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Sample records for molecular biological aspects

  1. Molecular and biological aspects of the bovine immunodeficiency virus.

    PubMed

    Corredor, Andrea G; St-Louis, Marie-Claude; Archambault, Denis

    2010-01-01

    The bovine immunodeficiency virus (BIV) was isolated in 1969 from a cow, R-29, with a wasting syndrome suggesting bovine leucosis. The virus, first designated bovine visna-like virus, remained unstudied until HIV was discovered in 1983. Then, it was demonstrated in 1987 that the bovine R-29 isolate was a lentivirus with striking similarity to the human immunodeficiency virus (HIV). Moreover, BIV has the most complex genomic structure among all identified lentiviruses shown by several regulatory/accessory genes encoding proteins, some of which are involved in the regulation of virus gene expression. This manuscript aims to review biological and molecular aspects of BIV, with emphasis on regulatory/accessory viral genes/proteins which are involved in virus expression. PMID:20210777

  2. Molecular biological aspects on canine and human mammary tumors.

    PubMed

    Rivera, P; von Euler, H

    2011-01-01

    The high incidence of mammary tumor disease reported in certain canine breeds suggests a significant genetic component, as has already been described in human familial breast cancer-in BRCA1- and BRCA2-associated breast cancer in particular. The identification of genetic risk factors is critical to improvements in the prevention, diagnosis, and treatment of these tumors. In recent years, there has been significant progress in developing the tools and reagents necessary to analyze the canine genome. This work has culminated in a high-quality draft genome sequence, as well as a single-nucleotide polymorphism map and single-nucleotide polymorphism arrays for genomewide association analysis. These tools provide an unprecedented opportunity to characterize the genetic influences in canine diseases such as cancer, eventually allowing for exploration of more effective therapies. Given the high homology between the canine genome sequence and its human counterpart--as well as the many similarities regarding the morphology, biological behavior, and clinical course of mammary tumors in both species--the dog has proven to be an excellent comparative model. This review highlights the comparative aspects regarding certain areas within molecular biology, and it discusses future perspectives. The findings in larger genomewide association analyses and cDNA expression arrays are described, and the BRCA1/BRCA2 complex is compared in detail between the 2 species. PMID:21147766

  3. Biochemical and molecular biological aspects of silverfish allergens.

    PubMed

    Barletta, Bianca; Di Felice, Gabriella; Pini, Carlo

    2007-01-01

    Insects and insect-derived materials have been implicated as a risk factor for sensitization and subsequent elicitation of allergic rhinitis and allergic bronchial asthma. During the last decades, insects other than those known as allergenic, were investigated for their potential role in inducing and triggering an IgE immune response. Among these, the silverfish, an insect belonging to the Thysanura order, appeared to be of particular interest. Silverfish (Lepisma saccharina) is the most primitive living insect, and represents a descendent of the ancestral wingless insects. They are 3-12 mm long, have three tail feelers and are covered with shiny scales. They shun light and need a humid environment and their diet consists of carbohydrate materials such as paper and book-binding glue, crumbs of bread and flour. Because of these features, silverfish finds an optimal habitat both in dwellings and workplaces and in spite of its antiquity, silverfish has succeeded in exploiting the new opportunity created by man. Although its importance significantly increased when it has been demonstrated that house dust contains significant silverfish levels even in houses where the inhabitants were unaware of its presence, no silverfish extract for diagnosis of allergic diseases is commercially available yet. Identification of optimal extraction conditions and characterization of allergenic extracts are the first steps to obtain an effective allergen preparation suitable for diagnosis and therapy, and will be useful as a reference preparation for assessing silverfish exposure in different indoor environments. It has been cloned and characterized a silverfish tropomyosin, named Lep s 1, which represents the first allergen identified in silverfish extract and can be regarded as a molecule cross-reactive among inhalant and edible invertebrates allergenic sources. rLep s 1 displayed biological activity, suggesting that it could be regarded as a useful tool to study the role of silverfish

  4. Glycoprotein Biochemistry (Biosynthesis)--A Vehicle for Teaching Many Aspects of Biochemistry and Molecular Biology.

    ERIC Educational Resources Information Center

    Cole, Clair R.; Smith, Christopher A.

    1990-01-01

    Information about the biosynthesis of the carbohydrate portions or glycans of glycoproteins is presented. The teaching of glycosylation can be used to develop and emphasize many general aspects of biosynthesis, in addition to explaining specific biochemical and molecular biological features associated with producing the oligosaccharide portions of…

  5. A review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination.

    PubMed

    Olsen, C W

    1993-07-01

    Feline infectious peritonitis (FIP) has been an elusive and frustrating problem for veterinary practitioners and cat breeders for many years. Over the last several years, reports have begun to elucidate aspects of the molecular biology of the causal virus (FIPV). These papers complement a rapidly growing base of knowledge concerning the molecular organization and replication of coronaviruses in general. The fascinating immunopathogenesis of FIPV infection and the virus' interaction with macrophages has also been the subject of several recent papers. It is now clear that FIPV may be of interest to scientists other than veterinary virologists since its pathogenesis may provide a useful model system for other viruses whose infectivity is enhanced in the presence of virus-specific antibody. With these advances and the recent release of the first commercially-available FIPV vaccine, it is appropriate to review what is known about the organization and replication of coronaviruses and the pathogenesis of FIPV infection.

  6. Particular aspects in the cytogenetics and molecular biology of salivary gland tumours - current review of reports.

    PubMed

    Ochal-Choińska, Aleksandra J; Osuch-Wójcikiewicz, Ewa

    2016-01-01

    Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours. The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours. PMID:27688723

  7. Humic substances biological activity at the plant-soil interface: from environmental aspects to molecular factors.

    PubMed

    Trevisan, Sara; Francioso, Ornella; Quaggiotti, Silvia; Nardi, Serenella

    2010-06-01

    Humic substances (HS) represent the organic material mainly widespread in nature. HS have positive effects on plant physiology by improving soil structure and fertility and by influencing nutrient uptake and root architecture. The biochemical and molecular mechanisms underlying these events are only partially known. HS have been shown to contain auxin and an "auxin-like" activity of humic substances has been proposed, but support to this hypothesis is fragmentary. In this review article, we are giving an overview of available data concerning molecular structures and biological activities of humic substances, with special emphasis on their hormone-like activities. PMID:20495384

  8. Biological and molecular aspects of lymph node metastasis in gastro-intestinal cancer.

    PubMed

    Mimori, Koshi; Shinden, Yoshiharu; Eguchi, Hidetoshi; Sudo, Tomoya; Sugimachi, Keishi

    2013-10-01

    Recently, the existence of lymph node micrometastasis, including isolated tumor cells, has been the focus of the development of molecular diagnostic tools for lymph node metastasis in various malignant neoplasms, including those of the GI tract. In this review, we summarize recent molecular biological studies that might provide two reasons to explain the survival of single isolated cancer cells in lymph nodes. One is the specific characteristics of cancer cells, which can exist under severe circumstances, along with recent technological innovations to obtain expression profiles and sequencing from a single cell. The other is microenvironmental factors that support the formation of micrometastasis even in small numbers of cancer cells. The expression profile of whole transcriptome sequencing, genomic sequencing and epigenetic sequencing of a single cancer cell with tumorigenic properties in lymph node metastases should be disclosed in the near future.

  9. Milk proteins-derived bioactive peptides in dairy products: molecular, biological and methodological aspects.

    PubMed

    Dziuba, Bartłomiej; Dziuba, Marta

    2014-01-01

    Proteins are one of the primary components of the food, both in terms of nutrition and function. They are main source of amino acids, essential for synthesis of proteins, and also source of energy. Additionally, many proteins exhibit specific biological activities, which may have effect on functional or pro-health properties of food products. These proteins and their hydrolysis products, peptides, may influence the properties of food and human organism. The number of commercially available food products containing bioactive peptides is very low, apart from that milk proteins are their rich source. It could be supposed that number of available products with declared activity will rise in near future because of observed strong uptrend on interest in such products. Molecular and biological properties of milk proteins, as precursors of bioactive peptides was characterised in the work. Therefore, the strategy of research and obtaining of such peptides both in laboratory and industrial scale, as well as the range of their commercial application, was presented. Several examples of research efforts presenting high potential to develop new products containing bioactive peptides from milk proteins and predetermined as nutraceuticals was described.

  10. Molecular biology of development

    SciTech Connect

    Davidson, E.H.; Firtel, R.A.

    1984-01-01

    This book is a compilation of papers presented at a symposium on the molecular biology of development. Topics discussed include: cytoplasmic localizations and pattern formations, gene expression during oogenesis and early development, developmental expression of gene families molecular aspects of plant development and transformation in whole organisms and cells.

  11. Particular aspects in the cytogenetics and molecular biology of salivary gland tumours – current review of reports

    PubMed Central

    Osuch-Wójcikiewicz, Ewa

    2016-01-01

    Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours. The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours. PMID:27688723

  12. Particular aspects in the cytogenetics and molecular biology of salivary gland tumours – current review of reports

    PubMed Central

    Osuch-Wójcikiewicz, Ewa

    2016-01-01

    Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours. The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours.

  13. The molecular aspects of chordoma.

    PubMed

    Gulluoglu, Sukru; Turksoy, Ozlem; Kuskucu, Aysegul; Ture, Ugur; Bayrak, Omer Faruk

    2016-04-01

    Chordomas are one of the rarest bone tumors, and they originate from remnants of embryonic notochord along the spine, more frequently at the skull base and sacrum. Although they are relatively slow growing and low grade, chordomas are highly recurrent, aggressive, locally invasive, and prone to metastasize to the lungs, bone, and the liver. Chordomas highly and generally show a dual epithelial-mesenchymal differentiation. These tumors resist chemotherapy and radiotherapy; therefore, radical surgery and high-dose radiation are the most used treatments, although there is no standard way to treat the disease. The molecular biology process behind the initiation and progression of a chordoma needs to be revealed for a better understanding of the disease and to develop more effective therapies. Efforts to discover the mysteries of these molecular aspects have delineated several molecular and genetic alterations in this tumor. Here, we review and describe the emerging insights into the molecular landscape of chordomas.

  14. Molecular biology of potyviruses.

    PubMed

    Revers, Frédéric; García, Juan Antonio

    2015-01-01

    Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.

  15. Preparation, Purification, and Secondary Structure Determination of Bacillus Circulans Xylanase. A Molecular Laboratory Incorporating Aspects of Molecular Biology, Biochemistry, and Biophysical Chemistry

    ERIC Educational Resources Information Center

    Russo, Sal; Gentile, Lisa

    2006-01-01

    A project module designed for biochemistry or cellular and molecular biology student which involves determining the secondary structure of Bacillus circulans xylanase (BCX) by circular dichroism (CD) spectroscopy under conditions that compromise its stabilizing intramolecular forces is described. The lab model enhanced students knowledge of the…

  16. The Molecular Crosstalk between the MET Receptor Tyrosine Kinase and the DNA Damage Response — Biological and Clinical Aspects

    PubMed Central

    Medová, Michaela; Aebersold, Daniel M.; Zimmer, Yitzhak

    2013-01-01

    Radiation therapy remains an imperative treatment modality for numerous malignancies. Enduring significant technical achievements both on the levels of treatment planning and radiation delivery have led to improvements in local control of tumor growth and reduction in healthy tissue toxicity. Nevertheless, resistance mechanisms, which presumably also involve activation of DNA damage response signaling pathways that eventually may account for loco-regional relapse and consequent tumor progression, still remain a critical problem. Accumulating data suggest that signaling via growth factor receptor tyrosine kinases, which are aberrantly expressed in many tumors, may interfere with the cytotoxic impact of ionizing radiation via the direct activation of the DNA damage response, leading eventually to so-called tumor radioresistance. The aim of this review is to overview the current known data that support a molecular crosstalk between the hepatocyte growth factor receptor tyrosine kinase MET and the DNA damage response. Apart of extending well established concepts over MET biology beyond its function as a growth factor receptor, these observations directly relate to the role of its aberrant activity in resistance to DNA damaging agents, such as ionizing radiation, which are routinely used in cancer therapy and advocate tumor sensitization towards DNA damaging agents in combination with MET targeting. PMID:24378750

  17. Chemical aspects of synthetic biology.

    PubMed

    Luisi, Pier Luigi

    2007-04-01

    Synthetic biology as a broad and novel field has also a chemical branch: whereas synthetic biology generally has to do with bioengineering of new forms of life (generally bacteria) which do not exist in nature, 'chemical synthetic biology' is concerned with the synthesis of chemical structures such as proteins, nucleic acids, vesicular forms, and other which do not exist in nature. Three examples of this 'chemical synthetic biology' approach are given in this article. The first example deals with the synthesis of proteins that do not exist in nature, and dubbed as 'the never born proteins' (NBPs). This research is related to the question why and how the protein structures existing in our world have been selected out, with the underlying question whether they have something very particular from the structural or thermodynamic point of view (for example, the folding). The NBPs are produced in the laboratory by the modern molecular biology technique, the phage display, so as to produce a very large library of proteins having no homology with known proteins. The second example of chemical synthetic biology has also to do with the laboratory synthesis of proteins, but, this time, adopting a prebiotic synthetic procedure, the fragment condensation of short peptides, where short means that they have a length that can be obtained by prebiotic methods; for example, from the condensation of N-carboxy anhydrides. The scheme is illustrated and discussed, being based on the fragment condensation catalyzed by peptides endowed with proteolitic activity. Selection during chain growth is determined by solubility under the contingent environmental conditions, i.e., the peptides which result insoluble are eliminated from further growth. The scheme is tested preliminarily with a synthetic chemical fragment-condensation method and brings to the synthesis of a 44-residues-long protein, which has no homology with known proteins, and which has a stable tertiary folding. Finally, the third

  18. Papillomaviruses: Molecular and clinical aspects

    SciTech Connect

    Howley, P.M.; Broker, T.R.

    1985-01-01

    This book contains nine sections, each consisting of several papers. The section headings are : Papillomaviruses and Human Genital Tract Diseases;Papillomaviruses and Human Cutaneous Diseases, Papillomaviruses and Human Oral and Laryngeal Diseases;Therapeutic Approaches to Papillomavirus Infections;Animal Papillomaviruses;Molecular Biology;Transcription, Replication, and Genome Organization;Epithelial Cell Culture;Papillomavirus Transformation;and Viral Vectors.

  19. Functional Aspects of Biological Networks

    NASA Astrophysics Data System (ADS)

    Sneppen, Kim

    2007-03-01

    We discuss biological networks with respect to 1) relative positioning and importance of high degree nodes, 2) function and signaling, 3) logic and dynamics of regulation. Visually the soft modularity of many real world networks can be characterized in terms of number of high and low degrees nodes positioned relative to each other in a landscape analogue with mountains (high-degree nodes) and valleys (low-degree nodes). In these terms biological networks looks like rugged landscapes with separated peaks, hub proteins, which each are roughly as essential as any of the individual proteins on the periphery of the hub. Within each sup-domain of a molecular network one can often identify dynamical feedback mechanisms that falls into combinations of positive and negative feedback circuits. We will illustrate this with examples taken from phage regulation and bacterial uptake and regulation of small molecules. In particular we find that a double negative regulation often are replaced by a single positive link in unrelated organisms with same functional requirements. Overall we argue that network topology primarily reflects functional constraints. References: S. Maslov and K. Sneppen. ``Computational architecture of the yeast regulatory network." Phys. Biol. 2:94 (2005) A. Trusina et al. ``Functional alignment of regulatory networks: A study of temerate phages". Plos Computational Biology 1:7 (2005). J.B. Axelsen et al. ``Degree Landscapes in Scale-Free Networks" physics/0512075 (2005). A. Trusina et al. ``Hierarchy and Anti-Hierarchy in Real and Scale Free networks." PRL 92:178702 (2004) S. Semsey et al. ``Genetic Regulation of Fluxes: Iron Homeostasis of Escherichia coli". (2006) q-bio.MN/0609042

  20. Biological aspects of gender disorders.

    PubMed

    Corsello, S M; Di Donna, V; Senes, P; Luotto, V; Ricciato, M P; Paragliola, R M; Pontecorvi, A

    2011-12-01

    The scientific community is very interested in the biological aspects of gender disorders and sexual orientation. There are different levels to define an individual's sex: chromosomal, gonadic, and phenotypic sex. Concerning the psychological sex, men and women are different by virtue of their own gender identity, which means they recognize themselves as belonging to a determinate sex. They are different also as a result of their own role identity, a set of behaviors, tendencies, and cognitive and emotional attitudes, commonly defined as "male" and "female". Transsexuality is a disorder characterized by the development of a gender identity opposed to phenotypic sex, whereas homosexuality is not a disturbance of gender identity but only of sexual attraction, expressing sexual orientation towards people of the same sex. We started from a critical review of literature on genetic and hormonal mechanisms involved in sexual differentiation. We re-examined the neuro-anatomic and functional differences between men and women, with special reference to their role in psychosexual differentiation and to their possible implication in the genesis of homosexuality and identity gender disorders. Homosexuality and transsexuality are conditions without a well defined etiology. Although the influence of educational and environmental factors in humans is undeniable, it seems that organic neurohormonal prenatal and postnatal factors might contribute in a determinant way in the development of these two conditions. This "organicistic neurohormal theory" might find support in the study of particular situations in which the human fetus is exposed to an abnormal hormonal environment in utero.

  1. Biosilica: Molecular Biology, Biochemistry and Function in Demosponges as well as its Applied Aspects for Tissue Engineering.

    PubMed

    Wang, Xiaohong; Schröder, Heinz C; Wiens, Matthias; Schloßmacher, Ute; Müller, Werner E G

    2012-01-01

    Biomineralization, biosilicification in particular (i.e. the formation of biogenic silica, SiO(2)), has become an exciting source of inspiration for the development of novel bionic approaches following 'nature as model'. Siliceous sponges are unique among silica-forming organisms in their ability to catalyze silica formation using a specific enzyme termed silicatein. In this study, we review the present state of knowledge on silicatein-mediated 'biosilica' formation in marine demosponges, the involvement of further molecules in silica metabolism and their potential applications in nano-biotechnology and bio-medicine. While most forms of multicellular life have developed a calcium-based skeleton, a few specialized organisms complement their body plan with silica. Only sponges (phylum Porifera) are able to polymerize silica enzymatically mediated in order to generate massive siliceous skeletal elements (spicules) during a unique reaction, at ambient temperature and pressure. During this biomineralization process (i.e. biosilicification), hydrated, amorphous silica is deposited within highly specialized sponge cells, ultimately resulting in structures that range in size from micrometres to metres. This peculiar phenomenon has been comprehensively studied in recent years, and in several approaches, the molecular background was explored to create tools that might be employed for novel bioinspired biotechnological and biomedical applications. Thus, it was discovered that spiculogenesis is mediated by the enzyme silicatein and starts intracellularly. The resulting silica nanoparticles fuse and subsequently form concentric lamellar layers around a central protein filament, consisting of silicatein and the scaffold protein silintaphin-1. Once the growing spicule is extruded into the extracellular space, it obtains final size and shape. Again, this process is mediated by silicatein and silintaphin-1/silintaphin-1, in combination with other molecules such as galectin and

  2. Molecular Models in Biology

    ERIC Educational Resources Information Center

    Goodman, Richard E.

    1970-01-01

    Describes types of molecular models (ball-and-stick, framework, and space-filling) and evaluates commercially available kits. Gives instructions for constructive models from polystyrene balls and pipe-cleaners. Models are useful for class demonstrations although not sufficiently accurate for research use. Illustrations show biologically important…

  3. Molecular aspects of multiple myeloma.

    PubMed

    Kastrinakis, N G; Gorgoulis, V G; Foukas, P G; Dimopoulos, M A; Kittas, C

    2000-10-01

    Multiple myeloma (MM) is a B-cell neoplasm characterized by bone marrow infiltration with malignant plasma cells, which synthesize and secrete monoclonal immunoglobulin (Ig) fragments. Despite the considerable progress in the understanding of MM biology, the molecular basis of the disease remains elusive. The initial transformation is thought to occur in a postgerminal center B-lineage cell, carrying a somatically hypermutated Ig heavy chain (IGH) gene. This plasmablastic precursor cell colonizes the bone marrow, propagates clonally and differentiates into a slowly proliferating myeloma cell population, all under the influence of specific cell adhesion molecules and cytokines. Production of interleukin-6 by stromal cells, osteoblasts and, in some cases, neoplastic cells is an essential element of myeloma cell growth, with the cytokine stimulus being delivered intracellularly via the Jack-STAT and ras signaling pathways. While karyotypic changes have been identified in up to 50% of MM patients, recent molecular cytogenetic techniques have revealed chromosomal abnormalities in the vast majority of examined cases. Translocations mostly involve illegal switch rearrangements of the IGH locus with various partner genes (CCND1, FGFR3, c-maf). Such events have been assigned a critical role in MM development. Mutations in coding and regulatory regions, as well as aberrant expression patterns of several oncogenes (c-myc, ras) and tumor suppressor genes (p16, p15) have been reported. Key regulators of programmed cell death (BCL-2, Fas), tumor expansion (metalloproteinases) and drug responsiveness (topoisomerase II alpha) have also been implicated in the pathogenesis of this hematologic malignancy. A tumorigenic role for human herpesvirus 8 (HHV8) was postulated recently, following the detection of viral sequences in bone marrow dendritic cells of MM patients. However, since several research groups were unable to confirm this observation, the role of HHV8 remains unclear

  4. Educational aspects of molecular simulation

    NASA Astrophysics Data System (ADS)

    Allen, Michael P.

    This article addresses some aspects of teaching simulation methods to undergraduates and graduate students. Simulation is increasingly a cross-disciplinary activity, which means that the students who need to learn about simulation methods may have widely differing backgrounds. Also, they may have a wide range of views on what constitutes an interesting application of simulation methods. Almost always, a successful simulation course includes an element of practical, hands-on activity: a balance always needs to be struck between treating the simulation software as a 'black box', and becoming bogged down in programming issues. With notebook computers becoming widely available, students often wish to take away the programs to run themselves, and access to raw computer power is not the limiting factor that it once was; on the other hand, the software should be portable and, if possible, free. Examples will be drawn from the author's experience in three different contexts. (1) An annual simulation summer school for graduate students, run by the UK CCP5 organization, in which practical sessions are combined with an intensive programme of lectures describing the methodology. (2) A molecular modelling module, given as part of a doctoral training centre in the Life Sciences at Warwick, for students who might not have a first degree in the physical sciences. (3) An undergraduate module in Physics at Warwick, also taken by students from other disciplines, teaching high performance computing, visualization, and scripting in the context of a physical application such as Monte Carlo simulation.

  5. Molecular Biology of Nitrogen Fixation

    ERIC Educational Resources Information Center

    Shanmugam, K. T.; Valentine, Raymond C.

    1975-01-01

    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  6. Molecular Mechanism of Biological Proton Transport

    SciTech Connect

    Pomes, R.

    1998-09-01

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  7. Molecular aspects of charm physics

    SciTech Connect

    Fernandez, F.; Ortega, P. G.; Entem, D. R.

    2013-03-25

    We study the influence of possible molecular structures in the charmonium spectrum. We focus on the 0{sup ++}, 1{sup ++} and 1{sup --} sectors. In the first one we coupled the 2{sup 3}P{sub 0}cc pair with DD, J/{psi}{omega}, D{sub s}D{sub s} and J/{psi}{phi} channels and we obtain two states compatibles with the X(3945) and the Y(3940). In the second one we couple the 2{sup 3}P{sub 1}cc state with the DD{sup *} channel and we obtain a dressed state compatible with the X(3940) and a new state that we assign to the X(3872). In the third one we include the 3{sup 3}S{sub 1} and 2{sup 3}D{sub 1} charmonium states coupled to DD, DD{sup *}, D{sup *}D{sup *}, D{sub s}D{sub s}, D{sub s}D{sup *}s and D{sup *}{sub s}D{sup *}{sub s}. In this calculation we obtain a new molecular state that could be the G(3900) or the controversial Y(4008) and two cc states dressed by the molecular components assigned to the {psi}(4040) and the {psi}(4160). Finally we perform a calculation in the five quark sector where we can describe the {Lambda}{sub c}(2940){sup +} as a ND{sup *} molecular state and predict a {Lambda}{sub b}(6248){sup +} state.

  8. Singlet molecular oxygen generated by biological hydroperoxides.

    PubMed

    Miyamoto, Sayuri; Martinez, Glaucia R; Medeiros, Marisa H G; Di Mascio, Paolo

    2014-10-01

    The chemistry behind the phenomenon of ultra-weak photon emission has been subject of considerable interest for decades. Great progress has been made on the understanding of the chemical generation of electronically excited states that are involved in these processes. Proposed mechanisms implicated the production of excited carbonyl species and singlet molecular oxygen in the mechanism of generation of chemiluminescence in biological system. In particular, attention has been focused on the potential generation of singlet molecular oxygen in the recombination reaction of peroxyl radicals by the Russell mechanism. In the last ten years, our group has demonstrated the generation of singlet molecular oxygen from reactions involving the decomposition of biologically relevant hydroperoxides, especially from lipid hydroperoxides in the presence of metal ions, peroxynitrite, HOCl and cytochrome c. In this review we will discuss details on the chemical aspects related to the mechanism of singlet molecular oxygen generation from different biological hydroperoxides.

  9. [Molecular aspects of renal desease].

    PubMed

    Nichik, T E; Lin'kova, N S; Kraskovskaia, N A; Dudkov, A V; Khavinson, V Kh

    2014-01-01

    The review considers molecular mechanisms of chronic renal failure and cancer kidney disease. The most important molecules inducing inflammation are cytokines (MCP-1, TNFalpha, IFN-gamma, IL-1,6,8,18), matrix metalloproteinases MMP-2,3,9,14, tissue inhibitors of metalloproteinases (TIMPs) and grow factors (VEGF PDGE FGF). This signal molecules regulate the activity of immune cells and remodeling extracellular matrix (ECM) components taken place in inflammatory reactions, proliferation, apoptosis and also in the differentiation of kidney cells. On the basis of these data nowadays developed new highly selective approaches to diagnosis, prediction, estimation of efficiency of treatment of renal disease and creating of target drugs. PMID:25707263

  10. Teaching Molecular Biology with Microcomputers.

    ERIC Educational Resources Information Center

    Reiss, Rebecca; Jameson, David

    1984-01-01

    Describes a series of computer programs that use simulation and gaming techniques to present the basic principles of the central dogma of molecular genetics, mutation, and the genetic code. A history of discoveries in molecular biology is presented and the evolution of these computer assisted instructional programs is described. (MBR)

  11. Molecular biomimetics: nanotechnology through biology

    NASA Astrophysics Data System (ADS)

    Sarikaya, Mehmet; Tamerler, Candan; Jen, Alex K.-Y.; Schulten, Klaus; Baneyx, François

    2003-09-01

    Proteins, through their unique and specific interactions with other macromolecules and inorganics, control structures and functions of all biological hard and soft tissues in organisms. Molecular biomimetics is an emerging field in which hybrid technologies are developed by using the tools of molecular biology and nanotechnology. Taking lessons from biology, polypeptides can now be genetically engineered to specifically bind to selected inorganic compounds for applications in nano- and biotechnology. This review discusses combinatorial biological protocols, that is, bacterial cell surface and phage-display technologies, in the selection of short sequences that have affinity to (noble) metals, semiconducting oxides and other technological compounds. These genetically engineered proteins for inorganics (GEPIs) can be used in the assembly of functional nanostructures. Based on the three fundamental principles of molecular recognition, self-assembly and DNA manipulation, we highlight successful uses of GEPI in nanotechnology.

  12. Molecular biomimetics: nanotechnology through biology.

    PubMed

    Sarikaya, Mehmet; Tamerler, Candan; Jen, Alex K-Y; Schulten, Klaus; Baneyx, François

    2003-09-01

    Proteins, through their unique and specific interactions with other macromolecules and inorganics, control structures and functions of all biological hard and soft tissues in organisms. Molecular biomimetics is an emerging field in which hybrid technologies are developed by using the tools of molecular biology and nanotechnology. Taking lessons from biology, polypeptides can now be genetically engineered to specifically bind to selected inorganic compounds for applications in nano- and biotechnology. This review discusses combinatorial biological protocols, that is, bacterial cell surface and phage-display technologies, in the selection of short sequences that have affinity to (noble) metals, semiconducting oxides and other technological compounds. These genetically engineered proteins for inorganics (GEPIs) can be used in the assembly of functional nanostructures. Based on the three fundamental principles of molecular recognition, self-assembly and DNA manipulation, we highlight successful uses of GEPI in nanotechnology.

  13. [Molecular biology of hearing].

    PubMed

    Stöver, T; Diensthuber, M

    2011-03-01

    The inner ear is our most sensitive sensory organ and can be subdivided into 3 functional units: organ of Corti, stria vascularis and spiral ganglion. The appropriate stimulus for the organ of hearing is sound which travels through the external auditory canal to the middle ear where it is transmitted to the inner ear. The inner ear habors the hair cells, the sensory cells of hearing. The inner hair cells are capable of mechanotransduction, the transformation of mechanical force into an electrical signal, which is the basic principle of hearing. The stria vascularis generates the endocochlear potential and maintains the ionic homeostasis of the endolymph. The dendrites of the spiral ganglion form synaptic contacts with the hair cells. The spiral ganglion is composed of neurons that transmit the electrical signals from the cochlea to the central nervous system. In the past years there was significant progress in research on the molecular basis of hearing. More and more genes and proteins which are related to hearing can be identified and characterized. The increasing knowledge on these genes contributes not only to a better understanding of the mechanism of hearing but also to a deeper understanding of the molecular basis of hereditary hearing loss. This basic research is a prerequisite for the development of molecular diagnostics and novel therapies for hearing loss.

  14. Molecular biology of hearing

    PubMed Central

    Stöver, Timo; Diensthuber, Marc

    2012-01-01

    The inner ear is our most sensitive sensory organ and can be subdivided into three functional units: organ of Corti, stria vascularis and spiral ganglion. The appropriate stimulus for the organ of hearing is sound, which travels through the external auditory canal to the middle ear where it is transmitted to the inner ear. The inner ear houses the hair cells, the sensory cells of hearing. The inner hair cells are capable of mechanotransduction, the transformation of mechanical force into an electrical signal, which is the basic principle of hearing. The stria vascularis generates the endocochlear potential and maintains the ionic homeostasis of the endolymph. The dendrites of the spiral ganglion form synaptic contacts with the hair cells. The spiral ganglion is composed of neurons that transmit the electrical signals from the cochlea to the central nervous system. In recent years there has been significant progress in research on the molecular basis of hearing. An increasing number of genes and proteins related to hearing are being identified and characterized. The growing knowledge of these genes contributes not only to greater appreciation of the mechanism of hearing but also to a deeper understanding of the molecular basis of hereditary hearing loss. This basic research is a prerequisite for the development of molecular diagnostics and novel therapies for hearing loss. PMID:22558056

  15. Measurement Frontiers in Molecular Biology

    NASA Astrophysics Data System (ADS)

    Laderman, Stephen

    2009-03-01

    Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

  16. Molecular biology of chromosome function

    SciTech Connect

    Adolph, K.W. )

    1989-01-01

    The structure and function of chromosomes are closely linked since chromosome organization profoundly influences the activity of the genome in replication and transcription. Many fundamental results originated from studies of bacterial and viral systems chosen for their less-complex cycles. However, the processes of replication and transcription show differences between the higher and simpler systems. Three important subjects are covered in this volume: DNA replication and recombination, gene transcription, and chromosome organization. Eukaryotic, prokaryotic, and viral systems are discussed. The information presented is derived from techniques of structural biology and biophysics, including computer graphics and X-ray crystallography, as well as biochemistry, molecular and cell biology.

  17. Information theory in molecular biology

    NASA Astrophysics Data System (ADS)

    Adami, Christoph

    2004-04-01

    This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identically prepared sets) of symbolic sequences. Such an approach can distinguish between entropy and information in genes, predict the secondary structure of ribozymes, and detect the covariation between residues in folded proteins. We also review applications to molecular sequence and structure analysis, and introduce new tools in the characterization of resistance mutations, and in drug design.

  18. Molecular aspects of DNA splicing system

    NASA Astrophysics Data System (ADS)

    Yusof, Yuhani; Lim, Wen Li; Goode, T. Elizabeth; Sarmin, Nor Haniza; Heng, Fong Wan; Wahab, Mohd Firdaus Abd

    2015-05-01

    The pioneer model of deoxyribonucleic acid (DNA) splicing system in a framework of Formal Language Theory was introduced by Head that led to the existence of other models of splicing system, namely Paun, Pixton and Yusof-Goode. These entire models are inspired by the molecular biological process of DNA splicing. Hence, this paper focuses on the translucent DNA splicing process, particularly on the generated language. Starting with some preliminaries in a limit graph, this paper also provides the experimental design with the predicted and actual result.

  19. The molecular biology of ilarviruses.

    PubMed

    Pallas, Vicente; Aparicio, Frederic; Herranz, Mari C; Sanchez-Navarro, Jesus A; Scott, Simon W

    2013-01-01

    Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses.

  20. Marine molecular biology: an emerging field of biological sciences.

    PubMed

    Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G

    2008-01-01

    An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

  1. Progressive multifocal leukoencephalopathy: Clinical and molecular aspects

    PubMed Central

    Tavazzi, Eleonora; White, Martyn K.; Khalili, Kamel

    2011-01-01

    The fatal CNS demyelinating disease, progressive multifocal leukoencephalopathy (PML), is rare and appears to occur almost always as a consequence of immune dysfunction. Thus it is associated with HIV/AIDS and also as a side-effect of certain immunomodulatory monoclonal antibody therapies. In contrast to the rarity of PML, the etiological agent of the disease, the polyomavirus JC (JCV) is widespread in populations worldwide. In the forty years since JCV was first isolated, much has been learned about the virus and the disease from laboratory and clinical observations. However, there are many aspects of the viral life cycle and the pathogenesis of the disease that still remain unclear and our understanding is constantly evolving. In this review, we will discuss our current understanding of the clinical features of PML and molecular characteristics of JCV and how they relate to each other. Clinical observations can inform molecular studies of the virus and likewise molecular findings concerning the life cycle of the virus can guide the development of novel therapeutic strategies. PMID:21936015

  2. Spatial Aspects in Biological System Simulations

    PubMed Central

    Resat, Haluk; Costa, Michelle N.; Shankaran, Harish

    2012-01-01

    Mathematical models of the dynamical properties of biological systems aim to improve our understanding of the studied system with the ultimate goal of being able to predict system responses in the absence of experimentation. Despite the enormous advances that have been made in biological modeling and simulation, the inherently multiscale character of biological systems and the stochasticity of biological processes continue to present significant computational and conceptual challenges. Biological systems often consist of well-organized structural hierarchies, which inevitably lead to multiscale problems. This chapter introduces and discusses the advantages and shortcomings of several simulation methods that are being used by the scientific community to investigate the spatiotemporal properties of model biological systems. We first describe the foundations of the methods and then describe their relevance and possible application areas with illustrative examples from our own research. Possible ways to address the encountered computational difficulties are also discussed. PMID:21187236

  3. [Meningiomas: anatomical pathology and molecular biology].

    PubMed

    Bekiashev, A Kh; Korshunov, A G; Cherekaev, V A

    2007-01-01

    In the past 5-10 years, there has been a considerable progress the understanding of the biology of meningioma. The most important advances have been made by comprehensive studies of the pathogenesis of meningioma in molecular genetics. Several target genes could be identified for mutation or inactivation. Additional chromosomal regions that are usually subject to deletion or amplification and point to the presence of tumor suppressor genes or proto-oncogenes were found. The revised and updated 2000 WHO Classification is a major innovation in the histopathology of meningiomas. The new classification system more precisely and objectively determines the grade of meningioma, which allows one to more logically make a prognosis of the recurrence and aggressive behavior of the tumor. The present overview places particular emphasis on recent advances in its molecular biology. It summarizes the most important aspects of the classification of meningiomas, which makes it possible to include the results of biological observations into the respective context, and also considers the mechanisms of angiogenesis and edema development and the role of hormonal receptors in meningiomas.

  4. The molecular biology of cancer.

    PubMed

    Bertram, J S

    2000-12-01

    identifies key genes directly involved in carcinogenesis and demonstrates how mutations in these genes allow cells to circumvent cellular controls. This detailed understanding of the process of carcinogenesis at the molecular level has only been possible because of the advent of modern molecular biology. This new discipline, by precisely identifying the molecular basis of the differences between normal and malignant cells, has created novel opportunities and provided the means to specifically target these modified genes. Whenever possible this review highlights these opportunities and the attempts being made to generate novel, molecular based therapies against cancer. Successful use of these new therapies will rely upon a detailed knowledge of the genetic defects in individual tumors. The review concludes with a discussion of how the use of high throughput molecular arrays will allow the molecular pathologist/therapist to identify these defects and direct specific therapies to specific mutations.

  5. Molecular characteristics versus biological activity

    USGS Publications Warehouse

    Applegate, Vernon C.; Smith, Manning A.; Willeford, Bennett R.

    1967-01-01

    The molecular characteristics of mononitrophenols containing halogens not only play a key role in their biological activity but provide a novel example of selective toxicity among vertebrate animals. It has been reported that efforts to control the parasitic sea lamprey in the Great Lakes are directed at present to the applications of a selective toxicant to streams inhabited by lamprey larvae. Since 1961, the larvicide that has been used almost exclusively in the control program has been 3-trifluoromethyl-4-nitrophenol (TFM). However, this is only one of about 15 closely related compounds, all halogen-containing mononitrophenols, that display a selectively toxic action upon lampreys. Although not all of the halogenated mononitrophenols are selectively toxic to lampreys (in fact, fewer than half of those tested), no other group of related compounds has displayed any useful larvicidal activity except for the substituted nitrosalicylanilides.

  6. History of the molecular biology of cytomegaloviruses.

    PubMed

    Stinski, Mark F

    2014-01-01

    The history of the molecular biology of cytomegaloviruses from the purification of the virus and the viral DNA to the cloning and expression of the viral genes is reviewed. A key genetic element of cytomegalovirus (the CMV promoter) contributed to our understanding of eukaryotic cell molecular biology and to the development of lifesaving therapeutic proteins. The study of the molecular biology of cytomegaloviruses also contributed to the development of antivirals to control the viral infection.

  7. Ricin Toxicity: Clinical and Molecular Aspects

    PubMed Central

    Moshiri, Mohammad; Hamid, Fatemeh; Etemad, Leila

    2016-01-01

    Seeds of the castor bean plant Ricinuscommunis L (CB) contain ricin toxin (RT), one of the most poisonous naturally-occurring substances known. Ricin toxin, a water-soluble glycoprotein that does not partition into the oil extract, is a ribosome-inactivating toxin composed of two chains, labeled A and B. Severity of the toxicity varies depending on the route of exposure to the toxin. Inhalational is the most toxic route, followed by oral ingestion. Orally-ingested RT accumulates in the liver and spleen but other cells are also affected. The main clinical manifestations are also related to the administration route. Oral ingestion of CB or RT results in abdominal pain, vomiting, diarrhea, and various types of gastrointestinal bleeding that leading to volume depletion, hypovolemic shock, and renal failure. Inhalation of the toxin presents with non-cardiogenic pulmonary edema, diffuse necrotizing pneumonia, interstitial and alveolar inflammation, and edema. Local injection of RT induces indurations at the injection site, swelling of regional lymph nodes, hypotension, and death. An enzyme-linked immunosorbent assay (ELISA) has been developed to detect RT in animal tissues and fluids. Ricinine, an alkaloid of CB, can be detected in rat urine within 48 h of RT exposure. Supportive care is the basic treatment and standard biowarfare decontamination protocols are used for RT intoxication. Dexamethasone and difluoromethylornithine might be effective treatments. This review examines the clinical and molecular aspects of ricin toxicity. PMID:27536698

  8. Ricin Toxicity: Clinical and Molecular Aspects.

    PubMed

    Moshiri, Mohammad; Hamid, Fatemeh; Etemad, Leila

    2016-04-01

    Seeds of the castor bean plant Ricinuscommunis L (CB) contain ricin toxin (RT), one of the most poisonous naturally-occurring substances known. Ricin toxin, a water-soluble glycoprotein that does not partition into the oil extract, is a ribosome-inactivating toxin composed of two chains, labeled A and B. Severity of the toxicity varies depending on the route of exposure to the toxin. Inhalational is the most toxic route, followed by oral ingestion. Orally-ingested RT accumulates in the liver and spleen but other cells are also affected. The main clinical manifestations are also related to the administration route. Oral ingestion of CB or RT results in abdominal pain, vomiting, diarrhea, and various types of gastrointestinal bleeding that leading to volume depletion, hypovolemic shock, and renal failure. Inhalation of the toxin presents with non-cardiogenic pulmonary edema, diffuse necrotizing pneumonia, interstitial and alveolar inflammation, and edema. Local injection of RT induces indurations at the injection site, swelling of regional lymph nodes, hypotension, and death. An enzyme-linked immunosorbent assay (ELISA) has been developed to detect RT in animal tissues and fluids. Ricinine, an alkaloid of CB, can be detected in rat urine within 48 h of RT exposure. Supportive care is the basic treatment and standard biowarfare decontamination protocols are used for RT intoxication. Dexamethasone and difluoromethylornithine might be effective treatments. This review examines the clinical and molecular aspects of ricin toxicity. PMID:27536698

  9. Strontium: Part II. Chemistry, Biological Aspects and Applications.

    ERIC Educational Resources Information Center

    Britton, G. C.; Johnson, C. H.

    1987-01-01

    Reviews basic information on the Chemistry of strontium and its compounds. Explains biological aspects of strontium and its pharmaceutical applications. Highlights industrial application of strontium and its components. (ML)

  10. Geometric Aspects of Biological Sequence Comparison

    PubMed Central

    Stojmirović, Aleksandar

    2009-01-01

    Abstract We introduce a geometric framework suitable for studying the relationships among biological sequences. In contrast to previous works, our formulation allows asymmetric distances (quasi-metrics), originating from uneven weighting of strings, which may induce non-trivial partial orders on sets of biosequences. The distances considered are more general than traditional generalized string edit distances. In particular, our framework enables non-trivial conversion between sequence similarities, both local and global, and distances. Our constructions apply to a wide class of scoring schemes and require much less restrictive gap penalties than the ones regularly used. Numerous examples are provided to illustrate the concepts introduced and their potential applications. PMID:19361329

  11. [Ethical aspects of biological sample banks].

    PubMed

    Cambon-Thomsen, A; Rial-Sebbag, E

    2003-02-01

    Numerous activities in the domain of epidemiology require the constitution or the use of biological sample banks. Such biobanks raise ethical issues. A number of recommendations are applicable to this field, in France and elsewhere. Major principles applicable to biobanks include the respect of person's autonomy, the respect of human body, the respect of confidentiality. These principles are translated into practices through the following procedures: relevant information to the persons regarding their sample management prior to informed consent, opinion of an independent ethics committee, actual implementation of conditions for protecting samples and data. However, although those principles may appear quite simple and obvious, in the context of a largely international practice of research and given the large variety of biobanks, it is not always obvious for researchers to find their way. The attitudes vary between countries, there are numerous texts for various types of biobanks, the same texts raise different interpretations in different institutions, there are new ethical opinions expressed, and mainly the novelty of questions raised by the uses of samples that are possible today, especially in genetics, and were not foreseeable at the time of sampling make the field difficult in practice. This article reviews the types of biobanks, the relevant ethical issues. It also underlines the still unclear or ambiguous situations using some examples of practical situations.

  12. Monod and the spirit of molecular biology.

    PubMed

    Morange, Michel

    2015-06-01

    The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly, Monod anticipated some recent evolutions of this discipline.

  13. Molecular ferroelectrics: where electronics meet biology

    PubMed Central

    Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

    2013-01-01

    In the last several years, we have witnessed significant advances in molecular ferroelectrics, with ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by overview on the fundamentals of ferroelectricity. Latest development in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also noted. PMID:24018952

  14. Molecular ferroelectrics: where electronics meet biology.

    PubMed

    Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

    2013-12-28

    In the last several years, we have witnessed significant advances in molecular ferroelectrics, with the ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by an overview of the fundamentals of ferroelectricity. The latest developments in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also described.

  15. [Aggressive behavior: theoretical and biological aspects].

    PubMed

    Giotakos, O

    2013-01-01

    The susceptibility to aggression may manifest differently depending on the psychological context in which it occurs. In the context of psychopathy, characterized by a lack of empathy, this may manifest in aggression with criminal acts, which is characteristic of antisocial personality disorder. When the susceptibility is associated with psychotic impairment, aggression may be manifested in highly deviant behavior, like murder or serial killing. While the great majority of persons with schizophrenia do not commit violent acts, clinicians suggest that some schizophrenics may pose a risk in the community, particularly those patients with co-occurring substance abuse diagnoses, those who are noncompliant with prescribed psychiatric treatment, and those with a history of frequent relapses resulting in hospitalization or arrest. Episodic violence and aggression often accompany dementia. When coupled with emotional dysregulation, impulsive aggression often occurs in an interpersonal context, as in borderline personality disorder. However, the most common comorbidity is the substance abuse disorder, which contributes to both the cognitive distortions and disinhibition associated with the substance use. According to the biological data, aggression seems to emerge when the drive of limbic-mediated affective prefrontal response to provocative producing stimuli is insufficiently constrained by inhibition. Thus, excessive reactivity in the amygdale, coupled with inadequate prefrontal regulation, increase the possibility of aggressive behavior. The PET/SPECT studies focusing on schizophrenia have shown reduced activity in fronto-temoral circuitry. The fMRI studies concord with the hypothesis that among violent persons with schizophrenia, those with sociopathetic features and/or substance abuse constitute a highly different subgroup, in which cognitive, neurological and behavioral patterns are more closely associated with the personality traits than schizophrenia. It is known

  16. Molecular biology for the computer scientist

    SciTech Connect

    Subramaniam, S.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial focuses on the following: the cell and the structural and energetic basis of life molecules; membrane structure; bioenergetics; eukaryotes and functional specialization; examples of molecular systems; evolution and diversity; and modern techniques in molecular biology.

  17. Molecular biology of microbial ureases.

    PubMed Central

    Mobley, H L; Island, M D; Hausinger, R P

    1995-01-01

    progress in our understanding of the molecular biology of microbial ureases is reviewed. PMID:7565414

  18. Origins of molecular biology in Japan.

    PubMed

    Obayashi, M

    1986-06-01

    The purpose of this paper is to discuss the origins of molecular biology in Japan. Japanese molecular biology does not have a long history since it started only after World War II. Especially, molecular genetics which uses "bacteriophage" had hardly been studied before the war and only a few scientists were interested in it immediately after the war. This is one of the origins of molecular biology in Japan. But there are other origins, one of which is the group formed by biologists, biochemists and physicists interested in nucleic acids. This group also started just after the war. Still another origin is the group of enzymologists. Enzymology was one of the main subjects of biochemistry from before the war. In Japan, biochemistry developed in conjunction with the medical and agricultural sciences from the pre-war era. These played an important role in introducing molecular biology from Europe and the United States after the war. A historical study of the development of molecular biology in Japan, comparing it with the history of molecular biology in Europe and the United States, should contribute to the elucidation of the features of the history of molecular biology in Japan.

  19. Molecular machines - a new dimension of biological sciences.

    PubMed

    Głogocka, Daria; Przybyło, Magdalena; Langner, Marek

    2015-06-01

    Biological systems are characterized by directional and precisely controlled flow of matter and information along with the maintenance of their structural patterns. This is possible thanks to sequential transformations of information, energy and structure carried out by molecular machines. The new perception of biological systems, including their mechanical aspects, requires the implementation of tools and approaches previously developed for engineering sciences. In this review paper, a biological system is presented in a new perspective as an ensemble of coordinated molecular devices functioning in the limited space confined by the biological membrane. The working of a molecular machine is presented using the example of F0F1 ATPase, and the general conditions necessary for the coordination of a large number of functional units are described.

  20. The Molecular Biology Capstone Assessment: A Concept Assessment for Upper-Division Molecular Biology Students

    ERIC Educational Resources Information Center

    Couch, Brian A.; Wood, William B.; Knight, Jennifer K.

    2015-01-01

    Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in…

  1. [Biochemistry, molecular mechanism of action and biological effects of endotoxin].

    PubMed

    Burgmann, H; Breyer, S

    1995-01-01

    This review is a brief attempt at providing an overview of a subject of enormous complexity-endotoxins and the mediators associated with its biological effects. More specifically it deals with biochemistry and biology of endotoxin, detection of endotoxin with the Limulus amebocyte lysate test, the molecular mechanisms and biological effects, and in the last part with future aspects of therapeutical strategies. It seems certain that the subject will become even more complex and possibly controversial as scientific knowledge further involves. However, because of the high mortality rate of patients suffering from gram-negative sepsis all efforts have to be made to find effective therapeutical strategies.

  2. Genetics and molecular biology of breast cancer

    SciTech Connect

    King, M.C.; Lippman, M.

    1992-12-31

    This volume contains the abstracts of oral presentations and poster sessions presented at the Cold Springs Harbor Meeting on Cancer Cells, this meeting entitled Genetics and Molecular Biology of Breast Cancer.

  3. Biological Aspects of Anorexia Nervosa and Bulimia Nervosa.

    ERIC Educational Resources Information Center

    Kaplan, Allan S.; Woodside, D. Blake

    1987-01-01

    Reviews biological factors relevant to the understanding of anorexia nervosa and bulimia nervosa. Considers the physical presentation of these disorders; the medical complications of starvation, binging, and purging; and the cognitive and behavioral effects of starvation. Reviews neurophysiological and neurochemical aspects of these illnesses and…

  4. The History, Biology and Medical Aspects of Leprosy.

    ERIC Educational Resources Information Center

    Eichman, Phillip

    1999-01-01

    Presents information about the history, biology, and medical aspects of leprosy, including its description in historical documents, its cause and effects, statistics on its prevalence, and various attempts at treatment. Notes that leprosy is one of the few infectious diseases that, although treatable with medication, remains incurable. Contains 30…

  5. Using Spreadsheets to Teach Aspects of Biology Involving Mathematical Models

    ERIC Educational Resources Information Center

    Carlton, Kevin; Nicholls, Mike; Ponsonby, David

    2004-01-01

    Some aspects of biology, for example the Hardy-Weinberg simulation of population genetics or modelling heat flow in lizards, have an undeniable mathematical basis. Students can find the level of mathematical skill required to deal with such concepts to be an insurmountable hurdle to understanding. If not used effectively, spreadsheet models…

  6. Molecular beacons: an optimal multifunctional biological probe.

    PubMed

    Li, Yongsheng; Zhou, Xiaoyan; Ye, Duyun

    2008-09-01

    Molecular beacon technology is set up based on fluorescence resonance energy transfer (FRET) and the complementary pairing principles. These fluorescent molecular probes, which are very highly specific and sensitive, have now become one important tool in medical and biological researches. This review introduces the molecular beacons structure, principle, the main impact factors, the labeling of the molecular beacons, and research progress on molecular beacons fluorescent-label in the polymerase chain reaction (PCR), DNA sequence analysis, gene dynamic detection in living cells, protein (enzyme)-nucleic acid interactions and applications in clinical medicine.

  7. Seeing the Unseen: Molecular Visualization in Biology

    ERIC Educational Resources Information Center

    Finnan, Jeff; Taylor-Papp, Kim; Duran, Mesut

    2005-01-01

    In high school biology, students are challenged by many molecular concepts and structures. They meander through a number of molecular structures, some in macromolecular form: carbohydrates, amino acids, fatty acids, nucleotides. Student difficulties arise in part from inability to visualize what they can't easily see. Students struggle moving from…

  8. Protein dynamics: Moore's law in molecular biology.

    PubMed

    Vendruscolo, Michele; Dobson, Christopher M

    2011-01-25

    The millisecond barrier has been broken in molecular dynamics simulations of proteins. Such simulations are increasingly revealing the inner workings of biological systems by generating atomic-level descriptions of their behaviour that make testable predictions about key molecular processes.

  9. Genetic and molecular aspects of spinocerebellar ataxias

    PubMed Central

    Honti, Viktor; Vécsei, László

    2005-01-01

    The group of spinocerebellar ataxias (SCAs) includes more than 20 subgroups based only on genetic research. The “ataxia genes” are autosomal; the “disease-alleles” are dominant, and many of them, but not all, encode a protein with an abnormally long polyglutamine domain. In DNA, this domain can be detected as an elongated CAG repeat region, which is the basis of genetic diagnostics. The polyglutamine tails often tend to aggregate and form inclusions. In some cases, protein–protein interactions are the key to understanding the disease. Protein partners of ataxia proteins include phosphatases and components of chromatin and the transcriptional machinery. To date, investigation of spinocerebellar ataxias involves population genetics, molecular methods, and studying model organisms. However, there is still no efficient therapy for patients. Here, we review the genetic and molecular data gained on spinocerebellar ataxias. PMID:18568057

  10. Molecular and clinical aspects of apoptosis.

    PubMed

    Uren, A G; Vaux, D L

    1996-01-01

    Unwanted cells are removed by physiological cell death processes that are highly conserved throughout the animal kingdom. Physiological cell death plays an important role in development, tissue homeostasis and defence against viral infection and mutation. This review describes the molecular components that implement this process, the relevance of these to a variety of human diseases, and discusses the potential for novel therapies based on our understanding of them. PMID:8981570

  11. Molecular and Functional Aspects of Bacterial Chemotaxis

    NASA Astrophysics Data System (ADS)

    Celani, A.; Shimizu, T. S.; Vergassola, M.

    2011-07-01

    We consider the dynamics of chemotaxis in the model bacterium Escherichia coli. We analyze both its molecular mechanisms and the functional causes governing the evolution of the observed behaviors. We review molecular models of the transduction network controlling the bacterial chemotaxis in response to chemoattractant binding to the receptors. In particular, recent progress stimulated by FRET experiments is presented for statistical physics allosteric models. The response function to a pulse of chemoattractant is expressed in terms of microscopic parameters of the allosteric models. The functional causes for the shape of the response function, as measured in experimental tethering assay, are then investigated. A hydrodynamic equation, valid for space-time scales larger than the microscopic running length and time, is derived for the position of a swimming bacterium. It is then shown how optimization over the microscopic parameters of the response function yields the curve observed experimentally. In particular, the observed property of adaptation to the background level of aspartate emerges as being produced by fluctuations in the space-time chemoattractant profiles sensed by bacteria along their trajectories. This functional cause is distinct from arguments based on the extension of the dynamical range. Future directions and experiments to probe the adaptation of E. coli chemotaxis to the environmental conditions and its response to realistic space-time chemoattractant stimuli are finally discussed.

  12. Molecular biology of pancreatic cancer.

    PubMed

    Zavoral, Miroslav; Minarikova, Petra; Zavada, Filip; Salek, Cyril; Minarik, Marek

    2011-06-28

    In spite of continuous research efforts directed at early detection and treatment of pancreatic cancer, the outlook for patients affected by the disease remains dismal. With most cases still being diagnosed at advanced stages, no improvement in survival prognosis is achieved with current diagnostic imaging approaches. In the absence of a dominant precancerous condition, several risk factors have been identified including family history, chronic pancreatitis, smoking, diabetes mellitus, as well as certain genetic disorders such as hereditary pancreatitis, cystic fibrosis, familial atypical multiple mole melanoma, and Peutz-Jeghers and Lynch syndromes. Most pancreatic carcinomas, however, remain sporadic. Current progress in experimental molecular techniques has enabled detailed understanding of the molecular processes of pancreatic cancer development. According to the latest information, malignant pancreatic transformation involves multiple oncogenes and tumor-suppressor genes that are involved in a variety of signaling pathways. The most characteristic aberrations (somatic point mutations and allelic losses) affect oncogenes and tumor-suppressor genes within RAS, AKT and Wnt signaling, and have a key role in transcription and proliferation, as well as systems that regulate the cell cycle (SMAD/DPC, CDKN2A/p16) and apoptosis (TP53). Understanding of the underlying molecular mechanisms should promote development of new methodology for early diagnosis and facilitate improvement in current approaches for pancreatic cancer treatment.

  13. Genetic and molecular aspects of hypertension.

    PubMed

    Padmanabhan, Sandosh; Caulfield, Mark; Dominiczak, Anna F

    2015-03-13

    Until recently, significant advances in our understanding of the mechanisms of blood pressure regulation arose from studies of monogenic forms of hypertension and hypotension, which identified rare variants that primarily alter renal salt handling. Genome-wide association and exome sequencing studies over the past 6 years have resulted in an unparalleled burst of discovery in the genetics of blood pressure regulation and hypertension. More importantly, genome-wide association studies, while expanding the list of common genetic variants associated with blood pressure and hypertension, are also uncovering novel pathways of blood pressure regulation that augur a new era of novel drug development, repurposing, and stratification in the management of hypertension. In this review, we describe the current state of the art of the genetic and molecular basis of blood pressure and hypertension.

  14. [Glucotransporters: clinical, molecular and genetic aspects].

    PubMed

    Sandoval-Muñiz, Roberto de Jesús; Vargas-Guerrero, Belinda; Flores-Alvarado, Luis Javier; Gurrola-Díaz, Carmen Magdalena

    2016-01-01

    Oxidation of glucose is the major source of obtaining cell energy, this process requires glucose transport into the cell. However, cell membranes are not permeable to polar molecules such as glucose; therefore its internalization is accomplished by transporter proteins coupled to the cell membrane. In eukaryotic cells, there are two types of carriers coupled to the membrane: 1) cotransporter Na+-glucose (SGLT) where Na+ ion provides motive power for the glucose´s internalization, and 2) the glucotransporters (GLUT) act by facilitated diffusion. This review will focus on the 14 GLUT so far described. Despite the structural homology of GLUT, different genetic alterations of each GLUT cause specific clinical entities. Therefore, the aim of this review is to gather the molecular and biochemical available information of each GLUT as well as the particular syndromes and pathologies related with GLUT´s alterations and their clinical approaches. PMID:27595260

  15. Molecular and cellular aspects of rhabdovirus entry.

    PubMed

    Albertini, Aurélie A V; Baquero, Eduard; Ferlin, Anna; Gaudin, Yves

    2012-01-01

    Rhabdoviruses enter the cell via the endocytic pathway and subsequently fuse with a cellular membrane within the acidic environment of the endosome. Both receptor recognition and membrane fusion are mediated by a single transmembrane viral glycoprotein (G). Fusion is triggered via a low-pH induced structural rearrangement. G is an atypical fusion protein as there is a pH-dependent equilibrium between its pre- and post-fusion conformations. The elucidation of the atomic structures of these two conformations for the vesicular stomatitis virus (VSV) G has revealed that it is different from the previously characterized class I and class II fusion proteins. In this review, the pre- and post-fusion VSV G structures are presented in detail demonstrating that G combines the features of the class I and class II fusion proteins. In addition to these similarities, these G structures also reveal some particularities that expand our understanding of the working of fusion machineries. Combined with data from recent studies that revealed the cellular aspects of the initial stages of rhabdovirus infection, all these data give an integrated view of the entry pathway of rhabdoviruses into their host cell.

  16. Molecular and Cellular Aspects of Rhabdovirus Entry

    PubMed Central

    Albertini, Aurélie A. V.; Baquero, Eduard; Ferlin, Anna; Gaudin, Yves

    2012-01-01

    Rhabdoviruses enter the cell via the endocytic pathway and subsequently fuse with a cellular membrane within the acidic environment of the endosome. Both receptor recognition and membrane fusion are mediated by a single transmembrane viral glycoprotein (G). Fusion is triggered via a low-pH induced structural rearrangement. G is an atypical fusion protein as there is a pH-dependent equilibrium between its pre- and post-fusion conformations. The elucidation of the atomic structures of these two conformations for the vesicular stomatitis virus (VSV) G has revealed that it is different from the previously characterized class I and class II fusion proteins. In this review, the pre- and post-fusion VSV G structures are presented in detail demonstrating that G combines the features of the class I and class II fusion proteins. In addition to these similarities, these G structures also reveal some particularities that expand our understanding of the working of fusion machineries. Combined with data from recent studies that revealed the cellular aspects of the initial stages of rhabdovirus infection, all these data give an integrated view of the entry pathway of rhabdoviruses into their host cell. PMID:22355455

  17. [Molecular biology methods in immunohematology].

    PubMed

    Tournamille, C

    2013-05-01

    The molecular basis of almost all antigens of the 33 blood group systems are known. These knowledge and the advent of the PCR technology have allowed the DNA-based genotyping in order to predict the presence or absence of a blood group antigen on the cell membrane of red blood cells. DNA genotyping is required in cases where red blood cells patient cannot be used for serological typing either after a recent transfusion or because of the presence of autoantibodies on the red blood cells. Numerous DNA assays are available to detect any nucleotide polymorphism on the genes encoding blood group antigens. The technologies have improved to answer quickly to any case of transfusion emergency and to limit the risk of DNA contamination in a molecular diagnostic laboratory. Some technologies are ready for high-throughput blood group genotyping. They will be used in the future to obtain a fully typed blood group card of each donor but also to detect blood donors with rare phenotypes to register them to the Banque Nationale de Sang de Phénotype Rare (BNSPR). PMID:23587623

  18. Molecular aspects of the endocytic pathway.

    PubMed Central

    Clague, M J

    1998-01-01

    Observation of the flow of material along the endocytic pathway has lead to the description of the basic architecture of the pathway and provided insight into the relationship between compartments. Significant advances have been made in the study of endocytic transport steps at the molecular level, of which studies of cargo selection, vesicle budding and membrane fusion events comprise the major part. Progress in this area has been driven by two approaches, yeast genetics and in vitro or cell-free assays, which reconstitute particular transport steps and allow biochemical manipulation. The complex protein machineries that control vesicle budding and fusion are significantly conserved between the secretory and endocytic pathways such that proteins that regulate particular steps are often part of a larger family of proteins which exercise a conserved function at other locations within the cell. Well characterized examples include vesicle coat proteins, rabs (small GTPases) and soluble N-ethylmaleimide-sensitive fusion protein (NSF) attachment protein (SNAP) receptors (SNAREs). Intracompartmental pH, lipid composition and cytoskeletal organization have also been identified as important determinants of the orderly flow of material within the endocytic pathway. PMID:9820800

  19. Molecular and Clinical Aspects of Angelman Syndrome

    PubMed Central

    Dagli, A.; Buiting, K.; Williams, C.A.

    2012-01-01

    The Angelman syndrome is caused by disruption of the UBE3A gene and is clinically delineated by the combination of severe mental disability, seizures, absent speech, hypermotoric and ataxic movements, and certain remarkable behaviors. Those with the syndrome have a predisposition toward apparent happiness and paroxysms of laughter, and this finding helps distinguish Angelman syndrome from other conditions involving severe developmental handicap. Accurate diagnosis rests on a combination of clinical criteria and molecular and/or cytogenetic testing. Analysis of parent-specific DNA methylation imprints in the critical 15q11.2–q13 genomic region identifies 75–80% of all individuals with the syndrome, including those with cytogenetic deletions, imprinting center defects and paternal uniparental disomy. In the remaining group, UBE3A sequence analysis identifies an additional percentage of patients, but 5–10% will remain who appear to have the major clinical phenotypic features but do not have any identifiable genetic abnormalities. Genetic counseling for recurrence risk is complicated because multiple genetic mechanisms can disrupt the UBE3A gene, and there is also a unique inheritance pattern associated with UBE3A imprinting. Angelman syndrome is a prototypical developmental syndrome due to its remarkable behavioral phenotype and because UBE3A is so crucial to normal synaptic function and neural plasticity. PMID:22670133

  20. Atomic and Molecular Aspects of Astronomical Spectra

    NASA Astrophysics Data System (ADS)

    Sochi, Taha

    2012-11-01

    In the first section we present the atomic part where a C2+ atomic target was prepared and used to generate theoretical data to investigate recombination lines arising from electron-ion collisions in thin plasma. R-matrix method was used to describe the C2+ plus electron system. Theoretical data concerning bound and autoionizing states were generated in the intermediate-coupling approximation. The data were used to generate dielectronic recombination data for C+ which include transition lines, oscillator strengths, radiative transition probabilities, emissivities and dielectronic recombination coefficients. The data were cast in a line list containing 6187 optically-allowed transitions which include many C II lines observed in astronomical spectra. This line list was used to analyze the spectra from a number of astronomical objects, mainly planetary nebulae, and identify their electron temperature. The electron temperature investigation was also extended to include free electron energy analysis to investigate the long-standing problem of discrepancy between the results of recombination and forbidden lines analysis and its possible connection to the electron distribution. In the second section we present the results of our molecular investigation; the generation of a comprehensive, calculated line list of frequencies and transition probabilities for H2D+. The line list contains over 22 million rotational-vibrational transitions occurring between more than 33 thousand energy levels and covers frequencies up to 18500 cm-1. About 15% of these levels are fully assigned with approximate rotational and vibrational quantum numbers. A temperature-dependent partition function and cooling function are presented. Temperature-dependent synthetic spectra for the temperatures T=100, 500, 1000 and 2000 K in the frequency range 0-10000 cm-1 were also generated and presented graphically.

  1. Molecular and Biotechnological Aspects of Microbial Proteases†

    PubMed Central

    Rao, Mala B.; Tanksale, Aparna M.; Ghatge, Mohini S.; Deshpande, Vasanti V.

    1998-01-01

    diverse origins have been analyzed with the aim of studying their evolutionary relationships. Despite the extensive research on several aspects of proteases, there is a paucity of knowledge about the roles that govern the diverse specificity of these enzymes. Deciphering these secrets would enable us to exploit proteases for their applications in biotechnology. PMID:9729602

  2. Molecular aspects of intestinal calcium absorption.

    PubMed

    Diaz de Barboza, Gabriela; Guizzardi, Solange; Tolosa de Talamoni, Nori

    2015-06-21

    Intestinal Ca(2+) absorption is a crucial physiological process for maintaining bone mineralization and Ca(2+) homeostasis. It occurs through the transcellular and paracellular pathways. The first route comprises 3 steps: the entrance of Ca(2+) across the brush border membranes (BBM) of enterocytes through epithelial Ca(2+) channels TRPV6, TRPV5, and Cav1.3; Ca(2+) movement from the BBM to the basolateral membranes by binding proteins with high Ca(2+) affinity (such as CB9k); and Ca(2+) extrusion into the blood. Plasma membrane Ca(2+) ATPase (PMCA1b) and sodium calcium exchanger (NCX1) are mainly involved in the exit of Ca(2+) from enterocytes. A novel molecule, the 4.1R protein, seems to be a partner of PMCA1b, since both molecules co-localize and interact. The paracellular pathway consists of Ca(2+) transport through transmembrane proteins of tight junction structures, such as claudins 2, 12, and 15. There is evidence of crosstalk between the transcellular and paracellular pathways in intestinal Ca(2+) transport. When intestinal oxidative stress is triggered, there is a decrease in the expression of several molecules of both pathways that inhibit intestinal Ca(2+) absorption. Normalization of redox status in the intestine with drugs such as quercetin, ursodeoxycholic acid, or melatonin return intestinal Ca(2+) transport to control values. Calcitriol [1,25(OH)₂D₃] is the major controlling hormone of intestinal Ca(2+) transport. It increases the gene and protein expression of most of the molecules involved in both pathways. PTH, thyroid hormones, estrogens, prolactin, growth hormone, and glucocorticoids apparently also regulate Ca(2+) transport by direct action, indirect mechanism mediated by the increase of renal 1,25(OH)₂D₃ production, or both. Different physiological conditions, such as growth, pregnancy, lactation, and aging, adjust intestinal Ca(2+) absorption according to Ca(2+) demands. Better knowledge of the molecular details of intestinal Ca(2

  3. Molecular aspects of intestinal calcium absorption

    PubMed Central

    Diaz de Barboza, Gabriela; Guizzardi, Solange; Tolosa de Talamoni, Nori

    2015-01-01

    Intestinal Ca2+ absorption is a crucial physiological process for maintaining bone mineralization and Ca2+ homeostasis. It occurs through the transcellular and paracellular pathways. The first route comprises 3 steps: the entrance of Ca2+ across the brush border membranes (BBM) of enterocytes through epithelial Ca2+ channels TRPV6, TRPV5, and Cav1.3; Ca2+ movement from the BBM to the basolateral membranes by binding proteins with high Ca2+ affinity (such as CB9k); and Ca2+ extrusion into the blood. Plasma membrane Ca2+ ATPase (PMCA1b) and sodium calcium exchanger (NCX1) are mainly involved in the exit of Ca2+ from enterocytes. A novel molecule, the 4.1R protein, seems to be a partner of PMCA1b, since both molecules co-localize and interact. The paracellular pathway consists of Ca2+ transport through transmembrane proteins of tight junction structures, such as claudins 2, 12, and 15. There is evidence of crosstalk between the transcellular and paracellular pathways in intestinal Ca2+ transport. When intestinal oxidative stress is triggered, there is a decrease in the expression of several molecules of both pathways that inhibit intestinal Ca2+ absorption. Normalization of redox status in the intestine with drugs such as quercetin, ursodeoxycholic acid, or melatonin return intestinal Ca2+ transport to control values. Calcitriol [1,25(OH)2D3] is the major controlling hormone of intestinal Ca2+ transport. It increases the gene and protein expression of most of the molecules involved in both pathways. PTH, thyroid hormones, estrogens, prolactin, growth hormone, and glucocorticoids apparently also regulate Ca2+ transport by direct action, indirect mechanism mediated by the increase of renal 1,25(OH)2D3 production, or both. Different physiological conditions, such as growth, pregnancy, lactation, and aging, adjust intestinal Ca2+ absorption according to Ca2+ demands. Better knowledge of the molecular details of intestinal Ca2+ absorption could lead to the development of

  4. Molecular aspects of intestinal calcium absorption.

    PubMed

    Diaz de Barboza, Gabriela; Guizzardi, Solange; Tolosa de Talamoni, Nori

    2015-06-21

    Intestinal Ca(2+) absorption is a crucial physiological process for maintaining bone mineralization and Ca(2+) homeostasis. It occurs through the transcellular and paracellular pathways. The first route comprises 3 steps: the entrance of Ca(2+) across the brush border membranes (BBM) of enterocytes through epithelial Ca(2+) channels TRPV6, TRPV5, and Cav1.3; Ca(2+) movement from the BBM to the basolateral membranes by binding proteins with high Ca(2+) affinity (such as CB9k); and Ca(2+) extrusion into the blood. Plasma membrane Ca(2+) ATPase (PMCA1b) and sodium calcium exchanger (NCX1) are mainly involved in the exit of Ca(2+) from enterocytes. A novel molecule, the 4.1R protein, seems to be a partner of PMCA1b, since both molecules co-localize and interact. The paracellular pathway consists of Ca(2+) transport through transmembrane proteins of tight junction structures, such as claudins 2, 12, and 15. There is evidence of crosstalk between the transcellular and paracellular pathways in intestinal Ca(2+) transport. When intestinal oxidative stress is triggered, there is a decrease in the expression of several molecules of both pathways that inhibit intestinal Ca(2+) absorption. Normalization of redox status in the intestine with drugs such as quercetin, ursodeoxycholic acid, or melatonin return intestinal Ca(2+) transport to control values. Calcitriol [1,25(OH)₂D₃] is the major controlling hormone of intestinal Ca(2+) transport. It increases the gene and protein expression of most of the molecules involved in both pathways. PTH, thyroid hormones, estrogens, prolactin, growth hormone, and glucocorticoids apparently also regulate Ca(2+) transport by direct action, indirect mechanism mediated by the increase of renal 1,25(OH)₂D₃ production, or both. Different physiological conditions, such as growth, pregnancy, lactation, and aging, adjust intestinal Ca(2+) absorption according to Ca(2+) demands. Better knowledge of the molecular details of intestinal Ca(2

  5. Molecular plasmonics for biology and nanomedicine

    PubMed Central

    Zheng, Yue Bing; Kiraly, Brian; Weiss, Paul S; Huang, Tony Jun

    2014-01-01

    The optical excitation of surface plasmons in metal nanoparticles leads to nanoscale spatial confinement of electromagnetic fields. The confined electromagnetic fields can generate intense, localized thermal energy and large near-field optical forces. The interaction between these effects and nearby molecules has led to the emerging field known as molecular plasmonics. Recent advances in molecular plasmonics have enabled novel optical materials and devices with applications in biology and nanomedicine. In this article, we categorize three main types of interactions between molecules and surface plasmons: optical, thermal and mechanical. Within the scope of each type of interaction, we will review applications of molecular plasmonics in biology and nanomedicine. We include a wide range of applications that involve sensing, spectral analysis, imaging, delivery, manipulation and heating of molecules, biomolecules or cells using plasmonic effects. We also briefly describe the physical principles of molecular plasmonics and progress in the nanofabrication, surface functionalization and bioconjugation of metal nanoparticles. PMID:22630155

  6. Molecular plasmonics for biology and nanomedicine.

    PubMed

    Zheng, Yue Bing; Kiraly, Brian; Weiss, Paul S; Huang, Tony Jun

    2012-05-01

    The optical excitation of surface plasmons in metal nanoparticles leads to nanoscale spatial confinement of electromagnetic fields. The confined electromagnetic fields can generate intense, localized thermal energy and large near-field optical forces. The interaction between these effects and nearby molecules has led to the emerging field known as molecular plasmonics. Recent advances in molecular plasmonics have enabled novel optical materials and devices with applications in biology and nanomedicine. In this article, we categorize three main types of interactions between molecules and surface plasmons: optical, thermal and mechanical. Within the scope of each type of interaction, we will review applications of molecular plasmonics in biology and nanomedicine. We include a wide range of applications that involve sensing, spectral analysis, imaging, delivery, manipulation and heating of molecules, biomolecules or cells using plasmonic effects. We also briefly describe the physical principles of molecular plasmonics and progress in the nanofabrication, surface functionalization and bioconjugation of metal nanoparticles.

  7. The molecular biology of galactosemia.

    PubMed

    Elsas, L J; Lai, K

    1998-01-01

    Classic galactosemia is an autosomal recessive disorder caused by the deficiency of galactose 1-phosphate uridyltransferase (GALT). Although the potentially lethal, neonatal hepatotoxic syndrome is prevented by newborn screening and galactose restriction, long-term outcome for older patients with galactosemia remains problematic. After the cloning and sequencing of the GALT gene, more than 130 mutations in the GALT gene have been associated with GALT deficiency; this review relates them to function and clinical outcome. Two common mutations, Q188R and K285N, account for more than 70% of G alleles in the white population and are associated with classic galactosemia and impaired GALT function. In the black population, S135L accounts for 62% of the alleles causing galactosemia and is associated with good outcomes. A large 5 kb deletion in the GALT gene is found in Ashkenazim Jews. The Duarte galactosemia variant is caused by N314D. Homozygosity for N314D reduces GALT activity to 50%. When either E203K or a 1721C-->T transition (Los Angeles variant) are present in cis with N314D, GALT activity reverts to normal. In this review, we discuss the structural biology of these mutations as they affect both the GALT enzyme and patient outcome.

  8. The Molecular Biology Database Collection: 2008 update

    PubMed Central

    Galperin, Michael Y.

    2008-01-01

    The Nucleic Acids Research online Molecular Biology Database Collection is a public repository that lists more than 1000 databases described in this and previous Nucleic Acids Research annual database issues, as well as a selection of molecular biology databases described in other journals. All databases included in this Collection are freely available to the public. The 2008 update includes 1078 databases, 110 more than the previous one. The links to more than 80 databases have been updated and 25 obsolete databases have been removed from the list. The complete database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oxfordjournals.org/. PMID:18025043

  9. BIONET: national computer resource for molecular biology.

    PubMed Central

    Smith, D H; Brutlag, D; Friedland, P; Kedes, L H

    1986-01-01

    This paper describes briefly the BIONET National Computer Resource for Molecular Biology. This presentation is intended as information for scientists in molecular biology and related disciplines who require access to computational methods for sequence analysis. We describe the goals, and the service and research opportunities offered to the community by BIONET, the relationship of BIONET to other national and regional resources, our recent efforts toward distribution of the resource to BIONET Satellites, and procedures for investigators to gain access to the Resource. PMID:3945548

  10. Frontiers of NMR in Molecular Biology

    SciTech Connect

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  11. Cellular and molecular aspects of plant adaptation to microgravity

    NASA Astrophysics Data System (ADS)

    Kordyum, Elizabeth; Kozeko, Liudmyla

    2016-07-01

    Elucidation of the range and mechanisms of the biological effects of microgravity is one of the urgent fundamental tasks of space and gravitational biology. The absence of forbidding on plant growth and development in orbital flight allows studying different aspects of plant adaptation to this factor that is directly connected with development of the technologies of bioregenerative life-support systems. Microgravity belongs to the environmental factors which cause adaptive reactions at the cellular and molecular levels in the range of physiological responses in the framework of genetically determined program of ontogenesis. It is known that cells of a multicellular organism not only take part in reactions of the organism but also carry out processes that maintain their integrity. In light of these principles, the problem of identification of biochemical, physiological and structural patterns that can have adaptive significance at the cellular and molecular levels in real and simulated microgravity is considered. It is pointed that plant cell responses in microgravity and under clinorotation vary according to growth phase, physiological state, and taxonomic position of the object. At the same time, the responses have, to some degree, a similar character reflecting the changes in the cell organelle functional load. The maintenance of the plasmalemma fluidity at the certain level, an activation of both the antioxidant system and expression of HSP genes, especially HSP70, under increasing reactive oxygen species, lipid peroxidation intensity and alteration in protein homeostasis, are a strategic paradigm of rapid (primary) cell adaptation to microgravity. In this sense, biological membranes, especially plasmalemma, and their properties and functions may be considered as the most sensitive indicators of the influence of gravity or altered gravity on a cell. The plasmalemma lipid bilayer is a border between the cell internal content and environment, so it is a mediator

  12. Salvia divinorum: toxicological aspects and analysis in human biological specimens.

    PubMed

    Margalho, Cláudia; Corte-Real, Francisco; López-Rivadulla, Manuel; Gallardo, Eugenia

    2016-07-01

    The identification and quantitation of the main psychoactive component of Salvia divinorum (salvinorin A) in biological specimens are crucial in forensic and clinical toxicology. Despite all the efforts made, its uncontrolled abuse has increased quickly, exposing its users' health to serious risks both in the short and long term. The use of alternative biological matrices in toxicological analyzes can be advantageous as complementary postmortem samples, or in situations when neither blood nor urine can be collected; they may be useful tools in those determinations, providing important information about prior exposure. The aim of this article is to present a brief summary of legal aspects of Salvia divinorum and salvinorin A, including the methods used for the determination of the latter in biological matrices. PMID:27277872

  13. The role of neutron scattering in molecular and cellular biology

    NASA Astrophysics Data System (ADS)

    Worcester, D. L.

    1982-09-01

    Neutron scattering measurements of biological macromolecules and materials have provided answers to numerous questions about molecular assemblies and arrangements. Studies of ribosomes, viruses, membranes, and other biological structures are reviewed, with emphasis on the importance of both deuterium labelling and contrast variation with H2O/D2O exchange. Although many studies of biological molecules have been made using contrast variation alone, it is the deuterium labelling experiments that have provided the most precise information and answers to major biological questions. This is largely the result of the low resolution of scattering data and the consequent rapid increase of information content that specific deuterium labelling provides. Procedures for specific deuterium labelling `in vivo' are described for recent work on myelin membranes together with basic aspects of such labelling useful for future research.

  14. Cellular and molecular aspects of plant adaptation to microgravity

    NASA Astrophysics Data System (ADS)

    Kordyum, Elizabeth; Kozeko, Liudmyla

    2016-07-01

    Elucidation of the range and mechanisms of the biological effects of microgravity is one of the urgent fundamental tasks of space and gravitational biology. The absence of forbidding on plant growth and development in orbital flight allows studying different aspects of plant adaptation to this factor that is directly connected with development of the technologies of bioregenerative life-support systems. Microgravity belongs to the environmental factors which cause adaptive reactions at the cellular and molecular levels in the range of physiological responses in the framework of genetically determined program of ontogenesis. It is known that cells of a multicellular organism not only take part in reactions of the organism but also carry out processes that maintain their integrity. In light of these principles, the problem of identification of biochemical, physiological and structural patterns that can have adaptive significance at the cellular and molecular levels in real and simulated microgravity is considered. It is pointed that plant cell responses in microgravity and under clinorotation vary according to growth phase, physiological state, and taxonomic position of the object. At the same time, the responses have, to some degree, a similar character reflecting the changes in the cell organelle functional load. The maintenance of the plasmalemma fluidity at the certain level, an activation of both the antioxidant system and expression of HSP genes, especially HSP70, under increasing reactive oxygen species, lipid peroxidation intensity and alteration in protein homeostasis, are a strategic paradigm of rapid (primary) cell adaptation to microgravity. In this sense, biological membranes, especially plasmalemma, and their properties and functions may be considered as the most sensitive indicators of the influence of gravity or altered gravity on a cell. The plasmalemma lipid bilayer is a border between the cell internal content and environment, so it is a mediator

  15. Molecular biology of Hendra and Nipah viruses.

    PubMed

    Wang, L; Harcourt, B H; Yu, M; Tamin, A; Rota, P A; Bellini, W J; Eaton, B T

    2001-04-01

    The structure and genetic organization of Hendra and Nipah viruses places them in the subfamily Paramyxovirinae. However, low homology with other subfamily members and several novel biological and molecular features such as genome length and F(0 )cleavage site suggest classification in a new genus within the Paramyxovirinae.

  16. Molecular Biology and Biotechnology of Bacteriophage

    NASA Astrophysics Data System (ADS)

    Onodera, Kazukiyo

    The development of the molecular biology of bacteriophage such as T4, lambda and filamentous phages was described and the process that the fundamental knowledge obtained in this field has subsequently led us to the technology of phage display was introduced.

  17. Systematic Representation of Molecular Biology Knowledge.

    ERIC Educational Resources Information Center

    Fisher, Kathleen M.

    A small set of relationships has been identified which appears to be sufficient for describing all molecular and cellular reactions and structures discussed in an introductory biology course. A precise definition has been developed for each relationship. These 20 relationships are of four types: (1) analytical; (2) spatial; (3) temporal; and (4)…

  18. Molecular profiles to biology and pathways: a systems biology approach.

    PubMed

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  19. Molecular biology of thermosensory transduction in C. elegans.

    PubMed

    Aoki, Ichiro; Mori, Ikue

    2015-10-01

    As the environmental temperature prominently influences diverse biological aspects of the animals, thermosensation and the subsequent information processing in the nervous system has attracted much attention in biology. Thermotaxis in the nematode Caenorhabditis elegans is an ideal behavioral paradigm by which to address the molecular mechanism underlying thermosensory transduction. Molecular genetic analysis in combination with other physiological and behavioral studies revealed that sensation of ambient temperature is mediated mainly by cyclic guanosine monophosphate (cGMP) signaling in thermosensory neurons. The information of the previously perceived temperature is also stored within the thermosensory neurons, and the consequence of the comparison between the past and the present temperature is conveyed to the downstream interneurons to further regulate the motor-circuits that encode the locomotion.

  20. Molecular knots in biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lim, Nicole C. H.; Jackson, Sophie E.

    2015-09-01

    Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

  1. Molecular biology of the human brain

    SciTech Connect

    Jones, E.G.

    1988-01-01

    This book examines new methods of molecular biology that are providing valuable insights into the human brain, the genes that govern its assembly and function, and the many genetic defects that cause neurological diseases such as Alzheimer's, Cri du Chat syndrome, Huntington's disease, and bipolar depression disorder. In addition, the book reviews techniques in molecular neurobiological research, including the use of affinity reagents, chimeric receptors, and site-directed mutagenesis in localizing the ion channel and cholinergic binding site, and the application of somatic cell genetics in isolating specific chromosomes or chromosomal segments.

  2. Informational Aspects of Isotopic Diversity in Biology and Medicine

    NASA Astrophysics Data System (ADS)

    Berezin, Alexander A.

    2004-10-01

    Use of stable and radioactive isotopes in biology and medicine is intensive, yet informational aspects of isotopes as such are largely neglected (A.A.Berezin, J.Theor.Biol.,1992). Classical distinguishability (``labelability'') of isotopes allows for pattern generation dynamics. Quantum mechanically advantages of isotopicity (diversity of stable isotopes) arise from (almost perfect) degeneracy of various isotopic configurations; this in turn allows for isotopic sweeps (hoppings) by resonance neutron tunneling (Eccles mechanism). Isotopic variations of de Broglie wavelength affect quantum tunneling, diffusivity, magnetic interactions (e.g. by Lorentz force), etc. Ergodicity principle (all isoenergetic states are eventually accessed) implies possibility of fast scanning of library of morphogenetic patterns (cf metaphors of universal ``Platonic'' Library of Patterns: e.g. J.L.Borges, R.Sheldrake) with subsequent Darwinian reinforcement (e.g. by targeted mutations) of evolutionary advantageous patterns and structures. Isotopic shifts in organisms, from viruses and protozoa to mammalians, (e.g. DNA with enriched or depleted C-13) are tools to elucidate possible informational (e.g. Shannon entropy) role of isotopicity in genetic (e.g. evolutionary and morphological), dynamical (e.g. physiological and neurological) as well as medical (e.g. carcinogenesis, aging) aspects of biology and medicine.

  3. The Boltzmann equation in molecular biology.

    PubMed

    Dubois, Jean-Marc; Ouanounou, Gilles; Rouzaire-Dubois, Béatrice

    2009-01-01

    In the 1870's, Ludwig Boltzmann proposed a simple equation that was based on the notion of atoms and molecules and that defined the probability of finding a molecule in a given state. Several years later, the Boltzmann equation was developed and used to calculate the equilibrium potential of an ion species that is permeant through membrane channels and to describe conformational changes of biological molecules involved in different mechanisms including: open probability of ion channels, effect of molecular crowding on protein conformation, biochemical reactions and cell proliferation. The aim of this review is to trace the history of the developments of the Boltzmann equation that account for the behaviour of proteins involved in molecular biology and physiology.

  4. Molecular neurodegeneration: basic biology and disease pathways.

    PubMed

    Vassar, Robert; Zheng, Hui

    2014-09-23

    The field of neurodegeneration research has been advancing rapidly over the past few years, and has provided intriguing new insights into the normal physiological functions and pathogenic roles of a wide range of molecules associated with several devastating neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, Huntington's disease, and Down syndrome. Recent developments have also facilitated initial efforts to translate preclinical discoveries toward novel therapeutic approaches and clinical trials in humans. These recent developments are reviewed in the current Review Series on "Molecular Neurodegeneration: Basic Biology and Disease Pathways" in a number of state-of-the-art manuscripts that cover themes presented at the Third International Conference on Molecular Neurodegeneration: "Basic biology and disease pathways" held in Cannes, France, September, 2013.

  5. 2012 PLANT MOLECULAR BIOLOGY GORDON RESEARCH CONFERENCE, JULY 15-20, 2012

    SciTech Connect

    Sussman, Michael

    2013-07-20

    The 2012 Gordon Conference on Plant Molecular Biology will present cutting-edge research on molecular aspects of plant growth and development, with particular emphasis on recent discoveries in molecular mechanisms involved with plant signaling systems. The Conference will feature a wide range of topics in plant molecular biology including hormone receptors and early events in hormone signaling, plant perception of and response to plant pathogen and symbionts, as well as technological and biological aspects of epigenomics particularly as it relates to signaling systems that regulate plant growth and development. Genomic approaches to plant signaling will be emphasized, including genomic profiling technologies for quantifying various biological subsystems, such as the epigenome, transcriptome, phosphorylome, and metabolome. The meeting will include an important session devoted to answering the question, "What are the biological and technological limits of plant breeding/genetics, and how can they be solved"?

  6. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  7. INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY (ISMB)

    SciTech Connect

    Debra Goldberg; Matthew Hibbs; Lukas Kall; Ravikumar Komandurglayavilli; Shaun Mahony; Voichita Marinescu; Itay Mayrose; Vladimir Minin; Yossef Neeman; Guy Nimrod; Marian Novotny; Stephen Opiyo; Elon Portugaly; Tali Sadka; Noboru Sakabe; Indra Sarkar; Marc Schaub; Paul Shafer; Olena Shmygelska; Gregory Singer; Yun Song; Bhattacharya Soumyaroop; Michael Stadler; Pooja Strope; Rong Su; Yuval Tabach; Hongseok Tae; Todd Taylor; Michael Terribilini; Asha Thomas; Nam Tran; Tsai-Tien Tseng; Akshay Vashist; Parthiban Vijaya; Kai Wang; Ting Wang; Lai Wei; Yong Woo; Chunlei Wu; Yoshihiro Yamanishi; Changhui Yan; Jack Yang; Mary Yang; Ping Ye; Miao Zhang

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on “intelligent systems” and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  8. Boswellic acids: biological actions and molecular targets.

    PubMed

    Poeckel, Daniel; Werz, Oliver

    2006-01-01

    Gum resin extracts of Boswellia species have been traditionally applied in folk medicine for centuries to treat various chronic inflammatory diseases, and experimental data from animal models and studies with human subjects confirmed the potential of B. spec extracts for the treatment of not only inflammation but also of cancer. Analysis of the ingredients of these extracts revealed that the pentacyclic triterpenes boswellic acids (BAs) possess biological activities and appear to be responsible for the respective pharmacological actions. Approaches in order to elucidate the molecular mechanisms underlying the biological effects of BAs identified 5-lipoxygenase, human leukocyte elastase, toposiomerase I and II, as well as IkappaB kinases as molecular targets of BAs. Moreover, it was shown that depending on the cell type and the structure of the BAs, the compounds differentially interfere with signal transduction pathways including Ca(2+/-) and MAPK signaling in various blood cells, related to functional cellular processes important for inflammatory reactions and tumor growth. This review summarizes the biological actions of BAs on the cellular and molecular level and attempts to put the data into perspective of the beneficial effects manifested in animal studies and trials with human subjects related to inflammation and cancer.

  9. The Molecular Biology Database Collection: 2002 update

    PubMed Central

    Baxevanis, Andreas D.

    2002-01-01

    The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org. PMID:11752241

  10. The Molecular Biology Database Collection: 2003 update

    PubMed Central

    Baxevanis, Andreas D.

    2003-01-01

    The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the jumping-off point from which to find specialized databases that may be of use in advancing biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in this Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org. PMID:12519937

  11. Can molecular cell biology explain chromosome motions?

    PubMed Central

    2011-01-01

    Background Mitotic chromosome motions have recently been correlated with electrostatic forces, but a lingering "molecular cell biology" paradigm persists, proposing binding and release proteins or molecular geometries for force generation. Results Pole-facing kinetochore plates manifest positive charges and interact with negatively charged microtubule ends providing the motive force for poleward chromosome motions by classical electrostatics. This conceptual scheme explains dynamic tracking/coupling of kinetochores to microtubules and the simultaneous depolymerization of kinetochore microtubules as poleward force is generated. Conclusion We question here why cells would prefer complex molecular mechanisms to move chromosomes when direct electrostatic interactions between known bound charge distributions can accomplish the same task much more simply. PMID:21619650

  12. A complex systems approach to computational molecular biology

    SciTech Connect

    Lapedes, A. |

    1993-09-01

    We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.

  13. Biological and Clinical Aspects of Lanthanide Coordination Compounds

    PubMed Central

    Misra, Sudhindra N.; M., Indira Devi; Shukla, Ram S.

    2004-01-01

    The coordinating chemistry of lanthanides, relevant to the biological, biochemical and medical aspects, makes a significant contribution to understanding the basis of application of lanthanides, particularly in biological and medical systems. The importance of the applications of lanthanides, as an excellent diagnostic and prognostic probe in clinical diagnostics, and an anticancer material, is remarkably increasing. Lanthanide complexes based X-ray contrast imaging and lanthanide chelates based contrast enhancing agents for magnetic resonance imaging (MRI) are being excessively used in radiological analysis in our body systems. The most important property of the chelating agents, in lanthanide chelate complex, is its ability to alter the behaviour of lanthanide ion with which it binds in biological systems, and the chelation markedly modifies the biodistribution and excretion profile of the lanthanide ions. The chelating agents, especially aminopoly carboxylic acids, being hydrophilic, increase the proportion of their complex excreted from complexed lanthanide ion form biological systems. Lanthanide polyamino carboxylate-chelate complexes are used as contrast enhancing agents for Magnetic Resonance Imaging. Conjugation of antibodies and other tissue specific molecules to lanthanide chelates has led to a new type of specific MRI contrast agents and their conjugated MRI contrast agents with improved relaxivity, functioning in the body similar to drugs. Many specific features of contrast agent assisted MRI make it particularly effective for musculoskeletal and cerebrospinal imaging. Lanthanide-chelate contrast agents are effectively used in clinical diagnostic investigations involving cerebrospinal diseases and in evaluation of central nervous system. Chelated lanthanide complexes shift reagent aided 23Na NMR spectroscopic analysis is used in cellular, tissue and whole organ systems. PMID:18365075

  14. The molecular biology of vertebrate olfaction.

    PubMed

    Hayden, Sara; Teeling, Emma C

    2014-11-01

    The importance of chemosensation for vertebrates is reflected in the vast and variable nature of their chemosensory tissues, neurons, and genes, which we explore in this review. Immense progress has been made in elucidating the molecular biology of olfaction since the discovery of the olfactory receptor genes by Buck and Axel, which eventually won the authors the Nobel Prize. In particular, research linking odor ligands to olfactory receptors (ORs) is truly revolutionizing our understanding of how a large but limited number of chemosensory receptors can allow us to perceive the massive diversity of odors in our habitat. This research is providing insight into the evolution of genomes and providing the raw data needed to explore links between genotype and phenotype, still a grand challenge in biology. Research into olfaction is still developing and will no doubt continue until we have a clear understanding of how all odors are detected and the evolutionary forces that have molded the chemosensory subgenome in vertebrates. This knowledge will not only be a huge step in elucidating olfactory function, advancing scientific knowledge and techniques, but there are also commercial applications for this research. This review focuses on the molecular basis of chemosensation, particularly olfaction, its evolution across vertebrates and the recent molecular advances linking odors to their cognate receptors. PMID:25312375

  15. The molecular biology of vertebrate olfaction.

    PubMed

    Hayden, Sara; Teeling, Emma C

    2014-11-01

    The importance of chemosensation for vertebrates is reflected in the vast and variable nature of their chemosensory tissues, neurons, and genes, which we explore in this review. Immense progress has been made in elucidating the molecular biology of olfaction since the discovery of the olfactory receptor genes by Buck and Axel, which eventually won the authors the Nobel Prize. In particular, research linking odor ligands to olfactory receptors (ORs) is truly revolutionizing our understanding of how a large but limited number of chemosensory receptors can allow us to perceive the massive diversity of odors in our habitat. This research is providing insight into the evolution of genomes and providing the raw data needed to explore links between genotype and phenotype, still a grand challenge in biology. Research into olfaction is still developing and will no doubt continue until we have a clear understanding of how all odors are detected and the evolutionary forces that have molded the chemosensory subgenome in vertebrates. This knowledge will not only be a huge step in elucidating olfactory function, advancing scientific knowledge and techniques, but there are also commercial applications for this research. This review focuses on the molecular basis of chemosensation, particularly olfaction, its evolution across vertebrates and the recent molecular advances linking odors to their cognate receptors.

  16. A comparative cellular and molecular biology of longevity database.

    PubMed

    Stuart, Jeffrey A; Liang, Ping; Luo, Xuemei; Page, Melissa M; Gallagher, Emily J; Christoff, Casey A; Robb, Ellen L

    2013-10-01

    Discovering key cellular and molecular traits that promote longevity is a major goal of aging and longevity research. One experimental strategy is to determine which traits have been selected during the evolution of longevity in naturally long-lived animal species. This comparative approach has been applied to lifespan research for nearly four decades, yielding hundreds of datasets describing aspects of cell and molecular biology hypothesized to relate to animal longevity. Here, we introduce a Comparative Cellular and Molecular Biology of Longevity Database, available at ( http://genomics.brocku.ca/ccmbl/ ), as a compendium of comparative cell and molecular data presented in the context of longevity. This open access database will facilitate the meta-analysis of amalgamated datasets using standardized maximum lifespan (MLSP) data (from AnAge). The first edition contains over 800 data records describing experimental measurements of cellular stress resistance, reactive oxygen species metabolism, membrane composition, protein homeostasis, and genome homeostasis as they relate to vertebrate species MLSP. The purpose of this review is to introduce the database and briefly demonstrate its use in the meta-analysis of combined datasets.

  17. Molecular cell biology and molecular genetics of Histoplasma capsulatum.

    PubMed

    Ignatov, Atanas; Keath, Elizabeth J

    2002-10-01

    Histoplasma capsulatum is a dimorphic ascomycete which is capable of producing a broad spectrum of disease ranging from mild asymptomatic, pulmonary illness to severe, life-threatening systemic mycosis. Regulatory mechanisms that use temperature and other environmental cues are paramount to the successful adaptation of the organism as an effective intracellular pathogenic yeast. Although the biochemistry and phenomenology of reversible morphogenesis have been well examined in Histoplasma, the identification and functional characterization of genes and their products that are required for early establishment or maintenance of the parasitic yeast phase in intracellular host compartments have only recently been fruitful. Advances in the molecular biology of Histoplasma, including approaches to introduce telomeric plasmids, reporter fusion constructs, and gene disruption cassettes into the fungus are poised to solidify the pre-eminence of this fungus as a model system which can be applied to other dimorphic fungal pathogens that exhibit similar cellular and immunological complexities. This review centers on recent developments in the molecular cell biology and molecular genetics of Histoplasma capsulatum that provide important new avenues for examining the mold-to-yeast phase transition beyond the historical, binary view of dimorphism and the implications that these successful approaches may have on seminal issues in fungal pathogenesis. PMID:12452281

  18. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    SciTech Connect

    Dr. Julie Maupin- Furlow

    2009-07-26

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  19. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    SciTech Connect

    Keneth Stedman

    2011-08-05

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  20. Molecular Biological Methods in Environmental Engineering.

    PubMed

    Zhang, Guocai; Wei, Li; Chang, Chein-Chi; Zhang, Yuhua; Wei, Dong

    2016-10-01

    Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification. 454 high throughput sequencing and Illumina MiSeq sequencing have been the primary and widely recognized methods to analyze the microbial. This review will provide environmental engineers and microbiologists an overview of important advancements in molecular techniques and highlight the application of these methods in diverse environments. PMID:27620079

  1. 2007 Archaea: Ecology, Metabolism and Molecular Biology

    SciTech Connect

    Imke Schroeder Nancy Ryan Gray

    2008-09-18

    The Archaea are a fascinating and diverse group of prokaryotic organisms with deep roots overlapping those of eukaryotes. The focus of this GRC conference, 'Archaea: Ecology Metabolism & Molecular Biology', expands on a number of emerging topics highlighting the evolution and composition of microbial communities and novel archaeal species, their impact on the environment, archaeal metabolism, and research that stems from sequence analysis of archaeal genomes. The strength of this conference lies in its ability to couple reputable areas with new scientific topics in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  2. Genetics and molecular biology of hypotension

    NASA Technical Reports Server (NTRS)

    Robertson, D.

    1994-01-01

    Major strides in the molecular biology of essential hypertension are currently underway. This has tended to obscure the fact that a number of inherited disorders associated with low blood pressure exist and that these diseases may have milder and underrecognized phenotypes that contribute importantly to blood pressure variation in the general population. This review highlights some of the gene products that, if abnormal, could cause hypotension in some individuals. Diseases due to abnormalities in the catecholamine enzymes are discussed in detail. It is likely that genetic abnormalities with hypotensive phenotypes will be as interesting and diverse as those that give rise to hypertensive disorders.

  3. Molecular biology approaches in bioadhesion research

    PubMed Central

    Rodrigues, Marcelo; Lengerer, Birgit; Ostermann, Thomas

    2014-01-01

    Summary The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1) generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2) setting up a BLAST search facility, (3) perform an in situ hybridization screen, and (4) functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives. PMID:25161834

  4. Rhabdomyosarcoma: Advances in Molecular and Cellular Biology

    PubMed Central

    Sun, Xin; Guo, Wei; Shen, Jacson K.; Mankin, Henry J.; Hornicek, Francis J.; Duan, Zhenfeng

    2015-01-01

    Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy in childhood and adolescence. The two major histological subtypes of RMS are alveolar RMS, driven by the fusion protein PAX3-FKHR or PAX7-FKHR, and embryonic RMS, which is usually genetically heterogeneous. The prognosis of RMS has improved in the past several decades due to multidisciplinary care. However, in recent years, the treatment of patients with metastatic or refractory RMS has reached a plateau. Thus, to improve the survival rate of RMS patients and their overall well-being, further understanding of the molecular and cellular biology of RMS and identification of novel therapeutic targets are imperative. In this review, we describe the most recent discoveries in the molecular and cellular biology of RMS, including alterations in oncogenic pathways, miRNA (miR), in vivo models, stem cells, and important signal transduction cascades implicated in the development and progression of RMS. Furthermore, we discuss novel potential targeted therapies that may improve the current treatment of RMS. PMID:26420980

  5. PATHOLOGIC AND IMPENDING FRACTURES: BIOLOGICAL AND CLINICAL ASPECTS.

    PubMed

    Spinelli, M S; Campi, S; Sacchetti, F M; Rossi, B; Di Martino, A; Giannini, S; Piccioli, A

    2015-01-01

    Bone metastases from carcinomas are epidemiologically rising because of the increased survival rate of oncologic patients, related to several factors such as improvement of primary and secondary screening, advancement of medical research and technology and the better understanding of mechanisms underlying bone metastases origination from primary tumor. Skeletal Related Events (SREs) can seriously affect quality of life in patients with metastatic disease. These events include the necessity of radiotherapy or bone surgery, malignant hypercalcemia, pathologic fractures and spinal cord compression. Among the SREs, pathologic fractures are the most disabling events and represent an emergency in these delicate patients. A pathologic fracture is defined as a fracture that occurs at the level of a pre-existing bone lesion (that is often a tumor), spontaneously or as the result of low-energy trauma (1). The pre-existence of the metastatic lesion in the bone, its evaluation and the assessment of progression can make these complications predictable and preventable. Pathologic fractures imply several severe consequences, including patient immobilization (in the case of fractures involving the lower limbs), loss of autonomy, anaemia, need of blood transfusion, discontinuation of medical therapies or radiotherapy and protracted hospitalization. Secondary effects of prolonged immobilization and loss of autonomy further lengthen this list of complications in patients who are already significantly limited in their activities. In the present paper, the authors present a review on the main aspects involved in bone metastastic disease: biology, quality of life, economic impact and survival. PMID:26652492

  6. Proteomics in reproductive biology: beacon for unraveling the molecular complexities.

    PubMed

    Upadhyay, Rahul D; Balasinor, N H; Kumar, Anita V; Sachdeva, Geetanjali; Parte, Priyanka; Dumasia, Kushaan

    2013-01-01

    Proteomics, an interface of rapidly evolving advances in physics and biology, is rapidly developing and expanding its potential applications to molecular and cellular biology. Application of proteomics tools has contributed towards identification of relevant protein biomarkers that can potentially change the strategies for early diagnosis and treatment of several diseases. The emergence of powerful mass spectrometry-based proteomics technique has added a new dimension to the field of medical research in liver, heart diseases and certain forms of cancer. Most proteomics tools are also being used to study physiological and pathological events related to reproductive biology. There have been attempts to generate the proteomes of testes, sperm, seminal fluid, epididymis, oocyte, and endometrium from reproductive disease patients. Here, we have reviewed proteomics based investigations in humans over the last decade, which focus on delineating the mechanism underlying various reproductive events such as spermatogenesis, oogenesis, endometriosis, polycystic ovary syndrome, embryo development. The challenge is to harness new technologies like 2-DE, DIGE, MALDI-MS, SELDI-MS, MUDPIT, LC-MS etc., to a greater extent to develop widely applicable clinical tools in understanding molecular aspects of reproduction both in health and disease.

  7. The molecular biology capstone assessment: a concept assessment for upper-division molecular biology students.

    PubMed

    Couch, Brian A; Wood, William B; Knight, Jennifer K

    2015-03-01

    Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty reviews and response validation through student interviews. The final assessment was taken online by 504 students in upper-division courses at seven institutions. Data from this administration indicate that the MBCA has acceptable levels of internal reliability (α=0.80) and test-retest stability (r=0.93). Students achieved a wide range of scores with a 67% overall average. Performance results suggest that students have an incomplete understanding of many molecular biology concepts and continue to hold incorrect conceptions previously documented among introductory-level students. By pinpointing areas of conceptual difficulty, the MBCA can provide faculty members with guidance for improving undergraduate biology programs.

  8. The Molecular Biology Capstone Assessment: A Concept Assessment for Upper-Division Molecular Biology Students

    PubMed Central

    Couch, Brian A.; Wood, William B.; Knight, Jennifer K.

    2015-01-01

    Measuring students’ conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty reviews and response validation through student interviews. The final assessment was taken online by 504 students in upper-division courses at seven institutions. Data from this administration indicate that the MBCA has acceptable levels of internal reliability (α = 0.80) and test–retest stability (r = 0.93). Students achieved a wide range of scores with a 67% overall average. Performance results suggest that students have an incomplete understanding of many molecular biology concepts and continue to hold incorrect conceptions previously documented among introductory-level students. By pinpointing areas of conceptual difficulty, the MBCA can provide faculty members with guidance for improving undergraduate biology programs. PMID:25713098

  9. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    PubMed

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  10. Molecular and Clinical Aspects of Drug-induced Gingival Overgrowth

    PubMed Central

    Kantarci, A.

    2015-01-01

    Drug-induced gingival overgrowth is a tissue-specific condition and is estimated to affect approximately one million North Americans. Lesions occur principally as side-effects from phenytoin, nifedipine, or ciclosporin therapy in approximately half of the people who take these agents. Due to new indications for these drugs, their use continues to grow. Here, we review the molecular and cellular characteristics of human gingival overgrowth lesions and highlight how they differ considerably as a function of the causative drug. Analyses of molecular signaling pathways in cultured human gingival fibroblasts have provided evidence for their unique aspects compared with fibroblasts from the lung and kidney. These findings provide insights into both the basis for tissue specificity and into possible therapeutic opportunities which are reviewed here. Although ciclosporin-induced gingival overgrowth lesions exhibit principally the presence of inflammation and little fibrosis, nifedipine- and especially phenytoin-induced lesions are highly fibrotic. The increased expression of markers of gingival fibrosis, particularly CCN2 [also known as connective tissue growth factor (CTGF)], markers of epithelial to mesenchymal transition, and more recently periostin and members of the lysyl oxidase family of enzymes have been documented in phenytoin or nifedipine lesions. Some oral fibrotic conditions such as leukoplakia and oral submucous fibrosis, after subsequent additional genetic damage, can develop into oral cancer. Since many pathways are shared, the study of gingival fibrosis and comparisons with characteristics and molecular drivers of oral cancer would likely enhance understandings and functional roles of molecular drivers of these oral pathologies. PMID:25680368

  11. Teaching Molecular Biological Techniques in a Research Content

    ERIC Educational Resources Information Center

    Stiller, John W.; Coggins, T. Chad

    2006-01-01

    Molecular biological methods, such as the polymerase chain reaction (PCR) and gel electrophoresis, are now commonly taught to students in introductory biology courses at the college and even high school levels. This often includes hands-on experience with one or more molecular techniques as part of a general biology laboratory. To assure that most…

  12. [Neuroblastoma. Current clinical and therapeutic aspects. Contributions of modern biology].

    PubMed

    Hartmann, O; Favrot, M C

    1993-11-01

    Neuroblastoma is a malignant tumour of the sympathetic tissue observed in children, generally before 6 years and before 1 year in one-third of the cases. In most cases the primary tumour lies in the retroperitoneal region, and in particular in the adrenal gland. Metastases affect the bones and bone-marrow after the age of 1 year and the liver in infants. Children whose metastases are present at the time of diagnosis are the most numerous. The therapeutic problems posed by non-metastatic forms are almost exclusively due to the difficulties encountered in complete excision of the tumour. For this reason, tumour reduction by preoperative chemotherapy plays a large role in the therapeutic approach. The prognosis of metastatic forms is totally different in infants and in older children: in infants, hepatic metastases without bone lesions have a favourable prognosis as a rule and sometimes regress without treatment. In older children, the usual osteomedullary damage still has a very sombre prognosis despite the recent therapeutic advances due to high-dose chemotherapy with bone-marrow transplantation. Cytogenetic studies and molecular biology have improved our understanding of these differences in the outcome of the disease. Amplification of Nmy cellular oncogene, ploidy and chromosome 1 short-arm deletion are essential prognostic factors in this particular tumour.

  13. A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

    ERIC Educational Resources Information Center

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

  14. Molecular aspects of stress-gene regulation during spaceflight

    NASA Technical Reports Server (NTRS)

    Paul, Anna-Lisa; Ferl, Robert J.

    2002-01-01

    Spaceflight-associated stress has been the topic of investigation since the first terrestrial organisms were exposed to this unique environment. Organisms that evolved under the selection pressures of earth-normal environments can perceive spaceflight as a stress, either directly because gravity influences an intrinsic biological process, or indirectly because of secondary effects imparted by spaceflight upon environmental conditions. Different organisms and even different organs within an organism adapt to a spaceflight environment with a diversity of tactics. Plants are keenly sensitive to gravity for directed development, and are also sensitive to other stresses associated with closed-system spaceflight environments. Within the past decade, the tools of molecular biology have begun to provide a sophisticated evaluation of spaceflight-associated stress and the genetic responses that accompany metabolic adaptation to spaceflight.

  15. 2010 Plant Molecular Biology Gordon Research Conference

    SciTech Connect

    Michael Sussman

    2010-07-23

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.

  16. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.

    1990-10-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka (Oryzias latipes), as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.

  17. Unconventional biological threats and the molecular biological response to biological threats.

    PubMed

    Greenfield, Ronald A; Lutz, Brock D; Huycke, Mark M; Gilmore, Michael S

    2002-06-01

    This article concludes this symposium on potential agents of warfare and terrorism with discussion of 3 topics. First, influenza A virus is discussed as a potential biological weapon. Although it does not receive much attention in this role, the potential for mass casualties and public panic certainly exist if an epidemic of a virulent influenza A virus were initiated. Second, agroterrorism, terrorism directed at livestock or poultry or crops, is briefly discussed. Finally, the potential role of techniques of modern molecular biology to create new agents for bioterrorism or enhance the terrorist potential of available agents, and the known roles of these techniques in defense against biological warfare or terrorism are discussed.

  18. Third international congress of plant molecular biology: Molecular biology of plant growth and development

    SciTech Connect

    Hallick, R.B.

    1995-02-01

    The Congress was held October 6-11, 1991 in Tucson with approximately 3000 scientists attending and over 300 oral presentations and 1800 posters. Plant molecular biology is one of the most rapidly developing areas of the biological sciences. Recent advances in the ability to isolate genes, to study their expression, and to create transgenic plants have had a major impact on our understanding of the many fundamental plant processes. In addition, new approaches have been created to improve plants for agricultural purposes. This is a book of presentation and posters from the conference.

  19. [Progress in molecular biology of a semi-mangrove, Millettia pinnata].

    PubMed

    Huang, Jianzi; Zhang, Wanke; Huang, Rongfeng; Zheng, Yizhi

    2015-04-01

    Millettia pinnata L. is a leguminous tree with great potential in biodiesel applications and also a typical semi-mangrove. In this review, we presented several aspects about the recent research progress in molecular biology of M. pinnata. We descrived several types of molecular markers used to assess the genetic diversity and phylogeny of this species, genome and transcriptome analyses based on high-throughput sequencing platform accomplished for this species, and several gene and genomic sequences of this species isolated for further research. Finally, based on the current research progress, we proposed some orientations for future molecular biology research on M. pinnata. PMID:26380403

  20. [Progress in molecular biology of a semi-mangrove, Millettia pinnata].

    PubMed

    Huang, Jianzi; Zhang, Wanke; Huang, Rongfeng; Zheng, Yizhi

    2015-04-01

    Millettia pinnata L. is a leguminous tree with great potential in biodiesel applications and also a typical semi-mangrove. In this review, we presented several aspects about the recent research progress in molecular biology of M. pinnata. We descrived several types of molecular markers used to assess the genetic diversity and phylogeny of this species, genome and transcriptome analyses based on high-throughput sequencing platform accomplished for this species, and several gene and genomic sequences of this species isolated for further research. Finally, based on the current research progress, we proposed some orientations for future molecular biology research on M. pinnata.

  1. 2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012

    SciTech Connect

    Judith Berman

    2012-06-22

    The Gordon Research Conference on CELLULAR & MOLECULAR FUNGAL BIOLOGY was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

  2. Molecular Aspects of Bone Resorption in β-Thalassemia Major

    PubMed Central

    Saki, Najmaldin; Abroun, Saeid; Salari, Fatemeh; Rahim, Fakher; Shahjahani, Mohammad; Javad, Mohammadi-Asl

    2015-01-01

    β-thalassemia is the most common single gene disorder worldwide, in which hemoglobin β-chain production is decreased. Today, the life expectancy of thalassemic patients is increased because of a variety of treatment methods; however treatment related complications have also increased. The most common side effect is osteoporosis, which usually occurs in early adulthood as a consequence of increased bone resorption. Increased bone resorption mainly results from factors such as delayed puberty, diabetes mellitus, hypothyroidism, ineffective hematopoiesis as well as hyperplasia of the bone marrow, parathyroid gland dysfunction, toxic effect of iron on osteoblasts, growth hormone (GH) and insulin-like growth factor-1 (IGF-1) deficiency. These factors disrupt the balance between osteoblasts and osteoclasts by interfering with various molecular mechanisms and result in decreased bone density. Given the high prevalence of osteopenia and osteoporosis in thalassemic patients and complexity of their development process, the goal of this review is to evaluate the molecular aspects involved in osteopenia and osteoporosis in thalassemic patients, which may be useful for therapeutic purposes. PMID:26199898

  3. Molecular biology and regulation of methane monooxygenase.

    PubMed

    Murrell, J C; Gilbert, B; McDonald, I R

    2000-01-01

    Methanotrophs are ubiquitous in the environment and play an important role in mitigating global warming due to methane. They are also potentially interesting for industrial applications such as production of bulk chemicals or bioremediation. The first step in the oxidation of methane is the conversion to methanol by methane monooxygenase, the key enzyme, which exists in two forms: the cytoplasmic, soluble methane monooxygenase (sMMO) and the membrane-bound, particulate methane monooxygenase (pMMO). This paper reviews the biochemistry and molecular biology of both forms of MMO. In the past few years there have been many exciting new findings. sMMO components have been expressed in heterologous and homologous hosts. The pMMO has been purified and biochemically studied in some detail and the genes encoding the pMMO have been sequenced. Copper ions have been shown to play a key role in regulating the expression of both MMO enzyme complexes. We also present a model for copper regulation based on results from Northern analysis, primer-extensions and new sequence data, and raise a number of unanswered questions for future studies.

  4. 2003 Archaea: Ecology, Metabolism and Molecular Biology

    SciTech Connect

    Richard F. Shand

    2004-09-21

    The Gordon Research Conference (GRC) on 2003 Archaea: Ecology, Metabolism and Molecular Biology was held at Proctor Academy, Andover, NH from August 3-8, 2003. The Conference was well-attended with 150 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, ''free time'' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field. I want to personally thank you for your support of this Conference. As you know, in the interest of promoting the presentation of unpublished and frontier-breaking research, Gordon Research Conferences does not permit publication of meeting proceedings. If you wish any further details, please feel free to contact me. Thank you, Dr. Richard F. Shand, 2003 Conference Chair.

  5. Commentary: Biochemistry and Molecular Biology Educators Launch National Network

    ERIC Educational Resources Information Center

    Bailey, Cheryl; Bell, Ellis; Johnson, Margaret; Mattos, Carla; Sears, Duane; White, Harold B.

    2010-01-01

    The American Society of Biochemistry and Molecular Biology (ASBMB) has launched an National Science Foundation (NSF)-funded 5 year project to support biochemistry and molecular biology educators learning what and how students learn. As a part of this initiative, hundreds of life scientists will plan and develop a rich central resource for…

  6. Digital Learning Material for Model Building in Molecular Biology

    ERIC Educational Resources Information Center

    Aegerter-Wilmsen, Tinri; Janssen, Fred; Hartog, Rob; Bisseling, Ton

    2005-01-01

    Building models to describe processes forms an essential part of molecular biology research. However, in molecular biology curricula little attention is generally being paid to the development of this skill. In order to provide students the opportunity to improve their model building skills, we decided to develop a number of digital cases about…

  7. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    ERIC Educational Resources Information Center

    Shi, Jia; Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed…

  8. [New concepts in molecular biology applied to traslational research].

    PubMed

    Mengual, Lourdes

    2013-06-01

    This chapter intends to introduce the new concepts that have been established in molecular biology over the last years and are being applied in translational research. The chapter is divided in four big blocks, which treat the molecular biology concepts and techniques in relation to DNA, RNA, proteins and metabolites, respectively. Moreover, we give examples of translational application of these new methodologies described.

  9. Molecular Biology and Pathogenicity of Mycoplasmas

    PubMed Central

    Razin, Shmuel; Yogev, David; Naot, Yehudith

    1998-01-01

    The recent sequencing of the entire genomes of Mycoplasma genitalium and M. pneumoniae has attracted considerable attention to the molecular biology of mycoplasmas, the smallest self-replicating organisms. It appears that we are now much closer to the goal of defining, in molecular terms, the entire machinery of a self-replicating cell. Comparative genomics based on comparison of the genomic makeup of mycoplasmal genomes with those of other bacteria, has opened new ways of looking at the evolutionary history of the mycoplasmas. There is now solid genetic support for the hypothesis that mycoplasmas have evolved as a branch of gram-positive bacteria by a process of reductive evolution. During this process, the mycoplasmas lost considerable portions of their ancestors’ chromosomes but retained the genes essential for life. Thus, the mycoplasmal genomes carry a high percentage of conserved genes, greatly facilitating gene annotation. The significant genome compaction that occurred in mycoplasmas was made possible by adopting a parasitic mode of life. The supply of nutrients from their hosts apparently enabled mycoplasmas to lose, during evolution, the genes for many assimilative processes. During their evolution and adaptation to a parasitic mode of life, the mycoplasmas have developed various genetic systems providing a highly plastic set of variable surface proteins to evade the host immune system. The uniqueness of the mycoplasmal systems is manifested by the presence of highly mutable modules combined with an ability to expand the antigenic repertoire by generating structural alternatives, all compressed into limited genomic sequences. In the absence of a cell wall and a periplasmic space, the majority of surface variable antigens in mycoplasmas are lipoproteins. Apart from providing specific antimycoplasmal defense, the host immune system is also involved in the development of pathogenic lesions and exacerbation of mycoplasma induced diseases. Mycoplasmas are

  10. Molecular biological enhancement of coal biodesulfurization

    SciTech Connect

    Litchfield, J.H.; Zupancic, T.J.; Kittle, J.D. Jr.; Baker, B.; Palmer, D.T.; Traunero, C.G.; Wyza, R.E.; Schweitzer, A.; Conkle, H.N. ); Chakravarty, L.; Tuovinen, O.H. )

    1992-10-08

    Progress is reported in understanding Thiobacillus molecular biology, specifically in the area of vector development. At the initiation of this program, the basic elements needed for performing genetic engineering in T. ferrooxidans were either not yet developed. Improved techniques are described which will make it easier to construct and analyze the genetic structure and metabolism of recombinant T. ferrooxidans. The metabolism of the model organic sulfur compound dibenzothiophene (DBT) by certain heterotrophic bacteria was confirmed and characterized. Techniques were developed to analyze the metabolites of DBT, so that individual 4S pathway metabolites could be distinguished. These techniques are expected to be valuable when engineering organic sulfur metabolism in Thiobacillus. Strain isolation techniques were used to develop pure cultures of T. ferrooxidans seven of which were assessed as potential recombinant hosts. The mixotrophic strain T. coprinus was also characterized for potential use as an electroporation host. A family of related Thiobacillus plasmids was discovered in the seven strains of P. ferrooxidans mentioned above. One of these plasmids, pTFI91, was cloned into a pUC-based plasmid vector, allowing it to propagate in E. coli. A key portion of the cloned plasmid was sequenced. This segment, which is conserved in all of the related plasmids characterized, contains the vegetative origin of DNA replication, and fortuitously, a novel insertion sequence, designated IS3091. The sequence of the DNA origin revealed that these Thiobacillus plasmids represent a unique class of replicons not previously described. The potentially useful insertion sequence IS3091 was identified as a new member of a previously undefined family of insertion sequences which include the E. coli element IS30.

  11. Molecular Aspect of Good Eating Quality Formation in Japonica Rice

    PubMed Central

    Sun, Ming-Mao; Abdula, Sailila E.; Lee, Hye-Jung; Cho, Young-Chan; Han, Long-Zhi; Koh, Hee-Jong; Cho, Yong-Gu

    2011-01-01

    The composition of amylopectin is the determinant of rice eating quality under certain threshold of protein content and the ratio of amylose and amylopectin. In molecular biology level, the fine structure of amylopectin is determined by relative activities of starch branching enzyme (SBE), granule-bound starch synthase (GBSS), and soluble starch synthase (SSS) in rice grain under the same ADP-Glucose level. But the underlying mechanism of eating quality in molecular biology level remains unclear. This paper reports the differences on major parameters such as SNP and insertion-deletion sites, RNA expressions, and enzyme activities associated with eating quality of japonica varieties. Eight japonica rice varieties with significant differences in various eating quality parameters such as palatability and protein content were used in this experiment. Association analysis between nucleotide polymorphism and eating quality showed that S12 and S13 loci in SBE1, S55 in SSS1, S58 in SSS2A were significantly associated with apparent amylose content, alkali digestion value, setback viscosity, consistency viscosity, pasting temperature, which explained most of the variation in apparent amylose content, setback viscosity, and consistency viscosity; and explained almost all variations in alkali digestion value and pasting temperature. Thirty-five SNPs and insertion-deletions from SBE1, SBE3, GBSS1, SSS1, and SSS2A differentiated high or intermediate palatability rice varieties from low palatability rice varieties. Correlation analysis between enzyme activities and eating quality properties revealed that SBE25 and SSS15/W15 were positively correlated with palatability, whereas GBSS10 and GBSS15 were negatively correlated. Gene expressions showed that SBE1 and SBE3 expressions in high palatability varieties tended to be higher than middle and low palatability varieties. Collectively, SBE1, SBE3, SSS1, and SSS2A, especially SBE1 and SBE3 could improve eating quality, but GBSS1

  12. Biological and molecular basis of human breast cancer.

    PubMed

    Russo, J; Yang, X; Hu, Y F; Bove, B A; Huang, Y; Silva, I D; Tahin, Q; Wu, Y; Higgy, N; Zekri, A; Russo, I H

    1998-09-01

    Human breast cancer remains the most common malignancy in the American women. The ultimate cure of this disease relies on a better understanding of the mechanisms underlying the initiation and progression of this disease. The neoplastic transformation of HBEC in vitro represents a successful model for obtaining knowledge on the molecular and biological alterations that may contribute to the tumorigenic mechanisms. We have presented here a current understanding of chemically transformed HBEC in the following aspects: 1. Factors affecting the transformation of HBEC such as genetic predisposition and differentiation status and prior immortalization; 2. New targets for studying the mechanism of cell immortalization such as alterations in telomerase activity and differential expression of cell cycle dependent genes as well as others recently isolated through differential cloning such as H-ferritin, and a calcium binding protein; 3. Epigenetic and genetic mechanisms underlying cell transformation; 4. The association of microsatellite instability in specific loci on chromosomes 11, 13, and 16 with the progression of cell transformation; and 5. The application of microcell mediated chromosome transfer technique as an approach to testing the functional role of specific genes whose dysregulation or loss of function may contribute to the ultimate cell transformation. Further efforts in this cell system will be directed to determine the roles of identified molecular changes as well as the mapping/cloning of tumor suppressor or senescence genes such as those that may reside on chromosomes 11 or 17. PMID:9727085

  13. Molecular codes in biological and chemical reaction networks.

    PubMed

    Görlich, Dennis; Dittrich, Peter

    2013-01-01

    Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

  14. Molecular Codes in Biological and Chemical Reaction Networks

    PubMed Central

    Görlich, Dennis; Dittrich, Peter

    2013-01-01

    Shannon’s theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process “meaningful” information from those that do not. Here, we present a formal method to assess a system’s semantic capacity by analyzing a reaction network’s capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems posses different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life. PMID:23372756

  15. Aspects of the political economy of development and synthetic biology.

    PubMed

    Wellhausen, Rachel; Mukunda, Gautam

    2009-12-01

    What implications might synthetic biology's potential as a wholly new method of production have for the world economy, particularly developing countries? Theories of political economy predict that synthetic biology can shift terms of trade and displace producers in developing countries. Governments, however, retain the ability to mitigate negative changes through social safety nets and to foster adaptation to some changes through research, education and investment. We consider the effects the synthetic production of otherwise naturally derived molecules are likely to have on trade and investment, particularly in developing countries. Both rubber in Malaysia and indigo dyes in India provide historical examples of natural molecules that faced market dislocations from synthetic competitors. Natural rubber was able to maintain significant market share, while natural indigo vanished from world markets. These cases demonstrate the two extremes of the impact synthetic biology might have on naturally derived products. If developing countries can cushion the pain of technological changes by providing producers support as they retool or exit, the harmful effects of synthetic biology can be mitigated while its benefits can still be captured.

  16. BRAIN DAMAGE IN CHILDREN, THE BIOLOGICAL AND SOCIAL ASPECTS.

    ERIC Educational Resources Information Center

    BIRCH, HERBERT G., ED.

    PAPERS AND DISCUSSION SUMMARIES ARE PRESENTED FROM A CONFERENCE ON THE BIOLOGICAL AND SOCIAL PROBLEMS OF CHILDHOOD BRAIN DAMAGE, HELD AT THE CHILDREN'S HOSPITAL OF PHILADELPHIA IN NOVEMBER 1962. A VARIETY OF DISCIPLINES IS REPRESENTED, AND THE FOLLOWING TOPICS ARE CONSIDERED--(1) "THE PROBLEM OF 'BRAIN DAMAGE' IN CHILDREN" BY HERBERT G. BIRCH, (2)…

  17. Fundamental approaches in molecular biology for communication sciences and disorders

    PubMed Central

    Bartlett, Rebecca; Jetté, Marie E; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

    2012-01-01

    Purpose This contemporary tutorial will introduce general principles of molecular biology, common DNA, RNA and protein assays and their relevance in the field of communication sciences and disorders (CSD). Methods Over the past two decades, knowledge of the molecular pathophysiology of human disease has increased at a remarkable pace. Most of this progress can be attributed to concomitant advances in basic molecular biology and, specifically, the development of an ever-expanding armamentarium of technologies for analysis of DNA, RNA and protein structure and function. Details of these methodologies, their limitations and examples from the CSD literature are presented. Results/Conclusions The use of molecular biology techniques in the fields of speech, language and hearing sciences is increasing, facilitating the need for an understanding of molecular biology fundamentals and common experimental assays. PMID:22232415

  18. Resistance to Tospoviruses in Vegetable Crops: Epidemiological and Molecular Aspects.

    PubMed

    Turina, Massimo; Kormelink, Richard; Resende, Renato O

    2016-08-01

    During the past three decades, the economic impact of tospoviruses has increased, causing high yield losses in a variety of crops and ornamentals. Owing to the difficulty in combating thrips vectors with insecticides, the best way to limit/prevent tospovirus-induced diseases involves a management strategy that includes virus resistance. This review briefly presents current tospovirus taxonomy, diversity, molecular biology, and cytopathology as an introduction to a more extensive description of the two main resistance genes employed against tospoviruses: the Sw5 gene in tomato and the Tsw in pepper. Natural and experimental resistance-breaking (RB) isolates allowed the identification of the viral avirulence protein triggering each of the two resistance gene products; epidemiology of RB isolates is discussed to reinforce the need for allelic variants and the need to search for new/alternative resistance genes. Ongoing efforts for alternative resistance strategies are described not only for Tomato spotted wilt virus (TSWV) in pepper and tomato but also for other vegetable crops heavily impacted by tospoviruses. PMID:27296139

  19. Molecular and Pathogenetic Aspects of Tumor Budding in Colorectal Cancer

    PubMed Central

    Dawson, Heather; Lugli, Alessandro

    2015-01-01

    In recent years, tumor budding in colorectal cancer has gained much attention as an indicator of lymph node metastasis, distant metastatic disease, local recurrence, worse overall and disease-free survival, and as an independent prognostic factor. Tumor buds, defined as the presence of single tumor cells or small clusters of up to five tumor cells at the peritumoral invasive front (peritumoral buds) or within the main tumor body (intratumoral buds), are thought to represent the morphological correlate of cancer cells having undergone epithelial–mesenchymal transition (EMT), an important mechanism for the progression of epithelial cancers. In contrast to their undisputed prognostic power and potential to influence clinical management, our current understanding of the biological background of tumor buds is less established. Most studies examining tumor buds have attempted to recapitulate findings of mechanistic EMT studies using immunohistochemical markers. The aim of this review is to provide a comprehensive summary of studies examining protein expression profiles of tumor buds and to illustrate the molecular pathways and crosstalk involved in their formation and maintenance. PMID:25806371

  20. Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects.

    PubMed

    Chenuil, Anne; Anne, Chenuil

    2006-05-01

    The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking genetic variability to the biological parameters of the studied organisms. MGM are defined by two components: the DNA region(s) screened, and the technique used to reveal its variation. Criteria of choice belong to three categories: (1) the level of variability, (2) the nature of the information (e.g. dominance vs. codominance, ploidy, ... ) which must be determined according to the biological question and (3) some practical criteria which mainly depend on the equipment of the laboratory and experience of the scientist. A three-step procedure is proposed for drawing up MGMs suitable to answer given biological questions, and compiled data are organized to guide the choice at each step: (1) choice, determined by the biological question, of the level of variability and of the criteria of the nature of information, (2) choice of the DNA region and (3) choice of the technique.

  1. Planetary Biology and Microbial Ecology: Molecular Ecology and the Global Nitrogen cycle

    NASA Technical Reports Server (NTRS)

    Nealson, Molly Stone (Editor); Nealson, Kenneth H. (Editor)

    1993-01-01

    This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

  2. Some aspects of the biological effects of space weather

    NASA Astrophysics Data System (ADS)

    Breus, T. K.; Ozheredov, V. A.; Syutkina, E. V.; Rogoza, A. N.

    2008-02-01

    Space weather hazards have been well-studied during the past few decades, mainly in connection with effects on technical systems. The biological effects of solar and geomagnetic activity have been largely ignored because the amplitudes of the electromagnetic fields (EMF) are small, typically one to several hundreds of nanoteslas. This is much weaker than electromagnetic noise of anthropogenic origin and about 10 orders of magnitude less than the characteristic energies of biochemical reactions. During the past 20 years, however, more careful consideration has been given to possible nonthermal mechanisms of interaction of biological systems with weak (<1 mT) low-frequency EMF, which are unavoidably present in the environment, and some progress has been made towards understanding how an interaction can occur.

  3. Jump-starting life? Fundamental aspects of synthetic biology

    PubMed Central

    2015-01-01

    What is life and how could it originate? This question lies at the core of understanding the cell as the smallest living unit. Although we are witnessing a golden era of the life sciences, we are ironically still far from giving a convincing answer to this question. In this short article, I argue why synthetic biology in conjunction with the quantitative sciences may provide us with new concepts and tools to address it. PMID:26323686

  4. Cell and molecular biology of Chlamydomonas

    SciTech Connect

    Not Available

    1988-01-01

    This document contains only the abstracts of 92 presentations on the biology of Chlamydomonas. Topics include gene transformations, gene regulation, biosynthetic pathways, cell surfaces, circadian clocks, and the development and structure of the flagellar apparatus. (TEM)

  5. Structural Biology and Molecular Applications Research

    Cancer.gov

    Part of NCI's Division of Cancer Biology's research portfolio, research and development in this area focuses on enabling technologies, models, and methodologies to support basic and applied cancer research.

  6. Computer Analogies: Teaching Molecular Biology and Ecology.

    ERIC Educational Resources Information Center

    Rice, Stanley; McArthur, John

    2002-01-01

    Suggests that computer science analogies can aid the understanding of gene expression, including the storage of genetic information on chromosomes. Presents a matrix of biology and computer science concepts. (DDR)

  7. Paper-based chemical and biological sensors: Engineering aspects.

    PubMed

    Ahmed, Snober; Bui, Minh-Phuong Ngoc; Abbas, Abdennour

    2016-03-15

    Remarkable efforts have been dedicated to paper-based chemosensors and biosensors over the last few years, mainly driven by the promise of reaching the best trade-off between performance, affordability and simplicity. Because of the low-cost and rapid prototyping of these sensors, recent research has been focused on providing affordable diagnostic devices to the developing world. The recent progress in sensitivity, multi-functionality and integration of microfluidic paper-based analytical devices (µPADs), increasingly suggests that this technology is not only attractive in resource-limited environments but it also represents a serious challenger to silicon, glass and polymer-based biosensors. This review discusses the design, chemistry and engineering aspects of these developments, with a focus on the past few years.

  8. Physical mechanisms of biological molecular motors

    NASA Astrophysics Data System (ADS)

    Miller, John H., Jr.; Vajrala, Vijayanand; Infante, Hans L.; Claycomb, James R.; Palanisami, Akilan; Fang, Jie; Mercier, George T.

    2009-03-01

    Biological motors generally fall into two categories: (1) those that convert chemical into mechanical energy via hydrolysis of a nucleoside triphosphate, usually adenosine triphosphate, regarded as life's chemical currency of energy and (2) membrane bound motors driven directly by an ion gradient and/or membrane potential. Here we argue that electrostatic interactions play a vital role for both types of motors and, therefore, the tools of physics can greatly contribute to understanding biological motors.

  9. The extracellular matrix of plants: Molecular, cellular and developmental biology

    SciTech Connect

    1996-12-31

    A symposium entitled ``The Extracellular Matrix of Plants: Molecular, Cellular and Developmental Biology was held in Tamarron, Colorado, March 15--21, 1996. The following topics were explored in addresses by 43 speakers: structure and biochemistry of cell walls; biochemistry, molecular biology and biosynthesis of lignin; secretory pathway and synthesis of glycoproteins; biosynthesis of matrix polysaccharides, callose and cellulose; role of the extracellular matrix in plant growth and development; plant cell walls in symbiosis and pathogenesis.

  10. A biochemistry and molecular biology course for secondary school teachers*.

    PubMed

    Fernández-Novell, J M; Cid, E; Gomis, R; Barberà, A; Guinovart, J J

    2004-11-01

    This article describes a course for reinforcing the knowledge of biochemistry in secondary school science teachers. The Department of Biochemistry and Molecular Biology of the University of Barcelona designed a course to bring these teachers up to date with this discipline. In addition to updating their knowledge of biochemistry and molecular biology, this course aims to provide teachers with a set of relevant laboratory practices that can be applied in their practical lessons.

  11. Immunoregulation by Mesenchymal Stem Cells: Biological Aspects and Clinical Applications

    PubMed Central

    Castro-Manrreza, Marta E.; Montesinos, Juan J.

    2015-01-01

    Mesenchymal stem cells (MSCs) are multipotent cells capable of differentiation into mesenchymal lineages and that can be isolated from various tissues and easily cultivated in vitro. Currently, MSCs are of considerable interest because of the biological characteristics that confer high potential applicability in the clinical treatment of many diseases. Specifically, because of their high immunoregulatory capacity, MSCs are used as tools in cellular therapies for clinical protocols involving immune system alterations. In this review, we discuss the current knowledge about the capacity of MSCs for the immunoregulation of immunocompetent cells and emphasize the effects of MSCs on T cells, principal effectors of the immune response, and the immunosuppressive effects mediated by the secretion of soluble factors and membrane molecules. We also describe the mechanisms of MSC immunoregulatory modulation and the participation of MSCs as immune response regulators in several autoimmune diseases, and we emphasize the clinical application in graft versus host disease (GVHD). PMID:25961059

  12. Luciferase Genes as Reporter Reactions: How to Use Them in Molecular Biology?

    PubMed

    Cevenini, L; Calabretta, M M; Calabria, D; Roda, A; Michelini, E

    2016-01-01

    : The latest advances in molecular biology have made available several biotechnological tools that take advantage of the high detectability and quantum efficiency of bioluminescence (BL), with an ever-increasing number of novel applications in environmental, pharmaceutical, food, and forensic fields. Indeed, BL proteins are being used to develop ultrasensitive binding assays and cell-based assays, thanks to their high detectability and to the availability of highly sensitive BL instruments. The appealing aspect of molecular biology tools relying on BL reactions is their general applicability in both in vitro assays, such as cell cultures or purified proteins, and in vivo settings, such as in whole-animal BL imaging. The aim of this chapter is to provide the reader with an overview of state-of-the-art bioluminescent tools based on luciferase genes, highlighting molecular biology strategies that have been applied so far, together with some selected examples.

  13. Computer-Based Semantic Network in Molecular Biology: A Demonstration.

    ERIC Educational Resources Information Center

    Callman, Joshua L.; And Others

    This paper analyzes the hardware and software features that would be desirable in a computer-based semantic network system for representing biology knowledge. It then describes in detail a prototype network of molecular biology knowledge that has been developed using Filevision software and a Macintosh computer. The prototype contains about 100…

  14. The molecular biology of Bluetongue virus replication.

    PubMed

    Patel, Avnish; Roy, Polly

    2014-03-01

    The members of Orbivirus genus within the Reoviridae family are arthropod-borne viruses which are responsible for high morbidity and mortality in ruminants. Bluetongue virus (BTV) which causes disease in livestock (sheep, goat, cattle) has been in the forefront of molecular studies for the last three decades and now represents the best understood orbivirus at a molecular and structural level. The complex nature of the virion structure has been well characterised at high resolution along with the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell as well as the protein and genome sequestration required for it; and the role of host proteins in virus entry and virus release. More recent developments of Reverse Genetics and Cell-Free Assembly systems have allowed integration of the accumulated structural and molecular knowledge to be tested at meticulous level, yielding higher insight into basic molecular virology, from which the rational design of safe efficacious vaccines has been possible. This article is centred on the molecular dissection of BTV with a view to understanding the role of each protein in the virus replication cycle. These areas are important in themselves for BTV replication but they also indicate the pathways that related viruses, which includes viruses that are pathogenic to man and animals, might also use providing an informed starting point for intervention or prevention.

  15. Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

    ERIC Educational Resources Information Center

    Bartlett, Rebecca S.; Jette, Marie E.; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

    2012-01-01

    Purpose: This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Method: Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has…

  16. Concepts and Skills in the Biochemistry/Molecular Biology Lab

    ERIC Educational Resources Information Center

    Boyer, Rodney

    2003-01-01

    Most colleges and universities throughout the world now offer a Biochemistry/Molecular Biology (BMB) lab course that is designed for undergraduate students in the molecular life sciences, chemistry, and related fields. To best serve our students, we must introduce them to the most current concepts, skills, and methods available. Suggestions for…

  17. The Macromolecular Concept and the Origins of Molecular Biology

    ERIC Educational Resources Information Center

    Olby, Robert

    1970-01-01

    Traces the origins of molecular biology to the work of 19th century biophysicists, ultrastructurists and collodial chemists. The development of the Aggregate Theory,and its overthrow by the Macromolecule Concept is described. Research in molecular genetics in the pre-second world war period, and the effects of the war on it, are briefly reviewed.…

  18. Using a Computer Animation to Teach High School Molecular Biology

    ERIC Educational Resources Information Center

    Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

    2008-01-01

    We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…

  19. Molecular biology of human muscle disease

    SciTech Connect

    Dunne, P.W.; Epstein, H.F. )

    1991-01-01

    The molecular revolution that is transforming the entire biomedical field has had far-reaching impact in its application to inherited human muscle disease. The gene for Duchenne muscular dystrophy was one of the first cloned without knowledge of the defective protein product. This success was based upon the availability of key chromosomal aberrations that provided molecular landmarks for the disease locus. Subsequent discoveries regarding the mode of expression for this gene, the structure and localization of its protein product dystrophin, and molecular diagnosis of affected and carrier individuals constitute a paradigm for investigation of human genetics. Finding the gene for myotonic muscular dystrophy is requiring the brute force approach of cloning several million bases of DNA, identifying expressed sequences, and characterizing candidate genes. The gene that causes hypertrophic cardiomyopathy has been found serendipitously to be one of the genetic markers on chromosome 14, the {beta} myosin heavy chain.

  20. Circulatory bubble dynamics: from physical to biological aspects.

    PubMed

    Papadopoulou, Virginie; Tang, Meng-Xing; Balestra, Costantino; Eckersley, Robert J; Karapantsios, Thodoris D

    2014-04-01

    Bubbles can form in the body during or after decompression from pressure exposures such as those undergone by scuba divers, astronauts, caisson and tunnel workers. Bubble growth and detachment physics then becomes significant in predicting and controlling the probability of these bubbles causing mechanical problems by blocking vessels, displacing tissues, or inducing an inflammatory cascade if they persist for too long in the body before being dissolved. By contrast to decompression induced bubbles whose site of initial formation and exact composition are debated, there are other instances of bubbles in the bloodstream which are well-defined. Gas emboli unwillingly introduced during surgical procedures and ultrasound microbubbles injected for use as contrast or drug delivery agents are therefore also discussed. After presenting the different ways that bubbles can end up in the human bloodstream, the general mathematical formalism related to the physics of bubble growth and detachment from decompression is reviewed. Bubble behavior in the bloodstream is then discussed, including bubble dissolution in blood, bubble rheology and biological interactions for the different cases of bubble and blood composition considered. PMID:24534474

  1. Taxonomy, biology, and periodontal aspects of Fusobacterium nucleatum.

    PubMed Central

    Bolstad, A I; Jensen, H B; Bakken, V

    1996-01-01

    The pathogenic potential of Fusobacterium nucleatum and its significance in the development of periodontal diseases, as well as in infections in other organs, have gained new interest for several reasons. First, this bacterium has the potential to be pathogenic because of its number and frequency in periodontal lesions, its production of tissue irritants, its synergism with other bacteria in mixed infections, and its ability to form aggregates with other suspected pathogens in periodontal disease and thus act as a bridge between early and late colonizers on the tooth surface. Second, of the microbial species that are statistically associated with periodontal disease, F. nucleatum is the most common in clinical infections of other body sites. Third, during the past few years, new techniques have made it possible to obtain more information about F. nucleatum on the genetic level, thereby also gaining better knowledge of the structure and functions of the outer membrane proteins (OMPs). OMPs are of great interest with respect to coaggregation, cell nutrition, and antibiotic susceptibility. This review covers what is known to date about F. nucleatum in general, such as taxonomy and biology, with special emphasis on its pathogenic potential. Its possible relationship to other periodontal bacteria in the development of periodontal diseases and the possible roles played by OMPs are considered. PMID:8665477

  2. Circulatory bubble dynamics: from physical to biological aspects.

    PubMed

    Papadopoulou, Virginie; Tang, Meng-Xing; Balestra, Costantino; Eckersley, Robert J; Karapantsios, Thodoris D

    2014-04-01

    Bubbles can form in the body during or after decompression from pressure exposures such as those undergone by scuba divers, astronauts, caisson and tunnel workers. Bubble growth and detachment physics then becomes significant in predicting and controlling the probability of these bubbles causing mechanical problems by blocking vessels, displacing tissues, or inducing an inflammatory cascade if they persist for too long in the body before being dissolved. By contrast to decompression induced bubbles whose site of initial formation and exact composition are debated, there are other instances of bubbles in the bloodstream which are well-defined. Gas emboli unwillingly introduced during surgical procedures and ultrasound microbubbles injected for use as contrast or drug delivery agents are therefore also discussed. After presenting the different ways that bubbles can end up in the human bloodstream, the general mathematical formalism related to the physics of bubble growth and detachment from decompression is reviewed. Bubble behavior in the bloodstream is then discussed, including bubble dissolution in blood, bubble rheology and biological interactions for the different cases of bubble and blood composition considered.

  3. [Volatile anaesthesias' molecular biological course of action].

    PubMed

    Søholm, Helle; Olsen, Niels Vidiendal

    2013-01-14

    Anaesthesia is extensively used worldwide and in Denmark alone more than 400,000 anaesthesias are performed each year. In spite of that the molecularly mechanism of anaesthesia has not been proven. Hypotheses have been suggested (lipid versus protein theory), but none has yet been able to explain the whole mechanism. Molecular targets for volatile anaesthetics (e.g. potassium and calcium channels) affected areas in the central nervous system and the impact on the cerebral metabolism versus the cerebral blood flow are discussed. PMID:23331943

  4. [Molecular biology for sarcoma: useful or necessary?].

    PubMed

    Neuville, Agnès; Coindre, Jean-Michel; Chibon, Frédéric

    2015-01-01

    Sarcomas are a heterogeneous group of tumors. Their diagnosis is based on morphology and immunohistochemical profile, with categories of tumors according to the type of tissue that they resemble. Nevertheless, for several tumors, cellular origin is unknown. Molecular analysis performed in recent years allowed, combining histophenotype and genomics, better classifying such sarcomas, individualizing new entities and grouping some tumors. Simple and recurrent genetic alterations, such as translocation, mutation, amplification, can be identified in one of two sarcomas and appear as new diagnostic markers. Their identification in specialized laboratories in molecular pathology of sarcomas is often useful and sometimes necessary for a good diagnosis, leading to a heavy and multidisciplinary multi-step treatment.

  5. 1-Dimensional nanoparticles - A brief critical review on biological, medical, and toxicological aspects

    NASA Astrophysics Data System (ADS)

    Popescu, B. M.; Ali, N.; Basturea, G.; Comsa, G. I.; Materon, L. A.; Chipara, M.

    2013-06-01

    A critical review of the biological and medical effects of one dimensional nanoparticles is presented. The review focuses on the toxicity of carbon nanotubes - a subject under strong debate and discusses briefly the most important concepts. It is tentatively suggested that the huge aspect ratio and the high Young modulus of carbon nanotubes are playing an important role in the biological, medical, and toxicological aspects of carbon nanotubes despite their low intrinsic biochemical activity. The most suitable biomedical model for the biological and medical effects of carbon nanotubes is described by the so-called impaling mode which appears to be qualitatively consistent with partial phagocytosis.

  6. Methods in molecular biology: plant cytogenetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cytogenetic studies have contributed greatly to our understanding of genetics, biology, reproduction, and evolution. From early studies in basic chromosome behavior the field has expanded enabling whole genome analysis to the manipulation of chromosomes and their organization. This book covers a ran...

  7. The molecular biology of meiosis in plants.

    PubMed

    Mercier, Raphaël; Mézard, Christine; Jenczewski, Eric; Macaisne, Nicolas; Grelon, Mathilde

    2015-01-01

    Meiosis is the cell division that reshuffles genetic information between generations. Recently, much progress has been made in understanding this process; in particular, the identification and functional analysis of more than 80 plant genes involved in meiosis have dramatically deepened our knowledge of this peculiar cell division. In this review, we provide an overview of advancements in the understanding of all aspects of plant meiosis, including recombination, chromosome synapsis, cell cycle control, chromosome distribution, and the challenge of polyploidy. PMID:25494464

  8. The molecular biology of meiosis in plants.

    PubMed

    Mercier, Raphaël; Mézard, Christine; Jenczewski, Eric; Macaisne, Nicolas; Grelon, Mathilde

    2015-01-01

    Meiosis is the cell division that reshuffles genetic information between generations. Recently, much progress has been made in understanding this process; in particular, the identification and functional analysis of more than 80 plant genes involved in meiosis have dramatically deepened our knowledge of this peculiar cell division. In this review, we provide an overview of advancements in the understanding of all aspects of plant meiosis, including recombination, chromosome synapsis, cell cycle control, chromosome distribution, and the challenge of polyploidy.

  9. Molecular biological enhancement of coal biodesulfurization

    SciTech Connect

    Kilbane, J.J. II; Bielaga, B.A.

    1991-12-01

    The overall objective of this project was to use molecular genetics to develop strains of bacteria with enhanced ability to remove sulfur from coal, and to obtain data that will allow the performance and economics of a coal biodesulfurization process to be predicted. (VC)

  10. Molecular biological enhancement of coal biodesulfurization

    SciTech Connect

    Bielaga, B.A.; Kilbane, J.J.

    1990-04-01

    The overall objectives of this project is to use Molecular Genetics to develop strains of bacteria (esp. Rhodococcus) with enhanced ability to remove sulfur from coal, and to obtain data that will allow the performance and economics of a coal biodesulfurization process to be predicted. 5 figs.

  11. Recent advances in the molecular and cellular biology of bunyaviruses.

    PubMed

    Walter, Cheryl T; Barr, John N

    2011-11-01

    The family Bunyaviridae of segmented, negative-stranded RNA viruses includes over 350 members that infect a bewildering variety of animals and plants. Many of these bunyaviruses are the causative agents of serious disease in their respective hosts, and are classified as emerging viruses because of their increased incidence in new populations and geographical locations throughout the world. Emerging bunyaviruses, such as Crimean-Congo hemorrhagic fever virus, tomato spotted wilt virus and Rift Valley fever virus, are currently attracting great interest due to migration of their arthropod vectors, a situation possibly linked to climate change. These and other examples of continued emergence suggest that bunyaviruses will probably continue to pose a sustained global threat to agricultural productivity, animal welfare and human health. The threat of emergence is particularly acute in light of the lack of effective preventative or therapeutic treatments for any of these viruses, making their study an important priority. This review presents recent advances in the understanding of the bunyavirus life cycle, including aspects of their molecular, cellular and structural biology. Whilst special emphasis is placed upon the emerging bunyaviruses, we also describe the extensive body of work involving model bunyaviruses, which have been the subject of major contributions to our overall understanding of this important group of viruses.

  12. The roles of integration in molecular systems biology.

    PubMed

    O'Malley, Maureen A; Soyer, Orkun S

    2012-03-01

    A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.

  13. Interactive analysis of systems biology molecular expression data

    PubMed Central

    Zhang, Mingwu; Ouyang, Qi; Stephenson, Alan; Kane, Michael D; Salt, David E; Prabhakar, Sunil; Burgner, John; Buck, Charles; Zhang, Xiang

    2008-01-01

    Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe) in growth media (an ionomics dataset). This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology. PMID:18312669

  14. The nucleic acid revolution continues - will forensic biology become forensic molecular biology?

    PubMed

    Gunn, Peter; Walsh, Simon; Roux, Claude

    2014-01-01

    Molecular biology has evolved far beyond that which could have been predicted at the time DNA identity testing was established. Indeed we should now perhaps be referring to "forensic molecular biology." Aside from DNA's established role in identifying the "who" in crime investigations, other developments in medical and developmental molecular biology are now ripe for application to forensic challenges. The impact of DNA methylation and other post-fertilization DNA modifications, plus the emerging role of small RNAs in the control of gene expression, is re-writing our understanding of human biology. It is apparent that these emerging technologies will expand forensic molecular biology to allow for inferences about "when" a crime took place and "what" took place. However, just as the introduction of DNA identity testing engendered many challenges, so the expansion of molecular biology into these domains will raise again the issues of scientific validity, interpretation, probative value, and infringement of personal liberties. This Commentary ponders some of these emerging issues, and presents some ideas on how they will affect the conduct of forensic molecular biology in the foreseeable future.

  15. Molecular biology of retinal ganglion cells.

    PubMed Central

    Xiang, M; Zhou, H; Nathans, J

    1996-01-01

    Retinal ganglion cells are the output neurons that encode and transmit information from the eye to the brain. Their diverse physiologic and anatomic properties have been intensively studied and appear to account well for a number of psychophysical phenomena such as lateral inhibition and chromatic opponency. In this paper, we summarize our current view of retinal ganglion cell properties and pose a number of questions regarding underlying molecular mechanisms. As an example of one approach to understanding molecular mechanisms, we describe recent work on several POU domain transcription factors that are expressed in subsets of retinal ganglion cells and that appear to be involved in ganglion cell development. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5 Fig. 6 PMID:8570601

  16. Molecular model for hydrated biological tissues

    NASA Astrophysics Data System (ADS)

    Sato, Erika Tiemi; Rocha, Alexandre Reily; de Carvalho, Luis Felipe das Chagas e. Silva; Almeida, Janete Dias; Martinho, Herculano

    2015-06-01

    A density-functional microscopic model for soft tissues (STmod) is presented. The model was based on a prototype molecular structure from experimentally resolved type I collagen peptide residues and water clusters treated in periodic boundary conditions. We obtained the optimized geometry, binding and coupling energies, dipole moments, and vibrational frequencies. The results concerning the stability of the confined water clusters, the water-water, and water-collagen interactions were successfully correlated to some important experimental trends of normal and inflammatory tissues.

  17. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    McCarthy, J.F.

    1990-04-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka, as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). 11 refs., 1 fig., 1 tab.

  18. Biochemistry and molecular biology of chromoplast development.

    PubMed

    Camara, B; Hugueney, P; Bouvier, F; Kuntz, M; Monéger, R

    1995-01-01

    Plant cells contain a unique class of organelles, designated the plastids, which distinguish them from animal cells. According to the largely accepted endosymbiotic theory of evolution, plastids are descendants of prokaryotes. This process requires several adaptative changes which involve the maintenance and the expression of part of the plastid genome, as well as the integration of the plastid activity to the cellular metabolism. This is illustrated by the diversity of plastids encountered in plant cells. For instance, in tissues undergoing color changes, i.e., flowers and fruits, the chromoplasts produce and accumulate excess carotenoids. In this paper we attempt to review the basic aspects of chromoplast development. PMID:8522420

  19. [The molecular biology of distraction osteogenesis].

    PubMed

    Boulétreau, P; Longaker, M T

    2004-02-01

    Distraction osteogenesis has become a mainstay in bone engineering and the recent application of this technique to the membranous craniofacial skeleton has significantly improved our armamentarium for reconstructive craniomaxillofacial procedures. However, if the biomechanical, histological and ultrastructural changes associated with distraction osteogenesis have been widely described, the molecular mechanisms governing the formation of new bone in the interfragmental gap of gradually distracted bone segments remain largely unclear. Recently, our laboratory has described a rat mandibular distraction model that provides an excellent environment for deciphering the molecular mechanisms that mediate distraction osteogenesis. In this Article, we present the hypotheses and current research that have furthered our knowledge of the molecular mechanisms that govern distraction osteogenesis. Recent studies have implicated a growing number of cytokines that are intimately involved in the regulation of bone synthesis and turnover. The gene regulation of numerous cytokines (Transforming Growth Factor-B, Bone Morphogenetic Proteins, Insulin-like Growth Factor-1, Fibroblast Growth Factor-2) during distraction osteogenesis have been best characterized and will be discussed in this text. We believe that novel systems like the rat model will facilitate our understanding of the biomolecular mechanisms that mediate membranous distraction osteogenesis and will ultimately guide the development of targeted-strategies designed to accelerate bone healing.

  20. Molecular model for hydrated biological tissues.

    PubMed

    Sato, Erika Tiemi; Rocha, Alexandre Reily; de Carvalho, Luis Felipe das Chagas e Silva; Almeida, Janete Dias; Martinho, Herculano

    2015-06-01

    A density-functional microscopic model for soft tissues (STmod) is presented. The model was based on a prototype molecular structure from experimentally resolved type I collagen peptide residues and water clusters treated in periodic boundary conditions. We obtained the optimized geometry, binding and coupling energies, dipole moments, and vibrational frequencies. The results concerning the stability of the confined water clusters, the water-water, and water-collagen interactions were successfully correlated to some important experimental trends of normal and inflammatory tissues. PMID:26172825

  1. The molecular biology of WHO grade I astrocytomas

    PubMed Central

    Marko, Nicholas F.; Weil, Robert J.

    2012-01-01

    World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood. PMID:23090984

  2. The molecular biology of WHO grade I astrocytomas.

    PubMed

    Marko, Nicholas F; Weil, Robert J

    2012-12-01

    World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood.

  3. Asymmetry at the molecular level in biology

    NASA Astrophysics Data System (ADS)

    Johnson, Louise N.

    2005-10-01

    Naturally occurring biological molecules are made of homochiral building blocks. Proteins are composed of L-amino acids (and not D-amino acids); nucleic acids such as DNA have D-ribose sugars (and not L-ribose sugars). It is not clear why nature selected a particular chirality. Selection could have occurred by chance or as a consequence of basic physical chemistry. Possible proposals, including the contribution of the parity violating the weak nuclear force, are discussed together with the mechanisms by which this very small contribution might be amplified. Homochirality of the amino acids has consequences for protein structure. Helices are right handed and beta sheets have a left-hand twist. When incorporated into the tertiary structure of a protein these chiralities limit the topologies of connections between helices and sheets. Polypeptides comprised of D-amino acids can be synthesized chemically and have been shown to adopt stable structures that are the mirror image of the naturally occurring L-amino acid polypeptides. Chirality is important in drug design. Three examples are discussed: penicillin; the CD4 antagonistic peptides; and thalidomide. The absolute hand of a biological structure can only be established by X-ray crystallographic methods using the technique of anomalous scattering.

  4. Evolution of egg coats: linking molecular biology and ecology.

    PubMed

    Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

    2015-08-01

    One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation.

  5. Overview of selected molecular biological databases

    SciTech Connect

    Rayl, K.D.; Gaasterland, T.

    1994-11-01

    This paper presents an overview of the purpose, content, and design of a subset of the currently available biological databases, with an emphasis on protein databases. Databases included in this summary are 3D-ALI, Berlin RNA databank, Blocks, DSSP, EMBL Nucleotide Database, EMP, ENZYME, FSSP, GDB, GenBank, HSSP, LiMB, PDB, PIR, PKCDD, ProSite, and SWISS-PROT. The goal is to provide a starting point for researchers who wish to take advantage of the myriad available databases. Rather than providing a complete explanation of each database, we present its content and form by explaining the details of typical entries. Pointers to more complete ``user guides`` are included, along with general information on where to search for a new database.

  6. pGLO Mutagenesis: A Laboratory Procedure in Molecular Biology for Biology Students

    ERIC Educational Resources Information Center

    Bassiri, Eby A.

    2011-01-01

    A five-session laboratory project was designed to familiarize or increase the laboratory proficiency of biology students and others with techniques and instruments commonly used in molecular biology research laboratories and industries. In this project, the EZ-Tn5 transposon is used to generate and screen a large number of cells transformed with…

  7. The molecular biology of WHO grade II gliomas.

    PubMed

    Marko, Nicholas F; Weil, Robert J

    2013-02-01

    The WHO grading scheme for glial neoplasms assigns Grade II to 5 distinct tumors of astrocytic or oligodendroglial lineage: diffuse astrocytoma, oligodendroglioma, oligoastrocytoma, pleomorphic xanthoastrocytoma, and pilomyxoid astrocytoma. Although commonly referred to collectively as among the "low-grade gliomas," these 5 tumors represent molecularly and clinically unique entities. Each is the subject of active basic research aimed at developing a more complete understanding of its molecular biology, and the pace of such research continues to accelerate. Additionally, because managing and predicting the course of these tumors has historically proven challenging, translational research regarding Grade II gliomas continues in the hopes of identifying novel molecular features that can better inform diagnostic, prognostic, and therapeutic strategies. Unfortunately, the basic and translational literature regarding the molecular biology of WHO Grade II gliomas remains nebulous. The authors' goal for this review was to present a comprehensive discussion of current knowledge regarding the molecular characteristics of these 5 WHO Grade II tumors on the chromosomal, genomic, and epigenomic levels. Additionally, they discuss the emerging evidence suggesting molecular differences between adult and pediatric Grade II gliomas. Finally, they present an overview of current strategies for using molecular data to classify low-grade gliomas into clinically relevant categories based on tumor biology.

  8. Genetics and molecular biology of Huntington's disease.

    PubMed

    Albin, R L; Tagle, D A

    1995-01-01

    In 1993, the genetic abnormality responsible for Huntington's disease was identified as a trinucleotide-repeat expansion in a novel gene. Much has been learned about the molecular genetics of Huntington's disease and the possible effects of the trinucleotide expansion in the development of this disease and other neurological disorders. The Huntington's disease locus is widely expressed throughout the brain and in many non-neural tissues. Current speculation about the pathogenesis of neuronal death concentrates on a 'gain of function' effect in which the abnormal protein has acquired a new and lethal property. Future research will define the normal function of the Huntington's disease locus, test hypotheses regarding the putative gain of function, and explore the factors that determine neuronal susceptibility to the effects of the abnormal allele.

  9. Plant synthetic biology for molecular engineering of signalling and development.

    PubMed

    Nemhauser, Jennifer L; Torii, Keiko U

    2016-03-02

    Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.

  10. The molecular biology of pulmonary metastasis.

    PubMed

    Krishnan, Kartik; Khanna, Chand; Helman, Lee J

    2006-05-01

    Curing cancer requires the treatment of metastatic disease. Whether this is a patient with advanced disease and clinically apparent metastases, or if the patient with localized disease is at risk for development of dissemination, failure to control metastasis will result in a poor outcome. Here, we have presented a molecular guide to our current understanding of the processes underlying metastasis. Experimental clinical trials designed to further the understanding of metastasis are often limited by selection of patients with advanced disease. Therefore, our understanding of the processes involved in the metastatic cascade is limited by the availability of comprehensive experimental model systems. The study of metastasis relies most heavily on xenografts, tumors using human cell lines, or tumor tissue that can grow in mice. These models present a limited recapitulation of the patients. Xenograft models require some degree of immunosuppression on the part of the host, because mice with native immune systems will reject transplanted human tumors, preventing their growth. As a result, mice with immune defects ranging from depleted T cells (nude mice) to absent T, B, and NK cells (SCID-Beige) are used as hosts. As the evasion of the immune system is a key function demonstrated by the metastatic cancer cell, xenograft models, by necessity, subvert this step. Furthermore, recent studies have established that angiogenesis in transplanted tumors is different than in native tumors, further highlighting the limitations of these models. With these limitations, studies of metastasis may require development of models of autochthonous tumors, that is, tumors originating in the study animals. A number of cell lines of autochthonous murine tumors have been established that generate metastatic disease after implantation into mice. Moreover, some transgenic animals spontaneously develop metastatic tumors that, although occurring in genetically engineered animals, may represent the

  11. A decade of molecular cell biology: achievements and challenges.

    PubMed

    Akhtar, Asifa; Fuchs, Elaine; Mitchison, Tim; Shaw, Reuben J; St Johnston, Daniel; Strasser, Andreas; Taylor, Susan; Walczak, Claire; Zerial, Marino

    2011-09-23

    Nature Reviews Molecular Cell Biology celebrated its 10-year anniversary during this past year with a series of specially commissioned articles. To complement this, here we have asked researchers from across the field for their insights into how molecular cell biology research has evolved during this past decade, the key concepts that have emerged and the most promising interfaces that have developed. Their comments highlight the broad impact that particular advances have had, some of the basic understanding that we still require, and the collaborative approaches that will be essential for driving the field forward.

  12. Where statistics and molecular microarray experiments biology meet.

    PubMed

    Kelmansky, Diana M

    2013-01-01

    This review chapter presents a statistical point of view to microarray experiments with the purpose of understanding the apparent contradictions that often appear in relation to their results. We give a brief introduction of molecular biology for nonspecialists. We describe microarray experiments from their construction and the biological principles the experiments rely on, to data acquisition and analysis. The role of epidemiological approaches and sample size considerations are also discussed.

  13. Molecular biology of coal bio-desulfurization

    SciTech Connect

    Young, K.D.; Gallagher, J.R.

    1991-07-18

    The aim of this project is to use the techniques of molecular genetics to identify, clone, sequence, and enhance the expression of proteins which remove sulfur covalently bound to coal. The cloned dox genes from strain C18 were more fully characterized. Another gene, doxG, is almost identical with the nahC gene, also involved in the naphthalene pathway. These results lead us to believe that dibenzothiophene (DBT) is degraded by the oxidative route along the naphthalene degradative pathway. At least one other gene, doxI, is implicated in the formation of the unidentified fluorescent product from DBT. The Rhodococcus rhodochrous isolate IGTS8 was mutated to produce a variant (strain UV1) that was negative for DBT utilization. This mutant was exposed to further rounds of UV mutagenesis and was used as the host for attempts to introduce various plasmid DNAs. Two plasmids could be introduced into UV1: pRF29 and pLAFR5. A cosmid library of IGTS8 DNA was constructed in pLAFR5 and was electroporated into UV1. Of over 2000 colonies tested three bulk batches, one flask of about 600 clones produced a fluorescent product from DBT. These are being screened to determine if one of these represents a clone that complements the DBT negative phenotype of the UV1 mutant. We obtained chloramphenicol resistant Thiobacillus ferrooxidans after electroporation but these transformants contained no plasmid or transposon sequences, so that insertion of DNA into T. ferrooxidans had not occurred.

  14. The molecular biology of Fanconi anemia.

    PubMed

    Tamary, Hannah; Bar-Yam, Raanan; Zemach, Michal; Dgany, Orly; Shalmon, Lea; Yaniv, Isaac

    2002-10-01

    Fanconi anemia is a rare autosomal recessive disorder characterized clinically by congenital abnormalities, progressive bone marrow failure, and a predisposition to malignancy. FA cells are sensitive to DNA cross-linking agents. Complementation analysis of FA cells using somatic cell fusion has facilitated the identification of eight complementation groups, suggesting that FA is a genetically heterogeneous disorder. Six genes (FANCA, FANCC, FANCD2, FANCE, FANGF, FANCG) have been cloned so far. The majority of affected patients belong to FA group A. Of the 32 unrelated Israeli patients with FA that we studied, 6 carried the FANCC mutations and 15 the FANCA mutations. Among the Jewish patients, ethnic-related mutations were common. Recent cumulative evidence suggests that the FA proteins are repair proteins. FANCC, FANCA and FANCG bind and interact in a protein complex found in the cytoplasm and nucleus of normal cells. FANCD2 exists in two isoforms; the long active form, FANCD2-L, is absent from FA cells of all complementation groups. FANCD2 colocalizes with BRCA1 in nuclear foci, probably as part of a large genomic surveillance complex. Studies using FANCA and FANCC knockout mice suggest that bone marrow precursors express interferon-gamma hypersensitivity and show progressive apoptosis. The definition of the molecular basis of FA in many affected families now enables prenatal diagnosis.

  15. Molecular aspects of flow-induced crystallization of polypropylene

    NASA Astrophysics Data System (ADS)

    Thurman, Derek W.

    Using a novel shearing device, we investigate-flow-induced crystallization of bimodal blends of polypropylenes (PP) in which we vary the molecular character (concentration, molecular weight, regularity) of the high molecular weight mode. We apply a number of in situ characterization tools (rheo-optics, rheo-WAXD) to the development of transient structure and interpret our findings in light of ex situ microscopic examination of the final morphology. Blending a well-characterized high molecular weight isotactic polypropylene into a "base iPP" at various concentrations (c), we determined that less than 1% of long chains with Mw five times larger than the Mw of the base resin profoundly affected the flow-induced crystallization kinetics and morphology. Varying the concentration from below to above c* indicated that the effect of the long chains involves cooperative interactions enhanced by long chain-long chain overlap. The long chains particularly influence the formation of anisotropic nuclei. Studying a series of bimodal blends in which the long chain molecular weight (ML) was varied, we found that increasing ML increased the tendency to form threadlike precursors to oriented crystallization. This was highlighted by a marked decrease in the threshold stress (sigma*) necessary to induce oriented crystallization. A minimum separation in relaxation time scales (˜100 times slower) between the long chains and the average was necessary to form long lived oriented precursor structures. A novel "depth sectioning" analysis technique allowed us to gain depth dependent information from real-time rheo-optical and rheo-WAXD experiments. We identify a promising set of conditions that may be used to measure the thread propagation velocity for this material if the appropriate length scale can be assigned by microscopy. Threads first form near the channel wall and grow in length with prolonged flow until thread length per unit volume saturates. Prior to saturation, the thread

  16. The role of molecular methods in evaluating biological treatment processes.

    PubMed

    Rittmann, Bruce E

    2002-01-01

    Methods derived from molecular biology provide powerful new tools to analyze biological treatment processes. Because molecular methods can be used to directly interrogate genetic information about the microbial community, they can provide the fine detail that is impossible with the blunt, nondiscriminating information usually obtained from more traditional measures such as biochemical oxygen demand and volatile suspended solids. Molecular methods allow tracking of critical groups of microorganisms, such as ammonia oxidizers, that comprise a small fraction of the total biomass. Molecular methods also allow tracking of specific metabolic reactions or other functions that are key to the satisfactory performance of a system. Despite their power, molecular methods do not provide sufficient information when used alone. Aggregated measures and quantitative modeling remain necessary to establish mass balances, quantify the function of the microbial community, and connect the results of molecular assays to practice. Several examples involving nitrifying bacteria in activated sludge illustrate the fine detail available with molecular methods and how they can be linked to traditional and quantitative analyses. Other manuscripts in this special issue also provide examples of the value of using molecular tools in combination with traditional methods.

  17. Modeling Molecular and Cellular Aspects of Human Disease using the Nematode Caenorhabditis elegans

    PubMed Central

    Silverman, Gary A.; Luke, Cliff J.; Bhatia, Sangeeta R.; Long, Olivia S.; Vetica, Anne C.; Perlmutter, David H.; Pak, Stephen C.

    2009-01-01

    As an experimental system, Caenorhabditis elegans, offers a unique opportunity to interrogate in vivo the genetic and molecular functions of human disease-related genes. For example, C. elegans has provided crucial insights into fundamental biological processes such as cell death and cell fate determinations, as well as pathological processes such as neurodegeneration and microbial susceptibility. The C. elegans model has several distinct advantages including a completely sequenced genome that shares extensive homology with that of mammals, ease of cultivation and storage, a relatively short lifespan and techniques for generating null and transgenic animals. However, the ability to conduct unbiased forward and reverse genetic screens in C. elegans remains one of the most powerful experimental paradigms for discovering the biochemical pathways underlying human disease phenotypes. The identification of these pathways leads to a better understanding of the molecular interactions that perturb cellular physiology, and forms the foundation for designing mechanism-based therapies. To this end, the ability to process large numbers of isogenic animals through automated work stations suggests that C. elegans, manifesting different aspects of human disease phenotypes, will become the platform of choice for in vivo drug discovery and target validation using high-throughput/content screening technologies. PMID:18852689

  18. Human papillomavirus molecular biology and disease association

    PubMed Central

    Egawa, Nagayasu; Griffin, Heather; Kranjec, Christian; Murakami, Isao

    2015-01-01

    Summary Human papillomaviruses (HPVs) have evolved over millions of years to propagate themselves in a range of different animal species including humans. Viruses that have co‐evolved slowly in this way typically cause chronic inapparent infections, with virion production in the absence of apparent disease. This is the case for many Beta and Gamma HPV types. The Alpha papillomavirus types have however evolved immunoevasion strategies that allow them to cause persistent visible papillomas. These viruses activate the cell cycle as the infected epithelial cell differentiates in order to create a replication competent environment that allows viral genome amplification and packaging into infectious particles. This is mediated by the viral E6, E7, and E5 proteins. High‐risk E6 and E7 proteins differ from their low‐risk counterparts however in being able to drive cell cycle entry in the upper epithelial layers and also to stimulate cell proliferation in the basal and parabasal layers. Deregulated expression of these cell cycle regulators underlies neoplasia and the eventual progression to cancer in individuals who cannot resolve high‐risk HPV infection. Most work to date has focused on the study of high‐risk HPV types such as HPV 16 and 18, which has led to an understanding of the molecular pathways subverted by these viruses. Such approaches will lead to the development of better strategies for disease treatment, including targeted antivirals and immunotherapeutics. Priorities are now focused toward understanding HPV neoplasias at sites other than the cervix (e.g. tonsils, other transformation zones) and toward understanding the mechanisms by which low‐risk HPV types can sometimes give rise to papillomatosis and under certain situations even cancers. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25752814

  19. A possible molecular metric for biological evolvability.

    PubMed

    Mittal, Aditya; Jayaram, B

    2012-07-01

    Proteins manifest themselves as phenotypic traits, retained or lost in living systems via evolutionary pressures. Simply put, survival is essentially the ability of a living system to synthesize a functional protein that allows for a response to environmental perturbations (adaptation). Loss of functional proteins leads to extinction. Currently there are no universally applicable quantitative metrics at the molecular level for either measuring 'evolvability' of life or for assessing the conditions under which a living system would go extinct and why. In this work, we show emergence of the first such metric by utilizing the recently discovered stoichiometric margin of life for all known naturally occurring (and functional) proteins. The constraint of having well-defined stoichiometries of the 20 amino acids in naturally occurring protein sequences requires utilization of the full scope of degeneracy in the genetic code, i.e. usage of all codons coding for an amino acid, by only 11 of the 20 amino acids. This shows that the non-availability of individual codons for these 11 amino acids would disturb the fine stoichiometric balance resulting in non-functional proteins and hence extinction. Remarkably, these amino acids are found in close proximity of any given amino acid in the backbones of thousands of known crystal structures of folded proteins. On the other hand, stoichiometry of the remaining 9 amino acids, found to be farther/distal from any given amino acid in backbones of folded proteins, is maintained independent of the number of codons available to synthesize them, thereby providing some robustness and hence survivability.

  20. Molecular biology of somatostatin receptor subtypes.

    PubMed

    Patel, Y C; Greenwood, M; Panetta, R; Hukovic, N; Grigorakis, S; Robertson, L A; Srikant, C B

    1996-08-01

    Somatostatin (SRIF) receptors (ssts) comprise a family of heptahelical membrane proteins encoded by five related genes that map to separate chromosomes and which, with the exception of sst1, are intronless. The ssts1-4 display weak selectivity for SRIF-14 binding, whereas sst5 is SRIF-28-selective. Based on structural similarity and reactivity for octapeptide and hexapeptide sst analogs, ssts2,3 and sst5 belong to a similar sst subclass; ssts1-4 react poorly with these analogs and belong to a separate subclass. All five ssts are functionally coupled to inhibition of adenylyl cyclase via pertussis toxin-sensitive guanosine triphosphate (GTP)-binding proteins. mRNA for ssts1-5 is widely expressed in brain and peripheral organs and displays an overlapping but characteristic pattern that is subtype-selective and tissue- and species-specific. All pituitary cell subsets express sst2 and sst5, with sst5 being more abundant. Individual pituitary cells coexpress multiple sst subtypes. The binding pocket for SRIF-14 ligand lies deep within the membrane in transmembrane domains (TMDs) 3 to 7. Except for extracellular loop 2, it does not involve the other exofacial structures. Human (h)sst2A and hsst5 undergo agonist-mediated desensitization, associated with receptor internalization. The C-tail segment of hsst5 displays positive molecular internalization signals. The ssts inhibit the growth of tumor cells directly, through blockade of mitogenic signaling leading to growth arrest and through induction of apoptosis. This process is associated with translocation of phosphotyrosine phosphatase (PTP) 1C from the cytosol to the membrane.

  1. Human papillomavirus molecular biology and disease association.

    PubMed

    Doorbar, John; Egawa, Nagayasu; Griffin, Heather; Kranjec, Christian; Murakami, Isao

    2015-03-01

    Human papillomaviruses (HPVs) have evolved over millions of years to propagate themselves in a range of different animal species including humans. Viruses that have co-evolved slowly in this way typically cause chronic inapparent infections, with virion production in the absence of apparent disease. This is the case for many Beta and Gamma HPV types. The Alpha papillomavirus types have however evolved immunoevasion strategies that allow them to cause persistent visible papillomas. These viruses activate the cell cycle as the infected epithelial cell differentiates in order to create a replication competent environment that allows viral genome amplification and packaging into infectious particles. This is mediated by the viral E6, E7, and E5 proteins. High-risk E6 and E7 proteins differ from their low-risk counterparts however in being able to drive cell cycle entry in the upper epithelial layers and also to stimulate cell proliferation in the basal and parabasal layers. Deregulated expression of these cell cycle regulators underlies neoplasia and the eventual progression to cancer in individuals who cannot resolve high-risk HPV infection. Most work to date has focused on the study of high-risk HPV types such as HPV 16 and 18, which has led to an understanding of the molecular pathways subverted by these viruses. Such approaches will lead to the development of better strategies for disease treatment, including targeted antivirals and immunotherapeutics. Priorities are now focused toward understanding HPV neoplasias at sites other than the cervix (e.g. tonsils, other transformation zones) and toward understanding the mechanisms by which low-risk HPV types can sometimes give rise to papillomatosis and under certain situations even cancers.

  2. Molecular aspects of prostate cancer with neuroendocrine differentiation

    PubMed Central

    Li, Qi; Zhang, Connie S.

    2016-01-01

    Neuroendocrine differentiation (NED), which is not uncommon in prostate cancer, is increases in prostate cancer after androgen-deprivation therapy (ADT) and generally appears in castration-resistant prostate cancer (CRPC). Neuroendocrine cells, which are found in normal prostate tissue, are a small subset of cells and have unique function in regulating the growth of prostate cells. Prostate cancer with NED includes different types of tumor, including focal NED, pure neuroendocrine tumor or mixed neuroendocrine-adenocarcinoma. Although more and more studies are carried out on NED in prostate cancer, the molecular components that are involved in NED are still poorly elucidated. We review neuroendocrine cells in normal prostate tissue, NED in prostate cancer, terminology of NED and biomarkers used for detecting NED in routine pathological practice. Some recently reported molecular components which drive NED in prostate cancer are listed in the review. PMID:27041934

  3. Molecular and genetic aspects of odontogenic tumors: a review

    PubMed Central

    Garg, Kavita; Chandra, Shaleen; Raj, Vineet; Fareed, Wamiq; Zafar, Muhammad

    2015-01-01

    Odontogenic tumors contain a heterogeneous collection of lesions that are categorized from hamartomas to benign and malignant neoplasms of inconstant aggressiveness. Odontogenic tumors are usually extraordinary with assessed frequency of short of 0.5 cases/100,000 population for every year. The lesions such as odontogenic tumors are inferred from the components of the tooth-structuring contraption. They are discovered solely inside the maxillary and mandibular bones. This audit speaks to experiences and cooperation of the molecular and genetic variations connected to the development and movement of odontogenic tumors which incorporate oncogenes, tumor-silencer genes, APC gene, retinoblastoma genes, DNA repair genes, onco-viruses, development components, telomerase, cell cycle controllers, apoptosis-related elements, and regulators/conttrollers of tooth development. The reasonable and better understanding of the molecular components may prompt new ideas for their detection and administrating a better prognosis of odontogenic tumors. PMID:26221475

  4. Theoretical aspects of gas-phase molecular dynamics

    SciTech Connect

    Muckerman, J.T.

    1993-12-01

    Research in this program is focused on the development and application of time-dependent quantum mechanical and semiclassical methods for treating inelastic and reactive molecular collisions, and the photochemistry and photophysics of atoms and molecules in laser fields. Particular emphasis is placed on the development and application of grid methods based on discrete variable representations, on time-propagation methods, and, in systems with more that a few degrees of freedom, on the combined use of quantal wavepackets and classical trajectories.

  5. Molecular diagnosis of sepsis: New aspects and recent developments

    PubMed Central

    Lehman, L.; Hunfeld, K.-P.; Kost, G.

    2014-01-01

    By shortening the time to pathogen identification and allowing for detection of organisms missed by blood culture, new molecular methods may provide clinical benefits for the management of patients with sepsis. While a number of reviews on the diagnosis of sepsis have recently been published we here present up-to-date new developments including multiplex PCR, mass spectrometry and array techniques. We focus on those techniques that are commercially available and for which clinical studies have been performed and published. PMID:24678402

  6. Collective aspects of singlet fission in molecular crystals

    SciTech Connect

    Teichen, Paul E.; Eaves, Joel D.

    2015-07-28

    We present a model to describe collective features of singlet fission in molecular crystals and analyze it using many-body theory. The model we develop allows excitonic states to delocalize over several chromophores which is consistent with the character of the excited states in many molecular crystals, such as the acenes, where singlet fission occurs. As singlet states become more delocalized and triplet states more localized, the rate of singlet fission increases. We also determine the conditions under which the two triplets resulting from fission are correlated. Using the Bethe Ansatz and an entanglement measure for indistinguishable bipartite systems, we calculate the triplet-triplet entanglement as a function of the biexciton interaction strength. The biexciton interaction can produce bound biexciton states and provides a source of entanglement between the two triplets even when the triplets are spatially well separated. Significant entanglement between the triplet pair occurs well below the threshold for bound pair formation. Our results paint a dynamical picture that helps to explain why fission has been observed to be more efficient in molecular crystals than in their covalent dimer analogues and have consequences for photovoltaic efficiency models that assume that the two triplets can be extracted independently.

  7. Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction.

    PubMed

    Boniolo, Giovanni; D'Agostino, Marcello; Di Fiore, Pier Paolo

    2010-03-03

    We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word zetaomegaeta, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical "deduction". Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction.

  8. A Streamlined Molecular Biology Module for Undergraduate Biochemistry Labs

    ERIC Educational Resources Information Center

    Muth, Gregory W.; Chihade, Joseph W.

    2008-01-01

    Site-directed mutagenesis and other molecular biology techniques, including plasmid manipulation and restriction analysis, are commonly used tools in the biochemistry research laboratory. In redesigning our biochemistry lab curricula, we sought to integrate these techniques into a term-long, project-based course. In the module presented here,…

  9. Positron emission tomography provides molecular imaging of biological processes

    PubMed Central

    Phelps, Michael E.

    2000-01-01

    Diseases are biological processes, and molecular imaging with positron emission tomography (PET) is sensitive to and informative of these processes. This is illustrated by detection of biological abnormalities in neurological disorders with no computed tomography or MRI anatomic changes, as well as even before symptoms are expressed. PET whole body imaging in cancer provides the means to (i) identify early disease, (ii) differentiate benign from malignant lesions, (iii) examine all organs for metastases, and (iv) determine therapeutic effectiveness. Diagnostic accuracy of PET is 8–43% higher than conventional procedures and changes treatment in 20–40% of the patients, depending on the clinical question, in lung and colorectal cancers, melanoma, and lymphoma, with similar findings in breast, ovarian, head and neck, and renal cancers. A microPET scanner for mice, in concert with human PET systems, provides a novel technology for molecular imaging assays of metabolism and signal transduction to gene expression, from mice to patients: e.g., PET reporter gene assays are used to trace the location and temporal level of expression of therapeutic and endogenous genes. PET probes and drugs are being developed together—in low mass amounts, as molecular imaging probes to image the function of targets without disturbing them, and in mass amounts to modify the target's function as a drug. Molecular imaging by PET, optical technologies, magnetic resonance imaging, single photon emission tomography, and other technologies are assisting in moving research findings from in vitro biology to in vivo integrative mammalian biology of disease. PMID:10922074

  10. An Inquiry-based Introduction to Molecular Biology.

    ERIC Educational Resources Information Center

    Levy, Foster

    2000-01-01

    Presents investigative approaches to teaching molecular biology. Emphasizes a deductive determination of the nature of nucleic acids visualized in a gel, and a comparison of different genomes. Asks why students should take it on faith that what they view on a gel is DNA. (SAH)

  11. Frontiers in nuclear medicine symposium: Nuclear medicine & molecular biology

    SciTech Connect

    1995-04-01

    This document contains the abstracts from the American College of Nuclear Physicians 1993 Fall Meeting entitled, `Frontiers in Nuclear Medicine Symposium: Nuclear Medicine and Molecular Biology`. This meeting was sponsored by the US DOE, Office of Health and Environmental Research, Office of Energy Research. The program chairman was Richard C. Reba, M.D.

  12. Gene Concepts in Higher Education Cell and Molecular Biology Textbooks

    ERIC Educational Resources Information Center

    Albuquerque, Pitombo Maiana; de Almeida, Ana Maria Rocha; El-Hani, Nino Charbel

    2008-01-01

    Despite being a landmark of 20th century biology, the "classical molecular gene concept," according to which a gene is a stretch of DNA encoding a functional product, which may be a single polypeptide or RNA molecule, has been recently challenged by a series of findings (e.g., split genes, alternative splicing, overlapping and nested genes, mRNA…

  13. Web Based Learning Support for Experimental Design in Molecular Biology.

    ERIC Educational Resources Information Center

    Wilmsen, Tinri; Bisseling, Ton; Hartog, Rob

    An important learning goal of a molecular biology curriculum is a certain proficiency level in experimental design. Currently students are confronted with experimental approaches in textbooks, in lectures and in the laboratory. However, most students do not reach a satisfactory level of competence in the design of experimental approaches. This…

  14. Assessing Practical Laboratory Skills in Undergraduate Molecular Biology Courses

    ERIC Educational Resources Information Center

    Hunt, Lynne; Koenders, Annette; Gynnild, Vidar

    2012-01-01

    This study explored a new strategy of assessing laboratory skills in a molecular biology course to improve: student effort in preparation for and participation in laboratory work; valid evaluation of learning outcomes; and students' employment prospects through provision of evidence of their skills. Previously, assessment was based on written…

  15. A Biochemistry and Molecular Biology Course for Secondary School Teachers

    ERIC Educational Resources Information Center

    Fernandez-Novell, J. M.; Cid, E.; Gomis, R.; Barbera, A.; Guinovart, J. J.

    2004-01-01

    This article describes a course for reinforcing the knowledge of biochemistry in secondary school science teachers. The Department of Biochemistry and Molecular Biology of the University of Barcelona designed a course to bring these teachers up to date with this discipline. In addition to updating their knowledge of biochemistry and molecular…

  16. Monogenec Arrhythmic Syndromes: From Molecular and Genetic Aspects to Bedside.

    PubMed

    E Z, Golukhova; O I, Gromova; R A, Shomahov; N I, Bulaeva; L A, Bockeria

    2016-01-01

    The abrupt cessation of effective cardiac function that is generally due to heart rhythm disorders can cause sudden and unexpected death at any age and is referred to as a syndrome called "sudden cardiac death" (SCD). Annually, about 400,000 cases of SCD occur in the United States alone. Less than 5% of the resuscitation techniques are effective. The prevalence of SCD in a population rises with age according to the prevalence of coronary artery disease, which is the most common cause of sudden cardiac arrest. However, there is a peak in SCD incidence for the age below 5 years, which is equal to 17 cases per 100,000 of the population. This peak is due to congenital monogenic arrhythmic canalopathies. Despite their relative rarity, these cases are obviously the most tragic. The immediate causes, or mechanisms, of SCD are comprehensive. Generally, it is arrhythmic death due to ventricular tachyarrythmias - sustained ventricular tachycardia (VT) or ventricular fibrillation (VF). Bradyarrhythmias and pulseless electrical activity account for no more than 40% of all registered cardiac arrests, and they are more often the outcome of the abovementioned arrhythmias. Our current understanding of the mechanisms responsible for SCD has emerged from decades of basic science investigation into the normal electrophysiology of the heart, the molecular physiology of cardiac ion channels, the fundamental cellular and tissue events associated with cardiac arrhythmias, and the molecular genetics of monogenic disorders of the heart rhythm (for example, the long QT syndrome). This review presents an overview of the molecular and genetic basis of SCD in the long QT syndrome, Brugada syndrome, short QT syndrome, catecholaminergic polymorphic ventricular tachycardia and idiopathic ventricular fibrillation, and arrhythmogenic right ventricular dysplasia, and sudden cardiac death prevention strategies by modern techniques (including implantable cardioverter-defibrillator). PMID:27437140

  17. Monogenec Arrhythmic Syndromes: From Molecular and Genetic Aspects to Bedside

    PubMed Central

    E.Z., Golukhova; O.I., Gromova; R.A., Shomahov; N.I., Bulaeva; L.A., Bockeria

    2016-01-01

    The abrupt cessation of effective cardiac function that is generally due to heart rhythm disorders can cause sudden and unexpected death at any age and is referred to as a syndrome called “sudden cardiac death” (SCD). Annually, about 400,000 cases of SCD occur in the United States alone. Less than 5% of the resuscitation techniques are effective. The prevalence of SCD in a population rises with age according to the prevalence of coronary artery disease, which is the most common cause of sudden cardiac arrest. However, there is a peak in SCD incidence for the age below 5 years, which is equal to 17 cases per 100,000 of the population. This peak is due to congenital monogenic arrhythmic canalopathies. Despite their relative rarity, these cases are obviously the most tragic. The immediate causes, or mechanisms, of SCD are comprehensive. Generally, it is arrhythmic death due to ventricular tachyarrythmias – sustained ventricular tachycardia (VT) or ventricular fibrillation (VF). Bradyarrhythmias and pulseless electrical activity account for no more than 40% of all registered cardiac arrests, and they are more often the outcome of the abovementioned arrhythmias. Our current understanding of the mechanisms responsible for SCD has emerged from decades of basic science investigation into the normal electrophysiology of the heart, the molecular physiology of cardiac ion channels, the fundamental cellular and tissue events associated with cardiac arrhythmias, and the molecular genetics of monogenic disorders of the heart rhythm (for example, the long QT syndrome). This review presents an overview of the molecular and genetic basis of SCD in the long QT syndrome, Brugada syndrome, short QT syndrome, catecholaminergic polymorphic ventricular tachycardia and idiopathic ventricular fibrillation, and arrhythmogenic right ventricular dysplasia, and sudden cardiac death prevention strategies by modern techniques (including implantable cardioverter-defibrillator) PMID:27437140

  18. Mathematical aspects of molecular replacement. II. Geometry of motion spaces.

    PubMed

    Chirikjian, Gregory S; Yan, Yan

    2012-03-01

    Molecular replacement (MR) is a well established computational method for phasing in macromolecular crystallography. In MR searches, spaces of motions are explored for determining the appropriate placement of rigid models of macromolecules in crystallographic asymmetric units. In the first paper of this series, it was shown that this space of motions, when endowed with an appropriate composition operator, forms an algebraic structure called a quasigroup. In this second paper, the geometric properties of these MR search spaces are explored and analyzed. This analysis includes the local differential geometry, global geometry and symmetry properties of these spaces.

  19. The Warburg effect: molecular aspects and therapeutic possibilities.

    PubMed

    Ngo, Hanh; Tortorella, Stephanie M; Ververis, Katherine; Karagiannis, Tom C

    2015-04-01

    It has been about nine decades since the proposal of Otto Warburg on the metabolism of cancer cells. Unlike normal cells which undergo glycolysis and oxidative phosphorylation in the presence of oxygen, proliferating and cancer cells exhibit an increased uptake of glucose and increased rate of glycolysis and predominantly undergo lactic acid fermentation. Whether this phenomenon is the consequence of genetic dysregulation in cancer or is the cause of cancer still remains unknown. However, there is certainly a strong link between the genetic factors, epigenetic modulation, cancer immunosurveillance and the Warburg effect, which will be discussed in this review. Dichloroacetate and 3-bromopyruvate are among the substances that have been studied as potential cancer therapies. With our expanding knowledge of cellular metabolism, therapies targeting the Warburg effect appear very promising. This review discusses different aspects of these emerging therapies. PMID:25253100

  20. Biological Diversity and Molecular Plasticity of FIC Domain Proteins.

    PubMed

    Harms, Alexander; Stanger, Frédéric V; Dehio, Christoph

    2016-09-01

    The ubiquitous proteins with FIC (filamentation induced by cyclic AMP) domains use a conserved enzymatic machinery to modulate the activity of various target proteins by posttranslational modification, typically AMPylation. Following intensive study of the general properties of FIC domain catalysis, diverse molecular activities and biological functions of these remarkably versatile proteins are now being revealed. Here, we review the biological diversity of FIC domain proteins and summarize the underlying structure-function relationships. The original and most abundant genuine bacterial FIC domain proteins are toxins that use diverse molecular activities to interfere with bacterial physiology in various, yet ill-defined, biological contexts. Host-targeted virulence factors have evolved repeatedly out of this pool by exaptation of the enzymatic FIC domain machinery for the manipulation of host cell signaling in favor of bacterial pathogens. The single human FIC domain protein HypE (FICD) has a specific function in the regulation of protein stress responses. PMID:27482742

  1. tRNA--the golden standard in molecular biology.

    PubMed

    Barciszewska, Mirosława Z; Perrigue, Patrick M; Barciszewski, Jan

    2016-01-01

    Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology. In 1965, Robert Holley determined the first nucleotide sequence of alanine transfer RNA (tRNA(Ala)) which earned him the 1968 Nobel Prize in Physiology or Medicine. Today, tRNA is one of the best described and characterized biological molecules. Here we review some of the key historical events in tRNA research which led to breakthrough discoveries and new developments in molecular biology.

  2. Chirality as a physical aspect of structure formation in biological macromolecular systems

    NASA Astrophysics Data System (ADS)

    Malyshko, E. V.; Tverdislov, V. A.

    2016-08-01

    A novel regularity of hierarchical structures is found in the formation of chiral biological macromolecular systems. The formation of structures with alternating chirality (helical structures) serves as an instrument of stratification. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development through a series of chiral bifurcations. In the course of biological evolution, the helical structures became basic elements of the molecular machines in the cell. The discreteness of structural levels allowed the mechanical degrees of freedom formation in the molecular machines in the cell.

  3. Apert and Crouzon syndromes-Cognitive development, brain abnormalities, and molecular aspects.

    PubMed

    Fernandes, Marilyse B L; Maximino, Luciana P; Perosa, Gimol B; Abramides, Dagma V M; Passos-Bueno, Maria Rita; Yacubian-Fernandes, Adriano

    2016-06-01

    Apert and Crouzon are the most common craniosynostosis syndromes associated with mutations in the fibroblast growth factor receptor 2 (FGFR2) gene. We conducted a study to examine the molecular biology, brain abnormalities, and cognitive development of individuals with these syndromes. A retrospective longitudinal review of 14 patients with Apert and Crouzon syndromes seen at the outpatient Craniofacial Surgery Hospital for Rehabilitation of Craniofacial Anomalies in Brazil from January 1999 through August 2010 was performed. Patients between 11 and 36 years of age (mean 18.29 ± 5.80), received cognitive evaluations, cerebral magnetic resonance imaging, and molecular DNA analyses. Eight patients with Apert syndrome (AS) had full scale intelligence quotients (FSIQs) that ranged from 47 to 108 (mean 76.9 ± 20.2), and structural brain abnormalities were identified in five of eight patients. Six patients presented with a gain-of-function mutation (p.Ser252Trp) in FGFR2 and FSIQs in those patients ranged from 47 to78 (mean 67.2 ± 10.7). One patient with a gain-of-function mutation (p.Pro253Arg) had a FSIQ of 108 and another patient with an atypical splice mutation (940-2A →G) had a FSIQ of 104. Six patients with Crouzon syndrome had with mutations in exons IIIa and IIIc of FGFR2 and their FSIQs ranged from 82 to 102 (mean 93.5 ± 6.7). These reveal that molecular aspects are another factor that can be considered in studies of global and cognitive development of patients with Apert and Crouzon syndrome (CS). © 2016 Wiley Periodicals, Inc. PMID:27028366

  4. Membrane curvature in cell biology: An integration of molecular mechanisms.

    PubMed

    Jarsch, Iris K; Daste, Frederic; Gallop, Jennifer L

    2016-08-15

    Curving biological membranes establishes the complex architecture of the cell and mediates membrane traffic to control flux through subcellular compartments. Common molecular mechanisms for bending membranes are evident in different cell biological contexts across eukaryotic phyla. These mechanisms can be intrinsic to the membrane bilayer (either the lipid or protein components) or can be brought about by extrinsic factors, including the cytoskeleton. Here, we review examples of membrane curvature generation in animals, fungi, and plants. We showcase the molecular mechanisms involved and how they collaborate and go on to highlight contexts of curvature that are exciting areas of future research. Lessons from how membranes are bent in yeast and mammals give hints as to the molecular mechanisms we expect to see used by plants and protists.

  5. Membrane curvature in cell biology: An integration of molecular mechanisms.

    PubMed

    Jarsch, Iris K; Daste, Frederic; Gallop, Jennifer L

    2016-08-15

    Curving biological membranes establishes the complex architecture of the cell and mediates membrane traffic to control flux through subcellular compartments. Common molecular mechanisms for bending membranes are evident in different cell biological contexts across eukaryotic phyla. These mechanisms can be intrinsic to the membrane bilayer (either the lipid or protein components) or can be brought about by extrinsic factors, including the cytoskeleton. Here, we review examples of membrane curvature generation in animals, fungi, and plants. We showcase the molecular mechanisms involved and how they collaborate and go on to highlight contexts of curvature that are exciting areas of future research. Lessons from how membranes are bent in yeast and mammals give hints as to the molecular mechanisms we expect to see used by plants and protists. PMID:27528656

  6. Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers

    NASA Astrophysics Data System (ADS)

    Newman, Dianne K.; Neubauer, Cajetan; Ricci, Jessica N.; Wu, Chia-Hung; Pearson, Ann

    2016-06-01

    Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record.

  7. [Molecular biology in myelodysplastic syndromes and acute myeloid leukemias "smoldering"].

    PubMed

    Martinelli, Giovanni; Sartor, Chiara; Papayannidis, Cristina; Iacobucci, Ilaria; Paolini, Stefania; Clissa, Cristina; Ottaviani, Emanuela; Finelli, Carlo

    2014-03-01

    Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic disorders of the myeloid lineage characterized by peripheral cytopenias and frequent leukemic evolution. MDS differ for clinical presentation, disease behavior and progression and this is the reflection of remarkable variability at molecular level. To this moment disease diagnosis is still dependent on bone marrow morphology that, although high concordance rates among experts are reported, remains subjective. Karyotype analysis is mandatory but diagnosis may be difficult in presence of normal karyotype or non-informative cytogenetics. Standardized molecular markers are needed to better define diagnosis, prediction of disease progression and prognosis. Furthermore, a molecular biology analysis could provide an important therapeutic tool towards tailored therapy and new insights in the disease's biology.

  8. Responses of plant seedlings to hypergravity: cellular and molecular aspects

    NASA Astrophysics Data System (ADS)

    Hoson, T.; Yoshioka, R.; Soga, K.; Wakabayashi, K.; Takeba, G.

    Hypergravity produced by centrifugation has been used to analyze the responses of plant seedlings to gravity stimulus. Elongation growth of stem organs is suppressed by hypergravity, which can be recognized as a way for plants to resist gravitational force. The mechanisms inducing growth suppression under hypergravity conditions were analyzed at cellular and molecular levels. When growth was suppressed by hypergravity, a decrease in the cell wall extensibility was brought about in various plants. Hypergravity also induced a cell wall thickening and an increase in the molecular mass of the certain hemicellulosic polysaccharides. Both a decrease in the activities hydrolyzing such polysaccharides and an increase in the apoplast pH were involved in such changes in the cell wall constituents. Thus, the cell wall metabolism is greatly modified under hypergravity conditions, which causes a decrease in the cell wall extensibility, thereby inhibiting elongation growth in stem organs. On the other hand, to identify genes involved in hypergravity-induced growth suppression, changes in gene expression by hypergravity treatment were analyzed in Arabidopsis hypocotyls by differential display method. Sixty-two genes were expressed differentially: expression levels of 39 genes increased, whereas those of 23 genes decreased under hypergravity conditions. The expression of these genes was further analyzed using RT-PCR. One of genes upregulated by hypergravity encoded hydroxymethylglutaryl-CoA reductase (HMGR), which catalyzes a reaction producing mevalonic acid, a key precursor of hormones such as gibberellic acid and abscisic acid. The expression of HMGR gene increased within several hours after hypergravity treatment. Also, compactin, an inhibitor of HMGR activity, prevented hypergravity-induced growth suppression, suggesting that HMGR is involved in suppression of Arabidopsis hypocotyl growth by hypergravity. In addition, hypergravity increased the expression levels of CCR1 and

  9. Autoimmune regulator and self-tolerance - molecular and clinical aspects.

    PubMed

    Abramson, Jakub; Husebye, Eystein S

    2016-05-01

    The establishment of central tolerance in the thymus is critical for avoiding deleterious autoimmune diseases. Autoimmune regulator (AIRE), the causative gene in autoimmune polyendocrine syndrome type-1 (APS-1), is crucial for the establishment of self-tolerance in the thymus by promoting promiscuous expression of a wide array of tissue-restricted self-antigens. This step is critical for elimination of high-affinity self-reactive T cells from the immunological repertoire, and for the induction of a specific subset of Foxp3(+) T-regulatory (Treg ) cells. In this review, we discuss the most recent advances in our understanding of how AIRE operates on molecular and cellular levels, as well as of how its loss of function results in breakdown of self-tolerance mechanisms characterized by a broad and heterogeneous repertoire of autoimmune phenotypes. PMID:27088911

  10. [Asbestos and malignant pleural mesothelioma: molecular, cellular and physiopathological aspects].

    PubMed

    Mohr, Steve; Keith, Gérard; Rihn, Bertrand

    2005-11-01

    Asbestos is known as mutagenic and carcinogenic for human and is responsible for many pulmonary diseases including asbestosis, bronchogenic carcinoma and malignant pleural mesothelioma. Occupational exposure to asbestos is involved in 70-80% of all malignant pleural mesothelioma. The later presents a growing challenge for both researcher and clinician. The diagnosis of malignant pleural mesothelioma is difficult and the current treatments did not show significant improvement of the survival. The increasing incidence of malignant pleural mesothelioma, its gravity and its human, social and financial consequences are of high concern in public health. In this paper we summarize the so far knowledge on cellular, molecular and pathophysiological events involved in genesis and development of malignant pleural mesothelioma. Finally, the paper also report recent data sourced from the study of malignant pleural mesothelioma transcriptome using high-throughput technologies such as gene expression array. These data should improve the accuracy of mesothelioma diagnosis and therapy.

  11. Angelman syndrome: review of clinical and molecular aspects.

    PubMed

    Bird, Lynne M

    2014-01-01

    "Angelman syndrome" (AS) is a neurodevelopmental disorder whose main features are intellectual disability, lack of speech, seizures, and a characteristic behavioral profile. The behavioral features of AS include a happy demeanor, easily provoked laughter, short attention span, hypermotoric behavior, mouthing of objects, sleep disturbance, and an affinity for water. Microcephaly and subtle dysmorphic features, as well as ataxia and other movement disturbances, are additional features seen in most affected individuals. AS is due to deficient expression of the ubiquitin protein ligase E3A (UBE3A) gene, which displays paternal imprinting. There are four molecular classes of AS, and some genotype-phenotype correlations have emerged. Much remains to be understood regarding how insufficiency of E6-AP, the protein product of UBE3A, results in the observed neurodevelopmental deficits. Studies of mouse models of AS have implicated UBE3A in experience-dependent synaptic remodeling. PMID:24876791

  12. Molecular Aspects of Flow-Induced Crystallization of Polymers

    NASA Astrophysics Data System (ADS)

    Kornfield, J.

    Like teeth, bone and sea shells, semicrystalline polymers combine strength with toughness by forming a nano-scale composite with platelet-like crystals stacked with noncrystalline material between them. The morphology and orientation distribution of the nanostructure dictate the material properties. Dynamics of polymer chains in the melt play an important role in controlling the morphology, especially under the influence of flow. Using bimodal isotactic polypropylenes to reveal the effects of small concentrations of very long chains, in collaboration with Mitsubishi Chemical, we show that long chains have a profound effect when they are so long that they can undergo chain stretching, particularly when the long chain concentration is at or above their overlap concentration. When subjected to identical stress at identical subcooling, the blends containing long chains undergo dramatically faster crystallization with very strong orientation. The ``long chains" enhance formatio n of highly oriented crystallization precursors (``shish") on which oriented lamellae (``kebabs") subsequently grow. In collaboration with Sumitomo Chemical and The University of Tokyo, we test the hypothesis that the kebabs are actually composed of long chains using isotopic labelling of selected fractions and small angle neutron scattering (SANS). The results show that long chains in the shish are at the same concentration as they are everywhere else: there is no neutron scattering contrast when the long chains are the deuterium labelled ones! The long chains are essential for the formation of shish and they play their role by ``recruiting" adjacent chains into formation of the shish. Placing molecular defects on the longest chains inhibits their ability to serve this role, providing a molecular tool to independently control the melt elasticity (by choice of the length and concentration of the long chains) and the flow-induced crystallization behavior (by selecting the com onomer content, for

  13. Mechanistic modeling confronts the complexity of molecular cell biology.

    PubMed

    Phair, Robert D

    2014-11-01

    Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build-and subject to exhaustive experimental tests-models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set.

  14. Mechanistic modeling confronts the complexity of molecular cell biology

    PubMed Central

    Phair, Robert D.

    2014-01-01

    Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist–electrical engineer–systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build—and subject to exhaustive experimental tests—models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set. PMID:25368428

  15. Molecular Aspects of Transport in Thin Films of Controlled Architecture

    SciTech Connect

    Paul W. Bohn

    2009-04-16

    Our laboratory focuses on developing spatially localized chemistries which can produce structures of controlled architecture on the supermolecular length scale -- structures which allow us to control the motion of molecular species with high spatial resolution, ultimately on nanometer length scales. Specifically, nanocapillary array membranes (NCAMs) contain an array of nanometer diameter pores connecting vertically separated microfluidic channels. NCAMs can manipulate samples with sub-femtoliter characteristic volumes and attomole sample amounts and are opening the field of chemical analysis of mass-limited samples, because they are capable of digital control of fluid switching down to sub-attoliter volumes; extension of analytical “unit operations” down to sub-femtomole sample sizes; and exerting spatiotemporal control over fluid mixing to enable studies of reaction dynamics. Digital flow switching mediated by nanocapillary array membranes can be controlled by bias, ionic strength, or pore diameter and is being studied by observing the temporal characteristics of transport across a single nanopore in thin PMMA membranes. The control of flow via nanopore surface characteristics, charge density and functional group presentation, is being studied by coupled conductivity and laser-induced fluorescence (LIF) measurements. Reactive mixing experiments previously established low millisecond mixing times for NCAM-mediated fluid transfer, and this has been exploited to demonstrate capture of mass-limited target species by Au colloids. Voltage and thermally-activated polymer switches have been developed for active control of transport in NCAMs. Thermally-switchable and size-selective transport was achieved by grafting poly(N-isopropylacrylamide) brushes onto the exterior surface of a Au-coated polycarbonate track-etched membrane, while the voltage-gated properties of poly(hydroxyethylmethacrylate) were characterized dynamically. Electrophoretic separations have been

  16. Biomining Microorganisms: Molecular Aspects and Applications in Biotechnology and Bioremediation

    NASA Astrophysics Data System (ADS)

    Jerez, Carlos A.

    The microbial solubilization of metals using chemolithoautotrophic microorganisms has successfully been used in industrial processes called biomining to extract metals such as copper, gold, uranium and others. The most studied leaching bacteria are from the genus Acidithiobacillus belonging to the Gram-negative γ-proteobacteria. Acidithiobacillus spp. obtain their energy from the oxidation of ferrous iron, elemental sulfur, or partially oxidized sulfur compounds. Other thermophilic archaeons capable of oxidizing sulfur and iron (II) have also been known for many years, and they are mainly from the genera Sulfolobus, Acidianus, Metallosphaera and Sulfurisphaera. Recently, some mesophilic iron (II)-oxidizing archaeons such as Ferroplasma acidiphilium and F. acidarmanus belonging to the Thermoplasmales have also been isolated and characterized. Recent studies of microorganisms consider them in their consortia, integrating fundamental biological knowledge with metagenomics, metaproteomics, and other data to obtain a global picture of how a microbial community functions. The understanding of microbial growth and activities in oxidizing metal ions will be useful for improving applied microbial biotechnologies such as biomining, bioshrouding, biomonitoring and bioremediation of metals in acidic environments.

  17. Molecular studies of functional aspects of plant mitochondria. Progress report

    SciTech Connect

    Siedow, J.N.

    1992-03-03

    The goal of this research is to characterize the mechanism by which a protein encoded by mitochondrial genome of cms-T maize (URF13) interacts with a family of the compounds produced by certain fungi (T-toxins) to permeabilize biological membranes. The research carried out during the current funding period has focused on the structure of URF13, and the results support the validity of the three-helix model of URF13 and provide direct evidence for the oligomeric nature of at least some of the URF13 molecules in the membrane. In addition, the toxin binding studies have provided insight into the dynamic nature of the T-toxin:URF13 interaction and the extent to which Asp-39 is crucial to the interaction that leads to membrane pore formation. Additional knowledge of the structure of URF13 is needed if the nature of the interaction between URF13 and T-toxin to produce a hydrophilic pore within the membrane is to ultimately be understood.

  18. Molecular studies of functional aspects of plant mitochondria

    SciTech Connect

    Siedow, J.N.

    1992-03-03

    The goal of this research is to characterize the mechanism by which a protein encoded by mitochondrial genome of cms-T maize (URF13) interacts with a family of the compounds produced by certain fungi (T-toxins) to permeabilize biological membranes. The research carried out during the current funding period has focused on the structure of URF13, and the results support the validity of the three-helix model of URF13 and provide direct evidence for the oligomeric nature of at least some of the URF13 molecules in the membrane. In addition, the toxin binding studies have provided insight into the dynamic nature of the T-toxin:URF13 interaction and the extent to which Asp-39 is crucial to the interaction that leads to membrane pore formation. Additional knowledge of the structure of URF13 is needed if the nature of the interaction between URF13 and T-toxin to produce a hydrophilic pore within the membrane is to ultimately be understood.

  19. [Dicentric Y chromosomes. First part: cytogenetic and molecular aspects].

    PubMed

    Bouayed Abdelmoula, N; Amouri, A

    2005-01-01

    Dicentric Y chromosomes have been reviewed twice in 1994 by Hsu et al. and in 1995 by Tuck-Muller et al. who showed that dic(Y) are the most common Y structural abnormalities and that their influence on gonadal and somatic development is extremely variable. The prediction of their phenotypic consequences is often difficult because of the variety of genomic sequences concerned by duplications and deletions, because of the variable degrees of mosaicism (cell line 45,X in particular) and at the end, because of identification and analysis technical difficulties of the structure of the rearranged Y chromosome. The clinical specter of this cytogenetic abnormality is rather wide going from almost-normal or infertile males, to females with or without stigmas of Turner syndrome. Middle phenotypes consist of various degrees of genital ambiguities. However, clinical expression seems to be related to the genomic capital of the Y chromosome, mainly the Y genes involved in the control of the process of the determination of gonads (Yp) and spermatogenesis (Yq) as well as control of the growth and the skeletal development (Yp). Here, we report a third comprehensive review of the literature concerning dicentric Y chromosomes reported since 1994. In the light of previous reviews as well as the recent data of the genetic cartography of the Y chromosome, we try, in this first part, to determine characteristics of reported dicentric Y chromosomes as well as their chromosomal mechanics, their mitotic stability and finally their cytogenetic and molecular investigations.

  20. Molecular layer interneurons of the cerebellum: developmental and morphological aspects.

    PubMed

    Sotelo, Constantino

    2015-10-01

    During the past 25 years, our knowledge on the development of basket and stellate cells (molecular layer interneurons [MLIs]) has completely changed, not only regarding their origin from the ventricular zone, corresponding to the primitive cerebellar neuroepithelium, instead of the external granular layer, but above all by providing an almost complete account of the genetic regulations (transcription factors and other genes) involved in their differentiation and synaptogenesis. Moreover, it has been shown that MLIs' precursors (dividing neuroblasts) and not young postmitotic neurons, as in other germinal neuroepithelia, leave the germinative zone and migrate all along a complex and lengthy path throughout the presumptive cerebellar white matter, which provides suitable niches exerting epigenetic influences on their ultimate neuronal identities. Recent studies carried out on the anatomical-functional properties of adult MLIs emphasize the importance of these interneurons in regulating PC inhibition, and point out the crucial role played by electrical synaptic transmission between MLIs as well as ephaptic interactions between them and Purkinje cells at the pinceaux level, in the regulation of this inhibition.

  1. Ferric Enterochelin Transport in Yersinia enterocolitica: Molecular and Evolutionary Aspects

    PubMed Central

    Schubert, S.; Fischer, D.; Heesemann, J.

    1999-01-01

    Yersinia enterocolitica is well equipped for siderophore piracy, encompassing the utilization of siderophores such as ferrioxamine, ferrichrome, and ferrienterochelin. In this study, we report on the molecular and functional characterization of the Yersinia fep-fes gene cluster orthologous to the Escherichia coli ferrienterochelin transport genes (fepA, fepDGC, and fepB) and the esterase gene fes. In vitro transcription-translation analysis identified polypeptides of 30 and 35 kDa encoded by fepC and fes, respectively. A frameshift mutation within the fepA gene led to expression of a truncated polypeptide of 40 kDa. The fepD, fepG, and fes genes of Y. enterocolitica were shown to complement corresponding E. coli mutants. Insertional mutagenesis of fepD or fes genes abrogates enterochelin-supported growth of Y. enterocolitica on iron-chelated media. In contrast to E. coli, the fep-fes gene cluster in Y. enterocolitica consists solely of genes required for uptake and utilization of enterochelin (fep) and not of enterochelin synthesis genes such as entF. By Southern hybridization, fepDGC and fes sequences could be detected in Y. enterocolitica biotypes IB, IA, and II but not in biotype IV strains, Yersinia pestis, and Yersinia pseudotuberculosis strains. According to sequence alignment data and the coherent structure of the Yersinia fep-fes gene cluster, we suggest early genetic divergence of ferrienterochelin uptake determinants among species of the family Enterobacteriaceae. PMID:10515929

  2. Molecular aspects of bovine cystic ovarian disease pathogenesis.

    PubMed

    Ortega, Hugo H; Marelli, Belkis E; Rey, Florencia; Amweg, Ayelen N; Díaz, Pablo U; Stangaferro, Matías L; Salvetti, Natalia R

    2015-06-01

    Cystic ovarian disease (COD) is one of the main causes of reproductive failure in cattle and causes severe economic loss to the dairy farm industry because it increases both days open in the post partum period and replacement rates due to infertility. This disease is the consequence of the failure of a mature follicle to ovulate at the time of ovulation in the estrous cycle. This review examines the evidence for the role of altered steroid and gonadotropin signaling systems and the proliferation/apoptosis balance in the ovary with cystic structures. This evidence suggests that changes in the expression of ovarian molecular components associated with these cellular mechanisms could play a fundamental role in the pathogenesis of COD. The evidence also shows that gonadotropin receptor expression in bovine cystic follicles is altered, which suggests that changes in the signaling system of gonadotropins could play a fundamental role in the pathogenesis of conditions characterized by altered ovulation, such as COD. Ovaries from animals with COD exhibit a disrupted steroid receptor pattern with modifications in the expression of coregulatory proteins. These changes in the pathways of endocrine action would trigger the changes in proliferation and apoptosis underlying the aberrant persistence of follicular cysts. Free Spanish abstract: A Spanish translation of this abstract is freely available at http://www.reproduction-online.org/content/149/6/R251/suppl/DC1.

  3. Serrated polyposis syndrome: molecular, pathological and clinical aspects.

    PubMed

    Guarinos, Carla; Sánchez-Fortún, Cristina; Rodríguez-Soler, María; Alenda, Cristina; Payá, Artemio; Jover, Rodrigo

    2012-05-28

    Hyperplastic polyps have traditionally been considered not to have malignant potential. New pathological classification of serrated polyps and recent discoveries about the serrated pathway of carcinogenesis have revolutionized the concepts and revitalized the research in this area. Until recently, it has been thought that most colorectal cancers arise from conventional adenomas via the traditional tumor suppressor pathway initiated by a mutation of the APC gene, but it has been found that this pathway accounts for only approximately 70%-80% of colorectal cancer (CRC) cases. The majority of the remaining colorectal cancer cases follow an alternative pathway leading to CpG island methylator phenotype carcinoma with BRAF mutation and with or without microsatellite instability. The mechanism of carcinomas arising from this alternative pathway seems to begin with an activating mutation of the BRAF oncogene. Serrated polyposis syndrome is a relatively rare condition characterized by multiple and/or large serrated polyps of the colon. Clinical characteristics, etiology and relationship of serrated polyposis syndrome to CRC have not been clarified yet. Patients with this syndrome show a high risk of CRC and both sporadic and hereditary cases have been described. Clinical criteria have been used for diagnosis and frequent colonoscopy surveillance should be performed in order to prevent colorectal cancer. In this review, we try to gather new insights into the molecular pathogenesis of serrated polyps in order to understand their possible clinical implications and to make an approach to the management of this syndrome.

  4. Molecular Aspects of Plasmodium falciparum Infection during Pregnancy

    PubMed Central

    Ndam, Nicaise Tuikue; Deloron, Philippe

    2007-01-01

    Cytoadherence of Plasmodium-falciparum-parasitized red blood cells (PRBCs) to host receptors is the key phenomenon in the pathological process of the malaria disease. Some of these interactions can originate poor outcomes responsible for 1 to 3 million annual deaths mostly occurring among children in sub-Saharan Africa. Pregnancy-associated malaria (PAM) represents an important exception of the disease occurring at adulthood in malaria endemic settings. Consequences of this are shared between the mother (maternal anemia) and the baby (low birth weight and infant mortality). Demonstrating that parasites causing PAM express specific variant surface antigens (VSAPAM), including the P. falciparum erythrocyte membrane protein 1 (P f EMP1) variant VAR2CSA, that are targets for protective immunity has strengthened the possibility for the development of PAM-specific vaccine. In this paper, we review the molecular basis of malaria pathogenesis attributable to the erythrocyte stages of the parasites, and findings supporting potential anti-PAM vaccine components evidenced in PAM. PMID:17641725

  5. A diagnostic assessment for introductory molecular and cell biology.

    PubMed

    Shi, Jia; Wood, William B; Martin, Jennifer M; Guild, Nancy A; Vicens, Quentin; Knight, Jennifer K

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed for use as a pre- and posttest to measure student learning gains. To develop the assessment, we first worked with faculty to create a set of learning goals that targeted important concepts in the field and seemed likely to be emphasized by most instructors teaching these subjects. We interviewed students using open-ended questions to identify commonly held misconceptions, formulated multiple-choice questions that included these ideas as distracters, and reinterviewed students to establish validity of the instrument. The assessment was then evaluated by 25 biology experts and modified based on their suggestions. The complete revised assessment was administered to more than 1300 students at three institutions. Analysis of statistical parameters including item difficulty, item discrimination, and reliability provides evidence that the IMCA is a valid and reliable instrument with several potential uses in gauging student learning of key concepts in molecular and cell biology.

  6. Molecular biology and genetics affecting pediatric solid tumors.

    PubMed

    Lugo-Vicente, H

    2000-01-01

    Since the discovery of oncogenes more than 20 years ago, it has been proven that cancer is a genetically determined disease. Multiple genetic alteration occurs during the course of an illness for neoplasia to develop. Transformation of positive cell growth regulators (oncogenes) and inactivations of negative cell growth regulators (tumor suppressor genes) merge to express a malignant phenotype. These genetic alterations occur as chromosomal translocations, deletions, inversion, amplification or point mutation. The objective of this review is to introduce basic concepts of molecular biology and describe the molecular genetics and biologic clinical findings of the most important solid malignant tumors in children, namely Neuroblastoma, Wilms and Rhabdomyosarcoma. It is the oncology surgeons responsibility to learn basic molecular genetics and tumor biology to provide rational and appropriate care in the setting of multidisciplinary management. Identifications of new oncogenes will continue to be important milestones in diagnosis, early detection of tumor recurrence, and as potential targets for gene therapy. Fusion proteins generated by mutated translocations are true tumor specific antigens and potential targets for therapy. The predicament is that they are proteins needing therapeutic manipulation within the tumor cell nuclei. Technological advances in molecular and genetics will develop tools necessary to manipulate the cell nuclear DNA and target cancer cell.

  7. [Molecular biology of familial cases of human melanoma].

    PubMed

    Kit, O I; Vodolazhsky, D L; Timoshkina, N N; Przhedetsky, Yu V; Khokhlova, O V

    2015-01-01

    Skin melanoma is an etiologically heterogeneous disease, the development of which is related to a complex interaction of environmental factors and individual genetic characteristics. This article provides current molecular-genetic aspects of familial cases of melanoma and polymorphism of genes directly related to the risk of developing this hereditary disease. The studies of hereditary cancer cases add our knowledge of mechanisms oncotransformation, genetic changes in signaling pathways, which are responsible for invasiveness, metastasis and drug resistance of melanoma cells of the skin.

  8. Molecular circuits, biological switches, and nonlinear dose-response relationships.

    PubMed Central

    Andersen, Melvin E; Yang, Raymond S H; French, C Tenley; Chubb, Laura S; Dennison, James E

    2002-01-01

    Signaling motifs (nuclear transcriptional receptors, kinase/phosphatase cascades, G-coupled protein receptors, etc.) have composite dose-response behaviors in relation to concentrations of protein receptors and endogenous signaling molecules. "Molecular circuits" include the biological components and their interactions that comprise the workings of these signaling motifs. Many of these molecular circuits have nonlinear dose-response behaviors for endogenous ligands and for exogenous toxicants, acting as switches with "all-or-none" responses over a narrow range of concentration. In turn, these biological switches regulate large-scale cellular processes, e.g., commitment to cell division, cell differentiation, and phenotypic alterations. Biologically based dose-response (BBDR) models accounting for these biological switches would improve risk assessment for many nonlinear processes in toxicology. These BBDR models must account for normal control of the signaling motifs and for perturbations by toxic compounds. We describe several of these biological switches, current tools available for constructing BBDR models of these processes, and the potential value of these models in risk assessment. PMID:12634127

  9. Time scale of diffusion in molecular and cellular biology

    NASA Astrophysics Data System (ADS)

    Holcman, D.; Schuss, Z.

    2014-05-01

    Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.

  10. The molecular biology of diffuse large B-cell lymphoma.

    PubMed

    Frick, Mareike; Dörken, Bernd; Lenz, Georg

    2011-12-01

    Diffuse large B-cell lymphoma (DLBCL) represents the most common type of malignant lymphoma. In the last few years, significant progress has been achieved in the understanding of the molecular pathogenesis of this entity. Gene expression profiling has identified three molecular DLBCL subtypes, termed germinal-center B-cell-like (GCB) DLBCL, activated B-cell-like (ABC) DLBCL, and primary mediastinal B-cell lymphoma (PMBL). In this review, we summarize our current understanding of the biology of these DLBCL subtypes with a special emphasis on novel diagnostic and therapeutic approaches. PMID:23556103

  11. Molecular biology of gliomas: present and future challenges

    PubMed Central

    Altieri, R.; Agnoletti, A.; Quattrucci, F.; Garbossa, D.; Calamo Specchia, F. M.; Bozzaro, M.; Fornaro, R.; Mencarani, C.; Lanotte, M.; Spaziante, R.; Ducati, A.

    2014-01-01

    Malignant brain tumours are one of the most relevant causes of morbidity and mortality across a wide range of individuals. Malignant glioma is the most common intra axial tumor in the adult. Many researches on this theme brought advances in the knowledge of gliomas biology and pathogenesis and to the development of new agents for targeted molecular therapy. Recent studies focused on either tumor metabolism analysis or epigenetic regulation in the pathogenesis or maintenance of brain tumors. This Review summarizes these developments analyzing molecular pathology and possible further developments for targeted therapies. PMID:25147764

  12. Molecular biology of gliomas: present and future challenges.

    PubMed

    Altieri, R; Agnoletti, A; Quattrucci, F; Garbossa, D; Calamo Specchia, F M; Bozzaro, M; Fornaro, R; Mencarani, C; Lanotte, M; Spaziante, R; Ducati, A

    2014-09-01

    Malignant brain tumours are one of the most relevant causes of morbidity and mortality across a wide range of individuals. Malignant glioma is the most common intra axial tumor in the adult. Many researches on this theme brought advances in the knowledge of gliomas biology and pathogenesis and to the development of new agents for targeted molecular therapy. Recent studies focused on either tumor metabolism analysis or epigenetic regulation in the pathogenesis or maintenance of brain tumors. This Review summarizes these developments analyzing molecular pathology and possible further developments for targeted therapies.

  13. New Tools and New Biology: Recent Miniaturized Systems for Molecular and Cellular Biology

    PubMed Central

    Hamon, Morgan; Hong, Jong Wook

    2013-01-01

    Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology. PMID:24305843

  14. Grete Kellenberger-Gujer: Molecular biology research pioneer

    PubMed Central

    Citi, Sandra; Berg, Douglas E.

    2016-01-01

    ABSTRACT Grete Kellenberger-Gujer was a Swiss molecular biologist who pioneered fundamental studies of bacteriophage in the mid-20th century at the University of Geneva. Her life and career stories are reviewed here, focusing on her fundamental contributions to our early understanding of phage biology via her insightful analyses of phenomena such as the lysogenic state of a temperate phage (λ), genetic recombination, radiation's in vivo consequences, and DNA restriction-modification; on her creative personality and interactions with peers; and how her academic advancement was affected by gender, societal conditions and cultural attitudes of the time. Her story is important scientifically, putting into perspective features of the scientific community from just before the molecular biology era started through its early years, and also sociologically, in illustrating the numerous “glass ceilings” that, especially then, often hampered the advancement of creative women.

  15. Grete Kellenberger-Gujer: Molecular biology research pioneer.

    PubMed

    Citi, Sandra; Berg, Douglas E

    2016-01-01

    Grete Kellenberger-Gujer was a Swiss molecular biologist who pioneered fundamental studies of bacteriophage in the mid-20(th) century at the University of Geneva. Her life and career stories are reviewed here, focusing on her fundamental contributions to our early understanding of phage biology via her insightful analyses of phenomena such as the lysogenic state of a temperate phage (λ), genetic recombination, radiation's in vivo consequences, and DNA restriction-modification; on her creative personality and interactions with peers; and how her academic advancement was affected by gender, societal conditions and cultural attitudes of the time. Her story is important scientifically, putting into perspective features of the scientific community from just before the molecular biology era started through its early years, and also sociologically, in illustrating the numerous "glass ceilings" that, especially then, often hampered the advancement of creative women. PMID:27607140

  16. Grete Kellenberger-Gujer: Molecular biology research pioneer

    PubMed Central

    Citi, Sandra; Berg, Douglas E.

    2016-01-01

    ABSTRACT Grete Kellenberger-Gujer was a Swiss molecular biologist who pioneered fundamental studies of bacteriophage in the mid-20th century at the University of Geneva. Her life and career stories are reviewed here, focusing on her fundamental contributions to our early understanding of phage biology via her insightful analyses of phenomena such as the lysogenic state of a temperate phage (λ), genetic recombination, radiation's in vivo consequences, and DNA restriction-modification; on her creative personality and interactions with peers; and how her academic advancement was affected by gender, societal conditions and cultural attitudes of the time. Her story is important scientifically, putting into perspective features of the scientific community from just before the molecular biology era started through its early years, and also sociologically, in illustrating the numerous “glass ceilings” that, especially then, often hampered the advancement of creative women. PMID:27607140

  17. Grete Kellenberger-Gujer: Molecular biology research pioneer.

    PubMed

    Citi, Sandra; Berg, Douglas E

    2016-01-01

    Grete Kellenberger-Gujer was a Swiss molecular biologist who pioneered fundamental studies of bacteriophage in the mid-20(th) century at the University of Geneva. Her life and career stories are reviewed here, focusing on her fundamental contributions to our early understanding of phage biology via her insightful analyses of phenomena such as the lysogenic state of a temperate phage (λ), genetic recombination, radiation's in vivo consequences, and DNA restriction-modification; on her creative personality and interactions with peers; and how her academic advancement was affected by gender, societal conditions and cultural attitudes of the time. Her story is important scientifically, putting into perspective features of the scientific community from just before the molecular biology era started through its early years, and also sociologically, in illustrating the numerous "glass ceilings" that, especially then, often hampered the advancement of creative women.

  18. Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

    PubMed

    Reinhold, William C

    2015-12-10

    There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

  19. A discussion of molecular biology methods for protein engineering.

    PubMed

    Zawaira, Alexander; Pooran, Anil; Barichievy, Samantha; Chopera, Denis

    2012-05-01

    A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. We discuss the basic principles of these methods in a repertoire that may be used to achieve the elemental steps in protein engineering. These include site-directed, deletion and insertion mutagenesis. We provide detailed case studies, drawn from our own experiences, packaged together with conceptual discussions and include an analysis of the techniques presented with regards to their uses in protein engineering.

  20. In focus: molecular and cell biology research in China.

    PubMed

    Yao, Xuebiao; Li, Dangsheng; Pei, Gang

    2013-09-01

    An interactive, intellectual environment with good funding opportunities is essential for the development and success of basic research. The fast-growing economy and investment in science, together with a visionary plan, have attracted foreign scholars to work in China, motivated world-class Chinese scientists to return and strengthened the country's international collaborations. As a result, molecular and cell biology research in China has evolved rapidly over the past decade.

  1. Biological Moleculars: Have Most of Our Problems Already Been Solved?

    NASA Technical Reports Server (NTRS)

    Downey, James P.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Evolution has resulted in biological machinery that engineers have great reason to envy and at present can only poorly mimic. This is not just a curiosity as biological systems perform many functions that are desired industrial processes. Examples include photosynthesis, chemosynthesis, energy storage, low temperature chemical conversion, reproducible manufacture of chemical compounds, etc. The bases of biological machinery are the proteins and nucleic acids that comprise living organisms. Each molecule functions as a part of a biological machine. In many cases the molecule can be properly regarded as a stand alone machine of its own. Concepts and methods for harnessing the power of biological molecules exist but are often overlooked in the industrial world. Some are old and appear crude but are quite effective, e.g. the fermentation of grains and fruits. Currently, there is a revolution in progress regarding the harnessing biological processes. These include techniques such as genetic manipulation via polymerase chain reaction, forced evolution also known as evolution in a test tube, determination of molecular structure, and combinatorial chemistry. The following is a brief discussion on how these processes are performed and how they may relate to industrial and aerospace processes.

  2. Protocols, practices, and the reproduction of technique in molecular biology.

    PubMed

    Lynch, Michael

    2002-06-01

    Protocols are one of the main organizational resources in molecular biology. They are written instructions that specify ingredients, equipment, and sequences of steps for making technical preparations. Some protocols are published in widely used manuals, while others are hand-written variants used by particular laboratories and individual technicians. It is widely understood, both in molecular biology and in social studies of science, that protocols do not describe exactly what practitioners do in the laboratory workplace. In social studies of science, the difference between protocols and the actual practices of doing them often is used to set up ironic contrasts between 'messy' laboratory practices and the appearance of technical order. Alternatively, in ethnomethodological studies of work, the difference is examined as a constitutive feature, both of the lived-work of doing technical projects, and of the administrative work of regulating and evaluating such projects. The present article takes its point of departure from ethnomethodology, and begins with a discussion of local problems with performing molecular biology protocols on specific occasions. The discussion then moves to particular cases in criminal law in which defense attorneys cross-examine forensic technicians and lab administrators. In these interrogations, the distinction between protocols and actual practices animates the dialogue and becomes consequential for judgments in the case at hand. The article concludes with a discussion of administrative science: the work of treating protocols and paper trails as proxies for actual 'scientific' practices.

  3. Topology and static response of interaction networks in molecular biology.

    PubMed

    Radulescu, Ovidiu; Lagarrigue, Sandrine; Siegel, Anne; Veber, Philippe; Le Borgne, Michel

    2006-02-22

    We introduce a mathematical framework describing static response of networks occurring in molecular biology. This formalism has many similarities with the Laplace-Kirchhoff equations for electrical networks. We introduce the concept of graph boundary and we show how the response of the biological networks to external perturbations can be related to the Dirichlet or Neumann problems for the corresponding equations on the interaction graph. Solutions to these two problems are given in terms of path moduli (measuring path rigidity with respect to the propagation of interaction along the graph). Path moduli are related to loop products in the interaction graph via generalized Mason-Coates formulae. We apply our results to two specific biological examples: the lactose operon and the genetic regulation of lipogenesis. Our applications show consistency with experimental results and in the case of lipogenesis check some hypothesis on the behaviour of hepatic fatty acids on fasting. PMID:16849230

  4. Topology and static response of interaction networks in molecular biology

    PubMed Central

    Radulescu, Ovidiu; Lagarrigue, Sandrine; Siegel, Anne; Veber, Philippe; Le Borgne, Michel

    2005-01-01

    We introduce a mathematical framework describing static response of networks occurring in molecular biology. This formalism has many similarities with the Laplace–Kirchhoff equations for electrical networks. We introduce the concept of graph boundary and we show how the response of the biological networks to external perturbations can be related to the Dirichlet or Neumann problems for the corresponding equations on the interaction graph. Solutions to these two problems are given in terms of path moduli (measuring path rigidity with respect to the propagation of interaction along the graph). Path moduli are related to loop products in the interaction graph via generalized Mason–Coates formulae. We apply our results to two specific biological examples: the lactose operon and the genetic regulation of lipogenesis. Our applications show consistency with experimental results and in the case of lipogenesis check some hypothesis on the behaviour of hepatic fatty acids on fasting. PMID:16849230

  5. Clinical Applications of Molecular Biology for Infectious Diseases

    PubMed Central

    Speers, David J

    2006-01-01

    Molecular biological methods for the detection and characterisation of microorganisms have revolutionised diagnostic microbiology and are now part of routine specimen processing. Polymerase chain reaction (PCR) techniques have led the way into this new era by allowing rapid detection of microorganisms that were previously difficult or impossible to detect by traditional microbiological methods. In addition to detection of fastidious microorganisms, more rapid detection by molecular methods is now possible for pathogens of public health importance. Molecular methods have now progressed beyond identification to detect antimicrobial resistance genes and provide public health information such as strain characterisation by genotyping. Treatment of certain microorganisms has been improved by viral resistance detection and viral load testing for the monitoring of responses to antiviral therapies. With the advent of multiplex PCR, real-time PCR and improvements in efficiency through automation, the costs of molecular methods are decreasing such that the role of molecular methods will further increase. This review will focus on the clinical utility of molecular methods performed in the clinical microbiology laboratory, illustrated with the many examples of how they have changed laboratory diagnosis and therefore the management of infectious diseases. PMID:16886046

  6. Molecular biology in studies of oceanic primary production

    SciTech Connect

    LaRoche, J.; Falkowski, P.G. ); Geider, R. . Coll. of Marine Studies)

    1992-01-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  7. Molecular biology in studies of oceanic primary production

    SciTech Connect

    LaRoche, J.; Falkowski, P.G.; Geider, R.

    1992-07-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  8. A national comparison of biochemistry and molecular biology capstone experiences.

    PubMed

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices.

  9. Genomic Signal Processing: Predicting Basic Molecular Biological Principles

    NASA Astrophysics Data System (ADS)

    Alter, Orly

    2005-03-01

    Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of

  10. Single-stranded DNA-binding proteins (SSBs) -- sources and applications in molecular biology.

    PubMed

    Kur, Józef; Olszewski, Marcin; Długołecka, Anna; Filipkowski, Paweł

    2005-01-01

    Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombination, and repair in bacteria, archaea and eukarya. The SSBs share a common core ssDNA-binding domain with a conserved OB (oligonucleotide/oligosaccharide binding) fold. This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life. In recent years, there has been an increasing interest in SSBs because they are useful for molecular biology methods and for analytical purposes. In this review, we concentrate on recent advances in the discovery of new sources of SSBs as well as certain aspects of their applications in analytical sciences.

  11. Zsyntax: A Formal Language for Molecular Biology with Projected Applications in Text Mining and Biological Prediction

    PubMed Central

    Boniolo, Giovanni; D'Agostino, Marcello; Di Fiore, Pier Paolo

    2010-01-01

    We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word ζωή, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical “deduction”. Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction. PMID:20209084

  12. [Molecular Biology on the Mechanisms of Autism Spectrum Disorder for Clinical Psychiatrists].

    PubMed

    Makinodan, Manabu

    2015-01-01

    While, in general, a certain number of clinical psychiatrists might not be familiar with molecular biology, the mechanisms of mental illnesses have been uncovered by molecular biology for decades. Among mental illnesses, even biological psychiatrists and neuroscientists have paid less attention to the biological treatment of autism spectrum disorder (ASD) than Alzheimer's disease and schizophrenia since ASD has been regarded as a developmental disorder that was seemingly untreatable. However, multifaceted methods of molecular biology have revealed the mechanisms that would lead to the medication of ASD. In this article, how molecular biology dissects the pathobiology of ASD is described in order to announce the possibilities of biological treatment for clinical psychiatrists.

  13. Student perceptions: Importance of and satisfaction with aspects of an online biology course

    NASA Astrophysics Data System (ADS)

    Hendry, Sheila R.

    Research of student satisfaction with various facets of an online biology course, as well as the perceived importance of these aspects, was conducted during the summer and fall 2004 semesters within a course, History of Biology, at a university in the southeastern United States. This research is based on the theory of transactional distance, which involves dialogue between the teacher and student, the physical environments of both the student and teacher, and the emotional environments of each. Student ratings of importance and satisfaction regarding aspects of convenience, grade earned/knowledge learned, emotional health, communication, and student support were collected toward the end of each semester, via the online course, using the researcher-designed Student Perceptions Survey. Statistics with repeated measures ANOVA, using an alpha of 0.05, determined differences between importance and satisfaction ratings for each of these aspects. Students perceived grade earned/knowledge learned to be the most important aspect of learning online, although it is not an aspect unique to online courses. All of the aspects included in the study were found to be at least somewhat important. Convenience was the aspect with which students were most satisfied, with students at least somewhat satisfied with the other aspects. Although convenience is an inherent strength of the online course format, instructors should be aware of how important it is to design requirements of the online class to help students acquire knowledge while allowing them to do so at their own pace. Well-structured content, prompt feedback, encouragement of quality student-instructor communication, and student support are all parts of a positive online course experience. The Student Perceptions Survey, created specifically for this research, can have substantial value both in the creation of new online courses and in the evaluation of pre-existing courses. It can provide important information that can be

  14. [Molecular biology of familial cases of human melanoma].

    PubMed

    Kit, O I; Vodolazhsky, D L; Timoshkina, N N; Przhedetsky, Yu V; Khokhlova, O V

    2015-01-01

    Skin melanoma is an etiologically heterogeneous disease, the development of which is related to a complex interaction of environmental factors and individual genetic characteristics. This article provides current molecular-genetic aspects of familial cases of melanoma and polymorphism of genes directly related to the risk of developing this hereditary disease. The studies of hereditary cancer cases add our knowledge of mechanisms oncotransformation, genetic changes in signaling pathways, which are responsible for invasiveness, metastasis and drug resistance of melanoma cells of the skin. PMID:26995975

  15. Support of the IMA summer program molecular biology. Final report

    SciTech Connect

    Friedman, A.

    1995-08-01

    The revolutionary progress in molecular biology within the last 30 years opens the way to full understanding of the molecular structures and mechanisms of living organisms. The mathematical sciences accompany and support much of the progress achieved by experiment and computation, as well as provide insight into geometric and topological properties of biomolecular structure and processes. The 4 week program at the IMA brought together biologists and mathematicians leading researchers, postdocs, and graduate students. It focused on genetic mapping and DNA sequencing, followed by biomolecular structure and dynamics. High-resolution linkage maps of genetic marker were discussed extensively in relation to the human genome project. The next level of DNA mapping is physical mapping, consisting of overlapping clones spanning the genome. These maps are extremely useful for genetic analysis. They provide the material for less redundant sequencing and for detailed searches for a gene among other things. This topic was also extensively studied by the participants. From there, the program moved to consider protein structure and dynamics; this is a broad field with a large array of interesting topics. It is of key importance in answering basic scientific questions about the nature of all living organisms, and has practical biomedical applications. The major subareas of structure prediction and classification, techniques and heuristics for the simulation of protein folding, and molecular dynamics provide a rich problem domain where mathematics can be helpful in analysis, modeling, and simulation. One of the important problems in molecular biology is the three-dimensional structure of proteins, DNA and RNA in the cell, and the relationship between structure and function. The program helped increased the understanding of the topology of cellular DNA, RNA and proteins and the various life-sustaining mechanisms used by the cell which modify this molecular topology.

  16. Towards molecular computers that operate in a biological environment

    NASA Astrophysics Data System (ADS)

    Kahan, Maya; Gil, Binyamin; Adar, Rivka; Shapiro, Ehud

    2008-07-01

    important consequences when performed in a proper context. We envision that molecular computers that operate in a biological environment can be the basis of “smart drugs”, which are potent drugs that activate only if certain environmental conditions hold. These conditions could include abnormalities in the molecular composition of the biological environment that are indicative of a particular disease. Here we review the research direction that set this vision and attempts to realize it.

  17. Extracting evidence from forensic DNA analyses: future molecular biology directions.

    PubMed

    Budowle, Bruce; van Daal, Angela

    2009-04-01

    Molecular biology tools have enhanced the capability of the forensic scientist to characterize biological evidence to the point where it is feasible to analyze minute samples and achieve high levels of individualization. Even with the forensic DNA field's maturity, there still are a number of areas where improvements can be made. These include: enabling the typing of samples of limited quantity and quality; using genetic information and novel markers to provide investigative leads; enhancing automation with robotics, different chemistries, and better software tools; employing alternate platforms for typing DNA samples; developing integrated microfluidic/microfabrication devices to process DNA samples with higher throughput, faster turnaround times, lower risk of contamination, reduced labor, and less consumption of evidentiary samples; and exploiting high-throughput sequencing, particularly for attribution in microbial forensics cases. Knowledge gaps and new directions have been identified where molecular biology will likely guide the field of forensics. This review aims to provide a roadmap to guide those interested in contributing to the further development of forensic genetics.

  18. MYC cofactors: molecular switches controlling diverse biological outcomes.

    PubMed

    Hann, Stephen R

    2014-06-17

    The transcription factor MYC has fundamental roles in proliferation, apoptosis, tumorigenesis, and stem cell pluripotency. Over the last 30 years extensive information has been gathered on the numerous cofactors that interact with MYC and the target genes that are regulated by MYC as a means of understanding the molecular mechanisms controlling its diverse roles. Despite significant advances and perhaps because the amount of information learned about MYC is overwhelming, there has been little consensus on the molecular functions of MYC that mediate its critical biological roles. In this perspective, the major MYC cofactors that regulate the various transcriptional activities of MYC, including canonical and noncanonical transactivation and transcriptional repression, will be reviewed and a model of how these transcriptional mechanisms control MYC-mediated proliferation, apoptosis, and tumorigenesis will be presented. The basis of the model is that a variety of cofactors form dynamic MYC transcriptional complexes that can switch the molecular and biological functions of MYC to yield a diverse range of outcomes in a cell-type- and context-dependent fashion.

  19. Using Molecular Biology to Develop Drugs for Renal Cell Carcinoma

    PubMed Central

    Cowey, C. Lance; Rathmell, W. Kimryn

    2010-01-01

    Background Renal cell carcinoma is a disease marked by a unique biology which has governed it’s long history of poor response to conventional cancer treatments. The discovery of the signaling pathway activated as a result of inappropriate constitutive activation of the hypoxia inducible factors (HIF), transcription factors physiologically and transiently stabilized in response to low oxygen, has provided a primary opportunity to devise treatment strategies to target this oncogenic pathway. Objective A review of the molecular pathogenesis of renal cell cancer as well as molecularly targeted therapies, both those currently available and those in development, will be provided. In addition, trials involving combination or sequential targeted therapy are discussed. Methods A detailed review of the literature describing the molecular biology of renal cell cancer and novel therapies was performed and summarized. Results/Conclusion Therapeutics targeting angiogenesis have provided the first class of agents which provide clinical benefit in a large majority of patients and heralded renal cell carcinoma as a solid tumor paradigm for the development of novel therapeutics. Multiple strategies targeting this pathway and now other identified pathways in renal cell carcinoma provide numerous potential opportunities to make major improvements in treating this historically devastating cancer. PMID:20648240

  20. Internal radiation therapy: a neglected aspect of nuclear medicine in the molecular era

    PubMed Central

    Lin, Yansong

    2015-01-01

    Abstract With increasing evidence, internal radiation therapy, also known as brachytherapy, has become a neglected aspect of nuclear medicine in the molecular era. In this paper, recent developments regarding internal radiation therapy, including developments in radioiodine-131 (131I) and thyroid, radioimmunotherapy (RIT) for non-Hodgkin lymphoma (NHL), and radiopharmaceuticals for bone metastases. Relevant differences and status of their applications in China were mentioned as well. These molecular mediated internal radiation therapies are gaining increasing importance by providing palliative and curative treatments for an increasing number of diseases and becoming one of the important parts of molecular nuclear medicine. PMID:26445567

  1. Basics of particle therapy II biologic and dosimetric aspects of clinical hadron therapy.

    PubMed

    Rong, Yi; Welsh, James

    2010-12-01

    Besides photons and electrons, high-energy particles like protons, neutrons, ⁴He ions or heavier ions (C, Ne, etc) have been finding increasing applications in the treatment of radioresistant tumors and tumors located near critical structures. The main difference between photons and hadrons is their different biologic effect and depth-dose distribution. Generally speaking, protons are superior in dosimetric aspects whereas neutrons have advantages in biologic effectiveness because of the high linear energy transfer. In 1946 Robert Wilson first published the physical advantages in dose distribution of ion particles for cancer therapy. Since that time hadronic radiotherapy has been intensively studied in physics laboratories worldwide and clinical application have gradually come to fruition. Hadron therapy was made possible by the advances in accelerator technology, which increases the particles' energy high enough to place them at any depth within the patient's body. As a follow-up to the previous article Introduction to Hadrons, this review discusses certain biologic and dosimetric aspects of using protons, neutrons, and heavy charged particles for radiation therapy. PMID:20395789

  2. Biodiversity: molecular biological domains, symbiosis and kingdom origins

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  3. Molecular Mechanisms of Biological Aging in Intervertebral Discs

    PubMed Central

    Vo, Nam V.; Hartman, Robert A.; Patil, Prashanti R.; Risbud, Makarand V.; Kletsas, Dimitris; Iatridis, James C.; Hoyland, Judith A.; Le Maitre, Christine L.; Sowa, Gwendolyn A.; Kang, James D.

    2016-01-01

    Advanced age is the greatest risk factor for the majority of human ailments, including spine-related chronic disability and back pain, which stem from age-associated intervertebral disc degeneration (IDD). Given the rapid global rise in the aging population, understanding the biology of intervertebral disc aging in order to develop effective therapeutic interventions to combat the adverse effects of aging on disc health is now imperative. Fortunately, recent advances in aging research have begun to shed light on the basic biological process of aging. Here we review some of these insights and organize the complex process of disc aging into three different phases to guide research efforts to understand the biology of disc aging. The objective of this review is to provide an overview of the current knowledge and the recent progress made to elucidate specific molecular mechanisms underlying disc aging. In particular, studies over the last few years have uncovered cellular senescence and genomic instability as important drivers of disc aging. Supporting evidence comes from DNA repair-deficient animal models that show increased disc cellular senescence and accelerated disc aging. Additionally, stress-induced senescent cells have now been well documented to secrete catabolic factors, which can negatively impact the physiology of neighboring cells and ECM. These along with other molecular drivers of aging are reviewed in depth to shed crucial insights into the underlying mechanisms of age-related disc degeneration. We also highlight molecular targets for novel therapies and emerging candidate therapeutics that may mitigate age-associated IDD. PMID:26890203

  4. Biodiversity: molecular biological domains, symbiosis and kingdom origins.

    PubMed

    Margulis, L

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  5. Biodiversity: molecular biological domains, symbiosis and kingdom origins.

    PubMed

    Margulis, L

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  6. Deep-UV biological imaging by lanthanide ion molecular protection

    PubMed Central

    Kumamoto, Yasuaki; Fujita, Katsumasa; Smith, Nicholas Isaac; Kawata, Satoshi

    2015-01-01

    Deep-UV (DUV) light is a sensitive probe for biological molecules such as nucleobases and aromatic amino acids due to specific absorption. However, the use of DUV light for imaging is limited because DUV can destroy or denature target molecules in a sample. Here we show that trivalent ions in the lanthanide group can suppress molecular photodegradation under DUV exposure, enabling a high signal-to-noise ratio and repetitive DUV imaging of nucleobases in cells. Underlying mechanisms of the photodegradation suppression can be excitation relaxation of the DUV-absorptive molecules due to energy transfer to the lanthanide ions, and/or avoiding ionization and reactions with surrounding molecules, including generation of reactive oxygen species, which can modify molecules that are otherwise transparent to DUV light. This approach, directly removing excited energy at the fundamental origin of cellular photodegradation, indicates an important first step towards the practical use of DUV imaging in a variety of biological applications. PMID:26819825

  7. Diagnosis of Whipple's disease using molecular biology techniques.

    PubMed

    Cosme, Ángel; Ojeda, Evelia; Muñagorri, Ana I; Gaminde, Eduardo; Bujanda, Luis; Larzabal, Mikel; Gil, Inés

    2011-04-01

    The diagnosis of Whipple's disease (WD) is based on the existence of clinical signs and symptoms compatible with the disease and in the presence of PAS-positive diastase-resistant granules in the macrophages of the small intestine. If there is suspicion of the disease but no histological findings or only isolated extraintestinal manifestations, species-specific PCR using different sequences of the T. whippleii genome from different tissue types and biological fluids is recommended.This study reports two cases: the first patient had diarrhea and the disease was suspected after an endoscopic examination of the ileum, while the second patient had multi-systemic manifestations,particularly abdominal, thoracic, and peripheral lymphadenopathies. In both cases, the diagnosis was confirmed using molecular biology techniques to samples from the small intestine or from a retroperineal lymph node, respectively. PMID:21526877

  8. Experiments with a universe for molecular modelling of biological processes.

    PubMed

    Jedruch, W T; Barski, M

    1990-01-01

    A computer simulation program and results of preliminary simulations of an abstract two-dimensional universe are presented, in which biological and physical processes can be modelled at the molecular level. Two types of permanent elements (atoms) occupy squares of the universe: called 0 and 1. Atoms sharing a common square form a particle, with properties determined by its component atoms. Atoms, particles, and complexes of particles move and collide according to rules like those of classical mechanics. At a higher level of organization, the string of atoms in a particle is viewed as a program, whose execution can affect the space around the particle. The computer program (written in Turbo-Pascal language) can simulate the evolution of the universe starting from any given initial configuration of the particles. Three examples of simulations, showing the development of ordered spatial structures from initial sets of randomly distributed particles, illustrate the universe's potential in modelling various molecular processes.

  9. Medical and molecular biological application in the FELI

    SciTech Connect

    Nishimura, E.; Ogino, S.; Suzuki, T.

    1995-12-31

    Some of the user`s rooms of the FELI have been equipped for medical and molecular biological research. Main subjects are immunological reaction and cell fusion induced by IR FEL. We are beginning to do the preliminary irradiation experiments. The cultured T lymphocytes (Molt-4, human) are irradiated to FEL at wavelength 6.3{mu}m with the power density approximate 500mW/mm{sup 2} for 10 minutes, in the culture media (RPMI-1640) including 10% fetal bovine serum. Swelling and consequent collapse of the cells can be observed, probably due to abrasion of the cell membranes.

  10. Mutants of Arabidopsis as tools for physiology and molecular biology

    SciTech Connect

    Somerville, C.R.; Artus, N.; Browse, J.; Caspar, T.; Estelle, M.; Haughn, G.; Kunst, L.; Martinez, J.; McCourt, P.; Moffatt, B.

    1986-04-01

    The authors discuss the importance of developing a facile system for genetic analysis in higher plants which can be used to approach problems specific to plant biology in much the same way that molecular genetic approaches have been used in other classes of organisms such as yeast and Drosophila. Toward this end, they have developed methods for the isolation and analysis of mutants of Arabidopsis with specific alterations in photosynthesis, photorespiration, starch metabolism, lipid metabolism, purine metabolism, amino acid metabolism and phytohormone responses. The utility of this collection of mutants for studying problems in physiology and biochemistry is illustrated with selected examples.

  11. Dictionary of microbiology and molecular biology. 2nd ed

    SciTech Connect

    Singleton, P.; Sainsbury, D.

    1988-01-01

    A newly revised edition of the standard reference for microbiology and molecular biology. Includes a multitude of new terms and designations which, although widely used in the literature, are seldom defined outside the book or paper in which they first appeared. Also accounts for the changes in the meanings of older terms brought about by advances in knowledge. Definition of all terms reflects their actual usage in current journals and texts, and also given (where appropriate) are former meanings, alternative meanings, and synonyms. Includes terms from such fields as mycology, protozoology, virology, etc.

  12. PALM--a pattern language for molecular biology.

    PubMed

    Helgesen, C; Sibbald, P R

    1993-01-01

    This paper presents a new pattern language, PALM, for describing patterns in molecular biology sequences. The language is intended for representing knowledge about such patterns in a declarative, clear and concise way. It is also shown that its expressive power enables the definition of any regular or context free language, and also higher languages in the Chomsky hierarchy by parameter attachment, variables and procedural attachment. It is also possible to define approximate patterns. The language is rigorously defined, and several examples of its use and expressive power are given. PMID:7584333

  13. How restriction enzymes became the workhorses of molecular biology

    PubMed Central

    Roberts, Richard J.

    2005-01-01

    Restriction enzymes have proved to be invaluable for the physical mapping of DNA. They offer unparalleled opportunities for diagnosing DNA sequence content and are used in fields as disparate as criminal forensics and basic research. In fact, without restriction enzymes, the biotechnology industry would certainly not have flourished as it has. The first experiments demonstrating the utility of restriction enzymes were carried out by Danna and Nathans and reported in 1971. This pioneering study set the stage for the modern practice of molecular biology in which restriction enzymes are ubiquitous tools, although they are often taken for granted. PMID:15840723

  14. Molecular Biology of Pediatric Hydrocephalus and Hydrocephalus-related Diseases.

    PubMed

    Yamasaki, Mami; Kanemura, Yonehiro

    2015-01-01

    We are beginning to understand the molecular biology of hydrocephalus and its related diseases. X-linked hydrocephalus (XLH), holoprosencephaly (HPE), Dandy-Walker malformation (DWM), and neural tube defect (NTD) can all be discussed with respect to their available molecular genetics knowledge base and its clinical applications. XLH is single gene disorder caused by mutations in the neural cell adhesion molecule-encoding L1CAM (L1) gene. Our knowledge of the molecular basis of XLH is already being applied clinically in disease diagnosis, disease classification, and prenatal diagnosis. However, the molecular mechanism underlying XLH-related hydrocephalus still needs to be clarified. Sixteen causative genes for HPE have been identified, of which mutations are most often found in SHH, ZIC2, SIX3, and TGIF. Genetic interactions, gene complexity, and the wide variety of HPE phenotypes and genotypes are topics for future study. For DWM, two important loci, 3q24, which includes the FOXC1 gene, and 6q25.3, which includes the ZIC1 and ZIC4 genes, were recently identified as causative areas. The planar cell polarity (PCP) genes CELSR1, CELSR2, VANGL1, and VANGL2 have been implicated in NTD; these genes have roles in neural tube closure and ependymal ciliary movement. PMID:26227058

  15. Developing protein documentaries and other multimedia presentations for molecular biology.

    PubMed

    Quinn, G; Wang, H P; Martinez, D; Bourne, P E

    1999-01-01

    Computer-based multimedia technology for distance learning and research has come of age--the price point is acceptable, domain experts using off-the-shelf software can prepare compelling materials, and the material can be efficiently delivered via the Internet to a large audience. While not presenting any new scientific results, this paper outlines experiences with a variety of commercial and free software tools and the associated protocols we have used to prepare protein documentaries and other multimedia presentations relevant to molecular biology. A protein documentary is defined here as a description of the relationship between structure and function in a single protein or in a related family of proteins. A description using text and images which is further enhanced by the use of sound and interactive graphics. Examples of documentaries prepared to describe cAMP dependent protein kinase, the founding structural member of the protein kinase family for which there is now over 40 structures can be found at http://franklin.burnham-inst.org/rcsb. A variety of other prototype multimedia presentations for molecular biology described in this paper can be found at http://fraklin.burnham-inst.org. PMID:10380212

  16. Errant life, molecular biology, and biopower: Canguilhem, Jacob, and Foucault.

    PubMed

    Talcott, Samuel

    2014-01-01

    This paper considers the theoretical circumstances that urged Michel Foucault to analyse modern societies in terms of biopower. Georges Canguilhem's account of the relations between science and the living forms an essential starting point for Foucault's own later explorations, though the challenges posed by the molecular revolution in biology and François Jacob's history of it allowed Foucault to extend and transform Canguilhem's philosophy of error. Using archival research into his 1955-1956 course on "Science and Error," I show that, for Canguilhem, it is inauthentic to treat a living being as an error, even if living things are capable of making errors in the domain of knowledge. The emergent molecular biology in the 1960s posed a grave challenge, however, since it suggested that individuals could indeed be errors of genetic reproduction. The paper discusses how Canguilhem and Foucault each responded to this by examining, among other texts, their respective reviews of Jacob's The Logic of the Living. For Canguilhem this was an opportunity to reaffirm the creativity of life in the living individual, which is not a thing to be evaluated, but the source of values. For Foucault, drawing on Jacob's work, this was the opportunity to develop a transformed account of valuation by posing biopower as the DNA of society. Despite their disagreements, the paper examines these three authors as different iterations of a historical epistemology attuned to errancy, error, and experimentation.

  17. Errant life, molecular biology, and biopower: Canguilhem, Jacob, and Foucault.

    PubMed

    Talcott, Samuel

    2014-01-01

    This paper considers the theoretical circumstances that urged Michel Foucault to analyse modern societies in terms of biopower. Georges Canguilhem's account of the relations between science and the living forms an essential starting point for Foucault's own later explorations, though the challenges posed by the molecular revolution in biology and François Jacob's history of it allowed Foucault to extend and transform Canguilhem's philosophy of error. Using archival research into his 1955-1956 course on "Science and Error," I show that, for Canguilhem, it is inauthentic to treat a living being as an error, even if living things are capable of making errors in the domain of knowledge. The emergent molecular biology in the 1960s posed a grave challenge, however, since it suggested that individuals could indeed be errors of genetic reproduction. The paper discusses how Canguilhem and Foucault each responded to this by examining, among other texts, their respective reviews of Jacob's The Logic of the Living. For Canguilhem this was an opportunity to reaffirm the creativity of life in the living individual, which is not a thing to be evaluated, but the source of values. For Foucault, drawing on Jacob's work, this was the opportunity to develop a transformed account of valuation by posing biopower as the DNA of society. Despite their disagreements, the paper examines these three authors as different iterations of a historical epistemology attuned to errancy, error, and experimentation. PMID:25515360

  18. Holism and life manifestations: molecular and space-time biology.

    PubMed

    Krecek, J

    2010-01-01

    Appeals of philosophers to look for new concepts in sciences are being met with a weak response. Limited attention is paid to the relation between synthetic and analytic approach in solving problems of biology. An attempt is presented to open a discussion on a possible role of holism. The term "life manifestations" is used in accordance with phenomenology. Multicellular creatures maintain milieu intérieur to keep an aqueous milieu intracellulair in order to transform the energy of nutrients into the form utilizable for driving cellular life manifestations. Milieu intérieur enables to integrate this kind of manifestations into life manifestations of the whole multicellular creatures. The integration depends on a uniqueness and uniformity of the genome of cells, on their mutual recognition and adherence. The processes of ontogenetic development represent the natural mode of integration of cellular life manifestations. Functional systems of multicellular creatures are being established by organization of integrable cells using a wide range of developmental processes. Starting from the zygote division the new being displays all properties of a whole creature, although its life manifestations vary. Therefore, the whole organism is not only more than its parts, as supposed by holism, but also more than developmental stages of its life manifestations. Implicitly, the units of whole multicellular creature are rather molecular and developmental events than the cells per se. Holism, taking in mind the existence of molecular and space-time biology, could become a guide in looking for a new mode of the combination of analytical and synthetic reasoning in biology.

  19. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented.

  20. Transmission electron microscopy in molecular structural biology: A historical survey.

    PubMed

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. PMID:25475529

  1. Review and application of group theory to molecular systems biology

    PubMed Central

    2011-01-01

    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer. PMID:21696623

  2. Advances in the cellular and molecular biology of angiogenesis.

    PubMed

    Egginton, Stuart; Bicknell, Roy

    2011-12-01

    Capillaries have been recognized for over a century as one of the most important components in regulating tissue oxygen transport, and their formation or angiogenesis a pivotal element of tissue remodelling during development and adaptation. Clinical interest stems from observations that both excessive and inadequate vascular growth plays a major role in human diseases, and novel developments in treatments for cancer and eye disease increasingly rely on anti-angiogenic therapies. Although the discovery of VEGF (vascular endothelial growth factor) provided the first clue for specificity of signalling in endothelial cell activation, understanding the integrative response that drives angiogenesis requires a much broader perspective. The Advances in the Cellular and Molecular Biology of Angiogenesis meeting brought together researchers at the forefront of this rapidly moving field to provide an update on current understanding, and the most recent insights into molecular and cellular mechanisms of vascular growth. The plenary lecture highlighted the integrative nature of the angiogenic process, whereas invited contributions from basic and clinician scientists described fundamental mechanisms and disease-associated issues of blood vessel formation, grouped under a number of themes to aid discussion. These articles will appeal to academic, clinical and pharmaceutical scientists interested in the molecular and cellular basis of angiogenesis, their modulation or dysfunction in human diseases, and application of these findings towards translational medicine. PMID:22103485

  3. Molecular Biology of Insect Sodium Channels and Pyrethroid Resistance

    PubMed Central

    Dong, Ke; Du, Yuzhe; Rinkevich, Frank; Nomura, Yoshiko; Xu, Peng; Wang, Lingxin; Silver, Kristopher; Zhorov, Boris S.

    2015-01-01

    Voltage-gated sodium channels are essential for the initiation and propagation of the action potential in neurons and other excitable cells. Because of their critical roles in electrical signaling, sodium channels are targets of a variety of naturally occurring and synthetic neurotoxins, including several classes of insecticides. This review is intended to provide an update on the molecular biology of insect sodium channels and the molecular mechanism of pyrethroid resistance. Although mammalian and insect sodium channels share fundamental topological and functional properties, most insect species carry only one sodium channel gene, compared to multiple sodium channel genes found in each mammalian species. Recent studies showed that two posttranscriptional mechanisms, alternative splicing and RNA editing, are involved in generating functional diversity of sodium channels in insects. More than 50 sodium channel mutations have been identified to be responsible for or associated with knockdown resistance (kdr) to pyrethroids in various arthropod pests and disease vectors. Elucidation of molecular mechanism of kdr led to the identification of dual receptor sites of pyrethroids on insect sodium channels. Most of the kdr mutations appear to be located within or close to the two receptor sites. The accumulating knowledge of insect sodium channels and their interactions with insecticides provides a foundation for understanding the neurophysiology of sodium channels in vivo and the development of new and safer insecticides for effective control of arthropod pests and human disease vectors. PMID:24704279

  4. The biology, pathogenesis and clinical aspects of acute lymphoblastic leukemia in children with Down syndrome.

    PubMed

    Lee, P; Bhansali, R; Izraeli, S; Hijiya, N; Crispino, J D

    2016-09-01

    Children with Down syndrome (DS) are at a 20-fold increased risk for acute lymphoblastic leukemia (DS-ALL). Although the etiology of this higher risk of developing leukemia remains largely unclear, the recent identification of CRLF2 (cytokine receptor like factor 2) and JAK2 mutations and study of the effect of trisomy of Hmgn1 and Dyrk1a (dual-specificity tyrosine phosphorylation-regulated kinase 1A) on B-cell development have shed significant new light on the disease process. Here we focus on the clinical features, biology and genetics of ALL in children with DS. We review the unique characteristics of DS-ALL on both the clinical and molecular levels and discuss the differences in treatments and outcomes in ALL in children with DS compared with those without DS. The identification of new biological insights is expected to pave the way for novel targeted therapies. PMID:27285583

  5. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry.

    PubMed

    Kalay, Ziya

    2011-08-01

    How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.

  6. Tagging and Purifying Proteins to Teach Molecular Biology and Advanced Biochemistry

    ERIC Educational Resources Information Center

    Roecklein-Canfield, Jennifer A.; Lopilato, Jane

    2004-01-01

    Two distinct courses, "Molecular Biology" taught by the Biology Department and "Advanced Biochemistry" taught by the Chemistry Department, complement each other and, when taught in a coordinated and integrated way, can enhance student learning and understanding of complex material. "Molecular Biology" is a comprehensive lecture-based course with a…

  7. Implementation and Assessment of a Molecular Biology and Bioinformatics Undergraduate Degree Program

    ERIC Educational Resources Information Center

    Pham, Daphne Q. -D.; Higgs, David C.; Statham, Anne; Schleiter, Mary Kay

    2008-01-01

    The Department of Biological Sciences at the University of Wisconsin-Parkside has developed and implemented an innovative, multidisciplinary undergraduate curriculum in Molecular Biology and Bioinformatics (MBB). The objective of the MBB program is to give students a hands-on facility with molecular biology theories and laboratory techniques, an…

  8. Oral flora in the age of molecular biology.

    PubMed

    Perea, Evelio J

    2004-01-01

    The present work describes the fundamental aspects of the molecular methods that are applied to oral microbiology: probes, PCR, multiple real time PCR, 16S rDNA, and proteomics. Likewise, it presents the results obtained by applying these methods to the study of the bacterial flora encountered inside the mouth. By identifying 16S rDNA, up to 132 known species and 215 new, unknown phylotypes have been detected inside patients s periodontal pockets. We are currently using a commercial system based on multiple PCR (genomic amplification), followed by reverse hybridization to detect the five species known to cause periodontal disease. We also summarize the findings derived from the application of proteomic techniques to the study of odontologic infections pathogenesis and from the use of molecular methods in the study of resistance to antimicrobial agents. Finally, it puts forth the problems that remain unsolved with respect to oral flora and the treatment of odontogenic infections. Traditional culture methods continue to be indispensable, as they make it possible to later work with the cultured microorganisms.

  9. Rectified Brownian movement in molecular and cell biology

    NASA Astrophysics Data System (ADS)

    Fox, Ronald F.

    1998-02-01

    A unified model is presented for rectified Brownian movement as the mechanism for a variety of putatively chemomechanical energy conversions in molecular and cell biology. The model is established by a detailed analysis of ubiquinone transport in electron transport chains and of allosteric conformation changes in proteins. It is applied to P-type ATPase ion transporters and to a variety of rotary arm enzyme complexes. It provides a basis for the dynamics of actin-myosin cross-bridges in muscle fibers. In this model, metabolic free energy does no work directly, but instead biases boundary conditions for thermal diffusion. All work is done by thermal energy, which is harnessed at the expense of metabolic free energy through the establishment of the asymmetric boundary conditions.

  10. Molecular biological characterization of equine surfactant protein A.

    PubMed

    Hospes, R; Hospes, B I L; Reiss, I; Bostedt, H; Gortner, L

    2002-12-01

    In the following, we describe the isolation and sequencing of the equine surfactant protein A (Sp-A) as found in both the cDNA and the genomic DNA. We found a length of the cDNA sequence of 747 bp (base pairs), in translation into amino acids of 248. Compared with the known molecular biological facts about Sp-A in other species, the cDNA sequence obtained showed highest homology with that of sheep (85.01%). The genomic DNA of equine Sp-A, as in other species, includes three introns. There were no hints for the existence of two different Sp-A genes. These results should form the basis for a better understanding of respiratory failure in foals and adult horses, and also lead to further studies on this item.

  11. Biomarkers of Aging: From Function to Molecular Biology

    PubMed Central

    Wagner, Karl-Heinz; Cameron-Smith, David; Wessner, Barbara; Franzke, Bernhard

    2016-01-01

    Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products. PMID:27271660

  12. Obstructive renal injury: from fluid mechanics to molecular cell biology.

    PubMed

    Ucero, Alvaro C; Gonçalves, Sara; Benito-Martin, Alberto; Santamaría, Beatriz; Ramos, Adrian M; Berzal, Sergio; Ruiz-Ortega, Marta; Egido, Jesus; Ortiz, Alberto

    2010-04-22

    Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1) and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making.

  13. Software library with applications in virology and molecular biology.

    PubMed

    Campione-Piccardo, J

    1986-06-01

    A menu-driven interactive package of computer programs has been developed to help in calculations commonly required in laboratories using virological and molecular biological techniques. Two of the programs use two of the most accurate methods available for determining viral titers, several programs were designed to optimize experimental parameters and others help in the analysis of recombinant DNA data. All of the programs use specially developed original algorithms which in some cases are based also on equations originally derived. The programs were written in Microsoft BASIC using mostly hardware independent commands and functions and should run without major modifications in most microcomputers with BASIC interpreters or compilers. The programs are menu-driven and fully interactive. PMID:3755444

  14. Escherichia coli and the French School of Molecular Biology.

    PubMed

    Ullmann, Agnes

    2010-09-01

    André Lwoff, Jacques Monod, and François Jacob, the leaders of the French school of molecular biology, greatly contributed between 1937 and 1965 to its development and triumph. The main discovery of Lwoff was the elucidation of the mechanism of bacteriophage induction, the phenomenon of lysogeny, that led to the model of genetic regulation uncovered later by Jacob and Monod. Working on bacterial growth, Monod discovered in 1941 the phenomenon of diauxy and uncovered the nature of enzyme induction. By combining genetic and biochemical approaches, Monod brought to light the structure and functions of the Escherichia coli lactose system, comprising the genes necessary for lactose metabolism, i.e., β-galactosidase and lactose permease, a pump responsible for accumulation of galactosides into the cells. An additional genetic factor (the i gene) determines the inducibility and constitutivity of enzyme synthesis. Around the same time, François Jacob and Elie Wollman dissected the main events of bacterial conjugation that enabled them to construct a map of the E. coli chromosome and to demonstrate its circularity. The genetic analysis of the lactose system led Monod and Jacob to elucidate the mechanism of the regulation of gene expression and to propose the operon model: a unit of coordinate transcription. One of the new concepts that emerged from the operon model was messenger RNA. In 1963, Monod developed one of the most elegant concepts of molecular biology, the theory of allostery. In 1965, Lwoff, Monod and Jacob were awarded the Nobel Prize in Physiology or Medicine. PMID:26443784

  15. Escherichia coli and the French School of Molecular Biology.

    PubMed

    Ullmann, Agnes

    2010-09-01

    André Lwoff, Jacques Monod, and François Jacob, the leaders of the French school of molecular biology, greatly contributed between 1937 and 1965 to its development and triumph. The main discovery of Lwoff was the elucidation of the mechanism of bacteriophage induction, the phenomenon of lysogeny, that led to the model of genetic regulation uncovered later by Jacob and Monod. Working on bacterial growth, Monod discovered in 1941 the phenomenon of diauxy and uncovered the nature of enzyme induction. By combining genetic and biochemical approaches, Monod brought to light the structure and functions of the Escherichia coli lactose system, comprising the genes necessary for lactose metabolism, i.e., β-galactosidase and lactose permease, a pump responsible for accumulation of galactosides into the cells. An additional genetic factor (the i gene) determines the inducibility and constitutivity of enzyme synthesis. Around the same time, François Jacob and Elie Wollman dissected the main events of bacterial conjugation that enabled them to construct a map of the E. coli chromosome and to demonstrate its circularity. The genetic analysis of the lactose system led Monod and Jacob to elucidate the mechanism of the regulation of gene expression and to propose the operon model: a unit of coordinate transcription. One of the new concepts that emerged from the operon model was messenger RNA. In 1963, Monod developed one of the most elegant concepts of molecular biology, the theory of allostery. In 1965, Lwoff, Monod and Jacob were awarded the Nobel Prize in Physiology or Medicine.

  16. US-Latin American Workshop on Molecular and Materials Sciences: Theoretical and Computational Aspects

    NASA Astrophysics Data System (ADS)

    Micha, David A.

    1994-08-01

    Partial contents include: time-dependent theory of photoabsorption processes; molecular simulation of a chemical reaction in supercritical water; many-body methods for electron correlation; conformational studies of PAF and PAF-antagonists; electric properties of atomic anions; theoretical interpretation of the Li4(-) spectrum using path integrals and ab initio methods; energy levels and structure of tetra-atomic van der Vaals clusters; technology for modern computational science: the John Slater Computing Facility; carbohydrates on the stabilization of biological structures: molecular dynamics simulation; the role of quantum chemistry in heterogeneous catalysis; and corrections to the Born-Oppenheimer approximation by means of perturbation theory.

  17. Molecular Biology and Infection of Hepatitis E Virus.

    PubMed

    Nan, Yuchen; Zhang, Yan-Jin

    2016-01-01

    Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus.

  18. Molecular Biology and Infection of Hepatitis E Virus.

    PubMed

    Nan, Yuchen; Zhang, Yan-Jin

    2016-01-01

    Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus. PMID:27656178

  19. Molecular Biology and Infection of Hepatitis E Virus

    PubMed Central

    Nan, Yuchen; Zhang, Yan-Jin

    2016-01-01

    Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus.

  20. Molecular Biology and Infection of Hepatitis E Virus

    PubMed Central

    Nan, Yuchen; Zhang, Yan-Jin

    2016-01-01

    Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus. PMID:27656178

  1. Molecular imaging of biological tissue using gas cluster ions

    PubMed Central

    Tian, Hua; Wucher, Andreas; Winograd, Nicholas

    2015-01-01

    An Arn+ (n = 1–6000) gas cluster ion source has been utilized to map the chemical distribution of lipids in a mouse brain tissue section. We also show that the signal from high mass species can be further enhanced by doping a small amount of CH4 into the Ar cluster to enhance the ionization of several biologically important molecules. Coupled with secondary ion mass spectrometry instrumentation which utilizes a continuous Ar cluster ion projectile, maximum spatial resolution and maximum mass resolution can be achieved at the same time. With this arrangement, it is possible to achieve chemically resolved molecular ion images at the 4-µm resolution level. The focused Arn+/[Arx(CH4)y]+ beams (4–10 µm) have been applied to the study of untreated mouse brain tissue. A high signal level of molecular ions and salt adducts, mainly from various phosphocholine lipids, has been seen and directly used to map the chemical distribution. The signal intensity obtained using the pure Ar cluster source, the CH4-doped cluster source and C60 is also presented. PMID:26207076

  2. Structural, chemical and biological aspects of antioxidants for strategies against metal and metalloid exposure

    PubMed Central

    2009-01-01

    Oxidative stress contributes to the pathophysiology of exposure to heavy metals/metalloid. Beneficial renal effects of some medications, such as chelation therapy depend at least partially on the ability to alleviate oxidative stress. The administration of various natural or synthetic antioxidants has been shown to be of benefit in the prevention and attenuation of metal induced biochemical alterations. These include vitamins, N-acetylcysteine, α-lipoic acid, melatonin, dietary flavonoids and many others. Human studies are limited in this regard. Under certain conditions, surprisingly, the antioxidant supplements may exhibit pro-oxidant properties and even worsen metal induced toxic damage. To date, the evidence is insufficient to recommend antioxidant supplements in subject with exposure to metals. Prospective, controlled clinical trials on safety and effectiveness of different therapeutic antioxidant strategies either individually or in combination with chelating agent are indispensable. The present review focuses on structural, chemical and biological aspects of antioxidants particularly related to their chelating properties. PMID:20716905

  3. Solar Disinfection of Water by TiO2 Photoassisted Processes: Physicochemical, Biological, and Engineering Aspects

    NASA Astrophysics Data System (ADS)

    Rincón, Angela Guiovana; Pulgarin, Cesar

    In this chapter, an overview of photocatalytic bacterial inactivation is given together with recent relevant literature examples and references. The most important parameters influencing the process are classified in physicochemical, biological, and engineering aspects. Experiments carried out at laboratory and field scale are illustrated and discussed. Limitations, advantages, and drawbacks are pointed out. Sensitivity of bacteria to solar disinfection in the absence and presence of TiO2 can vary for each species of microorganism according to strain, stage of the culture, growth medium, initial bacterial load, and type of plating medium used for bacterial cultivation and counting. Physicochemical parameters and reactor design among others also influence the process. However, to comply with requirements in the disinfection systems, it is important to determine for each condition the length of the irradiation period or effective disinfection time (EDT) that ensures death of the bacteria and consequently the end of the treatment.

  4. Cold Spring Harbor symposia on quantitative biology: Volume 51, Molecular biology of Homo sapiens

    SciTech Connect

    Not Available

    1986-01-01

    Thirteen years marked the time between the discovery of the double helix in 1953 and the elucidation of the genetic code in 1966. A similar interval has now passed since the development by Cohen and Boyer of a simple procedure for the cloning of selective DNA fragments. The scientific advances made possible by the subsequent modification and elaboration of these original cloning procedures now amaze, stimulate, and increasingly often overwhelm us. Facts that until recently were virtually unobtainable now flow forth almost effortlessly. Most excitingly, the frenetic pace of these new discoveries, instead of marking the impending end of a glorious moment of learning, give every indication of opening up scientific frontiers that will take hundreds if not thousands of years to explore thoroughly. This new era of enlightenment is nowhere more apparent than in our newfound ability to study ourselves at the molecular level. This volume is the first of two collections of papers submitted by the contributors to the Cold Spring Harbor symposia on quantitative biology for 1986 - molecular biology of Homo sapiens. Contained in this collection are 80 papers grouped into sessions entitled Human Gene Map, Genetic Diagnosis, Human Evolution, and Drugs Made Off Human Genes.

  5. Common practice in molecular biology may introduce statistical bias and misleading biological interpretation.

    PubMed

    Hocquette, Jean François; Brandstetter, Anna M.

    2002-06-01

    In studies on enzyme activity or gene expression at the protein level, data are usually analyzed by using a standard curve after subtracting blank values. In most cases and for most techniques (spectrophotometric assays, ELISA), this approach satisfies the basic principles of linearity and specificity. In our experience, this might be also the case for Western-blot analysis. By contrast, mRNA data are usually presented as arbitrary units of the ratio of a target RNA over levels of a control RNA species. We here demonstrate by simple experiments and various examples that this data-normalization procedure may result in misleading conclusions. Common molecular biology techniques have never been carefully tested according to the basic principles of validation of quantitative techniques. We thus prefer a regression-based approach for quantifying mRNA levels relatively to a control RNA species by Northern-blot, semi-quantitative RT-PCR or similar techniques. This type of techniques is also characterized by a lower reproducibility for repeated assays when compared to biochemical analyses. Therefore, we also recommend to design experiments, which allow the detection of a similar range of variance by biochemical and molecular biology techniques. Otherwise, spurious conclusions may be provided regarding the control level of gene expression.

  6. Antioxidant and cytotoxic activities of canadine: biological effects and structural aspects.

    PubMed

    Correché, Estela R; Andujar, Sebastian A; Kurdelas, Rita R; Gómez Lechón, María J; Freile, Mónica L; Enriz, Ricardo D

    2008-04-01

    The cytotoxic effects of four alkaloids, berberine, canadine, anonaine, and antioquine were evaluated using three different cell cultures, a primary culture (rat hepatocytes) and two cell lines (HepG2 and HeLa). Our results indicate that berberine, anonaine, and antioquine possess a significant the cytotoxic effect. In contrast, canadine does not possess cytotoxic effect at concentrations tested here. A molecular modeling study indicates that the quaternary nitrogen, the aromatic polycyclic and planar structure of berberine could be the pharmacophoric patron to produce the cytotoxic effect. In parallel our results demonstrated that canadine possess a significant antioxidant activity. Stereoelectronic aspects of this alkaloid were found to be closely related to those displayed by alpha-tocopherol and its water-soluble analogue trolox. The antioxidant activities of canadine, combined with its low-toxic effect, indicated that the potential of this alkaloid as a novel class of antioxidant agent is very interesting and deserves further research.

  7. [Aspects of the biological behaviour of the rubber RS 330T-RTV silicon material].

    PubMed

    Gheban, E; Forna, Norina Consuela

    2008-01-01

    The resorption and atrophy of the prosthodontic prosthetic field via the mobile restorations made of flexible acrylate, constitutes a controversial problem in the specialty literature, determining the interest of the clinicians with regard to the counterattacking or improving this process inherent to the indentation evolution. The study aims at analyzing the biological behavior of the silicon type RUBBER RS 330T-RTV, a material often used in the creation of the maxilo-facial prosthetics. The method proposed by us has the object of lining the prosthetics made of flexible acrylic type Valplast with this type of silicon. The practical aspects have been forwarded by the biocompatibility studies, applied to the silicon test-tubes, made in the dental technique laboratory, or to the hypodermic implants at the rodent laboratory animals. At the macroscopic examination it can be observed that the silicon fragment maintains it's almost parallelepiped form. The microscopic exam reveals structural mending phenomena, initially mainly the lymphohistocyte cells, and then mainly the fibrous cells. Biocompatibility aspects certifiable at the RUBBER RS 330T-RTV silicon material are fully according to the biocompatibility notions afferent to the silicon materials. Key words: PMID:20209792

  8. 59. Cold Spring Harbor symposium on quantitative biology: Molecular genetics of cancer

    SciTech Connect

    1994-12-31

    Investigation of the mechanistic aspects of cancer has its roots in the studies on tumor viruses and their effects on cell proliferation, function, and growth. This outstanding progress was well documented in previous Cold Spring Harbor Symposia on Quantitative Biology. In the early to mid 1980s, progress on the development of chromosome mapping strategies and the accumulation of DNA probes that identified polymorphisms, encouraged by the international Human Genome Project, enabled the identification of other genes that contributed to familial inheritance of high susceptibility to specific cancers. This approach was very successful and led to a degree of optimism that one aspect of cancer, the multistep genetic process from early neoplasia to metastatic tumors, was beginning to be understood. It therefore seemed appropriate that the 59th Symposium on Quantitative Biology focus attention on the Molecular Genetics of Cancer. The concept was to combine the exciting progress on the identification of new genetic alterations in human tumor cells with studies on the function of the cancer gene products and how they go awry in tumor cells.

  9. Mathematical Biology Modules Based on Modern Molecular Biology and Modern Discrete Mathematics

    PubMed Central

    Davies, Robin; Hodge, Terrell; Enyedi, Alexander

    2010-01-01

    We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network. PMID:20810955

  10. Mathematical biology modules based on modern molecular biology and modern discrete mathematics.

    PubMed

    Robeva, Raina; Davies, Robin; Hodge, Terrell; Enyedi, Alexander

    2010-01-01

    We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network.

  11. Local and global aspects of biological motion perception in children born at very low birth weight

    PubMed Central

    Williamson, K. E.; Jakobson, L. S.; Saunders, D. R.; Troje, N. F.

    2015-01-01

    Biological motion perception can be assessed using a variety of tasks. In the present study, 8- to 11-year-old children born prematurely at very low birth weight (<1500 g) and matched, full-term controls completed tasks that required the extraction of local motion cues, the ability to perceptually group these cues to extract information about body structure, and the ability to carry out higher order processes required for action recognition and person identification. Preterm children exhibited difficulties in all 4 aspects of biological motion perception. However, intercorrelations between test scores were weak in both full-term and preterm children—a finding that supports the view that these processes are relatively independent. Preterm children also displayed more autistic-like traits than full-term peers. In preterm (but not full-term) children, these traits were negatively correlated with performance in the task requiring structure-from-motion processing, r(30) = −.36, p < .05), but positively correlated with the ability to extract identity, r(30) = .45, p < .05). These findings extend previous reports of vulnerability in systems involved in processing dynamic cues in preterm children and suggest that a core deficit in social perception/cognition may contribute to the development of the social and behavioral difficulties even in members of this population who are functioning within the normal range intellectually. The results could inform the development of screening, diagnostic, and intervention tools. PMID:25103588

  12. Photosynthesis research in India: transition from yield physiology into molecular biology.

    PubMed

    Raghavendra, Agepati S; Vishnu Sane, Prafullachandra; Mohanty, Prasanna

    2003-01-01

    Photosynthesis research in India can be traced back several thousand years, with the mention of the Sun energizing the plants, which form food for all living creatures on the earth (from the Mahabharata, the great epic, ca. 2600 B.C.) and the report of Sage Parasara (ca. 100 B.C.) on the ability of plants to make their own food, due to their pigments. With the pioneering studies by Sir Jagdish Chandra Bose, work on photosynthesis proceeded steadily during the first half of the 20th century. Some of the classic reports during this period are: malate metabolism in Hydrilla, spectrophotometric estimation of chlorophylls, importance of spectral quality for photosynthesis - an indication of two photosystems, photoinactivation of photosynthesis, and importance of flag leaf photosynthesis to grain yield. After the 1960s, there was a burst of research in the areas of physiology and biochemistry of carbon assimilation and photochemistry. A significant transition occurred, before the beginning of new millennium, into the area of molecular biology of chloroplasts, regulation of photosynthesis and stress tolerance. Future research work in India is geared to focus on the following aspects of photosynthesis: elucidation/analysis of genes, molecular biology/evolution of enzymes, development/use of transgenics and modeling. PMID:16228599

  13. What Skills Should Students of Undergraduate Biochemistry and Molecular Biology Programs Have Upon Graduation?

    PubMed Central

    White, Harold B.; Benore, Marilee A.; Sumter, Takita F.; Caldwell, Benjamin D.; Bell, Ellis

    2014-01-01

    Biochemistry and molecular biology (BMB) students should demonstrate proficiency in the foundational concepts of the discipline and possess the skills needed to practice as professionals. To ascertain the skills that should be required, groups of BMB educators met in several focused workshops to discuss the expectations with the ultimate goal of clearly articulating the skills required. The results of these discussions highlight the critical importance of experimental, mathematical, and interpersonal skills including collaboration, teamwork, safety, and ethics. The groups also found experimental design, data interpretation and analysiand the ability to communicate findings to diverse audience to be essential skills. To aid in the development of appropriate assessments these skills are grouped into three categories, 1) Process of Science, 2) Communication and Comprehension of Science, and 3) Community of Practice Aspects of Science. Finally, the groups worked to align these competencies with the best practices in both teaching and in skills assessment. PMID:24019246

  14. What skills should students of undergraduate biochemistry and molecular biology programs have upon graduation?

    PubMed

    White, Harold B; Benore, Marilee A; Sumter, Takita F; Caldwell, Benjamin D; Bell, Ellis

    2013-01-01

    Biochemistry and molecular biology (BMB) students should demonstrate proficiency in the foundational concepts of the discipline and possess the skills needed to practice as professionals. To ascertain the skills that should be required, groups of BMB educators met in several focused workshops to discuss the expectations with the ultimate goal of clearly articulating the skills required. The results of these discussions highlight the critical importance of experimental, mathematical, and interpersonal skills including collaboration, teamwork, safety, and ethics. The groups also found experimental design, data interpretation and analysiand the ability to communicate findings to diverse audience to be essential skills. To aid in the development of appropriate assessments these skills are grouped into three categories, 1) Process of Science, 2) Communication and Comprehension of Science, and 3) Community of Practice Aspects of Science. Finally, the groups worked to align these competencies with the best practices in both teaching and in skills assessment.

  15. Molecular self-assembly for biological investigations and nanoscale lithography

    NASA Astrophysics Data System (ADS)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  16. Molecular motor traffic: From biological nanomachines to macroscopic transport

    NASA Astrophysics Data System (ADS)

    Lipowsky, Reinhard; Chai, Yan; Klumpp, Stefan; Liepelt, Steffen; Müller, Melanie J. I.

    2006-12-01

    All cells of animals and plants contain complex transport systems based on molecular motors which walk along cytoskeletal filaments. These motors are rather small and have a size of 20-100 nm but are able to pull vesicles, organelles and other types of cargo over large distances, from micrometers up to meters. There are several families of motors: kinesins, dyneins, and myosins. Most of these motors have two heads which are used as legs and perform discrete steps along the filaments. Several aspects of the motor behavior will be discussed: motor cycles of two-headed motors; walks of single motors or cargo particles which consist of directed movements interrupted by random, diffusive motion; cargo transport through tube-like compartments; active diffusion of cargo particles in slab-like compartments; cooperative transport of cargo by several motors which may be uni- or bi-directional; and systems with many interacting motors that exhibit traffic jams, self-organized density and flux patterns, and traffic phase transitions far from equilibrium. It is necessary to understand these traffic phenomena in a quantitative manner in order to construct and optimize biomimetic transport systems based on motors and filaments with many possible applications in bioengineering, pharmacology, and medicine.

  17. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    SciTech Connect

    Eisenberg, David S.

    2008-07-15

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  18. International Conference on the Cell and Molecular Biology of Chlamydomonas

    SciTech Connect

    Dr. Stephen Miller

    2010-06-10

    The 2010 Conference on the Cell and Molecular Biology of Chlamydomonas was held June 6-10 near Boston, MA, and attracted a record 273 participants, 146 from US labs, 10 from Canada, and the remainder from 18 other countries. The single-celled algal protist Chlamydomonas is a key research organism for many investigators, including those who study photosynthesis, cell motility, adaptation to environmental stresses, the evolution of multicellularity, and the production of biofuels. Chlamydomonas researchers gather every two years at a research conference to exchange methods, develop collaborative efforts, disseminate recent findings, and plan large-scale studies to improve the usefulness of this unique research organism. This conference provides the only opportunity for Chlamydomonas scientists who work on different research problems to meet face to face, and greatly speeds progress in their respective fields. An important function of these Chlamydomonas conferences is to promote and showcase the work of younger scientists, and to attract new investigators into the Chlamydomonas community. DOE award SC0004085 was used to offset the travel and registration costs for 18 young investigators, 9 of whom were women, including one African American. Most of these scientists would not have been able to attend the conference without DOE support. A total of 208 research presentations were made at the meeting, 80 talks (63 presented by students, postdocs, and pre-tenured faculty) and 128 posters. Cell motility and biofuels/metabolism were the best-represented research areas, with a total of 77 presentations. This fact underscores the growing importance of Chlamydomonas as a research and production tool in the rapidly expanding world of biofuels research. A total of 28 talks and posters were presented on the topics of photosynthesis and stress responses, which were among the next best-represented research areas. As at several recent Chlamydomonas meetings, important advances were

  19. Towards Microsecond Biological Molecular Dynamics Simulations on Hybrid Processors

    SciTech Connect

    Hampton, Scott S; Agarwal, Pratul K

    2010-01-01

    Biomolecular simulations continue to become an increasingly important component of molecular biochemistry and biophysics investigations. Performance improvements in the simulations based on molecular dynamics (MD) codes are widely desired. This is particularly driven by the rapid growth of biological data due to improvements in experimental techniques. Unfortunately, the factors, which allowed past performance improvements of MD simulations, particularly the increase in microprocessor clock frequencies, are no longer improving. Hence, novel software and hardware solutions are being explored for accelerating the performance of popular MD codes. In this paper, we describe our efforts to port and optimize LAMMPS, a popular MD framework, on hybrid processors: graphical processing units (GPUs) accelerated multi-core processors. Our implementation is based on porting the computationally expensive, non-bonded interaction terms on the GPUs, and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface (MPI) that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs as well as extend the implementation on GPU clusters. The results from a number of typically sized biomolecular systems are provided and analysis is performed on 3 generations of GPUs from NVIDIA. Our implementation allows up to 30-40 ns/day throughput on a single workstation as well as significant speedup over Cray XT5, a high-end supercomputing platform. Moreover, detailed analysis of the implementation indicates that further code optimization and improvements in GPUs will allow {approx}100 ns/day throughput on workstations and inexpensive GPU clusters, putting the widely-desired microsecond simulation time-scale within reach to a large user community.

  20. Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

    SciTech Connect

    Watson, J.D.; Siniscalco, M.

    1986-01-01

    This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

  1. Biological aspects of altered bone remodeling in multiple myeloma and possibilities of pharmacological intervention.

    PubMed

    Kupisiewicz, Kasia

    2011-05-01

    osteoclasts appear to resorb deeper compared to non-fluorescent osteoclasts. The preliminary data that need to be confirmed suggest that formation of hybrid cells by fusion of myeloma cells with osteoclasts may result in reprogramming of the osteoclasts and contribute to the more aggressive bone resorption by osteoclasts as it is typically seen in myeloma patients. Another aspect of multiple myeloma and associated bone disease is the unmet need for novel and more efficient therapeutic regiments. Resveratrol (trans-3, 4', 5-trihydroxystilbene; RSV) is a natural compound shown to target the key players of myeloma bone disease: bone resorbing osteoclasts, bone forming osteoblasts and myeloma cells. Our in vitro study on RSV showed that it possessed this ideal triad of properties appearing and thus might be of interest as a potential drug for the treatment of multiple myeloma. RSV suppresses the growth and survival of myeloma cells, inhibits osteoclasts and stimulates the formation of osteoblasts. However, the need for high concentrations combined with low biological availability after oral administration and risk of important side effects stimulated a search for RSV derivates with the same spectrum of actions but safer and with better bioavailability. As the other task of my PhD, I screened structurally modified RSV analogues in cultures of myeloma cells, osteoblasts and osteoclasts. Compared to resveratrol, some analogues showed an up to 5,000-times increased potency to inhibit osteoclast differentiation and could still promote osteoblast maturation but they did not antagonize myeloma cells. The potency of the best-performing candidate in vitro was tested in vivo in an ovariectomy-induced model of osteoporosis, but effect on bone loss could not be detected. During my PhD, I also participated in the studies of the effect of the proteasome inhibitor - bortezomib on osteoclasts conducted at the department. Based on its potent activity in multiple myeloma, bortezomib was accepted

  2. Microgravity research in plant biological systems: Realizing the potential of molecular biology

    NASA Technical Reports Server (NTRS)

    Lewis, Norman G.; Ryan, Clarence A.

    1993-01-01

    The sole all-pervasive feature of the environment that has helped shape, through evolution, all life on Earth is gravity. The near weightlessness of the Space Station Freedom space environment allows gravitational effects to be essentially uncoupled, thus providing an unprecedented opportunity to manipulate, systematically dissect, study, and exploit the role of gravity in the growth and development of all life forms. New and exciting opportunities are now available to utilize molecular biological and biochemical approaches to study the effects of microgravity on living organisms. By careful experimentation, we can determine how gravity perception occurs, how the resulting signals are produced and transduced, and how or if tissue-specific differences in gene expression occur. Microgravity research can provide unique new approaches to further our basic understanding of development and metabolic processes of cells and organisms, and to further the application of this new knowledge for the betterment of humankind.

  3. Hereditary nonpolyposis colorectal cancer: Review of clinical, molecular genetics, and counseling aspects

    SciTech Connect

    Bellacosa, A.; Genuardi, M.; Anti, M.; Viel, A.; Ponz de Leon, M.

    1996-04-24

    Lynch syndrome, or hereditary nonpolyposis colon cancer (HNPCC), is an autosomal dominant disease accounting for approximately 1-5% of all colorectal cancer cases. Due to the lack of pathognomonic morphological or biomolecular markers, HNPCC has traditionally posed unique problems to clinicians and geneticists alike, both in terms of diagnosis and clinical management. Recently, novel insight into the pathogenesis of this syndrome has been provided by the identification of its molecular basis. In HNPCC families, germline mutations in any of four genes encoding proteins of a specialized DNA repair system, the mismatch repair, predispose to cancer development. Mutations in mismatch repair genes lead to an overall increase of the mutation rate and are associated with a phenotype of length instability of microsatellite loci. The present report summarizes the clinicopathological aspects of HNPCC and reviews the most recent molecular and biochemical findings. 115 refs., 2 figs., 3 tabs.

  4. Synthesis, characterization, biological evaluation and molecular docking of steroidal spirothiazolidinones

    NASA Astrophysics Data System (ADS)

    Shamsuzzaman; Abdul Baqi, Khan A. A.; Ali, Abad; Asif, Mohd; Mashrai, Ashraf; Khanam, Hena; Sherwani, Asif; Yaseen, Zahid; Owais, Mohammad

    2015-04-01

    The present work describes a convenient synthesis of steroidal spirothiazolidinone derivatives (3, 10-12) in a two-step process. All the newly synthesized compounds have been characterized by means of elemental analyses, IR, 1H NMR, 13C NMR and MS. Lipinski's 'Rule of Five' analysis and biological score predicted higher intrinsic quality of the synthesized compounds and revealed that these compounds have good passive oral absorption. The DNA binding studies of the synthesized compounds with CT-DNA were carried out by UV-vis and fluorescence spectroscopy. The molecular docking study suggested electrostatic interaction between synthesized compounds and nucleotide base pairs. The antitumor activity was tested in vitro against human leukemia cancer cell (Jurkat) and blood peripheral mononuclear normal cell (PBMCs) lines by MTT method. In addition, apoptosis and nonenzymatic degradation of DNA have been investigated. The acetylcholinesterase (AChE) inhibitor activities of the derivatives were also evaluated using Ellman's method. The present study has shown that steroidal spirothiazolidinone derivatives (3, 10-12) can be used as template to design more potent and selective cytotoxic and AChE inhibition agents through modification and derivatization.

  5. Delta hepatitis: molecular biology and clinical and epidemiological features.

    PubMed Central

    Polish, L B; Gallagher, M; Fields, H A; Hadler, S C

    1993-01-01

    Hepatitis delta virus, discovered in 1977, requires the help of hepatitis B virus to replicate in hepatocytes and is an important cause of acute, fulminant, and chronic liver disease in many regions of the world. Because of the helper function of hepatitis delta virus, infection with it occurs either as a coinfection with hepatitis B or as a superinfection of a carrier of hepatitis B surface antigen. Although the mechanisms of transmission are similar to those of hepatitis B virus, the patterns of transmission of delta virus vary widely around the world. In regions of the world in which hepatitis delta virus infection is not endemic, the disease is confined to groups at high risk of acquiring hepatitis B infection and high-risk hepatitis B carriers. Because of the propensity of this viral infection to cause fulminant as well as chronic liver disease, continued incursion of hepatitis delta virus into areas of the world where persistent hepatitis B infection is endemic will have serious implications. Prevention depends on the widespread use of hepatitis B vaccine. This review focuses on the molecular biology and the clinical and epidemiologic features of this important viral infection. PMID:8358704

  6. Disciplinary baptisms: a comparison of the naming stories of genetics, molecular biology, genomics, and systems biology.

    PubMed

    Powell, Alexander; O'Malley, Maureen A; Müller-Wille, Staffan; Calvert, Jane; Dupré, John

    2007-01-01

    Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in which the processes of disciplinary demarcation fundamentally changed from those characteristic of the nineteenth century. We outline how the establishment of each discipline relies upon an interplay of factors that include paradigmatic achievements, technological innovation, and social formations. Our focus, however, is the baptism stories that give the new discipline a founding narrative and articulate core problems, general approaches and constitutive methods. The highly plastic process of achieving disciplinary identity is further marked by the openness of disciplinary definition, tension between technological possibilities and the ways in which scientific issues are conceived and approached, synthesis of reductive and integrative strategies, and complex social interactions. The importance--albeit highly variable--of naming stories in these four cases indicates the scope for future studies that focus on failed disciplines or competing names. Further attention to disciplinary histories could, we suggest, give us richer insight into scientific development. PMID:18411835

  7. Just Working with the Cellular Machine: A High School Game for Teaching Molecular Biology

    ERIC Educational Resources Information Center

    Cardoso, Fernanda Serpa; Dumpel, Renata; Gomes da Silva, Luisa B.; Rodrigues, Carlos R.; Santos, Dilvani O.; Cabral, Lucio Mendes; Castro, Helena C.

    2008-01-01

    Molecular biology is a difficult comprehension subject due to its high complexity, thus requiring new teaching approaches. Herein, we developed an interdisciplinary board game involving the human immune system response against a bacterial infection for teaching molecular biology at high school. Initially, we created a database with several…

  8. Incorporating Molecular and Cellular Biology into a Chemical Engineering Degree Program

    ERIC Educational Resources Information Center

    O'Connor, Kim C.

    2005-01-01

    There is a growing need for a workforce that can apply engineering principles to molecular based discovery and product development in the biological sciences. To this end, Tulane University established a degree program that incorporates molecular and cellular biology into the chemical engineering curriculum. In celebration of the tenth anniversary…

  9. A Curriculum Skills Matrix for Development and Assessment of Undergraduate Biochemistry and Molecular Biology Laboratory Programs

    ERIC Educational Resources Information Center

    Caldwell, Benjamin; Rohlman, Christopher; Benore-Parsons, Marilee

    2004-01-01

    We have designed a skills matrix to be used for developing and assessing undergraduate biochemistry and molecular biology laboratory curricula. We prepared the skills matrix for the Project Kaleidoscope Summer Institute workshop in Snowbird, Utah (July 2001) to help current and developing undergraduate biochemistry and molecular biology program…

  10. Molecular biology of major components of chloride cells.

    PubMed

    Hirose, Shigehisa; Kaneko, Toyoji; Naito, Nobuko; Takei, Yoshio

    2003-12-01

    Current understanding of chloride cells (CCs) is briefly reviewed with emphasis on molecular aspects of their channels, transporters and regulators. Seawater-type and freshwater-type CCs have been identified based on their shape, location and response to different ionic conditions. Among the freshwater-type CCs, subpopulations are emerging that are implicated in the uptake of Na(+), Cl(-) and Ca(2+), respectively, and can be distinguished by their shape of apical crypt and affinity for lectins. The major function of the seawater CC is transcellular secretion of Cl(-), which is accomplished by four major channels and transporters: (1). CFTR Cl(-) channel, (2). Na(+),K(+)-ATPase, (3). Na(+)/K(+)/2Cl(-) cotransporter and (4). a K(+) channel. The first three components have been cloned and characterized, but concerning the K(+) channel that is essential for the continued generation of the driving force by Na(+),K(+)-ATPase, only one candidate is identified. Although controversial, freshwater CCs seem to perform the uptake of Na(+), Cl(-) and Ca(2+) in a manner analogous to but slightly different from that seen in the absorptive epithelia of mammalian kidney and intestine since freshwater CCs face larger concentration gradients than ordinary epithelial cells. The components involved in these processes are beginning to be cloned, but their CC localization remains to be established definitively. The most important yet controversial issue is the mechanism of Na(+) uptake. Two models have been postulated: (i). the original one involves amiloride-sensitive electroneutral Na(+)/H(+) exchanger (NHE) with the driving force generated by Na(+),K(+)-ATPase and carbonic anhydrase (CA) and (ii). the current model suggests that Na(+) uptake occurs through an amiloride-sensitive epithelial sodium channel (ENaC) electrogenically coupled to H(+)-ATPase. While fish ENaC remains to be identified by molecular cloning and database mining, fish NHE has been cloned and shown to be highly

  11. Molecular Aspects of Mucoadhesive Carrier Development for Drug Delivery and Improved Absorption

    PubMed Central

    Peppas, Nicholas A; Thomas, J. Brock; McGinity, James

    2011-01-01

    Although the oral route remains the most favored route of drug administration, major scientific obstacles prevent the effective and efficient delivery of low-molecular-mass drugs, peptides and proteins that exhibit poor solubility and permeability. Mucoadhesive dosage forms and the associated drug carriers have the ability to interact at a molecular level with the mucus gel layer that lines the epithelial surfaces of the major absorptive regions of the body. This interaction provides an increased residence time of the therapeutic formulation while localizing the drug at the site of administration. Such local, non-specific targeting leads to an increase in both oral absorption and bioavailability. Fundamental understanding of the biological processes encountered along the gastrointestinal tract can provide a sufficient engineer of carriers that are capable to provide this increase in residence time. Here we discuss the theoretical framework for achieving mucoadhesive systems as related to biomaterials science and the structure of the biomaterials used. PMID:19105897

  12. [Research on polyhydroxyalkanoate form a key aspect to enhanced biological phosphorus transformation].

    PubMed

    Liu, Yan; Xing, Zhi-qiang; Chen, Yin-guang; Zhou, Qi

    2006-06-01

    To investigate the influence of PHB and PHV formed on phosphorus (P) release, uptake and removal during enhanced biological phosphorus removal (EBPR), anaerobic/aerobic batch experiments were conducted with biomass acclimated with propionic to acetic acid carbon molar ratios of 0.5 and 2 on two sequencing batch reactors (SBR1 and SBR2). Statistically significant correlations between polyhydroxyalkanoate (PHA) quantity and form and P release/uptake and removal were observed (R2 >0.90). The regression coefficients showed that for biomass cultured with customizing wastewater P release and uptake were both a function of PHB but not of PHV, but higher P removal was largely because of PHV as the predominant type rather than PHV. For biomass cultured with different ratios of propionic to acetic acid, the SBR2 biomass synthesized and utilized more PHB and less PHV and showed higher net P removal (average increase of 16.69%) than SBR1. Thus acetate/propionate content of influent had a major influenceon PHA type and quantity and determine phosphorus (P) release, uptake and removal. Accordingly, PHB and PHV transformations should be taken into account as key aspect for optimizing EBPR.

  13. Generation of Scalable, Metallic High-Aspect Ratio Nanocomposites in a Biological Liquid Medium.

    PubMed

    Cotton Kelly, Kinsey; Wasserman, Jessica R; Deodhar, Sneha; Huckaby, Justin; DeCoster, Mark A

    2015-01-01

    The goal of this protocol is to describe the synthesis of two novel biocomposites with high-aspect ratio structures. The biocomposites consist of copper and cystine, with either copper nanoparticles (CNPs) or copper sulfate contributing the metallic component. Synthesis is carried out in liquid under biological conditions (37 °C) and the self-assembled composites form after 24 hr. Once formed, these composites are highly stable in both liquid media and in a dried form. The composites scale from the nano- to micro- range in length, and from a few microns to 25 nm in diameter. Field emission scanning electron microscopy with energy dispersive X-ray spectroscopy (EDX) demonstrated that sulfur was present in the NP-derived linear structures, while it was absent from the starting CNP material, thus confirming cystine as the source of sulfur in the final nanocomposites. During synthesis of these linear nano- and micro-composites, a diverse range of lengths of structures is formed in the synthesis vessel. Sonication of the liquid mixture after synthesis was demonstrated to assist in controlling average size of the structures by diminishing the average length with increased time of sonication. Since the formed structures are highly stable, do not agglomerate, and are formed in liquid phase, centrifugation may also be used to assist in concentrating and segregating formed composites. PMID:26274773

  14. A comprehensive phylogenetic analysis of termites (Isoptera) illuminates key aspects of their evolutionary biology.

    PubMed

    Inward, Daegan J G; Vogler, Alfried P; Eggleton, Paul

    2007-09-01

    The first comprehensive combined molecular and morphological phylogenetic analysis of the major groups of termites is presented. This was based on the analysis of three genes (cytochrome oxidase II, 12S and 28S) and worker characters for approximately 250 species of termites. Parsimony analysis of the aligned dataset showed that the monophyly of Hodotermitidae, Kalotermitidae and Termitidae were well supported, while Termopsidae and Rhinotermitidae were both paraphyletic on the estimated cladogram. Within Termitidae, the most diverse and ecologically most important family, the monophyly of Macrotermitinae, Foraminitermitinae, Apicotermitinae, Syntermitinae and Nasutitermitinae were all broadly supported, but Termitinae was paraphyletic. The pantropical genera Termes, Amitermes and Nasutitermes were all paraphyletic on the estimated cladogram, with at least 17 genera nested within Nasutitermes, given the presently accepted generic limits. Key biological features were mapped onto the cladogram. It was not possible to reconstruct the evolution of true workers unambiguously, as it was as parsimonious to assume a basal evolution of true workers and subsequent evolution of pseudergates, as to assume a basal condition of pseudergates and subsequent evolution of true workers. However, true workers were only found in species with either separate- or intermediate-type nests, so that the mapping of nest habit and worker type onto the cladogram were perfectly correlated. Feeding group evolution, however, showed a much more complex pattern, particularly within the Termitidae, where it proved impossible to estimate unambiguously the ancestral state within the family (which is associated with the loss of worker gut flagellates). However, one biologically plausible optimization implies an initial evolution from wood-feeding to fungus-growing, proposed as the ancestral condition within the Termitidae, followed by the very early evolution of soil-feeding and subsequent re

  15. Monitoring molecular, functional and morphologic aspects of bone metastases using non-invasive imaging.

    PubMed

    Bauerle, Tobias; Komljenovic, Dorde; Semmler, Wolfhard

    2012-03-01

    Bone is among the most common locations of metastasis and therefore represents an important clinical target for diagnostic follow-up in cancer patients. In the pathogenesis of bone metastases, disseminated tumor cells proliferating in bone interact with the local microenvironment stimulating or inhibiting osteoclast and osteoblast activity. Non-invasive imaging methods monitor molecular, functional and morphologic changes in both compartments of these skeletal lesions - the bone and the soft tissue tumor compartment. In the bone compartment, morphologic information on skeletal destruction is assessed by computed tomography (CT) and radiography. Pathogenic processes of osteoclast and osteoblast activity, however, can be imaged using optical imaging, positron emission tomography (PET), single photon emission CT (SPECT) and skeletal scintigraphy. Accordingly, conventional magnetic resonance imaging (MRI) and CT as well as diffusion- weighted MRI and optical imaging are used to assess morphologic aspects on the macroscopic and cellular level of the soft tissue tumor compartment. Imaging methods such as PET, MR spectroscopy, dynamic contrast-enhanced techniques and vessel size imaging further elucidate on pathogenic processes in this compartment including information on metabolism and vascularization. By monitoring these aspects in bone lesions, new insights in the pathogenesis of skeletal metastases can be gained. In translation to the clinical situation, these novel methods for the monitoring of bone metastases might be applied in patients to improve follow-up of these lesions, in particular after therapeutic intervention. This review summarizes established and experimental imaging techniques for the monitoring of tumor and bone cell activity including molecular, functional and morphological aspects in bone metastases. PMID:22214500

  16. The molecular biology of the olive fly comes of age

    PubMed Central

    2014-01-01

    were shown to be differentially expressed in the female and male reproductive systems analyzed. Finally, the expression profile of the embryonic serendipity-α locus and the pre-apoptotic head involution defective gene were analyzed during embryonic developmental stages. Conclusions Several years of molecular studies on the olive fly can now be combined with new information from whole transcriptome analyses and lead to a deep understanding of the biology of this notorious insect pest. This is a prerequisite for the development of novel embryonic lethality female sexing strains for successful SIT efforts which, combined with improved mass-reared conditions, give new hope for efficient SIT applications for the olive fly. PMID:25472866

  17. Escherichia coli and the Emergence of Molecular Biology.

    PubMed

    Ullmann, Agnes

    2011-12-01

    The creation of the "Phage group" by M. Delbrück, S. E. Luria, and A. D. Hershey in 1940 at Cold Spring Harbor played a crucial role in the development of molecular biology. In the 1940s, working with Escherichia coli and its viruses, Luria and Delbrück discovered the spontaneous nature of bacterial mutations and Hershey described recombination in bacteriophages and demonstrated with M. Chase that the genetic material that infects bacteria is DNA. At the same time, S. Benzer defined the structure of a functional genetic unit and J. Lederberg and E. Tatum discovered sexual recombination between bacteria. Some years later, Lederberg's group discovered extrachromosomal particles, the plasmids, and a novel way of genetic transfer through bacteriophages, called transduction. In 1949, at the Pasteur Institute in Paris, A. Lwoff uncovered the mechanism of lysogeny. Shortly afterwards, F. Jacob and E. Wollman unraveled the mechanism of the sexual process in E. coli and established the circularity of the bacterial chromosome. In the 1960s, J. Monod and F. Jacob, by genetic analysis of the E. coli lactose system, proposed the operon model for gene regulation and introduced the concept of messenger RNA. The elucidation of the double helix structure of DNA in 1953 by F. Crick and J. Watson had major consequences: the establishment of the copying mechanism (Meselson and Stahl), the discovery of the nature of the genetic code (S. Brenner) leading to its deciphering. E. coli and its phages were instrumental in the development of recombinant DNA technology based on the discovery of the restriction-modification system by W. Arber. PMID:26442505

  18. Escherichia coli and the Emergence of Molecular Biology.

    PubMed

    Ullmann, Agnes

    2011-12-01

    The creation of the "Phage group" by M. Delbrück, S. E. Luria, and A. D. Hershey in 1940 at Cold Spring Harbor played a crucial role in the development of molecular biology. In the 1940s, working with Escherichia coli and its viruses, Luria and Delbrück discovered the spontaneous nature of bacterial mutations and Hershey described recombination in bacteriophages and demonstrated with M. Chase that the genetic material that infects bacteria is DNA. At the same time, S. Benzer defined the structure of a functional genetic unit and J. Lederberg and E. Tatum discovered sexual recombination between bacteria. Some years later, Lederberg's group discovered extrachromosomal particles, the plasmids, and a novel way of genetic transfer through bacteriophages, called transduction. In 1949, at the Pasteur Institute in Paris, A. Lwoff uncovered the mechanism of lysogeny. Shortly afterwards, F. Jacob and E. Wollman unraveled the mechanism of the sexual process in E. coli and established the circularity of the bacterial chromosome. In the 1960s, J. Monod and F. Jacob, by genetic analysis of the E. coli lactose system, proposed the operon model for gene regulation and introduced the concept of messenger RNA. The elucidation of the double helix structure of DNA in 1953 by F. Crick and J. Watson had major consequences: the establishment of the copying mechanism (Meselson and Stahl), the discovery of the nature of the genetic code (S. Brenner) leading to its deciphering. E. coli and its phages were instrumental in the development of recombinant DNA technology based on the discovery of the restriction-modification system by W. Arber.

  19. Molecular biological enhancement of coal biodesulfurization. Final technical report

    SciTech Connect

    Litchfield, J.H.; Zupancic, T.J.; Kittle, J.D. Jr.; Baker, B.; Palmer, D.T.; Traunero, C.G.; Wyza, R.E.; Schweitzer, A.; Conkle, H.N.; Chakravarty, L.; Tuovinen, O.H.

    1992-10-08

    Progress is reported in understanding Thiobacillus molecular biology, specifically in the area of vector development. At the initiation of this program, the basic elements needed for performing genetic engineering in T. ferrooxidans were either not yet developed. Improved techniques are described which will make it easier to construct and analyze the genetic structure and metabolism of recombinant T. ferrooxidans. The metabolism of the model organic sulfur compound dibenzothiophene (DBT) by certain heterotrophic bacteria was confirmed and characterized. Techniques were developed to analyze the metabolites of DBT, so that individual 4S pathway metabolites could be distinguished. These techniques are expected to be valuable when engineering organic sulfur metabolism in Thiobacillus. Strain isolation techniques were used to develop pure cultures of T. ferrooxidans seven of which were assessed as potential recombinant hosts. The mixotrophic strain T. coprinus was also characterized for potential use as an electroporation host. A family of related Thiobacillus plasmids was discovered in the seven strains of P. ferrooxidans mentioned above. One of these plasmids, pTFI91, was cloned into a pUC-based plasmid vector, allowing it to propagate in E. coli. A key portion of the cloned plasmid was sequenced. This segment, which is conserved in all of the related plasmids characterized, contains the vegetative origin of DNA replication, and fortuitously, a novel insertion sequence, designated IS3091. The sequence of the DNA origin revealed that these Thiobacillus plasmids represent a unique class of replicons not previously described. The potentially useful insertion sequence IS3091 was identified as a new member of a previously undefined family of insertion sequences which include the E. coli element IS30.

  20. The molecular biology of plastid division in higher plants.

    PubMed

    Aldridge, Cassie; Maple, Jodi; Møller, Simon G

    2005-04-01

    Plastids are essential plant organelles vital for life on earth, responsible not only for photosynthesis but for many fundamental intermediary metabolic reactions. Plastids are not formed de novo but arise by binary fission from pre-existing plastids, and plastid division therefore represents an important process for the maintenance of appropriate plastid populations in plant cells. Plastid division comprises an elaborate pathway of co-ordinated events which include division machinery assembly at the division site, the constriction of envelope membranes, membrane fusion and, ultimately, the separation of the two new organelles. Because of their prokaryotic origin bacterial cell division has been successfully used as a paradigm for plastid division. This has resulted in the identification of the key plastid division components FtsZ, MinD, and MinE, as well as novel proteins with similarities to prokaryotic cell division proteins. Through a combination of approaches involving molecular genetics, cell biology, and biochemistry, it is now becoming clear that these proteins act in concert during plastid division, exhibiting both similarities and differences compared with their bacterial counterparts. Recent efforts in the cloning of the disrupted loci in several of the accumulation and replication of chloroplasts mutants has further revealed that the division of plastids is controlled by a combination of prokaryote-derived and host eukaryote-derived proteins residing not only in the plastid stroma but also in the cytoplasm. Based on the available data to date, a working model is presented showing the protein components involved in plastid division, their subcellular localization, and their protein interaction properties. PMID:15753112

  1. The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools.

    PubMed

    Caron, David A; Countway, Peter D; Brown, Mark V

    2004-01-01

    Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.

  2. Testing Models: A Key Aspect to Promote Teaching Activities Related to Models and Modelling in Biology Lessons?

    ERIC Educational Resources Information Center

    Krell, Moritz; Krüger, Dirk

    2016-01-01

    This study investigated biology teachers' (N = 148) understanding of models and modelling (MoMo), their model-related teaching activities and relations between the two. A framework which distinguishes five aspects of MoMo in science ("nature of models," "multiple models," "purpose of models," "testing…

  3. Chemical and molecular aspects on interactions of galanthamine and its derivatives with cholinesterases.

    PubMed

    Gulcan, Hayrettin O; Orhan, Ilkay E; Sener, Bilge

    2015-01-01

    Dual action of galanthamine as potent cholinesterase inhibitor and nicotinic modulator has attracted a great attention to be used in the treatment of AD. Consequently, galanthamine, a natural alkaloid isolated from a Galanthus species (snowdrop, Amaryllidaceae), has become an attractive model compound for synthesis of its novel derivatives to discover new drug candidates. Numerous studies have been done to elucidate interactions between galanthamine and its different derivatives and the enzymes; acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) using in vitro and in silico experimental models. The in vitro studies revealed that galanthamine inhibits AChE in strong, competitive, long-acting, and reversible manner as well as BChE, although its selectivity towards AChE is much higher than BChE. The in silico studies carried out by employing molecular docking experiments as well as molecular dynamics simulations pointed out to existence of strong interactions of galanthamine with the active gorge of AChE, mostly of Torpedo californica (the Pasific electric ray) origin. In this review, we evaluate the mainstays of cholinesterase inhibitory action of galanthamine and its various derivatives from the point of view of chemical and molecular aspects. PMID:25483718

  4. Chemical and molecular aspects on interactions of galanthamine and its derivatives with cholinesterases.

    PubMed

    Gulcan, Hayrettin O; Orhan, Ilkay E; Sener, Bilge

    2015-01-01

    Dual action of galanthamine as potent cholinesterase inhibitor and nicotinic modulator has attracted a great attention to be used in the treatment of AD. Consequently, galanthamine, a natural alkaloid isolated from a Galanthus species (snowdrop, Amaryllidaceae), has become an attractive model compound for synthesis of its novel derivatives to discover new drug candidates. Numerous studies have been done to elucidate interactions between galanthamine and its different derivatives and the enzymes; acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) using in vitro and in silico experimental models. The in vitro studies revealed that galanthamine inhibits AChE in strong, competitive, long-acting, and reversible manner as well as BChE, although its selectivity towards AChE is much higher than BChE. The in silico studies carried out by employing molecular docking experiments as well as molecular dynamics simulations pointed out to existence of strong interactions of galanthamine with the active gorge of AChE, mostly of Torpedo californica (the Pasific electric ray) origin. In this review, we evaluate the mainstays of cholinesterase inhibitory action of galanthamine and its various derivatives from the point of view of chemical and molecular aspects.

  5. Unicellular eukaryotes as models in cell and molecular biology: critical appraisal of their past and future value.

    PubMed

    Simon, Martin; Plattner, Helmut

    2014-01-01

    Unicellular eukaryotes have been appreciated as model systems for the analysis of crucial questions in cell and molecular biology. This includes Dictyostelium (chemotaxis, amoeboid movement, phagocytosis), Tetrahymena (telomere structure, telomerase function), Paramecium (variant surface antigens, exocytosis, phagocytosis cycle) or both ciliates (ciliary beat regulation, surface pattern formation), Chlamydomonas (flagellar biogenesis and beat), and yeast (S. cerevisiae) for innumerable aspects. Nowadays many problems may be tackled with "higher" eukaryotic/metazoan cells for which full genomic information as well as domain databases, etc., were available long before protozoa. Established molecular tools, commercial antibodies, and established pharmacology are additional advantages available for higher eukaryotic cells. Moreover, an increasing number of inherited genetic disturbances in humans have become elucidated and can serve as new models. Among lower eukaryotes, yeast will remain a standard model because of its peculiarities, including its reduced genome and availability in the haploid form. But do protists still have a future as models? This touches not only the basic understanding of biology but also practical aspects of research, such as fund raising. As we try to scrutinize, due to specific advantages some protozoa should and will remain favorable models for analyzing novel genes or specific aspects of cell structure and function. Outstanding examples are epigenetic phenomena-a field of rising interest. PMID:24529723

  6. Unicellular eukaryotes as models in cell and molecular biology: critical appraisal of their past and future value.

    PubMed

    Simon, Martin; Plattner, Helmut

    2014-01-01

    Unicellular eukaryotes have been appreciated as model systems for the analysis of crucial questions in cell and molecular biology. This includes Dictyostelium (chemotaxis, amoeboid movement, phagocytosis), Tetrahymena (telomere structure, telomerase function), Paramecium (variant surface antigens, exocytosis, phagocytosis cycle) or both ciliates (ciliary beat regulation, surface pattern formation), Chlamydomonas (flagellar biogenesis and beat), and yeast (S. cerevisiae) for innumerable aspects. Nowadays many problems may be tackled with "higher" eukaryotic/metazoan cells for which full genomic information as well as domain databases, etc., were available long before protozoa. Established molecular tools, commercial antibodies, and established pharmacology are additional advantages available for higher eukaryotic cells. Moreover, an increasing number of inherited genetic disturbances in humans have become elucidated and can serve as new models. Among lower eukaryotes, yeast will remain a standard model because of its peculiarities, including its reduced genome and availability in the haploid form. But do protists still have a future as models? This touches not only the basic understanding of biology but also practical aspects of research, such as fund raising. As we try to scrutinize, due to specific advantages some protozoa should and will remain favorable models for analyzing novel genes or specific aspects of cell structure and function. Outstanding examples are epigenetic phenomena-a field of rising interest.

  7. MOLECULAR IMAGING OF PROSTATE CANCER: translating molecular biology approaches into the clinical realm

    PubMed Central

    Vargas, Hebert Alberto; Grimm, Jan; Donati, Olivio F.; Sala, Evis; Hricak, Hedvig

    2016-01-01

    The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980’s. Most prostate cancers today are detected at early stages of the disease and are considered “indolent”, however some patients’ prostate cancers demonstrate a more aggressive behavior which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterizes this disease has lead to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumor detection alone to distinguishing patients with indolent tumors that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumors that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualization of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. PMID:25693661

  8. Molecular targeted therapy in enteropancreatic neuroendocrine tumors: from biology to clinical practice.

    PubMed

    Fazio, N; Scarpa, A; Falconi, M

    2014-01-01

    Advanced enteropancreatic (EP) neuroendocrine tumors (NETs) can be treated with several different therapies, including chemotherapy, biotherapy, and locoregional treatments. Over the last few decades, impressive progress has been made in the biotherapy field. Three main druggable molecular targets have been studied and developed in terms of therapy: somatostatin receptor (sstr), mammalian target of rapamycin (mTOR), and angiogenic factors. In particular, research has moved from the old somatostatin analogs (SSAs), such as octreotide (OCT) and lanreotide (LAN), specifically binding to the sstr-2, to the newer pasireotide (PAS), which presents a wider sstr spectrum. Over the last ten years, several molecular targeted agents (MTAs) have been studied in phase II trials, and very few of them have reached phase III. The mTOR inhibitor everolimus and the multitargeted inhibitor sunitinib have been approved for clinical use by the FDA and EMA in advanced well/moderately-differentiated (WD, MD) progressive pancreatic neuroendocrine tumors (PNETs), on the basis of the positive results of two international large randomized phase III trials vs. placebo. Bevacizumab has been studied in a large US phase III trial vs. interferon (IFN)-alfa2b, and results are pending. In this review, the biological and clinical aspects of MTAs introduced into clinical practice or which are currently in an advanced phase of clinical investigation are addressed.

  9. Managing Abandoned Farmland: The Need to Link Biological and Sociological Aspects

    NASA Astrophysics Data System (ADS)

    Benjamin, Karyne; Bouchard, André; Domon, Gérald

    2008-10-01

    The lack of a particular use associated with abandoned farmland provides real opportunities with respect to the various land-use pressures occurring in productive territories. These environments remain generally poorly known and, because of this, require in-depth studies on the feasibility of management options, on biological as well as social grounds. This study, based on research on the biophysical potential and the perceptions by the owners of abandoned farmlands, analyzes the feasibility of silvicultural management options to improve forestry potential. Using a questionnaire, we surveyed abandoned farmland owners on different aspects of the status of their abandoned farmland in order to determine their willingness toward the management of these private lands. The land owners were also asked to express their interests and their constraints toward various types of interventions, with an emphasis on silvicultural work. The data were analyzed using multivariate methods to establish relationships between the questionnaire data and the characteristics of the land owners (socioeconomic profile and value system toward the environment). The results show that, in general, abandoned farmland is an unwanted space, is generally little used, is poorly known, and has little importance in the plans of its owners. We have found three types of owner profiles; the owners with a farmer’s profile are those who are the most interested in managing their abandoned farmland, whether for agriculture or silviculture. The desire to improve abandoned farmland seems less important to owners with an ecocentric profile (high awareness of the environment) and to older owners. Finally, by associating the type of abandoned farmland owned and the characteristics of the owners, it is possible to propose different management options that reconcile the wishes of the owners as well as the biophysical potential of their abandoned farmland.

  10. The Closed Equilibrated Biological Aquatic System: general concept and aspects of botanical research.

    PubMed

    Blum, V; Hollander-Czytko, H; Voeste, D

    1997-09-01

    The Closed Equilibrated Biological Aquatic System (CEBAS) consists of four subcomponents which form a closed (artificial) aquatic ecosystem initially designed to study the long-term influence of space conditions on several successive generations of aquatic organisms. Teleost fishes and water snails in the zoological component produce CO2 ammonium ions and waste compounds which can be utilized after ammonium is oxidised in a microbial component by the botanical component consisting of a rootless, aquatic higher plant species which eliminates ions, i.e. nitrate, and produces oxygen for animal respiration. An electronic component serves as a data-acquisition and regulation device for temperature and oxygen-dependent illumination of the plant chamber. A comprehensive interdisciplinary research programme, focused around the CEBAS, is especially well developed in the field of zoology. It covers a ground laboratory and preparations for two scheduled space flight projects, as well as aspects of combined animal-plant food production modules for human nutrition in bioregenerative space life-support systems and for terrestrial production sites. In the botanical research programme, morphological investigations on Ceratophyllum demersum L. performed with light and electron microscopy have demonstrated a gas lacuna system which, in addition to starch grains in the plastids, might regulate the buoyancy of the plant and/or serve as a 'gas skeleton'. Also, a remarkable symmetry in the arrangement of tissues was observed in stems and older leaves. The photosynthetic capacities of Ceratophyllum in the CEBAS-MINI MODULE proved to be more than sufficient for life support, and experiments on nitrate uptake into the plants showed their capacity to utilize ions from the water.

  11. Managing abandoned farmland: the need to link biological and sociological aspects.

    PubMed

    Benjamin, Karyne; Bouchard, André; Domon, Gérald

    2008-10-01

    The lack of a particular use associated with abandoned farmland provides real opportunities with respect to the various land-use pressures occurring in productive territories. These environments remain generally poorly known and, because of this, require in-depth studies on the feasibility of management options, on biological as well as social grounds. This study, based on research on the biophysical potential and the perceptions by the owners of abandoned farmlands, analyzes the feasibility of silvicultural management options to improve forestry potential. Using a questionnaire, we surveyed abandoned farmland owners on different aspects of the status of their abandoned farmland in order to determine their willingness toward the management of these private lands. The land owners were also asked to express their interests and their constraints toward various types of interventions, with an emphasis on silvicultural work. The data were analyzed using multivariate methods to establish relationships between the questionnaire data and the characteristics of the land owners (socioeconomic profile and value system toward the environment). The results show that, in general, abandoned farmland is an unwanted space, is generally little used, is poorly known, and has little importance in the plans of its owners. We have found three types of owner profiles; the owners with a farmer's profile are those who are the most interested in managing their abandoned farmland, whether for agriculture or silviculture. The desire to improve abandoned farmland seems less important to owners with an ecocentric profile (high awareness of the environment) and to older owners. Finally, by associating the type of abandoned farmland owned and the characteristics of the owners, it is possible to propose different management options that reconcile the wishes of the owners as well as the biophysical potential of their abandoned farmland.

  12. Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria.

    PubMed

    Jagielski, Tomasz; Minias, Alina; van Ingen, Jakko; Rastogi, Nalin; Brzostek, Anna; Żaczek, Anna; Dziadek, Jarosław

    2016-04-01

    Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

  13. Thermodynamic and structural aspects of novel 1,2,4-thiadiazoles in solid and biological mediums.

    PubMed

    Perlovich, German L; Proshin, Alexey N; Volkova, Tatyana V; Bui, Cong Trinh; Bachurin, Sergey O

    2011-10-01

    Novel 1,2,4-thiadiazoles were synthesized. Crystal structures of these compounds were solved by X-ray diffraction experiments, and comparative analysis of packing architecture and hydrogen bond networks was carried out. Thermodynamic aspects of sublimation processes of the compounds under study were analyzed using temperature dependencies of vapor pressure. Thermophysical characteristics of the molecular crystals were obtained and compared with the sublimation and structural parameters. The melting points correlate with sublimation Gibbs energies. Moreover, an increase of donor-acceptor interactions in crystal structures leads to growth of Gibbs energy values. Relationships between the melting points and the fragmental contributions to the packing energies were established: R(1)-R(4) fragmental interactions are responsible for the fusion processes of this class of compounds. Solubility and solvation processes of 1,2,4-thiadiazoles in buffer, n-hexane and n-octanol were studied within a wide range of temperature intervals, and their thermodynamic functions were calculated. Specific and nonspecific interactions of molecules resolved in crystals and solvents were estimated and compared. It was found that the melting points correlate with sublimation Gibbs energies. Distribution processes of compounds in buffer/n-octanol and buffer/n-hexane systems (describing different types of membranes) were investigated. Transfer processes of the studied molecules from the buffer to n-octanol/n-hexane phases were analyzed by the diagram method with evaluation of the enthalpic and entropic terms. This approach allowed us to design drug molecules with optimal passive transport properties. Calcium-blocking properties of the substances were evaluated. The trend between the ability to inhibit Glu-Ca uptake and the distribution coefficients in buffer/hexane system was observed.

  14. Modulation of HIV transmission by Neisseria gonorrhoeae: molecular and immunological aspects.

    PubMed

    Jarvis, Gary A; Chang, Theresa L

    2012-04-01

    Neisseria gonorrhoeae (GC), a major cause of pelvic inflammatory disease, can facilitate HIV transmission. In response to GC infection, genital epithelial cells can produce cytokines, chemokines and defensins to modulate HIV infection and infectivity. GC can also induce the production of cytokines and chemokines in monocytes and modulate T cell activation. In vivo, an increase in the number of endocervical CD4+ T cells has been found in GC-infected women. Additionally, GC appears to modulate HIV-specific immune responses in HIV-exposed sex workers. Interestingly, in vitro, GC exhibits HIV enhancing or inhibitory effects depending on the HIV target cells. This review summarizes molecular and immunological aspects of the modulation of HIV infection and transmission by GC. Future studies using a multi-cellular system or in animal models will offer insight into the mechanisms by which GC increases HIV transmission.

  15. Novel aspects of the Jahn-Teller effect in molecular and solid-state systems

    NASA Astrophysics Data System (ADS)

    Ernst, Wolfgang E.; Köppel, Horst

    2015-10-01

    The Jahn-Teller effect continues to be a source of insight and inspiration for the interpretation of structural instabilities and dynamic phenomena in molecules and solids. About two decades passed between the publication of the proof of the Jahn-Teller theorem in 1937 and broad scientific activity in the field (although clear experimental evidence of the effect in the ESR spectra of bivalent copper compounds became available in 1950). Then a rapid development set in, and suitable model treatments were set up in the literature and applied to various kinds of problems in molecular and solid-state spectroscopy. Different possibilities for structural distortions, and the associated dynamical (tunneling) processes, were explored, and consequences for magnetic resonance and optical spectra revealed. Key extensions followed, regarding the structural and also dynamic aspects of the Jahn-Teller effect (JTE): similar distortions may also occur in near-degeneracy situations, termed pseudo JTE, which enhances the importance of the effects.

  16. Philosophical basis and some historical aspects of systems biology: from Hegel to Noble - applications for bioenergetic research.

    PubMed

    Saks, Valdur; Monge, Claire; Guzun, Rita

    2009-03-01

    We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed.

  17. Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research

    PubMed Central

    Saks, Valdur; Monge, Claire; Guzun, Rita

    2009-01-01

    We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed. PMID:19399243

  18. A perfect time to harness advanced molecular technologies to explore the fundamental biology of Toxocara species.

    PubMed

    Gasser, Robin B

    2013-04-15

    Toxocarosis is of major canine health and socioeconomic importance worldwide. Although many studies have given insights into toxocarosis, to date, there has been limited exploration of the molecular biology, biochemistry, genetics, epidemiology and ecology of Toxocara species as well as parasite-host interactions using '-omic' technologies. The present article gives a background on Toxocara species and toxocarosis, describes molecular tools for specific identification and genetic analysis, and provides a prospective view of the benefits that advanced molecular technologies will have towards better understanding the parasites and disease. Tackling key biological questions employing a 'systems biology' approach should lead to new and improved strategies for the treatment, diagnosis and control of toxocarosis.

  19. Molecular Biology of Learning: Modulation of Transmitter Release.

    ERIC Educational Resources Information Center

    Kandel, Eric R.; Schwartz, James H.

    1982-01-01

    Describes how a behavioral system in Aplysia (marine snail) can be used to examine mechanisms of several forms of learning at different levels of analysis: behavioral, cell-physiological, ultrastructural, and molecular. Focusing on short-term sensitization, suggests how molecular mechanisms can be extended to explain long-term memory and classical…

  20. Who wrote the book of life? Information and the transformation of molecular biology, 1945-55.

    PubMed

    Kay, L E

    1995-01-01

    This paper focuses on the opening of a discursive space: the emergence of informational and scriptural representations of life and hereditiy and their self-negating consequences for the construction of biological meaning. It probes the notion of writing and the book of life and shows how molecular biology's claims to a status of language and texuality undermines its own objective of control. These textual significations were historically contingent. The informational representations of heredity and life were not an outcome of the internal cognitive momentum of molecular biology; they were not a logical necessity of the unravelling of the base-pairing of the DNA double-helix. They were transported into molecular biology still within the protein paradigm of the gene in the 1940s and permeated nearly every discipline in the life and social sciences. These information-based models, metaphors, linguistic, and semiotic tools which were central to the formulation of the genetic code were transported into molecular biology from cybernetics, information theory, electronic computing, and control and communication systems--technosciences that were deeply embedded with the military experiences of World War II and the Cold War. The information discourse thus became fixed in molecular biology not because it worked in the narrow epistemic sense (it did not), but because it positioned molecular biology within postwar discourse and culture, perhaps within the transition to a post-modern information-based society. PMID:11613275

  1. Batten Disease: Clinical Aspects, Molecular Mechanisms, Translational Science, and Future Directions

    PubMed Central

    Dolisca, Sarah-Bianca; Mehta, Mitali; Pearce, David A.; Mink, Jonathan W.; Maria, Bernard L.

    2014-01-01

    The neuronal ceroid lipofuscinoses, collectively the most common neurodegenerative disorders of childhood, are primarily caused by an autosomal recessive genetic mutation leading to a lysosomal storage disease. Clinically these diseases manifest at varying ages of onset, and associated symptoms include cognitive decline, movement disorders, seizures, and retinopathy. The underlying cell biology and biochemistry that cause the clinical phenotypes of neuronal ceroid lipofuscinoses are still being elaborated. The 2012 Neurobiology of Disease in Children Symposium, held in conjunction with the 41st Annual Meeting of the Child Neurology Society, aimed to (1) provide a survey of the currently accepted forms of neuronal ceroid lipofuscinoses and their associated genetic mutations and clinical phenotypes; (2) highlight the specific pathology of Batten disease; (3) discuss the contemporary understanding of the molecular mechanisms that lead to pathology; and (4) introduce strategies that are being translated from bench to bedside as potential therapeutics. PMID:23838031

  2. Systems biology for molecular life sciences and its impact in biomedicine.

    PubMed

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  3. Global Foot-and-Mouth Disease Research Update and Gap Analysis: 7 - Pathogenesis and Molecular Biology.

    PubMed

    Robinson, L; Knight-Jones, T J D; Charleston, B; Rodriguez, L L; Gay, C G; Sumption, K J; Vosloo, W

    2016-06-01

    We assessed research knowledge gaps in the fields of FMDV (foot-and-mouth disease virus) pathogenesis and molecular biology by performing a literature review (2011-15) and collecting research updates (2014) from 33 institutes from across the world. Findings were used to identify priority areas for future research. There have been important advances in FMDV pathogenesis; FMDV remains in lymph nodes of many recovered animals that otherwise do not appear persistently infected, even in species previously not associated with the carrier state. Whether virus retention helps maintain host immunity and/or virus survival is not known. Studies of FMDV pathogenesis in wildlife have provided insights into disease epidemiology, in endemic and epidemic settings. Many aspects of FMDV infection and virus entry remain unknown; however, at the cellular level, we know that expression level and availability of integrins (that permit viral entry), rate of clearance of infected cells and strength of anti-viral type I IFN (interferon) response are key determinants of tissue tropism. Extending findings to improved understanding of transmission requires a standardized approach and adoption of natural routes of infection during experimental study. There has been recognition of the importance of autophagosomes for FMDV entry into the cytoplasm following cell surface receptor binding, and that distinct internal cellular membranes are exploited for viral replication and immune evasion. New roles for viral proteins in blocking type I IFN production and downstream signalling have been identified facilitating research in anti-viral therapeutics. We know more about how infection affects cell protein expression, and research into molecular determinants of capsid stability has aided the development of stable vaccines. We have an expanding knowledge of viral and host molecular determinates of virulence and infectiousness, and of how phylogenetics may be used to estimate vaccine match and strain

  4. Global Foot-and-Mouth Disease Research Update and Gap Analysis: 7 - Pathogenesis and Molecular Biology.

    PubMed

    Robinson, L; Knight-Jones, T J D; Charleston, B; Rodriguez, L L; Gay, C G; Sumption, K J; Vosloo, W

    2016-06-01

    We assessed research knowledge gaps in the fields of FMDV (foot-and-mouth disease virus) pathogenesis and molecular biology by performing a literature review (2011-15) and collecting research updates (2014) from 33 institutes from across the world. Findings were used to identify priority areas for future research. There have been important advances in FMDV pathogenesis; FMDV remains in lymph nodes of many recovered animals that otherwise do not appear persistently infected, even in species previously not associated with the carrier state. Whether virus retention helps maintain host immunity and/or virus survival is not known. Studies of FMDV pathogenesis in wildlife have provided insights into disease epidemiology, in endemic and epidemic settings. Many aspects of FMDV infection and virus entry remain unknown; however, at the cellular level, we know that expression level and availability of integrins (that permit viral entry), rate of clearance of infected cells and strength of anti-viral type I IFN (interferon) response are key determinants of tissue tropism. Extending findings to improved understanding of transmission requires a standardized approach and adoption of natural routes of infection during experimental study. There has been recognition of the importance of autophagosomes for FMDV entry into the cytoplasm following cell surface receptor binding, and that distinct internal cellular membranes are exploited for viral replication and immune evasion. New roles for viral proteins in blocking type I IFN production and downstream signalling have been identified facilitating research in anti-viral therapeutics. We know more about how infection affects cell protein expression, and research into molecular determinants of capsid stability has aided the development of stable vaccines. We have an expanding knowledge of viral and host molecular determinates of virulence and infectiousness, and of how phylogenetics may be used to estimate vaccine match and strain

  5. Biological, Epidemiological, and Clinical Aspects of Echinococcosis, a Zoonosis of Increasing Concern

    PubMed Central

    Eckert, Johannes; Deplazes, Peter

    2004-01-01

    Echinococcosis in humans is a zoonotic infection caused by larval stages (metacestodes) of cestode species of the genus Echinococcus. Cystic echinococcosis (CE) is caused by Echinococcus granulosus, alveolar echinococcosis (AE) is caused by E. multilocularis, and polycystic forms are caused by either E. vogeli or E. oligarthrus. In untreated cases, AE has a high mortality rate. Although control is essentially feasible, CE remains a considerable health problem in many regions of the northern and southern hemispheres. AE is restricted to the northern hemisphere regions of North America and Eurasia. Recent studies have shown that E. multilocularis, the causative agent of AE, is more widely distributed than previously thought. There are also some hints of an increasing significance of polycystic forms of the disease, which are restricted to Central and South America. Various aspects of human echinococcosis are discussed in this review, including data on the infectivity of genetic variants of E. granulosus to humans, the increasing invasion of cities in Europe and Japan by red foxes, the main definitive hosts of E. multilocularis, and the first demonstration of urban cycles of the parasite. Examples of emergence or reemergence of CE are presented, and the question of potential spreading of E. multilocularis is critically assessed. Furthermore, information is presented on new and improved tools for diagnosing the infection in final hosts (dogs, foxes, and cats) by coproantigen or DNA detection and the application of molecular techniques to epidemiological studies. In the clinical field, the available methods for diagnosing human CE and AE are described and the treatment options are summarized. The development of new chemotherapeutic options for all forms of human echinococcosis remains an urgent requirement. A new option for the control of E. granulosus in the intermediate host population (mainly sheep and cattle) is vaccination. Attempts are made to reduce the

  6. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins

    NASA Astrophysics Data System (ADS)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-01

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm- 1 and 1545 cm- 1, respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties.

  7. Mathematical aspects of molecular replacement. I. Algebraic properties of motion spaces

    PubMed Central

    Chirikjian, Gregory S.

    2011-01-01

    Molecular replacement (MR) is a well established method for phasing of X-ray diffraction patterns for crystals composed of biological macromolecules of known chemical structure but unknown conformation. In MR, the starting point is known structural domains that are presumed to be similar in shape to those in the macromolecular structure which is to be determined. A search is then performed over positions and orientations of the known domains within a model of the crystallographic asymmetric unit so as to best match a computed diffraction pattern with experimental data. Unlike continuous rigid-body motions in Euclidean space and the discrete crystallographic space groups, the set of motions over which molecular replacement searches are performed does not form a group under the operation of composition, which is shown here to lack the associative property. However, the set of rigid-body motions in the asymmetric unit forms another mathematical structure called a quasigroup, which can be identified with right-coset spaces of the full group of rigid-body motions with respect to the chiral space group of the macromolecular crystal. The algebraic properties of this space of motions are articulated here. PMID:21844648

  8. Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

    ERIC Educational Resources Information Center

    Oerther, Daniel B.

    2002-01-01

    Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

  9. Synthesis of Charge Transfer Dyes for Use as Molecular Sensors in Biological Systems

    NASA Technical Reports Server (NTRS)

    Christie, Joseph J.

    2003-01-01

    This is a continuation of last year's project to synthesize tetraaryl substituted benzodifurans for use as molecular probes in biological systems. The project will involve the synthesis and chemical characterization of dyes and precursor molecules.

  10. Foundational concepts and underlying theories for majors in "biochemistry and molecular biology".

    PubMed

    Tansey, John T; Baird, Teaster; Cox, Michael M; Fox, Kristin M; Knight, Jennifer; Sears, Duane; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3) foundational skills that undergraduate majors in biochemistry and molecular biology must understand to complete their major coursework. Using information gained from these workshops, as well as from the ASBMB accreditation working group and the NSF Vision and Change report, the Core Concepts working group has developed a consensus list of learning outcomes and objectives based on five foundational concepts (evolution, matter and energy transformation, homeostasis, information flow, and macromolecular structure and function) that represent the expected conceptual knowledge base for undergraduate degrees in biochemistry and molecular biology. This consensus will aid biochemistry and molecular biology educators in the development of assessment tools for the new ASBMB recommended curriculum.

  11. Practicing Real Science in the Laboratory: A Project-Based Approach to Teaching Molecular Biology.

    ERIC Educational Resources Information Center

    Wimmers, Larry E.

    2001-01-01

    Describes a molecular biology laboratory in which students study the role of the enzyme polygalacturonase in the softening of tomatoes during ripening by developing their own hypotheses and designing their own experiments. (MM)

  12. Pathophysiology and molecular aspects of diffuse large B-cell lymphoma

    PubMed Central

    Gouveia, Gisele Rodrigues; Siqueira, Sheila Aparecida Coelho; Pereira, Juliana

    2012-01-01

    Diffuse large B-Cell lymphoma is the most common subtype of non-Hodgkin lymphoma in the West. In Brazil, it is the fifth cause of cancer, with more than 55,000 cases and 26,000 deaths per year. At Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo - HCFMUSP, diffuse large B-Cell lymphoma represents 49.7% of all non-Hodgkin lymphoma cases. Initially, the classification of non-Hodgkin lymphoma was based on morphology, but advances in immunology and molecular medicine allowed the introduction of a biological classification for these diseases. As for other cancers, non-Hodgkin lymphoma involves patterns of multifactorial pathogenesis with environmental factors, as well as genetic, occupational and dietary factors, contributing to its development. Multiple lesions involving molecular pathways of B-cell proliferation and differentiation may result in the activation of oncogenes such as the BCL2, BCL6, and MYC genes and the inactivation of tumor suppressor genes such as p53 and INK4, as well as other important transcription factors such as OCT-1 and OCT-2. A dramatic improvement in survival was seen after the recent introduction of the anti-CD20 monoclonal antibody. The association of this antibody to the cyclophosphamide, hydroxydaunorubicin, oncovin and prednisolone (CHOP) regimen has increased overall survival of diffuse large B-Cell lymphoma and follicular lymphoma patients by 20%. However, 50% of all diffuse large B-Cell lymphoma patients remain incurable, creating a demand for more research with new advances in treatment. Thus, it is important to know and understand the key factors and molecular pathways involved in the pathogenesis of diffuse large B-Cell lymphoma. PMID:23323070

  13. Progress in nucleic acid research and molecular biology

    SciTech Connect

    Cohn, W.E. ); Moldave, K. )

    1989-01-01

    This book is organized under the following headings: Transposable elements in Drosophilia; Regulation of gene expression; Structure and function of repetitive and unusual sequences; Retroviruses; Molecular analysis of chromosomal translocation and gene insertion.

  14. A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

    PubMed Central

    Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

    2011-01-01

    Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

  15. Workshop in computational molecular biology, April 15, 1991--April 14, 1994

    SciTech Connect

    Tavare, S.

    1995-04-12

    Funds from this award were used to the Workshop in Computational Molecular Biology, `91 Symposium entitled Interface: Computing Science and Statistics, Seattle, Washington, April 21, 1991; the Workshop in Statistical Issues in Molecular Biology held at Stanford, California, August 8, 1993; and the Session on Population Genetics a part of the 56th Annual Meeting, Institute of Mathematical Statistics, San Francisco, California, August 9, 1993.

  16. A Biochemistry and Molecular Biology Experiment and Evaluation System for Biotechnology Specialty Students: An Effective Evaluation System to Improve the Biochemistry and Molecular Biology Experiment Teaching

    ERIC Educational Resources Information Center

    Li, Suxia; Wu, Haizhen; Zhao, Jian; Ou, Ling; Zhang, Yuanxing

    2010-01-01

    In an effort to achieve high success in knowledge and technique acquisition as a whole, a biochemistry and molecular biology experiment was established for high-grade biotechnology specialty students after they had studied essential theory and received proper technique training. The experiment was based on cloning and expression of alkaline…

  17. Surface chemistry but not aspect ratio mediates the biological toxicity of gold nanorods in vitro and in vivo

    PubMed Central

    Wan, Jiali; Wang, Jia-Hong; Liu, Ting; Xie, Zhixiong; Yu, Xue-Feng; Li, Wenhua

    2015-01-01

    Gold nanorods are a promising nanoscale material in clinical diagnosis and treatment. The physicochemical properties of GNRs, including size, shape and surface features, are crucial factors affecting their cytotoxicity. In this study, we investigated the effects of different aspect ratios and surface modifications on the cytotoxicity and cellular uptake of GNRs in cultured cells and in mice. The results indicated that the surface chemistry but not the aspect ratio of GNRs mediates their biological toxicity. CTAB-GNRs with various aspect ratios had similar abilities to induce cell apoptosis and autophagy by damaging mitochondria and activating intracellular reactive oxygen species (ROS). However, GNRs coated with CTAB/PSS, CTAB/PAH, CTAB/PSS/PAH or CTAB/PAH/PSS displayed low toxicity and did not induce cell death. CTAB/PAH-coated GNRs caused minimally abnormal cell morphology compared with CTAB/PSS and CTAB/PSS/PAH coated GNRs. Moreover, the intravenous injection of CTAB/PAH GNRs enabled the GNRs to reach tumor tissues through blood circulation in animals and remained stable, with a longer half-life compared to the other GNRs. Therefore, our results demonstrated that further coating can prevent cytotoxicity and cell death upon CTAB-coated GNR administration, similar to changing the GNR aspect ratio and CTAB/PAH coated GNRs show superior biological properties with better biocompatibility and minimal cytotoxicity. PMID:26096816

  18. From Gene to Protein: A 3-Week Intensive Course in Molecular Biology for Physical Scientists

    ERIC Educational Resources Information Center

    Nadeau, Jay L.

    2009-01-01

    This article describes a 3-week intensive molecular biology methods course based upon fluorescent proteins, which is successfully taught at the McGill University to advanced undergraduates and graduates in physics, chemical engineering, biomedical engineering, and medicine. No previous knowledge of biological terminology or methods is expected, so…

  19. Size Matters: Molecular Weight Specificity of Hyaluronan Effects in Cell Biology

    PubMed Central

    Cyphert, Jaime M.; Trempus, Carol S.; Garantziotis, Stavros

    2015-01-01

    Hyaluronan signaling properties are unique among other biologically active molecules, that they are apparently not influenced by postsynthetic molecular modification, but by hyaluronan fragment size. This review summarizes the current knowledge about the generation of hyaluronan fragments of different size and size-dependent differences in hyaluronan signaling as well as their downstream biological effects. PMID:26448754

  20. Biological characterization of adult MYC-translocation-positive mature B-cell lymphomas other than molecular Burkitt lymphoma.

    PubMed

    Aukema, Sietse M; Kreuz, Markus; Kohler, Christian W; Rosolowski, Maciej; Hasenclever, Dirk; Hummel, Michael; Küppers, Ralf; Lenze, Dido; Ott, German; Pott, Christiane; Richter, Julia; Rosenwald, Andreas; Szczepanowski, Monika; Schwaenen, Carsten; Stein, Harald; Trautmann, Heiko; Wessendorf, Swen; Trümper, Lorenz; Loeffler, Markus; Spang, Rainer; Kluin, Philip M; Klapper, Wolfram; Siebert, Reiner

    2014-04-01

    Chromosomal translocations affecting the MYC oncogene are the biological hallmark of Burkitt lymphomas but also occur in a subset of other mature B-cell lymphomas. If accompanied by a chromosomal break targeting the BCL2 and/or BCL6 oncogene these MYC translocation-positive (MYC(+)) lymphomas are called double-hit lymphomas, otherwise the term single-hit lymphomas is applied. In order to characterize the biological features of these MYC(+) lymphomas other than Burkitt lymphoma we explored, after exclusion of molecular Burkitt lymphoma as defined by gene expression profiling, the molecular, pathological and clinical aspects of 80 MYC-translocation-positive lymphomas (31 single-hit, 46 double-hit and 3 MYC(+)-lymphomas with unknown BCL6 status). Comparison of single-hit and double-hit lymphomas revealed no difference in MYC partner (IG/non-IG), genomic complexity, MYC expression or gene expression profile. Double-hit lymphomas more frequently showed a germinal center B-cell-like gene expression profile and had higher IGH and MYC mutation frequencies. Gene expression profiling revealed 130 differentially expressed genes between BCL6(+)/MYC(+) and BCL2(+)/MYC(+) double-hit lymphomas. BCL2(+)/MYC(+) double-hit lymphomas more frequently showed a germinal center B-like gene expression profile. Analysis of all lymphomas according to MYC partner (IG/non-IG) revealed no substantial differences. In this series of lymphomas, in which immunochemotherapy was administered in only a minority of cases, single-hit and double-hit lymphomas had a similar poor outcome in contrast to the outcome of molecular Burkitt lymphoma and lymphomas without the MYC break. Our data suggest that, after excluding molecular Burkitt lymphoma and pediatric cases, MYC(+) lymphomas are biologically quite homogeneous with single-hit and double-hit lymphomas as well as IG-MYC and non-IG-MYC(+) lymphomas sharing various molecular characteristics.

  1. A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

    ERIC Educational Resources Information Center

    Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

    2015-01-01

    Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do…

  2. Design, synthesis, and biological evaluation of potent discodermolide fluorescent and photoaffinity molecular probes.

    PubMed

    Smith, Amos B; Rucker, Paul V; Brouard, Ignacio; Freeze, B Scott; Xia, Shujun; Horwitz, Susan Band

    2005-11-10

    [structure: see text] The design, synthesis, and biological evaluation of a series of (+)-discodermolide molecular probes possessing photoaffinity and fluorescent appendages has been achieved. Stereoselective olefin cross-metathesis comprised a key tactic for construction of two of the molecular probes. Three photoaffinity probes were radiolabeled with tritium.

  3. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    ERIC Educational Resources Information Center

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  4. Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

    ERIC Educational Resources Information Center

    Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

    2016-01-01

    Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

  5. Features of Knowledge Building in Biology: Understanding Undergraduate Students' Ideas about Molecular Mechanisms

    ERIC Educational Resources Information Center

    Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S.

    2016-01-01

    Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections…

  6. DAMBE: software package for data analysis in molecular biology and evolution.

    PubMed

    Xia, X; Xie, Z

    2001-01-01

    DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data with a user-friendly Windows 95/98/2000/NT interface. DAMBE is free and can be downloaded from http://web.hku.hk/~xxia/software/software.htm. The current version is 4.0.36.

  7. Clinical and molecular aspects of the live attenuated Oka varicella vaccine.

    PubMed

    Quinlivan, Mark; Breuer, Judy

    2014-07-01

    VZV is a ubiquitous member of the Herpesviridae family that causes varicella (chicken pox) and herpes zoster (shingles). Both manifestations can cause great morbidity and mortality and are therefore of significant economic burden. The introduction of varicella vaccination as part of childhood immunization programs has resulted in a remarkable decline in varicella incidence, and associated hospitalizations and deaths, particularly in the USA. The vaccine preparation, vOka, is a live attenuated virus produced by serial passage of a wild-type clinical isolate termed pOka in human and guinea pig cell lines. Although vOka is clinically attenuated, it can cause mild varicella, establish latency, and reactivate to cause herpes zoster. Sequence analysis has shown that vOka differs from pOka by at least 42 loci; however, not all genomes possess the novel vOka change at all positions, creating a heterogeneous population of genetically distinct haplotypes. This, together with the extreme cell-associated nature of VZV replication in cell culture and the lack of an animal model, in which the complete VZV life cycle can be replicated, has limited studies into the molecular basis for vOka attenuation. Comparative studies of vOka with pOka replication in T cells, dorsal root ganglia, and skin indicate that attenuation likely involves multiple mutations within ORF 62 and several other genes. This article presents an overview of the clinical aspects of the vaccine and current progress on understanding the molecular mechanisms that account for the clinical phenotype of reduced virulence.

  8. Enzymes used in molecular biology: a useful guide

    PubMed Central

    Rittié, Laure

    2008-01-01

    Since molecular cloning has become routine laboratory technique, manufacturers offer countless sources of enzymes to generate and manipulate nucleic acids. Thus, selecting the appropriate enzyme for a specific task may seem difficult to the novice. This review aims at providing the readers with some cues for understanding the function and specificities of the different sources of polymerases, ligases, nucleases, phosphatases, methylases, and topoisomerases used for molecular cloning. We provide a description of the most commonly used enzymes of each group, and explain their properties and mechanism of action. By pointing out key requirements for each enzymatic activity and clarifying their limitations, we aim at guiding the reader in selecting appropriate enzymatic source and optimal experimental conditions for molecular cloning experiments. PMID:18766469

  9. How was teleology eliminated in early molecular biology?

    PubMed

    Sloan, Phillip R

    2012-03-01

    This paper approaches the issue of the status of teleological reasoning in contemporary biology through a historical examination of events of the 1930s that surrounded Niels Bohr's efforts to introduce 'complementarity' into biological discussions. The paper examines responses of three theoretical physicists who engaged boundary questions between the biological and physical sciences in this period in response to Bohr-Ernst Pascual Jordan (1902-80), Erwin Schrödinger (1887-1961), and Max Delbrück (1906-81). It is claimed that none of these physicists sufficiently understood Bohr's 'critical' teleological arguments, which are traced to the lineage of Kant and Harald Høffding and their respective resolutions of the Antinomy of Teleological Judgment. The positions of these four historical actors are discussed in terms of Ernst Mayr's distinction of 'teleological,' 'teleomatic,' and 'teleonomic' explanations. A return to some of the views articulated by Bohr, and behind him, to Høffding and Kant, is claimed to provide a framework for reintroducing a 'critical' teleology into biological discussions.

  10. Teaching Cell and Molecular Biology for Gender Equity

    ERIC Educational Resources Information Center

    Sible, Jill C.; Wilhelm, Dayna E.; Lederman, Muriel

    2006-01-01

    Science, technology, engineering, and math (STEM) fields, including cell biology, are characterized by the "leaky pipeline" syndrome in which, over time, women leave the discipline. The pipeline itself and the pond into which it empties may not be neutral. Explicating invisible norms, attitudes, and practices by integrating social studies of…

  11. How was teleology eliminated in early molecular biology?

    PubMed

    Sloan, Phillip R

    2012-03-01

    This paper approaches the issue of the status of teleological reasoning in contemporary biology through a historical examination of events of the 1930s that surrounded Niels Bohr's efforts to introduce 'complementarity' into biological discussions. The paper examines responses of three theoretical physicists who engaged boundary questions between the biological and physical sciences in this period in response to Bohr-Ernst Pascual Jordan (1902-80), Erwin Schrödinger (1887-1961), and Max Delbrück (1906-81). It is claimed that none of these physicists sufficiently understood Bohr's 'critical' teleological arguments, which are traced to the lineage of Kant and Harald Høffding and their respective resolutions of the Antinomy of Teleological Judgment. The positions of these four historical actors are discussed in terms of Ernst Mayr's distinction of 'teleological,' 'teleomatic,' and 'teleonomic' explanations. A return to some of the views articulated by Bohr, and behind him, to Høffding and Kant, is claimed to provide a framework for reintroducing a 'critical' teleology into biological discussions. PMID:22326083

  12. Towards molecular medicine: a case for a biological periodic table.

    PubMed

    Gawad, Charles

    2005-01-01

    The recently amplified pace of development in the technologies to study both normal and aberrant cellular physiology has allowed for a transition from the traditional reductionist approaches to global interrogations of human biology. This transformation has created the anticipation that we will soon more effectively treat or contain most types of diseases through a 'systems-based' approach to understanding and correcting the underlying etiology of these processes. However, to accomplish these goals, we must first have a more comprehensive understanding of all the elements involved in human cellular physiology, as well as why and how they interact. With the vast number of biological components that have and are being discovered, creating methods with modern computational techniques to better organize biological elements is the next requisite step in this process. This article aims to articulate the importance of the organization of chemical elements into a periodic table had on the conversion of chemistry into a quantitative, translatable science, as well as how we can apply the lessons learned in that transition to the current transformation taking place in biology.

  13. The Use of MERLOT in Biochemistry and Molecular Biology Education

    ERIC Educational Resources Information Center

    Cooper, Scott

    2005-01-01

    The referatory, Multimedia Educational Resources for Learning and Online Teaching (MERLOT), contains links to 1300 electronic teaching resources in biology and chemistry. Approximately 20% have been peer reviewed, and most have user comments or assignments attached. In addition to being a source of educational resources, the MERLOT project seeks…

  14. Molecular probes for nonlinear optical imaging of biological membranes

    NASA Astrophysics Data System (ADS)

    Blanchard-Desce, Mireille H.; Ventelon, Lionel; Charier, Sandrine; Moreaux, Laurent; Mertz, Jerome

    2001-12-01

    Second-harmonic generation (SHG) and two-photon excited fluorescence (TPEF) are nonlinear optical (NLO) phenomena that scale with excitation intensity squared, and hence give rise to an intrinsic 3-dimensional resolution when used in microscopic imaging. TPEF microscopy has gained widespread popularity in the biology community whereas SHG microscopy promises to be a powerful tool because of its sensitivity to local asymmetry. We have implemented an approach toward the design of NLO-probes specifically adapted for SHG and/or TPEF imaging of biological membranes. Our strategy is based on the design of nanoscale amphiphilic NLO-phores. We have prepared symmetrical bolaamphiphilic fluorophores combining very high two-photon absorption (TPA) cross-sections in the visible red region and affinity for cellular membranes. Their incorporation and orientation in lipid membranes can be monitored via TPEF anisotropy. We have also prepared amphiphilic push-pull chromophores exhibiting both large TPA cross-sections and very large first hyperpolarizabilities in the near-IR region. These NLO-probes have proved to be particularly useful for imaging of biological membranes by simultaneous SHG and TPEF microscopy and offer attractive prospects for real-time imaging of fundamental biological processes such as adhesion, fusion or reporting of membrane potentials.

  15. Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: Model for intercalative drug DNA binding

    NASA Astrophysics Data System (ADS)

    Das, Suman; Kumar, Gopinatha Suresh

    2008-01-01

    The mode, mechanism and energetics of interaction of phenosafranine, the planar, cationic and rigid phenazium dye to calf thymus DNA was investigated from absorption, fluorescence, circular dichroism, isothermal titration calorimetry, thermal melting, and viscosity. The study revealed non-cooperative binding of the dye to DNA with an affinity in the range (3.81-4.22) × 10 5 M -1 as observed from diverse techniques and obeying neighbor exclusion principle. The stoichiometry of binding was characterized to be one phenosafranine molecule per two base pairs. The binding was characterized by strong stabilization of DNA against thermal strand separation, large intrinsic circular dichroic changes of DNA by itself and the generation of induced circular dichroism for the optically inactive phenosafranine molecules. Hydrodynamic and fluorescence quenching studies revealed strong evidence that the phenosafranine molecules are intercalated between every alternate base pairs of calf thymus DNA. Isothermal titration calorimetry studies suggested that the binding was exothermic and favoured by both negative enthalpy and positive entropy changes. This study for the first time presents the complete molecular aspects and energetics of phenosafranine complexation to DNA as model for intercalative drug-DNA interaction.

  16. Cellular and molecular aspects of rhabdovirus interactions with insect and plant hosts.

    PubMed

    Ammar, El-Desouky; Tsai, Chi-Wei; Whitfield, Anna E; Redinbaugh, Margaret G; Hogenhout, Saskia A

    2009-01-01

    The rhabdoviruses form a large family (Rhabdoviridae) whose host ranges include humans, other vertebrates, invertebrates, and plants. There are at least 90 plant-infecting rhabdoviruses, several of which are economically important pathogens of various crops. All definitive plant-infecting and many vertebrate-infecting rhabdoviruses are persistently transmitted by insect vectors, and a few putative plant rhabdoviruses are transmitted by mites. Plant rhabdoviruses replicate in their plant and arthropod hosts, and transmission by vectors is highly specific, with each virus species transmitted by one or a few related insect species, mainly aphids, leafhoppers, or planthoppers. Here, we provide an overview of plant rhabdovirus interactions with their insect hosts and of how these interactions compare with those of vertebrate-infecting viruses and with the Sigma rhabdovirus that infects Drosophila flies. We focus on cellular and molecular aspects of vector/host specificity, transmission barriers, and virus receptors in the vectors. In addition, we briefly discuss recent advances in understanding rhabdovirus-plant interactions.

  17. WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology.

    ERIC Educational Resources Information Center

    Epstein, Jonathan A.; Kans, Jonathan A.; Schuler, Gregory D.

    This article describes the World Wide Web (WWW) Entrez server which is based upon the National Center for Biotechnology Information's (NCBI) Entrez retrieval database and software. Entrez is a molecular sequence retrieval system that contains an integrated view of portions of Medline and all publicly available nucleotide and protein databases,…

  18. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  19. Roles of cell volume in molecular and cellular biology.

    PubMed

    Dubois, Jean-Marc; Rouzaire-Dubois, Béatrice

    2012-04-01

    Extracellular tonicity and volume regulation control a great number of molecular and cellular functions including: cell proliferation, apoptosis, migration, hormone and neuromediator release, gene expression, ion channel and transporter activity and metabolism. The aim of this review is to describe these effects and to determine if they are direct or are secondarily the result of the activity of second messengers. PMID:22192789

  20. Angiostrongylus cantonensis: a review of its distribution, molecular biology and clinical significance as a human pathogen.

    PubMed

    Barratt, Joel; Chan, Douglas; Sandaradura, Indy; Malik, Richard; Spielman, Derek; Lee, Rogan; Marriott, Deborah; Harkness, John; Ellis, John; Stark, Damien

    2016-08-01

    Angiostrongylus cantonensis is a metastrongyloid nematode found widely in the Asia-Pacific region, and the aetiological agent of angiostrongyliasis; a disease characterized by eosinophilic meningitis. Rattus rats are definitive hosts of A. cantonensis, while intermediate hosts include terrestrial and aquatic molluscs. Humans are dead-end hosts that usually become infected upon ingestion of infected molluscs. A presumptive diagnosis is often made based on clinical features, a history of mollusc consumption, eosinophilic pleocytosis in cerebral spinal fluid, and advanced imaging such as computed tomography. Serological tests are available for angiostrongyliasis, though many tests are still under development. While there is no treatment consensus, therapy often includes a combination of anthelmintics and corticosteroids. Angiostrongyliasis is relatively rare, but is often associated with morbidity and sometimes mortality. Recent reports suggest the parasites' range is increasing, leading to fatalities in regions previously considered Angiostrongylus-free, and sometimes, delayed diagnosis in newly invaded regions. Increased awareness of angiostrongyliasis would facilitate rapid diagnosis and improved clinical outcomes. This paper summarizes knowledge on the parasites' life cycle, clinical aspects and epidemiology. The molecular biology of Angiostrongylus spp. is also discussed. Attention is paid to the significance of angiostrongyliasis in Australia, given the recent severe cases reported from the Sydney region. PMID:27225800

  1. Angiostrongylus cantonensis: a review of its distribution, molecular biology and clinical significance as a human pathogen.

    PubMed

    Barratt, Joel; Chan, Douglas; Sandaradura, Indy; Malik, Richard; Spielman, Derek; Lee, Rogan; Marriott, Deborah; Harkness, John; Ellis, John; Stark, Damien

    2016-08-01

    Angiostrongylus cantonensis is a metastrongyloid nematode found widely in the Asia-Pacific region, and the aetiological agent of angiostrongyliasis; a disease characterized by eosinophilic meningitis. Rattus rats are definitive hosts of A. cantonensis, while intermediate hosts include terrestrial and aquatic molluscs. Humans are dead-end hosts that usually become infected upon ingestion of infected molluscs. A presumptive diagnosis is often made based on clinical features, a history of mollusc consumption, eosinophilic pleocytosis in cerebral spinal fluid, and advanced imaging such as computed tomography. Serological tests are available for angiostrongyliasis, though many tests are still under development. While there is no treatment consensus, therapy often includes a combination of anthelmintics and corticosteroids. Angiostrongyliasis is relatively rare, but is often associated with morbidity and sometimes mortality. Recent reports suggest the parasites' range is increasing, leading to fatalities in regions previously considered Angiostrongylus-free, and sometimes, delayed diagnosis in newly invaded regions. Increased awareness of angiostrongyliasis would facilitate rapid diagnosis and improved clinical outcomes. This paper summarizes knowledge on the parasites' life cycle, clinical aspects and epidemiology. The molecular biology of Angiostrongylus spp. is also discussed. Attention is paid to the significance of angiostrongyliasis in Australia, given the recent severe cases reported from the Sydney region.

  2. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology.

    PubMed

    Székely, Anna J; Breitbart, Mya

    2016-03-01

    Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics. PMID:26850442

  3. Exploring the free-energy landscapes of biological systems with steered molecular dynamics.

    PubMed

    Chen, L Y

    2011-04-01

    We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.

  4. Molecular biological approaches to study myosin functions in cytokinesis of Dictyostelium.

    PubMed

    Uyeda, T Q; Yumura, S

    2000-04-15

    The cellular slime mold Dictyostelium discoideum is amenable to biochemical, cell biological, and molecular genetic analyses, and offers a unique opportunity for multifaceted approaches to dissect the mechanism of cytokinesis. One of the important questions that are currently under investigation using Dictyostelium is to understand how cleavage furrows or contractile rings are assembled in the equatorial region. Contractile rings consist of a number of components including parallel filaments of actin and myosin II. Phenotypic analyses and in vivo localization studies of cells expressing mutant myosin IIs have demonstrated that myosin II's transport to and localization at the equatorial region does not require regulation by phosphorylation of myosin II, specific amino acid sequences of myosin II, or the motor activity of myosin II. Rather, the transport appears to depend on a myosin II-independent flow of cortical cytoskeleton. What drives the flow of cortical cytoskeleton is still elusive. However, a growing number of mutants that affect assembly of contractile rings have been accumulated. Analyses of these mutations, identification of more cytokinesis-specific genes, and information deriving from other experimental systems, should allow us to understand the mechanism of contractile ring formation and other aspects of cytokinesis. PMID:10816252

  5. Molecular communication among biological nanomachines: a layered architecture and research issues.

    PubMed

    Nakano, Tadashi; Suda, Tatsuya; Okaie, Yutaka; Moore, Michael J; Vasilakos, Athanasios V

    2014-09-01

    Molecular communication is an emerging communication paradigm for biological nanomachines. It allows biological nanomachines to communicate through exchanging molecules in an aqueous environment and to perform collaborative tasks through integrating functionalities of individual biological nanomachines. This paper develops the layered architecture of molecular communication and describes research issues that molecular communication faces at each layer of the architecture. Specifically, this paper applies a layered architecture approach, traditionally used in communication networks, to molecular communication, decomposes complex molecular communication functionality into a set of manageable layers, identifies basic functionalities of each layer, and develops a descriptive model consisting of key components of the layer for each layer. This paper also discusses open research issues that need to be addressed at each layer. In addition, this paper provides an example design of targeted drug delivery, a nanomedical application, to illustrate how the layered architecture helps design an application of molecular communication. The primary contribution of this paper is to provide an in-depth architectural view of molecular communication. Establishing a layered architecture of molecular communication helps organize various research issues and design concerns into layers that are relatively independent of each other, and thus accelerates research in each layer and facilitates the design and development of applications of molecular communication.

  6. Pulmonary adenocarcinoma: implications of the recent advances in molecular biology, treatment and the IASLC/ATS/ERS classification

    PubMed Central

    Thakur, Priyanka; Bhardwaj, Bhaskar; Susheela, Sridhar Papaiah; Madabhavi, Irappa

    2014-01-01

    A decade ago, lung cancer could conveniently be classified into two broad categories—either the small cell lung carcinoma (SCLC), or the non-small cell lung carcinoma (NSCLC), mainly to assist in further treatment related decision making. However, the understanding regarding the eligibility of adenocarcinoma histology for treatments with agents such as pemetrexed and bevacizumab made it a necessity for NSCLC to be classified into more specific sub-groups. Then, the availability of molecular targeted therapy with oral tyrosine kinase inhibitors (TKIs) such as gefitinib and erlotinib not only further emphasized the need for accurate sub-classification of lung cancer, but also heralded the important role of molecular profiling of lung adenocarcinomas. Given the remarkable advances in molecular biology, oncology and radiology, a need for felt for a revised classification for lung adenocarcinoma, since the existing World Health Organization (WHO) classification of lung cancer, published in the year 2004 was mainly a pathological system of classification. Thus, there was a combined effort by the International Association for the Study of Lung Cancer (IASLC), the American Thoracic Society (ATS) and the European Respiratory Society (ERS) with an effort to inculcate newly established perspectives from clinical, molecular and radiological aspects in evolving a modern classification for lung adenocarcinomas. This review provides a summary of the recent advances in molecular biology and molecular targeted therapy with respect to lung adenocarcinoma. Also, a brief summation of the salient recommendations provided in the IASLC/ATS/ERS classification of lung adenocarcinomas is provided. Lastly, a discussion regarding the future prospects with lung adenocarcinoma is included. PMID:25349702

  7. Molecular biology of mycoplasmas: from the minimum cell concept to the artificial cell.

    PubMed

    Cordova, Caio M M; Hoeltgebaum, Daniela L; Machado, Laís D P N; Santos, Larissa Dos

    2016-01-01

    Mycoplasmas are a large group of bacteria, sorted into different genera in the Mollicutes class, whose main characteristic in common, besides the small genome, is the absence of cell wall. They are considered cellular and molecular biology study models. We present an updated review of the molecular biology of these model microorganisms and the development of replicative vectors for the transformation of mycoplasmas. Synthetic biology studies inspired by these pioneering works became possible and won the attention of the mainstream media. For the first time, an artificial genome was synthesized (a minimal genome produced from consensus sequences obtained from mycoplasmas). For the first time, a functional artificial cell has been constructed by introducing a genome completely synthesized within a cell envelope of a mycoplasma obtained by transformation techniques. Therefore, this article offers an updated insight to the state of the art of these peculiar organisms' molecular biology.

  8. Case study: Using microbe molecular biology for Gulf oil spill clean up.

    PubMed

    Jones, Daniel R

    2011-01-01

    This case has the student actively investigate the regulation of expression of a novel bacterial gene in the context of attempts to solve a real world problem, clean up of the April 2010 Deep Water Horizon oil spill in the Gulf of Mexico. Although the case is fictitious, it is based on factual gene regulatory characteristics of oil-degrading microbes. The case is written for a sophomore Cell Biology lecture course at Indiana Wesleyan University that is taught to Biology/Pre-Med majors. This study is also appropriate for use in undergraduate microbiology, biochemistry, molecular biology, and molecular genetics courses. The case is intended to enhance coverage of transcription, translation, control of gene expression, and selected molecular biology techniques. Opportunities to practice critical thinking skills and to a lesser extent an introduction to the paradigm of life science research at the industry level are provided.

  9. Molecular biology of mycoplasmas: from the minimum cell concept to the artificial cell.

    PubMed

    Cordova, Caio M M; Hoeltgebaum, Daniela L; Machado, Laís D P N; Santos, Larissa Dos

    2016-01-01

    Mycoplasmas are a large group of bacteria, sorted into different genera in the Mollicutes class, whose main characteristic in common, besides the small genome, is the absence of cell wall. They are considered cellular and molecular biology study models. We present an updated review of the molecular biology of these model microorganisms and the development of replicative vectors for the transformation of mycoplasmas. Synthetic biology studies inspired by these pioneering works became possible and won the attention of the mainstream media. For the first time, an artificial genome was synthesized (a minimal genome produced from consensus sequences obtained from mycoplasmas). For the first time, a functional artificial cell has been constructed by introducing a genome completely synthesized within a cell envelope of a mycoplasma obtained by transformation techniques. Therefore, this article offers an updated insight to the state of the art of these peculiar organisms' molecular biology. PMID:27142538

  10. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

    PubMed

    Rigden, Daniel J; Fernández-Suárez, Xosé M; Galperin, Michael Y

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. PMID:26740669

  11. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

    PubMed Central

    Rigden, Daniel J.; Fernández-Suárez, Xosé M.; Galperin, Michael Y.

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. PMID:26740669

  12. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.

    PubMed

    Rigden, Daniel J; Fernández-Suárez, Xosé M; Galperin, Michael Y

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases.

  13. Systems theoretic analysis of the central dogma of molecular biology: some recent results.

    PubMed

    Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

    2010-03-01

    This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

  14. Recent Advances in Molecular Biology of Thyroid Cancer and Their Clinical Implications

    PubMed Central

    Xing, Mingzhao

    2009-01-01

    Synopsis Thyroid cancer is the most common endocrine malignancy with a rapid rising incidence in recent years. Novel efficient management strategies are increasingly needed for this cancer. Remarkable advances have occurred in recent years in understanding the molecular biology of thyroid cancer. This is reflected in several major biological areas of thyroid cancer, including the molecular alterations for the loss of radioiodine avidity of thyroid cancer, the pathogenic role of the MAP kinase and PI3K/Akt pathways and their related genetic alterations, and the aberrant methylation of functionally important genes in thyroid tumorigenesis and pathogenesis. These exciting advances in molecular biology of thyroid cancer provide unprecedented opportunities for the development of molecular-based novel diagnostic, prognostic, and therapeutic strategies for this cancer. PMID:19040974

  15. Introduction to the special issue on molecular imaging in radiation biology.

    PubMed

    Humm, John L; Dewhirst, Mark W; Bhujwalla, Zaver M

    2012-04-01

    Molecular imaging is an evolving science that is concerned with the development of novel imaging probes and biomarkers that can be used to non-invasively image molecular and cellular processes. This special issue approaches molecular imaging in the context of radiation research, focusing on biomarkers and imaging methods that provide measurable signals that can assist in the quantification of radiation-induced effects of living systems at the physical, chemical and biological levels. The potential to image molecular changes in response to a radiation insult opens new and exciting opportunities for a more profound understanding of radiation biology, with the possibility of translation of these techniques to radiotherapy practice. This special issue brings together 14 reviews dedicated to the use of molecular imaging in the field of radiation research. The initial three reviews are introductory overviews of the key molecular imaging modalities: magnetic resonance, nuclear and optical. This is followed by 11 reviews each focusing on a specialist area within the field of radiation research. These include: hypoxia and perfusion, tissue metabolism, normal tissue injury, cell death and viability, receptor targeting and nanotechnology, reporter genes, reactive oxygen species (ROS), and biological dosimetry. Over the preceding decade, molecular imaging brought significant new advances to our understanding of every area of radiation biology. This special issue shows us these advances and points to the vibrant future of our field armed with these new capabilities.

  16. Streptococcal M protein: molecular design and biological behavior.

    PubMed Central

    Fischetti, V A

    1989-01-01

    M protein is a major virulence determinant for the group A streptococcus by virtue of its ability to allow the organism to resist phagocytosis. Common in eucaryotes, the fibrillar coiled-coil design for the M molecule may prove to be a common motif for surface proteins in gram-positive organisms. This type of structure offers the organism several distinct advantages, ranging from antigenic variation to multiple functional domains. The close resemblance of this molecular design to that of certain mammalian proteins could help explain on a molecular level the formation of epitopes responsible for serological cross-reactions between microbial and mammalian proteins. Many of the approaches described in the elucidation of the M-protein structure may be applied for characterizing similar molecules in other microbial systems. Images PMID:2670192

  17. Molecular microbiology: new dimensions for cutaneous biology and wound healing.

    PubMed

    Martin, Jo M; Zenilman, Jonathan M; Lazarus, Gerald S

    2010-01-01

    The role of bacteria in the pathogenesis of chronic, nonhealing wounds is unclear. All wounds are colonized with bacteria, but differentiating colonizers from invading organisms is difficult, if not impossible, at the present time. Furthermore, robust new molecular genomic techniques have shown that only 1% of bacteria can be grown in culture; anaerobes are especially difficult to identify using standard culture methods. Recent studies utilizing microbial genomic methods have demonstrated that chronic wounds are host to a wide range of microorganisms. New techniques also show that microorganisms are capable of forming highly organized biofilms within the wound that differ dramatically in gene expression and phenotype from bacteria that are typically seen in planktonic conditions. The aim of this review is to present a concise description of infectious agents as defined by new molecular techniques and to summarize what is known about the microbiology of chronic wounds in order to relate them to the pathophysiology and therapy of chronic wounds.

  18. Hybrid molecular probe for nucleic acid analysis in biological samples.

    PubMed

    Yang, Chaoyong James; Martinez, Karen; Lin, Hui; Tan, Weihong

    2006-08-01

    The ability to detect changes in gene expression, especially in real-time and with sensitivity sufficient enough to monitor small variations in a single-cell, will have considerable value in biomedical research and applications. Out of the many available molecular probes for intracellular monitoring of nucleic acids, molecular beacon (MB) is the most frequently used probe with the advantages of high sensitivity and selectivity. However, any processes in which the MB stem-loop structure is broken will result in a restoration of the fluorescence in MB. This brings in a few possibilities for false positive signal such as nuclease degradation, protein binding, thermodynamic fluctuation, solution composition variations (such as pH, salt concentration) and sticky-end pairing. These unwanted processes do exist inside living cells, making nucleic acid monitoring inside living cells difficult. We have designed and synthesized a hybrid molecular probe (HMP) for intracellular nucleic acid monitoring to overcome these problems. HMP has two DNA probes, one labeled with a donor and the other an acceptor. The two DNA probes are linked by a poly(ethylene glycol) (PEG) linker, with each DNA being complementary to adjacent areas of a target sequence. Target binding event brings the donor and acceptor in proximity, resulting in quenching of the donor fluorescence and enhancement of the acceptor emission. The newly designed HMP has high sensitivity, selectivity, and fast hybridization kinetics. The probe is easy to design and synthesize. HMP does not generate any false positive signal upon digestion by nuclease, binding by proteins, forming complexes by sticky-end pairing, or by other molecular interaction processes. HMP is capable of selectively detecting nucleic acid targets from cellular samples.

  19. [Molecular biology of castration-resistant prostate cancer].

    PubMed

    Doucet, Ludovic; Terrisse, Safae; Gauthier, Hélène; Pouessel, Damien; Le Maignan, Christine; Teixeira, Luis; Culine, Stéphane

    2015-06-01

    Castration-resistant prostate cancer was subjected to a paradigm switch from hormone resistance to androgen deprivation therapy resistance during the last decade. Indeed, new therapeutics targeting the androgen receptor showed clinical efficacy in patients with progressive disease under castration. Thus, it is a proof that the AR remains a dominant driver of oncogenesis in earlier-called hormone resistant prostate cancer. This review summarizes the molecular mechanisms involved in castration-resistant prostate cancer.

  20. Molecular and genetic aspects of controlling the soilborne necrotrophic pathogens Rhizoctonia and Pythium.

    PubMed

    Okubara, Patricia A; Dickman, Martin B; Blechl, Ann E

    2014-11-01

    The soilborne necrotrophic pathogens Rhizoctonia and Pythium infect a wide range of crops in the US and worldwide. These pathogens pose challenges to growers because the diseases they cause are not adequately controlled by fungicides, rotation or, for many hosts, natural genetic resistance. Although a combination of management practices are likely to be required for control of Rhizoctonia and Pythium, genetic resistance remains a key missing component. This review discusses the recent deployment of introduced genes and genome-based information for control of Rhizoctonia, with emphasis on three pathosystems: Rhizoctonia solani AG8 and wheat, R. solani AG1-IA and rice, and R. solani AG3 or AG4 and potato. Molecular mechanisms underlying disease suppression will be addressed, if appropriate. Although less is known about genes and factors suppressive to Pythium, pathogen genomics and biological control studies are providing useful leads to effectors and antifungal factors. Prospects for resistance to Rhizoctonia and Pythium spp. will continue to improve with growing knowledge of pathogenicity strategies, host defense gene action relative to the pathogen infection process, and the role of environmental factors on pathogen-host interactions.

  1. Molecular and genetic aspects of controlling the soilborne necrotrophic pathogens Rhizoctonia and Pythium.

    PubMed

    Okubara, Patricia A; Dickman, Martin B; Blechl, Ann E

    2014-11-01

    The soilborne necrotrophic pathogens Rhizoctonia and Pythium infect a wide range of crops in the US and worldwide. These pathogens pose challenges to growers because the diseases they cause are not adequately controlled by fungicides, rotation or, for many hosts, natural genetic resistance. Although a combination of management practices are likely to be required for control of Rhizoctonia and Pythium, genetic resistance remains a key missing component. This review discusses the recent deployment of introduced genes and genome-based information for control of Rhizoctonia, with emphasis on three pathosystems: Rhizoctonia solani AG8 and wheat, R. solani AG1-IA and rice, and R. solani AG3 or AG4 and potato. Molecular mechanisms underlying disease suppression will be addressed, if appropriate. Although less is known about genes and factors suppressive to Pythium, pathogen genomics and biological control studies are providing useful leads to effectors and antifungal factors. Prospects for resistance to Rhizoctonia and Pythium spp. will continue to improve with growing knowledge of pathogenicity strategies, host defense gene action relative to the pathogen infection process, and the role of environmental factors on pathogen-host interactions. PMID:25438786

  2. DOE contractors' workshop: Cellular and molecular aspects of radiation induced DNA damage and repair

    SciTech Connect

    Not Available

    1987-01-01

    For four decades the US Department of Energy and its predecessors have been the lead federal agency in supporting radiation biology research. Over the years emphasis in this program has gradually shifted from dose-effect studies on animals to research on the effects of radiations of various qualities on cells and molecules. Mechanistic studies on the action of radiation at the subcellular level are few in number and there is a need for more research in this area if we are to gain a better understanding of how radiation affects living cells. The intent of this workshop was to bring together DOE contractors and grantees who are investigating the effects of radiation at the cellular and molecular levels. The aims were to foster the exchange of information on research projects and experimental results, promote collaborative research efforts, and obtain an overview of research currently supported by the Health Effects Research Division of the Office of Health and Environmental Research. The latter is needed by the Office for program planning purposes. This report on the workshop which took place in Albuquerque, New Mexico on March 10-11, 1987, includes an overview with future research recommendations, extended abstracts of the plenary presentations, shorter abstracts of each poster presentation, a workshop agenda and the names and addresses of the attendees.

  3. Animal models of osteoarthritis in an era of molecular biology.

    PubMed

    Bendele, A M

    2002-12-01

    Animal models of osteoarthritis (OA) are used to study the pathogenesis of cartilage degeneration and to evaluate potential anti-arthritic drugs for clinical use. In general, these models fall into 2 categories, spontaneous and induced (surgical instability or genetic manipulation). Animal models of naturally occurring OA occur in knee joints of guinea pigs, mice and Syrian hamsters. Commonly utilized surgical instability models include medial meniscal tear in guinea pigs and rats, medial or lateral partial meniscectomy in rabbits, medial partial or total meniscectomy or anterior cruciate transection in dogs. Transgenic models have been developed in mice. These models all have potential use in the study of molecular mechanisms associated with OA development via use of immunohistochemistry, biochemistry and molecular probes to identify altered matrix molecules at different stages in disease progression. Testing of specific types of inhibitors developed through evaluation of matrix changes in the disease process will ultimately help identify key processes which initiate and perpetuate the disease and will lead to discovery of new disease modifying pharmaceutical agents for OA patients. This paper will focus on the discussion of several models which are likely to be useful in the molecular dissection of processes involved in cartilage degeneration. PMID:15758375

  4. REVIEW ARTICLE: The physics of biological molecular motors

    NASA Astrophysics Data System (ADS)

    Thomas, N.; Thornhill, R. A.

    1998-02-01

    Molecular motors are the fundamental agents of movement in living organisms. A prime example is the actomyosin motor that powers muscle contraction. We illustrate the remarkable physics of this motor using a simplified three-state model, in which a myosin cross-bridge attaches to an actin filament, tilts over and then detaches. This `cross-bridge cycle', driven by ATP hydrolysis, is similar to a thermodynamic cycle, except that the molecular system is stochastic. Random transitions in the cycle therefore produce tension fluctuations, which have recently been observed in single-molecule experiments. Furthermore, since the rate constants for attachment and tilting depend on the elastic energy in the cross-bridge spring, the molecular motor is a highly nonlinear mechanical system. A bias tension `stretch activates' the motor, and it then develops the remarkable property of `negative viscosity', which allows it to perform as a self-sustained mechanical oscillator. However, when a series of attachment sites is available, the motor operates instead as a ratchet, pulling the actin filament rapidly forwards against a light load, whilst a heavy load pulls the filament only very slowly in the opposite direction. Similar ideas may apply to the dynein-tubulin motor that powers cilia and flagella and the kinesin-tubulin motor used in intracellular transport.

  5. Biological preservation of plant derived animal feed with antifungal microorganisms: safety and formulation aspects.

    PubMed

    Melin, Petter; Sundh, Ingvar; Håkansson, Sebastian; Schnürer, Johan

    2007-08-01

    During storage of moist animal feed, growth of detrimental fungi causing spoilage, or being mycotoxigenic or pathogenic, is a severe problem. Addition of biopreservative yeasts or lactic acid bacteria can significantly reduce this problem. However, their use requires several careful considerations. One is the safety to the animal, humans and the environment, tightly connected to legal aspects and the need for pre-market authorisation when supplementing feed with microorganisms. Although both yeasts and lactic acid bacteria are considered comparatively safe organisms due to low production of toxic metabolites, it is of great importance to understand the mechanisms behind the biopreservative abilities. Another important issue concerns practical aspects, such as the economic production of large amounts of the organisms and the development of a suitable formulation giving the organisms a long shelf life. These aspects are discussed and a recommendation of this review is that both safety and formulation aspects of a specific microbe should be considered at an early stage in the selection of new organisms with biopreservation potential.

  6. Combining Radiation Epidemiology With Molecular Biology-Changing From Health Risk Estimates to Therapeutic Intervention.

    PubMed

    Abend, Michael; Port, Matthias

    2016-08-01

    The authors herein summarize six presentations dedicated to the key session "molecular radiation epidemiology" of the ConRad meeting 2015. These presentations were chosen in order to highlight the promise when combining conventional radiation epidemiology with molecular biology. Conventional radiation epidemiology uses dose estimates for risk predictions on health. However, combined with molecular biology, dose-dependent bioindicators of effect hold the promise to improve clinical diagnostics and to provide target molecules for potential therapeutic intervention. One out of the six presentations exemplified the use of radiation-induced molecular changes as biomarkers of exposure by measuring stabile chromosomal translocations. The remaining five presentations focused on molecular changes used as bioindicators of the effect. These bioindicators of the effect could be used for diagnostic purposes on colon cancers (genomic instability), thyroid cancer (CLIP2), or head and neck squamous cell cancers. Therapeutic implications of gene expression changes were examined in Chernobyl thyroid cancer victims and Mayak workers. PMID:27356062

  7. Combining Radiation Epidemiology With Molecular Biology-Changing From Health Risk Estimates to Therapeutic Intervention.

    PubMed

    Abend, Michael; Port, Matthias

    2016-08-01

    The authors herein summarize six presentations dedicated to the key session "molecular radiation epidemiology" of the ConRad meeting 2015. These presentations were chosen in order to highlight the promise when combining conventional radiation epidemiology with molecular biology. Conventional radiation epidemiology uses dose estimates for risk predictions on health. However, combined with molecular biology, dose-dependent bioindicators of effect hold the promise to improve clinical diagnostics and to provide target molecules for potential therapeutic intervention. One out of the six presentations exemplified the use of radiation-induced molecular changes as biomarkers of exposure by measuring stabile chromosomal translocations. The remaining five presentations focused on molecular changes used as bioindicators of the effect. These bioindicators of the effect could be used for diagnostic purposes on colon cancers (genomic instability), thyroid cancer (CLIP2), or head and neck squamous cell cancers. Therapeutic implications of gene expression changes were examined in Chernobyl thyroid cancer victims and Mayak workers.

  8. Biologic and clinical aspects of integration of different bone substitutes in oral surgery: a literature review.

    PubMed

    Zizzari, Vincenzo Luca; Zara, Susi; Tetè, Giulia; Vinci, Raffaele; Gherlone, Enrico; Cataldi, Amelia

    2016-10-01

    Many bone substitutes have been proposed for bone regeneration, and researchers have focused on the interactions occurring between grafts and host tissue, as the biologic response of host tissue is related to the origin of the biomaterial. Bone substitutes used in oral and maxillofacial surgery could be categorized according to their biologic origin and source as autologous bone graft when obtained from the same individual receiving the graft; homologous bone graft, or allograft, when harvested from an individual other than the one receiving the graft; animal-derived heterologous bone graft, or xenograft, when derived from a species other than human; and alloplastic graft, made of bone substitute of synthetic origin. The aim of this review is to describe the most commonly used bone substitutes, according to their origin, and to focus on the biologic events that ultimately lead to the integration of a biomaterial with the host tissue.

  9. The Defence of Artificial Life by Synthetic Biology From Ethical and Social Aspects.

    PubMed

    Chen, Yiyi; Yin, Zhou; Shao, Zhexin; Xie, Qiong

    2015-07-01

    Synthetic biology opens up exciting new opportunities for research and industry. Although the work of synthetic biologists presents many beneficial applications, it also raises potentially serious ethical concerns. Therefore, clear ideas must be formed regarding its ethical and social implications, e.g., public perception, safety, security, intellectual property rights and so on. In this review, the authors identified four issues relevant to synthetic biology and discussed associated ethical and practical implications. By weighing these perspectives of all sides, this paper clarifies the point that synthetic biology, as an emerging discipline with many anticipated benefits and positive impacts on society, can acquire moral support and ethical defence. Therefore, synthetic biologists should not be shackled with heavy ethical chains, but we must ensure that research is conducted under strict control and effective supervisory methods.

  10. Influence of platelet aspect ratio on the mechanical behaviour of bio-inspired nanocomposites using molecular dynamics.

    PubMed

    Mathiazhagan, S; Anup, S

    2016-06-01

    Superior mechanical properties of biocomposites such as nacre and bone are attributed to their basic building blocks. These basic building blocks have nanoscale features and play a major role in achieving combined stiffening, strengthening and toughening mechanisms. Bioinspired nanocomposites based on these basic building blocks, regularly and stairwise staggered arrangements of hard platelets in soft matrix, have huge potential for developing advanced materials. The study of applicability of mechanical principles of biological materials to engineered materials will guide designing advanced materials. To probe the generic mechanical characteristics of these bioinspired nanocomposites, the model material concept in molecular dynamics (MD) is used. In this paper, the effect of platelets aspect ratio (AR) on the mechanical behaviour of bioinspired nanocomposites is investigated. The obtained Young׳s moduli of both the models and the strengths of the regularly staggered models agree with the available theories. However, the strengths of the stairwise staggered models show significant difference. For the stairwise staggered model, we demonstrate the existence of two critical ARs, a smaller critical AR above which platelet fracture occurs and a higher critical AR above which composite strength remains constant. Our MD study also shows the existence of mechanisms of platelet pull-out and breakage for lower and higher ARs. Pullout mechanism acts as a major source of plasticity. Further, we find that the regularly staggered model can achieve an optimal combination of high Young׳s modulus, flow strength and toughness, and the stairwise staggered model is efficient in obtaining high Young׳s modulus and tensile strength. PMID:26741376

  11. Insights into the immuno-molecular biology of Angiostrongylus vasorum through transcriptomics--prospects for new interventions.

    PubMed

    Ansell, Brendan R E; Schnyder, Manuela; Deplazes, Peter; Korhonen, Pasi K; Young, Neil D; Hall, Ross S; Mangiola, Stefano; Boag, Peter R; Hofmann, Andreas; Sternberg, Paul W; Jex, Aaron R; Gasser, Robin B

    2013-12-01

    Angiostrongylus vasorum is a metastrongyloid nematode of dogs and other canids of major clinical importance in many countries. In order to gain first insights into the molecular biology of this worm, we conducted the first large-scale exploration of its transcriptome, and predicted essential molecules linked to metabolic and biological processes as well as host immune responses. We also predicted and prioritized drug targets and drug candidates. Following Illumina sequencing (RNA-seq), 52.3 million sequence reads representing adult A. vasorum were assembled and annotated. The assembly yielded 20,033 contigs, which encoded proteins with 11,505 homologues in Caenorhabditis elegans, and additional 2252 homologues in various other parasitic helminths for which curated data sets were publicly available. Functional annotation was achieved for 11,752 (58.6%) proteins predicted for A. vasorum, including peptidases (4.5%) and peptidase inhibitors (1.6%), protein kinases (1.7%), G protein-coupled receptors (GPCRs) (1.5%) and phosphatases (1.2%). Contigs encoding excretory/secretory and immuno-modulatory proteins represented some of the most highly transcribed molecules, and encoded enzymes that digest haemoglobin were conserved between A. vasorum and other blood-feeding nematodes. Using an essentiality-based approach, drug targets, including neurotransmitter receptors, an important chemosensory ion channel and cysteine proteinase-3 were predicted in A. vasorum, as were associated small molecular inhibitors/activators. Future transcriptomic analyses of all developmental stages of A. vasorum should facilitate deep explorations of the molecular biology of this important parasitic nematode and support the sequencing of its genome. These advances will provide a foundation for exploring immuno-molecular aspects of angiostrongylosis and have the potential to underpin the discovery of new methods of intervention.

  12. Modeling human risk: Cell & molecular biology in context

    SciTech Connect

    1997-06-01

    It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response.

  13. Basal cell carcinoma — molecular biology and potential new therapies

    PubMed Central

    Kasper, Maria; Jaks, Viljar; Hohl, Daniel; Toftgård, Rune

    2012-01-01

    Basal cell carcinoma (BCC) of the skin, the most common malignancy in individuals of mixed European descent, is increasing in incidence due to an aging population and sun exposure habits. The realization that aberrant activation of Hedgehog signaling is a pathognomonic feature of BCC development has opened the way for exciting progress toward understanding BCC biology and translation of this knowledge to the clinic. Genetic mouse models closely mimicking human BCCs have provided answers about the tumor cell of origin, and inhibition of Hedgehog signaling is emerging as a potentially useful targeted therapy for patients with advanced or multiple BCCs that have hitherto lacked effective treatment. PMID:22293184

  14. Structural and dynamical aspects of Streptococcus gordonii FabH through molecular docking and MD simulations.

    PubMed

    Shamim, Amen; Abbasi, Sumra Wajid; Azam, Syed Sikander

    2015-07-01

    β-Ketoacyl-ACP-synthase III (FabH or KAS III) has become an attractive target for the development of new antibacterial agents which can overcome the multidrug resistance. Unraveling the fatty acid biosynthesis (FAB) metabolic pathway and understanding structural coordinates of FabH will provide valuable insights to target Streptococcus gordonii for curing oral infection. In this study, we designed inhibitors against therapeutic target FabH, in order to block the FAB pathway. As compared to other targets, FabH has more interactions with other proteins, located on the leading strand with higher codon adaptation index value and associated with lipid metabolism category of COG. Current study aims to gain in silico insights into the structural and dynamical aspect of S. gordonii FabH via molecular docking and molecular dynamics (MD) simulations. The FabH protein is catalytically active in dimerization while it can lock in monomeric state. Current study highlights two residues Pro88 and Leu315 that are close to each other by dimerization. The active site of FabH is composed of the catalytic triad formed by residues Cys112, His249, and Asn279 in which Cys112 is involved in acetyl transfer, while His249 and Asn279 play an active role in decarboxylation. Docking analysis revealed that among the studied compounds, methyl-CoA disulfide has highest GOLD score (82.75), binding affinity (-11 kcal/mol) and exhibited consistently better interactions. During MD simulations, the FabH structure remained stable with the average RMSD value of 1.7 Å and 1.6 Å for undocked protein and docked complex, respectively. Further, crucial hydrogen bonding of the conserved catalytic triad for exhibiting high affinity between the FabH protein and ligand is observed by RDF analysis. The MD simulation results clearly demonstrated that binding of the inhibitor with S. gordonii FabH enhanced the structure and stabilized the dimeric FabH protein. Therefore, the inhibitor has the potential to become

  15. [Metastasis tumors of the central nervous system: molecular biology].

    PubMed

    Bello, M Josefa; González-Gómez, P; Rey, J A

    2004-12-01

    Metastases in the nervous system represent an important and growing problem in the clinical practice, being the cause of a great mortality in the developed countries. This article reviews the few data available on the molecular mechanisms involved in the pathogenesis of these tumours, leading to oncogene activation, inactivation of tumour suppressor genes, not only by the classical mechanisms, but also by the tumour cell epigenetic balance alteration. We conclude that all this knowledge will lead in the future to a better diagnosis, treatment and clinic evolution of these patients.

  16. Biological and molecular characterizations of Toxoplasma gondii strains

    USGS Publications Warehouse

    Cole, R.A.; Lindsay, D.S.; Howe, D.K.; Roderick, Constance L.; Dubey, J.P.; Thomas, N.J.; Baeten, L.A.

    2000-01-01

    Toxoplasma gondii was isolated from brain or heart tissue from 15 southern sea otters (Enhydra lutris nereis) in cell cultures. These strains were used to infect mice that developed antibodies to T. gondii as detected in the modified direct agglutination test and had T. gondii tissue cysts in their brains at necropsy. Mouse brains containing tissue cysts from 4 of the strains were fed to 4 cats. Two of the cats excreted T. gondii oocysts in their feces that were infectious for mice. Molecular analyses of 13 strains indicated that they were all type II strains, but that they were genetically distinct from one another.

  17. Molecular Biology and Immunology of Head & Neck Cancer

    PubMed Central

    Guo, Theresa; Califano, Joseph A.

    2015-01-01

    Synopsis In recent years our knowledge and understanding of head and neck squamous cell carcinoma (HNSCC) has expanded dramatically. New high-throughput sequencing technologies have accelerated these discoveries since the first reports of whole exome sequencing of HNSCC tumors in 2011. In addition, the discovery of human papillomavirus (HPV) in relationship with oropharyngeal squamous cell carcinoma has shifted our molecular understanding of the disease. New investigation into the role of immune evasion in HNSCC has also led to potential novel therapies based on immune specific systemic therapies. PMID:25979390

  18. Molecular biology and immunology of head and neck cancer.

    PubMed

    Guo, Theresa; Califano, Joseph A

    2015-07-01

    In recent years, our knowledge and understanding of head and neck squamous cell carcinoma (HNSCC) has expanded dramatically. New high-throughput sequencing technologies have accelerated these discoveries since the first reports of whole-exome sequencing of HNSCC tumors in 2011. In addition, the discovery of human papillomavirus in relationship with oropharyngeal squamous cell carcinoma has shifted our molecular understanding of the disease. New investigation into the role of immune evasion in HNSCC has also led to potential novel therapies based on immune-specific systemic therapies.

  19. Protozoan HSP90-heterocomplex: molecular interaction network and biological significance.

    PubMed

    Figueras, Maria J; Echeverria, Pablo C; Angel, Sergio O

    2014-05-01

    The HSP90 chaperone is a highly conserved protein from bacteria to higher eukaryotes. In eukaryotes, this chaperone participates in different large complexes, such as the HSP90 heterocomplex, which has important biological roles in cell homeostasis and differentiation. The HSP90-heterocomplex is also named the HSP90/HSP70 cycle because different co-chaperones (HIP, HSP40, HOP, p23, AHA1, immunophilins, PP5) participate in this complex by assembling sequentially, from the early to the mature complex. In this review, we analyze the conservation and relevance of HSP90 and the HSP90-heterocomplex in several protozoan parasites, with emphasis in Plasmodium spp., Toxoplasma spp., Leishmania spp. and Trypanosoma spp. In the last years, there has been an outburst of studies based on yeast two-hybrid methodology, co-immunoprecipitation-mass spectrometry and bioinformatics, which have generated a most comprehensive protein-protein interaction (PPI) network of HSP90 and its co-chaperones. This review analyzes the existing PPI networks of HSP90 and its co-chaperones of some protozoan parasites and discusses the usefulness of these powerful tools to analyze the biological role of the HSP90-heterocomplex in these parasites. The generation of a T. gondii HSP90 heterocomplex PPI network based on experimental data and a recent Plasmodium HSP90 heterocomplex PPI network are also included and discussed. As an example, the putative implication of nuclear transport and chromatin (histones and Sir2) as HSP90-heterocomplex interactors is here discussed.

  20. Protozoan HSP90-heterocomplex: molecular interaction network and biological significance.

    PubMed

    Figueras, Maria J; Echeverria, Pablo C; Angel, Sergio O

    2014-05-01

    The HSP90 chaperone is a highly conserved protein from bacteria to higher eukaryotes. In eukaryotes, this chaperone participates in different large complexes, such as the HSP90 heterocomplex, which has important biological roles in cell homeostasis and differentiation. The HSP90-heterocomplex is also named the HSP90/HSP70 cycle because different co-chaperones (HIP, HSP40, HOP, p23, AHA1, immunophilins, PP5) participate in this complex by assembling sequentially, from the early to the mature complex. In this review, we analyze the conservation and relevance of HSP90 and the HSP90-heterocomplex in several protozoan parasites, with emphasis in Plasmodium spp., Toxoplasma spp., Leishmania spp. and Trypanosoma spp. In the last years, there has been an outburst of studies based on yeast two-hybrid methodology, co-immunoprecipitation-mass spectrometry and bioinformatics, which have generated a most comprehensive protein-protein interaction (PPI) network of HSP90 and its co-chaperones. This review analyzes the existing PPI networks of HSP90 and its co-chaperones of some protozoan parasites and discusses the usefulness of these powerful tools to analyze the biological role of the HSP90-heterocomplex in these parasites. The generation of a T. gondii HSP90 heterocomplex PPI network based on experimental data and a recent Plasmodium HSP90 heterocomplex PPI network are also included and discussed. As an example, the putative implication of nuclear transport and chromatin (histones and Sir2) as HSP90-heterocomplex interactors is here discussed. PMID:24694366

  1. Aspects of Theme in the Method and Discussion Sections of Biology Journal Articles in English.

    ERIC Educational Resources Information Center

    Martinez, Iliana A.

    2003-01-01

    Analyzes the thematic structure of the method and Discussion section of biology research articles. A corpus of 30 journal articles was analyzed using the categories of systematic functional linguistics and a semantic categorization for unmarked themes realized by subject. Revealed differences in the semantic construction of the sections. (VWL)

  2. ASPECTS OF BASIC REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY IN THE FATHEAD MINNOW (PIMEPHALES PROMELAS)

    EPA Science Inventory

    The fathead minnow has been proposed as a model species for assessing the adverse effects of endocrine-disrupting chemicals (EDCs) on reproduction and development. The purpose of these studies was to develop baseline reproductive biology and endocrinology data for this species to...

  3. Soluble Epidermal Growth Factor Receptors (sEGFRs) in Cancer: Biological Aspects and Clinical Relevance

    PubMed Central

    Maramotti, Sally; Paci, Massimiliano; Manzotti, Gloria; Rapicetta, Cristian; Gugnoni, Mila; Galeone, Carla; Cesario, Alfredo; Lococo, Filippo

    2016-01-01

    The identification of molecules that can reliably detect the presence of a tumor or predict its behavior is one of the biggest challenges of research in cancer biology. Biological fluids are intriguing mediums, containing many molecules that express the individual health status and, accordingly, may be useful in establishing the potential risk of cancer, defining differential diagnosis and prognosis, predicting the response to treatment, and monitoring the disease progression. The existence of circulating soluble growth factor receptors (sGFRs) deriving from their membrane counterparts has stimulated the interest of researchers to investigate the use of such molecules as potential cancer biomarkers. But what are the origins of circulating sGFRs? Are they naturally occurring molecules or tumor-derived products? Among these, the epidermal growth factor receptor (EGFR) is a cell-surface molecule significantly involved in cancer development and progression; it can be processed into biological active soluble isoforms (sEGFR). We have carried out an extensive review of the currently available literature on the sEGFRs and their mechanisms of regulation and biological function, with the intent to clarify the role of these molecules in cancer (and other pathological conditions) and, on the basis of the retrieved evidences, speculate about their potential use in the clinical setting. PMID:27104520

  4. GEOCHEMICAL AND BIOLOGICAL ASPECTS OF SULFIDE MINERAL DISSOLUTION: LESSONS FROM IRON MOUNTAIN, CALIFORNIA. (R826189)

    EPA Science Inventory

    Abstract

    The oxidative dissolution of sulfide minerals leading to acid mine drainage (AMD) involves a complex interplay between microorganisms, solutions, and mineral surfaces. Consequently, models that link molecular level reactions and the microbial communities that ...

  5. Molecular biology of maize Ac/Ds elements: an overview.

    PubMed

    Lazarow, Katina; Doll, My-Linh; Kunze, Reinhard

    2013-01-01

    Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.

  6. Direct evidence of the molecular basis for biological silicon transport.

    PubMed

    Knight, Michael J; Senior, Laura; Nancolas, Bethany; Ratcliffe, Sarah; Curnow, Paul

    2016-01-01

    Diatoms are an important group of eukaryotic algae with a curious evolutionary innovation: they sheath themselves in a cell wall made largely of silica. The cellular machinery responsible for silicification includes a family of membrane permeases that recognize and actively transport the soluble precursor of biosilica, silicic acid. However, the molecular basis of silicic acid transport remains obscure. Here, we identify experimentally tractable diatom silicic acid transporter (SIT) homologues and study their structure and function in vitro, enabled by the development of a new fluorescence method for studying substrate transport kinetics. We show that recombinant SITs are Na(+)/silicic acid symporters with a 1:1 protein: substrate stoichiometry and KM for silicic acid of 20 μM. Protein mutagenesis supports the long-standing hypothesis that four conserved GXQ amino acid motifs are important in SIT function. This marks a step towards a detailed understanding of silicon transport with implications for biogeochemistry and bioinspired materials.

  7. Molecular biological enhancement of coal biodesulfurization. [Rhodococcus rhodochrous

    SciTech Connect

    Kilbane, J.J.; Bielaga, B.A.

    1990-07-01

    The overall objective of this project is to sue molecular genetics to develop strains of bacteria with enhanced ability to remove sulfur from coal and to obtain data that will allow the performance and economics of a coal biodesulfurization process to be predicted. The work planned for the current quarter (May 1990 to July 1990) includes the following activities: (1) Construct a cloning vector that can be used in Rhodococcus rhodochrous IGTS8 from the small cryptic plasmid found in Rhodococcus rhodochrous ATCC 190607; (2) Develop techniques for the genetic analysis of IGTS8; (3) Continue biochemical experiments, particularly those that may allow the identification of desulfurization-related enzymes; (4) Continue experiments with coal to determine the kinetics of organic sulfur removal.

  8. Applications of Discrete Molecular Dynamics in biology and medicine.

    PubMed

    Proctor, Elizabeth A; Dokholyan, Nikolay V

    2016-04-01

    Discrete Molecular Dynamics (DMD) is a physics-based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease-implicated protein folding intermediates, study assembly of protein complexes, predict protein-protein binding conformations, engineer rescue mutations in disease-causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications. PMID:26638022

  9. Direct evidence of the molecular basis for biological silicon transport

    PubMed Central

    Knight, Michael J.; Senior, Laura; Nancolas, Bethany; Ratcliffe, Sarah; Curnow, Paul

    2016-01-01

    Diatoms are an important group of eukaryotic algae with a curious evolutionary innovation: they sheath themselves in a cell wall made largely of silica. The cellular machinery responsible for silicification includes a family of membrane permeases that recognize and actively transport the soluble precursor of biosilica, silicic acid. However, the molecular basis of silicic acid transport remains obscure. Here, we identify experimentally tractable diatom silicic acid transporter (SIT) homologues and study their structure and function in vitro, enabled by the development of a new fluorescence method for studying substrate transport kinetics. We show that recombinant SITs are Na+/silicic acid symporters with a 1:1 protein: substrate stoichiometry and KM for silicic acid of 20 μM. Protein mutagenesis supports the long-standing hypothesis that four conserved GXQ amino acid motifs are important in SIT function. This marks a step towards a detailed understanding of silicon transport with implications for biogeochemistry and bioinspired materials. PMID:27305972

  10. Enzymology and molecular biology of cell wall biosynthesis. Progress report

    SciTech Connect

    Ray, P.M.

    1993-03-20

    In order to be able to explore the control of cell wall polysaccharide synthesis at the molecular level, which inter alia might eventually lead to means for useful modification of plant biomass polysaccharide production, the immediate goals of this project are to identify polypeptides responsible for wall polysaccharide synthase activities and to obtain clones of the genes that encode them. We are concentrating on plasma membraneassociated (1,3)-{beta}-glucan synthase (glucan synthase-II or GS-II) and Golgi-associated (1,4)-{beta}-glucan synthase (glucan synthase-I or GS-I), of growing pea stem tissue. Our progress has been much more rapid with respect to GS-II than regarding GS-I.

  11. A role for molecular genetics in biological conservation.

    PubMed Central

    O'Brien, S J

    1994-01-01

    The recognition of recent accelerated depletion of species as a consequence of human industrial development has spawned a wide interest in identifying threats to endangered species. In addition to ecological and demographic perils, it has become clear that small populations that narrowly survive demographic contraction may undergo close inbreeding, genetic drift, and loss of overall genomic variation due to allelic loss or reduction to homozygosity. I review here the consequences of such genetic depletion revealed by applying molecular population genetic analysis to four endangered mammals: African cheetah, lion, Florida panther, and humpback whale. The accumulated genetic results, combined with physiological, ecological, and ethological data, provide a multifaceted perspective of the process of species diminution. An emerging role of population genetics, phylogenetics, and phylogeography as indicators of a population's natural history and its future prognosis provides valuable data of use in the development of conservation management plans for endangered species. PMID:7912434

  12. Applications of Discrete Molecular Dynamics in biology and medicine.

    PubMed

    Proctor, Elizabeth A; Dokholyan, Nikolay V

    2016-04-01

    Discrete Molecular Dynamics (DMD) is a physics-based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease-implicated protein folding intermediates, study assembly of protein complexes, predict protein-protein binding conformations, engineer rescue mutations in disease-causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications.

  13. Direct evidence of the molecular basis for biological silicon transport.

    PubMed

    Knight, Michael J; Senior, Laura; Nancolas, Bethany; Ratcliffe, Sarah; Curnow, Paul

    2016-01-01

    Diatoms are an important group of eukaryotic algae with a curious evolutionary innovation: they sheath themselves in a cell wall made largely of silica. The cellular machinery responsible for silicification includes a family of membrane permeases that recognize and actively transport the soluble precursor of biosilica, silicic acid. However, the molecular basis of silicic acid transport remains obscure. Here, we identify experimentally tractable diatom silicic acid transporter (SIT) homologues and study their structure and function in vitro, enabled by the development of a new fluorescence method for studying substrate transport kinetics. We show that recombinant SITs are Na(+)/silicic acid symporters with a 1:1 protein: substrate stoichiometry and KM for silicic acid of 20 μM. Protein mutagenesis supports the long-standing hypothesis that four conserved GXQ amino acid motifs are important in SIT function. This marks a step towards a detailed understanding of silicon transport with implications for biogeochemistry and bioinspired materials. PMID:27305972

  14. Cell and molecular biology for diagnostic and therapeutic technology

    NASA Astrophysics Data System (ADS)

    Tan, M. I.

    2016-03-01

    Our body contains 100 trillion cells. However, each cell has certain function and structure. For maintaining their integrity, cells will be collaborating with each other and with extracellular matrix surround them to form a tissue. These interactions effect internally on many networks or pathway such as signalling pathway, metabolic pathway and transport network in the cell. These networks interact with each other to maintain cell survival, cell structure and function and moreover the tissue as well as the organ which the cells built. Therefore, as part of a tissue, genetic and epigenetic abnormality of a cell can also alter these networks, and moreover disturb the function of the tissue itself. Hence, condition of genetic and epigenetic of the cell may affect other conditions in omics level such as transcriptomic, proteomic, metabolomics characteristics which can be differentiated by a particular unique molecular profile from each level, which can be used for diagnostic as well as for targeted therapy.

  15. The molecular biology and biochemistry of rice endosperm. alpha. -globulin

    SciTech Connect

    Shorrosh, B.S.

    1989-01-01

    The author's first objective was to isolate a cDNA clone that encodes the rice endosperm {alpha}-globulin. Purified antibodies against a rice storage protein, {alpha}-globulin, were used to screen a {lambda}gt11 cDNA expression library constructed from immature rice seed endosperm. The cDNA insert of clone 4A1 (identified by antibody screening) was used as a probe to identify long cDNA inserts in the library. The deduced amino acid sequence of clone A3-12 cDNA insert (identified by cDNA screening) contained the amino acid sequences of three cyanogen bromide peptides fragment of {alpha}-globulin. The calculated molecular weight and amino acid composition of the deduced amino acid sequence were similar to the {alpha}-globulin protein. Northern blot analysis indicated that mRNA of one size, approximately 1.0 kb, is expressed. Southern genomic blot analysis revealed one band with EcoRI or Hind III digestion. Cell-free translation and immunoprecipitation showed that the initial translation product is approximately 2,000 daltons larger than the mature protein. The amino acid sequence of {alpha}-globulin revealed limited regions of similarities with wheat storage proteins. The author concludes that the cDNA insert in clone A3-12 contained the entire coding region of {alpha}-globulin protein and that {alpha}-globulin is encoded by a single gene. My second objective was to inhibit the degradation of {alpha}-globulin in the salt extract of rice flour. The salt extract of rice flour contained an acid protease whose optimal pH was 3 for {sup 3}H-casein hydrolysis. A polypeptide with molecular weight of 20,000 was immunologically reactive with {alpha}-globulin antibodies and is produced by limited proteolysis in the extract. Pepstatin inhibited the proteolysis of 3H-casein and slowed the proteolysis of {alpha}-globulin.

  16. Clinical, morphological, and molecular aspects of sialic acid storage disease manifesting in utero

    PubMed Central

    Froissart, R; Cheillan, D; Bouvier, R; Tourret, S; Bonnet, V; Piraud, M; Maire, I

    2005-01-01

    Background: Sialic acid storage diseases (SASDs) are caused by the defective transport of free sialic acid outside the lysosome. Apart from the Salla presentation in Finland, SASD is a very rare form of lysosomal storage disease (LSD) with approximately 35 cases, all diagnosed after birth, having been reported worldwide. We report a series of 12 French patients with very early manifestations, including eight fetuses diagnosed in utero. Results: Ultrasound examination, fetal autopsy, or clinical examination showed prominent ascites, rarely progressing to complete hydrops, and highlighted the early severity of bone disease. Dramatic increase of free sialic acid in various biological samples confirmed the diagnosis in all cases. Storage staining affinities and storage distribution in placenta and fetal organs allowed differential diagnosis from other LSDs but cannot differentiate between SASD, sialidosis, and galactosialidosis. Fourteen different mutations were identified, showing the molecular heterogeneity of SASD in the French population. We found that the previously described p.Y306X mutation generated two different transcripts, and we identified seven novel mutations: three deletions (del exon 7, del exons10+11 and c.1296delT), one splice site mutation (c.1350+1G→T) one nonsense mutation (p.W339X), and two missense mutations (p.R57C and p.G127E). Conclusions: The severity of our patients' genotypes is in agreement with their phenotypes but not with the importance and early appearance of the very frequent in utero manifestations. Minimal fetal disease in some patients and a reported case of heterogeneity of fetal involvement within a family suggest that factors other than the genotype influence fetal manifestations. PMID:15805149

  17. HAMLET kills tumor cells by an apoptosis-like mechanism--cellular, molecular, and therapeutic aspects.

    PubMed

    Svanborg, Catharina; Agerstam, Helena; Aronson, Annika; Bjerkvig, Rolf; Düringer, Caroline; Fischer, Walter; Gustafsson, Lotta; Hallgren, Oskar; Leijonhuvud, Irene; Linse, Sara; Mossberg, Ann-Kristin; Nilsson, Hanna; Pettersson, Jenny; Svensson, Malin

    2003-01-01

    HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a protein-lipid complex that induces apoptosis-like death in tumor cells, but leaves fully differentiated cells unaffected. This review summarizes the information on the in vivo effects of HAMLET in patients and tumor models on the tumor cell biology, and on the molecular characteristics of the complex. HAMLET limits the progression of human glioblastomas in a xenograft model and removes skin papillomas in patients. This broad anti-tumor activity includes >40 different lymphomas and carcinomas and apoptosis is independent of p53 or bcl-2. In tumor cells HAMLET enters the cytoplasm, translocates to the perinuclear area, and enters the nuclei where it accumulates. HAMLET binds strongly to histones and disrupts the chromatin organization. In the cytoplasm, HAMLET targets ribosomes and activates caspases. The formation of HAMLET relies on the propensity of alpha-lactalbumin to alter its conformation when the strongly bound Ca2+ ion is released and the protein adopts the apo-conformation that exposes a new fatty acid binding site. Oleic acid (C18:1,9 cis) fits this site with high specificity, and stabilizes the altered protein conformation. The results illustrate how protein folding variants may be beneficial, and how their formation in peripheral tissues may depend on the folding change and the availability of the lipid cofactor. One example is the acid pH in the stomach of the breast-fed child that promotes the formation of HAMLET. This mechanism may contribute to the protective effect of breastfeeding against childhood tumors. We propose that HAMLET should be explored as a novel approach to tumor therapy.

  18. Aspects of Biology and Development of Xiphinema americanum and Related Species.

    PubMed

    Halbrendt, J M; Brown, D J

    1993-09-01

    Identification of Xiphinema americanum-group nematodes is based on relatively subtle morphological and morphometric differences, many of which overlap. The significance and importance of these separations cannot be assessed without a basic understanding of the biological differences between species. Currently, information is accumulating on Xiphinema biology, development, and genetics that will help to confirm or refute the current systematics of species in this group. Recently, it was demonstrated that Xiphinema species pass through either three or four juvenile stages before becoming adults. This new and fundamental information divides the genus and the X. americanum group into subgroups based on their developmental evolution and provides new insight into the taxonomy and systematic positions of the species.

  19. Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009

    PubMed Central

    Galperin, Michael Y.; Cochrane, Guy R.

    2009-01-01

    The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory comment, we briefly describe some of these new databases and review the principles guiding the selection of databases for inclusion in the Nucleic Acids Research annual Database Issue and the Nucleic Acids Research online Molecular Biology Database Collection. The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). PMID:19033364

  20. Computational local stiffness analysis of biological cell: High aspect ratio single wall carbon nanotube tip.

    PubMed

    TermehYousefi, Amin; Bagheri, Samira; Shahnazar, Sheida; Rahman, Md Habibur; Kadri, Nahrizul Adib

    2016-02-01

    Carbon nanotubes (CNTs) are potentially ideal tips for atomic force microscopy (AFM) due to the robust mechanical properties, nanoscale diameter and also their ability to be functionalized by chemical and biological components at the tip ends. This contribution develops the idea of using CNTs as an AFM tip in computational analysis of the biological cells. The proposed software was ABAQUS 6.13 CAE/CEL provided by Dassault Systems, which is a powerful finite element (FE) tool to perform the numerical analysis and visualize the interactions between proposed tip and membrane of the cell. Finite element analysis employed for each section and displacement of the nodes located in the contact area was monitored by using an output database (ODB). Mooney-Rivlin hyperelastic model of the cell allows the simulation to obtain a new method for estimating the stiffness and spring constant of the cell. Stress and strain curve indicates the yield stress point which defines as a vertical stress and plan stress. Spring constant of the cell and the local stiffness was measured as well as the applied force of CNT-AFM tip on the contact area of the cell. This reliable integration of CNT-AFM tip process provides a new class of high performance nanoprobes for single biological cell analysis. PMID:26652417