bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of cross-tolerance inDrosophila melanogasteras a result of increased resistance to cold stress
Authors: Singh Karan , Samant Manas Arun , Prasad Nagaraj Guru
Published: April 2020

Cold stress is a critical environmental challenge that affects an organism’s fitness-related traits. InDrosophila, increased resistance to specific environmental stress may lead to increased resistance to other kinds of stress. In the present study, we aimed to understand whether increased cold stress resistance inDrosophila melanogastercan facilitate their ability to tolerate other environmental stresses. For the current study, we used successfully selected replicate populations ofD. melanogasteragainst cold shock and their control population. These selected populations have evolved several reproductive traits, including increased egg viability, mating frequency, male mating ability, ability to sire progenies, and faster recovery for mating latency under cold shock conditions. In the present work, we investigated egg viability and mating frequency with and without heat and cold shock conditions in the selected and their control populations. We also examined resistance to cold shock, heat shock, desiccation, starvation, and survival post-challenge withStaphylococcus succinussubsp.succinusPK-1 in the selected and their control populations.

After cold-shock treatment, we found a 1.25 times increase in egg viability and a 1.57 times increase in mating frequency in the selected populations compared to control populations. Moreover, more males (0.87 times) and females (1.66 times) of the selected populations survived under cold shock conditions relative to their controls. After being subjected to heat shock, the selected population’s egg viability and mating frequency increased by 0.30 times and 0.57 times, respectively, compared to control populations. Additionally, more selected males (0.31 times) and females (0.98 times) survived under heat shock conditions compared to the control populations. Desiccation resistance slightly increased in the females of the selected populations relative to their control, but we observed no change in the case of males. Starvation resistance decreased in males and females of the selected populations compared to their controls.

Our findings suggest that the increased resistance to cold shock correlates with increased tolerance to heat stress, but this evolved resistance comes at a cost, with decreased tolerance to starvation.
The visual white matter connecting human area prostriata and the thalamus is retinotopically organized
Authors: Kurzawski Jan W. , Mikellidou Kyriaki , Morrone Maria Concetta , Pestilli Franco
Published: April 2020

The human visual system is capable of processing visual information from fovea to the far peripheral visual field. Recent fMRI studies have shown a full and detailed retinotopic map in area prostriata, located ventro-dorsally and anterior to the calcarine sulcus along the parietooccipital sulcus with strong preference for peripheral and wide-field stimulation. Here, we report the anatomical pattern of white-matter connections between area prostriata and the thalamus encompassing the lateral geniculate nucleus (LGN). We observe a continuous and extended bundle of white matter fibers from which two subcomponents can be extracted: one passing ventrally parallel to the optic radiations (OR) and another passing dorsally circumventing the lateral ventricle. Interestingly, the loop travelling dorsally connects the thalamus with the central visual field representation of prostriata, while the other loop travelling more ventrally connects the LGN with the more peripheral visual field representation. This is consistent with a retinotopic segregation recently demonstrated in the OR, connecting the LGN and V1 in humans. Our results demonstrate for the first time a retinotopic segregation regarding the trajectory of a fiber bundle between the thalamus and an associative visual area.
hogwash: Three Methods for Genome-Wide Association Studies in Bacteria
Authors: Saund Katie , Snitkin Evan S
Published: April 2020

Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence based bGWAS methods identify genomic mutations that occur independently multiple times on the phylogenetic tree in the presence of phenotypic variation more often than is expected by chance. This work introduces hogwash, an open source R package that implements three algorithms for convergence based bGWAS. Hogwash additionally contains two burden testing approaches to perform gene- or pathway-analysis to improve power and increase convergence detection for related but weakly penetrant genotypes. To identify optimal use cases, we applied hogwash to data simulated with a variety of phylogenetic signals and convergence distributions. These simulated data are publicly available and contain the relevant metadata regarding convergence and phylogenetic signal for each phenotype and genotype. Hogwash is available for download from GitHub.
Sexually dimorphic traits and male-specific differentiation are actively regulated by Doublesex during specific developmental windows inNasonia vitripennis
Authors: Wang Yidong , Rensink Anna , Fricke Ute , Riddle Megan C. , Trent Carol , van de Zande Louis , Verhulst Eveline C.
Published: April 2020

Sexually dimorphic traits in insects are rapidly evolving due to sexual selection which can ultimately lead to speciation. However, our knowledge of the underlying sex-specific molecular mechanisms is still scarce. Here we show that the highly conserved gene,Doublesex (Dsx),regulates rapidly diverging sexually dimorphic traits in the model parasitoid waspNasonia vitripennis(Hymenoptera: Pteromalidae). We present here the revised fullDsxgene structure with an alternative first exon, and two additional maleNvDsxisoforms, which gives important insights into the evolution of the sex-specific oligomerization domains and C-termini. We show the sex-specificNvDsxexpression throughout development, and demonstrate that transientNvDsxsilencing in different male developmental stages dramatically shifts the morphology of two sexually dimorphic traits from male to female, with the effect being dependent on the timing of silencing. In addition, transient silencing ofNvDsxin early male larvae affects male genitalia tissue growth but not morphology. This indicates that maleNvDsxis actively required to suppress female-specific traits and to promote male-specific traits during specific developmental windows. These results also strongly suggest that inN. vitripennismost sex-specific tissues fully differentiate in the embryonic stage and only need the input ofNvDsxfor growth afterwards. This provides a first insight into the regulatory activity ofDsxin the Hymenoptera and will help to better understand the evolutionary and molecular mechanisms involved in sex-specific development in this parasitoid wasp, which can eventually lead to the development of new synthetic genetics-based tools for biological pest control by parasitoid wasps.

Significance Statement

In insects, male and female differentiation is regulated by the highly conserved transcription factor Doublesex (Dsx). The role of Dsx in regulating rapidly evolving sexually dimorphic traits has received less attention, especially in wasps and bees. Here, we mainly focused on Dsx regulation of two sexually dimorphic traits and male genitalia morphology in the parasitoid wasp,Nasonia vitripennis.We demonstrate thatDsxactively regulates male-specific tissue growth and morphology during specific developmental windows. These findings will help to better understand the molecular mechanisms underlying the rapid evolution of sexual differentiation and sexually dimorphic traits in insects, but may also be the starting point for the development of new tools for biological control of pest insects by parasitoid wasps.
Broad and differential animal ACE2 receptor usage by SARS-CoV-2
Authors: Zhao Xuesen , Chen Danying , Szabla Robert , Zheng Mei , Li Guoli , Du Pengcheng , Zheng Shuangli , Li Xinglin , Song Chuan , Li Rui , Guo Ju-Tao , Junop Murray , Zeng Hui , Lin Hanxin
Published: April 2020

The COVID-19 pandemic has caused an unprecedented global public health and economy crisis. The origin and emergence of its causal agent, SARS-CoV-2, in the human population remains mysterious, although bat and pangolin were proposed to be the natural reservoirs. Strikingly, comparing to the SARS-CoV-2-like CoVs identified in bats and pangolins, SARS-CoV-2 harbors a polybasic furin cleavage site in its spike (S) glycoprotein. SARS-CoV-2 uses human ACE2 as its receptor to infect cells. Receptor recognition by the S protein is the major determinant of host range, tissue tropism, and pathogenesis of coronaviruses. In an effort to search for the potential intermediate or amplifying animal hosts of SARS-CoV-2, we examined receptor activity of ACE2 from 14 mammal species and found that ACE2 from multiple species can support the infectious entry of lentiviral particles pseudotyped with the wild-type or furin cleavage site deficient S protein of SARS-CoV-2. ACE2 of human/rhesus monkey and rat/mouse exhibited the highest and lowest receptor activity, respectively. Among the remaining species, ACE2 from rabbit and pangolin strongly bound to the S1 subunit of SARS-CoV-2 S protein and efficiently supported the pseudotyped virus infection. These findings have important implications for understanding potential natural reservoirs, zoonotic transmission, human-to-animal transmission, and use of animal models.

Importance

SARS-CoV-2 uses human ACE2 as primary receptor for host cell entry. Viral entry mediated by the interaction of ACE2 with spike protein largely determines host range and is the major constraint to interspecies transmission. We examined the receptor activity of 14 ACE2 orthologues and found that wild type and mutant SARS-CoV-2 lacking the furin cleavage site in S protein could utilize ACE2 from a broad range of animal species to enter host cells. These results have important implications in the natural hosts, interspecies transmission, animal models and molecular basis of receptor binding for SARS-CoV-2.
Production of a tributyltin-binding protein 2 knockout mutant strain of Japanese medaka,Oryzias latipes
Authors: Kato-Unoki Yoko , Takai Yuki , Nagano Yosuke , Matsunaga Satoshi , Enoki Shintaro , Takamura Takumi , Kim Sangwan , Kinoshita Masato , Kitano Takeshi , Shimasaki Yohei , Oshima Yuji
Published: April 2020

Tributyltin-binding proteins (TBT-bps), members of the lipocalin family, bind TBT in fish blood and are presumed to contribute to detoxification of TBT. Recent studies have shown that many fish species have TBT-bp genes, and that these genes are induced by stresses such as exposure to chemicals or fish pathogenic bacteria. However, the function of TBT-bps, and the mechanisms of their induction and detoxification activity are still unclear. Here, towards elucidating the functions of TBT-bp2, we produced a TBT-bp2 knockout (TBT-bp2-/-) strain of Japanese medaka,Oryzias latipes, by using the CRISPR/Cas9 system. Gene expression of the mutated TBT-bp2 was reduced, and the cDNA sequencing and predicted protein structure suggested possible loss of function. However, the fish could be grown under normal conditions. Exposure of the TBT-bp2-/-strain of medaka to various stresses in future experiments is expected to contribute to our understanding of this novel detoxification system in aquatic organisms.
Gene interfered-ferroptosis therapy of cancer
Authors: Gao Jinliang , Luo Tao , Lin Na , Wang Jinke
Published: April 2020

Although some effective therapies have been available for cancer, it still poses a great threat to human health and life due to its drug resistance and low response in patients. Here, we developed a novel therapy named as gene interfered-ferroptosis therapy (GIFT) by combining iron nanoparticles and cancer-specific gene interference. Using a promoter consisted of a NF-κB decoy and a minimal promoter (DMP), we knocked down the expression of two iron metabolism-related genes (FPN and Lcn2) selectively in cancer cells. At the same time, we treated cells with Fe3O4nanoparticles. As a result, a significant ferroptosis was induced in a wide variety of cancer cells representing various hematological and solid tumors. However, the same treatment had no effect on normal cells. By using AAV and PEI-coated Fe3O4nanoparticles as gene vectors, we found that the tumor growth in mice could be also significantly inhibited by the intravenously injected GIFT reagents. By detecting ROS, iron content and gene expression, we confirmed that the mechanism underlying the therapy is gene inference-enhanced ferroptosis.
A heuristic model of the effects of phenotypic robustness in adaptive evolution
Authors: Rigato Emanuele , Fusco Giuseppe
Published: April 2020

A recent theoretical, deterministic model of the effects of phenotypic robustness on adaptive evolutionary dynamics showed that a certain level of phenotypic robustness (critical robustness) is a necessary condition for adaptation to occur and to be maintained in the course of evolution in most real organismal systems. We built an individual-based heuristic model to verify the soundness of these theoretical results through computer simulation, testing expectations under a range of scenarios for the relevant parameters of the evolutionary dynamics. These include the mutation probability, the presence of stochastic effects, the introduction of environmental influences and the possibility for some features of the population (like selection coefficients and phenotypic robustness) to change themselves during adaptation. Overall, we found a good match between observed and expected results, even for evolutionary parameter values that violate some of the assumptions of the deterministic model, and that robustness can itself evolve. However, from more than one simulation it appears that very high robustness values, higher than the critical value, can limit or slow-down adaptation. This possible trade-off was not predicted by the deterministic model.
Circuits in the absence of cortical layers: increased callosal connectivity in reeler mice revealed by brain-wide input mapping of VIP neurons in barrel cortex
Authors: Hafner Georg , Guy Julien , Witte Mirko , Truschow Pavel , Rüppel Alina , Sirmpilatze Nikoloz , Dadarwal Rakshit , Boretius Susann , Staiger Jochen F.
Published: April 2020

The neocortex is composed of layers. Whether layers constitute an essential framework for the formation of functional circuits is not well understood. We investigated if neurons require the layer organization to be embedded into brain-wide circuits using the reeler mouse. This mutant is characterized by a migration deficit of cortical neurons so that no layers are formed. Still, neurons retain their properties and reeler mice show little cognitive impairment. We focused on VIP neurons because they are known to receive strong long-range inputs and have a typical laminar bias towards upper layers. In reeler these neurons are more distributed across the cortex. We mapped the brain-wide inputs of VIP neurons in barrel cortex of wildtype and reeler mice with rabies virus tracing. Innervation by subcortical inputs was not altered in reeler, in contrast to the cortical circuitry. Numbers of long-range ipsilateral cortical inputs were reduced in reeler, while contralateral inputs were strongly increased. Reeler mice had more callosal projection neurons. Hence, the corpus callosum was larger in reeler as shown by structural imaging. We argue that in the absence of cortical layers, circuits with subcortical structures are maintained but cortical neurons establish a different network capable to preserve cognitive functions.
Combining In Vivo Corneal Confocal Microscopy with Deep Learning-based Analysis Reveals Sensory Nerve Fiber Loss in Acute SIV Infection
Authors: McCarron Megan E. , Weinberg Rachel L. , Izzi Jessica M. , Queen Suzanne E. , Misra Stuti L. , Russakoff Daniel B. , Oakley Jonathan D. , Mankowski Joseph L.
Published: April 2020

Purpose

To characterize corneal subbasal nerve plexus morphologic features usingin vivocorneal confocal microscopy (IVCM) in normal and SIV-infected macaques and to implement automated assessments using novel deep learning-based methods customized for macaque studies.

Methods

In vivo corneal confocal microscopy images were collected from both male and female age-matched specific-pathogen free rhesus and pigtailed macaques housed at the Johns Hopkins University breeding colony using the Heidelberg HRTIII with Rostock Corneal Module. We also obtained repeat IVCM images of 12 SIV-infected animals including pre-infection and 10 day post-SIV infection time-points. All IVCM images were analyzed using a novel deep convolutional neural network architecture developed specifically for macaque studies.

Results

Deep learning-based segmentation of subbasal nerves in IVCM images from macaques demonstrated that corneal nerve fiber length (CNFL) and fractal dimension measurements did not differ between species, but pigtailed macaques had significantly higher baseline corneal nerve fiber tortuosity than rhesus macaques (P = 0.005). Neither sex nor age of macaques was associated with differences in any of the assessed corneal subbasal nerve parameters. In the SIV/macaque model of HIV, acute SIV infection induced significant decreases in both corneal nerve fiber length and fractal dimension (P= 0.01 and P= 0.008 respectively).

Conclusions

The combination of IVCM and objective, robust, and rapid deep-learning analysis serves as a powerful noninvasive research and clinical tool to track sensory nerve damage, enabling early detection of neuropathy. Adapting the deep-learning analyses to human corneal nerve assessments will refine our ability to predict and monitor damage to small sensory nerve fibers in a number of clinical settings including HIV, multiple sclerosis, Parkinson’s disease, diabetes, and chemotherapeutic neurotoxicity.
The effects of YKL-40 on angiogenic potential of HUVECs are partly mediated by syndecan-4
Authors: Zheng Jianlei , Xue Qi , Zhao Yan , Sun WeiJun
Published: April 2020

Objective

YKL-40, a secreted glycoprotein, has a role in promoting tumor angiogenesis through syndecan-1 receptor. As one of the members of syndecans family, syndecan-4 is also an important mediator for tube formation. However, the effects of YKL-40 on migration and tube formation of human umbilical vein cells (HUVECs) mediated by syndecan-4 receptor are unknown.

Methods

HUVECs were transfected with lentivirus encoding syndecan-4 short hairpin (sh) RNA (lenti-synd4 shRNA) and the efficiency of transfection was measured using reverse transcription quantitative real time polymerase chain reaction (qRT-PCR) and flow cytometry. The effects of recombinant protein of YKL-40 on migration and angiogenesis of HUVECs adjusted by syndecan-4 were determined by wound healing and tube formation assay. The expression of protein kinase Cα (PKCα) and extracellular signal regulated kinases (ERKs) 1 and 2 (ERK1/2) in HUVECs was measured using western blotting.

Results

Transfection of lenti-synd4 shRNA significantly decreased the membrane protein expression of syndecan-4 in HUVECs. HUVECs transfected with lenti-synd4 shRNA remarkably inhibited the migration and tube formation of endothelial cells stimulated by recombinant protein of YKL-40. The levels of PKCα and ratio of p-ERK1/2 to ERK1/2 in HUVECs were also down-regulated by silencing syndecan-4.

Conclusion

The effects of YKL-40-induced on migration and tube formation of HUVECs may partly be inhibited by knock-downing syndecan-4 through suppressing PKCα and ERK1/2 signaling pathways.
Natural variation in autumnFLClevels, rather than epigenetic silencing, aligns vernalization to different climates
Authors: Hepworth Jo , Antoniou-Kourounioti Rea L , Berggren Kristina , Selga Catja , Tudor Eleri , Yates Bryony , Cox Deborah , Collier Harris Barley R , Irwin Judith , Howard Martin , Säll Torbjörn , Holm Svante , Dean Caroline
Published: April 2020

Plants monitor temperatures over long timescales to assess seasons and time developmental transitions. InArabidopsis thaliana, winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressorFLOWERING LOCUS C (FLC). Natural Arabidopsis accessions show considerable variation in vernalization, however which aspect of theFLCrepression mechanism is most important for adaptation to different climates is not clear. By analyzingFLCsilencing in natural variants throughout winter in three field sites, we find thatFLCstarting levels and early phases of silencing are the major variables underlying vernalization response, rather than establishment of epigenetic silencing. This results in an intricate interplay between promotion and delay of flowering to balance survival, and through a post-vernalization effect ofFLC, reproductive effort via branch production. These data reveal how non-codingFLCvariation aligns vernalization response to different climatic conditions and year-on-year fluctuations in natural temperature profiles.

Impact Statement

Alleles of the major floral repressor vary in their initial expression to underpin the ability of Arabidopsis to survive year-on-year climatic fluctuations.
A visual encoding model links magnetoencephalography signals to neural synchrony in human cortex
Authors: Kupers Eline R. , Benson Noah C. , Winawer Jonathan
Published: April 2020

Synchronization of neuronal responses over large distances is hypothesized to be important for many cortical functions. However, no straightforward methods exist to estimate synchrony non-invasively in the living human brain. MEG and EEG measure the whole brain, but the sensors pool over large, overlapping cortical regions, obscuring the underlying neural synchrony. Here, we developed a model from stimulus to cortex to MEG sensors to disentangle neural synchrony from spatial pooling of the instrument. We find that synchrony across cortex has a surprisingly large and systematic effect on predicted MEG spatial topography. We then conducted visual MEG experiments and separated responses into stimulus-locked and broadband components. The stimulus-locked topography was similar to model predictions assuming synchronous neural sources, whereas the broadband topography was similar to model predictions assuming asynchronous sources. We infer that visual stimulation elicits two distinct types of neural responses, one highly synchronous and one largely asynchronous across cortex.
Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy
Authors: Chandak Shubham , Tatwawadi Kedar , Sridhar Srivatsan , Weissman Tsachy
Published: April 2020

Motivation

Nanopore sequencing provides a real-time and portable solution to genomic sequencing, enabling better assembly, structural variant discovery and modified base detection than second generation technologies. The sequencing process generates a huge amount of data in the form of raw signal contained in fast5 files, which must be compressed to enable efficient storage and transfer. Since the raw data is inherently noisy, lossy compression has potential to significantly reduce space requirements without adversely impacting performance of downstream applications.

Results

We explore the use of lossy compression for nanopore raw data using two state-of-the-art lossy time-series compressors, and evaluate the tradeoff between compressed size and basecalling/consensus accuracy. We test several basecallers and consensus tools on a variety of datasets at varying depths of coverage, and conclude that lossy compression can provide 35-50% further reduction in compressed size of raw data over the state-of-the-art lossless compressor with negligible impact on basecalling accuracy (≲0.2% reduction) and consensus accuracy (≲0.002% reduction). In addition, we evaluate the impact of lossy compression on methylation calling accuracy and observe that this impact is minimal for similar reductions in compressed size, although further evaluation with improved benchmark datasets is required for reaching a definite conclusion. The results suggest the possibility of using lossy compression, potentially on the nanopore sequencing device itself, to achieve significant reductions in storage and transmission costs while preserving the accuracy of downstream applications.

Availability

The code is available athttps://github.com/shubhamchandak94/lossy_compression_evaluation.

Supplementary information

Supplementary data are available atBioinformaticsonline.

Contact

schandak@stanford.edu
A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus
Authors: Rodriguez O. L. , Gibson W. S. , Parks T. , Emery M. , Powell J. , Strahl M. , Deikus G. , Auckland K. , Eichler E. E. , Marasco W. A. , Sebra R. , Sharp A. J. , Smith M. L. , Bashir A. , Watson C. T.
Published: April 2020

An incomplete ascertainment of genetic variation within the highly polymorphic immunoglobulin heavy chain locus (IGH) has hindered our ability to define genetic factors that influence antibody and B cell mediated processes. To date, methods for locus-wide genotyping of all IGH variant types do not exist. Here, we combine targeted long-read sequencing with a novel bioinformatics tool, IGenotyper, to fully characterize genetic variation within IGH in a haplotype-specific manner. We apply this approach to eight human samples, including a haploid cell line and two mother-father-child trios, and demonstrate the ability to generate high-quality assemblies (>98% complete and >99% accurate), genotypes, and gene annotations, including 2 novel structural variants and 16 novel gene alleles. We show that multiplexing allows for scaling of the approach without impacting data quality, and that our genotype call sets are more accurate than short-read (>35% increase in true positives and >97% decrease in false-positives) and array/imputation-based datasets. This framework establishes a foundation for leveraging IG genomic data to study population-level variation in the antibody response.
Rice lectin proteinOsr40c1imparts drought tolerance by modulatingOsSAM2,OsSAP8 and chromatin-associated proteins
Authors: Sahid Salman , Roy Chandan , Paul Soumitra , Datta Riddhi
Published: April 2020

Lectin proteins play an important role in biotic and abiotic stress responses in plants. Although the rice lectin protein,Osr40c1, has been reported to be regulated by drought stress, the mechanism of its drought tolerance activity has not been studied so far. In this study, it has been depicted that expression ofOsr40c1gene correlates with the drought tolerance potential of various rice cultivars. Transgenic rice plants overexpressingOsr40c1were significantly more tolerant to drought stress over the wild-type plants. Furthermore, ectopic expression of theOsr40c1gene in tobacco yielded a similar result. Interestingly, the protein displayed a nucleo-cytoplasmic localization and was found to interact with a number of drought-responsive proteins likeOsSAM2,OsSAP8,OsMNB1B, andOsH4. Fascinatingly, silencing of each of these protein partners led to drought susceptibility in the otherwise tolerantOsr40c1 expressing transgenic tobacco lines indicating that these partners were crucial for theOsr40c1-mediated drought tolerancein planta. Together, the present investigation delineated the novel role ofOsr40c1 protein in imparting drought tolerance by regulating the chromatin proteins,OsMNB1B andOsH4, which presumably enablesOsSAP8 to induce downstream gene expression. In addition, its interaction withOsSAM2 might induce polyamine biosynthesis thus further improving drought tolerance in plants.

Highlights

A rice lectin protein,Osr40c1, plays a crucial role in imparting drought stress tolerance in plants by modulatingOsSAM2 as well as the transcriptional regulatorsOsSAP8,OsMNB1B andOsH4.
Jacalin domain-containing protein OsSalT interacts with OsDREB2A and OsNAC1 to impart drought stress tolerance in planta
Authors: Sahid Salman , Roy Chandan , Shee Dibyendu , Datta Riddhi , Paul Soumitra
Published: April 2020

With the changing climatic conditions, drought has become one of the most threatening abiotic stress factors that adversely affect rice cultivation and productivity. Although the involvement of the jacalin domain-containing protein, OsSalT, has been reported in drought and salinity tolerance, its functional mechanism still remains largely unexplored. In this study, expression of the OsSalT gene was found to be positively correlated with the drought tolerance potential with its higher transcript abundance in the tolerant indica rice cultivar, Vandana and lower abundance in the susceptible cultivar, MTU1010. Moreover, the ectopic expression of OsSalT in tobacco imparted drought stress tolerance in the transgenic lines. The transgenic lines exhibited significantly improved growth and higher osmolyte accumulation over the wild-type (WT) plants together with the induction in the OsSalT expression under drought stress. Fascinatingly, the yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analyses confirmed the interaction of OsSalT protein with two interesting transcription factors (TFs), OsNAC1 and OsDREB2A. In silico analysis further revealed that the OsSalT protein interacted with the regulatory domain of OsDREB2A and the C-terminal domain of OsNAC1 leading to their activation and induction of their downstream drought-responsive genes. Together, this study unravels a novel model for OsSalT-mediated regulation of drought tolerance in plants.
An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity
Authors: Luna Lucas A. , Lesecq Zachary , White Katharine A. , Hoang An , Scott David A. , Zagnitko Olga , Bobkov Andrey A. , Barber Diane L. , Schiffer Jamie M. , Isom Daniel G. , Sohl Christal D.
Published: April 2020

Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to α-ketoglutarate (α-KG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasingkcatvalues for α-KG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKavalues. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKavalue upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue ∼12 Å from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.
MpsLDA-ProSVM: predicting multi-label protein subcellular localization by wMLDAe dimensionality reduction and ProSVM classifier
Authors: Zhang Qi , Li Shan , Yu Bin , Li Yang , Zhang Yandan , Ma Qin , Zhang Yusen
Published: April 2020

Proteins play a significant part in life processes such as cell growth, development, and reproduction. Exploring protein subcellular localization (SCL) is a direct way to better understand the function of proteins in cells. Studies have found that more and more proteins belong to multiple subcellular locations, and these proteins are called multi-label proteins. They not only play a key role in cell life activities, but also play an indispensable role in medicine and drug development. This article first presents a new prediction model, MpsLDA-ProSVM, to predict the SCL of multi-label proteins. Firstly, the physical and chemical information, evolution information, sequence information and annotation information of protein sequences are fused. Then, for the first time, use a weighted multi-label linear discriminant analysis framework based on entropy weight form (wMLDAe) to refine and purify features, reduce the difficulty of learning. Finally, input the optimal feature subset into the multi-label learning with label-specific features (LIFT) and multi-label k-nearest neighbor (ML-KNN) algorithms to obtain a synthetic ranking of relevant labels, and then use Prediction and Relevance Ordering based SVM (ProSVM) classifier to predict the SCLs. This method can rank and classify related tags at the same time, which greatly improves the efficiency of the model. Tested by jackknife method, the overall actual accuracy (OAA) on virus, plant, Gram-positive bacteria and Gram-negative bacteria datasets are 98.06%, 98.97%, 99.81% and 98.49%, which are 0.56%-9.16%, 5.37%-30.87%, 3.51%-6.91% and 3.99%-8.59% higher than other advanced methods respectively. The source codes and datasets are available athttps://github.com/QUST-AIBBDRC/MpsLDA-ProSVM/.
NAT8LmRNA oxidation is linked to neurodegeneration in multiple sclerosis
Authors: Kharel Prakash , Singhal Naveen Kumar , West Nicole , Rana Joram , Smith Lindsey , Freeman Ernest , Chattopadhyay Ansuman , McDonough Jennifer , Basu Soumitra
Published: April 2020

RNA oxidation has been implicated in neurodegeneration, but the underlying mechanism for such effects is unclear. Recently, we demonstrated extensive RNA oxidation within the neurons in multiple sclerosis (MS) brain. In this report we identified selectively oxidized mRNAs in neuronal cells that pertained to neuropathological pathways. N-acetyl aspartate transferase 8 like (NAT8L) mRNA is one such transcript, whose translated product enzymatically synthesizes N-acetyl aspartic acid (NAA), a neuronal metabolite important for myelin synthesis. We reasoned that impediment of translation of an oxidizedNAT8LmRNA will result in reduction in its cognate protein, thus lowering NAA level. This assertion is directly supported by our studies on a model cellular system, an MS animal model and postmortem human MS brain. Reduced NAA level in the brain hampers myelin integrity making neuronal axons more susceptible to damage, which contributes in MS neurodegeneration. Overall, this work provides a framework for mechanistic understanding of the link between RNA oxidation and neurodegenerative diseases.
Cell-intrinsic differences between human airway epithelial cells from children and adults
Authors: Maughan Elizabeth F. , Hynds Robert E. , Pennycuick Adam , Nigro Ersilia , Gowers Kate H.C. , Denais Celine , Gómez-López Sandra , Lazarus Kyren A. , Orr Jessica C. , Pearce David R. , Clarke Sarah E. , Lee Dani Do Hyang , Woodall Maximillian N. J. , Masonou Tereza , Case Katie-Marie , Teixeira Vitor H. , Hartley Benjamin E. , Hewitt Richard J. , Yaghchi Chadwan Al , Sandhu Gurpreet S. , Birchall Martin A. , O’Callaghan Christopher , Smith Claire M. , De Coppi Paolo , Butler Colin R. , Janes Sam M.
Published: April 2020

The airway epithelium is a key protective barrier, the integrity of which is preserved by the self-renewal and differentiation of basal stem cells. Epithelial cells are central to the pathogenesis of multiple lung diseases. In chronic lung diseases, increasing age is a principle risk factor. Few studies have explored the differences between airway epithelial cells in children and adults and how the function of basal stem cells changes during ageing is poorly understood. Here, we analyze airway epithelial cells from children and adults in homeostatic conditions (laser capture-microdissected whole epithelium and fluorescence-activated cell-sorted basal cells) and in proliferation-inducing cell culture conditions. We find that, while the cellular composition of the pediatric and adult tracheobronchial epithelium is broadly similar, in cell culture, pediatric airway epithelial cells displayed higher colony-forming ability, sustainedin vitrogrowth and outcompeted adult cells in competitive proliferation assays. In RNA sequencing experiments, we observed potentially important differences between epithelium from children and adults, including higher baseline interferon-associated gene expression in pediatric epithelium. Our results demonstrate cell-intrinsic differences in transcriptional profile and regenerative capacity between proximal airway epithelial cells of children and adults.

Graphical abstract
Chimpanzee Brain Morphometry Utilizing Standardized MRI Preprocessing and Macroanatomical Annotations
Authors: Vickery Sam , Hopkins William D. , Sherwood Chet C. , Schapiro Steven J. , Latzman Robert D. , Caspers Svenja , Gaser Christian , Eickhoff Simon B. , Dahnke Robert , Hoffstaedter Felix
Published: April 2020

Chimpanzees are among the closest living relatives to humans and, as such, provide a crucial comparative model for investigating primate brain evolution. In recent years, human brain mapping has strongly benefited from enhanced computational models and image processing pipelines that could also improve data analyses in animals by using species-specific templates. In this study, we use structural MRI data from the National Chimpanzee Brain Resource (NCBR) to develop the chimpanzee brain reference template Juna.Chimp for spatial registration and the macro-anatomical brain parcellation Davi130 for standardized whole-brain analysis. Additionally, we introduce a ready-to-use image processing pipeline built upon the CAT12 toolbox in SPM12, implementing a standard human image preprocessing framework in chimpanzees. Applying this approach to data from 178 subjects, we find strong evidence for age-related GM atrophy in multiple regions of the chimpanzee brain, as well as, a human-like anterior-posterior pattern of hemi-spheric asymmetry in medial chimpanzee brain regions.
Reprogramming acetogenic bacteria with CRISPR-targeted base editingviadeamination
Authors: Xia Peng-Fei , Casini Isabella , Schulz Sarah , Klask Christian-Marco , Angenent Largus T. , Molitor Bastian
Published: April 2020

Acetogenic bacteria are rising in popularity as chassis microbes in biotechnology due to their capability of converting inorganic one-carbon (C1) gases to organic chemicals. To fully uncover the potential of acetogenic bacteria, synthetic-biology tools are imperative to either engineer designed functions or to interrogate the physiology. Here, we report a genome-editing tool at a one-nucleotide resolution, namely base editing, for acetogenic bacteria based on CRISPR-targeted deamination. This tool combines nuclease deactivated Cas9 with activation-induced cytidine deaminase to enable cytosine-to-thymine substitution without DNA cleavage, homology-directed repair, and donor DNA, which are generally the bottlenecks for applying conventional CRISPR-Cas systems in bacteria. We designed and validated a modularized base-editing tool in the model acetogenic bacteriumClostridium ljungdahlii. The editing principles were investigated, and anin-silicoanalysis revealed the capability of base editing across the genome. Moreover, genes related to acetate and ethanol production were disrupted individually by installing premature STOP codons to reprogram carbon flux towards improved acetate production. This resulted in engineeredC. ljungdahliistrains with the desired phenotypes and stable genotypes. Our base-editing tool promotes the application and research in acetogenic bacteria and provides a blueprint to upgrade CRISPR-Cas-based genome editing in bacteria in general.

Significance

Acetogenic bacteria metabolize one-carbon (C1) gases, such as industrial waste gases, to produce fuels and commodity chemicals. However, the lack of efficient gene-manipulation approaches hampers faster progress in the application of acetogenic bacteria in biotechnology. We developed a CRISPR-targeted base-editing tool at a one-nucleotide resolution for acetogenic bacteria. Our tool illustrates great potential in engineering other A-T-rich bacteria and links designed single-nucleotide variations with biotechnology. It provides unique advantages for engineering industrially relevant bacteria without creating genetically modified organisms (GMOs) under the legislation of many countries. This base-editing tool provides an example for adapting CRISPR-Cas systems in bacteria, especially those that are highly sensitive to heterologously expressed Cas proteins and have limited ability of receiving foreign DNA.
Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions
Authors: Butler Daniel J. , Mozsary Christopher , Meydan Cem , Danko David , Foox Jonathan , Rosiene Joel , Shaiber Alon , Afshinnekoo Ebrahim , MacKay Matthew , Sedlazeck Fritz J. , Ivanov Nikolay A. , Sierra Maria , Pohle Diana , Zietz Michael , Gisladottir Undina , Ramlall Vijendra , Westover Craig D. , Ryon Krista , Young Benjamin , Bhattacharya Chandrima , Ruggiero Phyllis , Langhorst Bradley W. , Tanner Nathan , Gawrys Justyna , Meleshko Dmitry , Xu Dong , Steel Peter A. D. , Shemesh Amos J. , Xiang Jenny , Thierry-Mieg Jean , Thierry-Mieg Danielle , Schwartz Robert E. , Iftner Angelika , Bezdan Daniela , Sipley John , Cong Lin , Craney Arryn , Velu Priya , Melnick Ari M. , Hajirasouliha Iman , Horner Stacy M. , Iftner Thomas , Salvatore Mirella , Loda Massimo , Westblade Lars F. , Cushing Melissa , Levy Shawn , Wu Shixiu , Tatonetti Nicholas , Imielinski Marcin , Rennert Hanna , Mason Christopher E.
Published: April 2020

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
Anthrax Toxin Translocation Complex Reveals insight into the Lethal Factor Unfolding and Refolding Mechanism
Authors: Machen Alexandra J , Fisher Mark T , Freudenthal Bret D
Published: April 2020

Translocation is essential to the anthrax toxin mechanism. Protective antigen (PA), the translocon component of this AB toxin, forms an oligomeric pore with three key clamp sites that aid in the efficient entry of lethal factor (LF) or edema factor (EF), the enzymatic components of the toxin, into the cell. LF and EF translocate through the PA pore (PApore) with the pH gradient between the endosome and the cytosol facilitating rapid translocationin vivo. Structural details of the translocation process have remained elusive despite their biological importance. To overcome the technical challenges of studying translocation intermediates, we developed a novel method to immobilize, transition, and stabilize anthrax toxin to mimic important physiological steps in the intoxication process. Here, we report a cryoEM snapshot of PAporetranslocating the N-terminal domain of LF (LFN). The resulting 3.3 Å structure of the complex shows density of partially unfolded LFNnear the canonical PAporebinding site as well as in the α clamp, the Φ clamp, and the charge clamp. We also observe density consistent with an α helix emerging from the 100 Å β barrel channel suggesting LF secondary structural elements begin to refold in the pore channel. We conclude the anthrax toxin β barrel aids in efficient folding of its enzymatic payload prior to channel exit. Our hypothesized refolding mechanism has broader implications for pore length of other protein translocating toxins.

Significance Statement

Toxins like the anthrax toxin aid bacteria in establishing an infection, evading the immune system, and proliferating inside a host. The anthrax toxin, a proteinaceous AB toxin secreted byBacillus anthracis, consists of lethal factor and protective antigen. In this work, we explore the molecular details of lethal factor translocation through protective antigen pore necessary for cellular entry. Our cryo electron microscopy results provide evidence of lethal factor secondary structure refolding prior to protective antigen pore exit. Similar to the ribosome exit tunnel, the toxin pore channel likely contributes to native folding of lethal factor. We predict other AB toxins with extended pores also initiate substrate refolding inside the translocon for effective intoxication during bacterial infection, evasion, and proliferation.
Cells recognize osmotic stress through liquid-liquid phase separation lubricated with poly(ADP-ribose)
Authors: Watanabe Kengo , Morishita Kazuhiro , Zhou Xiangyu , Shiizaki Shigeru , Uchiyama Yasuo , Koike Masato , Naguro Isao , Ichijo Hidenori
Published: April 2020

Cells are under threat of osmotic perturbation; and cell volume maintenance is critical in cerebral edema, inflammation and aging, in which prominent changes in intracellular or extracellular osmolality emerge. After osmotic stress-enforced cell swelling or shrinkage, the cells regulate intracellular osmolality to recover their volume. However, the mechanisms recognizing osmotic stress remain obscured. We previously clarified that apoptosis signal-regulating kinase 3 (ASK3) bidirectionally responds to osmotic stress and regulates cell volume recovery. Here, we report that macromolecular crowding induces liquid-demixing condensates of ASK3 under hyperosmotic stress, which transduce osmosensing signal into ASK3 inactivation. A genome-wide small interfering RNA (siRNA) screen identified an ASK3 inactivation regulator, nicotinamide phosphoribosyltransferase (NAMPT), related to poly(ADP-ribose) signaling. Furthermore, we clarify that poly(ADP-ribose) keeps ASK3 condensates in the liquid phase and enables ASK3 to become inactivated under hyperosmotic stress. Our findings demonstrate that cells rationally incorporate physicochemical phase separation into their osmosensing systems.