bluuebunny/crossref_metadata_2025 huggingface dataset:
PII1: a protein involved in starch initiation that determines granule number and size in Arabidopsis chloroplast
Authors: Vandromme Camille , Spriet Corentin , Dauvillée David , Courseaux Adeline , Putaux Jean-Luc , Wychowski Adeline , Facon Maud , D’Hulst Christophe , Wattebled Fabrice
Published: April 2018

The initiation of starch granule formation is still poorly understood. However, soluble starch synthase 4 (SS4) appears to be a major component of this process since it is required to synthetize the correct number of starch granules in the chloroplasts of Arabidopsis thaliana plants. A yeast-2-hybrid screen allowed the identification of several putative SS4 interacting partners. We identified the product of At4g32190 locus as a chloroplast-targeted PROTEIN INVOLVED IN STARCH INITIATION (named PII1). Arabidopsis mutants devoid of PII1 display an alteration of starch initiation process and accumulate, on average, one starch granule per plastid instead of the 5 to 7 granules found in plastids of wild-type plants. These granules are larger than in wild type and they remain flat and lenticular. pii1 mutants display wild-type growth rates and accumulate standard starch amounts. Moreover, starch characteristics, such as amylopectin chain length distribution, remain unchanged. Our results reveal the involvement of PII1 in starch priming process in Arabidopsis leaves through interaction with SS4.
Adaptive protein evolution through length variation in short tandem repeats
Authors: Reinar William B. , Greulich Anne , Stø Ida M. , Knutsen Jonfinn B. , Reitan Trond , Tørresen Ole K. , Jentoft Sissel , Butenko Melinka A. , Jakobsen Kjetill S.
Published: April 2018

Intrinsically disordered protein regions are of high importance for temperature sensing and immune responses in plants. Tracts of identical amino acids accumulate in these regions and can vary in length over generations due to expansions and retractions of short tandem repeats at the genomic level. However, little attention has been paid to what extent length variation is shaped by natural selection. By environmental association analysis on 2,514 length variable tracts in 770 whole-genome sequenced wildArabidopsis thalianawe show that length variation in glutamine and asparagine amino acid homopolymers, as well as in interaction hotspots, correlate with local bio-climatic habitat. We determined experimentally that the promoter activity of a light-stress gene depended on polyglutamine length variants in a disordered transcription factor. Our results show that length variations impact protein function and are substantially shaped by natural selection. Length variants modulating protein function at a global genomic scale has implications for understanding protein evolution and eco-evolutionary biology.
Rescue of a developmental arrest caused by aC. elegansheat-shock transcription-factor mutation by loss of ribosomal S6-kinase activity
Authors: Chisnell Peter , Richard Parenteau T. , Tank Elizabeth , Ashrafi Kaveh , Kenyon Cynthia
Published: April 2018

The widely conserved heat-shock response, regulated by heat shock transcription factors, is not only essential for cellular stress resistance and adult longevity, but also for proper development. However, the genetic mechanisms by which heat-shock transcription factors regulate development are not well understood. InC. elegans, we conducted an unbiased genetic screen to identify mutations that could ameliorate the developmental arrest phenotype of a heat-shock factor mutant. Here we show that loss of the conserved translational activatorrsks-1/S6-Kinase, a downstream effector of TOR kinase, can rescue the developmental-arrest phenotype of hsf-1partial loss-of-function mutants. Unexpectedly, we show that the rescue is not likely caused by reduced translation, nor to activation of any of a variety of stress-protective genes and pathways. Our findings identify an as-yet unexplained regulatory relationship between the heat-shock transcription factor and the TOR pathway duringC. elegans’development.
Single cell RNA sequencing reveals a novel, microglia-like cell type in cerebrospinal fluid during virologically suppressed HIV
Authors: Farhadian Shelli F. , Mehta Sameet S. , Zografou Chrysoula , Pappalardo Jenna , Chiarella Jennifer , Hafler David A. , Spudich Serena S.
Published: April 2018

Central nervous system (CNS) immune activation in an important driver of neuronal injury during several neurodegenerative and neuroinflammatory diseases. During HIV infection, CNS immune activation is associated with high rates of neurocognitive impairment, even with sustained long-term suppressive antiretroviral therapy (ART). However, the cellular subsets that drive immune activation and neuronal damage in the CNS during HIV infection and neurological conditions remain unknown, in part because CNS cells are difficult to access in living humans. Using single cell RNA sequencing (scRNA-seq) on cerebrospinal fluid (CSF) and blood from adults with HIV, we identified a rare (<5% of cells) subset of myeloid cells in CSF presenting a gene expression signature consistent with neurodegenerative disease associated microglia. This highlights the power of scRNA-seq of CSF to identify rare CNS immune cell subsets that may perpetuate neuronal injury during HIV infection and other conditions.
Hydrogen-deuterium exchange coupled to top- and middle-down mass spectrometry enables high-resolution measurements of histone tail dynamics before and after nucleosome assembly
Authors: Karch Kelly R. , Coradin Mariel , Zandarashvili Levani , Kan Zhong-Yuan , Gerace Morgan , Englander S. Walter , Black Ben E. , Garcia Benjamin A.
Published: April 2018

Until recently, a major limitation of hydrogen deuterium exchange mass spectrometry (HDX-MS) was that resolution of deuterium localization information was limited to the length of the peptide generated during proteolysis. Recently, however, it has been demonstrated that electron transfer dissociation (ETD) allows for preservation of deuterium label in the gas phase and therefore can be used to obtain more resolved information. To date, this technology has remained mostly limited to single, small, already well-characterized model proteins. Here, we optimize, expand, and adapt HDX-MS/MS capabilities to accommodate histone and nucleosomal complexes on top-down (TD) HDX-MS/MS and middle-down (MD) HDX-MS/MS platforms and demonstrate that near site-specific resolution of deuterium localization can be obtained with high reproducibility. We are able to study histone tail dynamics in unprecedented detail, which have evaded rigorous analysis by traditional structural biology techniques for decades, revealing important novel insights into chromatin biology. This work represents the first heterogeneous protein complex and protein-DNA complex to be analyzed by TD- and MD-HDX-MS/MS, respectively. Together, the results of these studies highlight the versatility, reliability, and reproducibility of ETD-based HDX-MS/MS methodology to interrogate large protein and protein/DNA complexes.
A CRISPR/Cas9 based strategy to manipulate the Alzheimer’s amyloid pathway
Authors: Sun Jichao , Carlson-Stevermer Jared , Das Utpal , Shen Minjie , Delenclos Marion , Snead Amanda M. , Wang Lina , Loi Jonathan , Petersen Andrew J , Stockton Michael , Bhattacharyya Anita , Jones Mathew V. , Sproul Andrew A. , McLean Pamela J. , Zhao Xinyu , Saha Krishanu , Roy Subhojit
Published: April 2018

The gradual accumulation of amyloid-β (Aβ) is a neuropathologic hallmark of Alzheimer’s disease (AD); playing a key role in disease progression. Aβ is generated by the sequential cleavage of amyloid precursor protein (APP) by β- and γ-secretases, with BACE-1 (β-site APP cleaving enzyme-1) cleavage as the rate limiting step 1–3. CRISPR/Cas9 guided gene-editing is emerging as a promising tool to edit pathogenic mutations and hinder disease progression 4,5,6 However, few studies have applied this technology to neurologic diseases 7–9. Besides technical caveats such as low editing efficiency in brains and limited in vivo validation 7, the canonical approach of ‘mutation-correction’ would only be applicable to the small fraction of neurodegenerative cases that are inherited (i.e. < 10% of AD, Parkinson’s, ALS); with a new strategy needed for every gene. Moreover, feasibility of CRISPR/Cas9 as a therapeutic possibility in sporadic AD has not been explored. Here we introduce a strategy to edit endogenous APP at the extreme C-terminus and reciprocally manipulate the amyloid pathway – attenuating β-cleavage and Aβ, while up-regulating neuroprotective a-cleavage. APP N-terminus, as well as compensatory APP homologues remain intact, and key physiologic parameters remain unaffected. Robust APP-editing is seen in cell lines, cultured neurons, human embryonic stem cells/iPSC-neurons, and mouse brains. Our strategy works by limiting the physical association of APP and BACE-1, and we also delineate the mechanism that abrogates APP/BACE-1 interaction in this setting. Our work offers an innovative ‘cut and silence’ gene-editing strategy that could be a new therapeutic paradigm for AD.
Molecular Strategy for Blocking Isopeptide Bond Formation in Nascent Pilin Proteins
Authors: Rivas-Pardo Jaime Andrés , Badilla Carmen L. , Tapia-Rojo Rafael , Alonso-Caballero Álvaro , Fernández Julio M.
Published: April 2018

Bacteria anchor to their host cells through their adhesive pili, which must resist the large mechanical stresses induced by the host as it attempts to dislodge the pathogens. The pili of Gram-positive bacteria are constructed as a single polypeptide made of hundreds of pilin repeats, which contain intramolecular isopeptide bonds strategically located in the structure to prevent their unfolding under force, protecting the pilus from degradation by extant proteases and oxygen radicals. Here, we demonstrate the design of a short peptide that blocks the formation of the isopeptide bond present in the pilin Spy0128 from the human pathogen Streptococcus pyogenes, resulting in mechanically labile pilin domains. We use a combination of protein engineering and AFM force spectroscopy to demonstrate that the peptide blocks the formation of the native isopeptide bond and compromises the mechanics of the domain. While an intact Spy0128 is inextensible at any force, peptide-modified Spy0128 pilins readily unfold at very low forces, marking the abrogation of the intramolecular isopeptide bond as well as the absence of a stable pilin fold. We propose that isopeptide-blocking peptides could be further developed as a novel type of highly-specific anti-adhesive antibiotics to treat Gram-positive pathogens.

Significance

At the onset of an infection, Gram-positive bacteria adhere to host cells through their pili, filamentous structures built by hundreds of repeats of pilin proteins. These proteins can withstand large mechanical challenges without unfolding, remaining anchored to the host and resisting cleavage by proteases and oxygen radicals present in the targeted tissues. The key structural component that gives pilins mechanical resilience are internal isopeptide bonds, strategically placed so that pilins become inextensible structures. We target this bond by designing a blocking peptide that interferes with its formation during folding. We demonstrate that peptide-modified pilins lack mechanical stability and extend at low forces. We propose this strategy as a rational design of mechanical antibiotics, targeting the Achilles’ Heel of bacterial adhesion.
Gain of Function Analysis Reveals Non-Redundant Roles for theYersinia pestisType III Secretion System Effectors YopJ, YopT, and YpkA
Authors: Palace Samantha G. , Proulx Megan K. , Szabady Rose L. , Goguen Jon D.
Published: April 2018

Virulence ofYersinia pestisin mammals requires the type III secretion system, which delivers seven effector proteins into the cytoplasm of host cells to undermine immune responses. All seven of these effectors are conserved acrossY. pestisstrains, but three – YopJ, YopT, and YpkA – are apparently dispensable for virulence. Some degree of functional redundancy between effector proteins would explain both observations. Here, we use a combinatorial genetic approach to define the minimal subset of effectors required for full virulence in mice following subcutaneous infection. We found that aY. pestisstrain lacking YopJ, YopT, and YpkA is attenuated for virulence in mice, and that addition of any one of these effectors to this strain increases lethality significantly. YopJ, YopT, and YpkA likely contribute to virulence via distinct mechanisms. YopJ is uniquely able to cause macrophage cell deathin vitroand to suppress accumulation of inflammatory cells to foci of bacterial growth in deep tissue, whereas YopT and YpkA cannot. The synthetic phenotypes that emerge when YopJ, YopT, and YpkA are removed in combination provide evidence that each enhancesY. pestisvirulence, and that YopT and YpkA act through a mechanism distinct from that of YopJ.
Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge
Authors: Terwilliger Thomas C. , Adams Paul D. , Afonine Pavel V. , Sobolev Oleg V.
Published: April 2018

A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 cryo-EM model challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å to 2.1 Å.
High-throughput chromatin accessibility profiling at single-cell resolution
Authors: Mezger Anja , Klemm Sandy , Mann Ishminder , Brower Kara , Mir Alain , Bostick Magnolia , Farmer Andrew , Fordyce Polly , Linnarsson Sten , Greenleaf William
Published: April 2018

We have developed a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4-5 hour on-chip processing time) and cost (~98¢ per cell) compared to prior microfluidic implementations. We applied this method to measure regulatory variation in Peripheral Blood Mononuclear Cells (PBMCs) and show robust,de-novoclustering of single cells by hematopoietic cell type.
GnasR201C Induces Murine Pancreatic Cystic Neoplasms through Suppression of YAP1 Signaling and Transcriptional Reprogramming
Authors: Ideno Noboru , Yamaguchi Hiroshi , Ghosh Bidyut , Gupta Sonal , Okumura Takashi , Fisher Catherine G , Wood Laura D , Singhi Aatur D. , Nakamura Masafumi , Gutkind J Silvio , Maitra Anirban
Published: April 2018

Background & Aims

Somatic “hotspot” mutations of GNAS, which encodes for the alpha subunit of stimulatory G-protein, are present in ~60% of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas. There are currently no cognate animal models that recapitulate the biology of mutant Gnas-induced IPMNs, and the underlying mechanisms that lead to the cystic pathway of neoplasia in the pancreas remain unknown.

Methods

We generated p48-Cre; LSL-KrasG12D; Rosa26R-LSL-rtTA-TetO-GnasR201C mice (Kras; Gnas mice) where pancreas-specific GnasR201C expression was induced by doxycycline administration. In this model, mutant Kras is constitutively expressed, and control mice were produced through absence of doxycycline. Separate cohorts of mice were utilized for timed necropsies and for Kaplan-Meier survival analysis. Isogenic cell lines (with doxycycline inducible mutant Gnas expression) were propagated from the resulting pancreatic ductal adenocarcinoma (PDAC).

Results

Co-expression of KrasG12D and GnasR201C resulted in the development of pancreatic cystic lesions resembling human IPMNs in 100% of mice, with higher grades of epithelial dysplasia observed over time. Approximately one-third of Kras; Gnas mice developed PDAC at a median of 38 weeks post doxycycline induction. GnasR201C did not accelerate oncogenic transformation with KrasG12D, but rather, reprogrammed Ras-induced neoplasms towards a well-differentiated phenotype. GnasR201C induction led to activation of the inhibitory Hippo kinase cascade and cytoplasmic sequestration of phosphorylated YAP1 protein, a phenomenon that was also observed in human IPMN with GNAS mutations.

Conclusions

GNASR201C functions not as a traditional oncogene, but rather as an “oncomodulator” of KRAS-mediated pancreatic neoplasia, through suppression of YAP1 and transcriptional reprogramming towards a differentiated (large ductal) phenotype.
A constraints-based theory of the primary cause of senescence: imbalance of epigenetic and non-epigenetic information in histone crosstalk
Authors: Veloso Felipe A.
Published: April 2018

Cellular aging has been progressively elucidated by science. However, the fundamental cause of senescence—i.e., why organisms age at the multicellular-individual level—remains unclear. A recent theory of individuated multicellularity describes the emergence and growth of crucial information content for cell differentiation. This information is mostly conveyed in the non-epigenetic (i.e., transcription uncorrelated) histone crosstalk near transcription start sites. According to this theory, the non-epigenetic content emerges and grows at the expense of the information capacity for epigenetic content. If this “reassignment” of information capacity continues after adulthood, it may explain the senescence phenomenon. Here, I present a novel, falsifiable theory describing an uninterrupted growth of capacity for non-epigenetic information at the expense of that for epigenetic information not only during ontogeny but also throughout adulthood. As a byproduct, this continuous “reassignment” of capacity effectively creates an information imbalance in histone crosstalk, which in turn overregulates transcriptional levels. This overregulation is to be understood as transcriptional levels becoming more and more accurate but also less and less precise with respect to the needs of the multicellular individual—up to the point of dysfunctionality. This epigenetic/non-epigenetic information imbalance is proposed to be the primary reason why individuated multicellular organisms senesce.
Exploring sex differences in the prevention of ethanol drinking by naltrexone in dependent rats during abstinence
Authors: Matzeu A , Terenius L , Martin-Fardon R
Published: April 2018

Background

Despite considerable efforts, few drugs are available for the treatment of alcohol (ethanol [EtOH]) use disorders (AUDs). Ethanol directly or indirectly modulates several aspects of the central nervous system, including neurotransmitter/neuromodulator systems. Relapse vulnerability is a challenge for the treatment of EtOH addiction. Ethanol withdrawal symptoms create motivational states that lead to compulsive EtOH drinking and relapse even after long periods of abstinence. Among the therapeutics to treat AUDs, naltrexone (NTX) is a pharmacological treatment for relapse. The goal of the present study was to evaluate the effect of NTX on EtOH drinking in EtOH-dependent male and female rats during abstinence.

Methods

Wistar rats (males and females) were first trained to orally self-administer 10% EtOH. Half of them were then made dependent by chronic intermittent EtOH (CIE) vapor exposure, and the other half were exposed to air. Using this model, rats exhibit somatic and motivational signs of withdrawal. At the end of EtOH vapor (or air) exposure, the rats were tested for the effects of NTX (10 mg/kg, p.o.) on EtOH self-administration at three abstinence time points: acute abstinence (8 h, A-Abst), late abstinence (2 weeks, L-Abst), and protracted abstinence (6 weeks, P-Abst).

Results

NTX decreased EtOH intake in nondependent rats, regardless of sex and abstinence time point. In post-dependent rats, the effects of NTX improved with a longer abstinence time (i.e., L-Abst and P-Abst) in males, whereas it similarly reduced EtOH drinking in females at all abstinence points.

Conclusions

The data suggest that the therapeutic efficacy of NTX depends on the time of intervention during abstinence and sex. The data further suggest that EtOH dependence induces different neuroadaptations in male and female rats, reflected by differential effects of NTX. The results underscore the significance of considering the duration of EtOH abstinence and sex for the development of pharmacotherapeutic treatments for AUD.
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity
Authors: Chen Xingqi , Litzenburger Ulrike M. , Wei Yuning , Schep Alicia N. , LaGory Edward L. , Choudhry Hani , Giaccia Amato J. , Greenleaf William J. , Chang Howard Y.
Published: April 2018

Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironmentin vivo. We identify a dominant role for hypoxia, marked by HIF1α protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.
HDAC11 Deficiency Prevents High-Fat Diet-Induced Obesity and Metabolic Syndrome
Authors: Sun Lei , Marin De Evsikova Caralina , Bian Ka , Achille Alexandra , Telles Elphine , Seto Edward
Published: April 2018

Significance Statement

Obesity is a serious and widespread health problem which has become a growing concern in many societies. Most currently available weight-loss medications do not work for everyone, and the effects decline over time. Thus, there is an urgent need to identify new molecular targets to improve drug development for the treatment of obesity and obesity-related diseases. In this study, we discovered that the histone deacetylase 11 (HDAC11) enzyme is a key regulator of metabolism and obesity, and the absence of HDAC11 prevents obesity in mice. Our findings will facilitate the development of novel therapeutics to treat obesity by targeting HDAC11.

Obesity and its associated metabolic syndromes are the consequence of susceptible genes and obesogenic environments. We report here that histone deacetylase 11 (HDAC11) plays a critical role in the development of obesity and in metabolic homeostasis. HDAC11 knockout mice display resistance to high-fat diet-induced obesity and associated syndromes by enhancing glucose tolerance and insulin sensitivity, attenuating hypercholesterolemia and hyperinsulinemia, and blocking hepatosteatosis and liver damage. Mechanistically, HDAC11 deficiency boosts energy expenditure through promoting thermogenic capacity, which attributes to the elevation of uncoupling protein 1 (UCP1) expression and activity in brown adipose tissue. Moreover, loss of HDAC11 stimulates mitochondrial oxidation, elevates plasma adiponectin, and activates the adiponectin-AdipoR-AMPK pathway in the liver, which may contribute to a reversal in hepatosteatosis. These findings establish HDAC11 as a key regulator of metabolism and indicate that HDAC11 inhibitors may hold promise for treating overweight and obesity-related diseases.
Small-scale soil microbial community heterogeneity linked to landforms on King George Island, maritime Antarctica
Authors: Zhang Yumin , Lu Lu , xChang Xulu , Jiang Fan , Gao Xiangdong , Peng Fang
Published: April 2018

We analysed soil-borne microbial (bacterial, archaeal, and fungal) communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes (soil chemical parameters and vegetation conditions) located in Holocene raised beach and Tertiary volcanic stratigraphy. Prokaryotic communities of the two groups were well separated; they predominantly correlated with soil elemental compositions, and were secondly correlated with environmental attributes (e.g., soil pH, total organic carbon,, and vegetation coverage; Pearson test,r= 0.59 vs. 0.52, bothP< 0.01). The relatively high abundance of P, S, Cl, and Br in Group 1 was likely due to landform uplift. Lithophile-elements (Si, Al, Ca, Sr, Ti, V, and Fe) correlated with prokaryotic communities in Group 2 may originate from weathering of Tertiary volcanic rock. The elements and nutrients accumulated during formation of different landforms influenced the development of soils, plant growth, and microbial communities, and resulted in small-scale spatially heterogeneous biological distributions. We propose that the geological evolution of the Fildes Region was crucial to its microbial community development.

IMPORTANCE

This current study analyzed soil-borne microbial communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes. We provide new evidence for the crucial influence of landforms on small-scale structures and spatial heterogeneity of soil microbial communities.
Bacillus cereusHS24 Suppresses Conidia Germination ofMagnaporthe oryzaeby Inhibiting the Ca2+Signaling Pathway
Authors: Huang Wenxiang , Liu Xingyu , Zhou Xiaosi , Chen Yu , Li Ye , Liu Hongxia
Published: April 2018

Rice yield is greatly reduced due to rice blast, a worldwide multi-cycle fungal disease caused by the ascomyceteMagnaporthe oryzae.Previously,Bacillus cereusHS24 was isolated from rice growing area, which showed a strong bio-control effect onM. oryzae.In order to better exploit it as a bio-control agent, HS24 has been studied for its mechanism of controlling rice blast. Our results showed that conidial germination ofM. oryzaewas significantly inhibited by HS24 suspension,nand the inhibition rate reached to 97.83% at the concentration of 10 CFU/ml. The transcriptional level ofCAMKII, PMC1andCCH1,which are key genes involved in Ca2+signaling pathway, were significantly decreased in HS24-treated conidia. The treatment ofM. oryzaewith Ca2+signaling pathway inhibitors KN-93, Verapamil, and cyclopiazonic acid (CPA) significantly reduced conidial germination rate and inhibited germ tube elongation. This inhibition effect was found to be concentration-dependent, similar to the HS24 treatment. By quantifying free Ca2+inM. oryzaeconidia, a significant reduction of intracellular free Ca2+concentration in HS24-treated conidia in comparison to sterile water-treated conidia was found. The addition of exogenous Ca2+did not abolish the inhibitory effect of HS24 on the reduction of intracellular free Ca2+concentration and conidial germination. In conclusion,B. cereusHS24 can inhibit conidial germination by suppressing Ca2+signaling inM. oryzae,and thus offers a great potential as a bio-control agent in rice blast management.

Importance

In the bio-control of rice blast, most of researches focused on the inhibitory effect of bio-control agents on development ofM. oryzae, including inhibition of conidia germination, germ tube deformity, mycelium growth inhibition, etc, while little work has elucidated the molecular mechanisms underlying the various phenotypic change inM. oryzae.In order to better exploit HS24 as a potential bio-control agent, we studied the molecular mechanisms underlying the suppression ofB. cereusHS24 onM. oryzaeGuy11, and draw the conclusion that HS24 may inhibit conidia germination and germ tube elongation through inhibiting the Ca2+signaling pathway. In this study, we characterized the morphological and physiological changes ofM. oryzaewhen interacting withB. cereusHS24, and further investgated the responses ofM. oryzaeCa2+signallig pathway to HS24 treatment. Thus we have provided one more piece for theB. cereus/M. oryzaesupression puzzle at the molecular level.
Expectation of the intercept from bivariate LD score regression in the presence of population stratification
Authors: Yengo Loic , Yang Jian , Visscher Peter M.
Published: April 2018

Linkage disequilibrium (LD) score regression is an increasingly popular method used to quantify the level of confounding in genome-wide association studies (GWAS) or to estimate heritability and genetic correlation between traits. When applied to a pair of GWAS, the LD score regression (LDSC) methodology produces a statistic, referred to as the bivariate LDSC intercept, which deviation from 0 is classically interpreted as an indication of sample overlap between the two GWAS. Here we propose an extension of the theory underlying the bivariate LDSC methodology, which accounts for population stratification within and between GWAS. Our extended theory predicts an inflation of the bivariate LDSC intercept when sample sizes and heritability are large, even in the absence of sample overlap. We illustrate our theoretical results with simulations based on actual SNP genotypes and we propose a re-interpretation of previously published results in the light of our extended theory.
Structural basis for relief of the sarcoplasmic reticulum Ca2+-ATPase inhibition by phospholamban at saturating Ca2+conditions
Authors: Gortari Eli Fernández-de , Michel Espinoza-Fonseca L.
Published: April 2018

We have performed extensive atomistic molecular dynamics simulations to probe the structural mechanism for relief of sarcoplasmic reticulum Ca2+-ATPase (SERCA) inhibition by phospholamban (PLB) at saturating Ca2+conditions. Reversal of SERCA-PLB inhibition by saturating Ca2+operates as a physiological rheostat to reactivate SERCA function in the absence of PLB phosphorylation. Simulation of the inhibitory complex at super-physiological Ca2+concentrations ([Ca2+]=10 mM) revealed that calcium ions interact primarily with SERCA and the lipid headgroups, but not with the cytosolic domain of PLB or the cytosolic side of the SERCA-PLB interface. At this [Ca2+], a single Ca2+ion is translocated from the cytosol to the transmembrane transport sites. We used this Ca2+-bound complex as an initial structure to simulate the effects of saturating Ca2+at physiological conditions ([Ca2+]total≈400 μM). At these conditions, ~30% of the Ca2+-bound complexes exhibit structural features that correspond to an inhibited state. However, in ~70% of the Ca2+-bound complexes, Ca2+moves to transport site I, recruits Glu771 and Asp800, and disrupts key inhibitory contacts involving conserved PLB residue Asn34. Structural analysis showed that Ca2+induces only local changes in interresidue inhibitory interactions, but does not induce dissociation, repositioning or changes in the structural dynamics of PLB. Upon relief of SERCA inhibition, Ca2+binding produces a productive site I configuration that is sufficient for subsequent SERCA activation. We propose that at saturating [Ca2+] and in the absence of PLB phosphorylation, binding of a single Ca2+ion in the transport sites rapidly shifts the equilibrium toward a non-inhibited SERCA-PLB complex.
CAGEfightR: Cap Analysis of Gene Expression (CAGE) in R/Bioconductor
Authors: Thodberg Malte , Thieffry Axel , Vitting-Seerup Kristoffer , Andersson Robin , Sandelin Albin
Published: April 2018

We developed the CAGEfightR R/Biconductor-package for analyzing CAGE data. CAGEfightR allows for fast and memory efficient identification of transcription start sites (TSSs) and predicted enhancers. Downstream analysis, including annotation, quantification, visualization and TSS shape statistics are implemented in easy-to-use functions. The package is freely available at https://bioconductor.org/packages/CAGEfightR
Lymphoid origin of intrinsically activated plasmacytoid dendritic cells in mice
Authors: Araujo Alessandra M. , Dekker Joseph D. , Garrison Kendra , Su Zhe , Rhee Catherine , Hu Zicheng , Lee Bum-Kyu , Osorio Hurtado Daniel , Lee Jiwon , Iyer Vishwanath R. , Ehrlich Lauren I. R. , Georgiou George , Ippolito Gregory C. , Yi S. Stephen , Tucker Haley O.
Published: April 2018

We identified a novel mouse plasmacytoid dendritic cell (pDC) lineage derived from the common lymphoid progenitors (CLPs) that is dependent on expression ofBcl11a. These CLP-derived pDCs, which we refer to as “B-pDCs”, have a unique gene expression profile that includes hallmark B cell genes, normally not expressed in conventional pDCs. Despite expressing most classical pDC markers such as SIGLEC-H and PDCA1, B-pDCs lack IFN-α secretion, exhibiting a distinct inflammatory profile. Functionally, B-pDCs induce T cell proliferation more robustly than canonical pDCs following Toll-like receptor 9 (TLR9) engagement. B-pDCs, along with another homogeneous subpopulation of myeloid derived pDCs, display elevated levels of the cell-surface receptor tyrosine kinase AXL, mirroring human AXL+transitional DCs in function and transcriptional profile. Murine B-pDCs therefore represent a phenotypically and functionally distinct CLP-derived DC lineage specialized in T cell activation and previously not described in mice.
Protective immunity induced by an intranasal multivalent vaccine comprising 10 Lactococcus lactis strains expressing highly prevalent M‐protein antigens derived from Group A Streptococcus
Authors: Wozniak Aniela , Scioscia Natalia , García Patricia C. , Dale James B. , Paillavil Braulio A. , Legarraga Paulette , Salazar‐Echegarai Francisco J. , Bueno Susan M. , Kalergis Alexis M.
Published: April 2018

Streptococcus pyogenes (group A Streptococcus) causes diseases ranging from mild pharyngitis to severe invasive infections. The N‐terminal fragment of streptococcal M protein elicits protective antibodies and is an attractive vaccine target. However, this N‐ terminal fragment is hypervariable: there are more than 200 different M types. In this study, an intranasal live bacterial vaccine comprising 10 strains of Lactococcus lactis, each expressing one N‐terminal fragment of M protein, has been developed. Live bacterial‐vectored vaccines cost less to manufacture because the processes involved are less complex than those required for production of protein subunit vaccines. Moreover, intranasal administration does not require syringes or specialized personnel. Evaluation of individual vaccine types (M1, M2, M3, M4, M6, M9, M12, M22, M28 and M77) showed that most of them protected mice against challenge with virulent S. pyogenes. All 10 strains combined in a 10‐valent vaccine (M×10) induced serum and bronchoalveolar lavage IgG titers that ranged from three‐ to 10‐fold those of unimmunized mice. After intranasal challenge with M28 streptococci, survival of M×10‐immunized mice was significantly higher than that of unimmunized mice. In contrast, when mice were challenged with M75 streptococci, survival of M×10‐immunized mice did not differ significantly from that of unimmunized mice. Mx‐10 immunized mice had significantly less S. pyogenes in oropharyngeal washes and developed less severe disease symptoms after challenge than did unimmunized mice. Our L. lactis‐based vaccine may provide an alternative solution to development of broadly protective group A streptococcal vaccines.
Association of the hypha‐related protein Pra1 and zinc transporter Zrt1 with biofilm formation by the pathogenic yeast Candida albicans
Authors: Kurakado Sanae , Arai Rika , Sugita Takashi
Published: April 2018

Bloodstream infection by the pathogenic fungus Candida albicans is a major health problem. Candidemia is often associated with medical devices, which can act as substrates for biofilm development. Biofilm‐related infections are relatively difficult to treat because of their resistance to antimicrobial agents. It is therefore important to explore the mechanisms of biofilm formation. Dimorphism is a major contributor to biofilm formation in C. albicans. To determine whether the hypha‐related proteins Pra1 (pH‐regulated antigen) and Zrt1 (zinc transporter) are responsible for biofilm formation, the ability of pra1 and zrt1 deletion mutants to form biofilms was investigated. Biofilm formation by both deletion mutants was less than that of the wild‐type strain. Because Pra1 and Zrt1 are also related to the zinc homeostasis system, the effects of adding zinc on biofilm formation were also examined. Biofilm formation was increased in the presence of zinc. These data suggest that Pra1 and Zrt1 regulate biofilm formation through zinc homeostasis.
Transcytosis of Junonia coenia densovirus VP4 across the gut epithelium of Spodoptera frugiperda (Lepidoptera: Noctuidae)
Authors: Kemmerer Mariah , Bonning Bryony C.
Published: April 2018

The Junonia coenia densovirus rapidly traverses the gut epithelium of the host lepidopteran without replicating in the gut cells. The ability of this virus to transcytose across the gut epithelium is of interest for the potential use of virus structural proteins as delivery vehicles for insecticidal peptides that act within the insect hemocoel, rather than in the gut. In this study, we used fall armyworm, Spodoptera frugiperda to examine the binding of the virus to brush border membrane vesicle proteins by two‐dimensional ligand blot analysis. We also assessed the rate of flux of the primary viral structural protein, VP4 fused to eGFP with a proline‐rich linker (VP4‐P‐eGFP) through the gut epithelium ex vivo in an Ussing chamber. The mechanisms involved with transcytosis of VP4‐P‐eGFP were assessed by use of inhibitors. Bovine serum albumin (BSA) and eGFP were used as positive and negative control proteins, respectively. In contrast to BSA, which binds to multiple proteins on the brush border membrane, VP4‐P‐eGFP binding was specific to a protein of high molecular mass. Protein flux was significantly higher for VP4‐P‐eGFP after 2 h than for albumin or eGFP, with rapid transcytosis of VP4‐P‐eGFP within the first 30 min. In contrast to BSA which transcytosed following clathrin‐mediated endocytosis, the movement of VP4‐P‐eGFP was vesicle‐mediated but clathrin‐independent. The specificity of binding combined with the efficiency of transport across the gut epithelium suggest that VP4 will provide a useful carrier for insecticidal peptides active within the hemocoel of key lepidopteran pests including S. frugiperda.
dispRity: A modular R package for measuring disparity
Authors: Guillerme Thomas
Published: April 2018

Biological data is multivariate in essence: many traits in organisms covary with each other in space and time. This causes biologists to either reduce these to a manageable number of variables or, increasingly, to use multivariate toolkits. One such toolkit is based on creating a multidimensional space where the variables are the axes. It is then possible to measure diverse aspects of the distribution of some observation (e.g. species) in this space. For example, if studying morphology, one can create a morphospace for two groups of species, measure the volume occupied by each of these groups and then test whether these two volumes are significantly different or not.

There are as many definitions of these multidimensional spaces, metrics and tests as there are questions that can be tackled with such methods. Many of these methods are implemented in specific software or r packages. However, the definition of the space, metric and test is often dependent on the software/package and authors points of view or specific questions. This can unfortunately hamper researchers’ ability to apply different methods that best suits their specific questions.

Here I present the dispRity package, a flexible R package for performing multidimensional analysis. It allows users to define each step of the analysis (whether it is the space, the metric or the test) through a highly modular architecture where each definition can be passed as a function. It also provides a tidy interface through the dispRity object, allowing users to easily run reproducible multivariate analysis.

The dispRity package also comes with an extend manual regularly updated following users’ questions or suggestions. Furthermore, the package contains some simulation tools (e.g to simulate complex multidimensional space or morphological data). Finally, it also contains a suite of utility functions to work with dispRity objects aimed at helping users to develop their own multidimensional metrics and/or tests.
Physiological role of Kvβ2 (AKR6) in murine skeletal muscle growth and regulation
Authors: Chapalamadugu K. C. , Tur J. , Badole S. L. , Kukreja R. C. , Brotto M. , Tipparaju S. M.
Published: April 2018

Aim

Potassium channel accessory subunits (Kvβ) play a key role in cardiac electrical activity through ion channel modulation. In this study, we hypothesize that Kvβ2 regulates skeletal muscle growth and fibre phenotype via protein‐protein interactions.

Methods

Kvβ2 knockout mouse model was used for morphometric, immunohistochemical and biochemical analysis to evaluate the role of Kvβ2 in skeletal muscle physiology.

Results

Deletion of Kvβ2 gene in mice (Kvβ2 knockout, KO) leads to significant decrease in body weight along with skeletal muscle size. Key hindlimb muscles such as biceps, soleus and gastrocnemius were significantly smaller in size in KO mice compared to that of wild type. Morphometric measurements and histological analysis clearly point that the fibre size is decreased in each of the muscle type in KO compared with wild‐type mice. In addition, Kvβ2 deletion contributes to fibre‐type switching from fast to slow fibre as indicated by more abundant MHCI‐expressing fibres in gastrocnemius and soleus muscles, which may underscore the smaller muscle size alongside increase in U3 ubiquitin ligase; NEDD4 expression. Using targeted siRNA knockdown approach, we identified that Kvβ2 knockdown does not affect the myoblasts proliferation. However, Pax7 expression was significantly decreased in 4‐week‐old gastrocnemius muscle, suggesting that cellular reserve for growth may be deficient in KO mice. This is further supported by decreased migratory capacity of C2C12 cells upon siRNA‐targeted Kvβ2 knockdown.

Conclusion

Overall, this is the first report identifying that genetic deletion of Kvβ2 leads to decreased skeletal muscle size along with isotype switching.
Genotype‐guided warfarin dosing vs. conventional dosing strategies: a systematic review and meta‐analysis of randomized controlled trials
Authors: Tse Gary , Gong Mengqi , Li Guangping , Wong Sunny Hei , Wu William K. K. , Wong Wing Tak , Roever Leonardo , Lee Alex Pui Wai , Lip Gregory Y. H. , Wong Martin C. S. , Liu Tong ,   International Health Informatics Study (IHIS) Network
Published: April 2018

Aims

Previous trials on the effectiveness of genotype‐guided warfarin dosing vs. conventional dosing have been inconclusive. We conducted a systematic review and meta‐analysis of randomized trials comparing genotype‐guided to conventional dosing strategies.

Methods

PubMed and the Cochrane Library were searched up to 23 October 2017.

Results

A total of 76 and 94 entries were retrieved were retrieved from PubMed and the Cochrane Library, respectively. A total of 2626 subjects in the genotype‐guided dosing (mean age 63.3 ± 5.8 years; 46% male) and 2604 subjects in the conventional dosing (mean age 64.7 ± 6.1 years; 46% male) groups (mean follow‐up duration 64 days) from 18 trials were included. Compared with conventional dosing, genotype‐guided dosing significantly shortened the time to first therapeutic international normalized ratio (INR) (mean difference 2.6 days, standard error 0.3 days; P < 0.0001; I2 0%) and time to first stable INR (mean difference 5.9 days, standard error 2.0 days; P < 0.01; I2 94%). Genotype‐guided dosing also increased the time in therapeutic range (mean difference 3.1%, standard error 1.2%; P < 0.01; I2 80%) and reduced the risks of both excessive anticoagulation, defined as INR ≥4 [risk ratio (RR) 0.87; 95% confidence interval (CI) 0.78, 0.98; P < 0.05; I2: 0%), and bleeding (RR 0.82; 95% CI 0.69, 0.98; P < 0.05; I2 31%). No difference in thromboembolism (RR 0.84; 95% CI 0.56, 1.26; P = 0.40; I2 0%) or mortality (RR 1.16; 95% CI 0.46, 2.91; P = 0.76; I2 0%) was observed between the two groups.

Conclusions

Genotype‐guided warfarin dosing offers better safety with less bleeding compared with conventional dosing strategies. No significant benefit on thromboembolism or mortality was evident.
New insights on the functional role of URG7 in the cellular response to ER stress
Authors: Armentano Maria Francesca , Caterino Marianna , Miglionico Rocchina , Ostuni Angela , Pace Maria Carmela , Cozzolino Flora , Monti Maria , Milella Luigi , Carmosino Monica , Pucci Piero , Bisaccia Faustino
Published: April 2018

Background information

Up‐regulated Gene clone 7 (URG7) is an ER resident protein, whose expression is up‐regulated in the presence of hepatitis B virus X antigen (HBxAg) during HBV infection. In virus‐infected hepatocytes, URG7 shows an anti‐apoptotic activity due to the PI3K/AKT signalling activation, does not seem to have tumorigenic properties, but it appears to promote the development and progression of fibrosis. However, the molecular mechanisms underlying URG7 activity remain largely unknown.

Results

To shed light on URG7 activity, we first analysed its interactome in HepG2 transfected cells: this analysis suggests that URG7 could have a role in affecting protein synthesis, folding and promoting proteins degradation. Moreover, keeping into account its subcellular localisation in the ER and that several viral infections give rise to ER stress, a panel of experiments was performed to evaluate a putative role of URG7 in ER stress. Our main results demonstrate that in ER‐stressed cells URG7 is able to modulate the expression of Unfolded Protein Response (UPR) markers towards survival outcomes, up‐regulating GRP78 protein and down‐regulating the pro‐apoptotic protein CHOP. Furthermore, URG7 reduces the ER stress by decreasing the amount of unfolded proteins, by increasing both the total protein ubiquitination and the AKT activation and reducing Caspase 3 activation.

Conclusions

All together these data suggest that URG7 plays a pivotal role as a reliever of ER stress‐induced apoptosis.

Significance

This is the first characterisation of URG7 activity under ER stress conditions. The results presented here will help to hypothesise new strategies to counteract the antiapoptotic activity of URG7 in the context of the viral infection.