bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes
Authors: Jordan Katherine W. , He Fei , de Soto Monica Fernandez , Akhunova Alina , Akhunov Eduard
Published: May 2020

Background

We have a limited understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes. Using a differential nuclease sensitivity (DNS) assay, we investigated the chromatin states in the coding and transposon element (TE) -rich repetitive regions of the allopolyploid wheat genome.

Results

We observed a negative chromatin accessibility gradient along the telomere-centromere axis with mostly open and closed chromatin located in the distal and pericentromeric regions of chromosomes, respectively. This trend was mirrored by the TE-rich intergenic regions, but not by the genic regions, which showed similar averages of chromatin accessibility levels along the chromosomes. The genes’ proximity to TEs was negatively associated with chromatin accessibility. The chromatin states of TEs was dependent on their type, proximity to genes, and chromosomal position. Both the distance between genes and TE composition appear to play a more important role in the chromatin accessibility along the chromosomes than chromosomal position. The majority of MNase hypersensitive regions were located within the TEs. The DNS assay accurately predicted previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within closed chromatin.

Conclusions

The chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.
CHOP-c-JUN complex plays a critical role in liver proteotoxicity induced by mutant Z alpha-1 antitrypsin
Authors: Attanasio Sergio , Gernoux Gwladys , Ferriero Rosa , De Cegli Rossella , Carissimo Annamaria , Nusco Edoardo , Campione Severo , Teckman Jeffrey , Mueller Christian , Piccolo Pasquale , Brunetti-Pierri Nicola
Published: May 2020

Alpha-1 antitrypsin (AAT) deficiency is a common genetic disorder with lung and liver involvement. Most patients carry the Z allele inSERPINA1that encodes a mutant AAT (ATZ) forming hepatotoxic polymers. We foundCHOPupregulation and activation in both mouse (PiZ) and human livers expressing ATZ. Compared to controls, juvenile PiZ/Chop-/-mice showed reduction in hepatic ATZ and transcriptional response to endoplasmic reticulum stress, as consequence of CHOP-mediated increase ofSERPINA1transcription. CHOP was found to upregulateSERPINA1though binding with c-JUN onSERPINA1regulatory elements, thus aggravating hepatic accumulation of ATZ. IncreasedCHOPlevels were detected in diseased livers of children homozygous for the Z allele.

Compared to adults, AAT deficiency in infants has different severity and prognosis. Based on our findings, CHOP-c-JUN complex upregulatesSERPINA1transcription and play an important role in the hepatic disease pathogenesis by increasing the burden of proteotoxic ATZ, particularly in the pediatric population.
Syndecan 2 regulates hematopoietic lineages and infection resolution in zebrafish
Authors: Lamichhane Bhawika Sharma , Bisgrove Brent W. , Su Yi-Chu , Demarest Bradley L. , Yost H. Joseph
Published: May 2020

Syndecan 2 (Sdc2) is a transmembrane cell-surface heparan sulfate proteoglycan (HSPG) that has been implicated in the regulation of cell-cell signaling pathways and cell-matrix interactions. Surprisingly, homozygous recessive maternal zygotic (MZ)sdc2null mutants in zebrafish appear to have normal development, normal morphology and are viable and fertile in adulthood. Whole transcriptome RNA sequencing, FACS analyses, and imaging of transgenic reporter lines that distinguish specific hematopoietic lineages revealed thatsdc2mutants have defects in the specification and proportions of red blood cells and neutrophils that initiate during embryonic hematopoiesis and likely persist through adulthood. During bacterial infections, MZsdc2mutants have markedly reduced neutrophil recruitment and significantly higher death rates. Hematopoietic stem/progenitor cell (HSPC) numbers are also significantly reduced in MZsdc2mutants. In zebrafish, cells that bud off of the ventral region of somites are thought to give rise to the reticular stromal cells of the caudal hematopoietic tissue (CHT) stem cell niche. In MZsdc2mutants, these budding cells have abberant blebbing morphology associated with widespread apoptosis during induction of HSPCs and with changes in the vascularization and stromal cell structure of the CHT stem cell niche. This suggests that loss ofsdc2disrupts the earliest events of definitive hematopoiesis. Our findings of hematopoietic defects, nascent immune system alterations and inability to resolve infection insdc2mutants sets the stage for examining the roles of HSPG genes in a wide range of hematopoietic and immune defects in humans.

Key Points

Syndecan 2 regulates the formation of Hematopoietic Stem/Progenitor Cells, differentiation into hematopoietic populations and the CHT architecture

Syndecan 2 mutants are significantly more susceptible to bacterial infection
TheVibrio choleraequorum-sensing protein VqmA integrates cell density, environmental, and host-derived cues into the control of virulence
Authors: Mashruwala Ameya A. , Bassler Bonnie L.
Published: May 2020

Scientific Abstract

Quorum sensing is a chemical communication process in which bacteria use the production, release, and detection of signal molecules called autoinducers to orchestrate collective behaviors. The human pathogenVibrio choleraerequires quorum sensing to infect the small intestine. There,V. choleraeencounters the absence of oxygen and the presence of bile. We show that these two stimuli differentially affect quorum sensing function and, in turn,V. choleraepathogenicity. The quorum-sensing receptor-transcription factor called VqmA, that detects the autoinducer called DPO, also detects the lack of oxygen and the presence of bile. Detection occurs via DPO-, oxygen-, bile-, and redox-responsive disulfide bonds that alter VqmA DNA binding activity. We propose that VqmA serves as an information processing hub that integrates quorum- sensing information, redox status, the presence or absence of oxygen, and host cues. In response to the information acquired through this mechanism,V. choleraeappropriately modulates its virulence output.

Lay Abstract

Quorum sensing (QS) is a process of chemical communication bacteria use to orchestrate collective behaviors. QS communication relies on chemical signal molecules called autoinducers. QS regulates virulence inVibrio cholerae, the causative agent of the disease cholera. Transit into the human small intestine, the site of cholera infection, exposesV. choleraeto the host environment. In this study, we show that the combination of two stimuli encountered in the small intestine, the absence of oxygen and the presence of host-produced bile, impinge onV. choleraeQS function and, in turn, pathogenicity. We suggest that possessing a QS system that is responsive to multiple environmental, host, and cell density cues enablesV. choleraeto fine-tune its virulence capacity in the human intestine.
Leish-ExP: a database of exclusive proteins fromLeishmaniaparasite
Authors: Das Aneesha , Biswas Nupur , Chakrabarti Saikat
Published: May 2020

Leishmaniasis is a complex disease caused by different species of genusLeishmania, which affects millions of people spanning over 88 countries causing extensive mortality and morbidity. Leishmaniasis exists in three clinical forms; cutaneous, mucocutaneous and visceral. Anti-leishmanial therapy is one of the challenging fields due to the presence of wide range ofLeishmaniaspecies and host response against the pathogenic infection. Clinical survey reveals toxicity of drugs and trial compounds causing death among patients and predominant resistance to different class of antimonials among the leishmaniasis patient. Identification of appropriate target protein is a primary and important phase of drug development andLeishmaniais a suitable system for targeted drug development as it branched out quite early from the higher eukaryotes like human. With the advancement of genomic era and availability of whole genome sequences ofLeishmaniaspecies, relevant information on their respective genes and proteins are now easily extracted. Hence, in the current study, to aid the targeted drug therapy, an exhaustive whole genome scale comparative sequence analysis was performed to identify genes/proteins exclusive toLeishmania. Subsequently, further filtration was employed to identify the individualLeishmaniaspecies specific gene/proteins. Among such proteins, a considerable number was found to have no recognizable structure and functions. Hence, efforts were taken to characterize theseLeishmaniaexclusive gene/proteins via providing additional sequence, structure, localization and functional information. All the information about each of theseLeishmaniaexclusive gene/proteins from five differentLeishmaniaspecies has been systemically categorized and represented in the form a user-friendly database calledLeish-ExP, which is freely available athttp://www.hpppi.iicb.res.in/Leish-ex.
IDENTIFICATION AND CHARACTERIZATION OF A LARGE SOURCE OF PRIMARY MESENCHYMAL STEM CELLS TIGHTLY ADHERED TO BONE SURFACES OF HUMAN VERTEBRAL BODY MARROW CAVITIES
Authors: Johnstone Brian H. , Miller Hannah M. , Beck Madelyn R. , Gu Dongsheng , Thirumala Sreedhar , LaFontaine Michael , Brandacher Gerald , Woods Erik J.
Published: May 2020

Therapeutic allogeneic mesenchymal stem/stromal cells (MSC) are currently in clinical trials for evaluating their effectiveness in treating many different disease indications. Eventual commercialization for broad distribution will require further improvements in manufacturing processes to economically manufacture MSC at sufficient scales required to satisfy projected demands. A key contributor to the present high cost of goods (COG) for MSC manufacturing is the need to create master cell banks (MCBs) from multiple donors, which leads to variability in large-scale manufacturing runs. Therefore, the availability of large single donor depots of primary MSC would greatly benefit the cell therapy market by reducing costs associated with manufacturing.

We have discovered that an abundant population of cells possessing all the hallmarks of MSC is tightly associated with the vertebral body (VB) bone matrix and are only liberated by proteolytic digestion. Here we demonstrate that these vertebral bone-adherent (vBA) MSC possess all the International Society of Cell and Gene Therapy (ISCT)-defined characteristics (e.g., plastic adherence, surface marker expression, and trilineage differentiation) of MSC and, therefore, have termed them vBA-MSC, to distinguish this population from loosely associated MSC recovered through aspiration or rinsing of the bone marrow (BM) compartment.

Pilot banking and expansion was performed with vBA-MSC obtained from 3 deceased donors and it was demonstrated that bank sizes averaging 2.9×108± 1.35×108vBA-MSC at passage one were obtainable from only 5 g of digested VB bone fragments. Each bank of cells demonstrated robust proliferation through a total of 9 passages without significant reduction in population doubling times. The theoretical total cell yield from the entire amount of bone fragments (approximately 300g) from each donor with limited expansion through 4 passages is 100 trillion (1×1014) vBA-MSC, equating to over 105doses at 10×106cells/kg for an average 70 kg recipient. Thus, we have established a novel and plentiful source of MSC which will benefit the cell therapy market by overcoming manufacturing and regulatory inefficiencies due to donor-to-donor variability.
Tyrosine kinase inhibitors induce mitochondrial dysfunction during cardiomyocyte differentiation through alteration of GATA4-mediated networks
Authors: Liu Qing , Wu Haodi , Luo Qing-Jun , Jiang Chao , Duren Zhana , Van Bortle Kevin , Zhao Ming-tao , Zhao Bingqing , Liu Jun , Marciano David P , Lee-McMullen Brittany , Zhu Chenchen , Narasimha Anil M , Gruber Joshua J , Lipchik Andrew M , Guo Hongchao , Watson Nathaniel K , Tsai Ming-Shian , Furihata Takaaki , Tian Lei , Wei Eric , Li Yingxin , Steinmetz Lars M , Wong Wing Hung , Kay Mark A. , Wu Joseph C , Snyder Michael P
Published: May 2020

Maternal drug exposure during pregnancy increases the risks of developmental cardiotoxicity, leading to congenital heart defects (CHDs). In this study, we used human stem cells as anin-vitrosystem to interrogate the mechanisms underlying drug-induced toxicity during cardiomyocyte differentiation, including anticancer tyrosine kinase inhibitor (TKI) drugs (imatinib, sunitinib, and vandetanib). H1-ESCs were treated with these drugs at sublethal levels during cardiomyocyte differentiation. We found that early exposure to TKIs during differentiation induced obvious toxic effects in differentiated cardiomyocytes, including disarranged sarcomere structure, interrupted Ca2+-handling, and impaired mitochondrial function. As sunitinib exposure showed the most significant developmental cardiotoxicity of all TKIs, we further examine its effect with in-vivo experiments. Maternal sunitinib exposure caused fetal death, bioaccumulation, and histopathologic changes in the neonatal mice. Integrative analysis of both transcriptomic and chromatin accessibility landscapes revealed that TKI-exposure altered GATA4-mediated regulatory network, which included key mitochondrial genes. Overexpression of GATA4 with CRISPR-activation restored morphologies, contraction, and mitochondria function in cardiomyocytes upon TKI exposure early during differentiation. Altogether, our study identified a novel crosstalk mechanism between GATA4 activity and mitochondrial function during cardiomyocyte differentiation, and revealed potential therapeutic approaches for reducing TKI-induced developmental cardiotoxicity for human health.

Highlights

Early-stage exposure to TKIs induced cardiotoxicity and mitochondrial dysfunction

GATA4 transcriptional activity is inhibited by TKIs

Network analysis reveals interactions between GATA4 and mitochondrial genes

GATA4-overexpression rescues cardiomyocytes and mitochondria from TKI exposure
Allele-specific alternative splicing in human tissues
Authors: Amoah Kofi , Hsiao Yun-Hua Esther , Bahn Jae Hoon , Sun Yiwei , Burghard Christina , Tan Boon Xin , Yang Ei-Wen , Xiao Xinshu
Published: May 2020

Alternative splicing is an RNA processing mechanism that affects most genes in human, contributing to disease mechanisms and phenotypic diversity. The regulation of splicing involves an intricate network of cis-regulatory elements and trans-acting factors. Due to their high sequence specificity, cis-regulation of splicing can be altered by genetic variants, significantly affecting splicing outcomes. Recently, multiple methods have been applied to understanding the regulatory effects of genetic variants on splicing. However, it is still challenging to go beyond apparent association to pinpoint functional variants. To fill in this gap, we utilized large-scale datasets of the Genotype-Tissue Expression (GTEx) project to study genetically-modulated alternative splicing (GMAS) via identification of allele-specific splicing events. We demonstrate that GMAS events are shared across tissues and individuals more often than expected by chance, consistent with their genetically driven nature. Moreover, although the allelic bias of GMAS exons varies across samples, the degree of variation is similar across tissues vs. individuals. Thus, genetic background drives the GMAS pattern to a similar degree as tissue-specific splicing mechanisms. Leveraging the genetically driven nature of GMAS, we developed a new method to predict functional splicing-altering variants, built upon a genotype-phenotype concordance model across samples. Complemented by experimental validations, this method predicted >1000 functional variants, many of which may alter RNA-protein interactions. Lastly, 72% of GMAS-associated SNPs were in linkage disequilibrium with GWAS-reported SNPs, and such association was enriched in tissues of relevance for specific traits/diseases. Our study enables a comprehensive view of genetically driven splicing variations in human tissues.
Single Cell RNA Profiling Reveals Adipocyte to Macrophage Signaling Sufficient to Enhance Thermogenesis
Authors: Henriques Felipe , Bedard Alexander H. , Guilherme Adilson , Kelly Mark , Chi Jingyi , Zhang Peng , Lifshitz Lawrence M. , Bellvé Karl , Rowland Leslie , Yenilmez Batuhan , Kumar Shreya , Wang Yetao , Luban Jeremy , Weinstein Lee S. , Lin Jiandie D. , Cohen Paul , Czech Michael P.
Published: May 2020

The “browning” of inguinal white adipose tissue (iWAT) through increased abundance of thermogenic beige/brite adipocytes is induced by cold exposure and many other perturbations in association with beneficial systemic metabolic effects. Adipose browning is reported to require activation of sympathetic nerve fibers (SNF), aided by alternately activated macrophages within iWAT. Here we demonstrate the first example of a non-cell autonomous pathway for iWAT browning that is fully independent of SNF activity. Thus, the strong induction of thermogenic adipocytes prompted by deletion of adipocyte fatty acid synthase (iAdFASNKO mice) was unaffected by denervation or the deletion of SNF modulator Neuregulin-4. However, browning of iWAT in iAdFASNKO mice does require adipocyte cAMP/protein kinase A signaling, as it was blocked in adipocyte- selective Fasn/Gsα double KO mice. Single-cell transcriptomic analysis of iAdFASNKO mouse adipose stromal cells revealed increased macrophages displaying gene expression signatures of the alternately activated type. Mechanistically, depletion of such phagocytic immune cells in iAdFASNKO mice fully abrogated appearance of thermogenic adipocytes in iWAT. Altogether, these findings reveal an unexpected pathway of cAMP/PKA-dependent iWAT browning that is initiated by adipocyte signals and caused by macrophage-like cells independent of sympathetic neuron involvement.
Heritable functional architecture in human visual cortex
Authors: Alvarez Ivan , Finlayson Nonie J. , Ei Shwe , de Haas Benjamin , Greenwood John A. , Schwarzkopf D. Samuel
Published: May 2020

How much of the functional organization of our visual system is inherited? Here we tested the heritability of retinotopic maps in human visual cortex using functional magnetic resonance imaging. We demonstrate that retinotopic organization shows a closer correspondence in monozygotic (MZ) compared to dizygotic (DZ) twin pairs, suggesting a partial genetic determination. Using population receptive field (pRF) analysis to examine the preferred spatial location and selectivity of these neuronal populations, we estimate a heritability around 30% for polar angle preferences and spatial selectivity, as quantified by pRF size, in extrastriate areas V2 and V3. Our findings are consistent with heritability in both the macroscopic arrangement of visual regions and stimulus tuning properties of visual cortex. This could constitute a neural substrate for variations in a range of perceptual effects, which themselves have been found to be at least partially genetically determined. These findings also add convergent evidence for the hypothesis that functional map topology is linked with cortical morphology.

Highlights

We analyzed retinotopic maps from monozygotic and dizygotic twin pairs

Visual field maps in V1-V3 are more similar in monozygotic twins

Heritability is greater in V1 and V3 for polar angle and population receptive field sizes

Eccentricity maps show lesser degree of heritability

Further evidence for link between cortical morphology and topology of retinotopic maps

Graphical Abstract
Epigenetic modulation reveals differentiation state specificity of oncogene addiction
Authors: Khaliq Mehwish , Manikkam Mohan , Martinez Elisabeth D. , Fallahi-Sichani Mohammad
Published: May 2020

Hyperactivation of the MAPK signaling pathway motivates the clinical use of MAPK inhibitors for BRAF-mutant melanomas. Heterogeneity in differentiation state due to epigenetic plasticity, however, results in cell-to-cell variability in the state of MAPK dependency, diminishing the efficacy of MAPK inhibitors. To identify key regulators of such variability, we screened 276 epigenetic-modifying compounds, individually or combined with MAPK inhibitors, across genetically diverse and isogenic populations of melanoma cells. Following single-cell analysis and multivariate modeling, we identified three classes of epigenetic inhibitors that target distinct epigenetic states associated with either one of the lysine-specific histone demethylases KDM1A or KDM4B, or BET bromodomain proteins. While melanocytes remained insensitive, the anti-tumor efficacy of each inhibitor was predicted based on melanoma cells’ differentiation state and MAPK activity. Our systems pharmacology approach highlights a path toward identifying actionable epigenetic factors that extend the BRAF oncogene addiction paradigm on the basis of tumor cell differentiation state.
Change in terrestrial human footprint drives continued loss of intact ecosystems
Authors: Williams Brooke A. , Venter Oscar , Allan James R. , Atkinson Scott C. , Rehbein Jose A. , Ward Michelle S. , Marco Moreno Di , Grantham Hedley S. , Ervin Jamison , Goetz Scott , Hansen Andrew J. , Jantz Patrick , Pillay Rajeev , Rodríguez-Buriticá Susana , Supples Christina , Virnig Anne L. S. , Watson James E.M.
Published: May 2020

Our ability to map humanity’s influence across Earth has evolved, thanks to powerful computing, a network of earth observing satellites, and new bottom-up census and crowd-sourced data. Here, we provide the latest temporally inter-comparable maps of the terrestrial Human Footprint, and assessment of change in human pressure at global, biome, and ecoregional scales. In 2013, 42% of terrestrial Earth could be considered relatively free of anthropogenic disturbance, and 25% could be classed as ‘wilderness’ (the least degraded end of the human footprint spectrum). Between 2000 and 2013, 1.9 million km2- an area the size of Mexico - of land relatively free of human disturbance became highly modified. The majority of this occurred within tropical and subtropical grasslands, savannah, and shrubland ecosystems, but the rainforests of Southeast Asia also underwent rapid modification. Our results show that humanity’s footprint is eroding Earth’s last intact ecosystems, and greater efforts are urgently needed to retain them.
Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model
Authors: Miyoshi Jun , Lee Sonny T. M. , Kennedy Megan , Puertolas Mora , Frith Mary , Koval Jason C. , Miyoshi Sawako , Antonopoulos Dionysios A. , Leone Vanessa , Chang Eugene B.
Published: May 2020

Background & Aims

Inflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts.

Methods

Using the IL-10 gene-deficient (IL-10 KO) murine model where early life dysbiosis from antibiotic (cefoperozone, CPZ) treated dams vertically-transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to eventual clinical outcomes.

Results

Compared to controls, offspring acquiring maternal CPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership both in bacteriome and mycobiome that were associated with alterations in specific functional subsystems. Furthermore, among IL-10 KO offspring from CPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome.

Conclusions

Our findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD.

Synopsis

Currently, predictive markers for the development and course of inflammatory bowel diseases (IBD) are not available. This study supports the notion that gut microbiome metagenomic profiles could be developed into a useful tool to assess risk and manage human IBD.
High resolution imaging of nascent mitochondrial protein synthesis in cultured human cells
Authors: Zorkau Matthew , Albus Christin A , Berlinguer-Palmini Rolando , Chrzanowska-Lightowlers Zofia MA , Lightowlers Robert N.
Published: May 2020

Human mitochondria contain their own genome, mtDNA, that is expressed in the mitochondrial matrix. This genome encodes thirteen vital polypeptides that are components of the multi-subunit complexes that couple oxidative phosphorylation (OXPHOS). The inner mitochondrial membrane that houses these complexes comprises the inner boundary membrane that runs parallel to the outer membrane, infoldings that form the cristae membranes, and the cristae junctions that separate the two. It is in these cristae membranes that the OXPHOS complexes have been shown to reside in various species. The majority of the OXPHOS subunits are nuclear-encoded and must therefore be imported from the cytosol through the outer membrane at contact sites with the inner boundary membrane. As the mitochondrially-encoded components are also integral members of these complexes, where does nascent protein synthesis occur? Transcription, mRNA processing, maturation and at least part of the mitoribosome assembly process occur at the nucleoid and the spatially juxtaposed mitochondrial RNA granules, is protein synthesis also performed at the RNA granules close to these entities, or does it occur distal to these sites ? We have adapted a click chemistry based method, coupled with STED nanoscopy to address these questions. We report that in human cells in culture, within the limits of our methodology, the majority of mitochondrial protein synthesis occurs at the cristae membranes and is spatially separated from the sites of RNA processing and maturation.
On the functional annotation of open-channel structures in the glycine receptor
Authors: Cerdan Adrien Henri , Cecchini Marco
Published: May 2020

The glycine receptor (GlyR) is by far the best-characterized pentameric ligand-gated ion channel with several high-resolution structures from X-ray crystallography, cryo-EM and modeling. Nonetheless, the significance of the currently available open-pore conformations is debated due to their diversity in the pore geometry. Here, we discuss the physiological significance of existing models of the GlyR active state based on conductance and selectivity measurements by computational electrophysiology. The results support the conclusion that the original cryo-EM reconstruction of the active state obtained in detergents as well as its subsequent refinement by Molecular Dynamics simulations are likely to be non-physiological as they feature artificially dilated ion pores. In addition, the calculations indicate that a physiologically relevant open pore configuration should be constricted within a radius of 2.5 and 2.8Å, which is consistent with previous modeling, electrophysiology measurements, and the most recent cryo-EM structures obtained in a native lipid-membrane environment.
Structures of microRNA-precursor apical junctions and loops reveal non-canonical base pairs important for processing
Authors: Shoffner Grant M. , Peng Zhixiang , Guo Feng
Published: May 2020

Metazoan pri-miRNAs and pre-miRNAs fold into characteristic hairpins that are recognized by the processing machinery. Essential to the recognition of these miR-precursors are their apical junctions where double-stranded stems meet single-stranded hairpin loops. Little is known about how apical junctions and loops fold in three-dimensional space. Here we developed a scaffold-directed crystallography method and determined the structures of eight human miR-precursor apical junctions and loops. Six structures contain non-canonical base pairs stacking on top of the hairpin stem. U-U pair contributes to thermodynamic stability in solution and is highly enriched at human miR-precursor apical junctions. Our systematic mutagenesis shows that U-U is among the most efficiently processed variants. The RNA-binding heme domain of pri-miRNA-processing protein DGCR8 binds longer loops more tightly and non-canonical pairs at the junction appear to modulate loop length. Our study provides structural and biochemical bases for understanding miR-precursors and molecular mechanisms of microRNA maturation.
Extrapolating acute bee sensitivity to insecticides using a phylogenetically informed interspecies scaling framework
Authors: Pamminger Tobias
Published: May 2020

Plant protection products, including insecticides, are important for global food production. Historically, research of the adverse effects of insecticides on bees has focused on the honeybee (Apis mellifera), while non-Apisbee species remained understudied. Consequently, sensitivity assessment of insecticides for the majority of bees is lacking, which in turn hinders accurate risk characterization and consequently bee protection. Interspecies sensitivity extrapolation based on body weight offers a potential solution to this problem, but in the past such approaches have often ignored the phylogenetic background and consequently non independence of species used in such models. Using published data on the sensitivity of different bee species to commonly used insecticides, their body weight and phylogenetic background I build interspecies scaling models (ISMs) applying a phylogenetically informed framework. In addition, I compared, the relative sensitivity of the standard test speciesApis melliferato other bee species to evaluate their protectiveness when used as standards screening bee species in the risk assessment process. I found that overall 1) body weight is a predictor of bee sensitivity to insecticides for a range of insecticide classes and 2)A.melliferais the most sensitive standard test species currently available and consequently a suitable surrogate species for ecotoxicological risk assessment.
Targeted bisulfite sequencing: A novel tool for the assessment of DNA methylation with high sensitivity and increased coverage
Authors: Moser D.A. , Müller S. , Hummel E.M. , Limberg A.S. , Dieckmann L. , Frach L. , Pakusch J. , Flasbeck V , Brüne M. , Beygo J. , Klein-Hitpass L. , Kumsta R.
Published: May 2020

DNA methylation analysis is increasingly used in stress research. Available methods are expensive, laborious and often limited by either the analysis of short CpG stretches or low assay sensitivity. Here, we present a cost-efficient next generation sequencing-based strategy for the simultaneous investigation of multiple candidate genes in large cohorts. To illustrate the method, we present analysis of four candidate genes commonly assessed in psychoneuroendocrine research:Glucocorticoid receptor(NR3C1), Serotonin transporter (SLC6A4), FKBP Prolyl isomerase 5 (FKBP5), and theOxytocin receptor(OXTR).

DNA methylation standards and DNA of a female and male donor were bisulfite treated in three independent trials and were used to generate sequencing libraries for 42 CpGs from theNR3C1 1Fpromoter region, 83 CpGs of theSLC6A45’ regulatory region, 5 CpGs located inFKBP5intron 7, and additional 12 CpGs located in a potential enhancer element in intron 3 of theOXTR. In addition, DNA of 45 patients with borderline personality disorder (BPD) and 45 healthy controls was assayed. Multiplex libraries of all samples were sequenced on a MiSeq system and analyzed for mean methylation values of all CpG sites using amplikyzer2 software.

Results indicated excellent accuracy of the assays when investigating replicates generated from the same bisulfite converted DNA, and very high linearity (R2> 0.9) of the assays shown by the analysis of differentially methylated DNA standards. Comparing DNA methylation between BPD and healthy controls revealed no biologically relevant differences.

The technical approach as described here facilitates targeted DNA methylation analysis and represents a highly sensitive, cost-efficient and high throughput tool to close the gap between coverage and precision in epigenetic research of stress-associated phenotypes.
Proteomic Investigation of the Signal Transduction Pathways Controlling Colistin Resistance inKlebsiella pneumoniae
Authors: Cheung Ching Hei Phoebe , Dulyayangkul Punyawee , Heesom Kate J. , Avison Matthew B.
Published: May 2020

Colistin resistance inKlebsiella pneumoniaeis predominantly caused by mutations that increase expression of thearn(also known aspbgorpmrF) operon. Expression is activated by the PhoPQ and PmrAB two-component systems. Constitutive PhoPQ activation occurs directly by mutation or following loss of MgrB. PhoPQ may also cross-activate PmrAB via the linker protein PmrD. Using proteomics, we show that MgrB loss causes a wider proteomic effect than direct PhoPQ activation, suggesting additional targets for MgrB. DifferentmgrBmutations cause different amounts of Arn protein production, which correlated with colistin MIC. Disruption ofphoPin anmgrBmutant had a reciprocal effect to direct activation of PhoQ in a wild-type background, but the regulated proteins showed almost total overlap. Disruption ofpmrDorpmrAslightly reduced Arn protein production in anmgrBmutant, but production was still high enough to confer colistin resistance; disruption ofphoPconferred wild-type Arn production and colistin MIC. Activation of PhoPQ directly, or throughmgrBmutation did not significantly activate PmrAB or PmrC production but direct activation of PmrAB by mutation did, and also activated Arn production and conferred colistin resistance. There was little overlap between the PmrAB and PhoPQ regulons. We conclude that under the conditions used for colistin susceptibility testing, PhoPQ-PmrD-PmrAB cross-regulation is not significant and that independent activation of PhoPQ or PmrAB is the main reason that Arn protein production increases above the threshold required for colistin resistance.
Direct evidence for decreased presynaptic inhibition evoked by PBSt group I muscle afferents after chronic SCI and recovery with step-training in the decerebrated rat
Authors: Caron Guillaume , Bilchak Jadwiga N. , Côté Marie-Pascale
Published: May 2020

Spinal cord injury (SCI) results in the disruption of supraspinal control of spinal networks and an increase in the relative influence of afferent feedback to sublesional neural networks, both of which contribute to enhancing spinal reflex excitability. Hyperreflexia occurs in ~75% of individuals with chronic SCI and critically hinders functional recovery and quality of life. It is suggested to result from an increase in motoneuronal excitability and a decrease in presynaptic and postsynaptic inhibitory mechanisms. In contrast, locomotor training decreases hyperreflexia by restoring presynaptic inhibition.

Primary afferent depolarization (PAD) is a powerful presynaptic inhibitory mechanism that selectively gates primary afferent transmission to spinal neurons to adjust reflex excitability and ensure smooth movement. However, the effect of chronic SCI and step-training on the reorganization of presynaptic inhibition evoked by hindlimb afferents, and the contribution of PAD has never been demonstrated. The objective of this study is to directly measure changes in presynaptic inhibition through dorsal root potentials (DRPs) and its association to plantar H-reflex inhibition. We provide direct evidence that H-reflex hyperexcitability is associated with a decrease in transmission of PAD pathways activated by PBSt afferents after chronic SCI. More precisely, we illustrate that PBSt group I muscle afferents evoke a similar pattern of inhibition onto both L4-DRPs and plantar H-reflexes evoked by the tibial nerve in Control and step-trained animals, but not in chronic SCI rats. These changes are not observed after step-training, suggesting a role for activity-dependent plasticity to regulate PAD pathways activated by flexor muscle group I afferents.

Key point summary

Presynaptic inhibition is modulated by supraspinal centers and primary afferents in order to filter sensory information, adjust spinal reflex excitability, and ensure smooth movements.

After SCI, the supraspinal control of primary afferent depolarization (PAD) interneurons is disengaged, suggesting an increased role for sensory afferents. While increased H-reflex excitability in spastic individuals indicates a possible decrease in presynaptic inhibition, it remains unclear whether a decrease in sensory-evoked PAD contributes to this effect.

We investigated whether the PAD evoked by hindlimb afferents contributes to the change in presynaptic inhibition of the H-reflex in a decerebrated rat preparation. We found that chronic SCI decreases presynaptic inhibition of the plantar H-reflex through a reduction in PAD evoked by PBSt muscle group I afferents.

We further found that step-training restored presynaptic inhibition of the plantar H-reflex evoked by PBSt, suggesting the presence of activity-dependent plasticity of PAD pathways activated by flexor muscle group I afferents.
Chromosomal arrangement of synthetic lethal gene pairs: repulsion or attraction?
Authors: Hosseini Sayed-Rzgar , Wadie Bishoy , Petsalaki Evangelia
Published: May 2020

Synthetic lethal interactions are of paramount importance both in biology and in medicine, and hence increasing efforts have been devoted to their systematic identification. Our previous computational analysis revealed that in prokaryotic species, synthetic lethal genes tend to be further away in chromosomes than random (i.e. repulsion), which was shown to provide bacterial genomes with greater robustness to large-scale DNA deletions. To test the generalizability of this observation in eukaryotic genomes, we leveraged the wealth of experimentally determined synthetic lethal genetic interactions of yeast that are curated in the BioGRID (Biological General Repository for Interaction Datasets) database. We observed an opposite trend that is the genomic proximity of synthetic lethal gene pairs both on the 2D and 3D chromosomal space of the yeast genome (i.e. 2D and 3D attraction). To gain mechanistic insights into the origin of the attraction of synthetic lethal gene pairs inS. cerevisiae, we characterized four classes of genes, in which synthetic lethal interactions are enriched and partly explain the observed patterns of genomic attraction: i) gene pairs operating on the same pathways, 2) co-expressed genes, 3) gene pairs whose protein products physically interact and 4) the paralogs. However, our analysis revealed that the contribution of these four types of genes is not sufficient to fully explain the observed 2D and 3D attraction of synthetic lethal gene pairs and hence its evolutionary origin still remains as an open question.

Significance statement

Unravelling the organizing principles underlying gene arrangements is one of the fundamental questions of research in evolutionary biology. One understudied aspect of this organization is the relative chromosomal arrangement of synthetic lethal gene pairs. In this study, by analyzing a wealth of synthetic lethality data in yeast, we provide evidence that synthetic lethal gene pairs tend to be attracted to each other both on 2D and 3D chromosomal space of the yeast genome. This observation is in sharp contrast with the repulsion of synthetic lethal (metabolic) gene pairs that we observed previously in bacterial genomes. Characterizing the evolutionary forces underlying this genomic pattern in yeast can open the door towards an evolutionary theory of genome organization in eukaryotes.
Optimization of crystallization of biological macromolecules using dialysis combined with temperature control
Authors: Junius Niels , Vahdatahar Elham , Oksanen Esko , Ferrer Jean-Luc , Budayova-Spano Monika
Published: May 2020

A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone – which is the optimal location for slow and ordered crystal expansion – by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant–concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.
Equatorial aberration of powder diffraction data collected with an Si strip X-ray detector by a continuous-scan integration method
Authors: Ida Takashi
Published: May 2020

Exact and approximate mathematical formulas of equatorial aberration for powder diffraction data collected with an Si strip X-ray detector in continuous-scan integration mode are presented. An approximate formula is applied to treat the experimental data measured with a commercial powder diffractometer.
Heterogeneity in consumer preferences for ready-to-eat pomegranate: an empirical study in Italy
Authors: Stiletto Alice , Giampietri Elisa , Trestini Samuele
Published: May 2020

Purpose

The present study aims at analysing consumer preferences for the pomegranate fruit, focussing on the effect of ready-to-eat format (i.e. packaged arils) on the purchasing choice, together with several products’ attributes as the origin, the packaging typology and the price.

Design/methodology/approach

The paper presents a choice experiment (CE) among 626 Italian consumers from Veneto region through an online survey. The study estimates both a conditional logit (CL) and a latent class logit model (LCM).

Findings

By segmenting the sample based on the heterogeneous preferences of consumers, it can distinguish “eco-friendly consumers”, “time-saving lovers”, “nationalists” and “price sensitive” subjects. Interestingly, the marginal willingness to pay for ready-to-eat arils is positive for the “time-saving lovers” that are mainly young consumers. The Italian origin has always a positive effect on the choice, whereas a negative effect is found for the price. Finally, the eco-friendly package has both a negative and a positive effect.

Research limitations/implications

The sample of this study is not representative of the population and the CE has a hypothetical nature. It follows that further research will link the economic analysis to a consumer test on a more representative sample.

Practical implications

This study can be useful for the pomegranate producers and the industry because it provides original evidence that could drive their business and marketing strategies, for instance, the preference for ready-to-eat arils.

Originality/value

This study is one of the first seeking to determine the factors that affect consumers' preferences for pomegranate arils.
Cocreating social innovations between an agro-food company and rice farmers in Taiwan: exploring the process mechanisms
Authors: Huang Chao-Chin
Published: May 2020

Purpose

While literature discussed value cocreation, most still has its focus from customer perspective, this study fills up this gap by focusing on supplier perspective. Second, prior works discussed the outcomes of cocreation; however, the process mechanisms are still under-explored, this study thus aims to explore these process mechanisms that drive value co-creation in the agro-food industry.

Design/methodology/approach

Case study is used as the method; specifically, six in-depth interviews on an agro-food company and its suppliers (i.e. farmers) are conducted, and data are analyzed using the grounded theory approach.

Findings

(1). Agro-food company and its rice suppliers invest different resource types and resource density, and the agro-food company is a main actor, i.e. resource investor and integrator; (2). While motivations of the agro-food company and farmers are different, they are mutually fit in the sustainability value; (3). Both parties share similar process mechanisms, i.e. co-production, senses of identification and trust, mutual interaction and information sharing and (4). Both parties thus have similar consequences, i.e. sustainability, codevelopment.

Originality/value

This study (1) proposes an innovative model of what and how values are cocreated, particularly in the agro-food industry; (2). uses three theories, i.e. input–process–output (I–P–O) model (McGrath and Kelly, 1986), service-dominant logic (SD-L) (Vargo and Lusch, 2004), cocreation design framework (Frow et al., 2015), to understand this phenomenon and thus demonstrates and enriches these three theories, particularly applied in the agro-food contexts; (3).offfers practical suggestions to agro-food firms and social enterprises, particularly those having food safety and environment issues.