bluuebunny/crossref_metadata_2025_split huggingface dataset:
The MMSET histone methyl transferase switches global histone methylation and alters gene expression in t(4;14) multiple myeloma cells
Authors: Martinez-Garcia Eva , Popovic Relja , Min Dong-Joon , Sweet Steve M. M. , Thomas Paul M. , Zamdborg Leonid , Heffner Aaron , Will Christine , Lamy Laurence , Staudt Louis M. , Levens David L. , Kelleher Neil L. , Licht Jonathan D. 
Published: October 2010

Abstract
The multiple myeloma SET domain (MMSET) protein is overexpressed in multiple myeloma (MM) patients with the translocation t(4;14). Although studies have shown the involvement of MMSET/Wolf-Hirschhorn syndrome candidate 1 in development, its mode of action in the pathogenesis of MM is largely unknown. We found that MMSET is a major regulator of chromatin structure and transcription in t(4;14) MM cells. High levels of MMSET correlate with an increase in lysine 36 methylation of histone H3 and a decrease in lysine 27 methylation across the genome, leading to a more open structural state of the chromatin. Loss of MMSET expression alters adhesion properties, suppresses growth, and induces apoptosis in MM cells. Consequently, genes affected by high levels of MMSET are implicated in the p53 pathway, cell cycle regulation, and integrin signaling. Regulation of many of these genes required functional histone methyl-transferase activity of MMSET. These results implicate MMSET as a major epigenetic regulator in t(4;14)+ MM.
Mutational dynamics of murine angiogenin duplicates
Authors: Codoñer Francisco M , Alfonso-Loeches Silvia , Fares Mario A 
Published: October 2010

Abstract

Background
Angiogenin (Ang) is a protein involved in angiogenesis by inducing the formation of blood vessels. The biomedical importance of this protein has come from findings linking mutations in Ang to cancer progression and neurodegenerative diseases. These findings highlight the evolutionary constrain on Ang amino acid sequence. However, previous studies comparing human Angiogenin with homologs from other phylogenetically related organisms have led to the conclusion that Ang presents a striking variability. Whether this variability has an adaptive value per se remains elusive. Understanding why many functional Ang paralogs have been preserved in mouse and rat and identifying functional divergence mutations at these copies may explain the relationship between mutations and function. In spite of the importance of testing this hypothesis from the evolutionarily and biomedical perspectives, this remains yet unaccomplished. Here we test the main mutational dynamics driving the evolution and function of Ang paralogs in mammals.

Results
We analysed the phylogenetic asymmetries between the different Ang gene copies in mouse and rat in the context of vertebrate Ang phylogeny. This analysis shows strong evidence in support of accelerated evolution in some Ang murine copies (mAng). This acceleration is not due to non-functionalisation because constraints on amino acid replacements remain strong. We identify many of the amino acid sites involved in signal localization and nucleotide binding by Ang to have evolved under diversifying selection. Compensatory effects of many of the mutations at these paralogs and their key structural location in or nearby important functional regions support a possible functional shift (functional divergence) in many Ang copies. Similarities between 3D-structural models for mAng copies suggest that their divergence is mainly functional.

Conclusions
We identify the main evolutionary dynamics shaping the variability of Angiogenin in vertebrates and highlight the plasticity of this protein after gene duplication. Our results suggest functional divergence among mAng paralogs. This puts forward mAng as a good system candidate for testing functional plasticity of such an important protein while stresses caution when using mouse as a model to infer the consequences of mutations in the single Ang copy of humans.
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon
Authors: Tyler Ludmila , Bragg Jennifer N , Wu Jiajie , Yang Xiaohan , Tuskan Gerald A , Vogel John P 
Published: October 2010

AbstractBackgroundGlycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged forOryza sativa(rice), the model dicotyledonous plantArabidopsis thaliana, and the fast-growing treePopulustrichocarpa(poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grassesBrachypodiumdistachyon(an emerging monocotyledonous model) andSorghum bicolor(sorghum). We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families.ResultsWe identified 356 glycoside hydrolase genes inBrachypodiumand 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice,Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. For several glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51), we present a detailed literature review together with an examination of the family structures. This analysis of individual families revealed both similarities and distinctions between monocots and eudicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within GH families, theBrachypodiumand sorghum proteins generally cluster with those from other monocots.ConclusionsThis work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining theBrachypodiumglycoside hydrolases sets the stage forBrachypodiumto be a grass model for investigations of these enzymes and their diverse rolesin planta. Insights gained fromBrachypodiumwill inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.
A novel multifunctional oligonucleotide microarray for Toxoplasma gondii
Authors: Bahl Amit , Davis Paul H , Behnke Michael , Dzierszinski Florence , Jagalur Manjunatha , Chen Feng , Shanmugam Dhanasekaran , White Michael W , Kulp David , Roos David S 
Published: October 2010

Abstract

Background
Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators.

Results
Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals) and Plasmodium falciparum (a related parasite responsible for severe human malaria), we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP)-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis) and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at pilot scale to inform future array designs.

Conclusions
In addition to providing an initial global view of the T. gondii transcriptome across major lineages and permitting detailed resolution of recombination points in a historical sexual cross, the multifunctional nature of this array also allowed opportunities to exploit probes for purposes beyond their intended use, enhancing analyses. This array is in widespread use by the T. gondii research community, and several aspects of the design strategy are likely to be useful for other pathogens.
Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method
Authors: Wu Jin-Ya , Jiang Xiao-Tao , Jiang Yun-Xia , Lu Su-Ying , Zou Fei , Zhou Hong-Wei 
Published: October 2010

Abstract

Background
The primer and amplicon length have been found to affect PCR based estimates of microbial diversity by pyrosequencing, while other PCR conditions have not been addressed using any deep sequencing method. The present study determined the effects of polymerase, template dilution and PCR cycle number using the Solexa platform.

Results
The PfuUltra II Fusion HS DNA Polymerase (Stratagene) with higher fidelity showed lower amount of PCR artifacts and determined lower taxa richness than the Ex Taq (Takara). More importantly, the two polymerases showed different efficiencies for amplifying some of very abundant sequences, and determined significantly different community structures. As expected, the dilution of the DNA template resulted in a reduced estimation of taxa richness, particularly at the 200 fold dilution level, but the community structures were similar for all dilution levels. The 30 cycle group increased the PCR artifacts while comparing to the 25 cycle group, but the determined taxa richness was lower than that of the 25 cycle group. The PCR cycle number did not changed the microbial community structure significantly.

Conclusions
These results highlight the PCR conditions, particularly the polymerase, have significant effect on the analysis of microbial diversity with next generation sequencing methods.
Mitochondrially-targeted expression of a cytoplasmic male sterility-associated orf220 gene causes male sterility in Brassica juncea
Authors: Yang Jinghua , Liu Xunyan , Yang Xiaodong , Zhang Mingfang 
Published: October 2010

AbstractBackgroundThe novel chimeric open reading frame (orf) resulting from the rearrangement of a mitochondrial genome is generally thought to be a causal factor in the occurrence of cytoplasmic male sterility (CMS). Both positive and negative correlations have been found between CMS-associatedorfsand the occurrence of CMS when CMS-associatedorfswere expressed and targeted at mitochondria. Someorfscause male sterility or semi-sterility, while some do not. Little is currently known about how mitochondrial factor regulates the expression of the nuclear genes involved in male sterility. The purpose of this study was to investigate the biological function of a candidate CMS-associatedorf220gene, newly isolated from cytoplasmic male-sterile stem mustard, and show how mitochondrial retrograde regulated nuclear gene expression is related to male sterility.ResultsIt was shown that the ORF220 protein can be guided to the mitochondria using the mitochondrial-targeting sequence of theβsubunit of F1-ATPase (atp2-1). Transgenic stem mustard plants expressed the chimeric gene containing theorf220gene and a mitochondrial-targeting sequence of theβsubunit of F1-ATPase (atp2-1). Transgenic plants were male-sterile, most being unable to produce pollen while some could only produce non-vigorous pollen. The transgenic stem mustard plants also showed aberrant floral development identical to that observed in the CMS stem mustard phenotype. Results obtained from oligooarray analysis showed that some genes related to mitochondrial energy metabolism were down-regulated, indicating a weakening of mitochondrial function in transgenic stem mustard. Some genes related to pollen development were shown to be down-regulated in transgenic stem mustard and the expression of some transcription factor genes was also altered.ConclusionThe work presented furthers our understanding of how the mitochondrially-targeted expression of CMS-associatedorf220gene causes male sterility through retrograde regulation of nuclear gene expression inBrassica juncea.
The Ve-mediated resistance response of the tomato to Verticillium dahliae involves H2O2, peroxidase and lignins and drives PALgene expression
Authors: Gayoso Carmen , Pomar Federico , Novo-Uzal Esther , Merino Fuencisla , Martínez de Ilárduya Óskar 
Published: October 2010

Abstract

Background

Verticillium dahliae is a fungal pathogen that infects a wide range of hosts. The only known genes for resistance to Verticillium in the Solanaceae are found in the tomato (Solanum lycopersicum) Ve locus, formed by two linked genes, Ve1 and Ve2. To characterize the resistance response mediated by the tomato Ve gene, we inoculated two nearly isogenic tomato lines, LA3030 (ve/ve) and LA3038 (Ve/Ve), with V. dahliae.

Results
We found induction of H2O2 production in roots of inoculated plants, followed by an increase in peroxidase activity only in roots of inoculated resistant plants. Phenylalanine-ammonia lyase (PAL) activity was also increased in resistant roots 2 hours after inoculation, while induction of PAL activity in susceptible roots was not seen until 48 hours after inoculation. Phenylpropanoid metabolism was also affected, with increases in ferulic acid, p-coumaric acid, vanillin and p-hydroxybenzaldehyde contents in resistant roots after inoculation. Six tomato PAL cDNA sequences (PAL1 - PAL6) were found in the SolGenes tomato EST database. RT-PCR analysis showed that these genes were expressed in all organs of the plant, albeit at different levels. Real-time RT-PCR indicated distinct patterns of expression of the different PAL genes in V. dahliae-inoculated roots. Phylogenetic analysis of 48 partial PAL cDNAs corresponding to 19 plant species grouped angiosperm PAL sequences into four clusters, suggesting functional differences among the six tomato genes, with PAL2 and PAL6 presumably involved in lignification, and the remaining PAL genes implicated in other biological processes.
An increase in the synthesis of lignins was found 16 and 28 days after inoculation in both lines; this increase was greater and faster to develop in the resistant line. In both resistant and susceptible inoculated plants, an increase in the ratio of guaiacyl/syringyl units was detected 16 days after inoculation, resulting from the lowered amount of syringyl units in the lignins of inoculated plants.

Conclusions
The interaction between the tomato and V. dahliae triggered a number of short- and long-term defensive mechanisms. Differences were found between compatible and incompatible interactions, including onset of H2O2 production and activities of peroxidase and PAL, and phenylpropanoid metabolism and synthesis of lignins.
Bacteremic community-acquired pneumonia due to Klebsiella pneumoniae: Clinical and microbiological characteristics in Taiwan, 2001-2008
Authors: Lin Yi-Tsung , Jeng Yuan-Yu , Chen Te-Li , Fung Chang-Phone 
Published: October 2010

Abstract

Background

Klebsiella pneumoniae is the major cause of community-acquired pyogenic infections in Taiwan. This retrospective study evaluated the clinical and microbiological characteristics of bacteremic community-acquired pneumonia due to K. pneumoniae in Taiwanese adults.

Methods
The clinical characteristics of bacteremic community-acquired pneumonia (CAP) in adults due to K. pneumoniae were compared to those of adults with bacteremic CAP due to Streptococcus pneumoniae at a tertiary medical center in Taiwan from 2001-2008. Risk factors for mortality of bacteremic CAP due to K. pneumoniae were analyzed. All clinical isolates of K. pneumoniae were examined for capsular serotypes, hypermucoviscosity phenotype, aerobactin and rmpA gene.

Results

K. pneumoniae was the dominant cause of bacteremic CAP and was associated with a more fulminant course and a worse prognosis than bacteremic CAP due to Streptococcus pneumoniae. Initial presentation with septic shock and respiratory failure were independent risk factors for both early and total mortality. Serotype K1 and K2 comprised around half of all isolates. There were no significant differences in the clinical characteristics of patients with bacteremic CAP due to K1/K2 and non-K1/K2 isolates. Hypermucoviscosity phenotype as well as the aerobactin and rmpA genes were highly prevalent in the K. pneumoniae isolates.

Conclusions

K. pneumoniae continued to be the dominant cause of bacteremic CAP in Taiwanese adults during 2001-2008. Initial presentation with septic shock and respiratory failure were independent risk factors for both early and total mortality from K. pneumoniae bacteremic CAP. Serotypes K1/K2 comprised around half of all isolates, but did not predispose patients to a poor clinical outcome. Physicians should be aware of the poor prognosis of any patient with bacteremic K. pneumoniae CAP and monitor these patients more closely.
Use of antenatal care services in Kassala, eastern Sudan
Authors: Ali Abdel Aziem A , Osman Mohammed M , Abbaker Ameer O , Adam Ishag 
Published: October 2010

Abstract

Background
Antenatal care is named as one of the four pillars initiatives of the Safe Motherhood Initiative. While many of routine antenatal care procedure have little effect on maternal mortality and morbidity, some of these have been ascertained as beneficial. The aim of this study was to investigate coverage of antenatal care and identify factors associated with inadequacy of antenatal care in Kassala, eastern Sudan.

Methods
A cross-sectional community-based study was carried out in Kassala, eastern Sudan during September-October 2009. Household surveys were conducted. Structured questionnaires were used to gather data from women who had been pregnant within the last year, or pregnant more than 14 weeks.

Results
Out of 900 women investigated for antenatal care coverage, 811(90%) women had at least one visit. Only 11% of the investigated women had ≥ four antenatal visits, while 10.0% had not attended at all. Out of 811 women who attended at least one visit, 483 (59.6%), 303 (37.4%) and 25 (3.1%) women attended antenatal care in the first, second and third trimester, respectively. In logistic regression analyses, while maternal age and residence were not associated with inadequacy of antenatal care (<2 visits), high parity (OR = 2.0, CI = 1.1-3.5; P = 0.01) and husband education ≤ secondary level (OR = 2.4, CI = 1.3-4.2; P = 0.002) were associated with inadequacy of antenatal care.

Conclusions
Antenatal care showed a low coverage in Kassala, eastern Sudan. This low coverage was associated with high parity and low husband education.
Herbal compound "Songyou Yin" reinforced the ability of interferon-alfa to inhibit the enhanced metastatic potential induced by palliative resection of hepatocellular carcinoma in nude mice
Authors: Huang Xiu-Yan , Huang Zi-Li , Wang Lu , Xu Yong-Hua , Huang Xin-Yu , Ai Kai-Xing , Zheng Qi , Tang Zhao-You 
Published: October 2010

Abstract

Background
Liver resection is a widely accepted treatment for hepatocellular carcinoma (HCC). Our previous clinical study showed that the rate of palliative resection was 34.0% (1958-2008, 2754 of 8107). However, the influence of palliative resection on tumor metastasis remains controversial. The present study was conducted to evaluate the effect of palliative resection on residual HCC and to explore interventional approaches.

Methods
Palliative resection was done in an orthotopic nude mice model of HCC (MHCC97H) with high metastatic potential. Tumor growth, invasion, metastasis, lifespan, and some molecular alterations were examined in vivo and in vitro. Mice that underwent palliative resection were treated with the Chinese herbal compound "Songyou Yin," interferon-alfa-1b (IFN-α), or their combination to assess their effects.

Results
In the palliative resection group, the number of lung metastatic nodules increased markedly as compared to the sham operation group (14.3 ± 4.7 versus 8.7 ± 3.6, P < 0.05); tumor matrix metalloproteinase 2 (MMP2) activity was elevated by 1.4-fold, with up-regulation of vascular endothelial growth factor (VEGF) and down-regulation of tissue inhibitor of metalloproteinase 2 (TIMP2). The sera of mice undergoing palliative resection significantly enhanced cell invasiveness by 1.3-fold. After treatment, tumor volume was 1205.2 ± 581.3 mm3, 724.9 ± 337.6 mm3, 507.6 ± 367.0 mm3, and 245.3 ± 181.2 mm3 in the control, "Songyou Yin," IFN-α, and combination groups, respectively. The combined therapy noticeably decreased the MMP2/TIMP2 ratio and prolonged the lifespan by 42.2%. Moreover, a significant (P < 0.001) reduction of microvessel density was found: 43.6 ± 8.5, 34.5 ± 5.9, 23.5 ± 5.6, and 18.2 ± 8.0 in the control and treatment groups, respectively.

Conclusion
Palliative resection-stimulated HCC metastasis may occur, in part, by up-regulation of VEGF and MMP2/TIMP2. "Songyou Yin" reinforced the ability of IFN-α to inhibit the metastasis-enhancing potential induced by palliative resection, which indicated its potential postoperative use in patients with HCC.
Pressure pain sensitivity maps of the neck-shoulder and the low back regions in men and women
Authors: Binderup Asbjørn T , Arendt-Nielsen Lars , Madeleine Pascal 
Published: October 2010

Abstract

Background
Musculoskeletal pain in the low back and neck-shoulder regions is a major problem among the working population all over the world. The prevalence of musculoskeletal pain is found to be higher among women. Women also have lower pressure pain thresholds (PPTs) than men. Pressure pain topography aims at mapping the spatial distribution of PPT within a muscle in an attempt to track changes in mechanical sensitivity. In order to assess gender differences in the pain topography, it is necessary to map the distribution in both healthy men and women. The aim of this study was to assess PPT maps from the cervico-thoracic and lumbar regions in men and women.

Methods
Eleven men and eleven women without any known musculoskeletal disorders participated in the study. PPT was measured twice at 36 points over the trapezius muscle of the dominant arm, at 36 points over the trapezius muscle on the contralateral side and at 12 points over the spine between the left and right trapezius. Further, 11 points were measured over the erector spinae muscle on the left side of the spine between the first and the fifth lumbar vertebrae, 11 on the right side and 5 points on the spine itself. The measurements on each trapezius muscle were divided according to anatomical subdivisions. Three-way and two-way ANOVAs were used to analyse the differences in PPTs with the following factors: gender, locations and sub-divisions (only for cervico-thoracic region).

Results
There were no differences between left and right side in neither the cervico-thoracic nor the lumbar region, but there were (large effect) differences between the subdivisions in the trapezius with the lowest values in the upper part (P < 0.001; partial η2 = 0.19). Women had (small effect) lower PPT in both cervico-thoracic and lumbar regions (P ≤ 0.001; partial η2 = 0.02 for both regions), but gender had no effect on neither location nor subdivisions.

Conclusions
The pain topography was not found to be different between genders in the cervico-thoracic and lumbar regions. This study can be used as basis for further clinical studies on musculoskeletal disorders.