bluuebunny/crossref_metadata_2025_split huggingface dataset:
The homoeologous genes for the Rec8-like meiotic cohesin in wheat: structure, function, and evolutionary implication
Authors: Ma Guojia , Zhang Wei , Liu Liwang , Chao Wun S. , Gu Yong Qiang , Qi Lili , Xu Steven S. , Cai Xiwen 
Published: March 2018

ABSTRACTThe Rec8-like cohesin is a cohesion protein essential for orderly chromosome segregation in meiosis. Here, we cloned twoRec8-like homoeologous genes (homoeoalleles) from tetraploid wheat (TtRec8-A1andTtRec8-B1) and one from hexaploid wheat (TaRec8-D1), and performed expression and functional analyses of the homoeoalleles. Also, we identified other twoRec8homoeoalleles in hexaploid wheat (TaRec8-A1andTaRec8-B1) and the one inAegilops tauschii(AetRec8-D1) by comparative analysis. The coding DNA sequences (CDS) of these sixRec8homoeoalleles are all 1,827 bp in length, encoding 608 amino acids. They differed from each other primarily in introns although single nucleotide polymorphisms were detected in CDS. Substantial difference was observed between the homoeoalleles from the subgenome B (TtRec8-B1andTaRec8-B1) and those from the subgenomes A and D (TtRec8-A1, TaRec8-A1, andTaRec8-D1).TtRec8-A1expressed dominantly overTtRec8-B1, but comparably toTaRec8-D1. Therefore, theRec8homoeoalleles from the subgenomes A and D may be functionally more active than the one from the subgenome B in wheat. The structural variation and differential expression of theRec8homoeoalleles indicate a unique cross-genome coordination of the homoeologous genes in the polyploid, and imply the distinction of the wheat subgenome B from other subgenomes in the origin and evolution.HIGHLIGHTThis work revealed the structural and expression patterns of theRec8-like homoeologous genes in polyploid wheat, implying a unique origin and evolutionary route of the wheat B subgenome.
Comparative Analysis ofUL16Mutants Derived from Multiple Strains of HSV-2 and HSV-1 Reveals Species-Specific Requirements for the UL16 Protein
Authors: Gao Jie , Yan Xiaohu , Banfield Bruce W. 
Published: March 2018

AbstractOrthologs of the herpes simplex virus (HSV)UL16gene are conserved throughout theHerpesviridae. Because of this conservation, one might expect that these proteins perform similar functions for all herpesviruses. Previous studies on aUL16null mutant derived from HSV-2 strain 186 revealed a roughly 100-fold replication defect and a critical role for UL16 in the nuclear egress of capsids. These findings were in stark contrast to what has been observed withUL16mutants of HSV-1 and pseudorabies virus where roughly 10-fold replication deficiencies were reported that were accompanied by defects in the secondary envelopment of cytoplasmic capsids. One possible explanation for this discrepancy is that the HSV-2 186 strain is not representative of the HSV-2 species. To address this possibility, multipleUL16null mutants were constructed in multiple HSV-2 and HSV-1 strains by CRISPR/Cas9 mutagenesis and their phenotypes characterized side-by-side. This analysis showed that all the HSV-2UL16mutants had 50 to 100-fold replication deficiencies that were accompanied by defects in the nuclear egress of capsids as well as defects in the secondary envelopment of cytoplasmic capsids. By contrast, most HSV-1UL16mutants had 10-fold replication deficiencies that were accompanied by defects in secondary envelopment of cytoplasmic capsids. These findings indicated that UL16 has HSV species-specific functions. Interestingly, HSV-1 UL16 could promote the nuclear egress of HSV-2UL16null strains, suggesting that, unlike HSV-1, HSV-2 lacks an activity that can compensate for nuclear egress in the absence of UL16.ImportanceHSV-2 and HSV-1 are important human pathogens that cause distinct diseases in their hosts. A complete understanding of the morphogenesis of these viruses is expected to reveal vulnerabilities that can be exploited in the treatment of HSV disease. UL16 is a virion structural component that is conserved throughout theHerpesviridaeand functions in virus morphogenesis, however, previous studies have suggested different roles for UL16 in the morphogenesis of HSV-2 and HSV-1. This study sought to resolve this apparent discrepancy by analyzing multiple UL16 mutant viruses derived from multiple strains of HSV-2 and HSV-1. The data indicate that UL16 has HSV species-specific functions insofar as HSV-2 has a requirement for UL16 in the escape of capsids from the nucleus whereas both HSV-2 and HSV-1 require UL16 for final envelopment of capsids at cytoplasmic membranes.
Differential splicing of ANP32A in birds alters its ability to stimulate RNA synthesis by restricted influenza polymerase
Authors: Baker Steven F. , Ledwith Mitchell P. , Mehle Andrew 
Published: March 2018

AbstractAdaptation of viruses to their host can result in specialization and a restricted host range. Species-specific polymorphisms in the influenza virus polymerase restrict its host range during transmission from birds to mammals. ANP32A was recently been identified as a cellular co-factor impacting polymerase adaption and activity. Avian influenza polymerases require ANP32A containing an insertion resulting from an exon duplication uniquely encoded in birds. Here we find that natural splice variants surrounding this exon create avian ANP32A proteins with distinct effects on polymerase activity. We demonstrate species-independent direct interactions between all ANP32A variants and the PB2 polymerase subunit. This interaction is enhanced in the presence of viral genomic RNA. In contrast, only avian ANP32A restored ribonucleoprotein complex assembly for a restricted polymerase by enhancing RNA synthesis. Our data suggest that ANP32A splicing variation amongst birds differentially impacts viral replication, polymerase adaption, and the potential of avian hosts to be reservoirs.
Analysis ofEscherichia coliFlagellin Gene Expression in Simulated Spaceflight Growth Conditions
Authors: Hetrick Kyle M. , Juergensmeyer Elizabeth A. , Henderson Jeffrey O. 
Published: March 2018

SummaryPopulation growth curves ofEscherichia coli(E. coli) cultures propagated in spaceflight environments demonstrate an extended log phase duration and an increased final cell concentration compared toE. colicultures grown on Earth. We suggest that during spaceflight, a lack of convective mixing in the growth medium alters a cell’s microenvironment such that the cell at first devotes its resources primarily to motility and later shifts most of its resources to reproduction. As flagellin is the major protein component of flagella, the motility structure ofE. coli, we propose that the expression of the flagellin gene (fliC) can be used as a diagnostic marker for determining if the bacterium is in fact altering its allocation of cellular resources to motility during specific growth phases. We have used semiquantitative RT-PCR to analyze the expression offliCin cultures grown in laboratory apparatus that simulate various aspects of the spaceflight environment. The data from this pilot study indicate thatfliCexpression increases initially under stationary, slow clinorotation, and fast clinorotation growth conditions, peaking at mid-exponential phase and decreasing dramatically in stationary phase. These data support the hypothesis that metabolic resources are being directed towards forming the flagellum, the bacteria motile structure, before shifting resources to growth, reproduction, and maintenance.
Molecular Genetic Analysis of Rbm45/Drbp1: Genomic Structure, Expression, and Evolution
Authors: Price Lauren E. , Loewen Faul Abigail B. , Vuchkovska Aleksandra , Lopez Kevin J. , Fast Katie M. , Eck Andrew G. , Hoferer David W. , Henderson Jeffrey O. 
Published: March 2018

SummaryRNA recognition motif-type RNA-binding domain containing proteins (RBDPs) participate in RNA metabolism including regulating mRNA stability, nuclear-cytoplasmic shuttling, and splicing. Rbm45 is an RBDP first cloned from rat brain and expressed spatiotemporally during rat neural development. More recently, RBM45 has been associated with pathological aggregates in the human neurological disorders amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and Alzheimer’s. Rbm45 and the neural developmental protein musashi-1 are in the same family of RDBPs and have similar expression patterns. In contrast to Musashi-1, which is upregulated during colorectal carcinogenesis, we found no association ofRBM45overexpression in human colon cancer tissue. In order to begin characterizing RNA-binding partners of Rbm45, we have successfully cloned and expressed human RBM45 in an Intein fusion-protein expression system. Furthermore, to gain a better understanding of the molecular genetics and evolution of Rbm45, we used anin silicoapproach to analyze the gene structure of the human and mouse Rbm45 homologues and explored the evolutionary conservation of Rbm45 in metazoans. HumanRBM45and mouseRbm45span ∽17 kb and 13 kb, respectively, and contain 10 exons, one of which is non-coding. Both genes have TATA-less promoters with an initiator and a GC-rich element. Downstream of exon 10, both homologues have canonical polyadenylation signals and an embryonic cytoplasmic polyadenylation element. Moreover, our data indicate Rbm45 is conserved across all metazoan taxa from sponges (phylum Porifera) to humans (phylum Chordata), portending a fundamental role in metazoan development.
In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences
Authors: Mendoza Brian J , Trinh Cong T 
Published: March 2018

AbstractDespite extensive exploration of the diversity of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems, biological applications have been mostly confined to Class 2 systems, specifically the Cas9 and Cas12 (formerly Cpf1) single effector proteins. A key limitation of exploring and utilizing other CRISPR-Cas systems with unique functionalities, particularly Class I types and their multi-protein effector complex, is the knowledge of the system’s protospacer adjacent motif (PAM) sequence identity. In this work, we developed a systematic pipeline, named CASPERpam, that enables us to comprehensively assess the PAM sequences of all the available CRISPR-Cas systems in the NCBI database of bacterial genomes. The CASPERpam analysis revealed that within the 30,389 assemblies previously screen for CRISPR arrays, there exists 26,364 spacers that match somewhere in the viral, bacterial, and plasmid databases of NCBI, using the constraints of 95% sequence identity and 95% sequence coverage for blast hits. When grouping these results by species, we were able to identify putative PAM sequences for 1,049 among 1,493 unique species. The remaining species either have insufficient data or an undetermined result from the analysis. Finally, we were able to infer certain design principles that are relevant for understanding PAM diversity and a baseline for further experimental studies including PAM assays. We envision CASPERpam is a useful bioinformatic tool for understanding and harnessing the diversity of CRISPR systems.
Proteome-wide Prediction of Lysine Methylation Reveals Novel Histone Marks and Outlines the Methyllysine Proteome
Authors: Biggar Kyle K , Charih Francois , Liu Huadong , Ruiz-Blanco Yasser B , Stalker Leanne , Chopra Anand , Connolly Justin , Adhikary Hemanta , Frensemier Kristin , Galka Marek , Fang Qi , Wynder Christopher , Standford William L , Green James R , Li Shawn S-C. 
Published: March 2018

SUMMARYProtein Lys methylation plays a critical role in numerous cellular processes, yet it has been challenging to identify Lys methylation in a systematic manner. We present here an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We have developed MethylSight, a program that predicts Kme events solely on physicochemical and biochemical properties of putative methylation sites, which can then be validated by targeted MS. Using this approach, we have identified 70 new histone Kme marks with a 90% validation rate. H2BK43me2, which undergoes dynamic changes during stem cell differentiation, is found to be a substrate of KDM5b. Furthermore, MethylSight predicts ~50,000 Kme sites in non-histone proteins with high confidence, suggesting that Lys methylation is a prevalent post-translational modification. Our work provides a useful resource for systematic exploration of the role of Lys methylation in human health and disease.
Crowding tunes 3D collagen fibrils and reveals matrix regulation of cancer cell morphogenesis
Authors: Han A. , Ranamukhaarachchi S. , Velez D. O. , Kumar A. , Engler A. J. , Fraley S. I. 
Published: March 2018

AbstractIt is well established that the collagenous extracellular matrix surrounding solid tumors significantly influences the dissemination of cancer cells. However, the underlying mechanisms remain poorly understood, in part because of a lack of methods to modulate collagen fibril topology in the presence of embedded cells. In this work, we develop a technique to tune the fibril architecture of cell-laden 3D collagen matrices using PEG as an inert molecular crowding agent. With this approach, we demonstrate that fibril length and pore size can be modulated independently of bulk collagen density and stiffness. Using live cell imaging and quantitative analysis, we show that matrices with long fibrils induce cell elongation and single cell migration, while shorter fibrils induce cell rounding, collective migration, and morphogenesis. We conclude that fibril architecture is an independent regulator of cancer cell phenotype and that cell shape and invasion strategy are functions of collagen fibril length.
Construction of a Genetic Sexing Strain for Aedes albopictus: a promising tool for the development of sterilizing insect control strategies targeting the tiger mosquito
Authors: Lebon Cyrille , Benlali Aude , Atyame Célestine , Mavingui Patrick , Tortosa Pablo 
Published: March 2018

AbstractBackgroundAedes albopictus is an invasive mosquito species of global medical concern as its distribution has recently expanded to Africa, the Americas and Europe. In the absence of prophylaxis protecting human populations from emerging arboviruses transmitted by this mosquito species, the most straightforward control measures rely on the suppression or manipulation of vector natural populations. A number of environmental-friendly methods using innundative releases of sterilizing males are currently under development. However, these strategies are still lacking an efficient sexing method required for mass production of males.ResultsWe present the first Genetic Sexing Strain (GSS) in Ae. albopictus, hereafter referred as TiCoq, obtained by sex linkage of rdl gene conferring dieldrin resistance. Hatching rate, larval survival and sex ratio were followed during twelve generations. The use of dieldrin at third larval stage allowed selecting 98% of males on average.ConclusionA good production rate of TiCoq males makes this GSS suitable for any control method based on mass production of Ae. albopictus sterilizing males. Despite limitations resulting from affected egg hatch as well as the nature of the used insecticide, the construction of this GSS paves the way for industrial sex separation of Ae. albopictus.
Neural Modulation of Social Distance on Third-Party Punishment
Authors: Qu Chen , Tang Zixuan , Zhang Huijun , Hu Yang , Dreher Jean Claude 
Published: March 2018

AbstractAs a crucial mechanism to enforce social norms, people as third parties tend to punish the norm violators even it costs their own pay-off. However, people do not usually treat everyone equally, e.g., it is shown that people are nice to close others. Here, we investigated how third party punishment (TPP) and its neural correlates is modulated by social distance (SD) by using fMRI. Behaviorally, participants punished more when the unfair perpetrator was more distant to them. Such SD-modulation effect was stronger when the punishment was free. Model-based results showed that SD-dependent computational signals were encoded in right dlPFC. More interestingly, SD modulated the relationship between punishment levels and neural activities in default network including vmPFC and bilateral hippocampus. The explorative functional connectivity analysis further showed that the vmPFC increased the association with left dlPFC when participants punished close others. Finally, punishment type (costly vs. free) also modulated the relationship between punishment levels and neural correlates in dACC and the ventral striatum. Taken together, our results revealed the neurocomputational underpinnings of how SD plays an important role in affecting TPP.
Deep mutational scanning by FACS-sorting of encapsulated E. coli micro-colonies
Authors: Behrendt Lars , Stein Amelie , Shah Shiraz Ali , Zengler Karsten , Sørensen Søren J. , Lindorff-Larsen Kresten , Winther Jakob R. 
Published: March 2018

AbstractWe present a method for high-throughput screening of protein variants where the signal is enhanced by micro-encapsulation of single cells into 20-30 μm agarose beads. Cells inside beads are propagated using standard agitation in liquid media and grow clonally into micro-colonies harboring several hundred bacteria. We have, as a proof-of-concept, analyzed random amino acid substitutions in the five C-terminal β-strands of the Green Fluorescent Protein (GFP). Starting from libraries of variants, each bead represents a clonal line of cells that can be separated by Fluorescence Activated Cell Sorting (FACS). Pools representing collections of individual variants with desired properties are subsequently analyzed by deep sequencing. Notably, the encapsulation approach described holds the potential for high-throughput analysis of systems where the fluorescence signal from a single cell is insufficient for detection. Fusion to GFP, or use of fluorogenic substrates, allows coupling protein levels or activity to sequence for a wide range of proteins. Here we analyzed more than 10,000 individual variants to gauge the effect of mutations on GFP-fluorescence. In the mutated region, we observed virtually all amino acid substitutions that are accessible by single nucleotide exchange. Lastly, we assessed the performance of biophysical protein stability predictors, FoldX and Rosetta, in predicting the outcome of the experiment. Both tools display good performance on average, suggesting that loss of thermodynamic stability is a key mechanism for the observed variation of the mutants. This, in turn, suggests that deep mutational scanning datasets may be used to more efficiently fine-tune such predictors, especially for mutations poorly covered by current biophysical data.
Cross-regulation between CDK and MAPK control cellular fate
Authors: Durandau Eric , Pelet Serge 
Published: March 2018

AbstractCommitment to a new cell cycle is controlled by a number of cellular signals. Mitogen-Activated Protein Kinase pathways, which transduce multiple extracellular cues, have been shown to be interconnected with the cell cycle. Using budding yeast as a model system, we have quantified in hundreds of live single cells the interplay between the MAPK regulating the mating response and the Cyclin-Dependent Kinase controlling cell cycle progression. Different patterns of MAPK activity dynamics could be identified by clustering cells based on their CDK activity, denoting the tight relationship between these two cellular signals. In mating mixtures, we have verified that the interplay between CDK and MAPK activities allows cells to select their fate, preventing them from being blocked in an undesirable cellular program.
Spatial photosynthesis modelling sets guidelines to constructing a viable single-cell cytoplasm-to-stroma C4 cycle
Authors: Jurić Ivan , Hibberd Julian M. , Blatt Mike , Burroughs Nigel J. 
Published: March 2018

AbstractIt has been proposed that introducing C4 photosynthesis into C3 crops would increase yield. The simplest scheme in- volves concentrating carbon originating from the cytosol in the chloroplast stroma of mesophyll cells without altering leaf or cell anatomy. Photosynthetic efficiency would then strongly depend on the chloroplast envelope permeability to CO2. We examine the performance of this C4 cycle with a spatial model of carbon assimilation in C3 mesophyll cell geometry, conducting a thorough exploration of parameter space relevant to C4 photosynthesis. For envelope perme- abilities below 300 µm/s C4 photosynthesis has a higher quantum efficiency than C3. However, even when envelope permeability is above this threshold, the C4 pathway can provide a substantial boost to carbon assimilation with only a moderate decrease in efficiency. Depending on the available light-harvesting capacity of plastids, C4 photosynthesis could boost carbon assimilation anywhere from 20% to 100%. Gains are even more prominent under CO2 deprivation, and can be achieved in conjunction with lower investment in plastids if chloroplast surface coverage is also altered. A C4 pathway operating within individual mesophyll cells of C3 plants could hence lead to higher growth rates and better drought resistance in dry, high-sunlight climates.
PACAP neurons in the ventral premammillary nucleus regulate reproductive function in the female mouse
Authors: Ross Rachel A. , León Silvia , Madara Joseph C. , Schafer Danielle , Fergani Chrysanthi , Maguire Caroline A. , Verstegen Anne M. J. , Brengle Emily , Kong Dong , Herbison Allan E , Kaiser Ursula B. , Lowell Bradford B. , Navarro Victor M. 
Published: March 2018

AbstractPituitary adenylate cyclase activating polypeptide (PACAP) is a neuromodulator implicated in anxiety, metabolism and reproductive behavior. PACAP global knockout mice have decreased fertility and PACAP modulates LH release. However, its source and role at the hypothalamic level remain unknown. We demonstrate that PACAP-expressing neurons of the ventral premamillary nucleus of the hypothalamus (PMVPACAP) project to, and make direct contact with, kisspeptin neurons in the arcuate and AVPV/PeN nuclei and a subset of these neurons respond to PACAP exposure. Targeted deletion of PACAP from the PMV through stereotaxic virally mediated cre- injection or genetic cross to LepR-i-cre mice with PACAPfl/flmice led to delayed puberty onset and impaired reproductive function in female, but not male, mice. We propose a new, sex-specific role for PACAP-expressing neurons in the PMV in the relay of nutritional state information to regulate GnRH release by modulating the activity of kisspeptin neurons, thereby regulating reproduction.Disclosure statementThe authors have nothing to disclose.
Perforin-2 Permeabilizes the Envelope of Phagocytosed Bacteria
Authors: Bai Fangfang , McCormack Ryan M. , Hower Suzanne , Plano Gregory V. , Lichtenheld Mathias G. , Munson George P. 
Published: March 2018

AbstractPerforin-2, the product of theMPEG1gene, limits the spread and dissemination of bacterial pathogens in vivo. It is highly expressed in murine and human phagocytes, and macrophages lacking Perforin-2 are compromised in their ability to kill phagocytosed bacteria. In this study we usedSalmonella typhimuriumas a model intracellular pathogen to elucidate the mechanism of Perforin-2‘s bactericidal activity. In vitro Perforin-2 was found to facilitate the degradation of antigens contained within the envelope of phagocytosed bacteria. In contrast, degradation of a representative surface antigen was found to be independent of Perforin-2. Consistent with our in vitro results a protease sensitive, periplasmic superoxide disumutase (SodCII) contributed to the virulence ofS. typhimuriumin Perforin-2 knockout but not wild-type mice. In aggregate our studies indicate that Perforin-2 breaches the envelope of phagocytosed bacteria facilitating the delivery of proteases and other antimicrobial effectors to sites within the bacterial envelope.