bluuebunny/crossref_metadata_2025_split huggingface dataset:
The precise regulation of different COR genes by individual CBF transcription factors in Arabidopsis thaliana
Authors: Shi Yihao , Huang Jiaying , Sun Tianshu , Wang Xuefei , Zhu Chenqi , Ai Yuxi , Gu Hongya 
Published: December 2016

AbstractThe transcription factors CBF1/2/3 are reported to play a dominant role in the cold responsive network of Arabidopsis by directly regulating the expression levels of cold responsive (COR) genes. In this study, we obtained CRISPR/Cas9‐mediated loss‐of‐function mutants of cbf1∼3. Over 3,000 COR genes identified by RNA‐seq analysis showed a slight but significant change in their expression levels in the mutants compared to the wild‐type plants after being treated at 4 °C for 12 h. The C‐repeat (CRT) motif (5′‐CCGAC‐3′) was enriched in promoters of genes that were up‐regulated by CBF2 and CBF3 but not in promoters of genes up‐regulated by CBF1. These data suggest that CBF2 and CBF3 play a more important role in directing the cold response by regulating different sets of downstream COR genes. More than 2/3 of COR genes were co‐regulated by two or three CBFs and were involved mainly in cellular signal transduction and metabolic processes; less than 1/3 of the genes were regulated by one CBF, and those genes up‐regulated were enriched in cold‐related abiotic stress responses. Our results indicate that CBFs play an important role in the trade‐off between cold tolerance and plant growth through the precise regulation of COR genes in the complicated transcriptional network.
Effects of Orchidectomy and Testosterone Replacement on Numbers of Kisspeptin‐, Neurokinin B‐, and Dynorphin A‐Immunoreactive Neurones in the Arcuate Nucleus of the Hypothalamus in Obese and Diabetic Rats
Authors: Dudek M. , Kołodziejski P. A. , Pruszyńska‐Oszmałek E. , Ziarniak K. , Sliwowska J. H. 
Published: December 2016

Neurones expressing kisspeptin, neurokinin B and dynorphin A, located in the arcuate nucleus of the hypothalamus (ARC), are important regulators of reproduction. Their functions depend on metabolic and hormonal status. We hypothesised that male rats with high‐fat diet‐induced obesity (DIO) and/or streptozotocin‐induced diabetes mellitus type 1 (DM1) and type 2 (DM2) will have alterations in numbers of immunoreactive (‐IR) cells: kisspeptin‐IR and/or neurokinin B‐IR and dynorphin A‐IR neurones in the ARC in the sham condition. In addition, orchidectomy alone (ORX) and with testosterone treatment (ORX+T) will unmask possible deficits in the response of these neurones in DIO, and/or DM1 and DM2 rats. Rats were assigned to four groups: a control (C) and one diabetic group (DM1) were fed a regular chow diet, whereas the obese group (DIO) and the other diabetic group (DM2) were fed a high‐fat diet. To induce diabetes, streptozotocin was injected. After 6 weeks, each group was divided into three subgroups: ORX, ORX+T and sham. After another 2 weeks, metabolic and hormonal profiles were assessed and immunocytochemistry was performed. We found that: (1) under sham conditions: (i) DM1 and DM2 animals had higher numbers of kisspeptin‐IR cells than controls and (ii) DM2 rats had increased numbers of neurokinin B‐IR and dynorphin A‐IR cells compared to C animals; (2) ORX and ORX+T treatments unmasked deficits of the studied neurones in DM1 and DM2 but not in DIO animals; and (3) DIO, DM1 and DM2 rats had altered metabolic and hormonal profiles, in particular decreased levels of testosterone. We concluded that alterations in numbers of kisspeptin‐IR and neurokinin B‐IR neurones in the ARC and their response to ORX and ORX+T may account for disruptions of metabolic and reproductive functions in diabetic but not in obese rats.
Resource Dependence and Network Relations: A Test of Venture Capital Investment Termination in China
Authors: Zheng Yanfeng , Xia Jun 
Published: December 2016

ABSTRACTThis study examines how venture capital (VC) firms terminate investments in an emerging economy context. We contend that due to the weak institutional environment, it is appropriate to draw on insights from power and social relation perspectives for a better understanding of the phenomenon. Specifically, we argue that a termination decision hinges on not only the dependence relationship between a VC firm and its portfolio companies, but also the social relationships among VC firms. Event history analyses of approximately 12,000 VC deals made in China between 2001 and 2012 reveal that when a VC firm has a greater number of investments in an industry, it is more likely to terminate investments on a portfolio company in that industry. Moreover, such effect on termination is moderated by the focal VC's embeddedness with its syndicate partners and collaboration opportunities with other VC firms outside the immediate access of the syndicate partners. Our study sheds light on research on VC decision making in emerging markets by integrating insights from resource dependence relationships and interorganizational network characteristics.
Sonic hedgehog is present in parotid saliva and is decreased in patients with taste dysfunction
Authors: Henkin Robert I. , Knöppel Alexandra B. , Abdelmeguid Mona , Stateman William A. , Hosein Suzanna 
Published: December 2016

PurposeTo demonstrate that sonic hedgehog (Shh) is present in human parotid saliva and is decreased in human taste dysfunction.MethodsShh was measured in parotid saliva of 27 normal subjects and 81 patients with taste dysfunction of multiple etiologies using a sensitive spectrophotometricELISAassay. Taste dysfunction was defined clinically both by subjective decreases of taste acuity and flavor perception and by impaired gustometry.ResultsShh was found in parotid saliva of both normal subjects and patients with taste dysfunction. Levels were significantly lower in patients than in normal subjects. Both subjective loss of taste acuity and flavor perception and impaired gustometry was measured in untreated patients.ConclusionsThis is the first demonstration of Shh in human saliva. As Shh has been related to taste bud growth and development, its presence in saliva is consistent with its role as a cell signaling moiety involved with stimulation of taste bud stem cells to generate taste receptors. Decreased saliva Shh secretion can be considered a marker of taste dysfunction in patients with multiple pathologies for their dysfunction.
Drivers of genetic differentiation in a generalist insect‐pollinated herb across spatial scales
Authors: Muñoz‐Pajares A. J. , García C. , Abdelaziz M. , Bosch J. , Perfectti F. , Gómez J. M. 
Published: December 2016

AbstractThe isolation‐by‐distance model (IBD) predicts that genetic differentiation among populations increases with geographic distance. Yet, empirical studies show that a variety of ecological, topographic and historical factors may override the effect of geographic distance on genetic variation. This may particularly apply to species with narrow but highly heterogeneous distribution ranges, such as those occurring along elevational gradients. Using nine SSR markers, we study the genetic differentiation of the montane pollination‐generalist herb, Erysimum mediohispanicum. Because the effects of any given factor may depend on the geographic scale considered, we investigate the contribution of different environmental and historical factors at three different spatial scales. We evaluate five competing models that put forward the role of geographic distance, local environmental factors [biotic interactions (IBEb) and climatic variables (IBEa)], landscape resistance (IBR) and phylogeographic patterns (IBP), respectively. We find significant IBD regardless of the spatial scale and the genetic distance estimator considered. However, IBEa and IBP also play a prominent role in shaping genetic differentiation patterns at the larger spatial scales, and IBR is significant at the fine spatial scale. Overall, our results highlight the importance of combining different estimators, statistical approaches and spatial scales to disentangle the relative importance of the various ecological factors contributing to the shaping of genetic divergence patterns in natural populations.
Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates
Authors: Badouin H. , Gladieux P. , Gouzy J. , Siguenza S. , Aguileta G. , Snirc A. , Le Prieur S. , Jeziorski C. , Branca A. , Giraud T. 
Published: December 2016

AbstractIdentifying the genes underlying adaptation, their distribution in genomes and the evolutionary forces shaping genomic diversity are key challenges in evolutionary biology. Very few studies have investigated the abundance and distribution of selective sweeps in species with high‐quality reference genomes, outside a handful of model species. Pathogenic fungi are tractable eukaryote models for investigating the genomics of adaptation. By sequencing 53 genomes of two species of anther‐smut fungi and mapping them against a high‐quality reference genome, we showed that selective sweeps were abundant and scattered throughout the genome in one species, affecting near 17% of the genome, but much less numerous and in different genomic regions in its sister species, where they left footprints in only 1% of the genome. Polymorphism was negatively correlated with linkage disequilibrium levels in the genomes, consistent with recurrent positive and/or background selection. Differential expression in planta and in vitro, and functional annotation, suggested that many of the selective sweeps were probably involved in adaptation to the host plant. Examples include glycoside hydrolases, pectin lyases and an extracellular membrane protein with CFEM domain. This study thus provides candidate genes for being involved in plant–pathogen interaction (effectors), which have remained elusive for long in this otherwise well‐studied system. Their identification will foster future functional and evolutionary studies, in the plant and in the anther‐smut pathogens, being model species of natural plant–pathogen associations. In addition, our results suggest that positive selection can have a pervasive impact in shaping genomic variability in pathogens and selfing species, broadening our knowledge of the occurrence and frequency of selective events in natural populations.
Clones or clans: the genetic structure of a deep‐sea sponge,Aphrocallistes vastus,in unique sponge reefs of British Columbia, Canada
Authors: Brown Rachel R. , Davis Corey S. , Leys Sally P. 
Published: December 2016

AbstractUnderstanding patterns of reproduction, dispersal and recruitment in deep‐sea communities is increasingly important with the need to manage resource extraction and conserve species diversity. Glass sponges are usually found in deep water (>1000 m) worldwide but form kilometre‐long reefs on the continental shelf of British Columbia and Alaska that are under threat from trawling and resource exploration. Due to their deep‐water habitat, larvae have not yet been found and the level of genetic connectivity between reefs and nonreef communities is unknown. The genetic structure ofAphrocallistes vastus, the primary reef‐building species in the Strait of Georgia (SoG) British Columbia, was studied using single nucleotide polymorphisms (SNPs). Pairwise comparisons of multilocus genotypes were used to assess whether sexual reproduction is common. Structure was examined 1) between individuals in reefs, 2) between reefs and 3) between sites in and outside the SoG. Sixty‐sevenSNPs were genotyped in 91 samples from areas in and around the SoG, including four sponge reefs and nearby nonreef sites. The results show that sponge reefs are formed through sexual reproduction. Within a reef and across the SoG basin, the genetic distance between individuals does not vary with geographic distance (r = −0.005 to 0.014), but populations within the SoG basin are genetically distinct from populations in Barkley Sound, on the west coast of Vancouver Island. Population structure was seen across all sample sites (globalFST = 0.248), especially between SoG and non‐SoG locations (average pairwiseFST = 0.251). Our results suggest that genetic mixing occurs across sponge reefs via larvae that disperse widely.
1,2‐Diacylglycerol choline phosphotransferase catalyzes the final step in the unique Treponema denticola phosphatidylcholine biosynthesis pathway
Authors: Vences‐Guzmán Miguel Ángel , Paula Goetting‐Minesky M. , Guan Ziqiang , Castillo‐Ramirez Santiago , Córdoba‐Castro Luz América , López‐Lara Isabel M. , Geiger Otto , Sohlenkamp Christian , Christopher Fenno J. 
Published: December 2016

SummaryTreponema denticola synthesizes phosphatidylcholine through a licCA‐dependent CDP‐choline pathway identified only in the genus Treponema. However, the mechanism of conversion of CDP‐choline to phosphatidylcholine remained unclear. We report here characterization of TDE0021 (herein designated cpt) encoding a 1,2‐diacylglycerol choline phosphotransferase homologous to choline phosphotransferases that catalyze the final step of the highly conserved Kennedy pathway for phosphatidylcholine synthesis in eukaryotes. T. denticola Cpt catalyzed in vitro phosphatidylcholine formation from CDP‐choline and diacylglycerol, and full activity required divalent manganese. Allelic replacement mutagenesis of cpt in T. denticola resulted in abrogation of phosphatidylcholine synthesis. T. denticola Cpt complemented a Saccharomyces cerevisiae CPT1 mutant, and expression of the entire T. denticola LicCA‐Cpt pathway in E. coli resulted in phosphatidylcholine biosynthesis. Our findings show that T. denticola possesses a unique phosphatidylcholine synthesis pathway combining conserved prokaryotic choline kinase and CTP:phosphocholine cytidylyltransferase activities with a 1,2‐diacylglycerol choline phosphotransferase that is common in eukaryotes. Other than in a subset of mammalian host‐associated Treponema that includes T. pallidum, this pathway is found in neither bacteria nor Archaea. Molecular dating analysis of the Cpt gene family suggests that a horizontal gene transfer event introduced this gene into an ancestral Treponema well after its divergence from other spirochetes.
Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis
Authors: Molodtsov Vadim , Scharf Nathan T. , Stefan Maxwell A. , Garcia George A. , Murakami Katsuhiko S. 
Published: December 2016

SummarySince 1967, Rifampin (RMP, a Rifamycin) has been used as a first line antibiotic treatment for tuberculosis (TB), and it remains the cornerstone of current short‐term TB treatment. Increased occurrence of Rifamycin‐resistant (RIFR) TB, ∼41% of which results from the RpoB S531L mutation in RNA polymerase (RNAP), has become a growing problem worldwide. In this study, we determined the X‐ray crystal structures of the Escherichia coli RNAPs containing the most clinically important S531L mutation and two other frequently observed RIFR mutants, RpoB D516V and RpoB H526Y. The structures reveal that the S531L mutation imparts subtle if any structural or functional impact on RNAP in the absence of RIF. However, upon RMP binding, the S531L mutant exhibits a disordering of the RIF binding interface, which effectively reduces the RMP affinity. In contrast, the H526Y mutation reshapes the RIF binding pocket, generating significant steric conflicts that essentially prevent any RIF binding. While the D516V mutant does not exhibit any such gross structural changes, certainly the electrostatic surface of the RIF binding pocket is dramatically changed, likely resulting in the decreased affinity for RIFs. Analysis of interactions of RMP with three common RIFR mutant RNAPs suggests that modifications to RMP may recover its efficacy against RIFR TB.
Several Hfq‐dependent alterations in physiology of Yersinia enterocolitica O:3 are mediated by derepression of the transcriptional regulator RovM
Authors: Leskinen Katarzyna , Pajunen Maria I. , Varjosalo Markku , Fernández‐Carrasco Helena , Bengoechea José A. , Skurnik Mikael 
Published: December 2016

SummaryIn bacteria, the RNA chaperone Hfq enables pairing of small regulatory RNAs with their target mRNAs and therefore is a key player of post‐transcriptional regulation network. As a global regulator, Hfq is engaged in the adaptation to external environment, regulation of metabolism and bacterial virulence. In this study we used RNA‐sequencing and quantitative proteomics (LC‐MS/MS) to elucidate the role of this chaperone in the physiology and virulence of Yersinia enterocolitica serotype O:3. This global approach revealed the profound impact of Hfq on gene and protein expression. Furthermore, the role of Hfq in the cell morphology, metabolism, cell wall integrity, resistance to external stresses and pathogenicity was evaluated. Importantly, our results revealed that several alterations typical for the hfq‐negative phenotype were due to derepression of the transcriptional factor RovM. The overexpression of RovM caused by the loss of Hfq chaperone resulted in extended growth defect, alterations in the lipid A structure, motility and biofilm formation defects, as well as changes in mannitol utilization. Furthermore, in Y. enterocolitica RovM only in the presence of Hfq affected the abundance of RpoS. Finally, the impact of hfq and rovM mutations on the virulence was assessed in the mouse infection model.
Suppression and synthetic‐lethal genetic relationships of ΔgpsB mutations indicate that GpsB mediates protein phosphorylation and penicillin‐binding protein interactions in Streptococcus pneumoniaeD39
Authors: Rued Britta E. , Zheng Jiaqi J. , Mura Andrea , Tsui Ho‐Ching T. , Boersma Michael J. , Mazny Jeffrey L. , Corona Federico , Perez Amilcar J. , Fadda Daniela , Doubravová Linda , Buriánková Karolína , Branny Pavel , Massidda Orietta , Winkler Malcolm E. 
Published: December 2016

SummaryGpsB regulatory protein and StkP protein kinase have been proposed as molecular switches that balance septal and peripheral (side‐wall like) peptidoglycan (PG) synthesis in Streptococcus pneumoniae (pneumococcus); yet, mechanisms of this switching remain unknown. We report that ΔdivIVA mutations are not epistatic to ΔgpsB division‐protein mutations in progenitor D39 and related genetic backgrounds; nor is GpsB required for StkP localization or FDAA labeling at septal division rings. However, we confirm that reduction of GpsB amount leads to decreased protein phosphorylation by StkP and report that the essentiality of ΔgpsB mutations is suppressed by inactivation of PhpP protein phosphatase, which concomitantly restores protein phosphorylation levels. ΔgpsB mutations are also suppressed by other classes of mutations, including one that eliminates protein phosphorylation and may alter division. Moreover, ΔgpsB mutations are synthetically lethal with Δpbp1a, but not Δpbp2a or Δpbp1b mutations, suggesting GpsB activation of PBP2a activity. Consistent with this result, co‐IP experiments showed that GpsB complexes with EzrA, StkP, PBP2a, PBP2b and MreC in pneumococcal cells. Furthermore, depletion of GpsB prevents PBP2x migration to septal centers. These results support a model in which GpsB negatively regulates peripheral PG synthesis by PBP2b and positively regulates septal ring closure through its interactions with StkP‐PBP2x.
Sudan black: a fast, easy and non‐toxic method to assess myelin repair in demyelinating diseases
Authors: Ineichen Benjamin V. , Weinmann Oliver , Good Nicolas , Plattner Patricia S. , Wicki Carla , Rushing Elisabeth J. , Linnebank Michael , Schwab Martin E. 
Published: December 2016

AimsThe search for novel drugs that enhance myelin repair in entities such as multiple sclerosis has top priority in neurological research, not least because remyelination can hinder further neurodegeneration in neuro‐inflammatory conditions. Recently, several new compounds with the potential to boost remyelination have been identified using high‐throughput in vitro screening methods. However, assessing their potential to enhance remyelination in vivo using plastic embedded semi‐thin sections or electron microscopy, even though being the gold standard for assessing remyelination, is toxic, extremely time‐consuming and expensive.MethodsWe screened available myelin dyes for a staining candidate which offers a faster and easier alternative to visualize remyelination in cryo‐sections.ResultsWe identified sudan black as a candidate with excellent myelin resolution and we show that our adapted sudan black staining can demonstrate myelin repair in rodent spinal cord cryosections as reliable as in semithin sections, but much faster, easier, less toxic and less expensive. Besides that, it can resolve the small myelinated axons in the corpus callosum. The staining can yet readily be combined with immunostainings which can be challenging in semithin sections. We validated the method in human spinal cord tissue as well as in experimental demyelination of the rat spinal cord by a lysolecithin time course experiment. As proof‐of‐principle, we demonstrate that sudan black is able to reliably detect the remyelination enhancing properties of benztropine.ConclusionOur adapted sudan black staining can be used to rapidly and non‐toxically screen for remyelinating therapies in demyelinating diseases.
Myopathology in the times of modern genetics
Authors: Schuelke M. , Øien N. C. , Oldfors A. 
Published: December 2016

The advent of Next Generation Sequencing (NGS) technologies has accelerated the rate of novel disease gene discovery. Analysis of the large datasets generated by whole exome sequencing, whole genome sequencing, and other NGS approaches poses a challenge to physicians and pathologists searching for disease causing variants amongst the 50 000—3 million polymorphisms typically seen in these datasets. This review describes strategies that successfully combine classical neuropathological investigation (e.g. histology, immunostaining and electron microscopy) with modern NGS technologies to pinpoint the underlying genetic cause of a disease. We describe filtering techniques and free online bioinformatic tools that can help physicians and researchers establish a molecular diagnosis from NGS data. The ethical issues raised by NGS data are outlined. We provide specific examples that illustrate how traditional and contemporary approaches integrate to solve a difficult diagnosis or to correct initially wrong assumptions based on data generated from one method alone.