bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia
Authors: Asselman Jana , Pfrender Michael E. , Lopez Jacqueline A. , De Coninck Dieter I. M. , Janssen Colin R. , Shaw Joseph R. , De Schamphelaere Karel A. C. 
Published: March 2015

AbstractDespite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage‐specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment‐specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.
High Final Energy of Low‐Level Gallium Arsenide Laser Therapy Enhances Skeletal Muscle Recovery without a Positive Effect on Collagen Remodeling
Authors: de Freitas Carlos Eduardo Assumpção , Bertaglia Raquel Santilone , Vechetti Júnior Ivan José , Mareco Edson Assunção , Salomão Rondinelle Artur Simões , de Paula Tassiana Gutierrez , Nai Gisele Alborghetti , Carvalho Robson Francisco , Pacagnelli Francis Lopes , Dal‐Pai‐Silva Maeli 
Published: March 2015

AbstractThe aim of this study was to evaluate the effects of a Gallium Arsenide (GaAs) laser, using a high final energy of 4.8 J, during muscle regeneration after cryoinjury. Thirty Wistar rats were divided into three groups: Control (C,n = 10); Injured (I,n = 10) and Injured and laser treated (Injured/LLLT,n = 10). The cryoinjury was induced in the central region of the tibialis anterior muscle (TA). The applications of the laser (904 nm, 50 mW average power) were initiated 24 h after injury, at energy density of 69 J cm−1for 48 s, for 5 days, to two points of the lesion. Twenty‐four hours after the final application, theTAmuscle was removed and frozen in liquid nitrogen to assess the general muscle morphology and the gene expression ofTNF‐α,TGF‐β, MyoD, and Myogenin. The Injured/LLLTgroup presented a higher number of regenerating fibers and fewer degenerating fibers (P < 0.05) without changes in the collagen remodeling. In addition, the Injured/LLLTgroup presented a significant decrease in the expression ofTNF‐αand myogenin compared to the injured group (P < 0.05). The results suggest that the GaAs laser, using a high final energy after cryoinjury, promotes muscle recovery without changing the collagen remodeling in the muscle extracellular matrix.
P53‐Mediated Repression of the Reprogramming in Cloned Bovine Embryos Through Direct Interaction with HDAC1 and Indirect Interaction with DNMT3A
Authors: Ma PJ , Zhang H , Li R , Wang YS , Zhang Y , Hua S 
Published: March 2015

ContentsP53 is a transcriptional activator, regulating growth arrest, DNA repair and apoptosis. We found that the expression level of P53 and the epigenetic profiles were significantly different in bovine somatic cell nuclear transfer embryos from those in vitro fertilization (IVF) embryos. So we inferred that abnormally expression of P53 might contribute to the incomplete reprogramming. Using bovine foetal fibroblasts, we constructed and screened a highly efficient shRNA vector targeting bovine P53 gene and then reconstituted somatic cell nuclear transfer embryos (RNAi‐SCNT). The results indicated that expression levels of P53 were downregulated significantly in RNAi‐SCNT embryos, and the blastulation rate and the total number of cell increased significantly. Moreover, methylation levels of CpG islands located 5′ region of OCT4, NANOG, H19 and IGF2R in RNAi ‐SCNT embryos were significantly normalized to that IVF embryos, and the methylation levels of genome DNA, H3K9 and H4K5 acetylation levels were also returned to levels similar to the IVF embryos. Differentially expressed genes were identified by microarray, and 28 transcripts were found to be significantly different (> twofolds) in RNAi‐SCNT embryos compared to the control nuclear transfer embryos (SCNT). Among the 28 differentially expressed transcripts, just HDAC1 and DNMT3A were closely associated with the epigenetic modifications. Finally, ChIP further showed that P53 might repress the epigenetic reprogramming by regulating HDAC1 directly and DNMT3A indirectly. These findings offer significant references to further elucidate the mechanism of epigenetic reprogramming in SCNT embryos.
Dengue epidemiology in selected endemic countries: factors influencing expansion factors as estimates of underreporting
Authors: Toan Nguyen T. , Rossi Stefania , Prisco Gabriella , Nante Nicola , Viviani Simonetta 
Published: March 2015

AbstractObjectiveDengue fever is globally considered underestimated. This study provides expansion factors (EFs) for dengue endemic selected countries and highlights critical issues in the use of EFs.MethodsWe identified dengue epidemiological cohort studies from 2000 to July 2013 through a literature search using PubMed, Web of Science and Lilacs (Latin American and Caribbean Health Sciences Database), pre‐defined keywords and inclusion/exclusion criteria, and included Brazil, Colombia, Nicaragua, Peru, Puerto Rico, Venezuela, Bangladesh, Cambodia, India, Indonesia, Philippines, Singapore, Sri Lanka, Thailand and Vietnam. Dengue national and local passive surveillance data were derived from WHO regional websites, PAHO, SEARO and WPRO. EFs were calculated as CI cohort studies/CI passive data for both national and local levels.ResultsCohort studies differed in case definition, laboratory test used and surveillance methods. The information on SEARO, PAHO and WPRO websites differed in terms of dengue epidemiological variables, population denominators and completeness. The highest incidence was reported by PAHO countries followed by WPRO and SEARO countries. EFs may vary for the different variables and denominators used for calculation. EFs were the highest in SEARO countries and lowest in PAHO countries. A trend for lower local EFs was observed.ConclusionsThe use of EFs for quantifying dengue underreporting may be problematic due to lack of uniformity in reporting dengue both active and passive surveillance data. Quality dengue surveillance data are urgently needed for a better estimate of dengue disease burden and to measure the impact of preventive intervention.
Psychological interventions for Common Mental Disorders for People Living With HIV in Low‐ and Middle‐Income Countries: systematic review
Authors: Chibanda Dixon , Cowan Frances M. , Healy Jessica L. , Abas Melanie , Lund Crick 
Published: March 2015

AbstractObjectiveTo assess the effectiveness of structured psychological interventions against common mental disorders (CMD) in people living with HIV infection (PLWH), in low‐ and middle‐income countries (LMIC).MethodsSystematic review of psychological interventions for CMD from LMIC for PLWH, with two‐stage screening carried out independently by 2 authors.ResultsOf 190 studies, 5 met inclusion criteria. These were randomised‐controlled trials based on the principles of cognitive behaviour therapy (CBT) and were effective in reducing CMD symptoms in PLWH. Follow‐up of study participants ranged from 6 weeks to 12 months with multiple tools utilised to measure the primary outcome. Four studies showed a high risk of bias, while 1 study from Iran met low risk of bias in all 6 domains of the Cochrane risk of bias tool and all 22 items of the CONSORT instrument.ConclusionThere is a need for more robust and adequately powered studies to further explore CBT‐based interventions in PLWH. Future studies should report on components of the psychological interventions, fidelity measurement and training, including supervision of delivering agents, particularly where lay health workers are the delivering agent.
Feasibility and effectiveness of two community‐based HIV testing models in rural Swaziland
Authors: Parker Lucy Anne , Jobanputra Kiran , Rusike Lorraine , Mazibuko Sikhathele , Okello Velephi , Kerschberger Bernhard , Jouquet Guillaume , Cyr Joanne , Teck Roger 
Published: March 2015

AbstractObjectivesTo evaluate the feasibility (population reached, costs) and effectiveness (positivity rates, linkage to care) of two strategies of community‐based HIV testing and counselling (HTC) in rural Swaziland.MethodsStrategies used were mobile HTC (MHTC) and home‐based HTC (HBHTC). Information on age, sex, previous testing and HIV results was obtained from routine HTC records. A consecutive series of individuals testing HIV‐positive were followed up for 6 months from the test date to assess linkage to care.ResultsA total of 9 060 people were tested: 2 034 through MHTC and 7 026 through HBHTC. A higher proportion of children and adolescents (<20 years) were tested through HBHTC than MHTC (57% vs. 17%; P < 0.001). MHTC reached a higher proportion of adult men than HBHTC (42% vs. 39%; P = 0.015). Of 398 HIV‐positive individuals, only 135 (34%) were enrolled in HIV care within 6 months. Of 42 individuals eligible for antiretroviral therapy, 22 (52%) started treatment within 6 months. Linkage to care was lowest among people who had tested previously and those aged 20–40 years. HBHTC was 50% cheaper (US$11 per person tested; $797 per individual enrolled in HIV care) than MHTC ($24 and $1698, respectively).ConclusionIn this high HIV prevalence setting, a community‐based testing programme achieved high uptake of testing and appears to be an effective and affordable way to encourage large numbers of people to learn their HIV status (particularly underserved populations such as men and young people). However, for community HTC to impact mortality and incidence, strategies need to be implemented to ensure people testing HIV‐positive in the community are linked to HIV care.
‘I was thinking too much’: experiences ofHIV‐positive adults with common mental disorders and poor adherence to antiretroviral therapy in Zimbabwe
Authors: Kidia Khameer , Machando Debra , Bere Tarisai , Macpherson Kirsty , Nyamayaro Primrose , Potter Lucy , Makadzange Tariro , Munjoma Ronald , Marufu Marshall , Araya Ricardo , Safren Steven , O'Cleirigh Conall , Chibanda Dixon , Abas Melanie 
Published: March 2015

AbstractObjectiveTo document the lived experiences of people with both poor mental health and suboptimal adherence to antiretroviral therapy in highHIVprevalence settings.MethodsIn‐depth qualitative interviews were conducted with 47 (female = 31)HIV‐positive adults who scored above the cut‐point on a locally validated scale for common mental disorders (CMDs). Purposive sampling was used to recruit participants with evidence of poor adherence. Six additional key informant interviews (female = 6) were conducted with healthcare workers. Data were collected and analysed inductively by an interdisciplinary coding team.ResultsThe major challenges faced by participants were stressors (poverty, stigma, marital problems) and symptoms of CMDs (‘thinking too much’, changes to appetite and sleep, ‘burdened heart’ and low energy levels). Thinking too much, which appears closely related to rumination, was the symptom with the greatest negative impact on adherence to antiretroviral therapy amongHIV‐positive adults with CMDs. In turn, thinking too much was commonly triggered by the stressors faced by people living withHIV/AIDS, especially poverty. Finally, participants desired private counselling, access to income‐generating activities and family engagement in mental health care.ConclusionsBetter understanding of the local expression of mental disorders and of underlying stressors can inform the development of culturally sensitive interventions to reduce CMDs and poor adherence to antiretroviral therapy.
OsNAC2 encoding a NAC transcription factor that affects plant height through mediating the gibberellic acid pathway in rice
Authors: Chen Xu , Lu Songchong , Wang Yaofeng , Zhang Xuan , Lv Bo , Luo Liqiong , Xi Dandan , Shen Jiabin , Ma Hong , Ming Feng 
Published: March 2015

SummaryPlant height and flowering time are key agronomic traits affecting yield in rice (Oryza sativa). In this study, we investigated the functions in rice growth and development of OsNAC2, encoding a NAC transcription factor in rice. Transgenic plants that constitutively expressed OsNAC2 had shorter internodes, shorter spikelets, and were more insensitive to gibberellic acid (GA3). In addition, the levels of GAs decreased in OsNAC2 overexpression plants, compared with the wild‐type. Moreover, flowering was delayed for approximately 5 days in transgenic lines. The transcription of Hd3a, a flowering‐time related gene, was suppressed in transgenic lines. In addition, transgenic Arabidopsis plants expressing OsNAC2 were also more insensitive to GA3. The expression levels of GA biosynthetic genes OsKO2 and OsKAO were repressed. The expression of OsSLRL, encoding a repressor in the GA signal pathway, and OsEATB, which encodes a repressor of GA biosynthesis, were both enhanced. Western blotting indicated that DELLA also accumulated at the protein level. Dual‐luciferase reporter analyses, yeast one‐hybrid assays and ChIP‐qPCR suggested that OsNAC2 directly interacted with the promoter of OsEATB and OsKO2. Taken together, we proposed that OsNAC2 is a negative regulator of the plant height and flowering time, which acts by directly regulating key genes of the GA pathway in rice.
Brassinosteroids promote development of rice pollen grains and seeds by triggering expression of Carbon Starved Anther, a MYB domain protein
Authors: Zhu Xiaolei , Liang Wanqi , Cui Xiao , Chen Mingjiao , Yin Changsong , Luo Zhijing , Zhu Jiaying , Lucas William J. , Wang Zhiyong , Zhang Dabing 
Published: March 2015

SummaryTransport of photoassimilates from leaf tissues (source regions) to the sink organs is essential for plant development. Here, we show that a phytohormone, the brassinosteroids (BRs) promotes pollen and seed development in rice by directly promoting expression of Carbon Starved Anther (CSA) which encodes a MYB domain protein. Over‐expression of the BR‐synthesis gene D11 or a BR‐signaling factor OsBZR1 results in higher sugar accumulation in developing anthers and seeds, as well as higher grain yield compared with control non‐transgenic plants. Conversely, knockdown of D11 or OsBZR1 expression causes defective pollen maturation and reduced seed size and weight, with less accumulation of starch in comparison with the control. Mechanically, OsBZR1 directly promotes CSA expression and CSA directly triggers expression of sugar partitioning and metabolic genes during pollen and seed development. These findings provide insight into how BRs enhance plant reproduction and grain yield in an important agricultural crop.
Effects of VEGF and MSCs on vascular regeneration in a trauma model in rats
Authors: Niyaz Mehmet , Gürpınar Özer Aylin , Oktar Gürsel Levent , Günaydın Serdar , Onur Mehmet Ali , Özsin Kadir Kaan , Yener Ali 
Published: March 2015

ABSTRACTIn the human body, vascular injuries that are caused by trauma, vessel lumen stenosis, and occlusions are often irreversible and can lead to sequelae formation as the vessels cannot reproduce fast enough. To solve this problem, the blood flow must be returned to the region as fast as possible. The adipose tissue contains progenitor cells with angiogenic potential and can be used to resolve the issue.In the present study, mesenchymal stem cells (MSCs) derived from rat adipose tissue, vascular endothelial growth factor (VEGF), and their mixture were applied on the dorsum of a rat, which was traumatized and its contribution to vascular regeneration was reviewed. No application was made to the control group.The results showed that the percentage of necrotic area was significantly lower in the MSC group than that of all the other groups. When the VEGF group was compared to the VEGF + MSCs, the percentage of necrotic area was observed to be similiar. However, VEGF showed effects only when a large quantites of VEGF was applied to the flap area.VEGF could not fully respond to the needs, whereas MSCs can produce VEGF according to the needs of tissue. This makes them superior to stem cells.
Lactococcal 949 Group Phages Recognize a Carbohydrate Receptor on the Host Cell Surface
Authors: Mahony Jennifer , Randazzo Walter , Neve Horst , Settanni Luca , van Sinderen Douwe 
Published: March 2015

ABSTRACT
Lactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly that for the receptor binding protein required for host recognition. Furthermore, we demonstrate that the 949 phages target cell wall phospho-polysaccharides as their receptors, accounting for the specificity of the interactions of these phages with their lactococcal hosts. Such information may ultimately aid in the identification of strains/strain blends that do not present the necessary saccharidic target for infection by these problematic phages.
Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides
Authors: Oehlenschlæger Christian Berg , Løvgreen Monika Nøhr , Reinauer Eva , Lehtinen Emilia , Pind Marie-Louise Lindberg , Harris Pernille , Martinussen Jan , Willemoës Martin 
Published: March 2015

ABSTRACT

Analysis of the genome of
Bacillus halodurans
strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the
comEB
gene and the
dcdB
gene, encoding dCMP deaminase and the bifunctional dCTP deaminase:dUTPase (DCD:DUT), respectively, were both shown to be expressed in
B. halodurans
, and both genes were subject to repression by the nucleosides thymidine and deoxycytidine. The latter nucleoside presumably exerts its repression after deamination by cytidine deaminase. Both
comEB
and
dcdB
were cloned, overexpressed in
Escherichia coli
, and purified to homogeneity. Both enzymes were active and displayed the expected regulatory properties: activation by dCTP for dCMP deaminase and dTTP inhibition for both enzymes. Structurally, the
B. halodurans
enzyme resembled the
Mycobacterium tuberculosis
enzyme the most. An investigation of sequenced genomes from other species of the genus
Bacillus
revealed that not only the genome of
B. halodurans
but also the genomes of
Bacillus pseudofirmus
,
Bacillus thuringiensis
,
Bacillus hemicellulosilyticus
,
Bacillus marmarensis
,
Bacillus cereus
, and
Bacillus megaterium
encode both the dCMP deaminase and the DCD:DUT enzymes. In addition, eight
dcdB
homologs from
Bacillus
species within the genus for which the whole genome has not yet been sequenced were registered in the NCBI Entrez database.
Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up
Authors: Muhamadali Howbeer , Xu Yun , Ellis David I. , Allwood J. William , Rattray Nicholas J. W. , Correa Elon , Alrabiah Haitham , Lloyd Jonathan R. , Goodacre Royston 
Published: March 2015

ABSTRACT

During the industrial scale-up of bioprocesses it is important to establish that the biological system has not changed significantly when moving from small laboratory-scale shake flasks or culturing bottles to an industrially relevant production level. Therefore, during upscaling of biomass production for a range of metal transformations, including the production of biogenic magnetite nanoparticles by
Geobacter sulfurreducens
, from 100-ml bench-scale to 5-liter fermentors, we applied Fourier transform infrared (FTIR) spectroscopy as a metabolic fingerprinting approach followed by the analysis of bacterial cell extracts by gas chromatography-mass spectrometry (GC-MS) for metabolic profiling. FTIR results clearly differentiated between the phenotypic changes associated with different growth phases as well as the two culturing conditions. Furthermore, the clustering patterns displayed by multivariate analysis were in agreement with the turbidimetric measurements, which displayed an extended lag phase for cells grown in a 5-liter bioreactor (24 h) compared to those grown in 100-ml serum bottles (6 h). GC-MS analysis of the cell extracts demonstrated an overall accumulation of fumarate during the lag phase under both culturing conditions, coinciding with the detected concentrations of oxaloacetate, pyruvate, nicotinamide, and glycerol-3-phosphate being at their lowest levels compared to other growth phases. These metabolites were overlaid onto a metabolic network of
G. sulfurreducens
, and taking into account the levels of these metabolites throughout the fermentation process, the limited availability of oxaloacetate and nicotinamide would seem to be the main metabolic bottleneck resulting from this scale-up process. Additional metabolite-feeding experiments were carried out to validate the above hypothesis. Nicotinamide supplementation (1 mM) did not display any significant effects on the lag phase of
G. sulfurreducens
cells grown in the 100-ml serum bottles. However, it significantly improved the growth behavior of cells grown in the 5-liter bioreactor by reducing the lag phase from 24 h to 6 h, while providing higher yield than in the 100-ml serum bottles.