Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP).

PubMed

Guevara, María Ángeles; de María, Nuria; Sáez-Laguna, Enrique; Vélez, María Dolores; Cervera, María Teresa; Cabezas, José Antonio

2017-01-01

Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.

Prevalent genotypes of Toxoplasma gondii in pregnant women and patients from Crete and Cyprus.

PubMed

Messaritakis, Ippokratis; Detsika, Maria; Koliou, Maria; Sifakis, Stavros; Antoniou, Maria

2008-08-01

Molecular genotyping has been used to characterize Toxoplasma gondii strains into the three clonal lineages known as types I, II, and III. To characterize T. gondii strains from Greece and Cyprus, polymerase chain reaction-restriction fragment length polymorphism analysis on the GRA6 gene was performed directly on 20 clinical samples from 18 humans (11 pregnant women, six patients with lymphadenopathy, and one patient positive for human immunodeficiency virus) and two rats. Characterization of T. gondii types was performed after digestion of amplified products with Mse I. The 20 strains were characterized as type II (20%) and type III (80%). Of these strains, 19 originated from the island of Crete (4 strains type II and 15 strains type III), and 1 from the island of Cyprus (type III). Although both type II and type III strains were found, type III was the most prevalent in Crete.

Fragment-based design of symmetrical bis-benzimidazoles as selective inhibitors of the trimethoprim-resistant, type II R67 dihydrofolate reductase.

PubMed

Bastien, Dominic; Ebert, Maximilian C C J C; Forge, Delphine; Toulouse, Jacynthe; Kadnikova, Natalia; Perron, Florent; Mayence, Annie; Huang, Tien L; Vanden Eynde, Jean Jacques; Pelletier, Joelle N

2012-04-12

The continuously increasing use of trimethoprim as a common antibiotic for medical use and for prophylactic application in terrestrial and aquatic animal farming has increased its prevalence in the environment. This has been accompanied by increased drug resistance, generally in the form of alterations in the drug target, dihydrofolate reductase (DHFR). The most highly resistant variants of DHFR are known as type II DHFR, among which R67 DHFR is the most broadly studied variant. We report the first attempt at designing specific inhibitors to this emerging drug target by fragment-based design. The detection of inhibition in R67 DHFR was accompanied by parallel monitoring of the human DHFR, as an assessment of compound selectivity. By those means, small aromatic molecules of 150-250 g/mol (fragments) inhibiting R67 DHFR selectively in the low millimolar range were identified. More complex, symmetrical bis-benzimidazoles and a bis-carboxyphenyl were then assayed as fragment-based leads, which procured selective inhibition of the target in the low micromolar range (K(i) = 2-4 μM). The putative mode of inhibition is discussed according to molecular modeling supported by in vitro tests. © 2012 American Chemical Society

Evaluation of biomarkers for osteoarthritis caused by fragmented medial coronoid process in dogs.

PubMed

Hurlbeck, C; Einspanier, R; Pfeil, I; Bondzio, A

2014-06-01

The aim of the present work was to evaluate whether concentrations of the carboxy-terminal cross-linked fragment of type II collagen (CTX-II), the activities of matrix metalloproteinase-2 and -9 (MMP-2/-9) and Myeloperoxidase (MPO) in canine synovial fluids (SF) can reflect structural alterations of articular cartilage in dogs with fragmented medial coronoid process (FMCP). Elbow joints with FMCP underwent radiographic and arthroscopic examination. Commercially available assays were used to analyze SF for CTX-II concentration and MMP-2/-9 activity. MPO activity was measured by o-dianisidine-assay. The MMPs were further evaluated by zymography. CTX-II concentration and MMP-2 activity showed age-dependent trends in controls. Increased enzyme activities of MPO and MMP-2/-9 were found in diseased dogs. MMP-9activity seems suitable to underline the subjective assessment of the degree of cartilage damage. These initial data of the study suggest that MPO and MMP-2/9 may be used as objective biomarkers in the diagnosis of canine osteoarthritis due to FMCP. Copyright © 2014. Published by Elsevier Ltd.

Functional analysis of a frame-shift mutant of the dihydropyridine receptor pore subunit (α1S) expressing two complementary protein fragments

PubMed Central

Ahern, Chris A; Vallejo, Paola; Mortenson, Lindsay; Coronado, Roberto

2001-01-01

Background The L-type Ca2+ channel formed by the dihydropyridine receptor (DHPR) of skeletal muscle senses the membrane voltage and opens the ryanodine receptor (RyR1). This channel-to-channel coupling is essential for Ca2+ signaling but poorly understood. We characterized a single-base frame-shift mutant of α1S, the pore subunit of the DHPR, that has the unusual ability to function voltage sensor for excitation-contraction (EC) coupling by virtue of expressing two complementary hemi-Ca2+ channel fragments. Results Functional analysis of cDNA transfected dysgenic myotubes lacking α1S were carried out using voltage-clamp, confocal Ca2+ indicator fluoresence, epitope immunofluorescence and immunoblots of expressed proteins. The frame-shift mutant (fs-α1S) expressed the N-terminal half of α1S (M1 to L670) and the C-terminal half starting at M701 separately. The C-terminal fragment was generated by an unexpected restart of translation of the fs-α1S message at M701 and was eliminated by a M701I mutation. Protein-protein complementation between the two fragments produced recovery of skeletal-type EC coupling but not L-type Ca2+ current. Discussion A premature stop codon in the II-III loop may not necessarily cause a loss of DHPR function due to a restart of translation within the II-III loop, presumably by a mechanism involving leaky ribosomal scanning. In these cases, function is recovered by expression of complementary protein fragments from the same cDNA. DHPR-RyR1 interactions can be achieved via protein-protein complementation between hemi-Ca2+ channel proteins, hence an intact II-III loop is not essential for coupling the DHPR voltage sensor to the opening of RyR1 channel. PMID:11806762

Template-based de novo design for type II kinase inhibitors and its extented application to acetylcholinesterase inhibitors.

PubMed

Su, Bo-Han; Huang, Yi-Syuan; Chang, Chia-Yun; Tu, Yi-Shu; Tseng, Yufeng J

2013-10-31

There is a compelling need to discover type II inhibitors targeting the unique DFG-out inactive kinase conformation since they are likely to possess greater potency and selectivity relative to traditional type I inhibitors. Using a known inhibitor, such as a currently available and approved drug or inhibitor, as a template to design new drugs via computational de novo design is helpful when working with known ligand-receptor interactions. This study proposes a new template-based de novo design protocol to discover new inhibitors that preserve and also optimize the binding interactions of the type II kinase template. First, sorafenib (Nexavar) and nilotinib (Tasigna), two type II inhibitors with different ligand-receptor interactions, were selected as the template compounds. The five-step protocol can reassemble each drug from a large fragment library. Our procedure demonstrates that the selected template compounds can be successfully reassembled while the key ligand-receptor interactions are preserved. Furthermore, to demonstrate that the algorithm is able to construct more potent compounds, we considered kinase inhibitors and other protein dataset, acetylcholinesterase (AChE) inhibitors. The de novo optimization was initiated using a template compound possessing a less than optimal activity from a series of aminoisoquinoline and TAK-285 inhibiting type II kinases, and E2020 derivatives inhibiting AChE respectively. Three compounds with greater potency than the template compound were discovered that were also included in the original congeneric series. This template-based lead optimization protocol with the fragment library can help to design compounds with preferred binding interactions of known inhibitors automatically and further optimize the compounds in the binding pockets.

Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination.

PubMed

Woods, Lucy A; Dolezal, Olan; Ren, Bin; Ryan, John H; Peat, Thomas S; Poulsen, Sally-Ann

2016-03-10

Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.

A Novel Cryptic Binding Motif, LRSKSRSFQVSDEQY, in the C-Terminal Fragment of MMP-3/7-Cleaved Osteopontin as a Novel Ligand for α9β1 Integrin Is Involved in the Anti-Type II Collagen Antibody-Induced Arthritis

PubMed Central

Kon, Shigeyuki; Nakayama, Yosuke; Matsumoto, Naoki; Ito, Koyu; Kanayama, Masashi; Kimura, Chiemi; Kouro, Hitomi; Ashitomi, Dai; Matsuda, Tadashi; Uede, Toshimitsu

2014-01-01

Osteopontin (OPN) is a multifunctional protein that has been linked to various intractable inflammatory diseases. One way by which OPN induces inflammation is the production of various functional fragments by enzyme cleavage. It has been well appreciated that OPN is cleaved by thrombin, and/or matrix metalloproteinase-3 and -7 (MMP-3/7). Although the function of thrombin-cleaved OPN is well characterized, little is known about the function of MMP-3/7-cleaved OPN. In this study, we found a novel motif, LRSKSRSFQVSDEQY, in the C-terminal fragment of MMP-3/7-cleaved mouse OPN binds to α9β1 integrin. Importantly, this novel motif is involved in the development of anti-type II collagen antibody-induced arthritis (CAIA). This study provides the first in vitro and in vivo evidence that OPN cleavage by MMP-3/7 is an important regulatory mechanism for CAIA. PMID:25545242

Dynamic investigation of DNA bending and wrapping by type II topoisomerases

NASA Astrophysics Data System (ADS)

Shao, Qing; Finzi, Laura; Dunlap, David

2009-11-01

Type II topoisomerases catalyze DNA decatenation and unwinding which is crucial for cell division, and therefore type II topoisomerases are some of the main targets of anti-cancer drugs. A recent crystal structure shows that, during the catalytic cycle, a yeast type II topoimerase can bend a 10 base pair DNA segment by up to 150 degrees. Bacterial gyrase, another type II topoisomerase, can wrap DNA into a tight 180 degree turn. Bending a stiff polymer like DNA requires considerable energy and could represent the rate limiting step in the catalytic (topological) cycle. Using modified deoxyribonucleotides in PCR reactions, stiffer DNA fragments have been produced and used as substrates for topoisomerase II-mediated relaxation of plectonemes introduced in single molecules using magnetic tweezers. The wrapping ability of gyrase decreases for diamino-purine-substituted DNA in which every base pair has three hydrogen-bonds. The overall rate of relaxation of plectonemes by recombinant human topoisomerase II alpha also decreases. These results reveal the dynamic properties of DNA bending and wrapping by type II topisomerases and suggest that A:T base pair melting is a rate determining step for bending and wrapping.

Restriction Fragment Length Polymorphisms of Virulence Plasmids in Rhodococcus equi

PubMed Central

Takai, Shinji; Shoda, Masato; Sasaki, Yukako; Tsubaki, Shiro; Fortier, Guillaume; Pronost, Stephane; Rahal, Karim; Becu, Teotimo; Begg, Angela; Browning, Glenn; Nicholson, Vivian M.; Prescott, John F.

1999-01-01

Virulent Rhodococcus equi, which is a well-known cause of pyogranulomatous pneumonia in foals, possesses a large plasmid encoding virulence-associated 15- to 17-kDa antigens. Foal and soil isolates from five countries—Argentina, Australia, Canada, France, and Japan—were investigated for the presence of 15- to 17-kDa antigens by colony blotting, using the monoclonal antibody 10G5, and the gene coding for 15- to 17-kDa antigens by PCR. Plasmid DNAs extracted from positive isolates were digested with restriction endonucleases BamHI, EcoRI, EcoT22I, and HindIII, and the digestion patterns that resulted divided the plasmids of virulent isolates into five closely related types. Three of the five types had already been reported in Canadian and Japanese isolates, and the two new types had been found in French and Japanese isolates. Therefore, we tentatively designated these five types 85-kb type I (pREAT701), 85-kb type II (a new type), 87-kb type I (EcoRI and BamHI type 2 [V. M. Nicholson and J. F. Prescott, J. Clin. Microbiol. 35:738–740, 1997]), 87-kb type II (a new type), and 90-kb (pREL1) plasmids. The 85-kb type I plasmid was found in isolates from Argentina, Australia, Canada, and France. Plasmid 87-kb type I was isolated in specimens from Argentina, Canada, and France. The 85-kb type II plasmid appeared in isolates from France. On the other hand, plasmids 87-kb type II and 90-kb were found only in isolates from Japan. These results revealed geographic differences in the distribution of the virulence plasmids found in the five countries and suggested that the restriction fragment length polymorphism of virulence plasmids might be useful to elucidate the molecular epidemiology of virulent R. equi in the world. PMID:10488224

Botulinum neurotoxin D-C uses synaptotagmin I and II as receptors, and human synaptotagmin II is not an effective receptor for type B, D-C and G toxins.

PubMed

Peng, Lisheng; Berntsson, Ronnie P-A; Tepp, William H; Pitkin, Rose M; Johnson, Eric A; Stenmark, Pål; Dong, Min

2012-07-01

Botulinum neurotoxins (BoNTs) are classified into seven types (A-G), but multiple subtype and mosaic toxins exist. These subtype and mosaic toxins share a high sequence identity, and presumably the same receptors and substrates with their parental toxins. Here, we report that a mosaic toxin, type D-C (BoNT/D-C), uses different receptors from its parental toxin BoNT/C. BoNT/D-C, but not BoNT/C, binds directly to the luminal domains of synaptic vesicle proteins synaptotagmin (Syt) I and II, and requires expression of SytI/II to enter neurons. The SytII luminal fragment containing the toxin-binding site can block the entry of BoNT/D-C into neurons and reduce its toxicity in vivo in mice. We also found that gangliosides increase binding of BoNT/D-C to SytI/II and enhance the ability of the SytII luminal fragment to block BoNT/D-C entry into neurons. These data establish SytI/II, in conjunction with gangliosides, as the receptors for BoNT/D-C, and indicate that BoNT/D-C is functionally distinct from BoNT/C. We further found that BoNT/D-C recognizes the same binding site on SytI/II where BoNT/B and G also bind, but utilizes a receptor-binding interface that is distinct from BoNT/B and G. Finally, we also report that human and chimpanzee SytII has diminished binding and function as the receptor for BoNT/B, D-C and G owing to a single residue change from rodent SytII within the toxin binding site, potentially reducing the potency of these BoNTs in humans and chimpanzees.

Cytochrome oxidase subunit 2 gene allows simultaneous detection and typing of Trypanosoma rangeli and Trypanosoma cruzi.

PubMed

de Sá, Amanda Regina Nichi; Steindel, Mário; Demeu, Lara Maria Kalempa; Lückemeyer, Débora Denardin; Grisard, Edmundo Carlos; Neto, Quirino Alves de Lima; de Araújo, Silvana Marques; Toledo, Max Jean de Ornelas; Gomes, Mônica Lúcia

2013-12-23

The parasites Trypanosoma rangeli and Trypanosoma cruzi share vectors and hosts over a wide geographical area in Latin America. In this study, we propose a single molecular approach for simultaneous detection and typing of T. rangeli and T. cruzi. A restriction fragment length polymorphism analysis of the mitochondrial cytochrome oxidase II gene (COII-RFLP) using enzyme AluI and different amounts of DNA from the major genetic groups of T. rangeli and T. cruzi (KP1+/KP1- and DTU-I/DTU-II) was carried out. The same marker was tested on the other T. cruzi DTUs (DTU-III to DTU-VI) and on DNA extracted from gut contents of experimentally infected triatomines. The COII PCR generates a ~400 bp fragment, which after digestion with AluI (COII-RFLP) can be used to distinguish T. rangeli from T. cruzi and simultaneously differentiate the major genetic groups of T. rangeli (KP1+ and KP1-) and T. cruzi (DTU-I and DTU-II). The COII-RFLP generated bands of ~120 bp and ~280 bp for KP1+, whereas for KP1- no amplicon cleavage was observed. For T. cruzi, digestion of COII revealed a ~300 bp band for DTU-I and a ~250 bp band for DTU-II. For DTU-III to DTU-VI, COII-RFLP generated bands ranging from ~310 to ~330 bp, but the differentiation of these DTUs was not as clear as the separation between DTU-I and DTU-II. After AluI digestion, a species-specific fragment of ~80 bp was observed for all DTUs of T. cruzi. No cross-amplification was observed for Leishmania spp., T. vivax or T. evansi. The COII-RFLP allowed simultaneous detection and typing of T. rangeli and T. cruzi strains according to their major genetic groups (KP1+/KP1- and DTU-I/DTU-II) in vitro and in vivo, providing a reliable and sensitive tool for epidemiological studies in areas where T. rangeli and T. cruzi coexist.

Cytochrome oxidase subunit 2 gene allows simultaneous detection and typing of Trypanosoma rangeli and Trypanosoma cruzi

PubMed Central

2013-01-01

Background The parasites Trypanosoma rangeli and Trypanosoma cruzi share vectors and hosts over a wide geographical area in Latin America. In this study, we propose a single molecular approach for simultaneous detection and typing of T. rangeli and T. cruzi. Methods A restriction fragment length polymorphism analysis of the mitochondrial cytochrome oxidase II gene (COII-RFLP) using enzyme AluI and different amounts of DNA from the major genetic groups of T. rangeli and T. cruzi (KP1+/KP1- and DTU-I/DTU-II) was carried out. The same marker was tested on the other T. cruzi DTUs (DTU-III to DTU-VI) and on DNA extracted from gut contents of experimentally infected triatomines. Results The COII PCR generates a ~400 bp fragment, which after digestion with AluI (COII-RFLP) can be used to distinguish T. rangeli from T. cruzi and simultaneously differentiate the major genetic groups of T. rangeli (KP1+ and KP1-) and T. cruzi (DTU-I and DTU-II). The COII-RFLP generated bands of ~120 bp and ~280 bp for KP1+, whereas for KP1- no amplicon cleavage was observed. For T. cruzi, digestion of COII revealed a ~300 bp band for DTU-I and a ~250 bp band for DTU-II. For DTU-III to DTU-VI, COII-RFLP generated bands ranging from ~310 to ~330 bp, but the differentiation of these DTUs was not as clear as the separation between DTU-I and DTU-II. After AluI digestion, a species-specific fragment of ~80 bp was observed for all DTUs of T. cruzi. No cross-amplification was observed for Leishmania spp., T. vivax or T. evansi. Conclusions The COII-RFLP allowed simultaneous detection and typing of T. rangeli and T. cruzi strains according to their major genetic groups (KP1+/KP1- and DTU-I/DTU-II) in vitro and in vivo, providing a reliable and sensitive tool for epidemiological studies in areas where T. rangeli and T. cruzi coexist. PMID:24360167

Fragment profiling of low molecular weight heparins using reversed phase ion pair liquid chromatography-electrospray mass spectrometry.

PubMed

Xu, Xiaohui; Li, Daoyuan; Chi, Lequan; Du, Xuzhao; Bai, Xue; Chi, Lianli

2015-04-30

Low molecular weight heparins (LMWHs) are linear and highly charged carbohydrate polymers prepared by chemical or enzymatic depolymerization of heparin. Compared to unfractionated heparin (UFH), LMWHs are prevalently used as clinical anticoagulant drugs due to their lower side effects and better bioavailability. The work presented herein provides a rapid and powerful fragment mapping method for structural characterization of LMWHs. The chain fragments of two types of LMWHs, enoxaparin and nadroparin, were generated by controlled enzymatic digestion with each of heparinase I (Hep I, Enzyme Commission (EC) # 4.2.2.7), heparinase II (Hep II, no EC # assigned) and heparinase III (Hep III, EC # 4.2.2.8). Reversed phase ion pair high performance liquid chromatography (RPIP-HPLC) coupled with electrospray ion trap time-of-flight mass spectrometry (ESI-IT-TOF-MS) was used to profile the oligosaccharide chains ranging from disaccharides to decasaccharides. A database containing all theoretical structural compositions was established to assist the mass spectra interpretation. The six digests derived by three enzymes from two types of LMWHs exhibited distinguishable fingerprinting patterns. And a total of 94 enoxaparin fragments and 109 nadroparin fragments were detected and identified. Besides the common LMWH oligosaccharides, many components containing characteristic LMWH structures such as saturated L-idopyranosuronic acid, 2,5-anhydro-D-mannitol, 1,6-anhydro-D-aminopyranose, as well as odd number oligosaccharides were also revealed. Quantitative comparison of major components derived from innovator and generic nadroparin products was presented. This approach to profile LMWHs' fragments offers a highly reproducible, high resolution and information-rich tool for evaluating the quality of this category of anticoagulant drugs or comparing structural similarities among samples from various sources. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Na+-phosphate cotransport system (NaPi-II) with a cleaved protein backbone: implications on function and membrane insertion

PubMed Central

Kohl, Beate; Wagner, Carsten A; Huelseweh, Birgit; Busch, Andreas E; Werner, Andreas

1998-01-01

Renal handling of inorganic phosphate (Pi) involves a Na+-Pi cotransport system which is well conserved between vertebrates. The members of this protein family, denoted NaPi-II, share a topology with, it is thought, eight transmembrane domains. The transporter is proposed to be proteolytically cleaved within a large hydrophilic loop in vivo. The consequences of an interrupted backbone were tested by constructing cDNA clones encoding different N- (1-3 and 1-5) and C-terminal (4-8 and 6-8) complementary fragments of NaPi-II from winter flounder. When the cognate fragments were used in combination (1-3 plus 4-8; 1-5 plus 6-8) they comprised the full complement of the putative transporter domains. None of the four individual fragments or the 1-5 plus 6-8 combination when expressed in Xenopus oocytes increased Pi flux. Coexpression of fragments 1-3 plus 4-8 stimulated transport activity identical to that for expressed wild-type NaPi-II with regard to pH dependency and Km for Na+ and Pi binding; however, the maximal transport rate (vmax) was lower. Immunohistochemistry on cryosections confined the functionally active 1-3 plus 4-8 combination to the oocyte membrane. This was not the case for the 1-5 plus 6-8 combination or any of the individual fragments, all of which failed to induce fluorescence. A second immunohistochemical approach using intact oocytes allowed determination of the extracellular regions of the protein. Epitopes within the loop between transmembrane domains 3 and 4 enhanced fluorescence. Neither N- nor C-terminal tags induced fluorescence. PMID:9508800

Genetic diversity of Toxoplasma gondii isolates in Egyptian feral cats reveals new genotypes.

PubMed

Al-Kappany, Y M; Rajendran, C; Abu-Elwafa, S A; Hilali, M; Su, C; Dubey, J P

2010-12-01

Cats are important in the epidemiology of Toxoplasma gondii because they are the only hosts that excrete environmentally resistant oocysts in feces. In the present study, 115 viable T. gondii isolates from tissues of cats from Egypt were genotyped using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) and DNA from tachyzoites. Seven genotypes were recognized including the clonal Type II, Type III (2 genotypes), and 4 atypical genotypes. Ninety percent (103 of 115) of isolates were clonal, i.e., Type II (n  =  61) and Type III (n  =  42) strains. Of the 61 Type II strains, all had the Type II alleles at all loci, except for 2 strains that had allele I at Apico. Eight isolates were divided into 4 atypical genotypes. One of these genotypes (with 4 isolates) was previously reported in dogs from Sri Lanka and in sand cats from the United Arab Emirates. Four isolates had mixed infections. These results revealed a strong clonal population structure with the dominance of clonal Type II and III lineages of T. gondii in feral cats from Egypt.

Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.

PubMed

Tóth, Eszter; Huszár, Krisztina; Bencsura, Petra; Kulcsár, Péter István; Vodicska, Barbara; Nyeste, Antal; Welker, Zsombor; Tóth, Szilvia; Welker, Ervin

2014-01-01

The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease--a Body Double of the Type IIP enzyme--is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

2001-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

1999-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

The human T-cell leukemia virus type 1 p13II protein: effects on mitochondrial function and cell growth

PubMed Central

D’Agostino, DM; Silic-Benussi, M; Hiraragi, H; Lairmore, MD; Ciminale, V

2011-01-01

p13II of human T-cell leukemia virus type 1 (HTLV-1) is an 87-amino-acid protein that is targeted to the inner mitochondrial membrane. p13II alters mitochondrial membrane permeability, producing a rapid, membrane potential-dependent influx of K+. These changes result in increased mitochondrial matrix volume and fragmentation and may lead to depolarization and alterations in mitochondrial Ca2+ uptake/retention capacity. At the cellular level, p13II has been found to interfere with cell proliferation and transformation and to promote apoptosis induced by ceramide and Fas ligand. Assays carried out in T cells (the major targets of HTLV-1 infection in vivo) demonstrate that p13II-mediated sensitization to Fas ligand-induced apoptosis can be blocked by an inhibitor of Ras farnesylation, thus implicating Ras signaling as a downstream target of p13II function. PMID:15761473

Salter-Harris type II metacarpal and metatarsal fracture in three foals. Treatment by minimally-invasive lag screw osteosynthesis combined with external coaptation.

PubMed

Klopfenstein Bregger, Micaël D; Fürst, Anton E; Kircher, Patrick R; Kluge, Katharina; Kummer, Martin

2016-05-18

To describe minimally-invasive lag screw osteosynthesis combined with external coaptation for the treatment of Salter-Harris type II third metacarpal and third metatarsal bone fractures. Three foals aged two weeks to four months with a Salter-Harris type II third metacarpal or third metatarsal fracture. Surgery was carried out under general anaesthesia in lateral recumbency. After fracture reduction, the metaphyseal fragment was stabilized with two cortical screws placed in lag fashion under fluoroscopic control. A cast was applied for at least two weeks. All foals had a good outcome with complete fracture healing and return to complete soundness without any angular limb deformity. All foals had moderate transient digital hyperextension after cast removal. Internal fixation of Salter-Harris type II third metacarpal or third metatarsal fractures with two cortical screws in lag fashion, combined with external coaptation provided good stabilization and preserved the longitudinal growth potential of the injured physis.

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria.

PubMed

Bernheim, Aude; Calvo-Villamañán, Alicia; Basier, Clovis; Cui, Lun; Rocha, Eduardo P C; Touchon, Marie; Bikard, David

2017-12-12

Type II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. These breaks can be the substrate of several DNA repair pathways, paving the way for interactions. We report that non-homologous end-joining (NHEJ) and type II-A CRISPR-Cas systems only co-occur once among 5563 fully sequenced prokaryotic genomes. We investigated experimentally the possible molecular interactions using the NHEJ pathway from Bacillus subtilis and the type II-A CRISPR-Cas systems from Streptococcus thermophilus and Streptococcus pyogenes. Our results suggest that the NHEJ system has no effect on CRISPR immunity. On the other hand, we provide evidence for the inhibition of NHEJ repair by the Csn2 protein. Our findings give insights on the complex interactions between CRISPR-Cas systems and repair mechanisms in bacteria, contributing to explain the scattered distribution of CRISPR-Cas systems in bacterial genome.

Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases.

PubMed

Stephenson, F H; Ballard, B T; Boyer, H W; Rosenberg, J M; Greene, P J

1989-12-21

The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase. A clone containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic DNA library by hybridization with synthetic oligodeoxyribonucleotide probes based on the N-terminal amino acid (aa) sequence of RsrI. Extracts of E. coli containing a subclone of the 11-kb fragment display RsrI activity. Nucleotide sequence analysis reveals an 831-bp open reading frame encoding a polypeptide of 277 aa. A 50% identity exists within a 266-aa overlap between the deduced aa sequences of RsrI and EcoRI. Regions of 75-100% aa sequence identity correspond to key structural and functional regions of EcoRI. The type-II ENases have many common properties, and a common origin might have been expected. Nevertheless, this is the first demonstration of aa sequence similarity between ENases produced by different organisms.

Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 2: 2D NMR spectroscopy

NASA Astrophysics Data System (ADS)

Deshmukh, Ashish P.; Pacheco, Carlos; Hay, Michael B.; Myneni, Satish C. B.

2007-07-01

Carboxyl groups are abundant in natural organic molecules (NOM) and play a major role in their reactivity. The structural environments of carboxyl groups in IHSS soil and river humic samples were investigated using 2D NMR (heteronuclear and homonuclear correlation) spectroscopy. Based on the 1H- 13C heteronuclear multiple-bond correlation (HMBC) spectroscopy results, the carboxyl environments in NOM were categorized as Type I (unsubstituted and alkyl-substituted aliphatic/alicyclic), Type II (functionalized carbon substituted), Type IIIa, b (heteroatom and olefin substituted), and Type IVa, b (5-membered heterocyclic aromatic and 6-membered aromatic). The most intense signal in the HMBC spectra comes from the Type I carboxyl groups, including the 2JCH and 3JCH couplings of unsubstituted aliphatic and alicyclic acids, though this spectral region also includes the 3JCH couplings of Type II and III structures. Type II and III carboxyls have small but detectable 2JCH correlations in all NOM samples except for the Suwannee River humic acid. Signals from carboxyls bonded to 5-membered aromatic heterocyclic fragments (Type IVa) are observed in the soil HA and Suwannee River FA, while correlations to 6-membered aromatics (Type IVb) are only observed in Suwannee River HA. In general, aromatic carboxylic acids may be present at concentrations lower than previously imagined in these samples. Vibrational spectroscopy results for these NOM samples, described in an accompanying paper [Hay M. B. and Myneni S. C. B. (2007) Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy. Geochim. Cosmochim. Acta (in press)], suggest that Type II and Type III carboxylic acids with α substituents (e.g., -OH, -OR, or -CO 2H) constitute the majority of carboxyl structures in all humic substances examined. Furoic and salicylic acid structures (Type IV) are also feasible fragments, albeit as minor constituents. The vibrational spectroscopy results also suggest that much of the "Type I" signal observed in the HMBC spectrum is due to carboxylic acid esters and possibly α-substituted alicyclic acids.

Cloning and characterization of a cDNA encoding topoisomerase II in pea and analysis of its expression in relation to cell proliferation.

PubMed

Reddy, M K; Nair, S; Tewari, K K; Mudgil, Y; Yadav, B S; Sopory, S K

1999-09-01

We have isolated and sequenced four overlapping cDNA clones to identify the full-length cDNA for topoisomerase II (PsTopII) from pea. Using degenerate primers, based on the conserved amino acid sequences of other eukaryotic type II topoisomerases, a 680 bp fragment was PCR-amplified with pea cDNA as template. This fragment was used as a probe to screen an oligo-dT-primed pea cDNA library. A partial cDNA clone was isolated that was truncated at the 3' end. RACE-PCR was employed to isolate the remaining portion of the gene. The total size of PsTopII is 4639 bp with an open reading frame of 4392 bp. The deduced amino acid sequence shows a strong homology to other eukaryotic topoisomerase II (topo II) at the N-terminus end. The topo II transcript was abundant in proliferative tissues. We also show that the level of topo II transcripts could be stimulated by exogenous application of growth factors that induced proliferation in vitro cultures. Light irradiation to etiolated tissue strongly stimulated the expression of topo II. These results suggest that topo II gene expression is up-regulated in response to light and hormones and correlates with cell proliferation. Besides, we have also isolated and analysed the 5'-flanking region of the pea TopII gene. This is first report on the isolation of a putative promoter for topoisomerase II from plants.

The ATP-binding site of type II topoisomerases as a target for antibacterial drugs.

PubMed

Maxwell, Anthony; Lawson, David M

2003-01-01

DNA topoisomerases are essential enzymes in all cell types and have been found to be valuable drug targets both for antibacterial and anti-cancer chemotherapy. Type II topoisomerases possess a binding site for ATP, which can be exploited as a target for chemo-therapeutic agents. High-resolution structures of protein fragments containing this site complexed with antibiotics or an ATP analogue have provided vital information for the understanding of the action of existing drugs and for the potential development of novel anti-bacterial agents. In this article we have reviewed the structure and function of the ATPase domain of DNA gyrase (bacterial topoisomerase II), particularly highlighting novel information that has been revealed by structural studies. We discuss the efficacy and mode of action of existing drugs and consider the prospects for the development of novel agents.

Associated characteristics and impact on recurrence and survival of free-floating tumor fragments in the lumen of fallopian tubes in Type I and Type II endometrial cancer.

PubMed

Albright, Benjamin B; Black, Jonathan D; Passarelli, Rachel; Gysler, Stefan; Whicker, Margaret; Altwerger, Gary; Menderes, Gulden; Buza, Natalia; Hui, Pei; Santin, Alessandro D; Azodi, Masoud; Silasi, Dan-Arin; Ratner, Elena S; Litkouhi, Babak; Schwartz, Peter E

2018-02-01

This study sought to evaluate characteristics of cases of free-floating tumor fragments within the lumen of fallopian tubes ('floaters') on final pathology for Type I and Type II endometrial adenocarcinoma, including relationships with disease recurrence and mortality. A single institution experience of 1022 consecutive cases of uterine cancer presenting between 2005 and 2010 was retrospectively reviewed, with data extraction from electronic medical records. Associations of floaters with baseline characteristics were studied with logistic regression, and relationships with disease recurrence and survival were assessed with Cox proportional hazards models. Among 816 included cases of Type I or Type II endometrial adenocarcinoma, floaters were identified on final pathology for 20 patients (2.5%). Patient characteristics of cases with floaters mirrored the overall sample. With adjustment, presence of floaters trended towards association with laparoscopic/robotic approach (OR = 3.84; 95%CI 0.98-15.1), and was significantly associated with lymphovascular invasion (OR = 9.65; 95%CI 2.35-39.6) and higher stage disease. Although floaters were associated with increased risk of recurrence in unadjusted analysis (HR = 3.22; 95%CI 1.41-7.37), after adjustment for disease type, stage, and patient comorbidities, no evidence for impact on disease recurrence or overall survival was found. The presence of floaters is rare. Floaters were generally associated with more extensive disease, but no evidence was found to show any independent prognostic impact on risk of recurrence or death. In agreement with prior research, this study found a trend towards association of floaters with laparoscopic/robotic approach, indicating the possibility of floaters sometimes being the result of trauma from uterine manipulator insertion.

Identification of a New Zinc Binding Chemotype by Fragment Screening.

PubMed

Chrysanthopoulos, Panagiotis K; Mujumdar, Prashant; Woods, Lucy A; Dolezal, Olan; Ren, Bin; Peat, Thomas S; Poulsen, Sally-Ann

2017-09-14

The discovery of a new zinc binding chemotype from screening a nonbiased fragment library is reported. Using the orthogonal fragment screening methods of native state mass spectrometry and surface plasmon resonance a 3-unsubstituted 2,4-oxazolidinedione fragment was found to have low micromolar binding affinity to the zinc metalloenzyme carbonic anhydrase II (CA II). This affinity approached that of fragment sized primary benzenesulfonamides, the classical zinc binding group found in most CA II inhibitors. Protein X-ray crystallography established that 3-unsubstituted 2,4-oxazolidinediones bound to CA II via an interaction of the acidic ring nitrogen with the CA II active site zinc, as well as two hydrogen bonds between the oxazolidinedione ring oxygen and the CA II protein backbone. Furthermore, 3-unsubstituted 2,4-oxazolidinediones appear to be a viable starting point for the development of an alternative class of CA inhibitor, wherein the medicinal chemistry pedigree of primary sulfonamides has dominated for several decades.

Identification of Organics in Ice Grains from Enceladus

NASA Astrophysics Data System (ADS)

Khawaja, N.; Postberg, F.; Reviol, R.; Nölle, L.; Klenner, F.; Srama, R.

2015-12-01

The Cosmic Dust Analyzer (CDA) aboard the Cassini spacecraft performs in-situ measurements of the chemical composition of icy dust grains impinging onto the target surface. The instrument recorded cationic Time-of-Flight (ToF) mass spectra of organic-bearing ice grains emitted from Enceladus at different impact velocities causing different molecular fragmentation patterns [1,2]. Here we present a detailed analysis of these spectra (Type-2) to identify the composition of organic material embedded in Enceladus ice grains. The organic compounds display a great compositional diversity, which indicates varying contributions of several organic species. The spectra analysis is supported by a large-scale laboratory ground campaign yielding a library of analogue spectra for organic material embedded in a water ice matrix. To mimic the identified pattern of cationic fragments in organic enriched spectra we use a laboratory setup: Infrared Free Liquid MALDI ToF Mass Spectrometer (IR-FL-MALDI-ToF-MS). An infrared laser is used to disperse a liquid micro-beam of a water-solution to get cationic fragments. The laser energy is adjusted to simulate different impact velocities of ice particles on CDA [3]. So far we have identified characteristic fragment patterns of at least three classes of organic molecules: (i) aromatic species, (ii) amines, and (iii) carbonyl group species. (i) ice grains containing aromatic species are identified by a series of characteristic aromatic fragment cations (ii) ice grains containing amines are identified by a pronounced ammonium cation and (iii) ice grains containing carbonyl compounds are specified by a characteristic acylium cation in conjunction with certain others mass lines. Besides aromatic, amine and carbonyl species, Type-2 spectra also show contributions from other, yet un-specified, organic species. Typically, fragment cations of aromatic compounds are stable at impact velocities up-to 15km/s whereas cations of amines and carbonyl species are stable at velocities below 8km/s. Work is in progress to quantify concentrations of the identified species and to assign yet un-specified organic mass lines in Type 2 spectra. Ref: [1]Postberg et al., Icarus-193,2008. [2]Postberg et al., Nature-459,2009. [3]Beinsen, A., University of Göttingen, Dissertation (2011).

Mycobacterium avium restriction fragment length polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains.

PubMed

Sequeira, Patrícia Carvalho de; Fonseca, Leila de Souza; Silva, Marlei Gomes da; Saad, Maria Helena Féres

2005-11-01

Simple double repetitive element polymerase chain reaction (MaDRE-PCR) and Pvu II-IS1245 restriction fragment length polymorphism (RFLP) typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 AIDS inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

Characterisation of homoflavonoids from three Ophioglossum species using liquid chromatography with diode array detection and electrospray ionisation tandem mass spectrometry.

PubMed

Wan, Chuan-Xing; Luo, Jian-Guang; Gu, Yu-Cheng; Xu, De-Ran; Kong, Ling-Yi

2013-01-01

Homoflavonoids, characterised by one more carbon atom directly added to C6 -C3 -C6 backbone of flavonoids, are rich in the species of genus Ophioglossum. Up to now we have little knowledge about their MS fragmentation patterns. It is therefore necessary to investigate their MS fragmentation pathways so as to distinguish them from other types of flavonoids. To develop a rapid method for identifying homoflavonoids from Ophioglossum based on their characteristic MS fragmentation. Mass spectrometry fragmentation pathways and qualitative analysis of homoflavonoids in three ferns of Ophioglosssum were investigated by using high-performance liquid chromatography coupled with diode-array detection and electrospray ionisation tandem mass spectrometry (HPLC-DAD-ESI/MS(n) ). The analyses of the MS(n) spectra of the homoflavonoids allowed us to classify them into two types according to their fragmentation characteristics. The type I homoflavonoids, with an attached additional carbon atom to the C-3 position of the C-ring, presented the initial competing loss of H2 O and CH2 O from their aglycone ions, compared to the initial removal of H2 O or CO in the case of the type II homoflavonoids, which bear the additional carbon atom at the C-2' site of the B-ring and forming ring D. The above characteristic fragmentations of homoflavonoids were quite different from those of other flavonoids, and were successfully applied to identify homoflavonoids in the crude extracts of three Ophioglossum species. The HPLC-DAD-ESI/MS(n) method obtained in the present study provided a powerful tool for identifying homoflavonoids from ferns in the genus Ophioglossum. Copyright © 2013 John Wiley & Sons, Ltd.

The effects of metal ions on the DNA damage induced by hydrogen peroxide.

PubMed

Kobayashi, S; Ueda, K; Komano, T

1990-01-01

The effects of metal ions on DNA damage induced by hydrogen peroxide were investigated using two methods, agarose-gel electrophoretic analysis of supercoiled DNA and sequencing-gel analysis of single end-labeled DNA fragments of defined sequences. Hydrogen peroxide induced DNA damage when iron or copper ion was present. At least two classes of DNA damage were induced, one being direct DNA-strand cleavage, and the other being base modification labile to hot piperidine. The investigation of the damaged sites and the inhibitory effects of radical scavengers revealed that hydroxyl radical was the species which attacked DNA in the reaction of H2O2/Fe(II). On the other hand, two types of DNA damage were induced by H2O2/Cu(II). Type I damage was predominant and inhibited by potassium iodide, but type II was not. The sites of the base-modification induced by type I damage were similar to those by lipid peroxidation products and by ascorbate in the presence of Cu(II), suggesting the involvement of radical species other than free hydroxyl radical in the damaging reactions.

Identification of type II and type III pyoverdine receptors from Pseudomonas aeruginosa.

PubMed

de Chial, Magaly; Ghysels, Bart; Beatson, Scott A; Geoffroy, Valérie; Meyer, Jean Marie; Pattery, Theresa; Baysse, Christine; Chablain, Patrice; Parsons, Yasmin N; Winstanley, Craig; Cordwell, Stuart J; Cornelis, Pierre

2003-04-01

Pseudomonas aeruginosa produces, under conditions of iron limitation, a high-affinity siderophore, pyoverdine (PVD), which is recognized at the level of the outer membrane by a specific TonB-dependent receptor, FpvA. So far, for P. aeruginosa, three different PVDs, differing in their peptide chain, have been described (types I-III), but only the FpvA receptor for type I is known. Two PVD-producing P. aeruginosa strains, one type II and one type III, were mutagenized by a mini-TnphoA3 transposon. In each case, one mutant unable to grow in the presence of the strong iron chelator ethylenediaminedihydroxyphenylacetic acid (EDDHA) and the cognate PVD was selected. The first mutant, which had an insertion in the pvdE gene, upstream of fpvA, was unable to take up type II PVD and showed resistance to pyocin S3, which is known to use type II FpvA as receptor. The second mutant was unable to take up type III PVD and had the transposon insertion in fpvA. Cosmid libraries of the respective type II and type III PVD wild-type strains were constructed and screened for clones restoring the capacity to grow in the presence of PVD. From the respective complementing genomic fragments, type II and type III fpvA sequences were determined. When in trans, type II and type III fpvA restored PVD production, uptake, growth in the presence of EDDHA and, in the case of type II fpvA, pyocin S3 sensitivity. Complementation of fpvA mutants obtained by allelic exchange was achieved by the presence of cognate fpvA in trans. All three receptors posses an N-terminal extension of about 70 amino acids, similar to FecA of Escherichia coli, but only FpvAI has a TAT export sequence at its N-terminal end.

Haloacetic acid-degrading bacterial communities in drinking water systems as determined by cultivation and by terminal restriction fragment length polymorphism of PCR-amplified haloacid dehalogenase gene fragments.

PubMed

Grigorescu, A S; Hozalski, R M; Lapara, T M

2012-04-01

To characterize the HAA-degrading bacteria in drinking water systems. Haloacetic acid (HAA)-degrading bacteria were analysed in drinking water systems by cultivation and by a novel application of terminal restriction fragment length polymorphism (tRFLP). Substantial similarities were observed among the tRFLP patterns of dehI and dehII gene fragments in drinking water samples obtained from three different cities (Minneapolis, MN; St Paul, MN; Bucharest, Romania) and from one biologically active granular activated carbon filter (Hershey, PA). The dominant fragment in the tRFLP profiles of dehI genes from the drinking water samples matched the pattern from an Afipia sp. that was previously isolated from drinking water. In contrast, the dominant fragment in the tRFLP profiles of dehII genes did not match any previously characterized dehII gene fragment. PCR cloning was used to characterize this gene fragment, which had <65% nucleotide sequence identity with any previously characterized dehII gene. Afipia spp. are an appropriate model organism for studying the biodegradation of HAAs in drinking water distribution systems as encoded by dehI genes; the organism that harbours the most prominent dehII gene in drinking water has yet to be cultivated and identified. The development of a novel application of tRFLP targeting dehI and dehII genes could be broadly useful in understanding HAA-degrading bacteria in numerous environments. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Preliminary crystallographic analysis of mouse Elf3 C-terminal DNA-binding domain in complex with type II TGF-[beta] receptor promoter DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agarkar, Vinod B.; Babayeva, Nigar D.; Rizzino, Angie

2010-10-08

Ets proteins are transcription factors that activate or repress the expression of genes that are involved in various biological processes, including cellular proliferation, differentiation, development, transformation and apoptosis. Like other Ets-family members, Elf3 functions as a sequence-specific DNA-binding transcriptional factor. A mouse Elf3 C-terminal fragment (amino-acid residues 269-371) containing the DNA-binding domain has been crystallized in complex with mouse type II TGF-{beta} receptor promoter (TR-II) DNA. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 42.66, b = 52, c = 99.78 {angstrom}, and diffracted to a resolution of 2.2 {angstrom}.

Infection with Trypanosoma cruzi TcII and TcI in free-ranging population of lion tamarins (Leontopithecus spp): an 11-year follow-up.

PubMed

Lisboa, Cristiane Varella; Monteiro, Rafael Veríssimo; Martins, Andreia Fonseca; Xavier, Samantha Cristina das Chagas; Lima, Valdirene Dos Santos; Jansen, Ana Maria

2015-05-01

Here, we present a review of the dataset resulting from the 11-years follow-up of Trypanosoma cruzi infection in free-ranging populations of Leontopithecus rosalia (golden lion tamarin) and Leontopithecus chrysomelas (golden-headed lion tamarin) from distinct forest fragments in Atlantic Coastal Rainforest. Additionally, we present new data regarding T. cruzi infection of small mammals (rodents and marsupials) that live in the same areas as golden lion tamarins and characterisation at discrete typing unit (DTU) level of 77 of these isolates. DTU TcII was found to exclusively infect primates, while TcI infected Didelphis aurita and lion tamarins. The majority of T. cruzi isolates derived from L. rosalia were shown to be TcII (33 out 42) Nine T. cruzi isolates displayed a TcI profile. Golden-headed lion tamarins demonstrated to be excellent reservoirs of TcII, as 24 of 26 T. cruzi isolates exhibited the TcII profile. We concluded the following: (i) the transmission cycle of T. cruzi in a same host species and forest fragment is modified over time, (ii) the infectivity competence of the golden lion tamarin population fluctuates in waves that peak every other year and (iii) both golden and golden-headed lion tamarins are able to maintain long-lasting infections by TcII and TcI.

Infection with Trypanosoma cruzi TcII and TcI in free-ranging population of lion tamarins (Leontopithecus spp): an 11-year follow-up

PubMed Central

Lisboa, Cristiane Varella; Monteiro, Rafael Veríssimo; Martins, Andreia Fonseca; Xavier, Samantha Cristina das Chagas; Lima, Valdirene dos Santos; Jansen, Ana Maria

2015-01-01

Here, we present a review of the dataset resulting from the 11-years follow-up of Trypanosoma cruzi infection in free-ranging populations of Leontopithecus rosalia (golden lion tamarin) and Leontopithecus chrysomelas (golden-headed lion tamarin) from distinct forest fragments in Atlantic Coastal Rainforest. Additionally, we present new data regarding T. cruzi infection of small mammals (rodents and marsupials) that live in the same areas as golden lion tamarins and characterisation at discrete typing unit (DTU) level of 77 of these isolates. DTU TcII was found to exclusively infect primates, while TcI infected Didelphis aurita and lion tamarins. The majority of T. cruzi isolates derived from L. rosalia were shown to be TcII (33 out 42) Nine T. cruzi isolates displayed a TcI profile. Golden-headed lion tamarins demonstrated to be excellent reservoirs of TcII, as 24 of 26 T. cruzi isolates exhibited the TcII profile. We concluded the following: (i) the transmission cycle of T. cruzi in a same host species and forest fragment is modified over time, (ii) the infectivity competence of the golden lion tamarin population fluctuates in waves that peak every other year and (iii) both golden and golden-headed lion tamarins are able to maintain long-lasting infections by TcII and TcI. PMID:25946156

Genetic polymorphism of estrogen receptor alpha gene in Egyptian women with type II diabetes mellitus

PubMed Central

Motawi, Tarek M.K.; El-Rehany, Mahmoud A.; Rizk, Sherine M.; Ramzy, Maggie M.; el-Roby, Doaa M.

2015-01-01

Estrogen might play an important role in type 2 diabetes mellitus pathogenesis. A number of polymorphisms have been reported in the estrogen receptor alpha gene including the XbaI and PvuII restriction enzyme polymorphisms. The aim of this study was to determine if ESRα gene polymorphisms are associated with type 2 diabetes mellitus and correlated with lipid profile. Ninety diabetic Egyptian patients were compared with forty healthy controls. ESRα genotyping of PvuII and XbaI was performed using restriction fragment length polymorphism analysis. Our study showed that there is more significant difference in the frequency of C and G polymorphic allele between patients and control groups in PvuII and XbaI respectively. Also carriers of minor C and G alleles of PvuII and XbaI gene polymorphisms were associated with increased fasting blood glucose and disturbance in lipid profile as there is an increase in total cholesterol, triglycerides and Low density lipoprotein. So findings of present study suggest the possibility that PvuII and XbaI polymorphisms in ERα are related to T2DM and with increased serum lipids among Egyptian population. PMID:26401488

New half sandwich-type Ru(II) coordination compounds characterized by the fac-Ru(dmso-S)3 fragment: influence of the face-capping group on the chemical behavior and in vitro anticancer activity.

PubMed

Bratsos, Ioannis; Simonin, Camilla; Zangrando, Ennio; Gianferrara, Teresa; Bergamo, Alberta; Alessio, Enzo

2011-10-07

The Ru(II) complex fac-[RuCl(dmso-S)(3)(dmso-O)(2)][PF(6)] (P2) was found to be an excellent precursor for the facile preparation in high yield of half sandwich-type compounds of the general formula fac-[RuCl(dmso-S)(3)(N)(2)][PF(6)] (e.g. (N)(2) = 1,2-diaminoethane (en, 4), trans-1,2-diaminocyclohexane (dach, 5), or 2 NH(3) (6)). Neutral half sandwich-type compounds of the general formula fac-[RuCl(dmso-S)(3)(N-O)] where N-O is an anionic chelating ligand (e.g. N-O = picolinate (pic, 7)) are best prepared from the universal Ru(II)-dmso precursor cis-[RuCl(2)(dmso)(4)] (P1). These complexes, that were fully characterized in solution and in the solid state, are structurally similar to the anticancer organometallic compounds [Ru(η(6)-arene)(chel)Cl][PF(6)](n) but, in place of a face-capping arene, have the fac-Ru(dmso-S)(3) fragment. In contrast to what observed for the corresponding arene compounds, that rapidly hydrolyze the Cl ligand upon dissolution in water, compounds 4-6 are very stable and inert in aqueous solution. Probably their inertness is the reason why they showed no significant cytotoxicity against the MDA-MB-231 cancer cell line.

Transition-metal phosphors with cyclometalating ligands: fundamentals and applications.

PubMed

Chi, Yun; Chou, Pi-Tai

2010-02-01

One goal of this critical review is to provide advanced methodologies for systematic preparation of transition-metal based phosphors that show latent applications in the field of organic light emitting diodes (OLEDs). We are therefore reviewing various types of cyclometalating chelates for which the favorable metal-chelate bonding interaction, on the one hand, makes the resulting phosphorescent complexes highly emissive in both fluid and solid states at room temperature. On the other hand, fine adjustment of ligand-centered pi-pi* electronic transitions allows tuning of emission wavelength across the whole visible spectrum. The cyclometalating chelates are then classified according to types of cyclometalating groups, i.e. either aromatic C-H or azolic N-H fragment, and the adjacent donor fragment involved in the formation of metallacycles; the latter is an N-containing heterocycle, N-heterocyclic (NHC) carbene fragment or even diphenylphosphino group. These cyclometalating ligands are capable to react with heavy transition-metal elements, namely: Ru(II), Os(II), Ir(III) and Pt(II), to afford a variety of highly emissive phosphors, for which the photophysical properties as a function of chelate or metal characteristics are systematically discussed. Using Ir(III) complexes as examples, the C--N chelates possessing both C-H site and N-heterocyclic donor group are essential for obtaining phosphors with emission ranging from sky-blue to saturated red, while the N--N chelates such as 2-pyridyl-C-linked azolates are found useful for serving as true-blue chromophores due to their increased ligand-centered pi-pi* energy gap. Lastly, the remaining NHC carbene and benzyl phosphine chelates are highly desirable to serve as ancillary chelates in localizing the electronic transition between the metal and remaining lower energy chromophoric chelates. As for the potential opto-electronic applications, many of them exhibit remarkable performance data, which are convincing to pave a broad avenue for further development of all types of phosphorescent displays and illumination devices (94 references).

Substrate water exchange in photosystem II depends on the peripheral proteins.

PubMed

Hillier, W; Hendry, G; Burnap, R L; Wydrzynski, T

2001-12-14

The (18)O exchange rates for the substrate water bound in the S(3) state were determined in different photosystem II sample types using time-resolved mass spectrometry. The samples included thylakoid membranes, salt-washed Triton X-100-prepared membrane fragments, and purified core complexes from spinach and cyanobacteria. For each sample type, two kinetically distinct isotopic exchange rates could be resolved, indicating that the biphasic exchange behavior for the substrate water is inherent to the O(2)-evolving catalytic site in the S(3) state. However, the fast phase of exchange became somewhat slower (by a factor of approximately 2) in NaCl-washed membrane fragments and core complexes from spinach in which the 16- and 23-kDa extrinsic proteins have been removed, compared with the corresponding rate for the intact samples. For CaCl(2)-washed membrane fragments in which the 33-kDa manganese stabilizing protein (MSP) has also been removed, the fast phase of exchange slowed down even further (by a factor of approximately 3). Interestingly, the slow phase of exchange was little affected in the samples from spinach. For core complexes prepared from Synechocystis PCC 6803 and Synechococcus elongatus, the fast and slow exchange rates were variously affected. Nevertheless, within the experimental error, nearly the same exchange rates were measured for thylakoid samples made from wild type and an MSP-lacking mutant of Synechocystis PCC 6803. This result could indicate that the MSP has a slightly different function in eukaryotic organisms compared with prokaryotic organisms. In all samples, however, the differences in the exchange rates are relatively small. Such small differences are unlikely to arise from major changes in the metal-ligand structure at the catalytic site. Rather, the observed differences may reflect subtle long range effects in which the exchange reaction coordinates become slightly altered. We discuss the results in terms of solvent penetration into photosystem II and the regional dielectric around the catalytic site.

Restriction fragment length polymorphism of the major histocompatibility complex of the dog.

PubMed

Sarmiento, U M; Storb, R F

1988-01-01

Human major histocompatibility complex (HLA) cDNA probes were used to analyze the restriction fragment length polymorphism (RFLP) of the DLA-D region in dogs. Genomic DNA from peripheral blood leucocytes of 23 unrelated DLA-D-homozygous dogs representing nine DLA-D types (defined by mixed leucocyte reaction) was digested with restriction enzymes (Bam HI, Eco RI, Hind III, Pvu II, Taq I, Rsa I, Msp I, Pst I, and Bgl II), separated by agarose gel electrophoresis, and transferred onto Biotrace membrane. The Southern blots were successively hybridized with radiolabeled HLA cDNA probes corresponding to DR, DQ, DP, and DO beta genes. The autoradiograms for all nine enzyme digests displayed multiple bands with the DRb, DQb, and DPb probes while the DOb probe hybridized with one to two bands. The RFLP patterns were highly polymorphic but consistent within each DLA-D type. Standard RFLP patterns were established for nine DLA-D types which could be discriminated from each other by using two enzymes (Rsa I and Pst I) and the HLA-DPb probe. Cluster analysis of the polymorphic restriction fragments detected by the DRb probe revealed four closely related supertypic groups or DLA-DR families: Dw3 + Dw4 + D1, Dw8 + D10, D7 + D16 + D9, and Dw1. This study provides the basis for DLA-D genotyping at a population level by RFLP analysis. These results also suggest that the genetic organization of the DLA-D region may closely resemble that of the HLA complex.

Towards a population synthesis model of self-gravitating disc fragmentation and tidal downsizing II: the effect of fragment-fragment interactions

NASA Astrophysics Data System (ADS)

Forgan, D. H.; Hall, C.; Meru, F.; Rice, W. K. M.

2018-03-01

It is likely that most protostellar systems undergo a brief phase where the protostellar disc is self-gravitating. If these discs are prone to fragmentation, then they are able to rapidly form objects that are initially of several Jupiter masses and larger. The fate of these disc fragments (and the fate of planetary bodies formed afterwards via core accretion) depends sensitively not only on the fragment's interaction with the disc, but also with its neighbouring fragments. We return to and revise our population synthesis model of self-gravitating disc fragmentation and tidal downsizing. Amongst other improvements, the model now directly incorporates fragment-fragment interactions while the disc is still present. We find that fragment-fragment scattering dominates the orbital evolution, even when we enforce rapid migration and inefficient gap formation. Compared to our previous model, we see a small increase in the number of terrestrial-type objects being formed, although their survival under tidal evolution is at best unclear. We also see evidence for disrupted fragments with evolved grain populations - this is circumstantial evidence for the formation of planetesimal belts, a phenomenon not seen in runs where fragment-fragment interactions are ignored. In spite of intense dynamical evolution, our population is dominated by massive giant planets and brown dwarfs at large semimajor axis, which direct imaging surveys should, but only rarely, detect. Finally, disc fragmentation is shown to be an efficient manufacturer of free-floating planetary mass objects, and the typical multiplicity of systems formed via gravitational instability will be low.

Wide Distribution of Mitochondrial Genome Rearrangements in Wild Strains of the Cultivated Basidiomycete Agrocybe aegerita

PubMed Central

Barroso, G.; Blesa, S.; Labarere, J.

1995-01-01

We used restriction fragment length polymorphisms to examine mitochondrial genome rearrangements in 36 wild strains of the cultivated basidiomycete Agrocybe aegerita, collected from widely distributed locations in Europe. We identified two polymorphic regions within the mitochondrial DNA which varied independently: one carrying the Cox II coding sequence and the other carrying the Cox I, ATP6, and ATP8 coding sequences. Two types of mutations were responsible for the restriction fragment length polymorphisms that we observed and, accordingly, were involved in the A. aegerita mitochondrial genome evolution: (i) point mutations, which resulted in strain-specific mitochondrial markers, and (ii) length mutations due to genome rearrangements, such as deletions, insertions, or duplications. Within each polymorphic region, the length differences defined only two mitochondrial types, suggesting that these length mutations were not randomly generated but resulted from a precise rearrangement mechanism. For each of the two polymorphic regions, the two molecular types were distributed among the 36 strains without obvious correlation with their geographic origin. On the basis of these two polymorphisms, it is possible to define four mitochondrial haplotypes. The four mitochondrial haplotypes could be the result of intermolecular recombination between allelic forms present in the population long enough to reach linkage equilibrium. All of the 36 dikaryotic strains contained only a single mitochondrial type, confirming the previously described mitochondrial sorting out after cytoplasmic mixing in basidiomycetes. PMID:16534984

Abnormal expression of p27kip1 protein in levator ani muscle of aging women with pelvic floor disorders – a relationship to the cellular differentiation and degeneration

PubMed Central

Bukovsky, Antonin; Copas, Pleas; Caudle, Michael R; Cekanova, Maria; Dassanayake, Tamara; Asbury, Bridgett; Van Meter, Stuart E; Elder, Robert F; Brown, Jeffrey B; Cross, Stephanie B

2001-01-01

Background Pelvic floor disorders affect almost 50% of aging women. An important role in the pelvic floor support belongs to the levator ani muscle. The p27/kip1 (p27) protein, multifunctional cyclin-dependent kinase inhibitor, shows changing expression in differentiating skeletal muscle cells during development, and relatively high levels of p27 RNA were detected in the normal human skeletal muscles. Methods Biopsy samples of levator ani muscle were obtained from 22 symptomatic patients with stress urinary incontinence, pelvic organ prolapse, and overlaps (age range 38–74), and nine asymptomatic women (age 31–49). Cryostat sections were investigated for p27 protein expression and type I (slow twitch) and type II (fast twitch) fibers. Results All fibers exhibited strong plasma membrane (and nuclear) p27 protein expression. cytoplasmic p27 expression was virtually absent in asymptomatic women. In perimenopausal symptomatic patients (ages 38–55), muscle fibers showed hypertrophy and moderate cytoplasmic p27 staining accompanied by diminution of type II fibers. Older symptomatic patients (ages 57–74) showed cytoplasmic p27 overexpression accompanied by shrinking, cytoplasmic vacuolization and fragmentation of muscle cells. The plasma membrane and cytoplasmic p27 expression was not unique to the muscle cells. Under certain circumstances, it was also detected in other cell types (epithelium of ectocervix and luteal cells). Conclusions This is the first report on the unusual (plasma membrane and cytoplasmic) expression of p27 protein in normal and abnormal human striated muscle cells in vivo. Our data indicate that pelvic floor disorders are in perimenopausal patients associated with an appearance of moderate cytoplasmic p27 expression, accompanying hypertrophy and transition of type II into type I fibers. The patients in advanced postmenopause show shrinking and fragmentation of muscle fibers associated with strong cytoplasmic p27 expression. PMID:11696252

Decay of aspen (Populus tremuloides Michx.) wood in moist and dry boreal, temperate, and tropical forest fragments

Treesearch

Grizelle Gonzalez; William Gould; Andrew T. Hudak; Teresa Nettleton Hollingsworth

2008-01-01

In this study, we set up a wood decomposition experiment to i) quantify the percent of mass remaining, decay constant and performance strength of aspen stakes (Populus tremuloides) in dry and moist boreal (Alaska and Minnesota, USA), temperate (Washington and Idaho, USA), and tropical (Puerto Rico) forest types, and ii) determine the effects of...

Intravenous immunoglobulin in kidney transplantation.

PubMed

Tedla, Fasika M; Roche-Recinos, Andrea; Brar, Amarpali

2015-12-01

Antibody-mediated injury of renal allografts has assumed increasing importance with the availability of potent immunosuppressants directed against T-lymphocytes. Intravenous immunoglobulin (IVIG) has been used for prevention and treatment of antibody-mediated rejection. The review summarizes recent advances that shed light on mechanisms of action of IVIG and outlines current roles of IVIG in kidney transplantation. Observational studies support the use of IVIG for desensitization and treatment of acute rejection. Most studies are small and uncontrolled, but a matched case-control study reported a better survival with incompatible live-donor kidney transplant after desensitization using IVIG-containing regimens compared with dialysis or waiting for compatible transplant. Recent data indicate that variations in glycosylation and amino acid sequence cause the crystallizable fragment of immunoglobulin G to assume specific conformations that have high affinity for canonical crystallizable fragment receptors (FcR) or a newly discovered class of FcRs, labelled type II FcRs. Signaling through type II FcRs appears to trigger anti-inflammatory pathways. Recent discoveries expand our understanding of the mechanism of action of IVIG. Future research is expected to clarify the relevance of these findings to humans and could lead to the development of novel immunomodulatory agents.

Part II: arthroscopic treatment of tibial plateau fractures: intercondylar eminence avulsion fractures.

PubMed

Lubowitz, James H; Elson, Wylie S; Guttmann, Dan

2005-01-01

Arthroscopic reduction and internal fixation (ARIF) of tibial intercondylar eminence fractures is the emerging state-of-the-art. ARIF is recommended for displaced type III fractures and should be considered for all cases of displaced type II fractures. Fractures without displacement after closed reduction require careful evaluation to rule out meniscal entrapment. Subjective results of ARIF are uniformly excellent, despite reports of objective anteroposterior laxity. Early range-of-motion exercises are essential to prevent loss of extension. Repair using nonabsorbable suture fixation, when of adequate strength to allow early range-of-motion, has the advantages of eliminating the risks of comminution of the fracture fragment, posterior neurovascular injury, and need for hardware removal, compared with ARIF using screws.

Oligomeric state regulated trafficking of human platelet-activating factor acetylhydrolase type-II.

PubMed

Monillas, Elizabeth S; Caplan, Jeffrey L; Thévenin, Anastasia F; Bahnson, Brian J

2015-05-01

The intracellular enzyme platelet-activating factor acetylhydrolase type-II (PAFAH-II) hydrolyzes platelet-activating factor and oxidatively fragmented phospholipids. PAFAH-II in its resting state is mainly cytoplasmic, and it responds to oxidative stress by becoming increasingly bound to endoplasmic reticulum and Golgi membranes. Numerous studies have indicated that this enzyme is essential for protecting cells from oxidative stress induced apoptosis. However, the regulatory mechanism of the oxidative stress response by PAFAH-II has not been fully resolved. Here, changes to the oligomeric state of human PAFAH-II were investigated as a potential regulatory mechanism toward enzyme trafficking. Native PAGE analysis in vitro and photon counting histogram within live cells showed that PAFAH-II is both monomeric and dimeric. A Gly-2-Ala site-directed mutation of PAFAH-II demonstrated that the N-terminal myristoyl group is required for homodimerization. Additionally, the distribution of oligomeric PAFAH-II is distinct within the cell; homodimers of PAFAH-II were localized to the cytoplasm while monomers were associated to the membranes of the endoplasmic reticulum and Golgi. We propose that the oligomeric state of PAFAH-II drives functional protein trafficking. PAFAH-II localization to the membrane is critical for substrate acquisition and effective oxidative stress protection. It is hypothesized that the balance between monomer and dimer serves as a regulatory mechanism of a PAFAH-II oxidative stress response. Copyright © 2015 Elsevier B.V. All rights reserved.

Lowered Insulin Signalling Ameliorates Age-Related Sleep Fragmentation in Drosophila

PubMed Central

Hendrich, Oliver; Hinze, Yvonne; Birras, Ulrike; Partridge, Linda

2014-01-01

Sleep fragmentation, particularly reduced and interrupted night sleep, impairs the quality of life of older people. Strikingly similar declines in sleep quality are seen during ageing in laboratory animals, including the fruit fly Drosophila. We investigated whether reduced activity of the nutrient- and stress-sensing insulin/insulin-like growth factor (IIS)/TOR signalling network, which ameliorates ageing in diverse organisms, could rescue the sleep fragmentation of ageing Drosophila. Lowered IIS/TOR network activity improved sleep quality, with increased night sleep and day activity and reduced sleep fragmentation. Reduced TOR activity, even when started for the first time late in life, improved sleep quality. The effects of reduced IIS/TOR network activity on day and night phenotypes were mediated through distinct mechanisms: Day activity was induced by adipokinetic hormone, dFOXO, and enhanced octopaminergic signalling. In contrast, night sleep duration and consolidation were dependent on reduced S6K and dopaminergic signalling. Our findings highlight the importance of different IIS/TOR components as potential therapeutic targets for pharmacological treatment of age-related sleep fragmentation in humans. PMID:24690889

Evidence in Gabon for an intrafamilial clustering with mother-to-child and sexual transmission of a new molecular variant of human T-lymphotropic virus type-II subtype B.

PubMed

Tuppin, P; Gessain, A; Kazanji, M; Mahieux, R; Cosnefroy, J Y; Tekaia, F; Georges-Courbot, M C; Georges, A; de Thé, G

1996-01-01

Following the observation of an HTLV-II seropositive 60-year-old woman living in Gabon (Central Africa), a serologic and molecular study of her family members was conducted in an attempt to determine the duration of the HTLV-II infection and the modes of transmission of the virus. Among 41 family members, five were HTLV-I seropositive and 7 exhibited specific HTLV-II antibodies in their sera as demonstrated by high immunofluorescence titers on C19 cells and/or specific Western-blot pattern. The second husband of the index case and two of his sisters were infected by the virus, suggesting the presence of HTLV-II in this family over two generations. Sequence analysis of an amplified fragment of 172 nucleotides within the gp21 of the env region (6469-6640) of four HTLV-II infected individuals revealed a new HTLV-II molecular variant of the subtype b diverging from the prototypes NRA and G12 by seven (4.1%) and five (2.9%) bases substitutions, respectively. Molecular analysis of the total env gene (1462 bp) and fragments of the pol and pX regions confirmed that this new African variant was the most divergent HTLV-II subtype b yet described, exhibiting 2.3% of nucleotide substitutions in the env gene (33 bases) as compared to the two HTLV-II b prototypes. These data demonstrate, for the first time in Africa, intrafamilial both mother-to-child transmission and sexual transmission between spouses of an HTLV-II b molecular variant, and also suggest that this virus has been present in Gabon for a long period of time.

Peptide Fragmentation by Corona Discharge Induced Electrochemical Ionization

PubMed Central

Lloyd, John R.; Hess, Sonja

2010-01-01

Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M]+•, thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: 1. Complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; 2. Electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e− → Fe +•); 3. Radical fragmentation of the complexed compound. 4. Electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites. PMID:20869880

Fragment Screening of Human Kynurenine Aminotransferase-II.

PubMed

Jayawickrama, Gayan S; Nematollahi, Alireza; Sun, Guanchen; Church, W Bret

2018-03-01

Kynurenine aminotransferase-II (KAT-II) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that acts in the tryptophan metabolic pathway by catalyzing the transamination of kynurenine into kynurenic acid (KYNA). It is one of four isoforms in the KAT family, of which it is the primary homologue responsible for KYNA production in the mammalian brain. KAT-II is targeted for inhibition as KYNA is implicated in diseases such as schizophrenia, where it is found in elevated concentrations. Previously, many different approaches have been taken to develop KAT-II inhibitors, and herein fragment-based drug design (FBDD) approaches have been exploited to provide further lead compounds that can be designed into novel inhibitors. Surface plasmon resonance (SPR) was used to screen a fragment library containing 1000 compounds, of which 41 hits were identified. These hits were further evaluated with SPR, and 18 were selected for inhibition studies. From these hits, two fragments, F6037-0164 and F0037-7280, were pursued and determined to have an IC 50 of 524.5 (± 25.6) μM and 115.2 (± 4.5) μM, respectively. This strategy shows the viability of using FBDD in gleaning knowledge about KAT-II inhibition and generating leads for the production of KAT-II inhibitors.

[Radiation biology of structurally different Drosophila genes. Report 2. The vestigial gene: molecular characteristics of chromosome mutations].

PubMed

Afanas'eva, K P; Aleksandrova, M V; Aleksandrov, I D; Korablinova, S V

2012-01-01

The results of the PCR-assay of mutation lesions at each of 16 fragments overlapping the entire vestigial (vg) gene of Drosophila melanogaster in 52 gamma-ray-, neutron- and neutron + gamma-ray-induced vg mutants having the inversion or translocation breakpoint within the vg microregion are presented. 4 from 52 mutants studied were found to have large deletions of about 200 kb covering the entire vg gene and adjacent to sca and l(2)C gene-markers as well. 23 mutants from 48 (47.9%) were found to have a wild-type gene structure showing that the exchange breakpoints are located outside of the vg gene. 25 others display the intragenic lesions of different complexity detected by PCR as the absence of(i) either one fragment or (ii) two or more (6-7) adjacent fragments and (iii) simultaneously several (i) or (i) and (ii) types separated by normal gene regions. It is important that 6 from 25 mutants have the breakpoint inside the vg gene and display the (i) or (ii) type of lesions at the gene regions containing the putative break whereas 5 others from 25 with the above lesions have the exchange breakpoint outside the vg gene. Therefore, the breakpoints underlying either inversions or translocations induced by low- and high-LET radiation are likely to be located within and outside the gene under study. Thereby, the formation of exchanges is accompanied by DNA deletions of various sizes at the exchange breakpoints. The molecular model of formation of such exchange-deletion rearrangements is elaborated and presented. Also, conception of the predominately clustered action of both low- and high-LET radiation on the germ cell genome is suggested as the summing-up of the presented results. The ability of ionizing radiation to induce the clusters of genetic alterations in the form of hidden DNA damages as well as gene/chromosome mutations is determined by the track structure and hierarchical organization of the genome. To detect the quality and frequency patterns of all components of the cluster, joint molecular, genetic and cytological techniques need to be used.

Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

NASA Astrophysics Data System (ADS)

Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

2006-03-01

Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

A note on the self-similar solutions to the spontaneous fragmentation equation

NASA Astrophysics Data System (ADS)

Breschi, Giancarlo; Fontelos, Marco A.

2017-05-01

We provide a method to compute self-similar solutions for various fragmentation equations and use it to compute their asymptotic behaviours. Our procedure is applied to specific cases: (i) the case of mitosis, where fragmentation results into two identical fragments, (ii) fragmentation limited to the formation of sufficiently large fragments, and (iii) processes with fragmentation kernel presenting a power-like behaviour.

A Raman scattering and FT-IR spectroscopic study on the effect of the solar radiation in Antarctica on bovine cornea

NASA Astrophysics Data System (ADS)

Yamamoto, Tatsuyuki; Murakami, Naoki; Yoshikiyo, Keisuke; Takahashi, Tetsuya; Yamamoto, Naoyuki

2010-01-01

The Raman scattering and FT-IR spectra of the corneas, transported to the Syowa station in Antarctica and exposed to the solar radiation of the mid-summer for four weeks, were studied to reveal that type IV collagen involved in corneas were fragmented. The amide I and III Raman bands were observed at 1660 and 1245 cm -1, respectively, and the amide I and II infrared bands were observed at 1655 and 1545 cm -1, respectively, for original corneas before exposure. The background of Raman signals prominently increased and the ratio of amide II infrared band versus amide I decreased by the solar radiation in Antarctica. The control experiment using an artificial UV lamp was also performed in laboratory. The decline rate of the amide II/amide I was utilized for estimating the degree of fragmentation of collagen, to reveal that the addition of vitamin C suppressed the reaction while the addition of sugars promoted it. The effect of the solar radiation in Antarctica on the corneas was estimated as the same as the artificial UV lamp of four weeks (Raman) or one week (FT-IR) exposure.

Inhibiting prolyl isomerase activity by hybrid organic-inorganic molecules containing rhodium(II) fragments.

PubMed

Coughlin, Jane M; Kundu, Rituparna; Cooper, Julian C; Ball, Zachary T

2014-11-15

A small molecule containing a rhodium(II) tetracarboxylate fragment is shown to be a potent inhibitor of the prolyl isomerase FKBP12. The use of small molecules conjugates of rhodium(II) is presented as a general strategy for developing new protein inhibitors based on distinct structural and sequence features of the enzyme active site. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pattern of Cortical Fracture following Corticotomy for Distraction Osteogenesis.

PubMed

Luvan, M; Kanthan, S R; Roshan, G; Saw, A

2015-11-01

Corticotomy is an essential procedure for deformity correction and there are many techniques described. However there is no proper classification of the fracture pattern resulting from corticotomies to enable any studies to be conducted. We performed a retrospective study of corticotomy fracture patterns in 44 patients (34 tibias and 10 femurs) performed for various indications. We identified four distinct fracture patterns, Type I through IV classification based on the fracture propagation following percutaneous corticotomy. Type I transverse fracture, Type II transverse fracture with a winglet, Type III presence of butterfly fragment and Type IV fracture propagation to a fixation point. No significant correlation was noted between the fracture pattern and the underlying pathology or region of corticotomy.

rFN/Cad-11-Modified Collagen Type II Biomimetic Interface Promotes the Adhesion and Chondrogenic Differentiation of Mesenchymal Stem Cells

PubMed Central

Guo, Hongfeng; Zhang, Yuan; Li, Zhengsheng; Kang, Fei; Yang, Bo; Kang, Xia; Wen, Can; Yan, Yanfei; Jiang, Bo; Fan, Yujiang

2013-01-01

Properties of the cell-material interface are determining factors in the successful function of cells for cartilage tissue engineering. Currently, cell adhesion is commonly promoted through the use of polypeptides; however, due to their lack of complementary or modulatory domains, polypeptides must be modified to improve their ability to promote adhesion. In this study, we utilized the principle of matrix-based biomimetic modification and a recombinant protein, which spans fragments 7–10 of fibronectin module III (heterophilic motif ) and extracellular domains 1–2 of cadherin-11 (rFN/Cad-11) (homophilic motif ), to modify the interface of collagen type II (Col II) sponges. We showed that the designed material was able to stimulate cell proliferation and promote better chondrogenic differentiation of rabbit mesenchymal stem cells (MSCs) in vitro than both the FN modified surfaces and the negative control. Further, the Col II/rFN/Cad-11-MSCs composite stimulated cartilage formation in vivo; the chondrogenic effect of Col II alone was much less significant. These results suggested that the rFN/Cad-11-modified collagen type II biomimetic interface has dual biological functions of promoting adhesion and stimulating chondrogenic differentiation. This substance, thus, may serve as an ideal scaffold material for cartilage tissue engineering, enhancing repair of injured cartilage in vivo. PMID:23919505

A recombinant estrogen receptor fragment-based homogeneous fluorescent assay for rapid detection of estrogens.

PubMed

Wang, Dan; Xie, Jiangbi; Zhu, Xiaocui; Li, Jinqiu; Zhao, Dongqin; Zhao, Meiping

2014-05-15

In this work, we demonstrate a novel estrogenic receptor fragment-based homogeneous fluorescent assay which enables rapid and sensitive detection of 17β-estradiol (E2) and other highly potent estrogens. A modified human estrogenic receptor fragment (N-His × 6-hER270-595-C-Strep tag II) has been constructed that contains amino acids 270-595 of wild-type human estrogenic receptor α (hER270-595) and two specific tags (6 × His and Strep tag II) fused to the N and C terminus, respectively. The designed receptor protein fragment could be easily produced by prokaryotic expression with high yield and high purity. The obtained protein exhibits high binding affinity to E2 and the two tags greatly facilitate the application of the recombinant protein. Taking advantage of the unique spectroscopic properties of coumestrol (CS), a fluorescent phytoestrogen, a CS/hER270-595-based fluorescent assay has been developed which can sensitively respond to E2 within 1.0 min with a linear working range from 0.1 to 20 ng/mL and a limit of detection of 0.1 ng/mL. The assay was successfully applied for rapid detection of E2 in the culture medium of rat hippocampal neurons. The method also holds great potential for high-throughput monitoring the variation of estrogen levels in complex biological fluids, which is crucial for investigation of the molecular basis of various estrogen-involved processes. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of the metal environment on the ferromagnetic interaction in the Co-NC-W pairs of octacyanotungstate(V)-Cobalt(II) three-dimensional networks.

PubMed

Clima, Sergiu; Hendrickx, Marc F A; Chibotaru, Liviu F; Soncini, Alessandro; Mironov, Vladimir; Ceulemans, Arnout

2007-04-02

State of the art CASSCF and CASPT2 calculations have been performed to elucidate the nature of ferromagnetism of CoII-NC-WV pairs in the three-dimensional compound [[WV(CN)2]2[(micro-CN)4CoII(H2O)2]3.4H2O]n, which has been recently synthesized and investigated by a number of experimental techniques (Herrera, J. M.; Bleuzen, A.; Dromzée, Y.; Julve, M.; Lloret, F.; Verdaguer, M. Inorg. Chem. 2003, 42, 7052-7059). In this network, the Co ions are in the high-spin (S = 3/2) state, while the single unpaired electron on the W centers occupies the lowest orbital of the dz2 type of the 5d shell. In agreement with the suggestion made by Herrera et al., we find that the ferromagnetism is due to a certain occupation scheme of the orbitals from the parent octahedral t2g shell on CoII sites, in which the orbital accommodating the unpaired electron is orthogonal to the dz2 orbitals of the surrounding W ions. We investigate the stabilization of such an orbital configuration on the Co sites and find that it cannot be achieved in the ground state of isolated mononuclear fragments [CoII(NC)4(OH2)2]2- for any conformations of the coordinated water molecules and Co-N-C bond angles. On the other hand, it is stabilized by the interaction of the complex with neighboring W ions, which are simulated here by effective potentials. The calculated exchange coupling constants for the CoII-NC-WV binuclear fragments are in reasonable agreement with the measured Curie-Weiss constant for this compound. As additional evidence for the inferred electronic configuration on the Co sites, the ligand-field transitions, the temperature-dependent magnetic susceptibility, and the field-dependent low-temperature magnetization, simulated ab initio for the mononuclear Co fragments, are in agreement with the available data for another compound [WIV[(micro-CN)4-CoII(H2O)2]2.4H2O]n containing diamagnetic W and high-spin Co ions in an isostructural environment.

Gene Identification of Pheromone Gland Genes Involved in Type II Sex Pheromone Biosynthesis and Transportation in Female Tea Pest Ectropis grisescens

PubMed Central

Li, Zhao-Qun; Ma, Long; Yin, Qian; Cai, Xiao-Ming; Luo, Zong-Xiu; Bian, Lei; Xin, Zhao-Jun; He, Peng; Chen, Zong-Mao

2018-01-01

Moths can biosynthesize sex pheromones in the female sex pheromone glands (PGs) and can distinguish species-specific sex pheromones using their antennae. However, the biosynthesis and transportation mechanism for Type II sex pheromone components has rarely been documented in moths. In this study, we constructed a massive PG transcriptome database (14.72 Gb) from a moth species, Ectropis grisescens, which uses type II sex pheromones and is a major tea pest in China. We further identified putative sex pheromone biosynthesis and transportation-related unigenes: 111 cytochrome P450 monooxygenases (CYPs), 25 odorant-binding proteins (OBPs), and 20 chemosensory proteins (CSPs). Tissue expression and phylogenetic tree analyses showed that one CYP (EgriCYP341-fragment3), one OBP (EgriOBP4), and one CSP (EgriCSP10) gene displayed an enriched expression in the PGs, and that EgriOBP2, 3, and 25 are clustered in the moth pheromone-binding protein clade. We considered these our candidate genes. Our results yielded large-scale PG sequence information for further functional studies. PMID:29317471

Phytochemicals as Anticancer and Chemopreventive Topoisomerase II Poisons

PubMed Central

Ketron, Adam C.

2013-01-01

Phytochemicals are a rich source of anticancer drugs and chemopreventive agents. Several of these chemicals appear to exert at least some of their effects through interactions with topoisomerase II, an essential enzyme that regulates DNA supercoiling and removes knots and tangles from the genome. Topoisomerase II-active phytochemicals function by stabilizing covalent protein-cleaved DNA complexes that are intermediates in the catalytic cycle of the enzyme. As a result, these compounds convert topoisomerase II to a cellular toxin that fragments the genome. Because of their mode of action, they are referred to as topoisomerase II poisons as opposed to catalytic inhibitors. The first sections of this article discuss DNA topology, the catalytic cycle of topoisomerase II, and the two mechanisms (interfacial vs. covalent) by which different classes of topoisomerase II poisons alter enzyme activity. Subsequent sections discuss the effects of several phytochemicals on the type II enzyme, including demethyl-epipodophyllotoxins (semisynthetic anticancer drugs) as well as flavones, flavonols, isoflavones, catechins, isothiocyanates, and curcumin (dietary chemopreventive agents). Finally, the leukemogenic potential of topoisomerase II-targeted phytochemicals is described. PMID:24678287

Biofragments: An Approach towards Predicting Protein Function Using Biologically Related Fragments and its Application to Mycobacterium tuberculosis CYP126

PubMed Central

Hudson, Sean A; Mashalidis, Ellene H; Bender, Andreas; McLean, Kirsty J; Munro, Andrew W; Abell, Chris

2014-01-01

We present a novel fragment-based approach that tackles some of the challenges for chemical biology of predicting protein function. The general approach, which we have termed biofragments, comprises two key stages. First, a biologically relevant fragment library (biofragment library) can be designed and constructed from known sets of substrate-like ligands for a protein class of interest. Second, the library can be screened for binding to a novel putative ligand-binding protein from the same or similar class, and the characterization of hits provides insight into the basis of ligand recognition, selectivity, and function at the substrate level. As a proof-of-concept, we applied the biofragments approach to the functionally uncharacterized Mycobacterium tuberculosis (Mtb) cytochrome P450 isoform, CYP126. This led to the development of a tailored CYP biofragment library with notable 3D characteristics and a significantly higher screening hit rate (14 %) than standard drug-like fragment libraries screened previously against Mtb CYP121 and 125 (4 % and 1 %, respectively). Biofragment hits were identified that make both substrate-like type-I and inhibitor-like type-II interactions with CYP126. A chemical-fingerprint-based substrate model was built from the hits and used to search a virtual TB metabolome, which led to the discovery that CYP126 has a strong preference for the recognition of aromatics and substrate-like type-I binding of chlorophenol moieties within the active site near the heme. Future catalytic analyses will be focused on assessing CYP126 for potential substrate oxidative dehalogenation. PMID:24677424

A deletion in the chromosome of Bacteroides thetaiotaomicron that abolishes production of chondroitinase II does not affect survival of the organism in gastrointestinal tracts of exgermfree mice.

PubMed Central

Salyers, A A; Guthrie, E P

1988-01-01

Bacteroides thetaiotaomicron, an obligate anaerobe normally found in high concentrations in the human colon, is one of the few colon bacteria that can ferment host mucopolysaccharides such as chondroitin sulfate. Previously, we found that a directed insertional mutation in the gene that codes for the chondroitinase II gene of B. thetaiotaomicron did not affect growth on chondroitin sulfate despite the fact that chondroitinase II accounts for 70% of the total cellular chondroitinase activity. Thus, the chondroitinase II gene did not seem to contribute significantly to growth on chondroitin sulfate when the bacteria were grown in laboratory medium. To determine whether this enzyme is important for bacteria growing in the intestinal tract, we tested the ability of a strain that does not produce chondroitinase II to colonize the intestinal tracts of germfree mice and to compete with wild-type B. thetaiotaomicron. The mutant used in these experiments carried a 0.5-kilobase deletion in the chondroitinase II gene and was constructed so that, unlike the original insertion mutant, it contained no exogenous DNA. The deletion mutant colonized the intestinal tracts of germfree mice at the same levels as the wild type. When a mixture of the deletion mutant and wild type was used to colonize germfree mice, the percent wild type, measured by colony hybridization with the deleted 0.5-kilobase fragment as the hybridization probe, did not rise to 100% even after periods as long as 9 weeks. In most experiments, the percent wild type did not rise significantly above the percent in the original mixture.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:3140726

Genotyping of Chromobacterium violaceum isolates by recA PCR-RFLP analysis.

PubMed

Scholz, Holger Christian; Witte, Angela; Tomaso, Herbert; Al Dahouk, Sascha; Neubauer, Heinrich

2005-03-15

Intraspecies variation of Chromobacterium violaceum was examined by comparative sequence - and by restriction fragment length polymorphism analysis of the recombinase A gene (recA-PCR-RFLP). Primers deduced from the known recA gene sequence of the type strain C. violaceum ATCC 12472(T) allowed the specific amplification of a 1040bp recA fragment from each of the 13 C. violaceum strains investigated, whereas other closely related organisms tested negative. HindII-PstI-recA RFLP analysis generated from 13 representative C. violaceum strains enabled us to identify at least three different genospecies. In conclusion, analysis of the recA gene provides a rapid and robust nucleotide sequence-based approach to specifically identify and classify C. violaceum on genospecies level.

Pattern of Cortical Fracture following Corticotomy for Distraction Osteogenesis

PubMed Central

Luvan, M; Roshan, G; Saw, A

2015-01-01

Corticotomy is an essential procedure for deformity correction and there are many techniques described. However there is no proper classification of the fracture pattern resulting from corticotomies to enable any studies to be conducted. We performed a retrospective study of corticotomy fracture patterns in 44 patients (34 tibias and 10 femurs) performed for various indications. We identified four distinct fracture patterns, Type I through IV classification based on the fracture propagation following percutaneous corticotomy. Type I transverse fracture, Type II transverse fracture with a winglet, Type III presence of butterfly fragment and Type IV fracture propagation to a fixation point. No significant correlation was noted between the fracture pattern and the underlying pathology or region of corticotomy. PMID:28611907

Stoichiometry of DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein TF1.

PubMed

Schneider, G J; Geiduschek, E P

1990-06-25

The stoichiometry of DNA binding by the bacteriophage SP01-encoded type II DNA-binding protein TF1 has been determined. 3H-Labeled TF1 was allowed to bind to a 32P-labeled DNA fragment containing a TF1 binding site. Multiple TF1-DNA complexes were resolved from each other and from unbound DNA by native gel electrophoresis. DNA-protein complexes were cut from polyacrylamide gels, and the amounts of 3H and 32P contained in each slice were measured. A ratio of 1.12 +/- 0.06 TF1 dimer/DNA molecule was calculated for the fastest-migrating TF1-DNA complex. We conclude that TF1 has a DNA-binding unit of one dimer. More slowly migrating complexes are apparently formed by serial addition of single TF1 dimers.

Gene Scanning of an Internalin B Gene Fragment Using High-Resolution Melting Curve Analysis as a Tool for Rapid Typing of Listeria monocytogenes

PubMed Central

Pietzka, Ariane T.; Stöger, Anna; Huhulescu, Steliana; Allerberger, Franz; Ruppitsch, Werner

2011-01-01

The ability to accurately track Listeria monocytogenes strains involved in outbreaks is essential for control and prevention of listeriosis. Because current typing techniques are time-consuming, cost-intensive, technically demanding, and difficult to standardize, we developed a rapid and cost-effective method for typing of L. monocytogenes. In all, 172 clinical L. monocytogenes isolates and 20 isolates from culture collections were typed by high-resolution melting (HRM) curve analysis of a specific locus of the internalin B gene (inlB). All obtained HRM curve profiles were verified by sequence analysis. The 192 tested L. monocytogenes isolates yielded 15 specific HRM curve profiles. Sequence analysis revealed that these 15 HRM curve profiles correspond to 18 distinct inlB sequence types. The HRM curve profiles obtained correlated with the five phylogenetic groups I.1, I.2, II.1, II.2, and III. Thus, HRM curve analysis constitutes an inexpensive assay and represents an improvement in typing relative to classical serotyping or multiplex PCR typing protocols. This method provides a rapid and powerful screening tool for simultaneous preliminary typing of up to 384 samples in approximately 2 hours. PMID:21227395

Analysis of a two-domain binding site for the urokinase-type plasminogen activator-plasminogen activator inhibitor-1 complex in low-density-lipoprotein-receptor-related protein.

PubMed

Andersen, O M; Petersen, H H; Jacobsen, C; Moestrup, S K; Etzerodt, M; Andreasen, P A; Thøgersen, H C

2001-07-01

The low-density-lipoprotein-receptor (LDLR)-related protein (LRP) is composed of several classes of domains, including complement-type repeats (CR), which occur in clusters that contain binding sites for a multitude of different ligands. Each approximately 40-residue CR domain contains three conserved disulphide linkages and an octahedral Ca(2+) cage. LRP is a scavenging receptor for ligands from extracellular fluids, e.g. alpha(2)-macroglobulin (alpha(2)M)-proteinase complexes, lipoprotein-containing particles and serine proteinase-inhibitor complexes, like the complex between urokinase-type plasminogen activator (uPA) and the plasminogen activator inhibitor-1 (PAI-1). In the present study we analysed the interaction of the uPA-PAI-1 complex with an ensemble of fragments representing a complete overlapping set of two-domain fragments accounting for the ligand-binding cluster II (CR3-CR10) of LRP. By ligand blotting, solid-state competition analysis and surface-plasmon-resonance analysis, we demonstrate binding to multiple CR domains, but show a preferential interaction between the uPA-PAI-1 complex and a two-domain fragment comprising CR domains 5 and 6 of LRP. We demonstrate that surface-exposed aspartic acid and tryptophan residues at identical positions in the two homologous domains, CR5 and CR6 (Asp(958,CR5), Asp(999,CR6), Trp(953,CR5) and Trp(994,CR6)), are critical for the binding of the complex as well as for the binding of the receptor-associated protein (RAP) - the folding chaperone/escort protein required for transport of LRP to the cell surface. Accordingly, the present work provides (1) an identification of a preferred binding site within LRP CR cluster II; (2) evidence that the uPA-PAI-1 binding site involves residues from two adjacent protein domains; and (3) direct evidence identifying specific residues as important for the binding of uPA-PAI-1 as well as for the binding of RAP.

Characterization of class II alpha genes and DLA-D region allelic associations in the dog.

PubMed

Sarmiento, U M; Storb, R F

1988-10-01

Human major histocompatibility complex (HLA) cDNA probes were used to analyze the restriction fragment length polymorphism (RFLP) of the alpha genes of the DLA-D region in dogs. Genomic DNA from peripheral blood leucocytes of 23 unrelated DLA-D homozygous dogs representing nine DLA-D types (defined by mixed leucocyte reaction) was digested with restriction enzymes (BamHI, EcoRI, Hind III, Pvu II, Taq I, Rsa I, Msp I, Pst I and Bgl II), separated by agarose gel electrophoresis and transferred onto Biotrace membrane. The Southern blots were successively hybridized with radiolabelled HLA cDNA probes corresponding to DQ, DP, DZ and DR alpha genes. Clear evidence was obtained for the canine homologues of DQ and DR alpha genes with simple bi- or tri-allelic polymorphism respectively. Evidence for a single, nonpolymorphic DP alpha gene was also obtained. However, the presence of a DZ alpha gene could not be clearly demonstrated in canine genomic DNA. This report extends our previous RFLP analysis documenting polymorphism of DLA class II beta genes in the same panel of homozygous typing cell dogs, and provides the basis for DLA-D genotyping at a population level. This study also characterizes the RFLP-defined preferential allelic associations across the DLA-D region in nine different homozygous typing cell specificities.

Evidence that TMPRSS2 Activates the Severe Acute Respiratory Syndrome Coronavirus Spike Protein for Membrane Fusion and Reduces Viral Control by the Humoral Immune Response▿

PubMed Central

Glowacka, Ilona; Bertram, Stephanie; Müller, Marcel A.; Allen, Paul; Soilleux, Elizabeth; Pfefferle, Susanne; Steffen, Imke; Tsegaye, Theodros Solomon; He, Yuxian; Gnirss, Kerstin; Niemeyer, Daniela; Schneider, Heike; Drosten, Christian; Pöhlmann, Stefan

2011-01-01

The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) can be proteolytically activated by cathepsins B and L upon viral uptake into target cell endosomes. In contrast, it is largely unknown whether host cell proteases located in the secretory pathway of infected cells and/or on the surface of target cells can cleave SARS S. We along with others could previously show that the type II transmembrane protease TMPRSS2 activates the influenza virus hemagglutinin and the human metapneumovirus F protein by cleavage. Here, we assessed whether SARS S is proteolytically processed by TMPRSS2. Western blot analysis revealed that SARS S was cleaved into several fragments upon coexpression of TMPRSS2 (cis-cleavage) and upon contact between SARS S-expressing cells and TMPRSS2-positive cells (trans-cleavage). cis-cleavage resulted in release of SARS S fragments into the cellular supernatant and in inhibition of antibody-mediated neutralization, most likely because SARS S fragments function as antibody decoys. trans-cleavage activated SARS S on effector cells for fusion with target cells and allowed efficient SARS S-driven viral entry into targets treated with a lysosomotropic agent or a cathepsin inhibitor. Finally, ACE2, the cellular receptor for SARS-CoV, and TMPRSS2 were found to be coexpressed by type II pneumocytes, which represent important viral target cells, suggesting that SARS S is cleaved by TMPRSS2 in the lung of SARS-CoV-infected individuals. In summary, we show that TMPRSS2 might promote viral spread and pathogenesis by diminishing viral recognition by neutralizing antibodies and by activating SARS S for cell-cell and virus-cell fusion. PMID:21325420

Fragment and knowledge-based design of selective GSK-3beta inhibitors using virtual screening models.

PubMed

Vadivelan, S; Sinha, Barij Nayan; Tajne, Sunita; Jagarlapudi, Sarma A R P

2009-06-01

Glycogen Synthase Kinase 3beta is one of the important targets in the treatment of type II diabetes and Alzheimer's disease. Currently this target is in pursuit for type II diabetes and a few GSK-3beta inhibitors have been now advanced to Phases I and II of clinical trials. The best validated HypoGen model consists of four pharmacophore features; 1) two hydrogen bond acceptors, 2) one hydrogen bond donor and 3) one hydrophobic. This pharmacophore model correlates well with the docking model, one hydrogen bond acceptor is necessary for the H-bond interaction with VAL135, and second hydrogen bond acceptor is important for the H-bond interactions with ARG141 and the hydrophobic feature may be required for the weak H-bond interactions with ASP133. The comparative model was developed from analogue and structure-based models like Catalyst, Glide SP & XP, Gold Fitness & ChemScore and Ligand Fit using multiple linear regression analysis. A virtual library of 10,000 molecules was generated employing fragment and knowledge-based approach and the comparative model was used to predict the activities of these molecules. The H-bond with ARG141 appears to be unique to GSK-3beta and explains the high GSK-3beta selectivity observed for 1H-Quinazolin-4-ones and Benzo[e][1,3]oxazin-4-ones. This understanding of protein-ligand interactions and molecular recognition increases the rapid development of potent and selective inhibitors, and also helps to eliminate the increase in number of false positives and negatives.

Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

PubMed

Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

2017-12-01

Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

Specific binding of a naturally occurring amyloidogenic fragment of Streptococcus mutans adhesin P1 to intact P1 on the cell surface characterized by solid state NMR spectroscopy

PubMed Central

Tang, Wenxing; Bhatt, Avni; Smith, Adam N.; Crowley, Paula J.; Brady, L. Jeannine; Long, Joanna R.

2016-01-01

The P1 adhesin (aka Antigen I/II or PAc) of the cariogenic bacterium Streptococcus mutans is a cell surface-localized protein involved in sucrose-independent adhesion and colonization of the tooth surface. The immunoreactive and adhesive properties of S. mutans suggest an unusual functional quaternary ultrastructure comprised of intact P1 covalently attached to the cell wall and interacting with non-covalently associated proteolytic fragments thereof, particularly the ~57-kDa C-terminal fragment C123 previously identified as Antigen II. S. mutans is capable of amyloid formation when grown in a biofilm and P1 is among its amyloidogenic proteins. The C123 fragment of P1 readily forms amyloid fibers in vitro suggesting it may play a role in the formation of functional amyloid during biofilm development. Using wild-type and P1-deficient strains of S. mutans, we demonstrate that solid state NMR (ssNMR) spectroscopy can be used to 1) globally characterize cell walls isolated from a Gram-positive bacterium and 2) characterize the specific binding of heterologously expressed, isotopically-enriched C123 to cell wall-anchored P1. Our results lay the groundwork for future high-resolution characterization of the C123/P1 ultrastructure and subsequent steps in biofilm formation via ssNMR spectroscopy, and they support an emerging model of S. mutans colonization whereby quaternary P1-C123 interactions confer adhesive properties important to binding to immobilized human salivary agglutinin. PMID:26837620

Specific binding of a naturally occurring amyloidogenic fragment of Streptococcus mutans adhesin P1 to intact P1 on the cell surface characterized by solid state NMR spectroscopy.

PubMed

Tang, Wenxing; Bhatt, Avni; Smith, Adam N; Crowley, Paula J; Brady, L Jeannine; Long, Joanna R

2016-02-01

The P1 adhesin (aka Antigen I/II or PAc) of the cariogenic bacterium Streptococcus mutans is a cell surface-localized protein involved in sucrose-independent adhesion and colonization of the tooth surface. The immunoreactive and adhesive properties of S. mutans suggest an unusual functional quaternary ultrastructure comprised of intact P1 covalently attached to the cell wall and interacting with non-covalently associated proteolytic fragments thereof, particularly the ~57-kDa C-terminal fragment C123 previously identified as Antigen II. S. mutans is capable of amyloid formation when grown in a biofilm and P1 is among its amyloidogenic proteins. The C123 fragment of P1 readily forms amyloid fibers in vitro suggesting it may play a role in the formation of functional amyloid during biofilm development. Using wild-type and P1-deficient strains of S. mutans, we demonstrate that solid state NMR (ssNMR) spectroscopy can be used to (1) globally characterize cell walls isolated from a Gram-positive bacterium and (2) characterize the specific binding of heterologously expressed, isotopically-enriched C123 to cell wall-anchored P1. Our results lay the groundwork for future high-resolution characterization of the C123/P1 ultrastructure and subsequent steps in biofilm formation via ssNMR spectroscopy, and they support an emerging model of S. mutans colonization whereby quaternary P1-C123 interactions confer adhesive properties important to binding to immobilized human salivary agglutinin.

DNA fingerprinting of isolates of Streptococcus mutans by pulsed-field gel electrophoresis.

PubMed

Mineyama, R; Yoshino, S; Maeda, N

2007-01-01

Forty isolates and five standard laboratory strains, representing serotypes c, e and f of Streptococcus mutans were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of the genomic DNA with BssH II. The digestion patterns of standard laboratory strains were characteristic of serotypes c, e and f. Serotypes c and f generated diagnostic DNA fragments of approximately 145 kbp and of approximately 130-175 kbp in length, respectively. Serotype e generated a ladder of at least 14 fragments of 15-155 kbp in length. The digestion patterns of isolates were essentially similar to those of the standard laboratory strains. The patterns of almost all isolates obtained from a single individual were identical, but patterns of a few different types were also observed among isolates obtained from two individuals. Digestion with BssH II revealed differences among isolates obtained from different individuals. We used differences in banding patterns among isolates to construct a dendrogram. The dendrogram included two major clusters, one that consisted of isolates of serotypes c and f, and an other that consisted of isolates of serotype e. Our results indicate that BssH II is a useful enzyme for distinguishing among isolates of S. mutans and that digestion patterns obtained by PFGE can be used for chromosomal DNA fingerprinting.

Genetic Variation among Staphylococcus aureus Strains from Bovine Milk and Their Relevance to Methicillin-Resistant Isolates from Humans ▿

PubMed Central

Hata, Eiji; Katsuda, Ken; Kobayashi, Hideki; Uchida, Ikuo; Tanaka, Kiyoshi; Eguchi, Masashi

2010-01-01

In genetic analysis of bovine Staphylococcus aureus isolates that are recognized as an important pathogenic bacterium in bovine mastitis, multilocus sequence typing (MLST) showed strong correlation to the results of pulsed-field gel electrophoresis, coa PCR-restriction fragment length polymorphism (RFLP), spa typing, and the coagulase serotyping method. According to MLST results, strains derived from sequence type 97 (ST97) and ST705 were suggested as not only dominant bovine S. aureus lineages in Japan but also pandemic bovine S. aureus lineages. Although both lineages seem to be distantly related to each other by phylogenetic analysis, both had common characteristics, i.e., lukM/lukF′-PV and coagulase serotype VI. These characteristics were very rare among minor bovine strains and human strains and may contribute to the host specificity of these lineages. Four methicillin-resistant S. aureus (MRSA) isolates were first confirmed from bovine milk in Japan; these isolates showed geno- and serotypes that were identical or similar to those of human MRSA isolates in Japan (ST5, staphylococcal cassette chromosome mec type II [SCCmec II], Spa type t002 or t375, and coagulase serotype II, and ST89, SCCmec IIIa, Spa type t5266, and coagulase serotype I). ST5 and ST89 are uncommon among bovine isolates in the world, whereas these STs are common among human MRSA isolates in Japan. PMID:20392913

Truncated recombinant human SP-D attenuates emphysema and type II cell changes in SP-D deficient mice

PubMed Central

Knudsen, Lars; Ochs, Matthias; MacKay, Rosemarie; Townsend, Paul; Deb, Roona; Mühlfeld, Christian; Richter, Joachim; Gilbert, Fabian; Hawgood, Samuel; Reid, Kenneth; Clark, Howard

2007-01-01

Background Surfactant protein D (SP-D) deficient mice develop emphysema-like pathology associated with focal accumulations of foamy alveolar macrophages, an excess of surfactant phospholipids in the alveolar space and both hypertrophy and hyperplasia of alveolar type II cells. These findings are associated with a chronic inflammatory state. Treatment of SP-D deficient mice with a truncated recombinant fragment of human SP-D (rfhSP-D) has been shown to decrease the lipidosis and alveolar macrophage accumulation as well as production of proinflammatory chemokines. The aim of this study was to investigate if rfhSP-D treatment reduces the structural abnormalities in parenchymal architecture and type II cells characteristic of SP-D deficiency. Methods SP-D knock-out mice, aged 3 weeks, 6 weeks and 9 weeks were treated with rfhSP-D for 9, 6 and 3 weeks, respectively. All mice were sacrificed at age 12 weeks and compared to both PBS treated SP-D deficient and wild-type groups. Lung structure was quantified by design-based stereology at the light and electron microscopic level. Emphasis was put on quantification of emphysema, type II cell changes and intracellular surfactant. Data were analysed with two sided non-parametric Mann-Whitney U-test. Main Results After 3 weeks of treatment, alveolar number was higher and mean alveolar size was smaller compared to saline-treated SP-D knock-out controls. There was no significant difference concerning these indices of pulmonary emphysema within rfhSP-D treated groups. Type II cell number and size were smaller as a consequence of treatment. The total volume of lamellar bodies per type II cell and per lung was smaller after 6 weeks of treatment. Conclusion Treatment of SP-D deficient mice with rfhSP-D leads to a reduction in the degree of emphysema and a correction of type II cell hyperplasia and hypertrophy. This supports the concept that rfhSP-D might become a therapeutic option in diseases that are characterized by decreased SP-D levels in the lung. PMID:17915009

Phospholipase C/protein kinase C pathway mediates angiotensin II-dependent apoptosis in neonatal rat cardiac fibroblasts expressing AT1 receptor.

PubMed

Vivar, Raul; Soto, Cristian; Copaja, Miguel; Mateluna, Francisca; Aranguiz, Pablo; Muñoz, Juan Pablo; Chiong, Mario; Garcia, Lorena; Letelier, Alan; Thomas, Walter G; Lavandero, Sergio; Díaz-Araya, Guillermo

2008-08-01

Cardiac fibroblasts are the major non-myocyte cell constituent in the myocardium, and they are involved in heart remodeling. Angiotensin II type 1 receptor (AT1R) mediates the established actions of angiotensin II (Ang II), and changes in its expression have been reported in cardiac fibroblasts after myocardial infarction. However, the AT1R-dependent signaling pathways involved in cardiac fibroblast death remain unknown. Using adenovirus, we ectopically expressed AT1R in cultured neonatal rat cardiac fibroblasts and investigated the role of the phospholipase (PLC)/protein kinase C (PKC) pathway on Ang II-dependent death. Ang II induced cardiac fibroblast death characterized by an early loss of mitochondrial membrane potential, increased Bax/Bcl-2 ratio, caspase-3 activation, and DNA fragmentation. All these effects were prevented by the AT1R antagonist losartan, PLC inhibitor U73122, and PKC inhibitor Gö6976. We conclude that Ang II stimulates the intrinsic apoptotic pathway in cultured cardiac fibroblasts by the AT1R/PLC/PKC signaling pathway.

Comparison of Abbott RealTime genotype II, GeneMatrix restriction fragment mass polymorphism and Sysmex HISCL HCV Gr assays for hepatitis C virus genotyping.

PubMed

Han, Mi-Soon; Park, Yongjung; Kim, Hyon-Suk

2017-07-26

Hepatitis C virus (HCV) genotype is a predictive marker for treatment response. We sequentially evaluated the performances of two nucleic acid amplification tests (NAATs) and one serology assay for HCV genotype: Abbott RealTime genotype II (RealTime II), GeneMatrix restriction fragment mass polymorphism (RFMP), and Sysmex HISCL HCV Gr (HISCL Gr). We examined 281 clinical samples with three assays. The accuracy was assessed using the HCV Genotype Performance Panel PHW204 (SeraCare Life Sciences) for two NAATs. Discrepant cases were re-genotyped by the Versant HCV v.2.0 (line probe 2.0) assay. With the RealTime II assay, clinic samples were analyzed as follows: genotypes 1b (43.1%), 2 (40.2%), 1 subtypes other than 1a and 1b (12.5%), 3 (1.8%), 4 (1.4%), 1a (0.7%), 6 (0.4%), and mixed (1.1%). The RealTime II and RFMP assays showed a type concordance rate of 97.5% (274/281) (κ=0.80) and no significant discordance (p=0.25). Both assays accurately genotyped all samples in the Performance Panel by the subtype level. The HISCL Gr assay showed concordance rates of about 91% (κ<0.40) and statistically significant discordances with two NAATs (p<0.05). In confirmation tests, the results of RFMP assay were the most consistent with those of Versant 2.0 assay. The three HCV assays provided genotyping and serotyping results with good concordance rates. The two NAATs (RealTime II and RFMP) showed comparable performance and good agreement. However, the results of the HISCL Gr assay showed statistically significant differences with those of the NAATs.

Surgical management for avulsion fracture of the calcaneal tuberosity.

PubMed

Yu, Guang-rong; Pang, Qing-jiang; Yu, Xiao; Chen, Da-wei; Yang, Yun-feng; Li, Bing; Zhou, Jia-qian

2013-08-01

To discuss the operative methods and curative effect of calcaneal tuberosity fracture. A retrospective study was done to analyze 15 patients with calcaneal tuberosity fracture who received surgical management between January 2008 and June 2011. There were nine males and six females, with the age ranging from 31 to 68 years (average, 51.4 years). All the patients had unilateral acute injury, with the left foot in 7 cases and the right foot in 8 cases. According to the Beavis classification, there were three cases in type I and 12 cases in type II. All the cases in type I and 10 cases in type II were treated with open reduction and screw fixation. The other two cases in type II with larger fragment involving a portion of the subtalar joint were treated with plate and screw fixation. The effect of the treatment was assessed according to the ankle and hindfoot score system of American Orthopaedic Foot and Ankle Society (AOFAS) after the operation. Ten patients were followed up for 12 to 36 months (average, 20 months). The healing time in these patients ranged from 8 to 25 weeks (average, 12 weeks). The postoperative score ranged from 47 to 100 points (average, 91.1 points). Seven cases were rated as excellent, two as good, and one as poor. The rate of excellent and good was 90%. Necrosis of skin and soft tissue and exposure of the plate happened in one patient, who eventually healed after 3 weeks by debridement with plate preserved and peroneal artery perforator flap transplantation. Loss of reduction happened to another patient, who was treated with revision surgery by open reduction and screw fixation again. To patients with obvious fracture displacement, whose soft tissues are irritated severely, emergency open reduction and internal fixation operation should be offered to prevent the necrosis of the flaps as far as possible. To patients with small fractures, it is advisable to choose open reduction and large diameter screw fixation, while plate and screw fixation may be better for the patients with large fragments, especially for those with the fracture line extending to the subtalar joint. © 2013 Chinese Orthopaedic Association and Wiley Publishing Asia Pty Ltd.

Inhibitory effects of polyphenols in leaves of Artemisia princeps PAMP on protein fragmentation by Cu(II)-H2O2 in vitro.

PubMed

Toda, Shizuo

2004-01-01

The leaves of Artemisia princeps PAMP have traditionally been used as teas and foods in Japan. Polyphenols in Artemisia plants have been shown to have inhibitory effects against biological damages. The inhibitory effects of polyphenols in the leaves of A. princeps PAMP were investigated on protein fragmentation induced by Cu(II)-H(2)O(2) in vitro. The total polyphenol content in the leaves of A. princeps PAMP was 4.58%. The condensed tannin content was 0.62% by vanillin assay and 0.14% by proanthrocyanidin assay. The polyphenols in the leaves of A. princeps PAMP inhibited bovine albumin fragmentation by Cu(II)-H(2)O(2). The effects of polyphenols in the leaves of A. princeps PAMP were similar to those of tannic acid, studied as a related polyphenol. These results demonstrated that the leaves of A. princeps PAMP have inhibitory effects on protein fragmentation damage.

Excess Silica Substitution in Plagioclase Grains in the Pasamonte Eucrite

NASA Technical Reports Server (NTRS)

Mittlefehldt, D. W.; Le, L.; Berger, E. L.

2017-01-01

Pasamonte is a clast-rich polymict basaltic breccia with O- and Cr-isotopic compositions that are resolved from those of most eucrites. It is dominated by two mafic clast types: (i) very-fine- to fine-grained, variolitic, subophitic and ophitic basalts, usually containing zoned pyroxenes; and (ii) fine- to medium grained hypidiomorphic-granular and allotriomorphic-granular microgabbros containing pyroxenes composed of augite lamellae in homogeneous pigeonite hosts. Minor clast types are fine-grained impact-melt, mafic-breccia and mafic-granular clasts; coarse matrix mineral fragments include pyroxene, plagioclase, silica, ferroan olivine and ilmenite. Our petrologic studies include determination of plagioclase compositions for the two major clast types and matrix grains, which we report here.

[Expression in Escherichia coli of the gspd(l) gene of the type II secretion system in Leptospira borgpetersenii serovariety hardjo].

PubMed

Reyes, Ernesto Armando Rodríguez; Cullen, Paul; Bulach, Dieter; Adler, Ben; Haake, David; de la Peña-Moctezuma, Alejandro

2005-01-01

A fragment of 1.539 pb of the gene homologous to gspD of Hardjobovis was clonated in the pET28a vector and it was transformed into E. coli C43 and Rosetta strains. The sequence of GspD(L) showed 46 % of similitude with E. coli GspD secretin. The expression of recombinant GspD(L) was obtained in Rosetta strain.

Stronger enhancer II/core promoter activities of hepatitis B virus isolates of B2 subgenotype than those of C2 subgenotype

PubMed Central

Qin, Yanli; Zhou, Xueshi; Jia, Haodi; Chen, Chaoyang; Zhao, Weifeng; Zhang, Jiming; Tong, Shuping

2016-01-01

Hepatitis B virus (HBV) genotype C causes prolonged chronic infection and increased risk for liver cancer than genotype B. Our previous work revealed lower replication capacity of wild-type genotype C2 than B2 isolates. HBV DNA replication is driven by pregenomic RNA, which is controlled by core promoter (CP) and further augmented by enhancer I (ENI) and enhancer II (ENII). DNA fragments covering these regulatory elements were amplified from B2 and C2 isolates to generate luciferase reporter constructs. As ENII is fully embedded in CP, we inserted HBV DNA fragments in the sense orientation to determine their combined activities, and in the antisense orientation to measure enhancer activities alone. Genotype B2 isolates displayed higher ENI+ENII+CP, ENII+CP, and ENII activities, but not ENI or ENI+ENII activity, than C2 isolates. The higher ENII+CP activity was partly attributable to 4 positions displaying genotype-specific variability. Exchanging CP region was sufficient to revert the replication phenotypes of several B2 and C2 clones tested. These results suggest that a weaker ENII and/or CP at least partly accounts for the lower replication capacities of wild-type C2 isolates, which could drive the subsequent acquisition of CP mutations. Such mutations increase genome replication and are implicated in liver cancer development. PMID:27461034

Stronger enhancer II/core promoter activities of hepatitis B virus isolates of B2 subgenotype than those of C2 subgenotype.

PubMed

Qin, Yanli; Zhou, Xueshi; Jia, Haodi; Chen, Chaoyang; Zhao, Weifeng; Zhang, Jiming; Tong, Shuping

2016-07-27

Hepatitis B virus (HBV) genotype C causes prolonged chronic infection and increased risk for liver cancer than genotype B. Our previous work revealed lower replication capacity of wild-type genotype C2 than B2 isolates. HBV DNA replication is driven by pregenomic RNA, which is controlled by core promoter (CP) and further augmented by enhancer I (ENI) and enhancer II (ENII). DNA fragments covering these regulatory elements were amplified from B2 and C2 isolates to generate luciferase reporter constructs. As ENII is fully embedded in CP, we inserted HBV DNA fragments in the sense orientation to determine their combined activities, and in the antisense orientation to measure enhancer activities alone. Genotype B2 isolates displayed higher ENI+ENII+CP, ENII+CP, and ENII activities, but not ENI or ENI+ENII activity, than C2 isolates. The higher ENII+CP activity was partly attributable to 4 positions displaying genotype-specific variability. Exchanging CP region was sufficient to revert the replication phenotypes of several B2 and C2 clones tested. These results suggest that a weaker ENII and/or CP at least partly accounts for the lower replication capacities of wild-type C2 isolates, which could drive the subsequent acquisition of CP mutations. Such mutations increase genome replication and are implicated in liver cancer development.

Insights into the history of a bacterial group II intron remnant from the genomes of the nitrogen-fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae.

PubMed

Toro, N; Martínez-Rodríguez, L; Martínez-Abarca, F

2014-10-01

Group II introns are self-splicing catalytic RNAs that act as mobile retroelements. In bacteria, they are thought to be tolerated to some extent because they self-splice and home preferentially to sites outside of functional genes, generally within intergenic regions or in other mobile genetic elements, by mechanisms including the divergence of DNA target specificity to prevent target site saturation. RmInt1 is a mobile group II intron that is widespread in natural populations of Sinorhizobium meliloti and was first described in the GR4 strain. Like other bacterial group II introns, RmInt1 tends to evolve toward an inactive form by fragmentation, with loss of the 3' terminus. We identified genomic evidence of a fragmented intron closely related to RmInt1 buried in the genome of the extant S. meliloti/S. medicae species. By studying this intron, we obtained evidence for the occurrence of intron insertion before the divergence of ancient rhizobial species. This fragmented group II intron has thus existed for a long time and has provided sequence variation, on which selection can act, contributing to diverse genetic rearrangements, and to generate pan-genome divergence after strain differentiation. The data presented here suggest that fragmented group II introns within intergenic regions closed to functionally important neighboring genes may have been microevolutionary forces driving adaptive evolution of these rhizobial species.

Insights into the history of a bacterial group II intron remnant from the genomes of the nitrogen-fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae

PubMed Central

Toro, N; Martínez-Rodríguez, L; Martínez-Abarca, F

2014-01-01

Group II introns are self-splicing catalytic RNAs that act as mobile retroelements. In bacteria, they are thought to be tolerated to some extent because they self-splice and home preferentially to sites outside of functional genes, generally within intergenic regions or in other mobile genetic elements, by mechanisms including the divergence of DNA target specificity to prevent target site saturation. RmInt1 is a mobile group II intron that is widespread in natural populations of Sinorhizobium meliloti and was first described in the GR4 strain. Like other bacterial group II introns, RmInt1 tends to evolve toward an inactive form by fragmentation, with loss of the 3′ terminus. We identified genomic evidence of a fragmented intron closely related to RmInt1 buried in the genome of the extant S. meliloti/S. medicae species. By studying this intron, we obtained evidence for the occurrence of intron insertion before the divergence of ancient rhizobial species. This fragmented group II intron has thus existed for a long time and has provided sequence variation, on which selection can act, contributing to diverse genetic rearrangements, and to generate pan-genome divergence after strain differentiation. The data presented here suggest that fragmented group II introns within intergenic regions closed to functionally important neighboring genes may have been microevolutionary forces driving adaptive evolution of these rhizobial species. PMID:24736785

Substitution of aspartate for glycine 103 of the type II collagen triple helical domain: Identification of the minimal mutation which can produce Kniest dysplasia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkin, D.J.; Rimoin, D.L.; Cohn, D.H.

1994-09-01

Kniest dysplasia is an autosomal dominant chondrodysplasia which results from mutations in the gene for type II collagen, COL2A1. Characteristics of the disorder include a short trunk and extremities, mid-face hypoplasia, cleft palate, myopia, retinal detachment, and hearing loss. Recently, deletions of all or part of exon 12 have been identified in individuals with Kniest dysplasia, suggesting that mutations within this region of the protein may primarily result in the Kniest dysplasia phenotype. We used SSCP to analyze an amplified genomic DNA fragment containing exon 12 from 7 individuals with Kniest dysplasia. An abnormality was identified in one patient. DNAmore » sequence analysis demonstrated that the patient was heterozygous for a G to A transition that implied substitution of glycine{sup 103} of the triple helix by aspartate. The mutation was not observed in DNA from either of the proband`s parents. Protein microsequencing demonstrated expression of the abnormal allele in the proband`s cartilage, indicating that the Kniest phenotype results from the presence of abnormal type II collagen molecules in the extracellular matrix. These data demonstrate the minimal mutation which can produce Kniest dysplasia and further support the hypothesis that alteration of a domain which includes the region encoded by exon 12 in the type II collagen protein leads to this disorder. Experiments designed to identify specific effects that mutations in this region have on intermolecular interactions among abnormal type II collagen molecules and other components of the cartilage extracellular matrix may clarify the underlying pathophysiology of Kniest dysplasia.« less

Biological responses of Raw 264.7 macrophage exposed to two strains of Stachybotrys chartarum spores grown on four different wallboard types.

PubMed

Kim, J H; Harvey, L A; Evans, A L; Byfield, G E; Betancourt, D A; Dean, T R

2016-06-01

The many benefits of building "green" have motivated the use of sustainable products in the design and execution of the built environment. However, the use of these natural or recycled materials, some of which have been treated with antimicrobials, provides a growth opportunity for microorganisms with the potential to elicit adverse health effects especially in the presence of an antimicrobial. The focus of this research was to determine the effects of Stachybotrys chartarum (strains Houston and 51-11) grown under different conditions on a macrophage cell line (Raw 264.7) using endpoints, including cytotoxicity, and those associated with immunity specifically inflammation and MHC class II expression. The fungi were grown on four different gypsum products, and macrophages were exposed to whole spores of both strains and fragmented spores of strain 51-11. Whole spores of the Houston strain elicited no cytotoxicity with some level of inflammation, while exposure to whole spores of 51-11 caused variable responses depending on the wallboard type supporting the fungal growth. High concentrations of fragmented 51-11 spores primarily resulted in the apoptosis of macrophage with no inflammation. None of the fungal strains caused elevated levels of major histocompatibility complex (MHC) class II expression on the surface of Raw cells. Mycotoxin levels of 51-11 spores from all of the wallboard types measured  >250 ng/μL of T2 equivalent toxin based on activity. Collectively, the data demonstrated that all of the wallboard types supported growth of fungi with the ability to elicit harmful biological responses with the potential to negatively impact human health.

Methyl-CpG island-associated genome signature tags

DOEpatents

Dunn, John J

2014-05-20

Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

Genetic typing of feline rabies virus isolated in greater Bangkok, Thailand.

PubMed

Kasempimolporn, Songsri; Saengseesom, Wachiraporn; Tirawatnapong, Thaweesak; Puempumpanich, Sununta; Sitprija, Visith

2004-01-01

To study the molecular epidemiology of rabies virus that is prevalent among cats in greater Bangkok, Thailand, a total of 17 rabies virus isolates from cats were characterized and compared with 120 rabies virus isolates from dogs. Analyses were performed on the genetic polymorphism in the rabies virus nucleoprotein (N) gene. Rabies virus N gene of isolates was amplified by reverse transcriptionpolymerase chain reaction. The diversity of N gene was revealed by the restriction fragment length polymorphism (RFLP) method. The rabies virus isolates from cats could be classified into 5 types, designated as Dd I-Hf I, Dd II-Hf II, Dd III-Hf I, Dd IV-Hf I, and Dd IV-Hf III. Type Dd I-Hf I was encountered more frequently than the others. It was apparent that no less than five rabies virus types presented in the areas of Bangkok. Moreover, all five RFLP patterns were typical of those which had been observed in dogs. Our findings suggest that there had been viral transmission between the dogs and the cats.

A large-scale forest fragmentation experiment: the Stability of Altered Forest Ecosystems Project.

PubMed

Ewers, Robert M; Didham, Raphael K; Fahrig, Lenore; Ferraz, Gonçalo; Hector, Andy; Holt, Robert D; Kapos, Valerie; Reynolds, Glen; Sinun, Waidi; Snaddon, Jake L; Turner, Edgar C

2011-11-27

Opportunities to conduct large-scale field experiments are rare, but provide a unique opportunity to reveal the complex processes that operate within natural ecosystems. Here, we review the design of existing, large-scale forest fragmentation experiments. Based on this review, we develop a design for the Stability of Altered Forest Ecosystems (SAFE) Project, a new forest fragmentation experiment to be located in the lowland tropical forests of Borneo (Sabah, Malaysia). The SAFE Project represents an advance on existing experiments in that it: (i) allows discrimination of the effects of landscape-level forest cover from patch-level processes; (ii) is designed to facilitate the unification of a wide range of data types on ecological patterns and processes that operate over a wide range of spatial scales; (iii) has greater replication than existing experiments; (iv) incorporates an experimental manipulation of riparian corridors; and (v) embeds the experimentally fragmented landscape within a wider gradient of land-use intensity than do existing projects. The SAFE Project represents an opportunity for ecologists across disciplines to participate in a large initiative designed to generate a broad understanding of the ecological impacts of tropical forest modification.

A large-scale forest fragmentation experiment: the Stability of Altered Forest Ecosystems Project

PubMed Central

Ewers, Robert M.; Didham, Raphael K.; Fahrig, Lenore; Ferraz, Gonçalo; Hector, Andy; Holt, Robert D.; Kapos, Valerie; Reynolds, Glen; Sinun, Waidi; Snaddon, Jake L.; Turner, Edgar C.

2011-01-01

Opportunities to conduct large-scale field experiments are rare, but provide a unique opportunity to reveal the complex processes that operate within natural ecosystems. Here, we review the design of existing, large-scale forest fragmentation experiments. Based on this review, we develop a design for the Stability of Altered Forest Ecosystems (SAFE) Project, a new forest fragmentation experiment to be located in the lowland tropical forests of Borneo (Sabah, Malaysia). The SAFE Project represents an advance on existing experiments in that it: (i) allows discrimination of the effects of landscape-level forest cover from patch-level processes; (ii) is designed to facilitate the unification of a wide range of data types on ecological patterns and processes that operate over a wide range of spatial scales; (iii) has greater replication than existing experiments; (iv) incorporates an experimental manipulation of riparian corridors; and (v) embeds the experimentally fragmented landscape within a wider gradient of land-use intensity than do existing projects. The SAFE Project represents an opportunity for ecologists across disciplines to participate in a large initiative designed to generate a broad understanding of the ecological impacts of tropical forest modification. PMID:22006969

Multiplex PCR Targeting tpi (Triose Phosphate Isomerase), tcdA (Toxin A), and tcdB (Toxin B) Genes for Toxigenic Culture of Clostridium difficile

PubMed Central

Lemee, Ludovic; Dhalluin, Anne; Testelin, Sabrina; Mattrat, Marie-Andre; Maillard, Karine; Lemeland, Jean-François; Pons, Jean-Louis

2004-01-01

A multiplex PCR toxigenic culture approach was designed for simultaneous identification and toxigenic type characterization of Clostridium difficile isolates. Three pairs of primers were designed for the amplification of (i) a species-specific internal fragment of the tpi (triose phosphate isomerase) gene, (ii) an internal fragment of the tcdB (toxin B) gene, and (iii) an internal fragment of the tcdA (toxin A) gene allowing distinction between toxin A-positive, toxin B-positive (A+B+) strains and toxin A-negative, toxin B-positive (A−B+) variant strains. The reliability of the multiplex PCR was established by using a panel of 72 C. difficile strains including A+B+, A−B−, and A−B+ toxigenic types and 11 other Clostridium species type strains. The multiplex PCR assay was then included in a toxigenic culture approach for the detection, identification, and toxigenic type characterization of C. difficile in 1,343 consecutive human and animal stool samples. Overall, 111 (15.4%) of 721 human samples were positive for C. difficile; 67 (60.4%) of these samples contained A+B+ toxigenic isolates, and none of them contained A−B+ variant strains. Fifty (8%) of 622 animal samples contained C. difficile strains, which were toxigenic in 27 (54%) cases, including 1 A−B+ variant isolate. Eighty of the 721 human stool samples (37 positive and 43 negative for C. difficile culture) were comparatively tested by Premier Toxins A&B (Meridian Bioscience) and Triage C. difficile Panel (Biosite) immunoassays, the results of which were found concordant with toxigenic culture for 82.5 and 92.5% of the samples, respectively. The multiplex PCR toxigenic culture scheme described here allows combined diagnosis and toxigenic type characterization for human and animal C. difficile intestinal infections. PMID:15583303

Effect of Genetic Polymorphisms in GH/Hpa II and MSTN / Dra I Loci on Body Weight in Friesian Bull Calves.

PubMed

Nasr, S M; Ateya, A I; Sadek, K M; Radwan, H A

The GH and MSTN gene polymorphisms and their association with body weight were declared in a population of 100 Friesian bull calves. For DNA extraction, collection of blood samples was carried out from the studied animals. The PCR for GH and MSTN genes yielded fragments of 329 and 1346 bp, respectively. The PCR-HpaII digestion of 329 bp of GH gene revealed three genotypes: AA genotype possess undigested fragment (329 bp), AB genotype has three fragments (329, 224 and 105 bp) and BB genotype has two fragments (224 and 105 bp). The GH genotypes incidence and alleles frequency were calculated. For the 100 Friesian bull calves, genotypic frequencies for the AA, AB and BB genotypes were 0.1, 0.78 and 0.12, respectively and the allele frequencies for A and B allele frequencies were 0.49 and 0.51. Statistical analysis revealed that there was a significant effect of GH genotypes on body weight. The AB genotype possessed higher body weight than the other 2 genotypes. Regarding MSTN gene, PCR-DraI digestion of 1346 bp fragment was monomorphic; where it yielded four fragments (505, 427, 321 and 93 bp) in all animals under study. The outcome of this study is that it highlights the effectiveness of GH/HpaII locus as candidate marker for body weight in cattle rather than MSTN/DraI.

Randomized DNA libraries construction tool: a new 3-bp 'frequent cutter' TthHB27I/sinefungin endonuclease with chemically-induced specificity.

PubMed

Krefft, Daria; Papkov, Aliaksei; Prusinowski, Maciej; Zylicz-Stachula, Agnieszka; Skowron, Piotr M

2018-05-11

Acoustic or hydrodynamic shearing, sonication and enzymatic digestion are used to fragment DNA. However, these methods have several disadvantages, such as DNA damage, difficulties in fragmentation control, irreproducibility and under-representation of some DNA segments. The DNA fragmentation tool would be a gentle enzymatic method, offering cleavage frequency high enough to eliminate DNA fragments distribution bias and allow for easy control of partial digests. Only three such frequently cleaving natural restriction endonucleases (REases) were discovered: CviJI, SetI and FaiI. Therefore, we have previously developed two artificial enzymatic specificities, cleaving DNA approximately every ~ 3-bp: TspGWI/sinefungin (SIN) and TaqII/SIN. In this paper we present the third developed specificity: TthHB27I/SIN(SAM) - a new genomic tool, based on Type IIS/IIC/IIG Thermus-family REases-methyltransferases (MTases). In the presence of dimethyl sulfoxide (DMSO) and S-adenosyl-L-methionine (SAM) or its analogue SIN, the 6-bp cognate TthHB27I recognition sequence 5'-CAARCA-3' is converted into a combined 3.2-3.0-bp 'site' or its statistical equivalent, while a cleavage distance of 11/9 nt is retained. Protocols for various modes of limited DNA digestions were developed. In the presence of DMSO and SAM or SIN, TthHB27I is transformed from rare 6-bp cutter to a very frequent one, approximately 3-bp. Thus, TthHB27I/SIN(SAM) comprises a new tool in the very low-represented segment of such prototype REases specificities. Moreover, this modified TthHB27I enzyme is uniquely suited for controlled DNA fragmentation, due to partial DNA cleavage, which is an inherent feature of the Thermus-family enzymes. Such tool can be used for quasi-random libraries generation as well as for other DNA manipulations, requiring high frequency cleavage and uniform distribution of cuts along DNA.

Presence of a deletion mutation (c.716delA) in the ligand binding domain of the vitamin D receptor in an Indian patient with vitamin D-dependent rickets type II.

PubMed

Kanakamani, Jeyaraman; Tomar, Neeraj; Kaushal, Esha; Tandon, Nikhil; Goswami, Ravinder

2010-01-01

Vitamin D-dependent rickets type II (VDDR-type II) is a rare disorder caused by mutations in the vitamin D receptor (VDR) gene. Here, we describe a patient with VDDR-type II with severe alopecia and rickets. She had hypocalcemia, hypophosphatemia, secondary hyperparathyroidism, and elevated serum alkaline phosphatase and 1,25-dihydroxyvitamin D(3). Sequence analysis of the lymphocyte VDR cDNA revealed deletion mutation c.716delA. Sequence analysis of her genomic DNA fragment amplified from exon 6 of the VDR gene incorporating this mutation confirmed the presence of the mutation in homozygous form. This frameshift mutation in the ligand binding domain (LBD) resulted in premature termination (p.Lys240Argfs) of the VDR protein. The mutant protein contained 246 amino acids, with 239 normal amino acids at the N terminus, followed by seven changed amino acids resulting in complete loss of its LBD. The mutant VDR protein showed evidence of 50% reduced binding with VDR response elements on electrophoretic mobility assay in comparison to the wild-type VDR protein. She was treated with high-dose calcium infusion and oral phosphate. After 18 months of treatment, she gained 6 cm of height, serum calcium and phosphorus improved, alkaline phosphatase levels decreased, and intact PTH normalized. Radiologically, there were signs of healing of rickets. Her parents and one of her siblings had the same c.716delA mutation in heterozygous form. Despite the complete absence of LBD, the rickets showed signs of healing with intravenous calcium.

Chromosomal Fragmentation: A Possible Marker for the Selection of High Gymnemic Acid Yielding Accessions of Gymnema sylvestre R. Br.

PubMed

Verma, Ashutosh Kumar; Dhawan, Sunita Singh

2017-10-01

Gymnema sylvestre R. Br. a member of family Asclepiadaceae as mentioned in Indian Pharmacopoeia popular among the researchers because of stimulatory effect of its phytoconstituent on pancreatic cells and potential to treat Type I and II type of diabetes. Development of cost-effective marker system for the selection of high gymnemic acid yielding accessions of G. sylvestre . Presoaked seeds of Brassica campestris treated with different dilutions of gymnemagenin and 10% leaf extract of twenty different accessions of G. sylvestre . Root tips of germinated seeds were fixed, and chromosomal studies were made by root tip bioassay method. Exposure of seeds to treatment solutions promotes various types of chromosomal anomalies in root meristem, and surprisingly, direct correlation between the percentage of chromosomal fragmentation and the percentage of gymnemic acid shared by treatment solution were observed. Later finding may be explored for the development of a novel methodology or marker system for the selection of high active principle yielding accessions of G. sylvestre . An experiment was carried out using root tip bioassay method for the study of effect of different dilutions of standard gymnemic acid and 10% leaf extract of twenty different accessions of Gymnema sylvestre on root tip meristem of Brassica campestris . Various types of chromosomal anomalies were observed. Of which, percentage of chromosomal fragmentation was showed a direct (∞) relationship with the percentage of gymnemic acid shared by treatment solution. This interesting result after more and more exploration and revalidation could be utilized for the development of a novel methodology for the selection of high active principle yielding accessions of G. sylvestre . Abbreviations used: MI: Mitotic index; CP: Condensed prophase; CM: Clumped metaphase; MC: Metaphase cleft; FR: Fragmentation; AP: Anaphase with persistent nucleolous; LA: Laggard, BR: Bridge; BI: Bi-nucleated cell; DA: Disturbed anaphasic polarity.

Chromosomal Fragmentation: A Possible Marker for the Selection of High Gymnemic Acid Yielding Accessions of Gymnema sylvestre R. Br

PubMed Central

Verma, Ashutosh Kumar; Dhawan, Sunita Singh

2017-01-01

Background: Gymnema sylvestre R. Br. a member of family Asclepiadaceae as mentioned in Indian Pharmacopoeia popular among the researchers because of stimulatory effect of its phytoconstituent on pancreatic cells and potential to treat Type I and II type of diabetes. Objectives: Development of cost-effective marker system for the selection of high gymnemic acid yielding accessions of G. sylvestre. Materials and Methods: Presoaked seeds of Brassica campestris treated with different dilutions of gymnemagenin and 10% leaf extract of twenty different accessions of G. sylvestre. Root tips of germinated seeds were fixed, and chromosomal studies were made by root tip bioassay method. Results: Exposure of seeds to treatment solutions promotes various types of chromosomal anomalies in root meristem, and surprisingly, direct correlation between the percentage of chromosomal fragmentation and the percentage of gymnemic acid shared by treatment solution were observed. Conclusion: Later finding may be explored for the development of a novel methodology or marker system for the selection of high active principle yielding accessions of G. sylvestre. SUMMARY An experiment was carried out using root tip bioassay method for the study of effect of different dilutions of standard gymnemic acid and 10% leaf extract of twenty different accessions of Gymnema sylvestre on root tip meristem of Brassica campestris. Various types of chromosomal anomalies were observed. Of which, percentage of chromosomal fragmentation was showed a direct (∞) relationship with the percentage of gymnemic acid shared by treatment solution. This interesting result after more and more exploration and revalidation could be utilized for the development of a novel methodology for the selection of high active principle yielding accessions of G. sylvestre. Abbreviations used: MI: Mitotic index; CP: Condensed prophase; CM: Clumped metaphase; MC: Metaphase cleft; FR: Fragmentation; AP: Anaphase with persistent nucleolous; LA: Laggard, BR: Bridge; BI: Bi-nucleated cell; DA: Disturbed anaphasic polarity. PMID:29142402

A binary search approach to whole-genome data analysis.

PubMed

Brodsky, Leonid; Kogan, Simon; Benjacob, Eshel; Nevo, Eviatar

2010-09-28

A sequence analysis-oriented binary search-like algorithm was transformed to a sensitive and accurate analysis tool for processing whole-genome data. The advantage of the algorithm over previous methods is its ability to detect the margins of both short and long genome fragments, enriched by up-regulated signals, at equal accuracy. The score of an enriched genome fragment reflects the difference between the actual concentration of up-regulated signals in the fragment and the chromosome signal baseline. The "divide-and-conquer"-type algorithm detects a series of nonintersecting fragments of various lengths with locally optimal scores. The procedure is applied to detected fragments in a nested manner by recalculating the lower-than-baseline signals in the chromosome. The algorithm was applied to simulated whole-genome data, and its sensitivity/specificity were compared with those of several alternative algorithms. The algorithm was also tested with four biological tiling array datasets comprising Arabidopsis (i) expression and (ii) histone 3 lysine 27 trimethylation CHIP-on-chip datasets; Saccharomyces cerevisiae (iii) spliced intron data and (iv) chromatin remodeling factor binding sites. The analyses' results demonstrate the power of the algorithm in identifying both the short up-regulated fragments (such as exons and transcription factor binding sites) and the long--even moderately up-regulated zones--at their precise genome margins. The algorithm generates an accurate whole-genome landscape that could be used for cross-comparison of signals across the same genome in evolutionary and general genomic studies.

Treatment of type II and type III open tibia fractures in children.

PubMed

Bartlett, C S; Weiner, L S; Yang, E C

1997-07-01

To determine whether severe open tibial fractures in children behave like similar fractures in adults. A combined retrospective and prospective review evaluated treatment protocol for type II and type III open tibial fractures in children over a ten-year period from 1984 to 1993. Twenty-three fractures were studied in children aged 3.5 to 14.5 (18 boys and 5 girls). There were six type II, eight type IIIA, and nine type IIIB fractures. Type I fractures were not included. Seven fractures were comminuted with significant butterfly fragments or segmental patterns. Treatment consisted of adequate debridement of soft tissues, closure of dead space, and stabilization with external fixation. Bone debridement only included contaminated devitalized bone or devitalized bone without soft tissue coverage. Bone that could be covered despite periosteal stripping was preserved. Clinical and roentgenographic examinations were used to determine time to union. All fractures in this series healed between eight and twenty-six weeks. Wound coverage included two flaps, three skin grafts, and two delayed primary closures. No bone grafts were required. There were no deep infections, growth arrests, or malunions. Follow-up has ranged from six months to four years. Open tibia fractures in children differ from similar fractures in adults in the following ways: soft tissues have excellent healing capacity, devitalized bone that is not contaminated or exposed can be saved and will become incorporated, and external fixation can be maintained until the fracture has healed. Periosteum in young children can form bone even in the face of bone loss.

Precursor Ion Scan Mode-Based Strategy for Fast Screening of Polyether Ionophores by Copper-Induced Gas-Phase Radical Fragmentation Reactions.

PubMed

Crevelin, Eduardo J; Possato, Bruna; Lopes, João L C; Lopes, Norberto P; Crotti, Antônio E M

2017-04-04

The potential of copper(II) to induce gas-phase fragmentation reactions in macrotetrolides, a class of polyether ionophores produced by Streptomyces species, was investigated by accurate-mass electrospray tandem mass spectrometry (ESI-MS/MS). Copper(II)/copper(I) transition directly induced production of diagnostic acylium ions with m/z 199, 185, 181, and 167 from α-cleavages of [macrotetrolides + Cu] 2+ . A UPLC-ESI-MS/MS methodology based on the precursor ion scan of these acylium ions was developed and successfully used to identify isodinactin (1), trinactin (2), and tetranactin (3) in a crude extract of Streptomyces sp. AMC 23 in the precursor ion scan mode. In addition, copper(II) was also used to induce radical fragmentation reactions in the carboxylic acid polyether ionophore nigericin. The resulting product ions with m/z 755 and 585 helped to identify nigericin in a crude extract of Streptomyces sp. Eucal-26 by means of precursor ion scan experiments, demonstrating that copper-induced fragmentation reactions can potentially identify different classes of polyether ionophores rapidly and selectively.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marfa-Riera, V.; Gollin, D.; Mohnen, D.

An optimized tobacco thin-cell-layer (TCL) bioassay was used to study the induction of flowers by plant oligosaccharins. Endopolygalacturonase (EPG)-released fragments of suspension-cultured sycamore cell walls induced flowers on TCLs grown on a medium containing 1.5 {mu}M IBA and 0.9 {mu}M kinetin. The EPG-released fragments were primarily composed of the polysaccharides rhamnogalacturonan I (RG-I), rhamnogalacturonan II (RG-II), and {alpha}-1,4-linked oligogalacturonides. The {alpha}-1,4-linked oligogalacturonides, subsequently purified from the EPG-released sycamore cell wall fragment mixture, induced flowers on TCLs. Purified RG-I and RG-II did not induce flowers. Oligosaccharide fragments, generated by partial acid hydrolysis of citrus pectin, were also capable of inducing flowersmore » on the TCLs. The active components in the pectin fragment mixture were {alpha}-1,4-linked oligogalacturonides. Oligogalacturonides with a degree of polymerization (DP) of 8-16, at concentrations of {approx} 0.1 {mu}M, induced flowers, while oligogalacturonides with a DP 2-7, even at higher concentrations, did not. Oligogalacturonides have previously been shown to induce the synthesis of phytoalexins, protease inhibitors, lignin, and ethylene in other plant systems. Thus, the ability of {alpha}-1,4-linked oligogalacturonides to induce flower formation in the tobacco TCLs represents a new biological activity of these oligosaccharins.« less

A second gene for type I signal peptidase in Bradyrhizobium japonicum, sipF, is located near genes involved in RNA processing and cell division.

PubMed

Bairl, A; Müller, P

1998-11-01

The TnphoA-induced Bradyrhizobium japonicum mutant 184 shows slow growth and aberrant colonization of soybean nodules. Using a DNA fragment adjacent to the transposon insertion site as a probe, a 3.4-kb BglII fragment of B. japonicum 110spc4 DNA was identified and cloned. Sequence analysis indicated that two truncated ORFs and three complete ORFs were encoded on this fragment. A database search revealed homologies to several other prokaryotic proteins: PdxJ (an enzyme involved in vitamin B6 biosynthesis), AcpS (acyl carrier protein synthase), Lep or Sip (prokaryotic type I signal peptidase), RNase III (an endoribonuclease which processes double-stranded rRNA precursors and mRNA) and Era (a GTP-binding protein required for cell division). The mutation in strain 184 was found to lie within the signal peptidase gene, which was designated sipF. Therefore, sipF is located in a region that encodes gene products involved in posttranscriptional and posttranslational processing processes. By complementation of the lep(ts) E. coli mutant strain IT41 it was demonstrated that sipF indeed encodes a functional signal peptidase, and genetic complementation of B. japonicum mutant 184 by a 2.8-kb SalI fragment indicated that sipF is expressed from a promoter located directly upstream of sipF. Using a non-polar kanamycin resistance cassette, a specific sipF mutant was constructed which exhibited defects in symbiosis similar to those of the original mutant 184.

Formation of furan and methylfuran by maillard-type reactions in model systems and food.

PubMed

Limacher, Anita; Kerler, Josef; Davidek, Tomas; Schmalzried, Frank; Blank, Imre

2008-05-28

The formation of furan and 2-methylfuran was studied in model systems based on sugars and selected amino acids. Both compounds were preferably formed under roasting conditions in closed systems yielding up to 330 micromol of furan and 260 micromol of 2-methylfuran per mol of precursor. The amounts obtained under pressure cooking conditions were much lower, usually below 20 micromol/mol, except for 2-furaldehyde, which yielded 70-100 micromol/mol of furan. Labeling studies indicated two major formation pathways for both furans: (i) from the intact sugar skeleton and (ii) by recombination of reactive C(2) and/or C(3) fragments. Under roasting conditions in the absence of amino acids, furan was mainly formed from the intact sugar skeleton. Formic and acetic acid were identified as byproducts of sugar degradation, indicating the split off of C(1) and/or C(2) units from hexoses. The presence of alanine, threonine, or serine promoted furan formation by the recombination of C(2) fragments, such as acetaldehyde and glycolaldehyde, which may originate from both sugars and amino acids. In aqueous solution, about half of furan was generated by the recombination of sugar fragments. 2-Methylfuran was preferably formed in the presence of amino acids by aldol-type reactions of C(2) and C(3) fragments with lactaldehyde as a key intermediate, the Strecker aldehyde of threonine. The total furan levels in cooked vegetables were increased by spiking with hexoses. However, in pumpkin puree, only about 20% of furan was formed from sugars, preferably from the intact carbon skeleton.

Localizing National Fragmentation Statistics with Forest Type Maps

Treesearch

Kurt H. Riitters; John W. Coulston; James D. Wickham

2003-01-01

Fragmentation of forest types is an indicator of biodiversity in the Montreal Process, but the available national data permit assessment of only overall forestland fragmentation, not forest type fragmentation. Here we illustrate how to localize national statistics from the 2003 National Report on Sustainable Forests by combining state vegetation maps with national...

Antihypertensive effects of continuous oral administration of nattokinase and its fragments in spontaneously hypertensive rats.

PubMed

Fujita, Mitsugu; Ohnishi, Katsunori; Takaoka, Shinsaku; Ogasawara, Kazuya; Fukuyama, Ryo; Nakamuta, Hiromichi

2011-01-01

To determine whether the antihypertensive effect of nattokinase is associated with the protease activity of this enzyme, we compared nattokinase with the fragments derived from nattokinase, which possessed no protease activity, in terms of the effect on hypertension in spontaneously hypertensive rats (SHR). In the continuous oral administration test, the groups were given a basic diet alone (control), the basic diet containing nattokinase (0.2, 2.6 mg/g diet) or the basic diet containing the fragments derived from nattokinase (0.2, 0.6 mg/g diet). The group fed the basic diet containing high-dosage nattokinase (2.6 mg/g diet) showed significant reductions in systolic blood pressure (SBP), diastolic blood pressure (DBP) and plasma fibrinogen level, compared with control group and no influence on activities of renin and angiotensin-converting enzyme (ACE, EC 3.4.15.1), and plasma angiotensin II level in the renin-angiotensin system. The treatment of the basic diet containing high-dosage fragments (0.6 mg/g diet) significantly decreased SBP, DBP and plasma angiotensin II level in plasma but the treatment did not influence on plasma fibrinogen level. These results suggest that nattokinase and its fragments are different from each other in the mechanism to reduce hypertension. Nattokinase, retained its protease activity after absorbance across the intestines, may decrease blood pressure through cleavage of fibrinogen in plasma. The fragments, which absorbed as nattokinase-degradation products, prevents the elevation of plasma angiotensin II level to suppress hypertension.

Isolation and genotyping of Toxoplasma gondii causing fatal systemic toxoplasmosis in an immunocompetent 10-year-old cat.

PubMed

Spycher, Andrea; Geigy, Caroline; Howard, Judith; Posthaus, Horst; Gendron, Karine; Gottstein, Bruno; Debache, Karim; Herrmann, Daland C; Schares, Gereon; Frey, Caroline F

2011-01-01

A 10-year-old male, neutered domestic shorthair cat was presented with fever, anorexia, vomiting, and diarrhea. Serologic testing for Feline immunodeficiency virus and Feline leukemia virus were negative. Fine-needle aspirates of mesenteric lymph nodes revealed the presence of banana-shaped apicomplexan parasites. The cat died after 4 days of hospitalization. Postmortem polymerase chain reaction (PCR) analysis confirmed the presence of Toxoplasma gondii in all examined organs. Parasites were ex vivo isolated in outbred mice and subsequently transferred into cell culture. Genotyping, using genetic markers for SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico for PCR-restriction fragment length polymorphism, revealed infection with type II T. gondii displaying type II alleles at all loci except Apico, which exhibited a type I allele. This is the most frequently identified genotype among cats acting as definitive hosts in central Europe, but to the authors' knowledge, it has never been associated with systemic toxoplasmosis in an adult, immunocompetent cat.

Hydrogenotrophic methanogenesis is the dominant methanogenic pathway in neotropical tank bromeliad wetlands.

PubMed

Martinson, Guntars O; Pommerenke, Bianca; Brandt, Franziska B; Homeier, Jürgen; Burneo, Juan I; Conrad, Ralf

2018-02-01

Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that emits substantial amounts of CH 4 . Tank bromeliads growing in the forest canopy (functional type-II tank bromeliads) were found to emit more CH 4 than tank bromeliads growing on the forest floor (functional type-I tank bromeliads) but the reasons for this difference and the underlying microbial CH 4 -cycling processes have not been studied. Therefore, we characterized archaeal communities in bromeliad tanks of the two different functional types in a neotropical montane forest of southern Ecuador using terminal-restriction fragment length polymorphism (T-RFLP) and performed tank-slurry incubations to measure CH 4 production potential, stable carbon isotope fractionation and pathway of CH 4 formation. The archaeal community composition was dominated by methanogens and differed between bromeliad functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens and hydrogenotrophic methanogenesis was the dominant methanogenic pathway among all bromeliads. The relative abundance of aceticlastic Methanosaetaceae and the relative contribution of aceticlastic methanogenesis increased in type-I tank bromeliads probably due to more oxic conditions in type-I than in type-II bromeliads leading to the previously observed lower in situ CH 4 emissions from type-I tank bromeliads but to higher CH 4 production potentials in type-I tank bromeliad slurries. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryan, Q.C.

There are two nonallelic human {gamma} globin genes located on the short arm of chromosome No. 11 in the order 5{prime}-{sup G}{sub {gamma}}-{sup A}{sub {gamma}}-3{prime}. Various modifications of the two {gamma} genes have been reported and include: deletions, triplications, quadruplications and recently a quintuplication. These are generally created by one or more unequal crossovers in the {gamma} globin gene regions on adjacent chromosomes. During the course of looking for a {gamma}{sup {degree}} thalassemia, which might be due to a crossover of looking for a {gamma} genes, two cases were found in the family W. Bgl II mapping studies showed amore » 5 kb deletion at the {gamma} gene loci in these individuals. The Bgl II fragment from the {gamma} gene loci of R.W. was cloned into the phage vector QR1. Phage mapping showed that two out of the three Pst I sites within the Bgl II fragment were missing which suggested that the crossover might have occurred within the {gamma} gene, possibly within the {gamma}IVS II region. Sequence analysis of the cloned fragment revealed an unusual sequence which had no sequence homology with the {gamma} gene region except for a small 264 bp region near the 3{prime} end. The orientation of the 264 bp fragment is inverted relative to homologous sequences in the {sup G}{sub {gamma}} and {sup A}{sub {gamma}} IVS II. The unusual sequence was computer analyzed for homology with every DNA sequence file in the EMBL database and GenBank and did not show any significant homologies to all the available DNA sequences except for the 264 bp {gamma}IVS II homology.« less

A site-directed mutagenesis method particularly useful for creating otherwise difficult-to-make mutants and alanine scanning.

PubMed

Wan, Haisu; Li, Yongwen; Fan, Yu; Meng, Fanrong; Chen, Chen; Zhou, Qinghua

2012-01-15

Site-directed mutagenesis has become routine in molecular biology. However, many mutants can still be very difficult to create. Complicated chimerical mutations, tandem repeats, inverted sequences, GC-rich regions, and/or heavy secondary structures can cause inefficient or incorrect binding of the mutagenic primer to the target sequence and affect the subsequent amplification. In theory, these problems can be avoided by introducing the mutations into the target sequence using mutagenic fragments and so removing the need for primer-template annealing. The cassette mutagenesis uses the mutagenic fragment in its protocol; however, in most cases it needs to perform two rounds of mutagenic primer-based mutagenesis to introduce suitable restriction enzyme sites into templates and is not suitable for routine mutagenesis. Here we describe a highly efficient method in which the template except the region to be mutated is amplified by polymerase chain reaction (PCR) and the type IIs restriction enzyme-digested PCR product is directly ligated with the mutagenic fragment. Our method requires no assistance of mutagenic primers. We have used this method to create various types of difficult-to-make mutants with mutagenic frequencies of nearly 100%. Our protocol has many advantages over the prevalent QuikChange method and is a valuable tool for studies on gene structure and function. Copyright © 2011 Elsevier Inc. All rights reserved.

Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments.

PubMed

Nunoura, Takuro; Hirayama, Hisako; Takami, Hideto; Oida, Hanako; Nishi, Shinro; Shimamura, Shigeru; Suzuki, Yohey; Inagaki, Fumio; Takai, Ken; Nealson, Kenneth H; Horikoshi, Koki

2005-12-01

Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota.

FAST ROTATION AND TRAILING FRAGMENTS OF THE ACTIVE ASTEROID P/2012 F5 (GIBBS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drahus, Michał; Waniak, Wacław; Tendulkar, Shriharsh

While having a comet-like appearance, P/2012 F5 (Gibbs) has an orbit native to the Main Asteroid Belt, and physically is a km-sized asteroid which recently (mid 2011) experienced an impulsive mass ejection event. Here we report new observations of this object obtained with the Keck II telescope on UT 2014 August 26. The data show previously undetected 200 m scale fragments of the main nucleus, and reveal a rapid nucleus spin with a rotation period of 3.24 ± 0.01 hr. The existence of large fragments and the fast nucleus spin are both consistent with rotational instability and partial disruption ofmore » the object. To date, many fast rotators have been identified among the minor bodies, which, however, do not eject detectable fragments at the present-day epoch, and also fragmentation events have been observed, but with no rotation period measured. P/2012 F5 is unique in that for the first time we detected fragments and quantified the rotation rate of one and the same object. The rapid spin rate of P/2012 F5 is very close to the spin rates of two other active asteroids in the Main Belt, 133P/Elst-Pizarro and (62412), confirming the existence of a population of fast rotators among these objects. But while P/2012 F5 shows impulsive ejection of dust and fragments, the mass loss from 133P is prolonged and recurrent. We believe that these two types of activity observed in the rapidly rotating active asteroids have a common origin in the rotational instability of the nucleus.« less

A Dictyostelium mutant deficient in severin, an F-actin fragmenting protein, shows normal motility and chemotaxis

PubMed Central

1989-01-01

A severin deficient mutant of Dictyostelium discoideum has been isolated by the use of colony immunoblotting after chemical mutagenesis. In homogenates of wild-type cells, severin is easily detected as a very active F-actin fragmenting protein. Tests for severin in the mutant, HG1132, included viscometry for the assay of F- actin fragmentation in fractions from DEAE-cellulose columns, labeling of blots with monoclonal and polyclonal antibodies, and immunofluorescent-labeling of cryosections. Severin could not be detected in the mutant using these methods. The mutation in HG1132 is recessive and has been mapped to linkage group VII. The mutant failed to produce the normal severin mRNA, but small amounts of a transcript that was approximately 100 bases larger than the wild-type mRNA were detected in the mutant throughout all stages of development. On the DNA level a new Mbo II restriction site was found in the mutant within the coding region of the severin gene. The severin deficient mutant cells grew at an approximately normal rate, aggregated and formed fruiting bodies with viable spores. By the use of an image processing system, speed of cell movement, turning rates, and precision of chemotactic orientation in a stable gradient of cyclic AMP were quantitated, and no significant differences between wild-type and mutant cells were found. Thus, under the culture conditions used, severin proved to be neither essential for growth of D. discoideum nor for any cell function that is important for aggregation or later development. PMID:2537840

Analyzing Internal Fragmentation of Electrosprayed Ubiquitin Ions During Beam-Type Collisional Dissociation

NASA Astrophysics Data System (ADS)

Durbin, Kenneth R.; Skinner, Owen S.; Fellers, Ryan T.; Kelleher, Neil L.

2015-05-01

Gaseous fragmentation of intact proteins is multifaceted and can be unpredictable by current theories in the field. Contributing to the complexity is the multitude of precursor ion states and fragmentation channels. Terminal fragment ions can be re-fragmented, yielding product ions containing neither terminus, termed internal fragment ions. In an effort to better understand and capitalize upon this fragmentation process, we collisionally dissociated the high (13+), middle (10+), and low (7+) charge states of electrosprayed ubiquitin ions. Both terminal and internal fragmentation processes were quantified through step-wise increases of voltage potential in the collision cell. An isotope fitting algorithm matched observed product ions to theoretical terminal and internal fragment ions. At optimal energies for internal fragmentation of the 10+, nearly 200 internal fragments were observed; on average each of the 76 residues in ubiquitin was covered by 24.1 internal fragments. A pertinent finding was that formation of internal ions occurs at similar energy thresholds as terminal b- and y-ion types in beam-type activation. This large amount of internal fragmentation is frequently overlooked during top-down mass spectrometry. As such, we present several new approaches to visualize internal fragments through modified graphical fragment maps. With the presented advances of internal fragment ion accounting and visualization, the total percentage of matched fragment ions increased from approximately 40% to over 75% in a typical beam-type MS/MS spectrum. These sequence coverage improvements offer greater characterization potential for whole proteins with no needed experimental changes and could be of large benefit for future high-throughput intact protein analysis.

Gladiolus plants transformed with single-chain variable fragment antibodies to Cucumber mosaic virus

USDA-ARS?s Scientific Manuscript database

Transgenic plants of Gladiolus ‘Peter Pears’ or ‘Jenny Lee’ were developed that contain single-chain variable fragments (scFv) to Cucumber mosaic virus (CMV) subgroup I or II. The CMV subgroup I heavy and light chain scFv fragments were placed under control of either the duplicated CaMV 35S or suga...

LOCALIZING NATIONAL FRAGMENTATION STATISTICS WITH FOREST TYPE MAPS

EPA Science Inventory

Fragmmentation of forest types is an indicator of biodiversity in the Montreal Process, but the available national data permit assessment of only overall forestland fragmentation, not forest type fragmentation. Here we illustrate how to localize national statistics from the 2003...

Physics-Based Modeling of Meteor Entry and Breakup

NASA Technical Reports Server (NTRS)

Prabhu, Dinesh K.; Agrawal, Parul; Allen, Gary A., Jr.; Bauschlicher, Charles W., Jr.; Brandis, Aaron M.; Chen, Yih-Kang; Jaffe, Richard L.; Palmer, Grant E.; Saunders, David A.; Stern, Eric C.;

Physics-Based Modeling of Meteor Entry and Breakup

NASA Technical Reports Server (NTRS)

Prabhu, Dinesh K.; Agrawal, Parul; Allen, Gary A.; Brandis, Aaron M.; Chen, Yih-Kanq; Jaffe, Richard L.; Saunders, David A.; Stern, Eric C.; Tauber, Michael E.; Venkatapathy, Ethiraj

2015-01-01

A new research effort at NASA Ames Research Center has been initiated in Planetary Defense, which integrates the disciplines of planetary science, atmospheric entry physics, and physics-based risk assessment. This paper describes work within the new program and is focused on meteor entry and breakup. Over the last six decades significant effort was expended in the US and in Europe to understand meteor entry including ablation, fragmentation and airburst (if any) for various types of meteors ranging from stony to iron spectral types. These efforts have produced primarily empirical mathematical models based on observations. Weaknesses of these models, apart from their empiricism, are reliance on idealized shapes (spheres, cylinders, etc.) and simplified models for thermal response of meteoritic materials to aerodynamic and radiative heating. Furthermore, the fragmentation and energy release of meteors (airburst) is poorly understood. On the other hand, flight of human-made atmospheric entry capsules is well understood. The capsules and their requisite heatshields are designed and margined to survive entry. However, the highest speed Earth entry for capsules is less than 13 km/s (Stardust). Furthermore, Earth entry capsules have never exceeded diameters of 5 m, nor have their peak aerothermal environments exceeded 0.3 atm and 1 kW/cm2. The aims of the current work are: (i) to define the aerothermal environments for objects with entry velocities from 13 to greater than 20 km/s; (ii) to explore various hypotheses of fragmentation and airburst of stony meteors in the near term; (iii) to explore the possibility of performing relevant ground-based tests to verify candidate hypotheses; and (iv) to quantify the energy released in airbursts. The results of the new simulations will be used to anchor said risk assessment analyses. With these aims in mind, state-of-the-art entry capsule design tools are being extended for meteor entries. We describe: (i) applications of current simulation tools to spherical geometries of diameters ranging from 1 to 100 m for an entry velocity of 20 km/s and stagnation pressures ranging from 1 to 100 atm; (ii) the influence of shape and departure of heating environment predictions from those for a simple spherical geometry; (iii) assessment of thermal response models for silica subject to intense radiation; and (iv) results for porosity-driven gross fragmentation of meteors, idealized as a collection of smaller objects. Lessons learned from these simulations will be used to help understand the Chelyabinsk meteor entry up to its first point of fragmentation.

Physics-Based Modeling of Meteor Entry and Breakup

NASA Technical Reports Server (NTRS)

Prabhu, Dinesh K.; Agrawal, Parul; Allen, Gary A., Jr.; Bauschlicher, Charles W., Jr.; Brandis, Aaron M.; Chen, Yih-Kanq; Jaffe, Richard L.; Palmer, Grant E.; Saunders, David A.; Stern, Eric C.;

Anatomy and classification of the posterior tibial fragment in ankle fractures.

PubMed

Bartoníček, Jan; Rammelt, Stefan; Kostlivý, Karel; Vaněček, Václav; Klika, Daniel; Trešl, Ivo

2015-04-01

The aim of this study was to analyze the pathoanatomy of the posterior fragment on the basis of a comprehensive CT examination, including 3D reconstructions, in a large patient cohort. One hundred and forty one consecutive individuals with an ankle fracture or fracture-dislocation of types Weber B or Weber C and evidence of a posterior tibial fragment in standard radiographs were included in the study. The mean patient age was 49 years (range 19-83 years). The exclusion criteria were patients below 18 years of age, inability to provide written consent, fractures of the tibial pilon, posttraumatic arthritis and pre-existing deformities. In all patients, post-injury radiographs were obtained in anteroposterior, mortise and lateral views. All patients underwent CT scanning in transverse, sagittal and frontal planes. 3D CT reconstruction was performed in 91 patients. We were able to classify 137 cases into one of the following four types with constant pathoanatomic features: type 1: extraincisural fragment with an intact fibular notch, type 2: posterolateral fragment extending into the fibular notch, type 3: posteromedial two-part fragment involving the medial malleolus, type 4: large posterolateral triangular fragment. In the 4 cases it was not possible to classify the type of the posterior tibial fragment. These were collectively termed type 5 (irregular, osteoporotic fragments). It is impossible to assess the shape and size of the posterior malleolar fragment, involvement of the fibular notch, or the medial malleolus, on the basis of plain radiographs. The system that we propose for classification of fractures of the posterior malleolus is based on CT examination and takes into account the size, shape and location of the fragment, stability of the tibio-talar joint and the integrity of the fibular notch. It may be a useful indication for surgery and defining the most useful approach to these injuries.

Magnetic anisotropy of [Mo(CN)7]4- anions and fragments of cyano-bridged magnetic networks.

PubMed

Chibotaru, Liviu F; Hendrickx, Marc F A; Clima, Sergiu; Larionova, Joulia; Ceulemans, Arnout

2005-08-18

Quantum chemistry calculations of CASSCF/CASPT2 level together with ligand field analysis are used for the investigation of magnetic anisotropy of [Mo(CN)7]4- complexes. We have considered three types of heptacyano environments: two ideal geometries, a pentagonal bipyramid and a capped trigonal prism, and the heptacyanomolybdate fragment of the cyano-bridged magnetic network K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O. At all geometries the first excited Kramers doublet is found remarkably close to the ground one due to a small orbital energy gap in the ligand field spectrum, which ranges between a maximal value in the capped trigonal prism (800 cm(-1)) and zero in the pentagonal bipyramid. The small value of this gap explains (i) the axial form of the g tensor and (ii) the strong magnetic anisotropy even in strongly distorted complexes. Comparison with available experimental data for the g tensor of the mononuclear precursors reveals good agreement with the present calculations for the capped trigonal prismatic complex and a significant discrepancy for the pentagonal bipyramidal one. The calculations for the heptacyanomolybdate fragment of K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O give g(perpendicular)/g(parallel) approximately 0.5 and the orientation of the local anisotropy axis close to the symmetry axis of an idealized pentagonal bipyramid. These findings are expected to be important for the understanding of the magnetism of anisotropic Mo(III)-Mn(II) cyano-bridged networks based on the [Mo(CN)7]4- building block.

A multigene family related to chitin synthase genes of yeast in the opportunistic pathogen Aspergillus fumigatus.

PubMed

Mellado, E; Aufauvre-Brown, A; Specht, C A; Robbins, P W; Holden, D W

1995-02-06

Two approaches were used to isolate fragments of chitin synthase genes from the opportunistic human pathogen Aspergillus fumigatus. Firstly, regions of amino acid conservation in chitin synthases of Saccharomyces cerevisiae were used to design degenerate primers for amplification of portions of related genes, and secondly, a segment of the S. cerevisiae CSD2 gene was used to screen an A. fumigatus lambda genomic DNA library. the polymerase chain reaction (PCR)-based approach led to the identification of five different genes, designated chsA, chsB, chsC, chsD and chsE. chsA, chsB, and chsC fall into Classes I, II and III of the 'zymogen type' chitin synthases, respectively. The chsD fragment has approximately 35% amino acid sequence identity to both the zymogen type genes and the non-zymogen type CSD2 gene. chsF appears to be a homologue of CSD2, being 80% identical to CSD2 over 100 amino acids. An unexpected finding was the isolation by heterologous hybridization of another gene (chsE), which also has strong sequence similarity (54% identity at the amino acid level over the same region as chsF) to CSD2. Reverse transcriptase-PCR was used to show that each gene is expressed during hyphal growth in submerged cultures.

[The use of palisade technique in tympanoplasties after Heermann].

PubMed

Wielgosz, Romuald; Mroczkowski, Edward

2006-01-01

The palisade tympanoplasties-technique with using of tragal and conchal autografts for reconstruction of the tympanic membrane and the auditory canal wall was described. The operation started with the endaural incision. Tragal and conchal autograft palisade fragments with perichondrium for reconstruction of the tympanic membrane and the auditory canal wall have been used up to 1996 in 15,300 cases. We placed palisaded cartilage fragments parallel to the manubrium of the malleus in type I tympanoplasties and in type II or III procedures parallel to the long process of the incus. The "tunnel plasty" in the eustachian tubal entrance is performed with "simmering", "architrave" and "anti-architrave" to keep the tubal entrance open. This "tunnel plasty" results in a nice reconstruction of the tympano-meatal niche. The "annulus-stapes plate" in type III tympanoplasties replaces the function of the incus, crossing the promontory and reducing adhesions. This annulus-stapes bridge is fixed with a further palisade cartilage, "step plasty", which connects the "tunnel-plasty" with "annulus-stapes plate". The palisade-epitympanum-antrum plasty allows ventilation of the antrum via a tunnel constructed of well-fitting parallel pieces of cartilage fixed by self-tension (no glue) and replacing the bony canal wall. The "columella-tunnel plasty" has an L-shaped notch in the "annulus-stapes plate" fixing a columella of cartilage, placed in the oval window. Only in a case with a narrow oval window niche, a type IV palisade plasty can be performed or a prosthesis placed. The "annulus-stapes cartilage plate" is more stable reconstruction in type III tympanoplasties than are incus of foreign body interpositions. Adhesions on the promontory are found more often with fascia than with cartilage fragments. Histologic study of autograft cartilage showed good preservation of cartilage cells even 26 years after transplantation. The use of palisade cartilage technique brings very good functional and better long-term results.

The electroneutral sodium/bicarbonate cotransporter containing an amino terminal 123-amino-acid cassette is expressed predominantly in the heart

PubMed Central

Cooper, Deborah S.; Lee, Hye Jeong; Yang, Han Soo; Kippen, Joseph; Yun, C. Chris; Choi, Inyeong

2006-01-01

Summary In this study, we examined the tissue-specific expression of two electroneutral Na/HCO3 cotransporter (NBCn1) variants that differ from each other by the presence of the N-terminal 123 amino acids (cassette II). A rat Northern blot with the probe to nucleotides encoding cassette II detected a 9 kb NBCn1 mRNA strongly in the heart and weakly in skeletal muscles, but absent from most of the tissues including kidney, brain, and pancreas. In the rat heart, PCR with primers flanking cassette II preferentially amplified a DNA fragment that lacked cassette II. However, in the human heart, PCR preferentially amplified a fragment that contained cassette II. This larger PCR product was found virtually in all regions of the human cardiovascular system with strong amplification in the apex, atrium, and atrioventricular nodes. These findings indicate that the variant containing cassette II is almost absent in tissues including brain, kidney, and pancreas, where NBCn1 has been extensively examined. PMID:16547769

Improving of lipid productivity of the oleaginous microalgae Chlorella pyrenoidosa via atmospheric and room temperature plasma (ARTP).

PubMed

Cao, Song; Zhou, Xu; Jin, Wenbiao; Wang, Feng; Tu, Renjie; Han, Songfang; Chen, Hongyi; Chen, Chuan; Xie, Guo-Jun; Ma, Fang

2017-11-01

In this study, an efficient screening program was established with ARTP. Five strains from oleaginous microalgae Chlorella pyrenoidosa were screened from mutant library after mutagenizing by ARTP. Among them, the optimal mutant strain was named as II-H6. In the BG11 medium, the OD 680 of II-H6 in stationary phase were increased by 32.08% than the original strain. Meanwhile, compared with the original strain, the dry weight and lipid productivity of II-H6 were increased by 22.07% and 16.85%, respectively. II-H6 showed a good genetic stability in BG11 medium and the optimum growth temperature and pH were 33°C and 9.0. 18S gene fragment length of II-H6 strain were 1886bp. Analysis of the gene fragment showed that the II-H6 strain had a close relationship to the original strain, and it belonged to the mutation within the genus Chlorella. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation and characterization of a cDNA clone specific for avian vitellogenin II.

PubMed Central

Protter, A A; Wang, S Y; Shelness, G S; Ostapchuk, P; Williams, D L

1982-01-01

A clone for vitellogenin, a major avian, estrogen responsive egg yolk protein, was isolated from the cDNA library of estrogen-induced rooster liver. Two forms of plasma vitellogenin, vitellogenin I (VTG I) and vitellogenin II (VTG II), distinguishable on the basis of their unique partial proteolysis maps, have been characterized and their corresponding hepatic precursor forms identified. We have used this criterion to specifically characterize which vitellogenin protein had been cloned. Partial proteolysis maps of BTG I and VTG II standards, synthesized in vivo, were compared to maps of protein synthesized in vitro using RNA hybrid-selected by the vitellogenin plasmid. Eight major digest fragments were found common to the in vitro synthesized vitellogenin and the VTG II standard while no fragments were observed to correspond to the VTG I map. A restriction map of the VTG II cDNA clone permits comparison to previously described cDNA and genomic vitellogenin clones. Images PMID:6182527

On disciplinary fragmentation and scientific progress.

PubMed

Balietti, Stefano; Mäs, Michael; Helbing, Dirk

2015-01-01

Why are some scientific disciplines, such as sociology and psychology, more fragmented into conflicting schools of thought than other fields, such as physics and biology? Furthermore, why does high fragmentation tend to coincide with limited scientific progress? We analyzed a formal model where scientists seek to identify the correct answer to a research question. Each scientist is influenced by three forces: (i) signals received from the correct answer to the question; (ii) peer influence; and (iii) noise. We observed the emergence of different macroscopic patterns of collective exploration, and studied how the three forces affect the degree to which disciplines fall apart into divergent fragments, or so-called "schools of thought". We conducted two simulation experiments where we tested (A) whether the three forces foster or hamper progress, and (B) whether disciplinary fragmentation causally affects scientific progress and vice versa. We found that fragmentation critically limits scientific progress. Strikingly, there is no effect in the opposite causal direction. What is more, our results shows that at the heart of the mechanisms driving scientific progress we find (i) social interactions, and (ii) peer disagreement. In fact, fragmentation is increased and progress limited if the simulated scientists are open to influence only by peers with very similar views, or when within-school diversity is lost. Finally, disciplines where the scientists received strong signals from the correct answer were less fragmented and experienced faster progress. We discuss model's implications for the design of social institutions fostering interdisciplinarity and participation in science.

On Disciplinary Fragmentation and Scientific Progress

PubMed Central

Balietti, Stefano; Mäs, Michael; Helbing, Dirk

2015-01-01

Why are some scientific disciplines, such as sociology and psychology, more fragmented into conflicting schools of thought than other fields, such as physics and biology? Furthermore, why does high fragmentation tend to coincide with limited scientific progress? We analyzed a formal model where scientists seek to identify the correct answer to a research question. Each scientist is influenced by three forces: (i) signals received from the correct answer to the question; (ii) peer influence; and (iii) noise. We observed the emergence of different macroscopic patterns of collective exploration, and studied how the three forces affect the degree to which disciplines fall apart into divergent fragments, or so-called “schools of thought”. We conducted two simulation experiments where we tested (A) whether the three forces foster or hamper progress, and (B) whether disciplinary fragmentation causally affects scientific progress and vice versa. We found that fragmentation critically limits scientific progress. Strikingly, there is no effect in the opposite causal direction. What is more, our results shows that at the heart of the mechanisms driving scientific progress we find (i) social interactions, and (ii) peer disagreement. In fact, fragmentation is increased and progress limited if the simulated scientists are open to influence only by peers with very similar views, or when within-school diversity is lost. Finally, disciplines where the scientists received strong signals from the correct answer were less fragmented and experienced faster progress. We discuss model’s implications for the design of social institutions fostering interdisciplinarity and participation in science. PMID:25790025

Regulation of nonmuscle myosin II during 3-methylcholanthrene induced dedifferentiation of C2C12 myotubes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dey, Sumit K.; Saha, Shekhar; Das, Provas

2014-08-01

3-Methylcholanthrene (3MC) induces tumor formation at the site of injection in the hind leg of mice within 110 days. Recent reports reveal that the transformation of normal muscle cells to atypical cells is one of the causes for tumor formation, however the molecular mechanism behind this process is not well understood. Here, we show in an in vitro study that 3MC induces fragmentation of multinucleate myotubes into viable mononucleates. These mononucleates form colonies when they are seeded into soft agar, indicative of cellular transformation. Immunoblot analysis reveals that phosphorylation of myosin regulatory light chain (RLC{sub 20}) is 5.6±0.5 fold reducedmore » in 3MC treated myotubes in comparison to vehicle treated myotubes during the fragmentation of myotubes. In contrast, levels of myogenic factors such as MyoD, Myogenin and cell cycle regulators such as Cyclin D, Cyclin E1 remain unchanged as assessed by real-time PCR array and reverse transcriptase PCR analysis, respectively. Interestingly, addition of the myosin light chain kinase inhibitor, ML-7, enhances the fragmentation, whereas phosphatase inhibitor perturbs the 3MC induced fragmentation of myotubes. These results suggest that decrease in RLC{sub 20} phosphorylation may be associated with the fragmentation step of dedifferentiation. - Highlights: • 3-Methylcholanthrene induces fragmentation of C2C12-myotubes. • Dedifferentiation can be divided into two steps – fragmentation and proliferation. • Fragmentation is associated with rearrangement of nonmuscle myosin II. • Genes associated with differentiation and proliferation are not altered during fragmentation. • Phosphorylation of myosin regulatory light chain is reduced during fragmentation.« less

Habitat fragmentation in the temperate zone: a perspective for managers

Treesearch

John Faaborg; Margaret Brittingham; Therese Donovan; John Blake

1993-01-01

Habitat fragmentation occurs when a large, fairly continuous tract of vegetation is converted to other vegetation types such that only scattered fragments of the original type remain. Problems associated with habitat fragmentation include overall habitat loss, increase in edge habitat and edge effects (particularly higher parasitism and nest predation rates), and...

Impaired Vascular Contractility and Aortic Wall Degeneration in Fibulin-4 Deficient Mice: Effect of Angiotensin II Type 1 (AT1) Receptor Blockade

PubMed Central

Moltzer, Els; te Riet, Luuk; Swagemakers, Sigrid M. A.; van Heijningen, Paula M.; Vermeij, Marcel; van Veghel, Richard; Bouhuizen, Angelique M.; van Esch, Joep H. M.; Lankhorst, Stephanie; Ramnath, Natasja W. M.; de Waard, Monique C.; Duncker, Dirk J.; van der Spek, Peter J.; Rouwet, Ellen V.; Danser, A. H. Jan; Essers, Jeroen

2011-01-01

Medial degeneration is a key feature of aneurysm disease and aortic dissection. In a murine aneurysm model we investigated the structural and functional characteristics of aortic wall degeneration in adult fibulin-4 deficient mice and the potential therapeutic role of the angiotensin (Ang) II type 1 (AT1) receptor antagonist losartan in preventing aortic media degeneration. Adult mice with 2-fold (heterozygous Fibulin-4+/R) and 4-fold (homozygous Fibulin-4R/R) reduced expression of fibulin-4 displayed the histological features of cystic media degeneration as found in patients with aneurysm or dissection, including elastin fiber fragmentation, loss of smooth muscle cells, and deposition of ground substance in the extracellular matrix of the aortic media. The aortic contractile capacity, determined by isometric force measurements, was diminished, and was associated with dysregulation of contractile genes as shown by aortic transcriptome analysis. These structural and functional alterations were accompanied by upregulation of TGF-β signaling in aortas from fibulin-4 deficient mice, as identified by genome-scaled network analysis as well as by immunohistochemical staining for phosphorylated Smad2, an intracellular mediator of TGF-β. Tissue levels of Ang II, a regulator of TGF-β signaling, were increased. Prenatal treatment with the AT1 receptor antagonist losartan, which blunts TGF-β signaling, prevented elastic fiber fragmentation in the aortic media of newborn Fibulin-4R/R mice. Postnatal losartan treatment reduced haemodynamic stress and improved lifespan of homozygous knockdown fibulin-4 animals, but did not affect aortic vessel wall structure. In conclusion, the AT1 receptor blocker losartan can prevent aortic media degeneration in a non-Marfan syndrome aneurysm mouse model. In established aortic aneurysms, losartan does not affect aortic architecture, but does improve survival. These findings may extend the potential therapeutic application of inhibitors of the renin-angiotensin system to the preventive treatment of aneurysm disease. PMID:21858106

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

PubMed Central

Xiang, Jin Yu; Ponder, Jay W.

2014-01-01

An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies. PMID:25045338

The new intra-articular calcaneal fracture classification system in term of sustentacular fragment configurations and incorporation of posterior calcaneal facet fractures with fracture components of the calcaneal body.

PubMed

Harnroongroj, Thossart; Harnroongroj, Thos; Suntharapa, Thongchai; Arunakul, Marut

2016-10-01

The aim of this study was to develop a new calcaneal fracture classification system which will consider sustentacular fragment configuration and relation of posterior calcaneal facet to calcaneal body. The new classification system used sustentacular fragment configuration and relation of posterior calcaneal facet fracture with fracture components of calcaneal body as key aspects of main types and subtypes. Between 2000 and 2014, 126 intraarticular calcaneal fractures were classified according to the new classification system by using computed tomography images. The new classification system was studied in term of reliability, correlation to choices of treatment, implant fixation and quality of fracture reduction. Types of sustentacular fragment comprised type A, B and C. Type A sustentacular fragment included sustentacular tali containing middle calcaneal facet. In Type B and C fractures sustentacular fragment included medial aspect and entire posterior calcaneal facet as a single unit, respectively. The fractures with type A, B and C sustentacular fragments were classified as main type A, B and C intra-articular calcaneal fractures. The main type A and B comprised 4 subtypes. Subtypes A1, A3, B1, and B3 associated with avulsion and bending fragments of calcaneal body. Subtype A2, B2, and B4 associated with burst calcaneal body. Subtype B4 was not found in the study. Main type C had no subtype and associated with burst calcaneal body. The data showed good reliability. The study showed that our new intra-articular calcaneal fracture classification system correlates to choices of treatment, implant fixation and quality of fracture reduction. Level IV, Study of Diagnostic Test. Copyright © 2016 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

Genetic characterisation of Toxoplasma gondii in wildlife from North America revealed widespread and high prevalence of the fourth clonal type

USGS Publications Warehouse

Dubey, J.P.; Velmurugan, G.V.; Ragendran, C.; Yabsley, M.J.; Thomas, N.J.; Beckmen, K.B.; Sinnett, D.; Ruid, D.; Hart, J.; Fair, P.A.; McFee, W.E.; Shearn-Bochsler, V.; Kwok, O.C.H.; Ferreira, L.R.; Choudhary, S.; Faria, E.B.; Zhou, H.; Felix, T.A.; Su, C.

2011-01-01

Little is known of the genetic diversity of Toxoplasma gondii circulating in wildlife. In the present study wild animals, from the USA were examined for T. gondii infection. Tissues of naturally exposed animals were bioassayed in mice for isolation of viable parasites. Viable T. gondii was isolated from 31 animals including, to our knowledge for the first time, from a bald eagle (Haliaeetus leucocephalus), five gray wolves (Canis lupus), a woodrat (Neotoma micropus), and five Arctic foxes (Alopex lagopus). Additionally, 66 T. gondii isolates obtained previously, but not genetically characterised, were revived in mice. Toxoplasma gondii DNA isolated from these 97 samples (31+66) was characterised using 11 PCR-restriction fragment length polymorphism (RFLP) markers (SAG1, 5'- and 3'-SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico). A total of 95 isolates were successfully genotyped. In addition to clonal Types II, and III, 12 different genotypes were found. These genotype data were combined with 74 T. gondii isolates previously characterised from wildlife from North America and a composite data set of 169 isolates comprised 22 genotypes, including clonal Types II, III and 20 atypical genotypes. Phylogenetic network analysis showed limited diversity with dominance of a recently designated fourth clonal type (Type 12) in North America, followed by the Type II and III lineages. These three major lineages together accounted for 85% of strains in North America. The Type 12 lineage includes previously identified Type A and X strains from sea otters. This study revealed that the Type 12 lineage accounts for 46.7% (79/169) of isolates and is dominant in wildlife of North America. No clonal Type I strain was identified among these wildlife isolates. These results suggest that T. gondii strains in wildlife from North America have limited diversity, with the occurrence of only a few major clonal types.

Fatal Disseminated Toxoplasma gondii Infection in a Captive Harbour Porpoise (Phocoena phocoena).

PubMed

Herder, V; van de Velde, N; Højer Kristensen, J; van Elk, C; Peters, M; Kilwinski, J; Schares, G; Siebert, U; Wohlsein, P

2015-11-01

A 7-year-old female harbour porpoise (Phocoena phocoena), born and held in captivity, suffered from reduced consciousness, imprecise and circling swimming movements and long phases of immobility over a period of 3 weeks. The animal died during treatment in a Danish open sea facility. Pathological examination revealed multifocal pyogranulomatous to necrotizing meningoencephalomyelitis, ganglioneuritis, plexus chorioiditis, myocarditis, hepatitis and adrenalitis with few intralesional protozoal tachyzoites and bradyzoites within cysts. Immunohistochemistry was positive for Toxoplasma gondii antigen within the lesions. Using polymerase chain reaction (PCR), the presence of T. gondii-specific genome fragments was confirmed. A multilocus PCR-restriction fragment length polymorphism analysis using nine unlinked marker regions (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) resulted in the identification of T. gondii type II (variant Apico Type I), which is the T. gondii genotype dominating in Germany. This is the first description of disseminated fatal toxoplasmosis in a captive harbour porpoise that lived in an open sea basin. Surface water contaminated with toxoplasma oocysts is regarded as the most likely source of infection. Copyright © 2015 Elsevier Ltd. All rights reserved.

Lineage II (Serovar 1/2a and 1/2c) Human Listeria monocytogenes Pulsed-Field Gel Electrophoresis Types Divided into PFGE Groups Using the Band Patterns Below 145.5 kb.

PubMed

Lopez-Valladares, Gloria; Danielsson-Tham, Marie-Louise; Goering, Richard V; Tham, Wilhelm

2017-01-01

Among 504 clinical lineage II isolates of Listeria monocytogenes isolated during 1958-2010 in Sweden, 119 pulsed-field gel electrophoresis (PFGE) types (AscI) have been identified based on the number and distribution of all banding patterns in each DNA profile. In this study, these types were further divided into PFGE groups based on the configuration of small bands with sizes <145.5 kb. The 504 isolates included 483 serovar 1/2a isolates distributed into 114 PFGE types and 21 serovar 1/2c isolates distributed into 9 PFGE types; these were further divided into 21 PFGE groups. PFGE group, that is, configuration of small bands below 145.5 kb, and serovars were correlated. L. monocytogenes isolates belonging to PFGE groups A, B, C, E, F, H, K, L, M, S, V, W, Y, and Ö-6 to Ö-12 shared serovar 1/2a, with one exception. PFGE group E also included two PFGE types sharing serovar 1/2c and four PFGE types belonging to either serovar 1/2a or 1/2c. Isolates belonging to PFGE group N shared serovar 1/2c. In contrast to lineage I isolates, small fragments <33.3 kb were visible in all L. monocytogenes isolates belonging to lineage II. In the results from both the present and previous studies, the genomic region of small bands was genetically more conservative than in large bands. The distribution of these small bands established the relatedness of strains and defined a genetic marker for both lineages I and II, while also establishing their serogroup. The division of L. monocytogenes PFGE types into PFGE groups is advantageous as the profile of every new isolate can be identified easily and quickly through first studying the PFGE group affiliation of the isolate based on the smaller band patterns <145.5 kb, and then identifying the PFGE type based on the band patterns >145.5 kb.

Evaluation of Semiautomated IS6110-Based Restriction Fragment Length Polymorphism Typing for Mycobacterium tuberculosis in a High-Burden Setting.

PubMed

Said, Halima M; Krishnamani, Keshav; Omar, Shaheed V; Dreyer, Andries W; Sansom, Bianca; Fallows, Dorothy; Ismail, Nazir A

2016-10-01

The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing of Mycobacterium tuberculosis using the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing of M. tuberculosis isolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Combined EXAFS and DFT Structure Calculations Provide Structural Insights into the 1:1 Multi-Histidine Complexes of CuII, CuI and ZnII with the Tandem Octarepeats of the Mammalian Prion Protein

PubMed Central

Pushie, M. Jake; Nienaber, Kurt H.; McDonald, Alex; Millhauser, Glenn L.; George, Graham N.

2014-01-01

The metal coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of copper interaction with PrP just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, and yet the structural details of the various metal coordination modes have not been fully elucidated in some cases. Herein we employ X-ray absorption near edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for CuII, CuI and ZnII with an N-terminal fragment of PrP. The PrP fragment constitutes four tandem repeats representative of the mammalian octarepeat domain, designated OR4, which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations provide additional structural and thermodynamic data, and candidate structures are used to inform EXAFS data analysis. The optimized geometries from DFT calculations are used to identify potential coordination complexes for multi-histidine coordination of CuII, CuI and ZnII in an aqueous medium, modeled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve fitting, using full multiple scattering on candidate structures from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of CuII, CuI and ZnII with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as a square planar [CuII(His)4]2+, digonal [CuI(His)2]+ and tetrahedral [ZnII(His)3(OH2)]2+, respectively. PMID:25042361

Gas-phase behaviour of Ru(II) cyclopentadienyl-derived complexes with N-coordinated ligands by electrospray ionization mass spectrometry: fragmentation pathways and energetics.

PubMed

Madeira, Paulo J Amorim; Morais, Tânia S; Silva, Tiago J L; Florindo, Pedro; Garcia, M Helena

2012-08-15

The gas-phase behaviour of six Ru(II) cyclopentadienyl-derived complexes with N-coordinated ligands, compounds with antitumor activities against several cancer lines, was studied. This was performed with the intent of establishing fragmentation pathways and to determine the Ru-L(N) and Ru-L(P) ligand bond dissociation energies. Such knowledge can be an important tool for the postulation of the mechanisms of action of these anticancer drugs. Two types of instruments equipped with electrospray ionisation were used (ion trap and a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer). The dissociation energies were determined using energy-variable collision-induced dissociation measurements in the ion trap. The FTICR instrument was used to perform MS(n) experiments on one of the compounds and to obtain accurate mass measurements. Theoretical calculations were performed at the density functional theory (DFT) level using two different functionals (B3LYP and M06L) to estimate the dissociation energies of the complexes under study. The influence of the L(N) on the bond dissociation energy (D) of RuCp compounds with different nitrogen ligands was studied. The lability order of L(N) was: imidazole<1-butylimidazole<5-phenyl-1H-tetrazole<1-benzylimidazole. Both the functionals used gave the following ligand lability order: imidazole<1-benzylimidazole<5-phenyl-1H-tetrazole<1-butylimidazole. It is clear that there is an inversion between 1-benzylimidazole and 1-butylimidazole for the experimental and theoretical lability orders. The M06L functional afforded values of D closer to the experimental values. The type of phosphane (L(P) ) influenced the dissociation energies, with values of D being higher for Ru-L(N) with 1-butylimidazole when the phosphane was 1,2-bis(diphenylphosphino)ethane. The Ru-L(P) bond dissociation energy for triphenylphosphane was independent of the type of complex. The D values of Ru-L(N) and Ru-L(P) were determined for all six compounds and compared with the values calculated by the DFT method. For the imidazole-derived ligands the energy trend was rationalized in terms of the increasing extension of the σ-donation/π-backdonation effect. The bond dissociation energy of Ru-PPh(3) was independent of the fragmentations. Copyright © 2012 John Wiley & Sons, Ltd.

14-3-3 proteins tune non-muscle myosin II assembly.

PubMed

West-Foyle, Hoku; Kothari, Priyanka; Osborne, Jonathan; Robinson, Douglas N

2018-05-04

The 14-3-3 family comprises a group of small proteins that are essential, ubiquitous, and highly conserved across eukaryotes. Overexpression of the 14-3-3 proteins σ, ϵ, ζ, and η correlates with high metastatic potential in multiple cancer types. In Dictyostelium , 14-3-3 promotes myosin II turnover in the cell cortex and modulates cortical tension, cell shape, and cytokinesis. In light of the important roles of 14-3-3 proteins across a broad range of eukaryotic species, we sought to determine how 14-3-3 proteins interact with myosin II. Here, conducting in vitro and in vivo studies of both Dictyostelium (one 14-3-3 and one myosin II) and human proteins (seven 14-3-3s and three nonmuscle myosin IIs), we investigated the mechanism by which 14-3-3 proteins regulate myosin II assembly. Using in vitro assembly assays with purified myosin II tail fragments and 14-3-3, we demonstrate that this interaction is direct and phosphorylation-independent. All seven human 14-3-3 proteins also altered assembly of at least one paralog of myosin II. Our findings indicate a mechanism of myosin II assembly regulation that is mechanistically conserved across a billion years of evolution from amebas to humans. We predict that altered 14-3-3 expression in humans inhibits the tumor suppressor myosin II, contributing to the changes in cell mechanics observed in many metastatic cancers. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Global DNA methylation analysis using methyl-sensitive amplification polymorphism (MSAP).

PubMed

Yaish, Mahmoud W; Peng, Mingsheng; Rothstein, Steven J

2014-01-01

DNA methylation is a crucial epigenetic process which helps control gene transcription activity in eukaryotes. Information regarding the methylation status of a regulatory sequence of a particular gene provides important knowledge of this transcriptional control. DNA methylation can be detected using several methods, including sodium bisulfite sequencing and restriction digestion using methylation-sensitive endonucleases. Methyl-Sensitive Amplification Polymorphism (MSAP) is a technique used to study the global DNA methylation status of an organism and hence to distinguish between two individuals based on the DNA methylation status determined by the differential digestion pattern. Therefore, this technique is a useful method for DNA methylation mapping and positional cloning of differentially methylated genes. In this technique, genomic DNA is first digested with a methylation-sensitive restriction enzyme such as HpaII, and then the DNA fragments are ligated to adaptors in order to facilitate their amplification. Digestion using a methylation-insensitive isoschizomer of HpaII, MspI is used in a parallel digestion reaction as a loading control in the experiment. Subsequently, these fragments are selectively amplified by fluorescently labeled primers. PCR products from different individuals are compared, and once an interesting polymorphic locus is recognized, the desired DNA fragment can be isolated from a denaturing polyacrylamide gel, sequenced and identified based on DNA sequence similarity to other sequences available in the database. We will use analysis of met1, ddm1, and atmbd9 mutants and wild-type plants treated with a cytidine analogue, 5-azaC, or zebularine to demonstrate how to assess the genetic modulation of DNA methylation in Arabidopsis. It should be noted that despite the fact that MSAP is a reliable technique used to fish for polymorphic methylated loci, its power is limited to the restriction recognition sites of the enzymes used in the genomic DNA digestion.

C4d-negative antibody-mediated rejection with high anti-angiotensin II type I receptor antibodies in absence of donor-specific antibodies.

PubMed

Fuss, Alexander; Hope, Christopher M; Deayton, Susan; Bennett, Greg Donald; Holdsworth, Rhonda; Carroll, Robert P; Coates, P Toby H

2015-07-01

Acute antibody-mediated rejection can occur in absence of circulating donor-specific antibodies. Agonistic antibodies targeting the anti-angiotensin II type 1 receptor (anti-AT1 R) are emerging as important non-human leucocyte antigen (HLA) antibodies. Elevated levels of anti-angiotensin II receptor antibodies were first observed in kidney transplant recipients with malignant hypertension and allograft rejection. They have now been studied in three separate kidney transplant populations and associate to frequency of rejection, severity of rejection and graft failure. We report 11 cases of biopsy-proven, Complement 4 fragment d (C4d)-negative, acute rejection occurring without circulating donor-specific anti-HLA antibodies. In eight cases, anti-angiotensin receptor antibodies were retrospectively examined. The remaining three subjects were identified from our centre's newly instituted routine anti-angiotensin receptor antibody screening. All subjects fulfilled Banff 2013 criteria for antibody-mediated rejection and all responded to anti-rejection therapy, which included plasma exchange and angiotensin receptor blocker therapy. These cases support the routine assessment of anti-AT1 R antibodies in kidney transplant recipients to identify subjects at risk. Further studies will need to determine optimal assessment protocol and the effectiveness of pre-emptive treatment with angiotensin receptor blockers. © 2015 Asian Pacific Society of Nephrology.

Inhibition of the Hantavirus Fusion Process by Predicted Domain III and Stem Peptides from Glycoprotein Gc.

PubMed

Barriga, Gonzalo P; Villalón-Letelier, Fernando; Márquez, Chantal L; Bignon, Eduardo A; Acuña, Rodrigo; Ross, Breyan H; Monasterio, Octavio; Mardones, Gonzalo A; Vidal, Simon E; Tischler, Nicole D

2016-07-01

Hantaviruses can cause hantavirus pulmonary syndrome or hemorrhagic fever with renal syndrome in humans. To enter cells, hantaviruses fuse their envelope membrane with host cell membranes. Previously, we have shown that the Gc envelope glycoprotein is the viral fusion protein sharing characteristics with class II fusion proteins. The ectodomain of class II fusion proteins is composed of three domains connected by a stem region to a transmembrane anchor in the viral envelope. These fusion proteins can be inhibited through exogenous fusion protein fragments spanning domain III (DIII) and the stem region. Such fragments are thought to interact with the core of the fusion protein trimer during the transition from its pre-fusion to its post-fusion conformation. Based on our previous homology model structure for Gc from Andes hantavirus (ANDV), here we predicted and generated recombinant DIII and stem peptides to test whether these fragments inhibit hantavirus membrane fusion and cell entry. Recombinant ANDV DIII was soluble, presented disulfide bridges and beta-sheet secondary structure, supporting the in silico model. Using DIII and the C-terminal part of the stem region, the infection of cells by ANDV was blocked up to 60% when fusion of ANDV occurred within the endosomal route, and up to 95% when fusion occurred with the plasma membrane. Furthermore, the fragments impaired ANDV glycoprotein-mediated cell-cell fusion, and cross-inhibited the fusion mediated by the glycoproteins from Puumala virus (PUUV). The Gc fragments interfered in ANDV cell entry by preventing membrane hemifusion and pore formation, retaining Gc in a non-resistant homotrimer stage, as described for DIII and stem peptide inhibitors of class II fusion proteins. Collectively, our results demonstrate that hantavirus Gc shares not only structural, but also mechanistic similarity with class II viral fusion proteins, and will hopefully help in developing novel therapeutic strategies against hantaviruses.

Determinants of affinity and mode of DNA binding at the carboxy terminus of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1.

PubMed

Andera, L; Geiduschek, E P

1994-03-01

The role of the carboxy-terminal amino acids of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1, in DNA binding was analyzed. Chain-terminating mutations truncating the normally 99-amino-acid TF1 at amino acids 96, 97, and 98 were constructed, as were missense mutations substituting cysteine, arginine, and serine for phenylalanine at amino acid 97 and tryptophan for lysine at amino acid 99. The binding of the resulting proteins to a synthetic 44-bp binding site in 5-(hydroxymethyl)uracil DNA, to binding sites in larger SPO1 [5-(hydroxymethyl)uracil-containing] DNA fragments, and to thymine-containing homologous DNA was analyzed by gel retardation and also by DNase I and hydroxy radical footprinting. We conclude that the C tail up to and including phenylalanine at amino acid 97 is essential for DNA binding and that the two C-terminal amino acids, 98 and 99, are involved in protein-protein interactions between TF1 dimers bound to DNA.

A novel Alaska pollack-derived peptide, which increases glucose uptake in skeletal muscle cells, lowers the blood glucose level in diabetic mice.

PubMed

Ayabe, Tatsuhiro; Mizushige, Takafumi; Ota, Wakana; Kawabata, Fuminori; Hayamizu, Kohsuke; Han, Li; Tsuji, Tomoko; Kanamoto, Ryuhei; Ohinata, Kousaku

2015-08-01

We found that the tryptic digest of Alaska pollack protein exhibits a glucose-lowering effect in KK-Ay mice, a type II diabetic model. We then searched for glucose-lowering peptides in the digest. Ala-Asn-Gly-Glu-Val-Ala-Gln-Trp-Arg (ANGEVAQWR) was identified from a peak of the HPLC fraction selected based on the glucose-lowering activity in an insulin resistance test using ddY mice. ANGEVAQWR (3 mg kg(-1)) decreased the blood glucose level after intraperitoneal administration. Among its fragment peptides, the C-terminal tripeptide, Gln-Trp-Arg (QWR, 1 mg kg(-1)), lowered the blood glucose level, suggesting that the C-terminal is critical for glucose-lowering activity. QWR also enhanced glucose uptake into C2C12, a mouse skeletal muscle cell line. QWR did not induce the phosphorylation of serine/threonine protein kinase B (Akt) and adenosine monophosphate-activated protein kinase (AMPK). We also demonstrated that QWR lowered the blood glucose level in NSY and KK-Ay, type II diabetic models.

Antigenic structure of the herpes simplex virus type 1 glycoprotein C: demonstration of a linear epitope situated in an environment of highly conformation-dependent epitopes.

PubMed

Sjöblom, I; Glorioso, J C; Sjögren-Jansson, E; Olofsson, S

1992-03-01

A continuous epitope, situated within or in close proximity to antigenic site II of the herpes simplex virus type 1-specified glycoprotein C (gC-1), was identified. The continuous linear nature of the epitope, defined by a monoclonal antibody C2H12, was established by three independent lines of evidence: (i) The epitope was detectable by immunoblot under denaturing and reducing conditions. (ii) The epitope was detectable by RIPA of extracts from TM-treated HSV-infected cells, despite the malfolding caused by this treatment. (iii) The epitope was detected in an approximately 5,000-dalton papain fragment of gC-1. A mapping analysis, primarily based on use of mutant virus, expressing truncated gC-1 molecules, suggested that the mapping position of the epitope was delimited by amino acids 120 and 230. Other epitopes of this region of gC-1 are highly conformation-dependent, and the existence of a linear epitope, accessible on native gC-1, may facilitate the elucidation of the functional anatomy of gC-1.

An outbreak of toxoplasmosis in squirrel monkeys (Saimiri sciureus) in South Korea.

PubMed

Oh, Hanseul; Eo, Kyung-Yeon; Gumber, Sanjeev; Hong, Jung Joo; Kim, C-Yoon; Lee, Hyun-Ho; Jung, Young-Mok; Kim, Jin; Whang, Gyu-Whan; Lee, Ji-Min; Yeo, Yong-Gu; Ryu, Bokyeong; Ryu, Ji-Sook; Lee, Seul-Kee; Kim, Ukjin; Kang, Sin-Geun; Park, Jae-Hak

2018-04-30

Toxoplasma gondii (T. gondii) is an intracellular protozoan parasite that can infect warm-blooded animals including humans. New World monkeys, such as squirrel monkeys, are more susceptible to T. gondii than Old World monkeys, often developing fatal disease. In this study, seven of thirteen dead squirrel monkeys at Seoul Grand Park were tested to find the cause of sudden death. The main histopathological findings included interstitial pneumonia, necrotizing hepatitis, and splenitis. Periodic acid-Schiff staining of liver, spleen, and lung revealed cyst structures consistent with bradyzoites. Amplification of the B1 gene was detected in the liver or spleen of all monkeys. Additionally, a restriction fragment length polymorphism assay and phylogenetic analysis of the GRA6 amplicon revealed a consistent clustering with the type II strain of T. gondii. This study is the first report of T. gondii infection of squirrel monkeys in Korea, and the first report of type II T. gondii based on GRA6 analysis in Korea. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Caffeine-Induced Premature Chromosome Condensation Results in the Apoptosis-Like Programmed Cell Death in Root Meristems of Vicia faba

PubMed Central

Rybaczek, Dorota; Musiałek, Marcelina Weronika; Balcerczyk, Aneta

2015-01-01

We have demonstrated that the activation of apoptosis-like programmed cell death (AL-PCD) was a secondary result of caffeine (CF) induced premature chromosome condensation (PCC) in hydroxyurea-synchronized Vicia faba root meristem cells. Initiation of the apoptotic-like cell degradation pathway seemed to be the result of DNA damage generated by treatment with hydroxyurea (HU) [double-stranded breaks (DSBs) mostly] and co-treatment with HU/CF [single-stranded breaks (SSBs) mainly]. A single chromosome comet assay was successfully used to study different types of DNA damage (neutral variant–DSBs versus alkaline–DSBs or SSBs). The immunocytochemical detection of H2AXS139Ph and PARP-2 were used as markers for DSBs and SSBs, respectively. Acridine orange and ethidium bromide (AO/EB) were applied for quantitative immunofluorescence measurements of dead, dying and living cells. Apoptotic-type DNA fragmentation and positive TUNEL reaction finally proved that CF triggers AL-PCD in stressed V. faba root meristem cells. In addition, the results obtained under transmission electron microscopy (TEM) further revealed apoptotic-like features at the ultrastructural level of PCC-type cells: (i) extensive vacuolization; (ii) abnormal chromatin condensation, its marginalization and concomitant degradation; (iii) formation of autophagy-like vesicles (iv) protoplast shrinkage (v) fragmentation of cell nuclei and (vi) extensive degeneration of the cells. The results obtained have been discussed with respect to the vacuolar/autolytic type of plant-specific AL-PCD. PMID:26545248

β-Propeller Blades as Ancestral Peptides in Protein Evolution

PubMed Central

Kopec, Klaus O.; Lupas, Andrei N.

2013-01-01

Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD), type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world. PMID:24143202

Elemental analysis of glass by laser ablation inductively coupled plasma optical emission spectrometry (LA-ICP-OES).

PubMed

Schenk, Emily R; Almirall, José R

2012-04-10

The elemental analysis of glass evidence has been established as a powerful discrimination tool for forensic analysts. Laser ablation inductively coupled plasma optical emission spectrometry (LA-ICP-OES) has been compared to laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and energy dispersive micro X-ray fluorescence spectroscopy (μXRF/EDS) as competing instrumentation for the elemental analysis of glass. The development of a method for the forensic analysis of glass coupling laser ablation to ICP-OES is presented for the first time. LA-ICP-OES has demonstrated comparable analytical performance to LA-ICP-MS based on the use of the element menu, Al (Al I 396.15 nm), Ba (Ba II 455.40 nm), Ca (Ca II 315.88 nm), Fe (Fe II 238.20 nm), Li (Li I 670.78 nm), Mg (Mg I 285.21 nm), Sr (Sr II 407.77 nm), Ti (Ti II 368.51 nm), and Zr (Zr II 343.82 nm). The relevant figures of merit, such as precision, accuracy and sensitivity, are presented and compared to LA-ICP-MS. A set of 41 glass samples was used to assess the discrimination power of the LA-ICP-OES method in comparison to other elemental analysis techniques. This sample set consisted of several vehicle glass samples that originated from the same source (inside and outside windshield panes) and several glass samples that originated from different vehicles. Different match criteria were used and compared to determine the potential for Type I and Type II errors. It was determined that broader match criteria is more applicable to the forensic comparison of glass analysis because it can reduce the affect that micro-heterogeneity inherent in the glass fragments and a less than ideal sampling strategy can have on the interpretation of the results. Based on the test set reported here, a plus or minus four standard deviation (± 4s) match criterion yielded the lowest possibility of Type I and Type II errors. The developed LA-ICP-OES method has been shown to perform similarly to LA-ICP-MS in the discrimination among different sources of glass while offering the advantages of a lower cost of acquisition and operation of analytical instrumentation making ICP-OES a possible alternative elemental analysis method for the forensic laboratory. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Clinical and microbiological characteristics of cryptococcosis in Singapore: predominance of Cryptococcus neoformans compared with Cryptococcus gattii.

PubMed

Chan, Monica; Lye, David; Win, Mar Kyaw; Chow, Angela; Barkham, Tim

2014-09-01

To describe the clinical features, treatments, outcomes, and subtype prevalence of cryptococcosis in Singapore. All patients with laboratory confirmed cryptococcal infections admitted from 1999 to 2007 to a teaching hospital in Singapore were reviewed retrospectively. Identification and molecular types of Cryptococcus neoformans variants and Cryptococcus gattii were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Serotypes were inferred with a multiplex PCR method. Of 62 patients with cryptococcosis, C. neoformans var. grubii was the predominant subtype (in 95%), affecting mainly immunocompromised hosts (91%) with HIV infection (80%). Patients with HIV were younger (median age 36.5 vs. 49.5 years, p=0.006) and less likely to present with an altered mental status (14% vs. 50%, p=0.013). In contrast, delayed treatment (median 7 days vs. 2 days, p=0.03), pulmonary involvement (58% vs. 14%, p=0.03), and initial treatment with fluconazole (25% vs. 2%, p=0.02) were more common in HIV-negative patients. C. gattii was uncommon, affecting only three patients, all of whom were immunocompetent and had disseminated disease with pulmonary and neurological involvement. All C. gattii were RFLP type VG II, serotype B and all C. neoformans var. grubii were RFLP type VN I, serotype A, except for one that was RFLP type VN II. C. neoformans var. grubii, subtype VN I, was the predominant subtype in Singapore, infecting younger, mainly immunocompromised hosts with HIV. C. gattii was uncommon, causing pulmonary manifestations in older, immunocompetent patients and were RFLP type VG II. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Comparative study of CTX-II, Zn2+, and Ca2+ from the urine for knee osteoarthritis patients and healthy individuals

PubMed Central

Xin, Linwei; Wu, Zhihai; Qu, Quanli; Wang, Ruiying; Tang, Jichun; Chen, Lei

2017-01-01

Abstract The aim of the study was to explore the relationship between the concentration of C-telopeptide fragments of type II collagen (CTX-II), Zn2+, and Ca2+ in urine and knee osteoarthritis (KOA). Eighty-two patients with KOA and 20 healthy volunteers were enrolled. Anteroposterior and lateral position x-rays of knee joints were collected. The images were classified according to Kellgren-Lawrence radiographic grading criterion. The patients were divided into group grade I, group grade II, group grade III, and grade IV. The concentration of CTX-II in the urine was detected by enzyme-linked immunosorbent assay. The concentration of Zn2+ and Ca2+ in urine was detected by inductively coupled plasma atomic emission spectrometry. Compared with the healthy individuals, the concentration of CTX-II was significantly higher in KOA patients. The concentration of CTX-II in KOA patients from high to low was as follows: group IV, group III, group II, and group I. There was no significant difference between group I and healthy individuals. The concentration of Zn2+ and Ca2+ in urine of KOA patients was higher than that in healthy individuals. There was no difference in each KOA group. The concentration of CTX-II is instrumental to diagnose the progress of KOA. The concentration of Zn2+ and Ca2+ in urine is helpful for early diagnosis of KOA. PMID:28796042

An RNA-splicing mutation (G{sup +51VS20}) in the Type II collagen gene (COL2A1) in a family with spondyloepiphyseal dysplasia congenita

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tiller, G.E.; Polumbo, P.A.; Weis, M.A.

1995-02-01

Defects in type II collagen have been demonstrated in a phenotypic continuum of chondrodysplasias that includes achondrogenesis II, hypochondrogenesis, spondyloepiphyseal dysplasia congenita (SEDC), Kniest dysplasia, and Stickler syndrome. We have determined that cartilage from a terminated fetus with an inherited form of SEDC contained both normal {alpha}1(II) collagen chains and chains that lacked amino acids 256-273 of the triple-helical domain. PCR amplification of this region of COL2A1, from genomic DNA, yielded products of normal size, while amplification of cDNA yielded a normal sized species and a shorter fragment missing exon 20. Sequence analysis of genomic DNA from the fetus revealedmore » a G{yields}T transversion at position +5 of intron 20; the affected father was also heterozygous for the mutation. Allele-specific PCR and heteroduplex analysis of a VNTR in COL2A1 independently confirmed the unaffected status of a fetus in a subsequent pregnancy. Thermodynamic calculations suggest that the mutation prevents normal splicing of exon 20 by interfering with binding of U{sub 1} small-nuclear RNA to pre-mRNA, thus leading to skipping of exon 20 in transcripts from the mutant allele. Electron micrographs of diseased cartilage showed intracellular inclusion bodies, which were stained by an antibody to {alpha}1(II) procollagen. Our findings support the hypothesis that {alpha}-chain length alterations that preserve the Gly-X-Y repeat motif of the triple helix result in partial intracellular retention of {alpha}1(II) procollagen and produce mild to moderate chondrodysplasia phenotypes. 50 refs., 6 figs., 1 tab.« less

The fate of b-ions in the two worlds of collision-induced dissociation.

PubMed

Waldera-Lupa, Daniel M; Stefanski, Anja; Meyer, Helmut E; Stühler, Kai

2013-12-01

Fragment analysis of proteins and peptides by mass spectrometry using collision-induced dissociation (CID) revealed that the pairwise generated N-terminal b- and C-terminal y-ions have different stabilities resulting in underrepresentation of b-ions. Detailed analyses of large-scale spectra databases and synthetic peptides underlined these observations and additionally showed that the fragmentation pattern depends on utilized CID regime. To investigate this underrepresentation further we systematically compared resonant excitation energy and beam-type CID facilitated on different mass spectrometer platforms: (i) quadrupole time-of-flight, (ii) linear ion trap and (iii) three-dimensional ion trap. Detailed analysis of MS/MS data from a standard tryptic protein digest revealed that b-ions are significantly underrepresented on all investigated mass spectrometers. By N-terminal acetylation of tryptic peptides we show for the first time that b-ion cyclization reaction significantly contributes to b-ion underrepresentation even on ion trap instruments and accounts for at most 16% of b-ion loss. © 2013.

Effect of osmolytes on the conformation and aggregation of some amyloid peptides: CD spectroscopic data.

PubMed

Inayathullah, Mohammed; Rajadas, Jayakumar

2016-06-01

Protein misfolding and aggregation are responsible for a large number of diseases called protein conformational diseases or disorders that include Alzheimer׳s disease, Huntington׳s diseases, Prion related encephalopathies and type-II diabetes (http://dx.doi.org/10.1038/35041139) (Kopito and Ron, 2000) [1]. A variety of studies have shown that some small organic molecules, known as osmolytes have the ability to stabilize native conformation of proteins and prevent misfolding and aggregation (http://www.la-press.com/article.php?article_id=447) (Zhao et al., 2008) [2]. It has been shown that certain short segment or fragment of respective proteins can also form amyloids, and the segments also promote the aggregation in the full-length protein (http://dx.doi.org/10.2174/0929867023369187) (Gazit, 2002) [3]. This article presents circular dichroism spectroscopic data on conformational analysis and effect of osmolytes on Aβ peptide fragments, different lengths of polyglutamine peptide and the amyloidogenic segment of islet amyloid polypeptide.

alpha-Putrescinylthymine and the sensitivity of bacteriophage phi W-14 DNA to restriction endonucleases.

PubMed Central

Miller, P B; Wakarchuk, W W; Warren, R A

1985-01-01

The modified base alpha-putrescinylthymine (putT) in phi W-14 DNA blocks cleavage of the DNA by 17 of 32 Type II restriction endonucleases. The enzymes cleaving the DNA do so to widely varying extents. The frequencies of cleavage of three altered forms of the DNA show that putT blocks recognition sites either when it occurs within the site or when it is in a sequence flanking the site. The blocking is dependent on both charge and steric factors. The charge effects can be greater than the steric effects for some of the enzymes tested. All the enzymes cleaving phi W-14 DNA release discrete fragments, showing that the distribution of putT is ordered. The cleavage frequencies for different enzymes suggest that the sequence CAputTG occurs frequently in the DNA. Only TaqI of the enzymes tested appeared not to be blocked by putT, but it was slowed down. TaqI generated fragments are joinable by T4 DNA ligase. PMID:2987859

Acrylamide and 5-hydroxymethylfurfural formation during biscuit baking. Part II: Effect of the ratio of reducing sugars and asparagine.

PubMed

Nguyen, Ha T; van der Fels-Klerx, H J Ine; van Boekel, M A J S

2017-09-01

This study investigated acrylamide and 5-hydroxymethylfurfural (HMF) formation during biscuit baking. Four types of wheat flour with different molar ratios of total fructose and glucose to asparagine were investigated. Nevertheless, the molar ratio in all four biscuit doughs exceeded one after proofing due to enzyme action. Data obtained after baking were used to develop a mechanistic model, based on the asparagine-related pathway, for acrylamide and HMF formation in the four baked biscuit types. Asparagine reacted with fructose to form a Schiff base before decarboxylation to produce acrylamide without Amadori rearrangement product and sugar fragmentation. Fructose contributed considerably to acrylamide formation and to HMF formation via caramelization in all four biscuit types. No clear correlation was found between acrylamide and HMF in baked biscuits, nor between asparagine and the sum of glucose and fructose concentrations in the wheat flour. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Cytochrome b-559 photooxidation in the presence of carbonyl cyanide p-trifluorometh-oxyphenylhydrazone and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone or p-benzoquinone in three non-photosynthetic mutants of Chlamydomonas reinhardti (author's transl)].

PubMed

Maroc, J; Garnier, J

1975-04-14

Studies of absorbance related to the cytochrome b-559 photooxidation induced by FCCP, with and without addition of 3-p-chlorophenyl-1, 1-dimethylurea (CMU), DBMIB or p-benzoquinone, in whole cells and in chloroplast fragments of Chlamydomonas reinhardti, were carried out. In addition to the wild type, three strains of non-photosynthetic mutants were used: Fl 5, which lacks P 700; Fl 9 and Fl 15, which are deficient in bound cytochrome c-553 and in cytochrome b-563. In the presence of FCCP, whole cells and chloroplast fragments of the four strains showed a System II-dependent photooxidation of cytochrome b-559. This photooxidation was inhibited by CMU but it occurred again in presence of FCCP, CMU and DBMIB. In chloroplast fragments, cytochrome b-559 photooxidation was also inhibited by an excess of FCCP; it was recovered, likewise, by addition of DBMIB. In whole cells, the highest measured redox changes were: 1 mu mol oxidized cytochrome b-559 per 1 mmol chlorophyll, corresponding approximately to about one seventh (wild type, Fl5) or one fifth (Fl 9, Fl 15) of the total amount of this cytochrome. Another kind of cytochrome b-559 photooxidation, CMU-insensitive, also occurred in the mutants Fl 9 and Fl 15 and in the wild type, but not in the mutant Fl 5. This latter kind of photooxidation was observed with chloroplast fragments in the presence of FCCP and CMU and also with whole cells in the presence of FCCP, CMU and p-benzoquinone. These reactions can be attributed to the Photosystem I; they do not require the intervention of the cytochrome c-553. A high-potential form of cytochrome b-559, hydroquinone-reducible, was involved in these two kinds of photooxidation. In addition, a lower potential form, reducible only by ascorbate, appeared to be able to interfere also. An interpretation is attempted, taking into consideration the various effects of FCCP and DBMIB, at different concentrations, on photosynthetic electron transport.

Differences in the ovine HSP90AA1 gene expression rates caused by two linked polymorphisms at its promoter affect rams sperm DNA fragmentation under environmental heat stress conditions.

PubMed

Salces-Ortiz, Judit; Ramón, Manuel; González, Carmen; Pérez-Guzmán, M Dolores; Garde, J Julián; García-Álvarez, Olga; Maroto-Morales, Alejandro; Calvo, Jorge H; Serrano, M Magdalena

2015-01-01

Heat shock (HS) is one of the best-studied exogenous cellular stresses. Almost all tissues, cell types, metabolic pathways and biochemical reactions are affected in greater or lesser extent by HS. However, there are some especially thermo sensible cellular types such as the mammalian male germ cells. The present study examined the role of three INDELs in conjunction with the -660G/C polymorphism located at the HSP90AA1 promoter region over the gene expression rate under HS. Specially, the -668insC INDEL, which is very close to the -660G/C transversion, is a good candidate to be implied in the transcriptional regulation of the gene by itself or in a cooperative way with this SNP. Animals carrying the genotype II-668 showed higher transcription rates than those with ID-668 (FC = 3.07) and DD-668 (FC = 3.40) genotypes for samples collected under HS. A linkage between gene expression and sperm DNA fragmentation was also found. When HS conditions were present along or in some stages of the spermatogenesis, alternative genotypes of the -668insC and -660G/C mutations are involved in the effect of HS over sperm DNA fragmentation. Thus, unfavorable genotypes in terms of gene expression induction (ID-668GC-660 and DD-668GG-660) do not produce enough mRNA (stored as messenger ribonucleoprotein particles) and Hsp90α protein to cope with future thermal stress which might occur in posterior stages when transcriptional activity is reduced and cell types and molecular processes are more sensible to heat (spermatocytes in pachytene and spermatids protamination). This would result in the impairment of DNA packaging and the consequent commitment of the events occurring shortly after fertilization and during embryonic development. In the short-term, the assessment of the relationship between sperm DNA fragmentation sensitivity and ram's fertility will be of interest to a better understanding of the mechanisms of response to HS and its consequences on animal production and reproduction performance.

Archaelogical Excavations of the Gardens and Interior Areas of Houses B and C of the Southeast Row Houses Fort Michilimackinac, Michigan.

DTIC Science & Technology

1981-08-01

porcelain fragments recovered were Group I, Chinese Export Porcelain . No evidence of Group II, English Porcelain , was present. There were 40 fragments...earthenware, stoneware and porcelain . Distribution of colonial ceramics by unit and level appears in Appendices 2 31 and 3. Therefore, only classes and...unidentifiable fragments of stoneware. Similar to the earthenware, they were not identified because of being burned or too small. Class C Porcelain All

Global-scale patterns of forest fragmentation

USGS Publications Warehouse

Riitters, K.; Wickham, J.; O'Neill, R.; Jones, B.; Smith, E.

2000-01-01

We report an analysis of forest fragmentation based on 1-km resolution land-cover maps for the globe. Measurements in analysis windows from 81 km 2 (9 ?? 9 pixels, "small" scale) to 59,049 km 2 (243 ?? 243 pixels, "large" scale) were used to characterize the fragmentation around each forested pixel. We identified six categories of fragmentation (interior, perforated, edge, transitional, patch, and undetermined) from the amount of forest and its occurrence as adjacent forest pixels. Interior forest exists only at relatively small scales; at larger scales, forests are dominated by edge and patch conditions. At the smallest scale, there were significant differences in fragmentation among continents; within continents, there were significant differences among individual forest types. Tropical rain forest fragmentation was most severe in North America and least severe in Europe - Asia. Forest types with a high percentage of perforated conditions were mainly in North America (five types) and Europe - Asia (four types), in both temperate and subtropical regions. Transitional and patch conditions were most common in 11 forest types, of which only a few would be considered as "naturally patchy" (e.g., dry woodland). The five forest types with the highest percentage of interior conditions were in North America; in decreasing order, they were cool rain forest, coniferous, conifer boreal, cool mixed, and cool broadleaf. Copyright ?? 2000 by The Resilience Alliance.

Surgical treatment on displaced and dislocated sagittal fractures of the mandibular condyle.

PubMed

Jing, Jie; Han, Yu; Song, Yu; Wan, Yingbiao

2011-06-01

The purpose of this study was to evaluate the effect of surgical treatment on displaced and dislocated sagittal fractures of the mandibular condyle (SFMC). Twenty-four patients with 28 displaced and dislocated SFMCs were distinguished into type M, type C, and type L fractures according the location of the fracture line. The fractured fragment was reduced and fixated with two 0.6-mm 4-hole micro-plates via a preauricular temporal incision. The fragment was extirpated when it was too small to be fixated. The postoperative position and profile of the fragment was examined by orthopantomogram radiograph or computed tomography (CT). The function of the temporal and zygomatic branches of the facial nerve was inspected. The occluding relation was surveyed, the interincisal distance at maximum mouth opening was measured, and the deviation from the midline during mouth opening was recorded. Twenty-three condyles (82%) suffered dislocated fractures with the condylar fragment out of the glenoid fossa. Five condyles (18%) were displaced, but not dislocated. There were 2 (7%) type M, 19 (68%) type C (3 comminuted), and 7 (25%) type L fractures (1 comminuted), respectively. Twenty-one (75%) fractured fragments received free-graft procedures with 2 micro-plates. Four (14%) fragments were reduced and fixated without being dissected free of their attachments. Three (11%) fragments were extirpated. There were no permanent facial never branch injuries. Micro-plate removal was necessary because of postoperative infection and necrosis of the fractured fragment in 1 condylar process. No other patients could be found with obvious postoperative bone resorption. The average postoperative maximum mouth opening and deviation at 6 months were improved significantly. The postoperative occlusion was good in 22 cases. Access with the preauricular incision, and the dislocated and displaced fragment can be reduced and fixated to its normal position easily. Free-graft procedure is a suitable surgical treatment if the fractured fragment cannot be reduced without dissection free of the pterygoid muscle attachment. Although most fractured fragments in SFMCs have to be dissected free, there are no obvious complications in dislocated and displaced SFMCs after surgical treatment. Copyright © 2011 Mosby, Inc. All rights reserved.

Molecular analyses of the agouti allele in the Japanese house mouse identify a novel variant of the agouti gene.

PubMed

Iwasa, Masahiro A; Kawamura, Sayaka; Myoshu, Hikari; Suzuki, Taichi A

2018-03-01

It has been thought that the Japanese house mouse carries the A w allele at the agouti locus causing light-colored bellies, but they do not always show this coloration. Thus, the presence of the A w allele seems to be doubtful in them. To ascertain whether the A w allele is present, a two-pronged approach was used. First, we compared lengths of DNA fragments obtained from three PCRs conducted on them to the known fragment sizes generated from mouse strains exhibiting homozygosities of either a/a, A/A, or A w /A w . PCR I, PCR II, and PCR III amplify only in the A and A w alleles, the a and A w alleles, and the a allele, respectively, and we detected amplifications in strains with A/A and A w /A w by PCR I, in those with a/a and the Japanese house mouse by PCR II, and in those with a/a by PCR III. Second, we sequenced the exon 1A region of the agouti gene and obtained sequences corresponding to the above strains and the Japanese house mouse, but their sequences were similar to those of the a allele. We concluded that their agouti allele is not identical to the A w allele and seems to be a novel type similar to the a allele.

Palladium(II) complexes bearing di-(2-picolyl)amine functionalized chrysin fragments. An experimental and theoretical study

NASA Astrophysics Data System (ADS)

González-Montiel, Simplicio; Valdez-Calderón, Alejandro; Vásquez-Pérez, J. Manuel; Torres-Valencia, J. Martín; Martínez-Otero, Diego; López, Jorge A.; Cruz-Borbolla, Julián

2017-10-01

A new series of chrysin derivatives containing the di-(2-picolyl)amine (2a-d) moiety have been designed, synthesized, and treated with PdCl2·2CH3CN allowing the preparation of new cationic Palladium(II) complexes (3a-d). Solution-phase studies by 1H NMR spectroscopy of 3a-d revealed that the protons of the methylene groups of the di(2-picolyl)amine fragment are diasterotopic. GIAO/DFT studies were performed to predict the molecular structures of 3a-d by comparing the experimental and theoretical 1H-NMR chemical shifts. The molecular structure of 3c was determined by X-ray crystallographic analysis revealing that di-(2-picolyl)amine fragment is coordinated to the palladium center in a κ3-N,N,N-tridentate fashion in an overall square-planar geometry completed with a chloride atom.

The Munich accelerator for fission fragments MAFF

NASA Astrophysics Data System (ADS)

Habs, D.; Groß, M.; Assmann, W.; Ames, F.; Bongers, H.; Emhofer, S.; Heinz, S.; Henry, S.; Kester, O.; Neumayr, J.; Ospald, F.; Reiter, P.; Sieber, T.; Szerypo, J.; Thirolf, P. G.; Varentsov, V.; Wilfart, T.; Faestermann, T.; Krücken, R.; Maier-Komor, P.

2003-05-01

The Munich Accelerator for Fission Fragments MAFF has been designed for the new Munich research reactor FRM-II. It will deliver several intense beams (˜3×10 11 s -1) of very neutron-rich fission fragments with a final energy of 30 keV (low-energy beam) or energies between 3.7 and 5.9 MeV· A (high-energy beam). Such beams are of interest for the creation of super-heavy elements by fusion reactions, nuclear spectroscopy of exotic nuclei, but they also have a potential for applications, e.g. in medicine. Presently the Munich research reactor FRM-II is ready for operation, but authorities delay the final permission to turn the reactor critical probably till the end of 2002. Only after this final permission the financing of the major parts of MAFF can start. On the other hand all major components have been designed and special components have been tested in separate setups.

Characterization of renal amyloid derived from the variable region of the lambda light chain subgroup II.

PubMed Central

Picken, M. M.; Gallo, G.; Buxbaum, J.; Frangione, B.

1986-01-01

Amyloid fibrils were extracted from the kidney of a patient (CHE) shown to have tetramers and dimers of a monoclonal lambda light chain in his serum, and whose bone marrow cells in short-term culture synthesized these forms and a smaller lambda fragment of approximately 10,000 to 12,000 daltons. Biochemical and serologic analysis of a fraction of a size (obtained from amyloid fibrils extracted from the kidney) similar to that synthesized by the bone marrow cells revealed a light chain fragment corresponding to the amino terminal end of the variable region of the lambda light chain subgroup II. The presence of similarly sized short fragments of lambda light chain in both the synthesized and deposited protein suggests that aberrant synthesis and/or proteolytic degradation may play a pathogenetic role in the process of amyloidogenesis. Images Figure 1 PMID:3089021

Minim typing--a rapid and low cost MLST based typing tool for Klebsiella pneumoniae.

PubMed

Andersson, Patiyan; Tong, Steven Y C; Bell, Jan M; Turnidge, John D; Giffard, Philip M

2012-01-01

Here we report a single nucleotide polymorphism (SNP) based genotyping method for Klebsiella pneumoniae utilising high-resolution melting (HRM) analysis of fragments within the multilocus sequence typing (MLST) loci. The approach is termed mini-MLST or Minim typing and it has previously been applied to Streptococcus pyogenes, Staphylococcus aureus and Enterococcus faecium. Six SNPs were derived from concatenated MLST sequences on the basis of maximisation of the Simpsons Index of Diversity (D). DNA fragments incorporating these SNPs and predicted to be suitable for HRM analysis were designed. Using the assumption that HRM alleles are defined by G+C content, Minim typing using six fragments was predicted to provide a D = 0.979 against known STs. The method was tested against 202 K. pneumoniae using a blinded approach in which the MLST analyses were performed after the HRM analyses. The HRM-based alleles were indeed in accordance with G+C content, and the Minim typing identified known STs and flagged new STs. The tonB MLST locus was determined to be very diverse, and the two Minim fragments located herein contribute greatly to the resolving power. However these fragments are refractory to amplification in a minority of isolates. Therefore, we assessed the performance of two additional formats: one using only the four fragments located outside the tonB gene (D = 0.929), and the other using HRM data from these four fragments in conjunction with sequencing of the tonB MLST fragment (D = 0.995). The HRM assays were developed on the Rotorgene 6000, and the method was shown to also be robust on the LightCycler 480, allowing a 384-well high through-put format. The assay provides rapid, robust and low-cost typing with fully portable results that can directly be related to current MLST data. Minim typing in combination with molecular screening for antibiotic resistance markers can be a powerful surveillance tool kit.

Minim Typing – A Rapid and Low Cost MLST Based Typing Tool for Klebsiella pneumoniae

PubMed Central

Andersson, Patiyan; Tong, Steven Y. C.; Bell, Jan M.; Turnidge, John D.; Giffard, Philip M.

2012-01-01

Here we report a single nucleotide polymorphism (SNP) based genotyping method for Klebsiella pneumoniae utilising high-resolution melting (HRM) analysis of fragments within the multilocus sequence typing (MLST) loci. The approach is termed mini-MLST or Minim typing and it has previously been applied to Streptococcus pyogenes, Staphylococcus aureus and Enterococcus faecium. Six SNPs were derived from concatenated MLST sequences on the basis of maximisation of the Simpsons Index of Diversity (D). DNA fragments incorporating these SNPs and predicted to be suitable for HRM analysis were designed. Using the assumption that HRM alleles are defined by G+C content, Minim typing using six fragments was predicted to provide a D = 0.979 against known STs. The method was tested against 202 K. pneumoniae using a blinded approach in which the MLST analyses were performed after the HRM analyses. The HRM-based alleles were indeed in accordance with G+C content, and the Minim typing identified known STs and flagged new STs. The tonB MLST locus was determined to be very diverse, and the two Minim fragments located herein contribute greatly to the resolving power. However these fragments are refractory to amplification in a minority of isolates. Therefore, we assessed the performance of two additional formats: one using only the four fragments located outside the tonB gene (D = 0.929), and the other using HRM data from these four fragments in conjunction with sequencing of the tonB MLST fragment (D = 0.995). The HRM assays were developed on the Rotorgene 6000, and the method was shown to also be robust on the LightCycler 480, allowing a 384-well high through-put format. The assay provides rapid, robust and low-cost typing with fully portable results that can directly be related to current MLST data. Minim typing in combination with molecular screening for antibiotic resistance markers can be a powerful surveillance tool kit. PMID:22428067

Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of [alpha]- and PPII-helices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Matthew R.; Rajashankar, Kanagalaghatta R.; Patel, Manisha H.

2010-08-18

Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary pellicle. AgI/II contributes to virulence and has been studied as an immunological and structural target, but a fundamental understanding of its underlying architecture has been lacking. Here we report a high-resolution (1.8 {angstrom}) crystal structure of the A{sub 3}VP{sub 1} fragment of S. mutans AgI/II that demonstrates a unique fibrillar form (155 {angstrom}) through the interaction of two noncontiguous regions in the primary sequence. The A{sub 3} repeat of the alanine-rich domain adopts an extended {alpha}-helix that intertwines with the P{submore » 1} repeat polyproline type II (PPII) helix to form a highly extended stalk-like structure heretofore unseen in prokaryotic or eukaryotic protein structures. Velocity sedimentation studies indicate that full-length AgI/II that contains three A/P repeats extends over 50 nanometers in length. Isothermal titration calorimetry revealed that the high-affinity association between the A{sub 3} and P{sub 1} helices is enthalpically driven. Two distinct binding sites on AgI/II to the host receptor salivary agglutinin (SAG) were identified by surface plasmon resonance (SPR). The current crystal structure reveals that AgI/II family proteins are extended fibrillar structures with the number of alanine- and proline-rich repeats determining their length.« less

BIANCA, a biophysical model of cell survival and chromosome damage by protons, C-ions and He-ions at energies and doses used in hadrontherapy

NASA Astrophysics Data System (ADS)

Pietro Carante, Mario; Aimè, Chiara; Tello Cajiao, John James; Ballarini, Francesca

2018-04-01

An upgraded version of the BIANCA II biophysical model, which describes more realistically interphase chromosome organization and the link between chromosome aberrations and cell death, was applied to V79 and AG01522 cells exposed to protons, C-ions and He-ions over a wide LET interval (0.6–502 keV µm‑1), as well as proton-irradiated U87 cells. The model assumes that (i) ionizing radiation induces DNA ‘cluster lesions’ (CLs), where by definition each CL produces two independent chromosome fragments; (ii) fragment (distance-dependent) mis-rejoining, or un-rejoining, produces chromosome aberrations; (iii) some aberrations lead to cell death. The CL yield, which mainly depends on radiation quality but is also modulated by the target cell, is an adjustable parameter. The fragment un-rejoining probability, f, is the second, and last, parameter. The value of f, which is assumed to depend on the cell type but not on radiation quality, was taken from previous studies, and only the CL yield was adjusted in the present work. Good agreement between simulations and experimental data was obtained, suggesting that BIANCA II is suitable for calculating the biological effectiveness of hadrontherapy beams. For both V79 and AG01522 cells, the mean number of CLs per micrometer was found to increase with LET in a linear-quadratic fashion before the over-killing region, where a less rapid increase, with a tendency to saturation, was observed. Although the over-killing region deserves further investigation, the possibility of fitting the CL yields is an important feature for hadrontherapy, because it allows performing predictions also at LET values where experimental data are not available. Finally, an approach was proposed to predict the ion-response of the cell line(s) of interest from the ion-response of a reference cell line and the photon response of both. A pilot study on proton-irradiated AG01522 and U87 cells, taking V79 cells as a reference, showed encouraging results.

Stable MSAP markers for the distinction of Vitis vinifera cv Pinot noir clones.

PubMed

Ocaña, Juan; Walter, Bernard; Schellenbaum, Paul

2013-11-01

Grapevine is one of the most economically important fruit crops. Molecular markers have been used to study grapevine diversity. For instance, simple sequence repeats are a powerful tool for identification of grapevine cultivars, while amplified fragment length polymorphisms have shown their usefulness in intra-varietal diversity studies. Other techniques such as sequence-specific amplified polymorphism are based on the presence of mobile elements in the genome, but their detection lies upon their activity. Relevant attention has been drawn toward epigenetic sources of variation. In this study, a set of Vitis vinifera cv Pinot noir clones were analyzed using the methylation-sensitive amplified polymorphism technique with isoschizomers MspI and HpaII. Nine out of fourteen selective primer combinations were informative and generated two types of polymorphic fragments which were categorized as "stable" and "unstable." In total, 23 stable fragments were detected and they discriminated 92.5 % of the studied clones. Detected stable polymorphisms were either common to several clones, restricted to a few clones or unique to a single clone. The identification of these stable epigenetic markers will be useful in clonal diversity studies. We highlight the relevance of stable epigenetic variation in V. vinifera clones and analyze at which level these markers could be applicable for the development of forthright techniques for clonal distinction.

RAPID FORMATION OF SATURN AFTER JUPITER COMPLETION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobayashi, Hiroshi; Ormel, Chris W.; Ida, Shigeru, E-mail: hkobayas@nagoya-u.jp, E-mail: ormel@astro.berkeley.edu, E-mail: ida@geo.titech.ac.jp

We have investigated Saturn's core formation at a radial pressure maximum in a protoplanetary disk, which is created by gap opening by Jupiter. A core formed via planetesimal accretion induces the fragmentation of surrounding planetesimals, which generally inhibits further growth of the core by removal of the resulting fragments due to radial drift caused by gas drag. However, the emergence of the pressure maximum halts the drift of the fragments, while their orbital eccentricities and inclinations are efficiently damped by gas drag. As a result, the core of Saturn rapidly grows via accretion of the fragments near the pressure maximum.more » We have found that in the minimum-mass solar nebula, kilometer-sized planetesimals can produce a core exceeding 10 Earth masses within two million years. Since Jupiter may not have undergone significant type II inward migration, it is likely that Jupiter's formation was completed when the local disk mass has already decayed to a value comparable to or less than Jovian mass. The expected rapid growth of Saturn's core on a timescale comparable to or shorter than the observationally inferred disk lifetime enables Saturn to acquire the current amount of envelope gas before the disk gas is completely depleted. The high heat energy release rate onto the core surface due to the rapid accretion of the fragments delays onset of runaway gas accretion until the core mass becomes somewhat larger than that of Jupiter, which is consistent with the estimate based on interior modeling. Therefore, the rapid formation of Saturn induced by gap opening of Jupiter can account for the formation of multiple gas giants (Jupiter and Saturn) without significant inward migration and larger core mass of Saturn than that of Jupiter.« less

Calcium Handling by Endoplasmic Reticulum and Mitochondria in a Cell Model of Huntington’s Disease

PubMed Central

De Mario, Agnese; Scarlatti, Chiara; Costiniti, Veronica; Primerano, Simona; Lopreiato, Raffaele; Calì, Tito; Brini, Marisa; Giacomello, Marta; Carafoli, Ernesto

2016-01-01

Huntington disease (HD) is caused by the CAG (Q) expansion in exon 1 of the IT15 gene encoding a polyglutamine (poly-Q) stretch of the Huntingtin protein (Htt). In the wild type protein, the repeats specify a stretch of up 34 Q in the N-terminal portion of Htt. In the pathological protein (mHtt) the poly-Q tract is longer. Proteolytic cleavage of the protein liberates an N-terminal fragment containing the expanded poly-Q tract becomes harmful to cells, in particular to striatal neurons. The fragments cause the transcriptional dysfunction of genes that are essential for neuronal survival. Htt, however, could also have non-transcriptional effects, e.g. it could directly alter Ca2+ homeostasis and/or mitochondrial morphology and function. Ca2+ dyshomeostasis and mitochondrial dysfunction are considered important in the molecular aetiology of the disease. Here we have analyzed the effect of the overexpression of Htt fragments (18Q, wild type form, wtHtt and 150Q mutated form, mHtt) on Ca2+ homeostasis in striatal neuronal precursor cells (Q7/7). We have found that the transient overexpression of the Htt fragments increases Ca2+ transients in the mitochondria of cells stimulated with Ca2+-mobilizing agonists. The bulk Ca2+ transients in the cytosol were unaffected, but the Ca2+ content of the endoplasmic reticulum was significantly decreased in the case of mHtt expression. To rule out possible transcriptional effects due to the presence of mHtt, we have measured the mRNA level of a subunit of the respiratory chain complex II, whose expression is commonly altered in many HD models. No effects on the mRNA level was found suggesting that, in our experimental condition, transcriptional action of Htt is not occurring and that the effects on Ca2+ homeostasis were dependent to non-transcriptional mechanisms. PMID:26819834

Calcium Handling by Endoplasmic Reticulum and Mitochondria in a Cell Model of Huntington's Disease.

PubMed

De Mario, Agnese; Scarlatti, Chiara; Costiniti, Veronica; Primerano, Simona; Lopreiato, Raffaele; Calì, Tito; Brini, Marisa; Giacomello, Marta; Carafoli, Ernesto

2016-01-06

Huntington disease (HD) is caused by the CAG (Q) expansion in exon 1 of the IT15 gene encoding a polyglutamine (poly-Q) stretch of the Huntingtin protein (Htt). In the wild type protein, the repeats specify a stretch of up 34 Q in the N-terminal portion of Htt. In the pathological protein (mHtt) the poly-Q tract is longer. Proteolytic cleavage of the protein liberates an N-terminal fragment containing the expanded poly-Q tract becomes harmful to cells, in particular to striatal neurons. The fragments cause the transcriptional dysfunction of genes that are essential for neuronal survival. Htt, however, could also have non-transcriptional effects, e.g. it could directly alter Ca2+ homeostasis and/or mitochondrial morphology and function. Ca2+ dyshomeostasis and mitochondrial dysfunction are considered important in the molecular aetiology of the disease. Here we have analyzed the effect of the overexpression of Htt fragments (18Q, wild type form, wtHtt and 150Q mutated form, mHtt) on Ca2+ homeostasis in striatal neuronal precursor cells (Q7/7). We have found that the transient overexpression of the Htt fragments increases Ca2+ transients in the mitochondria of cells stimulated with Ca2+-mobilizing agonists. The bulk Ca2+ transients in the cytosol were unaffected, but the Ca2+ content of the endoplasmic reticulum was significantly decreased in the case of mHtt expression. To rule out possible transcriptional effects due to the presence of mHtt, we have measured the mRNA level of a subunit of the respiratory chain complex II, whose expression is commonly altered in many HD models. No effects on the mRNA level was found suggesting that, in our experimental condition, transcriptional action of Htt is not occurring and that the effects on Ca2+ homeostasis were dependent to non-transcriptional mechanisms.

Acemetacin cocrystal structures by powder X-ray diffraction.

PubMed

Bolla, Geetha; Chernyshev, Vladimir; Nangia, Ashwini

2017-05-01

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p -aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM-NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid-amide dimer three-point synthon R 3 2 (9) R 2 2 (8) R 3 2 (9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM-NAM, ACM-NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study.

Acemetacin cocrystal structures by powder X-ray diffraction

PubMed Central

Bolla, Geetha

2017-01-01

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthon R 3 2(9)R 2 2(8)R 3 2(9) with three different syn amides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, being anti (type I) or syn (type II). ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O⋯H, N⋯H, Cl⋯H and C⋯H interactions. The physicochemical properties of these cocrystals are under study. PMID:28512568

Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.

PubMed

Dubey, J P; Choudhary, S; Tilahun, G; Tiao, N; Gebreyes, W A; Zou, X; Su, C

2013-09-01

Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia. Published by Elsevier B.V.

Crystal structure of an Okazaki fragment at 2-A resolution

NASA Technical Reports Server (NTRS)

Egli, M.; Usman, N.; Zhang, S. G.; Rich, A.

1992-01-01

In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.

Crystal and electronic structures of magnesium(II), copper(II), and mixed magnesium(II)-copper(II) complexes of the quinoline half of styrylquinoline-type HIV-1 integrase inhibitors.

PubMed

Courcot, B; Firley, D; Fraisse, B; Becker, P; Gillet, J-M; Pattison, P; Chernyshov, D; Sghaier, M; Zouhiri, F; Desmaële, D; d'Angelo, J; Bonhomme, F; Geiger, S; Ghermani, N E

2007-05-31

A new target in AIDS therapy development is HIV-1 integrase (IN). It was proven that HIV-1 IN required divalent metal cations to achieve phosphodiester bond cleavage of DNA. Accordingly, all newly investigated potent IN inhibitors contain chemical fragments possessing a high ability to chelate metal cations. One of the promising leads in the polyhydroxylated styrylquinolines (SQLs) series is (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinoline carboxylic acid (1). The present study focuses on the quinoline-based progenitor (2), which is actually the most probable chelating part of SQLs. Conventional and synchrotron low-temperature X-ray crystallographic studies were used to investigate the chelating power of progenitor 2. Mg2+ and Cu2+ cations were selected for this purpose, and three types of metal complexes of 2 were obtained: Mg(II) complex (4), Cu(II) complex (5) and mixed Mg(II)-Cu(II) complexes (6 and 7). The analysis of the crystal structure of complex 4 indicates that two tridentate ligands coordinate two Mg2+ cations, both in octahedral geometry. The Mg-Mg distance was found equal to 3.221(1) A, in agreement with the metal-metal distance of 3.9 A encountered in the crystal structure of Escherichia coli DNA polymerase I. In 5, the complex is formed by two bidentate ligands coordinating one copper ion in tetrahedral geometry. Both mixed Mg(II)-Cu(II) complexes, 6 and 7 exhibit an original arrangement of four ligands linked to a central heterometallic cluster consisting of three octahedrally coordinated magnesium ions and one tetrahedrally coordinated copper ion. Quantum mechanics calculations were also carried out in order to display the electrostatic potential generated by the dianionic ligand 2 and complex 4 and to quantify the binding energy (BE) during the formation of the magnesium complex of progenitor 2. A comparison of the binding energies of two hypothetical monometallic Mg(II) complexes with that found in the bimetallic magnesium complex 4 was made.

Molecular characterization of the short interspersed repetitive element SIRE in the six discrete typing units (DTUs) of Trypanosoma cruzi.

PubMed

Pavia, Paula X; Thomas, M Carmen; López, Manuel C; Puerta, Concepción J

2012-10-01

Repetitive sequences constitute an important proportion of the Trypanosoma cruzi genome; hence, they have been used as molecular markers and as amplification targets to identify the parasite presence via PCR. In this study, a molecular characterization of the SIRE repetitive element was performed in the six discrete typing units (DTUs) of T. cruzi. The results evidenced that this element, located in multiple chromosomes, was interspersed in the genome of all DTUs of the parasite. The presence of several motifs implicated in element insertion, duplication, and functionality suggests that SIRE could be an active element in the parasite genome. Of interest, there were SIRE specific Alu I fragments that allowed to discriminate DTU I from the others DTUs. Moreover, an UPGMA phenetic tree constructed from fragment sharing Southern blot data showed that T. cruzi I isolates conform a cluster separated from the T. cruzi II-VI isolates. When the relative number of SIRE copies was determined, a variation from 105 to 2,000 copies per haploid genome was observed among the different isolates without kept a DTU-relationship. In all, these findings suggest that SIRE sequence is a good target for parasite DNA amplification. Copyright © 2012 Elsevier Inc. All rights reserved.

Profiling of acarviostatin family secondary metabolites secreted by Streptomyces coelicoflavus ZG0656 using ultraperformance liquid chromatography coupled with electrospray ionization mass spectrometry.

PubMed

Geng, Peng; Meng, Xiansheng; Bai, Gang; Luo, Guoan

2008-10-01

Profiling of acarviostatin family secondary metabolites secreted by Streptomyces coelicoflavus ZG0656 was performed by means of a rapid and facile procedure using ultraperformance liquid chromatography coupled with electrospray ionization mass spectrometry (UPLC/ESI-MS). The acarviostatins were separated on a C18 UPLC column with a series of acetonitrile-aqueous ammonia gradients. The target homologues were detected using the multiple reaction monitoring mode, and the chemical structures were confirmed by analyzing the diagnostic fragment ions in their MS/MS spectra. All six known reference acarviostatins (I03, II03, II13, II23, III03, IV03) were thus identified. In addition, at least 74 acarviostatin homologues, including 65 novel compounds, were characterized. Some of the features of the novel structures included having up to five acarviosine moieties, an acarviosine moiety at the reducing terminus, or an incomplete acarviosine moiety at the nonreducing terminus. This type of investigation may be useful for researchers who study secondary metabolomics in microorganisms and plants, especially those who perform metabolic profiling of aminooligosaccharides and other natural products with similar structures.

Electrochemical behavior of phytochelatins and related peptides at the hanging mercury drop electrode in the presence of cobalt(II) ions.

PubMed

Dorcák, Vlastimil; Sestáková, Ivana

2006-01-01

Direct current voltammetry and differential pulse voltammetry have been used to investigate the electrochemical behaviour of two phytochelatins: heptapeptide (gamma-Glu-Cys)3-Gly and pentapeptide (gamma-Glu-Cys)2-Gly, tripeptide glutathione gamma-Glu-Cys-Gly and its fragments: dipeptides Cys-Gly and gamma-Glu-Cys at the hanging mercury drop electrode in the presence of cobalt(II) ions. Most interesting results were obtained with direct current voltammetry in the potential region of -0.80 V up to -1.80 V. Differential pulse voltammetry of the same solutions of Co(II) with peptides gives more complicated voltammograms with overlapping peaks, probably in connection with the influence of adsorption at slow scan rates necessarily used in this method. However, in using Brdicka catalytic currents for analytical purposes, differential pulse voltammograms seem to be more helpful. Presented investigations have shown that particularly the prewave of cobalt(II) allows distinguishing among phytochelatins, glutathione, and its fragments.

[Poisons of DNA topoisomerases I and II].

PubMed

Charcosset, J Y; Soues, S; Laval, F

1993-11-01

Over the past decade, DNA topoisomerase I and II appeared to be the targets of some antitumor agents: CPT-11 and Topotecan derived from Camptothecin which interact with topoisomerase I; Actinomycin D, Adriamycin and Daunorubicin, Elliptinium Acetate, Mitoxantrone, Etoposide and Teniposide, Amsacrine which interact with topoisomerase II. The multiple functions of these enzymes are important as they play a role during replication, transcription, recombination, repair and chromatine organisation. Particularly, they relax torsional constraints which appear when intertwined DNA strands are separated while replication fork or RNA polymerases are moving. To some extent, topoisomerase I and II are structurally and functionally different. Moreover, topoisomerase I is not indispensable for a living cell whereas topoisomerase II is. Drug-topoisomerase interaction which probably leads to antitumoral effect of the compounds studied in this review is not a trivial inhibition of the enzyme but rather a poisoning due to stabilization of cleavable complexes between the enzyme and DNA. These stabilized complexes are likely to induce apoptosis-like programmed cell death, which is characterised by DNA fragmentation. However, it appears that it is the collision of the replication fork with the drug-stabilized cleavable complex that is responsible for the cytotoxicity of the drug: poisoning of topoisomerases by antitumor agents leads to a new concept of "dynamic toxicity". Although they interact with a common target, topoisomerase II poisons have differential effects on macromolecules syntheses, cell cycle and chromosome fragmentation; a few compounds may produce free radicals. Because of these differential effects in addition to quantitative and qualitative variations of stabilized cleavable complexes, in particular DNA sequences on which topoisomerase II is stabilized, these antitumor agents do not resemble each other. Cellular resistance to topoisomerases poisons results of two principal types of alteration: target and/or drug transport modification. Decreased ability to form the cleavable complex in resistant cells may be the consequence of both decreased amount of topoisomerase or altered enzyme. On the other hand, overexpression of membrane P-glycoprotein, which pumps drugs out of the cell by an energy dependent process provokes a decreased accumulation of these drugs. Cross resistances to other drugs are mainly under control of these two different mechanisms of resistance. A complete knowledge of their individual effects and mechanisms of resistance would allow a better clinical use of topoisomerases poisons, especially when administered in combination chemotherapy.

Effects of fragmentation on the spatial ecology of the California Kingsnake (Lampropeltis californiae)

USGS Publications Warehouse

Anguiano, Michael P.; Diffendorfer, James E.

2015-01-01

We investigated the spatial ecology of the California Kingsnake (Lampropeltis californiae) in unfragmented and fragmented habitat with varying patch sizes and degrees of exposure to urban edges. We radiotracked 34 Kingsnakes for up to 3 yr across four site types: interior areas of unfragmented ecological reserves, the urbanized edge of these reserves, large habitat fragments, and small habitat fragments. There was no relationship between California Kingsnake movements and the degree of exposure to urban edges and fragmentation. Home range size and movement patterns of Kingsnakes on edges and fragments resembled those in unfragmented sites. Average home-range size on each site type was smaller than the smallest fragment in which snakes were tracked. The persistence of California Kingsnakes in fragmented landscapes may be related directly to their small spatial movement patterns, home-range overlap, and ability to use urban edge habitat.

SO2 emissions at Semeru volcano, Indonesia: Characterization and quantification of persistent and periodic explosive activity

NASA Astrophysics Data System (ADS)

Smekens, Jean-François; Clarke, Amanda B.; Burton, Michael R.; Harijoko, Agung; Wibowo, Haryo E.

2015-07-01

We present the first measurements of SO2 emissions at Semeru volcano, Indonesia, using an SO2 camera. Activity at Semeru is characterized by quiescent degassing interspersed with short-lived explosive events with low ash burden. The interval between explosions was measured at 32.1 ± 15.7 min in a webcam survey of the volcano between the months of June and December 2013. We distinguish between two types of events: shorter events (type I: 5 min duration) with emissions returning quickly to baseline levels, and longer events (type II: 15 min duration) often showing multiple pulses and a longer period of increased emissions before a return to quiescent levels. Type I events represent > 90% of the activity and release an average of 200-500 kg of SO2 per event. The single type II event we documented with the SO2 camera released a total of 1460 kg of SO2. We estimate the daily average emissions of Semeru to be 21-71 t d- 1 of SO2, amounting to a yearly output of 8-26 Gg (8000-26,000 metric tons), with 35-65% released during explosive events. The time series patterns of degassing are consistent with the existence of a viscous plug at the top of the conduit, which seals the conduit immediately prior to explosive events, causing pressurization of the underlying magma followed by a sudden release of gas and fragmented magma.

A Selected Immunohistochemical Panel Aids in Differential Diagnosis and Prognostic Stratification of Subtypes of High-grade Endometrial Carcinoma: A Clinicopathologic and Immunohistochemical Study at a Single Institution.

PubMed

Taskin, Orhun Çiğ; Onder, Semen; Topuz, Samet; Sozen, Hamdullah; Sen, Fatma; Ilhan, Ridvan; Yavuz, Ekrem

This study aimed to investigate whether a selected immunohistochemical panel (estrogen receptor, p53, ARID1A, PPP2R1A, HNF-1β) could contribute to the diagnostic process of high-grade endometrial carcinomas (HG-ECs). We also aimed to analyze the correlation of these immunohistochemical results with several morphologic variables and survival data. After revising the diagnosis of 78 HG-ECs, immunohistochemical analysis was performed for each case. After immunohistochemical analysis, a specific diagnosis of prototypic HG-EC was established in most of the cases that were uncertain due to morphologic ambiguity. In the univariate analysis, older patient age, type II morphology, undifferentiated carcinoma and carcinosarcoma type of histology, altered p53 immunostaining, strong membranous staining of PPP2R1A, presence of lymphovascular invasion in serous carcinoma, and microcystic, elongated, and fragmented-type infiltration pattern in endometrioid carcinoma were significantly related to poor prognosis. In the multivariate analysis, only older patient age and carcinosarcoma or undifferentiated/dedifferentiated carcinoma type histology were found to be significantly poor prognostic factors (P=0.011), whereas advanced FIGO stage and type II histology were found to be correlated with poor prognosis, but did not reach statistical significance. We suggest that immunohistochemistry should be used in the differential diagnosis of HG-ECs, especially those with ambiguous morphology. Markers used in this study made a valuable contribution to the diagnostic process as well as prediction of prognosis.

An Early and Robust Activation of Caspases Heads Cells for a Regulated Form of Necrotic-like Cell Death.

PubMed

Garcia-Belinchón, Mercè; Sánchez-Osuna, María; Martínez-Escardó, Laura; Granados-Colomina, Carla; Pascual-Guiral, Sònia; Iglesias-Guimarais, Victoria; Casanelles, Elisenda; Ribas, Judit; Yuste, Victor J

2015-08-21

Apoptosis is triggered by the activation of caspases and characterized by chromatin condensation and nuclear fragmentation (type II nuclear morphology). Necrosis is depicted by a gain in cell volume (oncosis), swelling of organelles, plasma membrane leakage, and subsequent loss of intracellular contents. Although considered as different cell death entities, there is an overlap between apoptosis and necrosis. In this sense, mounting evidence suggests that both processes can be morphological expressions of a common biochemical network known as "apoptosis-necrosis continuum." To gain insight into the events driving the apoptosis-necrosis continuum, apoptotically proficient cells were screened facing several apoptotic inducers for the absence of type II apoptotic nuclear morphologies. Chelerythrine was selected for further studies based on its cytotoxicity and the lack of apoptotic nuclear alterations. Chelerythrine triggered an early plasma membrane leakage without condensed chromatin aggregates. Ultrastructural analysis revealed that chelerythrine-mediated cytotoxicity was compatible with a necrotic-like type of cell death. Biochemically, chelerythrine induced the activation of caspases. Moreover, the inhibition of caspases prevented chelerythrine-triggered necrotic-like cell death. Compared with staurosporine, chelerythrine induced stronger caspase activation detectable at earlier times. After using a battery of chemicals, we found that high concentrations of thiolic antioxidants fully prevented chelerythrine-driven caspase activation and necrotic-like cell death. Lower amounts of thiolic antioxidants partially prevented chelerythrine-mediated cytotoxicity and allowed cells to display type II apoptotic nuclear morphology correlating with a delay in caspase-3 activation. Altogether, these data support that an early and pronounced activation of caspases can drive cells to undergo a form of necrotic-like regulated cell death. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Atypical Strain of Toxoplasma gondii Causing Fatal Reactivation after Hematopoietic Stem Cell Transplantion in a Patient with an Underlying Immunological Deficiency

PubMed Central

Štajner, Tijana; Vasiljević, Zorica; Vujić, Dragana; Marković, Marija; Ristić, Goran; Mićić, Dragan; Pašić, Srdjan; Ivović, Vladimir; Ajzenberg, Daniel

2013-01-01

In immunocompromized patients, including hematopoietic stem cell transplant (HSCT) recipients, life-threatening toxoplasmosis may result from reactivation of previous infection. We report a case of severe disseminated toxoplasmosis that developed early after allogeneic HSCT for T-cell lymphoblastic leukemia/lymphoma in a 15-year-old Toxoplasma gondii-seropositive boy with Nijmegen breakage syndrome, a rare genetic DNA repair disorder associated with immunodeficiency. The donor was the patient's HLA-identical brother. Prophylaxis with cotrimoxazole was discontinued a day before the HSCT procedure. Signs of lung infection appeared as early as day 14 post-HSCT. The presence of tachyzoite-like structures on Giemsa-stained bronchoalveolar lavage (BAL) fluid smears suggested toxoplasmosis. Real-time PCR targeted at the T. gondii AF146527 gene revealed extremely high parasite burdens in both blood and BAL fluid. Although immediate introduction of specific treatment resulted in a marked reduction of the parasite load and transient clinical improvement, the patient deteriorated and died of multiple organ failure on day 39 post-HSCT. Direct genotyping of T. gondii DNA from blood and BAL fluid with the PCR-restriction fragment length polymorphism method revealed type II alleles with SAG1, SAG2, and GRA6 markers but alleles of both type I and type II with GRA7. Additional analysis with 15 microsatellite markers showed that the T. gondii DNA was atypical and genetically divergent from that of the clonal type I, II, and III strains. This is the first report of increased clinical severity of toxoplasmosis associated with an atypical strain in the setting of immunosuppression, which emphasizes the need to diagnose and monitor toxoplasmosis by quantitative molecular methods in cases of reactivation risk. PMID:23761151

An Early and Robust Activation of Caspases Heads Cells for a Regulated Form of Necrotic-like Cell Death*

PubMed Central

Garcia-Belinchón, Mercè; Sánchez-Osuna, María; Martínez-Escardó, Laura; Granados-Colomina, Carla; Pascual-Guiral, Sònia; Iglesias-Guimarais, Victoria; Casanelles, Elisenda; Ribas, Judit; Yuste, Victor J.

2015-01-01

Apoptosis is triggered by the activation of caspases and characterized by chromatin condensation and nuclear fragmentation (type II nuclear morphology). Necrosis is depicted by a gain in cell volume (oncosis), swelling of organelles, plasma membrane leakage, and subsequent loss of intracellular contents. Although considered as different cell death entities, there is an overlap between apoptosis and necrosis. In this sense, mounting evidence suggests that both processes can be morphological expressions of a common biochemical network known as “apoptosis-necrosis continuum.” To gain insight into the events driving the apoptosis-necrosis continuum, apoptotically proficient cells were screened facing several apoptotic inducers for the absence of type II apoptotic nuclear morphologies. Chelerythrine was selected for further studies based on its cytotoxicity and the lack of apoptotic nuclear alterations. Chelerythrine triggered an early plasma membrane leakage without condensed chromatin aggregates. Ultrastructural analysis revealed that chelerythrine-mediated cytotoxicity was compatible with a necrotic-like type of cell death. Biochemically, chelerythrine induced the activation of caspases. Moreover, the inhibition of caspases prevented chelerythrine-triggered necrotic-like cell death. Compared with staurosporine, chelerythrine induced stronger caspase activation detectable at earlier times. After using a battery of chemicals, we found that high concentrations of thiolic antioxidants fully prevented chelerythrine-driven caspase activation and necrotic-like cell death. Lower amounts of thiolic antioxidants partially prevented chelerythrine-mediated cytotoxicity and allowed cells to display type II apoptotic nuclear morphology correlating with a delay in caspase-3 activation. Altogether, these data support that an early and pronounced activation of caspases can drive cells to undergo a form of necrotic-like regulated cell death. PMID:26124276

Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant.

PubMed

Lei, Jiangtao; Qi, Ruxi; Wei, Guanghong; Nussinov, Ruth; Ma, Buyong

2016-03-21

Recent studies suggested that p53 aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, with adverse cancer consequences. The p53 aggregation-nucleating (251)ILTIITL(257) fragment is a key segment in wild-type p53 aggregation; however, an I254R mutation can prevent it. It was suggested that self-assembly of wild-type p53 and its cross-interaction with mutants differ from the classical amyloid nucleation-growth mechanism. Here, using replica exchange molecular dynamics (REMD) simulations, we studied the cross-interactions of this p53 core fragment and its aggregation rescue I254R mutant. We found that the core fragment displays strong aggregation propensity, whereas the gatekeeper I254R mutant tends to be disordered, consistent with experiments. Our cross-interaction results reveal that the wild-type p53 fragment promotes β-sheet formation of the I254R mutant by shifting the disordered mutant peptides into aggregating states. As a result, the system has similar oligomeric structures, inter-peptide interactions and free energy landscape as the wild type fragment does, revealing a prion-like process. We also found that in the cross-interaction system, the wild-type species has higher tendency to interact with the mutant than with itself. This phenomenon illustrates synergistic effects between the p53 (251)ILTIITL(257) fragment and the mutant resembling prion cross-species propagation, cautioning against exploiting it in drug discovery.

Characterization of the Origin of DNA Replication of the Coxiella burnetii Chromosome

DTIC Science & Technology

1990-01-26

chromosomal DNAs (FIG. IB): the 19.4-kb EcoR I fragment of Salmonella typhimurium DNA (lane 4),9 the 17.5-kb Sal I fragment of Enterobacter aerogenes ...IacZYA-argF) U 1694680d IacZAM15 Salmonella typhimurium Wild type WVUd Kiebsiella pneumoniae Wild type WVUd Enterobacter aero genes Wild type WVUd... aerogenes and K. pneumoniae were digested with appropriate restriction enzymes. The restriction fragments were separated on a 0.9% agarose gel, transferred to

Two reaction pathways for transformation of high potential cytochrome b559 of PS II into the intermediate potential form.

PubMed

Kaminskaya, Olga; Shuvalov, Vladimir A; Renger, Gernot

2007-06-01

This study describes an analysis of different treatments that influence the relative content and the midpoint potential of HP Cyt b559 in PS II membrane fragments from higher plants. Two basically different types of irreversible modification effects are distinguished: the HP form of Cyt b559 is either predominantly affected when the heme group is oxidized ("O-type" effects) or when it is reduced ("R-type" effects). Transformation of HP Cyt b559 to lower potential redox forms (IP and LP forms) by the "O-type" mechanism is induced by high pH and detergent treatments. In this case the effects consist of a gradual decrease in the relative content of HP Cyt b559 while its midpoint potential remains unaffected. Transformation of HP Cyt b559 via an "R-type" mechanism is caused by a number of exogenous compounds denoted L: herbicides, ADRY reagents and tetraphenylboron. These compounds are postulated to bind to the PS II complex at a quinone binding site designated as Q(C) which interacts with Cyt b559 and is clearly not the Q(B) site. Binding of compounds L to the Q(C) site when HP Cyt b559 is oxidized gives rise to a gradual decrease in the E(m) of HP Cyt b559 with increasing concentration of L (up to 10 K(ox)(L) values) while the relative content of HP Cyt b559 is unaffected. Higher concentrations of compounds L required for their binding to Q(C) site when HP Cyt b559 is reduced (described by K(red)(L)) induce a conversion of HP Cyt b559 to lower potential redox forms ("R-type" transformation). Two reaction pathways for transitions of Cyt b559 between the different protein conformations that are responsible for the HP and IP/LP redox forms are proposed and new insights into the functional regulation of Cyt b559 via the Q(C) site are discussed.

[Analysis of tension-distraction state in the shin bones fractures in conditions of external fixation with application of apparatuses with different spatially oriented supports].

PubMed

Hutsuliak, V I

2014-09-01

In Autodesk Inventor 11 program, using method of end-capping elements, a three- dimensional computeric modelling of biomechanical systems of two models was conducted: I - "tibia - Ilizarov's apparatus with concentric location of supports"; II - "tibia - Ilizarov's apparatus with excentric location of supports". The loading, which was applied towards distal fragment in 6 standard degrees of freedom, was modelled for studying of the fixation rigidity of tibial fragments in these systems. Determination of the loading value in various directions, in which the fragment have had shifted by 1 mm, have constituted the main task of the investigation. In a model II a rigidity of the fragments fixation, in comparison with such in a model I, is bigger by 631.43% - while applying a compression loading, by 8.35 - 31.75% - the transversal one and by 19.72% - the rotation loading. While choosing the method of transosteal osteosynthesis of the shin bones the advantage, have the apparatuses with excentric location of supports, what secures the enhanced rigidity of the fragments fixation in comparison with such in apparatuses with concentric location of supports. Although, even in excentric location of supports in the apparatus the fixation rigidity is insufficient for early full loading of the traumatized extremity while walking. It is necessary to elaborate such apparatus, the form of which may be adopted toanatomic configuration of segment.

Costs, outcomes and challenges for diabetes care in Spain

PubMed Central

2013-01-01

Background Diabetes is becoming of increasing concern in Spain due to rising incidence and prevalence, although little information is known with regards to costs and outcomes. The information on cost of diabetes in Spain is fragmented and outdated. Our objective is to update diabetes costs, and to identify outcomes and quality of care of diabetes in Spain. Methods We performed systematic searches from secondary sources, including scientific literature and government data and reports. Results Diabetes Type II prevalence is estimated at 7.8%, and an additional 6% of the population is estimated to be undiagnosed. Four Spanish diabetes cost studies were analyzed to create a projection of direct costs in the NHS and productivity losses, estimating €5.1 billion for direct costs along with €1.5 billion for diabetes-related complications (2009) and labour productivity losses represented €2.8 billion. Glycemic control (glycolysated hemoglobin) is considered acceptable in 59% of adult Type II cases, in addition to 85% with HDL cholesterol ≥40mg/dl and 65% with blood pressure <140/90 mmHg, pointing to good intermediate outcomes. However, annual figures indicate that over half of the Type II diabetics are obese (BMI >30), 15% have diabetic retinopathy, 16% with microalbuminuria, and 15% with cardiovascular disease. Conclusions The direct health care costs (8% of the total National Health System expenditure) and the loss of labour productivity are high. The importance of a multi-sectoral approach in prevention and improvements in management of diabetes are discussed, along with policy considerations to help modify the disease course. PMID:23635075

Long-term ultrastructural indices of lead intoxication in pulmonary tissue of the rat.

PubMed

Kaczyńska, Katarzyna; Walski, Michał; Szereda-Przestaszewska, Małgorzata

2013-12-01

In the present research long-term pulmonary toxicity of lead was investigated in rats treated by intraperitoneal administration of lead acetate for three consecutive days (25 mg/kg per day). Five weeks after treatment average lead content in the whole blood was 0.41 μg/dL ± 0.05, in the lung homogenates it measured 3.35 μg/g ± 0.54, as compared to the control values of 0.13 ± 0.07 μg/dL and 1.03 μg/g ± 0.59, respectively. X-ray microanalysis of lung specimens displayed lead localized mainly within type II pneumocytes and macrophages. At the ultrastructural level the effects of lead toxicity were found in lung capillaries, interstitium, epithelial cells, and alveolar lining. Alveolar septa showed intense fibrosis, consisting of collagen, elastin, and fibroblasts. Thinned alveolar septa had emphysematous tissue with some revealing signs of angiogenesis. Type II pneumocytes contained lamellar bodies with features of laminar destruction. Fragments of the surfactant layer were often detached from the alveolar epithelium. These findings indicate that 5 weeks after exposure, lead provokes reconstruction of the alveolar septa including fibrosis and emphysematous changes in the lung tissue.

Evaluation of androgen receptor gene as a candidate gene in female androgenetic alopecia.

PubMed

el-Samahy, May H; Shaheen, Maha A; Saddik, Dina E B; Abdel-Fattah, Nermeen S A; el-Sawi, Mohammad A; Mahran, Manal Z; Shehab, Abeer A A

2009-06-01

Genetic polymorphisms of the androgen receptor (AR) gene have been studied in male androgenetic alopecia (AGA); however, little is known about gene polymorphism and female AGA. To evaluate the AR gene as a candidate gene for female AGA. Thirty premenopausal Egyptian female patients with AGA (mean age, 32.3 +/- 7 years) and 11 age- and sex-matched controls were included. All subjects underwent laboratory and pelvic ultrasound evaluation to exclude other precipitating cause(s) of hair loss. Scalp biopsy was taken and the AR gene was evaluated using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). According to Ludwig's classification, all patients had type II AGA. Statistical analysis showed no statistically significant difference in genotype (chi(2) = 5.513, P > or = 0.05) or allele frequency (chi(2) = 1.312, P > or = 0.05) between patients and controls. There was also no statistically significant difference between the genotype and allele frequency with disease duration. In contrast with male AGA, no association was found between type II AGA in Egyptian women and the AR gene. Therefore, the genetic study of this gene does not serve as a biomarker for the identification of women with a predisposition to AGA.

Whole blood lead levels are associated with biomarkers of joint tissue metabolism in African American and white men and women: the Johnston County Osteoarthritis Project.

PubMed

Nelson, Amanda E; Chaudhary, Sanjay; Kraus, Virginia B; Fang, Fang; Chen, Jiu-Chiuan; Schwartz, Todd A; Shi, Xiaoyan A; Renner, Jordan B; Stabler, Thomas V; Helmick, Charles G; Caldwell, Kathleen; Poole, A Robin; Jordan, Joanne M

2011-11-01

To examine associations between biomarkers of joint tissue metabolism and whole blood lead (Pb), separately for men and women in an African American and Caucasian population, which may reflect an underlying pathology. Participants in the Johnston County Osteoarthritis Project Metals Exposure Sub-Study (329 men and 342 women) underwent assessment of whole blood Pb and biochemical biomarkers of joint tissue metabolism. Urinary cross-linked N telopeptide of type I collagen (uNTX-I) and C-telopeptide fragments of type II collagen (uCTX-II), serum cleavage neoepitope of type II collagen (C2C), serum type II procollagen synthesis C-propeptide (CPII), and serum hyaluronic acid (HA) were measured using commercially available kits; the ratio of [C2C:CPII] was calculated. Serum cartilage oligomeric matrix protein (COMP) was measured by an in-house assay. Multiple linear regression models were used to examine associations between continuous blood Pb and biomarker outcomes, adjusted for age, race, current smoking status, and body mass index. Results are reported as estimated change in biomarker level for a 5-unit change in Pb level. The median Pb level among men and women was 2.2 and 1.9μg/dL, respectively. Correlations were noted between Pb levels and the biomarkers uNTX-I, uCTX-II, and COMP in women, and between Pb and uCTX-II, COMP, CPII, and the ratio [C2C:CPII] in men. In adjusted models among women, a 5-unit increase in blood Pb level was associated with a 28% increase in uCTX-II and a 45% increase in uNTX-I levels (uCTX-II: 1.28 [95% CI: 1.04-1.58], uNTX-I: 1.45 [95% CI:1.21-1.74]). Among men, levels of Pb and COMP showed a borderline positive association (8% increase in COMP for a 5-unit change in Pb: 1.08 [95% CI: 1.00-1.18]); no other associations were significant after adjustment. Based upon known biomarker origins, the novel associations between blood Pb and biomarkers appear to be primarily reflective of relationships to bone and calcified cartilage turnover among women and cartilage metabolism among men, suggesting a potential gender-specific effect of Pb on joint tissue metabolism that may be relevant to osteoarthritis. Copyright © 2011 Elsevier Inc. All rights reserved.

Whole blood lead levels are associated with biomarkers of joint tissue metabolism in African American and White men and women: The Johnston County Osteoarthritis Project

PubMed Central

Nelson, Amanda E.; Chaudhary, Sanjay; Kraus, Virginia B.; Fang, Fang; Chen, Jiu-Chiuan; Schwartz, Todd A.; Shi, Xiaoyan A.; Renner, Jordan B.; Stabler, Thomas V.; Helmick, Charles G.; Caldwell, Kathleen; Poole, A. Robin; Jordan, Joanne M.

2011-01-01

Purpose To examine associations between biomarkers of joint tissue metabolism and whole blood lead (Pb), separately for men and women in an African American and Caucasian population, which may reflect an underlying pathology. Methods Participants in the Johnston County Osteoarthritis Project Metals Exposure Sub-study (329 men and 342 women) underwent assessment of whole blood Pb and biochemical biomarkers of joint tissue metabolism. Urinary cross-linked N telopeptide of type I collagen (uNTX-I) and C-telopeptide fragments of type II collagen (uCTX-II), and serum cleavage neoepitope of type II collagen (C2C), serum type II procollagen synthesis C-propeptide (CPII), and serum hyaluronic acid (HA) were measured using commercially available kits; the ratio of [C2C:CPII] was calculated. Serum cartilage oligomeric matrix protein (COMP) was measured by an in-house assay. Multiple linear regression models were used to examine associations between continuous blood Pb and biomarker outcomes, adjusted for age, race, current smoking status, and body mass index. Results are reported as estimated change in biomarker level for a 5-unit change in Pb level. Results The median Pb level among men and women was 2.2 and 1.9 µg/dL, respectively. Correlations were noted between Pb levels and the biomarkers uNTX-I, uCTX-II, and COMP in women, and between Pb and uCTX-II, COMP, CPII, and the ratio [C2C:CPII] in men. In adjusted models among women, a 5-unit increase in blood Pb level was associated with a 28% increase in uCTX-II and a 45% increase in uNTX-I levels (uCTX-II: 1.28 [95%CI: 1.04–1.58], uNTX-I: 1.45 [95%CI:1.21–1.74]). Among men, levels of Pb and COMP showed a borderline positive association (8% increase in COMP for a 5-unit change in Pb: 1.08 [95% CI: 1.00–1.18])); no other associations were significant after adjustment. Conclusions Based upon known biomarker origins, the novel associations between blood Pb and biomarkers appear to be primarily reflective of relationships to bone and calcified cartilage turnover among women and cartilage metabolism among men, suggesting a potential gender-specific effect of Pb on joint tissue metabolism that may be relevant to osteoarthritis. PMID:21839992

MAPPING THE SHORES OF THE BROWN DWARF DESERT. II. MULTIPLE STAR FORMATION IN TAURUS-AURIGA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kraus, Adam L.; Ireland, Michael J.; Martinache, Frantz

2011-04-10

We have conducted a high-resolution imaging study of the Taurus-Auriga star-forming region in order to characterize the primordial outcome of multiple star formation and the extent of the brown dwarf desert. Our survey identified 16 new binary companions to primary stars with masses of 0.25-2.5 M{sub sun}, raising the total number of binary pairs (including components of high-order multiples) with separations of 3-5000 AU to 90. We find that {approx}2/3-3/4 of all Taurus members are multiple systems of two or more stars, while the other {approx}1/4-1/3 appear to have formed as single stars; the distribution of high-order multiplicity suggests thatmore » fragmentation into a wide binary has no impact on the subsequent probability that either component will fragment again. The separation distribution for solar-type stars (0.7-2.5 M{sub sun}) is nearly log-flat over separations of 3-5000 AU, but lower-mass stars (0.25-0.7 M{sub sun}) show a paucity of binary companions with separations of {approx}>200 AU. Across this full mass range, companion masses are well described with a linear-flat function; all system mass ratios (q = M{sub B} /M{sub A} ) are equally probable, apparently including substellar companions. Our results are broadly consistent with the two expected modes of binary formation (free-fall fragmentation on large scales and disk fragmentation on small scales), but the distributions provide some clues as to the epochs at which the companions are likely to form.« less

Relative motions of fragments of the split comets. I - A new approach

NASA Technical Reports Server (NTRS)

Sekanina, Z.

1977-01-01

A hypothesis is proposed which interprets the relative motion of two fragments of a split comet in terms of a slight difference between their effective solar attraction rather than in terms of the impulse imparted to them at separation. A quantitative version of this hypothesis is formulated by assuming that the difference in effective solar attraction varies with heliocentric distance in direct proportion to the actual solar attraction so that the ratio of the two forces is constant and equal to a measure of the relative effect between the two fragments under consideration. Results obtained using this formulation are compared with observational evidence on the split comets P/Biela, Liais 1860 I, 1882 II, P/Brooks 2 1889 V, Swift 1899 I, Kopff 1905 IV, Mellish 1915 II, Taylor 1916 I, 1947 XII, Wirtanen 1957 VI, Ikeya-Seki 1965 VIII, Kohoutek 1970 III, and West 1975n. The hypothesis is found to fail only in the case of comet Wirtanen 1957 VI. Some unusual phenomena associated with split comets are examined.

An analysis of the wounding factors of four different shapes of fragments.

PubMed

Ma, Y Y; Feng, T S; Fu, R X; Li, M

1988-01-01

The wounding characteristics to a biological target of four typical shapes of fragments (square, triangular, cylindrical, and spherical) with masses of less than 1 gram and velocities between 460 and 1,500 m/s are studied in this paper. The following conclusions about the effects of the wounding factors, such as energy transfer, velocity, mass, and shape of fragment are presented: 1) For given target characteristics, the important wounding factors of fragments are impact velocity, mass, and shape, and of these velocity is the most important. 2) Besides direct effects, the fragment velocity has great influence on far-reaching, indirect wounding effects. When velocity increases, it not only increases the size of direct wound, but also the rate of indirect bone fracture. 3) The rate of energy transfer is affected by fragment shape, and it is also a decreasing function of mass. 4) Under the same conditions there are differences in wounding effectiveness among the four fragment shapes, the triangular with a comparatively high wounding effectiveness, followed by the square, cylindrical, and spherical. The types of wound channels are also different, the cylindrical and spherical making a "through" type, the square and triangular making a "blind-tube" type.

Oscar — Using Byte Pairs to Find File Type and Camera Make of Data Fragments

NASA Astrophysics Data System (ADS)

Karresand, Martin; Shahmehri, Nahid

Mapping out the contents of fragmented storage media is hard if the file system has been corrupted, especially as the current forensic tools rely on meta information to do their job. If it was possible to find all fragments belonging to a certain file type, it would also be possible to recover a lost file. Such a tool could for example be used in the hunt for child pornography. The Oscar method identifies the file type of data fragments based solely on statistics calculated from their structure. The method does not need any meta data to work. We have previously used the byte frequency distribution and the rate of change between consecutive bytes as basis for the statistics, as well as calculating the 2-gram frequency distribution to create a model of different file types. This paper present a variant of the 2-gram method, in that it uses a dynamic smoothing factor. In this way we take the amount of data used to create the centroid into consideration. A previous experiment on file type identification is extended with .mp3 files reaching a detection rate of 76% with a false positives rate of 0.4%. We also use the method to identify the camera make used to capture a .jpg picture from a fragment of the picture. The result shows that we can clearly separate a picture fragment coming from a Fuji or Olympus cameras from a fragment of a picture of the other camera makes used in our test.

[Restriction polymorphism of the proto-oncogene c-Ha-ras-1 in patients with multiple primary malignant neoplasms and non-small-cell lung cancer].

PubMed

Gaspar'ian, A V; Sel'chuk, V Iu; Iakubovskaia, M G; Zborovskaia, I B; Tatosian, A G

1997-01-01

Restriction fragment length polymorphism in the human c-Ha-ras-1 locus, associated with a minisatellite sequence, was examined in 45 multiple primary cancer (MPC) patients, 56 patients with squamous cell lung cancer (SCLC), 21 patients with lung adenocarcinoma (LAC), and 53 individuals having no oncopathology. Southern analysis of cellular DNA revealed the presence of 4 common alleles (with collective allele frequency close to 94% in the control group) and a set of rare alleles. Allele a3, (2.1 kb in size under MspI/HpaII digestion) was shown to be more frequent in the MPC than in the control group. The same tendency was observed in the patients with highly differentiated cell lung cancer. An increased frequency of the a4 allele (2.5 kb under MspI/HpaII digestion) was observed in the patients with adenocarcinomas as well as in the patients with metastases and low levels of tumor tissue differentiation. The elevated frequencies of a3 in the MPC group and of a4 in the LAC patients did not correlate with increased risk of the cancers mentioned above but was associated with type of tumor progression. Previously, it was reported that the mini-satellite sequence within the c-Ha-ras-1 locus possesses enhancer activity. Our data indirectly confirm the hypothesis that the efficiency of minisatellite modulator activity is associated with fragment size.

Left Ventricular Assist Device Design Reduces von Willebrand Factor Degradation: A Comparative Study Between the HeartMate II and the EVAHEART Left Ventricular Assist System.

PubMed

Bartoli, Carlo R; Kang, Jooeun; Zhang, David; Howard, Jessica; Acker, Michael; Atluri, Pavan; Motomura, Tadashi

2017-04-01

Supraphysiologic shear stress from continuous-flow left ventricular assist devices (LVADs) accelerates von Willebrand factor (vWF) degradation and predisposes patients to nonsurgical bleeding. It is unknown whether unique design characteristics of LVADs differentially affect vWF degradation. We tested the hypothesis that the centrifugal-flow EVAHEART (Evaheart, Houston, TX) left ventricular assist system (LVAS), which was designed to minimize shear stress (low operational revolutions per minute [rpm], larger flow gaps, low shear stress, flat H-Q curve), reduced vWF degradation versus the axial-flow HeartMate II (Thoratec, Pleasanton, CA) LVAD. Whole human blood was obtained from volunteer donors (n = 22). Blood was circulated for 12 hours in mock circulatory loops through a HeartMate II (n = 10; 11,400 rpm, 6.3 ± 0.8 L/min, 76 ± 2 mm Hg) or an EVAHEART LVAS (n = 12; 2,300 rpm, 5.7 ± 0.1 L/min, 80 ± 1 mm Hg). vWF degradation was characterized with electrophoresis and immunoblotting for large vWF multimers and 11 vWF degradation fragments. The HeartMate II eliminated large vWF multimers and significantly (p < 0.05) increased 10 of 11 vWF degradation fragments at 6 and 12 hours. The increase was approximately 2.0-fold at 6 hours and 2.2-fold at 12 hours. In contrast, the EVAHEART LVAS modestly reduced large vWF multimers and significantly increased 5 of 11 and 8 of 11 vWF degradation fragments at 6 and 12 hours, respectively. The increase was approximately 1.5-fold at 6 hours and 1.7-fold at 12 hours. The EVAHEART LVAS caused significantly less degradation (p < 0.01) than the HeartMate II of the 140 kDa vWF fragment (cleavage product of ADAMTS-13, the vWF protease). The EVAHEART LVAS caused significantly less vWF degradation than the HeartMate II in a mock circulatory loop with whole human blood. LVAD design features may minimize vWF degradation. These data may inform the design and operation of next-generation LVADs to minimize blood trauma. Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Development of molecular markers for zebrafish (Danio rerio) ovarian follicle growth assessment following in-vitro culture in cryopreservation studies.

PubMed

Anil, Siji; Rawson, David; Zhang, Tiantian

2018-05-29

Development of in vitro culture protocol for early stage ovarian follicles of zebrafish is important since cryopreserved early stage ovarian follicles would need to be matured in vitro following cryopreservation before they can be fertilised. Development of molecular markers for zebrafish (Danio rerio) ovarian follicle growth assessment following in vitro culture of early stage zebrafish ovarian follicles in ovarian tissue fragments is reported here for the first time although some work has been reported for in vitro culture of isolated early stage zebrafish ovarian follicles. The main aim of the present study was to develop molecular markers in an optimised in vitro culture protocol for stage I and stage II zebrafish ovarian follicles in ovarian tissue fragments. The effect of concentration of the hormones human chorionic gonadotropin and follicle stimulating hormones, and additives such as Foetal Bovine Serum and Bovine Serum Albumin were studied. The results showed that early stage zebrafish ovarian fragments containing stage I and stage II follicles which are cultured in vitro for 24 h in 20% FBS and 100mIU/ml FSH in 90% L-15 medium at 28 °C can grow to the size of stage II and stage III ovarian follicles respectively. More importantly the follicle growth from stage I to stage II and from stage II to stage III were confirmed using molecular markers such as cyp19a1a (also known as P450aromA) and vtg1 genes respectively. However, no follicle growth was observed following cryopreservation and in vitro culture. Copyright © 2018 Elsevier Inc. All rights reserved.

Low- Versus High-Intensity Plyometric Exercise During Rehabilitation After Anterior Cruciate Ligament Reconstruction.

PubMed

Chmielewski, Terese L; George, Steven Z; Tillman, Susan M; Moser, Michael W; Lentz, Trevor A; Indelicato, Peter A; Trumble, Troy N; Shuster, Jonathan J; Cicuttini, Flavia M; Leeuwenburgh, Christiaan

2016-03-01

Plyometric exercise is used during rehabilitation after anterior cruciate ligament (ACL) reconstruction to facilitate the return to sports participation. However, clinical outcomes have not been examined, and high loads on the lower extremity could be detrimental to knee articular cartilage. To compare the immediate effect of low- and high-intensity plyometric exercise during rehabilitation after ACL reconstruction on knee function, articular cartilage metabolism, and other clinically relevant measures. Randomized controlled trial; Level of evidence, 2. Twenty-four patients who underwent unilateral ACL reconstruction (mean, 14.3 weeks after surgery; range, 12.1-17.7 weeks) were assigned to 8 weeks (16 visits) of low- or high-intensity plyometric exercise consisting of running, jumping, and agility activities. Groups were distinguished by the expected magnitude of vertical ground-reaction forces. Testing was conducted before and after the intervention. Primary outcomes were self-reported knee function (International Knee Documentation Committee [IKDC] subjective knee form) and a biomarker of articular cartilage degradation (urine concentrations of crosslinked C-telopeptide fragments of type II collagen [uCTX-II]). Secondary outcomes included additional biomarkers of articular cartilage metabolism (urinary concentrations of the neoepitope of type II collagen cleavage at the C-terminal three-quarter-length fragment [uC2C], serum concentrations of the C-terminal propeptide of newly formed type II collagen [sCPII]) and inflammation (tumor necrosis factor-α), functional performance (maximal vertical jump and single-legged hop), knee impairments (anterior knee laxity, average knee pain intensity, normalized quadriceps strength, quadriceps symmetry index), and psychosocial status (kinesiophobia, knee activity self-efficacy, pain catastrophizing). The change in each measure was compared between groups. Values before and after the intervention were compared with the groups combined. The groups did not significantly differ in the change of any primary or secondary outcome measure. Of interest, sCPII concentrations tended to change in opposite directions (mean ± SD: low-intensity group, 28.7 ± 185.5 ng/mL; high-intensity group, -200.6 ± 255.0 ng/mL; P = .097; Cohen d = 1.03). Across groups, significant changes after the intervention were increased the IKDC score, vertical jump height, normalized quadriceps strength, quadriceps symmetry index, and knee activity self-efficacy and decreased average knee pain intensity. No significant differences were detected between the low- and high-intensity plyometric exercise groups. Across both groups, plyometric exercise induced positive changes in knee function, knee impairments, and psychosocial status that would support the return to sports participation after ACL reconstruction. The effect of plyometric exercise intensity on articular cartilage requires further evaluation. Clinicaltrials.gov NCT01851655. © 2016 The Author(s).

Low oxygen tension increased fibronectin fragment induced catabolic activities--response prevented with biomechanical signals.

PubMed

Parker, Eleanor; Vessillier, Sandrine; Pingguan-Murphy, Belinda; Abas, Wan; Bader, Dan L; Chowdhury, Tina T

2013-10-25

The inherent low oxygen tension in normal cartilage has implications on inflammatory conditions associated with osteoarthritis (OA). Biomechanical signals will additionally contribute to changes in tissue remodelling and influence the inflammatory response. In this study, we investigated the combined effects of oxygen tension and fibronectin fragment (FN-f) on the inflammatory response of chondrocytes subjected to biomechanical signals. Chondrocytes were cultured under free-swelling conditions at 1%, 5% and 21% oxygen tension or subjected to dynamic compression in an ex vivo 3D/bioreactor model with 29 kDa FN-f, interleukin-1beta (IL-1β) and/or the nitric oxide synthase (NOS) inhibitor for 6 and 48 hours. Markers for catabolic activity (NO, PGE2), tissue remodelling (GAG, MMPs) and cytokines (IL-1β, IL-6 and TNFα) were quantified by biochemical assay. Aggrecan, collagen type II, iNOS and COX-2 gene expression were examined by real-time quantitative PCR. Two-way ANOVA and a post hoc Bonferroni-corrected t-test were used to analyse data. Both FN-fs and IL-1β increased NO, PGE2 and MMP production (all P< 0.001). FN-f was more active than IL-1β with greater levels of NO observed at 5% than 1% or 21% oxygen tension (P < 0.001). Whilst FN-f reduced GAG synthesis at all oxygen tension, the effect of IL-1β was significant at 1% oxygen tension. In unstrained constructs, treatment with FN-f or IL-1β increased iNOS and COX-2 expression and reduced aggrecan and collagen type II (all P < 0.001). In unstrained constructs, FN-f was more effective than IL-1β at 5% oxygen tension and increased production of NO, PGE2, MMP, IL-1β, IL-6 and TNFα. At 5% and 21% oxygen tension, co-stimulation with compression and the NOS inhibitor abolished fragment or cytokine-induced catabolic activities and restored anabolic response. The present findings revealed that FN-fs are more potent than IL-1β in exerting catabolic effects dependent on oxygen tension via iNOS and COX-2 upregulation. Stimulation with biomechanical signals abolished catabolic activities in an oxygen-independent manner and NOS inhibitors supported loading-induced recovery resulting in reparative activities. Future investigations will utilize the ex vivo model as a tool to identify key targets and therapeutics for OA treatments.

Characterization of Bois noir isolates by restriction fragment length polymorphism of a Stolbur-specific putative membrane protein gene.

PubMed

Pacifico, D; Alma, A; Bagnoli, B; Foissac, X; Pasquini, G; Tessitori, M; Marzachì, C

2009-06-01

Bois noir phytoplasma (BNp), widespread in wine-producing areas of Europe and endemic in France and Italy, is classified in the 16SrXII-A subgroup, whose members are referred to as Stolbur phytoplasmas. The 16S rDNA gene of Stolbur phytoplasma shows low variability, and few non-ribosomal genes are available as markers to assess variation among isolates. We used the Stolbur-specific stol-1H10 gene, encoding a putative membrane-exposed protein, to investigate genetic diversity of French and Italian BNp isolates from plants and insects. Amplification of stol-1H10 from infected grapevines, weeds, and Hyalesthes obsoletus produced fragments of three sizes, and restriction fragment length polymorphism analysis divided these amplicons further into 12 profiles (V1 to V12). French BNp isolates were more variable than Italian ones, and different profiles were present in infected grapevines from France and Italy. Isolate V3, most abundant among Italian affected grapes but present among French ones, was found in one Urtica dioica sample and in all H. obsoletus collected on this species. Four Italian-specific profiles were represented among infected Convolvulus arvensis, the most frequent of which (V12) was also detected in H. obsoletus collected on this species. Most of the variability in the stol-1H10 sequence was associated with type II on the tuf gene.

Risk factors for intracranial infection secondary to penetrating craniocerebral gunshot wounds in civilian practice.

PubMed

Jimenez, Carlos Mario; Polo, Jonathan; España, Julian Andres

2013-01-01

To determine risk factors for intracranial infection secondary to penetrating craniocerebral gunshot wounds (PCGWs) in civilian practice, in patients who underwent surgery with removal of bullet fragments, wound debridement, and watertight dural closure. An observational, analytical, prospective, cohort-type study was conducted with follow-up in a group of patients with PCGWs caused by a low-velocity projectile admitted between January 2000 and November 2010. There were 160 patients, 59 of whom were administered prophylactic antibiotics based on the decision of the treating neurosurgeon. Average follow-up time was 39 months (range, 3-92 months). Infection occurred in 40 patients (25%); 20 patients received antibiotics (20 of 59 [33.9%]), and 20 patients did not receive antibiotics (20 of 101 [19.8%]). Three variables were independent risk factors for infection: (i) persistence of parenchymal osseous or metallic fragments after surgery (P < 0.0001, relative risk [RR] 7.45); (ii) projectile trajectory through a natural cavity with contaminating flora (P = 0.03, RR 2.84); and (iii) prolonged hospitalization time (P < 0.0001, RR 3.695). Administration of prophylactic antibiotics was not associated with the incidence of intracranial infection secondary to PCGWs. Projectile trajectory through potentially contaminating cavities, persistence of intraparenchymal osseous or metallic fragments after surgery, and prolonged hospital stay were independent risk factors for intracranial infection. Copyright © 2013 Elsevier Inc. All rights reserved.

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

PubMed

Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

2015-09-01

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Meta-analysis of the effects of forest fragmentation on interspecific interactions.

PubMed

Magrach, Ainhoa; Laurance, William F; Larrinaga, Asier R; Santamaria, Luis

2014-10-01

Forest fragmentation dramatically alters species persistence and distribution and affects many ecological interactions among species. Recent studies suggest that mutualisms, such as pollination and seed dispersal, are more sensitive to the negative effects of forest fragmentation than antagonisms, such as predation or herbivory. We applied meta-analytical techniques to evaluate this hypothesis and quantified the relative contributions of different components of the fragmentation process (decreases in fragment size, edge effects, increased isolation, and habitat degradation) to the overall effect. The effects of fragmentation on mutualisms were primarily driven by habitat degradation, edge effects, and fragment isolation, and, as predicted, they were consistently more negative on mutualisms than on antagonisms. For the most studied interaction type, seed dispersal, only certain components of fragmentation had significant (edge effects) or marginally significant (fragment size) effects. Seed size modulated the effect of fragmentation: species with large seeds showed stronger negative impacts of fragmentation via reduced dispersal rates. Our results reveal that different components of the habitat fragmentation process have varying impacts on key mutualisms. We also conclude that antagonistic interactions have been understudied in fragmented landscapes, most of the research has concentrated on particular types of mutualistic interactions such as seed dispersal, and that available studies of interspecific interactions have a strong geographical bias (arising mostly from studies carried out in Brazil, Chile, and the United States). © 2014 Society for Conservation Biology.

Analysis of In-Flight Collision Process During V-Type Firing Pattern in Surface Blasting Using Simple Physics

NASA Astrophysics Data System (ADS)

Chouhan, Lalit Singh; Raina, Avtar K.

2015-10-01

Blasting is a unit operation in Mine-Mill Fragmentation System (MMFS) and plays a vital role in mining cost. One of the goals of MMFS is to achieve optimum fragment size at minimal cost. Blast fragmentation optimization is known to result in better explosive energy utilization. Fragmentation depends on the rock, explosive and blast design variables. If burden, spacing and type of explosive used in a mine are kept constant, the firing sequence of blast-holes plays a vital role in rock fragmentation. To obtain smaller fragmentation size, mining professionals and relevant publications recommend V- or extended V-pattern of firing sequence. In doing so, it is assumed that the in-flight air collision breaks larger rock fragments into smaller ones, thus aiding further fragmentation. There is very little support to the phenomenon of breakage during in-flight collision of fragments during blasting in published literature. In order to assess the breakage of in-flight fragments due to collision, a mathematical simulation was carried over using basic principles of physics. The calculations revealed that the collision breakage is dependent on velocity of fragments, mass of fragments, the strength of the rock and the area of fragments over which collision takes place. For higher strength rocks, the in-flight collision breakage is very difficult to achieve. This leads to the conclusion that the concept demands an in-depth investigation and validation.

Effects of analogues of substance P fragments on the MAO activity in rat brain.

PubMed

Turska, E; Lachowicz, L; Koziołkiewicz, W; Wasiak, T

1985-01-01

The influence in vitro of analogues of Sp5-11 and SP6-11 substance P fragments on the activity of monoamine oxidase (MAO) in homogenates and crude mitochondrial fractions of rat brain was examined. The rat brain was divided into: I--cerebral cortex, II--hippocampus, III--midbrain, IV--thalamus with hypothalamus, V--cerebellum and VI--medulla oblongata. The obtained results proved that the analogues of SP fragments inhibit selectively the activity of the enzyme in the homogenates of cerebral cortex, hippocampus, midbrain and cerebellum. In the crude mitochondrial fractions the applied analogues of SP fragments caused a slight increase of the enzyme activity. The most significant changes in the activity of MAO were observed in hippocampus homogenate fraction.

Tungsten fragmentation in nuclear reactions induced by high-energy cosmic-ray protons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chechenin, N. G., E-mail: chechenin@sinp.msu.ru; Chuvilskaya, T. V.; Shirokova, A. A.

2015-01-15

Tungsten fragmentation arising in nuclear reactions induced by cosmic-ray protons in space-vehicle electronics is considered. In modern technologies of integrated circuits featuring a three-dimensional layered architecture, tungsten is frequently used as a material for interlayer conducting connections. Within the preequilibrium model, tungsten-fragmentation features, including the cross sections for the elastic and inelastic scattering of protons of energy between 30 and 240 MeV; the yields of isotopes and isobars; their energy, charge, and mass distributions; and recoil energy spectra, are calculated on the basis of the TALYS and EMPIRE-II-19 codes. It is shown that tungsten fragmentation affects substantially forecasts of failuresmore » of space-vehicle electronics.« less

Effects of script types of Japanese loan words on priming performance.

PubMed

Hayashi, Chiyoko

2005-04-01

23 female undergraduate students (M=20 yr., 10 mo., SD=15 mo.) were given a word-fragment completion task, containing a study and nonstudy list. In the present study, the effect of orthographic familiarity (e.g., script type) of a test item on a word-fragment completion task was examined. The script types of word stimuli (Katakana and Hiragana) were manipulated between a study and test phase. Priming effect was greater when the script type was the same between a study and test phase than in the cross-script condition. Further, even if the script type of word stimulus was different between study and test phases, a significant priming effect was obtained when the test fragment was orthographically familiar. These results suggested that not only the consistency of the perceptual feature of the stimulus word between study and test phases, but also orthographic familiarity of the stimulus word in the test phase facilitated priming effect in a word-fragment completion test.

Conformational heterogeneity in the C-terminal zinc fingers of human MTF-1: an NMR and zinc-binding study.

PubMed

Giedroc, D P; Chen, X; Pennella, M A; LiWang, A C

2001-11-09

The human metalloregulatory transcription factor, metal-response element (MRE)-binding transcription factor-1 (MTF-1), contains six TFIIIA-type Cys(2)-His(2) motifs, each of which was projected to form well-structured betabetaalpha domains upon Zn(II) binding. In this report, the structure and backbone dynamics of a fragment containing the unusual C-terminal fingers F4-F6 has been investigated. (15)N heteronuclear single quantum coherence (HSQC) spectra of uniformly (15)N-labeled hMTF-zf46 show that Zn(II) induces the folding of hMTF-zf46. Analysis of the secondary structure of Zn(3) hMTF-zf46 determined by (13)Calpha chemical shift indexing and the magnitude of (3)J(Halpha-HN) clearly reveal that zinc fingers F4 and F6 adopt typical betabetaalpha structures. An analysis of the heteronuclear backbone (15)N relaxation dynamics behavior is consistent with this picture and further reveals independent tumbling of the finger domains in solution. Titration of apo-MTF-zf46 with Zn(II) reveals that the F4 domain binds Zn(II) significantly more tightly than do the other two finger domains. In contrast to fingers F4 and F6, the betabetaalpha fold of finger F5 is unstable and only partially populated at substoichiometric Zn(II); a slight molar excess of zinc results in severe conformational exchange broadening of all F5 NH cross-peaks. Finally, although Cd(II) binds to apo-hMTF-zf46 as revealed by intense S(-)-->Cd(II) absorption, a non-native structure results; addition of stoichiometric Zn(II) to the Cd(II) complex results in quantitative refolding of the betabetaalpha structure in F4 and F6. The functional implications of these results are discussed.

Circular dichroism study of the carbohydrate-modified opioid peptides

NASA Astrophysics Data System (ADS)

Horvat, Štefica; Otvos, Laszlo; Urge, Laszlo; Horvat, Jaroslav; Čudić, Mare; Varga-Defterdarović, Lidija

1999-09-01

The conformational preferences of enkephalins and the related glycoconjugates in which free or protected carbohydrate moieties were linked to the opioid peptides through an ether, ester or amide bond were investigated by circular dichroism spectroscopy in water, trifluoroethanol and water-trifluoroethanol mixtures. The analysis of the spectra revealed that the conformation of the enkephalin molecule is very sensitive to slight changes in the peptide structure around the C-terminal region. It was found that the type II β-turn structures are populated in N-terminal tetrapeptide enkephalin fragment, while leucine-enkephalin amide feature a type I (III) β-turn structure in solution. Incorporation of the sugar moiety into opioid peptide compound did not significantly influence the overall conformation of the peptide backbone, although minor intensity changes may reflect shifts in the population of the different turn systems. These small structural alterations can be responsible for the receptor-subtype selectivity of the various carbohydrate-modified enkephalin analogs.

[Patella fractures in knee arthroplasty].

PubMed

Roth, A; Ghanem, M; Fakler, J

2016-05-01

Periprosthetic patella fractures occur both with and without retropatellar joint replacement. A non-operative treatment yields satisfactory results with low morbidity. It can be applied in minimally displaced fractures that have an intact retropatellar component and an intact extensor mechanism, combined with an initial immobilization. The surgical treatment is associated with relatively poor results and with high complication rates. There was only minor improvement of functional results, no matter which surgical technique was used. Surgical intervention is still required in fractures with a loosening of the patellar component, considerable dislocations of fragments, and damage to or rupture of the extensor mechanism. In particular, type II fractures require repair of the extensor mechanism and the fracture or patellectomy. Type III fractures require a revision or resection of the patella, a patelloplasty or total patellectomy. In addition, early or late reconstruction using allograft to restore the extensor mechanism can be taken in consideration.

Near-Earth Asteroid Returned Sample (NEARS)

NASA Technical Reports Server (NTRS)

Shoemaker, Eugene M.; Cheng, Andrew F.

1994-01-01

The concept of the Near-Earth Asteroid Returned Sample (NEARS) mission is to return to Earth 10-100 g from each of four to six sites on a near-Earth asteroid and to perform global characterization of the asteroid and measure mass, volume, and density to ten percent. The target asteroid for the mission is 4660 Nereus, probably a primitive C-type asteroid, with the alternate target being 1989ML, an extremely accessible asteroid of unknown type. Launch dates will be 1998, 2000, 2002, and 2004 on the Delta II-7925 launch vehicle. The mission objectives are three-fold. (1) Provide first direct and detailed petrological, chemical, age, and isotopic characterization of a near-Earth asteroid and relate it to terrestrial, lunar, and meteoritic materials. (2) Sample the asteroid regolith and characterize any exotic fragments. (3) Identify heterogeneity in the asteroid's isotopic properties, age, and elemental chemistry.

Functional association of Sun1 with nuclear pore complexes

PubMed Central

Liu, Qian; Pante, Nelly; Misteli, Tom; Elsagga, Mohamed; Crisp, Melissa; Hodzic, Didier; Burke, Brian; Roux, Kyle J.

2007-01-01

Sun1 and 2 are A-type lamin-binding proteins that, in association with nesprins, form a link between the inner nuclear membranes (INMs) and outer nuclear membranes of mammalian nuclear envelopes. Both immunofluorescence and immunoelectron microscopy reveal that Sun1 but not Sun2 is intimately associated with nuclear pore complexes (NPCs). Topological analyses indicate that Sun1 is a type II integral protein of the INM. Localization of Sun1 to the INM is defined by at least two discrete regions within its nucleoplasmic domain. However, association with NPCs is dependent on the synergy of both nucleoplasmic and lumenal domains. Cells that are either depleted of Sun1 by RNA interference or that overexpress dominant-negative Sun1 fragments exhibit clustering of NPCs. The implication is that Sun1 represents an important determinant of NPC distribution across the nuclear surface. PMID:17724119

Study of the peculiarities of multiparticle production via event-by-event analysis in asymmetric nucleus-nucleus interactions

NASA Astrophysics Data System (ADS)

Fedosimova, Anastasiya; Gaitinov, Adigam; Grushevskaya, Ekaterina; Lebedev, Igor

2017-06-01

In this work the study on the peculiarities of multiparticle production in interactions of asymmetric nuclei to search for unusual features of such interactions, is performed. A research of long-range and short-range multiparticle correlations in the pseudorapidity distribution of secondary particles on the basis of analysis of individual interactions of nuclei of 197 Au at energy 10.7 AGeV with photoemulsion nuclei, is carried out. Events with long-range multiparticle correlations (LC), short-range multiparticle correlations (SC) and mixed type (MT) in pseudorapidity distribution of secondary particles, are selected by the Hurst method in accordance with Hurst curve behavior. These types have significantly different characteristics. At first, they have different fragmentation parameters. Events of LC type are processes of full destruction of the projectile nucleus, in which multicharge fragments are absent. In events of mixed type several multicharge fragments of projectile nucleus are discovered. Secondly, these two types have significantly different multiplicity distribution. The mean multiplicity of LC type events is significantly more than in mixed type events. On the basis of research of the dependence of multiplicity versus target-nuclei fragments number for events of various types it is revealed, that the most considerable multiparticle correlations are observed in interactions of the mixed type, which correspond to the central collisions of gold nuclei and nuclei of CNO-group, i.e. nuclei with strongly asymmetric volume, nuclear mass, charge, etc. Such events are characterised by full destruction of the target-nucleus and the disintegration of the projectile-nucleus on several multi-charged fragments.

Three-dimensional structure and dynamics of wine tannin-saliva protein complexes. A multitechnique approach.

PubMed

Simon, Cécile; Barathieu, Karine; Laguerre, Michel; Schmitter, Jean-Marie; Fouquet, Eric; Pianet, Isabelle; Dufourc, Erick J

2003-09-09

The interactions between the B3 (catechin-4alpha,8-catechin) red wine tannin and the human salivary protein fragment IB7(14) (SPPGKPQGPPPQGG) were monitored by (1)H magic angle spinning NMR, circular dichroism, electrospray ionization mass spectrometry, and molecular modeling. It is found that the secondary structure of IB7(14) is made of a type II helix (collagen helix) and random coil. The central glycine 8 appears to act as a flexible rotula separating two helix II regions. Three tannin molecules tightly complex the peptide, without modifying its secondary structure, but seem to reduce its conformational dynamics. The binding dissociation constant is in the millimolar range. B3 tannins with a "tweezers" conformation bind to the hydrophilic side of the saliva peptide, suggesting that the principal driving forces toward association are governed by hydrogen bonding between the carbonyl functions of proline residues and both the phenol and catechol OH groups. These findings are further discussed in the frame of an astringency phenomenon.

A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA

PubMed Central

Martick, Monika; Horan, Lucas H.; Noller, Harry F.; Scott, William G.

2008-01-01

Structured RNAs embedded in the untranslated regions (UTRs) of messenger RNAs can regulate gene expression. In bacteria, control of a metabolite gene is mediated by the self-cleaving activity of a ribozyme embedded in its 5′ UTR1. This discovery has raised the question of whether gene-regulating ribozymes also exist in eukaryotic mRNAs. Here we show that highly active hammerhead ribozymes2,3 are present in the 3′ UTRs of rodent C-type lectin type II (Clec2) genes4–7. Using a hammerhead RNA motif search with relaxed delimitation of the non-conserved regions, we detected ribozyme sequences in which the invariant regions, in contrast to the previously identified continuous hammerheads8–10, occur as two fragments separated by hundreds of nucleotides. Notably, a fragment pair can assemble to form an active hammerhead ribozyme structure between the translation termination and the poly-adenylation signals within the 3′ UTR. We demonstrate that this hammerhead structure can self-cleave both in vitro and in vivo, and is able to reduce protein expression in mouse cells. These results indicate that an unrecognized mechanism of post-transcriptional gene regulation involving association of discontinuous ribozyme sequences within an mRNA may be modulating the expression of several CLEC2 proteins that function in bone remodelling and the immune response of several mammals. PMID:18615019

Fragment-based prediction of skin sensitization using recursive partitioning

NASA Astrophysics Data System (ADS)

Lu, Jing; Zheng, Mingyue; Wang, Yong; Shen, Qiancheng; Luo, Xiaomin; Jiang, Hualiang; Chen, Kaixian

2011-09-01

Skin sensitization is an important toxic endpoint in the risk assessment of chemicals. In this paper, structure-activity relationships analysis was performed on the skin sensitization potential of 357 compounds with local lymph node assay data. Structural fragments were extracted by GASTON (GrAph/Sequence/Tree extractiON) from the training set. Eight fragments with accuracy significantly higher than 0.73 ( p < 0.1) were retained to make up an indicator descriptor fragment. The fragment descriptor and eight other physicochemical descriptors closely related to the endpoint were calculated to construct the recursive partitioning tree (RP tree) for classification. The balanced accuracy of the training set, test set I, and test set II in the leave-one-out model were 0.846, 0.800, and 0.809, respectively. The results highlight that fragment-based RP tree is a preferable method for identifying skin sensitizers. Moreover, the selected fragments provide useful structural information for exploring sensitization mechanisms, and RP tree creates a graphic tree to identify the most important properties associated with skin sensitization. They can provide some guidance for designing of drugs with lower sensitization level.

Anti-aging Friction of Carbonate Fault Mirror and its Microstructural Interpretation

NASA Astrophysics Data System (ADS)

Park, Y.; Ree, J. H.; Hirose, T.

2017-12-01

In our slide-hold-slide (SHS) friction tests on carbonate fault rocks, fault mirror (FM), light reflective mirror-like fault surface, shows almost zero or slightly negative aging rate of friction (`anti-aging' friction), whereas carbonate faults without FM exhibit a positive aging rate. We analyzed microstructures from three types of carbonate faults to explore the cause of the anti-aging friction of FM. The three types of fault rocks before SHS tests were made from Carrara marble; (i) FM, (ii) crushed gouge of former FM (CF), and (iii) gouge produced by pre-shearing of Carrara marble (PR). The fault zone of FM before SHS tests consists of sintered nanograin patches smeared into negative asperities of wall rocks (thickness up to 150 μm) and a sintered gouge layer between wall rocks (thickness up to 200 μm) that is composed of tightly-packed nanograins (50-500 nm in size) with triple junctions and angular-subangular fragments (a few-100 μm) of sintered nanograin aggregates. A straight and discrete Y-shear surface defines a boundary between the gouge layer and the nanograin patches or between the layer and wall rock. CF specimens before SHS tests are composed of patches of sintered nanograins as in FM specimens and a porous gouge layer with finer nanograins (a few-20 nm in size) and angular fragments of former FM. PR specimens before SHS tests are composed of damaged wall rocks and porous gouge with finer nanograins (a few-tens of μm). After SHS tests, sintered appearance of grains within the fault zones of CF and PR indicates the increase in interparticle bonding and also in contact area by grain aggregation. In contrast, the gouge layer of FM specimens after SHS tests consists mostly of angular fragments of sintered nanograin aggregates. The angular shape of the fragments indicates little increase in bonding and contact area between the fragments. Tightly sintered nanograins in FM specimens would have a lower chemical reactivity with their size coarser and sintering stronger than those of CF and PR. Furthermore, a high wear resistance of sintered nanograins of FM would prohibit generation of fine wear debris which may have led to the strenghtened interparticle bonding. Our results imply that anti-aging friction may be a common behavior other rocks' FM too, once they are composed of tightly sintered nanograins.

Protective effects of blueberries (Vaccinium corymbosum L.) extract against cadmium-induced hepatotoxicity in mice.

PubMed

Gong, Pin; Chen, Fu-xin; Wang, Lan; Wang, Jing; Jin, Sai; Ma, Yang-min

2014-05-01

The oxidative status and morphological changes of mouse liver exposed to cadmium chloride (Cd(II)) and therapeutic potential of blueberry (Vaccinium corymbosum L.) extract against Cd(II)-induced hepatic injury were investigated. A variety of parameters were evaluated, including lipid peroxidation (LPO), protein carbonyl (PCO) level, DNA fragment, as well as antioxidative defense system (i.e., superoxide dismutase (SOD), catalase (CAT), reduced glutathione (GSH)). Elemental analysis and evaluation of morphological changes and NO levels were also performed. Exposure to Cd(II) led to increased LPO and PCO as well as DNA fragment and a reduction of SOD and CAT activities, however, the content of GSH elevated probably due to biological adaptive-response. In contrast, co-treatment of anthocyanin (Ay) inhibited the increased oxidative parameters as well as restored the activities of antioxidative defense system in a dose-dependent manner. Ay administration regained these morphological changes caused by intoxication of Cd(II) to nearly normal levels. Moreover, the accumulation of Cd(II) in liver may be one of the reasons for Cd(II) toxicity and Ay can chelate with Cd(II) to reduce Cd(II) burden. The influence of Cd(II) on the Zn and Ca levels can also be adjusted by the co-administration of Ay. Exposure to Cd(II) led to an increase of NO and Ay reduced NO contents probably by directly scavenging. Potential mechanisms for the protective effect of Ay have been proposed, including its anti-oxidative and anti-inflammatory effect along with the metal-chelating capacity. These results suggest that blueberry extract may be valuable as a therapeutic agent in combating Cd(II)-induced tissue injury. Copyright © 2014 Elsevier B.V. All rights reserved.

Effects of habitat fragmentation on wild mammal infection by Trypanosoma cruzi.

PubMed

Vaz, V C; D'Andrea, P S; Jansen, A M

2007-11-01

Expansion of human activities frequently results in habitat fragmentation, a phenomenon that has been widely recognized in the last decades as one of the major threats to world's biodiversity. The transformation of a continuous forest into a fragmented area results in a hyper-dynamic landscape with unpredictable consequences to overall ecosystem health. The effect of the fragmentation process on Trypanosoma cruzi infection among small wild mammals was studied in an Atlantic Rain Forest landscape. Comparing continous forest to fragmented habitat, marsupials were less abundant than rodents in the continuous landscape. An overall decrease in small wild mammal richness was observed in the smaller fragments. An anti-T. cruzi seroprevalence of 18% (82/440) was deteced by immunofluorescence assay. Moreover, this seroprevalence was higher in the fragmented habitat than in the continuous forest. According to the collected data, 3 main factors seem to modulate infection by T. cruzi in small wild mammals: (i) habitat fragmentation; (ii) biodiversity loss; (iii) increase of marsupial abundance in mammal communities. Furthermore, an extremely mild controlled infection by T. cruzi was detected since no patent parasitaemia could be detected in fresh blood samples, and no parasites were isolated by haemoculture.

Habitat fragmentation resulting in overgrazing by herbivores.

PubMed

Kondoh, Michio

2003-12-21

Habitat fragmentation sometimes results in outbreaks of herbivorous insect and causes an enormous loss of primary production. It is hypothesized that the driving force behind such herbivore outbreaks is disruption of natural enemy attack that releases herbivores from top-down control. To test this hypothesis I studied how trophic community structure changes along a gradient of habitat fragmentation level using spatially implicit and explicit models of a tri-trophic (plant, herbivore and natural enemy) food chain. While in spatially implicit model number of trophic levels gradually decreases with increasing fragmentation, in spatially explicit model a relatively low level of habitat fragmentation leads to overgrazing by herbivore to result in extinction of the plant population followed by a total system collapse. This provides a theoretical support to the hypothesis that habitat fragmentation can lead to overgrazing by herbivores and suggests a central role of spatial structure in the influence of habitat fragmentation on trophic communities. Further, the spatially explicit model shows (i) that the total system collapse by the overgrazing can occur only if herbivore colonization rate is high; (ii) that with increasing natural enemy colonization rate, the fragmentation level that leads to the system collapse becomes higher, and the frequency of the collapse is lowered.

STUDIES ON ISOLATED NUCLEI. II. ISOLATION AND CHEMICAL CHARACTERIZATION OF NUCLEOLAR AND NUCLEOPLASMIC SUBFRACTIONS.

PubMed

MAGGIO, R; SIEKEVITZ, P; PALADE, G E

1963-08-01

This paper describes the subfractionation of nuclei isolated from guinea pig liver by the procedure presented in the first article of the series (8). Centrifugation in a density gradient system of nuclear fractions disrupted by sonication permits the isolation of the following subfractions: (a) a nucleolar subfraction which consists mainly of nucleoli surrounded by a variable amount of nucleolus-associated chromatin and contaminated by chromatin blocks derived primarily from von Kupffer cell nuclei; (b) and (c), two nucleoplasmic subfractions (I and II) which consist mainly of chromatin threads in a coarser (I) or finer (II) degree of fragmentation. The protein, RNA, and DNA content of these subfractions was determined, and their RNA's characterized in terms of NaCl-solubility, nucleotide composition, and in vivo nucleotide turnover, using inorganic (32)P as a marker. The results indicate that there are at least three types of RNA in the nucleus (one in the nucleolus and two in the nucleoplasm or chromatin), which differ from one another in NaCl-solubility, nucleotide composition, turnover, and possibly sequence. Possible relations among these RNA's and those of the cytoplasm are discussed.

Energy production using fission fragment rockets

NASA Astrophysics Data System (ADS)

Chapline, G.; Matsuda, Y.

1991-08-01

Fission fragment rockets are nuclear reactors with a core consisting of thin fibers in a vacuum, and which use magnetic fields to extract the fission fragments from the reactor core. As an alternative to ordinary nuclear reactors, fission fragment rockets would have the following advantages: approximately twice the efficiency if the fission fragment energy can be directly converted into electricity; reduction of the buildup of a fission fragment inventory in the reactor could avoid a Chernobyl type disaster; and collection of the fission fragments outside the reactor could simplify the waste disposal problem.

Ambient light-based optical biosensing platform with smartphone-embedded illumination sensor.

PubMed

Park, Yoo Min; Han, Yong Duk; Chun, Hyeong Jin; Yoon, Hyun C

2017-07-15

We present a hand-held optical biosensing system utilizing a smartphone-embedded illumination sensor that is integrated with immunoblotting assay method. The smartphone-embedded illumination sensor is regarded as an alternative optical receiver that can replaces the conventional optical analysis apparatus because the illumination sensor can respond to the ambient light in a wide range of wavelengths, including visible and infrared. To demonstrate the biosensing applicability of our system employing the enzyme-mediated immunoblotting and accompanying light interference, various types of ambient light conditions including outdoor sunlight and indoor fluorescent were tested. For the immunoblotting assay, the biosensing channel generating insoluble precipitates as an end product of the enzymatic reaction is fabricated and mounted on the illumination sensor of the smartphone. The intensity of penetrating light arrives on the illumination sensor is inversely proportional to the amount of precipitates produced in the channel, and these changes are immediately analyzed and quantified via smartphone software. In this study, urinary C-terminal telopeptide fragment of type II collagen (uCTX-II), a biomarker of osteoarthritis diagnosis, was tested as a model analyte. The developed smartphone-based sensing system efficiently measured uCTX-II in the 0-5ng/mL concentration range with a high sensitivity and accuracy under various light conditions. These assay results show that the illumination sensor-based optical biosensor is suitable for point-of-care testing (POCT). Copyright © 2016 Elsevier B.V. All rights reserved.

Differentiation of isomeric 2-aryldimethyltetrahydro-5-quinolinones by electron ionization and electrospray ionization mass spectrometry.

PubMed

Kumar, Ch Dinesh; Chary, V Naresh; Dinesh, A; Reddy, P S; Srinivas, K; Gayatri, G; Sastry, G N; Prabhakar, S

2011-10-15

A series of isomeric 2-aryl-6,6-dimethyltetrahydro-5-quinolinones (set I) and 2-aryl-7,7-dimethyltetrahydro-5-quinolinones (set II) were studied under positive ion electron ionization (EI) and electrospray ionization (ESI) techniques. Under EI conditions, the molecular ions were found to be less stable in set I isomers, and they resulted in abundant fragment ions, i.e., [M-CH(3)](+), [M-CO](+.), [M-HCO](+), [M-(CH(3),CO)](+), and [M-(CH(3),CH(2)O)](+), when compared with set II isomers. In addition, the set I isomers showed specific fragment ions corresponding to [M-OH](+) and [M-OCH(3)](+). The retro-Diels-Alder (RDA) product ion was always higher in set II isomers. The ESI mass spectra produced [M + H](+) ions, and their decomposition showed favorable loss of CH(3) radical, CH(4) and C(2)H(6) molecules in set I isomers. The set II isomers, however, showed predominant RDA product ions, and specific loss of H(2)O. The selectivity in EI and ESI was attributed to the instability of set I isomers by the presence of a gem-dimethyl group at the α-position, and it was supported by the data from model compounds without a gem-dimethyl group. Density functional theory (DFT) calculations successfully corroborated the fragmentation pathways for diagnostic ions. This study revealed the effect of a gem-dimethyl group located at the α-position to the carbonyl having aromatic/unsaturated carbon on the other side of the carbonyl group. Copyright © 2011 John Wiley & Sons, Ltd.

Stat5-mediated regulation of the human type II 3beta-hydroxysteroid dehydrogenase/delta5-delta4 isomerase gene: activation by prolactin.

PubMed

Feltus, F A; Groner, B; Melner, M H

1999-07-01

Altered PRL levels are associated with infertility in women. Molecular targets at which PRL elicits these effects have yet to be determined. These studies demonstrate transcriptional regulation by PRL of the gene encoding the final enzymatic step in progesterone biosynthesis: 3beta-hydroxysteroid dehydrogenase/delta5-delta4 isomerase (3beta-HSD). A 9/9 match with the consensus Stat5 response element was identified at -110 to -118 in the human Type II 3beta-HSD promoter. 3beta-HSD chloramphenicol acetyltransferase (CAT) reporter constructs containing either an intact or mutated Stat5 element were tested for PRL activation. Expression vectors for Stat5 and the PRL receptor were cotransfected with a -300 --> +45 3beta-HSD CAT reporter construct into HeLa cells, which resulted in a 21-fold increase in reporter activity in the presence of PRL. Promoter activity showed an increased response with a stepwise elevation of transfected Stat5 expression or by treatment with increasing concentrations of PRL (max, 250 ng/ml). This effect was dramatically reduced when the putative Stat5 response element was removed by 5'-deletion of the promoter or by the introduction of a 3-bp mutation into critical nucleotides in the element. Furthermore, 32P-labeled promoter fragments containing the Stat5 element were shifted in electrophoretic mobility shift assay experiments using nuclear extracts from cells treated with PRL, and this complex was supershifted with antibodies to Stat5. These results demonstrate that PRL has the ability to regulate expression of a key human enzyme gene (type II 3beta-HSD) in the progesterone biosynthetic pathway, which is essential for maintaining pregnancy.

A hybrid ruthenium alkynyl/zinc porphyrin "Cross Fourchée" with large cubic NLO properties.

PubMed

Merhi, Areej; Grelaud, Guillaume; Green, Katy A; Minh, Ngo Hoang; Reynolds, Michael; Ledoux, Isabelle; Barlow, Adam; Wang, Genmiao; Cifuentes, Marie P; Humphrey, Mark G; Paul, Frédéric; Paul-Roth, Christine O

2015-05-07

A new Zn(ii) porphyrin-cored ruthenium alkynyl dendrimer (2) containing twelve Ru(κ(2)-dppe)2 bis-alkynyl fragments has been prepared in two steps from 5,10,15,20-tetra(4-ethynylphenyl)porphyrinatozinc(ii) and shown to be highly active for third-harmonic generation (THG) at 1907 nm.

Luminous Efficiency Estimates of Meteors. II. Application to Canadian Automated Meteor Observatory Meteor Events

NASA Astrophysics Data System (ADS)

Subasinghe, Dilini; Campbell-Brown, Margaret

2018-02-01

Luminous efficiency is a necessary parameter for determining meteoroid mass from optical emission. Despite this importance, it is very poorly known, with previous results varying by up to two orders of magnitude for a given speed. We present the most recent study of luminous efficiency values determined with modern high-resolution instruments, by directly comparing dynamic and photometric meteoroid masses. Fifteen non-fragmenting meteoroids were used, with a further five clearly fragmenting events for comparison. Twelve of the fifteen non-fragmenting meteoroids had luminous efficiencies less than 1%, while the fragmenting meteoroids had upper limits of a few tens of per cent. No clear trend with speed was seen, but there was a weak negative trend of luminous efficiency on meteoroid mass, implying that smaller meteoroids radiate more efficiently.

The fragmentation of 510 MeV/nucleon iron-56 in polyethylene. II. Comparisons between data and a model

NASA Technical Reports Server (NTRS)

Zeitlin, C.; Heilbronn, L.; Miller, J.; Schimmerling, W.; Townsend, L. W.; Tripathi, R. K.; Wilson, J. W.

1996-01-01

The results of a Monte Carlo model for calculating fragment fluences and LET spectra are compared to data taken with 600 MeV/nucleon iron ions incident on an accelerator beamline configured for irradiation of biological samples, with no target and with 2, 5 and 8 cm of polyethylene. The model uses a multi-generation nuclear fragmentation code, coupled with a formulation of ionization energy loss based on the Bethe-Bloch equation. In the region where the data are reliable and the experimental acceptance is well understood, many of the features of the experimental spectra are well replicated by the model. To obtain good agreement with the experimental data, the model must allow for at least two generations of fragment production in the target.

Mass spectrometry of cis-diamminedichloroplatinum(II) adducts with the dinucleosidemonophosphates d(ApG), d(GpG) and d(TpC) in an ion trap.

PubMed

Hagemeister, Timo; Linscheid, Michael

2002-07-01

The detection and fragmentation behaviour of adducts of the chemotherapeutic cis-diamminedichloroplatinum(II) (cisplatin) with the dinucleosidemonophosphates d(ApG), d(GpG) and d(TpC) as model compounds for DNA adducts in an ion trap with electrospray ionization were studied. Mainly the monofunctional adduct, the bifunctional adduct and the bifunctional adduct with platinum bridging two dinucleosidemonophosphates were detected. In addition, several more complex adducts were seen resulting from reactions among these species. Adduct formation was low in the case of d(TpC). Fragmentation could be controlled strongly by varying the temperature of the transfer capillary; furthermore, tandem mass spectrometric (MS/MS) experiments on both the monofunctional and the bifunctional adducts were performed. For the adducts of d(ApG) and d(GpG) losses of NH(3) and HCl were the most dominant reactions, followed by the losses of one, then another two units of 98 amu from the sugar-phosphate backbone, whereas d(TpC)-Pt predominantly forms the dinucleosidemonophosphate. In the gas phase, the conversion of the monofunctional into the bifunctional adducts through binding to another site in the dinucleotide accompanied by loss of NH(3) or HCl could also be observed. The removal of a ligand from the coordination sphere of the square-planar platinum complexes appeared to be the crucial step for the induction of further fragmentation of the dinucleotide ligand. MS(n) experiments of the bifunctional adducts of d(ApG) and d(GpG) revealed different fragmentation pathways involving the loss of phosphoric acid, metaphosphoric acid, deoxyribose units (intact or dehydrated) and the nucleobases in different orders, leaving characteristic binding site-determining fragments. Fragmentation of these ions was also performed, mainly resulting in fragmentation of the bases. The study confirmed the remarkable stability of the platinum-guanine bond compared with other nucleobases. Copyright 2002 John Wiley & Sons, Ltd.

Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding.

PubMed

Yang, A S; Hitz, B; Honig, B

1996-06-21

The stability of beta-turns is calculated as a function of sequence and turn type with a Monte Carlo sampling technique. The conformational energy of four internal hydrogen-bonded turn types, I, I', II and II', is obtained by evaluating their gas phase energy with the CHARMM force field and accounting for solvation effects with the Finite Difference Poisson-Boltzmann (FDPB) method. All four turn types are found to be less stable than the coil state, independent of the sequence in the turn. The free-energy penalties associated with turn formation vary between 1.6 kcal/mol and 7.7 kcal/mol, depending on the sequence and turn type. Differences in turn stability arise mainly from intraresidue interactions within the two central residues of the turn. For each combination of the two central residues, except for -Gly-Gly-, the most stable beta-turn type is always found to occur most commonly in native proteins. The fact that a model based on local interactions accounts for the observed preference of specific sequences suggests that long-range tertiary interactions tend to play a secondary role in determining turn conformation. In contrast, for beta-hairpins, long-range interactions appear to dominate. Specifically, due to the right-handed twist of beta-strands, type I' turns for -Gly-Gly- are found to occur with high frequency, even when local energetics would dictate otherwise. The fact that any combination of two residues is found able to adopt a relatively low-energy turn structure explains why the amino acid sequence in turns is highly variable. The calculated free-energy cost of turn formation, when combined with related numbers obtained for alpha-helices and beta-sheets, suggests a model for the initiation of protein folding based on metastable fragments of secondary structure.

Generalized Boltzmann-Type Equations for Aggregation in Gases

NASA Astrophysics Data System (ADS)

Adzhiev, S. Z.; Vedenyapin, V. V.; Volkov, Yu. A.; Melikhov, I. V.

2017-12-01

The coalescence and fragmentation of particles in a dispersion system are investigated by applying kinetic theory methods, namely, by generalizing the Boltzmann kinetic equation to coalescence and fragmentation processes. Dynamic equations for the particle concentrations in the system are derived using the kinetic equations of motion. For particle coalescence and fragmentation, equations for the particle momentum, coordinate, and mass distribution functions are obtained and the coalescence and fragmentation coefficients are calculated. The equilibrium mass and velocity distribution functions of the particles in the dispersion system are found in the approximation of an active terminal group (Becker-Döring-type equation). The transition to a continuum description is performed.

Assembly and analysis of fragmentation data for liquid propellant vessels

NASA Technical Reports Server (NTRS)

Baker, W. E.; Parr, V. B.; Bessey, R. L.; Cox, P. A.

1974-01-01

Fragmentation data was assembled and analyzed for exploding liquid propellant vessels. These data were to be retrieved from reports of tests and accidents, including measurements or estimates of blast yield, etc. A significant amount of data was retrieved from a series of tests conducted for measurement of blast and fireball effects of liquid propellant explosions (Project PYRO), a few well-documented accident reports, and a series of tests to determine auto-ignition properties of mixing liquid propellants. The data were reduced and fitted to various statistical functions. Comparisons were made with methods of prediction for blast yield, initial fragment velocities, and fragment range. Reasonably good correlation was achieved. Methods presented in the report allow prediction of fragment patterns, given type and quantity of propellant, type of accident, and time of propellant mixing.

Short mucin 6 alleles are associated with H pylori infection

PubMed Central

Nguyen, Thai V; Janssen, Marcel JR; Gritters, Paulien; te Morsche, René HM; Drenth, Joost PH; van Asten, Henri; Laheij, Robert JF; Jansen, Jan BMJ

2006-01-01

AIM: To investigate the relationship between mucin 6 (MUC6) VNTR length and H pylori infection. METHODS: Blood samples were collected from patients visiting the Can Tho General Hospital for upper gastrointestinal endoscopy. DNA was isolated from whole blood, the repeated section was cut out using a restriction enzyme (PvuII) and the length of the allele fragments was determined by Southern blotting. H pylori infection was diagnosed by 14C urea breath test. For analysis, MUC6 allele fragment length was dichotomized as being either long (> 13.5 kbp) or short (≤ 13.5 kbp) and patients were classified according to genotype [long-long (LL), long-short (LS), short-short (SS)]. RESULTS: 160 patients were studied (mean age 43 years, 36% were males, 58% H pylori positive). MUC6 PvuII-restricted allele fragment lengths ranged from 7 to 19 kbp. Of the patients with the LL, LS, SS MUC6 genotype, 43% (24/56), 57% (25/58) and 76% (11/46) were infected with H pylori, respectively (P = 0.003). CONCLUSION: Short MUC6 alleles are associated with H pylori infection. PMID:17009402

Short mucin 6 alleles are associated with H pylori infection.

PubMed

Nguyen, Thai V; Janssen, Marcel; Gritters, Paulien; te Morsche, René H M; Drenth, Joost P H; van Asten, Henri; Laheij, Robert J F; Jansen, Jan B M J

2006-10-07

To investigate the relationship between mucin 6 (MUC6) VNTR length and H pylori infection. Blood samples were collected from patients visiting the Can Tho General Hospital for upper gastrointestinal endoscopy. DNA was isolated from whole blood, the repeated section was cut out using a restriction enzyme (Pvu II) and the length of the allele fragments was determined by Southern blotting. H pylori infection was diagnosed by (14)C urea breath test. For analysis, MUC6 allele fragment length was dichotomized as being either long (> 13.5 kbp) or short (< or = 13.5 kbp) and patients were classified according to genotype [long-long (LL), long-short (LS), short-short (SS)]. 160 patients were studied (mean age 43 years, 36% were males, 58% H pylori positive). MUC6 Pvu II-restricted allele fragment lengths ranged from 7 to 19 kbp. Of the patients with the LL, LS, SS MUC6 genotype, 43% (24/56), 57% (25/58) and 76% (11/46) were infected with H pylori, respectively (P = 0.003). Short MUC6 alleles are associated with H pylori infection.

Areas influenced by multiple edges and their implications in fragmented landscapes

Treesearch

Qinglin Li; Jiquan Chen; Bo Song; Jacob L. LaCroix; Mary K. Breese; John A. Radmacher

2007-01-01

We introduced a new approach for delineating areas of multiple edge influence (AMEI) within a fragmented landscape using a geographic information system (GIS). AMEI was defined as the interface that is affected by more than two neighboring patch types. We decomposed AMEI into three components: AMEI1, the area where one patch type meets a different patch type; AMEI2,...

The Importance of Maize Management on Dung Beetle Communities in Atlantic Forest Fragments

PubMed Central

Campos, Renata Calixto; Hernández, Malva Isabel Medina

2015-01-01

Dung beetle community structures changes due to the effects of destruction, fragmentation, isolation and decrease in tropical forest area, and therefore are considered ecological indicators. In order to assess the influence of type of maize cultivated and associated maize management on dung beetle communities in Atlantic Forest fragments surrounded by conventional and transgenic maize were evaluated 40 Atlantic Forest fragments of different sizes, 20 surrounded by GM maize and 20 surrounded by conventional maize, in February 2013 and 2014 in Southern Brazil. After applying a sampling protocol in each fragment (10 pitfall traps baited with human feces or carrion exposed for 48 h), a total of 3454 individuals from 44 species were captured: 1142 individuals from 38 species in GM maize surrounded fragments, and 2312 from 42 species in conventional maize surrounded fragments. Differences in dung beetle communities were found between GM and conventional maize communities. As expected for fragmented areas, the covariance analysis showed a greater species richness in larger fragments under both conditions; however species richness was greater in fragments surrounded by conventional maize. Dung beetle structure in the forest fragments was explained by environmental variables, fragment area, spatial distance and also type of maize (transgenic or conventional) associated with maize management techniques. In Southern Brazil’s scenario, the use of GM maize combined with associated agricultural management may be accelerating the loss of diversity in Atlantic Forest areas, and consequently, important ecosystem services provided by dung beetles may be lost. PMID:26694874

The Importance of Maize Management on Dung Beetle Communities in Atlantic Forest Fragments.

PubMed

Campos, Renata Calixto; Hernández, Malva Isabel Medina

2015-01-01

Dung beetle community structures changes due to the effects of destruction, fragmentation, isolation and decrease in tropical forest area, and therefore are considered ecological indicators. In order to assess the influence of type of maize cultivated and associated maize management on dung beetle communities in Atlantic Forest fragments surrounded by conventional and transgenic maize were evaluated 40 Atlantic Forest fragments of different sizes, 20 surrounded by GM maize and 20 surrounded by conventional maize, in February 2013 and 2014 in Southern Brazil. After applying a sampling protocol in each fragment (10 pitfall traps baited with human feces or carrion exposed for 48 h), a total of 3454 individuals from 44 species were captured: 1142 individuals from 38 species in GM maize surrounded fragments, and 2312 from 42 species in conventional maize surrounded fragments. Differences in dung beetle communities were found between GM and conventional maize communities. As expected for fragmented areas, the covariance analysis showed a greater species richness in larger fragments under both conditions; however species richness was greater in fragments surrounded by conventional maize. Dung beetle structure in the forest fragments was explained by environmental variables, fragment area, spatial distance and also type of maize (transgenic or conventional) associated with maize management techniques. In Southern Brazil's scenario, the use of GM maize combined with associated agricultural management may be accelerating the loss of diversity in Atlantic Forest areas, and consequently, important ecosystem services provided by dung beetles may be lost.

Structural requirements for fibromodulin binding to collagen and the control of type I collagen fibrillogenesis--critical roles for disulphide bonding and the C-terminal region.

PubMed

Font, B; Eichenberger, D; Goldschmidt, D; Boutillon, M M; Hulmes, D J

1998-06-15

Fibromodulin belongs to the family of small, leucine-rich proteoglycans which have been reported to interact with collagens and to inhibit type I collagen fibrillogenesis. Decorin and fibromodulin exhibit a noticeable degree of sequence similarity. However, as previously reported [Font, B., Eichenberger, D., Rosenberg, L. M. & van der Rest, M. (1996) Matrix Biol. 15, 341-348] the domains of these molecules implicated in the interactions with type XII and type XIV collagens are different, these being the dermatan sulphate/chondroitin sulphate chain for decorin and the core protein for fibromodulin. At the present time the fibromodulin domains implicated in the interactions with fibrillar collagens remain unknown. In experiments reported here, we have sought to identify the structural requirements for fibromodulin interaction with collagen and for the control of type I collagen fibrillogenesis. Circular dichroism spectra and fibrillogenesis inhibition studies show that fibromodulin structure and its collagen fibrillogenesis control function are strictly dependent on the presence of intact disulphide bridge(s). In addition, we show that the binding of fibromodulin (or fibromodulin-derived fragments) to type I collagen is not necessarily correlated with fibrillogenesis inhibition. To isolate fibromodulin domains, the native proteoglycan was submitted to mild proteolysis. We have isolated an alpha-chymotrypsin-resistant fragment which contains the bulk of the N-terminal and central region of the molecule including the leucine-rich repeats 4 and 6 reported for decorin to be involved in type I collagen binding. This fragment does not bind to type I collagen. Using enzymes with different specificities, a number of large fragments of fibromodulin were obtained, suggesting a compact structure for this molecule which is relatively resistant to proteolysis. None of these N-glycosylated fragments were able to bind to type I collagen in co-sedimentation experiments. Taken together these results suggest that fibromodulin-type I collagen interactions leading to fibrillogenesis inhibition require more than one binding domain. One of these domains could be the C-terminal end of the molecule containing the disulphide loop which is absent in the chymotrypsin-resistant fragment.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient.

PubMed

Orihuela, Rodrigo L L; Peres, Carlos A; Mendes, Gabriel; Jarenkow, João A; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

PubMed Central

Orihuela, Rodrigo L. L.; Peres, Carlos A.; Mendes, Gabriel; Jarenkow, João A.; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide. PMID:26309252

PubChem atom environments.

PubMed

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased. The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log-log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.

Gold-Catalyzed Enantio- and Diastereoselective Syntheses of Left Fragments of Azadirachtin/Meliacarpin-Type Limonoids.

PubMed

Shi, Hang; Tan, Ceheng; Zhang, Weibin; Zhang, Zichun; Long, Rong; Gong, Jianxian; Luo, Tuoping; Yang, Zhen

2016-02-05

Meliacarpin-type limonoids are an important class of organic insecticides. Their syntheses are challenging due to their chemical complexity. Here, we report the highly enantio- and diastereoselective synthesis of the left fragments of azadirachtin I and 1-cinnamoylmelianolone, being two important family members of meliacarpin-type limonoids, via pairwise palladium- and gold-catalyzed cascade reactions. Gold-catalyzed reactions of 1,7-diynes were performed as model studies, and the efficient construction of tetracyclic late-stage intermediates was achieved on the basis of this key transformation. Our unique route gave both of the left fragments in 23 steps from the commercially available chiral starting material (-)-carvone. This study significantly advances research on the synthesis of the meliacarpin-type limonoids.

Epstein-Barr virus recombinants from overlapping cosmid fragments.

PubMed

Tomkinson, B; Robertson, E; Yalamanchili, R; Longnecker, R; Kieff, E

1993-12-01

Five overlapping type 1 Epstein-Barr virus (EBV) DNA fragments constituting a complete replication- and transformation-competent genome were cloned into cosmids and transfected together into P3HR-1 cells, along with a plasmid encoding the Z immediate-early activator of EBV replication. P3HR-1 cells harbor a type 2 EBV which is unable to transform primary B lymphocytes because of a deletion of DNA encoding EBNA LP and EBNA 2, but the P3HR-1 EBV can provide replication functions in trans and can recombine with the transfected cosmids. EBV recombinants which have the type 1 EBNA LP and 2 genes from the transfected EcoRI-A cosmid DNA were selectively and clonally recovered by exploiting the unique ability of the recombinants to transform primary B lymphocytes into lymphoblastoid cell lines. PCR and immunoblot analyses for seven distinguishing markers of the type 1 transfected DNAs identified cell lines infected with EBV recombinants which had incorporated EBV DNA fragments beyond the transformation marker-rescuing EcoRI-A fragment. Approximately 10% of the transforming virus recombinants had markers mapping at 7, 46 to 52, 93 to 100, 108 to 110, 122, and 152 kbp from the 172-kbp transfected genome. These recombinants probably result from recombination among the transfected cosmid-cloned EBV DNA fragments. The one recombinant virus examined in detail by Southern blot analysis has all the polymorphisms characteristic of the transfected type 1 cosmid DNA and none characteristic of the type 2 P3HR-1 EBV DNA. This recombinant was wild type in primary B-lymphocyte infection, growth transformation, and lytic replication. Overall, the type 1 EBNA 3A gene was incorporated into 26% of the transformation marker-rescued recombinants, a frequency which was considerably higher than that observed in previous experiments with two-cosmid EBV DNA cotransfections into P3HR-1 cells (B. Tomkinson and E. Kieff, J. Virol. 66:780-789, 1992). Of the recombinants which had incorporated the marker-rescuing cosmid DNA fragment and the fragment encoding the type 1 EBNA 3A gene, most had incorporated markers from at least two other transfected cosmid DNA fragments, indicating a propensity for multiple homologous recombinations. The frequency of incorporation of the nonselected transfected type 1 EBNA 3C gene, which is near the end of two of the transfected cosmids, was 26% overall, versus 3% in previous experiments using transfections with two EBV DNA cosmids. In contrast, the frequency of incorporation of a 12-kb EBV DNA deletion which was near the end of two of the transfected cosmids was only 13%.(ABSTRACT TRUNCATED AT 400 WORDS)

Expression of angiotensin II receptors in the caprine ovary and improvement of follicular viability in vitro.

PubMed

Bruno, J B; Lima-Verde, I B; Celestino, J J H; Lima, L F; Matos, M H T; Faustino, L R; Donato, M A M; Peixoto, C A; Campello, C C; Silva, J R V; Figueiredo, J R

2016-08-01

This study aimed to evaluate mRNA levels of angiotensin II (ANG II) receptors (AGTR1 and AGTR2) in caprine follicles and to investigate the influence of ANG II on the viability and in vitro growth of preantral follicles. Real-time polymerase chain reaction (PCR) was used to quantify AGTR1 and AGTR2 mRNA levels in the different follicular stages. For culture, caprine ovaries were collected, cut into 13 fragments and then either directly fixed for histological and ultrastructural analysis (fresh control) or placed in culture for 1 or 7 days in α-minumum essential medium plus (α-MEM+) with 0, 1, 5, 10, 50 or 100 ng/ml ANG II. Then, the fragments were destined to morphological, viability and ultrastructural analysis. The results showed that primordial follicles had higher levels of AGTR1 and AGTR2 mRNA than secondary follicles. Granulosa/theca cells from antral follicles had higher levels of AGTR1 mRNA than their respective cumulus-oocyte complex (COCs). After 7 days of culture, ANG II (10 or 50 ng/ml) maintained the percentages of normal follicles compared with α-MEM+. Fluorescence and ultrastructural microscopy confirmed follicular integrity in ANG II (10 ng/ml). In conclusion, a high expression of AGTR1 and AGTR2 is observed in primordial follicles. Granulosa/theca cells from antral follicles had higher levels of AGTR1 mRNA. Finally, 10 ng/ml ANG II maintained the viability of caprine preantral follicles after in vitro culture.

Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in beta-turns.

PubMed

Rotondi, Kenneth S; Gierasch, Lila M

2003-01-01

We have recently shown that two of the beta-turns (III and IV) in the ten-stranded, beta-clam protein, cellular retinoic acid-binding protein I (CRABP I), are favored in short peptide fragments, arguing that they are encoded by local interactions (K. S. Rotondi and L. M. Gierasch, Biochemistry, 2003, Vol. 42, pp. 7976-7985). In this paper we examine these turns in greater detail to dissect the specific local interactions responsible for their observed native conformational biases. Conformations of peptides corresponding to the turn III and IV fragments were examined under conditions designed to selectively disrupt stabilizing interactions, using pH variation, chaotrope addition, or mutagenesis to probe specific side-chain influences. We find that steric constraints imposed by excluded volume effects between near neighbor residues (i,i+2), favorable polar (i,i+2) interactions, and steric permissiveness of glycines are the principal factors accounting for the observed native bias in these turns. Longer-range stabilizing interactions across the beta-turns do not appear to play a significant role in turn stability in these short peptides, in contrast to their importance in hairpins. Additionally, our data add to a growing number of examples of the 3:5 type I turn with a beta-bulge as a class of turns with high propensity to form locally defined structure. Current work is directed at the interplay between the local sequence information in the turns and more long-range influences in the mechanism of folding of this predominantly beta-sheet protein. Copyright 2004 Wiley Periodicals, Inc.

Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A

PubMed Central

Shea, Joan-Emma; Onuchic, José N.; Brooks, Charles L.

1999-01-01

Topological frustration in an energetically unfrustrated off-lattice model of the helical protein fragment B of protein A from Staphylococcus aureus was investigated. This Gō-type model exhibited thermodynamic and kinetic signatures of a well-designed two-state folder with concurrent collapse and folding transitions and single exponential kinetics at the transition temperature. Topological frustration is determined in the absence of energetic frustration by the distribution of Fersht φ values. Topologically unfrustrated systems present a unimodal distribution sharply peaked at intermediate φ, whereas highly frustrated systems display a bimodal distribution peaked at low and high φ values. The distribution of φ values in protein A was determined both thermodynamically and kinetically. Both methods yielded a unimodal distribution centered at φ = 0.3 with tails extending to low and high φ values, indicating the presence of a small amount of topological frustration. The contacts with high φ values were located in the turn regions between helices I and II and II and III, intimating that these hairpins are in large part required in the transition state. Our results are in good agreement with all-atom simulations of protein A, as well as lattice simulations of a three- letter code 27-mer (which can be compared with a 60-residue helical protein). The relatively broad unimodal distribution of φ values obtained from the all-atom simulations and that from the minimalist model for the same native fold suggest that the structure of the transition state ensemble is determined mostly by the protein topology and not energetic frustration. PMID:10535953

Angiotensin converting enzyme DD genotype is associated with development of rheumatic heart disease in Egyptian children.

PubMed

Morsy, Mohamed-Mofeed Fawaz; Abdelaziz, Nada Abdelmohsen Mohamed; Boghdady, Ahmed Mohamed; Ahmed, Hydi; Abu Elfadl, Essam Mohamed; Ismail, Mohamed Ali

2011-01-01

Angiotensin converting enzyme (ACE) gene polymorphism was previously studied in some cardiovascular diseases. There are only few studies which investigated this polymorphism in patients with rheumatic heart disease (RHD). The results of these investigations are inconsistent. Furthermore, gene polymorphism distribution is different in various ethnic populations. We conducted this study to demonstrate this gene polymorphism in Egyptian children with RHD. Leukocytes DNA was extracted from 139 patients with RHD and 79 healthy control children. After amplification by the PCR, the products were separated by electrophoresis in 6% polyacrylamide gel and visualized after ethidium bromide staining with UV light. The PCR product is a 190-bp fragment in the absence of the insertion (D allele) and a 490-bp fragment in the presence of the insertion (I allele). Gene polymorphism was as follows: DD gene when lane contains only 190-bp fragment, II gene when lane contains only 490-bp fragment and ID gene when lane contains both fragments. We found that gene polymorphism in both control and patients groups followed the following order of distribution from highest to lowest: ID, II, DD gene. The frequency in control group was 49.4, 36.7, and 13.9%, respectively. In patients groups, the gene frequency was 42.5, 30.9, and 26.6%, respectively. DD gene frequency differs significantly between the two groups. We concluded that patients with RHD have a higher ACE-DD genotype than normal control. ACE-DD genotype may be a risk factor for RHD in Egyptian children.

Macroalgal Composition Determines the Structure of Benthic Assemblages Colonizing Fragmented Habitats.

PubMed

Matias, Miguel G; Arenas, Francisco; Rubal, Marcos; Pinto, Isabel S

2015-01-01

Understanding the consequences of fragmentation of coastal habitats is an important topic of discussion in marine ecology. Research on the effects of fragmentation has revealed complex and context-dependent biotic responses, which prevent generalizations across different habitats or study organisms. The effects of fragmentation in marine environments have been rarely investigated across heterogeneous habitats, since most studies have focused on a single type of habitat or patch. In this study, we assessed the effects of different levels of fragmentation (i.e. decreasing size of patches without overall habitat loss). We measured these effects using assemblages of macro-invertebrates colonizing representative morphological groups of intertidal macroalgae (e.g. encrusting, turf and canopy-forming algae). For this purpose, we constructed artificial assemblages with different combinations of morphological groups and increasing levels of fragmentation by manipulating the amount of bare rock or the spatial arrangement of different species in mixed assemblages. In general, our results showed that 1) fragmentation did not significantly affect the assemblages of macroinvertebrates; 2) at greater levels of fragmentation, there were greater numbers of species in mixed algal assemblages, suggesting that higher habitat complexity promotes species colonization. Our results suggest that predicting the consequences of fragmentation in heterogeneous habitats is dependent on the type and diversity of morphological groups making up those habitats.

Macroalgal Composition Determines the Structure of Benthic Assemblages Colonizing Fragmented Habitats

PubMed Central

Matias, Miguel G.; Arenas, Francisco; Rubal, Marcos; Pinto, Isabel S.

2015-01-01

Understanding the consequences of fragmentation of coastal habitats is an important topic of discussion in marine ecology. Research on the effects of fragmentation has revealed complex and context-dependent biotic responses, which prevent generalizations across different habitats or study organisms. The effects of fragmentation in marine environments have been rarely investigated across heterogeneous habitats, since most studies have focused on a single type of habitat or patch. In this study, we assessed the effects of different levels of fragmentation (i.e. decreasing size of patches without overall habitat loss). We measured these effects using assemblages of macro-invertebrates colonizing representative morphological groups of intertidal macroalgae (e.g. encrusting, turf and canopy-forming algae). For this purpose, we constructed artificial assemblages with different combinations of morphological groups and increasing levels of fragmentation by manipulating the amount of bare rock or the spatial arrangement of different species in mixed assemblages. In general, our results showed that 1) fragmentation did not significantly affect the assemblages of macroinvertebrates; 2) at greater levels of fragmentation, there were greater numbers of species in mixed algal assemblages, suggesting that higher habitat complexity promotes species colonization. Our results suggest that predicting the consequences of fragmentation in heterogeneous habitats is dependent on the type and diversity of morphological groups making up those habitats. PMID:26554924

Tropical forest fragmentation affects floral visitors but not the structure of individual-based palm-pollinator networks.

PubMed

Dáttilo, Wesley; Aguirre, Armando; Quesada, Mauricio; Dirzo, Rodolfo

2015-01-01

Despite increasing knowledge about the effects of habitat loss on pollinators in natural landscapes, information is very limited regarding the underlying mechanisms of forest fragmentation affecting plant-pollinator interactions in such landscapes. Here, we used a network approach to describe the effects of forest fragmentation on the patterns of interactions involving the understory dominant palm Astrocaryum mexicanum (Arecaceae) and its floral visitors (including both effective and non-effective pollinators) at the individual level in a Mexican tropical rainforest landscape. Specifically, we asked: (i) Does fragment size affect the structure of individual-based plant-pollinator networks? (ii) Does the core of highly interacting visitor species change along the fragmentation size gradient? (iii) Does forest fragment size influence the abundance of effective pollinators of A. mexicanum? We found that fragment size did not affect the topological structure of the individual-based palm-pollinator network. Furthermore, while the composition of peripheral non-effective pollinators changed depending on fragment size, effective core generalist species of pollinators remained stable. We also observed that both abundance and variance of effective pollinators of male and female flowers of A. mexicanum increased with forest fragment size. These findings indicate that the presence of effective pollinators in the core of all forest fragments could keep the network structure stable along the gradient of forest fragmentation. In addition, pollination of A. mexicanum could be more effective in larger fragments, since the greater abundance of pollinators in these fragments may increase the amount of pollen and diversity of pollen donors between flowers of individual plants. Given the prevalence of fragmentation in tropical ecosystems, our results indicate that the current patterns of land use will have consequences on the underlying mechanisms of pollination in remnant forests.

Mumps Hoshino and Torii vaccine strains were distinguished from circulating wild strains.

PubMed

Sawada, Akihito; Yamaji, Yoshiaki; Nakayama, Tetsuo

2013-06-01

Aseptic meningitis and acute parotitis have been observed after mumps vaccination. Mumps outbreaks have been reported in Japan because of low vaccine coverage, and molecular differentiation is required to determine whether these cases are vaccine associated. RT-nested PCR was performed in the small hydrophobic gene region, and viruses were differentiated by restriction fragment length polymorphism assay. A total of 584 nucleotides were amplified. The PCR product of the Hoshino strain was cut into two fragments (313 and 271 nucleotides) by MfeI; that of the Torii strain was digested with EcoT22I, resulting in 332- and 252-nucleotide fragments. Both strains were genotype B and had an XbaI site, resulting in two fragments: 299 and 285 nucleotides. Current circulating wild types were cut only by XbaI or MfeI. However, the MfeI site of the wild types was different from that of the Hoshino strain, resulting in 451- and 133-nucleotide fragments. Using three restriction enzymes, two mumps vaccine strains were distinguished from wild types, and this separation was applied to the identification of vaccine-related adverse events.

1,2,3-Triazole-Heme Interactions in Cytochrome P450: Functionally Competent Triazole-Water- Heme Complexes

PubMed Central

Conner, Kip P.; Vennam, Preethi; Woods, Caleb M.; Krzyaniak, Matthew D.; Bowman, Michael K.; Atkins, William M.

2012-01-01

In comparison to imidazole (IMZ) and 1,2,4-triazole (1,2,4-TRZ) the isosteric 1,2,3-triazole (1,2,3-TRZ) is unrepresented among CYP inhibitors. This is surprising because 1,2,3-TRZs are easily obtained via ‘click’ chemistry. To understand this underrepresentation of 1,2,3-TRZs among CYP inhibitors, thermodynamic and DFT computational studies were performed with unsusbstituted IMZ, 1,2,4-TRZ, and 1,2,3-TRZ. The results indicate that the lower affinity of 1,2,3-TRZ for the heme iron includes a large unfavorable entropy term likely originating in solvent – 1,2,3-TRZ interactions; the difference is not solely due to differences in the enthalpy of heme – ligand interactions. In addition, the 1,2,3-TRZ fragment was incorporated into a well-established CYP3A4 substrate and mechanism based inactivator, 17-α-ethynylestradiol (17EE), via click chemistry. This derivative, 17-click, yielded optical spectra consistent with low spin ferric heme iron (type II) in contrast to 17EE, which yields a high spin complex (type I). Furthermore, the rate of CYP3A4-mediated metabolism of 17-click was comparable to 17EE, and with different regioselectivity. Surprisingly, CW EPR and HYSCORE EPR spectroscopy indicate that the 17-click does not displace water from the 6th axial ligand position of CYP3A4 as expected for a type II ligand. We propose a binding model where 17-click pendant 1,2,3-TRZ hydrogen bonds with the 6th axial water ligand. The results demonstrate the potential for 1,2,3-TRZ to form metabolically labile water-bridged low spin heme complexes, consistent with recent evidence that nitrogenous type II ligands of CYPs can be efficiently metabolized. The specific case of [CYP3A4•17-click] highlights the risk of interpreting CYP-ligand complex structure on the basis of optical spectra. PMID:22809252

The CRISPR-Cas system - from bacterial immunity to genome engineering.

PubMed

Czarnek, Maria; Bereta, Joanna

2016-09-01

Precise and efficient genome modifications present a great value in attempts to comprehend the roles of particular genes and other genetic elements in biological processes as well as in various pathologies. In recent years novel methods of genome modification known as genome editing, which utilize so called "programmable" nucleases, came into use. A true revolution in genome editing has been brought about by the introduction of the CRISP-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) system, in which one of such nucleases, i.e. Cas9, plays a major role. This system is based on the elements of the bacterial and archaeal mechanism responsible for acquired immunity against phage infections and transfer of foreign genetic material. Microorganisms incorporate fragments of foreign DNA into CRISPR loci present in their genomes, which enables fast recognition and elimination of future infections. There are several types of CRISPR-Cas systems among prokaryotes but only elements of CRISPR type II are employed in genome engineering. CRISPR-Cas type II utilizes small RNA molecules (crRNA and tracrRNA) to precisely direct the effector nuclease - Cas9 - to a specific site in the genome, i.e. to the sequence complementary to crRNA. Cas9 may be used to: (i) introduce stable changes into genomes e.g. in the process of generation of knock-out and knock-in animals and cell lines, (ii) activate or silence the expression of a gene of interest, and (iii) visualize specific sites in genomes of living cells. The CRISPR-Cas-based tools have been successfully employed for generation of animal and cell models of a number of diseases, e.g. specific types of cancer. In the future, the genome editing by programmable nucleases may find wide application in medicine e.g. in the therapies of certain diseases of genetic origin and in the therapy of HIV-infected patients.

Dimeric MHC-peptides inserted into an immunoglobulin scaffold as new immunotherapeutic agents

PubMed Central

Goldberg, Burt; Bona, Constantin

2011-01-01

Abstract The interactions of the T cell receptor (TCR) with cognate MHC-peptide and co-stimulatory molecules expressed at surface of antigen presenting cells (APC) leads to activation or tolerance of T cells. The development of molecular biological tools allowed for the preparation of soluble MHC-peptide molecules as surrogate for the APC. A decade ago a monomeric class II MHC molecule in which the peptide was covalently linked to β-chain of class II molecule was generated. This type of molecule had a low-binding affinity and did not cause the multimerization of TCR. The requirement of multimerization of TCR led to development of a new class of reagents, chimeric peptides covalently linked to MHC that was dimerized via Fc fragment of an immunoglobulin and linked to 3′ end of the β-chain of MHC class II molecule. These soluble dimerized MHC-peptide chimeric molecules display high affinity for the TCR and caused multimerization of TCR without processing by an APC. Because dimeric molecules are devoid of co-stimulatory molecules interacting with CD28, a second signal, they induce anergy rather the activation of T cells. In this review, we compare the human and murine dimerized MHC class II-peptides and their effect on CD4+ T cells, particularly the generation of T regulatory cells, which make these chimeric molecules an appealing approach for the treatment of autoimmune diseases. PMID:21435177

Isolation and expression of recombinant antibody fragments to the biological warfare pathogen Brucella melitensis.

PubMed

Hayhurst, Andrew; Happe, Scott; Mabry, Robert; Koch, Zephyr; Iverson, Brent L; Georgiou, George

2003-05-01

Brucella melitensis is a highly infectious animal pathogen able to cause a recurring debilitating disease in humans and is therefore high on the list of biological warfare agents. Immunoglobulin genes from mice immunized with gamma-irradiated B. melitensis strain 16M were used to construct a library that was screened by phage display against similarly prepared bacteria. The selected phage particles afforded a strong enzyme-linked immunosorbent assay (ELISA) signal against gamma-irradiated B. melitensis cells. However, extensive efforts to express the respective single chain antibody variable region fragment (scFv) in soluble form failed due to: (i) poor solubility and (ii) in vivo degradation of the c-myc tag used for the detection of the recombinant antibodies. Both problems could be addressed by: (i) fusing a human kappa light chain constant domain (Ck) chain to the scFv to generate single chain antibody fragment (scAb) antibody fragments and (ii) by co-expression of the periplasmic chaperone Skp. While soluble, functional antibodies could be produced in this manner, phage-displaying scFvs or scAbs were still found to be superior ELISA reagents for immunoassays, due to the large signal amplification afforded by anti-phage antibodies. The isolated phage antibodies were shown to be highly specific to B. melitensis and did not recognize Yersinia pseudotuberculosis in contrast to the existing diagnostic monoclonal YST 9.2.1.

Molecular Determination of Fasciola Spp. Isolates from Domestic Ruminants Fecal Samples in the Northwest of Iran

PubMed Central

IMANI BARAN, Abbas; CHERAGHI SARAY, Habib; KATIRAEE, Farzad

2017-01-01

Background: Fasciola species are the main causes for fascioliasis with great financial losses and are among the most important food/water-borne parasites worldwide. The basic proceedings such as epidemiology and effective control of fascioliasis rely mainly on precise identification of Fasciola species. The present study was conducted to determine the Fasciola species in ruminant fecal samples from East Azerbaijan Province in Iran. Methods: Overall, 2012 fecal samples were collected and processed initially for microscopic examination of Fasciola eggs in 2014–15. Then, recovered eggs were subjected to molecular identification. A fragment of 618 bp of the 28S rRNA gene pertaining to Fasciola genus was amplified under PCR. The amplified fragment was restricted by fast digest Ava II enzyme in order to a Restriction Fragment Length Polymorphism. Results: Based on microscopic examination, 72 samples were infected, from which, 10 and 62 cases pertained to cattle and sheep samples respectively. Based on RFLP, the PCR products restricted by the Ava II restriction enzyme produced 529 bp fragments only. According to the positive controls, all restriction patterns were related to Fasciola hepatica, while no restriction patterns were linked to F. gigantica. Conclusion: Based on PCR-RFLP, F. hepatica was dominant species in animals of the studied areas and no evidence of F. gigantica was observed. Therefore, further field studies to verify these results are suggested. PMID:28761485

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D.

2016-04-01

Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

Richness and Abundance of Ichneumonidae in a Fragmented Tropical Rain Forest.

PubMed

Ruiz-Guerra, B; Hanson, P; Guevara, R; Dirzo, R

2013-10-01

Because of the magnitude of land use currently occurring in tropical regions, the local loss of animal species due to habitat fragmentation has been widely studied, particularly in the case of vertebrates. Many invertebrate groups and the ichneumonid wasps in particular, however, have been poorly studied in this context, despite the fact that they are one of the most species-rich groups and play an important role as regulators of other insect populations. Here, we recorded the taxonomic composition of ichneumonid parasitoids and assessed their species richness, abundance, similarity, and dominance in the Los Tuxtlas tropical rain forest, Mexico. We compared two forest types: a continuous forest (640 ha) and a forest fragment (19 ha). We sampled ichneumonids using four malaise traps in both forest types during the dry (September-October) and rainy (March-April) seasons. A total of 104 individuals of Ichneumonidae belonging to 11 subfamilies, 18 genera, and 42 species were collected in the continuous forest and 11 subfamilies, 15 genera, and 24 species were collected in the forest fragment. Species richness, abundance, and diversity of ichneumonids were greater in the continuous forest than in the forest fragment. We did not detect differences between seasons. Species rank/abundance curves showed that the ichneumonid community between the forest types was different. Species similarity between forest types was low. The most dominant species in continuous forest was Neotheronia sp., whereas in the forest fragment, it was Orthocentrus sp. Changes in the ichneumonid wasp community may compromise important tropical ecosystem processes.

Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans.

PubMed

Harvey, David J; Watanabe, Yasunori; Allen, Joel D; Rudd, Pauline; Pagel, Kevin; Crispin, Max; Struwe, Weston B

2018-06-01

Ion mobility mass spectrometry (IM-MS) holds great potential for structural glycobiology, in particular in its ability to resolve glycan isomers. Generally, IM-MS has largely been applied to intact glycoconjugate ions with reports focusing on the separation of different adduct types. Here, we explore IM separation and report the collision cross section (CCS) of complex type N-glycans and their fragments in negative ion mode following collision-induced dissociation (CID). CCSs of isomeric fragment ions were found, in some cases, to reveal structural details that were not present in CID spectra themselves. Many fragment ions were confirmed as possessing multiple structure, details of which could be obtained by comparing their drift time profiles to different glycans. By using fragmentation both before and after mobility separation, information was gathered on the fragmentation pathways producing some of the ions. These results help demonstrate the utility of IM and will contribute to the growing use of IM-MS for glycomics. Graphical Abstract ᅟ.

Collision Cross Sections and Ion Mobility Separation of Fragment Ions from Complex N-Glycans

NASA Astrophysics Data System (ADS)

Harvey, David J.; Watanabe, Yasunori; Allen, Joel D.; Rudd, Pauline; Pagel, Kevin; Crispin, Max; Struwe, Weston B.

2018-04-01

Ion mobility mass spectrometry (IM-MS) holds great potential for structural glycobiology, in particular in its ability to resolve glycan isomers. Generally, IM-MS has largely been applied to intact glycoconjugate ions with reports focusing on the separation of different adduct types. Here, we explore IM separation and report the collision cross section (CCS) of complex type N-glycans and their fragments in negative ion mode following collision-induced dissociation (CID). CCSs of isomeric fragment ions were found, in some cases, to reveal structural details that were not present in CID spectra themselves. Many fragment ions were confirmed as possessing multiple structure, details of which could be obtained by comparing their drift time profiles to different glycans. By using fragmentation both before and after mobility separation, information was gathered on the fragmentation pathways producing some of the ions. These results help demonstrate the utility of IM and will contribute to the growing use of IM-MS for glycomics. [Figure not available: see fulltext.

Production of haemolysins by strains of the Actinobacillus minor/"porcitonsillarum" complex.

PubMed

Arya, Gitanjali; Niven, Donald F

2010-03-24

Actinobacillus minor and "Actinobacillus porcitonsillarum" are distinguished by their haemolytic activities, the latter organism being haemolytic and the former, non-haemolytic. Analysis of a whole genome shotgun sequence, however, revealed that A. minor strain 202, like "A. porcitonsillarum", possesses a haemolysin-encoding apxII operon. The purpose of this study was therefore to investigate haemolysin production by this organism and also by three additional members of the A. minor/"porcitonsillarum" complex, strains 33PN and 7ATS and A. minor strain NM305(T). Primers based on sequences within the apxII genes of strain 202 allowed the amplification of appropriately sized fragments from DNA from strain 33PN suggesting that this organism also possesses an apxII operon. Analysis of a whole genome shotgun sequence failed to reveal any trace of an apxII operon in strain NM305(T) and attempts to amplify apxII genes from DNA from strain 7ATS also failed. Strains 202 and 33PN, and surprisingly, the type strain of A. minor and strain 7ATS, were all found to be haemolysin-positive as growth media from cultures of these organisms could promote the lysis of erythrocytes in suspension. The erythrocyte specificities of the haemolysins produced by strains 202 and 33PN indicated that the haemolytic activities exhibited by these organisms were due to ApxII. In keeping with the apparent lack of apxII genes in strains NM305(T) and 7ATS, the haemolysins produced by these organisms were not erythrocyte-specific and with both organisms, haemolytic activity appeared to be due to a combination of heat-stable and heat-labile components. The identities of these components, however, remain unknown. Copyright 2009 Elsevier B.V. All rights reserved.

Excessive Cytosolic DNA Fragments as a Potential Trigger of Graves’ Disease: An Encrypted Message Sent by Animal Models

PubMed Central

Luo, Yuqian; Yoshihara, Aya; Oda, Kenzaburo; Ishido, Yuko; Suzuki, Koichi

2016-01-01

Graves’ hyperthyroidism is caused by autoantibodies directed against the thyroid-stimulating hormone receptor (TSHR) that mimic the action of TSH. The establishment of Graves’ hyperthyroidism in experimental animals has proven to be an important approach to dissect the mechanisms of self-tolerance breakdown that lead to the production of thyroid-stimulating TSHR autoantibodies (TSAbs). “Shimojo’s model” was the first successful Graves’ animal model, wherein immunization with fibroblasts cells expressing TSHR and a major histocompatibility complex (MHC) class II molecule, but not either alone, induced TSAb production in AKR/N (H-2k) mice. This model highlights the importance of coincident MHC class II expression on TSHR-expressing cells in the development of Graves’ hyperthyroidism. These data are also in agreement with the observation that Graves’ thyrocytes often aberrantly express MHC class II antigens via mechanisms that remain unclear. Our group demonstrated that cytosolic self-genomic DNA fragments derived from sterile injured cells can induce aberrant MHC class II expression and production of multiple inflammatory cytokines and chemokines in thyrocytes in vitro, suggesting that severe cell injury may initiate immune responses in a way that is relevant to thyroid autoimmunity mediated by cytosolic DNA signaling. Furthermore, more recent successful Graves’ animal models were primarily established by immunizing mice with TSHR-expressing plasmids or adenovirus. In these models, double-stranded DNA vaccine contents presumably exert similar immune-activating effect in cells at inoculation sites and thus might pave the way toward successful Graves’ animal models. This review focuses on evidence suggesting that cell injury-derived self-DNA fragments could act as Graves’ disease triggers. PMID:27895620

Effects of patch size and type of coffee matrix on ithomiine butterfly diversity and dispersal in cloud-forest fragments.

PubMed

Muriel, Sandra B; Kattan, Gustavo H

2009-08-01

Determining the permeability of different types of landscape matrices to animal movement is essential for conserving populations in fragmented landscapes. We evaluated the effects of habitat patch size and matrix type on diversity, isolation, and dispersal of ithomiine butterflies in forest fragments surrounded by coffee agroecosystems in the Colombian Andes. Because ithomiines prefer a shaded understory, we expected the highest diversity and abundance in large fragments surrounded by shade coffee and the lowest in small fragments surrounded by sun coffee. We also thought shade coffee would favor butterfly dispersal and immigration into forest patches. We marked 9675 butterflies of 39 species in 12 forest patches over a year. Microclimate conditions were more similar to the forest interior in the shade-coffee matrix than in the sun-coffee matrix, but patch size and matrix type did not affect species richness and abundance in forest fragments. Furthermore, age structure and temporal recruitment patterns of the butterfly community were similar in all fragments, independent of patch size or matrix type. There were no differences in the numbers of butterflies flying in the matrices at two distances from the forest patch, but their behavior differed. Flight in the sun-coffee matrix was rapid and directional, whereas butterflies in shade-coffee matrix flew slowly. Seven out of 130 recaptured butterflies immigrated into patches in the shade-coffee matrix, and one immigrated into a patch surrounded by sun coffee. Although the shade-coffee matrix facilitated movement in the landscape, sun-coffee matrix was not impermeable to butterflies. Ithomiines exhibited behavioral plasticity in habitat use and high mobility. These traits favor their persistence in heterogeneous landscapes, opening opportunities for their conservation. Understanding the dynamics and resource requirements of different organisms in rural landscapes is critical for identifying management options that address both animals' and farmers' needs.

Antibody Fragments as Potential Biopharmaceuticals for Cancer Therapy: Success and Limitations.

PubMed

Kholodenko, Roman V; Kalinovsky, Daniel V; Doronin, Igor I; Ponomarev, Eugene D; Kholodenko, Irina V

2017-08-17

Monoclonal antibodies (mAbs) are an important class of therapeutic agents approved for the therapy of many types of malignancies. However, in certain cases applications of conventional mAbs have several limitations in anticancer immunotherapy. These limitations include insufficient efficacy and adverse effects. The antigen-binding fragments of antibodies have a considerable potential to overcome the disadvantages of conventional mAbs, such as poor penetration into solid tumors and Fc-mediated bystander activation of the immune system. Fragments of antibodies retain antigen specificity and part of functional properties of conventional mAbs and at the same time have much better penetration into the tumors and a greatly reduced level of adverse effects. Recent advantages in antibody engineering allowed to produce different types of antibody fragments with improved structure and properties for efficient elimination of tumor cells. These molecules opened up new perspectives for anticancer therapy. Here we will overview the structural features of the various types of antibody fragments and their applications for anticancer therapy as separate molecules and as part of complex conjugates or structures. Mechanisms of antitumor action of antibody fragments as well as their advantages and disadvantages for clinical application will be discussed in this review. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants.

PubMed

Stępniewska, Zofia; Goraj, Weronika; Kuźniar, Agnieszka; Łopacka, Natalia; Małysza, Magdalena

2017-09-01

Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland). Methanotrophic bacteria were isolated from plants by adding sterile fragments of different parts of plants (roots and stems) to agar mineral medium (nitrate mineral salts (NMS)) and incubated at different methane values (1-20% CH4). Single colonies were streaked on new NMS agar media and, after incubation, transferred to liquid NMS medium. Bacterial growth dynamics in the culture solution was studied by optical density-OD600 and methane consumption. Changes in the methane concentration during incubation were controlled by the gas chromatography technique. Characterization of methanotrophs was made by fluorescence in situ hybridization (FISH) with Mg705 and Mg84 for type I methanotrophs and Ma450 for type II methanotrophs. Identification of endophytes was performed after 16S ribosomal RNA (rRNA) and mmoX gene amplification. Our study confirmed the presence of both types of methanotrophic bacteria (types I and II) with the predominance of type I methanotrophs. Among cultivable methanotrophs, there were different strains of the genus Methylomonas and Methylosinus. Furthermore, we determined the potential of the examined bacteria for methane oxidation, which ranged from 0.463 ± 0.067 to 5.928 ± 0.169 μmol/L CH4/mL/day.

Recognition and characterization of hierarchical interstellar structure. II - Structure tree statistics

NASA Technical Reports Server (NTRS)

Houlahan, Padraig; Scalo, John

1992-01-01

A new method of image analysis is described, in which images partitioned into 'clouds' are represented by simplified skeleton images, called structure trees, that preserve the spatial relations of the component clouds while disregarding information concerning their sizes and shapes. The method can be used to discriminate between images of projected hierarchical (multiply nested) and random three-dimensional simulated collections of clouds constructed on the basis of observed interstellar properties, and even intermediate systems formed by combining random and hierarchical simulations. For a given structure type, the method can distinguish between different subclasses of models with different parameters and reliably estimate their hierarchical parameters: average number of children per parent, scale reduction factor per level of hierarchy, density contrast, and number of resolved levels. An application to a column density image of the Taurus complex constructed from IRAS data is given. Moderately strong evidence for a hierarchical structural component is found, and parameters of the hierarchy, as well as the average volume filling factor and mass efficiency of fragmentation per level of hierarchy, are estimated. The existence of nested structure contradicts models in which large molecular clouds are supposed to fragment, in a single stage, into roughly stellar-mass cores.

Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

PubMed Central

Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

2009-01-01

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

Fragment-based screening of the bromodomain of ATAD2

DOE PAGES

Harner, Mary J.; Chauder, Brian A.; Phan, Jason; ...

2014-10-14

Cellular and genetic evidence suggest that inhibition of ATAD2 could be a useful strategy to treat several types of cancer. To discover small-molecule inhibitors of the bromodomain of ATAD2, we used a fragment-based approach. As a result, fragment hits were identified using NMR spectroscopy, and ATAD2 was crystallized with three of the hits identified in the fragment screen.

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.

PubMed

Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

2016-07-01

Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment. Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality. Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/ It is bundled with a manual and example data. chengji@missouri.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Lithologic distribution and geologic history of the Apollo 17 site: The record in soils and small rock particles from the highland massifs

NASA Astrophysics Data System (ADS)

Jolliff, Bradley L.; Rockow, Kaylynn M.; Korotev, Randy L.; Haskin, Larry A.

1996-01-01

Through analysis by instrumental neutron activation (INAA) of 789 individual lithic fragments from the 2 mm-4 mm grain-size fractions of five Apollo 17 soil samples (72443, 72503, 73243, 76283, and 76503) and petrographic examination of a subset, we have determined the diversity and proportions of rock types recorded within soils from the highland massifs. The distribution of rock types at the site, as recorded by lithic fragments in the soils, is an alternative to the distribution inferred from the limited number of large rock samples. The compositions and proportions of 2 mm-4 mm fragments provide a bridge between compositions of <1 mm fines, and types and proportions of rocks observed in large collected breccias and their clasts. The 2 mm-4 mm fraction of soil from South Massif, represented by an unbiased set of lithic fragments from station-2 samples 72443 and 72503, consists of 71% noritic impact-melt breccia, 7% incompatible-trace-element-(ITE)-poor highland rock types (mainly granulitic breccias), 19% agglutinates and regolith breccias, 1% high-Ti mare basalt, and 2% others (very-low-Ti (VLT) basalt, monzogabbro breccia, and metal). In contrast, the 2 mm-4 mm fraction of a soil from the North Massif, represented by an unbiased set of lithic fragments from station-6 sample 76503, has a greater proportion of ITE-poor highland rock types and mare-basalt fragments: it consists of 29% ITE-poor highland rock types (mainly granulitic breccias and troctolitic anorthosite), 25% impact-melt breccia, 13% high-Ti mare basalt, 31% agglutinates and regolith breccias, 1% orange glass and related breccia, and 1% others. Based on a comparison of mass-weighted mean compositions of the lithic fragments with compositions of soil fines from all Apollo 17 highland stations, differences between the station-2 and station-6 samples are representative of differences between available samples from the two massifs. From the distribution of different rock types and their compositions, we conclude the following: (1) North-Massif and South-Massif soil samples differ significantly in types and proportions of ITE-poor highland components and ITE-rich impact-melt-breccia components. These differences reflect crudely layered massifs and known local geology. The greater percentage of impact-melt breccia in the South-Massif light-mantle soil stems from derivation of the light mantle from the top of the massif, which apparently is richer in noritic impact-melt breccia than are lower parts of the massifs. (2) At station 2, the 2 mm-4 mm grain-size fraction is enriched in impact-melt breccias compared to the <1 mm fraction, suggesting that the <1 mm fraction within the light mantle has a greater proportion of lithologies such as granulitic breccias which are more prevalent lower in the massifs and which we infer to be older (pre-basin) highland components. (3) Soil from station 6, North Massif, contains magnesian troctolitic anorthosite, which is a component that is rare in station-2 South-Massif soils. (4) Compositional differences between poikilitic impact-melt breccias from the two massifs suggest broad-scale heterogeneity in impact-melt breccia interpreted by most investigators to be ejecta from the Serenitatis basin. We have found rock types not previously recognized or uncommon at the Apollo 17 site. These include (1) ITE-rich impact-melt breccias that are compositionally distinct from previously recognized "aphanitic" and "poikilitic" groups at Apollo 17; (2) regolith breccias that are free of mare components and poor in impact melt of the types associated with the main melt-breccia groups, and that, if those groups derive from the Serenitatis impact, may represent the pre-Serenitatis surface; (3) several VLT basalts, including an unusual very-high-K basaltic breccia; (4) orange-glass regolith breccias; (5) aphanitic-matrix melt breccias at station 6; (6) fragments of alkali-rich composition, including alkali anorthosite, and monzogabbro; (7) one fragment of 72275-type KREEP basalt from station 3; (8) seven lithic fragments of ferroan-anorthositic-suite rocks; and (9) a fragment of metal, possibly from an L chondrite. Some of these lithologies have been found only as lithic fragments in the soils and not among the large rock samples. In contrast, we have not found among the 2 mm-4 mm lithic fragments individual samples of certain lithologies that have been recognized as clasts in breccias (e.g., dunite and spinel troctolite). The diversity of lithologic information contained in the lithic fragments of these soils nearly equals that found among large rock samples, and most information bearing on petrographic relationships is maintained, even in such small samples. Given a small number of large samples for "petrologic ground truth," small lithic fragments contained in soil "scoop" samples can provide the basis for interpreting the diversity of rock types and their proportions in remotely sensed geologic units. They should be considered essential targets for future automated sample-analysis and sample-return missions.

A desert of gas giant planets beyond tens of au: from feast to famine

NASA Astrophysics Data System (ADS)

Nayakshin, Sergei

2017-09-01

It is argued that frequency of gravitational fragmentation of young massive discs around FGK stars may be much higher than commonly believed. Numerical simulations presented here show that survival of gas giant planets at large separations from their host stars is very model dependent. Low-mass clumps in slowly cooling discs are found to accrete gas very slowly and migrate inward very rapidly in the well-known type I regime (no gap open). They are either tidally disrupted or survive as planets inwards of about 10 au. In this regime, probability of clump survival at large separations is extremely low, perhaps as low as 0.001, requiring up to a dozen clumps per star early on to explain the observed population. In contrast, initially massive clumps or low-mass clumps born in rapidly cooling discs accrete gas rapidly. Opening deep gaps in the disc, they migrate in the much slower type II regime and are more likely to survive beyond tens of au. The frequency of disc fragmentation in this case is at the per cent level if the clump growth saturates at brown dwarf masses but may be close to 100 per cent if clumps evolve into low stellar mass companions. Taking these theoretical uncertainties into account, current observations limit the number of planet mass clumps hatched by young massive discs around FGK stars to between 0.01 and ˜10. A deeper theoretical understanding of such discs is needed to narrow this uncertainty down.

Dulaglutide, a long-acting GLP-1 analog fused with an Fc antibody fragment for the potential treatment of type 2 diabetes.

PubMed

Jimenez-Solem, Espen; Rasmussen, Mette H; Christensen, Mikkel; Knop, Filip K

2010-12-01

Dulaglutide (LY-2189265) is a novel, long-acting glucagon-like peptide 1 (GLP-1) analog being developed by Eli Lilly for the treatment of type 2 diabetes mellitus (T2DM). Dulaglutide consists of GLP-1(7-37) covalently linked to an Fc fragment of human IgG4, thereby protecting the GLP-1 moiety from inactivation by dipeptidyl peptidase 4. In vitro and in vivo studies on T2DM models demonstrated glucose-dependent insulin secretion stimulation. Pharmacokinetic studies demonstrated a t1/2 in humans of up to 90 h, making dulaglutide an ideal candidate for once-weekly dosing. Clinical trials suggest that dulaglutide reduces plasma glucose, and has an insulinotropic effect increasing insulin and C-peptide levels. Two phase II clinical trials demonstrated a dose-dependent reduction in glycated hemoglobin (HbA1c) of up to 1.52% compared with placebo. Side effects associated with dulaglutide administration were mainly gastrointestinal. To date, there have been no reports on the formation of antibodies against dulaglutide, but, clearly, long-term data will be needed to asses this and other possible side effects. The results of several phase III clinical trials are awaited for clarification of the expected effects on HbA1c and body weight. If dulaglutide possesses similar efficacy to other GLP-1 analogs, the once-weekly treatment will most likely be welcomed by patients with T2DM.

Characterization of a major late herpes simplex virus type 1 mRNA.

PubMed

Costa, R H; Devi, B G; Anderson, K P; Gaylord, B H; Wagner, E K

1981-05-01

A major, late 6-kilobase (6-kb) mRNa mapping in the large unique region of herpes simplex virus type 1 (HSV-1) was characterized by using two recombinant DNA clones, one containing EcoRI fragment G (0.190 to 0.30 map units) in lambda. WES.B (L. Enquist, M. Madden, P. Schiop-Stansly, and G. Vandl Woude, Science 203:541-544, 1979) and one containing HindIII fragment J (0.181 to 0.259 map units) in pBR322. This 6-kb mRNA had its 3' end to the left of 0.231 on the prototypical arrangement of the HSV-1 genome and was transcribed from right to left. It was bounded on both sides by regions containing a large number of distinct mRNA species, and its 3' end was partially colinear with a 1.5-kb mRNA which encoded a 35,000-dalton polypeptide. The 6-kb mRNA encoded a 155,000-dalton polypeptide which was shown to be the only one of this size detectable by hybrid-arrested translation encoded by late polyadenylated polyribosomal RNA. The S1 nuclease mapping experiments indicated that there were no introns in the coding sequence for this mRNA and that its 3' end mapped approximately 800 nucleotides to the left of the BglII site at 0.231, whereas its 5' end extended very close to the BamHI site at 0.266.

Effect of postponed treatment with an anti-tumour necrosis factor (TNF) F(ab')2 fragment on endotoxin-induced cytokine and neutrophil responses in chimpanzees.

PubMed Central

van der Poll, T; Levi, M; ten Cate, H; Jansen, J; Biemond, B J; Haagmans, B L; Eerenberg, A; van Deventer, S J; Hack, C E; ten Cate, J W

1995-01-01

TNF is considered to be an intermediate factor in endotoxin-induced release of other cytokines and endotoxin-induced neutrophil degranulation. Little is known about the effect of postponed treatment with anti-TNF in primate endotoxin models. To assess the effect of delayed treatment with anti-TNF in endotoxaemia, six healthy adult chimpanzees were intravenously injected with Escherichia coli endotoxin (4 ng/kg). In three of these animals the administration of endotoxin was followed after 30 min by a bolus i.v. injection of the anti-TNF F(ab')2 fragment MAK 195F (0.1 mg/kg). Post-treatment with MAK 195F completely prevented the appearance of TNF activity in serum elicited by endotoxin, and markedly reduced the rises in the serum concentrations of IL-6 and IL-8. In addition, the endotoxin-induced increases in the type I and type II soluble TNF receptors were also profoundly inhibited by MAK 195F, suggesting that TNF is involved in the release of its own soluble receptors in endotoxaemia. Neutrophilic leucocytosis was not affected by MAK 195F. In contrast, MAK 195F did significantly abrogate neutrophil degranulation, as measured by the plasma concentrations of lactoferrin. These results indicate that treatment with anti-TNF 30 min after the administration of endotoxin is still effective in attenuating the induction of the cytokine network and of neutrophil degranulation. PMID:7697917

Synthesis of 4‧-substituted-2,2‧;6‧,2″-terpyridine Ru(II) complexes electrochemical, fluorescence quenching and antibacterial studies

NASA Astrophysics Data System (ADS)

Ezhilarasu, Tamilarasu; Sathiyaseelan, Anbazhagan; Kalaichelvan, Pudupalayam Thangavelu; Balasubramanian, Sengottuvelan

2017-04-01

Three new Ru(II) terpyridine complexes viz. [Ru(BBtpy)2](PF6)2 [Ru(L1)] (BBtpy = 4‧-(4-benzyloxybenzaldehyde)-2,2‧:6‧,2″-terpyridine), [Ru(BMBtpy)2](PF6)2 [Ru(L2)] (BMBtpy = 4‧-(4-benzyloxy-3-methoxybenzaldehyde)-2,2‧:6‧,2″-terpyridine) and [Ru(BEBtpy)2](PF6)2 [Ru(L3)] (BEBtpy = 4‧-(4-benzyloxy-3-ethoxybenzaldehyde)-2,2‧:6‧,2″-terpyridine) have been synthesized and characterized. The MALDI-TOF/MS fragmentation pattern of [Ru(BMBtpy)2](PF6)2 complex exhibits a molecular ion peak at m/z = 987.09 [M-2PF6]2+ fragment. These Ru(II) complexes are redox active, show both metal centered oxidation and ligand centered reduction processes. The peak potential and peak current Ipa and Ipc also undergo definite shift and increase with increase in the scan rate (20-120 mV/s). The fluorescence of Ru(II) complexes [Ru(L1)], [Ru(L2)] and [Ru(L3)] are effectively quenched by 1,4-benzoquinone and 1,4-naphthoquinone in acetonitrile. The antibacterial activity of ruthenium(II) complexes were screened against four human pathogens both gram-positive bacteria (Bacillus subtilis, Staphylococcus aureus) and gram negative bacteria (Escherichia coli, Klebsiella pneumonia) by the well diffusion method. The antibacterial activity of Ru(II) complexes is comparable to that of standard antibiotics like tetracycline.

Angiotensin II-Induced End-Organ Damage in Mice Is Attenuated by Human Exosomes and by an Exosomal Y RNA Fragment.

PubMed

Cambier, Linda; Giani, Jorge F; Liu, Weixin; Ijichi, Takeshi; Echavez, Antonio K; Valle, Jackelyn; Marbán, Eduardo

2018-06-04

Hypertension often leads to cardiovascular disease and kidney dysfunction. Exosomes secreted from cardiosphere-derived cells (CDC-exo) and their most abundant small RNA constituent, the Y RNA fragment EV-YF1, exert therapeutic benefits after myocardial infarction. Here, we investigated the effects of CDC-exo and EV-YF1, each administered individually, in a model of cardiac hypertrophy and kidney injury induced by chronic infusion of Ang (angiotensin) II. After 2 weeks of Ang II, multiple doses of CDC-exo or EV-YF1 were administered retro-orbitally. Ang II infusion induced an elevation in systolic blood pressure that was not affected by CDC-exo or EV-YF1. Echocardiography confirmed that Ang II infusion led to cardiac hypertrophy. CDC-exo and EV-YF1 both attenuated cardiac hypertrophy and reduced cardiac inflammation and fibrosis. In addition, both CDC-exo and EV-YF1 improved kidney function and diminished renal inflammation and fibrosis. The beneficial effects of CDC-exo and EV-YF1 were associated with changes in the expression of the anti-inflammatory cytokine IL (interleukin)-10 in plasma, heart, spleen, and kidney. In summary, infusions of CDC-exo or EV-YF1 attenuated cardiac hypertrophy and renal injury induced by Ang II infusion, without affecting blood pressure, in association with altered IL-10 expression. Exosomes and their defined noncoding RNA contents may represent potential new therapeutic approaches for hypertension-associated cardiovascular and renal damage. © 2018 American Heart Association, Inc.

Identification and characterization by LC-UV-MS/MS of melanotan II skin-tanning products sold illegally on the Internet.

PubMed

Breindahl, Torben; Evans-Brown, Michael; Hindersson, Peter; McVeigh, Jim; Bellis, Mark; Stensballe, Allan; Kimergård, Andreas

2015-02-01

New methods were developed and validated to determine the identity, contents, and purity of samples of melanotan II, a synthetic melanocortin receptor agonist, sold in vials as injectable skin-tanning products that were purchased from three online shops. Methods were based on liquid chromatography with ultra-violet detection (LC-UV) at wavelength 218 nm, and tandem mass spectrometric detection (MS/MS) after collision-induced fragmentation of the double charged [M+2H](2+) precursor ion (m/z 513). Identification of melanotan II was verified by correct chromatographic retention time, and relative abundance ratios of five qualifying fragment ions. LC-UV was used to quantify melanotan II as well as impurities. Method validation was performed with reference to guidelines for assessing active substances in authorized medicinal products to reach acceptable accuracy and precision. Vials from two shops contained unknown impurities ranging from 4.1 to 5.9%; impurities from one shop were below the quantification limit. The total amount of melanotan II in vials ranged between 4.32 and 8.84 mg, although each shop claimed that vials contained 10 mg melanotan II. A broad range of drugs used for enhancement purposes can be obtained from the illicit market. However, users of these drugs may be exposed to a range of potential harms, as shown in this study, given that these products are manufactured, distributed and supplied from an illicit market. Copyright © 2014 John Wiley & Sons, Ltd.

A recombinant flagellin fragment, which includes the epitopes flg22 and flgII-28, provides a useful tool to study flagellin-triggered immunity

USDA-ARS?s Scientific Manuscript database

Plants and animals both independently evolved the ability to recognize flagellin (also called FliC), the building block of the bacterial flagellum, as part of their innate immune response. Most plants recognize one or two short epitopes of FliC: flg22 and flgII-28. However, since most research in pl...

Differential compaction behaviour of roller compacted granules of clopidogrel bisulphate polymorphs.

PubMed

Khomane, Kailas S; Bansal, Arvind K

2014-09-10

In the present work, in-die and out-of-die compaction behaviour of dry-granulated powders of clopidogrel bisulphate (CLP) polymorphs, form I and form II, was investigated using a fully instrumented rotary tablet press. Each polymorph was compacted at three different roller pressures [70.3 (S1), 105.5 (S2) and 140.6 (S3)kgf/cm(2)], and obtained granules were characterized for their physico-mechanical properties. Compaction data were analyzed for out-of-die compressibility, tabletability and compactibility profiles, and in-die Heckel, Kawakita and Walker analysis. The roller compacted granules of both forms showed markedly different tabletting behaviour. Roller pressure exhibited a trend on compaction behaviour of form I granules, whereas, in case of form II, the effect was insignificant. Tabletability of the six granule batches follows the order; I_S1>I_S2>I_S3>II_S1≈II_S2≈II_S3. In case of form I, the reduced tabletability of the granules compacted at higher roller pressure was attributed to the decreased compressibility and plastic deformation. This was confirmed by compressibility plot and various mathematical parameters derived from Heckel (Py), Kawakita (1/b) and Walker (W) equations. The reduced tabletability of form I granules was due to 'granule hardening' during roller compaction. On the other hand, insignificant effect of roller compaction on tabletting behaviour of form II granules was attributed to brittle fragmentation. The extensive fragmentation of granules offered new 'clean' surfaces and higher contact points that negated the effect of granule hardening. Copyright © 2014 Elsevier B.V. All rights reserved.

Method for identifying mutagenic agents which induce large, multilocus deletions in DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bradley, W.E.C.; Belouchi, A.; Dewyse, P.

1993-07-13

A method of identifying a mutagenic agent is described which includes a large, multilocus deletions in DNA in mammalian cells comprising: (i) exposing a class III heterozygous CHO cell line to a potential mutagenic agent under investigation, and allowing any mutation of the cell line to proceed, said cell line being characterized in that a restriction fragment length variation exists in on mutation it becomes resistant to 2,6-diaminopurine and in that the DNA sequence adjacent to the two alleles of the APRT gene such that the DNA sequence adjacent to one of the two alleles can be digested with themore » enzyme BclI but the DNA sequence variation adjacent to the other of the two alleles cannot be digested with BclI, (ii) isolating induced mutations of the cell line deficient in APRT function, (iii) isolating DNA from the induced mutants, (iv) digesting the isolated DNA with BclI enzyme to produce digested fragments including a 19 kb fragment and any 2 kb fragment, which fragments hybridize with the labeled probe derived from DNA fragment PDI, (v) separating any digested fragments, (vi) transferring the separated fragments of (v) to a solid support, (vii) hybridizing the supported separated fragments with a labeled probe derived from the clone DNA fragment PD 1, (viii) determining fragments having undergone loss of the 2 kb band identified by the probe, as an identification of parent mutants in which the loss occurred, and (ix) evaluating the mutating ability of the potential mutagenic agent.« less

Association of angiotensin-converting enzyme (ACE) and fatty acid binding protein 2 (FABP2) genes polymorphism with type 2 diabetes mellitus in Northern India.

PubMed

Raza, Syed Tasleem; Fatima, Jalees; Ahmed, Faisal; Abbas, Shania; Zaidi, Zeashan Haider; Singh, Seema; Mahdi, Farzana

2014-12-01

Type 2 diabetes mellitus (T2DM) is growing in an epidemic manner across the world with an expected doubling of the incidence to millions of affected individuals in the last decades. At present, adequate data are not available regarding the ACE and FABP2 polymorphisms and their susceptibility with T2DM cases in the North Indian population. Thus we conceived the need for further study of ACE (I/D) and FABP2 (Ala54Thr) genes polymorphism and its susceptibility to T2DM in the North Indian population. In this study, a total of 300 subjects (including 190 T2DM cases and 110 controls) participated. ACE and FABP2 gene polymorphisms in the cases and controls were evaluated by polymerase chain reaction and restriction fragment length polymorphism. The frequencies of ACE I/I, I/D and D/D genotypes in T2DM cases and controls were 28.73%, 55.17%, 16.09% and 13.63%, 57.95%, 28.40%, respectively. The frequencies of FABP2 Ala54Ala, Ala54Thr and Thr54Thr in T2DM cases were 18.39%, 66.66%, 14.94% and 22.72%, 61.36%, 15.90% in controls, respectively. ACE I/I genotype was significantly more frequent in cases as compared to controls (p = 0.003, χ(2) = 9.13). It appears that the ACE I/I genotype frequency was significantly higher in the T2DM cases as compared to the controls. © The Author(s) 2013.

The Effects of Habitat Fragmentation on the Behavior of the Cotton Rat (Sigmodon hispidus):Phase II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barrett, G.W.; Drelin, E.A.; Mabry, K.E.

The authors studied the movements of cotton rats and cotton mice in experimental landscapes at the SRS in order to determine the effects of fragmentation and connectivity between habitat patches on dispersal movements and population dynamics. Densities between connected and isolated patches were not different. Small patches tended to support higher densities. Cotton rats were more common in corridors than expected and cotton mice were more likely to leave by a corridor.

Distinct oxidative cleavage and modification of bovine [Cu-Zn]-SOD by an ascorbic acid/Cu(II) system: Identification of novel copper binding site on SOD molecule

PubMed Central

Uehara, Hiroshi; Luo, Shen; Aryal, Baikuntha; Levine, Rodney L.; Rao, V. Ashutosh

2016-01-01

We investigated the combined effect of ascorbate and copper [Asc/Cu(II)] on the integrity of bovine [Cu-Zn]-superoxide dismutase (bSOD1) as a model system to study the metal catalyzed oxidation (MCO) and fragmentation of proteins. We found Asc/Cu(II) mediates specific cleavage of bSOD1 and generates 12.5 and 3.2 kDa fragments in addition to oxidation/carbonylation of the protein. The effect of other tested transition metals, a metal chelator, and hydrogen peroxide on the cleavage and oxidation indicated that binding of copper to a previously unknown site on SOD1 is responsible for the Asc/Cu(II) specific cleavage and oxidation. We utilized tandem mass spectrometry to identify the specific cleavage sites of Asc/Cu(II)-treated bSOD1. Analyses of tryptic- and AspN-peptides have demonstrated the cleavage to occur at Gly31 with peptide bond breakage with Thr30 and Ser32 through diamide and α-amidation pathways, respectively. The three-dimensional structure of bSOD1 reveals the imidazole ring of His19 localized within 5 Angstrom from the α-carbon of Gly31 providing a structural basis that copper ion, most likely coordinated by His19, catalyzes the specific cleavage reaction. PMID:26872685

Distinct oxidative cleavage and modification of bovine [Cu- Zn]-SOD by an ascorbic acid/Cu(II) system: Identification of novel copper binding site on SOD molecule.

PubMed

Uehara, Hiroshi; Luo, Shen; Aryal, Baikuntha; Levine, Rodney L; Rao, V Ashutosh

2016-05-01

We investigated the combined effect of ascorbate and copper [Asc/Cu(II)] on the integrity of bovine [Cu-Zn]-superoxide dismutase (bSOD1) as a model system to study the metal catalyzed oxidation (MCO) and fragmentation of proteins. We found Asc/Cu(II) mediates specific cleavage of bSOD1 and generates 12.5 and 3.2kDa fragments in addition to oxidation/carbonylation of the protein. The effect of other tested transition metals, a metal chelator, and hydrogen peroxide on the cleavage and oxidation indicated that binding of copper to a previously unknown site on SOD1 is responsible for the Asc/Cu(II) specific cleavage and oxidation. We utilized tandem mass spectrometry to identify the specific cleavage sites of Asc/Cu(II)-treated bSOD1. Analyses of tryptic- and AspN-peptides have demonstrated the cleavage to occur at Gly31 with peptide bond breakage with Thr30 and Ser32 through diamide and α-amidation pathways, respectively. The three-dimensional structure of bSOD1 reveals the imidazole ring of His19 localized within 5Å from the α-carbon of Gly31 providing a structural basis that copper ion, most likely coordinated by His19, catalyzes the specific cleavage reaction. Published by Elsevier Inc.

Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II.

PubMed

Barrera, Gloria Patricia; Villamizar, Laura Fernanda; Espinel, Carlos; Quintero, Edgar Mauricio; Belaich, Mariano Nicolás; Toloza, Deisy Liseth; Ghiringhelli, Pablo Daniel; Vargas, Germán

2017-01-01

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification.

Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II

PubMed Central

Villamizar, Laura Fernanda; Espinel, Carlos; Quintero, Edgar Mauricio; Belaich, Mariano Nicolás; Toloza, Deisy Liseth

2017-01-01

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification. PMID:28873431

APP Processing Induced by Herpes Simplex Virus Type 1 (HSV-1) Yields Several APP Fragments in Human and Rat Neuronal Cells

PubMed Central

Civitelli, Livia; Argnani, Rafaela; Piacentini, Roberto; Ripoli, Cristian; Manservigi, Roberto; Grassi, Claudio; Garaci, Enrico; Palamara, Anna Teresa

2010-01-01

Lifelong latent infections of the trigeminal ganglion by the neurotropic herpes simplex virus type 1 (HSV-1) are characterized by periodic reactivation. During these episodes, newly produced virions may also reach the central nervous system (CNS), causing productive but generally asymptomatic infections. Epidemiological and experimental findings suggest that HSV-1 might contribute to the pathogenesis of Alzheimer's disease (AD). This multifactorial neurodegenerative disorder is related to an overproduction of amyloid beta (Aβ) and other neurotoxic peptides, which occurs during amyloidogenic endoproteolytic processing of the transmembrane amyloid precursor protein (APP). The aim of our study was to identify the effects of productive HSV-1 infection on APP processing in neuronal cells. We found that infection of SH-SY5Y human neuroblastoma cells and rat cortical neurons is followed by multiple cleavages of APP, which result in the intra- and/or extra-cellular accumulation of various neurotoxic species. These include: i) APP fragments (APP-Fs) of 35 and 45 kDa (APP-F35 and APP-F45) that comprise portions of Aβ; ii) N-terminal APP-Fs that are secreted; iii) intracellular C-terminal APP-Fs; and iv) Aβ1-40 and Aβ1-42. Western blot analysis of infected-cell lysates treated with formic acid suggests that APP-F35 may be an Aβ oligomer. The multiple cleavages of APP that occur in infected cells are produced in part by known components of the amyloidogenic APP processing pathway, i.e., host-cell β-secretase, γ-secretase, and caspase-3-like enzymes. These findings demonstrate that HSV-1 infection of neuronal cells can generate multiple APP fragments with well-documented neurotoxic potentials. It is tempting to speculate that intra- and extracellular accumulation of these species in the CNS resulting from repeated HSV-1 reactivation could, in the presence of other risk factors, play a co-factorial role in the development of AD. PMID:21085580

A 1.5 Mb submicroscopic deletion in 17p11.2-p12 is frequently observed in Italian families with hereditary neuropathy with liability to pressure palsies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lorenzetti, D.; Roa, B.B.; Abbas, N.E.

1994-09-01

Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant disorder characterized by recurrent mononeuropathies that was recently associated with a 1.5 Mb deletion in chromosome 17p11.2-p12. Duplication of the same region is known to be associated with Charcot-Marie-Tooth disease type 1A (CMT1A), a more severe peripheral neuropathy characterized by symmetrically slowed nerve conduction velocity. The CMT1A duplication and HNPP deletion are reciprocal recombination products involving a repeat element (CMT1A-REP) which flanks the 1.5 Mb region involved in the duplication/deletion. Patients from 9 unrelated HNPP Italian families were clinically, electrophysiologically and histologically evaluated. Families were typed with amore » polymorphic (CA){sub n} repeat and with RFLPs corresponding to loci D17S122, D17S125 and D17S61, which all map within the deleted region. Lack of allelic transmission from affected parent to affected offspring was observed in four informative families, suggesting the presence of deletion. Southern blot analysis of EcoRI digested genomic DNA from HNPP patients and control subjects was performed using a probe mapping within the CMT1A-REP elements. A reduced hybridization signal of a 6.0 kb EcoRI fragment, mapping within the distal CMT1A-REP, was observed in all HNPP patients suggesting the loss of one copy of this fragment in the HNPP-deleted chromosome. PFGE analysis of SacII digested genomic DNA from selected HNPP subjects showed the presence of a junction fragment which has previously been found in association with the 1.5 Mb HNPP deletion. Evidence for deletion could be demonstrated in all 9 families suggesting that the 17p11.2-p12 deletion is commonly associated with HNPP.« less

Antitumor effect and toxicity of free rhodium (II) citrate and rhodium (II) citrate-loaded maghemite nanoparticles in mice bearing breast cancer.

PubMed

Carneiro, Marcella Lemos Brettas; Peixoto, Raphael C A; Joanitti, Graziela A; Oliveira, Ricardo G S; Telles, Luis A M; Miranda-Vilela, Ana L; Bocca, Anamélia L; Vianna, Leonora M S; da Silva, Izabel C R; de Souza, Aparecido R; Lacava, Zulmira G M; Báo, Sônia N

2013-02-16

Magnetic fluids containing superparamagnetic iron oxide nanoparticles represent an attractive platform as nanocarriers in chemotherapy. Recently, we developed a formulation of maghemite nanoparticles coated with rhodium (II) citrate, which resulted in in vitro cytotoxicity enhanced up to 4.6 times when compared to free rhodium (II) citrate formulation on breast carcinoma cells. In this work, we evaluate the antitumor activity and toxicity induced by these formulations in Balb/c mice bearing orthotopic 4T1 breast carcinoma. Mice were evaluated with regard to the treatments' toxicity through analyses of hemogram, serum levels of alanine aminotransferase, iron, and creatinine; DNA fragmentation and cell cycle of bone marrow cells; and liver, kidney and lung histology. In addition, the antitumor activity of rhodium (II) citrate and maghemite nanoparticles coated with rhodium (II) citrate was verified by tumor volume reduction, histology and immunohistochemistry. Regarding the treatments' toxicity, no experimental groups had alterations in levels of serum ALT or creatinine, and this suggestion was corroborated by the histopathologic examination of liver and kidney of mice. Moreover, DNA fragmentation frequency of bone marrow cells was lower than 15% in all experimental groups. On the other hand, the complexes rhodium (II) citrate-functionalized maghemite and free rhodium (II) citrate led to a marked growth inhibition of tumor and decrease in CD31 and Ki-67 staining. In summary, we demonstrated that both rhodium (II) citrate and maghemite nanoparticles coated with rhodium (II) citrate formulations exhibited antitumor effects against 4T1 metastatic breast cancer cell line following intratumoral administration. This antitumor effect was followed by inhibition of both cell proliferation and microvascularization and by tumor tissue injury characterized as necrosis and fibrosis. Remarkably, this is the first published report demonstrating the therapeutic efficacy of maghemite nanoparticles coated with rhodium (II) citrate. This treatment prolonged the survival period of treated mice without inducing apparent systemic toxicity, which strengthens its use for future breast cancer therapeutic applications.

Photosynthetic Electron Transport Chain of Chlamydomonas reinhardi VI. Electron Transport in Mutant Strains Lacking Either Cytochrome 553 or Plastocyanin 1

PubMed Central

Gorman, Donald S.; Levine, R. P.

1966-01-01

A mutant strain of Chlamydomonas reinhardi, ac-206, lacks cytochrome 553, at least in an active and detectable form. Chloroplast fragments of this mutant strain are inactive in the photoreduction of NADP when the source of electrons is water, but they are active when the electron source is 2,6-dichlorophenolindophenol and ascorbate. The addition of either cytochrome 553 or plastocyanin, obtained from the wild-type strain, has no effect upon the photosynthetic activities of the mutant strain. Cells of the mutant strain lack both the soluble and insoluble forms of cytochrome 553, but they possess the mitochondrial type cytochrome c. Thus, the loss of cytochrome 553 appears to be specific. Another mutant strain, ac-208, lacks plastocyanin, or possesses it in an inactive and undetectable form. Chloroplast fragments of ac-208 are inactive in the photoreduction of NADP with either water or 2,6-dichlorophenolindophenol and ascorbate as electron donors. However, these reactions are restored upon the addition of plastocyanin. The addition of cytochrome 553 has no effect. The measurement of light-induced absorbance changes with ac-208 reveal that, in the absence of plastocyanin, light fails to sensitize the oxidation of cytochrome 553, but it will sensitize its reduction. However, the addition of plastocyanin restores the light-induced cytochrome oxidation. A third mutant strain, ac-208 (sup.) carries a suppressor mutation that partially restores the wild phenotype. This mutant strain appears to possess a plastocyanin that is less stable than that of the wild-type strain. The observations with the mutant strains are discussed in terms of the sequence of electron transport System II → cytochrome 553 → plastocyanin → System I. PMID:16656453

Curcumin inhibits growth potential by G1 cell cycle arrest and induces apoptosis in p53-mutated COLO 320DM human colon adenocarcinoma cells.

PubMed

Dasiram, Jade Dhananjay; Ganesan, Ramamoorthi; Kannan, Janani; Kotteeswaran, Venkatesan; Sivalingam, Nageswaran

2017-02-01

Curcumin, a natural polyphenolic compound and it is isolated from the rhizome of Curcuma longa, have been reported to possess anticancer effect against stage I and II colon cancer. However, the effect of curcumin on colon cancer at Dukes' type C metastatic stage III remains still unclear. In the present study, we have investigated the anticancer effects of curcumin on p53 mutated COLO 320DM human colon adenocarcinoma cells derived from Dukes' type C metastatic stage. The cellular viability and proliferation were assessed by trypan blue exclusion assay and MTT assay, respectively. The cytotoxicity effect was examined by lactate dehydrogenase (LDH) cytotoxicity assay. Apoptosis was analyzed by DNA fragmentation analysis, Hoechst and propidium iodide double fluorescent staining and confocal microscopy analysis. Cell cycle distribution was performed by flow cytometry analysis. Here we have observed that curcumin treatment significantly inhibited the cellular viability and proliferation potential of p53 mutated COLO 320DM cells in a dose- and time-dependent manner. In addition, curcumin treatment showed no cytotoxic effects to the COLO 320DM cells. DNA fragmentation analysis, Hoechst and propidium iodide double fluorescent staining and confocal microscopy analysis revealed that curcumin treatment induced apoptosis in COLO 320DM cells. Furthermore, curcumin caused cell cycle arrest at the G1 phase, decreased the cell population in the S phase and induced apoptosis in COLO 320DM colon adenocarcinoma cells. Together, these data suggest that curcumin exerts anticancer effects and induces apoptosis in p53 mutated COLO 320DM human colon adenocarcinoma cells derived from Dukes' type C metastatic stage. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Antennal transcriptome analysis of the piercing moth Oraesia emarginata (Lepidoptera: Noctuidae)

PubMed Central

Feng, Bo; Guo, Qianshuang; Zheng, Kaidi; Qin, Yuanxia; Du, Yongjun

2017-01-01

The piercing fruit moth Oraesia emarginata is an economically significant pest; however, our understanding of its olfactory mechanisms in infestation is limited. The present study conducted antennal transcriptome analysis of olfactory genes using real-time quantitative reverse transcription PCR analysis (RT-qPCR). We identified a total of 104 candidate chemosensory genes from several gene families, including 35 olfactory receptors (ORs), 41 odorant-binding proteins, 20 chemosensory proteins, 6 ionotropic receptors, and 2 sensory neuron membrane proteins. Seven candidate pheromone receptors (PRs) and 3 candidate pheromone-binding proteins (PBPs) for sex pheromone recognition were found. OemaOR29 and OemaPBP1 had the highest fragments per kb per million fragments (FPKM) values in all ORs and OBPs, respectively. Eighteen olfactory genes were upregulated in females, including 5 candidate PRs, and 20 olfactory genes were upregulated in males, including 2 candidate PRs (OemaOR29 and 4) and 2 PBPs (OemaPBP1 and 3). These genes may have roles in mediating sex-specific behaviors. Most candidate olfactory genes of sex pheromone recognition (except OemaOR29 and OemaPBP3) in O. emarginata were not clustered with those of studied noctuid species (type I pheromone). In addition, OemaOR29 was belonged to cluster PRIII, which comprise proteins that recognize type II pheromones instead of type I pheromones. The structure and function of olfactory genes that encode sex pheromones in O. emarginata might thus differ from those of other studied noctuids. The findings of the present study may help explain the molecular mechanism underlying olfaction and the evolution of olfactory genes encoding sex pheromones in O. emarginata. PMID:28614384

A new assay based on terminal restriction fragment length polymorphism of homocitrate synthase gene fragments for Candida species identification.

PubMed

Szemiako, Kasjan; Śledzińska, Anna; Krawczyk, Beata

2017-08-01

Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.

Quantitative petrographic analysis of Desmoinesian sandstones from Oklahoma

USGS Publications Warehouse

Dyman, Thaddeus S.

1989-01-01

Desmoinesian sandstones from the northern Oklahoma platform and the Anadarko, Arkoma, and Ardmore basins record a complex interaction between mid-Pennsylvanian source-area tectonism and cyclic sedimentation patterns associated with numerous transgressions and regressions. Framework-grain summaries for 50 thin sections from sandstones of the Krebs, Cabaniss, and Marmaton Groups and their surface and subsurface equivalents were subjected to multivariate statistical analyses to establish regional compositional trends for provenance analysis. R-mode cluster and correspondence analyses were used to determine the contributing effect (total variance) of key framework grains. Fragments of monocrystalline and polycrystalline quartz; potassium and plagioclase feldspar; chert; and metamorphic, limestone, and mudstone-sandstone rock fragments contribute most to the variation in the grain population. Q-mode cluster and correspondence analyses were used to identify four petrofacies and establish the range of compositional variation in Desmoinesian sandstones. Petrofacies I is rich in monocrystalline quartz (78-98%); mica and rock fragments are rare. Petrofacies II is also rich in monocrystalline quartz (60-84%) and averages 12% total rock fragments. Petrofacies III and IV are compositionally heterogeneous and contain variable percentages of monocrystalline and polycrystalline quartz, potassium feldspar, mica, chert, and metamorphic and sedimentary rock fragments. Quantitative analyses indicate that Desmoinesian sandstones were derived from sedimentary, igneous, and metamorphic source areas. Sandstones of petrofacies I and II occur mostly in the lower Desmoinesian and are widely distributed, although they are most abundant in eastern and central Oklahoma; sandstones of petrofacies III and IV are widely distributed and occur primarily in the middle and upper Desmoinesian. The range of compositional variation and the distribution of petrofacies are related to paleotectonics and basin development, sediment recycling, and varying depositional environments.

Molecular Identification and Genetic Analysis of Norovirus Genogroups I and II in Water Environments: Comparative Analysis of Different Reverse Transcription-PCR Assays▿

PubMed Central

La Rosa, G.; Fontana, S.; Di Grazia, A.; Iaconelli, M.; Pourshaban, M.; Muscillo, M.

2007-01-01

Noroviruses have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Our inability to grow them in cell culture and the lack of an animal model hinder the characterization of these viruses. More recently, molecular approaches have been used to study the genetic relationships that exist among them. In the present study, environmental samples from seawater, estuarine water, and effluents of sewage treatment plants were analyzed in order to evaluate the role of environmental surface contamination as a possible vehicle for transmission of norovirus genogroups I and II. Novel broad-range reverse transcription-PCR/nested assays targeting the region coding for the RNA-dependent RNA polymerase were developed, amplifying fragments of 516 bp and 687 bp in the nested reactions for genogroups II and I, respectively. The assays were evaluated and compared against widely used published assays. The newly designed assays provide long regions for high-confidence BLAST searches in public databases and therefore are useful diagnostic tools for molecular diagnosis and typing of human noroviruses in clinical and environmental samples, as well as for the study of molecular epidemiology and the evolution of these viruses. PMID:17483265

Degradation pattern of photosystem II reaction center protein D1 in intact leaves. The major photoinhibition-induced cleavage site in D1 polypeptide is located amino terminally of the DE loop.

PubMed

Kettunen, R; Tyystjärvi, E; Aro, E M

1996-08-01

Photoinhibition-induced degradation of the D1 protein of the photosystem II reaction center was studied in intact pumpkin (Cucurbita pepo L.) leaves. Photoinhibition was observed to cause the cleavage of the D1 protein at two distinct sites. The main cleavage generated an 18-kD N-terminal and a 20-kD C-terminal degradation fragment of the D1 protein. this cleavage site was mapped to be located clearly N terminally of the DE loop. The other, less-frequent cleavage occurred at the DE loop and produced the well-documented 23-kD, N-terminal D1 degradation product. Furthermore, the 23-kD, N-terminal D1 fragment appears to be phosphorylated and can be detected only under severe photoinhibition in vivo. Comparison of the D1 degradation pattern after in vivo photoinhibition to that after in vitro acceptor-side and donor-side photoinhibition, performed with isolated photosystem II core particles, gives indirect evidence in support of donor-side photoinhibition in intact leaves.

ToF-SIMS Parallel Imaging MS/MS of Lipid Species in Thin Tissue Sections.

PubMed

Bruinen, Anne Lisa; Fisher, Gregory L; Heeren, Ron M A

2017-01-01

Unambiguous identification of detected species is essential in complex biomedical samples. To date, there are not many mass spectrometry imaging techniques that can provide both high spatial resolution and identification capabilities. A new and patented imaging tandem mass spectrometer, exploiting the unique characteristics of the nanoTOF II (Physical Electronics, USA) TOF-SIMS TRIFT instrument, was developed to address this.Tandem mass spectrometry is based on the selection of precursor ions from the full secondary ion spectrum (MS 1 ), followed by energetic activation and fragmentation, and collection of the fragment ions to obtain a tandem MS spectrum (MS 2 ). The PHI NanoTOF II mass spectrometer is equipped with a high-energy collision induced dissociation (CID) fragmentation cell as well as a second time-of-flight analyzer developed for simultaneous ToF-SIMS and tandem MS imaging experiments.We describe here the results of a ToF-SIMS imaging experiment on a thin tissue section of an infected zebrafish as a model organism for tuberculosis. The focus is on the obtained ion distribution plot of a fatty acid as well as its identification by tandem mass spectrometry.

[Classification and Treatment of Sacroiliac Joint Dislocation].

PubMed

Tan, Zhen; Huang, Zhong; Li, Liang; Meng, Wei-Kun; Liu, Lei; Zhang, Hui; Wang, Guang-Lin; Huang, Fu-Guo

2017-09-01

To develop a renewed classification and treatment regimen for sacroiliac joint dislocation. According to the direction of dislocation of sacroiliac joint,combined iliac,sacral fractures,and fracture morphology,sacroiliac joint dislocation was classified into 4 types. Type Ⅰ (sacroiliac anterior dislocation): main fracture fragments of posterior iliac wing dislocated in front of sacroiliac joint. Type Ⅱ (sacroiliac posterior dislocation): main fracture fragments of posterior iliac wing dislocated in posterior of sacroiliac joint. Type Ⅲ (Crescent fracturedislocation of the sacroiliac joint): upward dislocation of posterior iliac wing with oblique fracture through posterior iliac wing. Type ⅢA: a large crescent fragment and dislocation comprises no more than onethird of sacroiliac joint,which is typically inferior. Type ⅢB: intermediatesize crescent fragment and dislocation comprises between one and twothirds of joint. Type ⅢC: a small crescent fragment where dislocation comprises most,but not the entire joint. Different treatment regimens were selected for different types of fractures. Treatment for type Ⅰ sacroiliac joint dislocation: anterior iliac fossa approach pry stripping reset; sacroiliac joint fixed with sacroiliac screw through percutaneous. Treatment for type Ⅱ sacroiliac joint dislocation: posterior sacroiliac joint posterior approach; sacroiliac joint fixed with sacroiliac screw under computer guidance. Treatment for type ⅢA and ⅢB sacroiliac joint dislocation: posterior sacroiliac joint approach; sacroiliac joint fixed with reconstruction plate. Treatment for type ⅢC sacroiliac joint dislocation: sacroiliac joint closed reduction; sacroiliac joint fixed with sacroiliac screw through percutaneous. Treatment for type Ⅳ sacroiliac joint dislocation: posterior approach; sacroiliac joint fixed with spinal pelvic fixation. Results of 24 to 72 months patient follow-up (mean 34.5 months): 100% survival,100% wound healing,and 100% fracture healing. Two cases were identified as type Ⅰ sacroiliac joint dislocation,including one with coexistence of nerve injury. Patients recovered completely 12 months after surgery. Eight cases were identified as type Ⅱ sacroiliac joint dislocation; none had obvious nerve injury during treatments. Twelve cases were identified as type Ⅲ sacroiliac joint dislocation,including one with coexistence of nerve injury. Patients recovered completely 12 months after surgery. Three cases were identified as type Ⅳ sacroiliac joint dislocation with coexistence of nerve injury. Two patients fully recovered 12 months after surgery. One had partial recovery of neurological function. The classification and treatment regimen for sacroiliac joint dislocation have achieved better therapeutic effect,which is worth promoting.

DebriSat Fragment Characterization System and Processing Status

NASA Technical Reports Server (NTRS)

Rivero, M.; Shiotani, B.; M. Carrasquilla; Fitz-Coy, N.; Liou, J. C.; Sorge, M.; Huynh, T.; Opiela, J.; Krisko, P.; Cowardin, H.

2016-01-01

The DebriSat project is a continuing effort sponsored by NASA and DoD to update existing break-up models using data obtained from hypervelocity impact tests performed to simulate on-orbit collisions. After the impact tests, a team at the University of Florida has been working to characterize the fragments in terms of their mass, size, shape, color and material content. The focus of the post-impact effort has been the collection of 2 mm and larger fragments resulting from the hypervelocity impact test. To date, in excess of 125K fragments have been recovered which is approximately 40K more than the 85K fragments predicted by the existing models. While the fragment collection activities continue, there has been a transition to the characterization of the recovered fragments. Since the start of the characterization effort, the focus has been on the use of automation to (i) expedite the fragment characterization process and (ii) minimize the effects of human subjectivity on the results; e.g., automated data entry processes were developed and implemented to minimize errors during transcription of the measurement data. At all steps of the process, however, there is human oversight to ensure the integrity of the data. Additionally, repeatability and reproducibility tests have been developed and implemented to ensure that the instrumentations used in the characterization process are accurate and properly calibrated.

Regional forest fragmentation effects on bottomland hardwood community types and resource values

Treesearch

Victor A. Rudis

1995-01-01

In human-dominated regions, forest vegetation removal impacts remaining ecosystems but regional-scale biological consequences and resource value changes are not well known. Using forest resource survey data, I examined current bottomland hardwood community types and a range of fragment size classes in the south central United States. Analyses examined resource value...

Morphological, chemical and molecular differentiation of Fusarium equiseti isolated from Norwegian cereals.

PubMed

Kosiak, Elzbieta Barbara; Holst-Jensen, Arne; Rundberget, Thomas; Gonzalez Jaen, Maria Teresa; Torp, Mona

2005-03-15

The morphological variation, secondary metabolite profiles and restriction fragment length polymorphisms (RFLPs) of PCR amplified intergenic spacer (IGS) ribosomal DNA (rDNA) were studied in 27 isolates of Fusarium equiseti, 25 isolated from Norwegian cereals and 2 from soil obtained from the IBT culture collection (BioCentrum, Technical University of Denmark). All 27 isolates were tested for production of fusarochromanone (FUSCHR), zearalenone (ZEA) and the trichothecenes: 15-monoacetoxy-scirpentriol (MAS), diacetoxy-scirpenol (DAS), T-2 and HT-2 toxins, T2-triol, neosolaniol (NEO), deoxynivalenol (DON), nivalenol (NIV) and 4-acetylnivalenol (Fus-X). The trichothecenes were analysed by GC-MS in a selected ion monitoring mode, while FUSCHR was determined by ion pair HPLC with fluorometric detection and production of ZEA by TLC. For amplification of IGS rDNA primers CNL12 and CNS1 were applied. IGS rDNA was digested with the four restriction enzymes: AvaII, CfoI, EcoRI and Sau3A. In addition, we sequenced the IGS rDNA region of three of the Norwegian isolates. There were two morphological types among the Norwegian strains of F. equiseti, type I with short apical cells (dominating) and type II with long apical cells, with four haplotypes identified based on the RFLP data. Variation in secondary metabolite profiles within and between the morphological groups was observed and the levels of produced toxins were: FUSCHR 3000-42,500 and 25-30 ng/g, NIV 20-2500 and 120-700 ng/g, FUS-X 20-15,000 and 0 ng/g, DAS 30-7500 and 0-600 ng/g, and MAS 10-600 and 0-500 ng/g, for strains with short and long apical cells, respectively. NEO was detected in 16/27 strains tested (all morphotype I). All but four strains of type I (these four lacked a restriction site for EcoRI) had identical RFLP profiles. The isolates of type II had two haplotypes. The IGS sequence similarity data indicated differences between these morphotypes corresponding to two separate lineages apparently at the species level.

Syntactic Structure and Information Structure: The Acquisition of Portuguese Clefts and "Be"-Fragments

ERIC Educational Resources Information Center

Lobo, Maria; Santos, Ana Lúcia; Soares-Jesel, Carla

2016-01-01

This article investigates the acquisition of different types of clefts and of "be"-fragments in European Portuguese. We first present the main syntactic and discourse properties of different cleft structures and of "be"-fragments in European Portuguese, and we discuss how data from first language acquisition may contribute to…

Regulation of apoptosis by low serum in cells of different stages of neoplastic progression: enhanced susceptibility after loss of a senescence gene and decreased susceptibility after loss of a tumor suppressor gene.

PubMed

Preston, G A; Lang, J E; Maronpot, R R; Barrett, J C

1994-08-01

A cell culture model system has been used to study the susceptibility of cells to apoptotic cell death during different stages of neoplastic progression. This system consists of normal diploid Syrian hamster embryo (SHE) cells, two preneoplastic cell lines [tumor suppressor stage I (sup +I) and non-tumor suppressor stage II (sup -II)], and hamster tumor cell lines. Stage I preneoplastic cells are nontumorigenic immortal clones that suppress tumorigenicity when hybridized to tumor cells, whereas stage II cells have lost the ability to suppress tumorigenicity in cell hybrids. We refer to these two types of preneoplastic cells as sup +I and sup -II, respectively. Neoplastic progression is generally associated with cellular alterations in growth factor responsiveness. Therefore, to study the regulation of apoptosis in the system described above, cells were cultured in low serum (0.2%) as a means of withdrawing growth factors. In low serum, normal SHE cells were quiescent (labeling index of 0.2%), with little cell death. The sup +I cells showed a relatively low labeling index (1.6%) but, in contrast to the normal cells, died at a high rate (55% cell loss after 48 h) by apoptosis, as evidenced by morphology, DNA fragmentation, and in situ end-labeling of fragmented DNA. The apoptotic cells did not go through a replicative cycle while in low serum, implying that apoptosis was initiated in the G0/G1 phase of the cell cycle. The sup -II cell line showed a high labeling index (40%) after 48 h, but cell growth was balanced by cell death that occurred at approximately the same rate. The cells died, however, predominantly by necrosis. The tumor cell lines continued to proliferate in low serum, with high labeling indices (ranging from 27% to 43%) and a low level of apoptotic or necrotic cell death. To determine the relative ability of these cells to survive in vivo, normal SHE cells, sup +I cells, and sup -II cells were injected s.c. into nude mice. At 5 or 21 days after injection, the normal SHE cells were readily retrieved from the mice and grew well in culture. In contrast, few sup +I cells were retrieved 5 days after injection and no viable cells were retrieved after 21 days. Sup -II cells were not retrieved at either the 5-day or 21-day harvest, and histological examinations of the sites of injection showed the presence of macrophages, eosinophils, and neutrophils, indicating an inflammatory response associated with necrotic cell death.(ABSTRACT TRUNCATED AT 400 WORDS)

Autoantibodies to human tryptophan hydroxylase and aromatic L-amino acid decarboxylase.

PubMed

Dal Pra, Chiara; Chen, Shu; Betterle, Corrado; Zanchetta, Renato; McGrath, Vivienne; Furmaniak, Jadwiga; Rees Smith, Bernard

2004-03-01

To assess the prevalence of autoantibodies (Abs) to tryptophan hydroxylase (TPH) and aromatic l-amino acid decarboxylase (AADC) in patients with different autoimmune diseases and to analyse their respective epitopes. TPH and AADC Abs were measured in an immunoprecipitation assay using (35)S-labelled full-length and fragments of TPH and AADC. Patients with different autoimmune adrenal diseases (n=84), non-adrenal autoimmune diseases (n=37), idiopathic vitiligo (n=8) and 56 healthy blood donors were studied. Fourteen of twenty-three (61%) of patients with autoimmune polyglandular syndrome (APS) type I and 1/34 (3%) of patients with isolated Addison's disease (AD) were positive for TPH Abs. None of the patients with APS type II (n=27), coeliac disease (n=10), autoimmune thyroid disease (AITD) (n=11), type 1 diabetes mellitus (DM) (n=16) or idiopathic vitiligo (n=8) was positive for TPH Abs. AADC Abs were detected in 12/23 (52%) patients with APS type I, in 1/29 (3%) patients with APS type II and 1/34 (3%) patients with isolated AD. None of the patients with coeliac disease, type 1 DM, AITD or idiopathic vitiligo was positive for AADC Abs. TPH Abs were found to interact with the C-terminal amino acids (aa) 308-423, central aa 164-205 and N-terminal aa 1-105 of the TPH molecule. AADC Ab binding epitopes were within the C-terminal aa 382-483, the central aa 243-381 and the N-terminal aa 1-167. Our study suggests that TPH Abs and AADC Abs react with several different epitopes and that different epitopes are recognized by different sera. The prevalence of TPH Abs and AADC Abs in patients with APS type I in our study is in agreement with previous reports. TPH Abs and AADC Abs were found very rarely in patients with other forms of autoimmune adrenal disease and were not detected in patients with non-adrenal autoimmune diseases.

Grafting transition metal-organophosphonate fragments onto heteropolyoxomolybdate: activity in photocatalysis.

PubMed

Sun, Xiaopeng; Liang, Zhijie; Ma, Pengtao; Ban, Ran; Jiang, Mingshuang; Zhang, Dongdi; Wang, Jingping; Niu, Jingyang

2015-10-28

A novel organophosphonate-functionalized heteropolyoxomolybdate incorporated nickel cluster, CsNa9[H2{Ni3O2(H2O)6}(PMo6O21)2{Ni(OOCCH2NHCH2PO3)2}3]·21H2O (1), has been synthesized, which represents the first member of the family of oxomolybdenum organophosphonate containing hexa-nuclear Ni(ii) in a polyanion framework. The polyanion comprises a unique ladder-type {Ni3O10(H2O)6} cluster and three {Ni(OOCCH2NHCH2PO3)2} bridgings, which are capped on either end by a {PMo6O28} group. Photocatalytic experiments indicate that 1 exhibits catalytic activity for the photodegradation of RhB solution. Furthermore, magnetic studies indicate that 1 displays antiferromagnetic interactions.

Is the gravity effect of radiographic anatomic features enough to justify stone clearance or fragments retention following extracorporeal shock wave lithotripsy (SWL).

PubMed

Mustafa, Mahmoud

2012-08-01

We determined whether the gravity effect of radiographic anatomic features on the preoperative urography (IVP) are enough to predict fragments clearance after shock wave lithotripsy (SWL). A Total of 282 patients with mean age 45.8 ± 13.2 years (189 male, 93 female), who underwent SWL due to renal calculi between October 2005 and August 2009 were enrolled. The mean calculi load was 155.72 ± 127.66 mm². The patients were stratified into three groups: patients with pelvis calculi (group 1); patients with upper or middle pole calculi (group 2) and patients with lower pole calculi (group 3). Three angles on the pretreatment IVP were measured: the inner angle between the axis of the lower pole infundibular and ureteropelvic axis (angle I); the inner angle between the lower pole infundibular axis and main axis of pelvis-ureteropelvic (UP) junction point (angle II) and the inner angle between the lower pole infundibular axis and perpendicular line (angle III). Multivariate analysis was used to define the significant predictors of stone clearance. The overall success rate was 85.81%. All angles, sessions number, shock waves number and stone burden were significant predictors of success in patients in group 1. However, in group 2 only angle II and in group 3 angles I and II had significant effect on stone clearance. Radiographic anatomic features have significant role in determining the stone-free rate following satisfactory fragmentation of renal stones with SWL. The measurement of infundibulopelvic angle in different manner helps to predict the stone-free status in patients with renal calculi located not only in lower pole, but also in renal pelvis and upper or middle pole. Gravity effect is not enough to justify the significant influence of the radiographic anatomic features on the stone clearance and fragments retention after SWL.

Increasing methylation of the calcitonin gene during disease progression in sequential samples from CML patients.

PubMed

Mills, K I; Guinn, B A; Walsh, V A; Burnett, A K

1996-09-01

In chronic myeloid leukaemia (CML), disease progression from the initial chronic phase to the acute phase or blast crisis has previously been shown to be correlated with progressive increases in hyper-methylation of the calcitonin gene, located at chromosome 11p15. However, sequential studies of individual patients were not performed in these investigations. We have analysed 44 samples from nine patients with typical Philadelphia chromosome positive CML throughout their disease progression to determine the methylation state of the calcitonin gene at these time points. Densitometry was used to quantitate the ratio of the normal 2.0 kb Hpa II fragments, indicating normal methylation status of the gene, compared to the intensity of the abnormal, hyper-methylated, 2.6-3.1 kb Hpa II fragments. We found a gradual increase in the ratio of methylated:unmethylated calcitonin gene during chronic phase with a dramatic rise at blast crisis. Further, the ratio of the abnormal hypermethylated 3.1 kb fragments to the methylated 2.6 kb fragment resulted in the identification of a clonal expansion of abnormally methylated cells. This expansion of cells with hypermethylation of the calcitonin gene during chronic phase was shown to coincide with the presence of a mutation in the p53 gene. The data presented in this study would suggest that an increased methylation status of the calcitonin gene during disease progression may indicate the expansion of abnormal blast cell populations and subsequent progression to blast crisis.

Fragmentation-fraction ratio f_{Ξ _b}/f_{Λ _b} in b- and c-baryon decays

NASA Astrophysics Data System (ADS)

Jiang, Hua-Yu; Yu, Fu-Sheng

2018-03-01

We study the ratio of fragmentation fractions, f_{Ξ _b}/f_{Λ _b}, from the measurement of Ξ _b^0→ Ξ _c^+π ^- and Λ _b^0→ Λ _c^+π ^- with Ξ c+/Λ c+→ p K^-π ^+. With the branching fraction B(Ξ _c^+→ pK^-π ^+)=(2.2± 0.8)% obtained under the U-spin symmetry, the fragmentation ratio is determined as f_{Ξ _b}/f_{Λ _b} =0.054± 0.020. To reduce the above uncertainties, we suggest to measure the branching fractions of Ξ _c^+→ p \\overline{K}^{*0} and Λ _c^+→ Σ ^+ K^{*0} at BESIII, Belle II and LHCb.

Analysis of mexicanolide- and phragmalin-type limonoids from Heynea trijuga using high-performance liquid chromatography/electrospray tandem mass spectrometry.

PubMed

Yang, Wei; Fang, Dong-Mei; He, Hong-Ping; Hao, Xiao-Jiang; Wu, Zhi-Jun; Zhang, Guo-Lin

2013-06-15

Limonoids, a class of tetranortriterpenoids, exhibit various biological effects, including acting as potent antifeedants and insect growth-regulators against various pests. The analysis of phragmalin- and mexicanolide-type limonoids by collision-induced dissociation tandem mass spectrometry (CID-MS/MS) has not been reported. A high-performance liquid chromatography/electrospray ionization (HPLC/ESI)-MS/MS method was developed to investigate the fragmentation patterns of [M+NH4 ](+) ions for nine reference phragmalin- and mexicanolide-type limonoids. The method was also used in the identification of limonoid compounds in botanic extracts of Heynea trijuga. The losses of side chains and the furan part were the major fragmentation patterns. However, there was variation in the relative abundances of product ions resulting from the same fragmentation pathways. A total of 89 phragmalin- and mexicanolide-type limonoids in botanic extracts of Heynea trijuga were detected and 50 of these compounds were identified or tentatively characterized based on elemental constituents, fragmentation pathways, and the profile of the major product ions of reference compounds. In addition, the isomers could be tentatively distinguished. An HPLC/ESI-MS/MS method was developed and could be used to simultaneously identify and screen phragmalin- and mexicanolide-type limonoids in botanic extracts of Heynea trijuga. Copyright © 2013 John Wiley & Sons, Ltd.

WHAT IS CONTROLLING THE FRAGMENTATION IN THE INFRARED DARK CLOUD G14.225–0.506?: DIFFERENT LEVELS OF FRAGMENTATION IN TWIN HUBS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Busquet, Gemma; Girart, Josep Miquel; Estalella, Robert

We present observations of the 1.3 mm continuum emission toward hub-N and hub-S of the infrared dark cloud G14.225–0.506 carried out with the Submillimeter Array, together with observations of the dust emission at 870 and 350 μm obtained with APEX and CSO telescopes. The large-scale dust emission of both hubs consists of a single peaked clump elongated in the direction of the associated filament. At small scales, the SMA images reveal that both hubs fragment into several dust condensations. The fragmentation level was assessed under the same conditions and we found that hub-N presents 4 fragments while hub-S is moremore » fragmented, with 13 fragments identified. We studied the density structure by means of a simultaneous fit of the radial intensity profile at 870 and 350 μm and the spectral energy distribution adopting a Plummer-like function to describe the density structure. The parameters inferred from the model are remarkably similar in both hubs, suggesting that density structure could not be responsible for determining the fragmentation level. We estimated several physical parameters, such as the level of turbulence and the magnetic field strength, and we found no significant differences between these hubs. The Jeans analysis indicates that the observed fragmentation is more consistent with thermal Jeans fragmentation compared with a scenario in which turbulent support is included. The lower fragmentation level observed in hub-N could be explained in terms of stronger UV radiation effects from a nearby H ii region, evolutionary effects, and/or stronger magnetic fields at small scales, a scenario that should be further investigated.« less

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

PubMed Central

Ikonen, Suvi; Auvinen, Petri; Paulin, Lars; Koskinen, Patrik; Holm, Liisa; Taipale, Minna; Duplouy, Anne; Ruokolainen, Annukka; Saarnio, Suvi; Sirén, Jukka; Kohonen, Jukka; Corander, Jukka; Frilander, Mikko J.; Ahola, Virpi; Hanski, Ilkka

2014-01-01

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation. PMID:24988207

Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

PubMed

Somervuo, Panu; Kvist, Jouni; Ikonen, Suvi; Auvinen, Petri; Paulin, Lars; Koskinen, Patrik; Holm, Liisa; Taipale, Minna; Duplouy, Anne; Ruokolainen, Annukka; Saarnio, Suvi; Sirén, Jukka; Kohonen, Jukka; Corander, Jukka; Frilander, Mikko J; Ahola, Virpi; Hanski, Ilkka

2014-01-01

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.

F-actin clustering and cell dysmotility induced by the pathological W148R missense mutation of filamin B at the actin-binding domain.

PubMed

Zhao, Yongtong; Shapiro, Sandor S; Eto, Masumi

2016-01-01

Filamin B (FLNB) is a dimeric actin-binding protein that orchestrates the reorganization of the actin cytoskeleton. Congenital mutations of FLNB at the actin-binding domain (ABD) are known to cause abnormalities of skeletal development, such as atelosteogenesis types I and III and Larsen's syndrome, although the underlying mechanisms are poorly understood. Here, using fluorescence microscopy, we characterized the reorganization of the actin cytoskeleton in cells expressing each of six pathological FLNB mutants that have been linked to skeletal abnormalities. The subfractionation assay showed a greater accumulation of the FLNB ABD mutants W148R and E227K than the wild-type protein to the cytoskeleton. Ectopic expression of FLNB-W148R and, to a lesser extent, FLNB-E227K induced prominent F-actin accumulations and the consequent rearrangement of focal adhesions, myosin II, and septin filaments and results in a delayed directional migration of the cells. The W148R protein-induced cytoskeletal rearrangement was partially attenuated by the inhibition of myosin II, p21-activated protein kinase, or Rho-associated protein kinase. The expression of a single-head ABD fragment with the mutations partially mimicked the rearrangement induced by the dimer. The F-actin clustering through the interaction with the mutant FLNB ABD may limit the cytoskeletal reorganization, preventing normal skeletal development. Copyright © 2016 the American Physiological Society.

New steroid 5alpha-reductase type I (SRD5A1) homologous sequences on human chromosomes 6 and 8.

PubMed

Eminović, I; Liović, M; Prezelj, J; Kocijancic, A; Rozman, D; Komel, R

2001-01-01

To date, two genes encoding 5alpha-reductase isoenzymes are known (type I, type II), and one type I pseudogene. The divergent localization of these genes and the still not fully understood function of the encoded enzymes as well as the perplexing results we obtained after sequencing PCR-amplified SRD5A1 gene fragments (out of genomic DNA), made us assume that, in addition to the known SRD5A1 gene, one or more different human 5alpha-reductase type I coding genes may exist. Our research provide the first evidence for the existence of two new SRD5A1 related, previously unidentified sequences in the human genome. These sequences which were localized to chromosomes 6 and 8 are highly homologous (> 99%) to SRD5A1, and also do not contain any deletions or insertions that are otherwise a characteristic of the SRD5API pseudogene. Our results imply that these sequences may be either coding parts of yet unknown, active SRD5A1 genes, and/or of previously unidentified pseudogenes. These findings additionally support data of Chen et al. who confirmed the existence of various SRD5A1 proteins in cultured human skin cells.

Morphology of the posteromedial fragment in pertrochanteric fractures: A three-dimensional computed tomography analysis.

PubMed

Sharma, Gaurav; Gn, Kiran Kumar; Khatri, Kavin; Singh, Ravijot; Gamanagatti, Shivanand; Sharma, Vijay

2017-02-01

In this study we describe the morphology of the posteromedial fragment in pertrochanteric fractures using 3D CT scans and answer two questions 1) Do differences exist between the 3D CT appearances of posteromedial fragments and the depictions made in the AO classification 2) Does the posteromedial fragment affect stability in pertrochanteric fractures, in terms of fracture collapse? Preoperative CT scans of eight 31-A1 and fifty 31-A2 fractures were analysed. The presence of PM fragment, its fragmentation, greater trochanter (GT) involvement, lesser trochanter (LT) fragment size (in terms of its posterior and medial extent as well as LT length), LT fragment displacement (in terms of medial displacement and rotation) were determined. All fractures were treated with a DHS. Fracture collapse was determined on postoperative radiographs. The relationship between fracture collapse and patient factors including age, gender, fracture type (A1 versus A2), characteristics of the posteromedial fragment, and the presence of a lateral wall fracture were determined. Three out of eight 31-A1 fractures demonstrated a separate GT fragment (three part fracture). Out of the 50 31-A2 fractures, 12 had a single PM fragment, which included the LT and GT in continuity. The more common four part fractures seem to form by further fragmentation of this basic form. In A2 fractures, the GT was almost always broken and the broken fragment comprised a mean 56% of normal GT. The LT fragment involved an average of 74% of the posterior wall, and an average of 36% of the medial wall of the proximal femur. Larger LT fragments were less displaced as compared to smaller fragments. Univariate regression analyses revealed that fracture collapse was significantly correlated with fracture type (A1 versus A2, p 0.036), GT size (p 0.002) and the presence of a lateral wall fracture (p<0.001). This study revealed some important differences between the 3D CT appearances and AO classification of pertrochanteric fractures. Further, neither fragmentation of the posteromedial fragment, nor the size of the lesser trochanter fragment was found to predict stability in pertrochanteric fractures. A perioperative lateral wall fracture is the main determinant of stability in these fractures. Copyright © 2016 Elsevier Ltd. All rights reserved.

First Partial Skeleton of a 1.34-Million-Year-Old Paranthropus boisei from Bed II, Olduvai Gorge, Tanzania

PubMed Central

Domínguez-Rodrigo, Manuel; Pickering, Travis Rayne; Baquedano, Enrique; Mabulla, Audax; Mark, Darren F.; Musiba, Charles; Bunn, Henry T.; Uribelarrea, David; Smith, Victoria; Diez-Martin, Fernando; Pérez-González, Alfredo; Sánchez, Policarpo; Santonja, Manuel; Barboni, Doris; Gidna, Agness; Ashley, Gail; Yravedra, José; Heaton, Jason L.; Arriaza, Maria Carmen

2013-01-01

Recent excavations in Level 4 at BK (Bed II, Olduvai Gorge, Tanzania) have yielded nine hominin teeth, a distal humerus fragment, a proximal radius with much of its shaft, a femur shaft, and a tibia shaft fragment (cataloged collectively as OH 80). Those elements identified more specifically than to simply Hominidae gen. et sp. indet are attributed to Paranthropus boisei. Before this study, incontrovertible P. boisei partial skeletons, for which postcranial remains occurred in association with taxonomically diagnostic craniodental remains, were unknown. Thus, OH 80 stands as the first unambiguous, dentally associated Paranthropus partial skeleton from East Africa. The morphology and size of its constituent parts suggest that the fossils derived from an extremely robust individual who, at 1.338±0.024 Ma (1 sigma), represents one of the most recent occurrences of Paranthropus before its extinction in East Africa. PMID:24339873

Experimental constraints on phreatic eruption processes at Whakaari (White Island volcano)

NASA Astrophysics Data System (ADS)

Mayer, Klaus; Scheu, Bettina; Gilg, H. Albert; Heap, Michael J.; Kennedy, Ben M.; Lavallée, Yan; Letham-Brake, Mark; Dingwell, Donald B.

2015-09-01

Vigorous hydrothermal activity interspersed by sequences of phreatic and phreatomagmatic eruptions occur at Whakaari (White Island volcano), New Zealand. Here, we investigate the influence of sample type (hydrothermally altered cemented ash tuffs and unconsolidated ash/lapilli) and fragmentation mechanism (steam flashing versus gas expansion) on fragmentation and ejection velocities as well as on particle-size and shape. Our rapid decompression experiments show that fragmentation and ejection speeds of two ash tuffs, cemented by alunite and amorphous opal, increase with increasing porosity and that both are significantly enhanced in the presence of steam flashing. Ejection speeds of unconsolidated samples are higher than ejection speeds of cemented tuffs, as less energy is consumed by fragmentation. Fragmentation dominated by steam flashing results in increased fragmentation energy and a higher proportion of fine particles. Particle shape analyses before and after fragmentation reveal that both steam flashing and pure gas expansion produce platy or bladed particles from fracturing parallel to the decompression front. Neither fragmentation mechanisms nor sample type show a significant influence on the shape. Our results emphasize that, under identical pressure and temperature conditions, eruptions accompanied by the process of liquid water flashing to steam are significantly more violent than those driven simply by gas expansion. Therefore, phase changes during decompression and cementation are both important considerations for hazard assessment and modeling of eruptions in hydrothermally active environments.

Biomechanical aspects of lower limb torsional deformation correction with the Ilizarov external fixator.

PubMed

Morasiewicz, Piotr; Filipiak, Jarosław; Krysztoforski, Krzysztof; Dragan, Szymon

2014-03-01

The correction of torsional deformities with the Ilizarov apparatus is accompanied by rotational and translational displacement, which affects the biomechanics of the bone fragments. Understanding the biomechanical factors will assist in designing the optimal treatment strategy and mechanical properties of the fixator, thus shortening the duration of treatment and improving the outcomes. In order to determine the impact of different types of derotators on the kinematics of bone fragments in Ilizarov apparatus, physical models were studied. Translational and derotational displacement was measured using non-contact method (Optotrak Certus Motion Capture System). The results of the studies conducted on physical models have shown that regardless of the type of the derotator, the divergence between the applied angle of derotation and the obtained angle of rotation relative to fragments needs to be taken into account. Transverse displacement of fragments occur by 3.5 mm to approximately 9 mm, depending on the angle of derotation. For correction of rotational deformities up to 30°, it is advisable to use the type Z derotators because of its higher accuracy of derotation. Different types of derotators can affect the biomechanical conditions in the regenerating bone tissue through different kinematics characteristics.

Episodic Aging and End States of Comets

NASA Technical Reports Server (NTRS)

Sekanina, Zdenek

2008-01-01

It is known that comets are aging very rapidly on cosmic scales, because they rapidly shed mass. The processes involved are (i) normal activity - sublimation of ices and expulsion of dust from discrete emission sources on and/or below the surface of a comet's nucleus, and (ii) nuclear fragmentation. Both modes are episodic in nature, the latter includes major steps in the comet's life cycle. The role and history of dynamical techniques used are described and results on mass losses due to sublimation and dust expulsion are reviewed. Studies of split comets, Holmes-like exploding comets, and cataclysmically fragmenting comets show that masses of 10 to 100 million tons are involved in the fragmentation process. This and other information is used to investigate the nature of comets' episodic aging. Based on recent advances in understanding the surface morphology of cometary nuclei by close-up imaging, a possible mechanism for large-scale fragmentation events is proposed and shown to be consistent with evidence available from observations. Strongly flattened pancake-like shapes appear to be required for comet fragments by conceptual constraints. Possible end states are briefly examined.

Identification of transmembrane domain 6 & 7 residues that contribute to the binding pocket of the urotensin II receptor.

PubMed

Holleran, Brian J; Domazet, Ivana; Beaulieu, Marie-Eve; Yan, Li Ping; Guillemette, Gaétan; Lavigne, Pierre; Escher, Emanuel; Leduc, Richard

2009-04-15

Urotensin II (U-II), a cyclic undecapeptide, is the natural ligand of the urotensin II (UT) receptor, a G protein-coupled receptor. In the present study, we used the substituted-cysteine accessibility method to identify specific residues in transmembrane domains (TMDs) six and seven of the rat urotensin II receptor (rUT) that contribute to the formation of the binding pocket of the receptor. Each residue in the R256(6.32)-Q283(6.59) fragment of TMD6 and the A295(7.31)-T321(7.57) fragment of TMD7 was mutated, individually, to a cysteine. The resulting mutants were expressed in COS-7 cells, which were subsequently treated with the positively charged methanethiosulfonate-ethylammonium (MTSEA) or the negatively charged methanethiosulfonate-ethylsulfonate (MTSES) sulfhydryl-specific alkylating agents. MTSEA treatment resulted in a significant reduction in the binding of TMD6 mutants F268C(6.44) and W278C(6.54) and TMD7 mutants L298C(7.34), T302C(7.38), and T303C(7.39) to (125)I-U-II. MTSES treatment resulted in a significant reduction in the binding of two additional mutants, namely L282C(6.58) in TMD6 and Y300C(7.36) in TMD7. These results suggest that specific residues orient themselves within the water-accessible binding pocket of the rUT receptor. This approach, which allowed us to identify key determinants in TMD6 and TMD7 that contribute to the UT receptor binding pocket, enabled us to further refine our homology-based model of how U-II interacts with its cognate receptor.

Forest structure and downed woody debris in boreal temperate, and tropical forest fragments

Treesearch

William A. Gould; Grizelle Gonzalez; Andrew T. Hudak; Teresa Nettleton Hollingsworth; Jamie Hollingsworth

2008-01-01

Forest fragmentation affects the heterogeneity of accumulated fuels by increasing the diversity of forest types and by increasing forest edges. This heterogeneity has implications in how we manage fuels, fire, and forests. Understanding the relative importance of fragmentation on woody biomass within a single climatic regime, and along climatic gradients, will improve...

Fragmentation of eastern United States forest types

Treesearch

Kurt H. Riitters; John W. Coulston

2013-01-01

Fragmentation is a continuing threat to the sustainability of forests in the Eastern United States, where land use changes supporting a growing human population are the primary driver of forest fragmentation (Stein and others 2009). While once mostly forested, approximately 40 percent of the original forest area has been converted to other land uses, and most of the...

Comparative analysis by polymerase chain reaction amplified minicircles of kinetoplast DNA of a stable strain of Trypanosoma cruzi from São Felipe, Bahia, its clones and subclones: possibility of predominance of a principal clone in this area.

PubMed

Campos, R F; Gonçalves, M S; dos Reis, E A; dos Reis, M G; Andrade, S G

1999-01-01

Molecular characterization of one stable strain of Trypanosoma cruzi, the 21 SF, representative of the pattern of strains isolated from the endemic area of São Felipe, State of Bahia, Brazil, maintained for 15 years in laboratory by serial passages in mice and classified as biodeme Type II and zymodeme 2 has been investigated. The kinetoplast DNA (kDNA) of parental strain, 5 clones and 14 subclones were analyzed. Schizodeme was established by comparative study of the fragments obtained from digestion of the 330-bp fragments amplified by polymerase chain reaction (PCR) from the variable regions of the minicircles, and digested by restriction endonucleases Rsa I and Hinf I. Our results show a high percentual of similarity between the restriction fragment length polymorphism (RFLP) for the parental strain and its clones and among these individual clones and their subclones at a level of 80 to 100%. This homology indicates a predominance of the same "principal clone" in the 21SF strain and confirms the homogeneity previously observed at biological and isozymic analysis. These results suggest the possibility that the T. cruzi strains with similar biological and isoenzymic patterns, circulating in this endemic area, are representative of one dominant clone. The presence of "principal clones" could be responsible for a predominant tropism of the parasites for specific organs and tissues and this could contribute to the pattern of clinico-pathological manifestations of Chagas's disease in one geographical area.

Use of indicator chemicals to characterize the plastic fragments ingested by Laysan albatross.

PubMed

Nilsen, Frances; David Hyrenbach, K; Fang, Jiasong; Jensen, Brenda

2014-10-15

Laysan albatross (Phoebastria immutabilis) ingest plastic marine debris of a wide range of shape, sizes and sources. To better characterize this plastic and provide insights regarding its provenance and persistence in the environment, we developed a simple method to classify plastic fragments of unknown origin according to the resin codes used by the Society of Plastics Industry. Known plastics were analyzed by gas chromatography-mass spectroscopy (GC-MS) to identify indicator chemicals characteristic of each plastic resin. Application of this method to fragments of ingested plastic debris from boluses of Laysan albatross from Kure Atoll, Hawai'i, yielded proportions of 0.8% High Density Polyethylene, 6.8% Polystyrene, 8.5% Polyethylene Terephthalate, 20.5% Polyvinyl Chloride and 68.4% Polypropylene. Some fragments were composed of multiple resin types. These results suggest that infrequently recycled plastics are the dominant fragments ingested by albatross, and that these are the most prevalent and persistent resin types in the marine environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mycoplasma-induced BALB/c 3T3 collagenase is a mammalian enzyme.

PubMed Central

Kluve, B; Merrick, W C; Gershman, H

1983-01-01

A collagenase previously reported to accumulate in the medium of cultures of BALB/c 3T3 cells on infection with Mycoplasma orale [Kluve, Merrick, Stanbridge & Gershman (1981) Nature (London) 292, 855-857] was partially purified and characterized. With regard to purification properties, activation, sensitivity to inhibitors and relative molecular mass the enzyme was similar to previously reported vertebrate collagenases, but could not be unequivocally distinguished from bacterial collagenases. With regard to substrate-specificity and reaction products, however, the collagenase was typical of vertebrate collagenases and distinct from bacterial collagenases. Specifically, the enzyme displayed a preference for type III collagen and type I collagen, a somewhat decreased ability to degrade type II collagen, and a very limited ability to degrade type IV collagen. The initial products of the action of the collagenase on type I collagen were characterized as fragments one-quarter and three-quarters of the length of the intact collagen molecule. Because the properties of the collagenase produced by cultures of mycoplasma-infected BALB/c 3T3 cells are those of a mammalian-type (vertebrate-type) enzyme, we have concluded that the collagenase is a product of the mouse (BALB/c 3T3) genome, and is not produced by the mycoplasma. Therefore it appears that infection of BALB/c 3T3 mouse fibroblasts with Mycoplasma orale induces the mouse cells to produce and secrete collagenase. PMID:6309150

Detection of Methanotroph Diversity on Roots of Submerged Rice Plants by Molecular Retrieval of pmoA, mmoX, mxaF, and 16S rRNA and Ribosomal DNA, Including pmoA-Based Terminal Restriction Fragment Length Polymorphism Profiling

PubMed Central

Horz, Hans-Peter; Yimga, Merlin Tchawa; Liesack, Werner

2001-01-01

The diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. The research focused mainly on the retrieval of pmoA, which encodes the α subunit of the particulate methane monooxygenase. A novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (T-RFLP) technique. The T-RFLP profiles clearly revealed a more complex root-associated methanotrophic community than did banding patterns obtained by pmoA-based denaturing gradient gel electrophoresis. The comparison of pmoA-based T-RFLP profiles obtained from rice roots and bulk soil of flooded rice microcosms suggested that there was a substantially higher abundance of type I methanotrophs on rice roots than in the bulk soil. These were affiliated to the genera Methylomonas, Methylobacter, Methylococcus, and to a novel type I methanotroph sublineage. By contrast, type II methanotrophs of the Methylocystis-Methylosinus group could be detected with high relative signal intensity in both soil and root compartments. Phylogenetic treeing analyses and a set of substrate-diagnostic amino acid residues provided evidence that a novel pmoA lineage was detected. This branched distinctly from all currently known methanotrophs. To examine whether the retrieval of pmoA provided a complete view of root-associated methanotroph diversity, we also assessed the diversity detectable by recovery of genes coding for subunits of soluble methane monooxygenase (mmoX) and methanol dehydrogenase (mxaF). In addition, both 16S rRNA and 16S ribosomal DNA (rDNA) were retrieved using a PCR primer set specific to type I methanotrophs. The overall methanotroph diversity detected by recovery of mmoX, mxaF, and 16S rRNA and 16S rDNA corresponded well to the diversity detectable by retrieval of pmoA. PMID:11526021

A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis.

PubMed

Gòdia, Marta; Mayer, Fabiana Quoos; Nafissi, Julieta; Castelló, Anna; Rodríguez-Gil, Joan Enric; Sánchez, Armand; Clop, Alex

2018-04-26

The study of the boar sperm transcriptome by RNA-seq can provide relevant information on sperm quality and fertility and might contribute to animal breeding strategies. However, the analysis of the spermatozoa RNA is challenging as these cells harbor very low amounts of highly fragmented RNA, and the ejaculates also contain other cell types with larger amounts of non-fragmented RNA. Here, we describe a strategy for a successful boar sperm purification, RNA extraction and RNA-seq library preparation. Using these approaches our objectives were: (i) to evaluate the sperm recovery rate (SRR) after boar spermatozoa purification by density centrifugation using the non-porcine-specific commercial reagent BoviPure TM ; (ii) to assess the correlation between SRR and sperm quality characteristics; (iii) to evaluate the relationship between sperm cell RNA load and sperm quality traits and (iv) to compare different library preparation kits for both total RNA-seq (SMARTer Universal Low Input RNA and TruSeq RNA Library Prep kit) and small RNA-seq (NEBNext Small RNA and TailorMix miRNA Sample Prep v2) for high-throughput sequencing. Our results show that pig SRR (~22%) is lower than in other mammalian species and that it is not significantly dependent of the sperm quality parameters analyzed in our study. Moreover, no relationship between the RNA yield per sperm cell and sperm phenotypes was found. We compared a RNA-seq library preparation kit optimized for low amounts of fragmented RNA with a standard kit designed for high amount and quality of input RNA and found that for sperm, a protocol designed to work on low-quality RNA is essential. We also compared two small RNA-seq kits and did not find substantial differences in their performance. We propose the methodological workflow described for the RNA-seq screening of the boar spermatozoa transcriptome. FPKM: fragments per kilobase of transcript per million mapped reads; KRT1: keratin 1; miRNA: micro-RNA; miscRNA: miscellaneous RNA; Mt rRNA: mitochondrial ribosomal RNA; Mt tRNA: mitochondrial transference RNA; OAZ3: ornithine decarboxylase antizyme 3; ORT: osmotic resistance test; piRNA: Piwi-interacting RNA; PRM1: protamine 1; PTPRC: protein tyrosine phosphatase receptor type C; rRNA: ribosomal RNA; snoRNA: small nucleolar RNA; snRNA: small nuclear RNA; SRR: sperm recovery rate; tRNA: transfer RNA.

Spatial distribution of soil properties on a landslide in Taiwan: effects of movement types and vegetation

NASA Astrophysics Data System (ADS)

Lee, Pei-Chen; Cheng, Chih-Hsin

2017-04-01

Landslides are critical natural disturbances in tropical and temperate areas and exert immense impacts on forest ecosystems and soil properties. The impacts of landslides on soil properties not only vary with their movement type, scale, or location but also have great spatial variation inside landslide. In this study, the effects of movement type (erosion and deposition) and succeeding vegetation on soil properties inside a landslide scar were evaluated. The study site was located in Chiufenernshan, central Taiwan. The landslide was triggered by the Chi-Chi Earthquake (Ritch magnitude 7.3) in 1999. A huge amount of waste debris (30 million m3) was moved along the sliding slope (with a tipping degree at 26o) and deposited in the lower parts. Total area size of landslide scar was 200 ha and about 30 - 50 m depth waste material was eroded/deposited in the upper/lower scar areas. After 17 years, the succeeding vegetation varied inside landslide scar. The erosion areas were covered with grass (Miscanthus floridulus) or left barren in some slopes. In contrast, a secondary forest, dominated with Trema orientalis, Lithocarpus konishii, Mallotus paniculatus, and Smilax bracteata, developed in the deposition areas. We collected soil samples in different landscape areas including (i) erosion areas without vegetation, (ii) erosion areas with grass vegetation, (iii) deposition areas, and (iv) adjacent undisturbed areas. Our results indicated that the erosion areas had higher bulk density, rock fragment and pH value, but less soil organic carbon, total nitrogen, total phosphorus and N-mineralization rate than both deposition and adjacent undisturbed areas. The soil properties without vegetation even showed the extreme end compared to the soils with grass vegetation. Soils at the deposition zone had similar rock fragment, bulk density, soil pH, soil organic carbon and N-mineralization rate values to the undisturbed site (p > 0.05). We speculate that movement types could determine the initial establishment of vegetation types and then influence soil properties under vegetation succession. Therefore, both waste movement types and vegetation and their interactions play important roles on soil properties.

In vitro inhibition of African swine fever virus-topoisomerase II disrupts viral replication.

PubMed

Freitas, Ferdinando B; Frouco, Gonçalo; Martins, Carlos; Leitão, Alexandre; Ferreira, Fernando

2016-10-01

African swine fever virus (ASFV) is the etiological agent of a highly-contagious and fatal disease of domestic pigs, leading to serious socio-economic impact in affected countries. To date, neither a vaccine nor a selective anti-viral drug are available for prevention or treatment of African swine fever (ASF), emphasizing the need for more detailed studies at the role of ASFV proteins involved in viral DNA replication and transcription. Notably, ASFV encodes for a functional type II topoisomerase (ASFV-Topo II) and we recently showed that several fluoroquinolones (bacterial DNA topoisomerase inhibitors) fully abrogate ASFV replication in vitro. Here, we report that ASFV-Topo II gene is actively transcribed throughout infection, with transcripts being detected as early as 2 hpi and reaching a maximum peak concentration around 16 hpi, when viral DNA synthesis, transcription and translation are more active. siRNA knockdown experiments showed that ASFV-Topo II plays a critical role in viral DNA replication and gene expression, with transfected cells presenting lower viral transcripts (up to 89% decrease) and reduced cytopathic effect (-66%) when compared to the control group. Further, a significant decrease in the number of both infected cells (75.5%) and viral factories per cell and in virus yields (up to 99.7%, 2.5 log) was found only in cells transfected with siRNA targeting ASFV-Topo II. We also demonstrate that a short exposure to enrofloxacin during the late phase of infection (from 15 to 1 hpi) induces fragmentation of viral genomes, whereas no viral genomes were detected when enrofloxacin was added from the early phase of infection (from 2 to 16 hpi), suggesting that fluoroquinolones are ASFV-Topo II poisons. Altogether, our results demonstrate that ASFV-Topo II enzyme has an essential role during viral genome replication and transcription, emphasizing the idea that this enzyme can be a potential target for drug and vaccine development against ASF. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis of the human insulin gene. Part II. Further improvements in the modified phosphotriester method and the synthesis of seventeen deoxyribooligonucleotide fragments constituting human insulin chains B and mini-CDNA.

PubMed Central

Sung, W L; Hsiung, H M; Brousseau, R; Michniewicz, J; Wu, R; Narang, S A

1979-01-01

The purification of protected deoxyribooligonucleotides containing phosphotriester internucleotidic linkages has been improved by developing a deactivated silica gel chromatographic technique. The efficiency of this technique as applied in the modified phosphotriester approach has been demonstrated in the rapid synthesis of seventeen pure fragments constituting the sequence of human insulin B and mini-C DNA. The sequence of each oligomer was confirmed by the two-dimensional mobility shift method of fingerprinting. Images PMID:230464

Degradation of glyceraldehyde-3-phosphate dehydrogenase triggered by 4-hydroxy-2-nonenal and 4-hydroxy-2-hexenal.

PubMed

Tsuchiya, Yukihiro; Yamaguchi, Mitsune; Chikuma, Toshiyuki; Hojo, Hiroshi

2005-06-15

Lipid peroxidation products such as 4-hydroxy-2-nonenal (HNE) may be responsible for various pathophysiological events under oxidative stress, since they injure cellular components such as proteins and DNA. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is a key enzyme of glycolysis and has been reported to be a multifunctional enzyme, is one of the enzymes inhibited by HNE. Previous studies showed that GAPDH is degraded when incubated with acetylleucine chloromethyl ketone (ALCK), resulting in the liberation of a 23-kDa fragment. In this study, we examined whether GAPDH incubated with HNE or other aldehydes of lipid peroxidation products are degraded similarly to that with ALCK. The U937 cell extract was incubated with these aldehydes at 37 degrees C and analyzed by Western blotting using anti-GAPDH antibodies. Incubation with HNE or 4-hydroxy-2-hexenal (HHE) decreased GAPDH activity and GAPDH protein level, and increased the 23-kDa fragment, in time- and dose-dependent manners, but that with other aldehydes did not. Gel filtration using the Superose 6 showed that the GAPDH-degrading activity was eluted in higher molecular fractions than proteasome activity. The enzyme activity was detected at the basic range of pH and inhibited by serine protease inhibitors, diisopropyl fluorophosphate and phenylmethylsulfonyl fluoride, but not by other protease inhibitors including a proteasome inhibitor, MG-132, and a tripeptidyl peptidase II (TPP II) inhibitor, AAF-CMK. These results suggest that GAPDH modified by HNE and HHE is degraded by a giant serine protease, releasing the 23-kDa fragment, not by proteasome or TPP II.

Products of Submarine Fountains and Bubble-burst Eruptive Activity at 1200 m on West Mata Volcano, Lau Basin

NASA Astrophysics Data System (ADS)

Clague, D. A.; Rubin, K. H.; Keller, N. S.

2009-12-01

An eruption was observed and sampled at West Mata Volcano using ROV JASON II for 5 days in May 2009 during the NSF-NOAA eruption response cruise to this region of suspected volcanic activity. Activity was focused near the summit at the Prometheus and Hades vents. Prometheus erupted almost exclusively as low-level fountains. Activity at Hades cycled between vigorous degassing, low fountains, and bubble-bursts, building up and partially collapsing a small spatter/scoria cone and feeding short sheet-like and pillow flows. Fire fountains at Prometheus produced mostly small primary pyroclasts that include Pele's hair and fluidal fragments of highly vesicular volcanic glass. These fragments have mostly shattered and broken surfaces, although smooth spatter-like surfaces also occur. As activity wanes, glow in the vent fades, and denser, sometimes altered volcanic clasts are incorporated into the eruption. The latter are likely from the conduit walls and/or vent-rim ejecta, drawn back into the vent by inrushing seawater that replaces water entrained in the rising volcanic plume. Repeated recycling of previously erupted materials eventually produces rounded clasts resembling beach cobbles and pitted surfaces on broken phenocrysts of pyroxene and olivine. We estimate that roughly 33% of near vent ejecta are recycled. Our best sample of this ejecta type was deposited in the drawer of the JASON II ROV during a particularly large explosion that occurred during plume sampling immediately above the vent. Elemental sulfur spherules up to 5 mm in diameter are common in ejecta from both vents and occur inside some of the lava fragments Hades activity included dramatic bubble-bursts unlike anything previously observed under water. The lava bubbles, sometimes occurring in rapid-fire sequence, collapsed in the water-column, producing fragments that are quenched in less than a second to form Pele's hair, limu o Pele, spatter-like lava blobs, and scoria. All are highly vesicular, including the hairs and limu, unlike similar fragments from Loihi Seamount, Axial Seamount, and mid-ocean ridges that have <10% vesicles. The lava bubbles were observed to reach about 1 m in diameter, sometimes appearing to separate from the lava surface, suggesting that they are fed by gasses rising directly from the conduit. Slow-motion video analysis shows that the lava skin stretches to form thin regions that then separate, exposing still incandescent gas within. Bubbles collapse as the lava skin disrupts (usually at the top of the bubble), producing a shower of convex spatter-like lava fragments. Sheet-like lava flows are associated with collapse of the spatter cone and change to pillow lobe extrusion about 5 m from the vent orifice. One pillow lobe sample collected molten contains ~60% vesicles. We suggest that the erupting melt contains large coalesced slugs of magmatic gas and abundant small expanding vesicles that have yet to be incorporated into the large gas slugs. The contrast with Prometheus suggests highly localized conditions of magma devolatilization at W. Mata.

Morph-specific differences in reproductive success in the distylous Primula veris in a context of habitat fragmentation

NASA Astrophysics Data System (ADS)

Van Rossum, Fabienne; De Sousa, Sara Campos; Triest, Ludwig

2006-11-01

Heterostylous self-incompatible plant species are particularly sensitive to habitat fragmentation and to disruption of pollination processes because of the need of intermorph cross-pollination for producing seeds. Heterostyly is characterized by sexual polymorphism through the occurrence of two (distyly) or three (tristyly) morph types that differ in floral traits (style length and anther position). We examined whether the long-styled (pin) and short-styled (thrum) morph types show differences in reproductive components and responses to habitat fragmentation in the distylous, self-incompatible perennial herb Primula veris. We documented reproductive components for pin and thrum individuals and their relationships with population size, plant density and morph ratio (pin frequency), in nine populations from Flanders (northern Belgium) located in fragmented habitats of the intensively used agricultural landscape. Seed abortion increased in small populations as a result of inbreeding depression. Fruit set increased with plant density. Seed set was positively related to pin proportion. Seed set was higher for pin than thrum in small populations, but lower in large populations. Two hypotheses can be considered to explain these morph-specific differences: a pollen transfer asymmetry, and a reproductive advantage for the partially self-compatible pin morph. Morph types appear to respond differently to habitat fragmentation constraints. A floral morph type showing partial self-compatibility may be favored in populations under pollination failure, because it can increase reproductive success and mating opportunities through intramorph crosses.

FAST TRACK COMMUNICATION: The nonlinear fragmentation equation

NASA Astrophysics Data System (ADS)

Ernst, Matthieu H.; Pagonabarraga, Ignacio

2007-04-01

We study the kinetics of nonlinear irreversible fragmentation. Here, fragmentation is induced by interactions/collisions between pairs of particles and modelled by general classes of interaction kernels, for several types of breakage models. We construct initial value and scaling solutions of the fragmentation equations, and apply the 'non-vanishing mass flux' criterion for the occurrence of shattering transitions. These properties enable us to determine the phase diagram for the occurrence of shattering states and of scaling states in the phase space of model parameters.

Complexation humic substances of soils with metal ions as the main way migration of matals from soil to water

NASA Astrophysics Data System (ADS)

Dinu, Marina

2013-04-01

Organic matter (OM) of natural waters can bind with the ions metals (IM) entering the system, thus reducing their toxic properties. OM in water consists predominantly (up to 80%) of humic acids (HA), represented by highmolecular, dyed, polyfunctional compounds. The natural-climatic zones feature various ratios of fulvic (FA) and humic acids. An important specific feature of metals as contamination elements is the fact that when they occur in the environment, their potential toxicity and bioavailability depend significantly on their speciation. In recent years, lakes have been continuously enriched in hazardous elements such as Pb, Cd, Al, and Cr on a global (regional) basis. The most important organic ligands are humic matter (HM) washed out from soils in water and metals occur in natural waters as free ions, simple complexes with inorganic and organic ligands, and mineral and organic particles of molecules and ions sorbed on the surface. The occurrence of soluble metal forms in natural waters depends on the presence of organic and inorganic anions. However, direct determinations are rather difficult. The goal was the calculation and analysis of the forms of metals in the system catchment basin, based on the chemical composition of the water body and the structural features of soil humic substances (HS).We used the following analytical techniques - leaching of humic substances from soil and sample preparation (Orlov DS, 1985), the functional characteristics of humic substances - spectral analysis methods, the definition of conditional stability constants of complexes - electrochemical methods of analysis. Our results show thet HAs of selected soil types are different in functions, and these differences effect substantially the complexing process. When analyzing the results obtained in the course of spectrometric investigation of HMs in selected soil types, we determined the following main HA characteristics: (1) predominance of oxygen bearing groups in HM of the northern taiga soils; (2) similar amounts of oxygen bearing fragments, hydrocarbon constituents, and nitrogen bearing components in the mixed forest zones; (3) occurrence of aromatic and aliphatic hydrocarbons in HM of steppe soils. The HM functional characteristics influence substantially the stability constants of complexes with metal ions and complex stoichiometry: Fe(III)>Cu(II)>Pb(II)>Al(III)>Co(II)>Ni(II)>Cd(II)>Zn(II)>Cr(III)>Mg(II)>Sr(II)>Ca(II)>Mn(II) - northern taiga soils; Cu(II)>Fe(III)>Al(III)>Ni(II)>Zn(II)>Pb(II)>Co(II)>Cd(II)>Sr(II)>Mn(II)>Cr(III)>Ca(II)>Mg(II) - mixed forest zones; Fe(III)>Cu(II)>Al(III)>Pb(II)>Ni(II)>Zn(II)>Co(II)>Ca(II)>Cd(II)>Sr(II)>Mg(II)>Cr(III)>Mn(II) - steppe soils. 1. T.I. Moiseenko, L.P. Kudryavtseva, and N.A. Gashkina, Scattered Element in Surface Land Waters: Technophility, Bioaccumulation, and Ecotoxicology (Nauka, Moscow, 2006) 2. G. M. Varshal, Ext. Abstr. Doct. Dis. Chem. (Inst. Geokh. Analit. Khim. RAN, Moscow, 1994).. 4. D.S. Orlov, Humic Acids (MGU, Moscow, 1986) 5. D.V. Kovalevsky, Ext. Abstr. Cand. Dis. Chem. (MGU, Moscow, 1998). 6. I.A. Linnik and B. I. Nabivanets, Metal Migration Forms in Surface Fresh Waters (Gidrometizdat, Leningrad, 1985) 7. Hartley, F., Burgess, C., and Alcoc, R., Solution Equilibria (Ellis Horwood, Chichester (UK), 1980). 8. Yu. Yu. Lur'e, Reference Book of Physicochemical Values (Nauka, Moscow, 2000)

Cadmium-induced immune abnormality is a key pathogenic event in human and rat models of preeclampsia.

PubMed

Zhang, Qiong; Huang, Yinping; Zhang, Keke; Huang, Yanjun; Yan, Yan; Wang, Fan; Wu, Jie; Wang, Xiao; Xu, Zhangye; Chen, Yongtao; Cheng, Xue; Li, Yong; Jiao, Jinyu; Ye, Duyun

2016-11-01

With increased industrial development, cadmium is an increasingly important environmental pollutant. Studies have identified various adverse effects of cadmium on human beings. However, the relationships between cadmium pollution and the pathogenesis of preeclampsia remain elusive. The objective of this study is to explore the effects of cadmium on immune system among preeclamptic patients and rats. The results showed that the cadmium levels in the peripheral blood of preeclamptic patients were significantly higher than those observed in normal pregnancy. Based on it, a novel rat model of preeclampsia was established by the intraperitoneal administration of cadmium chloride (CdCl2) (0.125 mg of Cd/kg body weight) on gestational days 9-14. Key features of preeclampsia, including hypertension, proteinuria, placental abnormalities and small foetal size, appeared in pregnant rats after the administration of low-dose of CdCl2. Cadmium increased immunoglobulin production, mainly angiotensin II type 1-receptor-agonistic autoantibodies (AT1-AA), by increasing the expression of activation-induced cytosine deaminase (AID) in B cells. AID is critical for the maturation of antibody and autoantibody responses. In addition, angiotensin II type 1-receptor-agonistic autoantibody, which emerged recently as a potential pathogenic contributor to PE, was responsible for the deposition of complement component 5 (C5) in kidneys of pregnant rats via angiotensin II type 1 receptor (AT1R) activation. C5a is a fragment of C5 that is released during C5 activation. Selectively interfering with C5a signalling by a complement C5a receptor-specific antagonist significantly attenuated hypertension and proteinuria in Cd-injected pregnant rats. Our results suggest that cadmium induces immune abnormalities that may be a key pathogenic contributor to preeclampsia and provide new insights into treatment strategies of preeclampsia. Copyright © 2016 Elsevier Ltd. All rights reserved.

When and how to operate the posterior malleolus fragment in trimalleolar fractures: a systematic literature review.

PubMed

Verhage, Samuel Marinus; Hoogendoorn, Jochem Maarten; Krijnen, Pieta; Schipper, Inger Birgitta

2018-05-12

Whether or not and how to fixate the posterior malleolus fracture seems to depend on the fracture fragment size and its amount of dislocation, but clear guidelines for daily practice are lacking. In this review, we summarize the literature on preferred treatment of the posterior fragment in trimalleolar fractures. A systematic review of publications between January 1995 and April 30 2017 on this topic in the PubMed, Embase, and Cochrane databases was performed according to the PRISMA statement. Seventeen (2 prospective and 15 retrospective) of the 180 identified studies were included. Six studies report on indications for fixation of posterior malleolus fracture fragments. Eleven studies compare different fixation approaches and techniques for the posterior fragment. Meta-analysis was not possible due to varying fixation criteria and outcomes. There was no clear association between posterior fragment size and functional outcome or development of osteoarthritis. The non-anatomical reduction of the fragment was of more influence on outcome. Radiological and functional outcome was better after open reduction and internal fixation via the posterolateral approach than after percutaneous anterior-to-posterior screw fixation. The posterior fragment size is not a clear indication for its fixation. A step-off, however, seems an important indicator for developing posttraumatic osteoarthritis and worse functional outcome. Posterior fragments involving the intra-articular surface need to be reduced and fixated to prevent postoperative persisting step-off. Furthermore, fixation of the posterior malleolus via an open posterolateral approach seems superior to percutaneous anterior-to-posterior fixation. However, these results need to be confirmed in a prospective comparative trial. Therapeutic level II.

Linkage map of the fragments of herpesvirus papio DNA.

PubMed Central

Lee, Y S; Tanaka, A; Lau, R Y; Nonoyama, M; Rabin, H

1981-01-01

Herpesvirus papio (HVP), an Epstein-Barr-like virus, causes lymphoblastoid disease in baboons. The physical map of HVP DNA was constructed for the fragments produced by cleavage of HVP DNA with restriction endonucleases EcoRI, HindIII, SalI, and PvuI, which produced 12, 12, 10, and 4 fragments, respectively. The total molecular size of HVP DNA was calculated as close to 110 megadaltons. The following methods were used for construction of the map; (i) fragments near the ends of HVP DNA were identified by treating viral DNA with lambda exonuclease before restriction enzyme digestion; (ii) fragments containing nucleotide sequences in common with fragments from the second enzyme digest of HVP DNA were examined by Southern blot hybridization; and (iii) the location of some fragments was determined by isolating individual fragments from agarose gels and redigesting the isolated fragments with a second restriction enzyme. Terminal heterogeneity and internal repeats were found to be unique features of HVP DNA molecule. One to five repeats of 0.8 megadaltons were found at both terminal ends. Although the repeats of both ends shared a certain degree of homology, it was not determined whether they were identical repeats. The internal repeat sequence of HVP DNA was found in the EcoRI-C region, which extended from 8.4 to 23 megadaltons from the left end of the molecule. The average number of the repeats was calculated to be seven, and the molecular size was determined to be 1.8 megadaltons. Similar unique features have been reported in EBV DNA (D. Given and E. Kieff, J. Virol. 28:524-542, 1978). Images PMID:6261015

Epidemiologic and Molecular Relationship Between Vaccine Manufacture and Autism Spectrum Disorder Prevalence.

PubMed

Deisher, Theresa A; Doan, Ngoc V; Koyama, Kumiko; Bwabye, Sarah

2015-01-01

To assess the public health consequences of fetal cell line manufactured vaccines that contain residual human fetal DNA fragments utilizing laboratory and ecological approaches including statistics, molecular biology and genomics. MMR coverage and autism disorder or autism spectrum disorder prevalence data for Norway, Sweden and the UK were obtained from public and government websites as well as peer reviewed published articles. Biologically, the size and quantity of the contaminating fetal DNA in Meruvax II and Havrix as well as the propensity of various cell lines for cellular and nuclear uptake of primitive human DNA fragments were measured and quantified using gel electrophoresis, fluorescence microscopy and fluorometry. Lastly, genomic analysis identified the specific sites where fetal DNA fragment integration into a child's genome is most likely to occur. The average MMR coverage for the three countries fell below 90% after Dr. Wakefield's infamous 1998 publication but started to recover slowly after 2001 until reaching over 90% coverage again by 2004. During the same time period, the average autism spectrum disorder prevalence in the United Kingdom, Norway and Sweden dropped substantially after birth year 1998 and gradually increased again after birth year 2000. Average single stranded DNA and double stranded DNA in Meruvax II were 142.05 ng/vial and 35.00 ng/vial, respectively, and 276.00 ng/vial and 35.74 ng/vial in Havrix respectively. The size of the fetal DNA fragments in Meruvax II was approximately 215 base pairs. There was spontaneous cellular and nuclear DNA uptake in HFF1 and NCCIT cells. Genes that have been linked to autism (autism associated genes; AAGs) have a more concentrated susceptibility for insults to genomic stability in comparison to the group of all genes contained within the human genome. Of the X chromosome AAGs, 15 of 19 have double strand break motifs less than 100 kilobases away from the center of a meiotic recombination hotspot located within an exon. Vaccines manufactured in human fetal cell lines contain unacceptably high levels of fetal DNA fragment contaminants. The human genome naturally contains regions that are susceptible to double strand break formation and DNA insertional mutagenesis. The "Wakefield Scare" created a natural experiment that may demonstrate a causal relationship between fetal cell-line manufactured vaccines and ASD prevalence.

Negative Impacts of Human Land Use on Dung Beetle Functional Diversity

PubMed Central

Barragán, Felipe; Moreno, Claudia E.; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

2011-01-01

The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed. PMID:21448292

Native and exotic plants of fragments of sagebrush steppe produced by geomorphic processes versus land use

USGS Publications Warehouse

Huntly, N.; Bangert, R.; Hanser, S.E.

2011-01-01

Habitat fragmentation and invasion by exotic species are regarded as major threats to the biodiversity of many ecosystems. We surveyed the plant communities of two types of remnant sagebrush-steppe fragments from nearby areas on the Snake River Plain of southeastern Idaho, USA. One type resulted from land use (conversion to dryland agriculture; hereafter AG Islands) and the other from geomorphic processes (Holocene volcanism; hereafter kipukas). We assessed two predictions for the variation in native plant species richness of these fragments, using structural equation models (SEM). First, we predicted that the species richness of native plants would follow the MacArthur-Wilson (M-W) hypothesis of island biogeography, as often is expected for the communities of habitat fragments. Second, we predicted a negative relationship between native and exotic plants, as would be expected if exotic plants are decreasing the diversity of native plants. Finally, we assessed whether exotic species were more strongly associated with the fragments embedded in the agricultural landscape, as would be expected if agriculture had facilitated the introduction and naturalization of non-native species, and whether the communities of the two types of fragments were distinct. Species richness of native plants was not strongly correlated with M-W characteristics for either the AG Islands or the **kipukas. The AG Islands had more species and higher cover of exotics than the kipukas, and exotic plants were good predictors of native plant species richness. Our results support the hypothesis that proximity to agriculture can increase the diversity and abundance of exotic plants in native habitat. In combination with other information, the results also suggest that agriculture and exotic species have caused loss of native diversity and reorganization of the sagebrush-steppe plant community. ?? 2011 Springer Science+Business Media B.V.

Negative impacts of human land use on dung beetle functional diversity.

PubMed

Barragán, Felipe; Moreno, Claudia E; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

2011-03-23

The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed.

Forest fragments as barriers to fruit fly dispersal: Anastrepha (Diptera: Tephritidae) populations in orchards and adjacent forest fragments in Puerto Rico

USDA-ARS?s Scientific Manuscript database

McPhail-type traps baited with ammonium acetate and putrescine were used to monitor populations of Anastrepha obliqua and A. suspensa at four sites in Guánica, Puerto Rico; one forest fragment in Ponce, Puerto Rico; in a commercial mango orchard in Guayanilla, PR; and an experimental carambola orcha...

Atmospheric-pressure ionization and fragmentation of peptides by solution-cathode glow discharge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwartz, Andrew J.; Shelley, Jacob T.; Walton, Courtney L.

Modern “-omics” (e.g., proteomics, glycomics, metabolomics, etc.) analyses rely heavily on electrospray ionization and tandem mass spectrometry to determine the structural identity of target species. Unfortunately, these methods are limited to specialized mass spectrometry instrumentation. Here in this paper, a novel approach is described that enables ionization and controlled, tunable fragmentation of peptides at atmospheric pressure. In the new source, a direct-current plasma is sustained between a tapered metal rod and a flowing sample-containing solution. As the liquid stream contacts the electrical discharge, peptides from the solution are volatilized, ionized, and fragmented. At high discharge currents (e.g., 70 mA), electrospray-likemore » spectra are observed, dominated by singly and doubly protonated molecular ions. At lower currents (35 mA), many peptides exhibit extensive fragmentation, with a-, b-, c-, x-, and y-type ion series present as well as complex fragments, such as d-type ions, not previously observed with atmospheric-pressure dissociation. Though the mechanism of fragmentation is currently unclear, observations indicate it could result from the interaction of peptides with gas-phase radicals or ultraviolet radiation generated within the plasma.« less

Atmospheric-pressure ionization and fragmentation of peptides by solution-cathode glow discharge

DOE PAGES

Schwartz, Andrew J.; Shelley, Jacob T.; Walton, Courtney L.; ...

2016-06-27

Modern “-omics” (e.g., proteomics, glycomics, metabolomics, etc.) analyses rely heavily on electrospray ionization and tandem mass spectrometry to determine the structural identity of target species. Unfortunately, these methods are limited to specialized mass spectrometry instrumentation. Here in this paper, a novel approach is described that enables ionization and controlled, tunable fragmentation of peptides at atmospheric pressure. In the new source, a direct-current plasma is sustained between a tapered metal rod and a flowing sample-containing solution. As the liquid stream contacts the electrical discharge, peptides from the solution are volatilized, ionized, and fragmented. At high discharge currents (e.g., 70 mA), electrospray-likemore » spectra are observed, dominated by singly and doubly protonated molecular ions. At lower currents (35 mA), many peptides exhibit extensive fragmentation, with a-, b-, c-, x-, and y-type ion series present as well as complex fragments, such as d-type ions, not previously observed with atmospheric-pressure dissociation. Though the mechanism of fragmentation is currently unclear, observations indicate it could result from the interaction of peptides with gas-phase radicals or ultraviolet radiation generated within the plasma.« less

A global analysis of traits predicting species sensitivity to habitat fragmentation

USGS Publications Warehouse

Keinath, Douglas; Doak, Daniel F.; Hodges, Karen E.; Prugh, Laura R.; Fagan, William F.; Sekercioglu, Cagan H.; Buchart, Stuart H. M.; Kauffman, Matthew J.

2017-01-01

AimElucidating patterns in species responses to habitat fragmentation is an important focus of ecology and conservation, but studies are often geographically restricted, taxonomically narrow or use indirect measures of species vulnerability. We investigated predictors of species presence after fragmentation using data from studies around the world that included all four terrestrial vertebrate classes, thus allowing direct inter-taxonomic comparison.LocationWorld-wide.MethodsWe used generalized linear mixed-effect models in an information theoretic framework to assess the factors that explained species presence in remnant habitat patches (3342 patches; 1559 species, mostly birds; and 65,695 records of patch-specific presence–absence). We developed a novel metric of fragmentation sensitivity, defined as the maximum rate of change in probability of presence with changing patch size (‘Peak Change’), to distinguish between general rarity on the landscape and sensitivity to fragmentation per se.ResultsSize of remnant habitat patches was the most important driver of species presence. Across all classes, habitat specialists, carnivores and larger species had a lower probability of presence, and those effects were substantially modified by interactions. Sensitivity to fragmentation (measured by Peak Change) was influenced primarily by habitat type and specialization, but also by fecundity, life span and body mass. Reptiles were more sensitive than other classes. Grassland species had a lower probability of presence, though sample size was relatively small, but forest and shrubland species were more sensitive.Main conclusionsHabitat relationships were more important than life-history characteristics in predicting the effects of fragmentation. Habitat specialization increased sensitivity to fragmentation and interacted with class and habitat type; forest specialists and habitat-specific reptiles were particularly sensitive to fragmentation. Our results suggest that when conservationists are faced with disturbances that could fragment habitat they should pay particular attention to specialists, particularly reptiles. Further, our results highlight that the probability of presence in fragmented landscapes and true sensitivity to fragmentation are predicted by different factors.

Development of a Multiplex Single Base Extension Assay for Mitochondrial DNA Haplogroup Typing

PubMed Central

Nelson, Tahnee M.; Just, Rebecca S.; Loreille, Odile; Schanfield, Moses S.; Podini, Daniele

2007-01-01

Aim To provide a screening tool to reduce time and sample consumption when attempting mtDNA haplogroup typing. Methods A single base primer extension assay was developed to enable typing, in a single reaction, of twelve mtDNA haplogroup specific polymorphisms. For validation purposes a total of 147 samples were tested including 73 samples successfully haplogroup typed using mtDNA control region (CR) sequence data, 21 samples inconclusively haplogroup typed by CR data, 20 samples previously haplogroup typed using restriction fragment length polymorphism (RFLP) analysis, and 31 samples of known ancestral origin without previous haplogroup typing. Additionally, two highly degraded human bones embalmed and buried in the early 1950s were analyzed using the single nucleotide polymorphisms (SNP) multiplex. Results When the SNP multiplex was used to type the 96 previously CR sequenced specimens, an increase in haplogroup or macrohaplogroup assignment relative to conventional CR sequence analysis was observed. The single base extension assay was also successfully used to assign a haplogroup to decades-old, embalmed skeletal remains dating to World War II. Conclusion The SNP multiplex was successfully used to obtain haplogroup status of highly degraded human bones, and demonstrated the ability to eliminate possible contributors. The SNP multiplex provides a low-cost, high throughput method for typing of mtDNA haplogroups A, B, C, D, E, F, G, H, L1/L2, L3, M, and N that could be useful for screening purposes for human identification efforts and anthropological studies. PMID:17696300

Chronic shin splints. Classification and management of medial tibial stress syndrome.

PubMed

Detmer, D E

1986-01-01

A clinical classification and treatment programme has been developed for chronic medial tibial stress syndrome. Medial tibial stress syndrome has been reported to be either tibial stress fracture or microfracture, tibial periostitis, or distal deep posterior chronic compartment syndrome. Three chronic types exist and may coexist: Type I (tibial microfracture, bone stress reaction or cortical fracture); type II (periostalgia from chronic avulsion of the periosteum at the periosteal-fascial junction); and type III (chronic compartment syndrome syndrome). Type I disease is treated nonoperatively. Operations for resistant types II and III medial tibial stress syndrome were performed in 41 patients. Bilaterality was common (type II, 50% type III, 88%). Seven had coexistent type II/III; one had type I/II. Preoperative symptoms averaged 24 months in type II, 6 months in type III, and 33 months in types II/III. Mean age was 22 years (15 to 51). Resting compartment pressures were normal in type II (mean 12 mm Hg) and elevated in type III and type II/III (mean 23 mm Hg). Type II and type II/III patients received fasciotomy plus periosteal cauterisation. Type III patients had fasciotomy only. All procedures were performed on an outpatient basis using local anaesthesia. Follow up was complete and averaged 6 months (2 to 14 months). Improved performance was as follows: type II, 93%, type III, 100%; type II/III, 86%. Complete cures were as follows: type II, 78%; type III, 75%; and type II/III, 57%. This experience suggests that with precise diagnosis and treatment involving minimal risk and cost the athlete has a reasonable chance of return to full activity.

An 'instant gene bank' method for gene cloning by mutant complementation.

PubMed

Gems, D; Aleksenko, A; Belenky, L; Robertson, S; Ramsden, M; Vinetski, Y; Clutterbuck, A J

1994-02-01

We describe a new method of gene cloning by complementation of mutant alleles which obviates the need for construction of a gene library in a plasmid vector in vitro and its amplification in Escherichia coli. The method involves simultaneous transformation of mutant strains of the fungus Aspergillus nidulans with (i) fragmented chromosomal DNA from a donor species and (ii) DNA of a plasmid without a selectable marker gene, but with a fungal origin of DNA replication ('helper plasmid'). Transformant colonies appear as the result of the joining of chromosomal DNA fragments carrying the wild-type copies of the mutant allele with the helper plasmid. Joining may occur either by ligation (if the helper plasmid is in linear form) or recombination (if it is cccDNA). This event occurs with high efficiency in vivo, and generates an autonomously replicating plasmid cointegrate. Transformants containing Penicillium chrysogenum genomic DNA complementing A. nidulans niaD, nirA and argB mutations have been obtained. While some of these cointegrates were evidently rearranged or consisted only of unaltered replicating plasmid, in other cases plasmids could be recovered into E. coli and were subsequently shown to contain the selected gene. The utility of this "instant gene bank" technique is demonstrated here by the molecular cloning of the P. canescens trpC gene.

Role of reef fauna in sediment transport and distribution - Studies from Tektite I and II

USGS Publications Warehouse

Clifton, H.E.

1973-01-01

1. Reef organisms may play a major role in the transport and distribution of sediment on the sea floor adjacent to coral reefs. 2. Some fish such as Malacanthus plumieri (Bloch) selectively transport and collect certain types of sediment (such as larger coral and shell fragments). 3. The random movement of crawling or burrowing organisms may cause a large amount of sediment to be shifted laterally on the sea floor. On slopes, a net downhill displacement may result. 4. The surface configuration and internal structure of the sediment is rapidly changed by faunal mixing. Ripple marks formed by waves or currents are obliterated by the activity of organisms in only a few weeks in the environment studied. Internal structure (bedding) near the sediment-water interface is similarly destroyed in a short period of time. 5. Larger clasts (including empty shells) on the sea floor tend to be buried by faunal undermining. The rate of burial depends primarily on the grain size of the substrate. 6. The random movement of fauna on the sea floor may produce a predominantly concave-up orientation of pelecypod shells and shell fragments on the sea floor - the opposite of that produced by the activity of waves or currents. ?? 1973 Biologischen Anstalt Helgoland.

Propagation of shock waves in elastic solids caused by cavitation microjet impact. II: Application in extracorporeal shock wave lithotripsy.

PubMed

Zhong, P; Chuong, C J; Preminger, G M

1993-07-01

To better understand the mechanism of stone fragmentation during extracorporeal shock wave lithotripsy (ESWL), the model developed in Part I [P. Zhong and C.J. Chuong, J. Acoust. Soc. Am. 94, 19-28 (1993)] is applied to study cavitation microjet impingement and its resultant shock wave propagation in renal calculi. Impact pressure at the stone boundary and stress, strain at the propagating shock fronts in the stone were calculated for typical ESWL loading conditions. At the anterior surface of the stone, the jet induced compressive stress can vary from 0.82 approximately 4 times that of the water hammer pressure depending on the contact angles; whereas the jet-induced shear stress can achieve its maximum, with a magnitude of 30% approximately 54% of the water hammer pressure, near the detachment of the longitudinal (or P) wave in the solid. Comparison of model predictions with material failure strengths of renal calculi suggests that jet impact can lead to stone surface erosion by combined compressive and shear loadings at the jet impacting surface, and spalling failure by tensile forces at the distal surface of the stone. Comparing responses from four different stone types suggests that cystine is the most difficult stone to fragment in ESWL, as observed from clinical experience.

Time-aware service-classified spectrum defragmentation algorithm for flex-grid optical networks

NASA Astrophysics Data System (ADS)

Qiu, Yang; Xu, Jing

2018-01-01

By employing sophisticated routing and spectrum assignment (RSA) algorithms together with a finer spectrum granularity (namely frequency slot) in resource allocation procedures, flex-grid optical networks can accommodate diverse kinds of services with high spectrum-allocation flexibility and resource-utilization efficiency. However, the continuity and the contiguity constraints in spectrum allocation procedures may always induce some isolated, small-sized, and unoccupied spectral blocks (known as spectrum fragments) in flex-grid optical networks. Although these spectrum fragments are left unoccupied, they can hardly be utilized by the subsequent service requests directly because of their spectral characteristics and the constraints in spectrum allocation. In this way, the existence of spectrum fragments may exhaust the available spectrum resources for a coming service request and thus worsens the networking performance. Therefore, many reactive defragmentation algorithms have been proposed to handle the fragmented spectrum resources via re-optimizing the routing paths and the spectrum resources for the existing services. But the routing-path and the spectrum-resource re-optimization in reactive defragmentation algorithms may possibly disrupt the traffic of the existing services and require extra components. By comparison, some proactive defragmentation algorithms (e.g. fragmentation-aware algorithms) were proposed to suppress spectrum fragments from their generation instead of handling the fragmented spectrum resources. Although these proactive defragmentation algorithms induced no traffic disruption and required no extra components, they always left the generated spectrum fragments unhandled, which greatly affected their efficiency in spectrum defragmentation. In this paper, by comprehensively considering the characteristics of both the reactive and the proactive defragmentation algorithms, we proposed a time-aware service-classified (TASC) spectrum defragmentation algorithm, which simultaneously employed proactive and reactive mechanisms in suppressing spectrum fragments with the awareness of services' types and their duration times. By dividing the spectrum resources into several flexible groups according to services' types and limiting both the spectrum allocation and the spectrum re-tuning for a certain service inside one specific spectrum group according to its type, the proposed TASC defragmentation algorithm cannot only suppress spectrum fragments from generation inside each spectrum group, but also handle the fragments generated between two adjacent groups. In this way, the proposed TASC algorithm gains higher efficiency in suppressing spectrum fragments than both the reactive and the proactive defragmentation algorithms. Additionally, as the generation of spectrum fragments is retrained between spectrum groups and the defragmentation procedure is limited inside each spectrum group, the induced traffic disruption for the existing services can be possibly reduced. Besides, the proposed TASC defragmentation algorithm always re-tunes the spectrum resources of the service with the maximum duration time first in spectrum defragmentation procedure, which can further reduce spectrum fragments because of the fact that the services with longer duration times always have higher possibility in inducing spectrum fragments than the services with shorter duration times. The simulation results show that the proposed TASC defragmentation algorithm can significantly reduce the number of the generated spectrum fragments while improving the service blocking performance.

Morphological characteristics of the posterior malleolar fragment according to ankle fracture patterns: a computed tomography-based study.

PubMed

Yi, Young; Chun, Dong-Il; Won, Sung Hun; Park, Suyeon; Lee, Sanghyeon; Cho, Jaeho

2018-02-13

The posterior malleolar fragment (PMF) of an ankle fracture can have various shapes depending on the injury mechanism. The purpose of this study was to evaluate the morphological characteristics of the PMF according to the ankle fracture pattern described in the Lauge-Hansen classification by using computed tomography (CT) images. We retrospectively analyzed CT data of 107 patients (107 ankles) who underwent surgery for trimalleolar fracture from January 2012 to December 2014. The patients were divided into two groups: 76 ankles in the supination-external rotation (SER) stage IV group and 31 ankles in the pronation-external rotation (PER) stage IV group. The PMF type of the two groups was assessed using the Haraguchi and Jan Bartonicek classification. The cross angle (α), fragment length ratio (FLR), fragment area ratio (FAR), sagittal angle (θ), and fragment height (FH) were measured to assess the morphological characteristics of the PMF. The PMF in the SER group mainly had a posterolateral shape, whereas that in the PER group mainly had a posteromedial two-part shape or a large posterolateral triangular shape (P = 0.02). The average cross angle was not significantly different between the two groups (SER group = 19.4°, PER group = 17.6°). The mean FLR and FH were significantly larger in the PER group than in the SER group (P = 0.024, P = 0.006). The mean fragment sagittal angle in the PER group was significantly smaller than that in the SER group (P = 0.017). With regard to the articular involvement, volume, and vertical nature, the SER-type fracture tends to have a smaller fragment due to the rotational force, whereas the PER-type fracture tends to have a larger fragment due to the combination of rotational and axial forces.

High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq).

PubMed

Jiao, Yang; Li, Ran; Wu, Chao; Ding, Yibin; Liu, Yanning; Jia, Danmei; Wang, Lifeng; Xu, Xiang; Zhu, Jing; Zheng, Min; Jia, Junling

2018-01-15

Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine. Here, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing. STC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine.

Dynamic NMR study of ethene exchange in cationic CNN-type platinum(II) complexes.

PubMed

Plutino, M Rosaria; Fenech, Lucia; Stoccoro, Sergio; Rizzato, Silvia; Castellano, Carlo; Albinati, Alberto

2010-01-18

Cationic ethylene platinum(II) complexes of the type [Pt(CNN)(C(2)H(4))](+), containing a methyl fragment and different diimines (NN), or terdentate (kappaC-kappa(2)NN') anionic ligands, were synthesized and fully characterized both as solids and in solution [NN = 2,2'-dipyridylamine, 1; 2,2'-dipyridylsulfide, 2; 1,10-phenanthroline, 3; 4,7-diphenyl-1,10-phenanthroline, 4; 3,4,7,8-tetramethyl-1,10-phenanthroline, 5; 2,2'-bipyridine, 6; HC-NN = 6-tert-butyl-2,2'-bipyridine, 7; 6-neo-pentyl-2,2'-bipyridine, 8; 6-phenyl-2,2'-bipyridine, 9; 6-(alpha-methyl)benzyl-2,2'-bipyridine, 10; 6-(alpha-ethyl)benzyl-2,2'-bipyridine, 11; 6-(alpha,alpha-dimethyl)benzyl-2,2'-bipyridine, 12]. Crystals suitable for X-ray analysis of complexes 5 and 7 were obtained. Ethene exchange at the cyclometalated platinum(II) complexes 7, 8, and 10-12 was studied by (1)H NMR line-broadening experiments in chloroform-d, as a function of both temperature and olefin concentrations. For the other prepared complexes the process was too fast to be monitored on the NMR time scale even at the lowest temperature. The ethylene exchange rates show a linear dependence on the concentration of the free ligand, with a negligible k(1) term indicating that either a solvolytic or a dissociative pathway to the products is absent or negligible. The values of the second-order rate constants k(exc), as obtained by linear regression analysis of the experimental data at 298 K, are in a range of ca. 10(4)-10(5) s(-1) m(-1). The activation entropies are negative, ranging between -129 and -112 J K(-1) mol(-1), as expected for associative processes. The activation process is largely entropy controlled: the TDeltaS()() contribution to the free energy of activation is extremely large, amounting to more than 80% for all complexes, with a smaller enthalpy contribution. All the experimental findings evidence that the mechanism takes place via an associative attack by the entering olefin, through a well-ordered, stable pentacoordinated transition state with the two ethene molecules on the trigonal plane. The reactivity of [Pt(CNN)(C(2)H(4))](+) complexes is strongly dependent on the choice of coordinated 6-substituted-2,2'-bipyridines, especially when the terdentate anionic fragment is capable of generating steric crowding and congestion on the coordination plane.

From Protein Structure to Small-Molecules: Recent Advances and Applications to Fragment-Based Drug Discovery.

PubMed

Ferreira, Leonardo G; Andricopulo, Adriano D

2017-01-01

Fragment-based drug discovery (FBDD) is a broadly used strategy in structure-guided ligand design, whereby low-molecular weight hits move from lead-like to drug-like compounds. Over the past 15 years, an increasingly important role of the integration of these strategies into industrial and academic research platforms has been successfully established, allowing outstanding contributions to drug discovery. One important factor for the current prominence of FBDD is the better coverage of the chemical space provided by fragment-like libraries. The development of the field relies on two features: (i) the growing number of structurally characterized drug targets and (ii) the enormous chemical diversity available for experimental and virtual screenings. Indeed, fragment-based campaigns have contributed to address major challenges in lead optimization, such as the appropriate physicochemical profile of clinical candidates. This perspective paper outlines the usefulness and applications of FBDD approaches in medicinal chemistry and drug design. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Differentiation of mycoplasmalike organisms (MLOs) in European fruit trees by PCR using specific primers derived from the sequence of a chromosomal fragment of the apple proliferation MLO.

PubMed Central

Jarausch, W; Saillard, C; Dosba, F; Bové, J M

1994-01-01

A 1.8-kb chromosomal DNA fragment of the mycoplasmalike organism (MLO) associated with apple proliferation was sequenced. Three putative open reading frames were observed on this fragment. The protein encoded by open reading frame 2 shows significant homologies with bacterial nitroreductases. From the nucleotide sequence four primer pairs for PCR were chosen to specifically amplify DNA from MLOs associated with European diseases of fruit trees. Primer pairs specific for (i) Malus-affecting MLOs, (ii) Malus- and Prunus-affecting MLOs, and (iii) Malus-, Prunus-, and Pyrus-affecting MLOs were obtained. Restriction enzyme analysis of the amplification products revealed restriction fragment length polymorphisms between Malus-, Prunus, and Pyrus-affecting MLOs as well as between different isolates of the apple proliferation MLO. No amplification with either primer pair could be obtained with DNA from 12 different MLOs experimentally maintained in periwinkle. Images PMID:7916180

Templated synthesis of copper(II) azacyclam complexes using urea as a locking fragment and their metal-enhanced binding tendencies towards anions.

PubMed

Boiocchi, Massimo; Fabbrizzi, Luigi; Garolfi, Mauro; Licchelli, Maurizio; Mosca, Lorenzo; Zanini, Cristina

2009-10-26

Copper(II) azacyclam complexes 3(2+) and 4(2+) were obtained through a metal-templated procedure involving the pertinent open-chain tetramine, formaldehyde and a phenylurea derivative as a locking fragment. Both metal complexes can establish interactions with anions through the metal centre and the amide NH group. Equilibrium studies in DMSO by a spectrophotometric titration technique were carried out to assess the affinity of 3(2+) and 4(2+) towards anions. While the NH group of an amide model compound and the metal centre of the plain Cu(II)(azacyclam)(2+) complex do not interact at all with anions, 3(2+) and 4(2+) establish strong interactions with oxo anions, profiting from a pronounced cooperative effect. In particular, 1) they form stable 1:1 and 1:2 complexes with H(2)PO(4) (-) ions in a stepwise mode with both hydrogen-bonding and metal-ligand interactions, and 2) in the presence of CH(3)COO(-), they undergo deprotonation of the amido NH group and thus profit from axial coordination of the partially negatively charged carbonyl oxygen atom in a scorpionate binding mode.

Stability and Unimolecular Reactivity of Palladate(II) Complexes [Ln PdR3 ]- (L=Phosphine, R=Organyl, n=0 and 1).

PubMed

Kolter, Marlene; Koszinowski, Konrad

2016-10-24

The reduction of Pd II precatalysts to catalytically active Pd 0 species is a key step in many palladium-mediated cross-coupling reactions. Besides phosphines, the stoichiometrically used organometallic reagents can afford this reduction, but do so in a poorly understood way. To elucidate the mechanism of this reaction, we have treated solutions of Pd(OAc) 2 and a phosphine ligand L in tetrahydrofuran with RMgCl (R=Ph, Bn, Bu) as well as other organometallic reagents. Analysis of these model systems by electrospray- ionization mass spectrometry found palladate(II) complexes [L n PdR 3 ] - (n=0 and 1), thus pointing to the occurrence of transmetallation reactions. Upon gas-phase fragmentation, the [L n PdR 3 ] - anions preferentially underwent a reductive elimination to yield Pd 0 species. The sequence of the transmetallation and reductive elimination, thus, constitutes a feasible mechanism for the reduction of the Pd(OAc) 2 precatalyst. Other species of interest observed include the Pd IV complex [PdBn 5 ] - , which did not fragment via a reductive elimination but lost BnH instead. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Life Origination Hydrate Theory (LOH-Theory) and Mitosis and Replication Hydrate Theory (MRH-Theory): three-dimensional PC validation

NASA Astrophysics Data System (ADS)

Kadyshevich, E. A.; Dzyabchenko, A. V.; Ostrovskii, V. E.

2014-04-01

Size compatibility of the CH4-hydrate structure II and multi-component DNA fragments is confirmed by three-dimensional simulation; it is validation of the Life Origination Hydrate Theory (LOH-Theory).

Antitumor effect and toxicity of free rhodium (II) citrate and rhodium (II) citrate-loaded maghemite nanoparticles in mice bearing breast cancer

PubMed Central

2013-01-01

Background Magnetic fluids containing superparamagnetic iron oxide nanoparticles represent an attractive platform as nanocarriers in chemotherapy. Recently, we developed a formulation of maghemite nanoparticles coated with rhodium (II) citrate, which resulted in in vitro cytotoxicity enhanced up to 4.6 times when compared to free rhodium (II) citrate formulation on breast carcinoma cells. In this work, we evaluate the antitumor activity and toxicity induced by these formulations in Balb/c mice bearing orthotopic 4T1 breast carcinoma. Methods Mice were evaluated with regard to the treatments’ toxicity through analyses of hemogram, serum levels of alanine aminotransferase, iron, and creatinine; DNA fragmentation and cell cycle of bone marrow cells; and liver, kidney and lung histology. In addition, the antitumor activity of rhodium (II) citrate and maghemite nanoparticles coated with rhodium (II) citrate was verified by tumor volume reduction, histology and immunohistochemistry. Results Regarding the treatments’ toxicity, no experimental groups had alterations in levels of serum ALT or creatinine, and this suggestion was corroborated by the histopathologic examination of liver and kidney of mice. Moreover, DNA fragmentation frequency of bone marrow cells was lower than 15% in all experimental groups. On the other hand, the complexes rhodium (II) citrate-functionalized maghemite and free rhodium (II) citrate led to a marked growth inhibition of tumor and decrease in CD31 and Ki-67 staining. Conclusions In summary, we demonstrated that both rhodium (II) citrate and maghemite nanoparticles coated with rhodium (II) citrate formulations exhibited antitumor effects against 4T1 metastatic breast cancer cell line following intratumoral administration. This antitumor effect was followed by inhibition of both cell proliferation and microvascularization and by tumor tissue injury characterized as necrosis and fibrosis. Remarkably, this is the first published report demonstrating the therapeutic efficacy of maghemite nanoparticles coated with rhodium (II) citrate. This treatment prolonged the survival period of treated mice without inducing apparent systemic toxicity, which strengthens its use for future breast cancer therapeutic applications. PMID:23414068

Le Phénomène Wolf-Rayet au Sein des Etoiles chaudes de Populations I et II: Histoire des Vents stellaires et Impact sur la Structure nébulaire circumstellaire

NASA Astrophysics Data System (ADS)

Grosdidier, Yves

2000-12-01

Les spectres des étoiles Wolf-Rayet pop. I (WR) présentent de larges raies en émission dues à des vents stellaires chauds en expansion rapide (vitesse terminale de l'ordre de 1000 km/s). Le modèle standard des étoiles WR reproduit qualitativement le profil général et l'intensité des raies observées. Mais la spectroscopie intensive à moyenne résolution de ces étoiles révèle l'existence de variations stochastiques dans les raies (sous-pics mobiles en accélération échelles de temps: environ 10-100 min.). Ces variations ne sont pas comprises dans le cadre du modèle standard et suggèrent une fragmentation intrinsèque des vents. Cette thèse de doctorat présente une étude de la variabilité des raies spectrales en émission des étoiles WR pop. II; la question de l'impact d'un vent WR fragmenté sur le milieu circumstellaire est aussi étudiée: 1) à partir du suivi spectroscopique intensif des raies CIIIl5696 et CIVl5801/12, nous analysons quantitativement (via le calcul des Spectres de Variance Temporelle) les vents issus de 5 étoiles centrales de nébuleuses planétaires (NP) galactiques présentant le phénomène WR; 2) nous étudions l'impact de la fragmentation des vents issus de deux étoiles WR pop. I sur le milieu circumstellaire via: i) l'imagerie IR (NICMOS2/HST) de WR 137, et ii) l'imagerie H-alpha (WFPC2/HST) et l'interférométrie Fabry-Perot H-alpha (SIS-CFHT) de la nébuleuse M 1-67 (étoile centrale: WR 124). Les principaux résultats sont les suivants: VENTS WR POP. II: (1) Nous démontrons la variabilité spectroscopique intrinsèque des vents issus des noyaux de NP HD 826 ([WC 8]), BD +30 3639 ([WC 9]) et LSS 3169 ([WC 9]), observés durant respectivement 22, 15 et 1 nuits, et rapportons des indications de variabilité pour les noyaux [WC 9] HD 167362 et He 2-142. Les variabilités de HD 826 et BD +30 3639 apparaissent parfois plus soutenues (``bursts'' qui se maintiennent durant plusieurs nuits); (2) La cinématique des sous-pics de BD +30 3639 suggère une anisotropie transitoire de la distribution des fragments dans le vent; (3) Le phénomène WR apparaît purement atmosphérique: la cinématique des sous-pics, les amplitudes et les échelles de temps caractéristiques des variations, ainsi que les accélérations observées sont similaires pour les deux populations. Mais, pour HD 826, une accélération maximale d'environ 70 m/s2 est détectée, valeur significativement plus importante que celles rapportées pour les autres étoiles WR pop. I & II (environ 15 m/s2). La petitesse du rayon de HD 826 en serait la cause; (4) Comme pour les WR pop. I, de grands paramètres (β supérieur ou égal à 3-10) sont requis pour ajuster les accélérations observées avec une loi de vitesse de type beta. La loi beta sous-estime systématiquement les gradients de vitesse au sein de la région de formation de la raie CIIIl5696; (5) Les vents WR pop. II étant fragmentés, l'estimation des taux de perte de masse actuels à partir de méthodes supposant les atmosphères homogènes conduit à une surestimation i) des taux de perte de masse eux-mêmes, et ii) des masses initiales des étoiles avant qu'elles n'entrent dans la phase WR. IMPACT DES VENTS: (1) Au périastre, de la poussière est détectée dans l'environnement de la binaire WC+OB WR 137. La formation de poussières est soit facilitée, soit provoquée par la collision des deux vents chauds; le rôle capital de la fragmentation des vents (fournissant une compression localisée supplémentaire du plasma) est suggéré (2) La nébuleuse M 1-67 affiche une interaction avec le milieu interstellaire (MIS) non-négligeable (``bow-shock''). Les champs de densité et de vitesse sont très perturbés. Ces perturbations sont reliées, d'une part, à l'histoire des vents issus de WR 124 durant sa propre évolution, d'autre part, à l'interaction avec le MIS. Les fonctions de structure des champs de densitéet de vitesse de M 1-67 ne révèlent aucun indice en faveur d'une turbulence au sein de la nébuleuse (3) Des simulations hydrodynamiques 2D réalisées avec le code ZEUS-3D montrent qu'un fragment dense formé près du coeur hydrostatique stellaire ne peut probablement pas, sans adjoindre les effets de bouclier et de confinement radiatifs, atteindre des distances nébulaires.

Subtypes of the Type II Pit Pattern Reflect Distinct Molecular Subclasses in the Serrated Neoplastic Pathway.

PubMed

Aoki, Hironori; Yamamoto, Eiichiro; Yamano, Hiro-O; Sugai, Tamotsu; Kimura, Tomoaki; Tanaka, Yoshihito; Matsushita, Hiro-O; Yoshikawa, Kenjiro; Takagi, Ryo; Harada, Eiji; Nakaoka, Michiko; Yoshida, Yuko; Harada, Taku; Sudo, Gota; Eizuka, Makoto; Yorozu, Akira; Kitajima, Hiroshi; Niinuma, Takeshi; Kai, Masahiro; Nojima, Masanori; Suzuki, Hiromu; Nakase, Hiroshi

2018-03-15

Colorectal serrated lesions (SLs) are important premalignant lesions whose clinical and biological features are not fully understood. We aimed to establish accurate colonoscopic diagnosis and treatment of SLs through evaluation of associations among the morphological, pathological, and molecular characteristics of SLs. A total of 388 premalignant and 18 malignant colorectal lesions were studied. Using magnifying colonoscopy, microsurface structures were assessed based on Kudo's pit pattern classification system, and the Type II pit pattern was subcategorized into classical Type II, Type II-Open (Type II-O) and Type II-Long (Type II-L). BRAF/KRAS mutations and DNA methylation of CpG island methylator phenotype (CIMP) markers (MINT1, - 2, - 12, - 31, p16, and MLH1) were analyzed through pyrosequencing. Type II-O was tightly associated with sessile serrated adenoma/polyps (SSA/Ps) with BRAF mutation and CIMP-high. Most lesions with simple Type II or Type II-L were hyperplastic polyps, while mixtures of Type II or Type II-L plus more advanced pit patterns (III/IV) were characteristic of traditional serrated adenomas (TSAs). Type II-positive TSAs frequently exhibited BRAF mutation and CIMP-low, while Type II-L-positive TSAs were tightly associated with KRAS mutation and CIMP-low. Analysis of lesions containing both premalignant and cancerous components suggested Type II-L-positive TSAs may develop into KRAS-mutated/CIMP-low/microsatellite stable cancers, while Type II-O-positive SSA/Ps develop into BRAF-mutated/CIMP-high/microsatellite unstable cancers. These results suggest that Type II subtypes reflect distinct molecular subclasses in the serrated neoplasia pathway and that they could be useful hallmarks for identifying SLs at high risk of developing into CRC.

Establishment of reference intervals for osteoarthritis-related soluble biomarkers: the FNIH/OARSI OA Biomarkers Consortium.

PubMed

Kraus, Virginia B; Hargrove, David E; Hunter, David J; Renner, Jordan B; Jordan, Joanne M

2017-01-01

To establish reference intervals for osteoarthritis (OA)-related biomarkers used in the Foundation for the National Institutes of Health (FNIH) OA Biomarkers Consortium Project. A total of 129 'multijoint controls' were selected from 2722 African-American and Caucasian men and women in the Johnston County Osteoarthritis Project. The majority (79%) of those eligible (with biospecimens and baseline data) also had one or more follow-up evaluations 5-15 years later. Multijoint controls were selected to be free of radiographic hand, hip, knee and lumbar spine osteoarthritis (OA), to have no knee or hip symptoms, and minimal hand and spine symptoms at all available time points. Eighteen biomarkers were evaluated in serum (s) and/or urine (u) by ELISA. Reference intervals and partitioning by gender and race were performed with EP Evaluator software. Controls were 64% women, 33% African-Americans, mean age 59 years and mean body mass index 29 kg/m 2 . Three biomarkers were associated with age: sHyaluronan (positively), sN-terminal propeptide of collagen IIA (positively) and sCol2-3/4 C-terminal cleavage product of types I and II collagen (negatively). Exploratory analyses suggested that separate reference intervals may be warranted on the basis of gender for uC-terminal cross-linked telopeptide of type II collagen (uCTXII), sMatrix metalloproteinase-3, uNitrated type II collagen degradation fragment (uCol2-1 NO2) and sHyaluronan, and on the basis of race for uCTXII, sCartilage oligomeric matrix protein, sC-terminal cross-linked telopeptide of type I collagen and uCol2-1 NO2. To our knowledge, this represents the best and most stringent control group ever assayed for OA-related biomarkers. These well-phenotyped controls, representing a similar age demographic to that of the OA Initiative-FNIH main study sample, provide a context for interpretation of OA subject biomarker data. The freely available data set also provides a reference for future human studies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Cartilage collagen type II seromarker patterns in axial spondyloarthritis and psoriatic arthritis: associations with disease activity, smoking and HLA-B27.

PubMed

Munk, Heidi Lausten; Gudmann, Natasja Staehr; Christensen, Anne Friesgaard; Ejstrup, Leif; Sorensen, Grith Lykke; Loft, Anne Gitte; Bay-Jensen, Anne C; Siebuhr, Anne Sofie; Junker, Peter

2016-04-01

The aim of the study was to assess the possible association between type II collagen turnover seromarkers and disease profile in patients with axial spondyloarthritis (SpA) and psoriatic arthritis (PsA). Outpatients with axial SpA (n = 110) or PsA (n = 101) underwent clinical examination including disease activity measures and HLA-B27 typing. The procollagen IIA N-terminal peptide (PIIANP) and a matrix metalloproteinase-generated type II collagen fragment (C2M) were quantified in serum by ELISA. C2M was higher in SpA than in controls, 0.41 versus 0.36 ng/ml (p = 0.004), while PIIANP did not differ between patients and healthy subjects, 2252 versus 2142 ng/ml (p = 0.13). However, DMARD-naïve SpA patients had higher PIIANP, 2461 ng/ml (p = 0.01) and C2M, 0.44 ng/ml (p = 0.0007) levels than controls, and PIIANP correlated with CRP (ρ = 0.34). C2M was lower in SpA smokers, 0.36 ng/ml versus non-smokers, 0.43 ng/ml (p = 0.02), while PIIANP was higher in HLA-B27 positive, 2312 ng/ml versus negative patients, 2021 ng/ml (p = 0.03). In PsA, PIIANP and C2M did not differ between patients and controls, but PIIANP was elevated in patients not receiving DMARDs, 2726 ng/ml. In PsA, PIIANP and C2M did not differ according to smoking and HLA-B27. Cartilage degradation assessed by C2M is increased in SpA irrespective of treatment but not in PsA. Cartilage synthesis reflected by PIIANP is increased in untreated SpA and PsA. PIIANP correlates with CRP in SpA while not in PsA. In DMARD-naïve SpA but not in PsA, HLA-B27 positivity and smoking are associated with a chondro-proliferative metabolic pattern.

Changes in copper sulfate crystal habit during cooling crystallization

NASA Astrophysics Data System (ADS)

Giulietti, M.; Seckler, M. M.; Derenzo, S.; Valarelli, J. V.

1996-09-01

The morphology of technical grade copper(II) sulfate pentahydrate crystals produced from batch cooling experiments in the temperature range of 70 to 30°C is described and correlated with the process conditions. A slow linear cooling rate (batch time of 90 min) predominantly caused the appearance of well-formed crystals. Exponential cooling (120 min) resulted in the additional formation of agglomerates and twins. The presence of seeds for both cooling modes led to round crystals, agglomerates and twins. Fast linear cooling (15 min) gave rise to a mixture of the former types. Broken crystals and adhering fragments were often found. Growth zoning was pronounced in seeded and linear cooling experiments. Fluid inclusions were always found and were more pronounced for larger particles. The occurrence of twinning, zoning and fluid inclusions was qualitatively explained in terms of fundamental principles.

Design and construction of multigenic constructs for plant biotechnology using the GoldenBraid cloning strategy.

PubMed

Sarrion-Perdigones, Alejandro; Palaci, Jorge; Granell, Antonio; Orzaez, Diego

2014-01-01

GoldenBraid (GB) is an iterative and standardized DNA assembling system specially designed for Multigene Engineering in Plant Synthetic Biology. GB is based on restriction-ligation reactions using type IIS restriction enzymes. GB comprises a collection of standard DNA pieces named "GB parts" and a set of destination plasmids (pDGBs) that incorporate the multipartite assembly of standardized DNA parts. GB reactions are extremely efficient: two transcriptional units (TUs) can be assembled from several basic GBparts in one T-DNA less than 24 h. Moreover, larger assemblies comprising 4-5 TUs are routinely built in less than 2 working weeks. Here we provide a detailed view of the GB methodology. As a practical example, a Bimolecular Fluorescence Complementation construct comprising four TUs in a 12 kb DNA fragment is presented.

Automated glycan assembly of xyloglucan oligosaccharides.

PubMed

Dallabernardina, Pietro; Schuhmacher, Frank; Seeberger, Peter H; Pfrengle, Fabian

2016-01-07

We report the automated glycan assembly of oligosaccharide fragments related to the hemicellulose xyloglucan (XG). Iterative addition of monosaccharide and disaccharide building blocks to a solid support provided seven cellulose and xyloglucan fragments including XXGG- and XXXG-type oligosaccharides.

Differentiation of three pairs of aconite alkaloid isomers from Aconitum nagarum var. lasiandrum by electrospray ionization tandem mass spectrometry.

PubMed

Li, Rui; Wu, Zhijun; Zhang, Fan; Ding, Lisheng

2006-01-01

Three pairs of isomers of aconite alkaloids from Aconitum nagarum var. lasiandrum have been investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) employing ion-trap and quadrupole time-of-flight mass spectrometers in positive mode. Based on the differences of their fragmentation pathways and special fragment ions, three pairs of isomers of aconite alkaloids were differentiated. In addition, fragmentation laws of some veatchines and the discrepancy of fragmentation mechanisms between veatchine-type and aconitine-type alkaloid were also concluded. In the case of veatchines, a radical would be formed by homolysis of C18--C4 or C18--H bonds, followed by elimination of a series of C(2)H(2) and C(2)H(4). Moreover, the retro-Diels-Alder (RDA) reaction occurred in the E-ring and double-electron transfer triggered by the positive charge on C1 led to the formation of diagnostic ions at m/z 216. With regard to aconitine-type alkaloids, the N-substituent is not eliminated easily. Although there is no carbonyl group on some aconitine-type alkaloids, with hydroxyl and methoxyl on C15 and C16 respectively, CO was readily eliminated through tautomerization.

Extracting Both Peptide Sequence and Glycan Structural Information by 157 nm Photodissociation of N-Linked Glycopeptides

PubMed Central

Zhang, Liangyi; Reilly, James P.

2009-01-01

157 nm photodissociation of N-linked glycopeptides was investigated in MALDI tandem time-of-flight (TOF) and linear ion trap mass spectrometers. Singly-charged glycopeptides yielded abundant peptide and glycan fragments. The peptide fragments included a series of x-, y-, v- and w- ions with the glycan remaining intact. These provide information about the peptide sequence and the glycosylation site. In addition to glycosidic fragments, abundant cross-ring glycan fragments that are not observed in low-energy CID were detected. These fragments provide insight into the glycan sequence and linkages. Doubly-charged glycopeptides generated by nanospray in the linear ion trap mass spectrometer also yielded peptide and glycan fragments. However, the former were dominated by low-energy fragments such as b- and y- type ions while glycan was primarily cleaved at glycosidic bonds. PMID:19113943

Collision-induced fragmentation of negative ions from N-linked glycans derivatized with 2-aminobenzoic acid.

PubMed

Harvey, David J

2005-05-01

N-Linked glycans from bovine ribonuclease B, chicken ovalbumin, bovine fetuin, porcine thyroglobulin and human alpha(1)-acid glycoprotein were derivatized with 2-aminobenzoic acid by reductive amination and their tandem mass spectra were recorded by negative ion electrospray ionization with a quadrupole time-of-flight mass spectrometer. Derivatives were also prepared from 2-amino-5-methyl- and 2-amino-4,5-dimethoxybenzoic acid in order to confirm the identity of fragment ions containing the reducing terminus. Major fragments from the [M - H](-) ions from the neutral glycans retained the derivative (Y-type cleavages) and provided information on sequence and branching. Other major fragments were products of A-type cross-ring cleavages giving information on antenna structure. Singly doubly and triply charged ions were formed from sialylated glycans. They produced major fragments by loss of sialic acid and a series of singly charged ions that were similar to those from the neutral analogues. Doubly charge ions were also produced by the neutral glycans and were fragmented to form product ions with one and two charges. Again, the fragment ions with a single charge were similar to those from the singly charged parents, but branching information was less obvious because of the occurrence of more abundant ions produced by multiple cleavages. Detection limits were around 200 fmol (3 : 1 signal-to-noise ratio). Copyright 2005 John Wiley & Sons, Ltd.

Concomitant presence of endothelial nitric oxide 894T and angiotensin II-converting enzyme D alleles are associated with diabetic nephropathy in a Kurdish population from Western Iran.

PubMed

Rahimi, Zohreh; Vaisi-Raygani, Asad; Rahimi, Ziba; Parsian, Abbas

2012-02-01

The present study investigated the influence of insertion (I)/deletion (D) polymorphism of the angiotensin II-converting enzyme (ACE) gene in combination with endothelial nitric oxide (eNOS) G894T polymorphism on the predisposition to diabetic nephropathy (DN). Using polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP) method, the ACE and eNOS polymorphisms were genotyped in 72 microalbuminuric, 68 macroalbuminuric and 72 normoalbuinuric type 2 diabetes mellitus (T2DM) patients from Western Iran. The presence of eNOS T or ACE D allele was not associated with increased risk of macroalbuminuria (odds ratio (OR) = 1.36, P = 0.27 and OR = 1.6, P = 0.062, respectively). However, in the presence of both alleles there was a trend towards increased risk of macroalbuminuria (fivefold, P = 0.05). Our study indicates that the concomitant presence of both ACE D and eNOS T alleles tends to be associated with an elevation risk of macroalbuminuria compared with the presence of each polymorphism alone. This risk could be attributed to the increasing activity of ACE and angiotensin II level in the presence of D allele and decreasing NO production in the presence of T allele accelerating diabetic nephropathy. © 2011 The Authors. Nephrology © 2011 Asian Pacific Society of Nephrology.

Structural Vulnerability of the Boeing B-29 Aircraft Wing to Damage by Warhead Fragments

NASA Technical Reports Server (NTRS)

Kordes, Eldon E.; OSullivan, William J., Jr.

1952-01-01

An elementary type of analysis has been used to determine the amount of wing tip that must be severed to produce irrevocable loss of control of a B-29 airplane. The remaining inboard structure of the Boeing B-29 wing has then been analyzed and curves are presented for the estimated reduction in structural strength due to four general types of damage produced by rod-type warhead fragments. The curves indicate the extent of structural damage required to produce a kill of the aircraft within 10 seconds.

Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.

PubMed

Cubero, Elena; Luque, F Javier; Orozco, Modesto

2006-02-01

A series of d (AT)(n) oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation.

Theoretical Study of the Hoogsteen–Watson-Crick Junctions in DNA

PubMed Central

Cubero, Elena; Luque, F. Javier; Orozco, Modesto

2006-01-01

A series of d (AT)n oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation. PMID:16287814

Invasion vs insurgency: US Navy/Marine Corps forward surgical care during Operation Iraqi Freedom.

PubMed

Brethauer, Stacy A; Chao, Alex; Chambers, Lowell W; Green, Donald J; Brown, Carlos; Rhee, Peter; Bohman, Harold R

2008-06-01

The transition from maneuver warfare to insurgency warfare has changed the mechanism and severity of combat wounds treated by US Marine Corps forward surgical units in Iraq. Case series comparison. Forward Resuscitative Surgical System units in Iraq. Three hundred thirty-eight casualties treated during the invasion of Iraq in 2003 (Operation Iraqi Freedom I [OIF I]) and 895 casualties treated between March 2004 and February 2005 (OIF II). Definitive and damage control procedures for acute combat casualties. Mechanism of injury, procedures performed, time to presentation, and killed in action (KIA) and died of wounds (DOW) rates. More major injuries occurred per patient (2.4 vs 1.6) during OIF II. There were more casualties with fragment wounds (61% vs 48%; P = .03) and a trend toward fewer gunshot wounds (33% vs 43%; P = .15) during OIF II. More damage control laparotomies (P = .04) and more soft tissue debridements (P < .001) were performed during OIF II. The median time to presentation for critically injured US casualties during OIF I and OIF II were 30 and 59 minutes, respectively. The KIA rate increased from 13.5% to 20.2% and the DOW rate increased from 0.88% to 5.5% for US personnel in the First Marine Expeditionary Force area of responsibility. The transition from maneuver to insurgency warfare has changed the type and severity of casualties treated by US Marine Corps forward surgical units in Iraq. Improvised explosive devices, severity and number of injuries per casualty, longer transport times, and higher KIA and DOW rates represent major differences between periods. Further data collection is necessary to determine the association between transport times and mortality rates.

Structural Insights into Antibody Sequestering and Neutralizing of Na+ Channel α-Type Modulator from Old World Scorpion Venom

PubMed Central

Fabrichny, Igor P.; Mondielli, Grégoire; Conrod, Sandrine; Martin-Eauclaire, Marie-France; Bourne, Yves; Marchot, Pascale

2012-01-01

The Old World scorpion Androctonus australis hector (Aah) produces one of the most lethal venoms for humans. Peptidic α-toxins AahI to AahIV are responsible for its potency, with AahII accounting for half of it. All four toxins are high affinity blockers of the fast inactivation phase of mammalian voltage-activated Na+ channels. However, the high antigenic polymorphism of α-toxins prevents production of a polyvalent neutralizing antiserum, whereas the determinants dictating their trapping by neutralizing antibodies remain elusive. From an anti-AahII mAb, we generated an antigen binding fragment (Fab) with high affinity and selectivity for AahII and solved a 2.3 Å-resolution crystal structure of the complex. Sequestering of the C-terminal region of the bound toxin within a groove formed by the Fab combining loops is associated with a toxin orientation and main and side chain conformations that dictate the AahII antigenic specificity and efficient neutralization. From an anti-AahI mAb, we also preformed and crystallized a high affinity AahI-Fab complex. The 1.6 Å-resolution structure solved revealed a Fab molecule devoid of a bound AahI and with combining loops involved in packing interactions, denoting expulsion of the bound antigen upon crystal formation. Comparative analysis of the groove-like combining site of the toxin-bound anti-AahII Fab and planar combining surface of the unbound anti-AahI Fab along with complementary data from a flexible docking approach suggests occurrence of distinctive trapping orientations for the two toxins relative to their respective Fab. This study provides complementary templates for designing new molecules aimed at capturing Aah α-toxins and suitable for immunotherapy. PMID:22371498

Xenoliths in maars and diatremes with inferences for the moon, Mars, and Venus.

NASA Technical Reports Server (NTRS)

Mcgetchin, T. R.; Ullrich, G. W.

1973-01-01

Some field observations of the occurrence of deep-seated rock fragments in three terrestrial volcanic features that may have counterparts on the moon or Mars are reviewed, and results of numerical hydrodynamic calculations of the eruption of these types of volcanoes are presented. In particular, the transport of entrained fragmental debris is investigated for the surface (muzzle) velocity of fragments that it yields as a function of fragment size and various values of surface gravity. The implications of these observations and inferences for possible future space missions are examined.

Capturing Nature's Diversity

PubMed Central

Pascolutti, Mauro; Campitelli, Marc; Nguyen, Bao; Pham, Ngoc; Gorse, Alain-Dominique; Quinn, Ronald J.

2015-01-01

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products. PMID:25902039

Detection of Acoustic/Infrasonic/Seismic Waves Generated by Hypersonic Re-Entry of the HAYABUSA Capsule and Fragmented Parts of the Spacecraft

NASA Astrophysics Data System (ADS)

Yamamoto, Masa-Yuki; Ishihara, Yoshiaki; Hiramatsu, Yoshihiro; Kitamura, Kazuki; Ueda, Masayoshi; Shiba, Yasuo; Furumoto, Muneyoshi; Fujita, Kazuhisa

2011-10-01

Acoustic/infrasonic/seismic waves were observed during the re-entry of the Japanese asteroid explorer ``HAYABUSA'' at 6 ground sites in Woomera, Australia, on 2010 June 13. Overpressure values of infrasound waves were detected at 3 ground sites in a range from 1.3 Pa, 1.0 Pa, and 0.7 Pa with each distance of 36.9 km, 54.9 km, and 67.8 km, respectively, apart from the SRC trajectory. Seismic waveforms through air-to-ground coupling processes were also detected at 6 sites, showing a one-to-one correspondence to infrasound waves at all simultaneous observation sites. Audible sound up to 1 kHz was recorded at one site with a distance of 67.8 km. The mother spacecraft was fragmented from 75 km down to 38 km with a few explosive enhancements of emissions. A persistent train of HAYABUSA re-entry was confirmed at an altitude range of between 92 km down to 82 km for about 3 minutes. Light curves of 136 fragmented parts of the spacecraft were analyzed in detail based on video observations taken at multiple ground sites, being classified into three types of fragmentations, i.e., melting, explosive, and re-fragmented types. In a comparison between infrasonic waves and video-image analyses, regarding the generation of sonic-boom type shock waves by hypersonically moving artificial meteors, both the sample return capsule and fragmented parts of the mother spacecraft, at an altitude of 40 ± 1 km were confirmed with a one-to-one correspondence with each other.

Mimicry by asx- and ST-turns of the four main types of beta-turn in proteins.

PubMed

Duddy, William J; Nissink, J Willem M; Allen, Frank H; Milner-White, E James

2004-11-01

Hydrogen-bonded beta-turns in proteins occur in four categories: type I (the most common), type II, type II', and type I'. Asx-turns resemble beta-turns, in that both have an NH. . .OC hydrogen bond forming a ring of 10 atoms. Serine and threonine side chains also commonly form hydrogen-bonded turns, here called ST-turns. Asx-turns and ST-turns can be categorized into four classes, based on side chain rotamers and the conformation of the central turn residue, which are geometrically equivalent to the four types of beta-turns. We propose asx- and ST-turns be named using the type I, II, I', and II' beta-turn nomenclature. Using this, the frequency of occurrence of both asx- and ST-turns is: type II' > type I > type II > type I', whereas for beta-turns it is type I > type II > type I' > type II'. Almost all type II asx-turns occur as a recently described three residue feature named an asx-nest.

Experimental use of new absorbable tracheal stent.

PubMed

Schopf, Luciano F; Fraga, José Carlos; Porto, Rodrigo; Santos, Luis A; Marques, Douglas R; Sanchez, Paulo R; Meyer, Fabíola S; Ulbrich, Jane M

2017-11-16

Silicone and metallic stents are not effective in children with tracheobronchial stenosis or tracheomalacia. Herein, we aimed to evaluate the clinical manifestations and histological reaction of rabbit trachea to the presence of a new poly(lactic-co-glycolic acid) with polyisoprene (PLGA/PI) polymer absorbable stent. Fourteen adult white rabbits (weight, 3.0-3.5kg) were randomly assigned to three groups: Group I (n=6): PLGA/PI spiral stent; Group II (n=6): PLGA/PI fragment; and Group III (n=2): controls. After a longitudinal incision on three cervical tracheal rings, the stents and fragments were inserted into the trachea and fixed onto the lateral wall with nonabsorbable sutures. The stented group showed significantly more stridor at rest (p=0.0041), agitation (p=0.014), and use of accessory muscles (p=0.0002) and required more emergency endoscopies than the fragment group. Further, it showed significantly more remarkable histological inflammatory damage than the fragment and control groups (p=0.002). The new PLGA/PI polymeric stent implanted into the trachea of rabbits caused more clinical manifestations and histologically verified inflammatory reaction than the PLGA/PI polymeric fragment. Future studies should be aimed at reducing the stent-wall thickness. Copyright © 2017 Elsevier Inc. All rights reserved.

The Effect of Stone Composition on the Efficacy of Retrograde Intrarenal Surgery: Kidney Stones 1 - 3 cm in Diameter.

PubMed

Xue, Yuquan; Zhang, Peng; Yang, Xiaojie; Chong, Tie

2015-05-01

The goal of this study was to analyze the effect of stone composition on the efficacy of retrograde intrarenal surgery (RIRS) with kidney stones of 1-3 cm, 1-2 cm, and 2-3 cm in diameter. We undertook a retrospective analysis of 74 patients with kidney stones who underwent RIRS. The patients were divided into two groups based on stone composition: Group I (n=47) (calcium oxalate monohydrate and calcium phosphate) was the hard to fragment stone group and group II (n=27) (calcium oxalate dihydrate, magnesium ammonium phosphate, and uric acid) was the easy to fragment stone group. Forty-six patients with kidney stones 1 to 2 cm in diameter were divided into group A (n=30) (smaller than 20 mm, hard to fragment stones) and group B (n=16) (smaller than 20 mm, easy to fragment stones). Twenty-eight patients with stones 2 to 3 cm in diameter were divided into group C (n=17) (larger than 20 mm, hard to fragment stones) and group D (n=11) (larger than 20 mm, easy-to-crush stones). The stone clearance rates of group I and group II were 66.0% and 88.9%, respectively (P<0.05). The stone clearance rates of group A and group B were 73.3% and 100% (P<0.05). The stone clearance rates of group C and group D were 52.9% and 72.7%, respectively. Stone composition has a significant impact on the efficacy of RIRS in the management of 1 to 3 cm kidney stones. For 2-3 cm calcium oxalate dihydrate stones, uric acid stones, and magnesium ammonium phosphate stones, the outcome of RIRS treatment was relatively good, and RIRS is recommended.

Extracellular matrix fragmentation in young, healthy cartilaginous tissues.

PubMed

Craddock, R J; Hodson, N W; Ozols, M; Shearer, T; Hoyland, J A; Sherratt, M J

2018-02-09

Although the composition and structure of cartilaginous tissues is complex, collagen II fibrils and aggrecan are the most abundant assemblies in both articular cartilage (AC) and the nucleus pulposus (NP) of the intervertebral disc (IVD). Whilst structural heterogeneity of intact aggrecan ( containing three globular domains) is well characterised, the extent of aggrecan fragmentation in healthy tissues is poorly defined. Using young, yet skeletally mature (18-30 months), bovine AC and NP tissues, it was shown that, whilst the ultrastructure of intact aggrecan was tissue-dependent, most molecules (AC: 95 %; NP: 99.5 %) were fragmented (lacking one or more globular domains). Fragments were significantly smaller and more structurally heterogeneous in the NP compared with the AC (molecular area; AC: 8543 nm2; NP: 4625 nm2; p < 0.0001). In contrast, fibrillar collagen appeared structurally intact and tissue-invariant. Molecular fragmentation is considered indicative of a pathology; however, these young, skeletally mature tissues were histologically and mechanically (reduced modulus: AC: ≈ 500 kPa; NP: ≈ 80 kPa) comparable to healthy tissues and devoid of notable gelatinase activity (compared with rat dermis). As aggrecan fragmentation was prevalent in neonatal bovine AC (99.5 % fragmented, molecular area: 5137 nm2) as compared with mature AC (95.0 % fragmented, molecular area: 8667 nm2), it was hypothesised that targeted proteolysis might be an adaptive process that modified aggrecan packing (as simulated computationally) and, hence, tissue charge density, mechanical properties and porosity. These observations provided a baseline against which pathological and/or age-related fragmentation of aggrecan could be assessed and suggested that new strategies might be required to engineer constructs that mimic the mechanical properties of native cartilaginous tissues.

Blast and Fragments from Superpressure Vessel Rupture

DTIC Science & Technology

1976-02-09

hemispheres. These plecs were accelerated to velocities of about 300 ft/second; about half the calculated fragment velocities. MCEBION Wllltl...8217 i i i i i T T i r t i t T T—T T i i i i i i i ^ T r i i i ! i-i-1 r r" rT *TT"T- rT i ’ ’FIG. 3.1 ESTIMATED DIRECTION OF ARGON JETTING...the box (line 2) are higher than along the other two lines but no higher than was predicted for a free field burst. Pressures behind the box are

Synthesis of the human insulin gene. Part III. Chemical synthesis of 5'-phosphomonoester group containing deoxyribooligonucleotides by the modified phosphotriester method. Its application in the synthesis of seventeen fragments constituting human insulin C-chain DNA.

PubMed Central

Hsiung, H M; Sung, W L; Brousseau, R; Wu, R; Narang, S A

1980-01-01

A method for phosphorylating a protected deoxyribooligonucleotide containing phosphotriester linkages is described. The modified phosphotriester method of chemical synthesis is further refined in terms of (i) better final deblocking conditions and (ii) new chromatography solvent systems containing acetone-water-ethyl acetate to yield pure oligomers. The effectiveness of these improvements has been demonstrated in the rapid and efficient synthesis of seventeen fragments constituting the sequence of human insulin C-chain DNA. Images PMID:7008029

[Radiation biology of structurally different Drosophila melanogaster genes. Report I. The vestigial gene: molecular characteristic of "point" mutations].

PubMed

Aleksandrov, I D; Afanas'eva, K P; Aleksandrova, M V; Lapidus, I L

2012-01-01

The screening of PCR-detected DNA alterations in 9 spontaneous and 59 gamma-ray-, neutron - or neutron + gamma-ray-induced Drosophila vestigial (vg) gene/"point" mutations was carried out. The detected patterns of existence or absence of either of 16 overlapping fragments into which vg gene (15.1 kb, 8 exons, 7 introns) was divided enable us to subdivide all mutants into 4 classes: (i) PCR+ (40.7%) without the detected changes; (ii) "single-site" (33.9%) with the loss of a single fragment; (iii) partial detections (15.2%) as a loss of 2-9 adjacent fragments and (iv) "cluster" mutants (10.2%) having 2-3 independent changes of(ii) and/or (iii) classes. All spontaneous mutants except one were found to be classified as (ii) whereas radiation-induced mutants are represented by all 4 classes whose interrelation is determined by the dose and radiation quality. In particular, the efficacy of neutrons was found to be nine times as large as that of gamma-rays under the "cluster" mutant induction. Essentially, the distribution of DNA changes along the gene is uneven. CSGE-assay of PCR+-exon 3 revealed DNA heteroduplexes in 5 out of 17 PCR+-mutants studied, 2 of which had small deletions (5 and 11 b) and 3 others made transitions (A --> G) as shown by the sequencing. Therefore, gamma-rays and neutrons seem to be significant environmental agents increasing the SNP risk for the population through their action on the germ cells. The results obtained are also discussed within the framework of the track structure theory and the notion of quite different chromatin organization in somatic and germ cells.

Assembly of the intrinsic factor domains and oligomerization of the protein in the presence of cobalamin.

PubMed

Fedosov, Sergey N; Fedosova, Natalya U; Berglund, Lars; Moestrup, Søren K; Nexø, Ebba; Petersen, Torben E

2004-11-30

Human intrinsic factor (IF) was purified from the recombinant plant Arabidopsis thaliana by affinity chromatography. Cobalamin (Cbl) saturated protein was separated by gel filtration into peaks I and II, which contained according to SDS electrophoresis the 50 kDa full-length protein IF(50) and a mixture of two fragments, respectively. Two components of peak II were identified as the 30 kDa N-terminal peptide IF(30) and the 20 kDa C-terminal glycopeptide IF(20). Measurements of M(w) under the nondenaturing conditions were conducted by static light scattering. They revealed 100 kDa IF dimers in peak I, whereas 50 kDa cleaved monomers were found in peak II. The protein devoid of Cbl dissociated to the elementary units incapable of association in the absence of Cbl. The individual proteolytic fragments bound Cbl at high concentration of the ligand; however, neither IF(30).Cbl nor IF(20).Cbl oligomerized. A mixture of two fragments IF(30) + IF(20) and Cbl produced a firm complex, IF(30+20).Cbl, which could not associate to dimers. In contrast to IF(30+20).Cbl, the saturated full-length monomers IF(50).Cbl dimerized with K(d) approximately 1 microM. We suggest a two-domain organization of the full-length protein, where two distant units, IF(30) and IF(20), can be assembled only by Cbl. They are connected by a protease-sensitive link, whose native structure is likely to be important for dimerization. However, linkage between two domains is not compulsory for Cbl binding. Advantages of the two-domain structure of IF are discussed.

Mechanical properties of resin cements with different activation modes.

PubMed

Braga, R R; Cesar, P F; Gonzaga, C C

2002-03-01

Dual-cured cements have been studied in terms of the hardness or degree of conversion achieved with different curing modes. However, little emphasis is given to the influence of the curing method on other mechanical properties. This study investigated the flexural strength, flexural modulus and hardness of four proprietary resin cements. Materials tested were: Enforce and Variolink II (light-, self- and dual-cured), RelyX ARC (self- and dual-cured) and C & B (self-cured). Specimens were fractured using a three-point bending test. Pre-failure loads corresponding to specific displacements of the cross-head were used for flexural modulus calculation. Knoop hardness (KHN) was measured on fragments obtained after the flexural test. Tests were performed after 24 h storage at 37 degrees C. RelyX ARC dual-cured showed higher flexural strength than the other groups. RelyX ARC and Variolink II depended upon photo-activation to achieve higher hardness values. Enforce showed similar hardness for dual- and self-curing modes. No correlation was found between flexural strength and hardness, indicating that other factors besides the degree of cure (e.g. filler content and monomer type) affect the flexural strength of composites. No statistical difference was detected in the flexural modulus among the different groups.

Phage idiotype vaccination: first phase I/II clinical trial in patients with multiple myeloma

PubMed Central

2014-01-01

Background Multiple myeloma is characterized by clonal expansion of B cells producing monoclonal immunoglobulins or fragments thereof, which can be detected in the serum and/or urine and are ideal target antigens for patient-specific immunotherapies. Methods Using phage particles as immunological carriers, we employed a novel chemically linked idiotype vaccine in a clinical phase I/II trial including 15 patients with advanced multiple myeloma. Vaccines composed of purified paraproteins linked to phage were manufactured successfully for each patient. Patients received six intradermal immunizations with phage idiotype vaccines in three different dose groups. Results Phage idiotype was well tolerated by all study participants. A subset of patients (80% in the middle dose group) displayed a clinical response indicated by decrease or stabilization of paraprotein levels. Patients exhibiting a clinical response to phage vaccines also raised idiotype-specific immunoglobulins. Induction of a cellular immune response was demonstrated by a cytotoxicity assay and delayed type hypersensitivity tests. Conclusion We present a simple, time- and cost-efficient phage idiotype vaccination strategy, which represents a safe and feasible patient-specific therapy for patients with advanced multiple myeloma and produced promising anti-tumor activity in a subset of patients. PMID:24885819

Systemic reduction of soluble complement receptor II/CD21 during pregnancy to levels reminiscent of autoimmune disease.

PubMed

Masilamani, Madhan; Rajasekaran, Narendiran; Singh, Anjana; Low, Hui-Zhi; Albus, Kerstin; Anders, Swantje; Behne, Frank; Eiermann, Peter; König, Katharina; Mindnich, Clarissa; Ribarska, Teodora; Illges, Harald

2008-09-01

Complement receptor type II/CD21 is the functional receptor for complement fragments such as C3d, iC3b and the Epstein Barr Virus. A soluble form of CD21 (sCD21) is shed from lymphocytes surface and is able to bind to its ligands found in the plasma. The amount of sCD21 in serum may modulate immunity as the plasma levels are correlated with autoimmune conditions, such as Systemic Lupus Erythematosus, Rheumatoid Arthritis and Sjoegren's Syndrome. Because of the fact that pregnancy may lead to remission of autoimmune diseases we determined the serum levels of sCD21 during pregnancy and postpartum. The serum sCD21 levels during pregnancy are significantly lower as compared to that of the healthy controls. There were no significant differences in sCD21 levels between the mother and the cord blood also immediately after parturition. Restoration of sCD21 levels to normal values takes between 6 weeks and 1 year after childbirth. Our study indicates that CD21-shedding is affected during pregnancy comparable to that of autoimmunity.

Fragment-Based Drug Discovery of Potent Protein Kinase C Iota Inhibitors.

PubMed

Kwiatkowski, Jacek; Liu, Boping; Tee, Doris Hui Ying; Chen, Guoying; Ahmad, Nur Huda Binte; Wong, Yun Xuan; Poh, Zhi Ying; Ang, Shi Hua; Tan, Eldwin Sum Wai; Ong, Esther Hq; Nurul Dinie; Poulsen, Anders; Pendharkar, Vishal; Sangthongpitag, Kanda; Lee, May Ann; Sepramaniam, Sugunavathi; Ho, Soo Yei; Cherian, Joseph; Hill, Jeffrey; Keller, Thomas H; Hung, Alvin W

2018-05-24

Protein kinase C iota (PKC-ι) is an atypical kinase implicated in the promotion of different cancer types. A biochemical screen of a fragment library has identified several hits from which an azaindole-based scaffold was chosen for optimization. Driven by a structure-activity relationship and supported by molecular modeling, a weakly bound fragment was systematically grown into a potent and selective inhibitor against PKC-ι.

Atmospheric-pressure ionization and fragmentation of peptides by solution-cathode glow discharge† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc02032a Click here for additional data file.

PubMed Central

Schwartz, Andrew J.; Walton, Courtney L.; Williams, Kelsey L.; Hieftje, Gary M.

2016-01-01

Modern “-omics” (e.g., proteomics, glycomics, metabolomics, etc.) analyses rely heavily on electrospray ionization and tandem mass spectrometry to determine the structural identity of target species. Unfortunately, these methods are limited to specialized mass spectrometry instrumentation. Here, a novel approach is described that enables ionization and controlled, tunable fragmentation of peptides at atmospheric pressure. In the new source, a direct-current plasma is sustained between a tapered metal rod and a flowing sample-containing solution. As the liquid stream contacts the electrical discharge, peptides from the solution are volatilized, ionized, and fragmented. At high discharge currents (e.g., 70 mA), electrospray-like spectra are observed, dominated by singly and doubly protonated molecular ions. At lower currents (35 mA), many peptides exhibit extensive fragmentation, with a-, b-, c-, x-, and y-type ion series present as well as complex fragments, such as d-type ions, not previously observed with atmospheric-pressure dissociation. Though the mechanism of fragmentation is currently unclear, observations indicate it could result from the interaction of peptides with gas-phase radicals or ultraviolet radiation generated within the plasma. PMID:28451101

Analysis of stone fragility in vitro and in vivo with piezoelectric shock waves using the EDAP LT-01.

PubMed

Wang, Y H; Grenabo, L; Hedelin, H; Pettersson, S; Wikholm, G; Zachrisson, B F

1993-04-01

A total of 100 whole stones was fragmented in vitro at 3-minute intervals with piezoelectric shock waves using the EDAP LT-01 device until all fragments were less than 2 mm. Larger stones and stones with a high computerized tomography attenuation needed longer treatments for fragmentation. Smoothly bulging stones with an even structure according to plain x-ray films were also more resistant to the shock wave treatment. Calcium oxalate monohydrate stones were not more difficult to break than other types of calculi. Stone fragments from 100 patients after extracorporeal shock wave lithotripsy were also analyzed. The average size of the fragments collected was less than 1 mm. Larger stones produced larger fragments and required more treatment sessions.

Computed tomography of calcaneal fractures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heger, L.; Wulff, K.; Seddiqi, M.S.A.

1985-07-01

Computed tomography (CT) of 25 fractured calcanei was performed to investigate the potential of CT in evaluating the pattern and biomechanics of these fractures. The characteristic findings of typical fractures are presented, including the number and type of principal fragments, size and dislocation of the sustentacular fragment, and involvement of the anterior and posterior facets of the subtalar joint. In 17 cases, the calcaneus consisted of four or more fragments. Furthermore, in 17 cases the sustentacular fragment included all or part of the posterior facet joint. In 18 of the 25 cases, the sustentacular fragment was displaced. It is concludedmore » that well performed CT is an invaluable adjunct in understanding the fracture mechanism and in detecting pain-provoking impingement between the fibular malleolus and the tuberosity fragment.« less

Synthesis of Methylenebicyclo[3.2.1]octanol by a Sm(II)-Induced 1,2-Rearrangement Reaction with Ring Expansion of Methylenebicyclo[4.2.0]octanone.

PubMed

Takatori, Kazuhiko; Ota, Shoya; Tendo, Kenta; Matsunaga, Kazuma; Nagasawa, Kokoro; Watanabe, Shinya; Kishida, Atsushi; Kogen, Hiroshi; Nagaoka, Hiroto

2017-07-21

Direct conversion of methylenebicyclo[4.2.0]octanone to methylenebicyclo[3.2.1]octanol by a Sm(II)-induced 1,2-rearrangement with ring expansion of the methylenecyclobutane is described. Three conditions were optimized to allow the adaptation of this approach to various substrates. A rearrangement mechanism is proposed involving the generation of a ketyl radical and cyclopentanation by ketyl-olefin cyclization, followed by radical fragmentation and subsequent protonation.

Differences in the motility of Amoeba proteus isolated fragments are determined by F-actin arrangement and cell nucleus presence.

PubMed

Grebecka, L; Pomorski, P; Lopatowska, A

1995-10-01

Isolated fragments produced by bisection of Amoeba proteus differ by their position in the original cell and by the presence or absence of the cell nucleus. Immediately after the operation, both types of anterior fragments preserve the former motory polarity, and do not interrupt locomotion. In the same time, all posterior fragments stop, round up and fail to react stimuli. In the second phase of experiment, these anterior fragments, which had no nucleus ceased to move, whereas the nucleated posterior ones resumed locomotion. It was demonstrated, that the behaviour of a fragment is primarily determined by the peripheral F-actin distribution, which is different depending on the origin of the fragment either from the anterior or from the posterior cell region. Later, the "inherited" F-actin distribution may be stabilized or reorganized in the presence of the nucleus, or desorganized in its absence.

Universality of fragment shapes.

PubMed

Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

2015-03-16

The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism.

Universality of fragment shapes

PubMed Central

Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

2015-01-01

The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

A mechanism for negative gene regulation in Autographa californica multinucleocapsid nuclear polyhedrosis virus

USGS Publications Warehouse

Leisy, D.J.; Rasmussen, C.; Owusu, E.O.; Rohrmann, G.F.

1997-01-01

The Autographa californica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is thought to play a central role in stimulating early viral transcription. IE-1 has been demonstrated to activate several early viral gene promoters and to negatively regulate the promoters of two other AcMNPV regulatory genes, ie-0 and ie-2. Our results indicate that IE-1 negatively regulates the expression of certain genes by binding directly, or as part of a complex, to promoter regions containing a specific IE-1-binding motif (5'-ACBYGTAA-3') near their mRNA start sites. The IE-1 binding motif was also found within the palindromic sequences of AcMNPV homologous repeat (hr) regions that have been shown to bind IE-1. The role of this IE-1 binding motif in the regulation of the ie-2 and pe-38 promoters was examined by introducing mutations in these promoters in which the central 6 bp were replaced with Bg/II sites. GUS reporter constructs containing ie-2 and pe-38 promoter fragments with and without these specific mutations were cotransfected into Sf9 cells with various amounts of an ie-1-containing plasmid (ple-1). Comparisons of GUS expression produced by the mutant and wild-type constructs demonstrated that the IE-1 binding motif mediated a significant decrease in expression from the ie-2 and pe-38 promoters in response to increasing pIe-1 concentrations. Electrophoretic mobility shift assays with pIe-1-transfected cell extracts and supershift assays with IE-1- specific antiserum demonstrated that IE-1 binds to promoter fragments containing the IE-1 binding motif but does not bind to promoter fragments lacking this motif.

Analysis of a Hypergolic Propellant Explosion During Processing of Launch Vehicles in the VAB

NASA Technical Reports Server (NTRS)

Chrostowski, Jon D.; Gan Wenshui; Campbell, Michael D.

2010-01-01

NASA is developing launch vehicles to support missions to Low Earth Orbit (LEO), the moon and deep space. Whether manned or unmanned, the vehicle components will likely be integrated in the Vehicle Assembly Building (VAB) at Kennedy Space Center (KSC) and typically include a fueled spacecraft (SC) that sits on top of one or more stages. The processing of a fueled SC involves hazardous operations when it is brought into the VAB Transfer Aisle and lifted a significant height for mating with lower stages. Accidents resulting from these hazardous operations could impact unrelated personnel working in buildings adjacent to the VAB. Safe separation distances based on the DOD Explosives Standards Quantity-Distance (Q-D) approach result in large IBD arcs. This paper presents site-specific air blast and fragmentation hazard analyses for comparison with the Q-D arcs as well as consequence and risk analyses to provide added information for the decision maker. A new physics-based fragmentation model is presented that includes: a) the development of a primary fragment list (which defines the fragment characteristics) associated with a hypergolic propellant explosion, b) a description of a 3D fragment bounce model, c) the results of probabilistic Monte-Carlo simulations (that include uncertainties in the fragment characteristics) to determine: i) the hazardous fragment density distance, ii) the expected number of wall/roof impacts and penetrations to over 40 buildings adjacent to the VAB, and iii) the risk to building occupants.

Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

PubMed Central

Hadifar, Shima; Moghim, Sharareh; Fazeli, Hossein; GhasemianSafaei, Hajieh; Havaei, Seyed Asghar; Farid, Fariba; Esfahani, Bahram Nasr

2015-01-01

Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species. PMID:26380237

The novel monoclonal antibody 9F5 reveals expression of a fragment of GPNMB/osteoactivin processed by furin‐like protease(s) in a subpopulation of microglia in neonatal rat brain

PubMed Central

Hirata, Hiroshi; Ohbuchi, Kengo; Nishi, Kentaro; Maeda, Akira; Kuniyasu, Akihiko; Yamada, Daisuke; Maeda, Takehiko; Tsuji, Akihiko; Sawada, Makoto

2016-01-01

To differentiate subtypes of microglia (MG), we developed a novel monoclonal antibody, 9F5, against one subtype (type 1) of rat primary MG. The 9F5 showed high selectivity for this cell type in Western blot and immunocytochemical analyses and no cross‐reaction with rat peritoneal macrophages (Mφ). We identified the antigen molecule for 9F5: the 50‐ to 70‐kDa fragments of rat glycoprotein nonmetastatic melanoma protein B (GPNMB)/osteoactivin, which started at Lys170. In addition, 9F5 immunoreactivity with GPNMB depended on the activity of furin‐like protease(s). More important, rat type 1 MG expressed the GPNMB fragments, but type 2 MG and Mφ did not, although all these cells expressed mRNA and the full‐length protein for GPNMB. These results suggest that 9F5 reactivity with MG depends greatly on cleavage of GPNMB and that type 1 MG, in contrast to type 2 MG and Mφ, may have furin‐like protease(s) for GPNMB cleavage. In neonatal rat brain, amoeboid 9F5+ MG were observed in specific brain areas including forebrain subventricular zone, corpus callosum, and retina. Double‐immunοstaining with 9F5 antibody and anti‐Iba1 antibody, which reacts with MG throughout the CNS, revealed that 9F5+ MG were a portion of Iba1+ MG, suggesting that MG subtype(s) exist in vivo. We propose that 9F5 is a useful tool to discriminate between rat type 1 MG and other subtypes of MG/Mφ and to reveal the role of the GPNMB fragments during developing brain. GLIA 2016;64:1938–1961 PMID:27464357

Fragman: an R package for fragment analysis

USDA-ARS?s Scientific Manuscript database

Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and QTL mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available softw...

Genetic differentiation and phylogeny relationships of functional ApoVLDL-II gene in red jungle fowl and domestic chicken populations.

PubMed

Musa, Hassan H; Cheng, Jin H; Bao, Wen B; Li, Bi C; Mekki, Dafaalla M; Chen, Guo H

2007-08-01

A total of 243 individuals from Red Jungle Fowl (Gallus gallus spadiceus), Rugao, Anka, Wenchang and Silikes chicken populations were used for polymorphism analysis in functional apoVLDL-II gene by Restriction fragment length polymorphism and single strand conformation polymorphism markers. The results show that Anka population has highest gene diversity and Shannon information index, while Red jungle fowl shows highest effective number of allele. In addition, the higher coefficient of genetic differentiation (Gst) across all loci in apoVLDL-II was indicating that high variation is proportioned among populations. As expected total gene diversity (Ht) has upper estimate compared with within population genetic diversity (Hs) across all loci. The mean Gst value across all loci was (0.194) indicating about 19.4% of total genetic variation could be explained by breeds differences, while the remaining 80.6% was accounted for differences among individuals. The average apoVLDL-II gene flow across all loci in five chicken populations was 1.189. The estimates of genetic identity and distance confirm that these genes are significantly different between genetically fat and lean population, because fat type breed Anka shows highest distance with the other Silikes and Rugao whish are genetically lean. In addition, Wenchang and Red jungle fowl were found more closely and genetically related than the other breeds with 49.4% bootstrapping percentages, then they were related to Silikes by 100% bootstrapping percentages followed by Rugao and finally all of them are related with exotic fat breed Anka.

[Application of rafting K-wire technique for tibial plateau fractures].

PubMed

Zhang, Xing-zhou; Yu, Wei-zhong; Li, Yun-feng; Liu, Yan-hui

2015-12-01

To summarize application of rafting K-wires technique for tibial plateau fractures. From January 2013 to January 2015,45 patients with tibial plateau fractures were treated by locking plate with rafting K-wires, including 33 males and 12 females with an average of 44.2 years old ranging from 22 to 56 years old. According to Schatzker classification, 6 cases were type II, 8 were type Ill, 4 were type IV, 4 were type V, and 5 were type VI. Allogeneic bone graft were performed for bone defects. All patients were fixed with two to five K-wires. Part of weight loading were encouraged at 3 months after operation,and full weight-loading were done at 5 months after operation. Postoperative complications were observed,and Rasmussen clinical and radiological assessment were used to evaluate clinical results. All Patients were followed up from 10 to 23 months with average of 14 months. According to Rasmussen clinical and radiological assessment, clinical scores 23.58 ± 6.33, radiological scores were 14.00 ± 6.33; and excellent and good rates were 82.2% and 77.8% respectively. Four patients occurred severe osteoporosis and collapse of articular surface; 5 patients occurred traumatic arthritis. Rafting K-wires technique with anatomized armor plate could effective fix and support platform collapse and joint bone fragments, increase support surface area and reduce postoperative reduction loss rate.

Characteristics of Pebble- and Cobble-Sized Clasts Along the Curiosity Rover Traverse from Sol 0 to 800.

NASA Astrophysics Data System (ADS)

Aileen Yingst, R.; Cropper, Kevin; Blank, Jennifer; Goetz, Walter; Hamilton, Victoria; Hipkin, Victoria; Kah, Linda; Madsen, Morten Bo; Newsom, Horton; Williams, Rebecca; Bridges, John; Martinez-Frias, Jesús; King, Penelope

2015-04-01

The transport, sorting and abrasive processes that modify the loose surface fragments comprising a sedimentary population are best recorded in the morphologic characteristics of those fragments (also termed clasts or particles). Here we assess morphologic characteristics (size, shape, roundness, texture) of clasts in the pebble to cobble size range (2-256 mm) in Gale Crater imaged along the path of the Curisoty rover from sols 0 to 800. Pebble- to cobble-sized clasts along Curiosity's traverse most likely include geologic materials from the walls of fluvial canyons that debouch onto the crater floor, fragments shed from the central mound of the crater, and grains from modern eolian dunes. Our goal is to help constrain the boundaries of potential transport mechanisms important throughout the geologic history of the crater interior. Clast survey observations were taken on 162 sols. Most common clast types include: Type 1. These grey, fine-grained clasts are the most common type between sols 0 to ~650. Particles are angular to sub-angular (though sub-rounded clasts appear beginning ~sol 548), with flat facets terminating in sharp or slightly rounded edges. Surface texture is often smooth, but fresher facets can be rough and knobby at the sub-mm scale; occasionally, faint layers can be discerned. Wind-eroded features are common. Type 2. These clasts are gray and angular to sub-angular, displaying faces with circular or elongated concave-outward ellipsoids averaging 0.5-1.5 mm long-axis. A potential variant of this clast type is one in which ellipsoids are so deeply weathered that the particle takes on a scoria-like shape. Type 3. This class consists of angular to sub-angular void-rich clasts. These are rare, and disappear after ~sol 50, but reappear around sol 672. Type 4. These particles are angular to sub-angular and clast-rich. Clasts protrude as they wear, making surface textures jagged-looking. Type 5. Particles in this class vary in color, are equidimensional or somewhat elongate, and tend to be subrounded to well-rounded. Such fragments are a significant component of the clast population in some areas along traverse, often littering the surface surrounding larger conglomerate fragments. Type 6. These particles are angular to sub-rounded in shape, with a knobby, rugged surface texture. This type weathers to similar shapes as Type 4 but lacks protruding grains. Type 7. This class consists of platy or chunky fragments with a grainy surface texture. This type begins to appear around sol 746 and is the predominant clast type starting sol 780. This type is similar to the surrounding outcrop and thus likely did not travel far. The diverse morphology indicates that a complex interplay of varying lithologies, transport mechanisms, and environmental circumstances is responsible for the morphology observed. Morphology of clasts suggests that the majority of pebbles and cobbles have not been significantly altered in transport. The exceptions are pebbles that likely wore out of conglomerates, and a sub-rounded population near the base of Mt. Sharp that we are beginning to explore.

Toll-like receptors-2 and -9 (TLR2 and TLR9) gene polymorphism in patients with type 2 diabetes and diabetic foot.

PubMed

Wifi, Mohamed-Naguib Abdalla; Assem, Maha; Elsherif, Rasha Hamed; El-Azab, Hameda Abdel-Fattah; Saif, Aasem

2017-04-01

Toll-like receptors (TLRs) are innate immune receptors that mediate the inflammatory response in diabetes mellitus (DM). The aim of this study is to evaluate the association of TLR2 and TLR9 gene polymorphism in patients with type 2 DM (T2DM) and diabetic foot (DF).The study included 90 subjects divided into group I (30 patients with T2DM and DF), group II (30 patients with T2DM and no evidence of DF), and group III (normal control subjects). TLR2 (1350 T/C, rs3804100) and TLR9 (1237 T/C, rs5743836) genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique for all subjects.There was a statistically significant difference in the distribution of TLR9-1237 T/C genotypes between groups I and II (P < .029) as well as between groups I and III (P < .001). Calculated risk estimation revealed that TLR9-1237 polymorphism conferred almost 20 times increased risk of DF disorders in T2DM (OR = 20, 95% CI = 5.38-74.30). There was no statistical difference in the distribution of TLR2-1350T/C genotypes between the 3 groups.TLR9-1237 T/C gene polymorphism may be considered as a molecular risk for DF among patients with T2DM.

Toll-like receptors-2 and -9 (TLR2 and TLR9) gene polymorphism in patients with type 2 diabetes and diabetic foot

PubMed Central

Wifi, Mohamed-Naguib Abdalla; Assem, Maha; Elsherif, Rasha Hamed; El-Azab, Hameda Abdel-Fattah; Saif, Aasem

2017-01-01

Abstract Toll-like receptors (TLRs) are innate immune receptors that mediate the inflammatory response in diabetes mellitus (DM). The aim of this study is to evaluate the association of TLR2 and TLR9 gene polymorphism in patients with type 2 DM (T2DM) and diabetic foot (DF). The study included 90 subjects divided into group I (30 patients with T2DM and DF), group II (30 patients with T2DM and no evidence of DF), and group III (normal control subjects). TLR2 (1350 T/C, rs3804100) and TLR9 (1237 T/C, rs5743836) genotyping was performed by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) technique for all subjects. There was a statistically significant difference in the distribution of TLR9-1237 T/C genotypes between groups I and II (P < .029) as well as between groups I and III (P < .001). Calculated risk estimation revealed that TLR9-1237 polymorphism conferred almost 20 times increased risk of DF disorders in T2DM (OR = 20, 95% CI = 5.38–74.30). There was no statistical difference in the distribution of TLR2-1350T/C genotypes between the 3 groups. TLR9-1237 T/C gene polymorphism may be considered as a molecular risk for DF among patients with T2DM. PMID:28445304

Hydroxyl Radical Modification of Collagen Type II Increases Its Arthritogenicity and Immunogenicity

PubMed Central

Shahab, Uzma; Ahmad, Saheem; Moinuddin; Dixit, Kiran; Habib, Safia; Alam, Khursheed; Ali, Asif

2012-01-01

Background The oxidation of proteins by endogenously generated free radicals causes structural modifications in the molecules that lead to generation of neo-antigenic epitopes that have implications in various autoimmune disorders, including rheumatoid arthritis (RA). Collagen induced arthritis (CIA) in rodents (rats and mice) is an accepted experimental model for RA. Methodology/Principal Findings Hydroxyl radicals were generated by the Fenton reaction. Collagen type II (CII) was modified by •OH radical (CII-OH) and analysed by ultraviolet-visible (UV-VIS), fluorescence and circular dichroism (CD) spectroscopy. The immunogenicity of native and modified CII was checked in female Lewis rats and specificity of the induced antibodies was ascertained by enzyme linked immunosorbent assay (ELISA). The extent of CIA was evaluated by visual inspection. We also estimated the oxidative and inflammatory markers in the sera of immunized rats. A slight change in the triple helical structure of CII as well as fragmentation was observed after hydroxyl radical modification. The modified CII was found to be highly arthritogenic and immunogenic as compared to the native form. The CII-OH immunized rats exhibited increased oxidative stress and inflammation as compared to the CII immunized rats in the control group. Conclusions/Significance Neo-antigenic epitopes were generated on •OH modified CII which rendered it highly immunogenic and arthritogenic as compared to the unmodified form. Since the rodent CIA model shares many features with human RA, these results illuminate the role of free radicals in human RA. PMID:22319617

Antibody Prevalence and Isolation of Viable Toxoplasma gondii from Raptors in the Southeastern USA.

PubMed

Love, David; Kwok, Oliver C; Verma, Shiv Kumar; Dubey, Jitender P; Bellah, Jamie

2016-07-01

Raptors are good indicators of the prevalence of Toxoplasma gondii in the environment because they prey on small mammals and birds. These prey species are a major source of infection in domestic cats ( Felis catus ), which shed the environmentally resistant oocysts. We assessed T. gondii infection in 281 opportunistically available raptors at a rehabilitation facility between 2012 and 2014. Antibodies to T. gondii were assayed by a modified agglutination test (cutoff 1:25) and found in serum of 22/71 Red-tailed Hawks ( Buteo jamaicensis ), 25/54 Barred Owls ( Strix varia ), 9/41 Red-shouldered Hawks ( Buteo lineatus ), 13/28 Great Horned Owls ( Bubo virginianus ), 6/20 Broad-winged Hawks ( Buteo platypterus ), 2/16 Eastern Screech Owls (Megascops asio), 12/13 Bald Eagles ( Haliaeetus leucocephalus ), 6/12 Cooper's Hawks ( Accipiter cooperii ), 1/8 Black Vultures ( Coragyps atratus ), and 1/1 Golden Eagle ( Aquila chrysaetos ). Antibodies were not detected in 5 Barn Owls ( Tyto alba ), 3 American Kestrels ( Falco sparverius ), 1 Mississippi Kite ( Ictinia mississippiensis ), and 1 Osprey ( Pandion haliaetus ). Viable T. gondii was isolated from the tissues of 1 antibody-positive Barred Owl and identified as a strain having type II alleles at all 10 loci tested, except one (ToxoDB polymerase chain reaction-restriction fragment length polymorphism genotype 3). Type II strain is the most common strain in the US. Results of this study indicate a high prevalence of T. gondii in some raptor species and the first reported genotyping from a Barred Owl.

[Expression of Dengue virus type 2 nonstructural protein 3 and isolation of host proteins interacting with it].

PubMed

Weng, Daihui; Lei, Yingfeng; Dong, Yangchao; Han, Peijun; Ye, Chuantao; Yang, Jing; Wang, Yuan; Yin, Wen

2015-12-01

To construct the plasmid expressing the fusion protein of Dengue virus type 2 (DENV2) nonstructural protein 3 (NS3) with affinity tag, and isolate the cellular proteins interacting with NS3 protein using tandem affinity purification (TAP) assay. Primers for amplifying NS3 gene were designed according to the sequence of DENV2 genome and chemically synthesized. The NS3 fragments, after amplified by PCR with DENV2 cDNA as template, were digested and cloned into the mammalian eukaryotic expression vector pCI-SF with the tandem affinity tag (FLAG-StrepII). The recombinant pCI-NS3-SF was transiently transformed by Lipofectamine(TM) 2000 into HEK293T cells, and the expression of the fusion protein was confirmed by Western blotting. Cellular proteins that interacted with NS3 were isolated and purified by TAP assay. The eukaryotic expression vector expressing NS3 protein was successfully constructed. The host proteins interacting with NS3 protein were isolated by TAP system. TAP is an efficient method to isolate the cellular proteins interacting with DENV2 NS3.

Cloning, cell-type specificity, and regulatory function of the mouse alpha(1B)-adrenergic receptor promoter.

PubMed

Zuscik, M J; Piascik, M T; Perez, D M

1999-12-01

The functionality of a 3422-base pair promoter fragment from the mouse alpha(1B)-adrenergic receptor (alpha(1B)AR) gene was examined. This fragment, cloned from a mouse genomic library, was found to have significant sequence homology to the known human and rat alpha(1B)AR promoters. However, the consensus motif of several key cis-acting elements is not conserved among the rat, human, and mouse genes, suggesting species specificity. Confirming fidelity of the murine promoter, robust in vitro expression of a chloramphenicol acetyltransferase (CAT) reporter was detected in known alpha(1B)AR-expressing BC(3)H1, NB41A3, and DDT(1)MF-2 cells transiently transfected with a promoter-CAT construct. Conversely, minimal CAT expression was detected in known alpha(1B)AR-negative RAT-1 and R3T3 cells. These findings were extended by transfecting the same promoter-CAT construct into various primary cell types. In support of the hypothesis that alpha(1)ARs are differentially expressed in the smooth muscle of the vasculature, primary cultures of superior mesenteric and renal artery vascular smooth muscle cells showed significantly stronger CAT expression than did vascular smooth muscle cells derived from pulmonary, femoral, and iliac arteries. Primary osteoblastic bone-forming cells, which are known to be alpha(1B)AR negative, showed minimal CAT expression. Indicating regulatory function through cis-acting elements, RAT-1, R3T3, NB41A3, BC(3)H1, and DDT(1)MF2 cells transfected with the promoter-CAT construct all showed increased CAT production when challenged with forskolin or hypoxic conditions. Additionally, tissue-specific regulation of the promoter was observed when cells were simultaneously challenged with both forskolin and hypoxia. These results collectively demonstrate that a 3.4-kb PvuII fragment of the murine alpha(1B)AR gene promoter can: 1) drive tissue-specific production of a CAT reporter in both clonal and primary cell lines; and 2) confer tissue-specific regulation of that CAT reporter when induced by challenge with forskolin and/or hypoxic conditions.

Hydrothermal quartz formation during fluctuations of brittle shear-zone activity and fluid flow: grain growth and deformation structures of the Pfahl shear zone (Germany)

NASA Astrophysics Data System (ADS)

Yilmaz, T.; Prosser, G.; Liotta, D.; Kruhl, J. H.

2012-12-01

The Bavarian Pfahl shear zone is a WNW-ESE trending dextral strike-slip shear zone at the SW margin of the Bohemian Massif (Central Europe). It was discontinuously active during decreasing PT-conditions, i.e. from ductile to brittle, from the late-Carboniferous to the late-Cretaceous - Paleocene times. Triassic hydrothermal activity produced a 150 km long and 30-100 m wide quartz dyke along the main fault, surrounded by sheared basement rocks. Within a zone of >10 m metasomatism transformed the wall rocks to mostly kaolinite, chlorite and phyllosilicates. The quartz dyke exhibits a layered to lenticular and partly symmetric structure with different types of quartz masses, transected by a complex quartz vein network. This already indicates pulses of fluid flux and fragmentation during the lifetime of the shear zone. Analyses by optical microscopy, cathodoluminescence (CL) and SEM-EDX reveal at least four subsequent stages of quartz crystallization and fragmentation. (i) The oldest generation of quartz is represented by a homogeneous dark grey to reddish quartz mass made up by ~10-20 μm-sized crystals. It contains mm- to cm-sized angular wall-rock fragments, completely altered to kaolinite, indicating intense wall-rock alteration prior to the earliest event of silica precipitation. This rules out the possibility that the quartz mass developed from silicification of the wall rocks. This first type of quartz occurs as cm- to dm-large angular fragments in (ii) a light grey to pink quartz mass formed by ~10-50 μm-sized crystals. The different colours result from variable types and amounts of inclusions. Quartz of both generations shows random crystallographic orientations and complex inclusion structures. It probably developed during two fragmentation events and possibly from a silica gel precursor that crystallized after precipitation. (iii) The third quartz generation formed as a set of mm- to dm-wide veins roughly parallel to the trend of the Pfahl zone, crosscutting the first generations of fine-grained quartz mass and the wall rocks, in connection to intense fracturing and brecciation. The complex geometry of the vein sets points to multiple fluid injections and brecciation, as additionally indicated by coarse quartz with different inclusion and CL intensity. Temporal changes of strain rate are indicated by crystal plastic deformation structures in quartz, which overprint brittle structures. (iv) The fourth quartz generation occurs in mm- to dm-thick quartz veins, partly open as geodes, filling N-S oriented cm- to dm-spaced fractures that crosscut the earlier quartz masses and veins and extend at least several meters into the wall rock. They indicate the last activity of the shear-zone in a constant kinematic framework. Summarizing, the Pfahl shear zone shows brittle-ductile deformation during the long-term activity of a large-scale hydrothermal system. Consequently, it represents an excellent example where different generations of quartz precipitation can be connected to fluctuations of fluid flow and strain rate.

A comparison of charcoal measurements for reconstruction of Mediterranean paleo-fire frequency in the mountains of Corsica

NASA Astrophysics Data System (ADS)

Leys, Bérangère; Carcaillet, Christopher; Dezileau, Laurent; Ali, Adam A.; Bradshaw, Richard H. W.

2013-05-01

Fire-history reconstructions inferred from sedimentary charcoal records are based on measuring sieved charcoal fragment area, estimating fragment volume, or counting fragments. Similar fire histories are reconstructed from these three approaches for boreal lake sediment cores, using locally defined thresholds. Here, we test the same approach for a montane Mediterranean lake in which taphonomical processes might differ from boreal lakes through fragmentation of charcoal particles. The Mediterranean charcoal series are characterized by highly variable charcoal accumulation rates. Results there indicate that the three proxies do not provide comparable fire histories. The differences are attributable to charcoal fragmentation. This could be linked to fire type (crown or surface fires) or taphonomical processes, including charcoal transportation in the catchment area or in the sediment. The lack of correlation between the concentration of charcoal and of mineral matter suggests that fragmentation is not linked to erosion. Reconstructions based on charcoal area are more robust and stable than those based on fragment counts. Area-based reconstructions should therefore be used instead of the particle-counting method when fragmentation may influence the fragment abundance.

Land Use Change and Agricultural Land Fragmentation due to Anthropogenic Activities in an Hot Spot Area: A Case Study for Thrace Region of Turkey

NASA Astrophysics Data System (ADS)

Altürk, Bahadır; Konukcu, Fatih

2017-04-01

Agricultural lands that supply food, energy and ecosystem services for human life have been lost due to anthropogenic activities such as construction of roads, urban and industry areas. The significant reasons for the increase of artificial surfaces were poorly planned economic decisions by the government and internal migration due to this poorly planning. Unplanned urban sprawl also give rise to land fragmentation. Fragmentation of agricultural land affects both the agricultural production capacity and rural sustainable employment. In this study: i) Land use changes between 1990-2014 period were assessed using remotely sensed data and ii) Spatial and temporal agricultural land fragmentation were investigated using landscape pattern indice (effective mesh size), Morphological Spatial Pattern Analysis (MSPA) and Entropy method for 25 years period. The selected"hot spot" study area is located on east Thrace region of Turkey, being the service and industrial development zone where agricultural activities, water resources and natural habitat have been damaged due to rapid urban and industrial development for about 25 years. The results showed that agricultural lands decreased 6.44%, urban areas increased 111.68% and industry areas increased 251.19% during this 25 years period. Additionally, fragmentation analyses demonstrated that core agricultural areas sharply decreased and relative fragmentation (effective mesh size) increased from 50.68% to 56.77% during 1990 and 2014.

Heterogeneous Distributions of Amino Acids Provide Evidence of Multiple Sources Within the Almahata Sitta Parent Body, Asteroid 2008 TC(sub 3)

NASA Technical Reports Server (NTRS)

Burton, Aaron S.; Glavin, Daniel P.; Callahan, Michael P.; Dworkin, Jason P.; Jenniskens, Peter; Shaddad, Muawia H.

2011-01-01

Two new fragments of the Almahata Sitta meteorite and a sample of sand from the related strewn field in the Nubian Desert, Sudan, were analyzed for two to six carbon aliphatic primary amino acids by ultrahigh performance liquid chromatography with UV-fluorescence detection and time-of-flight mass spectrometry (LC-FT/ToF-MS). The distribution of amino acids in fragment #25, an H5 ordinary chondrite, and fragment #27, a polymict ureilite, were compared with results from the previously analyzed fragment #4, also a polymict ureilite. All three meteorite fragments contain 180-270 parts-per-billion (ppb) of amino acids, roughly 1000-fold lower than the total amino acid abundance of the Murchison carbonaceous chondrite. All of the Almahata Sitta fragments analyzed have amino acid distributions that differ from the Nubian Desert sand, which primarily contains L-alpha-amino acids. In addition, the meteorites contain several amino acids that were not detected in the sand, indicating that many of the amino acids are extraterrestrial in origin. Despite their petrological differences, meteorite fragments #25 and #27 contain similar amino acid compositions; however, the distribution of amino acids in fragment #27 was distinct from those in fragment #4, even though both arc polymict ureilites from the same parent body. Unlike in CM2 and CR2/3 meteorites, there are low relative abundances of alpha-amino acids in the Almahata Sitta meteorite fragments, which suggest that Strecker-type chemistry was not a significant amino acid formation mechanism. Given the high temperatures that asteroid 2008 TC3 appears to have experienced and lack of evidence for aqueous alteration on the asteroid, it is possible that the extraterrestrial amino acids detected in Almahata Sitta were formed by Fischer-Tropsch/Haber-Bosch type gas-grain reactions at elevated temperatures.

Management of combined knee medial compartmental and patellofemoral osteoarthritis with lateral closing wedge osteotomy with anterior translation of the distal tibial fragment: Does the degree of anteriorization affect the functional outcome and posterior tibial slope?

PubMed

Sadek, Ahmed F; Osman, Mohammed K; Laklok, Mohamed A

2016-10-01

The aim of this study was to assess the effect of degree of anterior translation of the distal tibial fragment after lateral closing wedge high tibial osteotomy in patients having combined knee medial compartmental and patellofemoral osteoarthritis. A retrospective study was conducted on 64 patients who were operated on for combined knee medial compartmental and patellofemoral osteoarthritis, by lateral closing wedge high tibial osteotomy with anterior translation of the distal tibial fragment. They were divided into two groups; Group I comprising 32 patients (34 knees, mean age of 51.4±7years) whose degree of anterior translation was <1cm and Group II comprising 32 patients (33 knees, mean age of 52.2±8.3years) whose degree of anterior translation was >1.5cm. The final assessment was performed via: visual analog scale, postoperative Knee Society clinical rating system function score, active range of motion, time to union, degree of correction of mechanical axis, posterior tibial slope, and Insall-Salvati ratio. Group II patients exhibited statistically superior mean postoperative score and better return to their work than Group I (P=0.013, 0.076, respectively). Both groups showed statistically significant differences between the preoperative and postoperative evaluation parameters (P<0.001). The posterior tibial slope was decreased in both groups but with no significant difference (P=0.527). Lateral closing wedge high tibial osteotomy combined with anterior translation of the distal tibial fragment more than 1.5cm achieved significantly better postoperative functional knee score. Both groups exhibited comparatively decreased posterior tibial slope. Copyright © 2016 Elsevier B.V. All rights reserved.

Differentiation of highly virulent strains of Streptococcus suis serotype 2 according to glutamate dehydrogenase electrophoretic and sequence type.

PubMed

Kutz, Russell; Okwumabua, Ogi

2008-10-01

The glutamate dehydrogenase (GDH) enzymes of 19 Streptococcus suis serotype 2 strains, consisting of 18 swine isolates and 1 human clinical isolate from a geographically varied collection, were analyzed by activity staining on a nondenaturing gel. All seven (100%) of the highly virulent strains tested produced an electrophoretic type (ET) distinct from those of moderately virulent and nonvirulent strains. By PCR and nucleotide sequence determination, the gdh genes of the 19 strains and of 2 highly virulent strains involved in recent Chinese outbreaks yielded a 1,820-bp fragment containing an open reading frame of 1,344 nucleotides, which encodes a protein of 448 amino acid residues with a calculated molecular mass of approximately 49 kDa. The nucleotide sequences contained base pair differences, but most were silent. Cluster analysis of the deduced amino acid sequences separated the isolates into three groups. Group I (ETI) consisted of the seven highly virulent isolates and the two Chinese outbreak strains, containing Ala(299)-to-Ser, Glu(305)-to-Lys, and Glu(330)-to-Lys amino acid substitutions compared with groups II and III (ETII). Groups II and III consisted of moderately virulent and nonvirulent strains, which are separated from each other by Tyr(72)-to-Asp and Thr(296)-to-Ala substitutions. Gene exchange studies resulted in the change of ETI to ETII and vice versa. A spectrophotometric activity assay for GDH did not show significant differences between the groups. These results suggest that the GDH ETs and sequence types may serve as useful markers in predicting the pathogenic behavior of strains of this serotype and that the molecular basis for the observed differences in the ETs was amino acid substitutions and not deletion, insertion, or processing uniqueness.

Effects of the novel angiotensin II receptor type I antagonist, fimasartan on myocardial ischemia/reperfusion injury.

PubMed

Han, Jin; Park, Sung-Ji; Thu, Vu Thi; Lee, Sung-Ryul; Long, Le Thanh; Kim, Hyoung Kyu; Kim, Nari; Park, Seung Woo; Jeon, Eun-Seok; Kim, Eun-Ji; Yoon, Chang-Hwan; Cho, Goo-Young; Choi, Dong-Ju

2013-10-03

The aim of this study was to investigate the cardioprotective effect of fimasartan, a newly developed angiotensin II receptor type I blocker (ARB), against myocardial ischemia/reperfusion (I/R) injury and to identify the mechanism by which it reduces mitochondrial damage. Fimasartan was administered intravenously to Sprague-Dawley rats (3mg/kg), cardiomyocytes (50 μM), and H9c2 cells (50 μM) before ischemia or hypoxia. Myocardial infarction (MI), echocardiograms, DNA fragmentation, terminal deoxynucleotidyl transferase-mediated dUTP in situ nick-end labeling, immunoblotting, oxygen consumption, confocal microscopic appearance, and L-type Ca(2+) current (ICa,L) were then assessed. Fimasartan pretreatment remarkably reduced the rate of MI and improved cardiac performance well after I/R (n = 9/group). Fimasartan also reduced apoptotic cell death both in vivo and in hypoxia/reoxygenation (H/R)-treated H9c2 cells (n = 5~8/group). H/R-induced mitochondrial O2(-) production and collapse of membrane potential were markedly attenuated in fimasartan-treated cardiomyocytes (n = 4 ~ 6/group). Additionally, mitochondrial Ca(2+) overload during reoxygenation was suppressed by fimasartan (n = 4~6/group), and this was found to be possibly related to the inhibition of ICa,L and mitochondrial Ca(2+) uniporter. Furthermore, fimasartan pretreatment increased phosphorylations of Akt and glycogen synthase kinase-3β (n = 5 ~ 7/group), decreased pro-apoptotic p53 levels, and increased anti-apoptotic Bcl-2 levels (n = 4) during reperfusion. Fimasartan preconditioning has the potential to modulate Bcl-2 and suppress I/R-induced Ca(2+) overload by inhibiting ICa,L and MCU. These beneficial effects could prevent the mitochondrial dysfunction and apoptosis accompanied by I/R. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Utilization of Seismic and Infrasound Signals for Characterizing Mining Explosions

DTIC Science & Technology

2001-10-01

different types of mining operations exist, ranging from surface coal cast blasting to hard rock fragmentation blasting in porphyry copper mines. The study...both seismic and infrasound signals. The seismic coupling of large-scale cast blasts in Wyoming, copper fragmentation blasts in Arizona and New Mexico...mining explosions from the copper fragmentation blasts in SE Arizona were observed at Los Alamos. Detected events were among the largest of the blasts

An energy-dependent numerical model for the condensation probability, γ j

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerby, Leslie Marie

The “condensation” probability, γ j, is an important variable in the preequilibrium stage of nuclear spallation reactions. It represents the probability that p j excited nucleons (excitons) will “condense” to form complex particle type j in the excited residual nucleus. In addition, it has a significant impact on the emission width, or probability of emitting fragment type j from the residual nucleus. Previous formulations for γ j were energy-independent and valid for fragments up to 4He only. This paper explores the formulation of a new model for γ j, one which is energy-dependent and valid for up to 28Mg, andmore » which provides improved fits compared to experimental fragment spectra.« less

An energy-dependent numerical model for the condensation probability, γ j

DOE PAGES

Kerby, Leslie Marie

2016-12-09

The “condensation” probability, γ j, is an important variable in the preequilibrium stage of nuclear spallation reactions. It represents the probability that p j excited nucleons (excitons) will “condense” to form complex particle type j in the excited residual nucleus. In addition, it has a significant impact on the emission width, or probability of emitting fragment type j from the residual nucleus. Previous formulations for γ j were energy-independent and valid for fragments up to 4He only. This paper explores the formulation of a new model for γ j, one which is energy-dependent and valid for up to 28Mg, andmore » which provides improved fits compared to experimental fragment spectra.« less

Clinical characteristics and surgical experience of Type III Wagstaffe fractures: Pay attention to concomitant chondral injury of the talus.

PubMed

Zhang, Ming; Chen, Yun-Feng; Wang, Lei; Li, Fan; Wei, Hai-Feng; Shi, Zhong-Min

2017-04-27

The purpose of this study was to investigate clinical characteristics and surgical management of Type III Wagstaffe fracture. From August 2012 to July 2015, 13 patients with Type III Wagstaffe fractures were surgically treated. During operation, the cartilage of joint surface was explored. Wagstaffe fragment was fixed with cannulated screw or suture, Chaput fragment was fixed with cannulated screw or plate, and Cotton test was performed to evaluate the stability of syndesmosis during the operation. All the patients were followed up for 14.3 months in average. Clinical outcome was assessed with Olerud-Molander score and American Orthopedic Foot and Ankle Society (AOFAS) score. The traumatic arthritis was evaluated with osteoarthritis-score (OA-score). During the operation, chondral injury was found on the lateral top of the talus in 8 cases, as "kissing lesion" of Chaput fragment. The fractures healed uneventfully and all the patients recovered satisfactorily except two had moderate restriction in ankle movement. The average Olerud-Molander score and AOFAS score were 82.3 and 86.1, respectively. Type III Wagstaffe is a rare and often missed fracture. 61% are associated with a chondral lesion on the lateral top of the talus. Anatomical reduction and rigid fixation of both fragments are mandatory to obtain ankle stability and good results. Copyright © 2017 European Foot and Ankle Society. Published by Elsevier Ltd. All rights reserved.

From vein precipitates to deformation and fluid rock interaction within a SSZ: Insights from the Izu-Bonin-Mariana fore arc

NASA Astrophysics Data System (ADS)

Micheuz, Peter; Quandt, Dennis; Kurz, Walter

2017-04-01

International Ocean Discovery Program (IODP) expeditions 352 and 351 drilled through oceanic crust of the Philippine Sea plate. The two study areas are located near the outer Izu-Bonin-Mariana (IBM) fore arc and in the Amami Sankaku Basin. The primary objective was to improve our understanding of supra-subduction zones (SSZ) and the process of subduction initiation. The recovered drill cores during IODP expedition 352 represent approximately 50 Ma old fore arc basalts (FAB) and boninites revealing an entire volcanic sequence of a SSZ. Expedition 351 drilled FAB like oceanic crust similar in age to the FABs of expedition 352. In this study we present data on vein microstructures, geochemical data and isotopic signatures of vein precipitates to give new insights into fluid flow and precipitation processes and deformation within the Izu-Bonin fore arc. Veins formed predominantly as a consequence of hydrofracturing resulting in the occurrence of branched vein systems and brecciated samples. Along these hydrofractures the amount of altered host rock fragments varies and locally alters the host rock completely to zeolites and carbonates. Subordinately extensional veins released after the formation of the host rocks. Cross-cutting relationships of different vein types point to multiple fracturing events subsequently filled with minerals originating from a fluid with isotopic seawater signature. Based on vein precipitates, their morphology and their growth patterns four vein types have been defined. Major vein components are (Mg-) calcite and various zeolites determined by Raman spectra and electron microprobe analyses. Zeolites result from alteration of volcanic glass during interaction with a seawaterlike fluid. Type I veins which are characterized by micritic infill represent neptunian dykes. They predominantly occur in the upper levels of drill cores being the result of an initial volume change subsequently to crystallization of the host rocks. Type II veins are characterized by blocky carbonates and idiomorphic to blocky zeolites. Blocky carbonates locally exhibit zonation patterns. Type III and type IV veins are both assumed to be extensional veins. Type III is characterized by syntaxial growth and elongate blocky carbonate minerals. They predominantly occur as asymmetric syntaxial veins, locally exhibiting more than one crack-seal event. Type IV veins are defined as antitaxial fibrous carbonates. Type II veins commonly show deformation microstructures like twinning (type I/II twins), slightly curved twins, and subgrain boundaries indicative of incipient plastic deformation. Based on these observations differential stresses around 50 MPa were needed to deform vein minerals, presumably related to IBM fore arc extension due to the retreat of the subducted Pacific plate. We acknowledge financial support by the Austrian Research Fund (P27982-N29) to W. Kurz

Landscape composition and configuration in the central highlands of Ethiopia.

PubMed

Tolessa, Terefe; Senbeta, Feyera; Kidane, Moges

2016-10-01

Landscape dynamics are common phenomenon in the human-dominated environments whereby it can be observed that the composition and configuration between landscape elements change over time. This dynamism brings about habitat loss and fragmentation that can greatly alter ecosystem services at patch, class, and landscape levels. We conducted a study to examine composition and configuration of forested landscape in the central highlands of Ethiopia using satellite images of over a period of four decades, and FRAGSTAT raster dataset was used to analyze fragmentation. Our result showed five land use/land cover (LULC) types in the study area. Cultivated land and settlement land increased at the expense of forestland, shrubland, and grassland. Fragmentation analysis showed the number of patches increased for all LULC types, indicating the level of fragmentation and interspersion. Juxtaposition increased for shrubland, grassland, and cultivated lands and decreased for settlement and forestland resulting in the fragmentation and isolation of patches. The study of LULC along with fragmentation at the landscape level can help improve our understanding of the pace at which conversion of landscape elements is happening and the impacts on ecosystem services as studies of LULC are courser in nature and would not show how each land use is reducing in size, proximity and shape among other things that determine ecosystem services. Such type of studies in rural landscapes are very vital to consider appropriate land management policies for the landscape level by taking into account the interaction between each element for sustainable development. We recommend land managers, conservationists, and land owners for observing the roles of each patch in the matrix to maximize the benefits than focusing on a single element.

Reconstruction of Traumatic Bone Defect With In Situ Implantation of Dropped Traumatic Segmental Bone Fragments.

PubMed

Lin, Dasheng; Luo, Deqing; Lian, Kejian; Zhai, Wenliang; Ding, Zhenqi

2016-01-01

This study was conducted to determine whether in situ implantation of a dropped traumatic segmental bone fragment is safe and whether the authors' method would reduce the incidence of infectious and related complications. The authors retrospectively reviewed 16 patients with open fractures, including 11 with Gustilo-Anderson type IIIA fractures and 5 with Gustilo-Anderson type IIIB fractures who had a dropped traumatic segmental bone fragment between January 2002 and January 2012. Mean patient age was 35.4 years (range, 19-47 years). There were 10 femurs and 6 tibias. Average postoperative follow-up was 26.8 months (range, 12-60 months). The dropped traumatic segmental bone fragments were cleaned with 3% hydrogen peroxide, placed in separate sterile cups, and soaked in 1% iodophor for 30 minutes. Initial treatment included surgical debridement, wound irrigation, in situ implantation of the dropped traumatic segmental bone fragment, and temporary external fixation. Approximately 4 to 8 weeks later, after successful reconstruction of the soft tissue envelope, minimally invasive plate osteosynthesis was performed. Mean duration of treatment was 8 weeks (range, 6-14 weeks). All patients had fracture union at final follow-up. Mean healing time was 21.8 weeks (range, 14-48 weeks). One patient did not achieve primary union and required bone grafting. One patient with a Gustilo-Anderson type IIIB fracture had deep infection and removal of the dropped traumatic segmental bone fragment and bone grafting. According to the Klemm and Börner classification, 11 patients had excellent results, 3 had good results, and 2 had poor results. With adequate soft tissue coverage, this method was acceptable for the management of open fractures with bone defects. Copyright 2016, SLACK Incorporated.

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts. II. IR spectral studies.

PubMed Central

Krzyzosiak, W; Jaskólski, M; Sierzputowska-Gracz, H; Wiewiórowski, M

1982-01-01

The IR spectra of crystalline cytidine (Cyd), ethenocytidine (epsilon Cyd), and their hydrochlorides (Cyd-Hcl and epsilon CyD-HCl) have been analyzed to determine the spectroscopic manifestations of the structural differences that were previously established for these nucleosides from X-ray studies. O,N-Deuteration of the samples turned out to be a successful approach to obtaining interpretable spectra. The analysis was carried out in three frequency ranges: (i) The 2600-1900 cm-1 range originating from the vO-D and VN-D vibrations. All intermolecular hydrogen bonds could be recognized here. The positions of the individual vO-D (vN-D) bands were correlated with the geometrical delta HB parameters presenting the strengths of hydrogen bonds in which these groups act as donors (ii) The 1750-1500 cm-1 region originating from the stretching vibrations of double bonds. All absorption bands in this region were interpreted in terms of electronic structures of the base fragments. (iii) The region of the C-H stretching vibrations of the base fragments (3200-3000 cm-1) and sugar moieties (3000-2800 cm-1). The Csp2-H vibrations also reflect the electronic structures of the base fragments, whereas the vCsp-H frequencies seem to be sensitive to etheno-bridging and to the presence of an intramolecular C6-H...05' hydrogen bond. PMID:7079184

Morphological and Molecular Discrimination of Fasciola Species Isolated From Domestic Ruminants of Urmia City, Iran

PubMed Central

YAKHCHALI, Mohammad; MALEKZADEH-VIAYEH, Reza; IMANI-BARAN, Abbas; MARDANI, Karim

2015-01-01

Background: The trematodes of the genus Fasciola (the liver flukes) are among the well-known instances of food-borne parasites worldwide. Differentiation of Fasciola species is important because of their different transmission and epidemiological characteristics. The current study was undertaken to discriminate Fasciola species in the domestic ruminants of Urmia city, Iran. Methods: Adult flukes were isolated from the naturally infected livers of the slaughtered water buffaloes and sheep. The flukes were initially identified based on morphological and morphometric parameters. A 618-bp-long fragment of the 28SrRNA gene of Fasciola was amplified by polymerase chain reaction (PCR). The amplified fragment was digested by DraII or AvaII enzymes for a restriction fragment length polymorphism (RFLP) analysis and sequenced for the phylogenetic tree construction. Results: Based on the morphometric examination, the flukes belonged to F. hepatica, F. gigantica and an intermediate Fasciola form. The PCR-RFLP analysis was able to differentiate F. hepatica from F. gigantica. While the phylogenetic reconstruction justified, to some extent, the morphological diagnosis, it failed to segregate F. hepatica from F. gigantica identified in this and the previous studies. Conclusion: To resolve fully the problem of taxonomy and evolution in Fasciola species, employing a broad range of molecular and morphological approaches is necessary. This is crucial for epidemiological surveys and successful clinical management of their infection. PMID:25904945

Novel Bioinformatics-Based Approach for Proteomic Biomarkers Prediction of Calpain-2 & Caspase-3 Protease Fragmentation: Application to βII-Spectrin Protein

NASA Astrophysics Data System (ADS)

El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges; Kobeissy, Firas

2017-01-01

The crucial biological role of proteases has been visible with the development of degradomics discipline involved in the determination of the proteases/substrates resulting in breakdown-products (BDPs) that can be utilized as putative biomarkers associated with different biological-clinical significance. In the field of cancer biology, matrix metalloproteinases (MMPs) have shown to result in MMPs-generated protein BDPs that are indicative of malignant growth in cancer, while in the field of neural injury, calpain-2 and caspase-3 proteases generate BDPs fragments that are indicative of different neural cell death mechanisms in different injury scenarios. Advanced proteomic techniques have shown a remarkable progress in identifying these BDPs experimentally. In this work, we present a bioinformatics-based prediction method that identifies protease-associated BDPs with high precision and efficiency. The method utilizes state-of-the-art sequence matching and alignment algorithms. It starts by locating consensus sequence occurrences and their variants in any set of protein substrates, generating all fragments resulting from cleavage. The complexity exists in space O(mn) as well as in O(Nmn) time, where N, m, and n are the number of protein sequences, length of the consensus sequence, and length per protein sequence, respectively. Finally, the proposed methodology is validated against βII-spectrin protein, a brain injury validated biomarker.

Immobilization methods for the rapid total chemical synthesis of proteins on microtiter plates.

PubMed

Zitterbart, Robert; Krumrey, Michael; Seitz, Oliver

2017-07-01

The chemical synthesis of proteins typically involves the solid-phase peptide synthesis of unprotected peptide fragments that are stitched together in solution by native chemical ligation (NCL). The process is slow, and throughput is limited because of the need for repeated high performance liquid chromatography purification steps after both solid-phase peptide synthesis and NCL. With an aim to provide faster access to functional proteins and to accelerate the functional analysis of synthetic proteins by parallelization, we developed a method for the high performance liquid chromatography-free synthesis of proteins on the surface of microtiter plates. The method relies on solid-phase synthesis of unprotected peptide fragments, immobilization of the C-terminal fragment and on-surface NCL with an unprotected peptide thioester in crude form. Herein, we describe the development of a suitable immobilization chemistry. We compared (i) formation of nickel(II)-oligohistidine complexes, (ii) Cu-based [2 + 3] alkine-azide cycloaddition and (iii) hydrazone ligation. The comparative study identified the hydrazone ligation as most suitable. The sequence of immobilization via hydrazone ligation, on-surface NCL and radical desulfurization furnished the targeted SH3 domains in near quantitative yield. The synthetic proteins were functional as demonstrated by an on-surface fluorescence-based saturation binding analysis. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP)

PubMed Central

Suzuki, Masako; Greally, John M.

2010-01-01

The HELP assay is a technique that allows genome-wide analysis of cytosine methylation. Here we describe the assay, its relative strengths and weaknesses, and the transition of the assay from a microarray to massively-parallel sequencing-based foundation. PMID:20434563

Effects of meteoroid fragmentation on radar observations of meteor trails

NASA Astrophysics Data System (ADS)

Elford, W. Graham; Campbell, L.

2001-11-01

Radar reflections from meteor trails often differ from the predictions of simple models. There is general consensus that these differences are probably the result of fragmentation of the meteoroid. Several examples taken from different types of meteor radar observations are considered in order to test the validity of the fragmentation hypothesis. The absence of the expected Fresnel oscillations in many observations of transverse scatter from meteor trails is readily explained by assuming a number of ablating fragments spread out along the trails. Observations of amplitude fluctuations in head echoes from "down-the-beam" meteoroids are explained by gross fragmentation of a meteoroid into two or more pieces. Another down-the-beam event is modeled by simulation of the differential retardation of two fragments of different mass, giving reasonable agreement between the observed and predicted radar signals.

Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) II: Spectral Homogeneity Among Hungaria Family Asteroids

NASA Astrophysics Data System (ADS)

Lucas, Michael P.; Emery, Joshua; Pinilla-Alonso, Noemi; Lindsay, Sean S.; MacLennan, Eric M.; Cartwright, Richard; Reddy, Vishnu; Sanchez, Juan A.; Thomas, Cristina A.; Lorenzi, Vania

2017-10-01

Spectral observations of asteroid family members provide valuable information regarding parent body interiors, the source regions of near-Earth asteroids, and the link between meteorites and their parent bodies. Hungaria family asteroids constitute the closest samples to the Earth from a collisional family (~1.94 AU), permitting observations of smaller fragments than accessible for Main Belt families. We have carried out a ground-based observational campaign - Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) - to record reflectance spectra of these preserved samples from the inner-most primordial asteroid belt. During HARTSS phase one (Lucas et al. [2017]. Icarus 291, 268-287) we found that ~80% of the background population is comprised of stony S-complex asteroids that exhibit considerable spectral and mineralogical diversity. In HARTSS phase two, we turn our attention to family members and hypothesize that the Hungaria collisional family is homogeneous. We test this hypothesis through taxonomic classification, albedo estimates, and spectral properties.During phase two of HARTSS we acquired near-infrared (NIR) spectra of 50 new Hungarias (19 family; 31 background) with SpeX/IRTF and NICS/TNG. We analyzed X-type family spectra for NIR color indices (0.85-J J-K), and a subtle ~0.9 µm absorption feature that may be attributed to Fe-poor orthopyroxene. Surviving fragments of an asteroid collisional family typically exhibit similar taxonomies, albedos, and spectral properties. Spectral analysis of X-type Hungaria family members and independently calculated WISE albedo determinations for 428 Hungaria asteroids is consistent with this scenario. Furthermore, ~1/4 of the background population exhibit similar spectral properties and albedos to family X-types.Spectral observations of 92 Hungaria region asteroids acquired during both phases of HARTSS uncover a compositionally heterogeneous background and spectral homogeneity down to ~2 km for collisional family members. Taxonomy, albedos, and spectral properties reveal that the Hungaria family progenitor was an igneous body that formed under reduced conditions, and was compositionally consistent with the enstatite achondrite (i.e., aubrite) meteorite group.

Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation.

PubMed

Brodie, Nicholas I; Huguet, Romain; Zhang, Terry; Viner, Rosa; Zabrouskov, Vlad; Pan, Jingxi; Petrotchenko, Evgeniy V; Borchers, Christoph H

2018-03-06

Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.

Evaluation of a Modified Single-Enzyme Amplified-Fragment Length Polymorphism Technique for Fingerprinting and Differentiating of Mycobacterium kansasii Type I Isolates

PubMed Central

Gaafar, Ayman; Josebe Unzaga, M.; Cisterna, Ramón; Clavo, Felicitas Elena; Urra, Elena; Ayarza, Rafael; Martín, Gloria

2003-01-01

The usefulness of single-enzyme amplified-fragment length polymorphism (AFLP) analysis for the subtyping of Mycobacterium kansasii type I isolates was evaluated. This simplified technique classified 253 type I strains into 12 distinct clusters. The discriminating power of this technique was high, and the technique easily distinguished between the epidemiologically unrelated control strains and our clinical isolates. Overall, the technique was relatively rapid and technically simple, yet it gave reproducible and discriminatory results. This technique provides a powerful typing tool which may be helpful in solving many questions concerning the reservoirs, pathogenicities, and modes of transmission of these isolates. PMID:12904399

Fungal Fragments in Moldy Houses: A Field Study in Homes in New Orleans and Southern Ohio

PubMed Central

Reponen, Tiina; Seo, Sung-Chul; Grimsley, Faye; Lee, Taekhee; Crawford, Carlos; Grinshpun, Sergey A.

2007-01-01

Smaller-sized fungal fragments (<1 μm) may contribute to mold-related health effects. Previous laboratory-based studies have shown that the number concentration of fungal fragments can be up to 500 times higher than that of fungal spores, but this has not yet been confirmed in a field study due to lack of suitable methodology. We have recently developed a field-compatible method for the sampling and analysis of airborne fungal fragments. The new methodology was utilized for characterizing fungal fragment exposures in mold-contaminated homes selected in New Orleans, Louisiana and Southern Ohio. Airborne fungal particles were separated into three distinct size fractions: (i) >2.25 μm (spores); (ii) 1.05–2.25 μm (mixture); and (iii) < 1.0 μm (submicrometer-sized fragments). Samples were collected in five homes in summer and winter and analyzed for (1→3)-β-D-glucan. The total (1→3)-β-D-glucan varied from 0.2 to 16.0 ng m−3. The ratio of (1→3)-β-D-glucan mass in fragment size fraction to that in spore size fraction (F/S) varied from 0.011 to 2.163. The mass ratio was higher in winter (average = 1.017) than in summer (0.227) coinciding with a lower relative humidity in the winter. Assuming a mass-based F/S-ratio=1 and the spore size = 3 μm, the corresponding number-based F/S-ratio (fragment number/spore number) would be 103 and 106, for the fragment sizes of 0.3 and 0.03 μm, respectively. These results indicate that the actual (field) contribution of fungal fragments to the overall exposure may be very high, even much greater than that estimated in our earlier laboratory-based studies. PMID:19050738

Micro-fragmented adipose tissue injection for the treatment of complex anal fistula: a pilot study accessing safety and feasibility.

PubMed

Naldini, G; Sturiale, A; Fabiani, B; Giani, I; Menconi, C

2018-02-01

The aim of the present study was to evaluate the safety and efficacy of autologous, micro-fragmented and minimally manipulated adipose tissue injection associated closure of the internal opening in promoting healing of complex anal fistula. A pilot study was conducted on patients referred to our center with anal fistula, from April 2015-December 2016. Inclusion criteria were age over 16 years old and a diagnosis of complex anal fistula according to the American Gastroenterological Association classification The patients were divided into 2 groups; the "first time group" (Group I) in which micro-fragmented adipose tissue injection with closure of the internal opening was the first sphincter-saving procedure, and the "recurrent group" (Group II) consisting of patients who had failed prior sphincter-saving procedures. The procedure was carried out 4-6 weeks after seton placement. Follow-up visits were scheduled at 7 days, and 1, 3, 6 and 12 months after surgery. Fistula healing was defined as the closure of the internal and external openings without any discharge. Out of 47 patients with complex transsphincteric anal fistula, 19 met the inclusion criteria and were selected to undergo the procedure. Twelve of these patients (Group I) had micro-fragmented adipose tissue injection as first-line treatment, and 7 (Group II) had failed previous sphincter-saving procedures. The mean operative time was 55 ± 6 min (range 50-70 min). The mean postoperative pain score measured with the visual analog pain scale was 2 ± 1.4 (range 0-4). No intraoperative difficulties related to the use of the kit were recorded. There were no cases of postoperative fever or abdominal sepsis related to the procedure and no post-treatment perianal bleeding or impaired anal continence. Only 3 cases of minor abdominal wall hematoma that did not require any treatment and 1 case of perianal abscess were observed. Patients were evaluated for a mean follow-up time of 9 ± 3.1 months (range 3-12 months). The overall healing rate was 73.7, 83.3% for Group I and 57.1% for Group II. The injection of autologous, micro-fragmented and minimally manipulated adipose tissue associated with closure of the internal opening is a safe, feasible and reproducible procedure and may enhance complex anal fistula healing.

Factors influencing the detection of beach plastic debris.

PubMed

Lavers, Jennifer L; Oppel, Steffen; Bond, Alexander L

2016-08-01

Marine plastic pollution is a global problem with considerable ecological and economic consequences. Quantifying the amount of plastic in the ocean has been facilitated by surveys of accumulated plastic on beaches, but existing monitoring programmes assume the proportion of plastic detected during beach surveys is constant across time and space. Here we use a multi-observer experiment to assess what proportion of small plastic fragments is missed routinely by observers, and what factors influence the detection probability of different types of plastic. Detection probability across the various types of plastic ranged from 60 to 100%, and varied considerably by observer, observer experience, and biological material present on the beach that could be confused with plastic. Blue fragments had the highest detection probability, while white fragments had the lowest. We recommend long-term monitoring programmes adopt survey designs accounting for imperfect detection or at least assess the proportion of fragments missed by observers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

NASA Astrophysics Data System (ADS)

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H.; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10 2+ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10 2+ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10 2+, suggesting that b10 2+ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10 2+; over 30 % of the observed SORI-CID fragment ions from substance P b10 2+ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10 2+, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10 2+.

Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions.

PubMed

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.

PubMed

Bai, Fang; Morcos, Faruck; Cheng, Ryan R; Jiang, Hualiang; Onuchic, José N

2016-12-13

Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

Emergence of Pathogenic Coronaviruses in Cats by Homologous Recombination between Feline and Canine Coronaviruses

PubMed Central

Terada, Yutaka; Matsui, Nobutaka; Noguchi, Keita; Kuwata, Ryusei; Shimoda, Hiroshi; Soma, Takehisa; Mochizuki, Masami; Maeda, Ken

2014-01-01

Type II feline coronavirus (FCoV) emerged via double recombination between type I FCoV and type II canine coronavirus (CCoV). In this study, two type I FCoVs, three type II FCoVs and ten type II CCoVs were genetically compared. The results showed that three Japanese type II FCoVs, M91-267, KUK-H/L and Tokyo/cat/130627, also emerged by homologous recombination between type I FCoV and type II CCoV and their parent viruses were genetically different from one another. In addition, the 3′-terminal recombination sites of M91-267, KUK-H/L and Tokyo/cat/130627 were different from one another within the genes encoding membrane and spike proteins, and the 5′-terminal recombination sites were also located at different regions of ORF1. These results indicate that at least three Japanese type II FCoVs emerged independently. Sera from a cat experimentally infected with type I FCoV was unable to neutralize type II CCoV infection, indicating that cats persistently infected with type I FCoV may be superinfected with type II CCoV. Our previous study reported that few Japanese cats have antibody against type II FCoV. All of these observations suggest that type II FCoV emerged inside the cat body and is unable to readily spread among cats, indicating that these recombination events for emergence of pathogenic coronaviruses occur frequently. PMID:25180686

First report of Sapajus cay naturally infected by Trypanosoma cruzi in San Pedro Department, Paraguay.

PubMed

Acosta, Nidia; Miret, Jorge; López, Elsa; Schinini, Alicia

2016-08-29

To verify the occurrence of natural Trypanosoma cruzi infection in non-human primates from a rural endemic area of the east region of Paraguay, xenodiagnosis was performed in 35 animals belonging to two species. For genotyping and T. cruzi discrete typing unit (DTU) assignment, a combination of four markers was used, including amplification products of the small (18S) and large (24Sα) subunits of ribosomal ribonucleic acid gene, the intergenic region of mini-exon gene and the heat shock protein 60 Eco-RV polymerase chain reaction-restriction fragment length polymorphism (HSP60/EcoRV-PCR-RFLP). One specimen of Sapajus cay was found positive and infected by the DTU TcII. This result constitutes the first record of natural T. cruzi infection in a sylvatic monkey in Paraguay, harbouring a DTU associated with severe Chagas disease in humans.

Biodegradation of trichloroethylene (TCE) by methanotrophic community.

PubMed

Shukla, Awadhesh K; Vishwakarma, Pranjali; Upadhyay, S N; Tripathi, Anil K; Prasana, H C; Dubey, Suresh K

2009-05-01

Laboratory incubation experiments were carried out to assess the potential of methanotrophic culture for degrading TCE. Measurements of the growth rate and TCE degradation showed that the methanotrophs not only grew in presence of TCE but also degraded TCE. The rate of TCE degradation was found to be 0.19 ppm h(-1). The reverse transcriptase-PCR test was conducted to quantify expression of pmoA and mmoX genes. RT-PCR revealed expression of pmoA gene only. This observation provides evidence that the pmoA gene was functionally active for pMMO enzyme during the study. The diversity of the methanotrophs involved in TCE degradation was assessed by PCR amplification, cloning, restriction fragment length polymorphism and phylogenetic analysis of pmoA genes. Results suggested the occurrence of nine different phylotypes belonging to Type II methanotrophs in the enriched cultures. Out of the nine, five clustered with, genera Methylocystis and rest got clustered in to a separate group.

The chloroplast and mitochondrial DNA type are correlated with the nuclear composition of somatic hybrid calli of Solanum tuberosum and Nicotiana plumbaginifolia.

PubMed

Wolters, A M; Koornneef, M; Gilissen, L J

1993-09-01

This paper describes the analysis of chloroplast (cp) DNA and mitochondrial (mt) DNA in 21 somatic hybrid calli of Solanum tuberosum and Nicotiana plumbaginifolia by means of Southern-blot hybridization. Each of these calli contained only one type of cpDNA; 14 had the N. plumbaginifolia (Np) type and seven the S. tuberosum (St) type. N. plumbaginifolia cpDNA was present in hybrids previously shown to contain predominantly N. plumbaginifolia chromosomes whereas hybrids in which S. tuberosum chromosomes predominated possessed cpDNA from potato. We have analyzed the mtDNA of these 21 somatic hybrid calli using four restriction enzyme/probe combinations. Most fusion products had only, or mostly, mtDNA fragments from the parent that predominated in the nucleus. The hybrids containing mtDNA fragments from only one parent (and new fragments) also possessed chloroplasts from the same species. The results suggest the existence of a strong nucleo-cytoplasmic incongruity which affects the genome composition of somatic hybrids between distantly related species.

[Dichlorido (2-(2-(1H-benzo[d]thiazol-2-yl)hydrazono)propan-1-ol) Cu(II)]: Crystal structure, Hirshfeld surface analysis and correlation of its ESI-MS behavior with [Dichlorido 3-(hydroxyimino)-2-butanone-2-(1H-benzo[d]thiazol-2-yl)hydrazone Cu(II)

NASA Astrophysics Data System (ADS)

Kamat, Vinayak; Kumara, Karthik; Naik, Krishna; Kotian, Avinash; Netalkar, Priya; Shivalingegowda, Naveen; Neratur, Krishnappagowda Lokanath; Revankar, Vidyanand

2017-12-01

In the present work, Cu(II) complexes of 2-(2-benzo[d]thiazol-2-yl)hydrazono)propan-1-ol (L1) and 3-(hydroxyimino)-2-butanone-2-(1H-benzo[d]thiazol-2-yl)hydrazone (L2) are synthesized and characterized by various spectro-analytical techniques. The structure of Cu(II) complex of L1 i.e., [CuL1Cl2], is unambiguously determined by single crystal X-ray diffraction method. While similar efforts were unsuccessful in the case of Cu(II) complex of L2 i.e., [CuL2Cl2]. Hence, to avail the structural facts, various cationic/anionic fragments or adducts formed during positive/negative mode electrospray ionization (ESI) of CuL1Cl2 and CuL2Cl2 have been identified with the help of their charge, monoisotopic masses and isotopic distributions. The similarity in the ESI behavior of two complexes has inferred their structural resemblance, which is further supported by DFT optimized structures, EPR spectral studies and analytical measurements. The EPR spectral behavior (g|| > g⊥ > 2.02) of the complexes are attributed to an axial symmetry with the dx2-y2 ground state having square pyramidal Cu(II) ion. CuL1Cl2 has crystallized in monoclinic crystal system in P21/c space group. The molecular complex has ring-metal (Cg-Me) interactions of the type Cg···>Cu, which contributes to the crystal packing. The Cl⋯H (30.6%) interactions have the major contribution among all intermolecular contacts and have played a vital role in the stabilization of the molecular structure, which is extended to 3D network through Csbnd H···Cg and Cg-Cg interactions.

On High and Low Starting Frequencies of Type II Radio Bursts

NASA Astrophysics Data System (ADS)

Sharma, J.; Mittal, N.

2017-06-01

We have studied the characteristics of type II radio burst during the period May 1996 to March 2015, for the solar cycle 23 and 24, observed by WIND/WAVES radio instrument. A total of 642 events were recorded by the instrument during the study period. We have divided the events with two starting frequency range (high > 1 MHz; low ≤ 1MHz) as type II1 (i.e., 1-16 MHz) radio burst and type II2 (i.e., 20 KHz - 1020 KHz) radio burst which constitute the DH and km type II radio burst observed by WIND spacecraft, and determined their time and frequency characteristics. The mean drift rate of type II1 and type II2 radio bursts is 29.76 × 10-4 MHz/s and 0.17 × 10-4 MHz/s respectively, which shows that type II1 with high start frequency hase larger drift rate than the type II2 with low starting frequencies. We have also reported that the start frequency and the drift rate of type II1 are in good correlation, with a linear correlation coefficient of 0.58.

Differential activation of human T cells to allogeneic endothelial cells, epithelial cells and fibroblasts in vitro

PubMed Central

2012-01-01

Background In the direct pathway, T cells recognize intact donor major histocompatability complexes and allogeneic peptide on the surface of donor antigen presenting cells (APCs). Indirect allorecognition results from the recognition of processed alloantigen by self MHC complexes on self APCs. In this study, we wished to evaluate the relative contribution of different intragraft cells to the alloactivation of nave and memory T cells though the direct and the indirect pathway of allorecognition. Methods The processing of membrane fragments from IFN-treated single donor endothelial cells (EC), fibroblasts or renal epithelial cells (RPTEC) was evaluated by DiOC labeling of each cell type and flow cytometry following interaction with PBMC. Direct pathway activation of nave CD45RA+ or memory CD45RO+ CD4+ T cells was evaluated following coculture with IFN-treated and MHC class II-expressing EC, fibroblasts or RPTEC. Indirect pathway activation was assessed using CD45RA+ or CD45RO+ CD4+ T cells cocultured with autologous irradiated APCs in the absence or presence of sonicates derived from IFN-treated allogeneic EC, fibroblasts or RPTEC. Activation of T cells was assessed by [3H]thymidine incorporation and by ELISpot assays. Results We find that CD14+ APCs readily acquire membrane fragments from fibroblasts and RPTEC, but fail to acquire membrane fragments from intact EC. However, APCs process membranes from EC undergoing apoptosis.There was a notable direct pathway alloproliferative response of CD45RO+ CD4+ T cells to IFN-treated EC, but not to fibroblasts or RPTEC. Also, there was a minimal direct pathway response of CD45RA+ CD4+ T cells to all cell types. In contrast, we found that both CD45RA+ and CD45RO+ CD4+ T cells proliferated following coculture with autologous APCs in the presence of sonicates derived from IFN-treated EC, fibroblasts or RPTEC. By ELISpot, we found that these T cells stimulated via the indirect pathway also produced the cytokines IFN, IL-2, IL-4 and IL-5. Conclusions Recipient APCs may readily process membrane fragments from allogeneic intragraft cells, but not from EC unless they are undergoing apoptosis. This processing is sufficient for indirect pathway alloactivation of both CD45RA+ and CD45RO+ CD4+ T cells. Only graft vascular EC mediate direct pathway reactivation of CD4+ T cells. PMID:23369287

The cancellation of magnetic flux. II - In a decaying active region. [of sun

NASA Technical Reports Server (NTRS)

Martin, S. F.; Livi, S. H. B.; Wang, J.

1985-01-01

H-alpha filtergrams and videomagnetograms are used to study an active region during its period of decay on August 3-8, 1984; the decay had been initiated by a fragmentation process in which very small knots of magnetic flux separated from larger concentration of flux. The disappearance of magnetic flux was always observed when the small fragments of flux encountered other small fragments or concentrations of flux of opposite polarity. Such 'cancellations' are shared by both polarities of magnetic field, and it is deduced that the disappearance of flux occurred either at or within 5 arcsec of the apparent dividing line between the opposite polarities. All of the 22 flares observed during the decay of this region were initiated around sites where magnetic flux was cancelling or was deduced to be cancelling during the flares. It is hypothesized that cancellation was one of the necessary conditions for flaring in this active region.

Properties of promoters cloned randomly from the Saccharomyces cerevisiae genome.

PubMed Central

Santangelo, G M; Tornow, J; McLaughlin, C S; Moldave, K

1988-01-01

Promoters were isolated at random from the genome of Saccharomyces cerevisiae by using a plasmid that contains a divergently arrayed pair of promoterless reporter genes. A comprehensive library was constructed by inserting random (DNase I-generated) fragments into the intergenic region upstream from the reporter genes. Simple in vivo assays for either reporter gene product (alcohol dehydrogenase or beta-galactosidase) allowed the rapid identification of promoters from among these random fragments. Poly(dA-dT) homopolymer tracts were present in three of five randomly cloned promoters. With two exceptions, each RNA start site detected was 40 to 100 base pairs downstream from a TATA element. All of the randomly cloned promoters were capable of activating reporter gene transcription bidirectionally. Interestingly, one of the promoter fragments originated in a region of the S. cerevisiae rDNA spacer; regulated divergent transcription (presumably by RNA polymerase II) initiated in the same region. Images PMID:2847031

Negative Ion CID Fragmentation of O-linked Oligosaccharide Aldoses—Charge Induced and Charge Remote Fragmentation

NASA Astrophysics Data System (ADS)

Doohan, Roisin A.; Hayes, Catherine A.; Harhen, Brendan; Karlsson, Niclas Göran

2011-06-01

Collision induced dissociation (CID) fragmentation was compared between reducing and reduced sulfated, sialylated, and neutral O-linked oligosaccharides. It was found that fragmentation of the [M - H]- ions of aldoses with acidic residues gave unique Z-fragmentation of the reducing end GalNAc containing the acidic C-6 branch, where the entire C-3 branch was lost. This fragmentation pathway, which is not seen in the alditols, showed that the process involved charge remote fragmentation catalyzed by a reducing end acidic anomeric proton. With structures containing sialic acid on both the C-3 and C-6 branch, the [M - H]- ions were dominated by the loss of sialic acid. This fragmentation pathway was also pronounced in the [M - 2H]2- ions revealing both the C-6 Z-fragment plus its complementary C-3 C-fragment in addition to glycosidic and cross ring fragmentation. This generation of the Z/C-fragment pairs from GalNAc showed that the charges were not participating in their generation. Fragmentation of neutral aldoses showed pronounced Z-fragmentation believed to be generated by proton migration from the C-6 branch to the negatively charged GalNAc residue followed by charge remote fragmentation similar to the acidic oligosaccharides. In addition, A-type fragments generated by charge induced fragmentation of neutral oligosaccharides were observed when the charge migrated from C-1 of the GalNAc to the GlcNAc residue followed by rearrangement to accommodate the 0,2A-fragmentation. LC-MS also showed that O-linked aldoses existed as interchangeable α/β pyranose anomers, in addition to a third isomer (25% of the total free aldose) believed to be the furanose form.

Synthetic Progress toward Azadirachtins. 1. Enantio- and Diastereoselective Synthesis of the Left-Wing Fragment of 11-epi-Azadirachtin I.

PubMed

Shi, Hang; Tan, Ceheng; Zhang, Weibin; Zhang, Zichun; Long, Rong; Luo, Tuoping; Yang, Zhen

2015-05-15

A highly enantio- and diastereoselective synthesis of the left-wing fragment of 11-epi-azadirachtin I characterized with the pairwise use of palladium- and gold-catalyzed cascade reactions is presented. By enlisting a sequence of stereocontrolled transformations, our 21-step route established the stereocenters of the left-wing fragment from one chiral starting material, (-)-carvone, which would significantly facilitate the synthetic studies of the azadirachtin-type limonoids.

The impact of homologous recombination repair deficiency on depleted uranium clastogenicity in Chinese hamster ovary cells: XRCC3 protects cells from chromosome aberrations, but increases chromosome fragmentation.

PubMed

Holmes, Amie L; Joyce, Kellie; Xie, Hong; Falank, Carolyne; Hinz, John M; Wise, John Pierce

2014-04-01

Depleted uranium (DU) is extensively used in both industry and military applications. The potential for civilian and military personnel exposure to DU is rising, but there are limited data on the potential health hazards of DU exposure. Previous laboratory research indicates DU is a potential carcinogen, but epidemiological studies remain inconclusive. DU is genotoxic, inducing DNA double strand breaks, chromosome damage and mutations, but the mechanisms of genotoxicity or repair pathways involved in protecting cells against DU-induced damage remain unknown. The purpose of this study was to investigate the effects of homologous recombination repair deficiency on DU-induced genotoxicity using RAD51D and XRCC3-deficient Chinese hamster ovary (CHO) cell lines. Cells deficient in XRCC3 (irs1SF) exhibited similar cytotoxicity after DU exposure compared to wild-type (AA8) and XRCC3-complemented (1SFwt8) cells, but DU induced more break-type and fusion-type lesions in XRCC3-deficient cells compared to wild-type and XRCC3-complemented cells. Surprisingly, loss of RAD51D did not affect DU-induced cytotoxicity or genotoxicity. DU induced selective X-chromosome fragmentation irrespective of RAD51D status, but loss of XRCC3 nearly eliminated fragmentation observed after DU exposure in wild-type and XRCC3-complemented cells. Thus, XRCC3, but not RAD51D, protects cells from DU-induced breaks and fusions and also plays a role in DU-induced chromosome fragmentation. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular analysis of RAPD DNA based markers: their potential use for the detection of genetic variability in jojoba (Simmondsia chinensis L Schneider).

PubMed

Amarger, V; Mercier, L

1995-01-01

We have applied the recently developed technique of random amplified polymorphic DNA (RAPD) for the discrimination between two jojoba clones at the genomic level. Among a set of 30 primers tested, a simple reproducible pattern with three distinct fragments for clone D and two distinct fragments for clone E was obtained with primer OPB08. Since RAPD products are the results of arbitrarily priming events and because a given primer can amplify a number of non-homologous sequences, we wondered whether or not RAPD bands, even those of similar size, were derived from different loci in the two clones. To answer this question, two complementary approaches were used: i) cloning and sequencing of the amplification products from clone E; and ii) complementary Southern analysis of RAPD gels using cloned or amplified fragments (directly recovered from agarose gels) as RFLP probes. The data reported here show that the RAPD reaction generates multiple amplified fragments. Some fragments, although resolved as a single band on agarose gels, contain different DNA species of the same size. Furthermore, it appears that the cloned RAPD products of known sequence that do not target repetitive DNA can be used as hybridization probes in RFLP to detect a polymorphism among individuals.

Iron overload promotes mitochondrial fragmentation in mesenchymal stromal cells from myelodysplastic syndrome patients through activation of the AMPK/MFF/Drp1 pathway.

PubMed

Zheng, Qingqing; Zhao, Youshan; Guo, Juan; Zhao, Sida; Fei, Chengming; Xiao, Chao; Wu, Dong; Wu, Lingyun; Li, Xiao; Chang, Chunkang

2018-05-03

Iron overload (IO) has been reported to contribute to mesenchymal stromal cell (MSC) damage, but the precise mechanism has yet to be clearly elucidated. In this study, we found that IO increased cell apoptosis and lowered cell viability in MSCs, accompanied by extensive mitochondrial fragmentation and autophagy enhancement. All these effects were reactive oxygen species (ROS) dependent. In MSCs with IO, the ATP concentrations were significantly reduced due to high ROS levels and low electron respiratory chain complex (ETC) II/III activity. Reduced ATP phosphorylated AMP-activated protein kinase (AMPK). Activation of AMPK kinase complexes triggered mitochondrial fission. Moreover, gene knockout of AMPK via CRISPR/Cas9 reduced cell apoptosis, enhanced cell viability and attenuated mitochondrial fragmentation and autophagy caused by IO in MSCs. Further, AMPK-induced mitochondrial fragmentation of MSCs with IO was mediated via phosphorylation of mitochondrial fission factor (MFF), a mitochondrial outer-membrane receptor for the GTPase dynamin-related protein 1 (Drp1). Gene knockdown of MFF reversed AMPK-induced mitochondrial fragmentation in MSCs with IO. In addition, MSCs from IO patients with myelodysplastic syndrome (MDS) showed increased cell apoptosis, decreased cell viability, higher ROS levels, lower ATP concentrations and increased mitochondrial fragmentation compared with MSCs from non-IO patients. In addition, iron chelation or antioxidant weakened the activity of the AMPK/MFF/Drp1 pathway in MDS-MSCs with IO from several patients, accompanied by attenuation of mitochondrial fragmentation and autophagy. Taken together, the AMPK/MFF/Drp1 pathway has an important role in the damage to MDS-MSCs caused by IO.

Number of fragments, margin status and thermal artifacts of conized specimens from LLETZ surgery to treat cervical intraepithelial neoplasia.

PubMed

Bittencourt, Dulcimary Dias; Zanine, Rita Maira; Sebastião, Ana Martins; Taha, Nabiha Saadi; Speck, Neila Góis; Ribalta, Julisa Chamorro Lascasas

2012-01-01

Large loop excision of the transformation zone (LLETZ) is a nontraumatic cut and coagulation method with several advantages, but it induces thermal artifacts in the cut region. The aim here was to assess the correlations of age, number of fragments, lesion grade and degree of thermal artifacts with margin quality in conized specimens from LLETZ for cervical intraepithelial neoplasia (CIN). Cross-sectional study at Universidade Federal de São Paulo (Unifesp). The records and histopathology findings of 118 women who underwent LLETZ between 1999 and 2007 were reviewed. Age, number of fragments, lesion grade, degree of thermal artifacts and margin quality were assessed. The patients' mean age was 27.14 years; 63.6% had been diagnosed with CIN II and 36.4% with CIN III. The lesion was removed as a single fragment in 79.6% of the cases. The margins were free from intraepithelial neoplasia in 85.6% and compromised in the endocervical margin in 6.8%. Fragment damage due to artifacts occurred in 2.5%. Severe artifacts occurred in 22.8%. Women aged 30 years or over presented more cases of CIN III (P < 0.0004). Neoplastic compromising of surgical margins and severe artifacts occurred more often in cases in which two or more fragments were removed, and in patients aged 30 years or over. CIN III in women aged 30 or over, when removed in two or more fragments during LLETZ, presented a greater number of compromised margins and greater severity of thermal artifacts.

Proportion of collagen type II in the extracellular matrix promotes the differentiation of human adipose-derived mesenchymal stem cells into nucleus pulposus cells.

PubMed

Tao, Yiqing; Zhou, Xiaopeng; Liu, Dongyu; Li, Hao; Liang, Chengzhen; Li, Fangcai; Chen, Qixin

2016-01-01

During degeneration process, the catabolism of collagen type II and anabolism of collagen type I in nucleus pulposus (NP) may influence the bioactivity of transplanted cells. Human adipose-derived mesenchymal stem cells (hADMSCs) were cultured as a micromass or in a series of gradual proportion hydrogels of a mix of collagen types I and II. Cell proliferation and cytotoxicity were detected using CCK-8 and LDH assays respectively. The expression of differentiation-related genes and proteins, including SOX9, aggrecan, collagen type I, and collagen type II, was examined using RT-qPCR and Western blotting. Novel phenotypic genes were also detected by RT-qPCR and western blotting. Alcian blue and dimethylmethylene blue assays were used to investigate sulfate proteoglycan expression, and PI3K/AKT, MAPK/ERK, and Smad signaling pathways were examined by Western blotting. The results showed collagen hydrogels have good biocompatibility, and cell proliferation increased after collagen type II treatment. Expressions of SOX9, aggrecan, and collagen type II were increased in a collagen type II dependent manner. Sulfate proteoglycan synthesis increased in proportion to collagen type II concentration. Only hADMSCs highly expressed NP cell marker KRT19 in collagen type II culture. Additionally, phosphorylated Smad3, which is associated with phosphorylated ERK, was increased after collagen type II-stimulation. The concentration and type of collagen affect hADMSC differentiation into NP cells. Collagen type II significantly ameliorates hADMSC differentiation into NP cells and promotes extracellular matrix synthesis. Therefore, anabolism of collagen type I and catabolism of type II may attenuate the differentiation and biosynthesis of transplanted stem cells. © 2016 International Union of Biochemistry and Molecular Biology.

Young Stellar Objects in the Massive Star-forming Regions W51 and W43

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saral, G.; Audard, M.; Hora, J. L.

We present the results of our investigation of the star-forming complexes W51 and W43, two of the brightest in the first Galactic quadrant. In order to determine the young stellar object (YSO) populations in W51 and W43 we used color–magnitude relations based on Spitzer mid-infrared and 2MASS/UKIDSS near-infrared data. We identified 302 Class I YSOs and 1178 Class II/transition disk candidates in W51, and 917 Class I YSOs and 5187 Class II/transition disk candidates in W43. We also identified tens of groups of YSOs in both regions using the Minimal Spanning Tree (MST) method. We found similar cluster densities inmore » both regions, even though Spitzer was not able to probe the densest part of W43. By using the Class II/I ratios, we traced the relative ages within the regions and, based on the morphology of the clusters, we argue that several sites of star formation are independent of one another in terms of their ages and physical conditions. We used spectral energy distribution-fitting to identify the massive YSO (MYSO) candidates since they play a vital role in the star formation process, and then examined them to see if they are related to any massive star formation tracers such as UCH ii regions, masers, or dense fragments. We identified 17 MYSO candidates in W51, and 14 in W43, respectively, and found that groups of YSOs hosting MYSO candidates are positionally associated with H ii regions in W51, though we do not see any MYSO candidates associated with previously identified massive dense fragments in W43.« less

Azide derivatized anticancer agents of Vitamin K 3: X-ray structural, DSC, resonance spectral and API studies

NASA Astrophysics Data System (ADS)

Badave, Kirti; Patil, Yogesh; Gonnade, Rajesh; Srinivas, Darbha; Dasgupta, Rajan; Khan, Ayesha; Rane, Sandhya

2011-12-01

Compound 1 [1-imino (acetyl hydrazino)-Vitamin K 3], displays valence tautomerically related electronic isomers as Form I and Form II. Form I exhibits 2D packing fragment with 1D ribbon chains of N-H⋯O hydrogen bonds and shows EPR silent features. While Form II is EPR active and exhibits biradical nature with double quantum transitions at g = 2.0040. 1H NMR of compound 2, [1-imino (hydrazino carboxylate)-Vitamin K 3] and Form II exhibit π delocalization via resonance assisted H-bonding [RAHB] effect compared to Form I. Molecular interactions in Form I and II are visualized by DSC. The electronic structures of compounds 1 and 2 have been correlated to their API values by measuring anticancer activities, mitochondrial potentials and DNA shearing patterns. Form II and compound 2 indicate mitochondria mediated apoptosis (˜75% cell death) while Form I causes 35% cell death.

[Anatomy of fractures of the inferior scapular angle].

PubMed

Bartoníček, J; Tuček, M; Malík, J

2018-01-01

The aim of this study is to describe the anatomy of fractures of the inferior angle and the adjacent part of the scapular body, based on 3D CT reconstructions. In a series of 375 scapular fractures, we identified a total of 20 fractures of the inferior angle of the scapular body (13 men, 7 women), with a mean patient age of 50 years (range 3373). In all fractures, 3D CT reconstructions were obtained, allowing an objective evaluation of the fracture pattern with a focus on the size and shape of the inferior angle fragment, propagation of the fracture line to the lateral and medial borders of the infraspinous part of the scapular body, fragment displacement and any additional fracture of the ipsilateral scapula and the shoulder girdle. We identified a total of 5 types of fracture involving the distal half of the infraspinous part of the scapular body. The first type, recorded in 5 cases, affected only the apex of the inferior angle, with a small part of the adjacent medial border. The second type, occurring in 4 cases, involved fractures separating the entire inferior angle. The third type, represented by 4 cases, was characterized by a fracture line starting medially close above the inferior angle and passing proximolaterally. The separated fragment had a shape of a big drop, carrying also the distal half of the lateral pillar in addition to the inferior angle. In the fourth type identified in 5 fractures, the separated fragment was formed both by the inferior angle and a variable part of the medial border. The fifth type, being by its nature a transition to the fracture of the infraspinous part of the body, was recorded in 2 cases, with the same V-shaped fragment. Fractures of the inferior angle and the adjacent part of the scapular body are groups of fractures differing from other infraspinous fractures of the scapular body. Although these fractures are highly variable in terms of shape, they have the same course of fracture line and the manner of displacement.Key words: scapula scapula fractures scapular body fractures inferior angle classification of scapular body fractures.

Fragment screening by SPR and advanced application to GPCRs.

PubMed

Shepherd, Claire A; Hopkins, Andrew L; Navratilova, Iva

2014-01-01

Surface plasmon resonance (SPR) is one of the primary biophysical methods for the screening of low molecular weight 'fragment' libraries, due to its low protein consumption and 'label-free' methodology. SPR biosensor interaction analysis is employed to both screen and confirm the binding of compounds in fragment screening experiments, as it provides accurate information on the affinity and kinetics of molecular interactions. The most advanced application of the use of SPR for fragment screening is against membrane protein drug targets, such G-protein coupled receptors (GPCRs). Biophysical GPCR assays using SPR have been validated with pharmacological measurements approximate to cell-based methods, yet provide the advantage of biophysical methods in their ability to measure the weak affinities of low molecular weight fragments. A number of SPR fragment screens against GPCRs have now been disclosed in the literature. SPR fragment screening is proving versatile to screen both thermostabilised GPCRs and solubilised wild type receptors. In this chapter, we discuss the state-of-the-art in GPCR fragment screening by SPR and the technical considerations in performing such experiments. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Modic changes in lumbar spine: prevalence and distribution patterns of end plate oedema and end plate sclerosis.

PubMed

Xu, Lei; Chu, Bin; Feng, Yang; Xu, Feng; Zou, Yue-Fen

2016-01-01

The purpose of this study is to evaluate the distribution of end plate oedema in different types of Modic change especially in mixed type and to analyze the presence of end plate sclerosis in various types of Modic change. 276 patients with low back pain were scanned with 1.5-T MRI. Three radiologists assessed the MR images by T1 weighted, T2 weighted and fat-saturation T2 weighted sequences and classified them according to the Modic changes. Pure oedematous end plate signal changes were classified as Modic Type I; pure fatty end plate changes were classified as Modic Type II; and pure sclerotic end plate changes as Modic Type III. A mixed feature of both Types I and II with predominant oedematous signal change is classified as Modic I-II, and a mixture of Types I and II with predominant fatty change is classified as Modic II-I. Thus, the mixed types can further be subdivided into seven subtypes: Types I-II, Types II-I, Types I-III, Types III-I, Types II-III, Types III-II and Types I-III. During the same period, 52 of 276 patients who underwent CT and MRI were retrospectively reviewed to determine end plate sclerosis. (1) End plate oedema: of the 2760 end plates (276 patients) examined, 302 end plates showed Modic changes, of which 82 end plates showed mixed Modic changes. The mixed Modic changes contain 92.7% of oedematous changes. The mixed types especially Types I-II and Types II-I made up the majority of end plate oedematous changes. (2) End plate sclerosis: 52 of 276 patients were examined by both MRI and CT. Of the 520 end plates, 93 end plates showed Modic changes, of which 34 end plates have shown sclerotic changes in CT images. 11.8% of 34 end plates have shown Modic Type I, 20.6% of 34 end plates have shown Modic Type II, 2.9% of 34 end plates have shown Modic Type III and 64.7% of 34 end plates have shown mixed Modic type. End plate oedema makes up the majority of mixed types especially Types I-II and Types II-I. The end plate sclerosis on CT images may not just mean Modic Type III but does exist in all types of Modic changes, especially in mixed Modic types, and may reflect vertebral body mineralization rather than change in the bone marrow. End plate oedema and end plate sclerosis are present in a large proportion of mixed types.

Effect of transverse vibrations of fissile nuclei on the angular and spin distributions of low-energy fission fragments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bunakov, V. E.; Kadmensky, S. G., E-mail: kadmensky@phys.vsu.ru; Lyubashevsky, D. E.

2016-05-15

It is shown that A. Bohr’s classic theory of angular distributions of fragments originating from low-energy fission should be supplemented with quantum corrections based on the involvement of a superposition of a very large number of angular momenta L{sub m} in the description of the relative motion of fragments flying apart along the straight line coincidentwith the symmetry axis. It is revealed that quantum zero-point wriggling-type vibrations of the fissile system in the vicinity of its scission point are a source of these angular momenta and of high fragment spins observed experimentally.

The PCC assay can be used to predict radiosensitivity in biopsy cultures irradiated with different types of radiation.

PubMed

Suzuki, Masao; Tsuruoka, Chizuru; Nakano, Takashi; Ohno, Tatsuya; Furusawa, Yoshiya; Okayasu, Ryuichi

2006-12-01

The aim of this study was to identify potential biomarkers for radiosensitivity using the relationship between cell killing and the yield of excess chromatin fragments detected with the premature chromosome condensation (PCC) technique. This method was applied to primary cultured cells obtained from biopsies from patients. Six primary culture biopsies were obtained from 6 patients with carcinoma of the cervix before starting radiotherapy. The cultures were irradiated with two different LET carbon-ion beams (LET = 13 keV/microm, 77.1+/-2.8 keV/microm) and 200 kV X-rays. The carbon-ion beams were produced by Heavy Ion Medical Accelerator in Chiba (HIMAC). PCC was performed using the polyethylene glycol-mediated cell fusion technique. The yield of excess chromatin fragments were measured by counting the number of unrejoined chromatin fragments detected with the PCC technique after a 24-h post-irradiation incubation period. Obtained results indicated that cultures which were more sensitive to killing were also more susceptible to the induction of excess chromatin fragments. Furthermore there was a good correlation between cell killing and excess chromatin fragments among the 6 cell cultures examined. There is also evidence that the induction of excess chromatin fragments increased with increasing LET as well as cell-killing effect in the same cell culture. The data reported here support the idea that the yield of excess chromatin fragments detected with the PCC technique might be useful for predicting the radiosensitivity of cells contained in tumor tissue, and to predict responses to different radiation types.

Adenovirus type 2 DNA replication. I. Evidence for discontinuous DNA synthesis.

PubMed Central

Winnacker, E L

1975-01-01

Isolated nuclei from adenovirus type 2-infected HeLa cells catalyze the incorporation of all four deoxyribonucleoside triphosphates into viral DNA. The observed DNA synthesis occurs via a transient formation of DNA fragments with a sedimentation coefficient of 10S. The fragments are precursors to unit-length viral DNA, they are self-complementary to an extent of at least 70%, and they are distributed along most of the viral chromosome. In addition, accumulation of 10S DNA fragments is observed either in intact, virus-infected HeLa cells under conditions where viral DNA synthesis is inhibited by hydroxyurea or in isolated nuclei from virus-infected HeLa cells at low concentrations of deoxyribonucleotides. Under these suboptimal conditions for DNA synthesis in isolated nuclei, ribonucleoside triphosphates determine the size distribution of DNA intermediates. The evidence presented suggests that a ribonucleoside-dependent initiation step as well at two DNA polymerase catalyzed reactions are involved in the discontinuous replication of adenovirus type 2 DNA. PMID:1117487

Fragmentation increases wind disturbance impacts on forest structure and carbon stocks in a western Amazonian landscape.

PubMed

Schwartz, Naomi B; Uriarte, María; DeFries, Ruth; Bedka, Kristopher M; Fernandes, Katia; Gutiérrez-Vélez, Victor; Pinedo-Vasquez, Miguel A

2017-09-01

Tropical second-growth forests could help mitigate climate change, but the degree to which their carbon potential is achieved will depend on exposure to disturbance. Wind disturbance is common in tropical forests, shaping structure, composition, and function, and influencing successional trajectories. However, little is known about the impacts of extreme winds on second-growth forests in fragmented landscapes, though these ecosystems are often located in mosaics of forest, pasture, cropland, and other land cover types. Indirect evidence suggests that fragmentation increases risk of wind damage in tropical forests, but no studies have found such impacts following severe storms. In this study, we ask whether fragmentation and forest type (old vs. second growth) were associated with variation in wind damage after a severe convective storm in a fragmented production landscape in western Amazonia. We applied linear spectral unmixing to Landsat 8 imagery from before and after the storm, and combined it with field observations of damage to map wind effects on forest structure and biomass. We also used Landsat 8 imagery to map land cover with the goals of identifying old- and second-growth forest and characterizing fragmentation. We used these data to assess variation in wind disturbance across 95,596 ha of forest, distributed over 6,110 patches. We find that fragmentation is significantly associated with wind damage, with damage severity higher at forest edges and in edgier, more isolated patches. Damage was also more severe in old-growth than in second-growth forests, but this effect was weaker than that of fragmentation. These results illustrate the importance of considering landscape context in planning tropical forest restoration and natural regeneration projects. Assessments of long-term carbon sequestration potential need to consider spatial variation in disturbance exposure. Where risk of extreme winds is high, minimizing fragmentation and isolation could increase carbon sequestration potential. © 2017 by the Ecological Society of America.

Large Gliadin Peptides Detected in the Pancreas of NOD and Healthy Mice following Oral Administration

PubMed Central

Sidenius, Ulrik; Heegaard, Niels H.

2016-01-01

Gluten promotes type 1 diabetes in nonobese diabetic (NOD) mice and likely also in humans. In NOD mice and in non-diabetes-prone mice, it induces inflammation in the pancreatic lymph nodes, suggesting that gluten can initiate inflammation locally. Further, gliadin fragments stimulate insulin secretion from beta cells directly. We hypothesized that gluten fragments may cross the intestinal barrier to be distributed to organs other than the gut. If present in pancreas, gliadin could interact directly with the immune system and the beta cells to initiate diabetes development. We orally and intravenously administered 33-mer and 19-mer gliadin peptide to NOD, BALB/c, and C57BL/6 mice and found that the peptides readily crossed the intestinal barrier in all strains. Several degradation products were found in the pancreas by mass spectroscopy. Notably, the exocrine pancreas incorporated large amounts of radioactive label shortly after administration of the peptides. The study demonstrates that, even in normal animals, large gliadin fragments can reach the pancreas. If applicable to humans, the increased gut permeability in prediabetes and type 1 diabetes patients could expose beta cells directly to gliadin fragments. Here they could initiate inflammation and induce beta cell stress and thus contribute to the development of type 1 diabetes. PMID:27795959