bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim
Authors: Zeng Shaohua , Xiao Gong , Guo Juan , Fei Zhangjun , Xu Yanqin , Roe Bruce A , Wang Ying 
Published: February 2010

Abstract

Background

Epimedium sagittatum (Sieb. Et Zucc.) Maxim, a traditional Chinese medicinal plant species, has been used extensively as genuine medicinal materials. Certain Epimedium species are endangered due to commercial overexploition, while sustainable application studies, conservation genetics, systematics, and marker-assisted selection (MAS) of Epimedium is less-studied due to the lack of molecular markers. Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for E. sagittatum.

Results
cDNAs of E. sagittatum are sequenced using 454 GS-FLX pyrosequencing technology. The raw reads are cleaned and assembled into a total of 76,459 consensus sequences comprising of 17,231 contigs and 59,228 singlets. About 38.5% (29,466) of the consensus sequences significantly match to the non-redundant protein database (E-value < 1e-10), 22,295 of which are further annotated using Gene Ontology (GO) terms. A total of 2,810 EST-SSRs is identified from the Epimedium EST dataset. Trinucleotide SSR is the dominant repeat type (55.2%) followed by dinucleotide (30.4%), tetranuleotide (7.3%), hexanucleotide (4.9%), and pentanucleotide (2.2%) SSR. The dominant repeat motif is AAG/CTT (23.6%) followed by AG/CT (19.3%), ACC/GGT (11.1%), AT/AT (7.5%), and AAC/GTT (5.9%). Thirty-two SSR-ESTs are randomly selected and primer pairs are synthesized for testing the transferability across 52 Epimedium species. Eighteen primer pairs (85.7%) could be successfully transferred to Epimedium species and sixteen of those show high genetic diversity with 0.35 of observed heterozygosity (Ho) and 0.65 of expected heterozygosity (He) and high number of alleles per locus (11.9).

Conclusion
A large EST dataset with a total of 76,459 consensus sequences is generated, aiming to provide sequence information for deciphering secondary metabolism, especially for flavonoid pathway in Epimedium. A total of 2,810 EST-SSRs is identified from EST dataset and ~1580 EST-SSR markers are transferable. E. sagittatum EST-SSR transferability to the major Epimedium germplasm is up to 85.7%. Therefore, this EST dataset and EST-SSRs will be a powerful resource for further studies such as taxonomy, molecular breeding, genetics, genomics, and secondary metabolism in Epimedium species.
Genome-wide analysis of rice ClpB/HSP100, ClpC and ClpD genes
Authors: Singh Amanjot , Singh Upasana , Mittal Dheeraj , Grover Anil 
Published: February 2010

AbstractBackgroundClpB-cyt/HSP100 protein acts as chaperone, mediating disaggregation of denatured proteins. Previous studies have shown that ClpB-cyt/HSP100 gene belongs to the group class I Clp ATPase proteins and ClpB-cyt/HSP100 transcript is regulated by heat stress and developmental cues.ResultsNine ORFs were noted to constitute rice class I Clp ATPases in the following manner: 3 ClpB proteins (ClpB-cyt, Os05g44340; ClpB-m, Os02g08490; ClpB-c, Os03g31300), 4 ClpC proteins (ClpC1, Os04g32560; ClpC2, Os12g12580; ClpC3, Os11g16590; ClpC4, Os11g16770) and 2 ClpD proteins (ClpD1, Os02g32520; ClpD2, Os04g33210). Using the respective signal sequences cloned upstream to GFP/CFP reporter proteins and transient expression studies with onion epidermal cells, evidence is provided that rice ClpB-m and Clp-c proteins are indeed localized to their respective cell locations mitochondria and chloroplasts, respectively. Associated with their diverse cell locations, domain structures of OsClpB-c, OsClpB-m and OsClpB-cyt proteins are noted to possess a high-level conservation.OsClpB-cyttranscript is shown to be enriched at milk and dough stages of seed development. While expression ofOsClpB-mwas significantly less as compared to its cytoplasmic and chloroplastic counterparts in different tissues, this transcript showed highest heat-induced expression amongst the 3 ClpB proteins. OsClpC1 and OsClpC2 are predicted to be chloroplast-localized as is the case with all known plant ClpC proteins. However, the fact that OsClpC3 protein appears mitochondrial/chloroplastic with equal probability and OsClpC4 a plasma membrane protein reflects functional diversity of this class. Different class I Clp ATPase transcripts were noted to be cross-induced by a host of different abiotic stress conditions. Complementation assays ofΔhsp104mutant yeast cells showed thatOsClpB-cyt,OsClpB-m,OsClpC1andOsClpD1have significantly positive effects. Remarkably,OsClpD1gene imparted appreciably high level tolerance to the mutant yeast cells.ConclusionsRice class I Clp ATPase gene family is constituted of 9 members. Of these 9, only 3 belonging to ClpB group are heat stress regulated. Distribution of ClpB proteins to different cell organelles indicates that their functioning might be critical in different cell locations. From the complementation assays, OsClpD1 appears to be more effective than OsClpB-cyt protein in rescuing the thermosensitive defect of the yeastScΔhsp104mutant cells.
Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics
Authors: Noël Christophe J , Diaz Nicia , Sicheritz-Ponten Thomas , Safarikova Lucie , Tachezy Jan , Tang Petrus , Fiori Pier-Luigi , Hirt Robert P 
Published: February 2010

Abstract

Background

Trichomonas vaginalis is the most common non-viral human sexually transmitted pathogen and importantly, contributes to facilitating the spread of HIV. Yet very little is known about its surface and secreted proteins mediating interactions with, and permitting the invasion and colonisation of, the host mucosa. Initial annotations of T. vaginalis genome identified a plethora of candidate extracellular proteins.

Results
Data mining of the T. vaginalis genome identified 911 BspA-like entries (TvBspA) sharing TpLRR-like leucine-rich repeats, which represent the largest gene family encoding potential extracellular proteins for the pathogen. A broad range of microorganisms encoding BspA-like proteins was identified and these are mainly known to live on mucosal surfaces, among these T. vaginalis is endowed with the largest gene family. Over 190 TvBspA proteins with inferred transmembrane domains were characterised by a considerable structural diversity between their TpLRR and other types of repetitive sequences and two subfamilies possessed distinct classic sorting signal motifs for endocytosis. One TvBspA subfamily also shared a glycine-rich protein domain with proteins from Clostridium difficile pathogenic strains and C. difficile phages. Consistent with the hypothesis that TvBspA protein structural diversity implies diverse roles, we demonstrated for several TvBspA genes differential expression at the transcript level in different growth conditions. Identified variants of repetitive segments between several TvBspA paralogues and orthologues from two clinical isolates were also consistent with TpLRR and other repetitive sequences to be functionally important. For one TvBspA protein cell surface expression and antibody responses by both female and male T. vaginalis infected patients were also demonstrated.

Conclusions
The biased mucosal habitat for microbial species encoding BspA-like proteins, the characterisation of a vast structural diversity for the TvBspA proteins, differential expression of a subset of TvBspA genes and the cellular localisation and immunological data for one TvBspA; all point to the importance of the TvBspA proteins to various aspects of T. vaginalis pathobiology at the host-pathogen interface.
Pseudomonas aeruginosa Cystic Fibrosis isolates of similar RAPD genotype exhibit diversity in biofilm forming ability in vitro
Authors: Deligianni Elena , Pattison Sally , Berrar Daniel , Ternan Nigel G , Haylock Richard W , Moore John E , Elborn Stuart J , Dooley James SG 
Published: February 2010

Abstract

Background

Pseudomonas aeruginosa is considered to grow in a biofilm in cystic fibrosis (CF) chronic lung infections. Bacterial cell motility is one of the main factors that have been connected with P. aeruginosa adherence to both biotic and abiotic surfaces. In this investigation, we employed molecular and microscopic methods to determine the presence or absence of motility in P. aeruginosa CF isolates, and statistically correlated this with their biofilm forming ability in vitro.

Results
Our investigations revealed a wide diversity in the production, architecture and control of biofilm formation. Of 96 isolates, 49% possessed swimming motility, 27% twitching and 52% swarming motility, while 47% were non-motile. Microtitre plate assays for biofilm formation showed a range of biofilm formation ability from biofilm deficient phenotypes to those that formed very thick biofilms. A comparison of the motility and adherence properties of individual strains demonstrated that the presence of swimming and twitching motility positively affected biofilm biomass. Crucially, however, motility was not an absolute requirement for biofilm formation, as 30 non-motile isolates actually formed thick biofilms, and three motile isolates that had both flagella and type IV pili attached only weakly. In addition, CLSM analysis showed that biofilm-forming strains of P. aeruginosa were in fact capable of entrapping non-biofilm forming strains, such that these 'non-biofilm forming' cells could be observed as part of the mature biofilm architecture.

Conclusions
Clinical isolates that do not produce biofilms in the laboratory must have the ability to survive in the patient lung. We propose that a synergy exists between isolates in vivo, which allows "non biofilm-forming" isolates to be incorporated into the biofilm. Therefore, there is the potential for strains that are apparently non-biofilm forming in vitro to participate in biofilm-mediated pathogenesis in the CF lung.
Transcriptional profiling reveals the expression of novel genes in response to various stimuli in the human dermatophyte Trichophyton rubrum
Authors: Peres Nalu TA , Sanches Pablo R , Falcão Juliana P , Silveira Henrique CS , Paião Fernanda G , Maranhão Fernanda CA , Gras Diana E , Segato Fernando , Cazzaniga Rodrigo A , Mazucato Mendelson , Cursino-Santos Jeny R , Aquino-Ferreira Roseli , Rossi Antonio , Martinez-Rossi Nilce M 
Published: February 2010

Abstract

Background
Cutaneous mycoses are common human infections among healthy and immunocompromised hosts, and the anthropophilic fungus Trichophyton rubrum is the most prevalent microorganism isolated from such clinical cases worldwide. The aim of this study was to determine the transcriptional profile of T. rubrum exposed to various stimuli in order to obtain insights into the responses of this pathogen to different environmental challenges. Therefore, we generated an expressed sequence tag (EST) collection by constructing one cDNA library and nine suppression subtractive hybridization libraries.

Results
The 1388 unigenes identified in this study were functionally classified based on the Munich Information Center for Protein Sequences (MIPS) categories. The identified proteins were involved in transcriptional regulation, cellular defense and stress, protein degradation, signaling, transport, and secretion, among other functions. Analysis of these unigenes revealed 575 T. rubrum sequences that had not been previously deposited in public databases.

Conclusion
In this study, we identified novel T. rubrum genes that will be useful for ORF prediction in genome sequencing and facilitating functional genome analysis. Annotation of these expressed genes revealed metabolic adaptations of T. rubrum to carbon sources, ambient pH shifts, and various antifungal drugs used in medical practice. Furthermore, challenging T. rubrum with cytotoxic drugs and ambient pH shifts extended our understanding of the molecular events possibly involved in the infectious process and resistance to antifungal drugs.
Food seeking in spite of harmful consequences is under prefrontal cortical noradrenergic control
Authors: Latagliata Emanuele Claudio , Patrono Enrico , Puglisi-Allegra Stefano , Ventura Rossella 
Published: February 2010

Abstract

Background
Eating disorders are multifactorial psychiatric disorders. Chronic stressful experiences and caloric restriction are the most powerful triggers of eating disorders in human and animals. Although compulsive behavior is considered to characterize pathological excessive food intake, to our knowledge, no evidence has been reported of continued food seeking/intake despite its possible harmful consequences, an index of compulsive behavior. Brain monoamine transmission is considered to have a key role in vulnerability to eating disorders, and norepinephrine in medial prefrontal cortex has been shown to be critical for food-related motivated behavior.
Here, using a new paradigm of conditioned suppression, we investigated whether the ability of a foot-shock-paired conditioned stimulus to suppress chocolate-seeking behavior was reversed by previous exposure to a food restriction experience, thus modeling food seeking in spite of harmful consequences in mice. Moreover, we assessed the effects of selective norepinephrine inactivation in medial prefrontal cortex on conditioned suppression test in stressed and caloric restricted mice.

Results
While Control (non food deprived) animals showed a profound conditioned suppression of chocolate seeking during presentation of conditioned stimulus, previously food restricted animals showed food seeking/intake despite its possible harmful consequences. Moreover, food seeking in spite of harmful consequences was prevented by selective norepinephrine inactivation, thus showing that prefrontal cortical norepinephrine is critical also for maladaptive food-related behavior.

Conclusions
These findings indicate that adaptive food seeking/intake can be transformed into maladaptive behaviors and point to "top-down" influence on eating disturbances and to new targets for therapy of aberrant eating behaviors.
BDNF Val66Met polymorphism and protein levels in Amniotic Fluid
Authors: Cattaneo Annamaria , Bocchio-Chiavetto Luisella , Zanardini Roberta , Marchina Eleonora , Bellotti Daniela , Milanesi Elena , Moraschi Stefania , Calabrese Francesca , Barlati Sergio , Riva Marco Andrea , Gennarelli Massimo 
Published: February 2010

Abstract

Background
Brain-Derived Neurotrophic Factor (BDNF) is a neurotrophin which plays survival- and growth-promoting activity in neuronal cells and it is involved in cellular plasticity mechanisms as it controls activity dependent synaptic transmission. A functional polymorphism (Val66Met) in the pro-region of BDNF, which affects the intracellular trafficking of proBDNF has been associated with memory and cognitive deficits as well as to an increased susceptibility for several psychiatric disorders especially those with a neurodevelopmental origin. To date, no study has evaluated the influence of the Val66Met polymorphism on BDNF levels in a peripheral system that may reflect fetal neurodevelopment. Therefore we investigated in amniotic fluids (AF) obtained from 139 healthy women during 15-17 week of pregnancy, BDNF protein levels in correlation with the Val66Met polymorphism.

Results
Interestingly we found a significant BDNF protein levels reduction in 55 Met carriers (Val/Met and Met/Met) (p = 0.002) as compared to 84 non carriers (Val/Val), and no effect of fetus gender, maternal age or gestation week on BDNF levels has been observed.

Conclusion
These results, although explorative, indicate that during fetal life the Val66Met genotype might influences BDNF protein levels in AF supporting the involvement of this polymorphism in behavioral and functional brain individual differences in the adulthood.
The origin of populations of Arabidopsis thalianain China, based on the chloroplast DNA sequences
Authors: Yin Ping , Kang Juqing , He Fei , Qu Li-Jia , Gu Hongya 
Published: February 2010

Abstract

Background
In the studies incorporating worldwide sampling of A. thaliana populations, the samples from East Asia, especially from China, were very scattered; and the studies focused on global patterns of cpDNA genetic variation among accessions of A. thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China.

Results
A data set comprising 77 accessions of A. thaliana, including 19 field-collected Chinese accessions together with three related species (A. arenosa, A. suecica, and Olimarabidopsis cabulica) as the out-group, was compiled. The analysis of the nucleotide sequences showed that the 77 accessions of A. thaliana were partitioned into two major differentiated haplotype classes (MDHCs). The estimated divergence time of the two MDHCs was about 0.39 mya. Forty-nine haplotypes were detected among the 77 accessions, which exhibited nucleotide diversity (π) of 0.00169. The Chinese populations along the Yangtze River were characterized by five haplotypes, and the two accessions collected from the middle range of the Altai Mountains in China shared six specific variable sites.

Conclusions
The dimorphism in the chloroplast DNA could be due to founder effects during late Pleistocene glaciations and interglacial periods, although introgression cannot be ruled out. The Chinese populations along the Yangtze River may have dispersed eastwards to their present-day locations from the Himalayas. These populations originated from a common ancestor, and a rapid demographic expansion began approximately 90,000 years ago. Two accessions collected from the middle range of the Altai Mountains in China may have survived in a local refugium during late Pleistocene glaciations. The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections.
The Manchester Color Wheel: development of a novel way of identifying color choice and its validation in healthy, anxious and depressed individuals
Authors: Carruthers Helen R , Morris Julie , Tarrier Nicholas , Whorwell Peter J 
Published: February 2010

Abstract

Background
For the purposes of our research programme we needed a simple, reliable and validated method for allowing choice of a color in response to a series of questions. On reviewing the literature no such instrument was available and this study aimed to rectify this situation. This was achieved by developing a simple method of presenting a series of colors to people validating it in healthy volunteers and in individuals where color choice might be distorted, namely anxiety and depression.

Methods
A series of different presentations of four shades of eight colors and grey, as well as black and white were evaluated. 'Mood', 'favourite' and 'drawn to' colors were assessed in 105 healthy, 108 anxious and 110 depressed participants. The positive, neutral or negative attribution of these colors was recorded in a further 204 healthy volunteers.

Results
The circular presentation of colors was most favoured (Color Wheel). Yellow was the most 'drawn to' color and blue the commonest 'favourite' color in all subjects. Yellow was most often associated with a normal mood and grey with an anxious or depressed mood. Different shades of the same color had completely different positive or negative connotations. Reproducibility was exceptionally high when color choice was recorded in positive, neutral or negative terms.

Conclusions
The Color Wheel could be used to assess health status, mood or even treatment outcome in a variety of clinical situations. It may also have utility in circumstances where verbal communication may not be optimal, such as with children.
Chromosome 7p linkage and association study for diabetes related traits and type 2 diabetes in an African-American population enriched for nephropathy
Authors: Leak Tennille S , Langefeld Carl D , Keene Keith L , Gallagher Carla J , Lu Lingyi , Mychaleckyj Josyf C , Rich Stephen S , Freedman Barry I , Bowden Donald W , Sale Michèle M 
Published: February 2010

Abstract

Background
Previously we performed a linkage scan of 638 African American affected sibling pairs (ASP) with type 2 diabetes (T2D) enriched for end-stage renal disease (ESRD). Ordered subset linkage analysis (OSA) revealed a linkage peak on chromosome 7p in the subset of families with earlier age of T2D diagnosis.

Methods
We fine mapped this region by genotyping 11 additional polymorphic markers in the same ASP and investigated a total of 68 single nucleotide polymorphisms (SNPs) in functional candidate genes (GCK1, IL6, IGFBP1 and IGFBP3) for association with age of T2D diagnosis, age of ESRD diagnosis, duration of T2D to onset of ESRD, body mass index (BMI) in African American cases and T2D-ESRD in an African American case-control cohort. OSA of fine mapping markers supported linkage at 28 cM on 7p (near D7S3051) in early-onset T2D families (max. LOD = 3.61, P = 0.002). SNPs in candidate genes and 70 ancestry-informative markers (AIMs) were evaluated in 577 African American T2D-ESRD cases and 596 African American controls.

Results
The most significant association was observed between ESRD age of diagnosis and SNP rs730497, located in intron 1 of the GCK1 gene (recessive T2D age-adjusted P = 0.0006). Nominal associations were observed with GCK1 SNPs and T2D age of diagnosis (BMI-adjusted P = 0.014 to 0.032). Also, one IGFBP1 and four IGFBP3 SNPs showed nominal genotypic association with T2D-ESRD (P = 0.002-0.049). After correcting for multiple tests, only rs730497 remanined significant.

Conclusion
Variant rs730947 in the GCK1 gene appears to play a role in early ESRD onset in African Americans.
A polymorphism at the 3'-UTR region of the aromatase gene defines a subgroup of postmenopausal breast cancer patients with poor response to neoadjuvant letrozole
Authors: Garcia-Casado Zaida , Guerrero-Zotano Angel , Llombart-Cussac Antonio , Calatrava Ana , Fernandez-Serra Antonio , Ruiz-Simon Amparo , Gavila Joaquin , Climent Miguel A , Almenar Sergio , Cervera-Deval Jose , Campos Josefina , Albaladejo Carlos Vazquez , Llombart-Bosch Antonio , Guillem Vicente , Lopez-Guerrero Jose A 
Published: February 2010

AbstractBackgroundAromatase (CYP19A1) regulates estrogen biosynthesis. Polymorphisms inCYP19A1have been related to the pathogenesis of breast cancer (BC). Inhibition of aromatase with letrozole constitutes the best option for treating estrogen-dependent BC in postmenopausal women. We evaluate a series of polymorphisms ofCYP19A1and their effect on response to neoadjuvant letrozole in early BC.MethodsWe analyzed 95 consecutive postmenopausal women with stage II-III ER/PgR [+] BC treated with neoadjuvant letrozole. Response to treatment was measured by radiology at 4thmonth by World Health Organization (WHO) criteria. Three polymorphisms ofCYP19A1, one in exon 7 (rs700519) and two in the 3'-UTR region (rs10046 and rs4646) were evaluated on DNA obtained from peripheral blood.ResultsThirty-five women (36.8%) achieved a radiological response to letrozole. The histopathological and immunohistochemical parameters, including hormonal receptor status, were not associated with the response to letrozole. Only the genetic variants (AC/AA) of the rs4646 polymorphism were associated with poor response to letrozole (p = 0.03). Eighteen patients (18.9%) reported a progression of the disease. Those patients carrying the genetic variants (AC/AA) of rs4646 presented a lower progression-free survival than the patients homozygous for the reference variant (p = 0.0686). This effect was especially significant in the group of elderly patients not operated after letrozole induction (p = 0.009).ConclusionsOur study reveals that the rs4646 polymorphism identifies a subgroup of stage II-III ER/PgR [+] BC patients with poor response to neoadjuvant letrozole and poor prognosis. Testing for the rs4646 polymorphism could be a useful tool in order to orientate the treatment in elderly BC patients.