bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nutrient parsimony shapes diversity and functionality in hyper-oligotrophic Antarctic soils
Authors: Van Goethem Marc W. , Vikram Surendra , Hopkins David W. , Hall Grant , Woodborne Stephan , Aspray Thomas J. , Hogg Ian D. , Cowan Don A. , Makhalanyane Thulani P. 
Published: February 2020

AbstractThe balance of nutrients in soil is critical for microbial growth and function, and stoichiometric values below the Redfield ratio for C:N:P can negatively affect microbial ecosystem services. However, few studies have assessed the relationships between nutrient balance and biological productivity in extremely nutrient-poor habitats. The Mackay Glacier region of Eastern Antarctica is a hyper-oligotrophic ice-free desert and is an appropriate landscape to evaluate the effects of nutrient deficiency and imbalance on microbial community ecology. In a survey of multiple, widely dispersed soil samples from this region, we detected only low rates of microbial respiration, and observed that C:N:P ratios were well below those required for optimal activity. In silico metagenomic and soil isotopic ratio (δ15N) analyses indicated that the capacity for nitrogen fixation was low, but that soil microbial communities were enriched for soil nitrate assimilation processes, mostly associated with heterotrophic taxa. δ13C isotope ratio data suggested that carbon dioxide was fixed principally via the Calvin cycle. Genes involved in this pathway were common to all metagenomes and were primarily attributed to members of the dominant soil bacterial phyla: Bacteroidetes and Acidobacteria. The identification of multiple genes encoding non-photoautotrophic RUBISCO and carbon dioxide dehydrogenase enzymes in both the metagenomic sequences and assembled MAGs is suggestive of a trace-gas scavenging physiology in members of these soil communities.
Modeling and Analysis of the Macronutrient Signaling Network in Budding Yeast
Authors: Jalihal Amogh P. , Kraikivski Pavel , Murali T. M. , Tyson John J. 
Published: February 2020

AbstractIn eukaryotes, distinct nutrient signals are relayed by specific plasma membrane receptors to signal transduction pathways that are interconnected in complex information-processing networks. The function of these networks is to govern robust cellular responses to unpredictable changes in the nutritional environment of the cell. In the budding yeast,Saccharomyces cerevisiae, these nutrient signaling pathways and their interconnections have been well characterized. However the complexity of the signaling network confounds the interpretation of the overall regulatory ‘logic’ of the control system. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling network in budding yeast, focusing on early temporal responses to carbon and nitrogen signaling. We build a computational model of this network to reconcile literature-curated quantitative experimental data with our proposed molecular mechanism. We evaluate the robustness of our estimates of the model’s kinetic parameter values. We test the model by comparing predictions made in mutant strains with qualitative experimental observations made in the same strains. Finally, we use the model to predict nutrient-responsive transcription factor activities in a number of mutant strains undergoing complex nutrient shifts.
In and outs of Chuviridae endogenous viral elements: origin of a retrovirus and signature of ancient and ongoing arms race in mosquito genomes
Authors: Dezordi Filipe Zimmer , dos Santos Vasconcelos Crhisllane Rafaele , Rezende Antonio Mauro , Wallau Gabriel Luz 
Published: February 2020

AbstractBackgroundEndogenous viral elements (EVEs) are sequences of viral origin integrated into the host genome. EVEs have been characterized in various insect genomes, including mosquitoes. A large EVE content has been found inAedes aegyptiandAedes albopictusgenomes among which a recently describedChuviridaeviral family is of particular interest, owing to the abundance of EVEs derived from it, the discrepancy in the endogenized gene regions and the frequent association with retrotransposons from the BEL-Pao superfamily. In order to better understand the endogenization process of chuviruses and the association between chuvirus glycoproteins and BEL-Pao retrotransposons, we performed a comparative genomics and evolutionary analysis of chuvirus-derived EVEs found in 37 mosquito genomes.ResultsWe identified 428 EVEs belonging to theChuviridaefamily confirming the wide discrepancy between the number of genomic regions endogenized: 409 glycoproteins, 18 RNA-dependent RNA polymerases and one nucleoprotein region. Most of the glycoproteins (263 out of 409) are associated specifically with retroelements from the Pao family. Focusing only on well assembled Pao retroelement copies, we estimated that 263 out of 379 Pao elements are associated with chuvirus-derived glycoproteins. Seventy-three potentially active Pao copies were found to contain glycoproteins into their LTR boundaries. Thirteen out of these were classified as complete and likely autonomous copies, with a full LTR structure and protein domains. We also found 116 Pao copies with no trace of glycoproteins and 37 solo glycoproteins. All potential autonomous Pao copies, contained highly similar LTRs, suggesting a recent/current activity of these elements in the mosquito genomes.ConclusionEvolutionary analysis revealed that most of the glycoproteins found are likely derived from a single or few glycoprotein endogenization events associated with a recombination event with a Pao ancestral element. A potential fully functional Pao-chuvirus hybrid (named Anakin) emerged and the glycoprotein was further replicated through retrotransposition. However, a number of solo glycoproteins, not associated with Pao elements, can still be found in some mosquito genomes 114 million years later, suggesting that these glycoproteins were likely domesticated by the host genome and may participate in an antiviral defense mechanism against both chuvirus and Anakin retrovirus.
Non-photopic and photopic visual cycles differentially regulate immediate, early and late-phases of cone photoreceptor-mediated vision
Authors: Ward Rebecca , Kaylor Joanna J. , Cobice Diego F. , Pepe Dionissia A. , McGarrigle Eoghan M. , Brockerhoff Susan E. , Hurley James B. , Travis Gabriel H. , Kennedy Breandán N. 
Published: February 2020

AbstractCone photoreceptors in the retina enable vision over a wide range of light intensities. However, the processes enabling cone vision in bright light (i.e.photopic vision) are not adequately understood. Chromophore regeneration of cone photopigments may require the retinal pigment epithelium (RPE) and/or retinal Müller glia. In the RPE, isomerization of all-trans-retinyl esters (atRE) to 11-cis-retinol (11cROL) is mediated by the retinoid isomerohydrolase Rpe65. An alternative retinoid isomerase, dihydroceramide desaturase-1 (DES1), is expressed in RPE and Müller cells. The retinol-isomerase activities of Rpe65 and Des1 are inhibited by emixustat and fenretinide, respectively. Here, we tested the effects of these visual cycle inhibitors on immediate, early and late phases of cone photopic vision. In zebrafish larvae raised under cyclic light conditions, fenretinide impaired late cone photopic vision, whereas emixustat-treated zebrafish unexpectedly had normal vision. In contrast, emixustat-treated larvae raised under extensive dark-adaption displayed significantly attenuated immediate photopic vision concomitantly with significantly reduced 11-cis-retinaldehyde (11cRAL). Following 30 minutes of light, early photopic vision recovered, despite 11cRAL levels remaining significantly reduced. Defects in immediate cone photopic vision were rescued in emixustat- or fenretinide-treated larvae following exogenous 9-cis-retinaldehyde (9cRAL) supplementation. Genetic knockout ofdegs1or retinaldehyde-binding protein 1b (rlbp1b)revealed that neither are required for photopic vision in zebrafish. Our findings define the molecular and temporal requirements of the non-photopic and photopic visual cycles for mediating vision in bright light.
Dynamic molecular architecture of the synaptonemal complex
Authors: Köhler Simone , Wojcik Michal , Xu Ke , Dernburg Abby F. 
Published: February 2020

AbstractDuring meiosis, pairing between homologous chromosomes is stabilized by the assembly of a protein lattice known as the synaptonemal complex (SC). The SC ensures the formation of crossovers between homologous chromosomes and also regulates their distribution. However, how the SC regulates crossover formation remains elusive. We isolated an unusual mutation inC. elegansthat disrupts crossover interference but not the assembly of the SC. This mutation alters the unique C-terminal domain of an essential SC protein, SYP-4, a likely ortholog of the vertebrate SC protein SIX6OS1. To characterize the structure of the SC in wild-type and mutant animals, we use three-dimensional STochastic Optical Reconstruction Microscopy (3D-STORM) to interrogate the molecular architecture of the SC in intact germline tissue fromC. elegans. The approach enabled us to define positions of protein epitopes with respect to the 3D architecture of this complex. Using a probabilistic mapping approach to analyze super-resolution image data, we detect a marked structural transition in wild-type animals that coincides with crossover designation. We also found that oursyp-4mutant subtly perturbs SC architecture. Our findings add to growing evidence that the SC is an active material whose molecular organization contributes to chromosome-wide crossover regulation.
Aberrant astrocyte protein secretion contributes to altered neuronal development in diverse disorders
Authors: Caldwell Alison L.M. , Diedrich Jolene K. , Shokhirev Maxim N. , Allen Nicola J. 
Published: February 2020

AbstractAstrocytes negatively impact neuronal development in many neurodevelopmental disorders (NDs), however how they do this, and if mechanisms are shared across disorders, is not known. We developed an in vitro system to ask how astrocyte protein secretion and gene expression change in three genetic NDs. We identified disorder specific changes, and changes common to all disorders. ND astrocytes increase release of Igfbp2, a secreted inhibitor of IGF. IGF rescues neuronal deficits in many NDs, and we found blocking Igfbp2 partially rescues inhibitory effects of Rett Syndrome astrocytes, suggesting increased astrocyte Igfbp2 contributes to decreased IGF signaling in NDs. We identified increased BMP signaling in ND astrocytes is upstream of protein secretion changes, including Igfbp2, and blocking BMP signaling in Fragile X Syndrome astrocytes reverses inhibitory effects on neurite outgrowth. We provide a resource of astrocyte secreted proteins in health and NDs, and identify novel targets for intervention in diverse NDs.
Comprehensive Network Analysis and Experimental Verification of Dedu Safflower’s Influence on Ascites Hepatocarcinoma
Authors: Wang Lu , Li Sha , Bao Lidao 
Published: February 2020

AbstractBackgroundDedu Safflower Powder is a kind of classical prescription of Mongolian Medicine, and its main ingredients are the safflower and the Scabiosa tschiliensis. In the former Mongolian Medicine clinical practice, Dedu Safflower Powder, etc. had obvious effect on curing hepatocarcinoma so as to ease ascites. But the principle of Dedu Safflower Powder’s curing ascites hepatocarcinoma has been not clear.AimH22 mouse hepatocarcinoma ascites models are used for researching the safflower and the Scabiosa tschiliensis’s function of jointly being against hepatocarcinoma ascites, and for verifying their possible combination principle (miR-23a-DAPK1-PVT1 signal axis).MethodThrough simulating an interaction network of the safflower and the Scabiosa tschiliensis with target spots, the function target was predicted. H22 mouse hepatocarcinoma ascites models were randomly divided into a blank contrast group, a model contrast group, a safflower group, a Scabiosa tschiliensis group and a compatibility group of the safflower/the Scabiosa tschiliensis. On the 10thday, mice were killed to measure their weights and abdominal perimeters, also to collect ascites and blood for physical examinations. Kidney tissues were dissected at once and fixed in paraformaldehyde, for a real-time quantitative polymerase chain reaction (qRT-PCR) analysis.ResultIn the network, the DAPK1-PVT1 interaction showed the biggest edge betweenness, so it was predicted that DAPK1 and PVT1 were respectively presumed targets of the safflower and the Scabiosa tschiliensis. Compared with the model contrast group, the safflower group, the Scabiosa tschiliensis group and the safflower/Scabiosa tschiliensis group all had decreasing ascites volumes, body weights, abdominal perimeters. Compared with the model group, the safflower group and the safflower/Scabiosa tschiliensis group had rising DAPK1 expressions (p<0.05), while the safflower group had more obvious increasing DAPK1 (p<0.01); the Scabiosa tschiliensis group and the safflower/Scabiosa tschiliensis group had lowering PVT1 expressions (p<0.05), while the Scabiosa tschiliensis group had more obvious lowering PVT1 (p<0.01); the safflower group, the Scabiosa tschiliensis group and the safflower/Scabiosa tschiliensis group had lowering miR-23a expressions (p<0.05), while the safflower/Scabiosa tschiliensis group had more obvious lowering (p<0.01).ConclusionDAPK1 and PVT1 are respectively the presumed targets of the safflower and the Scabiosa tschiliensis. So Dedu Safflower Powder has good effects on ascites hepatocarcinoma, and that function may be partly related to regulation of miR-23a-DAPK1-PVT1 signal axis.
Trans-generational effect of protein restricted diet on adult body and wing size ofDrosophila melanogaster
Authors: Krittika Sudhakar , Yadav Pankaj 
Published: February 2020

AbstractDietary Restriction (DR) via protein restriction (PR) has become an inquisitive field and has established feasible trade-offs between various fitness and behavioral traits inDrosophila melanogasterto understand lifespan or aging in a nutritionally challenged environment. However, the phenotypes of body size, weight and wing length respond according to factors such as flies’ genotype, environmental exposure, and parental diet. Hence, understanding the long-term effect of PR on these phenotypes is essential. Here, we demonstrate the effect of PR diet on body size, weight and normal & dry wing length of flies subjected to PR50 and PR70 (50% and 70% protein content present in control food respectively) for 20 generations from pre-adult stage. We found that PR fed flies have lower body weight, relative water content (in males), unaltered (PR50%) and higher (PR70%) relative fat content in males, smaller normal and dry body size as compared to control and generations 1 and 2. Interestingly, wing size and pupal size of PR flies are smaller and showed significant effects of diet and generation. Thus, these traits are sex and generation dependent along with an interaction of diet, which is capable of modulating these results variably. Our study suggests that trans-generational effect is more prominent in influencing these traits and wing length might not be a predictor for body size. Taken together, the trans-generational effect of PR on fitness and fitness-related traits might be helpful to understand the underpinning mechanisms of evolution and aging in fruit fliesD. melanogaster.Summary statementTwenty generations of protein restricted diet have a diet and generation dependent effect on adult body size, wing length and body weight.
Nutritional stress alone can controlin vitrotumor formation and its invasive nature
Authors: Gayan Sukanya , Teli Abhishek , Nair Anish , Dey Tuli 
Published: February 2020

AbstractThe metastatic nature is an inherent property of the tumor. However, the effect of the environmental stress conditions on tumor microcosm in the context of metastasis needs to be analyzed. This work is proposed to analyze the tumor behavior under multiple metabolic stress conditions, such as deprivation of glucose, protein, and oxygen. The spheroid proliferation rate is observed to be influenced profoundly by the stress level where minimal stress produces compact spheroid and severe stress makes unstable aggregate like structures. It is observed that the non-invasive cancer cells cannot form spheroids under extreme stress. Stress conditions influence the mRNA levels of hypoxic, angiogenic and ECM deformation specific gene clusters. Spheroid reversal assay reveals the quiescent nature of the stressed spheroids under continuous stress conditions. However, after the rescue, the stressed spheroids were found to opt for different migration modalities. Extremely stressed non-invasive spheroids display atypical sprout-like growth within the invasion matrix and severely stressed spheroids can control the migration pattern of mesenchymal stem cells. Thus, it is concluded that multiple nutritional stress influences the spheroid formation and physiology along with the conversion of a non-invasive spheroid into quasi-invasive one.
Enhanced inhibitor tolerance and increased lipid productivity through adaptive laboratory evolution in the oleaginous yeastMetshnikowia pulcherrima
Authors: Hicks Robert H. , Sze Yuxin , Chuck Christopher J. , Henk Daniel A. 
Published: February 2020

AbstractMicrobial lipid production from second generation feedstocks presents a sustainable route to future fuels, foods and bulk chemicals. The oleaginous yeastMetshnikowia pulcherrimahas previously been investigated as a potential platform organism for lipid production due to its ability to be grown in non-sterile conditions and metabolising a wide range of oligo- and monosaccharide carbon sources within lignocellulosic hydrolysates. However, the generation of inhibitors from depolymerisation causes downstream bioprocessing complications, and despiteM. pulcherrima’scomparative tolerance, their presence is deleterious to both biomass and lipid formation. Using either a single inhibitor (formic acid) or an inhibitor cocktail (formic acid, acetic acid, fufural and HMF), two strategies of adaptive laboratory evolution were performed to improveM. pulcherrima’sfermentation inhibitor tolerance. Using a sequential batch culturing approach, the resulting strains from both strategies had increased growth rates and reduced lag times under inhibiting conditions versus the progenitor. Interestingly, the lipid production of the inhibitor cocktail evolved strains markedly increased, with one strain producing 41% lipid by dry weight compared to 22% of the progenitor. The evolved species was cultured in a non-sterile 2L stirred tank bioreactor and accumulated lipid rapidly, yielding 6.1 g/L of lipid (35% cell dry weight) within 48 hours; a lipid productivity of 0.128 g L-1 h-1. Furthermore, the lipid profile was analogous to palm oil, consisting of 39% C16:0 and 56% C18:1 after 48 hours.
Branched chain amino acid aminotransferase 2 Regulates Ferroptotic Cell Death in Cancer Cells
Authors: Wang Kang , Zhang Zhengyang , Hsiang-i Tsai , Liu Yanfang , Wang Ming , Song Lian , Cao Xiongfeng , Xu Zhanxue , Chen Hongbo , Gong Aihua , Wang Dongqing , Cheng Fang , Zhu Haitao 
Published: February 2020

AbstractFerroptosis has been implicated as a tumor-suppressor function for cancer therapy. Recently the sensitivity to ferroptosis was tightly linked to numerous biological processes, including metabolism of amino acid. Here, using a high-throughput CRISPR/Cas9 based genetic screen in HepG2 cells to search for metabolic proteins inhibiting ferroptosis, we identified branched chain amino acid aminotransferase 2 (BCAT2) as a novel suppressor of ferroptosis. Mechanistically, ferroptosis inducers (erastin, sorafenib and sulfasalazine) activated AMPK/SREBP1 signaling pathway through ferritinophagy, which in turn inhibited BCAT2 transcription. We further confirmed that BCAT2 mediating the metabolism of sulfur amino acid, regulated intracellular glutamate level, whose activation by ectopic expression specifically antagonize system Xc– inhibition and protected liver and pancreatic cancer cells from ferroptosis in vitro and in vivo. Finally, our results demonstrate the synergistic effect of sorafenib and sulfasalazine in downregulating BCAT2 expression and dictating ferroptotic death, where BCAT2 can also be used to predict the responsiveness of cancer cells to ferroptosis-inducing therapies. Collectively, these findings identify a novel role of BCAT2 in ferroptosis, suggesting a potential therapeutic strategy for overcoming sorafenib resistance.
Oocytes, a single cell and a tissue
Authors: Wu Di , Dean Jurrien 
Published: February 2020

AbstractDevelopment of single cell sequencing allows detailing the transcriptome of individual oocytes. Here, we compare different RNA-seq datasets from single and pooled mouse oocytes and show higher reproducibility using single oocyte RNA-seq. We further demonstrate that UMI (unique molecular identifiers) based and other deduplication methods are limited in their ability to improve the precision of these datasets. Finally, for normalization of sample differences in cross-stage comparisons, we propose that external spike-in molecules are comparable to using the endogenous genes stably expressed during oocyte maturation. The ability to normalize data among single cells provides insight into the heterogeneity of mouse oocytes.
Workplace incivility and knowledge hiding: a research agenda
Authors: Irum Ayesha , Ghosh Koustab , Pandey Agrata 
Published: February 2020

PurposeContemporary organizations report a sharp increase in the incidences of workplace incivility. The purpose of this paper is to capture the impact of workplace incivility on the victimized employee's knowledge-hiding behaviours. The paper proposes that the victim will hide knowledge by playing dumb, evasive hiding and rationalized hiding behaviour.Design/methodology/approachThe paper first focusses on a review of literature on workplace incivility and summarizes the findings through a conceptual review model. Subsequently, the paper puts forth a conceptual model depicting the relationship of incivility with knowledge hiding.FindingsDrawing from the affective events theory, the paper demonstrates that incivility will arouse negative emotions in the victim, enticing the individual to respond by engaging in knowledge hiding. It establishes knowledge hiding to be more than just a consequence of reciprocal exchange relationships. The authors also propose this positive relationship to vary with gender.Originality/valueThe paper draws attention towards the counterproductive knowledge behaviours that can be stirred as a result of negative emotional experiences. It explores the employee’s response to an active form of workplace mistreatment, workplace incivility. It advocates the need to check uncivil and disrespectful behaviours in the organization so as to build a healthy work environment.