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Small RNAs were involved in homozygous state-associated silencing of a marker gene (Neomycin phosphotransferase II: nptII) in transgenic tomato plants.  


Homozygous state-associated co-suppression is not a very common phenomenon. In our experiments, two transgenic plants 3A29 and 1195A were constructed by being transformed with the constructs pBIN-353A and pBIN119A containing nptII gene as a marker respectively. The homozygous progeny from these two independent transgenic lines 3A29 and 1195A, displayed kanamycin-sensitivity and produced a short main root without any lateral roots as untransformed control (wild-type) seedlings when germinated on kanamycin media. For the seedlings derived from putative hemizygous plants, the percentage of the seedlings showing normal growth on kanamycin media was about 50% and lower than the expected percentage (75%). Southern analysis of the genomic DNA confirmed that the homozygous and hemizygous plants derived from the same lines contained the same multiple nptII transgenes, which were located on the same site of chromosome. Northern analysis suggested that the marker nptII gene was expressed in the primary and the hemizygous transformants, but it was silenced in the homozygous transgenic plants. Further Northern analysis indicated that antisense and sense small nptII-derived RNAs were present in the transgenic plants and the blotting signal of nptII-derived small RNA was much higher in the homozygous transgenic plants than that of hemizygous transgenic plants. Additionally, read-through transcripts from the TRAMP gene to the nptII gene were detected. These results suggest that the read-through transcripts may be involved in homozygous state-associated silencing of the nptII transgene in transgenic tomato plants and a certain threshold level of the nptII-derived small RNAs is required for the homozygous state-associated co-suppression of the nptII transgene. PMID:23612328

Deng, Lei; Pan, Yu; Chen, Xuqing; Chen, Guoping; Hu, Zongli



Nucleotide substitutions in rolC and nptII gene sequences during long-term cultivation of Panax ginseng cell cultures  

Microsoft Academic Search

It has been shown previously that the rolC gene from Agrobacterium tumefaciens gene was stably and highly expressed in 15-year-old Panax ginseng transgenic cell cultures. In the present report, we analyze in detail the nucleotide composition of the rolC and nptII (neomycin phosphotransferase) genes, which is the selective marker used for transgenic cell cultures of P.\\u000a ginseng. It has been

Konstantin V. Kiselev; Anna V. Turlenko; Galina K. Tchernoded; Yuri N. Zhuravlev



Light-induced expression of the chimeric chalcone synthase-NPTII gene in tobacco cells  

PubMed Central

A chimeric gene was constructed containing the light-inducible chalcone synthase (chs) promoter from Antirrhinum majus, the neomycin phosphotransferase structural sequence from Tn5 as a reporter gene (NPTII) and the termination region from chs gene 1 from Petroselinum hortense. This gene was introduced into tobacco plants with the help of Ti plasmid-derived plant vectors and NPTII expression was measured. Analysis of the chs promoter sequence indicated the position of several possible regulatory regions. These were deleted to test their influence on the expression of the chs-NPTII gene. The different chimeric genes were all shown to be active after transfer to tobacco with the exception of one, in which the entire 5' upstream sequence from ?1200 to ?39 was deleted. The transcription of a chimeric gene with a 1.2-kbp 5' upstream promoter sequence was shown to be light inducible in tobacco plants. The analysis of various deletions of this 5' upstream sequence indicates that a number of sequence motifs have a quantitative effect on gene expression. One of these sequence motifs (?564 to ?661) contains a direct repeat of 47 bp and the sequence GTGGTTAG which corresponds to the consensus core sequences observed in animal gene enhancer sequences. Deletion of a fragment containing this direct repeat resulted in a reduction of NPTII expression by a factor of 5. ImagesFig. 4.Fig. 5.Fig. 6.Fig. 7.Fig. 8.

Kaulen, Hildegard; Schell, Jeff; Kreuzaler, Fritz



Survival of plant seeds, their UV screens, and nptII DNA for 18 months outside the International Space Station.  


The plausibility that life was imported to Earth from elsewhere can be tested by subjecting life-forms to space travel. Ultraviolet light is the major liability in short-term exposures (Horneck et al., 2001 ), and plant seeds, tardigrades, and lichens-but not microorganisms and their spores-are candidates for long-term survival (Anikeeva et al., 1990 ; Sancho et al., 2007 ; Jönsson et al., 2008 ; de la Torre et al., 2010 ). In the present study, plant seeds germinated after 1.5 years of exposure to solar UV, solar and galactic cosmic radiation, temperature fluctuations, and space vacuum outside the International Space Station. Of the 2100 exposed wild-type Arabidopsis thaliana and Nicotiana tabacum (tobacco) seeds, 23% produced viable plants after return to Earth. Survival was lower in the Arabidopsis Wassilewskija ecotype and in mutants (tt4-8 and fah1-2) lacking UV screens. The highest survival occurred in tobacco (44%). Germination was delayed in seeds shielded from solar light, yet full survival was attained, which indicates that longer space travel would be possible for seeds embedded in an opaque matrix. We conclude that a naked, seed-like entity could have survived exposure to solar UV radiation during a hypothetical transfer from Mars to Earth. Chemical samples of seed flavonoid UV screens were degraded by UV, but their overall capacity to absorb UV was retained. Naked DNA encoding the nptII gene (kanamycin resistance) was also degraded by UV. A fragment, however, was detected by the polymerase chain reaction, and the gene survived in space when protected from UV. Even if seeds do not survive, components (e.g., their DNA) might survive transfer over cosmic distances. PMID:22680697

Tepfer, David; Zalar, Andreja; Leach, Sydney



Hybrid genes in the analysis of transformation conditions. 3. Temporal\\/spatial fate of NPTII gene integration, its inheritance and factors affecting these processes in Nicotiana plumbaginifolia  

Microsoft Academic Search

Freshly isolated haploid mesophyll protoplasts of Nicotiana plumbaginifolia were transformed for kanamycin resistance. In 38% of the 224 transformants analysed, transmission of the NPTII gene occurred as a homozygous trait, while 62% of the transformants were heterozygous for the trait. In the first case, the foreign DNA integration predominantly (95%) resulted in monogenic inheritance. The second group was characterized by

G. B. Gharti-Chhetri; W. Cherdshewasart; J. Dewulf; J. Paszkowski; M. Jacobs; I. Negrutiu



Hybrid genes in the analysis of transformation conditions. 3. Temporal/spatial fate of NPTII gene integration, its inheritance and factors affecting these processes in Nicotiana plumbaginifolia.  


Freshly isolated haploid mesophyll protoplasts of Nicotiana plumbaginifolia were transformed for kanamycin resistance. In 38% of the 224 transformants analysed, transmission of the NPTII gene occurred as a homozygous trait, while 62% of the transformants were heterozygous for the trait. In the first case, the foreign DNA integration predominantly (95%) resulted in monogenic inheritance. The second group was characterized by a significant (46%) proportion of multiple insertions. However, there was no clear-cut difference in the integration pattern between the two groups. Furthermore, transformation rates were increased by 4- to 10-fold when transformed diploid protoplasts were treated with UV light or with 3-aminobenzamide. The number of insertion sites was also increased by these treatments. These results shed further light on the fate of the foreign DNA in transformed plants and on means to control or manipulate the integration event(s). PMID:1966385

Gharti-Chhetri, G B; Cherdshewasart, W; Dewulf, J; Paszkowski, J; Jacobs, M; Negrutiu, I



Genetic transformation of potato with nptII-gus marker genes enhances foliage consumption by Colorado potato beetle larvae  

Microsoft Academic Search

Little is known about the effect of transgenic plants containing commonly used marker genes, such as aph(3')II (nptII encoding neomycinphosphotransferase) and uidA (gus encoding ß-glucuronidase) on insect feeding behaviour. We report here, for the first time, that transgenic potato plants containing only nptII and gus marker genes enhance foliage consumption by the Colorado potato beetle (CPB, Leptinotarsa decemlineata S.). Transformation

Anne Lecardonnel; Genevičve Prévost; Antony Beaujean; Rajbir S. Sangwan; Brigitte S. Sangwan-Norreel



Detection of npt II Activity in Transgenic Apple Fruits  

Microsoft Academic Search

It receives much concern whether the transgenic foods, especially the antibiotic marker genes, are safe for human health all the time. In this paper, the transgenic Malus domestica Borkh. cv. Royal Gala carrying exogenous neomycin phosphotransferase (nptII) was used to study the npt II gene activity in transgenic apple fruits. The result showed that the npt II activities were detected

Rui Jin Zhou; Qiang Fang; Xiao Xin Shi; Guo Qiang Du



Stable transformation via electroporation into maize Type II callus and regeneration of fertile transgenic plants  

Microsoft Academic Search

Maize Type II callus tissue was used as the plant material for genetic transformation via electroporation. Plasmid DNA containing a selectable marker gene (either neomycin phosphotransferase (npt-II) or phosphinothricin acetyl transferase (bar)), and a screenable marker gene (gus A) was incubated with the tissue prior to electroporation. Electroporated callus tissue was placed on selection medium containing kanamycin sulfate or Bast.

S. M. Pescitelli; K. Sukhapinda



Agrobacterium T-DNA-mediated integration and gene replacement in the brown rot pathogen Monilinia fructicola  

Microsoft Academic Search

A transformation system utilizing Agrobacterium tumefaciens was developed for targeted gene disruption in Monilinia fructicola, a fungal pathogen that causes brown rot disease of stone fruits. Transformation with a vector containing the neomycin phosphotransferase II (nptII) cassette flanked with 4 kb cutinase gene (Mfcut1) flanking sequences resulted in an average of 13 transformants per 105 spores. When assayed by PCR and

Miin-Huey Lee; Richard M. Bostock



Detection of the reporter and selection genes in transformed hop (Humulus lupulus L.)  

Microsoft Academic Search

Agrobacterium-mediated transformation of hop nodal explants with meristems was used for the introduction of a gus reporter gene and nptII plant selection gene into Slovenian hop cv. Aurora. Emerging hop regenerants were previously tested for the gus gene expression by histochemical analysis of ?-glucoronidase (GUS) activity. Approximately six months after the transformation procedure, PCR molecular analysis of shoots originating from




Production of ROL gene transformed plants of Rosa hybrida L. and characterization of their rooting ability  

Microsoft Academic Search

Transgenic plants of the rootstock Rosa hybrida L. cv. Moneyway were produced via a two-step procedure. First, kanamycin-resistant roots were generated on stem slices from micropropagated shoots, which were cocultivated with Agrobacterium tumefaciens containing the neomycin phosphotransferase II (NPTII) gene for conferring kanamycin resistance, together with individual ROL genes from A. rhizogenes. Root formation was quite efficient and up to

Theo P. M. van der Salm; Caroline J. G. van der Toorn; Reinoud Bouwer; Charlotte H. Hänisch ten Cate; Hans J. M. Dons



Transformation of Brassica napus L. using Agrobacterium tumefaciens : developmentally regulated expression of a reintroduced napin gene  

Microsoft Academic Search

Genetically transformed plants of Brassica napus L. (oilseed rape) were obtained from hypocotyl expiants using Agrobacterium tumefaciens vectors. Hypocotyl explants were inoculated with disarmed or oncogenic A. tumefaciens strains, EHA101 and A281, and then cultured on media containing kanamycin. The A. tumefaciens strains harbored a binary vector, which contained a neomycin phosphotransferase II (NPTII) gene driven by the 35S promoter

S. E. Radke; B. M. Andrews; M. M. Moloney; M. L. Crouch; J. C. Kridl; V. C. Knauf



Deletion analysis of the mannopine synthase gene promoter in sunflower crown gall tumors and Agrobacterium tumefaciens  

Microsoft Academic Search

We have used deletion mutagenesis to analyze a TR-DNA promoter from the octopine-type Ti plasmid pTiB6806. The promoter for the gene encoding mannopine synthase (mas) was cloned upstream of the bacterial kanamycin-resistance gene neomycin phosphotransferase II (NPT II). Bal31 deletion mutagenesis was used to generate deletion derivatives of the mas\\/NPTII gene beginning 1353 bp upstream of the initiation of transcription

Victor J. DiRita; Stanton B. Gelvin



Transfer of the yeast salt tolerance gene HAL1 to Cucumis melo L. cultivars and in vitro evaluation of salt tolerance  

Microsoft Academic Search

An Agrobacterium-mediated gene transfer method for production of transgenic melon plants has been optimized. The HAL1 gene, an halotolerance gene isolated from yeast, was inserted in a chimaeric construct and joined to two marker genes: a selectable-neomycin phosphotransferase-II (nptII)-, and a reporter-ß-glucuronidase (gus)-. The entire construct was introduced into commercial cultivars of melon. Transformants were selected for their ability to

Mireia Bordas; Consuelo Montesinos; Mercedes Dabauza; Aurora Salvador; Luis Antonio Roig; Ramon Serrano; VICENTE Moreno



Transformation of Japanese persimmon (Diospyros kaki Thunb.) with a bacterial gene for choline oxidase  

Microsoft Academic Search

This report describes the first successful genetic engineering of tolerance to salt in an agriculturally important species of woody plants by Agrobacterium-mediated transformation with the codA gene of Arthrobacter globiformis. This gene encodes choline oxidase, which catalyzes the oxidation of choline to glycinebetaine. The binary plasmid vector pGC95.091, containing a kanamycin-resistance gene (nptII), a gene for ß-glucuronidase (gusA) and the

Mei Gao; Atsushi Sakamoto; Keisuke Miura; Norio Murata; Akira Sugiura; Ryutaro Tao



Transient gene expression and influence of promoters on foreign gene expression in Arabidopsis thaliana  

Microsoft Academic Search

Summary  The influence of a variety of parameters was investigated on polyethylene glycol (PEG)-mediated transient nptII and gus gene expression in mesophyll protoplasts of Arabidopsis thaliana ecotype, Estland, in order to develop a suitable transient gene expression system. The investigation revealed that a combination\\u000a of 20% PEG, incubation time of 15 min, 20–30 g plasmid concentration per ml along with 50

Rita Gandhi; Satish C. Maheshwari; Paramjit Khurana



A co-transformation system to produce transgenic grapevines free of marker genes  

Microsoft Academic Search

A co-transformation system was developed to produce grapevines free of selectable marker genes. This was achieved by transforming Vitis vinifera L. ‘Thompson Seedless’ somatic embryos with a mixture of two Agrobacterium strains. The first strain contained a binary plasmid with an egfp gene of interest between the T-DNA borders. The second strain harbored the neomycin phosphotransferase (nptII) gene for positive

M. Dutt; Z. T. Li; S. A. Dhekney; D. J. Gray



Efficient production of transgenic citrus plants using isopentenyl transferase positive selection and removal of the marker gene by site-specific recombination  

Microsoft Academic Search

The presence of marker genes conferring antibiotic resistance in transgenic plants represents a serious obstacle for their public acceptance and future commercialization. In citrus, selection using the selectable marker gene nptII, that confers resistance to the antibiotic kanamycin, is in general very effective. An attractive alternative is offered by the MAT system (Multi-Auto-Transformation), which combines the ipt gene for positive

Alida Ballester; Magdalena Cervera; Leandro Peńa



Gene Manipulation of a Heavy Metal Hyperaccumulator Species Thlaspi caerulescens L. via Agrobacterium -mediated Transformation  

Microsoft Academic Search

Thlaspi caerulescens L. is well known as a Zn\\/Cd hyperaccumulator. The genetic manipulation of T. caerulescens through transgenic technology can modify plant features for use in phytoremediation. Here, we describe the efficient transformation\\u000a of T. caerulescens using Agrobacterium tumefaciens strain EHA105 harboring a binary vector pBI121 with the nptII gene as a selectable marker, the gus gene as a reporter and a

Zi Qiu Guan; Tuan Yao Chai; Yu Xiu Zhang; Jin Xu; Wei Wei; Lu Han; Lin Cong



Expression of the rol B gene enhances adventitious root formation in hardwood cuttings of aspen  

Microsoft Academic Search

Summary  An elite aspen hybrid (Populus × canescens × P. grandidentata) was transformed with Agrobacterium tumefaciens strain EHA105 that harbored a binary vector (pBI121) carrying the nptII gene under the nos promoter and tandem rolB-uidA (GUS) genes with the CaMV 35S or heat shock promoter. Among 32 independent kanamycin-resistant plants, 25 plants were confirmed\\u000a by polymerase chain reaction and Southern blot

Wenhao Dai; Zong-Ming Cheng; Wayne A. Sargent



Overexpression of the feedback-insensitive anthranilate synthase gene in tobacco causes tryptophan accumulation  

Microsoft Academic Search

A total of 35 independent transgenic tobacco plants were produced using the Agrobacterium tumefaciens-leaf segment co-cultivation method followed by selection with kanamycin for the nptII gene. The vector also carried the tobacco feedback-insensitive anthranilate synthase gene ( ASA2). Many of the lines showed increased ASA2 mRNA levels but only three contained increased free tryptophan (Trp) and many lines contained lower

F.-Y. Tsai; J. E. Brotherton; J. M. Widholm



Selection for kanamycin resistance in transformed petunia cells leads to the co-amplification of a linked gene  

Microsoft Academic Search

A cell suspension culture was established from a transgenic petunia (Petunia hybrida L.) plant which carried genes encoding neomycin phosphotransferase II (nptII) and ß-glucuronidase (uidA, GUS). Two selection experiments were performed to obtain cell lines with increased resistance to kanamycin. In the first, two independently selected cell lines grown in the presence of 350 µg\\/ml kanamycin were eight to ten-fold

James D. Jones; Stephen C. Weller; Peter B. Goldsbrough



Agrobacterium tumefaciens -mediated transformation of blackgram: An assessment of factors influencing the efficiency of uidA gene transfer  

Microsoft Academic Search

Agrobacterium tumefaciens strain EHA105 carrying a binary vector pCAMBIA2301, which contains a neomycin phosphotransferase gene (nptII) and a ?-glucuronidase (GUS) gene (uidA) interrupted with an intron, was used for transformation of Vigna mungo cotyledonary node explants. Various factors such as preculture and wounding of explants, manipulations in inoculation and\\u000a co-cultivation conditions were found to play a significant role in influencing

R. Saini; P. K. Jaiwal



Real-time PCR methods for the detection of DNA constructs with the nptII gene for the detection of genetically modified plants in food, feed and seed  

Microsoft Academic Search

For routine analysis of the most different food and feed matrices for genetical modification screening methods have increasingly\\u000a been applied during the past years as the first step of detection. Screening for frequently used regulation elements and recombinant\\u000a DNA-constructs by the use of real-time PCR is the state of the art. By combining several screening methods, the number of\\u000a lines

Ralf Reiting



Transformation of a recalcitrant grain legume, Vigna mungo L. Hepper, using Agrobacterium tumefaciens -mediated gene transfer to shoot apical meristem cultures  

Microsoft Academic Search

The efficiency of Vigna mungo L. Hepper transformation was significantly increased from an average of 1% to 6.5% by using shoot apices excised from embryonic axes precultured on 10 µM benzyl-6-aminopurine (BAP) for 3 days and wounded prior to inoculation in Agrobacterium tumefaciens strain EHA105 carrying the binary vector pCAMBIA2301, which contains a neomycin phosphotransferase gene (nptII) and a ß-glucuronidase (GUS) gene

Raman Saini; Pawan K. Jaiwal



Angiotensin II Regulation of Adrenocortical Gene Transcription  

PubMed Central

Angiotensin II (Ang II) is the key peptide hormone in the renin-angiotensin-aldosterone system (RAAS). Its ability to regulate levels of circulating aldosterone relies on actions on adrenal glomerulosa cells. Many of the Ang II effects on glomerulosa cells involve a precisely coordinated regulation of signaling cascades and gene expression. The development of genome-wide gene arrays has allowed the definition of transcriptome-wide effects of Ang II in adrenocortical cells. Analysis of the Ang II gene targets reveals broad effects on cellular gene expression, particularly the rapid induction of numerous transcription factors that may regulate long-term steroid metabolism and cell growth/proliferation. Herein we discuss the Ang II-induced genes in adrenocortical cells and review the progress in defining the role of these genes in zona glomerulosa function.

Nogueira, Edson F.; Bollag, Wendy B.; Rainey, William E.



Agrobacterium -mediated transformation in chickpea ( Cicer arietinum L.) with an insecticidal protein gene: optimisation of different factors  

Microsoft Academic Search

Agrobacterium-mediated transformation in chickpea was developed using strain LBA4404 carrying nptII, uidA and cryIAc genes and transformants selected on Murashige and Skoog’s basal medium supplemented with benzyladenine, kinetin and kanamycin.\\u000a Integration of transgenes was demonstrated using polymerase chain reaction and Southern blot hybridization of T0 plants. The expression of CryIAc delta endotoxin and GUS enzyme was shown by enzyme linked

Shivani Indurker; Hari S. Misra; Susan Eapen



Transformation of a recalcitrant grain legume, Vigna mungo L. Hepper, using Agrobacterium tumefaciens-mediated gene transfer to shoot apical meristem cultures.  


The efficiency of Vigna mungo L. Hepper transformation was significantly increased from an average of 1% to 6.5% by using shoot apices excised from embryonic axes precultured on 10 microM benzyl-6-aminopurine (BAP) for 3 days and wounded prior to inoculation in Agrobacterium tumefaciens strain EHA105 carrying the binary vector pCAMBIA2301, which contains a neomycin phosphotransferase gene (nptII) and a beta-glucuronidase (GUS) gene (gusA) interrupted by an intron. The transformed green shoots that were selected and rooted on medium containing kanamycin, and which tested positive for nptII gene by polymerase chain reaction, were established in soil to collect seeds. GUS activity was detected in whole T(0) shoots and T(1) seedlings. All T(0) plants were morphologically normal, fertile and the majority of them transmitted transgenes in a 3:1 ratio to their progenies. Southern analysis of T(1) plants showed integration of nptII into the plant genome. PMID:15815929

Saini, Raman; Jaiwal, Pawan K



ROR1/RPA2A, a Putative Replication Protein A2, Functions in Epigenetic Gene Silencing and in Regulation of Meristem Development in ArabidopsisW?  

PubMed Central

We screened for suppressors of repressor of silencing1 (ros1) using the silenced 35S promoter-neomycin phosphotransferase II (Pro35S:NPTII) gene as a marker and identified two allelic mutants, ror1-1 and ror1-2 (for suppressor of ros1). Map-based cloning revealed that ROR1 encodes a 31-kD protein similar to DNA replication protein A2 (RPA2A). Mutations in ROR1 reactivate the silenced Pro35S:NPTII gene but not RD29A promoter-luciferase in the ros1 mutant. DNA methylation in rDNA, centromeric DNA, and RD29A promoter regions is not affected by ror1. However, chromatin immunoprecipitation data suggest that histone H3 acetylation is increased and histone H3K9 dimethylation is decreased in the 35S promoter in the ror1 ros1 mutant compared with ros1. These results indicate that release of silenced Pro35S:NPTII by ror1 mutations is independent of DNA methylation. ROR1/RPA2A is strongly expressed in shoot and root meristems. Mutations in ROR1/RPA2A affect cell division in meristems but not final cell sizes. Our work suggests important roles of ROR1/RPA2A in epigenetic gene silencing and in the regulation of plant development.

Xia, Ran; Wang, Junguo; Liu, Chunyan; Wang, Yu; Wang, Youqun; Zhai, Jixian; Liu, Jun; Hong, Xuhui; Cao, Xiaofeng; Zhu, Jian-Kang; Gong, Zhizhong



Protocol for transformation of the apple rootstock Jork 9 with the rol B gene and its influence on rooting  

Microsoft Academic Search

A suitable protocol for transformation has been developed for the apple rootstock Jork 9 using Agrobacterium tumefaciens strain EHA101A(pEHA101A)(pSCV1.6). Root formation was increased by transforming the rootstock with A. tumefaciens strain C58C1(pGV3850)(pB-B:GUS), which contains the nptII, rolB and gus genes on the T-DNA. Transformation for all of the introduced genes was confirmed by polymerase chain reaction and Southern blot analyses.

M. Sedira; A. Holefors; M. Welander



Gene Transfer by Transduction in the Marine Environment  

PubMed Central

To determine the potential for bacteriophage-mediated gene transfer in the marine environment, we established transduction systems by using marine phage host isolates. Plasmid pQSR50, which contains transposon Tn5 and encodes kanamycin and streptomycin resistance, was used in plasmid transduction assays. Both marine bacterial isolates and concentrated natural bacterial communities were used as recipients in transduction studies. Transductants were detected by a gene probe complementary to the neomycin phosphotransferase (nptII) gene in Tn5. The transduction frequencies ranged from 1.33 × 10?7 to 5.13 × 10?9 transductants/PFU in studies performed with the bacterial isolates. With the mixed bacterial communities, putative transductants were detected in two of the six experiments performed. These putative transductants were confirmed and separated from indigenous antibiotic-resistant bacteria by colony hybridization probed with the nptII probe and by PCR amplification performed with two sets of primers specific for pQSR50. The frequencies of plasmid transduction in the mixed bacterial communities ranged from 1.58 × 10?8 to 3.7 × 10?8 transductants/PFU. Estimates of the transduction rate obtained by using a numerical model suggested that up to 1.3 × 1014 transduction events per year could occur in the Tampa Bay Estuary. The results of this study suggest that transduction could be an important mechanism for horizontal gene transfer in the marine environment.

Jiang, Sunny C.; Paul, John H.



Gene manipulation of a heavy metal hyperaccumulator species Thlaspi caerulescens L. via Agrobacterium-mediated transformation.  


Thlaspi caerulescens L. is well known as a Zn/Cd hyperaccumulator. The genetic manipulation of T. caerulescens through transgenic technology can modify plant features for use in phytoremediation. Here, we describe the efficient transformation of T. caerulescens using Agrobacterium tumefaciens strain EHA105 harboring a binary vector pBI121 with the nptII gene as a selectable marker, the gus gene as a reporter and a foreign catalase gene. Based on the optimal concentration of growth regulators, the shoot cluster regeneration system via callus phase provided the basis of the genetic transformation in T. caerulescens. The key variables in transformation were examined, such as co-cultivation period and bacterial suspension density. Optimizing factors for T-DNA delivery resulted in kanamycin-resistant transgenic shoots with transformation efficiency more than 20%, proven by histochemical GUS assay and PCR analysis. Southern analysis of nptII and RT-PCR of catalase gene demonstrated that the foreign genes were integrated in the genome of transformed plantlets. Moreover, the activity of catalase enzyme in transgenic plants was obviously higher than in wild-type plants. This method offers new prospects for the genetic engineering of this important hyperaccumulator species. PMID:18427996

Guan, Zi Qiu; Chai, Tuan Yao; Zhang, Yu Xiu; Xu, Jin; Wei, Wei; Han, Lu; Cong, Lin



The Class II Transactivator Requires brahma-Related Gene 1 To Activate Transcription of Major Histocompatibility Complex Class II Genes  

Microsoft Academic Search

The class II transactivator (CIITA) is the key regulator of major histocompatibility complex (MHC) class II gene transcription. We demonstrate here that CIITA requires the ATPase subunit of an hSWI\\/SNF complex, brahma-related gene 1 (BRG-1), to activate transcription. When introduced into a cell line lacking BRG-1, CIITA was unable to activate cellular MHC class II genes. Reexpression of the wild-type

Rajini Mudhasani; Joseph D. Fontes




Technology Transfer Automated Retrieval System (TEKTRAN)

Rainbow trout (Oncorhynchus mykiss) has two types of lysozyme. Type II lysozyme differs from type I by only one amino acid, but only type II lysozyme has significant bactericidal activity. Due to this novel antibacterial property, lysozyme II appears to be a candidate gene for potentially enhancing ...


Transcript levels and synthesis of photosystem II components in cyanobacterial mutants with inactivated photosystem II genes  

SciTech Connect

After interruption or deletion of the photosystem II genes psbB, psbC, and psbD in the cyanobacterium Synechocystis sp. PCC 6803, thylakoids from such mutants were found to be depleted in a number of photosystem II proteins in addition to those for which the gene(s) had been inactivated. Transcript levels of photosystem II genes were measured and protein pulse-labeling was carried out to determine the reason for this effect. Transcripts of all photosystem II genes except the inactivated one(s) were found to be present in the various mutants. In certain cases, inactivation of one photosystem II gene led to overexpression of another. Protein pulse-labeling experiments using {sup 35}S-methionine, in which not only the rapidly turing over D1 protein but also D2, CP43, and CP47 appear to be preferentially labeled, showed that the mutants studied synthesize the D1 protein as well as other photosystem II proteins whose genes were not inactivated. The fact that, in the various mutants, photosystem II proteins for which the gene is not inactivated are synthesized but do not accumulate in the thylakoid indicates that the psbB, psbC, and psbD gene products are all required for a stable assembly of the photosystem II complex.

Jiujiang Yu; Vermaas, W.F.J. (Arizona State Univ., Tempe (United States))



Homology-dependent DNA Transfer from Plants to a Soil Bacterium Under Laboratory Conditions: Implications in Evolution and Horizontal Gene Transfer  

Microsoft Academic Search

DNA transfer was demonstrated from six species of donor plants to the soil bacterium, Acinetobacter spp. BD413, using neomycin phosphotransferase (nptII) as a marker for homologous recombination. These laboratory results are compatible with, but do not prove, DNA transfer in nature. In tobacco carrying a plastid insertion of nptII, transfer was detected with 0.1 g of disrupted leaves and in

David Tepfer; Rolando Garcia-Gonzales; Hounayda Mansouri; Martina Seruga; Brigitte Message; Francesca Leach; Mirna Curkovic Perica



MicroRNA genes are transcribed by RNA polymerase II  

Microsoft Academic Search

MicroRNAs (miRNAs) constitute a large family of noncod- ing RNAs that function as guide molecules in diverse gene silencing pathways. Current efforts are focused on the regulatory function of miRNAs, while little is known about how these unusual genes themselves are regulated. Here we present the first direct evidence that miRNA genes are transcribed by RNA polymerase II (pol II).

Yoontae Lee; Minju Kim; Jinju Han; Kyu-Hyun Yeom; Sanghyuk Lee; Sung Hee Baek; V Narry Kim



Norway spruce (Picea abies) genetic transformation with modified Cry3A gene of Bacillus thuringiensis.  


Modified versions of the Cry3A gene of Bacillus thuringiensis (Bt) were transferred into Norway spruce (Picea abies). Both the biolistic approach and Agrobacterium tumefaciens mediated procedure were employed for transformation of embryogenic tissue (ET) cultures. The latter method proved to be more efficient yielding 70 transgenic embryogenic tissue lines compared with 18 lines obtained by biolistics. The modified Cry3A genes were driven by a 35S promoter and the nptII screenable selection marker gene was used in all vectors. The transgenic ETs were molecularly characterized and converted into mature somatic embryos. Germinating embryos formed plantlets which were finally planted into perlite and their Cry3A gene transcription activities were demonstrated by RT-PCR. PMID:23888296

B?íza, Jind?ich; Pavingerová, Daniela; Vlasák, Josef; Niedermeierová, Hana



Co-transformation of grapevine somatic embryos to produce transgenic plants free of marker genes.  


A cotransformation system using somatic embryos was developed to produce grapevines free of selectable marker genes. This was achieved by transforming Vitis vinifera L. "Thompson Seedless" somatic embryos with a mixture of two Agrobacterium strains. The first strain contained a binary plasmid with an egfp gene of interest between the T-DNA borders. The second strain harbored the neomycin phosphotransferase (nptII) gene for positive selection and the cytosine deaminase (codA) gene for negative selection, linked together by a bidirectional dual promoter complex. Our technique included a short positive selection phase of cotransformed somatic embryos on liquid medium containing 100 mg/L kanamycin before subjecting cultures to prolonged negative selection on medium containing 250 mg/L 5-fluorocytosine. PMID:22351010

Dutt, Manjul; Li, Zhijian T; Dhekney, Sadanand A; Gray, Dennis J



Bacterial control of host gene expression through RNA polymerase II  

PubMed Central

The normal flora furnishes the host with ecological barriers that prevent pathogen attack while maintaining tissue homeostasis. Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation in which some patients infected with Escherichia coli develop acute pyelonephritis, while other patients with bacteriuria exhibit an asymptomatic carrier state similar to bacterial commensalism. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease-associated responses in the host. Here, we identify a new mechanism of bacterial adaptation through broad suppression of RNA polymerase II–dependent (Pol II–dependent) host gene expression. Over 60% of all genes were suppressed 24 hours after human inoculation with the prototype asymptomatic bacteriuria (ABU) strain E. coli 83972, and inhibition was verified by infection of human cells. Specific repressors and activators of Pol II–dependent transcription were modified, Pol II phosphorylation was inhibited, and pathogen-specific signaling was suppressed in cell lines and inoculated patients. An increased frequency of strains inhibiting Pol II was epidemiologically verified in ABU and fecal strains compared with acute pyelonephritis, and a Pol II antagonist suppressed the disease-associated host response. These results suggest that by manipulating host gene expression, ABU strains promote tissue integrity while inhibiting pathology. Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that potentially destructive immune activation will not occur.

Lutay, Nataliya; Ambite, Ines; Hernandez, Jenny Gronberg; Rydstrom, Gustav; Ragnarsdottir, Bryndis; Puthia, Manoj; Nadeem, Aftab; Zhang, Jingyao; Storm, Petter; Dobrindt, Ulrich; Wullt, Bjorn; Svanborg, Catharina



Group II Intron-Anchored Gene Deletion in Clostridium  

PubMed Central

Clostridium plays an important role in commercial and medical use, for which targeted gene deletion is difficult. We proposed an intron-anchored gene deletion approach for Clostridium, which combines the advantage of the group II intron “ClosTron” system and homologous recombination. In this approach, an intron carrying a fragment homologous to upstream or downstream of the target site was first inserted into the genome by retrotransposition, followed by homologous recombination, resulting in gene deletion. A functional unknown operon CAC1493–1494 located in the chromosome, and an operon ctfAB located in the megaplasmid of C. acetobutylicum DSM1731 were successfully deleted by using this approach, without leaving antibiotic marker in the genome. We therefore propose this approach can be used for targeted gene deletion in Clostridium. This approach might also be applicable for gene deletion in other bacterial species if group II intron retrotransposition system is established.

Jia, Kaizhi; Zhu, Yan; Zhang, Yanping; Li, Yin



A Role for KNAT Class II Genes in Root Development  

PubMed Central

Homeodomain proteins set up domains of gene expression during the development of animal and plant body plans. In plants, homeodomain proteins of the KNOX class I family have been shown to play a role in shoot apical meristem development. Recently, we have investigated the role of the Arabidopsis thaliana KNOX class II genes KNAT3, KNAT4 and KNAT5 in root development. These genes showed root domain and cell type specific expression patterns, and their expression was regulated by hormones that influence root growth. Moreover, sub-cellular localization of the KNAT proteins exhibited regulation, suggesting that post-transcriptional control contributes to KNOX class II protein activity. Our data provide a survey of KNAT gene expression in the root and indicate that the investigated KNAT genes might play distinct roles during root development.

Haseloff, Jim



DNase II: genes, enzymes and function  

Microsoft Academic Search

Deoxyribonuclease (DNase) II, which was discovered more than 50 years ago, is a mammalian endonuclease that functions optimally at acid pH in the absence of divalent cations. Its lysosomal localization and ubiquitous tissue distribution suggested that this enzyme played a role in the degradation of exogenous DNA encountered by phagocytosis, although the relative importance of such a role was unknown.

Cory J. Evans; Renato J. Aguilera



Topoisomerase II is required for the production of long Pol II gene transcripts in yeast  

PubMed Central

The extent to which the DNA relaxation activities of eukaryotic topoisomerases (topo I and topo II) are redundant during gene transcription is unclear. Although both enzymes can often substitute for each other in vivo, studies in vitro had revealed that the DNA cross-inversion mechanism of topo II relaxes chromatin more efficiently than the DNA strand-rotation mechanism of topo I. Here, we show that the inactivation of topo II in budding yeast produces an abrupt decrease of virtually all polyA+ RNA transcripts of length above ?3?kb, irrespective of their function. This reduction is not related to transcription initiation but to the stall of RNA polymerase II (Pol II) during elongation. This reduction does not occur in topo I mutants; and it is not avoided by overproducing yeast topo I or bacterial topo I, which relaxes (?) DNA supercoils. It is rescued by catalytically active topo II or a GyrBA enzyme, which relaxes (+) DNA supercoils. These findings demonstrate that DNA relaxation activities of topo I and topo II are not interchangeable in vivo. Apparently, only topo II relaxes efficiently the (+) DNA supercoils that stall the advancement of Pol II in long genes. A mechanistic model is proposed.

Joshi, Ricky S.; Pina, Benjamin; Roca, Joaquim



[Genetic transformation of flax (Linum usitatissimum L.) with chimeric GFP-TUA6 gene for visualisation of microtubules].  


The data of Agrobacterium-mediated transformation of some Linum usitatissimum cultivars zoned on the territories of Belarus and Ukraine with the plasmid carrying chimeric GFP-TUA6 gene and nptII gene as selectable marker conferring resistance to kanamycin are presented in this study. Transformation was affected by a number of factors including optical density (OD600), time of inoculation of explants with Agrobacterium and co-culture conditions. Transgenic nature of obtained lines was confirmed by PCR analysis. Expression of GFP-TUA6 gene was detected with confocal laser scanning microscopy. The obtained transgenic lines can be used for further functional studies the role of microtubules in the processes of building the flax fibres and resistance to wind. PMID:23745358

Shisha, E N; Korkhovo?, V I; Baer, G Ia; Guzenko, E V; Lemesh, V A; Kartel', N A; Emets, A I; Blium, Ia B


Retargeting mobile group II introns to repair mutant genes.  


Retroposable elements such as retroviral and lentiviral vectors have been employed for many gene therapy applications. Unfortunately, such gene transfer vectors integrate genes into many different DNA sequences and unintended integration of the vector near a growth-promoting gene can engender pathological consequences. For example, retroviral vector-mediated gene transfer induced leukemia in 2 of 11 children treated for severe combined immunodeficiency, raising significant safety issues for gene transfer strategies that cannot be targeted to specific sequences. Here, we examine the use of a mobile retroposable genetic element that can be targeted to introduce therapeutic sequences site specifically into mutant genes. The data demonstrate that the mobile group II intron from Lactococcus lactis can be targeted to insert into and repair mutant lacZ (approved gene symbol GLB1) and beta-globin (approved gene symbol HBB) genes with high efficiency and fidelity in model systems in bacteria. These results suggest that these mobile genetic elements represent a novel class of agents for performing targeted genetic repair. PMID:15851007

Jones, John Patrick; Kierlin, Monique N; Coon, Robert G; Perutka, Jiri; Lambowitz, Alan M; Sullenger, Bruce A



Angiotensin II-regulated transcription regulatory genes in adrenal steroidogenesis  

PubMed Central

Transcription regulatory genes are crucial modulators of cell physiology and metabolism whose intracellular levels are tightly controlled in response to extracellular stimuli. We previously reported a set of 29 transcription regulatory genes modulated by angiotensin II in H295R human adrenocortical cells and their roles in regulating the expression of the last and unique enzymes of the glucocorticoid and mineralocorticoid biosynthetic pathways, 11?-hydroxylase and aldosterone synthase, respectively, using gene expression reporter assays. To study the effect of this set of transcription regulatory genes on adrenal steroidogenesis, H295R cells were transfected by high-efficiency nucleofection and aldosterone and cortisol were measured in cell culture supernatants under basal and angiotensin II-stimulated conditions. BCL11B, BHLHB2, CITED2, ELL2, HMGA1, MAFF, NFIL3, PER1, SERTAD1, and VDR significantly stimulated aldosterone secretion, while EGR1, FOSB, and ZFP295 decreased aldosterone secretion. BTG2, HMGA1, MITF, NR4A1, and ZFP295 significantly increased cortisol secretion, while BCL11B, NFIL3, PER1, and SIX2 decreased cortisol secretion. We also report the effect of some of these regulators on the expression of endogenous aldosterone synthase and 11?-hydroxylase under basal and angiotensin II-stimulated conditions. In summary, this study reports for the first time the effects of a set of angiotensin II-modulated transcription regulatory genes on aldosterone and cortisol secretion and the expression levels of the last and unique enzymes of the mineralocorticoid and glucocorticoid biosynthetic pathways. Abnormal regulation of mineralocorticoid or glucocorticoid secretion is involved in several pathophysiological conditions. These transcription regulatory genes may be involved in adrenal steroidogenesis pathologies; thus they merit additional study as potential candidates for therapeutic intervention.

Gomez-Sanchez, Elise P.; Gomez-Sanchez, Celso E.



Overview of BioCreative II gene mention recognition  

PubMed Central

Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions.

Smith, Larry; Tanabe, Lorraine K; Ando, Rie Johnson nee; Kuo, Cheng-Ju; Chung, I-Fang; Hsu, Chun-Nan; Lin, Yu-Shi; Klinger, Roman; Friedrich, Christoph M; Ganchev, Kuzman; Torii, Manabu; Liu, Hongfang; Haddow, Barry; Struble, Craig A; Povinelli, Richard J; Vlachos, Andreas; Baumgartner, William A; Hunter, Lawrence; Carpenter, Bob; Tsai, Richard Tzong-Han; Dai, Hong-Jie; Liu, Feng; Chen, Yifei; Sun, Chengjie; Katrenko, Sophia; Adriaans, Pieter; Blaschke, Christian; Torres, Rafael; Neves, Mariana; Nakov, Preslav; Divoli, Anna; Mana-Lopez, Manuel; Mata, Jacinto; Wilbur, W John



OntoGene in BioCreative II.5.  


We describe a system for the detection of mentions of protein-protein interactions in the biomedical scientific literature. The original system was developed as a part of the OntoGene project, which focuses on using advanced computational linguistic techniques for text mining applications in the biomedical domain. In this paper, we focus in particular on the participation to the BioCreative II.5 challenge, where the OntoGene system achieved best-ranked results. Additionally, we describe a feature-analysis experiment performed after the challenge, which shows the unexpected result that one single feature alone performs better than the combination of features used in the challenge. PMID:20671319

Rinaldi, Fabio; Schneider, Gerold; Kaljurand, Kaarel; Clematide, Simon; Vachon, Thérčse; Romacker, Martin


Genomic isolation of genes encoding starch branching enzyme II (SBEII) in apple: toward characterization of evolutionary disparity in SbeII genes between monocots and eudicots.  


Two genes encoding starch branching enzyme II (SBEII) have been identified in apple. These genes share 94 and 92% identity in coding DNA sequences and amino acid sequences, respectively; moreover, they have similar expression patterns. Both genes are expressed in vegetative and reproductive tissues, including leaves, buds, flowers, and fruits. Based on genomic Southern blots, there are two copies of SbeII genes in the apple genome. Comparisons of genomic sequences between monocots and eudicots have revealed that the genomic structure of SbeII genes is conserved. However, the 5'-terminal region of coding DNA sequences of SbeII genes shows greater divergence than the 3'-terminal region between monocots and eudicots. Phylogenetic analysis of DNA sequences has demonstrated that the duplication patterns of SbeII genes are different between monocots and eudicots. In monocots, the duplication of SbeII genes must have occurred prior to the radiation of grasses (Poaceae); while, in eudicots, the expansion of SbeII genes must have followed the process of speciation. PMID:17564724

Han, Yuepeng; Bendik, Elise; Sun, Feng-Jie; Gasic, Ksenija; Korban, Schuyler S



Organization and expression of the chum salmon insulin-like growth factor II gene.  


IGF-II plays an important role in growth and development of vertebrates. In the present study, the characterization of the first fish IGF-II gene, chum salmon IGF-II, is described. The sIGF-II gene consists of four exons, spanning a region of 9 kbp, that encode the 214 aa IGF-II precursor. While the amino acid sequences of fully processed IGF-II of salmon and mammalian species are very similar, the prepro-peptide sequence deviates extensively in the signal- and E-peptide domains. The transcription initiation site of the sIGF-II gene was localized within a 30 nt region employing RT-PCR. Using sIGF-II promoter-luciferase constructs it was demonstrated that the sIGF-II gene has a relatively strong promoter that contains tissue-specific regulatory elements. PMID:9373182

Palamarchuk, A Y; Holthuizen, P E; Müller, W E; Sussenbach, J S; Kavsan, V M



Gene regulation and priming by topoisomerase II? in embryonic stem cells.  


Topoisomerases resolve torsional stress, while their function in gene regulation, especially during cellular differentiation, remains unknown. Here we find that the expression of topo II isoforms, topoisomerase II? and topoisomerase II?, is the characteristic of dividing and postmitotic tissues, respectively. In embryonic stem cells, topoisomerase II? preferentially occupies active gene promoters. Topoisomerase II? inhibition compromises genomic integrity, which results in epigenetic changes, altered kinetics of RNA Pol II at target promoters and misregulated gene expression. Common targets of topoisomerase II? and topoisomerase II? are housekeeping genes, while unique targets are involved in proliferation/pluripotency and neurogenesis, respectively. Topoisomerase II? targets exhibiting bivalent chromatin resolve upon differentiation, concomitant with their activation and occupancy by topoisomerase II?, features further observed for long genes. These long silent genes display accessible chromatin in embryonic stem cells that relies on topoisomerase II? activity. These findings suggest that topoisomerase II? not only contributes to stem-cell transcriptome regulation but also primes developmental genes for subsequent activation upon differentiation. PMID:24072229

Thakurela, Sudhir; Garding, Angela; Jung, Johannes; Schübeler, Dirk; Burger, Lukas; Tiwari, Vijay K



Effect of Ni(II) on inflammatory gene expression in THP1 monocytic cells.  


Nickel-containing alloys are in common use for dental restorations, but tend to corrode and release Ni(II) in service. Ni(II) increases secretion of several inflammatory cytokines from activated monocytic cells, suggesting that nickel alloys may exaggerate inflammatory responses in adjacent periodontal tissues. In this work, the effects of Ni(II) on expression of inflammatory cytokine and receptor genes as well as nuclear factor-kappa B (NF?B)-related genes were assessed using quantitative real-time polymerase chain reaction (PCR) and PCR-based arrays in the human THP1 monocytic cell line pre-exposed to Ni(II) for 72 h, then activated by lipopolysaccharide. The expression of 10 inflammatory genes was down-regulated ?50% by Ni(II) versus non-Ni(II) controls, whereas some genes like IL8 were up-regulated significantly by Ni(II). Expression of seven NF?B-related genes was up-regulated by Ni(II) by ?50%, and HMOX1 expression, a redox protein regulated by NRF2, was increased by >500%. The current results suggest that Ni(II) has diverse effects on inflammatory gene expression, which may partly account for previous reports of Ni(II)-induced changes in inflammatory cytokine secretion from monocytes and alterations in NF?B regulation. Further work is needed to verify these effects in primary cells and to ascertain how Ni(II) alters gene expression. PMID:23090859

Li, Lei; Drury, Jeanie L; Zhang, Hai; Sun, Jianxun; DiJulio, Dennis; Chung, Whasun O; Wataha, John C



Complete nucleotide sequence of the chum salmon insulin-like growth factor II gene.  


Insulin-like growth factor II (IGF-II) is thought to play an important role in development and growth of vertebrates. In contrast to mammals, the IGF-II gene is expressed at a high level from the early stages of embryonic development until the adult stage and IGF-II peptide is produced in virtually all organs of bony fish, indicating a physiological importance of IGF-II 'under water'. Therefore, we describe here the complete nucleotide sequence (accession no. X97225) and organization of the chum salmon IGF-II gene. In addition, the phylogenetic relationship of the IGF-II hormones is analysed. Although the chum salmon contains two non-allelic insulin and IGF-I genes, only one IGF-II gene could be identified. The chum salmon IGF-II gene consists of four exons and is comprised of 7992 bp from the putative transcription initiation site to the poly(A) site. Activation of the only promoter of the salmon IGF-II gene gives rise to a single 4 kb transcript. The fish IGF-II gene is much smaller and simpler organized than its known mammalian counterparts that are governed by several tissue-specific and developmental stage-dependent promoters. All known mammalian IGF-II genes to date have been found to form a conserved linkage group with the insulin and tyrosine hydroxylase (TH) genes and are organized as TH-insulin-IGF-II genomic locus. However, in our study we could find no linkage between the insulin and IGF-II genes, or between the insulin, TH and IGF-II genes, at least within approximately 20 kb of the chum salmon IGF-II genomic sequence. In spite of minor differences, the overall organization of the IGF-II genes turned out to be very similar in bony fish. A limited analysis of the phylogenetic relationship between IGF-II prohormones indeed showed a very conservative phylogenesis of IGF-II in bony fish that may indicate the particular significance of IGF-II in these animals. PMID:12354657

Palamarchuk, Alex; Gritsenko, Olga; Holthuizen, Elly; Sussenbach, John; Caelers, Antje; Reinecke, Manfred; Kavsan, Vadym



Regulation, linkage, and sequence of mouse metallothionein I and II genes.  

PubMed Central

The mouse metallothionein II (MT-II) gene is located approximately 6 kilobases upstream of the MT-I gene. A comparison of the sequences of mouse MT-I and MT-II genes (as well as those of other mammals) reveals that the coding regions are highly conserved even at "silent" positions but that the noncoding regions and introns are extremely divergent between primates and rodents. There are four blocks of conserved sequences in the promoters of mouse MT-I, mouse MT-II, and human MT-IIA genes; one includes the TATAAA sequence, and another has been implicated in regulation by heavy metals. Mouse MT-I and MT-II mRNAs are induced to approximately the same extent in vivo in response to cadmium, dexamethasone, or lipopolysaccharide. Mouse MT-I and MT-II genes are regulated by metals but not by glucocorticoids after transfection into HeLa cells. Images

Searle, P F; Davison, B L; Stuart, G W; Wilkie, T M; Norstedt, G; Palmiter, R D



Molecular basis of iduronate-2-sulphatase gene mutations in patients with mucopolysaccharidosis type II (Hunter syndrome)  

Microsoft Academic Search

Mucopolysaccharidosis type II (Hunter syndrome) is an X linked lysosomal storage disorder resulting from heterogeneous mutations in the iduronate-2-sulphatase (IDS) gene. To detect IDS gene mutations, direct sequencing of IDS cDNA fragments coupled with assays on IDS genomic amplicons was applied to 18 unrelated patients with MPS II. Seventeen mutations were detected from the 18 patients including seven missense mutations

Peining Li; Amy B Bellows; Jerry N Thompson



Exchange of RNA Polymerase II Initiation and Elongation Factors during Gene Expression In Vivo  

Microsoft Academic Search

We have systematically explored the in vivo occupancy of promoters and open reading frames by components of the RNA polymerase II transcription initiation and elongation apparatuses in yeast. RNA polymerase II, Mediator, and the general transcription factors (GTFs) were recruited to all promoters tested upon gene activation. RNA polymerase II, TFIIS, Spt5, and, unexpectedly, the Paf1\\/Cdc73 complex, were found associated

Dmitry K Pokholok; Nancy M Hannett; Richard A Young



Association of polymorphism of IGF-II gene with growth traits in Nanyang cattle  

Microsoft Academic Search

Insulin-like growth factor II (IGF-II) plays a key role in preadolescent growth, influencing fetal cell division and differentiation. It is assumed to be a candidate\\u000a gene involved in growth and carcass traits.We investigated the polymorphism of exon 2 of IGF-II gene and its relationship with growth traits in 126 Nanyang cattle by PCR-RFLP with BsrI. Two alleles, C and T,

Zhengfeng Zhang; Qiuling Li


Methylation of class II transactivator gene promoter IV is not associated with susceptibility to Multiple Sclerosis  

Microsoft Academic Search

BACKGROUND: Multiple sclerosis (MS) is a complex trait in which alleles at or near the class II loci HLA-DRB1 and HLA-DQB1 contribute significantly to genetic risk. The MHC class II transactivator (MHC2TA) is the master controller of expression of class II genes, and methylation of the promoter of this gene has been previously been shown to alter its function. In

Sreeram V Ramagopalan; David A Dyment; Katie M Morrison; Blanca M Herrera; Gabriele C DeLuca; Matthew R Lincoln; Sarah M Orton; Lahiru Handunnetthi; Michael J Chao; A Dessa Sadovnick; George C Ebers



The nucleotide sequence of the sheep MHC class II DNA gene  

SciTech Connect

The human MHC class II DNA gene was identified and sequenced by Trowsdale and Kelly. When a molecular map of the HLA-D region became available, it was shown that the HLA-DNA gene was unusual in not having a B gene partner situated within a few kilobases (kb), the nearest B gene being HLA-DPB1. The nearest unpaired B gene is HLA-DOB which is approximately 160 kb telomeric of HLA-DNA. More recently, the mouse MHC class II genes H-20A and H-20B were shown to be equivalent to the HLA-DNA and HLA-DOB genes. Moreover, the mouse genes expressed an MHC class II protein whose tissue distribution was restricted to B cells and epithelial cell of the thymic medulla. No corresponding HLA-DN protein has been reported. 21 refs., 3 figs.

Wright, H.; Redmond, J.; Ballingall, K.T. [Moredun Research Institute, Edinburgh (United Kingdom); Wright, F. [Univ. of Edinburgh (United Kingdom)



Overview of BioCreative II gene normalization  

Microsoft Academic Search

BACKGROUND:: The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the human expert; genes are often described rather than referred to by gene symbol and, confusingly, one gene

Alexander A Morgan; Zhiyong Lu; Xinglong Wang; Aaron M Cohen; Juliane Fluck; Patrick Ruch; Anna Divoli; Katrin Fundel; Robert Leaman; Jörg Hakenberg; Chengjie Sun; Heng-hui Liu; Rafael Torres; Michael Krauthammer; William W Lau; Hongfang Liu; Chun-Nan Hsu; Martijn Schuemie; K Bretonnel Cohen; Lynette Hirschman



Serial Analysis of Gene Expression Identifies Metallothionein-II as Major Neuroprotective Gene in Mouse Focal Cerebral Ischemia  

Microsoft Academic Search

We applied serial analysis of gene expression (SAGE) to study differentially expressed genes in mouse brain 14 hr after the induction of focal cerebral ischemia. Analysis of 60,000 tran- scripts revealed 83 upregulated and 94 downregulated tran- scripts (more than or equal to eightfold). Reproducibility was demonstrated by performing SAGE in duplicate on the same starting material. Metallothionein-II (MT-II) was

George Trendelenburg; Konstantin Prass; Josef Priller; Krisztian Kapinya; Andreas Polley; Claudia Muselmann; Karsten Ruscher; Ute Kannbley; Armin O. Schmitt; Stefanie Castell; Frank Wiegand; Andreas Meisel; Ulrich Dirnagl



Identification and Characterization of an Antigen I\\/II Homologous Gene, pah , from Streptococcus downei  

Microsoft Academic Search

Antigen I\\/II of Streptococcus mutans is a cell surface protein involved in the adherence of cells to tooth surfaces. In this study, an antigen I\\/II homologous\\u000a gene, pah, was identified and sequenced from Streptococcus downei MFe28 using degenerate polymerase chain reaction (PCR) and the gene-walking method. The pah gene encodes a cell-wall-anchoring protein, PAh, containing 1565 amino acids. At the

Haruki Tamura; Arisa Yamada; Hirohisa Kato



Genomic isolation of genes encoding starch branching enzyme II (SBEII) in apple: toward characterization of evolutionary disparity in Sbe II genes between monocots and eudicots  

Microsoft Academic Search

Two genes encoding starch branching enzyme II (SBEII) have been identified in apple. These genes share 94 and 92% identity\\u000a in coding DNA sequences and amino acid sequences, respectively; moreover, they have similar expression patterns. Both genes\\u000a are expressed in vegetative and reproductive tissues, including leaves, buds, flowers, and fruits. Based on genomic Southern\\u000a blots, there are two copies of

Yuepeng Han; Elise Bendik; Feng-Jie Sun; Ksenija Gasic; Schuyler S. Korban



TM6, a novel nuclear matrix attachment region, enhances its flanking gene expression through influencing their chromatin structure.  


Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription. PMID:23852133

Ji, Lusha; Xu, Rui; Lu, Longtao; Zhang, Jiedao; Yang, Guodong; Huang, Jinguang; Wu, Changai; Zheng, Chengchao



Activation of class II MHC genes requires both the X box region and the class II transactivator (CIITA).  


CIITA, a gene that can complement a transcriptional mutation of the major histocompatibility complex (MHC) class II genes, was tested for its ability to function as a coactivator, CIITA cDNA clones isolated showed alternative RNA splicing, but only one splice site combination was able to restore class II MHC gene expression. DNA-mediated transfection experiments showed that CIITA directs its activity through the X box element; the presence of CIITA leads to the formation of a higher order complex at the X box region; and CIITA contains a potent activation domain. These findings support the hypothesis that CIITA directly interacts with the MHC class II-specific transcription factors and is required for expression. PMID:7749984

Riley, J L; Westerheide, S D; Price, J A; Brown, J A; Boss, J M



Asparaginase II of Saccharomyces cerevisiae. Characterization of the ASP3 gene.  


Purified preparations of asparaginase II of Saccharomyces cerevisiae exhibit two protein bands upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Cloning and sequencing of the ASP3 gene, and partial amino acid sequencing as asparaginase II, imply that both bands are encoded by ASP3 but have different N termini. Northern blot analysis using the cloned ASP3 gene as a probe indicates that nitrogen catabolite repression of asparaginase II is achieved by alteration in mRNA levels. Deletion of sequences greater than 600 base pairs upstream from the initiation AUG codon results in an altered response to certain nitrogen sources in strains containing the truncated gene. PMID:3042786

Kim, K W; Kamerud, J Q; Livingston, D M; Roon, R J



Differential gene expression signatures for cell wall integrity found in chitin synthase II (chs2?) and myosin II (myo1?) deficient cytokinesis mutants of Saccharomyces cerevisiae  

Microsoft Academic Search

BACKGROUND: Myosin II-dependent contraction of the cytokinetic ring and primary septum formation by chitin synthase II are interdependent processes during cytokinesis in Saccharomyces cerevisiae. Hence, null mutants of myosin II (myo1?) and chitin synthase II (chs2?) share multiple morphological and molecular phenotypes. To understand the nature of their interdependent functions, we will seek to identify genes undergoing transcriptional regulation in

José F Rodríguez-Quińones



Glucose catabolism in cancer cells: amplification of the gene encoding type II hexokinase.  


Hexokinase type II is highly overexpressed in many cancer cells, where it plays a pivotal role in the high glycolytic phenotype. Here we demonstrate by Southern blot analysis and fluorescence in situ hybridization (FISH) that in the rapidly growing rat AS-30D hepatoma cell line, enhanced hexokinase activity is associated with at least a 5-fold amplification of the type II gene relative to normal hepatocytes. This amplification is located chromosomally, extends to the whole gene, and most likely occurs at the site of the resident gene. No rearrangement of the gene could be detected. Therefore, overexpression of hexokinase type II in AS-30D hepatoma cells may be based, at least in part, on a stable gene amplification. This is the first report describing the amplification of a hexokinase gene in a tumor cell line expressing the high glycolytic phenotype. PMID:8653677

Rempel, A; Mathupala, S P; Griffin, C A; Hawkins, A L; Pedersen, P L



PKR-Dependent Mechanisms of Gene Expression from a Subgenomic Hepatitis C Virus Clone  

PubMed Central

Studies on hepatitis C virus (HCV) replication have been greatly advanced by the development of cell culture models for HCV known as replicon systems. The prototype replicon consists of a subgenomic HCV RNA in which the HCV structural region is replaced by the neomycin phosphotransferase II (NPTII) gene, and translation of the HCV proteins NS3 to NS5 is directed by the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES). The interferon (IFN)-inducible protein kinase PKR plays an important role in cell defense against virus infection by impairing protein synthesis as a result of eIF-2? phosphorylation. Here, we show that expression of the viral nonstructural (NS) and PKR proteins and eIF-2? phosphorylation are all variably regulated in proliferating replicon Huh7 cells. In proliferating cells, induction of PKR protein by IFN-? is inversely proportional to viral RNA replication and NS protein expression, whereas eIF-2? phosphorylation is induced by IFN-? in proliferating but not in serum-starved replicon cells. The role of PKR and eIF-2? phosphorylation was further addressed in transient-expression assays in Huh7 cells. These experiments demonstrated that activation of PKR results in the inhibition of EMCV IRES-driven NS protein synthesis from the subgenomic viral clone through mechanisms that are independent of eIF-2? phosphorylation. Unlike NS proteins, HCV IRES-driven NPTII protein synthesis from the subgenomic clone was resistant to PKR activation. Interestingly, activation of PKR could induce HCV IRES-dependent mRNA translation from dicistronic constructs, but this stimulatory effect was mitigated by the presence of the viral 3? untranslated region. Thus, PKR may assume multiple roles in modulating HCV replication and protein synthesis, and tight control of PKR activity may play an important role in maintaining virus replication and allowing infection to evade the host's IFN system.

Rivas-Estilla, Ana Maria; Svitkin, Yuri; Lopez Lastra, Marcelo; Hatzoglou, Maria; Sherker, Averell; Koromilas, Antonis E.



Localization of the synapsin II (SYN2) gene to human chromosome 3 and mouse chromosome 6  

SciTech Connect

The synapsins are a family of four synaptic vesicle-associated proteins, synapsins Ia, Ib, IIa, and IIb, that have been implicated in modulation of neurotransmitter release and in synaptogenesis . They are products from alternative splicing of two distinct genes, the synapsin I and synapsin II genes. The synapsin I (SYN1) gene has been mapped to the X chromosome in human and mouse. In this study, we have determined the chromosomal location of the synapsin II (SYN2) gene in both and human and mouse. 10 refs., 1 fig.

Lian Li; Lih-Shen Chin; Greengard, P. [Rockefeller Univ., New York, NY (United States)] [and others



Chromosomal localization and structure of the human type II IMP dehydrogenase gene  

SciTech Connect

We determined the chromosomal localization and structure of the gene encoding human type II inosine 5{prime}-monophosphate dehydrogenase (IMPDH, EC, an enzyme associated with cellular proliferation, malignant transformation, and differentiation. Using polymerase chain reaction (PCR) primers specific for type II IMPDH, we screened a panel of human-Chinese hamster cell somatic hybrids and a separate deletion panel of chromosome 3 hybrids and localized the gene to 3p21.1{yields}p24.2. Two overlapping yeast artificial chromosome clones containing the full gene for type II IMPDH were isolated and a physical map of 117 kb of human genomic DNA in this region of chromosome 3 was constructed. The gene for type II IMPDH was localized and oriented on this map and found to span no more than 12.5 kb.

Glesne, D.; Huberman, E. [Chicago Univ., IL (United States). Dept. of Molecular Genetics and Cell Biology]|[Argonne National Lab., IL (United States); Collart, F. [Argonne National Lab., IL (United States); Varkony, T.; Drabkin, H. [Colorado Univ., Denver, CO (United States). Health Sciences Center



Tissue-specific expression of the human type II collagen gene in mice  

SciTech Connect

Type II collagen is crucial to the development of form in vertebrates as it is the major protein of cartilage. To study the factors regulating its expression the authors introduced a cosmid containing the human type II collagen gene, including 4.5 kilobases of 5' and 2.2 kilobases of 3' flanking DNA, into embryonic stem cells in vitro. The transformed cells contribute to all tissues in chimeric mice allowing the expression of the exogenous gene to be studied in vivo. Human type II collagen mRNA is restricted to tissues showing transcription from the endogenous gene and human type II collagen is found in extracellular matrix surrounding chondrocytes in cartilage. The results indicate that the cis-acting requirements for correct temporal and spatial regulation of the gene are contained with the introduced DNA.

Lovell-Badge, R.H.; Bygrave, A.; Bradley, A.; Robertson, E.; Tilly, R.; Cheah, K.S.E.



Chromosomal localization and structure of the human type II IMP dehydrogenase gene (IMPDH2)  

SciTech Connect

The authors determined the chromosomal localization and structure of the gene encoding human type II inosine 5[prime]-monophosphate dehydrogenase (IMPDH, EC, an enzyme associated with cellular proliferation, malignant transformation, and differentiation. Using polymerase chain reaction (PCR) primers specific for type II IMPDH, they screened a panel of human-Chinese hamster cell somatic hybrids and a separate deletion panel of chromosome 3 hybrids and localized the gene to 3p21.2 [yields] p24.2. Two overlapping yeast artificial chromosome clones containing the full gene for type II IMPDH (IMPDH2) were isolated, and a physical map of 117 kb of human genomic DNA in this region of chromosome 3 was constructed. The gene for type II IMPDH was localized and oriented on this map and found to span no more than 12.5 kb. 14 refs., 2 figs., 1 tab.

Glesne, D.; Huberman, E. (Univ. of Chicago, IL (United States) Argonne National Lab., IL (United States)); Collart, F. (Argonne National Lab., IL (United States)); Varkony, T.; Drabkin, H. (Univ. of Colorado, Denver (United States))



Chromosomal localization and structure of the human type II IMP dehydrogenase gene.  

National Technical Information Service (NTIS)

We determined the chromosomal localization and structure of the gene encoding human type II inosine 5(prime)-monophosphate dehydrogenase (IMPDH, EC, an enzyme associated with cellular proliferation, malignant transformation, and differentiation...

D. Glesne E. Huberman F. Collart T. Varkony H. Drabkin



Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila  

Microsoft Academic Search

We have characterized RpII215, the gene encoding the largest subunit of RNA polymerase II in Drosophila melanogaster. DNA sequencing and nuclease S1 analyses provided the primary structure of this gene, its 7 kb RNA and 215 kDa protein products. The amino-terminal 80% of the subunit harbors regions with strong homology to the ß' subunit of Escherichia coli RNA polymerase and

R. S. Jokerst; W. A. Zehring; A. L. Greenleaf



Characterization and Evolution of MHC Class II B Genes in Ardeid Birds  

Microsoft Academic Search

Major histocompatibility complex (MHC) is a multi-gene family that is very suitable to investigate a wide range of open questions\\u000a in evolutionary ecology. In this study, we characterized two expressed MHC class II B genes (DAB1 and DAB2) in the Grey Heron\\u000a (Aves: Ardea cinerea). We further developed the primer pairs to amplify and sequence two MHC class II B

Li Li; Xiaopin Zhou; Xiaolin Chen


An omp gene enhances cell tolerance of Cu(II) in Sinorhizobium meliloti CCNWSX0020.  


The main aim of this work was to study molecular characterization of a DNA fragment conferring resistance to Cu(II) in Sinorhizobium meliloti CCNWSX0020. The strain CCNWSX0020, resistant to 1.4 mmol l(-1) Cu(II) in tryptone-yeast extract medium was isolated from Medicago lupulina growing in mine tailings of Fengxian County, China. The availability of the complete genome sequence of S. meliloti CCNWSX0020 provides an opportunity for investigating genes that play significant roles in Cu(II) resistance. A copper resistance gene, with a length of 1,445 bp, encoding 481 amino acids, designated omp, was identified by cDNA-amplified fragment length polymorphism from S. meliloti CCNWSX0020. The expression of omp gene strongly increased in the presence of Cu(II). The omp-defective mutants display sensitivities to Cu(II) compared with their wild types. The Cu(II)-sensitive phenotype of the mutant was complemented by a 1.5-kb DNA fragment containing omp gene. BLAST analysis revealed that this gene encoded a hypothetical outer membrane protein with 75 % similarity to outer membrane efflux protein in Rhizobium leguminosarum bv. viciae 3841. These studies suggested that the omp product was involved in the Cu(II) tolerance of S. meliloti CCNWSX0020. PMID:23526229

Li, Zhefei; Lu, Mingmei; Wei, Gehong



Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria  

Microsoft Academic Search

Mobile group II introns can be retargeted to insert into virtually any desired DNA target. Here we show that retargeted group II introns can be used for highly specific chromosomal gene disruption in Escherichia coli and other bacteria at frequencies of 0.1–22%. Furthermore, the introns can be used to introduce targeted chromosomal breaks, which can be repaired by transformation with

Michael Karberg; Huatao Guo; Jin Zhong; Robert Coon; Jiri Perutka; Alan M. Lambowitz



PEG and electroporation-induced transformation in Nicotiana tabacum: influence of genotype on transformation frequencies  

Microsoft Academic Search

Experimental parameters for direct gene transfer with recombinant DNA encoding neomycin phosphotransferase II (NPTII) under control of eukaryotic expression signals were established. The introduced gene was shown by the growth of transformants on media containing kanamycin, by genomic blotting and by assaying NPTII activity. Leaf protoplasts from three green genotypes of varieties xanthii and petit havanna, and from four plastome-encoded

S. Tyagi; B. Spiirlein; A. K. Tyagi; R. G. Herrmann; H. U. Koop



Development of transformation vectors based upon a modified plant alpha-tubulin gene as the selectable marker.  


A plant transformation and selection system has been developed utilizing a modified tubulin gene as a selectable marker. The vector constructs carrying a mutant alpha-tubulin gene from goosegrass conferring resistance to dinitroaniline herbicides were created for transformation of monocotyledonous and dicotyledonous plants. These constructs contained beta- and/or mutant alpha-tubulin genes driven either by ubiquitin or CaMV 35S promoter. The constructs were used for biolistic transformation of finger millet and soybean or for Agrobacterium-mediated transformation of flax and tobacco. Trifluralin, the main representative of dinitroaniline herbicides, was used as a selective agent in experiments to select transgenic cells, tissues and plantlets. Selective concentrations of trifluralin estimated for each species were as follows: 10 microM for Eleusine coracana, Glycine max, Nicotiana plumbaginifolia and Nicotiana sylvestris; 3 microM for Linum usitatissimum. PCR and Southern blotting analyses of transformed lines with a specific probe to nptII, alpha-tubulin or beta-tubulin genes were performed to confirm the transgenic nature of regenerated plants. Band specific for the mutant alpha-tubulin gene was identified in transformed plant lines. Results confirmed the stable integration of the mutant tubulin gene into the plant genomes. The present study clearly demonstrates the use of a plant mutant tubulin as a selective gene for plant transformation. PMID:18180180

Yemets, Alla; Radchuk, Vladimir; Bayer, Oleg; Bayer, Galina; Pakhomov, Alexey; Vance Baird, W; Blume, Yaroslav B



DNA Topoisomerase II Is Involved in Regulation of Cyst Wall Protein Genes and Differentiation in Giardia lamblia  

PubMed Central

The protozoan Giardia lamblia differentiates into infectious cysts within the human intestinal tract for disease transmission. Expression of the cyst wall protein (cwp) genes increases with similar kinetics during encystation. However, little is known how their gene regulation shares common mechanisms. DNA topoisomerases maintain normal topology of genomic DNA. They are necessary for cell proliferation and tissue development as they are involved in transcription, DNA replication, and chromosome condensation. A putative topoisomerase II (topo II) gene has been identified in the G. lamblia genome. We asked whether Topo II could regulate Giardia encystation. We found that Topo II was present in cell nuclei and its gene was up-regulated during encystation. Topo II has typical ATPase and DNA cleavage activity of type II topoisomerases. Mutation analysis revealed that the catalytic important Tyr residue and cleavage domain are important for Topo II function. We used etoposide-mediated topoisomerase immunoprecipitation assays to confirm the binding of Topo II to the cwp promoters in vivo. Interestingly, Topo II overexpression increased the levels of cwp gene expression and cyst formation. Microarray analysis identified up-regulation of cwp and specific vsp genes by Topo II. We also found that the type II topoisomerase inhibitor etoposide has growth inhibition effect on Giardia. Addition of etoposide significantly decreased the levels of cwp gene expression and cyst formation. Our results suggest that Topo II has been functionally conserved during evolution and that Topo II plays important roles in induction of the cwp genes, which is key to Giardia differentiation into cysts.

Lin, Bo-Chi; Pan, Yu-Jiao; Chan, Nei-Li; Li, Tsai-Kun; Wang, Hsin-Chih; Sun, Chin-Hung



In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster.  

PubMed Central

We describe a method for examining the in vivo distribution of a protein on specific eucaryotic DNA sequences. In this method, proteins are cross-linked to DNA in intact cells, and the protein-DNA adducts are isolated by immunoprecipitation with antiserum against the protein. Characterization of the DNA cross-linked to the precipitated protein identifies the sequences with which the protein is associated in vivo. Here, we applied these methods to detect RNA polymerase II-DNA interactions in heat-shocked and untreated Drosophila melanogaster Schneider line 2 cells. The level of RNA polymerase II associated with several heat shock genes increased dramatically in response to heat shock, whereas the level associated with the copia genes decreased, indicating that both induction of heat shock gene expression and repression of the copia gene expression by heat shock occur at the transcriptional level. Low levels of RNA polymerase II were present on DNA outside of the transcription units, and for at least two genes, hsp83 and hsp26, RNA polymerase II initiated binding near the transcription start site. Moreover, for hsp70, the density of RNA polymerase II on sequences downstream of the polyadenylate addition site was much lower than that observed on the gene internal sequences. Examination of the amount of specific restriction fragments cross-linked to RNA polymerase II provides a means of detecting RNA polymerase II on individual members of multigene families. This analysis shows that RNA polymerase II is associated with only one of the two cytoplasmic actin genes. Images

Gilmour, D S; Lis, J T



Isolation of the Human Insulin-Like Growth Factor Genes: Insulin-Like Growth Factor II and Insulin Genes are Contiguous  

Microsoft Academic Search

Overlapping recombinant clones that encompass the insulin-like growth factor (IGF) I and II genes have been isolated from a human genomic DNA library. Each gene is present once per haploid genome; the IGF-I gene spans >35 kilobase pairs (kbp) and the IFG-II gene is at least 15 kbp. The exon-intron organization of these genes is similar, each having four exons,

Graeme I. Bell; Daniela S. Gerhard; Noel M. Fong; Ray Sanchez-Pescador; Leslie B. Rall



Regulation of the renal angiotensin II receptor gene in acute unilateral ureteral obstruction  

Microsoft Academic Search

Regulation of the renal angiotensin II receptor gene in acute unilateral ureteral obstruction. We have shown that acute (24-hr) unilateral ureteral obstruction (UUO) induces the genes encoding for renin, in juxtaglomerular apparatuses and in tubules, for angiotensin converting enzyme in vascular endothelial cells, and for angiotensinogen in perivascular fat. These molecular changes occur in temporal association to marked reductions in

J Luis Pimentel; Susheng Wang; Manuel Martinez-Maldonado



Wound-inducible potato inhibitor II genes: enhancement of expression by sucrose  

Microsoft Academic Search

Expression of a chimeric potato Inhibitor II-CAT gene in transgenic tobacco plants was enhanced 50-fold when leaf tissue was floated on solutions containing 1% sucrose. The expression of the chimeric gene was also enhanced when leaf sections were floated on solutions of glucose, fructose, and maltose, but not when floated on solutions of mannitol. The increased expression due to sucrose

Russell Johnson; Clarence A. Ryan



Trans-Species Polymorphism and Selection in the MHC Class II DRA Genes of Domestic Sheep  

Microsoft Academic Search

Highly polymorphic genes with central roles in lymphocyte mediated immune surveillance are grouped together in the major histocompatibility complex (MHC) in higher vertebrates. Generally, across vertebrate species the class II MHC DRA gene is highly conserved with only limited allelic variation. Here however, we provide evidence of trans-species polymorphism at the DRA locus in domestic sheep (Ovis aries). We describe

Keith T. Ballingall; Mara S. Rocchi; Declan J. McKeever; Frank Wright; Etienne Joly




Technology Transfer Automated Retrieval System (TEKTRAN)

A 5586-bp sequence (accession No. DQ278491) which contains the DNA-dependent RNA polymerase II gene (RPB2) encoding the second largest protein subunit (Rpb2) was obtained from the wheat-biotype Phaeosphaeria nodorum by PCR amplification. The RPB2 gene structure and its associated signals were analyz...


Cloning in Streptococcus pneumoniae of the gene for DpnII DNA methylase.  

PubMed Central

The gene coding for the pneumococcal DNA adenine methylase that recognizes the sequence 5'-GATC-3' was cloned in a strain of Streptococcus pneumoniae that lacked both restriction endonucleases DpnI and DpnII. The gene was cloned as a 3.7-kilobase fragment of chromosomal DNA from a DpnII-containing strain inserted in both possible orientations in the multicopy plasmid vector pMP5 to give recombinant plasmids pMP8 and pMP10. Recombinant plasmids were selected by their resistance to DpnII cleavage. Cells carrying the recombinant plasmids modified phage in vivo so that it was restricted by DpnI- but not DpnII-containing hosts. They also showed levels of DNA methylase activity five times higher than that in cells of the original DpnII strain. No DpnII activity was observed in the clones; therefore, it was concluded that the insert did not contain an intact DpnII endonuclease gene and that methylation of host DNA did not turn on a latent form of the gene.

Lacks, S A; Springhorn, S S



Cloning in Streptococcus pneumoniae of the gene for DpnII DNA methylase  

SciTech Connect

The gene coding for the pneumococcal DNA adenine methylase that recognizes the sequence 5'-GATC-3' was cloned in a strain of Streptococcus pneumoniae that lacked both restriction endonucleases DpnI and DpnII. The gene was cloned as a 3.7-kilobase fragment of chromosomal DNA from a DpnII-containing strain inserted in both possible orientations in the multicopy plasmid vector pMP5 to give recombinant plasmids pMP8 and pMP10. Recombinant plasmids were selected by their resistance to DpnII cleavage. Cells carrying the recombinant plasmids modified phage in vivo so that it was restricted by DpnI- but not DpnII-containing hosts. They also showed levels of DNA methylase activity five times higher than that in cells of the original DpnII strain. No DpnII activity was observed in the clones; therefore, it was concluded that the insert did not contain an intact DpnII endonuclease gene and that methylation of host DNA did not turn on a latent form of the gene. 16 references, 1 figure, 2 tables.

Lacks, S.A.; Springhorn, S.S.



Evolutionary genetics of MHC class II beta genes in the brown hare, Lepus europaeus.  


The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. High levels of diversity at the MHC are thought to be the result of parasite-mediated selection and there is growing evidence to support this theory. Most studies, however, target just a single gene within the MHC and infer any evidence of selection to be representative of the entire gene region. Here we present data from three MHC class II beta genes (DPB, DQB, and DRB) for brown hares in two geographic regions and compare them against previous results from a class II alpha-chain gene (DQA). We report moderate levels of diversity and high levels of population differentiation in the DQB and DRB genes (Na ?=? 11, D (est)?=? 0.071 and Na ?= 15, D (est)?=? 0.409, respectively), but not for the DPB gene (Na ?=? 4, D (est)?=? 0.00). We also detected evidence of positive selection within the peptide binding region of the DQB and DRB genes (95% CI, ? ?>? 1.0) but found no signature of selection for DPB. Mutation and recombination were both found to be important processes shaping the evolution of the class II genes. Our findings suggest that while diversifying selection is a significant contributor to the generally high levels of MHC diversity, it does not act in a uniform manner across the entire MHC class II region. The beta-chain genes that we have characterized provide a valuable set of MHC class II markers for future studies of the evolution of adaptive variation in Leporids. PMID:21688061

Smith, Steve; de Bellocq, Joëlle Goüy; Suchentrunk, Franz; Schaschl, Helmut



Linkage of regression and malignant conversion of rabbit viral papillomas to MHC class II genes.  


Human papillomaviruses associated with cutaneous and anogenital cancers induce intraepithelial precursor lesions which may regress spontaneously or progress into invasive carcinomas. Cell-mediated immune responses are probably involved in regression of precancerous lesions and the polymorphism of the genes responsible may thus have a key role in the variability of the host response. Skin warts and cancers induced in rabbits by Shope papillomavirus provide a model to test this hypothesis. We analysed a restriction-fragment-length polymorphism of major histocompatibility complex class I and class II genes and T-cell receptor beta-chain genes in infected domestic rabbits. We found a strong linkage between wart regression and a DR alpha EcoRI fragment, and an increased relative risk of malignant transformation associated with a DQ alpha PvuII fragment. This indicates a genetic control of wart evolution, involving genes in the class II region of the major histocompatibility complex. PMID:1347151

Han, R; Breitburd, F; Marche, P N; Orth, G



Finding regulatory modules from gene expression data II  

NASA Astrophysics Data System (ADS)

We tested the Progressive Iterative Signature Algorithm (PISA) on synthetic data and on a large gene-expression data set for the yeast Saccharomyces cerevisiae. For synthetic data, the false-positive rate for identifying transcriptional modules was extremely low. For the yeast data set of 1012 experimental conditions for 6206 genes, PISA identified a large number of modules, most of which could be readily assigned to specific biological functions. These included many small modules (with as few as five genes) that could not be easily found by ISA. We compared the set of modules we found to the Gene Ontology annotation database and found many significant overlaps. The modules identified by PISA also compare favorably to experimentally and theoretically determined sets of genes regulated by individual transcription factors.

Tang, Chao; Kloster, Morten; Wingreen, Ned



Microarray analysis of altered gene expression in murine fibroblasts transformed by nickel(II) to nickel(II)-resistant malignant phenotype  

Microsoft Academic Search

B200 cells are Ni(II)-transformed mouse BALB\\/c-3T3 fibroblasts displaying a malignant phenotype and increased resistance to Ni(II) toxicity. In an attempt to find genes whose expression has been altered by the transformation, the Atlas Mouse Stress\\/Toxicology cDNA Expression Array (Clontech Laboratories, Inc., Palo Alto, CA) was used to analyze the levels of gene expression in both parental and Ni(II)-transformed cells. Comparison

Renata. Kowara; Aldona Karaczyn; Robert Y. S. Cheng; Konstantin Salnikow; Kazimierz S. Kasprzak



Bovine and Ovine Gonadotropin-Releasing Hormone (GnRH)-II Ligand Precursors and Type II GnRH Receptor Genes Are Functionally Inactivated  

Microsoft Academic Search

The decapeptide sequence of GnRH-II is conserved in all jawed vertebrate species studied to date. New data for cattle (Bos taurus) indicates a gene encoding GnRH-II decapeptide possessing arginine (codon: CGG) rather than tryptophan (TGG) at position three in the mature peptide. This substitu- tion is unique. We confirmed the DNA sequence after cloning part of the bovine prepro-GnRH-II gene.

Kevin Morgan; Robin Sellar; Adam J. Pawson; Zhi-Liang Lu; Robert P. Millar



Factors affecting gene expression of patatin and proteinase-inhibitor-II gene families in detached potato leaves  

Microsoft Academic Search

In whole intact potato (Solanum tuberosum L.) plants, the gene families of class-I patatin and proteinase inhibitor II (Pin 2) are constitutively expressed in the tubers. However, they are also induced in detached potato leaves in the presence of light. To further characterize this light action, the detached leaves were subjected to monochromatic light of different wavelengths and to darkness

Hugo Peńa-Cortés; Xiangjun Liu; José Sanchez Serrano; Rainer Schmid; Lothar Willmitzer



Involvement of reactive oxygen species in angiotensin II-induced endothelin-1 gene expression in rat cardiac fibroblasts  

Microsoft Academic Search

ObjectivesThe aim of this study was to investigate the effects of angiotensin II (Ang II) on fibroblast proliferation and endothelin-1 (ET-1) gene induction, focusing especially on reactive oxygen species (ROS)-mediated signaling in cardiac fibroblasts.

Tzu-Hurng Cheng; Pao-Yun Cheng; Neng-Lang Shih; Iuan-Bor Chen; Danny Ling Wang; Jin-Jer Chen



Poised RNA polymerase II changes over developmental time and prepares genes for future expression.  


Poised RNA polymerase II (Pol II) is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. A comparison with other tissues shows that these changes are stage specific and not tissue specific. In contrast, Polycomb group repression is tissue specific, and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data with findings in mammalian embryonic stem cells and discuss a framework for predicting developmental programs on the basis of the chromatin state. PMID:23260668

Gaertner, Bjoern; Johnston, Jeff; Chen, Kai; Wallaschek, Nina; Paulson, Ariel; Garruss, Alexander S; Gaudenz, Karin; De Kumar, Bony; Krumlauf, Robb; Zeitlinger, Julia



Allelic variation adjacent to the human insulin and apolipoprotein C-II genes in different ethnic groups  

Microsoft Academic Search

Summary  We have used DNA probes for the human insulin gene and apolipoprotein C-II (apo C-II) gene to determine the extent of allelic\\u000a variation in different ethnic groups. The distribution of an apo C-II DNA polymorphism revealed by the restriction endonuclease\\u000a Taq I showed no significant variation amongst racial groups; in contrast, an insulin gene-related DNA polymorphism showed\\u000a marked variability. In

L. G. Williams; N. I. Jowett; M. A. Vella; S. Humphries; D. J. Galton



Horticultural characteristics of transgenic tobacco expressing the rolC gene from Agrobacterium rhizogenes  

SciTech Connect

Wisconsin 38 tobacco (Nicotiana tabacum L.) leaf discs were transformed with the disarmed Agrobacterium tumefaciens strain EHA 101 carrying the rolC gene from A. rhizogenes and NPT II and GUS genes. Shoots that regenerated on kanamycin-containing medium were confirmed as transgenic through GUS assays, polymerase chain reaction (PCR), Southern blot analyses, and transmission of the foreign genes through the sexual cycle. Transgenic plants were as short as half the height of control plants; were earlier flowering by up to 35 days; and had smaller leaves, shorter internodes, smaller seed capsules, fewer seeds, smaller flowers, and reduced pollen viability. The number of seed capsules, leaf number, and specific root length were similar between transgenic and control plants. Transgenic clones varied in the expression of the rolC-induced growth alterations as did the first generation of seedlings from these clones. Such differences suggested the potential for selecting for different levels of expression. Transformation with the rolC gene presents a potentially useful method of genetically modifying horticultural crops, particularly for flowering date, height, and leaf and flower size. Chemical names used: neomycin phosphotransferase (NPTII), [beta]-glucuronidase (GUS).

Scorza, R.; Zimmerman, T.W.; Cordts, J.M.; Footen, K.J. (Dept. of Agriculture, Kearneysville, WV (United States)); Ravelonandro, M. (Inst. National Recherche Agronomique, Villenave d'Ornon (France). Station de Pathologie Vegetale)



Identification of cis-elements conferring high levels of gene expression in non-green plastids.  


Although our knowledge about the mechanisms of gene expression in chloroplasts has increased substantially over the past decades, next to nothing is known about the signals and factors that govern expression of the plastid genome in non-green tissues. Here we report the development of a quantitative method suitable for determining the activity of cis-acting elements for gene expression in non-green plastids. The in vivo assay is based on stable transformation of the plastid genome and the discovery that root length upon seedling growth in the presence of the plastid translational inhibitor kanamycin is directly proportional to the expression strength of the resistance gene nptII in transgenic tobacco plastids. By testing various combinations of promoters and translation initiation signals, we have used this experimental system to identify cis-elements that are highly active in non-green plastids. Surprisingly, heterologous expression elements from maize plastids were significantly more efficient in conferring high expression levels in root plastids than homologous expression elements from tobacco. Our work has established a quantitative method for characterization of gene expression in non-green plastid types, and has led to identification of cis-elements for efficient plastid transgene expression in non-green tissues, which are valuable tools for future transplastomic studies in basic and applied research. PMID:22639905

Zhang, Jiang; Ruf, Stephanie; Hasse, Claudia; Childs, Liam; Scharff, Lars B; Bock, Ralph



Organization of genes required for the oxidation of methanol to formaldehyde in three type II methylotrophs  

SciTech Connect

Restriction maps of genes required for the synthesis of active methanol dehydrogenase in Methylobacterium organophilum XX and Methylobacterium sp. strain AM1 have been completed and compared. In these two species of pink-pigmented, type II methylotrophs, 15 genes were identified that were required for the expression of methanol dehydrogenase activity. None of these genes were required for the synthesis of the prosthetic group of methanol dehydrogenase, pyrroloquinoline quinone. The structural gene required for the synthesis of cytochrome c{sub L}, an electron acceptor uniquely required for methanol dehydrogenase, and the genes encoding small basic peptides that copurified with methanol dehydrogenases were closely linked to the methanol dehydrogenase structural genes. A cloned 22-kilobase DNA insert from Methylsporovibrio methanica 81Z, an obligate type II methanotroph, complemented mutants that contained lesions in four genes closely linked to the methanol dehydrogenase structural genes. The methanol dehydrogenase and cytochrome c{sub L} structural genes were found to be transcribed independently in M. organophilum XX. Only two of the genes required for methanol dehydrogenase synthesis in this bacterium were found to be cotranscribed.

Bastien, C.; Machlin, S.; Zhang, Y.; Donaldson, K.; Hanson, R.S. (Univ. of Minnesota, Navarre (USA))



Gene insulation. Part II: natural strategies in vertebrates.  


The way a gene is insulated from its genomic environment in vertebrates is not basically different from what is observed in yeast and Drosophila (preceding article in this issue). If the formation of a looped chromatin domain, whether generated by attachment to the nuclear matrix or not, has become a classic way to confine an enhancer to a specific genomic domain and to coordinate, sequentially or simultaneously, gene expression in a given program, its role has been extended to new networks of genes or regulators within the same gene. A wider definition of the bases of the chromatin loops (nonchromosomal nuclear structures or genomic interacting elements) is also available. However, whereas insulation in Drosophila is due to a variety of proteins, in vertebrates insulators are still practically limited to CTCF (the CCCTC-binding factor), which appears in all cases to be the linchpin of an architecture that structures the assembly of DNA-protein interactions for gene regulation. As in yeast and Drosophila, the economy of means is the rule and the same unexpected diversion of known transcription elements (active or poised RNA polymerases, TFIIIC elements out of tRNA genes, permanent histone replacement) is observed, with variants peculiar to CTCF. Thus, besides structuring DNA looping, CTCF is a barrier to DNA methylation or interferes with all sorts of transcription processes, such as that generating heterochromatin. PMID:21102651

Amouyal, Michčle



The chum salmon IGF-II gene promoter is activated by hepatocyte nuclear factor 3beta.  


IGF-II plays an important role in growth and development of vertebrates and is highly expressed in adult salmon liver. In the present study, we demonstrate that a liver-enriched transcription factor, hepatocyte nuclear factor 3beta (HNF-3beta), is an activator of the chum salmon IGF-II gene. Multiple binding sites for HNF-3beta were identified within the 5'-UTR using electrophoretic mobility shift assays and mutation of these sites prevents binding of HNF-3beta. In transient transfection assays it was shown that mutation of the HNF-3beta binding sites results in a substantial decrease of HNF-3beta-activated salmon IGF-II gene expression. This is the first identified transcription factor that is functionally involved in the regulation of fish IGF-II expression. PMID:10100852

Palamarchuk, A Y; Kavsan, V M; Sussenbach, J S; Holthuizen, P E



Inducible Gene Expression in Lactobacillus reuteri LTH5531 during Type II Sourdough Fermentation  

Microsoft Academic Search

Lactobacillus reuteri LTH5531 is a dominant member of the microbiota of type II sourdough fermentations. To investigate the genetic background of the ecological performance of LTH5531, in vivo expression technology was used to identify promoters that show elevated levels of expression during growth of this organism in a type II sourdough fermentation. Thirty-eight sourdough-induced fusions were detected, and 29 genes

Fabio Dal Bello; Jens Walter; Stefan Roos; Hans Jonsson; Christian Hertel



RNA Polymerase II Binding Patterns Reveal Genomic Regions Involved in MicroRNA Gene Regulation  

PubMed Central

MicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression. Due to the poor annotation of primary microRNA (pri-microRNA) transcripts, the precise location of promoter regions driving expression of many microRNA genes is enigmatic. This deficiency hinders our understanding of microRNA-mediated regulatory networks. In this study, we develop a computational approach to identify the promoter region and transcription start site (TSS) of pri-microRNAs actively transcribed using genome-wide RNA Polymerase II (RPol II) binding patterns derived from ChIP-seq data. Based upon the assumption that the distribution of RPol II binding patterns around the TSS of microRNA and protein coding genes are similar, we designed a statistical model to mimic RPol II binding patterns around the TSS of highly expressed, well-annotated promoter regions of protein coding genes. We used this model to systematically scan the regions upstream of all intergenic microRNAs for RPol II binding patterns similar to those of TSS from protein coding genes. We validated our findings by examining the conservation, CpG content, and activating histone marks in the identified promoter regions. We applied our model to assess changes in microRNA transcription in steroid hormone-treated breast cancer cells. The results demonstrate many microRNA genes have lost hormone-dependent regulation in tamoxifen-resistant breast cancer cells. MicroRNA promoter identification based upon RPol II binding patterns provides important temporal and spatial measurements regarding the initiation of transcription, and therefore allows comparison of transcription activities between different conditions, such as normal and disease states.

Wang, Guohua; Wang, Yadong; Shen, Changyu; Huang, Yi-wen; Huang, Kun; Huang, Tim H. M.; Nephew, Kenneth P.; Li, Lang; Liu, Yunlong



Gene Induction during Differentiation of Human Pulmonary Type II Cells In Vitro  

PubMed Central

Mature alveolar type II cells that produce pulmonary surfactant are essential for adaptation to extrauterine life. We profiled gene expression in human fetal lung epithelial cells cultured in serum-free medium containing dexamethasone and cyclic AMP, a treatment that induces differentiation of type II cells. Microarray analysis identified 388 genes that were induced > 1.5-fold by 72 h of hormone treatment. Induced genes represented all categories of molecular function and subcellular location, with increased frequency in the categories of ionic channel, cell adhesion, surface film, lysosome, extracellular matrix, and basement membrane. In time-course experiments, self-organizing map analysis identified a cluster of 17 genes that were slowly but highly induced (5- to ? 190-fold) and represented four functional categories: surfactant-related (SFTPC, SFTPA, PGC, SFTPB, LAMP3, LPL), regulatory (WIF2, IGF2, IL1RL1, NR4A2, HIF3A), metabolic (MAOA, ADH1B, SEPP1), and transport (SCNN1A, CLDN18, AQP4). Induction of both mRNA and protein for these genes, which included nine newly identified regulated genes, was confirmed, and cellular localization was determined in both fetal and postnatal tissue. Induction of lysosomal-associated membrane protein 3 required both hormones, and expression was localized to limiting membranes of lamellar bodies. Hormone-induced differentiation of human type II cells is associated with genome-wide increased expression of genes with diverse functions.

Wade, Kelly C.; Guttentag, Susan H.; Gonzales, Linda W.; Maschhoff, Kathryn L.; Gonzales, John; Kolla, Venkatadri; Singhal, Sunil; Ballard, Philip L.



PPARdelta increases expression of the human apolipoprotein A-II gene in human liver cells.  


The peroxisome proliferator-activated receptor delta (PPARdelta) is a transcription factor that regulates genes of importance in lipid and glucose metabolism. ApoA-II is one of the major proteins of the HDL-particle. The aim of this study was to investigate the regulation of apoA-II gene expression by PPARdelta. Treatment of HepG2 cells with the PPARdelta specific agonist GW501516 increased apoA-II mRNA expression. Likewise, reporter gene assays using a construct containing 2.7 kb of the proximal apoA-II promoter showed increased activity after treatment with GW501516, both in HepG2 and in HuH-7 cells. Mutation of two putative PPAR response elements (PPREs) in this region showed that the PPRE at position -737/-717 is the functional site. Binding of PPARdelta to this site was confirmed by chromatin immunoprecipitation and gel retardation analyses. In conclusion, PPARdelta increases the expression of the human apoA-II gene in liver cells via a PPRE in the proximal promoter. PMID:18506377

Thulin, Petra; Glinghammar, Björn; Skogsberg, Josefin; Lundell, Kerstin; Ehrenborg, Ewa



Detection of Gene Expression in Genetically Engineered Microorganisms and Natural Phytoplankton Populations in the Marine Environment by mRNA Analysis  

PubMed Central

A simple method that combines guanidinium isothiocyanate RNA extraction and probing with antisense and sense RNA probes is described for analysis of microbial gene expression in planktonic populations. Probing of RNA sample extracts with sense-strand RNA probes was used as a control for nonspecific hybridization or contamination of mRNA with target DNA. This method enabled detection of expression of a plasmid-encoded neomycin phosphotransferase gene (nptII) in as few as 104Vibrio cells per ml in 100 ml of seawater. We have used this method to detect expression of the ribulose-1,5-bisphosphate carboxylase large-subunit gene (rbcL) in Synechococcus cultures and natural phytoplankton populations in the Dry Tortugas, Florida. During a 36-h diel study, rbcL expression of the indigenous phytoplankton was greatest in the day, least at night (1100, 0300, and 0100 h), and variable at dawn or dusk (0700 and 1900 h). These results are the first report of gene expression in natural populations by mRNA isolation and probing. This methodology should be useful for the study of gene expression in microorganisms released into the environment for agricultural or bioremediation purposes and indigenous populations containing highly conserved target gene sequences. Images

Pichard, Scott L.; Paul, John H.



Multiple light-harvesting II polypeptides from maize mesophyll chloroplasts are distinct gene products.  


The major light-harvesting complex of photosystem II in higher plants is known as LHCII. It is composed of a number of chlorophyll-binding proteins sharing epitopes with each other. The number of apoproteins resolved by fully denaturing sodium dodecylsulfate polyacrylamide gel electrophoresis varies in different species. In order to know if this heterogeneity is caused by the expression of a number of homologous genes or if it is the product of post-translational modifications, we have resolved the six major apoproteins of Zea mays LHCII. Each protein is purified to homogeneity, subjected to direct protein sequencing and the sequences compared with those deduced from lhcb genes in maize and other organisms. All of the six proteins are distinct gene products, since they show differences in their primary structure. Three apoproteins are identified as products of type I lhcb genes and one each as type II and type III gene products. A sixth protein does not fit the requirements for any of the lhcb genes so far cloned and is therefore probably the product of an lhcb gene type not yet described. Our results clearly show that the major source of LHCII protein heterogeneity is the expression of many lhcb genes. Fractionation of maize LHCII by non-denaturing flat-bed isoelectric focusing resolves at least five major isoforms showing distinct differences in their polypeptide composition and also differing in their spectroscopic properties, thus suggesting that individual Lhcb gene products have distinct pigment-binding properties. PMID:10365446

De Luca, C; Varotto, C; Svendsen, I; Polverino De Laureto, P; Bassi, R



[Mutational analysis of the genes encoding the photosystem II proteins in Cyanobacterium synechocystis sp. 6803].  


Chlorophyll--binding protein CP43 and cytochrome b559, encoded by psbC and psbE/F genes, are the components of photosystem II (PS II). Three psbC- and four psbE/F- mutants were isolated from the collection of PS II-deficient mutants of the cyanobacterium Synechocystis sp. 6803. Restoration of photosynthetic activity was achieved by transformation of psbE/F- mutants with cloned psbE/F gene cluster from wild type cells and each of psbC- mutants--with specific part of wild type psbC gene. DNA fragments carrying the mutations were isolated from mutant cells and sequenced. The mutations which affect PS II activity were identified in psbC gene as "frameshift" mutation, stop-codon formation, or as deletion of three nucleotides resulting in loss of one of three Phe residues in position 422-424 of CP43. Sequence of mutant psbE/F genes revealed single mutations resulting in deletion of Phe-36 or substitution of Pro-63 for Leu in alpha-subunit and Val-29 for Phe in beta-subunit of cytochrome b559. PMID:8307353

Elanskaia, I V; Broun, M N; Gadzhiev, A G; Shestakov, S V



Differential expression of the topoisomerase II alpha and beta genes in human breast cancers.  

PubMed Central

Topoisomerase II is a key target for several anti-cancer drugs used for breast cancer therapy, including doxorubicin, epirubicin and mitoxantrone. Two isoforms of topoisomerase II (alpha and beta) have been described in human cells which differ in their subcellular localisation, biochemical properties and susceptibility to inhibition by anti-cancer drugs. The relative level of expression of the alpha and beta isoforms may contribute to the degree of tumour responsiveness to different chemotherapeutic agents. To assess the relationship between expression of topoisomerase II isoforms and established prognostic factors and pathological variables, 56 primary breast tumour samples were studied. The expression of the two topoisomerase II genes was apparently not co-ordinately regulated in these tissue samples. There was no relationship between any of the commonly used pathological variables [tumour size, lymph node status, S-phase fraction (SPF)] and the level of expression of topoisomerase II beta mRNA. However, high topoisomerase II alpha gene expression was significantly associated with a high SPF (sign-rank test; P = 0.01). Moreover, the ratio of mRNA levels for topoisomerase II alpha and beta showed a stronger relationship to SPF (median raito 0.62 for tumours with SPF < 10, and 1.64 for SPF > 10; P = 0.0021, sign-rank test). As expected from previous studies, an SPF > 10 was associated with poor overall survival (P = 0.01). Immunohistochemical analysis revealed that topoisomerase II beta was widely distributed ( > 90% positive tumour cells), but that topoisomerase II alpha expression was less widely expressed, with a pattern of expression similar to that of the proliferation-dependent antigen recognised by Ki67. Because topoisomerase II gene expression showed a log-normal distribution, log-transformed data were used in multivariate analysis of relapse-free survival. This showed that lymph node status and topoisomerase II beta mRNA expression were the only significant survival factors (P = 0.001 and 0.05, respectively, with relative risks of 1.3 and 1.8). These results indicate that topoisomerase II alpha, but not beta, expression is dependent upon cellular proliferation status, but that the more widely expressed topoisomerase II beta protein may play a significant role as a target for anti-tumour therapy. Images Figure 1 Figure 6

Sandri, M. I.; Hochhauser, D.; Ayton, P.; Camplejohn, R. C.; Whitehouse, R.; Turley, H.; Gatter, K.; Hickson, I. D.; Harris, A. L.



A Mutant Neomycin Phosphotransferase II Gene Reduces the Resistance of Transformants to Antibiotic Selection Pressure  

Microsoft Academic Search

The neo (neomycin-resistance) gene of transposon Tn5 encodes the enzyme neomycin phosphotransferase II (EC, which confers resistance to various aminoglycoside antibiotics, including kanamycin and G418. The gene is widely used as a selectable marker in the transformation of organisms as diverse as bacteria, yeast, plants, and animals. We found a mutation that involves a glutamic to aspartic acid conversion

Richard L. Yenofsky; Miriam Fine; John W. Pellow



Relaxation of insulin-like growth factor II gene imprinting implicated in Wilms' tumour  

Microsoft Academic Search

GENOMIC imprinting has been implicated in the onset of several embryonal tumours but the mechanism is not well understood1-3. Maternal chromosome 11p15 loss of heterozygosity4 and paternal chromosome 11 isodisomy5,6 suggest that imprinted genes are involved in the onset of Wilms' tumour and the Beckwith-Wiedemann syndrome. The insulin-like growth factor II (IGF2) gene located at 11pl5.5 has been put forward

Osamu Ogawa; Michael R. Eccles; Jenny Szeto; Leslie A. McNoe; Kankatsu Yun; Marion A. Maw; Peter J. Smith; Anthony E. Reeve



Recent duplication and inter-locus gene conversion in major histocompatibility class II genes in a teleost, the three-spined stickleback  

Microsoft Academic Search

Using a bacterial artificial chromosome (BAC) library, we analysed a 99.5 kb genomic segment containing the major histocompatibility class II genes of a teleost, the three-spined stickleback Gasterosteus aculeatus. Experiments with G. aculeatus have provided direct evidence for balancing selection by pathogens and mate choice driving MH class II beta polymorphism. Two sets of paralogous class II alpha genes and beta

Thorsten B. H. Reusch; Helmut Schaschl; K. Mathias Wegner



Conservation of DNA photolyase genes in group II nucleopolyhedroviruses infecting plusiine insects.  


DNA photolyase genes (phr) encode photoreactive enzymes, which are involved in the repair of UV-damaged DNA. Cyclobutane pyrimidine dimer (CPD) specific photolyase genes are present in nucleopolyhedroviruses isolated from Chrysodeixis chalcites (ChchNPV) and Trichoplusia ni (TnSNPV), insects belonging to the Plusiinae (Noctuidae). To better understand the occurrence and evolution of these genes in baculoviruses, we investigated their possible conservation in other group II NPVs, which infect plusiine insects. A PCR based strategy using degenerate phr-specific primers was designed to detect and analyze possible photolyase genes. Six additional Plusiinae-infecting NPVs were analyzed and all, except Thysanoplusia oricalcea NPV A28-1, which is a group I NPV, contained one or more phr-like sequences. Phylogenetic analysis revealed that all photolyase genes of the tested Plusiinae-infecting baculoviruses group in a single clade, separated into three subgroups. The phylogeny of the polyhedrin sequences of these viruses confirmed that the analyzed viruses also formed a single clade in group II NPVs. We hypothesize that all plusiine group II NPVs contain one or more photolyase genes and that these have a common ancestor. PMID:18513819

Xu, Fang; Vlak, Just M; van Oers, Monique M



Association of transcriptionally active vitellogenin II gene with the nuclear matrix of chicken liver.  

PubMed Central

Supercoiled DNA loops linked to the nuclear matrix can be progressively cleaved with deoxyribonuclease I. The DNA which remains associated with the nuclear matrix can be purified and analysed for vitellogenin II sequence content by dot blot hybridization. Using this technique we show that vitellogenin II gene sequences are selectively associated with the nuclear matrix of liver but not with oviduct of laying hens. Following primary stimulation in immature chicks of vitellogenin synthesis with estradiol, the association of the gene with the nuclear matrix precedes vitellogenin mRNA synthesis. After 15 days when the level of vitellogenin mRNA has returned to zero, the gene is no longer preferentially associated with the nuclear matrix. At this time a second stimulation with estradiol results in a reassociation of the vitellogenin II gene with the nuclear matrix. In addition to the structural gene, both the 3' and 5' end flanking regions (1.5-2 kb) also bind to the nuclear matrix. However, beyond the limit of 1.5-2 kb upstream from the 5' end of the gene, there is no preferential binding of DNA to the nuclear matrix. Images Fig. 1. Fig. 2. Fig. 4.

Jost, J P; Seldran, M



Molecular cloning, sequencing, and expression of the glutamine synthetase II (glnII) gene from the actinomycete root nodule symbiont Frankia sp. strain CpI1.  

PubMed Central

In common with other plant symbionts, Frankia spp., the actinomycete N2-fixing symbionts of certain nonleguminous woody plants, synthesize two glutamine synthetases, GSI and GSII. DNA encoding the Bradyrhizobium japonicum gene for GSII (glnII) hybridized to DNA from three Frankia strains. B. japonicum glnII was used as a probe to clone the glnII gene from a size-selected KpnI library of Frankia strain CpI1 DNA. The region corresponding to the Frankia sp. strain CpI1 glnII gene was sequenced, and the amino acid sequence was compared with that of the GS gene from the pea and glnII from B. japonicum. The Frankia glnII gene product has a high degree of similarity with both GSII from B. japonicum and GS from pea, although the sequence was about equally similar to both the bacterial and eucaryotic proteins. The Frankia glnII gene was also capable of complementing an Escherichia coli delta glnA mutant when transcribed from the vector lac promoter, but not when transcribed from the Frankia promoter. GSII produced in E. coli was heat labile, like the enzyme produced in Frankia sp. strain CpI1 but unlike the wild-type E. coli enzyme. Images

Rochefort, D A; Benson, D R



DNA topoisomerase II is involved in regulation of cyst wall protein genes and differentiation in Giardia lamblia.  


The protozoan Giardia lamblia differentiates into infectious cysts within the human intestinal tract for disease transmission. Expression of the cyst wall protein (cwp) genes increases with similar kinetics during encystation. However, little is known how their gene regulation shares common mechanisms. DNA topoisomerases maintain normal topology of genomic DNA. They are necessary for cell proliferation and tissue development as they are involved in transcription, DNA replication, and chromosome condensation. A putative topoisomerase II (topo II) gene has been identified in the G. lamblia genome. We asked whether Topo II could regulate Giardia encystation. We found that Topo II was present in cell nuclei and its gene was up-regulated during encystation. Topo II has typical ATPase and DNA cleavage activity of type II topoisomerases. Mutation analysis revealed that the catalytic important Tyr residue and cleavage domain are important for Topo II function. We used etoposide-mediated topoisomerase immunoprecipitation assays to confirm the binding of Topo II to the cwp promoters in vivo. Interestingly, Topo II overexpression increased the levels of cwp gene expression and cyst formation. Microarray analysis identified up-regulation of cwp and specific vsp genes by Topo II. We also found that the type II topoisomerase inhibitor etoposide has growth inhibition effect on Giardia. Addition of etoposide significantly decreased the levels of cwp gene expression and cyst formation. Our results suggest that Topo II has been functionally conserved during evolution and that Topo II plays important roles in induction of the cwp genes, which is key to Giardia differentiation into cysts. PMID:23696909

Lin, Bo-Chi; Su, Li-Hsin; Weng, Shih-Che; Pan, Yu-Jiao; Chan, Nei-Li; Li, Tsai-Kun; Wang, Hsin-Chih; Sun, Chin-Hung



Successive silencing of tandem reporter genes in potato (Solanum tuberosum) over 5 years of vegetative propagation  

PubMed Central

Background and Aims Transgenic plants represent an excellent tool for experimental plant biology and are an important component of modern agriculture. Fully understanding the stability of transgene expression is critical in this regard. Most changes in transgene expression occur soon after transformation and thus unwanted lines can be discarded easily; however, transgenes can be silenced long after their integration. Methods To study the long-term changes in transgene expression in potato (Solanum tuberosum), the activity of two reporter genes, encoding green fluorescent protein (GFP) and neomycin phosphotransferase (NPTII), was monitored in a set of 17 transgenic lines over 5 years of vegetative propagation in vitro. Key Results A decrease in transgene expression was observed mainly in lines with higher initial GFP expression and a greater number of T-DNA insertions. Complete silencing of the reporter genes was observed in four lines (nearly 25 %), all of which successively silenced the two reporter genes, indicating an interconnection between their silencing. The loss of GFP fluorescence always preceded the loss of kanamycin resistance. Treatment with the demethylation drug 5-azacytidine indicated that silencing of the NPTII gene, but probably not of GFP, occurred directly at the transcriptional level. Successive silencing of the two reporter genes was also reproduced in lines with reactivated expression of previously silenced transgenes. Conclusions We suggest a hypothetical mechanism involving the successive silencing of the two reporter genes that involves the switch of GFP silencing from the post-transcriptional to transcriptional level and subsequent spreading of methylation to the NPTII gene.

Nocarova, Eva; Opatrny, Zdenek; Fischer, Lukas



Characterization of a Cis-Acting Regulatory Element which Silences Expression of the Class II-A ~ Gene in Epithelium  

Microsoft Academic Search

Summary Class II major histocompatibility complex (MHC) genes encode for oe\\/13 chain pairs that are constitutively expressed principally on mature B cells and dendritic cells in mice. These gene products are easily induced on macrophages with cytokines, and may also aberrantly appear on the surface of epithelium during immune injury. The appearance of class II determinants in parenchymal tissue potentially

Shelley E. Albert; Frank Strutz; Kathleen Shelton; Thomas Haverty; Mac Jane Sun; Shao-ran Li; Amy Denham; Richard A. Maki; Eric G. Neilson


Characterization of photosystem II mutants of Chlamydomonas reinhardii lacking the psbA gene  

Microsoft Academic Search

We have examined 78 chloroplast mutants of Chlamydomonas reinhardii lacking photosystem II activity. Most of them are unable to synthesize the 32 Kdalton protein. Analysis of 22 of these mutants reveals that they have deleted both copies of the psbA gene (which codes for the 32 Kdalton protein) in their chloroplast genome. Although these mutants are able to synthesize and

Pierre Bennoun; Muriel Spierer-Herz; Jeanne Erickson; Jacqueline Girard-Bascou; Yves Pierre; Monique Delosme; J.-D. Rochaix



Characterization of the Major Histocompatibility Complex Class II Genes in Miiuy Croaker  

Microsoft Academic Search

Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. In order to study the molecular function and genomic characteristic of class II genes in teleost, the full lengths of MHC class IIA and IIB cDNA and genomic sequence were cloned from miiuy croaker (Miichthys miiuy). As in other

Tianjun Xu; Yuena Sun; Ge Shi; Yuanzhi Cheng; Rixin Wang; Zhanjiang Liu



Role of the Bradyrhizobium japonicum ntrC gene product in differential regulation of the glutamine synthetase II gene (glnII)  

SciTech Connect

We isolated the ntrC gene from Bradyrhizobium japonicum, the endosymbiont of soybean (Glycine max), and examined its role in regulating nitrogen assimilation. Two independent ntrC mutants were constructed by gene replacement techniques. One mutant was unable to produce NtrC protein, while the other constitutively produced a stable, truncated NtrC protein. Both ntrC mutants were unable to utilize potassium nitrate as a sole nitrogen source. In contrast to wild-type B. japonicum, the NtrC null mutant lacked glnII transcripts in aerobic, nitrogen-starved cultures. However, the truncated-NtrC mutant expressed glnII in both nitrogen-starved and nitrogen-excess cultures. Both mutants expressed glnII under oxygen-limited culture conditions and in symbiotic cells. These results suggest that nitrogen assimilation in B. japonicum is regulated in response to both nitrogen limitation and oxygen limitation and that separate regulatory networks exist in free-living and symbiotic cells.

Martin, G.B.; Chapman, K.A.; Chelm, B.K. (Michigan State Univ., East Lansing (USA))



Transactivation of mouse insulin-like growth factor II (IGF-II) gene promoters by the AP-1 complex.  

PubMed Central

The mouse insulin-like growth factor II gene (Igf2) is transcribed from three promoters (P1, P2 and P3), and is expressed in a tissue-specific and developmentally regulated fashion; however, little information is available on the transcription factors controlling Igf2 expression. The AP-1 complex is a transcription factor involved in the regulation of a variety of genes, including those encoding certain growth factors. We show that Igf2 P3 is transactivated by AP-1 in a transient expression assay, and that this effect is mediated through two non-consensus AP-1 binding sites characterised by DNA-protein interaction studies. Mutational analysis indicates these sites are required for AP-1 responsiveness and full promoter activity. Images

Caricasole, A; Ward, A



Expression Regulation of Major Histocompatibility Complex Class I and Class II Encoding Genes  

PubMed Central

Major histocompatibility complex (MHC)-I and MHC-II molecules play an essential role in the immune response to pathogens by virtue of their ability to present peptides to CD8+ and CD4+ T cells, respectively. Given this critical role, MHC-I and MHC-II genes are regulated in a tight fashion at the transcriptional level by a variety of transcription factors that interact with conserved cis-acting regulatory promoter elements. In addition to the activities of these regulatory factors, modification of chromatin also plays an essential role in the efficient transcription of these genes to meet with local requirement for an effective immune response. The focus of this review is on the transcription factors that interact with conserved cis-acting promoter elements and the epigenetic mechanisms that modulate induced and constitutive expression of these MHC genes.

van den Elsen, Peter J.



Transcriptional effects of the signal transduction protein P(II) (glnB gene product) on NtcA-dependent genes in Synechococcus sp. PCC 7942.  


P(II) proteins signal the cellular nitrogen status in numerous bacteria, and in cyanobacteria P(II) is subjected to serine phosphorylation when the cells experience a high C to N balance. In the unicellular cyanobacterium Synechococcus sp. PCC 7942, the P(II) protein (glnB gene product) is known to mediate the ammonium-dependent inhibition of nitrate and nitrite uptake. The analysis of gene expression through RNA/DNA hybridization indicated that a P(II)-null mutant was also impaired in the induction of NtcA-dependent, nitrogen assimilation genes amt1 (ammonium permease), glnA (glutamine synthetase) and nir (nitrite reductase), as well as of the N-control gene ntcA, mainly under nitrogen deprivation. This gene expression phenotype of the glnB mutant could be complemented by wild-type P(II) protein or by modified P(II) proteins that cannot be phosphorylated and mimic either the phosphorylated (GlnB(S49D) and GlnB(S49E)) or unphosphorylated (GlnB(S49A)) form of P(II). However, strains carrying the GlnB(S49D) and GlnB(S49E) mutant proteins exhibited higher levels of expression of nitrogen-regulated genes than the strains carrying the wild-type P(II) or the GlnB(S49A) protein. PMID:12753902

Paz-Yepes, Javier; Flores, Enrique; Herrero, Antonia



Characterization of MHC class II genes from an ancient reptile lineage, Sphenodon (tuatara).  


The organization and evolution of major histocompatibility complex (MHC) genes vary considerably among vertebrate lineages. MHC genes have been well characterized in mammals, birds, amphibians and fish, but little is known about their organization in reptiles, despite the fact that reptiles occupy an important phylogenetic position for understanding the evolutionary history of both mammalian and avian MHC genes. Here we describe the characterization of the first MHC class II B cDNA sequences from a non-avian reptile, the tuatara (Sphenodon spp.). Three class II B sequences were isolated from a tuatara cDNA library, and four additional partial sequences were isolated by reverse transcriptase-polymerase chain reaction. Six of these sequences appear to belong to the same gene family, which we have named SppuDAB. The remaining sequence (named SppuDBB) shares only 43.9% amino acid similarity with SppuDAB and thus appears to represent a separate gene family. SppuDBB may be a non-classical locus as it does not contain all the conserved residues expected of a classical MHC class II gene. Southern blot analysis indicates that only a single copy of SppuDBB exists in tuatara, but that multiple loci related to SppuDAB are present. The SppuDAB sequences have the highest amino acid similarity (57.2-62.4%) with class II B sequences from the spectacled caiman, but only 26.4-48.7% similarity with sequences from other vertebrates. The tuatara sequences do not strongly group with other reptile sequences on a phylogenetic tree, reflecting the antiquity of the Sphenodon lineage and the lack of closely related sequences for comparison. PMID:16261382

Miller, Hilary C; Belov, Katherine; Daugherty, Charles H



MHC class II and non-MHC class II genes differentially influence humoral immunity to Bacillus anthracis lethal factor and protective antigen.  


Anthrax Lethal Toxin consists of Protective Antigen (PA) and Lethal Factor (LF), and current vaccination strategies focus on eliciting antibodies to PA. In human vaccination, the response to PA can vary greatly, and the response is often directed toward non-neutralizing epitopes. Variable vaccine responses have been shown to be due in part to genetic differences in individuals, with both MHC class II and other genes playing roles. Here, we investigated the relative contribution of MHC class II versus non-MHC class II genes in the humoral response to PA and LF immunization using three immunized strains of inbred mice: A/J (H-2k at the MHC class II locus), B6 (H-2b), and B6.H2k (H-2k). IgG antibody titers to LF were controlled primarily by the MHC class II locus, whereas IgG titers to PA were strongly influenced by the non-MHC class II genetic background. Conversely, the humoral fine specificity of reactivity to LF appeared to be controlled primarily through non-MHC class II genes, while the specificity of reactivity to PA was more dependent on MHC class II. Common epitopes, reactive in all strains, occurred in both LF and PA responses. These results demonstrate that MHC class II differentially influences humoral immune responses to LF and PA. PMID:23342680

Garman, Lori; Dumas, Eric K; Kurella, Sridevi; Hunt, Jonathan J; Crowe, Sherry R; Nguyen, Melissa L; Cox, Philip M; James, Judith A; Farris, A Darise



RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes  

Microsoft Academic Search

We investigated co-transcriptional recruitment of pre-mRNA processing factors to human genes. Capping factors associate with paused RNA polymerase II (pol II) at the 5? ends of quiescent genes. They also track throughout actively transcribed genes and accumulate with paused polymerase in the 3? flanking region. The 3? processing factors cleavage stimulation factor and cleavage polyadenylation specificity factor are maximally recruited

Kira Glover-Cutter; Soojin Kim; Joaquin Espinosa; David L Bentley



Hemizygous mice for the angiotensin II type 2 receptor gene have attenuated susceptibility to azoxymethane-induced colon tumorigenesis  

Microsoft Academic Search

Evidence suggests that the use of angiotensin-converting enzyme inhibitors potentially reduces the risk of cancer, though the mechanism is unclear. To clarify a potential involvement of angiotensin II (Ang II) signaling in cancer risk, we have examined the effect of Ang II receptor deficiency on azoxymethane (AOM)-induced colon tumori- genesis. Male Ang II type 2 receptor gene-disrupted (AT2-null) mice with

Tetsuo Takagi; Yuichiro Nakano; Susumu Takekoshi; Tadashi Inagami; Masaaki Tamura


Human chromosomal mapping of genes for insulin-like growth factors I and II and epidermal growth factor  

Microsoft Academic Search

Many of the actions previously attributed to pituitary-derived growth hormone are mediated by polypeptide growth factors1-3. These include the insulin-like growth factors I and II (IGF-I and IGF-II)4-6, which are members of the insulin family of proteins7. We report here the chromosomal mapping of the human genes for IGF-I and IGF-II. IGF-II maps to the short arm of chromosome 11,

Jane E. Brissenden; Axel Ullrich; Uta Francke



Major histocompatibility (MH) class II B gene polymorphism influences disease resistance of common carp ( Cyprinus carpio L.)  

Microsoft Academic Search

Genes of the major histocompatibility complex (MHC) are crucial elements of adaptive immunity. High polymorphism renders the MHC genes highly suitable for studies on association with disease resistance. In common carp (Cyprinus carpio L.), there are two paralogous groups of MH class II B genes, Cyca-DAB1-like and Cyca-DAB3-like genes. The Cyca-DAB1-like genes especially, could be linked to high polymorphism and

Krzysztof ?. Rakus; Geert F. Wiegertjes; Patrycja Jurecka; Peter D. Walker; Andrzej Pilarczyk; Ilgiz Irnazarow



Embryo and anther regulation of the mabinlin II sweet protein gene in Capparis masaikai Lévl.  


Mabinlin II is one of the major sweet proteins stored in the seeds of Capparis masaikai Lévl. Its promoter region (779 bp) located 5' upstream of the mabinlin II gene has been isolated and named as MBL-779 (GenBank accession number, EU014073). This promoter contains two typical TATA box regions and a series of motifs related to seed-specific promoters, such as ACGT motifs, RY motif, napin motif, and G box. The MBL-779 promoter drove GUS gene to transiently express in the embryos of bean, maize, and rice seeds or to constantly express in the embryos and anthers of the transgenic Arabidopsis. The MBL-779 promoter regulated gene expression from approximately the 12th day and peaked on approximately the 16th day after flowering in Arabidopsis. The -300-bp promoter region is a minimal sequence required to functionally regulate gene expression. The CAATs at -325 to -322 bp and -419 to -416 bp and the region at -485 to -770 bp play a role in the quantitative regulation of gene expression. The RY motif, CATGAC, at -117 to -112 bp and the ACGT within the G box (CACGTG) at -126 to -123 bp positively regulate gene expression. PMID:19266222

Hu, Xin-Wen; Liu, Si-Xin; Guo, Jian-Chun; Li, Ji-Tao; Duan, Rui-Jun; Fu, Shao-Ping



ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.  


Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction database (ATTED-II) that provides co-regulated gene relationships based on co-expressed genes deduced from microarray data and the predicted cis elements. ATTED-II ( includes the following features: (i) lists and networks of co-expressed genes calculated from 58 publicly available experimental series, which are composed of 1388 GeneChip data in A.thaliana; (ii) prediction of cis-regulatory elements in the 200 bp region upstream of the transcription start site to predict co-regulated genes amongst the co-expressed genes; and (iii) visual representation of expression patterns for individual genes. ATTED-II can thus help researchers to clarify the function and regulation of particular genes and gene networks. PMID:17130150

Obayashi, Takeshi; Kinoshita, Kengo; Nakai, Kenta; Shibaoka, Masayuki; Hayashi, Shinpei; Saeki, Motoshi; Shibata, Daisuke; Saito, Kazuki; Ohta, Hiroyuki



Inflammatory bowel disease associations with HLA Class II genes  

SciTech Connect

A PCR-SSOP assay has been used to analyze HLA-Class II DRB1 and DQB1 alleles in 378 Caucasians from a population in Southern California. The data has been analyzed separately for the Ashkenasi Jews and non-Jewish patients (n=286) and controls (n=92). Two common clinical forms of inflammatory bowel disease (IBD) have been studied: ulcerative colitis (UC) and Crohn`s disease (CD). In CD, we observed a susceptible effect with the rare DR1 allele - DRB*0103 [O.R.=4.56; 95% CI (0.96, 42.97); p=0.03]; a trend for an increase in DRB1*0103 was also observed in UC patients. A susceptible effect with DRB1*1502 [O.R.=5.20; 95% CI (1.10, 48.99); p=0.02] was observed in non-Jewish UC patients. This susceptible effect was restricted to UC ANCA-positive (antineutrophil cytoplasmic antibodies) patients. In addition, a significant association with DRB1*1101-DQB1*0301 [O.R.=9.46; 95% CI (1.30, 413.87); p=0.01] was seen with UC among non-Jewish patients: this haplotype was increased with CD among non-Jewish patients. Two protective haplotypes were detected among CD non-Jewish patients: DRB1*1301-DQB1*0603 [O.R.=0.34; 95% CI (0.09, 1.09); p=0.04], and DRB*0404-DQB1*0302 [O.R.=<0.08; 95% CI (0.0, 0.84); p=0.01]. When the same data were analyzed at the serology level, we observed a positive association in UC with DR2 [O.R.6.77; 95% CI (2.47, 22.95); p=2 x 10{sup -4}], and a positive association in CD with DR1 [O.R.=2.63; 95% CI (1.14, 6.62); p=0.01] consistent with previous reports. Thus, some IBD disease associations appear to be common to both UC and CD, while some are unique to one disease.

Castro, R. [Cedars-Sinai Medical Center, Los Angeles, CA (United States); Yang, H.; Targan, S. [Roche Molecular Systems, Inc., Alameda, CA (United States)] [and others



Evolution of major histocompatibility complex class I and class II genes in the brown bear  

PubMed Central

Background Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae. Results We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Conclusions Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South–north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia.



Identification of a Melanosomal Membrane Protein Encoded by the PinkEyed Dilution (Type II Oculocutaneous Albinism) Gene  

Microsoft Academic Search

The pink-eyed dilution (p) locus in the mouse is critical to melanogenesis; mutations in the homologous locus in humans, P, are a cause of type II oculocutaneous albinism. Although a cDNA encoded by the p gene has recently been identified, nothing is known about the protein product of this gene. To characterize the protein encoded by the p gene, we

Susana Rosemblat; Donna Durham-Pierre; John M. Gardner; Yoshimichi Nakatsu; Murray H. Brilliant; Seth J. Orlow



Class II cytokine receptor gene cluster is a major locus for hepatitis B persistence  

PubMed Central

Persistent hepatitis B virus infection is a major risk factor for hepatocellular carcinoma, the most frequent cancer in some developing countries. Up to 95% of those infected at birth and 15% of those infected after the neonatal period fail to clear hepatitis B virus, together resulting in ?350 million persistent carriers worldwide. Via a whole genome scan in Gambian families, we have identified a major susceptibility locus as a cluster of class II cytokine receptor genes on chromosome 21q22. Coding changes in two of these genes, the type I IFN receptor gene, IFN-AR2, and the IL-10RB gene that encodes a receptor chain for IL-10-related cytokines including the IFN-?s, are associated with viral clearance (haplotype P value = 0.0003), and in vitro assays support functional roles for these variants in receptor signaling.

Frodsham, Angela J.; Zhang, Lyna; Dumpis, Uga; Taib, Nor Azizah Mohd; Best, Steve; Durham, Andrew; Hennig, Branwen J. W.; Hellier, Simon; Knapp, Susanne; Wright, Mark; Chiaramonte, Maria; Bell, John I.; Graves, Mary; Whittle, Hilton C.; Thomas, Howard C.; Thursz, Mark R.; Hill, Adrian V. S.



Study on the Imprinting Status of Insulin-Like Growth Factor II (IGF-II) Gene in Villus during 6-10 Gestational Weeks  

PubMed Central

Objective. To compare the difference of imprinting status of insulin-like growth factor II (IGF-II) gene in villus between normal embryo development group and abnormal embryo development group and to investigate the relationship between karyotype and the imprinting status of IGF-II gene. Methods. A total of 85 pregnant women with singleton pregnancy were divided into two groups: one with abnormal embryo development (n = 38) and the other with normal embryo development (n = 47). Apa I polymorphism of IGF-II gene in chorionic villus was assayed with reverse transcriptase polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). The relationship between chromosomal abnormal karyotype and IGF-II gene imprinting status was analyzed by primary cell culture and G-banding chromosomal karyotype analysis. Results. IGF-II imprinting loss rate was higher in the abnormal embryo development group than the normal embryo development group (44.7% versus 31.6%), but without significant difference (P > .05). The percentage of abnormal chromosomes of chorionic villus in the abnormal embryo development group was 42.5%, in which IGF-II imprinting loss rate reached 64.7%. No abnormal karyotypes were found in the normal embryo development group. However, there was significant difference in IGF-II imprinting loss rate between two groups (P > .05). Conclusion. During weeks 6–10 of gestation, abnormal embryonic development is correlated with chromosomal abnormalities. The imprinting status of IGF-II gene played important roles in embryonic development, and imprinting loss might be related to chromosomal abnormalities.

Chen, Jianhong; Fang, Qun; Chen, Baojiang; Zhou, Yi; Luo, Yanmin



Molecular analysis of iduronate -2- sulfatase gene in Tunisian patients with mucopolysaccharidosis type II  

PubMed Central

Mucopolysaccharidosis type II (MPS II, Hunter syndrome) is X-linked recessive lysosomal storage disorder resulting from the defective activity of the enzyme iduronate-2-sulfatase (IDS). Hunter disease can vary from mild to severe, depending on the level of enzyme deficiency. We report the IDS mutation and polymorphisms causing the Hunter syndrome in patients from one family in Tunisia Patients and methods A preliminary diagnosis was made by qualitative detection of urinary glycosaminoglycans of the suspected MPS II probands. The IDS mutation and polymorphisms were determined on these probands and their family members by amplifying and sequencing each of the exons and intron-exon junctions of IDS gene. Results The studied probands were homoallelic for p.R88P mutation. In addition, three known polymorphisms/sequence variants: IVS3-16 (c.419-16 delT), T214M (c.641C > T), T146T (c.438 C > T), IVS5-87(c.709-87G > A) and one previously unknown: IVS7+38(c.1006+38T > C were identified in the MPS II patients. These are the first Tunisian MPS II patients to be genotyped. Conclusion The identification of these mutation and polymorphisms and their genotype-phenotype correlation should facilitate prenatal diagnosis and counseling for MPS II in Tunisia, where a very high rate of consanguinity exists.



Coordinate amplification of metallothionein I and II gene sequences in cadmium-resistant CHO variants  

SciTech Connect

Cadmium-resistanc (Cd/sup r/) variants of the Chinese hamster cell line, CHO, have been derived by stepwise selection for growth in medium containing CdCl/sub 2/. These variants show coordinately increased production of both metallothionein (MT) I and II and were stably resistant to Cd/sup 2 +/ in the absence of continued selection. Genomic DNAs from these Cd/sup r/ sublines were analyzed for both MT gene copy number and MT gene organization, using cDNA sequence probes specific for each of the two Chinese hamster isometallothioneins. These analyses revealed coordinate amplification of MT I and II genes in all Cd/sup r/ variants which had increased copies of MT-encoding sequences. In situ hybridization of an MT-encoding probe to mitotic chromosomes of a Cd/sup r/ variant, which has amplified MT genes at least 14-fold, revealed a single chromosomal site of hybridization. These results suggest that the isoMTs constitute a functionally related gene cluster which amplifies coordinately in response to toxic metal stress.

Hildebrand, C.E.; Crawford, B.D.; Enger, M.D.



Characterization and evolution of MHC class II B genes in Ardeid birds.  


Major histocompatibility complex (MHC) is a multi-gene family that is very suitable to investigate a wide range of open questions in evolutionary ecology. In this study, we characterized two expressed MHC class II B genes (DAB1 and DAB2) in the Grey Heron (Aves: Ardea cinerea). We further developed the primer pairs to amplify and sequence two MHC class II B loci in ten ardeid birds. Phylogenetic analysis revealed that different parts of the genes showed different evolutionary patterns. The exon 2 sequences tended to cluster two gene-specific lineages. In each lineage, exon 2 sequences from several species showed closer relationships than sequences within species, and two shared identical alleles were found between species (Egretta sacra and Nycticorax nycticorax; Egretta garzetta and Bubulcus ibis), supporting the hypothesis of trans-species polymorphism. In contrast, the species-specific intron 2 plus partial exon 3 tree suggested that DAB1 and DAB2 were subject to concerted evolution. GENECONV analyses showed the gene exchange played an important role in the ardeid MHC evolution. PMID:21590337

Li, Li; Zhou, Xiaopin; Chen, Xiaolin



Characterization of the Major Histocompatibility Complex Class II Genes in Miiuy Croaker  

PubMed Central

Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. In order to study the molecular function and genomic characteristic of class II genes in teleost, the full lengths of MHC class IIA and IIB cDNA and genomic sequence were cloned from miiuy croaker (Miichthys miiuy). As in other teleost, four exons and three introns were identified in miiuy croaker class IIA gene; but the difference is that six exons and five introns were identified in the miiuy croaker class IIB gene. The deduced amino acid sequence of class IIA and class IIB had 26.3–85.7% and 11.0–88.8% identity with those of mammal and teleost, respectively. Real-time quantitative RT-PCR demonstrated that the MHC class IIA and IIB were ubiquitously expressed in ten normal tissues; expression levels of MHC genes were found first upregulated and then downregulated, and finally by a recovery to normal level throughout the pathogenic bacteria infection process. In addition, we report on the underlying mechanism that maintains sequences diversity among many fish species. A series of site-model tests implemented in the CODEML program revealed that positive Darwinian selection is likely the cause of the molecular evolution in the fish MHC class II genes.

Xu, Tianjun; Sun, Yuena; Shi, Ge; Cheng, Yuanzhi; Wang, Rixin



DNA typing of HLA class II genes in native inhabitants of Chukotka  

SciTech Connect

Polymorphism of HLA class II genes was studied in native Chukotka inhabitants with the use of DNA oligotyping. The characteristics of the distribution of allelic variants of the loci HLA-DRB1, -DQA1, -DQB1, and -DPB1 were revealed; they were similar to those of other Subarctic Mongoloid populations and different from those for comparable populations of other climatic and geographic zones. Our data suggest that the specific features found for the distributions of some alleles of the loci examined are related to the geographic variation in the HLA gene system studied. 20 refs., 4 tabs.

Krylov, M.Yu.; Erdesz, S.; Alexeeva, L.I. [Institute of Rheumatology, Moscow (Russian Federation)



[Genetic transformation of OSISAP1 gene to onion (Allium cepa L.) mediated by amicroprojectile bombardment].  


Microprojectile bombardment-mediated transformation method has been developed for onion (Allium cepa L.) using embryogenic calli, induced from stem discs, as target tissue. Zinc-finger protein gene OSISAP1 (Oryza sative subspecies indica stress-associated protein gene) was introduced into the open-pollinated onion cultivar (subs.) 'HG400B'. Bombardment parameters were optimized as: the pressure is 1,100 psi, the distance is 6 cm, two times, the ratio of mass between plasmid DNA and golden particles is 1:320. An efficient microprojectile bombardment-mediated transformation system of onion (Allium cepa L.) callus has been established. The binary vector used carried the nptII gene for kanamycin resistance and the GUS reporter gene. Transgenic cultures were screened for their ability to express the GUS reporter gene and to grow in the presence of kanamycin (150 mg/L). Transient expression of GUS reporter gene was observed through histochemical staining of embryogenic callus transformed by microprojectile bombardment. The putative transgenic plants were analysed at the molecular level using PCR, southern hybridization, and RT-PCR. The results confirmed that the OSISAP1 gene was integrated as one copy into the genome of onion and expression. Transgenic plants were produced efficiently with a transformation frequency of about 10%. Test of salinity-alkali stress showed that sodium chloride and sodium bicarbonate at 200 mmol/L effectively killed non-transgenic plants within 1 week of irrigation, while the transgenic plants were completely unaffected by salinity of 400 mmol/L. So transformation with the OSISAP1 gene raised the salinity-alkali-tolerance of the transgenic plants to a high level. PMID:17556805

Xu, Qi-Jiang; Cui, Cheng-Ri



Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler  

PubMed Central

Background The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. There are two bat genome projects currently underway, a circumstance that promises to speed the discovery host factors important in the coevolution of bats with their viruses. These genomes, however, are not yet assembled and one of them will provide only low coverage, making the inference of most genes of immunological interest error-prone. Many more wildlife genome projects are underway and intend to provide only shallow coverage. Results We have developed a statistical method for the assembly of gene families from partial genomes. The method takes full advantage of the quality scores generated by base-calling software, incorporating them into a complete probabilistic error model, to overcome the limitation inherent in the inference of gene family members from partial sequence information. We validated the method by inferring the human IFNA genes from the genome trace archives, and used it to infer 61 type-I interferon genes, and single type-II interferon genes in the bats Pteropus vampyrus and Myotis lucifugus. We confirmed our inferences by direct cloning and sequencing of IFNA, IFNB, IFND, and IFNK in P. vampyrus, and by demonstrating transcription of some of the inferred genes by known interferon-inducing stimuli. Conclusion The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.



Regulation of Nrf2-Mediated Phase II Detoxification and Anti-oxidant Genes  

PubMed Central

The molecular mechanisms by which a variety of naturally-occurring dietary compounds exert chemopreventive effects have been a subject of intense scientific investigations. Induction of phase II detoxification and anti-oxidant enzymes through activation of Nrf2/ARE-dependent gene is recognized as one of the major cellular defense mechanisms against oxidative or xenobiotic stresses and currently represents a critical chemopreventive mechanism of action. In the present review, the functional significance of Keap1/Nrf2 protein module in regulating ARE-dependent phase II detoxification and anti-oxidant gene expression is discussed. The biochemical mechanisms underlying the phosphorylation and expression of Keap1/Nrf2 proteins that are controlled by the intracellular signaling kinases and ubiquitin-mediated E3 ligase system as well as control of nucleocytoplasmic translocation of Nrf2 by its innate nuclear export signal (NES) are described.

Keum, Young-Sam



Mutations in the human CYP11B2 (aldosterone synthase) gene causing corticosterone methyloxidase II deficiency.  

PubMed Central

Corticosterone methyloxidase II (CMO-II) deficiency is an autosomal recessive disorder of aldosterone biosynthesis, characterized by an elevated ratio of 18-hydroxycorticosterone to aldosterone in serum. It is genetically linked to the CYP11B1 and CYP11B2 genes that, respectively, encode two cytochrome P450 isozymes, P450XIB1 and P450XIB2. Whereas P450XIB1 only catalyzes hydroxylation at position 11 beta of 11-deoxycorticosterone and 11-deoxycortisol, P450XIB2 catalyzes the synthesis of aldosterone from deoxycorticosterone, a process that successively requires hydroxylation at positions 11 beta and 18 and oxidation at position 18. To determine the molecular genetic basis of CMO-II deficiency, seven kindreds of Iranian-Jewish origin were studied in which members suffered from CMO-II deficiency. No mutations were found in the CYP11B1 genes, but two candidate mutations, R181W and V386A, were found in the CYP11B2 genes. When these mutations were individually introduced into CYP11B2 cDNA and expressed in cultured cells, R181W reduced 18-hydroxylase and abolished 18-oxidase activities but left 11 beta-hydroxylase activity intact, whereas V386A caused a small but consistent reduction in the production of 18-hydroxycorticosterone. All individuals affected with CMO-II deficiency were homozygous for both mutations, whereas eight asymptomatic subjects were homozygous for R181W alone and three were homozygous for V386A alone. These findings confirm that P450XIB2 is the major enzyme mediating oxidation at position 18 in the adrenal and suggest that a small amount of residual activity undetectable in in vitro assays is sufficient to synthesize normal amounts of aldosterone. Images

Pascoe, L; Curnow, K M; Slutsker, L; Rosler, A; White, P C



Novel and recurrent tyrosine aminotransferase gene mutations in tyrosinemia typeII  

Microsoft Academic Search

Tyrosinemia typeII (Richner-Hanhart syndrome, RHS) is a disorder of autosomal recessive inheritance characterized by keratitis,\\u000a palmoplantar hyperkeratosis, mental retardation, and elevated blood tyrosine levels. The disease results from deficiency in\\u000a hepatic tyrosine aminotransferase (TAT). We have previously described one deletion and six different point mutations in four\\u000a RHS patients. We have now analyzed the TAT genes in a further seven

Regina Hühn; Heike Stoermer; Beate Klingele; Elke Bausch; Alberto Fois; Mariangela Farnetani; Maja Di Rocco; Joelle Boué; Jean M. Kirk; Rosalind Coleman; G. Scherer



IGF-II gene region polymorphisms related to exertional muscle damage  

Microsoft Academic Search

ABSTRACT We examined the association of a novel SNP in IFG-I (IGF-I -C1245T located in the promoter) and eight SNPs in the IGF-II gene region with indicators of muscle damage (strength loss, muscle soreness, and increases in circulating levels of creatine kinase [CK] and myoglobin) after eccentric exercise. We also examined 2 SNPs in the IGF binding protein-3 (IGFBP-3). The

Joseph M. Devaney; Eric P. Hoffman; Heather Gordish-Dressman; Amy Kearns; Edward Zambraski; Priscilla M. Clarkson



PapilioPhylogeny Based on Mitochondrial Cytochrome Oxidase I and II Genes  

Microsoft Academic Search

Butterflies of the genusPapiliohave served as the basis for numerous studies in insect physiology, genetics, and ecology. However, phylogenetic work on relationships among major lineages in the genus has been limited and inconclusive. We have sequenced 2.3 kb of DNA from the mitochondrial cytochrome oxidase I and II genes (COI and COII) for 23Papiliotaxa and two outgroups,Pachliopta neptunusandEurytides marcellus,in order

Michael S. Caterino; Felix A. H. Sperling



Gene Duplication and the Evolution of Group II Chaperonins: Implications for Structure and Function  

Microsoft Academic Search

Chaperonins are multisubunit protein-folding assemblies. They are composed of two distinct structural classes, which also have a characteristic phylogenetic distribution. Group I chaperonins (called GroEL\\/cpn60\\/hsp60) are present in Bacteria and eukaryotic organelles while group II chaperonins are found in Archaea (called the thermosome or TF55) and the cytoplasm of eukaryotes (called CCT or TriC). Gene duplication has been an important

John M. Archibald; Christian Blouin; W. Ford Doolittle



The isolation and characterisation of type II metallothionein-like genes from tomato (Lycopersicon esculentum L.)  

Microsoft Academic Search

Two cDNAs encoding putative metallothionein (MT)-like peptides have been isolated from tomato (L. esculentum L.). The predicted protein products of these two cDNAs (LeMTA and LeMTB) are 72 and 83 amino acids respectively and both encode peptides with arrangements of cysteine residues characteristic of type II plant MTs. In other plants which possess more than one gene expressing MT proteins

C. A. Whitelaw; J. A. Le Huquet; D. A. Thurman; A. B. Tomsett



The zinc finger proteins ZXDA and ZXDC form a complex that binds CIITA and regulates MHC II gene transcription.  


The transcription of major histocompatibility complex class II (MHC II) genes depends critically upon the activity of the class II trans-activator (CIITA) protein. We previously described a novel CIITA-binding protein named zinc finger X-linked duplicated family member C (ZXDC) that contributes to the activity of CIITA and the transcription of MHC II genes. Here, we examined the contribution of a closely related family member of ZXDC, the ZXDA protein, to MHC II gene transcription. ZXDA has a domain organization similar to ZXDC, containing ten zinc fingers and a transcriptional activation domain. Knockdown and overexpression of ZXDA demonstrated its importance in the transcriptional activation of MHC II genes. We found that ZXDA and ZXDC can self-associate, and also form a complex with each other. The regions of the two proteins that contain zinc fingers mediate these interactions. Importantly, we found that the ZXDA-ZXDC complex interacts with CIITA, rather than either protein alone. Given our additional finding that ZXDC is present at MHC II promoters in HeLa cells, prior to and after treatment with IFN-gamma, it appears that ZXDA and ZXDC form an important regulatory complex for MHC II gene transcription. PMID:17493635

Al-Kandari, Wafa; Koneni, Rupa; Navalgund, Vandana; Aleksandrova, Anastasiia; Jambunathan, Srikarthika; Fontes, Joseph D



The zinc finger proteins ZXDA and ZXDC form a complex that binds CIITA and regulates MHC II gene transcription  

PubMed Central

Summary The transcription of major histocompatibility complex class II (MHC II) genes depends critically upon the activity of the class II trans-activator (CIITA) protein. We previously described a novel CIITA-binding protein named zinc finger X-linked duplicated family member C (ZXDC) that contributes to the activity of CIITA and the transcription of MHC II genes. In the present study, we examined the contribution of a closely related family member of ZXDC, the ZXDA protein, to MHC II gene transcription. ZXDA has a domain organization similar to ZXDC, containing ten zinc fingers and a transcriptional activation domain. Knockdown and overexpression of ZXDA demonstrated its importance in the transcriptional activation of MHC II genes. We found that ZXDA and ZXDC can self-associate, and also form a complex with each other. The regions of the two proteins that contain zinc fingers mediate these interactions. Importantly, we found that the ZXDA-ZXDC complex interacts with CIITA, rather than either protein alone. Given our additional finding that ZXDC is present at MHC II promoters in HeLa cells, prior to and after treatment with IFN-?, it appears that ZXDA and ZXDC form an important regulatory complex for MHC II gene transcription.

Al-Kandari, Wafa; Koneni, Rupa; Navalgund, Vandana; Aleksandrova, Anastasiia; Jambunathan, Srikarthika



Regulation of MHC class II gene expression, genetic variation and disease  

PubMed Central

Major histocompatibility complex (MHC) class II molecules are central to adaptive immune responses and maintenance of self-tolerance. Since the early 1970s the MHC class II region at chromosome 6p21 has been shown to be associated with a remarkable number of autoimmune, inflammatory and infectious diseases. Given that a full explanation for most MHC class II disease associations has not been reached through analysis of structural variation alone, in this review we explore the role of genetic variation in modulating gene expression. We describe the intricate architecture of the MHC class II regulatory system, indicating how its unique characteristics may relate to observed associations with disease. There is evidence that haplotype-specific variation involving proximal promoter sequences can alter the level of gene expression, potentially modifying the emergence and expression of key phenotypic traits. Although much emphasis has been placed on cis-regulatory elements, we also explore the role of more distant enhancer elements together with the evidence of dynamic inter- and intra-chromosomal interactions and epigenetic processes. The role of genetic variation in such mechanisms may hold profound implications for susceptibility to common disease.

Handunnetthi, Lahiru; Ramagopalan, Sreeram V.; Ebers, George C.; Knight, Julian C.



Correction of renal tubular acidosis in carbonic anhydrase II-deficient mice with gene therapy.  

PubMed Central

Carbonic anhydrase II (CAII) deficiency in humans is associated with a syndrome of renal tubular acidosis, osteopetrosis, and cerebral calcification. A strain of mice of CAII deficiency due to a point mutation also manifests renal tubular acidosis. We report here that retrograde injection of cationic liposome complexed with a CAII chimeric gene, using a cytomegalovirus (CMV) promoter/enhancer as an expression cassette to drive human CAII cDNA, into the renal pelvis of CAII-deficient mice results in expression of CAII in the kidney. The levels of both the CAII gene and its corresponding mRNA were highest by day 3 after treatment, diminishing thereafter, but remaining detectable by 1 mo. After gene therapy, CAII-deficient mice restored the ability to acidify urine after oral administration of ammonium chloride. The ability to acidify urine was maintained at 3 wk after gene therapy, and was eventually lost by 6 wk. Immunohistochemistry studies using anti-CAII antibodies showed that CAII was expressed in tubular cells of the outer medulla and corticomedullary junction. The gene therapy was not associated with nephrotoxicity as assessed by blood urea nitrogen levels and renal histology. To our knowledge, this is the first successful gene therapy of a genetic renal disease. Our results demonstrate the potential of gene therapy as a novel treatment for hereditary renal tubular defects.

Lai, L W; Chan, D M; Erickson, R P; Hsu, S J; Lien, Y H



MHC Class II ? Genes in the Endangered Hainan Eld's Deer (Cervus eldi hainanus).  


Contrary to neutral markers, the major histocompatibility complex (MHC) can reflect the fitness and adaptive potential of a given species due to its association with the immune system. For this reason, the use of MHC in endangered wildlife management has increased greatly in recent years. Here, we isolated complementary DNA (cDNA) and genomic DNA (gDNA) sequences to characterize the MHC class II ? genes in Hainan Eld's deer (Cervus eldi hainanus), a highly endangered cervid, which recovered from a severe population bottleneck consisting of 26 animals. Analysis of 7 individuals revealed the presence of 3 DRB and 3 DQB putatively functional gDNA sequences. The Ceel-DRB and DQB sequences displayed high variability in exon 2, and most nonsynonymous substitutions were detected in this region. Phylogenetic analysis indicated that trans-species evolution of MHC class II ? might occur in the Cervinae subfamily. Comparison of the number of sequences between gDNA and cDNA revealed that all sequences isolated from the genome were detectable in the cDNA libraries derived from different tissues (including the liver, kidney, and spleen), suggesting none of these sequences were derived from silent genes or pseudogenes. Characterization of the MHC class II ? genes may lay the foundation for future studies on genetic structure, mate choice, and viability analysis in Hainan Eld's deer. PMID:24078679

Liu, Hong-Yi; Xue, Fei; Wan, Qiu-Hong; Ge, Yun-Fa



Selection of a subpopulation with fewer DNA topoisomerase II alpha gene copies in a doxorubicin-resistant cell line panel.  

PubMed Central

A panel of doxorubicin-resistant sublines of the human small-cell lung carcinoma cell line GLC4 displays decreasing DNA topoisomerase II alpha (TopoII alpha) mRNA levels with increasing resistance. In the present study we describe how this decrease may be regulated. No significant differences in TopoII alpha mRNA stability or gene arrangement were found, using mRNA slot-blotting and Southern blotting, in the most resistant cell line compared with the parental cell line. To investigate if TopoII alpha gene copy loss contributed to the mRNA decrease, fluorescence in situ hybridisation using a TopoII alpha-specific probe was performed. During doxorubicin resistance development, the composition of the population in each cell line shifted with increasing resistance, from a population in which most cells contain three TopoII alpha gene copies (GLC4) to a population in which most cells contain only two copies. A partial revertant of the most resistant cell line displayed a shift back to the original situation. We conclude that the TopoII alpha gene copy number decrease per cell line is in good agreement with the decreased TopoII alpha mRNA and protein levels, and TopoII activity levels in these cell lines which were described previously. Images Figure 3 Figure 2

Withoff, S.; Keith, W. N.; Knol, A. J.; Coutts, J. C.; Hoare, S. F.; Mulder, N. H.; de Vries, E. G.



The mouse insulin-like growth factor II/cation-independent mannose 6-phosphate (IGF-II/MPR) receptor gene: Molecular cloning and genomic organization  

SciTech Connect

The mammalian insulin-like growth factor III/cation-independent mannose 6-phosphate receptor (IGF-II/MPR) is a multifunctional protein that binds both IGF-II and ligands containing a mannose 6-phosphate recognition marker through distinct high-affinity sites. This receptor plays an integral part in lysosomal enzyme transport, has a potential role in growth factor maturation and clearance, and may mediate IGF-II-activated signal transduction through a G-protein-coupled mechanism. Recent studies have shown that production of IGF-II/MPR mRNA and protein begins in the mouse embryo soon after fertilization and have demonstrated that the receptor gene is on mouse chromosome 17 and is maternally imprinted. In this paper, the authors report the cloning and characterization of the mouse IGF-II/MPR gene. The gene is 93 kb long, is composed of 48 exons, and codes for a predicted protein of 2482 amino acids. The extracellular part of the receptor is encoded by exons 1-46, with each of 15 related repeating motifs being determined by parts of 3-5 exons. A single fibronectin type II-like element is found in exon 39. The transmembrane portion of the receptor also is encoded by exon 46, and the cytoplasmic region by exons 46-48. The positions of exon-intron splice junctions are conserved between several of the repeats in the IGF-II/MPR and the homologous extracellular region of the gene for the other known lysosomal sorting receptor, the cation-dependent mannose 6-phosphate receptor. The gene duplications that gave rise to the modern IGF-II/MPR probably occurred before the divergence of mammals, since there is more extensive protein sequence conservation between receptors from different species than between any pair of repeating motifs within a single receptor. 55 refs., 7 figs., 1 tab.

Szebenyi, G.; Rotwein, P. (Washington Univ. School of Medicine, St. Louis, MO (United States))



Role of tfdC(I)D(I)E(I)F(I) and tfdD(II)C(II)E(II)F(II) gene modules in catabolism of 3-chlorobenzoate by Ralstonia eutropha JMP134(pJP4).  


The enzymes chlorocatechol-1,2-dioxygenase, chloromuconate cycloisomerase, dienelactone hydrolase, and maleylacetate reductase allow Ralstonia eutropha JMP134(pJP4) to degrade chlorocatechols formed during growth in 2,4-dichlorophenoxyacetate or 3-chlorobenzoate (3-CB). There are two gene modules located in plasmid pJP4, tfdC(I)D(I)E(I)F(I) (module I) and tfdD(II)C(II)E(II)F(II) (module II), putatively encoding these enzymes. To assess the role of both tfd modules in the degradation of chloroaromatics, each module was cloned into the medium-copy-number plasmid vector pBBR1MCS-2 under the control of the tfdR regulatory gene. These constructs were introduced into R. eutropha JMP222 (a JMP134 derivative lacking pJP4) and Pseudomonas putida KT2442, two strains able to transform 3-CB into chlorocatechols. Specific activities in cell extracts of chlorocatechol-1,2-dioxygenase (tfdC), chloromuconate cycloisomerase (tfdD), and dienelactone hydrolase (tfdE) were 2 to 50 times higher for microorganisms containing module I compared to those containing module II. In contrast, a significantly (50-fold) higher activity of maleylacetate reductase (tfdF) was observed in cell extracts of microorganisms containing module II compared to module I. The R. eutropha JMP222 derivative containing tfdR-tfdC(I)D(I)E(I)F(I) grew four times faster in liquid cultures with 3-CB as a sole carbon and energy source than in cultures containing tfdR-tfdD(II)C(II)E(II)F(II). In the case of P. putida KT2442, only the derivative containing module I was able to grow in liquid cultures of 3-CB. These results indicate that efficient degradation of 3-CB by R. eutropha JMP134(pJP4) requires the two tfd modules such that TfdCDE is likely supplied primarily by module I, while TfdF is likely supplied by module II. PMID:10742248

Pérez-Pantoja, D; Guzmán, L; Manzano, M; Pieper, D H; González, B



Isolation, sequencing, and disruption of the yeast CKA2 gene: casein kinase II is essential for viability in Saccharomyces cerevisiae.  

PubMed Central

Casein kinase II of Saccharomyces cerevisiae contains two distinct catalytic subunits, alpha and alpha', which are encoded by the CKA1 and CKA2 genes, respectively. Null mutations in the CKA1 gene do not confer a detectable phenotype (J. L.-P. Chen-Wu, R. Padmanabha, and C. V. C. Glover, Mol. Cell. Biol. 8:4981-4990, 1988), presumably because of the presence of the CKA2 gene. We report here the cloning, sequencing, and disruption of the CKA2 gene. The alpha' subunit encoded by the CKA2 gene is 60% identical to the CKA1-encoded alpha subunit and 55% identical to the Drosophila alpha subunit (A. Saxena, R. Padmanabha, and C. V. C. Glover, Mol. Cell. Biol. 7:3409-3417, 1987). Deletions of the CKA2 gene were constructed by gene replacement techniques. Haploid cells in which the CKA2 gene alone is disrupted show no detectable phenotype, but haploid cells carrying disruptions in both the CKA1 and CKA2 genes are inviable. Cells in which casein kinase II activity is depleted increase substantially in size prior to growth arrest, and a significant fraction of the arrested cells exhibit a pseudomycelial morphology. Disruption of the activity also results in flocculation. Yeast strains lacking both endogenous catalytic subunit genes can be rescued by expression of the alpha and beta subunits of Drosophila casein kinase II or by expression of the Drosophila alpha subunit alone, suggesting that casein kinase II function has been conserved through evolution. Images

Padmanabha, R; Chen-Wu, J L; Hanna, D E; Glover, C V



Role of Fosinopril and Valsartan on Klotho Gene Expression Induced by Angiotensin II in Rat Renal Tubular Epithelial Cells  

Microsoft Academic Search

Background\\/Aims: Klotho gene, a new anti-aging gene, is mainly expressed in the kidney tubules. Several studies have found the relationship between klotho and emergence and development of renal diseases. This study set out to explore the role of fosinopril (Fos) and valsartan (Val) on klotho expression induced by angiotensin II (Ang II) in rat renal tubular epithelial cells (NRK-52E). Methods:

Q. Zhou; S. Lin; R. Tang; P. Veeraragoo; W. Peng; R. Wu



Localization of Eight Additional Genes in the Human Major Histocompatibility Complex, Including the Gene Encoding the Casein Kinase II ? Subunit (CSNK2B)  

Microsoft Academic Search

A wide range of autoimmune and other diseases are known to be associated with the major histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility antigens in the class I and class II regions, but some appear to be more strongly associated with genes in the central 1100-kb class III region, making it important

Mark R. Albertella; Helene Jones; Wendy Thomson; Mark G. Olavesen; R. Duncan Campbell



Microarray gene expression profiling reveals antioxidant-like effects of angiotensin II inhibition in atherosclerosis.  


Reactive oxygen species (ROS) is a significant feature of atherosclerosis but the impact of ROS on atherogenesis is not clear since antioxidants such as vitamin E have little effect on atherosclerosis development in vivo. To investigate the role of ROS in atherosclerosis, we used ApoE-deficient mice, and compared the treatment effect of the antioxidant vitamin E with that of the angiotensin-converting enzyme (ACE) inhibitor, captopril, because angiotensin II is a major source of ROS in the vasculature. Dihydroethidium (DHE) staining demonstrated that vitamin E and captopril both prevented the atherosclerosis-induced increase in aortic superoxide content. In contrast, seven months of vitamin E treatment retarded the development of atherosclerotic lesions by only 45.8 ± 11.5% whereas captopril reduced the aortic plaque area by 88.1 ± 7.5%. To discriminate between vitamin E-sensitive and -insensitive effects of ACE inhibition, we performed whole genome microarray gene expression profiling. Gene ontology (GO) and immunohistology analyses showed that vitamin E and captopril prevented atherosclerosis-related changes of aortic intima and media genes. However, vitamin E did not reduce the expression of probe sets detecting the aortic recruitment of pro-inflammatory immune cells while immune cell-specific genes were normalized by captopril treatment. Moreover, vitamin E did not prevent the atherosclerosis-dependent down-regulation of perivascular nerve-specific genes, which were preserved in captopril-treated aortas. Taken together, our study detected antioxidant vitamin E-like effects of angiotensin II inhibition in atherosclerosis treatment regarding preservation of aortic intima and media genes. Additional vitamin E-insensitive effects targeting atherosclerosis-enhancing aortic immune cell recruitment and perivascular nerve degeneration could account for the stronger anti-atherogenic activity of ACE inhibition compared to vitamin E. PMID:23801967

Abd Alla, Joshua; El Faramawy, Yasser; Quitterer, Ursula



Stem Cell-Like Gene Expression in Ovarian Cancer Predicts Type II Subtype and Prognosis  

PubMed Central

Although ovarian cancer is often initially chemotherapy-sensitive, the vast majority of tumors eventually relapse and patients die of increasingly aggressive disease. Cancer stem cells are believed to have properties that allow them to survive therapy and may drive recurrent tumor growth. Cancer stem cells or cancer-initiating cells are a rare cell population and difficult to isolate experimentally. Genes that are expressed by stem cells may characterize a subset of less differentiated tumors and aid in prognostic classification of ovarian cancer. The purpose of this study was the genomic identification and characterization of a subtype of ovarian cancer that has stem cell-like gene expression. Using human and mouse gene signatures of embryonic, adult, or cancer stem cells, we performed an unsupervised bipartition class discovery on expression profiles from 145 serous ovarian tumors to identify a stem-like and more differentiated subgroup. Subtypes were reproducible and were further characterized in four independent, heterogeneous ovarian cancer datasets. We identified a stem-like subtype characterized by a 51-gene signature, which is significantly enriched in tumors with properties of Type II ovarian cancer; high grade, serous tumors, and poor survival. Conversely, the differentiated tumors share properties with Type I, including lower grade and mixed histological subtypes. The stem cell-like signature was prognostic within high-stage serous ovarian cancer, classifying a small subset of high-stage tumors with better prognosis, in the differentiated subtype. In multivariate models that adjusted for common clinical factors (including grade, stage, age), the subtype classification was still a significant predictor of relapse. The prognostic stem-like gene signature yields new insights into prognostic differences in ovarian cancer, provides a genomic context for defining Type I/II subtypes, and potential gene targets which following further validation may be valuable in the clinical management or treatment of ovarian cancer.

Schwede, Matthew; Spentzos, Dimitrios; Bentink, Stefan; Hofmann, Oliver; Haibe-Kains, Benjamin; Harrington, David; Quackenbush, John; Culhane, Aedin C.



mRNA up-regulation of MHC II and pivotal pro-inflammatory genes in normal brain aging  

Microsoft Academic Search

In normal brain aging, CNS resident macrophages exhibit increased expression of major histocompatibility complex (MHC) II expression. However, the transcriptional basis for this observation has not been clarified nor have age-related alterations in pivotal pro-inflammatory genes been characterized. Age-related mRNA alterations in MHC II, MHC II accessory molecules and several pro-inflammatory mediators were measured in older (24 months) and younger

Matthew G. Frank; Ruth M. Barrientos; Joseph C. Biedenkapp; Jerry W. Rudy; Linda R. Watkins; Steven F. Maier



Association between HLA class II genes and autoantibodies to cyclic citrullinated peptides (CCPs) influences the severity of rheumatoid arthritis  

Microsoft Academic Search

OBJECTIVE: The functional role of HLA class II molecules in the pathogenesis of rheumatoid arthritis (RA) is unclear. HLA class II molecules are involved in the interaction between T and B lymphocytes required for long-lived B cell responses and generation of high-affinity IgG antibodies. We undertook this study to investigate the relationship between HLA class II gene polymorphisms and RA-specific

Floris A. Van Gaalen; Jill Van Aken; Tom W. J. Huizinga; Geziena M. Th. Schreuder; Ferdinand C. Breedveld; Eric Zanelli; Walther J. Van Venrooij; Cornelis L. Verweij



Transcriptional Upregulation of Nrf2Dependent Phase II Detoxification Genes in the Involved Epidermis of Vitiligo Vulgaris  

Microsoft Academic Search

Oxidative stress is widely believed to be a contributing factor in vitiligo pathogenesis. To explore mechanisms by which epidermis responds to mounting oxidative stress, we investigated the involvement of phase II detoxification genes in vitiligo. Phase II detoxification pathways have recently been identified as being important in the regulation of epidermal skin homeostasis. In this study we show that the

Vivek T Natarajan; Archana Singh; Avinash A Kumar; Pankaj Sharma; Hemanta K Kar; Laurent Marrot; Jean-Roch Meunier; Krishnamurthy Natarajan; Rajni Rani; Rajesh S Gokhale



IGF2 gene polymorphisms and IGF-II concentration are determinants of longitudinal weight trends in type 2 diabetes.  


The hypothesis of the study was that IGF2 gene polymorphisms were associated with longitudinal trends in weight through modification of IGF-II concentration.Observational study that explored associations of the IGF2 gene and baseline circulating IGF-II concentration with 'real-world' longitudinal trends in body-mass index in a type 2 diabetes population.26 haplotype tagging single nucleotide polymorphisms (SNPs) from the IGF2 and H19 genes were studied in 485 Caucasian individuals in the Salford Longitudinal Diabetes Cohort. A generalised-estimating equation (GEE) model was used to separately study the association of SNPs and IGF-II concentration with 8-year longitudinal trends in body-mass index.High serum IGF-II concentration at baseline was associated with weight loss over the study period (?=-0.006, 95% CI -0.009 to -0.002, p<0.001). 8 SNPs were associated with longitudinal body-mass index trends, of which 4 retained significance after multiple -testing correction. 2 SNPs rs10770063 and rs3842767 were associated with both IGF-II concentration as well as longitudinal weight changes.We report novel associations between polymorphisms in the IGF2 gene, with concentration of circulating IGF-II and also with longitudinal weight change in type 2 diabetes. Our data indicate that the IGF2 gene and its gene product may be important determinants of longitudinal weight trends in type 2 diabetes. PMID:23757053

Narayanan, R P; Fu, B; Payton, A; Hudson, J E; Oliver, R L; Anderson, S G; Siddals, K W; White, A; Ollier, W E R; Heald, A H; Gibson, J M



Evolution of Type II Antifreeze Protein Genes in Teleost Fish: A Complex Scenario Involving Lateral Gene Transfers and Episodic Directional Selection  

PubMed Central

I examined hypotheses about lateral transfer of type II antifreeze protein (AFP) genes among “distantly” related teleost fish. The effects of episodic directional selection on amino acid evolution were also investigated. The strict consensus results showed that the type II AFP and type II antifreeze-like protein genes were transferred from Osmerus mordax to Clupea harengus, from the ancestral lineage of the Brachyopsis rostratus—Hemitripterus americanus clade to the ancestor of the Hypomesus nipponensis—Osmerus mordax group and from the ancestral lineage of Brachyopsis rostratus—Hemitripterus americanus—Siniperca chuatsi—Perca flavescens to Perca flavescens. At the present time, the available evidence is more consistent with the LGT hypothesis than with other alternative explanations. The overall results indicate that evolutionary history of the type II AFP gene is complex, and that episodic directional selection was instrumental in the evolution of this freeze-preventing protein from a C-type lectin precursor.

Sorhannus, Ulf



The Occurrence of Antibiotic Resistance Genes in Taq Polymerases and a Decontamination Method Applied to the Detection of Genetically Modified Crops  

Microsoft Academic Search

Different antibiotic resistance (AR) genes, such as Bla, Tet and NPTII, contaminate commercially available Taq polymerases. The specificity of the AR gene PCR can be increased when using a restriction enzyme-based decontamination of\\u000a polymerase. The elimination of Taq polymerase contamination allows the use of PCR tests to screen seeds (corn) and processed food for the presence of genetically\\u000a modified organisms

André Perron; Philippe Raymond; Robin Simard



An efficient method for the production of transgenic plants of peanut ( Arachis hypogaea L .) through Agrobacterium tumefaciens-mediated genetic transformation  

Microsoft Academic Search

Cotyledon explants from mature peanut seeds (Arachis hypogaea L.) were optimized to obtain adventitious shoot buds with high frequencies (>90%). Efficient transformation of these cotyledons by using Agrobacterium tumefaciens strain C58 carrying neomycin phosphotransferase II (nptII) and ß-glucuronidase (GUS; uidA), or coat protein gene of the Indian peanut clump virus (IPCVcp) and nptII on binary vectors (pBI121; pROKII:IPCVcp) led to

Kiran K Sharma; Vanamala Anjaiah



Regulation of gene transcription of angiotensin II receptor subtypes in myocardial infarction.  

PubMed Central

Increasing evidence suggests that angiotensin II (AngII) acts as a modulator for ventricular remodeling after myocardial infarction. Using competitive reverse-transcriptase polymerase chain reaction, nuclear runoff, and binding assays, we examined the regulation of AngII type 1a and 1b (AT1a-R and AT1b-R) and type 2 receptor (AT2-R) expression in the infarcted rat heart as well as the effects of AngII receptor antagonists. AT1a-R mRNA levels were increased in the infarcted (4.2-fold) and noninfarcted portions (2.2-fold) of the myocardium 7 d after myocardial infarction as compared with those in sham-operated controls, whereas AT1b-R mRNA levels were unchanged. The amount of detectable AT2-R mRNA increased in infarcted (3.1-fold) and noninfarcted (1.9-fold) portions relative to that in the control. The transcription rates for AT1a-R and AT2-R genes, determined by means of a nuclear runoff assay, were significantly increased in the infarcted heart. The AngII receptor numbers were elevated (from 12 to 35 fmol/mg protein) in the infarcted myocardium in which the increases in AT1-R and AT2-R were 3.2- and 2.3-fold, respectively, while the receptor affinity was unchanged. Therapy with AT1-R antagonist for 7 d reduced the increase in AT1-R and AT2-R expressions in the infarcted heart together with a decrease in blood pressure, whereas therapy with an AT2-R antagonist did not affect mRNA levels and blood pressure. Neither AT1-R nor AT2-R antagonists affected the infarct sizes. These results demonstrated that myocardial infarction causes an increase in the gene transcription and protein expression of cardiac AT1a-R and AT2-R, whereas the AT1b-R gene is unaffected, and that therapy with an AT1-R antagonist, but not with an AT2-R antagonist, is effective in reducing the increased expression of AngII receptor subtypes induced by myocardial infarction. Images

Nio, Y; Matsubara, H; Murasawa, S; Kanasaki, M; Inada, M



Sequence of the 18S-5S ribosomal gene region and the cytochrome oxidase II gene from mtDNA of Zea diploperennis  

Microsoft Academic Search

The coding and flanking sequences of the 18S-5S ribosomal RNA genes and the cytochrome oxidase subunit II gene of Zea diploperennis mitochondrial DNA have been determined and compared to the corresponding sequences of normal maize (Zea mays L.) Both length and substitution mutations are found in the coding region of the 18S rRNA gene, whereas only one substitution mutation is

B. Gwynn; R. E. Dewey; R. R. Sederoff; D. H. Timothy; C. S. Levjngs



Effects of naringenin and its phase II metabolites on in vitro human macrophage gene expression.  


Abstract Naringenin, together with its glycosidic forms, is a flavanone abundant in grapefruit and orange. It has been detected in human plasma, following citrus juice intake, at sub-µmolar concentrations, and its main phase II conjugated metabolites (naringenin-7-O-glucuronide and narigenin-4'-O-glucuronide) have been identified in urine. Recent evidence suggests a potential active anti-inflammatory role of flavonoids on macrophages, cells actively involved in atherogenesis. The aim of this study was to evaluate the effects of naringenin and its phase II metabolites on the expression of specific genes in differently activated macrophages at concentrations coherent with dietary exposure. Results suggest that phase II metabolites, as well as the aglyconic form of naringenin, were able to perturb macrophage gene expression in directions that are not always consistent with anti-inflammatory effects. Moreover, the effects of metabolites were not always consistent with each other and with those of their aglycone, underlining the paramount importance of testing physiological forms of phytochemicals within in vitro experimental models. In vivo studies are needed to further explore these observations and investigate their practical consequences. PMID:23883170

Dall'asta, Margherita; Derlindati, Eleonora; Curella, Valentina; Mena, Pedro; Calani, Luca; Ray, Sumantra; Zavaroni, Ivana; Brighenti, Furio; Del Rio, Daniele



Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways  

PubMed Central

The yeast URA2 gene, encoding the rate-limiting enzyme of UTP biosynthesis, is transcriptionally activated by UTP shortage. In contrast to other genes of the UTP pathway, this activation is not governed by the Ppr1 activator. Moreover, it is not due to an increased recruitment of RNA polymerase II at the URA2 promoter, but to its much more effective progression beyond the URA2 mRNA start site(s). Regulatory mutants constitutively expressing URA2 resulted from cis-acting deletions upstream of the transcription initiator region, or from amino-acid replacements altering the RNA polymerase II Switch 1 loop domain, such as rpb1-L1397S. These two mutation classes allowed RNA polymerase to progress downstream of the URA2 mRNA start site(s). rpb1-L1397S had similar effects on IMD2 (IMP dehydrogenase) and URA8 (CTP synthase), and thus specifically activated the rate-limiting steps of UTP, GTP and CTP biosynthesis. These data suggest that the Switch 1 loop of RNA polymerase II, located at the downstream end of the transcription bubble, may operate as a specific sensor of the nucleoside triphosphates available for transcription.

Kwapisz, Marta; Wery, Maxime; Despres, Daphne; Ghavi-Helm, Yad; Soutourina, Julie; Thuriaux, Pierre; Lacroute, Francois



Persistent Ehrlichia chaffeensis infection occurs in the absence of functional major histocompatibility complex class II genes.  


Human monocytic ehrlichiosis is an emerging tick-borne disease caused by the rickettsia Ehrlichia chaffeensis. We investigated the impact of two genes that control macrophage and T-cell function on murine resistance to E. chaffeensis. Congenic pairs of wild-type and toll-like receptor 4 (tlr4)- or major histocompatibility complex class II (MHC-II)-deficient mice were used for these studies. Wild-type mice cleared the infection within 2 weeks, and the response included macrophage activation and the synthesis of E. chaffeensis-specific Th1-type immunoglobulin G response. The absence of a functional tlr4 gene depressed nitric oxide and interleukin 6 secretion by macrophages and resulted in short-term persistent infections for > or =30 days. In the absence of MHC-II alleles, E. chaffeensis infections persisted throughout the entire 3-month evaluation period. Together, these data suggest that macrophage activation and cell-mediated immunity, orchestrated by CD4(+) T cells, are critical for conferring resistance to E. chaffeensis. PMID:11748204

Ganta, Roman Reddy; Wilkerson, Melinda J; Cheng, Chuanmin; Rokey, Aaron M; Chapes, Stephen K



Persistent Ehrlichia chaffeensis Infection Occurs in the Absence of Functional Major Histocompatibility Complex Class II Genes  

PubMed Central

Human monocytic ehrlichiosis is an emerging tick-borne disease caused by the rickettsia Ehrlichia chaffeensis. We investigated the impact of two genes that control macrophage and T-cell function on murine resistance to E. chaffeensis. Congenic pairs of wild-type and toll-like receptor 4 (tlr4)- or major histocompatibility complex class II (MHC-II)-deficient mice were used for these studies. Wild-type mice cleared the infection within 2 weeks, and the response included macrophage activation and the synthesis of E. chaffeensis-specific Th1-type immunoglobulin G response. The absence of a functional tlr4 gene depressed nitric oxide and interleukin 6 secretion by macrophages and resulted in short-term persistent infections for ?30 days. In the absence of MHC-II alleles, E. chaffeensis infections persisted throughout the entire 3-month evaluation period. Together, these data suggest that macrophage activation and cell-mediated immunity, orchestrated by CD4+ T cells, are critical for conferring resistance to E. chaffeensis.

Ganta, Roman Reddy; Wilkerson, Melinda J.; Cheng, Chuanmin; Rokey, Aaron M.; Chapes, Stephen K.



Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin.  

PubMed Central

A number of activators are known to increase transcription by RNA polymerase (pol) II through protein acetylation. While the physiological substrates for those acetylases are poorly defined, possible targets include general transcription factors, activator proteins and histones. Using a cell-free system to reconstitute chromatin with increased histone acetylation levels, we directly tested for a causal role of histone acetylation in transcription by RNA pol II. Chromatin, containing either control or acetylated histones, was reconstituted to comparable nucleosome densities and characterized by electron microscopy after psoralen cross-linking as well as by in vitro transcription. While H1-containing control chromatin severely repressed transcription of our model hsp26 gene, highly acetylated chromatin was significantly less repressive. Acetylation of histones, and particularly of histone H4, affected transcription at the level of initiation. Monitoring the ability of the transcription machinery to associate with the promoter in chromatin, we found that heat shock factor, a crucial regulator of heat shock gene transcription, profited most from histone acetylation. These experiments demonstrate that histone acetylation can modulate activator access to their target sites in chromatin, and provide a causal link between histone acetylation and enhanced transcription initiation of RNA pol II in chromatin.

Nightingale, K P; Wellinger, R E; Sogo, J M; Becker, P B



Mutations in exons of the CYP17-II gene affect sex steroid concentration in male Japanese flounder ( Paralichthys olivaceus)  

NASA Astrophysics Data System (ADS)

As a specific gene of fish, cytochrome P450c17-II ( CYP17-II) gene plays a key role in the growth, development an reproduction level of fish. In this study, the single-stranded conformational polymorphism (SSCP) technique was used to characterize polymorphisms within the coding region of CYP17-II gene in a population of 75 male Japanese flounder ( Paralichthys olivaceus). Three single nucleotide polymorphisms (SNPs) were identified in CYP17-II gene of Japanese flounder. They were c.G594A (p.G188R), c.G939A and c.G1502A (p.G490D). SNP1 (c.G594A), located in exon 4 of CYP17-II gene, was significantly associated with gonadosomatic index (GSI). Individuals with genotype GG of SNP1 had significantly lower GSI ( P < 0.05) than those with genotype AA or AG. SNP2 (c.G939A) located at the CpG island of CYP17-II gene. The mutation changed the methylation of exon 6. Individuals with genotype AA of SNP2 had significantly lower serum testosterone (T) level and hepatosomatic index (HSI) compared to those with genotype GG. The results suggested that SNP2 could influence the reproductive endocrine of male Japanese flounder. However, the SNP3 (c.G1502A) located in exon 9 did not affect the four measured reproductive traits. This study showed that CYP17-II gene could be a potentially useful candidate gene for the research of genetic breeding and physiological aspects of Japanese flounder.

Ma, Ruiqin; He, Feng; Wen, Haishen; Li, Jifang; Shi, Bao; Shi, Dan; Liu, Miao; Mu, Weijie; Zhang, Yuanqing; Hu, Jian; Han, Weiguo; Zhang, Jianan; Wang, Qingqing; Yuan, Yuren; Liu, Qun



Exonuclease III and the catalase hydroperoxidase II in Escherichia coli are both regulated by the katF gene product  

Microsoft Academic Search

The levels of both exonuclease III (exo III, product of xthA) and hydroperoxidase II (HP-II, product of katE) activity in Escherichia coli were influenced by a functional katF gene. The katF gene product is also necessary for synthesis of HP-II. Mutations in either katF or xthA, but not katE, result in sensitivity to HâOâ and near-UV (300-400 nm) radiation. Exo

B. D. Sak; A. Eisenstark; D. Touati



Functional association of Gdown1 with RNA polymerase II poised on human genes  

PubMed Central

Summary Most human genes are loaded with promoter proximally paused RNA polymerase II (Pol II) molecules that are poised for release into productive elongation by P-TEFb. We present evidence that Gdown1, a protein that renders Pol II responsive to mediator, is involved in Pol II elongation control. During in vitro transcription assays Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. Supporting these mechanistic insights, ChIP-Seq demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Our results establish that Gdown1 increases the stability of poised polymerases while maintaining their responsiveness to P-TEFb and suggest that mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function.

Cheng, Bo; Li, Tiandao; Rahl, Peter B.; Adamson, Todd E.; Loudas, Nicholas B.; Guo, Jiannan; Varzavand, Katayoun; Cooper, Jeffrey J.; Hu, Xiaopeng; Gnatt, Averell; Young, Richard A.; Price, David H.



Dual requirement for the yeast MMS19 gene in DNA repair and RNA polymerase II transcription.  

PubMed Central

Genetic and biochemical studies of Saccharomyces cerevisiae have indicated the involvement of a large number of protein factors in nucleotide excision repair (NER) of UV-damaged DNA. However, how MMS19 affects this process has remained unclear. Here, we report on the isolation of the MMS19 gene and the determination of its role in NER and other cellular processes. Genetic and biochemical evidence indicates that besides its function in NER, MMS19 also affects RNA polymerase II (Pol II) transcription. mms19delta cells do not grow at 37 degrees C, and mutant extract exhibits a thermolabile defect in Pol II transcription. Thus, Mms19 protein resembles TFIIH in that it is required for both transcription and DNA repair. However, addition of purified Mms19 protein does not alleviate the transcriptional defect of the mms19delta extract, nor does it stimulate the incision of UV-damaged DNA reconstituted from purified proteins. Interestingly, addition of purified TFIIH corrects the transcriptional defect of the mms19delta extract. Mms19 is, however, not a component of TFIIH or of Pol II holoenzyme. These and other results suggest that Mms19 affects NER and transcription by influencing the activity of TFIIH as an upstream regulatory element. It is proposed that mutations in the human MMS19 counterpart could result in syndromes in which both NER and transcription are affected.

Lauder, S; Bankmann, M; Guzder, S N; Sung, P; Prakash, L; Prakash, S



A new point mutation in the ND1 mitochondrial gene identified in a type II diabetic patient  

SciTech Connect

A novel mutation in a mitochondrial gene was identified in a patient with type II diabetes mellitus. G-to-A transition was localized at the nt3316 position of gene ND1 and resulted in alanine threonine replacement at position 4 of mitochondrial NAD-H-dehydrogenase. 6 refs., 2 figs.

Kalinin, V.N. [Research Center of Medical Genetics, Moscow (Russian Federation); Schmidt, W.; Olek, K. [Institut fuer Molekularbiologische Diagnostik, Bonn (Germany)] [and others



How GeneChipĂ® was developed (Part II), Stephen FodorSite: DNA Interactive (  

NSDL National Science Digital Library

Interviewee: Stephen Fodor DNAi Location:Applications>Genes and medicine>genetic profiling>Stephen Fodor How the chip was developed (Part II) Stephen Fodor continues his discussion of the experiments that laid the groundwork for GeneChipĂ® technology.



A class II gene conversion event defines an antigen-specific Ir gene epitope  

PubMed Central

To assess the role of Ia epitopes in conferring specificity for the immune response to nominal antigen, we compared the insulin response of mice with a defined mutation in the I-Ab beta gene, the B6.C-H-2bm12 (bm12), with that of wild-type H-2b C57BL/6 (B6) mice. We report that the bm 12 mutation resulted in a selective alteration of the specificity of insulin recognition, such that bm 12 mice responded upon immunization with sheep but not beef insulin, which differ by only one amino acid at position 9 of the insulin A chain. Thus, the bm12 mutation allows for the definition of the actual nucleotide sequence coding for an Ia epitope that is responsible for controlling the specificity of immune recognition of insulin. Furthermore, we show that the sheep insulin response of H-2k mice is controlled by the E molecule and that sheep insulin can be recognized by primed bm12 and H-2k T cells in the context of either bm12, B10.A, or B10.A(5R) antigen- presenting cells. Our data suggest that the mechanism for the bm12 mutation was the intergenic transfer of a hypervariable region in the first domain that is identical in the I-Abm12 beta, I-Eb beta, and I-Ek beta genes.



Silencing of hypoxia inducible factor-1? gene attenuated angiotensin II-induced renal injury in Sprague-Dawley rats  

PubMed Central

Although it has been shown that up-regulation of hypoxia-inducible factor (HIF)-1? is protective in acute ischemic renal injury, long-term over-activation of HIF-1? is implicated to be injurious in chronic kidney diseases. Angiotensin II (ANG II) is a well-known pathogenic factor producing chronic renal injury and has also been shown to increase HIF-1?. However, the contribution of HIF-1? to ANG II-induced renal injury has not been evidenced. The present study tested the hypothesis that HIF-1? mediates ANG II-induced renal injury in Sprague-Dawley rats. Chronic renal injury was induced by ANG II infusion (200ng/kg/min) for 2 weeks in uninephrectomized rats. Transfection of vectors expressing HIF-1? shRNA into the kidneys knocked down HIF-1? gene expression by 70%, blocked ANG II-induced HIF-1? activation and significantly attenuated ANG II-induced albuminuria, which was accompanied by inhibition of ANG II-induced vascular endothelial growth factor, a known glomerular permeability factor, in glomeruli. HIF-1? shRNA also significantly improved the glomerular morphological damage induced by ANG II. Furthermore, HIF-1? shRNA blocked ANG II-induced upregulation of collagen and ?-smooth muscle actin in tubulointerstitial region. There was no difference in creatinine clearance and ANG II-induced increase in blood pressure. HIF-1? shRNA had no effect on ANG II-induced reduction in renal blood flow and hypoxia in the kidneys. These data suggested that over-activation of HIF-1?-mediated gene regulation in the kidney is a pathogenic pathway mediating ANG II-induced chronic renal injuries and normalization of over-activated HIF-1? may be used as a treatment strategy for chronic kidney damages associated with excessive ANG II.

Zhu, Qing; Wang, Zhengchao; Xia, Min; Li, Pin-Lan; Van Tassell, Benjamin W.; Abbate, Antonio; Dhaduk, Romesh; Li, Ningjun



DMA and DMB are the only genes in the class II region of the human MHC needed for class II-associated antigen processing  

SciTech Connect

Previous studies have shown that homozygous mutations between the LMP2 and DNA loci in the human MHC cause class II molecules to be abnormally conformed and unstable in the presence of SDS at low temperature, and impede class II-associated Ag processing and presentation. These abnormalities result from impaired ability to form intracellular class II/peptide complexes that predominate in normal cells. We show in this work that this defect results from deficient expression of either the DMA or the DMB gene. Human B-LCL.174 (DR3) cells, which have a deletion of all known expressible genes in the class II region, express transgene-encoded HLA-DR3, but have the abnormalities. Transfer of cosmid HA14, which contains the DMA and DMB genes, into .174 (DR3) cells restored normal DR3 conformation, stability in 0.4% SDS at 0{degrees}, and ability to process and present tetanus toxoid, but only when both DMA and DMB mRNAs were present. The requirement for both genetic expressions in engendering normal phenotypes was confirmed by transferring the cloned genes into .174 (DR3) cells separately or together. Because normal phenotypes were fully restored in transferent cells expressing DMA plus DMB, other genes in the {approximately} 1-mb homozygous class II region deletion in .174 (DR3) cells either do not participate in or are dispensable for apparently normal production of intracellular class II/peptide complexes. The properties of DM-deficient EBV-transformed B lymphoblastoid cell lines (LCLs) suggest ways of identifying humans in whom DM deficiency contributes to congenital immunodeficiency and malignancy. 67 refs., 5 figs., 1 tab.

Ceman, S.; Rudersdorf, R.A.; Petersen, J.M. [Univ. of Wisconsin, Madison, WI (United States)] [and others



Inhibition of major histocompatibility complex class II gene transcription by nitric oxide and antioxidants.  


Interferon (IFN)-gamma facilitates cellular immune response, in part, by inducing the expression of major histocompatibility complex class II (MHC-II) molecules. We demonstrate that IFN-gamma induces the expression of HLA-DRA in vascular endothelial cells via mechanisms involving reactive oxygen species. IFN-gamma-induced HLA-DRA expression was inhibited by nitric oxide (NO) and antioxidants such as superoxide dismutase, catalase, pyrrolidine dithiocarbamate, and N-acetylcysteine. Nuclear run-on assays demonstrated that NO and antioxidants inhibited IFN-gamma-induced HLA-DRA gene transcription. Transient transfection studies using a fully functional HLA-DRA promoter construct ([-300]DR alpha.CAT) showed that inhibition of endogenous NO synthase activity by N(omega)-monomethyl-l-arginine or addition of exogenous hydrogen peroxide (H(2)O(2)) augmented basal and IFN-gamma-stimulated [-300]DR alpha.CAT activity. However, H(2)O(2) and N(omega)-monomethyl-l-arginine could induce HLA-DRA expression suggesting that H(2)O(2) is a necessary but not a sufficient mediator of IFN-gamma-induced HLA-DRA expression. Electrophoretic mobility shift assay and Western blotting demonstrated that NO and antioxidants had little or no effect on IFN-gamma-induced IRF-1 activation or MHC-II transactivator (CIITA) expression but did inhibit IFN-gamma-induced activation of STAT1 alpha (p91) and Y box transcription factors, NF-Y(A) and NF-Y(B). These results indicate that NO and antioxidants may attenuate vascular inflammation by antagonizing the effects of intracellular reactive oxygen species generation by IFN-gamma, which is necessary for MHC-II gene transcription. PMID:12006557

Grimm, Michael; Spiecker, Martin; De Caterina, Raffaele; Shin, Wee Soo; Liao, James K



Altered gene expression of cytokine, ICAM-1, and class II molecules precedes mouse intestinal allograft rejection.  


Rapid and severe rejection remains a major obstacle to successful clinical intestinal transplantation (IT). The aggressive nature of rejection in IT has been attributed to the increased massive immune stimulus provided by large numbers of resident lymphocytes, antigen presentation capacity of enterocytes, and graft damage mediated by luminal microflora. Early small bowel expression of proinflammatory cytokines, MHC class II, and adhesion molecules may also promote IT rejection, but the lack of a mouse model has hampered extensive studies of gene expression in IT. Using a recently developed surgical model, we examined the temporal pattern of gene expression in CB6F1 (H-2b/d) vascularized, heterotopic intestinal allografts transplanted into BALB/c (H-2d) mice. Although histological evidence of rejection was not present until day 7 in allografts, Northern blot analysis demonstrated increases in TNF alpha gene transcripts as early as day 3, followed by the expression of IL-1 beta, intercellular adhesion molecule-1, and MHC class II by day 5. Using reverse-transcriptase polymerase chain reaction, IFN-gamma was detected in allografts by day 3 and persisted to day 10. In contrast, IL-2, IL-4, IL-5, and IL-6 mRNA transcripts peaked by day 5 and then decreased, suggesting that both Th1 and Th2 subsets are involved in the rejection of unmodified small bowel allografts. The early and progressive expression of TNF alpha and IL-1 beta as well as IFN-gamma, intercellular adhesion molecule-1, and MHC class II in IT rejection may contribute to the difficulty in controlling IT rejection with present immunosuppression. PMID:7940716

Quan, D; Grant, D R; Zhong, R Z; Zhang, Z; Garcia, B M; Jevnikar, A M



Major Histocompatibility Complex Haplotypes and Class II Genes in Non Jewish Patients with Pemphigus Vulgaris  

Microsoft Academic Search

Previous studies demonstrated that HLA-DR4 was markedly increased among Ashkenazi Jewish patients with pemphigus vulgaris (PV), almost entirely as the common Jewish extended haplotype [HLA-B38, SC21, DR4, DQw8] or as the haplotype HLA-B35, SC31, DR4, DQw8, and that HLA-DR4, DQw8 was distributed among patients in a manner consistent with dominant expression of a class II (D-region or D-region-linked) susceptibility gene.

A. Razzaque Ahmed; Rene Wagner; Khalil Khatri; Gur Notani; Zuheir Awdeh; Chester A. Alper; Edmond J. Yunis



Gene Context and DNA rearrangements in the carbapenemase locus of division II strains of Bacteroides fragilis.  


The cfiA gene is clustered in a bicistronic operon encoding an N-acetyltransferase and an O-acetyltransferase related to resistance markers. This genetic context, exclusively found in strains of Bacteroides fragilis division II, has been highly rearranged by the successive integration of two new mobile sequences, a miniature element and ISBf9. Besides that, among the DNA polymorphisms detected in the cfiA locus, only the integration of IS942 at its promoter was a determinant for expression of carbapenemase activity. PMID:19364865

García, Nuria; Gutiérrez, Gloria; Lorenzo, María; Vadillo, Santiago; Píriz, Segundo; Quesada, Alberto



Gene Context and DNA Rearrangements in the Carbapenemase Locus of Division II Strains of Bacteroides fragilis?  

PubMed Central

The cfiA gene is clustered in a bicistronic operon encoding an N-acetyltransferase and an O-acetyltransferase related to resistance markers. This genetic context, exclusively found in strains of Bacteroides fragilis division II, has been highly rearranged by the successive integration of two new mobile sequences, a miniature element and ISBf9. Besides that, among the DNA polymorphisms detected in the cfiA locus, only the integration of IS942 at its promoter was a determinant for expression of carbapenemase activity.

Garcia, Nuria; Gutierrez, Gloria; Lorenzo, Maria; Vadillo, Santiago; Piriz, Segundo; Quesada, Alberto



Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data  

Microsoft Academic Search

Background: Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) or massive parallel sequencing (ChIP-seq) are enabling genome-wide identification of active promoters in different cellular conditions using antibodies against Pol-II. However, these methods produce enrichment not only near the gene

Ravi Gupta; Priyankara Wikramasinghe; Anirban Bhattacharyya; Francisco A. Perez; Sharmistha Pal; Ramana V. Davuluri



The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation.  


Enhancers play a central role in precisely regulating the expression of developmentally regulated genes. However, the machineries required for enhancer-promoter communication have remained largely unknown. We have found that Ell3, a member of the Ell (eleven-nineteen lysine-rich leukemia gene) family of RNA Pol II elongation factors, occupies enhancers in embryonic stem cells. Ell3's association with enhancers is required for setting up proper Pol II occupancy at the promoter-proximal regions of developmentally regulated genes and for the recruitment of the super elongation complex (SEC) to these loci following differentiation signals. Furthermore, Ell3 binding to inactive or poised enhancers is essential for stem cell specification. We have also detected the presence of Pol II and Ell3 in germ cell nuclei. These findings raise the possibility that transcription factors could prime gene expression by marking enhancers in ES cells or even as early as in the germ cell state. PMID:23273992

Lin, Chengqi; Garruss, Alexander S; Luo, Zhuojuan; Guo, Fengli; Shilatifard, Ali



Effect of transfection of a Drosophila topoisomerase II gene into a human brain tumour cell line intrinsically resistant to etoposide.  

PubMed Central

The human brain tumour cell line HBT20 is intrinsically resistant to etoposide and does not express mdr-1 mRNA. These studies were conducted to determine whether transfecting a Drosophila (D) topoisomerase II (topo II) gene into HBT20 cells could increase their sensitivity to etoposide. A D-topo II construct in a pMAMneo vector under the control of a mouse mammary tumour virus (MMTV) promoter was transfected into HBT20 cells. The gene is inducible by dexamethasone (Dex). The growth rate of the transfected cells and percentage of the cells in G1, S and G2M was no different than the parental cells. Survival after etoposide exposure (10 microM x 2 h) was measured by colony formation. Parental cells and cells transfected by pMAMneo vector alone showed no enhanced etoposide sensitivity after 24 h of Dex stimulation. By contrast, D-topo II transfected cells were sensitised 3-fold when etoposide treatment was preceded by 24 h Dex stimulation. Northern blotting and Western blotting confirmed that Dex had induced D-topo II expression in the sensitised cells. However, in D-topo II-transfected cells increasing the duration of Dex stimulation to 48 h eliminated the sensitisation to etoposide although increased MMTV promoter activity and expression of the D-topo II gene persisted. Measurement of endogenous human topo-II mRNA and protein revealed a decrease after Dex exposure of greater than 24 h. At these distal times, the total cellular topo II levels (endogenous + exogenous) may be decreased, which may explain why increased sensitivity to etoposide could no longer be demonstrated. This model suggests that D-topo II gene transfection can sensitise de novo resistant HBT20 cells to etoposide but that the time frame of that sensitisation is limited. Images Figure 1 Figure 2 Figure 3 Figure 5

Asano, T.; Zwelling, L. A.; An, T.; McWatters, A.; Herzog, C. E.; Mayes, J.; Loughlin, S. M.; Kleinerman, E. S.



Tyrosinemia type II (Richner-Hanhart syndrome): a new mutation in the TAT gene.  


In the present study we report the clinical features and the molecular genetic investigation of the tyrosine aminotransferase (TAT) gene in a young girl from Croatia with Richner-Hanhart syndrome, mainly suffering from photophobia, hyperkeratosis of the palmes and soles and slight neurological abnormalities. Sequencing analysis of the TAT gene revealed a novel homozygous missense mutation c.1250G>A (p.R417Q) in exon 12, and herewith confirmed the clinical diagnosis. Showing the first symptoms in babyhood, at the age of 8 years it was for the first time clinically diagnosed that the patient suffers from tyrosinemia type II and a therapy with tyrosine and phenylalanine reduced diet has been started successfully. All symptoms disappeared within 2-4 weeks. Since that time, we have been following the girl until today for more than ten years. She is in a good condition, and attends the normal high school program. PMID:21145993

Culic, Vida; Betz, Regina C; Refke, Melanie; Fumic, Ksenija; Pavelic, Jasminka



Expressed MHC class II genes in sea otters (Enhydra lutris) from geographically disparate populations.  


The major histocompatibility complex (MHC) is central to maintaining the immunologic vigor of individuals and populations. Classical MHC class II genes were targeted for partial sequencing in sea otters (Enhydra lutris) from populations in California, Washington, and Alaska. Sequences derived from sea otter peripheral blood leukocyte mRNAs were similar to those classified as DQA, DQB, DRA, and DRB in other species. Comparisons of the derived amino acid compositions supported the classification of these as functional molecules from at least one DQA, DQB, and DRA locus and at least two DRB loci. While limited in scope, phylogenetic analysis of the DRB peptide-binding region suggested the possible existence of distinct clades demarcated by geographic region. These preliminary findings support the need for additional MHC gene sequencing and expansion to a comprehensive study targeting additional otters. PMID:16671948

Bowen, L; Aldridge, B M; Miles, A K; Stott, J L



Differential expression of secretogranin II and chromogranin A genes in the female rat pituitary through sexual maturation and estrous cycle  

SciTech Connect

Secretogranin II (SgII) is a protein of pituitary secretory granules released by LHRH-stimulated gonadotrope cells. Estrogens and androgens are modulators of SgII release. Experiments were performed to determine the regulation of expression of the SgII gene in the female rat pituitary, during sexual maturation and according to the estrous cycle. Age- and cycle-related changes in SgII mRNA content were estimated through cytoplasmic slot blot; SgII content was determined by western blotting; maturation of the protein was controlled through (35S)sulfate labeling. Variations in chromogranin A (CgA), another protein of secretory granules, were analyzed in the same experimental conditions to assess the specificity of SgII regulation. The pituitary SgII concentration increased between days 7 and 21 (2.2-fold) and then declined to the initial 7-day-old value. Simultaneously, the CgA concentration went through a maximum between days 14 and 21 and then strongly dropped to barely detectable levels in the adult pituitary. The SgII mRNA concentration followed roughly the same pattern as the protein. Moreover, the sulfation level remained constant between days 14 and 60. These results demonstrated a regulatory mechanism operating, during sexual maturation, on the SgII gene and not on the protein processing or on storage/release steps. In the 4-day cycling females, the pituitary SgII mRNA and protein contents were the lowest during estrus. They then increased to their highest values in diestrus II. Moreover, the sulfation level of SgII was significantly higher during estrus than during any other stage. Due to its low content level, variations in pituitary CgA could not be demonstrated during the cycle.

Anouar, Y.; Duval, J. (C.U.R.A. 256, Rennes (France))



Lack of HLA class II antigen expression in microsatellite unstable colorectal carcinomas is caused by mutations in HLA class II regulatory genes.  


Colorectal cancers (CRCs) develop on the basis of a deficient DNA mismatch repair (MMR) system in about 15% of cases. MMR-deficient CRC lesions show high-level microsatellite instability (MSI-H) and accumulate numerous mutations located at coding microsatellite loci that lead to the generation of immunogenic neopeptides. Consequently, the host's antitumoral immune response is of high importance for the course of the disease in MSI-H CRC patients. Accordingly, immune evasion mediated by impairment of HLA class I antigen presentation is frequently observed in these cancers. In this study, we aimed at a systematic analysis of alterations affecting HLA class II antigen expression in MSI-H CRC. HLA class II antigens are expressed by only two-thirds of MSI-H CRCs. The mechanisms underlying the lack of HLA class II antigens in a subset of MSI-H CRCs remain unknown. We here screened HLA class II regulatory genes for the presence of coding microsatellites and identified mutations of the essential regulator genes RFX5 in 9 (26.9%) out of 34 and CIITA in 1 (2.9%) out of 34 MSI-H CRCs. RFX5 mutations were related to lack of or faint HLA class II antigen expression (p = 0.006, Fisher's exact test). Transfection with wild-type RFX5 was sufficient to restore interferon gamma-inducible HLA class II antigen expression in the RFX5-mutant cell line HDC108. We conclude that somatic mutations of the RFX5 gene represent a novel mechanism of loss of HLA class II antigen expression in tumor cells, potentially contributing to immune evasion in MSI-H CRCs. PMID:20013806

Michel, Sara; Linnebacher, Michael; Alcaniz, Joshua; Voss, Maike; Wagner, Rudolf; Dippold, Wolfgang; Becker, Christina; von Knebel Doeberitz, Magnus; Ferrone, Soldano; Kloor, Matthias



Sheep exhibit novel variations in the organization of the mammalian type II gonadotropin-releasing hormone receptor gene.  


Species-specific differences in genes encoding type II GnRH receptor indicate that a functional hepta-helical receptor is produced in monkeys but not in rodents, cows, chimpanzees, or humans. To further investigate the extent of evolutionary differences, we sequenced the type II GnRH receptor gene from wild-type Soay sheep. The gene was isolated by long-distance PCR using primers to PEX11beta and RBM8A genes known to flank type II GnRH receptor gene homologues. The gene spans 5.7-kb DNA and was sequenced after shot-gun subcloning. Its novel features include absence of a Pit-1 transcription factor binding site, a premature stop codon (TAG) in exon 1, an in-frame deletion of 51 bp (17 codons) in exon 2, and several nonconservative codon changes. Sheep breed variation in the gene was assessed using genomic DNA in PCR-restriction digest assays for the premature stop codon and in a PCR assay for the deletion. Both characteristics were present in all 15 breeds tested. Receptor gene expression was investigated using poly-A(+) RNA Northern analysis, RT-PCR, and in situ hybridization. An oligonucleotide probe to exon 1 revealed an alternative transcript in testis but not in pituitary gland. No transcripts in testis or pituitary were detectable using an exon 2-3 probe. All tissues examined including multiple brain areas and gonadotrope-enriched cell cultures were negative for type II GnRH receptor in RT-PCR. Testis and pituitary sections were negative with exon 1 riboprobes and exon 1 or 2-3 oligonucleotide probes in in situ hybridization. A hepta-helical type II GnRH receptor is therefore not expressed from this sheep gene. PMID:14749360

Gault, Paula M; Morgan, Kevin; Pawson, Adam J; Millar, Robert P; Lincoln, Gerald A



Microarray analysis of altered gene expression in murine fibroblasts transformed by nickel(II) to nickel(II)-resistant malignant phenotype  

SciTech Connect

B200 cells are Ni(II)-transformed mouse BALB/c-3T3 fibroblasts displaying a malignant phenotype and increased resistance to Ni(II) toxicity. In an attempt to find genes whose expression has been altered by the transformation, the Atlas Mouse Stress/Toxicology cDNA Expression Array (Clontech Laboratories, Inc., Palo Alto, CA) was used to analyze the levels of gene expression in both parental and Ni(II)-transformed cells. Comparison of the results revealed a significant up- or downregulation of the expression of 62 of the 588 genes present in the array (approximately 10.5%) in B200 cells. These genes were assigned to different functional groups, including transcription factors and oncogenes (9/14; fractions in parentheses denote the number of up-regulated versus the total number of genes assigned to this group), stress and DNA damage response genes (11/12), growth factors and hormone receptors (6/9), metabolism (7/7), cell adhesion (2/7), cell cycle (3/6), apoptosis (3/4), and cell proliferation (2/3). Among those genes, overexpression of beta-catenin and its downstream targets c-myc and cyclin D1, together with upregulated cyclin G, points at the malignant character of B200 cells. While the increased expression of glutathione (GSH) synthetase, glutathione-S-transferase A4 (GSTA4), and glutathione-S-transferase theta (GSTT), together with high level of several genes responding to oxidative stress, suggests the enforcement of antioxidant defenses in Ni-transformed cells.

Kowara, Renata [Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, MD 21702 (United States)]. E-mail:; Karaczyn, Aldona [Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, MD 21702 (United States); Cheng, Robert Y.S. [Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, MD 21702 (United States); Salnikow, Konstantin [Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, MD 21702 (United States); Kasprzak, Kazimierz S. [Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, MD 21702 (United States)



Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II {beta} subunit (CSNK2B)  

SciTech Connect

A wide range of autoimmune and other diseases are known to be associated with the major histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility antigens in the class I and class II regions, but some appear to be more strongly associated with genes in the central 1100-kb class III region, making it important to characterize this region fully for the presence of novel genes. An {approximately}220-kb segment of DNA in the class III region separating the Hsp70 (HSPA1L) and BAT1 (D6S8IE) genes, which was previously known to contain 14 genes. Genomic DNA fragments spanning the gaps between the known genes were used as probes to isolate cDNAs corresponding to five new genes within this region. Evidence from Northern blot analysis and exon trapping experiments that suggested the presence of at least two more new genes was also obtained. Partial cDNA and complete exonic genomic sequencing of one of the new genes has identified it as the casein kinase II{beta} subunit (CSNK2B). Two of the other novel genes lie within a region syntenic to that implicated in susceptibility to experimental allergic orchitis in the mouse, an autoimmune disease of the testis, and represent additional candidates for the Orch-1 locus associated with this disease. In addition, characterization of the 13-kb intergenic gap separating the RD (D6545) and G11 (D6S60E) genes has revealed the presence of a gene encoding a 1246-amino-acid polypeptide that shows significant sequence similarity to the yeast anti-viral Ski2p gene product. 49 refs., 8 figs.

Albertella, M.R.; Jones, H.; Thomson, W. [Oxford Univ. (United Kingdom)] [and others



Identification of forensically important Sarcophagidae (Diptera) based on partial mitochondrial cytochrome oxidase I and II genes.  


Entomological evidence is of great importance in forensic cases for postmortem interval calculation. The use of Sarcophagidae (Diptera) for postmortem interval estimation is limited because morphological determination is often hampered because of similar characteristics in the larval, pupal, and even adult stage. To make the species identification more accurate and reliable, DNA-based identification is considered. In this study, we assessed the use of partial mitochondrial cytochrome oxidase I and II genes for discrimination of forensically important Sarcophagidae from Egypt and China [Sarcophaga argyrostoma (Robineau-Desvoidy), Sarcophaga dux (Thomson), Sarcophaga albiceps (Meigen), and Wohlfahrtia nuba (Wiedemann)]. This region was amplified using polymerase chain reaction followed by direct sequencing of the amplification products and using restriction enzymes HinfI and MfeI. Nucleotide sequence divergences were calculated using the Kimura 2-parameter distance model, and a neighbor-joining phylogenetic tree was generated. All examined specimens were assigned to the correct species. Combinations of the restriction enzymes HinfI and MfeI provide different restriction fragment length polymorphism profiles even among 3 sympatric species that belong to the Sarcophaga genus. Therefore, this study demonstrates that the studied partial mitochondrial cytochrome oxidase I and II genes were found to be instrumental for the molecular identification of these forensically important flesh fly species. PMID:23629402

Aly, Sanaa Mohamed; Wen, Jifang; Wang, Xiang



Association of angiotensin-converting enzyme and angiotensin II type I receptor gene polymorphisms with extreme obesity in Polish individuals.  


There is strong evidence for the presence of a functional renin-angiotensin system in human adipose tissue. The aim of our study was to investigate the association of polymorphic variants of angiotensin-converting enzyme gene (ACE I/D) and angiotensin II type I receptor gene (AGTR1 A1166C) with extreme obesity and obesity-associated type 2 diabetes mellitus (T2DM) and to examine their combined effect on extremely obese patients. Overall, no significant associations were detected between ACE and AGTR1 gene polymorphisms and extreme obesity. However, extremely obese patients with T2DM showed an increased frequency of ACE II genotype compared with controls (p<0.05) and with non-diabetic extremely obese patients (p<0.01). The results suggest that II genotype of ACE was a significant contributor to extreme obesity in AA homozygotes of AGTR1 gene, regardless of the presence of T2DM. Moreover, the analysis of genetic polymorphisms demonstrated that ACE II and AGTR1 AC genotypes were most frequently observed in patients with extreme obesity and T2DM. On the basis of our results, we suggest that ACE II homozygosity may be a significant predictor of extreme obesity and T2DM and that the interaction between ACE and AGTR1 genes may be considered a predisposing factor for extreme obesity and extreme obesity-associated T2DM development. PMID:23745680

Pacholczyk, Marta; Ferenc, Tomasz; Kowalski, Jan; Adamczyk, Przemys?aw; Chojnowski, Jacek; Ponikowska, Irena



DEK binding to class II MHC Y-box sequences is gene- and allele-specific.  


Using electrophoretic mobility shift assays, we examined sequence-specific binding of DEK, a potential autoantigen in juvenile rheumatoid arthritis, to conserved Y-box regulatory sequences in class II MHC gene promoters. Nuclear extracts from several cell lines of different phenotypes contained sequence-specific binding activity recognizing DRA, DQA1*0101, and DQA1*0501 Y-box sequences. Participation of both DEK and NF-Y in the DQA1 Y-box binding complex was confirmed by 'supershifting' with anti-DEK and anti-NF-Y antibodies. Recombinant DEK also bound specifically to the DQA1*0101 Y box and to the polymorphic DQA1*0501 Y box, but not to the consensus DRA Y box. Measurement of the apparent dissociation constants demonstrated a two- to fivefold difference in DEK binding to the DQA1 Y-box sequence in comparison with other class II MHC Y-box sequences. Residues that are crucial for DEK binding to the DQA1*0101 Y box were identified by DNase I footprinting. The specific characteristics of DEK binding to these related sequences suggests a potential role for DEK in differential regulation of class II MHC expression, and thus in the pathogenesis of juvenile rheumatoid arthritis and other autoimmune diseases. PMID:12823858

Adams, Barbara S; Cha, Hyuk C; Cleary, Joanne; Haiying, Tan; Wang, Hongling; Sitwala, Kajal; Markovitz, David M



Spread of Recombinant DNA by Roots and Pollen of Transgenic Potato Plants, Identified by Highly Specific Biomonitoring Using Natural Transformation of an Acinetobacter sp  

Microsoft Academic Search

Transgenic potato plants with the nptII gene coding for neomycin phosphotransferase (kanamycin resis- tance) as a selection marker were examined for the spread of recombinant DNA into the environment. We used the recombinant fusion of nptII with the tg4 terminator for a novel biomonitoring technique. This depended on natural transformation of Acinetobacter sp. strain BD413 cells having in their genomes

Johann de Vries; Martin Heine; Klaus Harms; Wilfried Wackernagel



Identification and mapping of two divergent, unlinked major histocompatibility complex class II B genes in Xiphophorus fishes.  

PubMed Central

We have isolated two major histocompatibility complex (MHC) class II B genes from the inbred fish strain Xiphophorus maculatus Jp 163 A. We mapped one of these genes, designated here as DXB, to linkage group III, linked to a malic enzyme locus, also syntenic with human and mouse MHC. Comparison of genomic and cDNA clones shows the gene consists of six exons and five introns. The encoded beta1 domain has three amino acids deleted and a cytoplasmic tail nine amino acids longer than in other teleost class II beta chains, more similar to HLA-DRB, clawed frog Xela-F3, and nurse shark Gici-B. Key residues for disulfide bonds, glycosylation, and interaction with alpha chains are conserved. These same features are also present in a swordtail (Xiphophorus helleri) genomic DXB PCR clone. A second type of class II B clone was amplified by PCR from X. maculatus and found to be orthologous to class II genes identified in other fishes. This DAB-like gene is 63% identical to the X. maculatus DXB sequence in the conserved beta2-encoding exon and was mapped to new unassigned linkage group LG U24. The DXB gene, then, represents an unlinked duplicated locus not previously identified in teleosts.

McConnell, T J; Godwin, U B; Norton, S F; Nairn, R S; Kazianis, S; Morizot, D C



Genetic diversity of the flagellin genes of Clostridium botulinum groups I and II.  


Botulinum neurotoxins (BoNTs) are produced by phenotypically and genetically different Clostridium species, including Clostridium botulinum and some strains of Clostridium baratii (serotype F) and Clostridium butyricum (serotype E). BoNT-producing clostridia responsible for human botulism encompass strains of group I (secreting proteases, producing toxin serotype A, B, or F, and growing optimally at 37°C) and group II (nonproteolytic, producing toxin serotype E, B, or F, and growing optimally at 30°C). Here we report the development of real-time PCR assays for genotyping C. botulinum strains of groups I and II based on flaVR (variable region sequence of flaA) sequences and the flaB gene. Real-time PCR typing of regions flaVR1 to flaVR10 and flaB was optimized and validated with 62 historical and Canadian C. botulinum strains that had been previously typed. Analysis of 210 isolates of European origin allowed the identification of four new C. botulinum flaVR types (flaVR11 to flaVR14) and one new flaVR type specific to C. butyricum type E (flaVR15). The genetic diversity of the flaVR among C. botulinum strains investigated in the present study reveals the clustering of flaVR types into 5 major subgroups. Subgroups 1, 3, and 4 contain proteolytic Clostridium botulinum, subgroup 2 is made up of nonproteolytic C. botulinum only, and subgroup 5 is specific to C. butyricum type E. The genetic variability of the flagellin genes carried by C. botulinum and the possible association of flaVR types with certain geographical areas make gene profiling of flaVR and flaB promising in molecular surveillance and epidemiology of C. botulinum. PMID:23603687

Woudstra, Cedric; Lambert, Dominic; Anniballi, Fabrizio; De Medici, Dario; Austin, John; Fach, Patrick



Structure, expression and function of Allomyces arbuscula CDP II (metacaspase) gene.  


Allomyces arbuscula, a primitive chytridiomycete fungus, has two Ca(2+)-dependent cysteine proteases, the CDP I and CDP II. We have cloned and analyzed the nucleotide sequence of CDP II gene and domain structure of the protein. Blast analysis of the sequence has shown that the protein belongs to a newly described member of caspase superfamily protein, the metacaspase, a CD clan of C14 family cysteine protease, we hence-forth name it as AMca 2 (Allomyces metacaspase 2). Southern hybridization studies have shown that the gene exists in a single copy per genome. The transcriptional analysis by Northern hybridization has confirmed our previous results that the protein is developmentally regulated, i.e. present in active growth phase but disappears during nutritional stress which also induces reproductive differentiation, indicating that the protein promotes cell growth, not death. The recombinant gene product expressed in Escherichiacoli has all the catalytic properties of native enzyme, i.e. sensitivity to protease inhibitors and substrate specificity. There is an absolute requirement of Ca(2+) for the activation of catalytic activity and the presence of R residue at the cleavage site (P1 position) in the substrate. The presence of a second basic residue, either R or K, in the P2 position strongly inhibits the catalytic activity which is stimulated by the presence of P and to a lesser extent G at this site. Peptide substrates with D at the cleavage site are not recognised and therefore not cleaved. The enzyme activity is inhibited by EDTA-EGTA, cysteine protease inhibitors and a specific peptide inhibitor Ac GVRCHCL TFA, but not by E64, although a potent inhibitor of cysteine proteases. PMID:20214955

Ojha, Mukti; Cattaneo, Arlette; Hugh, Séverine; Pawlowski, Jan; Cox, Jos A



Restriction for gene insertion within the Lactococcus lactis Ll.LtrB group II intron.  


The Ll.LtrB intron, from the low G+C gram-positive bacterium Lactococcus lactis, was the first bacterial group II intron shown to splice and mobilize in vivo. The detailed retrohoming and retrotransposition pathways of Ll.LtrB were studied in both L. lactis and Escherichia coli. This bacterial retroelement has many features that would make it a good gene delivery vector. Here we report that the mobility efficiency of Ll.LtrB expressing LtrA in trans is only slightly affected by the insertion of fragments <100 nucleotides within the loop region of domain IV. In contrast, Ll.LtrB mobility efficiency is drastically decreased by the insertion of foreign sequences >1 kb. We demonstrate that the inhibitory effect caused by the addition of expression cassettes on Ll.LtrB mobility efficiency is not sequence specific, and not due to the expression, or the toxicity, of the cargo genes. Using genetic screens, we demonstrate that in order to maintain intron mobility, the loop region of domain IV, more specifically domain IVb, is by far the best region to insert foreign sequences within Ll.LtrB. Poisoned primer extension and Northern blot analyses reveal that Ll.LtrB constructs harboring cargo sequences splice less efficiently, and show a significant reduction in lariat accumulation in L. lactis. This suggests that cargo-containing Ll.LtrB variants are less stable. These results reveal the potential, yet limitations, of the Ll.LtrB group II intron to be used as a gene delivery vector, and validate the random insertion approach described in this study to create cargo-containing Ll.LtrB variants that are mobile. PMID:16973892

Plante, Isabelle; Cousineau, Benoit



RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes  

PubMed Central

We investigated co-transcriptional recruitment of pre-mRNA processing factors to human genes. Capping factors associate with paused RNA pol II at the 5? ends of quiescent genes. They also track throughout actively transcribed genes, and accumulate with paused polymerase in the 3? flanking region. 3? processing factors CstF and CPSF are maximally recruited 0.5-1.5 kb downstream of poly(A) sites where they coincide with capping factors, Spt5, and Ser2 hyperphosphorylated, paused pol II. 3? end processing factors also localize at transcription start sites, and this early recruitment is enhanced after polymerase arrest with DRB. These results suggest that promoters may help specify recruitment of 3? end processing factors. We propose a dual pausing model where elongation arrests near the transcription start site and in the 3? flank to allow co-transcriptional processing by factors recruited to the pol II ternary complex.

Glover-Cutter, Kira; Kim, Soojin; Espinosa, Joaquin; Bentley, David L.



ZBTB32 is an early repressor of the class II transactivator and MHC class II gene expression during B cell differentiation to plasma cells1  

PubMed Central

The MHC class II transactivator (CIITA) and MHC class II expression is silenced during the differentiation of B cells to plasma cells. When B cell differentiation is carried out ex vivo, CIITA silencing occurs rapidly but the factors contributing to this event are not known. ZBTB32, also known as repressor of GATA3, was identified as an early repressor of CIITA in an ex vivo plasma cell differentiation model. ZBTB32 activity occurred at a time when Blimp-1, the regulator of plasma cell fate and suppressor of CIITA, was minimally induced. Ectopic expression of ZBTB32 suppressed CIITA and I-A gene expression in B cells. ShRNA depletion of ZBTB32 in a plasma cell line resulted in reexpression of CIITA and I-A. Compared to conditional Blimp-1 knock out and wild-type B cells, B cells from ZBTB32/ROG-knock out mice displayed delayed kinetics in silencing CIITA during ex vivo plasma cell differentiation. ZBTB32 was found to bind to the CIITA gene, suggesting that ZBTB32 directly regulates CIITA. Lastly, ZBTB32 and Blimp-1 coimmunoprecipitated, suggesting that the two repressors may ultimately function together to silence CIITA expression. These results introduce ZBTB32 as a novel regulator of MHC-II gene expression and a potential regulatory partner of Blimp-1 in repressing gene expression.

Yoon, Hyesuk; Scharer, Christopher D.; Majumder, Parimal; Davis, Carl W.; Butler, Royce; Zinzow-Kramer, Wendy; Skountzou, Ioanna; Koutsonanos, Dimitrios G.; Ahmed, Rafi; Boss, Jeremy M.



The gene encoding the large subunit of human RNA polymerase II is located on the short arm of chromosome 17.  

PubMed Central

We have used chromosomal in situ hybridization and Southern blot analysis of DNA from somatic cell hybrids to determine the chromosomal localization of the subgenomic DNA fragment that encodes part of the large subunit of human RNA polymerase II. The results of our analysis demonstrate localization of the human RNA polymerase II large subunit gene to the short arm of chromosome 17. Images Fig. 2 Fig. 4

Cannizzaro, L A; Emanuel, B S; Cho, K W; Weinmann, R



Support for the minimal essential MHC hypothesis: a parrot with a single, highly polymorphic MHC class II B gene  

Microsoft Academic Search

We characterized the MHC class II B gene in the green-rumped parrotlet, Forpus passerinus. Three approaches were used: polymerase chain reaction amplification using primers complementary to conserved regions of\\u000a exon 2, sequencing clones from a genomic library, and amplification of exon 2 using species-specific primers. All three methods\\u000a indicate that there is only a single class II B locus in

Colin R. Hughes; Shana Miles; Jaclyn M. Walbroehl



Characterization of a 300 kbp Region of Human DNA Containing the Type II Hair Keratin Gene Domain  

Microsoft Academic Search

Screening of an arrayed human genomic P1 artificial chromosome DNA library by means of the polymerase chain reaction with a specific primer pair from the human type II hair keratin hHb5 yielded two P1 artificial chromosome clones covering ?300 kb of genomic DNA. The contig contained six type II hair keratin genes, hHb1–hHb6, and four keratin pseudogenes ?hHbA–?hHbD. This hair

Michael A. Rogers; Hermelita Winter; Lutz Langbein; Christian Wolf; Jürgen Schweizer



DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli.  

PubMed Central

The structural gene for DNA polymerase II was cloned by using a synthetic inosine-containing oligonucleotide probe corresponding to 11 amino acids, which were determined by sequencing the amino terminus of the purified protein. The labeled oligonucleotide hybridized specifically to the lambda clone 7H9 from the Kohara collection as well as to plasmid pGW511 containing the SOS-regulated dinA gene. Approximately 1400 base pairs of dinA sequence were determined. The predicted amino-terminal sequence of dinA demonstrated that this gene encoded DNA polymerase II. Sequence analysis of the upstream region localized a LexA binding site overlapping the -35 region of the dinA promoter, and this promoter element was found to be only two nucleotides downstream from the 3' end of the araD gene. These results demonstrate that the gene order is thr-dinA (pol II)-ara-leu on the Escherichia coli chromosome and that the DNA polymerase II structural gene is transcribed in the same direction as the araBAD operon. Based on the analysis of the predicted protein, we have identified a sequence motif Asp-Xaa-Xaa-Ser-Leu-Tyr-Pro-Ser in DNA polymerase II that is highly conserved among a diverse group of DNA polymerases, which include those from humans, yeast, Herpes and vaccinia viruses, and phages T4 and PRD1. The demonstration that DNA polymerase II is a component of the SOS response in E. coli suggests that it plays an important role in DNA repair and/or mutagenesis. Images

Bonner, C A; Hays, S; McEntee, K; Goodman, M F



Expression of carbonic anhydrase II (CA II) promoter-reporter fusion genes in multiple tissues of transgenic mice does not replicate normal patterns of expression indicating complexity of CA II regulation in vivo  

SciTech Connect

Although the proximal, 5{prime} 115 bp of the human carbonic anhydrase II (CA II) gene was sufficient for expression of a reporter gene in some transfected cell lines, we found previously that 1100 bp of this promoter (or 500 bp of the mouse CA II promoter) was not sufficient for expression in transgenic mice. We have now studied the expression of linked reporter genes in mice transgenic for either (1) 11 kb of the human 5{prime} promoter or (2) 8 kb of the human 5{prime} promoter with mouse sequences from the first exon, part of the first intron (since a CpG island spans this region), and the 3{prime} sequences of the gene. Expression was found in both cases, but the tissue specificity was not appropriate for CA II. Although there was a difference in the sensitivity of the assays used, the first construct led to expression in many tissues, while the second construct was expressed only in spleen. These findings indicate considerable complexity of DNA control regions for in vivo CA II expression. 34 refs., 6 figs., 2 tabs.

Erickson, R.P.; Grimes, J. [Univ. of Arizona, Tucson, AZ (United States); Venta, P.J.; Tashian, R.E. [Univ. of Michigan School of Medicine, Ann Arbor, MI (United States)



Identification of the HSP70-II gene in Leishmania braziliensis HSP70 locus: genomic organization and UTRs characterization  

PubMed Central

Background The heat stress suffered by Leishmania sp during its digenetic life-cycle is a key trigger for its stage differentiation. In Leishmania subgenera two classes of HSP70 genes differing in their 3' UTR were described. Although the presence of HSP70-I genes was previously suggested in Leishmania (Viannia) braziliensis, HSP70-II genes had been reluctant to be uncovered. Results Here, we report the existence of two types of HSP70 genes in L. braziliensis and the genomic organization of the HSP70 locus. RT-PCR experiments were used to map the untranslated regions (UTR) of both types of genes. The 3' UTR-II has a low sequence identity (55-57%) when compared with this region in other Leishmania species. In contrast, the 5' UTR, common to both types of genes, and the 3' UTR-I were found to be highly conserved among all Leishmania species (77-81%). Southern blot assays suggested that L. braziliensis HSP70 gene cluster may contain around 6 tandemly-repeated HSP70-I genes followed by one HSP70-II gene, located at chromosome 28. Northern blot analysis indicated that levels of both types of mRNAs are not affected by heat shock. Conclusions This study has led to establishing the composition and structure of the HSP70 locus of L. braziliensis, complementing the information available in the GeneDB genome database for this species. L. braziliensis HSP70 gene regulation does not seem to operate by mRNA stabilization as occurs in other Leishmania species.



Role of Reactive Oxygen Species-Sensitive Extracellular Signal-Regulated Kinase Pathway in Angiotensin II-Induced Endothelin1 Gene Expression in Vascular Endothelial Cells  

Microsoft Academic Search

Background: Circulating angiotensin II (Ang II) increases vascular endothelin-1 (ET-1) tissue levels, which in turn mediate a major part of Ang II-stimulated vascular growth and hypertension in vivo. Ang II also stimulates the generation of reactive oxygen species (ROS) within vascular endothelial cells. However, whether ROS are involved in Ang II-induced ET-1 gene expression, and the related intracellular mechanisms occurring

Yung-Ho Hsu; Jin-Jer Chen; Nen-Chung Chang; Cheng-Hsien Chen; Ju-Chi Liu; Tso-Hsiao Chen; Cherng-Jye Jeng; Hung-Hsing Chao; Tzu-Hurng Cheng



Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation  

PubMed Central

Purpose During retinal development, post-mitotic neural progenitor cells must activate thousands of genes to complete synaptogenesis and terminal maturation. While many of these genes are known, others remain beyond the sensitivity of expression microarray analysis. Some of these elusive gene activation events can be detected by mapping changes in RNA polymerase-II (Pol-II) association around transcription start sites. Methods High-resolution (35 bp) chromatin immunoprecipitation (ChIP)-on-chip was used to map changes in Pol-II binding surrounding 26,000 gene transcription start sites during photoreceptor maturation of the mouse neural retina, comparing postnatal age 25 (P25) to P2. Coverage was 10–12 kb per transcription start site, including 2.5 kb downstream. Pol-II-active regions were mapped to the mouse genomic DNA sequence by using computational methods (Tiling Analysis Software-TAS program), and the ratio of maximum Pol-II binding (P25/P2) was calculated for each gene. A validation set of 36 genes (3%), representing a full range of Pol-II signal ratios (P25/P2), were examined with quantitative ChIP assays for transcriptionally active Pol-II. Gene expression assays were also performed for 19 genes of the validation set, again on independent samples. FLT-3 Interacting Zinc-finger-1 (FIZ1), a zinc-finger protein that associates with active promoter complexes of photoreceptor-specific genes, provided an additional ChIP marker to highlight genes activated in the mature neural retina. To demonstrate the use of ChIP-on-chip predictions to find novel gene activation events, four additional genes were selected for quantitative PCR analysis (qRT–PCR analysis); these four genes have human homologs located in unidentified retinal disease regions: Solute carrier family 25 member 33 (Slc25a33), Lysophosphatidylcholine acyltransferase 1 (Lpcat1), Coiled-coil domain-containing 126 (Ccdc126), and ADP-ribosylation factor-like 4D (Arl4d). Results ChIP-on-chip Pol-II peak signal ratios >1.8 predicted increased amounts of transcribing Pol-II and increased expression with an estimated 97% accuracy, based on analysis of the validation gene set. Using this threshold ratio, 1,101 genes were predicted to experience increased binding of Pol-II in their promoter regions during terminal maturation of the neural retina. Over 800 of these gene activations were additional to those previously reported by microarray analysis. Slc25a33, Lpcat1, Ccdc126, and Arl4d increased expression significantly (p<0.001) during photoreceptor maturation. Expression of all four genes was diminished in adult retinas lacking rod photoreceptors (Rd1 mice) compared to normal retinas (90% loss for Ccdc126 and Arl4d). For rhodopsin (Rho), a marker of photoreceptor maturation, two regions of maximum Pol-II signal corresponded to the upstream rhodopsin enhancer region and the rhodopsin proximal promoter region. Conclusions High-resolution maps of Pol-II binding around transcription start sites were generated for the postnatal mouse retina; which can predict activation increases for a specific gene of interest. Novel gene activation predictions are enriched for biologic functions relevant to vision, neural function, and chromatin regulation. Use of the data set to detect novel activation increases was demonstrated by expression analysis for several genes that have human homologs located within unidentified retinal disease regions: Slc25a33, Lpcat1, Ccdc126, and Arl4d. Analysis of photoreceptor-deficient retinas indicated that all four genes are expressed in photoreceptors. Genome-wide maps of Pol-II binding were developed for visual access in the University of California, Santa Cruz (UCSC) Genome Browser and its eye-centric version EyeBrowse (National Eye Institute-NEI). Single promoter resolution of Pol-II distribution patterns suggest the Rho enhancer region and the Rho proximal promoter region become closely associated with the activated gene’s promoter complex.

Tummala, Padmaja; Mali, Raghuveer S.; Guzman, Eduardo; Zhang, Xiao



Laminar Shear Stress Modulates Phosphorylation and Localization of RNA Polymerase II on the Endothelial Nitric Oxide Synthase Gene  

PubMed Central

Objective In endothelial cells exposed to unidirectional, laminar shear stress (LSS), eNOS transcription, mRNA stability, and protein levels are enhanced. We have previously demonstrated that these changes are associated with increased 3? polyadenylation of eNOS mRNA. Here, we investigated the effect of LSS on the phosphorylation and localization RNA Polymerase (Pol) II, the enzyme primarily responsible for coordinating transcription and posttranscriptional processing. Methods and Results Using Western and chromatin immunoprecipitation (ChIP) analyses, Pol II phosphorylation and localization on the eNOS gene were assessed in bovine aortic endothelial cells (BAECs) exposed to LSS. Total Pol II (phosphorylated and unphosphorylated) levels were increased 65% in response to LSS. This was associated with an increase in Pol II phospho-serine 2, but no change in levels of the unphosphorylated or phospho-serine 5 isoforms. Quantitative ChIP analysis showed that LSS enhanced binding of Pol II phospho-serine 2 to the 3? end of the eNOS gene, particularly exon 26, which encodes the 3?UTR. Treatment of cells with DRB attenuated LSS-induced Pol II phosphorylation, eNOS 3? polyadenylation, and eNOS expression. Conclusion These data suggest that LSS enhances eNOS mRNA 3? polyadenylation by modulating phosphorylation and localization of Pol II.

Moore, Jeffrey P.; Weber, Martina; Searles, Charles D.



Contact with a component of the polymerase II holoenzyme suffices for gene activation.  


In yeast strains bearing the point mutation called GAL11P (for potentiator), certain GAL4 derivatives lacking any classical activating region work as strong activators. The P mutation confers upon GAL11, a component of the RNA polymerase II holoenzyme, the ability to interact with a portion of the dimerization region of GAL4. The region of GAL11 affected by the P mutation is evidently functionally inert in ordinary cells, suggesting that this mutation is of no functional significance beyond creating an artificial target for the GAL4 dimerization fragment. From these observations and further analyses of GAL11, we propose that a single activator-holoenzyme contact can trigger gene activation simply by recruiting the latter to DNA. PMID:7736588

Barberis, A; Pearlberg, J; Simkovich, N; Farrell, S; Reinagel, P; Bamdad, C; Sigal, G; Ptashne, M



DNA Polymerase II is Encoded by the DNA Damage-Inducible dinA Gene of Escherichia coli  

Microsoft Academic Search

The structural gene for DNA polymerase II was cloned by using a synthetic inosine-containing oligonucleotide probe corresponding to 11 amino acids, which were determined by sequencing the amino terminus of the purified protein. The labeled oligonucleotide hybridized specifically to the lambda clone 7H9 from the Kohara collection as well as to plasmid pGW511 containing the SOS-regulated dinA gene. Approximately 1400

Cynthia A. Bonner; Sharon Hays; Kevin McEntee; Myron F. Goodman



A genetic variation in the PGC1 gene could confer insulin resistance and susceptibility to Type II diabetes  

Microsoft Academic Search

Aims\\/hypothesis. Peroxisome proliferator activated receptor % coactivator-1 (PGC-1), a transcriptional coactivator of the nuclear receptor PPAR%, plays a role in adaptive thermogenesis and insulin sensitivity. Plasma fasting insulin has been linked to the chromosomal region where the PGC-1 gene is located. Thus, PGC-1 can be viewed as a functional and positional candidate for the susceptibility gene for Type II (non-insulin-dependent)

K. Hara; K. Tobe; T. Okada; H. Kadowaki; Y. Akanuma; C. Ito; S. Kimura; T. Kadowaki



Molecular analysis and mapping of two genes encoding maize glutathione S-transferases (GST I and GST II)  

Microsoft Academic Search

Maize glutathione S-transferase (GST) isozymes are encoded by a gene family comprising at least five genes, three of which\\u000a (Gst I, II andIII) have recently been isolated and sequenced. The enzymes are active as homo or heterodimers and exhibit intraspecific polymorphism\\u000a including a “null” variant for the two major isoforms expressed in roots. Northern blot analyses performed on total root

L. Rossini; M. E. Pč; C. Frova; K. Hein; M. Sari-Gorla



Majewski osteodysplastic primordial dwarfism type II (MOPD II) syndrome previously diagnosed as Seckel syndrome: report of a novel mutation of the PCNT gene.  


We report on a 3-year-old boy with prenatal onset of proportionate dwarfism, postnatal severe microcephaly, high forehead with receded hairline, sparse scalp hair, beaked nose, mild retrognathia and hypotonia diagnosed at birth as Seckel syndrome. At age 3 years, he became paralyzed due to a cerebrovascular malformation. Based on the clinical and radiological features showing evidence of skeletal dysplasia, the diagnosis was revised to Majewski osteodysplastic primordial dwarfism type II (MOPD II) syndrome. Western blot analysis of the patient's lymphoblastoid cell line lysate showed the absence of the protein pericentrin. Subsequent molecular analysis identified a novel homozygous single base insertion (c.1527_1528insA) in exon 10 of the PCNT gene, which leads to a frameshift (Treo510fs) and to premature protein truncation. PCNT mutations must be considered diagnostic of MOPD II syndrome. A possible role of pericentrin in the development of cerebral vessels is suggested. PMID:19839044

Piane, Maria; Della Monica, Matteo; Piatelli, Gianluca; Lulli, Patrizia; Lonardo, Fortunato; Chessa, Luciana; Scarano, Gioacchino



Type I collagen formation in rat type II alveolar cells immortalised by viral gene products.  

PubMed Central

BACKGROUND--Alveolar type II (T2) cells synthesise matrix proteins such as type IV collagen and fibronectin. In contrast, a fetal rat T2 cell line has been shown to synthesise type I and III collagen as well as type IV collagen. To study regulation of collagen production in T2 cells, neonatal T2 cells immortalised by adenoviral 12SE1A gene transfer were used. It was previously reported that this immortalised cell line (E1A-T2) retains epithelial features such as tight junctions and cytokeratins but also expresses mesenchymal features such as vimentin. METHODS--Collagen production was examined in E1A-T2 and primary neonatal T2 cells using polyacrylamide gel electrophoresis. Electron microscopy was used to examine collagen deposition in E1A-T2 cell culture. To define the mechanism by which alpha 1(I) type I collagen gene expression was activated in E1A-T2 cells, a deletional analysis of alpha 1(I) promoter constructs linked to the bacterial chloramphenicol acetyltransferase gene was performed. RESULTS--E1A-T2 cells produced large amounts of type I collagen with a predominance of alpha 1(I) homotrimers; alpha 2(I) peptides were detected only in the cell layer. In contrast, primary neonatal rat T2 cell cultures produced a trace amount of type I collagen. Production of alpha 1(I) peptide chains (per microgram DNA) in E1A-T2 cell cultures was 30 times higher than that observed in primary neonatal T2 cell cultures. Electron microscopy showed deposition of type I collagen fibrils in the extracellular matrix of E1A-T2 cell cultures. Transfection studies suggested at least two cis-acting elements which mediate increased alpha 1(I) gene expression in E1A-T2 cells. CONCLUSIONS--These studies indicate that the E1A-T2 cell line may be useful for studying type I collagen gene regulation in alveolar T2 cells. These findings also raise the possibility that viral activation of type I collagen genes in alveolar epithelium may be involved in certain forms of pulmonary fibrosis. Images

Matsui, R; Goldstein, R H; Mihal, K; Brody, J S; Steele, M P; Fine, A



Interfacial stress affects rat alveolar type II cell signaling and gene expression  

PubMed Central

Previous work from our group (Ravasio A, Hobi N, Bertocchi C, Jesacher A, Dietl P, Haller T. Am J Physiol Cell Physiol 300: C1456–C1465, 2011.) showed that contact of alveolar epithelial type II cells with an air-liquid interface (IAL) leads to a paradoxical situation. It is a potential threat that can cause cell injury, but also a Ca2+-dependent stimulus for surfactant secretion. Both events can be explained by the impact of interfacial tensile forces on cellular structures. Here, the strength of this mechanical stimulus became also apparent in microarray studies by a rapid and significant change on the transcriptional level. Cells challenged with an IAL in two different ways showed activation/inactivation of cellular pathways involved in stress response and defense, and a detailed Pubmatrix search identified genes associated with several lung diseases and injuries. Altogether, they suggest a close relationship of interfacial stress sensation with current models in alveolar micromechanics. Further similarities between IAL and cell stretch were found with respect to the underlying signaling events. The source of Ca2+ was extracellular, and the transmembrane Ca2+ entry pathway suggests the involvement of a mechanosensitive channel. We conclude that alveolar type II cells, due to their location and morphology, are specific sensors of the IAL, but largely protected from interfacial stress by surfactant release.

Hobi, Nina; Ravasio, Andrea



Interfacial stress affects rat alveolar type II cell signaling and gene expression.  


Previous work from our group (Ravasio A, Hobi N, Bertocchi C, Jesacher A, Dietl P, Haller T. Am J Physiol Cell Physiol 300: C1456-C1465, 2011.) showed that contact of alveolar epithelial type II cells with an air-liquid interface (I(AL)) leads to a paradoxical situation. It is a potential threat that can cause cell injury, but also a Ca(2+)-dependent stimulus for surfactant secretion. Both events can be explained by the impact of interfacial tensile forces on cellular structures. Here, the strength of this mechanical stimulus became also apparent in microarray studies by a rapid and significant change on the transcriptional level. Cells challenged with an I(AL) in two different ways showed activation/inactivation of cellular pathways involved in stress response and defense, and a detailed Pubmatrix search identified genes associated with several lung diseases and injuries. Altogether, they suggest a close relationship of interfacial stress sensation with current models in alveolar micromechanics. Further similarities between I(AL) and cell stretch were found with respect to the underlying signaling events. The source of Ca(2+) was extracellular, and the transmembrane Ca(2+) entry pathway suggests the involvement of a mechanosensitive channel. We conclude that alveolar type II cells, due to their location and morphology, are specific sensors of the I(AL), but largely protected from interfacial stress by surfactant release. PMID:22610352

Hobi, Nina; Ravasio, Andrea; Haller, Thomas



Cellulosic Ethanol Production by Recombinant Cellulolytic Bacteria Harbouring pdc and adh II Genes of Zymomonas mobilis  

PubMed Central

The ethanol fermenting genes such as pyruvate decarboxylase (pdc) and alcohol dehydrogenase II (adh II) were cloned from Zymomonas mobilis and transformed into three different cellulolytic bacteria, namely Enterobacter cloacae JV, Proteus mirabilis JV and Erwinia chrysanthemi and their cellulosic ethanol production capability was studied. Recombinant E. cloacae JV was found to produce 4.5% and 3.5% (v/v) ethanol, respectively, when CMC and 4% NaOH pretreated bagasse were used as substrates, whereas recombinant P. mirabilis and E. chrysanthemi with the same substrates could only produce 4%, 3.5%, 1%, and 1.5 % of ethanol, respectively. The recombinant E. cloacae strain produced twofold higher percentage of ethanol than the wild type. The recombinant E. cloacae strain could be improved further by increasing its ethanol tolerance capability through media optimization and also by combining multigene cellulase expression for enhancing ethanol production from various types of lignocellulosic biomass so that it can be used for industrial level ethanol production.

Piriya, P. Sobana; Vasan, P. Thirumalai; Padma, V. S.; Vidhyadevi, U.; Archana, K.; Vennison, S. John



Regulation of genes encoding PS I and PS II proteins in Synechocystis  

SciTech Connect

The mechanisms of regulation of the genes encoding PS I and PS II components are largely unknown for the unicellular cyanobacterium Synechocystis sp. PCC 6803. In an attempt to elucidate how PS I and PS II biogenesis is controlled, we have isolated RNA from cells grown in various light conditions and analyzed relative steady-state levels of transcripts on Northern blots. Results from blots probed with psaA and psaB (which we recently cloned and sequenced) as well as previously isolated clones for psbA1, psbA2, psbD2, psaD, rbcL, and rrn will be presented. Preliminary data indicate the psbA and psaA-psaB transcripts accumulate in cells put in the dark, although the psaA-psaB transcript levels are somewhat reduced in the dark. Future experiments will focus on molecular analysis of the promoter region for the psaA-psaB operon.

Smart, L.B.; McIntosh, L. (Michigan State Univ., East Lansing (USA))



?????????? ??? ?????? ?????????? ????????????: ????????? II ??????? ??????? ?? ????  

Microsoft Academic Search

The article discusses the image of Catherine II in the context of the French anti-monarchist pamphlets that abounded after the French revolution and were often directed at the Russian empress as well, representing her as the “Semiramis of the North”. A special case is Marquis de Sade?s Histoire de Juliette, ou les Prospérités du vice, which unmistakably refers to Catherine

Alexandre Stroev



Major histocompatibility complex haplotypes and class II genes in non-Jewish patients with pemphigus vulgaris  

SciTech Connect

Previous studies demonstrated that HLA-DR4 was markedly increased among Ashkenazi Jewish patients with pemphigus vulgaris (PV), almost entirely as the common Jewish extended haplotype (HLA-B38, SC21, DR4, DQw8) or as the haplotype HLA-B35, SC31, DR4, DQw8, and that HLA-DR4, DQw8 was distributed among patients in a manner consistent with dominant expression of a class II (D-region or D-region-linked) susceptibility gene. In the present study of major histocompatibility complex (MHC) halotypes in 25 non-Jewish PV patients, DR4, DQw8 was found in 12 of the patients and DRw6, DQw5 was found in 15. Only 3 patients had neither. The non-Jewish patients were of more Southern European extraction than our controls. This suggests that there are two major MHC susceptibility alleles in American patients with PV. The more ancient apparently arose on a haplotype in the Jews, HLA-B38(35), SC21(SC31), DR4, DQw8, and spread to other populations largely as D-region segments. The other arose in or near Italy on the haplotype HLA-Bw55, SB45, DRw14, DQw5 amd has also partially fragmented so that many patients carry only DRw14, DQw5. The available data do not permit the specific localization of either the DR4, DQw8-or the DRw14, DQw5-linked susceptibility genes.

Ahmed, A.R. (Harvard School of Dental Medicine, Boston, MA (United States) Center for Blood Research, Boston, MA (United States) American Red Cross Blood Services-Northeast Region, Dedham, MA (United States)); Wagner, R.; Khatri, K.; Notani, G.; Awdeh, Z.; Alper, C.A. (Center for Blood Research, Boston, MA (United States)); Yunis, E.J. (Center for Blood Research, Boston, MA (United States) American Red Cross Blood Services-Northeast Region, Dedham, MA (United States))



Genetic and expression studies of SMN2 gene in Russian patients with spinal muscular atrophy type II and III  

PubMed Central

Background Spinal muscular atrophy (SMA type I, II and III) is an autosomal recessive neuromuscular disorder caused by mutations in the survival motor neuron gene (SMN1). SMN2 is a centromeric copy gene that has been characterized as a major modifier of SMA severity. SMA type I patients have one or two SMN2 copies while most SMA type II patients carry three SMN2 copies and SMA III patients have three or four SMN2 copies. The SMN1 gene produces a full-length transcript (FL-SMN) while SMN2 is only able to produce a small portion of the FL-SMN because of a splice mutation which results in the production of abnormal SMN?7 mRNA. Methods In this study we performed quantification of the SMN2 gene copy number in Russian patients affected by SMA type II and III (42 and 19 patients, respectively) by means of real-time PCR. Moreover, we present two families consisting of asymptomatic carriers of a homozygous absence of the SMN1 gene. We also developed a novel RT-qPCR-based assay to determine the FL-SMN/SMN?7 mRNA ratio as SMA biomarker. Results Comparison of the SMN2 copy number and clinical features revealed a significant correlation between mild clinical phenotype (SMA type III) and presence of four copies of the SMN2 gene. In both asymptomatic cases we found an increased number of SMN2 copies in the healthy carriers and a biallelic SMN1 absence. Furthermore, the novel assay revealed a difference between SMA patients and healthy controls. Conclusions We suggest that the SMN2 gene copy quantification in SMA patients could be used as a prognostic tool for discrimination between the SMA type II and SMA type III diagnoses, whereas the FL-SMN/SMN?7 mRNA ratio could be a useful biomarker for detecting changes during SMA pharmacotherapy.



A novel P gene missense mutation in a Japanese patient with oculocutaneous albinism type II (OCA2)  

Microsoft Academic Search

Background: Oculocutaneous albinism type II (OCA2) is an autosomal recessively inherited disorder, characterized by white hair and skin, and loss of pigment in the eyes. Mutaions in P gene have been shown to result in OCA2. So far, two cases have been reported from Japan. Objective: We had an opportunity to examine a case of albinism, and screened the mutations

Atsushi Kato; Kazuyoshi Fukai; Naoki Oiso; Naoko Hosomi; Shinji Saitoh; Takahito Wada; Hiroshi Shimizu; Masamitsu Ishii



Low diversity in the major histocompatibility complex class II DRB1 gene of the Spanish ibex, Capra pyrenaica  

Microsoft Academic Search

During the last two centuries, the Spanish ibex (Capra pyrenaica) has shown a significant demographic decline as a result of the progressive destruction of its natural habitat, disease epidemics, and uncontrolled hunting. Partial sequencing of the class II MHC DRB1 gene revealed that the Spanish ibex has remarkably low levels of genetic variation at this locus, with only six different

M Amills; N Jiménez; J Jordana; A Riccardi; A Fernández-Arias; J Guiral; J L Bouzat; J Folch; A Sŕnchez



Description of the Cytochrome c Oxidase Subunit II Gene in Some Genera of New World Monkeys (Primates, Platyrrhini)  

Microsoft Academic Search

Nucleotide sequence variation at the mitochondrial cytochrome c oxidase subunit II gene (COII) was analyzed in 27 New World monkey specimens, nine newly reported herein. The study involved comparisons among platyrrhines and also between platyrrhines and catarrhines. The analysis of the frequencies of transitions and transversions at each codon position showed transitional saturation at third codon position. Neighbor-Joining trees obtained

Marina S. Ascunce; Esteban Hasson; Marta D. Mudry



Genetic History of Aleuts of the Commander Islands as Revealed by the Analysis of the HLA Class II Gene Variability  

Microsoft Academic Search

Variability of the HLA class II genes (alleles of the DRB1, DQA1, and DQB1 loci) was investigated in a sample of Aleuts of the Commanders (n = 31), whose ancestors inhabited the Commander Islands for many thousand years. Among 19 haplotypes revealed in the Aleuts of the Commanders, at most eight were inherited from the native inhabitants of the Commander

N. V. Volodko; O. A. Derbeneva; T. S. Uinuk-ool; R. I. Sukernik



Ectopic Expression of the Agouti Gene in Transgenic Mice Causes Obesity, Features of Type II Diabetes, and Yellow Fur  

Microsoft Academic Search

Mice that carry the lethal yellow (A^y) or viable yellow (Avy) mutation, two dominant mutations of the agouti (a) gene in mouse chromosome 2, exhibit a phenotype that includes yellow fur, marked obesity, a form of type II diabetes associated with insulin resistance, and an increased susceptibility to tumor development. Molecular analyses of these and several other dominant \\

M. L. Klebig; J. E. Wilkinson; J. G. Geisler; R. P. Woychik



Ectopic expression of the agouti gene in transgenic mice causes obesity, features of type II diabetes, and yellow fur  

Microsoft Academic Search

Mice that carry the lethal yellow (A{sup y}) or viable yellow (A{sup vy}) mutation, two dominant mutations of the agouti (a) gene in mouse chromosome 2, exhibit a phenotype that includes yellow fur, marked obesity, a form of type II diabetes associated with insulin resistance, and an increased susceptibility to tumor development. Molecular analyses of these and several other dominant

M. L. Klebig; R. P. Woychik; J. E. Wilkinson; J. G. Geisler



Chicken quantitative trait loci for growth and body composition associated with the very low density apolipoprotein-II gene.  


Very low density apolipoprotein-II (apoVLDL-II) is a major constituent of very low density lipoprotein and is involved in lipid transportation in chickens. The current study was designed to investigate the associations of an apoVLDL-II gene polymorphism on chicken growth and body composition traits. The Iowa Growth and Composition Resource Population was established by crossing broiler sires with dams from 2 unrelated highly inbred lines (Leghorn and Fayoumi). The F1 birds were intercrossed, within dam line, to produce 2 related F2 populations. Body weight and body composition traits were measured in the F2 population. Primers for the 5'-flanking region in apoVLDL-II were designed from database chicken genomic sequence. Single nucleotide polymorphisms (SNP) between parental lines were detected by DNA sequencing, and PCR-RFLP methods were then developed to genotype SNP in the F2 population. There was no polymorphism in the 492 bp sequenced between broiler and Leghorn. The apoVLDL-II polymorphism between broiler and Fayoumi was associated with multiple traits of growth and body composition in the 148 male F2 individuals, including BW, breast muscle weight, drumstick weight, and tibia length. This research suggests that apoVLDL-II or a tightly linked gene has broad effects on growth and development in the chicken. PMID:15913180

Li, H; Deeb, N; Zhou, H; Ashwell, C M; Lamont, S J



Model for MLL translocations in therapy-related leukemia involving topoisomerase II?-mediated DNA strand breaks and gene proximity.  


Topoisomerase poisons such as the epipodophyllotoxin etoposide are widely used effective cytotoxic anticancer agents. However, they are associated with the development of therapy-related acute myeloid leukemias (t-AMLs), which display characteristic balanced chromosome translocations, most often involving the mixed lineage leukemia (MLL) locus at 11q23. MLL translocation breakpoints in t-AMLs cluster in a DNase I hypersensitive region, which possesses cryptic promoter activity, implicating transcription as well as topoisomerase II activity in the translocation mechanism. We find that 2-3% of MLL alleles undergoing transcription do so in close proximity to one of its recurrent translocation partner genes, AF9 or AF4, consistent with their sharing transcription factories. We show that most etoposide-induced chromosome breaks in the MLL locus and the overall genotoxicity of etoposide are dependent on topoisomerase II?, but that topoisomerase II? and -? occupancy and etoposide-induced DNA cleavage data suggest factors other than local topoisomerase II concentration determine specific clustering of MLL translocation breakpoints in t-AML. We propose a model where DNA double-strand breaks (DSBs) introduced by topoisomerase II? into pairs of genes undergoing transcription within a common transcription factory become stabilized by antitopoisomerase II drugs such as etoposide, providing the opportunity for illegitimate end joining and translocation. PMID:22615413

Cowell, Ian G; Sondka, Zbyslaw; Smith, Kayleigh; Lee, Ka Cheong; Manville, Catriona M; Sidorczuk-Lesthuruge, Malgorzata; Rance, Holly Ashlene; Padget, Kay; Jackson, Graham Hunter; Adachi, Noritaka; Austin, Caroline A



Angiotensin II induces gene transcription through cell-type-dependent effects on the nuclear factor-?B (NF-?B) transcription factor  

Microsoft Academic Search

The vasopressor octapeptide, angiotensin II (Ang II), exerts homeostatic responses in cardiovascular tissues, including the heart, blood vessel wall, adrenal cortex and liver (a major source of circulating plasma proteins). One of the effects of Ang II is to induce expression of regulatory, structural and cytokine genes that play important roles in long-term control of blood pressure, vascular remodeling, cardiac

Allan R. Brasier; M. Jamaluddin; Youqui Han; Cam Patterson; Marschall S. Runge



Variations of the angiotensin II type 1 receptor gene are associated with extreme human longevity.  


Longevity phenotype in humans results from the influence of environmental and genetic factors. Few gene polymorphisms have been identified so far with a modest effect on lifespan leaving room for the search of other players in the longevity game. It has been recently demonstrated that targeted disruption of the mouse homolog of the human angiotensin II type 1 receptor (AT1R) gene (AGTR1) translates into marked prolongation of animal lifespan (Benigni et al., J Clin Invest 119(3):524-530, 2009). Based on the above study in mice, here we sought to search for AGTR1 variations associated to reduced AT1 receptor protein levels and to prolonged lifespan in humans. AGTR1 was sequenced in 173 Italian centenarians and 376 younger controls. A novel non-synonymous mutation was detected in a centenarian. Two polymorphisms in AGTR1 promoter, rs422858 and rs275653, in complete linkage disequilibrium, were significantly associated with the ability to attain extreme old age. We then replicated the study of rs275653 in a large independent cohort of Japanese origin (598 centenarians and semi-supercentenarians, 422 younger controls) and indeed confirmed its association with exceptional old age. In combined analyses, rs275653 was associated to extreme longevity either at recessive model (P = 0.007, odds ratio (OR) 3.57) or at genotype level (P = 0.015). Significance was maintained after correcting for confounding factors. Fluorescence activated cell sorting analysis revealed that subjects homozygous for the minor allele of rs275653 had less AT1R-positive peripheral blood polymorphonuclear cells. Moreover, rs275653 was associated to lower blood pressure in centenarians. These findings highlight the role of AGTR1 as a possible candidate among longevity-enabling genes. PMID:22569962

Benigni, Ariela; Orisio, Silvia; Noris, Marina; Iatropoulos, Paraskevas; Castaldi, Davide; Kamide, Kei; Rakugi, Hiromi; Arai, Yasumichi; Todeschini, Marta; Ogliari, Giulia; Imai, Enyu; Gondo, Yasuyuki; Hirose, Nobuyoshi; Mari, Daniela; Remuzzi, Giuseppe



Molecular polymorphism and expression analysis of MHC class II B gene from red sea bream (Chrysophrys major).  


MHC class II (major histocompatibility complex class II) plays an important role in the immune response of vertebrates. Its function is to present antigenic peptides to the T-cell receptor. In order to study the function and molecular polymorphism of class II B gene in fish, we have isolated cDNAs encoding class II B from spleen cDNA library of red sea bream (Chrysophrys major) by using EST sequencing, and examined genomic organization, molecular polymorphism and expression of red sea bream class II B gene. As in other vertebrates, five exons and four introns were identified in red sea bream class II B gene. Seven class II B alleles were identified from seven individuals of red sea bream. The deduced amino acid sequence of red sea bream MHC class II B 1(Chma-DAB*0101) had 87.1, 85.1, 87.1, 90.4, 87.1, 90.8% identity with those of red sea bream class II B 2, 3, 4, 5, 6, 7(Chma-DAB*0201-Chma-DAB*0701), respectively, and had 75.2, 74.5, 55.9, 55.1, 34.3 and 30.4% identity with those of striped sea bass, cichlid, rainbow trout, Atlantic salmon, mouse and human, respectively. Four different class II B alleles were observed in a single individual and two different 3' untranslated region (3' UTR) sequences from this individual may infer the existence of two loci at least. Semi-quantitative RT-PCR demonstrated that high expression was detected in liver, head kidney, kidney, intestine, gill, stomach, hear and spleen, low expression in muscle and blood. Challenge of red sea bream with the pathogenic bacteria, Vibrio anguillarum, resulted in a significant decrease in the expression of MHC class II B mRNA from 5 to 72 h after infection in liver, spleen, head kidney and intestine, followed by a recovery to normal level after 96 h. PMID:16045985

Chen, Song-Lin; Zhang, Yu-Xi; Xu, Mei-Yu; Ji, Xiang-Shan; Yu, Guo-Cai; Dong, Cheng-Fang



Alternative gene expression in type I and type II cells may enable further nuclear changes during conjugation of Blepharisma japonicum.  


In contrast to most ciliates, meiosis and successive nuclear changes during conjugation occur only in heterotypic pairs in Blepharisma. It has been suggested that homotypic pairs are ready for conjugation, but lack a trigger to initiate the nuclear changes, and the conjugation process is arrested before the onset of meiosis. To explore the possible nature of the trigger, we previously identified the genes BjCdk1 (homologous to cdk1/cdc2), Bj4HPPD (4-hydroxy-phenylpyruvate dioxygenase) and BjCks (cyclin dependent kinase regulatory subunit) whose expression is up-regulated in gamone1-treated type II cells. In this study, we investigated the molecular structures of these three genes, and compared their expression patterns in homotypic and heterotypic pairs, finding remarkable differences. BjCdk1, Bj4HPPD and BjCks were expressed specifically in gamone1-treated type II cells, but not in gamone2-treated type I cells. In heterotypic pairs, the expression of these genes stayed at the same level or gradually decreased throughout the entire process of conjugation, but it rapidly decreased and ceased after 10hours in homotypic pairs. These results indicate that some genes are expressed in a mating-type specific manner. Alternative gene expression in mating type I and type II cells and merging of individual factors in a heterotypic pair may induce nuclear changes including meiosis. PMID:21840256

Sugiura, Mayumi; Tanaka, Yuri; Suzaki, Toshinobu; Harumoto, Terue



Characterization of major histocompatibility complex class I and class II genes from the Tasmanian devil (Sarcophilus harrisii).  


The Tasmanian devil (Sarcophilus harrisii) is currently threatened by an emerging wildlife disease, devil facial tumour disease. The disease is decreasing devil numbers dramatically and may lead to the extinction of the species. At present, nothing is known about the immune genes or basic immunology of the devil. In this study, we report the construction of the first genetic library for the Tasmanian devil, a spleen cDNA library, and the isolation of full-length MHC Class I and Class II genes. We describe six unique Class II beta chain sequences from at least three loci, which belong to the marsupial Class II DA gene family. We have isolated 13 unique devil Class I sequences, representing at least seven Class I loci, two of which are most likely non-classical genes. The MHC Class I sequences from the devil have little heterogeneity, indicating recent divergence. The MHC genes described here are most likely involved in antigen presentation and are an important first step for studying MHC diversity and immune response in the devil. PMID:17673996

Siddle, Hannah V; Sanderson, Claire; Belov, Katherine



RNA polymerase II pauses at the 5 prime end of the transcriptionally induced Drosophila hsp70 gene  

SciTech Connect

An RNA polymerase II molecule is associated with the 5{prime} end of the Drosophila melanogaster hsp70 gene under non-heat shock conditions. This polymerase is engaged in transcription but has paused, or arrested, after synthesizing about 25 nucleotides. Resumption of elongation by this paused polymerase appears to be the rate-limiting step in hsp70 transcription in uninduced cells. Here the authors report results of nuclear run-on assays that measure the distribution of elongating and paused RNA polymerase molecules on the hsp70 gene in induced cells. Pausing of polymerase was detected at the 5{prime} end of hsp70 was transcribed approximately five times during the 25-min heat shock that they used. Therefore, once the hsp70 gene is induced to an intermediate level, initiation of transcription by RNA polymerase II remains more rapid than the resumption of elongation by a paused polymerase molecule.

O'Brien, T.; Lis, J.T. (Cornell Univ., Ithaca, NY (United States))



RNA polymerase II progression through H3K27me3-enriched gene bodies requires JMJD3 histone demethylase  

PubMed Central

JMJD3 H3K27me3 demethylase plays an important role in the transcriptional response to different signaling pathways; however, the mechanism by which it facilitates transcription has been unclear. Here we show that JMJD3 regulates transcription of transforming growth factor ? (TGF?)–responsive genes by promoting RNA polymerase II (RNAPII) progression along the gene bodies. Using chromatin immunoprecipitation followed by sequencing experiments, we show that, upon TGF? treatment, JMJD3 and elongating RNAPII colocalize extensively along the intragenic regions of TGF? target genes. According to these data, genome-wide analysis shows that JMJD3-dependent TGF? target genes are enriched in H3K27me3 before TGF? signaling pathway activation. Further molecular analyses demonstrate that JMJD3 demethylates H3K27me3 along the gene bodies, paving the way for the RNAPII progression. Overall these findings uncover the mechanism by which JMJD3 facilitates transcriptional activation.

Estaras, Conchi; Fueyo, Raquel; Akizu, Naiara; Beltran, Sergi; Martinez-Balbas, Marian A.



Natriuretic peptides inhibit angiotensin II-induced proliferation of rat cardiac fibroblasts by blocking endothelin-1 gene expression.  

PubMed Central

The present study was aimed to test the role of endothelin-1 (ET-1) as a possible autocrine/paracrine growth factor for cardiac fibroblasts, and to examine its interaction with cardiac natriuretic hormones. Expression of preproET-1 (ppET-1) mRNA by cultured cardiac fibroblasts from neonatal rats was demonstrated by Northern blot analysis using cDNA for rat ppET-1 as a probe. Angiotensin II (ANG II) and ET-1 transiently (30 min) increased steady-state ppET-1 mRNA levels in cardiac fibroblasts. Both ET-1 and ANG II significantly stimulated [3H] thymidine incorporation into cardiac fibroblasts, whose effects were dose-dependently inhibited by an ETA receptor antagonist (BQ123), BQ123 also inhibited both ET-1- and ANG II-induced ppET-1 mRNA expression. Both atrial and brain natriuretic peptides (ANP, BNP), which activate particulate guanylate cyclase, inhibited ppET-1 mRNA expression and [3H]thymidine incorporation stimulated by ANG II and ET-1. Sodium nitroprusside, a soluble guanylate cyclase activator, and 8-bromocyclic GMP, a membrane-permeable cGMP derivative, similarly inhibited ppET-1 mRNA expression and [3H]-thymidine incorporation. BNP was more potent than ANP to inhibit ANG II- and ET-1-stimulated DNA synthesis, whereas BNP and ANP were almost equipotent in stimulating cGMP generation in cardiac fibroblasts. Our data demonstrated that ANG II and ET-1 upregulate ET-1 gene expression in rat cardiac fibroblasts partly via cyclic GMP-dependent mechanism, and that natriuretic peptides inhibit ANG II-stimulated proliferation of cardiac fibroblasts, possibly by inhibiting ET-1 gene expression. Our data suggest the possible role of endogenous ET-1 as an autocrine/paracrine growth factor for cardiac fibroblasts and its close interaction with natriuretic peptides in the regulation of cardiac fibrosis. Images

Fujisaki, H; Ito, H; Hirata, Y; Tanaka, M; Hata, M; Lin, M; Adachi, S; Akimoto, H; Marumo, F; Hiroe, M



Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells  

PubMed Central

Background The signal transducer and activator of transcription 3 (STAT3) mediates gene expression in response to numerous growth factors and cytokines, playing an important role in many cellular processes. To better understand the molecular mechanisms by which Stat3 influences gene expression in the lung, the effect of pulmonary epithelial cell specific deletion of Stat3 on genome wide mRNA expression profiling was assessed. Differentially expressed genes were identified from Affymetrix Murine GeneChips analysis and subjected to gene ontology classification, promoter analysis, pathway mapping and literature mining. Results Total of 791 mRNAs were significantly increased and 314 mRNAs were decreased in response to the deletion of Stat3?/? in the lung. STAT is the most enriched cis-elements in the promoter regions of those differentially expressed genes. Deletion of Stat3 induced genes influencing protein metabolism, transport, chemotaxis and apoptosis and decreased the expression of genes mediating lipid synthesis and metabolism. Expression of Srebf1 and 2, genes encoding key regulators of fatty acid and steroid biosynthesis, was decreased in type II cells from the Stat3?/? mice, consistent with the observation that lung surfactant phospholipids content was decreased. Stat3 influenced both pro- and anti-apoptotic pathways that determine cell death or survival. Akt, a potential transcriptional target of Stat3, was identified as an important participant in Stat3 mediated pathways including Jak-Stat signaling, apoptosis, Mapk signaling, cholesterol and fatty acid biosynthesis. Conclusion Deletion of Stat3 from type II epithelial cells altered the expression of genes regulating diverse cellular processes, including cell growth, apoptosis and lipid metabolism. Pathway analysis indicates that STAT3 regulates cellular homeostasis through a complex regulatory network that likely enhances alveolar epithelial cell survival and surfactant/lipid synthesis, necessary for the protection of the lung during injury.

Xu, Yan; Ikegami, Machiko; Wang, Yanhua; Matsuzaki, Yohei; Whitsett, Jeffrey A



'Energy expenditure genes' or 'energy absorption genes': a new target for the treatment of obesity and Type II diabetes.  


Several hundred genes associated or linked to obesity have been described in the scientific literature. Whereas many of these genes are potential targets for the treatment of obesity and associated conditions, none of them have permitted the developement of an efficient drug therapy. As proposed by the 'thrifty genotype' theory, obesity genes may have conferred an evolutionary advantage in times of food shortage through efficient energy exploitation, while 'lean' or 'energy expenditure' genes may have become very rare during the same periods. It is therefore a challenge to identify 'energy expenditure genes' or 'energy absorption genes,' whose mutations or single nucleotide polymorphisms do result in reduced energy intake. We submit that such 'energy absorption' or 'energy expenditure' genes (crucial genes) are potential new targets for the treatment of obesity. These genes can be identified in rare genetic diseases that produce a lean, failure-to-thrive, energy malabsorption or starvation phenotype. PMID:21428800

Braud, Sandrine; Ciufolini, Marco; Harosh, Itzik



Light-Intensity-Dependent Expression of Lhc Gene Family Encoding Light-Harvesting Chlorophyll-a\\/b Proteins of Photosystem II in Chlamydomonas reinhardtii  

Microsoft Academic Search

Excessive light conditions repressed the levels of mRNAs accumulation of multiple Lhc genes encoding light-harvesting chlorophyll-a\\/b (LHC) proteins of photosystem (PS)II in the unicellular green alga, Chlamydomonas reinhardtii. The light intensity required for the repression tended to decrease with lowering temperature or CO2 concentration. The responses of six LhcII genes encoding the major LHC (LHCII) proteins and two genes (Lhcb4

Haruhiko Teramoto; Akira Nakamori; Jun Minagawa; Taka-aki Ono



The p53 Tumor Suppressor Protein Represses Human snRNA Gene Transcription by RNA Polymerases II and III Independently of Sequence-Specific DNA Binding  

Microsoft Academic Search

Human U1 and U6 snRNA genes are transcribed by RNA polymerases II and III, respectively. While the p53 tumor suppressor protein is a general repressor of RNA polymerase III transcription, whether p53 regulates snRNA gene transcription by RNA polymerase II is uncertain. The data presented herein indicate that p53 is an effective repressor of snRNA gene transcription by both polymerases.

Anastasia A. Gridasova; R. William Henry



Homologous nonallelic recombinations between the iduronate-sulfatase gene and pseudogene cause various intragenic deletions and inversions in patients with mucopolysaccharidosis type II  

Microsoft Academic Search

About 20% of patients with mucopolysaccharidosis type II (MPS II) have gross structural rearrangements involving the iduronate-sulfatase (IDS) gene in Xq27.3–q28. A nearby IDS pseudogene (IDS-2) promotes nonallelic recombination between highly homologous sequences. Here we describe major rearrangements due to gene\\/pseudogene recombination. In two unrelated patients, partial IDS gene deletions were found joining introns 3 and 7 of the IDS

Susanna Bunge; Michaela Rathmann; Cordula Steglich; Marie-Louise Bondeson; Anna Tylki-Szymanska; Ewa Popowska; Andreas Gal



Exonuclease III and the catalase hydroperoxidase II in Escherichia coli are both regulated by the katF gene product  

SciTech Connect

The levels of both exonuclease III (exo III, product of xthA) and hydroperoxidase II (HP-II, product of katE) activity in Escherichia coli were influenced by a functional katF gene. The katF gene product is also necessary for synthesis of HP-II. Mutations in either katF or xthA, but not katE, result in sensitivity to H/sub 2/O/sub 2/ and near-UV (300-400 nm) radiation. Exo III, encoded by the xthA locus, recognizes and removes nucleoside 5'-monophosphates near apurinic and apyrimidinic sites in damaged DNA. Extracts of katF mutant strains had little detectable exo III activity. When a katF+ plasmid was introduced into the katF mutant, exo III activity exceeded wild-type levels. We propose that the katF gene is a trans-acting positive regulator of exo III and HP-II enzymes, both of which are involved in cellular recovery from oxidative damage.

Sak, B.D.; Eisenstark, A.; Touati, D.



Targeting and Eradicating Hepatic Cancer Cells with a Cancer-Specific Vector Carrying the Buforin II Gene.  


Abstract Objective: The aim of this study was to investigate the suppressive effects of Buforin II on the growth of HepG2 cells. To accomplish this, we created a recombinant plasmid (pSUR-Buforin2) in which the survivin promoter was modified to drive the Buforin II gene. Methods: The DNA fragment encoding the Buforin II gene was obtained by gene synthesis and cloned into the pSUR-Luc plasmid behind the survivin promoter. The vector was subsequently transfected into HepG2 and LO2 cells. Cell proliferation was measured by the MTT assay, cell cytotoxicity detected by the LDH assay, and cell apoptosis determined by flow cytometry, DNA ladder assays, and immunoblot analysis. Results: The pSUR-Buforin2 vector effectively suppressed the proliferation of HepG2 cells. The MTT and LDH assay demonstrated that under control of the survivin promoter, Buforin II was not expressed in LO2 cells, but it was expressed in tumor cells where cell death was also observed. AnnexinV-PI staining, DNA ladder assays, and western blots showed massive apoptosis in HepG2 cells transfected with pSUR-Buforin2. Conclusion: pSUR-Buforin2 can significantly inhibit the growth of HepG2 cells, resulting in increased cancer cell apoptosis. Thus, this newly designed plasmid might provide a potent and selective anticancer therapy. PMID:24041444

Wang, Yanyun; Qu, Lili; Gong, Lailing; Sun, Li; Gong, Rujun; Si, Jin



Support for the minimal essential MHC hypothesis: a parrot with a single, highly polymorphic MHC class II B gene.  


We characterized the MHC class II B gene in the green-rumped parrotlet, Forpus passerinus. Three approaches were used: polymerase chain reaction amplification using primers complementary to conserved regions of exon 2, sequencing clones from a genomic library, and amplification of exon 2 using species-specific primers. All three methods indicate that there is only a single class II B locus in this species and no pseudogenes. We suggest that this is the ancestral state for birds. The gene is highly polymorphic; 33 alleles were found in a sample of 25 individuals. Variation in exon 2 is concentrated in the peptide binding residues which show a significant excess of non-synonymous substitutions consistent with the operation of selection in maintaining this extraordinary polymorphism. Genomic clones show that major histocompatibility complex (MHC) gene organization is different from that of chickens; the class II A locus is close to II B. These data provide support for the hypothesis that the bird MHC constitutes a "minimal essential MHC" for responding to infectious disease. PMID:18431567

Hughes, Colin R; Miles, Shana; Walbroehl, Jaclyn M



A Zn(II)2Cys6 DNA binding protein regulates the sirodesmin PL biosynthetic gene cluster in Leptosphaeria maculans  

PubMed Central

A gene, sirZ, encoding a Zn(II)2Cys6 DNA binding protein is present in a cluster of genes responsible for the biosynthesis of the epipolythiodioxopiperazine (ETP) toxin, sirodesmin PL in the ascomycete plant pathogen, Leptosphaeria maculans. RNA-mediated silencing of sirZ gives rise to transformants that produce only residual amounts of sirodesmin PL and display a decrease in the transcription of several sirodesmin PL biosynthetic genes. This indicates that SirZ is a major regulator of this gene cluster. Proteins similar to SirZ are encoded in the gliotoxin biosynthetic gene cluster of Aspergillus fumigatus (gliZ) and in an ETP-like cluster in Penicillium lilacinoechinulatum (PlgliZ). Despite its high level of sequence similarity to gliZ, PlgliZ is unable to complement the gliotoxin-deficiency of a mutant of gliZ in A. fumigatus. Putative binding sites for these regulatory proteins in the promoters of genes in these clusters were predicted using bioinformatic analysis. These sites are similar to those commonly bound by other proteins with Zn(II)2Cys6 DNA binding domains.

Fox, Ellen M.; Gardiner, Donald M.; Keller, Nancy P.; Howlett, Barbara J.



Interleukin-7 mediates glucose utilization in lymphocytes through transcriptional regulation of the hexokinase II gene  

PubMed Central

The cytokine interleukin-7 (IL-7) has essential growth activities that maintain the homeostatic balance of the immune system. Little is known of the mechanism by which IL-7 signaling regulates metabolic activity in support of its vital function in lymphocytes. We observed that IL-7 deprivation caused a rapid decline in the metabolism of glucose that was attributable to loss of intracellular glucose retention. To identify the transducer of the IL-7 metabolic signal, we examined the expression of three important regulators of glucose metabolism, the glucose transporter GLUT-1 and two glycolytic enzymes, hexokinase II (HXKII) and phosphofructokinase-1 (PFK-1), using an IL-7-dependent T-cell line and primary lymphocytes. We found that in lymphocytes deprived of IL-7 loss of glucose uptake correlated with decreased expression of HXKII. Readdition of IL-7 to cytokine-deprived lymphocytes restored the transcription of the HXKII gene within 2 h, but not that of GLUT-1 or PFK-1. IL-7-mediated increases in HXKII, but not GLUT-1 or PFK-1, were also observed at the protein level. Inhibition of HXKII with 3-bromopyruvate or specific small-interfering RNA decreased glucose utilization, as well as ATP levels, in the presence of IL-7, whereas overexpression of HXKII, but not GLUT-1, restored glucose retention and increased ATP levels in the absence of IL-7. We conclude that IL-7 controls glucose utilization by regulating the gene expression of HXKII, suggesting a mechanism by which IL-7 supports bioenergetics that control cell fate decisions in lymphocytes.

Chehtane, Mounir



Interleukin-7 mediates glucose utilization in lymphocytes through transcriptional regulation of the hexokinase II gene.  


The cytokine interleukin-7 (IL-7) has essential growth activities that maintain the homeostatic balance of the immune system. Little is known of the mechanism by which IL-7 signaling regulates metabolic activity in support of its vital function in lymphocytes. We observed that IL-7 deprivation caused a rapid decline in the metabolism of glucose that was attributable to loss of intracellular glucose retention. To identify the transducer of the IL-7 metabolic signal, we examined the expression of three important regulators of glucose metabolism, the glucose transporter GLUT-1 and two glycolytic enzymes, hexokinase II (HXKII) and phosphofructokinase-1 (PFK-1), using an IL-7-dependent T-cell line and primary lymphocytes. We found that in lymphocytes deprived of IL-7 loss of glucose uptake correlated with decreased expression of HXKII. Readdition of IL-7 to cytokine-deprived lymphocytes restored the transcription of the HXKII gene within 2 h, but not that of GLUT-1 or PFK-1. IL-7-mediated increases in HXKII, but not GLUT-1 or PFK-1, were also observed at the protein level. Inhibition of HXKII with 3-bromopyruvate or specific small-interfering RNA decreased glucose utilization, as well as ATP levels, in the presence of IL-7, whereas overexpression of HXKII, but not GLUT-1, restored glucose retention and increased ATP levels in the absence of IL-7. We conclude that IL-7 controls glucose utilization by regulating the gene expression of HXKII, suggesting a mechanism by which IL-7 supports bioenergetics that control cell fate decisions in lymphocytes. PMID:20200205

Chehtane, Mounir; Khaled, Annette R



DSIF and RNA Polymerase II CTD Phosphorylation Coordinate the Recruitment of Rpd3S to Actively Transcribed Genes  

PubMed Central

Histone deacetylase Rpd3 is part of two distinct complexes: the large (Rpd3L) and small (Rpd3S) complexes. While Rpd3L targets specific promoters for gene repression, Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II, to prevent cryptic initiation within genes. Methylation of histone H3 at lysine 36 by the Set2 methyltransferase is thought to mediate the recruitment of Rpd3S. Here, we confirm by ChIP–Chip that Rpd3S binds active ORFs. Surprisingly, however, Rpd3S is not recruited to all active genes, and its recruitment is Set2-independent. However, Rpd3S complexes recruited in the absence of H3K36 methylation appear to be inactive. Finally, we present evidence implicating the yeast DSIF complex (Spt4/5) and RNA polymerase II phosphorylation by Kin28 and Ctk1 in the recruitment of Rpd3S to active genes. Taken together, our data support a model where Set2-dependent histone H3 methylation is required for the activation of Rpd3S following its recruitment to the RNA polymerase II C-terminal domain.

Drouin, Simon; Forest, Audrey; Bergeron, Maxime; Robert, Francois



Mutations That Affect the Efficiency of Translation of mRNA for the cII Gene of Coliphage Lambda  

PubMed Central

Starting with the ? pRE- strain ?ctr1 cy3008, which forms clear plaques, we have isolated two mutant strains, ?dya2 ctr1 cy3008 and ? dya3 ctr1 cy3008, that form plaques with very slightly turbid centers. The dya2 and dya3 mutations lie in the region of overlap between the PRE promoter and the ribosome recognition region of the cII gene, and have nucleotide alterations at positions -1 and +5 of pRE, and alterations of cII mRNA at -16 and -21 nucleotides before the initial AUG codon of the gene. Both mutations destabilize a stem structure that may be formed by cII mRNA, and dya2 also changes the sequence on cII mRNA that is complementary to the 3'-end of 16 S rRNA from 5'-UAAGGA-3' to 5'-UGAGGA-3'.—The dya2 and dya3 mutations, along with the ctr1 mutation, which destabilizes either of two alternate stem structures which may be formed by cII mRNA (these being more stable stem structures than the one affected by dya2 and dya3), were tested for their ability to reverse two cII- mutations that are characterized by inefficient translation of cII mRNA. These are cII3088, an A ? G mutation four bases before the initial AUG codon, and cII3059 , a GUU ? GAU (Val2 ? Asp) second codon mutation. It was found that ctr1 completely reverses the translation defects of these two mutations, while dya2 partially reverses these translation defects. The dya3 mutation has no effect on translation efficiency under any condition tested. However neither the ctr1 mutation nor the dya2 mutation has much effect on translation efficiency in an otherwise cII+ background, indicating that other factors must limit the rate of translation of cII mRNA under these conditions.

Dul, Ed; Mahoney, Michael E.; Wulff, Daniel L.



Differential alleleic expression of the type II collagen gene (COL2A2) in osteoarthritic cartilage  

SciTech Connect

Osteoarthritis (OA) is a common debilitating disease resulting from the degeneration of articular cartilage. The major protein of cartilage is type II collagen, which is encoded by the COL2A1 gene. Mutations at this locus have been discovered in several individuals with inherited disorders of cartilage. We have identified 27 primary OA patients who are heterozygous for sequence dimorphisms located in the coding region of COL2A1. These dimorphisms were used to distinguish the mRNA output from each of the two COL2A1 alleles in articular cartilage obtained from each patient. Three patients demonstrated differential allelic expression and produced <12% of the normal level of mRNA from one of their COL2A1 alleles. The same allele shows reduced expression in a well-defined OA population than in a control group, suggesting the possible existence of a rare COL2A1 allele that predisposes to OA. 31 refs., 4 figs., 3 tabs.

Loughlin, J.; Irven, C.; Sykes, B. [Univ. of Oxford (United Kingdom); Athanasou, N.; Carr, A. [Nuffield Orthopaedic Centre, Oxford (United Kingdom)



The RNA polymerase II holoenzyme and its implications for gene regulation  

Microsoft Academic Search

The RNA polymerase II (Pol II) transcription initiation apparatus consists of several multisubunit complexes, including Pol II, general transcription factors and suppressor of RNA polymerase B (SRB) proteins. Recent evidence indicates that many of these components assemble into a large complex, called the RNA polymerase holoenzyme, the SRB components of which participate in the response to transcriptional regulators. We discuss

Anthony J. Koleske; Richard A. Young



Effects of angiotensin II and aldosterone on collagen gene expression and protein turnover in cardiac fibroblasts  

Microsoft Academic Search

Earlier studies have demonstrated angiotensin II (AngII) and aldosterone (ALDO) each augment cultured adult rat cardiac fibroblast (CFb) collagen synthesis. Whether this involves type I collagen, the major structural protein of the myocardium, and represents a transcriptional event, is uncertain. Accordingly, the influence of AngII and ALDO on transcription and synthesis of fibrillar collagen and on collagenolytic activity was examined

Guoping Zhou; Jagannadha C. Kandala; Suresh C. Tyagi; Laxmansa C. Katwa; Karl T. Weber



Over-expression of angiotensin II type 2 receptor gene induces cell death in lung adenocarcinoma cells  

PubMed Central

The endogenous angiotensin II (Ang II) type 2 receptor (AT2) has been shown to mediate apoptosis in cardiovascular tissues. Thus, the aim of this study was to explore the anti-cancer effect of AT2 over-expression on lung adenocarcinoma cells in vitro using adenoviral (Ad), FuGENE, and nanoparticle vectors. All three gene transfection methods efficiently transfected AT2 cDNA into lung cancer cells but caused minimal gene transfection in normal lung epithelial cells. Ad-AT2 significantly attenuated multiple human lung cancer cell growth (A549 and H358) as compared to the control viral vector, Ad-LacZ, when cell viability was examined by direct cell count. Examination of annexin V by flow cytometry revealed the activation of the apoptotic pathway via AT2 over-expression. Western Blot analysis confirmed the activation of caspase-3. Similarly, poly (lactide-co-glycolic acid) (PLGA) biodegradable nanoparticles encapsulated AT2 plasmid DNA were shown to be effectively taken up into the lung cancer cell. Nanoparticle-based AT2 gene transfection markedly increased AT2 expression and resultant cell death in A549 cells. These results indicate that AT2 over-expression effectively attenuates growth of lung adenocarcinoma cells through intrinsic apoptosis. Our results also suggest that PLGA nanoparticles can be used as an efficient gene delivery vector for lung adenocarcinoma targeted therapy.

Pickel, Lara; Matsuzuka, Takaya; Doi, Chiyo; Ayuzawa, Rie; Maurya, Dharmendra Kumar; Xie, Sheng-Xue; Berkland, Cory; Tamura, Masaaki



Linkage map of the short arm of human chromosome 11: location of the genes for catalase, calcitonin, and insulin-like growth factor II.  

PubMed Central

The following order of genes on the short arm of human chromosome 11 (11p) was determined previously: parathyroid hormone (PTH)-the beta-globin gene cluster (HBBC)-HRAS1/insulin. Although it is generally agreed that HRAS1 (formerly termed c-Ha-ras-1) and the insulin gene are close to each other [1-4 centimorgans (cM)], their order on chromosome 11p is still in question. We have now added three other genes, those for catalase, calcitonin, and insulin-like growth factor II (IGF-II), to this map of chromosome 11p by use of restriction site polymorphisms adjacent to these genes in classical linkage analysis. Most importantly, we find no evidence of linkage between the catalase and HBBC loci. In addition, our data indicate that the calcitonin gene is located between the catalase gene and the PTH gene. Our best estimate of the distance between the catalase and calcitonin gene is approximately 16 cM, while that between the calcitonin and PTH genes is approximately equal to 8 cM. In agreement, very loose linkage was found between the catalase and PTH loci (approximately 26 cM). Since the catalase locus has been mapped to 11p13, these data support the view that the PTH, HBBC, HRAS1, and insulin loci are located on the distal short arm of chromosome 11. The IGF-II gene is tightly linked to both the HRAS1 oncogene and the insulin gene since no recombinants were observed between the IGF-II and the HRAS1/insulin loci. Thus, based on our linkage analysis we propose that the most likely gene order for the short arm of chromosome 11 is centromere-catalase-calcitonin-PTH-HBBC-HRAS1/insulin-tel ome re and that the IGF-II gene is very close to both the HRAS1 and the insulin genes.

Kittur, S D; Hoppener, J W; Antonarakis, S E; Daniels, J D; Meyers, D A; Maestri, N E; Jansen, M; Korneluk, R G; Nelkin, B D; Kazazian, H H



Gene-specific requirement for P-TEFb activity and RNA polymerase II phosphorylation within the p53 transcriptional program  

PubMed Central

Activation of the p53 pathway mediates cellular responses to diverse forms of stress. Here we report that the p53 target gene p21CIP1 is regulated by stress at post-initiation steps through conversion of paused RNA polymerase II (RNAP II) into an elongating form. High-resolution chromatin immunoprecipitation assays (ChIP) demonstrate that p53-dependent activation of p21CIP1 transcription after DNA damage occurs concomitantly with changes in RNAP II phosphorylation status and recruitment of the elongation factors DSIF (DRB Sensitivity-Inducing Factor), P-TEFb (Positive Transcription Elongation Factor b), TFIIH, TFIIF, and FACT (Facilitates Chromatin Transcription) to distinct regions of the p21CIP1 locus. Paradoxically, pharmacological inhibition of P-TEFb leads to global inhibition of mRNA synthesis but activation of the p53 pathway through p53 accumulation, expression of specific p53 target genes, and p53-dependent apoptosis. ChIP analyses of p21CIP1 activation in the absence of functional P-TEFb reveals the existence of two distinct kinases that phosphorylate Ser5 of the RNAP II C-terminal domain (CTD). Importantly, CTD phosphorylation at Ser2 is not required for p21CIP1 transcription, mRNA cleavage, or polyadenylation. Furthermore, recruitment of FACT requires CTD kinases, yet FACT is dispensable for p21CIP1 expression. Thus, select genes within the p53 pathway bypass the requirement for P-TEFb and RNAP II phosphorylation to trigger a cellular response to inhibition of global mRNA synthesis.

Gomes, Nathan P.; Bjerke, Glen; Llorente, Briardo; Szostek, Stephanie A.; Emerson, Beverly M.; Espinosa, Joaquin M.



Type II Toxoplasma gondii KU80 Knockout Strains Enable Functional Analysis of Genes Required for Cyst Development and Latent Infection ? †  

PubMed Central

Type II Toxoplasma gondii KU80 knockouts (?ku80) deficient in nonhomologous end joining were developed to delete the dominant pathway mediating random integration of targeting episomes. Gene targeting frequency in the type II ?ku80 ?hxgprt strain measured at the orotate (OPRT) and the uracil (UPRT) phosphoribosyltransferase loci was highly efficient. To assess the potential of the type II ?ku80 ?hxgprt strain to examine gene function affecting cyst biology and latent stages of infection, we targeted the deletion of four parasite antigen genes (GRA4, GRA6, ROP7, and tgd057) that encode characterized CD8+ T cell epitopes that elicit corresponding antigen-specific CD8+ T cell populations associated with control of infection. Cyst development in these type II mutant strains was not found to be strictly dependent on antigen-specific CD8+ T cell host responses. In contrast, a significant biological role was revealed for the dense granule proteins GRA4 and GRA6 in cyst development since brain tissue cyst burdens were drastically reduced specifically in mutant strains with GRA4 and/or GRA6 deleted. Complementation of the ?gra4 and ?gra6 mutant strains using a functional allele of the deleted GRA coding region placed under the control of the endogenous UPRT locus was found to significantly restore brain cyst burdens. These results reveal that GRA proteins play a functional role in establishing cyst burdens and latent infection. Collectively, our results suggest that a type II ?ku80 ?hxgprt genetic background enables a higher-throughput functional analysis of the parasite genome to reveal fundamental aspects of parasite biology controlling virulence, pathogenesis, and transmission.

Fox, Barbara A.; Falla, Alejandra; Rommereim, Leah M.; Tomita, Tadakimi; Gigley, Jason P.; Mercier, Corinne; Cesbron-Delauw, Marie-France; Weiss, Louis M.; Bzik, David J.



Frequent intragenic deletion of the P gene in Tanzanian patients with Type II oculocutaneous albinism (OCA2)  

Microsoft Academic Search

Type II oculocutaneous albinism (OCA2) is an autosomal recessive disorder in which the biosynthesis of melanin pigment is reduced in the skin, hair, and eyes. OCA2, which results from mutations of the P gene, is the most frequent type of albinism in African and African-American patients. OCA2 is especially frequent in Tanzania, where it occurs with an incidence of âĽ1\\/1,400.

R. Spritz; K. Fukai; S. A. Holmes



Regulation of Major Histocompatibility Class II Gene Expression in FRTL-5 Thyrocytes: Opposite Effects of Interferon and Methimazole  

Microsoft Academic Search

Aberrant expression of major histocompatibility complex (MHC) class II antigens is associated with autoimmune thyroid disease; aberrant expression duplicating the autoimmune state can be induced by interferon-g (IFNg). We have studied IFNg-induced human leu- kocyte antigen (HLA)-DRa gene expression in rat FRTL-5 thyroid cells to identify the elements and factors important for aberrant expression. Using an HLA-DRa 59-flanking region construct




HLA class II, MICA and PRL gene polymorphisms: the common contribution to the systemic lupus erythematosus development in Czech population  

Microsoft Academic Search

The genetic components contribute to the systemic lupus erythematosus development. This study for the first time determined\\u000a the distribution of the polymorphisms and linkage disequilibrium in HLA class II, MICA and PRL gene among patients suffering\\u000a from SLE and healthy Czech individuals. DNA was obtained from the peripheral blood cells of 123 SLE patients and 96 healthy\\u000a people. Allele variants

Markéta Fojtíková; Peter Novota; Pavlína ?ejková; Satu Peši?ková; Dana Tegzová; Marie ?erná


Vitamin D-Dependent Rickets Type II: Report of a Novel Mutation in the Vitamin D Receptor Gene  

Microsoft Academic Search

Hereditary vitamin D-resistant rickets type or vitamin D-dependent rickets type II is a genetically determined and rare autosomal recessive disorder, most often caused by mutations in the vitamin D receptor gene. It usually presents with rachitic changes not responsive to vitamin D treatment and the circulating levels of 1,25 (OH)2 vitamin D-3 are elevated, differentiating it from vitamin D- dependent

Yousef Shafeghati; Nima Momenin; Taher Esfahani; Edwin Reyniers; Wim Wuyts


Characterization of MHC class I and II genes in a subantarctic seabird, the blue petrel, Halobaena caerulea (Procellariiformes)  

Microsoft Academic Search

The great polymorphism observed in the major histocompatibility complex (MHC) genes is thought to be maintained by pathogen-mediated\\u000a selection possibly combined with MHC-disassortative mating, guided by MHC-determined olfactory cues. Here, we partly characterize\\u000a the MHC class I and II B of the blue petrel, Halobaena caerulea (Procellariiformes), a bird with significant olfactory abilities that lives under presumably low pathogen burdens

Maria Strandh; Mimi Lannefors; Francesco Bonadonna; Helena Westerdahl


Analyses of RNA Polymerase II Genes from Free-Living Protists: Phylogeny, Long Branch Attraction, and the Eukaryotic Big Bang  

Microsoft Academic Search

The phylogenetic relationships among major eukaryotic protist lineages are largely uncertain. Two significant ob- stacles in reconstructing eukaryotic phylogeny are long-branch attraction (LBA) effects and poor taxon sampling of free-living protists. We have obtained and analyzed gene sequences encoding the largest subunit of RNA Poly- merase II (RPB1) from Naegleria gruberi (a heterolobosean), Cercomonas ATCC 50319 (a cercozoan), and Och-

Joel B. Dacks; Alexandra Marinets; W. Ford Doolittle; Thomas Cavalier-Smith; John M. Logsdon


Association between angiotensin II receptor gene polymorphism and serum angiotensin converting enzyme (SACE) activity in patients with sarcoidosis  

PubMed Central

BACKGROUND—Serum angiotensin converting enzyme (SACE) is considered to reflect disease activity in sarcoidosis. SACE activity is increased in many patients with active sarcoid lesions. The mechanism for the increased SACE activity in this disease has not been clarified. ACE insertion/deletion (I/D) gene polymorphism has been reported to have an association with SACE levels in sarcoidosis, but no evidence of an association between angiotensin II receptor gene polymorphism and SACE in this disease has been found. A study of the association of angiotensin II receptor gene polymorphisms with sarcoidosis was therefore undertaken.?METHODS—ACE (I/D), angiotensin II type 1 receptor (AGTR1), and angiotensin II type 2 receptor (AGTR2 ) gene polymorphisms were investigated by polymerase chain reaction (PCR) and SACE levels were measured in three groups of patients: those with sarcoidosis or tuberculosis and normal controls.?RESULTS—There was no difference in allele frequency of AGTR1 and AGTR2 polymorphism among the three groups. Neither AGTR1 nor AGTR2 polymorphisms were associated with sarcoidosis. SACE activity was higher in patients with sarcoidosis with the AGTR1 A/C genotype than in others. However, this tendency was not detected in patients with tuberculosis.?CONCLUSIONS—The AGTR1 allele C is associated with high activity of SACE in patients with sarcoidosis. It is another predisposing factor for high levels of SACE in patients with sarcoidosis and is considered to be an independent factor from the ACE D allele for high levels of SACE in sarcoidosis. This fact could be one of the explanations for the increased SACE activity in sarcoidosis.??

Takemoto, Y.; Sakatani, M.; Takami, S.; Tachibana, T.; Higaki, J.; Ogihara, T.; Miki, T.; Katsuya, T.; Tsuchiyama, T.; Yoshida, A.; Yu, H.; Tanio, Y.; Ueda, E.



Peripherin: An Islet Antigen that is Cross-Reactive with Nonobese Diabetic Mouse Class II Gene Products  

Microsoft Academic Search

The nonobese diabetic (NOD) mouse, in which major histocompatibility complex genes may be involved in the susceptibility to diabetes, has been developed as a model of autoimmune diabetes. The NOD mouse expresses I-A-encoded class II major histocompatibility complex antigens, which differ from those of other mouse haplotypes by the presence of a serine at position 57 of the A_beta chain.

C. Boitard; M. C. Villa; C. Becourt; H. Pham Gia; C. Huc; P. Sempe; M. M. Portier; J. F. Bach



Transformation of miniature potted rose (Rosa hybrida cv. Linda) with P( SAG12 )-ipt gene delays leaf senescence and enhances resistance to exogenous ethylene.  


KEY MESSAGE : The P ( SAG12 ) -ipt gene was transferred to miniature rose, as the first woody species, resulting in increased ethylene resistance due to specific up-regulation of the ipt gene under senescence promoting conditions. Transgenic plants of Rosa hybrida 'Linda' were obtained via transformation with Agrobacterium tumefaciens strain harboring the binary vector pSG529(+) containing the P( SAG12 )-ipt construct. A. tumefaciens strains AGL1, GV3850 and LBA4404 (containing P(35S)-INTGUS gene) were used for transformation of embryogenic callus, but transgenic shoots were obtained only when AGL1 was applied. The highest transformation frequency was 10 % and it was achieved when half MS medium was used for the dilution of overnight culture of Agrobacterium. Southern blot confirmed integration of 1-6 copies of the nptII gene into the rose genome in the tested lines. Four transgenic lines were obtained which were morphologically true-to-type and indistinguishable from Wt shoots while they were in in vitro cultures. Adventitious root induction was more difficult in transgenic shoots compared to the Wt shoots, however, one of the transgenic lines (line 6) was rooted and subsequently analyzed phenotypically. The ipt expression levels were determined in this line after exposure to exogenous ethylene (3.5 ?l l(-1)) and/or darkness. Darkness resulted in twofold up-regulation of ipt expression, whereas darkness combined with ethylene caused eightfold up-regulation in line 6 compared to Wt plants. The transgenic line had significantly higher content of chlorophyll at the end of the treatment period compared to Wt plants. PMID:23207761

Zakizadeh, Hedayat; Lütken, Henrik; Sriskandarajah, Sridevy; Serek, Margrethe; Müller, Renate



A mutation in the type II hair keratin KRT86 gene in a Han family with monilethrix?  

PubMed Central

Monilethrix, a congenital disease of hair, is usually associated with mutations in keratin genes, like KRT81, KRT83 and KRT86. We conducted this study to investigate the mutation of type II human basic hair keratin hHb/KRT gene in a Han family with monilethrix and obtain information for potential pathogenic mechanism study of monilethrix. Peripheral blood samples were drawn for genomic DNA detection. Exon 1 and exon 7 of the KRT81, KRT83 and KRT86 genes were amplified by PCR. All PCR products were sequenced directly using an ABI 310 DNA sequencer. These sequences were aligned with the standard sequences in GenBank using the BLAST software. PCR products were digested with restriction endonuclease and restriction fragment length polymorphism (RFLP) analysis was performed. In this study, we identified one novel mutation, which is a heterozygous transitional mutation of G?A at position 1,289 in exon 7 of the KRT86 gene [R430Q (KRT86)]. RFLP assays for the novel mutation excluded the possibility of polymorphism. The R430Q mutation of the KRT86 gene may be pathogenic for monilethrix. Meanwhile, we did not find any novel mutation or recurrent mutation in exons 1 and 7 of KRT81 and KRT83 and exon 1 of KRT86. There is a potential pathogenic gene in the subjects and our results expand the spectrum of mutations in the hHb6 gene.

Wu, Jin; Lin, Yongli; Xu, Wenrong; Li, Zhongming; Fan, Weixin



Melatonin attenuates clock gene cryptochrome1, which may aggravate mouse anti-type II collagen antibody-induced arthritis.  


Very recently, the circadian rhythm was proved to play an important role in the pathogenesis of arthritis. The role of melatonin in the development and progress of rheumatoid arthritis has been implicated for decades. This study was aimed to investigate the effect of melatonin on the expression of circadian clock genes in mouse anti-type II collagen antibody-induced arthritis (CIA). Mice were divided into 3 groups: control, CIA, and CIA + melatonin treatment (MLT). Both mRNA and protein levels of circadian clock gene Cryptochrome1 (Cry1) were markedly decreased in CIA + MEL group compared with those in control and CIA groups. MLT increased paw thickness. Histologic and X-ray assessment also revealed increased infiltration of inflammatory cells, synovial hyperplasia, and the destruction of articular cartilage and bone by MLT. The concentrations of anti-type II collagen antibody in CIA + MEL group mice were significantly higher than those in control and CIA groups (P < 0.05). Serum concentrations of TNF-? (P < 0.005) and IL-6 (P < 0.05) in CIA + MLT group were also increased. Taken together, these results implicate that clock gene Cry1 may be involved in the aggravation of MLT-mediated arthritis in mice anti-type II collagen antibody-induced arthritis. PMID:21113809

Bang, Jihye; Chang, Hyuk Won; Jung, Hae-Ra; Cho, Chul-Hyun; Hur, Ji-An; Lee, Sang-Il; Choi, Tae Hyun; Kim, Sang-Hyon; Ha, Eunyoung



Inherited immunodeficiency with a defect in a major histocompatibility complex class II promoter-binding protein differs in the chromatin structure of the HLA-DRA gene.  


A defect in a trans-regulatory factor which controls major histocompatibility complex class II gene expression is responsible for an inherited form of immunodeficiency with a lack of expression of human leukocyte antigen (HLA) class II antigens. We have recently described and cloned an HLA class II promoter DNA-binding protein, RF-X, present in normal B cells and absent in these class II-deficient regulatory mutants. Here we report that these in vitro results correlate with a specific change in the chromatin structure of the class II promoter: two prominent DNase I-hypersensitive sites were identified in the promoter of the HLA-DRA gene in normal B lymphocytes and found to be absent in the class II-deficient mutant cells. The same two prominent DNase I-hypersensitive sites were observed in normal fibroblastic cells induced by gamma interferon to express class II genes. Interestingly, they were also observed in the uninduced class II-negative fibroblastic cells, which have also been shown to have a normal RF-X binding pattern. We conclude that the two DNase I-hypersensitive sites in the HLA-DRA promoter reflect features in chromatin structure which correlate with the binding of the trans-acting factor RF-X and which are necessary but not sufficient for the expression of class II genes. PMID:2467188

Gönczy, P; Reith, W; Barras, E; Lisowska-Grospierre, B; Griscelli, C; Hadam, M R; Mach, B



MHC class II genes in the European badger (Meles meles): characterization, patterns of variation, and transcription analysis.  


The major histocompatibility complex (MHC) comprises many genes, some of which are polymorphic with numerous alleles. Sequence variation among alleles is most pronounced in exon 2 of the class II genes, which encodes the ?1 and ?1 domains that form the antigen-binding site (ABS) for the presentation of peptides. The MHC thus plays an important role in pathogen defense. European badgers (Meles meles) are a good species in which to study the MHC, as they harbor a variety of pathogens. We present the first characterization of MHC class II genes, isolated from genomic DNA (gDNA) and complementary DNA (cDNA), in the European badger. Examination of seven individuals revealed four DRB, two DQB, two DQA, and two DRA putatively functional gDNA sequences. All of these sequences, except DRA, exhibited high variability in exon 2; DRB had the highest variability. The ABS codons demonstrated high variability, due potentially to balancing selection, while non-ABS codons had lower variability. Positively selected sites were detected in DRB and DQA. Phylogenetic analysis demonstrated trans-species polymorphism of class II genes. Comparison with cDNA from whole blood revealed that only DRB had a transcription pattern reflecting the alleles that were present in the gDNA, while the other three genes had disparities between gDNA and cDNA. Only one sequence was transcribed, even though two gDNA sequences were present, from each of both DQB and DRA. Our characterization of badger MHC sequences forms a basis for further studies of MHC variability, mate choice, and pathogen resistance in this, and other, species. PMID:22038175

Sin, Yung Wa; Dugdale, Hannah L; Newman, Chris; Macdonald, David W; Burke, Terry



Positive and negative hepatic regulation of the human type II phospholipase A2 gene.  


To identify the elements which regulate the liver transcription of the human type II phospholipase A2 gene and its stimulation by interleukin 6, the 5' flanking region from -1614 to +806 and several 3' and 5' deleted fragments have been analyzed in CAT assays. Negative regulatory elements have been located in the regions -1614 to -326 and +20 to +806. The fragment -326 to +20 contains the main elements required for the transcription as well as for the stimulation by interleukin 6. Footprinting assays have been performed on this region and showed four protected elements, A [-35;-6], B [-125;-86], C [-209;-176], and D [-247;-211]. Deletion of element D enhanced the transcription of the reporter gene 10.5-fold compared to the [-326;+20]-CAT construct. Further deletions up to position -87 which removed both the elements B and C or the substitution of element C by a nonspecific sequence lowered the promoter activity to 23% and 70% of the control, respectively. These results indicate that element C binds positive regulatory factors and element D binds a negative regulatory factor. Furthermore, stimulation by interleukin 6 is lost when element C is substituted or deleted. As shown by the footprinting and band shift assays, the transcription factors C/EBP alpha and C/EBP beta can bind to elements C and D but the dissociation constant (Kd) of C/EBP alpha is 10 times lower for element C (0.6 nM) than for element D (5.8 nM). Band shift experiments using rat liver nuclear extracts showed that element C formed four heat stable complexes, some of which could be supershifted by anti C/EBP alpha antibodies. The binding of C/EBP factors to element C was confirmed by competition with previously described oligonucleotide and nucleotide substitution of element C. Band shift experiments using rat liver nuclear extracts showed that element D formed one major DNA-protein complex. This complex could be competed out by oligonucleotides containing a cAMP responsive element (CRE) but not by oligonucleotides containing the binding site of C/EBP. However, anti-CREB antibodies did not supershift this complex. Methylation interference experiments showed the involvement of a G nucleotide upstream to the sequence homologous to CRE in the binding of the hepatic nuclear factors.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:8003480

Olivier, J L; Fan, Q; Salvat, C; Ziari, M; Kong, L; Mangeney, M; Bereziat, G



Preliminary Characterizationof zntA a Gene Which Encodes a Zn(II)\\/Cd(II)Export Protein in Escherichia coli  

Microsoft Academic Search

Abstract An increasing number,of proteins from both prokaryotic and eukaryotic organisms which transport and\\/or bind transition metal ions contain sequences,corresponding,to the conserved,heavy metal associated motif (GMTCXXC). Those proteins in this group which translocate metal ions across membranes,also show,primary sequence,similarity to the P-type ATPase family of membrane,transport proteins. Database,analysis identified a gene encoding a candidate metal ion transport ATPase in the

Dayle K. Blencowe; Samantha J. Marshall; Andrew P. Morby


Transcription Unit Mapping in Bacteriophage T7 II. Proportionality of Number of Gene Copies, mRNA, and Gene Product  

PubMed Central

The effect of UV irradiation of bacteriophage T7 on in vivo early RNA synthesis has been studied by direct quantitation of the gene-specific RNA transcripts. The results show that the early region of phage T7 is transcribed from left to right as a single unit. Furthermore, gene inactivation, the UV sensitivity of synthesis of gene-specific RNA, and the UV sensitivity of synthesis of the corresponding proteins all follow pseudo first-order kinetics in multiply infected cells, demonstrating a random statistical correlation between both transcriptional sampling of gene copies and translational sampling of the resultant RNA transcripts. In addition, these simple kinetics imply an absence of positive feedback mechanisms compensating for the differential decline of individual early gene products in cells multiply infected with phage T7.

Brautigam, Alan R.; Sauerbier, Walter



[Role of the class II tumor suppressor gene maspin in thyroid carcinogenesis].  


The presented study was aimed to investigate new mechanisms of carcinogenesis in thyroids at the molecular level and to find potential protein markers involved in the initiation of the different histological subtypes of thyroid carcinoma. For this, we performed differential proteome analysis on primary cultured thyrocytes and transformed thyrocytes derived from 238Pu alpha-particle irradiation using two-dimensional electrophoresis (2-DE) and peptide mass fingerprinting (PMF) with matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS). Proteome analysis identified a strong upregulation of maspin, a serine protease inhibitor and class II tumor suppressor, in irradiated thyrocytes. To clarify the role of maspin in thyroid carcinogenesis, we searched for mRNA/protein expression in 30 normal (tumor-free) thyroid tissues, 35 follicular adenomas, 68 papillary carcinomas, 38 follicular carcinomas, 25 poorly differentiated carcinomas, and 34 undifferentiated carcinomas and compared the results with maspin promoter methylation status, p53 expression, clinicopathological data and prognosis. Maspin expression was detectable in 48 of 68 papillary carcinomas exclusively. There was a low methylation rate of 28% in papillary carcinomas in contrast to the other tissues (89-100%). p53 was positive in 2% of maspin positive cases, and in 80% of maspin negative cases. After 110 month follow-up 83% of the maspin positive patients had recurrence-free disease, whereas only 40% of the maspine negative patients were recurrence-free. Our data suggest: (1) maspin expression is a special feature of papillary thyroid carcinomas, (2) promotor methylation-caused maspin repression plays a major role in gene balance and in the process of tumor determination, (3) maspin protein possibly functions as a clinically relevant inhibitor of tumor progression, (4) our data delivers the hints for a p53-depentent regulatory pathway of the maspin protein in human cancer. PMID:16892558

Boltze, C; Hoang-Vu, C; Schneider-Stock, R; Lehnert, H; Roessner, A



Functional Gene-Guided Discovery of Type II Polyketides from Culturable Actinomycetes Associated with Soft Coral Scleronephthya sp  

PubMed Central

Compared with the actinomycetes in stone corals, the phylogenetic diversity of soft coral-associated culturable actinomycetes is essentially unexplored. Meanwhile, the knowledge of the natural products from coral-associated actinomycetes is very limited. In this study, thirty-two strains were isolated from the tissue of the soft coral Scleronephthya sp. in the East China Sea, which were grouped into eight genera by 16S rDNA phylogenetic analysis: Micromonospora, Gordonia, Mycobacterium, Nocardioides, Streptomyces, Cellulomonas, Dietzia and Rhodococcus. 6 Micromonospora strains and 4 Streptomyces strains were found to be with the potential for producing aromatic polyketides based on the analysis of KS? (ketoacyl-synthase) gene in the PKS II (type II polyketides synthase) gene cluster. Among the 6 Micromonospora strains, angucycline cyclase gene was amplified in 2 strains (A5-1 and A6-2), suggesting their potential in synthesizing angucyclines e.g. jadomycin. Under the guidance of functional gene prediction, one jadomycin B analogue (7b, 13-dihydro-7-O-methyl jadomycin B) was detected in the fermentation broth of Micromonospora sp. strain A5-1. This study highlights the phylogenetically diverse culturable actinomycetes associated with the tissue of soft coral Scleronephthya sp. and the potential of coral-derived actinomycetes especially Micromonospora in producing aromatic polyketides.

Sun, Wei; Peng, Chongsheng; Zhao, Yunyu; Li, Zhiyong



Negative Elongation Factor-Mediated Suppression of RNA Polymerase II Elongation of Kaposi's Sarcoma-Associated Herpesvirus Lytic Gene Expression  

PubMed Central

Genome-wide chromatin immunoprecipitation assays indicate that the promoter-proximal pausing of RNA polymerase II (RNAPII) is an important postinitiation step for gene regulation. During latent infection, the majority of Kaposi's sarcoma-associated herpesvirus (KSHV) genes is silenced via repressive histone marks on their promoters. Despite the absence of their expression during latency, however, several lytic promoters are enriched with activating histone marks, suggesting that mechanisms other than heterochromatin-mediated suppression contribute to preventing lytic gene expression. Here, we show that the RNAPII-mediated transcription of the KSHV OriLytL, K5, K6, and K7 (OriLytL-K7) lytic genes is paused at the elongation step during latency. Specifically, the RNAPII-mediated transcription is stalled by the host's negative elongation factor (NELF) at the promoter regions of OriLytL-K7 lytic genes during latency, leading to the hyperphosphorylation of the serine 5 residue and the hypophosphorylation of the serine 2 of the C-terminal domain of the RNAPII large subunit, a hallmark of stalled RNAPII. Consequently, depletion of NELF expression induced transition of stalled RNAPII into a productive transcription elongation at the promoter-proximal regions of OriLytL-K7 lytic genes, leading to their RTA-independent expression. Using an RTA-deficient recombinant KSHV, we also showed that expression of the K5, K6, and K7 lytic genes was highly inducible upon external stimuli compared to other lytic genes that lack RNAPII on their promoters during latency. These results indicate that the transcription elongation of KSHV OriLytL-K7 lytic genes is inhibited by NELF during latency, but can also be promptly reactivated in an RTA-independent manner upon external stimuli.

Toth, Zsolt; Brulois, Kevin F.; Wong, Lai-Yee; Lee, Hye-Ra; Chung, Brian



Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices  

Microsoft Academic Search

BACKGROUND: The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K+, Ca2+ and Na2+ concentrations. The presence of P-type II gene subfamilies that are specific for certain kingdoms has been reported but was sometimes contradicted by discovery of previously unknown homologous sequences in newly sequenced genomes. Members of

Nicolas Corradi; Ian R Sanders



The YeastTFB1andSSL1Genes, Which Encode Subunits of Transcription Factor IIH, Are Required for Nucleotide Excision Repair and RNA Polymerase II Transcription  

Microsoft Academic Search

The essential TFB1 and SSL1 genes of the yeast Saccharomyces cerevisiae encode two subunits of the RNA polymerase II transcription factor TFIIH (factor b). Here we show that extracts of temperature-sensitive mutants carrying mutations in both genes (tfb1-101 and ssl1-1) are defective in nucleotide excision repair (NER) and RNA polymerase II transcription but are proficient for base excision repair. RNA



Intratracheal administration of a nanoparticle-based therapy with the angiotensin II type 2 receptor gene attenuates lung cancer growth  

PubMed Central

Targeted gene delivery, transfection efficiency and toxicity concerns remain a challenge for effective gene therapy. In this study, we dimerized the HIV-1 TAT peptide and formulated a nanoparticle vector (dTAT NP) to leverage the efficiency of this cell penetrating strategy for tumor-targeted gene delivery in the setting of intratracheal administration. Expression efficiency for dTAT NP-encapsulated luciferase or angiotensin II type 2 receptor (AT2R) plasmid DNA (pDNA) was evaluated in Lewis Lung carcinoma (LLC) cells cultured in vitro or in vivo in orthotopic tumor grafts in syngeneic mice. In cell culture, dTAT NP was an effective pDNA transfection vector with negligible cytotoxicity. Transfection efficiency was further increased by addition of calcium and glucose to dTAT/pDNA NP. In orthotopic tumor grafts, immunohistochemical analysis confirmed that dTAT NP successfully delivered pDNA to the tumor, where it was expressed primarily in tumor cells along with the bronchial epithelium. Notably, gene expression in tumor tissues persisted at least 14 days after intratracheal administration. Moreover, bolus administration of dTAT NP-encapsulated AT2R or TRAIL pDNA markedly attenuated tumor growth. Taken together, our findings offer a preclinical proof of concept for a novel gene delivery system that offers an effective intratracheal strategy for administering lung cancer gene therapy.

Kawabata, Atsushi; Baoum, Abdul; Ohta, Naomi; Jacquez, Stephanie; Seo, Gwi-Moon; Berkland, Cory; Tamura, Masaaki



GENETICS Chicken Quantitative Trait Loci for Growth and Body Composition Associated with the Very Low Density Apolipoprotein-II Gene1  

Microsoft Academic Search

Very low density apolipoprotein-II (apoVLDL-II) is a major constituent of very low density lipoprotein and is involved in lipid transportation in chickens. The current study was designed to investigate the associations of an apoVLDL-II gene polymorphism on chicken growth and body composition traits. The Iowa GrowthandCompositionResourcePopulationwasestab- lished by crossing broiler sires with dams from 2 unre- lated highly inbred lines

H. Li; N. Deeb; H. Zhou; C. M. Ashwell; S. J. Lamont


HLA-DMA and -DMB genes are both required for MHC class II\\/peptide complex formation in antigen-presenting cells  

Microsoft Academic Search

MAJOR histocompatibility complex (MHC) class II molecules are highly polymorphic cell-surface glycoproteins that present antigenic peptides to CD4+ T lymphocytes. The normal assembly of class II molecules with cognate peptides for antigen presentation requires an accessory function provided by a gene mapping to the class II region of the HLA complex1,2. The isolation of somatic cell mutants of antigen-presenting cells

Steven P. Fling; Benjamin Arp; Donald Pious



Resistance to Cucumber mosaic virus in Gladiolus plants transformed with either a defective replicase or coat protein subgroup II gene from Cucumber mosaic virus  

Microsoft Academic Search

Transgenic Gladiolus plants that contain either Cucumber mosaic virus (CMV) subgroup I coat protein, CMV subgroup II coat protein, CMV replicase, a combination of the CMV subgroups I and II coat\\u000a proteins, or a combination of the CMV subgroup II coat protein and replicase genes were developed. These plants were multiplied\\u000a in vitro and challenged with purified CMV isolated from

Kathryn Kamo; Ramon Jordan; Mary Ann Guaragna; Hei-ti Hsu; Peter Ueng



Synergistic Action of Transforming Growth Factor-? and Insulin-like Growth Factor-I Induces Expression of Type II Collagen and Aggrecan Genes in Adult Human Articular Chondrocytes  

Microsoft Academic Search

Reexpression of aggrecan and type II collagen genes in dedifferentiated adult human articular chondrocytes (AHAC) in suspension culture varied widely depending on the specific lot of bovine serum used to supplement the culture medium. Some lots of serum provided strong induction of aggrecan and type II collagen expression by AHAC while others did not stimulate significant production of these hyaline

Peter C. Yaeger; Terése L. Masi; Juliana L. Buck de Ortiz; François Binette; Ross Tubo; John M. McPherson



Mutations in the COL5A1 gene are causal in the Ehlers-Danlos syndromes I and II  

SciTech Connect

The Ehlers-Danlos syndrome (EDS) is a heterogeneous connective-tissue disorder of which at least nine subtypes are recognized. Considerable clinical overlap exists between the EDS I and II subtypes, suggesting that both are allelic disorders. Recent evidence based on linkage and transgenic mice studies suggest that collagen V is causally involved in human EDS. Collagen V forms heterotypic fibrils with collagen I in many tissues and plays an important role in collagen I fibrillogenesis. We have identified a mutation in COL5A1, the gene encoding the pro{alpha}1(V) collagen chain, segregating with EDS I in a four-generation family. The mutation causes the substitution of the most 5{prime} cysteine residue by a serine within a highly conserved sequence of the pro{alpha}1(V) C-propeptide domain and causes reduction of collagen V by preventing incorporation of the mutant pro{alpha}1 (V) chains in the collagen V trimers. In addition, we have detected splicing defects in the COL5A1 gene in a patient with EDS I and in a family with EDS II. These findings confirm the causal role of collagen V in at least a subgroup of EDS I, prove that EDS I and II are allelic conditions, and represent a, so far, unique example of a human collagen disorder caused by substitution of a highly conserved cysteine residue in the C-propeptide domain of a fibrillar collagen. 30 refs., 6 figs., 2 tabs.

De Paepe, A.; Nuytinck, L.; Naeyaert, J.M. [Universitaets-Hautklinik Heidelberg (Germany)] [and others



The DNA Binding Protein BTEB Mediates Acetaldehyde-Induced, Jun N-Terminal Kinase-Dependent ?I(I) Collagen Gene Expression in Rat Hepatic Stellate Cells  

PubMed Central

Alcohol-induced cirrhosis results partially from the excessive production of collagen matrix proteins, which, predominantly ?I(I) collagen, are produced and secreted by activated hepatic stellate cells (HSC). The accumulation of ?I(I) collagen in HSC during cirrhosis is largely due to an increase in ?I(I) collagen gene expression. Acetaldehyde, the major active metabolite of alcohol, is known to stimulate ?I(I) collagen production in HSC. However, the mechanisms responsible for it remain unknown. The aim of this study was to elucidate the mechanisms by which ?I(I) collagen gene expression is induced by acetaldehyde in rat HSC. In the present study, the acetaldehyde response element was located in a distal GC box, previously described as the UV response element, in the promoter of the ?I(I) collagen gene (?1484 to ?1476). The GC box was predominantly bound by the DNA binding transcription factor BTEB (basic transcription element binding protein), expression of which was acetaldehyde and UV inducible. Blocking BTEB protein expression significantly reduced the steady-state levels of the acetaldehyde-induced ?I(I) collagen mRNA, suggesting that BTEB is required for this gene expression. Further studies found that acetaldehyde activated Jun N-terminal kinase (JNK) 1 and 2 and activator protein 1 (AP-1) transactivating activity. Inhibition of JNK activation resulted in the reduction of the acetaldehyde-induced BTEB protein abundance and ?I(I) collagen mRNA levels, indicating that the expression of both genes is JNK dependent in HSC. Taken together, these studies demonstrate that BTEB mediates acetaldehyde-induced, JNK-dependent ?I(I) collagen gene expression in HSC.

Chen, Anping; Davis, Bernard H.



Stable integration and expression of wasabi defensin gene in "Egusi" melon (Colocynthis citrullus L.) confers resistance to Fusarium wilt and Alternaria leaf spot.  


Production of "Egusi" melon (Colocynthis citrullus L.) in West Africa is limited by fungal diseases, such as Alternaria leaf spot and Fusarium wilt. In order to engineer "Egusi" resistant to these diseases, cotyledonary explants of two "Egusi" genotypes, 'Ejagham' and NHC1-130, were transformed with Agrobacterium tumefaciens strain EHA101 harbouring wasabi defensin gene (isolated from Wasabia japonica L.) in a binary vector pEKH1. After co-cultivation for 3 days, infected explants were transferred to MS medium containing 100 mg l(-l) kanamycin to select transformed tissues. After 3 weeks of culture, adventitious shoots appeared directly along the edges of the explants. As much as 19 out of 52 (36.5%) and 25 out of 71 (35.2%) of the explants in genotype NHC1-130 and 'Ejagham', respectively, formed shoots after 6 weeks of culture. As much as 74% (14 out of 19) of the shoots regenerated in genotype NHC1-130 and 72% (18 out of 25) of those produced in genotype 'Ejagham' were transgenic. A DNA fragment corresponding to the wasabi defensin gene or the selection marker nptII was amplified by PCR from the genomic DNA of all regenerated plant clones rooted on hormone-free MS medium under the same selection pressure, suggesting their transgenic nature. Southern blot analysis confirmed successful integration of 1-5 copies of the transgene. RT-PCR, northern and western blot analyses revealed that wasabi defensin gene was expressed in transgenic lines. Transgenic lines showed increased levels of resistance to Alternaria solani, which causes Alternaria leaf spot and Fusarium oxysporum, which causes Fusarium wilt, as compared to that of untransformed plants. PMID:20552202

Ntui, Valentine Otang; Thirukkumaran, Gunaratnam; Azadi, Pejman; Khan, Raham Sher; Nakamura, Ikuo; Mii, Masahiro



The lspA Gene, Encoding the Type II Signal Peptidase of Rickettsia typhi: Transcriptional and Functional Analysis?  

PubMed Central

Lipoprotein processing by the type II signal peptidase (SPase II) is known to be critical for intracellular growth and virulence for many bacteria, but its role in rickettsiae is unknown. Here, we describe the analysis of lspA, encoding a putative SPase II, an essential component of lipoprotein processing in gram-negative bacteria, from Rickettsia typhi. Alignment of deduced amino acid sequences shows the presence of highly conserved residues and domains that are essential for SPase II activity in lipoprotein processing. The transcription of lspA, lgt (encoding prolipoprotein transferase), and lepB (encoding type I signal peptidase), monitored by real-time quantitative reverse transcription-PCR, reveals a differential expression pattern during various stages of rickettsial intracellular growth. The higher transcriptional level of all three genes at the preinfection time point indicates that only live and metabolically active rickettsiae are capable of infection and inducing host cell phagocytosis. lspA and lgt, which are involved in lipoprotein processing, show similar levels of expression. However, lepB, which is involved in nonlipoprotein secretion, shows a higher level of expression, suggesting that LepB is the major signal peptidase for protein secretion and supporting our in silico prediction that out of 89 secretory proteins, only 14 are lipoproteins. Overexpression of R. typhi lspA in Escherichia coli confers increased globomycin resistance, indicating its function as SPase II. In genetic complementation, recombinant lspA from R. typhi significantly restores the growth of temperature-sensitive E. coli Y815 at the nonpermissive temperature, supporting its biological activity as SPase II in prolipoprotein processing.

Rahman, M. Sayeedur; Ceraul, Shane M.; Dreher-Lesnick, Sheila M.; Beier, Magda S.; Azad, Abdu F.



The Super Elongation Complex Family of RNA Polymerase II Elongation Factors: Gene Target Specificity and Transcriptional Output  

PubMed Central

The elongation stage of transcription is highly regulated in metazoans. We previously purified the AFF1- and AFF4-containing super elongation complex (SEC) as a major regulator of development and cancer pathogenesis. Here, we report the biochemical isolation of SEC-like 2 (SEC-L2) and SEC-like 3 (SEC-L3) containing AFF2 and AFF3 in association with P-TEFb, ENL/MLLT1, and AF9/MLLT3. The SEC family members demonstrate high levels of polymerase II (Pol II) C-terminal domain kinase activity; however, only SEC is required for the proper induction of the HSP70 gene upon stress. Genome-wide mRNA-Seq analyses demonstrated that SEC-L2 and SEC-L3 control the expression of different subsets of genes, while AFF4/SEC plays a more dominant role in rapid transcriptional induction in cells. MYC is one of the direct targets of AFF4/SEC, and SEC recruitment to the MYC gene regulates its expression in different cancer cells, including those in acute myeloid or lymphoid leukemia. These findings suggest that AFF4/SEC could be a potential therapeutic target for the treatment of leukemia or other cancers associated with MYC overexpression.

Luo, Zhuojuan; Lin, Chengqi; Guest, Erin; Garrett, Alexander S.; Mohaghegh, Nima; Swanson, Selene; Marshall, Stacy; Florens, Laurence; Washburn, Michael P.



No association between MTHFR gene polymorphism and diabetic nephropathy in Japanese type II diabetic patients with proliferative diabetic retinopathy.  


The development of diabetic nephropathy shows marked variation among individuals. Not only hyperglycemia, but also genetic factors may contribute to the development of diabetic nephropathy. Methylenetetrahydrofolate reductase (MTHFR) is involved in remethylation of homocysteine to methionine. Decreased activity of MTHFR which can result in hyperhomocysteinemia may lead to cerebrovascular disease and coronary artery disease. Recently, a common C to T mutation at nucleotide position 677 of the MTHFR gene (MTHFR677CT) has been reported to be correlated with hyperhomocysteinemia and the severity of coronary artery disease as macroangiopathy. In the present study, we recruited 173 of Japanese type II diabetic patients with proliferative diabetic retinopathy who would be exposed to long-term hyperglycemia, and examined the contribution of the MTHFR gene polymorphism to the development of diabetic nephropathy as microangiopathy. The frequency of the mutated allele was 43.3% in patients with nephropathy (n = 105) versus 41.9% in those without nephropathy (n = 68). The genotype frequencies were +/+, 16.2%; +/-, 54.3%; -/-, 29.5% in patients with nephropathy versus +/+, 13.2%; +/-, 57.4%; -/-, 29.4% in those without nephropathy (+ indicates the presence of the mutation). The MTHFR genotype and allele frequencies were not significantly different between patients with and without nephropathy. Therefore, we conclude that the MTHFR gene polymorphism is not associated with the development of diabetic nephropathy in Japanese type II diabetic patients. PMID:10765003

Fujita, H; Narita, T; Meguro, H; Ishii, T; Hanyu, O; Suzuki, K; Kamoi, K; Ito, S


Isolation and functional characterization of Sporothrix schenckii ROT2, the encoding gene for the endoplasmic reticulum glucosidase II.  


The N-linked glycosylation is a ubiquitous protein modification in eukaryotic cells. During the N-linked glycan synthesis, the precursor Glc(3)Man(9)GlcNAc(2) is processed by endoplasmic reticulum (ER) glucosidases I, II and ?1,2-mannosidase, before transporting to the Golgi complex for further structure modifications. In fungi of medical relevance, as Candida albicans and Aspergillus, it is well known that ER glycosidases are important for cell fitness, cell wall organization, virulence, and interaction with the immune system. Despite this, little is known about these enzymes in Sporothrix schenckii, the causative agent of human sporotrichosis. This limited knowledge is due in part to the lack of a genome sequence of this organism. In this work we used degenerate primers and inverse PCR approaches to isolate the open reading frame of S. schenckii ROT2, the encoding gene for ? subunit of ER glucosidase II. This S. schenckii gene complemented a Saccharomyces cerevisiae rot2? mutant; however, when expressed in a C. albicans rot2? mutant, S. schenckii Rot2 partially increased the levels of ?-glucosidase activity, but failed to restore the N-linked glycosylation defect associated to the mutation. To our knowledge, this is the first report where a gene involved in protein N-linked glycosylation is isolated from S. schenckii. PMID:22862919

Robledo-Ortiz, Claudia I; Flores-Carreón, Arturo; Hernández-Cervantes, Arturo; Álvarez-Vargas, Aurelio; Lee, Keunsook K; Díaz-Jiménez, Diana F; Munro, Carol A; Cano-Canchola, Carmen; Mora-Montes, Héctor M



The type F6 neurotoxin gene cluster locus of group II clostridium botulinum has evolved by successive disruption of two different ancestral precursors.  


Genome sequences of five different Group II (nonproteolytic) Clostridium botulinum type F6 strains were compared at a 50-kb locus containing the neurotoxin gene cluster. A clonal origin for these strains is indicated by the fact that sequences were identical except for strain Eklund 202F, with 10 single-nucleotide polymorphisms and a 15-bp deletion. The essential topB gene encoding topoisomerase III was found to have been split by the apparent insertion of 34.4 kb of foreign DNA (in a similar manner to that in Group II C. botulinum type E where the rarA gene has been disrupted by a neurotoxin gene cluster). The foreign DNA, which includes the intact 13.6-kb type F6 neurotoxin gene cluster, bears not only a newly introduced topB gene but also two nonfunctional botulinum neurotoxin gene remnants, a type B and a type E. This observation combined with the discovery of bacteriophage integrase genes and IS4 elements suggest that several rounds of recombination/horizontal gene transfer have occurred at this locus. The simplest explanation for the current genotype is that the ancestral bacterium, a Group II C. botulinum type B strain, received DNA firstly from a strain containing a type E neurotoxin gene cluster, then from a strain containing a type F6 neurotoxin gene cluster. Each event disrupted the previously functional neurotoxin gene. This degree of successive recombination at one hot spot is without precedent in C. botulinum, and it is also the first description of a Group II C. botulinum genome containing more than one neurotoxin gene sequence. PMID:23645598

Carter, Andrew T; Stringer, Sandra C; Webb, Martin D; Peck, Michael W



Cloning and analysis of the genes encoding the type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.  

PubMed Central

The genomic region encoding the type IIS restriction-modification (R-M) system HphI (enzymes recognizing the asymmetric sequence 5'-GGTGA-3'/5'-TCACC-3') from Haemophilus parahaemolyticus were cloned into Escherichia coli and sequenced. Sequence analysis of the R-M HphI system revealed three adjacent genes aligned in the same orientation: a cytosine 5 methyltransferase (gene hphIMC), an adenine N6 methyltransferase (hphIMA) and the HphI restriction endonuclease (gene hphIR). Either methyltransferase is capable of protecting plasmid DNA in vivo against the action of the cognate restriction endonuclease. hphIMA methylation renders plasmid DNA resistant to R.Hindill at overlapping sites, suggesting that the adenine methyltransferase modifies the 3'-terminal A residue on the GGTGA strand. Strong homology was found between the N-terminal part of the m6A methyltransferasease and an unidentified reading frame interrupted by an incomplete gaIE gene of Neisseria meningitidis. The HphI R-M genes are flanked by a copy of a 56 bp direct nucleotide repeat on each side. Similar sequences have also been identified in the non-coding regions of H.influenzae Rd DNA. Possible involvement of the repeat sequences in the mobility of the HphI R-M system is discussed.

Lubys, A; Lubiene, J; Kulakauskas, S; Stankevicius, K; Timinskas, A; Janulaitis, A



Cloning and analysis of the genes encoding the type IIS restriction-modification system HphI from Haemophilus parahaemolyticus.  


The genomic region encoding the type IIS restriction-modification (R-M) system HphI (enzymes recognizing the asymmetric sequence 5'-GGTGA-3'/5'-TCACC-3') from Haemophilus parahaemolyticus were cloned into Escherichia coli and sequenced. Sequence analysis of the R-M HphI system revealed three adjacent genes aligned in the same orientation: a cytosine 5 methyltransferase (gene hphIMC), an adenine N6 methyltransferase (hphIMA) and the HphI restriction endonuclease (gene hphIR). Either methyltransferase is capable of protecting plasmid DNA in vivo against the action of the cognate restriction endonuclease. hphIMA methylation renders plasmid DNA resistant to R.Hindill at overlapping sites, suggesting that the adenine methyltransferase modifies the 3'-terminal A residue on the GGTGA strand. Strong homology was found between the N-terminal part of the m6A methyltransferasease and an unidentified reading frame interrupted by an incomplete gaIE gene of Neisseria meningitidis. The HphI R-M genes are flanked by a copy of a 56 bp direct nucleotide repeat on each side. Similar sequences have also been identified in the non-coding regions of H.influenzae Rd DNA. Possible involvement of the repeat sequences in the mobility of the HphI R-M system is discussed. PMID:8759008

Lubys, A; Lubienč, J; Kulakauskas, S; Stankevicius, K; Timinskas, A; Janulaitis, A



Hypomorphic mutations of SEC23B gene account for mild phenotypes of congenital dyserythropoietic anemia type II  

PubMed Central

Congenital dyserythropoietic anemia type II, a recessive disorder of erythroid differentiation, is due to mutations in SEC23B, a component of the core trafficking machinery COPII. In no case homozygosity or compound heterozygosity for nonsense mutation(s) was found. This study represents the first description of molecular mechanisms underlying SEC23B hypomorphic genotypes by the analysis of five novel mutations. Our findings suggest that reduction of SEC23B gene expression is not associated with CDA II severe clinical presentation; conversely, the combination of a hypomorphic allele with one functionally altered results in more severe phenotypes. We propose a mechanism of compensation SEC23A-mediated which justifies these observations.

Russo, Roberta; Langella, Concetta; Esposito, Maria Rosaria; Gambale, Antonella; Vitiello, Francesco; Vallefuoco, Fara; Ek, Torben; Yang, Elizabeth; Iolascon, Achille



Ang II induce kidney damage by recruiting inflammatory cells and up regulates PPAR gamma and Renin 1 gene: effect of ? carotene on chronic renal damage.  


Antioxidants are widely used for prevention of diseases associated with oxidative stress and ischemic disorder. We investigated the hypothesis of antioxidants (?-tocopherol and ?-carotene) can suppress the renal disorder in apo E-/-mice. Renal damage induced by chronic infusion of Angiotensin II (Ang II) into 4 month old male apo E-/-mice. After that the mice were treated with diet enriched ? tocopherol and ? carotene (800 mg/kg) for 150 days. Ang II treated kidney showed polycystic appearance with accumulation of clear fluid and constriction of renal artery and renal vein was noticed. Vacuolar/cystic degeneration as well as inflammatory reactions was noticed in the tubules/glomerulus of Ang II treated mice. ? carotene treated mice showed enormous numbers of regenerated tubules in the kidney and over expression of ICAM proteins in the regenerated tubules. CD 45.2, MAC 3 proteins were over expressed in the inflammatory cells infiltrated into the tubular region of Ang II treated kidney. Gene expression studies revealed up regulation of Renin 1 (Ren 1) and PPAR? genes in the kidney of Ang II treated animals, but the ? carotene treatment controlled the expression of these genes in the regenerated kidneys. ? carotene may have protective effective on chronic renal disorder. It may repress the inflammatory genes (Ren 1, PPAR?) to achieve the protective effect on Ang II induced renal damage. PMID:23117547

Kaliappan, Gopal; Nagarajan, P; Moorthy, Ramya; Kalai Gana Selvi, S; Avinash Raj, T; Mahesh Kumar, Jerald



Expression of the insulin-like growth factor II gene in polychlorinated biphenyl exposed female mink (Mustela vison) and their fetuses.  

PubMed Central

AIM: To study how polychlorinated biphenyls (PCBs) affect fetal growth and the expression of the insulin-like growth factor (IGF II) gene in the mink (Mustela vision). METHODS: Ten female mink were each exposed to 0.65 or 1.3 mg Clophen A50/day, respectively, during the reproductive season. The numbers and sizes of viable fetuses were recorded. The expression of the IGF II gene was studied by northern blotting using a mink specific IGF II cDNA probe. RESULTS: The number of viable fetuses decreased after PCB exposure in a dose dependent fashion. Expression of the IGF II gene in adult livers from PCB exposed animals was decreased, compared with control animals, in a dose dependent fashion. In contrast, IGF II expression in placentas and fetuses was unaltered. Furthermore, the maternal excretion of urinary cortisol increased in both exposed groups during the implantation period. CONCLUSIONS: Expression of the IGF II gene is downregulated by PCB exposure in the adult liver. There is also an indication that the regulation of the expression of this gene differs between adult and fetal life.

Backlin, B M; Gessbo, A; Forsberg, M; Shokrai, A; Rozell, B; Engstrom, W



Linkage Analysis of Candidate Genes in Autoimmune Thyroid Disease. II. Selected Gender-Related Genes and the X-Chromosome  

Microsoft Academic Search

Hashimoto's thyroiditis (HT) and Graves' disease (GD) are auto- immune thyroid diseases (AITD) in which multiple genetic factors are suspected to play an important role. Until now, only a few minor risk factors for these diseases have been identified. Susceptibility seems to be stronger in women, pointing toward a possible role for genes related to sex steroid action or mechanisms



A luminescent tetranuclear ruthenium(II) complex as a tracking non-viral gene vector.  


A luminescent tetranuclear ruthenium(II) complex was developed to act as a DNA carrier and at the same time offer luminescent imaging to follow the DNA intracellular trafficking with time. PMID:23235506

Yu, Bole; Chen, Yu; Ouyang, Cheng; Huang, Huaiyi; Ji, Liangnian; Chao, Hui



Glucose Catabolism in Cancer Cells: Amplification of the Gene Encoding Type II Hexokinase1  

Microsoft Academic Search

Hexokinasetype II is highly overexpressedin manycancercells, where it plays a pivotal role in the high glycolytic phenotype.Here we demon strate by Southern blot analysis and fluorescence in situ hybridization (FISH) that in the rapidly growing rat AS-30D hepatoma cell line, en hanced hexokinase activity is associated with at least a 5-fold amplification of the typeII generelativeto normalhepatocytes. Thisamplification is located

Annette Rempel; Saroj P. Mathupala; Constance A. Griffin; Anita L. Hawkins; Peter L Pedersen


Regulation of major histocompatibility complex class II gene expression in trophoblast cells  

Microsoft Academic Search

Trophoblast cells are unique because they are one of the few mammalian cell types that do not express major histocompatibility\\u000a complex (MHC) class II antigens, either constitutively or after exposure to IFN-?. The absence of MHC class II antigen expression\\u000a on trophoblast cells has been postulated to be one of the essential mechanisms by which the semi-allogeneic fetus evades immune

Shawn P Murphy; Jason C Choi; Renae Holtz



Characterization of a class II pilin expression locus from Neisseria meningitidis: evidence for increased diversity among pilin genes in pathogenic Neisseria species.  

PubMed Central

Strains of Neisseria meningitidis elaborate one of two classes of pili. Meningococcal class I pili have many features in common with pili produced by N. gonorrhoeae, including the ability to bind monoclonal antibody SM1 and a common gene and protein structure consisting of conserved, semivariable, and hypervariable regions. Class II pili are SM1 nonreactive and display smaller subunit molecular weights than do gonococcal or meningococcal class I pili. In this study, we have determined the N-terminal amino acid sequence for class II pilin and isolated the expression locus encoding class II pilin from N. meningitidis FAM18. Meningococcal class II pilin displays features typical of type IV pili and shares extensive amino acid identity with the N-terminal conserved regions of other neisserial pilin proteins. However, the deduced class II pilin sequence displays several unique features compared with previously reported meningococcal class I and gonococcal pilin sequences. Class II pilin lacks several conserved peptide regions found within the semivariable and hypervariable regions of other neisserial pilins and displays a large deletion in a hypervariable region of the protein believed to be exposed on the pilus face in gonococcal pili. DNA sequence comparisons within all three regions of the coding sequence also suggest that the meningococcal class II pilin gene is the most dissimilar of the three types of neisserial pilE loci. Additionally, the class II locus fails to display flanking-sequence homology to class I and gonococcal genes and lacks a downstream Sma/Cla repeat sequence, a feature present in all other neisserial pilin genes examined to date. These data indicate meningococcal class II pili represent a structurally distinct class of pili and suggest that relationships among pilin genes in pathogenic Neisseria do not necessarily follow species boundaries.

Aho, E L; Botten, J W; Hall, R J; Larson, M K; Ness, J K



Prevention of radiation-induced pneumonitis by recombinant adenovirus-mediated transferring of soluble TGF-? type II receptor gene  

Microsoft Academic Search

To investigate whether radiation-induced pneumonitis in the mouse-irradiated lung could be prevented by recombinant adenovirus-mediated soluble transforming growth factor-beta (TGF-?) type II receptor gene therapy. Radiation fibrosis-prone mice (C57BL\\/6J) were randomly divided into four groups consisting of a (1) control group (sham-irradiated); (2) radiation (RT)-alone group; (3) RT+AdCMVsT?R group and (4) RT+AdCMVluc group. The RT-alone and sham-irradiated mice were killed

Z Haiping; K Takayama; J Uchino; A Harada; Y Adachi; S Kura; Z Caicun; T Tsuzuki; Y Nakanishi



Characterization of MHC class II genes from an ancient reptile lineage, Sphenodon (tuatara)  

Microsoft Academic Search

The organization and evolution of major histocompatibility complex (MHC) genes vary considerably among vertebrate lineages.\\u000a MHC genes have been well characterized in mammals, birds, amphibians and fish, but little is known about their organization\\u000a in reptiles, despite the fact that reptiles occupy an important phylogenetic position for understanding the evolutionary history\\u000a of both mammalian and avian MHC genes. Here we

Hilary C. Miller; Katherine Belov; Charles H. Daugherty



DNA methylation status of cyp17-II gene correlated with its expression pattern and reproductive endocrinology during ovarian development stages of Japanese flounder (Paralichthys olivaceus).  


Cytochrome P450c17-II (cyp17-II, 17?-hydroxylase) is responsible for the production of steroid hormones during oocyte maturation in vertebrates. The comparative expression pattern of cyp17-II gene during the gonadal development stages will provide important insights into its function of gonadal development. In addition, epigenetic modification especially DNA methylation plays a vital role in regulation of gene expression. The adult female Japanese flounder at different ovarian development stage (from stages II to V) was obtained in this experiment. The expression of cyp17-II gene in the ovary of Japanese flounder during the gonadal development stages was measured by quantitative PCR. Reproductive traits included gonadosomatic index (GSI), plasma estradiol-17? (E2) and testosterone (T) were also measured. Moreover, whole CpG dinucleotides methylation status of the two CpG rich regions in cyp17-II coding region was detected by bisulfate sequencing. In the ovary, the cyp17-II gene had the lowest mRNA expression at the early ovarian development stage, but then increased afterward. The variation trends of T and E2 level were consistent with the cyp17-II expression pattern in ovary. In contrast, the whole methylation levels of each CpG rich region (exon 4 and 6) in cyp17-II coding region were declined from stages II to IV, then increased at stage V. The methylation levels of whole CpG sites in each CpG rich region were inversely correlated with the values of ovarian cyp17-II gene expression, T and E2 level, and GSI. Based on the present study, we proposed that cyp17-II may regulate the level of steroid hormone, and then stimulate the oocyte growth and maturation. The cyp17-II gene transcriptional activity was possibly affected by the methylation level of CpG rich regions in coding region. These findings will help in the study of the molecular mechanism of fish reproduction and endocrine physiology. PMID:23747405

Ding, YuXia; He, Feng; Wen, HaiShen; Li, JiFang; Ni, Meng; Chi, MeiLi; Qian, Kun; Bu, Yan; Zhang, DongQian; Si, YuFeng; Zhao, JunLi



Organization of the Chorion Genes of BOMBYX MORI, a Multigene Family. II. Partial Localization of Three Gene Clusters  

PubMed Central

Chorion genes of the inbred stock Ascoli have been localized to three linked clusters by analysis of testcross progeny. Electrophoretic variants screened by isoelectric focusing served as markers. The clusters are designated Ch 1, Ch 2, and Ch 3. The gene order is Ch 1–Ch 2–Ch 3–Y, with relative map distances of approximately 0.4 m.u. for Ch 1–2, 3.3 ± 0.9 m.u. for Ch 2–3, and 21 m.u. for Ch 3-Y. In a separate testcross using different markers, two chorion regions were localized 2.3 m.u. and 3.1 m.u. from p. These markers could not be assigned to Ch 1, 2, or 3 because there is at present no test for allelism in this system.

Goldsmith, Marian R.; Clermont-Rattner, Eileen



Studies of three genes encoding Cinnamomin (a type II RIP) isolated from the seeds of camphor tree and their expression patterns.  


Cinnamomin, which has three isoforms, is a type II ribosome-inactivating protein (RIP) purified from the mature seeds of camphor tree (Cinnamomum camphora). In a previous study, an incomplete cDNA that encoded the A- and B-chain of Cinnamomin but lacked signal peptide sequence was cloned. In the present paper, its full-length cDNA was obtained by 5' rapid amplification of cDNA ends (5'RACE). Subsequently, polymerase chain reaction (PCR) amplification of its genomic DNA was performed. Unexpectedly, sequence analysis of the PCR products revealed three cinnamomin genes with >98.0% sequence identity. One of them corresponded to the published cDNA and was designated as cinnamomin I, whereas the other two genes were named as cinnamomin II and cinnamomin III, respectively. RT-PCR amplification of the cDNAs of cinnamomin II and III manifested that these two genes were functional. The three genes have no intron. Three Cinnamomin precursors that were inferred from the cDNA sequence of three cinnamomin genes exhibited relatively high sequence homology with other type II RIPs. Northern blot analysis demonstrated that the cinnamomin genes only expressed in cotyledons of C. camphora seeds and the acmes of expression emerged at 75-90 DAF when seeds were close to maturity. It is proposed that the three cinnamomin genes may encode three isoforms of Cinnamomin. The physiological function of Cinnamomin in C. camphora seeds is briefly discussed. PMID:11891062

Yang, Qiang; Liu, Ren-shui; Gong, Zhen-zhen; Liu, Wang-Yi



Probing the Drosophila retinal determination gene network in Tribolium (II): The Pax6 genes eyeless and twin of eyeless.  


The Pax6 genes eyeless (ey) and twin of eyeless (toy) are upstream regulators in the retinal determination gene network (RDGN), which instructs the formation of the adult eye primordium in Drosophila. Most animals possess a singleton Pax6 ortholog, but the dependence of eye development on Pax6 is widely conserved. A rare exception is given by the larval eyes of Drosophila, which develop independently of ey and toy. To obtain insight into the origin of differential larval and adult eye regulation, we studied the function of toy and ey in the red flour beetle Tribolium castaneum. We find that single and combinatorial knockdown of toy and ey affect larval eye development strongly but adult eye development only mildly in this primitive hemimetabolous species. Compound eye-loss, however, was provoked when ey and toy were RNAi-silenced in combination with the early retinal gene dachshund (dac). We propose that these data reflect a role of Pax6 during regional specification in the developing head and that the subsequent maintenance and growth of the adult eye primordium is regulated partly by redundant and partly by specific functions of toy, ey and dac in Tribolium. The results from embryonic knockdown and comparative protein sequence analysis lead us further to conclude that Tribolium represents an ancestral state of redundant control by ey and toy. PMID:19527703

Yang, Xiaoyun; Weber, Markus; Zarinkamar, Nazanin; Posnien, Nico; Friedrich, Frank; Wigand, Barbara; Beutel, Rolf; Damen, Wim G M; Bucher, Gregor; Klingler, Martin; Friedrich, Markus



The Emerging Importance of Genetics in Epidemiologic Research II. Issues in Study Design and Gene Mapping  

Microsoft Academic Search

PURPOSE: To provide a synthesis of current approaches to the discovery of genes associated with complex human diseases by examining the joint potential of traditional epidemiologic methods and current molecular techniques for gene discovery.METHODS: A discussion of optimal approaches for defining complex disease phenotypes in genetic epidemiology, ascertainment strategies for estimating genetic influences on disease risk, genomic approaches for localizing

Darrell L. Ellsworth; Teri A. Manolio



Glucose metabolism in cancer. Evidence that demethylation events play a role in activating type II hexokinase gene expression.  


One of the "signature" phenotypes of highly malignant, poorly differentiated tumors, including hepatomas, is their remarkable propensity to utilize glucose at a much higher rate than normal cells, a property frequently dependent on the marked overexpression of type II hexokinase (HKII). As the expression of the gene for this enzyme is nearly silent in liver tissue, we tested the possibility that DNA methylation/demethylation events may be involved in its regulation. Initial studies employing methylation restriction endonuclease analysis provided evidence for differential methylation patterns for the HKII gene in normal hepatocytes and hepatoma cells, the latter represented by a highly glycolytic model cell line (AS-30D). Subsequently, sequencing following sodium bisulfite treatment revealed 18 methylated CpG sites within a CpG island (-350 to +781 bp) in the hepatocyte gene but none in that of the hepatoma. In addition, treatment of a hepatocyte cell line with the DNA methyltransferase inhibitors, 5'-azacytidine and 5'-aza-2'-deoxycytidine, activated basal expression levels of HKII mRNA and protein. Finally, stably transfecting the hepatocyte cell line with DNA demethylase also resulted in activating the basal expression levels of HKII mRNA and protein. These novel observations indicate that one of the initial events in activating the HKII gene during either transformation or tumor progression may reside at the epigenetic level. PMID:12566445

Goel, Ashish; Mathupala, Saroj P; Pedersen, Peter L



Genetic diversity of the MHC class-II DQA gene in brown bears (Ursus arctos) on Hokkaido, Northern Japan.  


To investigate genetic diversity of a major histocompatibility complex (MHC) gene in the brown bear (Ursus arctos) population on Hokkaido Island, northern Japan, we cloned and sequenced parts of exon 2 and intron 2 of the MHC class-II DQA gene from 32 brown bears. According to strict criteria for allele identification established by mammalian MHC nomenclature committees, four DQA types (Urar-DQA*01 to Urar-DQA*04) were identified. Of the four, however, Urar-DQA*04 had a 12-bp deletion not detected in a cDNA analysis, indicating that this is a pseudogene at a distinct locus generated by gene duplication. The nucleotide sequences of the other three DQA alleles, which were expressed (because detected from cDNA), were very similar, indicating lower DQA variation In the Hokkaido brown bear population than in other mammals. We attribute this low genetic diversity to (1) some limited effect of possible balancing selection; (2) bottlenecks and inbreeding after migration and isolation of the Hokkaido brown bear population from the Eurasian Continent; (3) a much slower evolutionary rate in DQA than in other MHC genes in the Hokkaido brown bear population. PMID:19719404

Goda, Naoki; Mano, Tsutomu; Masuda, Ryuichi



RSF1010 and a conjugative plasmid contain sulII, one of two known genes for plasmid-borne sulfonamide resistance dihydropteroate synthase.  

PubMed Central

The nucleotide sequence of the type II sulfonamide resistance dihydropteroate synthase (sulII) gene was determined. The molecular weight determined by maxicells was 30,000, and the predicted molecular weight for the polypeptide was 28,469. Comparison with the sulI gene encoded by Tn21 showed 57% DNA similarity. The sulII-encoded polypeptide has 138 of 271 amino acids in common with the polypeptide encoded by sulI. The sulII gene is located on various IncQ (broad-host-range) plasmids and other small nonconjugative resistance plasmids. Detailed restriction maps were constructed to compare the different plasmids in which sulII is found. The large conjugative plasmid pGS05 and the IncQ plasmid RSF1010 contained identical nucleotide sequences for the sulII gene. This type of sulfonamide resistance is very frequently found among gram-negative bacteria because of its efficient spread to various plasmids. Images

Radstrom, P; Swedberg, G



A specific collagen type II gene (COL2A1) mutation presenting as spondyloperipheral dysplasia  

SciTech Connect

We report on a patient with a skeletal dysplasia characterized by short stature, spondylo-epiphyseal involvement, and brachydactyly E-like changes. This condition has been described as spondyloperipheral dysplasia and the few published cases suggest autosomal dominant inheritance with considerable clinical variability. We found our sporadic case to be due to a collagen type II defect resulting from a specific COL2A1 mutation. This mutation is the first to be located at the C-terminal outside the helical domain of COL2A1. A frameshift as consequence of a 5 bp duplication in exon 51 leads to a stop codon. The resulting truncated C-propeptide region seems to affect helix formation and produces changes of chondrocyte morphology, collagen type II fibril structure and cartilage matrix composition. Our case with its distinct phenotype adds another chondrodysplasia to the clinical spectrum of type II collagenopathies. 16 refs., 4 figs.

Zabel, B.; Hilbert, K.; Spranger, J.; Winterpacht, A. [Univ. of Mainz (Germany); Stoeb, H. [Inst. of Pathology St. Johannisstift, Paderborn (Germany); Superti-Furga, A. [Univ. of Zuerich (Switzerland)



Polymorphism analysis of MTHFR, factor II, and factor V genes in the Pomeranian population of Espirito Santo, Brazil.  


Pomeranian populations worldwide immigrated originally from the north of Europe, and because of their preferential marriage, religion, and cultural habits, they show little or no reproductive mixing with local populations. Methylenetetrahydrofolate reductase gene (MTHFR) C677T, Factor V Leiden, and Factor II G20210A polymorphisms are linked to augmented clotting and their frequencies may vary according to population ethnicity. We aimed to assess the frequencies of these thrombophilic alleles in the Pomeranian population residing in Espirito Santo and compare with the general population of the Espirito Santo state, Brazil. A total of 200 individuals were analyzed. The intrapopulation fixation index of the MTHFR C677T polymorphism was 0.03736. The observed heterozygosity was 0.44 and 0.4 for the general and Pomeranian populations, respectively. According to the chi-square test, both populations are in Hardy-Weinberg equilibrium. Four polymorphic alleles were detected for Factor II (2.02%) and 8 for Factor V (4.81%). Our results show that there is gene flow between the general and the Pomeranian population of Espirito Santo, which should no longer be considered an isolated population. PMID:21919702

Stur, Elaine; Silveira, Amanda Nunes; Selvatici, Livia Serra; Alves, Lyvia Neves Rebello; de Vargas Wolfgramm, Eldamária; Tovar, Thaís Tristăo; De Nadai Sartori, Mariana Penha; de Paula, Flavia; Louro, Iuri Drumond



Predicting BRCA1 and BRCA2 gene mutation carriers: comparison of PENN II model to previous study  

PubMed Central

A number of models have been developed to predict the probability that a person carries a detectable germline mutation in the BRCA1 or BRCA2 genes. Their relative performance in a clinical setting is variable. To compare the performance characteristics of a web-based BRCA1/BRCA2 gene mutation prediction model: the PENNII model (, with studies done previously at our institution using four other models including LAMBDA, BRCAPRO, modified PENNI (Couch) tables, and Myriad II tables collated by Myriad Genetics Laboratories. Proband and family cancer history data were analyzed from 285 probands from unique families (27 Ashkenazi Jewish; 277 female) seen for genetic risk assessment in a multispecialty tertiary care group practice. All probands had clinical testing for BR.CA1 and BRCA2 mutations conducted in the same single commercial laboratory. The performance for PENNII results were assessed by the area under the receiver operating characteristic curve (AUC) of sensitivity versus 1-specificity, as a measure of ranking. The AUCs of the PENNII model were higher for predicting BRCA1 than for BRCA2 (81 versus 72%). The overall AUC was 78.7%. PENN II model for BRCA1/2 prediction performed well in this population with higher AUC compared with our experience using four other models. The ease of use of the PENNII model is compatible with busy clinical practices.

Johnson, Kiley J.; Harvey, Hayden; Pankratz, V. Shane; Domchek, Susan M.; Hunt, Katherine; Wilson, Marcia; Smith, M. Cathie; Couch, Fergus



Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans  

PubMed Central

Some inducible yeast genes relocate to nuclear pores upon activation, but the general relevance of this phenomenon has remained largely unexplored. Here we show that the bidirectional hsp-16.2/41 promoter interacts with the nuclear pore complex upon activation by heat shock in the nematode Caenorhabditis elegans. Direct pore association was confirmed by both super-resolution microscopy and chromatin immunoprecipitation. The hsp-16.2 promoter was sufficient to mediate perinuclear positioning under basal level conditions of expression, both in integrated transgenes carrying from 1 to 74 copies of the promoter and in a single-copy genomic insertion. Perinuclear localization of the uninduced gene depended on promoter elements essential for induction and required the heat-shock transcription factor HSF-1, RNA polymerase II, and ENY-2, a factor that binds both SAGA and the THO/TREX mRNA export complex. After induction, colocalization with nuclear pores increased significantly at the promoter and along the coding sequence, dependent on the same promoter-associated factors, including active RNA polymerase II, and correlated with nascent transcripts.

Rohner, Sabine; Kalck, Veronique; Wang, Xuefei; Ikegami, Kohta; Lieb, Jason D.; Meister, Peter



Efficient silencing of gene expression with modular trimeric Pol II expression cassettes comprising microRNA shuttles  

PubMed Central

Expressed polycistronic microRNA (miR) cassettes have useful properties that can be utilized for RNA interference (RNAi)-based gene silencing. To advance their application we generated modular trimeric anti-hepatitis B virus (HBV) Pol II cassettes encoding primary (pri)-miR-31-derived shuttles that target three different viral genome sites. A panel of six expression cassettes, comprising each of the possible ordering combinations of the pri-miR-31 shuttles, was initially tested. Effective silencing of individual target sequences was achieved in transfected cells and transcribed pri-miR trimers generated intended guide strands. There was, however, variation in processing and silencing by each of the shuttles. In some cases the monomers’ position within the trimers influenced processing and this correlated with target silencing. Compromised efficacy could be compensated by substituting the pri-miR-31 backbone with a pri-miR-30a scaffold. Inhibition of HBV replication was achieved in vivo, and in cell culture without disruption of endogenous miR function or induction of the interferon response. A mutant HBV target sequence, with changes in one of the guide cognates, was also silenced by the trimeric cassettes. The modular nature of the cassettes together with compatibility with expression from Pol II promoters should be advantageous for gene silencing applications requiring simultaneous targeting of different sites.

Ely, Abdullah; Naidoo, Tanusha; Arbuthnot, Patrick



Polymorphisms of the angiotensin II type 1 receptor gene affect antihypertensive response to angiotensin receptor blockers in hypertensive Chinese.  


The renin-angiotensin-aldosterone system plays a key role in regulating blood pressure by maintaining vascular tone and the water/sodium balance. Many antihypertensive drugs target the renin-angiotensin-aldosterone system, but the effect differs considerably among hypertensive patients. We investigated whether genetic variants of the angiotensin II type 1 receptor are associated with blood pressure response to angiotensin II receptor blockers in hypertensive Chinese patients. After a 2-week single-blind placebo run-in period, 148 patients with mild-to-moderate primary hypertension received monotherapy with 80 mg/day telmisartan and then were followed up for 8 weeks. The 1166A/C, 573T/C, -810A/T, and -521C/T polymorphisms of the AT1R gene were determined through PCR and RFLP analysis. The relationship between these polymorphisms and changes in blood pressure was observed and evaluated after 8 weeks of treatment. Patients with the AT1R -521CC genotype had a significant reduction in diastolic blood pressure compared to those carrying the T allele. No significant reduction in blood pressure was found in individuals with the 1166A/C, 573T/C, or -810A/T polymorphisms of the AT1R gene. We conclude that only the AT1R -521CC genotype is associated with a significant decrease in blood pressure in response to telmisartan treatment in Chinese hypertensive patients. PMID:23913386

Gong, H T; Ma, X L; Chen, B X; Xu, X Y; Li, Q; Guo, C X; Du, F H



MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris).  


Bengal tigers are highly endangered and knowledge on adaptive genetic variation can be essential for efficient conservation and management. Here we present the first assessment of allelic variation in major histocompatibility complex (MHC) class I and MHC class II DRB genes for wild and captive tigers from India. We amplified, cloned, and sequenced alpha-1 and alpha-2 domain of MHC class I and beta-1 domain of MHC class II DRB genes in 16 tiger specimens of different geographic origin. We detected high variability in peptide-binding sites, presumably resulting from positive selection. Tigers exhibit a low number of MHC DRB alleles, similar to other endangered big cats. Our initial assessment-admittedly with limited geographic coverage and sample size-did not reveal significant differences between captive and wild tigers with regard to MHC variability. In addition, we successfully amplified MHC DRB alleles from scat samples. Our characterization of tiger MHC alleles forms a basis for further in-depth analyses of MHC variability in this illustrative threatened mammal. PMID:20821315

Pokorny, Ina; Sharma, Reeta; Goyal, Surendra Prakash; Mishra, Sudanshu; Tiedemann, Ralph



Heme oxygenase-1 gene expression modulates angiotensin II-induced increase in blood pressure.  


The heme-heme oxygenase (HO) system has been implicated in the regulation of vascular reactivity and blood pressure. This study examines the notion that overexpression of HO decreases pressor responsiveness to angiotensin II (Ang II). Five-day-old Sprague-Dawley rats received an intraleft ventricular injection of approximately 5x10(9) cfu/mL of retroviruses containing human HO-1 sense (LSN-HHO-1), rat HO-1 antisense (LSN-RHO-1-AS), or control retrovirus (LXSN). Three months later, rats were instrumented with femoral arterial and venous catheters for mean arterial pressure (MAP) determination and Ang II administration, respectively. Rats injected with LSN-HHO-1, but not with LXSN, expressed human HO-1 mRNA and protein in several tissues. BP increased with administration of Ang II in rats expressing and not expressing human HO-1. However, the Ang II-induced pressor response (mm Hg) in LSN-HHO-1 rats (16+/-3, 27+/-3, and 38+/-3 at 0.5, 2, and 10 ng) was surpassed (P<0.05) in LXSN rats (23+/-1, 37+/-2, and 52+/-2 at 0.5, 2, and 10 ng). Importantly, treating LSN-HHO-1 rats with the HO inhibitor tin mesoporphyrin (SnMP) enhanced (P<0.05) the Ang II-induced pressor response to a level not different from that observed in LXSN rats. Rats injected with LSN-RHO-1-AS showed a decrease in renal HO-1 protein expression and HO activity relative to control LXSN rats. Administration of Ang II (0.1 to 2 ng) caused small (4 to 5 mm Hg) but significant increases in MAP in rats injected with LSN-RHO-1-AS (P<0.05) compared with rats injected with LXSN. These data demonstrate that overexpression of HO-1 brings about a reduction in pressor responsiveness to Ang II, which is most likely due to increased generation of an HO-1 product, presumably CO, with the ability to inhibit vascular reactivity to constrictor stimuli. PMID:15166181

Yang, Liming; Quan, Shuo; Nasjletti, Alberto; Laniado-Schwartzman, Michal; Abraham, Nader G



Differential gene expression for glutamic acid decarboxylase and type II calcium-calmodulin-dependent protein kinase in basal ganglia, thalamus, and hypothalamus of the monkey  

SciTech Connect

In situ hybridization histochemistry, using cRNA probes, revealed a complementarity in the distributions of cells in the basal ganglia, basal nucleus of Meynert, thalamus, hypothalamus, and rostral part of the midbrain that showed gene expression for glutamic acid decarboxylase (GAD) or the alpha-subunit of type II calcium-calmodulin-dependent protein kinase (CAM II kinase-alpha). Cells in certain nuclei such as the thalamic reticular nucleus, globus pallidus, and pars reticulata of the substantia nigra show GAD gene expression only; others in nuclei such as the basal nucleus of Meynert, medial mamillary nuclei, and ventromedial hypothalamic nuclei show CAM II kinase-alpha gene expression only. A few nuclei, for example, the pars compacta of the substantia nigra and the greater part of the subthalamic nucleus, display gene expression for neither GAD nor CAM II kinase-alpha. In other nuclei, notably those of the dorsal thalamus, and possibly in the striatum, GAD- and CAM II kinase-expressing cells appear to form two separate populations that, in most thalamic nuclei, together account for the total cell population. In situ hybridization reveals large amounts of CAM II kinase-alpha mRNA in the neuropil of most nuclei containing CAM II kinase-alpha-positive cells, suggesting its association with dendritic polyribosomes. The message may thus be translated at those sites, close to the synapses with which the protein is associated. The in situ hybridization results, coupled with those from immunocytochemical staining for CAM II kinase-alpha protein, indicate that CAM II kinase-alpha is commonly found in certain non-GABAergic afferent fiber systems but is not necessarily present in the postsynaptic cells on which they terminate. It appears to be absent from most GABAergic fiber systems but can be present in the cells on which they terminate.

Benson, D.L.; Isackson, P.J.; Hendry, S.H.; Jones, E.G. (Department of Anatomy, University of California, Irvine (USA))



Adenoid cystic carcinomas of the breast have low Topo II? expression but frequently overexpress EGFR protein without EGFR gene amplification.  


Adenoid cystic carcinoma of the breast is a rare subtype of breast cancer with basal-like features. Published studies on breast adenoid cystic carcinoma are limited, resulting in relatively scarce information on the value of predictive tumor markers. We studied 20 primary cases of adenoid cystic carcinoma of the breast for expression of estrogen receptor, progesterone receptor, androgen receptor, epidermal growth factor receptor, HER-2/neu, and topoisomerase II? using immunohistochemistry and fluorescent in situ hybridization methods. Estrogen and progesterone receptor expression were detected in 1 case each. All tumors were uniformly negative for Her-2/neu expression. Androgen receptor and topoisomerase II? expression were weakly positive in three cases and 7 cases, respectively. Epidermal growth factor receptor overexpression was detected in 13 cases (65% of all cases). Amplification of TOP2A or HER-2/neu gene was not detected in any of the cases. Our study shows that the majority of adenoid cystic carcinomas of the breast do not overexpress Her-2/neu, topoisomerase II?, or estrogen receptor, and thus, they are unlikely to respond to therapies targeting these proteins. However, these tumors frequently over-express epidermal growth factor receptor, indicating a potential benefit from anti-epidermal growth factor receptor therapy for patients with advanced adenoid cystic carcinomas of the breast. PMID:20688355

Vranic, Semir; Frkovic-Grazio, Snjezana; Lamovec, Janez; Serdarevic, Fadila; Gurjeva, Olga; Palazzo, Juan; Bilalovic, Nurija; Lee, Lisa M J; Gatalica, Zoran



Occurrence, genes and expression of the W/Se-containing class II benzoyl-coenzyme A reductases in anaerobic bacteria.  


Benzoyl-coenzyme A (CoA) reductases (BCRs) are key enzymes in the anaerobic degradation of aromatic compounds and catalyse the reductive dearomatization of benzoyl-CoA to cyclohexa-1,5-dienoyl-1-carboxyl-CoA. Class I BCRs are ATP-dependent FeS enzymes, whereas class II BCRs are supposed to be ATP-independent and contain W, FeS clusters, and most probably selenocysteine. The active site components of a putative eight subunit class II BCR, BamBCDEFGHI, were recently characterized in Geobacter metallireducens. In this organism bamB was identified as structural gene for the W-containing active site subunit; bamF was predicted to code for a selenocysteine containing electron transfer subunit. In this work the occurrence and expression of BCRs in a number of anaerobic, aromatic compound degrading model microorganisms was investigated with a focus on the BamB and BamF components. Benzoate-induced class II BCR in vitro activities were determined in the soluble protein fraction in all obligately anaerobic bacteria tested. Where applicable, the results were in agreement with Western blot analysis using BamB targeting antibodies. By establishing a specific bamB targeting PCR assay, bamB homologues were identified in all tested obligately anaerobic bacteria with the capacity to degrade aromatic compounds; a number of bamB sequences from Gram-negative/positive sulfate-reducing bacteria were newly sequenced. In several organisms at least two bamB paralogues per genome were identified; however, in nearly all cases only one of them was transcribed during growth on an aromatic substrate. These benzoate-induced bamB genes are proposed to code for the active site subunit of class II BCRs; the major part of them group into a phylogenetic subcluster within the bamB homologues. Results from in silico analysis suggested that all class II BCRs contain selenocysteine in the BamF, and in many cases also in the BamE subunit. The results obtained indicate that the distribution of the two classes of BCRs in anaerobic bacteria appears to be strictly ruled by the available free energy from the oxidation of the aromatic carbon source rather than by phylogenetic relationships. PMID:21087381

Löffler, Claudia; Kuntze, Kevin; Vazquez, José Ramos; Rugor, Agnieszka; Kung, Johannes W; Böttcher, Annette; Boll, Matthias



Molecular cloning of cDNA of mammalian and chicken II gonadotropin-releasing hormones (mGnRHs and cGnRH-II) in the beluga ( Huso huso ) and the disruptive effect of methylmercury on gene expression  

Microsoft Academic Search

Two gonadotropin-releasing hormone (GnRH) isoforms were identified in the beluga (Huso huso) brain by cDNA sequencing: prepro-mammalian GnRH (mGnRH) and prepro-chicken GnRH-II (cGnRH-II). The nucleotide sequences\\u000a of the beluga mGnRH and cGnRH-II precursors are 273 and 258 base pairs (bp) long, encoding peptides of 91 and 86 amino acids,\\u000a respectively. To investigate the effect of methylmercury (MeHg) on GnRH gene

Ahmad Gharaei; Fereidoun Mahboudi; Abbas Esmaili-Sari; Rozita Edalat; Ahmad Adeli; Saeed Keyvanshokooh



Tumor rejection by gene transfer of the MHC class II transactivator in murine mammary adenocarcinoma cells.  


The murine mammary adenocarcinoma cell line TS/A is a highly malignant MHC class II-negative tumor. We show that transfection of TS/A cells with the MHC class II transactivator CIITA renders them MHC class II-positive and highly immunogenic in vivo. These cells were fully rejected by 51% of syngeneic recipients and had a significantly lower growth rate in the remaining 49% of animals. This directly correlated to the amount of MHC class II molecules expressed in the transfected tumor. Tumor rejecting animals were protected against rechallenge with the parental TS/A tumor. The rejection required CD4(+) and CD8(+) T cells. CD4(+) T cells were fundamental in the priming phase of the antitumor response. CTL-specific for a peptide of the envelope gp70 of an endogenous ecotropic retrovirus were identified and explained the specificity of the effector mechanism of rejection against the TS/A and the antigenically related C26 carcinoma cells but not against the unrelated gp70-negative syngeneic fibrosarcoma F1F cells. This is the first example of successful tumor vaccination by genetic transfer of CIITA. These results open the way to a possible use of CIITA for increasing both the inducing and the effector phase of the antitumor immune response. PMID:12731043

Meazza, Raffaella; Comes, Alberto; Orengo, Anna M; Ferrini, Silvano; Accolla, Roberto S



Patterns of Historical Balancing Selection on the Salmonid Major Histocompatibility Complex Class II ? Gene  

Microsoft Academic Search

Allelic variation in the major histocompatibility class (MHC) IIB gene of salmonids is analyzed for patterns indicative of\\u000a natural selection acting at the molecular level. Sequence data for the second exon of this MHC gene were generated for 11\\u000a species in three salmonid genera: Oncorhynchus, Salmo, and Salvelinus. Phylogenetic analysis of nucleotide sequences revealed: (1) monophyletic grouping of alleles from

Andres Aguilar; John Carlos Garza



A novel splice acceptor mutation in the DSPP gene causing dentinogenesis imperfecta type II  

Microsoft Academic Search

The dentin sialophosphoprotein (DSPP) gene (4q21.3) encodes two major noncollagenous dentin matrix proteins: dentin sialoprotein (DSP) and dentin phosphoprotein (DPP). Defects in the human gene encoding DSPP cause inherited dentin defects, and these defects can be associated with bilateral progressive high-frequency sensorineural hearing loss. Clinically, five different patterns of inherited dentin defects are distinguished and are classified as dentinogenesis imperfecta

J.-W. Kim; S.-H. Nam; K.-T. Jang; S.-H. Lee; C.-C. Kim; S.-H. Hahn; J. C.-C. Hu; J. P. Simmer



Molecular characterization of major histocompatibility complex class II gene expression and demonstration of antigen-specific T cell response indicate a new phenotype in class II-deficient patients  

PubMed Central

Major histocompatibility complex (MHC) class II deficiency is an inherited autosomal recessive combined immunodeficiency. The disease is known as bare lymphocyte syndrome (BLS). BLS is characterized by a lack of constitutive MHC class II expression on macrophages and B cells as well as a lack of induced MHC class II expression on cells other than professional antigen-presenting cells (APCs) due to the absence of mRNA and protein of the human leukocyte antigen (HLA) class II molecules, designated HLA-DR, -DQ, and -DP. The defect in gene expression is located at the transcriptional level and affects all class II genes simultaneously. Here we have analyzed transcription and protein expression of class II antigens in Epstein-Barr virus (EBV)-transformed B lymphoblastoid cell lines and mononuclear cells (MNCs) of twin brothers. Whereas flow cytometric analysis failed to detect class II antigens on the cell surface of the patients' EBV-B cells and MNCs, examination of the genes coding for HLA-DR, -DQ, -DP, and the invariant chain (Ii) by reverse transcriptase-polymerase chain reaction amplification resulted in an unusual mRNA pattern in the B cell lines of the patients (HLA-DR alpha +, -DR beta, -DQ alpha +, -DQ beta -, -DP alpha -; -DP beta +, Ii+). In accordance with these findings no HLA-DR beta-specific protein was detected by immunoblotting, whereas low levels of HLA-DR alpha and normal levels of Ii were present. In contrast to EBV-B cells, the MNCs of both patients displayed a residual HLA-DR beta, -DQ beta, and -DP alpha mRNA signal. Furthermore, HLA-DR beta-specific protein was found in addition to HLA-DR alpha by immunoblotting of cell lysates, even though it was clearly decreased as compared with controls. Our results indicate that the defect in class II antigen expression is not necessarily present to the same extent in B cells and cells of other lineages. mRNA levels of HLA-DR beta were found to be enriched in adherent cells within the MNC fraction. Further investigations indicated that the MHC class II expressed is functional in antigen presentation, as the two boys' CD4+ T cells became activated and expressed interleukin-2R after stimulation of peripheral blood mononuclear cell cultures with recall antigen (tetanus toxoid). Furthermore, T cells tested in one of the two patients responded to both MHC class I and II allostimulation, and this response was inhibited by monoclonal antibodies of the respective specificity.(ABSTRACT TRUNCATED AT 400 WORDS)



Stable transformation of Theobroma cacao L. and influence of matrix attachment regions on GFP expression  

Microsoft Academic Search

We describe a protocol for Agrobacterium-mediated genetic transformation of Theobroma cacao L. using cotyledonary explants from primary somatic embryos (SEs) and A. tumefaciens strain AGL1. Transgenic plants carrying the visible marker, gene green fluorescent protein (EGFP), the selectable marker gene neomycin phosphotransferase II (NPTII), the class I chitinase gene from cacao (Chi), and tobacco nuclear matrix attachment regions (MARs) in

S. Maximova; C. Miller; G. Antúnez de Mayolo; S. Pishak; A. Young; M. J. Guiltinan



Multiple Sites of Type II Site Ligand (Luteolin and BMHPC) Regulation of Gene Expression in PC-3 Cells  

PubMed Central

Type II [3H]estradiol binding site ligands including luteolin (a naturally occurring bioflavonoid) and synthetic compounds such as 2,6-bis((3-methoxy-4-hydroxyphenyl)methylene)cyclohexanone (BMHPC) inhibit normal and malignant prostate cell (PC-3, LNCaP, DU-145) proliferation in vitro and in vivo. Type II sites represent a binding domain on histone H4 possibly involved in an epigenetic mechanism for controlling gene transcription. Treatment of PC-3 human prostate cancer cells with luteolin or BMHPC modulated the expression of a number of genes in the epidermal growth factor receptor signaling pathway (EGFRSP) and cell cycle pathway (CCP). Pronounced stimulation (400-2000% of control) of c-FOS and p21 RNA expression was observed, suggesting that these were primary sites of action. Both compounds also caused irreversible G2/M arrest (p<0.001). siRNA’s for c-FOS or p21 reduced the RNA expression of their respective targets by 85-95%, with minimal effects on cell proliferation. Furthermore, neither siRNA alone (single knockdown), or in combination (double knockdown), blocked luteolin or BMHPC inhibition of PC-3 cell proliferation. Thus, although c-FOS and p21 are known to modulate the expression of genes in the ESGRSP (EGFR, SOS, GRB2, JNK1, MKK4, RasGAP) and CCP (CCNA2, CCNE2, CDC25A, CDKN1A, CDKN1B, p27, PLK1) involved in the regulation of cell proliferation by luteolin and BMHPC, the c-FOS and p21 siRNA knockdown studies reported here suggest that c-FOS and p21 may be secondary bystanders in the overall response to these ligands in the regulation of PC-3 cell proliferation.

Markaverich, Barry M.; Vijjeswarapu, Mary



Genome-wide analysis of the Zn(II)?Cys? zinc cluster-encoding gene family in Aspergillus flavus.  


Proteins with a Zn(II)?Cys? domain, Cys-X?-Cys-X?-Cys-X????-Cys-X?-Cys-X???-Cys (hereafter, referred to as the C6 domain), form a subclass of zinc finger proteins found exclusively in fungi and yeast. Genome sequence databases of Saccharomyces cerevisiae and Candida albicans have provided an overview of this family of genes. Annotation of this gene family in most fungal genomes is still far from perfect and refined bioinformatic algorithms are urgently needed. Aspergillus flavus is a saprophytic soil fungus that can produce the carcinogenic aflatoxin. It is the second leading causative agent of invasive aspergillosis. The 37-Mb genome of A. flavus is predicted to encode 12,000 proteins. Two and a half percent of the total proteins are estimated to contain the C6 domain, more than twofold greater than those estimated for yeast, which is about 1 %. The variability in the spacing between cysteines, C?-C? and C?-C?, in the zinc cluster enables classification of the domains into distinct subgroups, which are also well conserved in Aspergillus nidulans. Sixty-six percent (202/306) of the A. flavus C6 proteins contain a specific transcription factor domain, and 7 % contain a domain of unknown function, DUF3468. Two A. nidulans C6 proteins containing the DUF3468 are involved in asexual conidiation and another two in sexual differentiation. In the anamorphic A. flavus, a homolog of the latter lacks the C6 domain. A. flavus being heterothallic and reproducing mainly through conidiation appears to have lost some components involved in homothallic sexual development. Of the 55 predicted gene clusters thought to be involved in production of secondary metabolites, only about half have a C6-encoding gene in or near the gene clusters. The features revealed by the A. flavus C6 proteins likely are common for other ascomycete fungi. PMID:23563886

Chang, Perng-Kuang; Ehrlich, Kenneth C



Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts  

PubMed Central

Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this expanded dataset with published data for nine other cyanophages, we found that 88% of the phage genomes contain psbA, and 50% contain both psbA and psbD. The psbA gene was found in all myoviruses and Prochlorococcus podoviruses, but could not be amplified from Prochlorococcus siphoviruses or Synechococcus podoviruses. Nearly all of the phages that encoded both psbA and psbD had broad host ranges. We speculate that the presence or absence of psbA in a phage genome may be determined by the length of the latent period of infection. Whether it also carries psbD may reflect constraints on coupling of viral- and host-encoded PsbA–PsbD in the photosynthetic reaction center across divergent hosts. Phylogenetic clustering patterns of these genes from cultured phages suggest that whole genes have been transferred from host to phage in a discrete number of events over the course of evolution (four for psbA, and two for psbD), followed by horizontal and vertical transfer between cyanophages. Clustering patterns of psbA and psbD from Synechococcus cells were inconsistent with other molecular phylogenetic markers, suggesting genetic exchanges involving Synechococcus lineages. Signatures of intragenic recombination, detected within the cyanophage gene pool as well as between hosts and phages in both directions, support this hypothesis. The analysis of cyanophage psbA and psbD genes from field populations revealed significant sequence diversity, much of which is represented in our cultured isolates. Collectively, these findings show that photosynthesis genes are common in cyanophages and that significant genetic exchanges occur from host to phage, phage to host, and within the phage gene pool. This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution.

Lee, Jessica A; Thompson, Luke R; Bielawski, Joseph P



Construction of an Alpha Toxin Gene Knockout Mutant of Clostridium perfringens Type A by Use of a Mobile Group II Intron  

PubMed Central

In developing Clostridium perfringens as a safe vaccine vector, the alpha toxin gene (plc) in the bacterial chromosome must be permanently inactivated. Disrupting genes in C. perfringens by traditional mutagenesis methods is very difficult. Therefore, we developed a new strategy using group II intron-based Target-Tron technology to inactivate the plc gene in C. perfringens ATCC 3624. Western blot analysis showed no production of alpha toxin protein in the culture supernatant of the plc mutant. Advantages of this technology, such as site specificity, relatively high frequency of insertion, and introduction of no antibiotic resistance genes into the chromosome, could facilitate construction of other C. perfringens mutants.

Chen, Yue; McClane, Bruce A.; Fisher, Derek J.; Rood, Julian I.; Gupta, Phalguni



Increased Angiotensin II AT1 Receptor Expression in Paraventricular Nucleus and Hypothalamic-Pituitary-Adrenal Axis Stimulation in AT2 Receptor Gene Disrupted Mice  

Microsoft Academic Search

Angiotensin II AT2 receptor gene-disrupted mice have increased blood pressure and response to angiotensin II, behavioral alterations, greater response to stress, and increased adrenal AT1 receptors. We studied hypothalamic AT1 receptor binding and mRNA by receptor autoradiography and in situ hybridization, adrenal catecholamines by HPLC, adrenal tyrosine hydroxylase mRNA by in situ hybridization and pituitary and adrenal hormones by RIA

Inés Armando; José A. Terrón; Alicia Falcón-Neri; Ito Takeshi; Walter Häuser; Tadashi Inagami; Juan M. Saavedra



Genes of the major histocompatibility complex class II influence the outcome of hepatitis C virus infection  

Microsoft Academic Search

BACKGROUND & AIMS: The host's immune response may influence the course of hepatitis C virus (HCV) infection. The aim of this study was to investigate the distribution of HLA class II alleles in white subjects who spontaneously recovered from HCV infection compared with that in patients with persistent infection.METHODS: HLA-DRB1 and -DQB1 typing were performed in 103 consecutive patients with

L Alric; M Fort; J Izopet; JP Vinel; JP Charlet; J Selves; J Puel; JP Pascal; M Duffaut; M Abbal



Transcriptional regulation of the mouse steroid 5?-reductase type II gene by progesterone in brain  

Microsoft Academic Search

The steroid 5?-reductase (5?-R) plays an important physiological role in the conversion of steroid hormones such as androgen and progesterone to their 5?-reduced derivatives. 5?-R type II (5?-R2), one of two 5?-R isoforms, is thought to be a key enzyme in the generation of neuroactive steroids in the brain, particularly allopregnanolone (AP), via the production of its precursor dihydroprogesterone from

Daisuke Matsui; Matomo Sakari; Takashi Sato; Akiko Murayama; Ichiro Takada; Misun Kim; Ken-ichi Takeyama; Shigeaki Kato



Variable properties of transgenic cucumber plants containing the thaumatin II gene from Thaumatococcus daniellii  

Microsoft Academic Search

Thaumatin represents a unique class of the sweet-tasting plant proteins. Transgenic cucumber (Cucumis sativus L.) plants with stable integrated constructs consisting of the cauliflower mosaic virus 35S promoter and thaumatin II cDNA\\u000a were produced. Transformed cucumber plants were obtained using Agrobacterium tumefaciens, with one, two or five integration sites in diploid cucumber and with inheritance confirmed by a 3:1 Mendelian

Maria Szwacka I; Magdalena Krzymowska; Anita Osuch; Magdalena Ewa Kowalczyk; Stefan Malepszy



USF and NF-E2 cooperate to regulate the recruitment and activity of RNA polymerase II in the beta-globin gene locus.  


The human beta-globin gene is expressed at high levels in erythroid cells and regulated by proximal and distal cis-acting DNA elements, including promoter, enhancer, and a locus control region (LCR). Transcription complexes are recruited not only to the globin gene promoters but also to the LCR. Previous studies have implicated the ubiquitously expressed transcription factor USF and the tissue-restricted activator NF-E2 in the recruitment of transcription complexes to the beta-globin gene locus. Here we demonstrate that although USF is required for the efficient association of RNA polymerase II (Pol II) with immobilized LCR templates, USF and NF-E2 together regulate the association of Pol II with the adult beta-globin gene promoter. Recruitment of Pol II to the LCR occurs in undifferentiated murine erythroleukemia cells, but phosphorylation of LCR-associated Pol II at serine 5 of the C-terminal domain is mediated by erythroid differentiation and requires the activity of NF-E2. Furthermore, we provide evidence showing that USF interacts with NF-E2 in erythroid cells. The data provide mechanistic insight into how ubiquitous and tissue-restricted transcription factors cooperate to regulate the recruitment and activity of transcription complexes in a tissue-specific chromatin domain. PMID:20236933

Zhou, Zhuo; Li, Xingguo; Deng, Changwang; Ney, Paul A; Huang, Suming; Bungert, Jörg



USF and NF-E2 Cooperate to Regulate the Recruitment and Activity of RNA Polymerase II in the ?-Globin Gene Locus*  

PubMed Central

The human ?-globin gene is expressed at high levels in erythroid cells and regulated by proximal and distal cis-acting DNA elements, including promoter, enhancer, and a locus control region (LCR). Transcription complexes are recruited not only to the globin gene promoters but also to the LCR. Previous studies have implicated the ubiquitously expressed transcription factor USF and the tissue-restricted activator NF-E2 in the recruitment of transcription complexes to the ?-globin gene locus. Here we demonstrate that although USF is required for the efficient association of RNA polymerase II (Pol II) with immobilized LCR templates, USF and NF-E2 together regulate the association of Pol II with the adult ?-globin gene promoter. Recruitment of Pol II to the LCR occurs in undifferentiated murine erythroleukemia cells, but phosphorylation of LCR-associated Pol II at serine 5 of the C-terminal domain is mediated by erythroid differentiation and requires the activity of NF-E2. Furthermore, we provide evidence showing that USF interacts with NF-E2 in erythroid cells. The data provide mechanistic insight into how ubiquitous and tissue-restricted transcription factors cooperate to regulate the recruitment and activity of transcription complexes in a tissue-specific chromatin domain.

Zhou, Zhuo; Li, Xingguo; Deng, Changwang; Ney, Paul A.; Huang, Suming; Bungert, Jorg



Genomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by Both Enzymes and a Broad Use of Common Activators  

PubMed Central

SNAPc is one of a few basal transcription factors used by both RNA polymerase (pol) II and pol III. To define the set of active SNAPc-dependent promoters in human cells, we have localized genome-wide four SNAPc subunits, GTF2B (TFIIB), BRF2, pol II, and pol III. Among some seventy loci occupied by SNAPc and other factors, including pol II snRNA genes, pol III genes with type 3 promoters, and a few un-annotated loci, most are primarily occupied by either pol II and GTF2B, or pol III and BRF2. A notable exception is the RPPH1 gene, which is occupied by significant amounts of both polymerases. We show that the large majority of SNAPc-dependent promoters recruit POU2F1 and/or ZNF143 on their enhancer region, and a subset also recruits GABP, a factor newly implicated in SNAPc-dependent transcription. These activators associate with pol II and III promoters in G1 slightly before the polymerase, and ZNF143 is required for efficient transcription initiation complex assembly. The results characterize a set of genes with unique properties and establish that polymerase specificity is not absolute in vivo.

Praz, Viviane; Michaud, Joelle; Romascano, David; Hernandez, Nouria



Molecular cloning and expression of the Candida albicans TOP2 gene allows study of fungal DNA topoisomerase II inhibitors in yeast.  

PubMed Central

Candida albicans topoisomerase II, encoded by the TOP2 gene, mediates chromosome segregation by a double-strand DNA break mechanism and is a potential target for anti-fungal therapy. In this paper, we report the characterization of the C. albicans TOP2 gene and its use to develop a yeast system that allows the identification and study of anti-fungal topoisomerase II inhibitors in vivo. The gene, specifying a 1461-residue polypeptide with only 40% identity with human topoisomerase IIalpha and beta isoforms, was isolated from C. albicans on a 6.3 kb EcoRI fragment that mapped to chromosome 4. It was used to construct a plasmid in which TOP2 expresses a recombinant enzyme (residues 57-1461 of C. albicans topoisomerase II fused to the first five residues of Saccharomyces cerevisiae topoisomerase II) under the control of a galactose-inducible promoter. The plasmid rescued the lethal phenotype of a temperature-sensitive S. cerevisiae DNA topoisomerase II mutant allowing growth at 35 degrees C. Yeast cells, bearing ISE2 permeability and rad52 double-strand-break-repair mutations the growth of which at 35 degrees C was dependent on C. albicans topoisomerase II, were killed by the known topoisomerase II inhibitors amsacrine and doxorubicin. Parallel experiments in yeast expressing human topoisomerase IIalpha allowed the relative sensitivities of the fungal and host topoisomerases to be examined in the same genetic background. To compare the killing in vivo with drug inhibition in vitro, the recombinant C. albicans topoisomerase II protein was expressed and purified to near-homogeneity from S. cerevisiae yielding a 160 kDa polypeptide that displayed the expected ATP-dependent DNA-relaxation and DNA-decatenation activities. The enzyme, whether examined in vitro or complementing in S. cerevisiae, was comparably sensitive to amsacrine and doxorubicin. Our results suggest that potential topoisomerase II-targeting anti-fungal inhibitors can be identified and studied in S. cerevisiae.

Keller, B A; Patel, S; Fisher, L M



Gold induced nephropathy in rheumatoid arthritis and HLA class II genes.  

PubMed Central

OBJECTIVES--To elucidate the role of HLA-DRB, -DQA, and -DQB genes in patients with rheumatoid arthritis (RA) who developed gold induced nephropathy. METHODS--Southern blot analysis of HLA-DRB, -DQA, and -DQB genes was performed on DNA from 27 patients with RA with gold induced nephropathy, 37 patients with RA who were treated with gold but did not develop nephropathy, and 122 ethnically matched normal subjects. RESULTS--The 4.7 kb DQA1/Taq I band associated with DQA1*0501 and DR3 and DR5 was found in 16 (59%) patients with gold induced nephropathy compared with five (14%) patients without gold induced nephropathy. CONCLUSION--It is concluded that HLA-DQA region genes may be an important susceptibility factor for the development of gold induced nephropathy in patients with RA.

Sakkas, L I; Chikanza, I C; Vaughan, R W; Welsh, K I; Panayi, G S



Differential gene expression of IGF-I, IGF-II, and toll-like receptors 3 and 5 during embryogenesis in hybrid (channel x blue) and channel catfish.  


Insulin-like growth factors-I and-II (IGF-I and IGF-II) play important roles in growth and development of mammals. Toll-like receptors (TLRs) are pattern recognition molecules that orchestrate the induction of early innate immune response by recognition of specific sequences. Evidence is growing that suggests a relationship between growth and immune function. The objective of the study was to examine changes in gene expression of IGF-I, IGF-II, TLR3, and TLR5 during embryogenesis and early larval development in hybrid (channel catfishxblue catfish) and channel catfish. Egg samples were taken pre- and post-fertilization; embryos were collected at two stages of embryogenesis, at hatch, and at swim-up. All genes were detected in unfertilized catfish eggs. Expression levels of TLR5 and IGF-I mRNA in channel catfish and expression levels of TLR3, IGF-I, and IGF-II mRNA in hybrids increased over time (P<0.01). Effect of time was not significant for expression of IGF-II or TLR3 mRNA in channel catfish and for TLR5 mRNA in hybrid catfish. Results of this study suggest growth (IGF-I and IGF-II) and immune (TLR3 and TLR5) associated genes could be functional and play important roles during embryogenesis and early development of hybrid and channel catfish. PMID:15882955

Peterson, Brian C; Bosworth, Brian G; Bilodeau, A Lelania



Adenovirus-mediated E2F-1 gene transfer sensitizes melanoma cells to apoptosis induced by topoisomerase II inhibitors.  


Melanoma has proven to be resistant to conventional chemotherapy; however,the mechanism of chemoresistance is still unclear. Recent reports show that the transcription factor, E2F-1, may play a role in mediating cytotoxicity of certain chemotherapeutic agents. We have shown in a previous study that adenovirus-mediated overexpression of E2F-1 can efficiently induce apoptosis in melanoma cells. In the present study, the effect of E2F-1 expression on drug sensitivity of melanoma cells was evaluated. Two human melanoma cell lines, SK-MEL-28 and SK-MEL-2, were treated with drugs (etoposide, Adriamycin, roscovitine, cisplatin, 5-fluorouracil, or cycloheximide), alone or in combination with adenoviral vectors expressing beta-galactosidase (Ad-LacZ) or E2F-1 (Ad-E2F-1) at a multiplicity of infection of 1 in vitro. E2F-1 expression was confirmed by Western blot analysis. Sublethal concentrations of each drug alone or infection with Ad-E2F-1 alone produced <5% apoptosis by 3 days posttreatment. Conversely, cotreatment with Ad-E2F-1 and low concentrations of etoposide or Adriamycin markedly sensitized melanoma cells to apoptotic cell death. A slight enhancement of the cytotoxicity of roscovitine was demonstrated in combination with E2F-1 overexpression, but not to cisplatin, 5-fluorouracil, or cycloheximide. Ad-LacZ infection showed no obvious effects on drug sensitivity. Overexpression of p21 can block apoptosis induced by the combination chemogene therapy of Ad-E2F-1 and topoisomerase II poisons and does not require its proliferating cell nuclear antigen-binding ability. The protein synthesis inhibitor cycloheximide also has a cytotoxicity-protective effect against topoisomerase II inhibitor/E2F-1-induced apoptosis and suggests that new protein synthesis is required for this process. Topoisomerase II inhibitors also cooperated with Ad-E2F-1 to enhance antitumor activity in an in vivo model using xenografts in nude mice. When combined with Adriamycin or etoposide, E2F-1 adenovirus therapy resulted in an 87% or 91% decrease in tumor size, respectively, compared with controls (P < 0.002). Our results show that adenovirus-mediated E2F-1 gene transfer can sensitize melanoma cells to some chemotherapeutic agents, particularly topoisomerase II poisons, in vitro and in vivo. These results suggest a new chemosensitization strategy for melanoma gene therapy. PMID:11912154

Dong, Yan Bin; Yang, Hai Liang; Elliott, Mary Jane; McMasters, Kelly M



RIM2, MSI1 and PGI1 are located within an 8 kb segment of Saccharomyces cerevisiae chromosome II, which also contains the putative ribosomal gene L21 and a new putative essential gene with a leucine zipper motif.  


We report the DNA sequence of an 8 kb segment localized on the right arm of chromosome II from Saccharomyces cerevisiae. The sequence reveals the presence of eight open reading frames (ORFs). Three of them, YBR1402, YBR1405 and YBR1406 are previously sequenced genes, respectively the RIM2 (replication in mitochondria), MSI1 (multicopy suppressor of IRA1 gene) and PGI1 (phosphoglucoisomerase) genes. The predicted product of the ORF YBR1401 could be the putative yeast ribosomal protein L21. A new essential gene, YBR1403, has been identified by disruption; it possesses a leucine zipper motif. PMID:8346681

Démolis, N; Mallet, L; Bussereau, F; Jacquet, M



Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation  

PubMed Central

The Arabidopsis histone deacetylase HDA6 is required to silence transgenes, transposons, and ribosomal RNA (rRNA) genes subjected to nucleolar dominance in genetic hybrids. In nonhybrid Arabidopsis thaliana, we show that a class of 45S rRNA gene variants that is normally inactivated during development fails to be silenced in hda6 mutants. In these mutants, symmetric cytosine methylation at CG and CHG motifs is reduced, and spurious RNA polymerase II (Pol II) transcription occurs throughout the intergenic spacers. The resulting sense and antisense spacer transcripts facilitate a massive overproduction of siRNAs that, in turn, direct de novo cytosine methylation of corresponding gene sequences. However, the resulting de novo DNA methylation fails to suppress Pol I or Pol II transcription in the absence of HDA6 activity; instead, euchromatic histone modifications typical of active genes accumulate. Collectively, the data reveal a futile cycle of unregulated transcription, siRNA production, and siRNA-directed DNA methylation in the absence of HDA6-mediated histone deacetylation. We propose that spurious Pol II transcription throughout the intergenic spacers in hda6 mutants, combined with losses of histone deacetylase activity and/or maintenance DNA methylation, eliminates repressive chromatin modifications needed for developmental rRNA gene dosage control.

Earley, Keith W.; Pontvianne, Frederic; Wierzbicki, Andrzej T.; Blevins, Todd; Tucker, Sarah; Costa-Nunes, Pedro; Pontes, Olga; Pikaard, Craig S.



cAMP-dependent protein kinase types I and II differentially regulate cAMP response element-mediated gene expression: implications for neuronal responses to ethanol.  


We have shown that ethanol induces translocation of cAMP-dependent protein kinase (PKA) to the nucleus, cAMP response element-binding protein (CREB) phosphorylation, and cAMP response element-mediated gene transcription in NG108-15 cells. However, little is known about which PKA types regulate this process. We show here that under basal conditions NG108-15 cells contain type I PKA (CbetaRIbeta) primarily in cytosol and type II PKA (CalphaRIIbeta) in the particulate and nuclear fractions. Antagonists of both type I and type II PKA inhibit forskolin- and ethanol-induced cAMP response element-mediated gene transcription. However, only the type II PKA antagonist inhibits forskolin-induced Calpha and ethanol-induced Calpha and RIIbeta translocation to the nucleus and CREB phosphorylation; the type I antagonist is without effect. Our data suggest that forskolin- and ethanol-induced CREB phosphorylation and gene activation are differentially mediated by the two types of PKA. We propose that type II PKA is translocated and activated in the nucleus and induces CREB phosphorylation that is necessary but not sufficient for gene transcription. By contrast, type I PKA is activated in the cytoplasm, turning on a downstream pathway that activates other transcription cofactors that interact with phosphorylated CREB to induce gene transcription. PMID:11886856

Constantinescu, Anastasia; Gordon, Adrienne S; Diamond, Ivan



Giant panda genomic data provide insight into the birth-and-death process of mammalian major histocompatibility complex class II genes.  


To gain an understanding of the genomic structure and evolutionary history of the giant panda major histocompatibility complex (MHC) genes, we determined a 636,503-bp nucleotide sequence spanning the MHC class II region. Analysis revealed that the MHC class II region from this rare species contained 26 loci (17 predicted to be expressed), of which 10 are classical class II genes (1 DRA, 2 DRB, 2 DQA, 3 DQB, 1 DYB, 1 DPA, and 2 DPB) and 4 are non-classical class II genes (1 DOA, 1 DOB, 1 DMA, and 1 DMB). The presence of DYB, a gene specific to ruminants, prompted a comparison of the giant panda class II sequence with those of humans, cats, dogs, cattle, pigs, and mice. The results indicated that birth and death events within the DQ and DRB-DY regions led to major lineage differences, with absence of these regions in the cat and in humans and mice respectively. The phylogenetic trees constructed using all expressed alpha and beta genes from marsupials and placental mammals showed that: (1) because marsupials carry loci corresponding to DR, DP, DO and DM genes, those subregions most likely developed before the divergence of marsupials and placental mammals, approximately 150 million years ago (MYA); (2) conversely, the DQ and DY regions must have evolved later, but before the radiation of placental mammals (100 MYA). As a result, the typical genomic structure of MHC class II genes for the giant panda is similar to that of the other placental mammals and corresponds to BTNL2 approximately DR1 approximately DQ approximately DR2 approximately DY approximately DO_box approximately DP approximately COL11A2. Over the past 100 million years, there has been birth and death of mammalian DR, DQ, DY, and DP genes, an evolutionary process that has brought about the current species-specific genomic structure of the MHC class II region. Furthermore, facing certain similar pathogens, mammals have adopted intra-subregion (DR and DQ) and inter-subregion (between DQ and DP) convergent evolutionary strategies for their alpha and beta genes, respectively. PMID:19127303

Wan, Qiu-Hong; Zeng, Chang-Jun; Ni, Xiao-Wei; Pan, Hui-Juan; Fang, Sheng-Guo




Technology Transfer Automated Retrieval System (TEKTRAN)

Many taxonomic families of agarics are not monophyletic and require re-evaluation by molecular phylogenetic methods. Using over 5600 nucleotide characters from rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes, we recover six major clades of Agaricales with Bayesian and parsimony ...


Why do young women smoke? II. Role of traumatic life experience, psychological characteristics and serotonergic genes  

Microsoft Academic Search

Cigarette smoking is a complex behavioral phenotype to which environmental, psychological and genetic factors contribute. The purpose of this study was to investigate these multifactorial effects with a specific focus on young women and on genes that encode serotonin (5-HT) receptors and the 5-HT transporter. A case–control sample of female Israeli college students provided comprehensive background data and details of

E Lerer; K Kanyas; O Karni; R P Ebstein; B Lerer



Molecular phylogeny of Fusarium inferred from partial RNA polymerase II gene sequences  

Technology Transfer Automated Retrieval System (TEKTRAN)

Currently there are no robust phylogenetic hypotheses for Fusarium based on large-scale sampling across the breadth of this important group of mycotoxigenic phytopathogens. Nucleotide variation within the second largest RNA polymerase subunit (RPB2) protein-coding gene, however, has clearly demonst...


The Type II Pullulanase of Thermococcus hydrothermalis: Molecular Characterization of the Gene and Expression of the Catalytic Domain  

PubMed Central

The gene encoding a hyperthermostable type II pullulanase produced by Thermococcus hydrothermalis (Th-Apu) has been isolated. Analysis of a total of 5.2 kb of genomic DNA has revealed the presence of three open reading frames, one of which (apuA) encodes the pullulanase. This enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. In addition to a typical N-terminal signal peptide, Th-Apu possesses a catalytic domain, a domain bearing S-layer homology-like motifs, a Thr-rich region, and a potential C-terminal transmembrane domain. The presence of these noncatalytic domains suggests that Th-Apu may be anchored to the cell surface and be O glycosylated.

Erra-Pujada, Marta; Debeire, Philippe; Duchiron, Francis; O'Donohue, Michael J.



Effect of HLA class II gene disparity on clinical outcome in unrelated donor hematopoietic cell transplantation for chronic myeloid leukemia: the US National Marrow Donor Program Experience  

Microsoft Academic Search

The clinical importance of HLA class II gene disparity in unrelated stem cell trans- plantation is not entirely known. The im- pact was evaluated of matching donors and recipients for HLA-DR, HLA-DQ, and HLA-DP genes on clinical outcome after stem cell transplantation for chronic my- eloid leukemia (CML) performed between 1988 and 1997. HLA-DRB1, -DQA1, -DQB1, -DPA1, and -DPB1 alleles

Effie W. Petersdorf; Craig Kollman; Carolyn Katovich Hurley; Bo Dupont; Auayporn Nademanee; Ann B. Begovich; Daniel Weisdorf; Philip McGlave


An Alternative, Nonkinase Product of the Brain-Specifically Expressed Ca21\\/Calmodulin-Dependent Kinase II aIsoform Gene in Skeletal Muscle  

Microsoft Academic Search

The gene for the aisoform of Ca21\\/calmodulin-dependent kinase II (aCaMKII) codes for a multifunctional protein kinase that is found exclusively in the brain. Here we show that in skeletal muscle, an alternative nonkinase product, hereafter referred to as aKAP (aCaMKII association protein), is expressed from the same gene. aKAP consists of a C-terminal region that is identical to the association




Cloning and expression of a gene coding for the major light-harvesting chlorophyll a\\/b protein of photosystem II in the green alga Dunaliella salina  

Microsoft Academic Search

Genes encoding proteins of the major light-harvesting complex of photosystem II (LHCII) in higher plants are well studied.\\u000a However, little is known about the corresponding genes in the green alga Dunaliella salina, although this knowledge might provide valuable information about the respective roles of each LHCII protein at the molecular\\u000a level under extreme environmental conditions. Here, we describe an additional

Liang Wei; Yi Cao; Linhan Bai; Xue Liang; Tingting Deng; Jing Li; Dairong Qiao



Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger  

Microsoft Academic Search

The expression of inulinolytic genes in Aspergillus niger is co-regulated and induced by inulin and sucrose. We have identified a positive acting transcription factor InuR, which\\u000a is required for the induced expression of inulinolytic genes. InuR is a member of the fungal specific class of transcription\\u000a factors of the Zn(II)2Cys6 type. Involvement of InuR in inulin and sucrose metabolism was

Xiao-Lian Yuan; Johannes A. Roubos; Cees A. M. J. J. van den Hondel; Arthur F. J. Ram



Abnormal Response to Physical Activity in Femurs after Heterozygous Inactivation of One Allele of the Col2a1 Gene for Type II Collagen in Mice  

Microsoft Academic Search

The objective of this study was to evaluate the influence of heterozygous inactivation of one allele of the type II collagen gene (Col2a1) on biomechanical properties and mineral density of bone under physical loading conditions. C57BL\\/6?TGN mice with heterozygous knockout (HZK) inactivation of Col2a1 gene and their nontransgenic littermate controls were housed in individual cages with running wheels for 9

J. Nieminen; J. Sahlman; T. Hirvonen; T. Jämsä; J. Tuukkanen; V. Kovanen; H. Kröger; J. Jurvelin; M. Arita; S. W. Li; D. J. Prockop; M. M. Hyttinen; H. J. Helminen; T. Lapveteläinen; K. Puustjärvi



Suppression of the {alpha}-isoform of class II phosphoinositide 3-kinase gene expression leads to apoptotic cell death  

SciTech Connect

Phosphoinositide 3-kinases (PI3Ks) have known to be key enzymes activating intracellular signaling molecules when a number of growth factors bind to their cell surface receptors. PI3Ks are divided into three classes (I, II, and III) and enzymes of each class have different tissue-specificities and physiological functions. Class II PI3Ks consist of three isoforms ({alpha}, {beta}, {gamma}). Although the {alpha}-isoform (PI3K-C2{alpha}) is considered ubiquitous and preferentially activated by insulin rather than the {beta}-isoform, the physiological significance of PI3K-C2{alpha} is poorly understood. The present study aimed to determine whether PI3K-C2{alpha} is associated with the suppression of apoptotic cell death. Different sense- and antisense oligonucleotides (ODNs) were synthesized based on the sequence of C2 domain of PI3K-C2{alpha} gene. Transfection of CHO-IR cells with two different antisense ODNs clearly reduced the protein content as well as mRNA levels of PI3K-C2{alpha} whereas neither the nonspecific mock- nor sense ODNs affected. The decrease of PI3K-C2{alpha} gene expression was paralleled by cellular changes indicating apoptotic cell death such as nuclear condensation, formation of apoptotic bodies, and DNA fragmentation. PI3K-C2{alpha} mRNA levels were also reduced when cells were incubated in growth factor-deficient medium. Supplementing growth factors (serum or insulin) into medium lead to an increase of PI3K-C2{alpha} mRNA levels. This finding strongly suggests that PI3K-C2{alpha} is a crucial survival factor.

Kang, Shinhae [Technology Innovation Center, Cheju National University, Jeju, Jeju 690-756 (Korea, Republic of); Song, Jihoon [Department of Life Science, Cheju National University, Jeju, Jeju 690-756 (Korea, Republic of); Kang, Jihoon [Department of Medicine, Cheju National University, Jeju, Jeju 690-756 (Korea, Republic of); Kang, Heekyoung [Department of Medicine, Cheju National University, Jeju, Jeju 690-756 (Korea, Republic of); Lee, Daeho [Department of Medicine, Cheju National University, Jeju, Jeju 690-756 (Korea, Republic of); Lee, Youngki [Department of Medicine, Cheju National University, Jeju, Jeju 690-756 (Korea, Republic of); Park, Deokbae [Department of Medicine, Cheju National University, Jeju, Jeju 690-756 (Korea, Republic of)]. E-mail:



Association of kynurenine aminotransferase II gene C401T polymorphism with immune response in patients with meningitis  

PubMed Central

Background The kynurenine (KYN) pathway has been shown to be altered in several diseases which compromise the central nervous system (CNS) including infectious diseases such as bacterial meningitis (BM). The aim of this study was to assess single nucleotide polymorphisms (SNPs) in four genes of KYN pathway in patients with meningitis and their correlation with markers of immune response in BM. Methods One hundred and one individuals were enrolled in this study to investigate SNPs in the following genes: indoleamine-2,3-dioxygenase (IDO1 gene), kynureninase (KYNU gene), kynurenine aminotransferase I (CCBL1 gene), and kynurenine aminotransferase II (AADAT gene). SNP analyses were performed by primer-introduced restriction analysis-PCR (PIRA-PCR) followed by RFLP. Cytokines were measured using multiplex bead assay while immunoglobulins (IG) by immunodiffusion plates and NF-kappaB and c-Jun by dot blot assay. Results The variant allele of SNP AADAT+401C/T showed prevalent frequency in patients with BM. A significant decrease (p < 0.05) in TNF-?, IL-1?, IL-6, MIP-1?CCL3 and MIP-1?/CCL4 levels was observed in BM patients homozygous (TT) to the SNP AADAT+401C/T. Furthermore, a significant (p < 0.05) decrease in cell count was observed in cerebrospinal fluid (CSF) from patients with TT genotype. In addition, an increase in the IgG level in adults (p < 0.05) was observed. The variant allele for KYNU+715G/A was found with low frequency in the groups, and the SNPs in IDO1+434T/G, KYNU+693G/A, CCBL1+164T/C, and AADAT+650C/T had no frequency in this population. Conclusions This study is the first report of an association of SNP AADAT+401C/T with the host immune response to BM, suggesting that this SNP may affect the host ability in recruitment of leukocytes to the infection site. This finding may contribute to identifying potential targets for pharmacological intervention as adjuvant therapy for BM.



Correlation between microtubule-associated gene expression and chemosensitivity of patients with stage II non-small cell lung cancer  

PubMed Central

The aim of this study was to explore the correlation between mRNA expression of ?-tubulin-III and stathmin in patients with stage II non-small cell lung cancer (NSCLC) and the chemosensitivity to Navelbine plus cisplatin (NP), as well as to provide a basis for personalized treatment. A single-gene quantitative test was performed to detect the mRNA expression of ?-tubulin-III and stathmin in the tumor tissue of patients with stage II NSCLC. All the patients underwent NP treatment following surgery and were followed-up to record their disease-free survival (DFS) and overall survival (OS). Statistical analyses were conducted to investigate the correlation between ?-tubulin-III and stathmin mRNA expression and DFS and OS in the patients. ?-tubulin-III mRNA expression was associated with OS in the 73 patients (P=0.003) and DFS was correlated with ?-tubulin-III mRNA expression and lymphatic metastasis (P<0.01). Stathmin mRNA expression was not correlated with OS or DFS (P>0.05). OS and DFS were longer in the patients with low ?-tubulin-III mRNA expression than in those with high ?-tubulin-III mRNA expression (P<0.01); there was no significant change in OS and DFS between the patients with high and low mRNA expression of stathmin (P>0.05). The mRNA expression levels of ?-tubulin-III in the tumor tissue of patients with stage II NSCLC may be considered as an index of prognosis and chemosensitivity, as well as a reference for personalized chemotherapeutic applications in patients.




Effects of targeted disruption of the mouse angiotensin II type 2 receptor gene on stress-induced hyperthermia.  


1. We have previously reported that brain angiotensin II type 2 receptors (AT2) contribute to immunological stress-induced hyperthermia (fever) in rats. Now, in mice, we report the effect of AT2 gene disruption on the hyperthermia induced by immunological (interleukin-1 (IL-1) injection) and non-immunological (saline injection or cage switch) stress. 2. AT2-deficient and control mice both showed typical circadian rhythmicity in body temperature and physical activity. During the latter half of the dark period, AT2-deficient mice exhibited a lower body temperature than the controls. 3. By comparison with the controls, AT2-deficient mice exhibited: (i) a significantly smaller hyperthermia after intraperitoneal (i.p.) injection of IL-1beta; (ii) significantly greater increases in body temperature and physical activity after i. p. saline; and (iii) a significantly greater hyperthermia (but a similar increase in activity) during cage-switch stress. 4. These results suggest that AT2, presumably in the brain, plays important roles in stress-induced hyperthermia in mice. PMID:10066912

Watanabe, T; Hashimoto, M; Okuyama, S; Inagami, T; Nakamura, S



Effects of targeted disruption of the mouse angiotensin II type 2 receptor gene on stress-induced hyperthermia  

PubMed Central

We have previously reported that brain angiotensin II type 2 receptors (AT2) contribute to immunological stress-induced hyperthermia (fever) in rats. Now, in mice, we report the effect of AT2 gene disruption on the hyperthermia induced by immunological (interleukin-1 (IL-1) injection) and non-immunological (saline injection or cage switch) stress. AT2-deficient and control mice both showed typical circadian rhythmicity in body temperature and physical activity. During the latter half of the dark period, AT2-deficient mice exhibited a lower body temperature than the controls. By comparison with the controls, AT2-deficient mice exhibited: (i) a significantly smaller hyperthermia after intraperitoneal (i.p.) injection of IL-1?; (ii) significantly greater increases in body temperature and physical activity after i.p. saline; and (iii) a significantly greater hyperthermia (but a similar increase in activity) during cage-switch stress. These results suggest that AT2, presumably in the brain, plays important roles in stress-induced hyperthermia in mice.

Watanabe, Tatsuo; Hashimoto, Makoto; Okuyama, Shigeru; Inagami, Tadashi; Nakamura, Shoji



The expression of class II MHC gene products by fallopian tube epithelium in pregnancy and throughout the menstrual cycle.  

PubMed Central

The expression of HLA class II antigens by human fallopian tube epithelium was investigated in ectopic tubal pregnancy, in normal early and full-term intrauterine pregnancy, and during the menstrual cycle. Monoclonal antibodies directed against non-polymorphic (DA6.231, CR3/43, B7/21) and polymorphic (DA6.147, DA6.164, anti-leu-10) determinants of the HLA-D locus were used in a standard indirect immunoperoxidase method on fresh cryostat sections of fallopian tube. In ectopic pregnancy the tube epithelium showed uniform, intense reactivity for DR, DP and DQ. A similar reaction pattern was observed in normal first-trimester pregnancy. At term, most epithelial cells were DR-, DP- and DQ-positive, but a few were DP- and DQ-negative. In fallopian tubes from non-pregnant individuals, a variable number of epithelial cells labelled for DR alpha and DR beta but there was essentially no reactivity for DP or DQ. These results suggest differential regulation of class II MHC gene expression by tube epithelial cells, possibly mediated by hormones and/or a trophoblast product. Images Figure 1 Figure 2 Figure 3

Bulmer, J N; Earl, U



Characterization of a cis-acting regulatory element which silences expression of the class II-A beta gene in epithelium  

PubMed Central

Class II major histocompatibility complex (MHC) genes encode for alpha/beta chain pairs that are constitutively expressed principally on mature B cells and dendritic cells in mice. These gene products are easily induced on macrophages with cytokines, and may also aberrantly appear on the surface of epithelium during immune injury. The appearance of class II determinants in parenchymal tissue potentially renders these somatic cells capable of antigen presentation to circulating CD4+ T lymphocytes, and their absence may be protective for normal tissues expressing self-antigens. The low surface class II expression observed on parenchymal cells generally correlates with low levels of mRNA, suggesting that transcription rate is a major element in class II regulation. To understand the transcriptional mechanism maintaining low basal surface expression of class II in somatic cells, we transiently transfected mini-gene reporter constructs to study the regulation of the murine A beta promoter in a cultured renal epithelial cell line. We describe here a negative cis-acting regulatory region located between -552 and -489 bp upstream of the A beta cap site that silences the transcriptional activity of the A beta promoter in epithelial cells in an orientation-dependent manner, and is also able to silence a heterologous promoter. This region is not active in class II-expressing B cells (BAL-17) in culture, but is functional in two other murine class II-negative cell lines, fibroblasts and thymoma T cells. Using competition electrophoretic mobility shift assays, we have localized the core protein binding site within this region to an 8-10- bp response element, designated A beta NRE, at -543 to -534 bp. A nuclear extract from BAL-17 cells does not bind to this element. Mutation of this site abrogates the transcriptional silencing activity of the region. We conclude that the transcription of class II-A beta in parenchymal cells, and some lymphocytes, can be actively repressed by an upstream silencing element.



Gene expression of herpes simplex virus. II. Uv radiological analysis of viral transcription units  

SciTech Connect

The transcriptional organization of the genome of herpes simplex virus type 1 was analyzed by measuring the sensitivity of viral polypeptide synthesis to uv irradiation of the infecting virus. Herpes simplex virus type 1 was irradiated with various doses of uv light and used to infect xeroderma pigmentosum fibroblasts. Immediate early transcription units were analyzed by having cycloheximide present throughout the period of infection, removing the drug at 8 h postinfection, and pulse-labeling proteins with (355)methionine. Delayed early transcription units were analyzed in similar studies by having 9-beta-D-arabinofuranosyladenine present during the experiment to block replication of the input irradiated genome. The results indicate that none of the immediate early genes analyzed can be cotranscribed, whereas some of the delayed early genes might be cotranscribed. No evidence was found for the existence of large, multigene transcription units.

Millette, R. L.; Klaiber, R.



MHC class II genes in European wolves: a comparison with dogs.  


The genome of the grey wolf, one of the most widely distributed land mammal species, has been subjected to both stochastic factors, including biogeographical subdivision and population fragmentation, and strong selection during the domestication of the dog. To explore the effects of drift and selection on the partitioning of MHC variation in the diversification of species, we present nine DQA, 10 DQB, and 17 DRB1 sequences of the second exon for European wolves and compare them with sequences of North American wolves and dogs. The relatively large number of class II alleles present in both European and North American wolves attests to their large historical population sizes, yet there are few alleles shared between these regions at DQB and DRB1. Similarly, the dog has an extensive array of class II MHC alleles, a consequence of a genetically diverse origin, but allelic overlap with wolves only at DQA. Although we might expect a progression from shared alleles to shared allelic lineages during differentiation, the partitioning of diversity between wolves and dogs at DQB and DRB1 differs from that at DQA. Furthermore, an extensive region of nucleotide sequence shared between DRB1 and DQB alleles and a shared motif suggests intergenic recombination may have contributed to MHC diversity in the Canidae. PMID:12389097

Seddon, Jennifer M; Ellegren, Hans



Diversification of porcine MHC class II genes: evidence for selective advantage  

Microsoft Academic Search

The major histocompatibility complex (MHC) is an immunological gene-dense region of high diversity in mammalian species. Sus scrofa was domesticated by at least six independent events over Eurasia during the Holocene period. It has been hypothesized that\\u000a the level and distribution of MHC variation in pig populations reflect genetic selection and environmental influences. In\\u000a an effort to define the complexity

Erin S. Luetkemeier; Ripan S. Malhi; Jonathan E. Beever; Lawrence B. Schook



Frequency of angiotensin II type 1 receptor gene polymorphism in Turkish acute stroke patients.  


This study was performed in acute stroke patients in the Turkish population to determine the frequency of the A1166C polymorphism in the AT1 gene and to examine the role of this polymorphism in acute stroke development. In this study, 257 genomic DNA samples were analysed (from 206 acute stroke patients and 51 healthy individuals). Genomic DNA was prepared from peripheral blood using the salt-extraction method. The presence of the A1166C polymorphism in the AT1 gene was determined using the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method. PCR products were separated by 2% agarose gel electrophoresis and visualized by a charge-coupled device (CCD) camera. In this study, the allele frequency at the A1166C position was 92% A and 8% C for control and 97% A and 3% C for patients. This difference in allele frequency between the control group and the patient group was not statistically significant. However, genotype and allele frequencies showed a significant difference (P < 0.001) in the control and the patient groups. The results of this study show no relationship between the A1166C polymorphism in the AT1 gene and acute stroke in the Turkish population. PMID:23480670

Hulyam, Kurt; Aysegul, Bayramoglu; Veysi, Gunes Hasan; Demet, Ozbabalik; Irfan, Degirmenci; Ertugrul, Colak; Didem, Cosan Turgut; Banu, Bayram; Miris, Dikmen



Variation in USF1 shows haplotype effects, gene : gene and gene : environment associations with glucose and lipid parameters in the European Atherosclerosis Research Study II  

Microsoft Academic Search

Upstream stimulatory factor 1 (USF 1), is a transcription factor controlling expression of several genes involved in lipid and glucose homeostasis and co-localizes with familial combined hyperlipidemia (FCHL) and type 2 diabetes on chromosome 1q22 -2 3. We sequenced USF1 in 24 UK FCHL probands, but found no rare or common cSNPs. Three common intronic single nucleotide ploymorphisms (SNP), 306A>G,

Wendy Putt; Jutta Palmen; Viviane Nicaud; David-Alexandre Tregouet; Nadia Tahri-Daizadeh; David M. Flavell; Steve E. Humphries; Philippa J. Talmud



Toward understanding the role of mitochondrial complex II in the intraerythrocytic stages of Plasmodium falciparum: gene targeting of the Fp subunit.  


Malaria parasites in human hosts depend on glycolysis for most of their energy production, and the mitochondrion of the intraerythrocytic form is acristate. Although the genes for all tricarboxylic acid (TCA) cycle members are found in the parasite genome, the presence of a functional TCA cycle in the intraerythrocytic stage is still controversial. To elucidate the physiological role of Plasmodium falciparum mitochondrial complex II (succinate-ubiquinone reductase (SQR) or succinate dehydrogenase (SDH)) in the TCA cycle, the gene for the flavoprotein subunit (Fp) of the enzyme, pfsdha (P.falciparum gene for SDH subunit A, PlasmoDB ID: PF3D7_1034400) was disrupted. SDH is a well-known marker enzyme for mitochondria. In the pfsdha disruptants, Fp mRNA and polypeptides were decreased, and neither SQR nor SDH activity of complex II was detected. The suppression of complex II caused growth retardation of the intraerythrocytic forms, suggesting that complex II contributes to intraerythrocytic parasite growth, although it is not essential for survival. The growth retardation in the pfsdha disruptant was rescued by the addition of succinate, but not by fumarate. This indicates that complex II functions as a quinol-fumarate reductase (QFR) to form succinate from fumarate in the intraerythrocytic parasite. PMID:22698672

Tanaka, Takeshi Q; Hirai, Makoto; Watanabe, Yoh-ichi; Kita, Kiyoshi



Transcriptional up-regulation of antioxidant genes by PPAR? inhibits angiotensin II-induced premature senescence in vascular smooth muscle cells.  


This study evaluated peroxisome proliferator-activated receptor (PPAR) ? as a potential target for therapeutic intervention in Ang II-induced senescence in human vascular smooth muscle cells (hVSMCs). Activation of PPAR? by GW501516, a specific agonist of PPAR?, significantly inhibited the Ang II-induced premature senescence of hVSMCs. Agonist-activated PPAR? suppressed the generation of Ang II-triggered reactive oxygen species (ROS) with a concomitant reduction in DNA damage. Notably, GW501516 up-regulated the expression of antioxidant genes, such as glutathione peroxidase 1, thioredoxin 1, manganese superoxide dismutase and heme oxygenase 1. siRNA-mediated down-regulation of these antioxidant genes almost completely abolished the effects of GW501516 on ROS production and premature senescence in hVSMCs treated with Ang II. Taken together, the enhanced transcription of antioxidant genes is responsible for the PPAR?-mediated inhibition of premature senescence through sequestration of ROS in hVSMCs treated with Ang II. PMID:21352808

Kim, Hyo Jung; Ham, Sun Ah; Paek, Kyung Shin; Hwang, Jung Seok; Jung, Si Young; Kim, Min Young; Jin, Hanna; Kang, Eun Sil; Woo, Im Sun; Kim, Hye Jung; Lee, Jae Heun; Chang, Ki Churl; Han, Chang Woo; Seo, Han Geuk



Resemblance and Dissemblance of Arabidopsis Type II Peroxiredoxins: Similar Sequences for Divergent Gene Expression, Protein Localization, and Activity1  

PubMed Central

The Arabidopsis type II peroxiredoxin (PRXII) family is composed of six different genes, five of which are expressed. On the basis of the nucleotide and protein sequences, we were able to define three subgroups among the PRXII family. The first subgroup is composed of AtPRXII-B, -C, and -D, which are highly similar and localized in the cytosol. AtPRXII-B is ubiquitously expressed. More striking is the specific expression of AtPRXII-C and AtPRXII-D localized in pollen. The second subgroup comprises the mitochondrial AtPRXII-F, the corresponding gene of which is expressed constitutively. We show that AtPRXII-E, belonging to the last subgroup, is expressed mostly in reproductive tissues and that its product is addressed to the plastid. By in vitro enzymatic experiments, we demonstrate that glutaredoxin is the electron donor of recombinant AtPRXII-B for peroxidase reaction, but the donors of AtPRXII-E and AtPRXII-F have still to be identified.

Brehelin, Claire; Meyer, Etienne H.; de Souris, Jean-Paul; Bonnard, Geraldine; Meyer, Yves



Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells  

PubMed Central

Argonaute proteins are often credited for their cytoplasmic activities in which they function as central mediators of the RNAi platform and microRNA (miRNA)-mediated processes. They also facilitate heterochromatin formation and establishment of repressive epigenetic marks in the nucleus of fission yeast and plants. However, the nuclear functions of Ago proteins in mammalian cells remain elusive. In the present study, we combine ChIP-seq (chromatin immunoprecipitation coupled with massively parallel sequencing) with biochemical assays to show that nuclear Ago1 directly interacts with RNA Polymerase II and is widely associated with chromosomal loci throughout the genome with preferential enrichment in promoters of transcriptionally active genes. Additional analyses show that nuclear Ago1 regulates the expression of Ago1-bound genes that are implicated in oncogenic pathways including cell cycle progression, growth, and survival. Our findings reveal the first landscape of human Ago1-chromosomal interactions, which may play a role in the oncogenic transcriptional program of cancer cells.

Qi, Zhongxia; Wang, Ji; Place, Robert F.; Yu, Jingwei; Li, Hao; Li, Long-Cheng



Gene expression in the DpnI and DpnII restriction enzyme systems of Streptococcus pneumoniae  

SciTech Connect

Although a number of bacterial species are naturally transformable, that is, their cells are able to take up external DNA in substantial amounts and integrate it into the chromosome without artificial manipulation of the cell surface, Streptococcus pneumoniae, the first species in which this phenomenon was detected, remains a prototype of such transformation. Cells of S. pneumonias also contain potent restriction endonucleases able to severely restrict DNA introduced during viral infection. Our current understanding of the genetic basis of the complementary DpnI and DpnII restriction systems and of the biochemistry of their component enzymes are briefly reviewed. The manner in which these enzymes impinge on the transfer of chromosomal genes and of plasmeds will be examined in detail. It will be seen that far from acting against foreign DNA in general, the restriction systems seem to be designed to exclude only infecting viral DNA The presence of complementary restriction systems in different cells of S. pneumonias enhances their effectiveness in blocking viral infection and promoting species survival. This enhanced effectiveness requires the expression of alternative restriction systems. Therefore, the ability of the cells to transfer the restriction enzyme genes and to regulate their expression are important for survival of the species.

Lacks, S.A.; Sabelnikov, A.G.; Chen, Jau-Der; Greenberg, B.



cAMP Prevents Glucose-mediated Modifications of Histone H3 and Recruitment of the RNA Polymerase II Holoenzyme to the L-PK Gene Promoter  

PubMed Central

Glucose and cAMP reciprocally regulate expression of the L-type pyruvate kinase (L-PK) gene by controlling the formation of a complex containing Carbohydrate Response Element Binding Protein (ChREBP) and the coactivator CREB Binding Protein (CBP) on the L-PK promoter. However, the role of post-translational histone modifications on the opposing effects of glucose and cAMP on the L-PK gene are unknown. Using the highly glucose-sensitive 832/13 rat insulinoma cell line, we demonstrated that glucose regulates acetylation and methylation of various histone residues at the L-PK gene promoter. These glucose-dependent histone modifications correlated with an increase in the recruitment and phosphorylation of RNA Polymerase II (Pol II) on the L-PK gene promoter. Conversely, the cAMP agonist forskolin prevented glucose-mediated expression of the L-PK gene by decreasing the acetylation of histones H3 and H4 on the promoter, decreasing the methylation of H3-K4 on the coding region and increasing the methylation of H3-K9 on the coding region. These changes induced by cAMP culminated with a decrease in the glucose-dependent recruitment of phosphorylated Pol II to the L-PK gene promoter. Furthermore, maneuvers that interfere with the glucose-dependent assembly of ChREBP and CBP on the L-PK promoter, such as: 1) increasing intracellular cAMP levels; 2) overexpression of a dominant-negative form of ChREBP; or 3) siRNA-mediated suppression of CBP abundance all altered the acetylation and methylation of histones on the L-PK promoter, which decreased Pol II recruitment and subsequently inhibited transcriptional activation of the L-PK gene. We conclude that the effects of glucose and cAMP are mediated in part by epigenetic modulation of histones.

Burke, Susan J.; Collier, J. Jason; Scott, Donald K.



cAMP prevents glucose-mediated modifications of histone H3 and recruitment of the RNA polymerase II holoenzyme to the L-PK gene promoter.  


Glucose and cAMP reciprocally regulate expression of the L-type pyruvate kinase (L-PK) gene by controlling the formation of a complex containing the carbohydrate response element binding protein (ChREBP) and the coactivator CREB binding protein (CBP) on the L-PK promoter. However, the role of posttranslational histone modifications on the opposing effects of glucose and cAMP on the L-PK gene is unknown. Using the highly glucose-sensitive 832/13 rat insulinoma cell line, we demonstrated that glucose regulates acetylation and methylation of various histone residues at the L-PK gene promoter. These glucose-dependent histone modifications correlated with an increase in the recruitment and phosphorylation of RNA polymerase II (Pol II) on the L-PK gene promoter. Conversely, the cAMP agonist forskolin prevented glucose-mediated expression of the L-PK gene by decreasing the acetylation of histones H3 and H4 on the promoter, decreasing the methylation of H3-K4 on the coding region, and increasing the methylation of H3-K9 on the coding region. These changes induced by cAMP culminated with a decrease in the glucose-dependent recruitment of phosphorylated Pol II to the L-PK gene promoter. Furthermore, maneuvers that interfere with the glucose-dependent assembly of ChREBP and CBP on the L-PK promoter, such as increasing intracellular cAMP levels, overexpression of a dominant-negative form of ChREBP, and small-interfering-RNA-mediated suppression of CBP abundance, all altered the acetylation and methylation of histones on the L-PK promoter, which decreased Pol II recruitment and subsequently inhibited transcriptional activation of the L-PK gene. We conclude that the effects of glucose and cAMP are mediated in part by epigenetic modulation of histones. PMID:19631660

Burke, Susan J; Collier, J Jason; Scott, Donald K



Clinical and molecular analysis of three families with autosomal dominant neurohypophyseal diabetes insipidus associated with a novel and recurrent mutations in the vasopressin-neurophysin II gene  

Microsoft Academic Search

Objective: To test further the hypothesis that autosomal dominant neurohypophyseal diabetes insipi- dus (adFNDI) is caused by heterozygous mutations in the vasopressin - neurophysin II (AVP-NPII ) gene that exert a dominant negative effect by producing a precursor that misfolds, accumulates and eventually destroys the neurosecretory neurons. Methods: Antidiuretic function, magnetic resonance imaging (MRI) of the posterior pituitary and AVP-NPII

Jonas Rutishauser; Peter Kopp; Mary Beth Gaskill; Thomas J Kotlar; Gary L Robertson



Expression of the Insulin-Like Growth Factor II Gene in the Choroid Plexus and the Leptomeninges of the Adult Rat Central Nervous System  

Microsoft Academic Search

The rat insulin-like growth factor II gene, encoding a fetal somatomedin, expresses a multitranscript family in embryonic\\/fetal tissues and in the adult brain and spinal cord. By performing in situ hybridization on tissue sections of adult brain and spinal cord, we have found that these transcripts are not expressed in neural or glial cells but are expressed in the epithelium

Fotini Stylianopoulou; Joseph Herbert; Marcelo Bento Soares; Argiris Efstratiadis



Possible association of sudden infant death with partial complement C4 deficiency revealed by post-mortem DNA typing of HLA class II and III genes  

Microsoft Academic Search

Based on evidence of an increased rate of respiratory infections in sudden infant death (SID) infants as well as the observation of familial occurrence, we analysed in a retrospective study class II and class III genes of the major histocompatibility complex in 40 cases of SID by Southern blot analysis of DNA obtained post mortem from tissue samples. In 24

P. M. Schneider; C. Wendler; T. Riepert; L. Braun; U. Schacker; M. Horn; H. Althoff; R. Mattern; C. Rittner



Localization of the gene for the vitamin B12 binding protein, transcobalamin II, near the centromere on mouse chromosome 11, linked with the hemoglobin alpha-chain locus  

Microsoft Academic Search

Somatic cell hybrids, recombinant inbred (RI) mouse strains, and backcross breeding experiments were used to locate the gene of transcobalamin II (Tcn-2), the vitamin B12 binding protein in mouse serum. TCN-2 was found to be a useful genetic marker in the somatic cell hybrids. Selected hybrid clones were derived from fusions between GR mouse cells and the Chinese hamster cell

M. Frŕter-Schröder; M. Prochazka; O. Haller; F. Arwert; H. J. Porck; L. C. Skow; L.-G. Lundin; J. Hilkens; J. Hilgers



scully, an Essential Gene of Drosophila, is Homologous to Mammalian Mitochondrial Type II L-3-hydroxyacyl-CoA Dehydrogenase\\/Amyloid-beta Peptide-binding Protein  

Microsoft Academic Search

The characterization of scully , an essential gene of Drosophila with phenocritical phases at embry- onic and pupal stages, shows its extensive homology with vertebrate type II l -3-hydroxyacyl-CoA dehydro- genase\\/ERAB. Genomic rescue demonstrates that four different lethal mutations are scu alleles, the molecular nature of which has been established. One of them, scu 3127 , generates a nonfunctional truncated

Laura Torroja; Daniel Ortuńo-Sahagún; Alberto Ferrús; Barbara Hämmerle; Julio A. Barbas



Expression of a partially deleted gene of human type II procollagen (COL2A1) in transgenic mice produces a chondrodysplasia.  

PubMed Central

A minigene version of the human gene for type II procollagen (COL2A1) was prepared that lacked a large central region containing 12 of the 52 exons and therefore 291 of the 1523 codons of the gene. The construct was modeled after sporadic in-frame deletions of collagen genes that cause synthesis of shortened pro alpha chains that associate with normal pro alpha chains and thereby cause degradation of the shortened and normal pro alpha chains through a process called procollagen suicide. The gene construct was used to prepare five lines of transgenic mice expressing the minigene. A large proportion of the mice expressing the minigene developed a phenotype of a chondrodysplasia with dwarfism, short and thick limbs, a short snout, a cranial bulge, a cleft palate, and delayed mineralization of bone. A number of mice died shortly after birth. Microscopic examination of cartilage revealed decreased density and organization of collagen fibrils. In cultured chondrocytes from the transgenic mice, the minigene was expressed as shortened pro alpha 1(II) chains that were disulfide-linked to normal mouse pro alpha 1(II) chains. Therefore, the phenotype is probably explained by depletion of the endogenous mouse type II procollagen through the phenomenon of procollagen suicide. Images

Vandenberg, P; Khillan, J S; Prockop, D J; Helminen, H; Kontusaari, S; Ala-Kokko, L



HLA class II gene frequencies in Crohn's disease: a population based analysis in Germany.  

PubMed Central

BACKGROUND--Ulcerative colitis is the only known inflammatory bowel disease associated with particular HLA alleles. Whereas the association with the HLA-DRB1*15 allele has been described in several independent studies for ulcerative colitis, no contribution of HLA alleles to susceptibility in Crohn's disease has yet been shown. AIM--This study was designed to study the strength of association of HLA class II alleles as risk markers for Crohn's disease in a homogenous population in Germany. PATIENTS--A total of 4251 randomly selected control subjects, and 162 unrelated subjects with Crohn's disease were studied. Subjects were studied for their HLA-DRB1, HLA-DQA1, and HLA-DQB1 alleles. METHOD--HLA DNA typing was performed after locus specific amplification with the polymerase chain reaction and reverse dot blot hybridisation. RESULTS--The HLA-DRB1*07 was the only HLA class II allele found to be significantly associated with Crohn's disease (relative risk (RR) = 1.9, 95% CI: 1.66 to 2.14; p = 0.0001). This association remained significant after correction for the number of DRB1 alleles compared. In patients with disease onset before 35 years the RR for the disease in HLA-DRB1*07 positive subjects was found to be higher (RR = 3.1, 95% CI: 2.44 to 3.76). The HLA-DRB1*03 was significantly decreased in frequency in Crohn's disease (RR = 0.5, 95% CI: 0.39 to 0.61; p = 0.0028). CONCLUSION--The HLA-DRB1*07 allele provides risk for the disease especially in patients with younger ages of onset. These data also provide indirect evidence for an immunogenetically based heterogeneity of the disease.

Reinshagen, M; Loeliger, C; Kuehnl, P; Weiss, U; Manfras, B J; Adler, G; Boehm, B O



Sccmec type II gene is common among clinical isolates of methicillin-resistant Staphylococcus aureus in Jakarta, Indonesia  

PubMed Central

Background Community Acquired Methicillin Resistant Staphylococcus aureus (CA-MRSA) is a strain of MRSA that can cause infections in patients in the community, in which these patients had no previous risk factors for MRSA infection and the patient received 72?hours prior to infection when admitted to hospital. This study aims to determine and compare the characteristics of epidemiological, clinical, and molecular biology of CA-MRSA with HA-MRSA. Methods A total of 11 clinical strains of Methicillin-resistant Staphylococcus aureus (MRSA) and Methicillin-sensitive Stapylococcus aureus (MSSA) were collected from 2 hospitals in Jakarta, Indonesia in 2012. SCCmec typing was performed by multiplex polymerase chain reaction (PCR) and the presence of six genes (vraR, vraG, vraA, vraF,fruA, and fruB) associated with vancomycin resistance was examined by simple PCR analysis. Results We found three strains of community-acquired MRSA with SCCmec type II and one strain of hospital-acquired MRSA with SCCmec type IV. The other seven strains did not contain mecA genes and SCCmec. Plasmid pUB110 was found in one strain of community-acquired MRSA and two strains of hospital-acquired MRSA. vraA genes were present in 9 of the 11 strains, vraF in 4, vraG in 5, and vraR in 4. Note worthily, three quarters of strains without pUB110 contained vraR and vraF, and 70% contained vraA, whereas 60% of strains with pUB110 contained vraG. Conclusion Based on these results, we should be concerned about the possibility of transition from MRSA strains sensitive to vancomycin in VISA strains of MRSA strains obtained in clinical trials. But first we need to look the existence of natural VISA or hVISA among these MRSA strains.