bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of computational codon usage models and their association with translationally slow codons
Authors: Wright Gabriel , Rodriguez Anabel , Li Jun , Clark Patricia L. , Milenković Tijana , Emrich Scott
Published: March 2020

Improved computational modeling of protein translation rates, including better prediction of where translational slowdowns along an mRNA sequence may occur, is critical for understanding co-translational folding. Because codons within a synonymous codon group are translated at different rates, many computational translation models rely on analyzing synonymous codons. Some models rely ongenome-widecodon usage bias (CUB), believing that globally rare and common codons are the most informative of slow and fast translation, respectively. Others use the CUB observed only inhighly expressedgenes, which should be under selective pressure to be translated efficiently (and whose CUB may therefore be more indicative of translation rates). No prior work has analyzed these models for their ability to predict translational slowdowns. Here, we evaluate five models for their association with slowly translated positions as denoted by two independent ribosome footprint (RFP) count experiments fromS. cerevisiae, because RFP data is often considered as a “ground truth” for translation rates across mRNA sequences. We show that all five considered models strongly associate with the RFP data and therefore have potential for estimating translational slowdowns. However, we also show that there is a weak correlation between RFP counts for the same genes originating from independent experiments, even when their experimental conditions are similar. This raises concerns about the efficacy of using current RFP experimental data for estimating translation rates and highlights a potential advantage of using computational models to understand translation rates instead.
Amino acid quality modifies the quantitative availability of protein for reproduction inDrosophila melanogaster
Authors: Ma Carolyn , Mirth Christen K. , Hall Matthew D. , Piper Matthew D.W.
Published: March 2020

Diet composition, especially the relative abundance of key macronutrients, is well known to affect animal wellbeing by changing reproductive output, metabolism and length of life. However, less attention has been paid to the ways the quality of these nutrients modify these macronutrient interactions. Nutritional Geometry can be used to model the effects of multiple dietary components on life-history traits and to compare these responses when diet quality is varied. Previous studies have shown that dietary protein quality can be increased for egg production inDrosophila melanogasterby matching the dietary amino acid proportions to the balance of amino acids used by the sum of proteins in the fly’sin silicotranslated exome. Here, we show that dietary protein quality dramatically alters the effect of protein quantity on female reproduction across a broad range of diets varying in both protein and carbohydrate concentrations. These data show that when sources of ingredients vary, their relative value to the consumer can vastly differ and yield very different physiological outcomes. Such variations could be particularly important for meta analyses that look to draw generalisable conclusions from diverse studies.
A global Ramachandran score identifies protein structures with unlikely stereochemistry
Authors: Sobolev Oleg V. , Afonine Pavel V. , Moriarty Nigel W. , Hekkelman Maarten L. , Joosten Robbie P. , Perrakis Anastassis , Adams Paul D.
Published: March 2020

Ramachandran plots report the distribution of the (φ, Ψ) torsion angles of the protein backbone and are one of the best quality metrics of experimental structure models. Typically, validation software reports the number of residues belonging to “outlier”, “allowed” and “favored” regions. While “zero unexplained outliers” can be considered the current “gold standard”, this can be misleading if deviations from expected distributions, even within the favored region, are not considered. We therefore revisited the Ramachandran Z-score (Rama-Z), a quality metric introduced more than two decades ago, but underutilized. We describe a re-implementation of the Rama-Z score in the Computational Crystallography Toolbox along with a new algorithm to estimate its uncertainty for individual models; final implementations are available both in Phenix and in PDB-REDO. We discuss the interpretation of the Rama-Z score and advocate including it in the validation reports provided by the Protein Data Bank. We also advocate reporting it alongside the outlier/allowed/favored counts in structural publications.
Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of Norway spruce
Authors: Zhou Linghua , Chen Zhiqiang , Olsson Lars , Grahn Thomas , Karlsson Bo , Wu Harry X. , Lundqvist Sven-Olof , García-Gil María Rosario
Published: March 2020

Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce(Picea abies(L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. GS predictive abilities were comparable with those based on pedigree-based prediction. The highest PAs were reached with at least 80-90% of the dataset used as training set. Use of different statistical methods had no significant impact on the estimated PAs. We also compared the abilities to predict density, MFA and MOE of 19 year old trees with models trained on data from coring at different ages and to different depths into the stem. 78-95% of the maximal PAs obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3-5 rings towards the pith at tree age 10-12, thereby shortening the cycle and reducing the impact on the tree.
The Nucleocapsid Protein of SARS-CoV-2 Abolished Pluripotency in Human Induced Pluripotent Stem Cells
Authors: Lin Zebin , Wu Zhiming , Mai Jinlian , Zhou Lishi , Qian Yu , Cai Tian , Chen Zhenhua , Wang Ping , Lin Bin
Published: March 2020

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raging across the world, leading to a global mortality rate of 3.4% (estimated by World Health Organization in March 2020). As a potential vaccine and therapeutic target, the nucleocapsid protein of SARS-CoV-2 (nCoVN) functions in packaging the viral genome and viral self-assembly. To investigate the biological effects of nCoVN to human stem cells, genetically engineered human induced pluripotent stem cells (iPSC) expressing nCoVN (iPSC-nCoVN) were generated by lentiviral expression systems, in which the expression of nCoVN could be induced by the doxycycline. The proliferation rate of iPSC-nCoVN was decreased. Unexpectedly, the morphology of iPSC started to change after nCoVN expression for 7 days. The pluripotency marker TRA-1-81 were not detectable in iPSC-nCoVN after a four-day induction. Meanwhile, iPSC-nCoVN lost the ability for differentiation into cardiomyocytes with a routine differentiation protocol. The RNA-seq data of iPSC-nCoVN (induction for 30 days) and immunofluorescence assays illustrated that iPSC-nCoVN were turning to fibroblast-like cells. Our data suggested that nCoVN disrupted the pluripotent properties of iPSC and turned them into other types of cells, which provided a new insight to the pathogenic mechanism of SARS-CoV-2.
Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras
Authors: Vatansever Sezen , Erman Burak , Gümüş Zeynep H.
Published: March 2020

K-Ras is the most frequently mutated protein in human cancers. However, until very recently, its oncogenic mutants were viewed as undruggable. To develop inhibitors that directly target oncogenic K-Ras mutants, we need to understand both their mutant-specific and pan-mutant dynamics and conformations. Recently, we have investigated how the most frequently observed K-Ras mutation in cancer patients, G12D, changes its local dynamics and conformations1. Here, we extend our analysis to study and compare the local effects of other frequently observed oncogenic mutations, G12C, G12V, G13D and Q61H. For this purpose, we have performed Molecular Dynamics (MD) simulations of each mutant when active (GTP-bound) and inactive (GDP-bound), analyzed their trajectories, and compared how each mutant changes local residue conformations, inter-protein distance distributions, local flexibility and residue pair correlated motions. Our results reveal that in the four active oncogenic mutants we have studied, the α2 helix moves closer to the C-terminal of the α3 helix. However, P-loop mutations cause α3 helix to move away from Loop7, and only G12 mutations change the local conformational state populations of the protein. Furthermore, the motions of coupled residues are mutant-specific: G12 mutations lead to new negative correlations between residue motions, while Q61H destroys them. Overall, our findings on the local conformational states and protein dynamics of oncogenic K-Ras mutants can provide insights for both mutant-selective and pan-mutant targeted inhibition efforts.
Cell–cell adhesion in plant grafting is facilitated by β-1,4-glucanases
Authors: Notaguchi Michitaka , Kurotani Ken-ichi , Sato Yoshikatsu , Tabata Ryo , Kawakatsu Yaichi , Okayasu Koji , Sawai Yu , Okada Ryo , Asahina Masashi , Ichihashi Yasunori , Shirasu Ken , Suzuki Takamasa , Niwa Masaki , Higashiyama Tetsuya
Published: March 2020

Plant grafting is conducted for vegetative propagation in plants, whereby a piece of living tissue is attached to another tissue through establishment of cell–cell adhesion. Plant grafting has a long history in agriculture and has been applied to improve crop traits for thousands of years1. Plant grafting has mostly relied on the natural ability of a plant for wound healing. However, the compatibility of cell–cell adhesion typically limits graft combinations to closely related species2–4, and the mechanism by which cell–cell adhesion of injured tissues is established is largely unknown. Here, we show that a subclade of β-1,4-glucanases secreted into the extracellular region facilitates cell–cell adhesion near the graft interface.Nicotianashows a propensity for cell–cell adhesion with a diverse range of angiosperms, including vegetables, fruit trees, and monocots, in which cell wall reconstruction was promoted in a similar manner to conventional intrafamily grafting5–7. Using transcriptomic approaches, we identified a specific clade of β-1,4-glucanases that is upregulated during grafting in successful graft combinations but not in incompatible grafts and precedes graft adhesion in inter- and intrafamily grafts. Grafting was facilitated with an overexpressor of the β-1,4-glucanase and, usingNicotianastem as an interscion, we produced tomato fruits on rootstocks from other plant families. Our results demonstrate that the mechanism of cell–cell adhesion is partly conserved in plants and is a potential target to enhance plant grafting techniques.
A Reference Feature based method for Quantification and Identification of LC-MS based untargeted metabolomics
Authors: Luan Enhui , Cheng Ken , Long Qiaoyun , Li Dehua , Li Zhenyu , Liu Binghang , Wang Yalan , Li Wei , Guo Baosen , Tan Fengji , Yi Xiaoyi , Feng Lei , Song Jiaping , Zheng Hancheng
Published: March 2020

Batch inconsistency is a major problem when applying LC-MS based untargeted metabolomics in real-time analysis situation such as clinical diagnosis or health monitoring. And inefficiency of collecting MS2 is a major problem for metabolite identification. Here, we developed a reference-feature based quantification and identification strategy (RFQI). In RFQI, samples are individually profiled using a pre-fixed reference feature table. Quantification results show that RFQI improves features’ overlap rate and reduce variance across batches significantly in real-time-analysis mode, and can find more than 4-fold numbers of features. Besides, RFQI collects MS2 from consecutive increasing samples for metabolite identification of pre-fixed features, thus it can effectively compensate for the poor efficiency of MS2 collection in data-dependent acquisition mode. In summary, RFQI can make full advantage of consecutive increasing samples in real-time analysis situation, both for quantification and identification.
Identification and Expression Analysis of Heat Shock Proteins in Wheat Infected with Powdery Mildew and Stripe Rust
Authors: Zhang Hong , Guo Huan , Wang Guanghao , Wang Changyou , Wang Yajuan , Liu Xinlun , Ji Wanquan
Published: March 2020

Heat shock proteins (HSPs), which are encoded by conserved gene families in plants, are crucial for development and responses to diverse stresses. However, the wheat (Triticum aestivum) HSPs have not been systematically classified, especially those involved in protecting plants from disease. Here, we classified 119 DnaJ (Hsp40) proteins (TaDnaJs; encoded by 313 genes) and 41 Hsp70 proteins (TaHsp70s; encoded by 95 genes) into six and four groups, respectively, via a phylogenetic analysis. An examination of protein structures and a multiple sequence alignment revealed diversity in the TaDnaJ structural organization, but a highly conserved J-domain, which was usually characterized by an HPD motif followed by DRD or DED motifs. The expression profiles of these HSP-encoding homologous genes varied in response toBlumeria graminisf. sp.triticiandPuccinia striiformisf. sp.tritici. A quantitative real-time PCR analysis indicated a lack of similarity in the expression ofDnaJ70b, Hsp70-30b, andHsp90-4bin wheat infected byB. graminisf. sp.tritici, although the expression levels of these genes were abnormal in the infected resistant and susceptible lines. Furthermore, a direct interaction between DnaJ70 and TaHsp70-30 was not detected in a yeast two-hybrid assay. This study revealed the structure and expression profiles of the HSP-encoding genes in wheat. The resulting data may be useful for future functional analyses and for further elucidating the roles of wheat HSPs during responses to fungal infections.
Pseudomonas aeruginosaenhances the efficacy of norfloxacin againstStaphylococcus aureusbiofilms
Authors: Orazi Giulia , Jean-Pierre Fabrice , O’Toole George A.
Published: March 2020

The thick mucus within the airways of individuals with cystic fibrosis (CF) promotes frequent respiratory infections that are often polymicrobial.Pseudomonas aeruginosaandStaphylococcus aureusare two of the most prevalent pathogens that cause CF pulmonary infections, and both have been associated with worse lung function. Furthermore, the ability ofP. aeruginosaandS. aureusto form biofilms promotes the establishment of chronic infections that are often difficult to eradicate using antimicrobial agents. In this study, we found that multiple LasR-regulated exoproducts ofP. aeruginosa, including HQNO, siderophores, phenazines, and rhamnolipids, likely contribute to the ability ofP. aeruginosato shiftS. aureusnorfloxacin susceptibility profiles. Here, we observe that exposure toP. aeruginosaexoproducts leads to an increase in intracellular norfloxacin accumulation byS. aureus. We previously showed thatP. aeruginosasupernatant dissipatesS. aureusmembrane potential, and furthermore, depletion of theS. aureusproton-motive force recapitulates the effect ofP. aeruginosasupernatant on shifting norfloxacin sensitivity profiles of biofilm-grownS. aureus. From these results, we hypothesize that exposure toP. aeruginosaexoproducts leads to increased uptake of the drug and/or an impaired ability ofS. aureusto efflux norfloxacin. Our results illustrate that microbially-derived products can greatly alter the ability of antimicrobial agents to kill bacterial biofilms.

Importance

Pseudomonas aeruginosaandStaphylococcus aureusare frequently co-isolated from multiple infection sites, including the lungs of individuals with cystic fibrosis (CF) and non-healing diabetic foot ulcers. Co-infection withP. aeruginosaandS. aureushas been shown to produce worse outcomes compared to infection with one organism alone. Furthermore, the ability of these pathogens to form biofilms enables them to cause persistent infection and withstand antimicrobial therapy. In this study, we found thatP. aeruginosa-secreted products dramatically increase the ability of the antibiotic norfloxacin to killS. aureusbiofilms. Understanding how interspecies interactions alter the antibiotic susceptibility of bacterial biofilms may inform treatment decisions and inspire the development of new therapeutic strategies.
Sterol-response pathways mediate alkaline survival in diverse fungi
Authors: Brown Hannah E. , Telzrow Calla L. , Saelens Joseph W. , Fernandes Larissa , Alspaugh J. Andrew
Published: March 2020

The ability for cells to maintain homeostasis in the presence of extracellular stress is essential for their survival. Stress adaptations are especially important for microbial pathogens to respond to rapidly changing conditions, such as those encountered during the transition from the environment to the infected host. Many fungal pathogens have acquired the ability to quickly adapt to changes in extracellular pH to promote their survival in the various micro-environments encountered during a host infection. For example, the fungal-specific Rim/Pal alkaline response pathway has been well characterized in many fungal pathogens, includingCryptococcus neoformans. However, alternative mechanisms for sensing and responding to host pH have yet to be extensively studied. Recent observations from a genetic screen suggest that theC. neoformanssterol homeostasis pathway is required for growth at elevated pH. This work explores interactions among mechanisms of membrane homeostasis, alkaline pH tolerance, and Rim pathway activation. We find that the sterol homeostasis pathway is necessary for growth in an alkaline environment, and that an elevated pH is sufficient to induce Sre1 activation. This pH-mediated activation of the Sre1 transcription factor is linked to the biosynthesis of ergosterol, but is not dependent on Rim pathway signaling, suggesting that these two pathways are responding to alkaline pH independently. Furthermore, we discover thatC. neoformansis more susceptible to membrane-targeting antifungals in alkaline conditions highlighting the impact of micro-environmental pH on the treatment of invasive fungal infections. Together, these findings further connect membrane integrity and composition with the fungal pH response and pathogenesis.
SARS-CoV-2 proteome microarray for mapping COVID-19 antibody interactions at amino acid resolution
Authors: Wang Hongye , Hou Xin , Wu Xian , Liang Te , Zhang Xiaomei , Wang Dan , Teng Fei , Dai Jiayu , Duan Hu , Guo Shubin , Li Yongzhe , Yu Xiaobo
Published: March 2020

COVID-19 has quickly become a worldwide pandemic, which has significantly impacted the economy, education, and social interactions. Understanding the humoral antibody response to SARS-CoV-2 proteins may help identify biomarkers that can be used to detect and treat COVID-19 infection. However, no immuno-proteomics platform exists that can perform such proteome-wide analysis. To address this need, we created a SARS-CoV-2 proteome microarray to analyze antibody interactions at amino acid resolution by spotting peptides 15 amino acids long with 5-amino acid offsets representing full-length SARS-CoV-2 proteins. Moreover, the array processing time is short (1.5 hours), the dynamic range is ~2 orders of magnitude, and the lowest limit of detection is 94 pg/mL. Here, the SARS-CoV-2 proteome array reveals that antibodies commercially available for SARS-CoV-1 proteins can also target SARS-CoV-2 proteins. These readily available reagents could be used immediately in COVID-19 research. Second, IgM and IgG immunogenic epitopes of SARS-CoV-2 proteins were profiled in the serum of ten COVID-19 patients. Such epitope biomarkers provide insight into the immune response to COVID-19 and are potential targets for COVID-19 diagnosis and vaccine development. Finally, serological antibodies that may neutralize viral entry into host cells via the ACE2 receptor were identified. Further investigation into whether these antibodies can inhibit the propagation of SARS-CoV-2 is warranted. Antibody and epitope profiling in response to COVID-19 is possible with our peptide-based SARS-COV-2 proteome microarray. The data gleaned from the array could provide invaluable information to the scientific community to understand, detect, and treat COVID-19.
Structure based virtual screening identifies novel competitive inhibitors for the sialoglycan binding protein Hsa
Authors: Agarwal Rupesh , Bensing Barbara A. , Mi Dehui , Vinson Paige N. , Baudry Jerome , Iverson Tina M. , Smith Jeremy C.
Published: March 2020

Infective endocarditis (IE) is a cardiovascular disease often caused by bacteria of theviridansgroup of streptococci, which includesStreptococcus gordoniiandStreptococcus sanguinis. Previous research has found that a serine-rich repeat (SRR) proteins on theS. gordoniibacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialyated glycans displayed on human platelets. Despite its important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel inhibitors against the sialoglycan binding domain of the SRR adhesin protein Hsa from theS. gordoniistrain DL1.In silicocross screening against the glycan binding domains of closely related SRR proteins from five otherS. gordoniiorS. sanguinisstrains was also performed to further reduce false positives. Using ourin silicoscreening strategy we successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in anin vitroassay and bind competitively to adhesin protein Hsa (∼20% hit rate).
Immunological cross-reactions with paramyxovirus nucleoproteins may explain sporadic apparent ebolavirus seropositivity in European populations
Authors: Bishop Lisa A. , Müllner Marcell , Bjurhult-Kennedy Amalie , Lauder Robert M. , Gatherer Derek
Published: March 2020

Although confirmed outbreaks of Ebola Virus Disease (EVD) have been confined to central and west Africa, seropositivity to Zaire ebolavirus (EBOV) has been reported in other parts of Africa and even in one study from the early 1990s in Germany. The possible reasons for the discrepancy between serological studies and clinical evidence, remain uncertain. Here, we report anonymous serum donors sampled in Lancaster (UK) with seropositivity by ELISA to EBOV nucleoprotein at a frequency of approximately 2%. In one serum donor, we confirm the result using Western blot. This is only the second report of seropositivity for EBOV outside of Africa. Our samples are negative to EBOV glycoprotein, suggesting that the seropositivity is specific to the nucleoprotein and may be due to cross-reaction with antibodies produced by exposure to another virus. To investigate potential candidates for this cross-reacting virus, we perform bioinformatics analysis that suggests that EBOV nucleoprotein has structural similarity to paramyxovirus nucleoproteins at a candidate immunological epitope. Cross-reaction of antibodies against paramyxovirus nucleoproteins, with EBOV nucleoprotein antigens used in serological testing, may be the cause of the rare instances of ebolavirus seropositivity in Europe, and may also be a confounding factor in African serosurveys.
Molecular architecture of the luminal ring of theXenopus laevisnuclear pore complex
Authors: Zhang Yanqing , Li Sai , Zeng Chao , Huang Gaoxingyu , Zhu Xuechen , Wang Qifan , Wang Kunpeng , Zhou Qiang , Zhang Wusheng , Yang Guangwen , Liu Minhao , Tao Qinghua , Lei Jianlin , Shi Yigong
Published: March 2020

Nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC fromXenopus laevisoocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes, and a Grid domain, which serves as a rigid base for the Finger domain. Two neighbouring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighbouring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC.
“DOCK3 is a dosage-sensitive regulator of skeletal muscle and Duchenne muscular dystrophy-associated pathologies”
Authors: Reid Andrea L. , Wang Yimin , Samani Adrienne , Hightower Rylie M. , Lopez Michael A. , Gilbert Shawn R. , Ianov Lara , Crossman David K. , Dell’Italia Louis J. , Millay Douglas P. , van Groen Thomas , Halade Ganesh V. , Alexander Matthew S.
Published: March 2020

DOCK3 is a member of the DOCK family of guanine nucleotide exchange factors that function to regulate cell migration, fusion, and overall viability. Previously, we identified a miR-486/Dock3 signaling cascade that was dysregulated in dystrophin-deficient muscle which resulted in the overexpression ofDOCK3, however not much else is known about the role of DOCK3 in muscle. In this work, we characterize the functional role of DOCK3 in normal and dystrophic skeletal muscle. By utilizingDock3global knockout (Dock3KO) mice, we found reducingDock3gene via haploinsufficiency in DMD mice improved dystrophic muscle histology, however complete loss ofDock3worsened overall muscle function on a dystrophin-deficient background. Consistent with this,Dock3KO mice have impaired muscle architecture and myogenic differentiation defects. Moreover, transcriptomic analyses ofDock3knockout muscles reveal a decrease in factors known for myogenesis, suggesting a possible mechanism of action. These studies identifyDOCK3as a novel modulator of muscle fusion and muscle health and may yield additional therapeutic targets for treating dystrophic muscle symptoms.
A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples
Authors: Chen Wanqiu , Zhao Yongmei , Chen Xin , Xu Xiaojiang , Yang Zhaowei , Bi Yingtao , Chen Vicky , Li Jing , Choi Hannah , Ernest Ben , Tran Bao , Mehta Monika , Moos Malcolm , Farmer Andrew , Mir Alain , Kumar Parimal , Mehra Urvashi , Li Jian-Liang , Xiao Wenming , Wang Charles
Published: March 2020

Single-cell RNA sequencing (scRNA-seq) has become a very powerful technology for biomedical research and is becoming much more affordable as methods continue to evolve, but it is unknown how reproducible different platforms are using different bioinformatics pipelines, particularly the recently developed scRNA-seq batch correction algorithms. We carried out a comprehensive multi-center cross-platform comparison on different scRNA-seq platforms using standard reference samples. We compared six pre-processing pipelines, seven bioinformatics normalization procedures, and seven batch effect correction methods including CCA, MNN, Scanorama, BBKNN, Harmony, limma and ComBat to evaluate the performance and reproducibility of 20 scRNA-seq data sets derived from four different platforms and centers. We benchmarked scRNA-seq performance across different platforms and testing sites using global gene expression profiles as well as some cell-type specific marker genes. We showed that there were large batch effects; and the reproducibility of scRNA-seq across platforms was dictated both by the expression level of genes selected and the batch correction methods used. We found that CCA, MNN, and BBKNN all corrected the batch variations fairly well for the scRNA-seq data derived from biologically similar samples across platforms/sites. However, for the scRNA-seq data derived from or consisting of biologically distinct samples, limma and ComBat failed to correct batch effects, whereas CCA over-corrected the batch effect and misclassified the cell types and samples. In contrast, MNN, Harmony and BBKNN separated biologically different samples/cell types into correspondingly distinct dimensional subspaces; however, consistent with this algorithm’s logic, MNN required that the samples evaluated each contain a shared portion of highly similar cells. In summary, we found a great cross-platform consistency in separating two distinct samples when an appropriate batch correction method was used. We hope this large cross-platform/site scRNA-seq data set will provide a valuable resource, and that our findings will offer useful advice for the single-cell sequencing community.
On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation
Authors: Kordi Misagh , Kundu Soumya , Bansal Mukul S.
Published: March 2020

Horizontal gene transfer is one of the most important mechanisms for microbial evolution and adaptation. It is well known that horizontal gene transfer can be eitheradditiveorreplacingdepending on whether the transferred gene adds itself as a new gene in the recipient genome or replaces an existing homologous gene. Yet, all existing phylogenetic techniques for the inference of horizontal gene transfer assume either that all transfers are additive or that all transfers are replacing. This limitation not only affects the applicability and accuracy of these methods but also makes it difficult to distinguish between additive and replacing transfers.

Here, we address this important problem by formalizing a phylogenetic reconciliation framework that simultaneously models both additive and replacing transfer events. Specifically, we (1) introduce theDTRLreconciliation framework that explicitly models both additive and replacing transfer events, along with gene duplications and losses, (2) prove that the underlying computational problem is NP-hard, (3) perform the first experimental study to assess the impact of replacing transfer events on the accuracy of the traditional DTL reconciliation model (which assumes that all transfers are additive) and demonstrate that traditional DTL reconciliation remains highly robust to the presence of replacing transfers, (4) propose a simple heuristic algorithm for DTRL reconciliation based on classifying transfer events inferred through DTL reconciliation as being replacing or additive, and (5) evaluate the classification accuracy of the heuristic under a range of evolutionary conditions. Thus, this work lays the methodological and algorithmic foundations for estimating DTRL reconciliations and distinguishing between additive and replacing transfers.

An implementation of our heuristic for DTRL reconciliation is freely available open-source as part of the RANGER-DTL software package fromhttps://compbio.engr.uconn.edu/software/ranger-dtl/.
A Self-Immobilizing NIR Probe for Non-invasive Imaging of Senescence
Authors: Liu Jun , Ma Xiaowei , Cui Chao , Wang Ying , Deenik Philip R. , Cui Lina
Published: March 2020

Cellular senescence, a process that arrests the cell cycle, is a cellular stress response to various stimuli and is implicated in aging and age-related diseases. However, the understanding of senescence in living organisms is insufficient, largely due to the scarcity of sensitive tools for the detection of cellular senescencein vivo. Herein, we describe the development of a self-immobilizing near-infrared (NIR) probe that can be activated by senescence-associatedβ-Galactosidase (SA-β-Gal), a widely accepted senescence marker. The NIR fluorophore is turned on in the presence of SA-β-Gal, and the self-immobilizing group, based on quinone methide chemistry, retains the fluorescence signal to the site of activation. This strategy significantly improves the sensitivity of the probe from the one we developed before. We demonstrate the non-invasive imaging of drug-induced senescence in mice models.
CyclinD1 controls development of cerebellar granule cell progenitors through phosphorylation and stabilization of ATOH1
Authors: Miyashita Satoshi , Owa Tomoo , Seto Yusuke , Yamashita Mariko , Aida Shogo , Nishioka Tomoki , Kaibuchi Kozo , Kawaguchi Yoshiya , Taya Shinichiro , Hoshino Mikio
Published: March 2020

Here we report that CyclinD1 (CCND1) directly regulates both the proliferative and immature states of cerebellar granule cell progenitors (GCPs). CCND1 not only accelerates cell cycle but also upregulates ATOH1 protein, an essential transcription factor that maintains GCPs in an immature state. In cooperation with CDK4, CCND1 directly phosphorylates Ser309 of ATOH1, which inhibits additional phosphorylation at S328, consequently preventing Ser328 phosphorylation-dependent ATOH1 degradation. PROX1 downregulates Ccnd1 expression by histone-deacetylation of Ccnd1 promoter in GCPs, leading to cell cycle exit and differentiation. WNT signaling upregulates PROX1 expression in GCPs. These findings suggest that WNT-PROX1-CCND1-ATOH1 signaling cascade cooperatively controls proliferation and immaturity of GCPs. We revealed that the expression and phosphorylation levels of these molecules dynamically change during cerebellar development, which was suggested to determine appropriate differentiation rates from GCPs to GCs at distinct developmental stages. This study contributes to understanding the regulatory mechanism of GCPs as well as neural progenitors.
The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling
Authors: Fan Haoliang , Du Zhengming , Wang Fenfen , Wang Xiao , Wen Shao-Qing , Wang Lingxiang , Du Panxin , Liu Hai , Cao Shengping , Luo Zhenming , Han Bingbing , Huang Peiyu , Zhu Bofeng , Qiu Pingming
Published: March 2020

Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai-language speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics, however, the forensic associated studies on Hainan Li population are still insufficient.

Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™DNA Signature Prep Kit (DNA Primer Set A) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DAPA, it demonstrated that the STRs and iiSNPs in DAPA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three Datasets, which included the genetic data of (I). iiSNPs (27 populations, 2640 individuals), (II). Y-STRs (42 populations, 8281 individuals), and (III). Y-haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives.

In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
A NanoFE Simulation-based Surrogate Machine Learning Model to Predict Mechanical Functionality of Protein Networks from Live Confocal Imaging
Authors: Asgharzadeh Pouyan , Birkhold Annette I. , Triverdi Zubin , Özdemir Bugra , Reski Ralf , Röhrle Oliver
Published: March 2020

Sub-cellular mechanics plays a crucial role in a variety of biological functions and dysfunctions. Due to the strong structure-function relationship in cytoskeletal protein networks, light can be shed on their mechanical functionality by investigating their structures. Here, we present a data-driven approach employing a combination of confocal live imaging of fluorescent tagged protein networks, in-silico mechanical experiments and machine learning to investigate this relationship. Our designed image processing and nanoFE mechanical simulation framework resolves the structure and mechanical behaviour of cytoskeletal networks and the developed gradient boosting surrogate models link network structure to its functionality. In this study, for the first time, we perform mechanical simulations of Filamentous Temperature Sensitive Z (FtsZ) complex protein networks with close-to-reality network geometry depicting its skeletal functionality inside organelles (here, chloroplasts) of the mossPhyscomitrella patens. Training on synthetically produced simulation data enables predicting the mechanical characteristics of FtsZ network mechanics purely based on its structural features (R2≥ 0.93), therefore allowing to extract structural principles enabling specific mechanical traits of FtsZ, such as load bearing and resistance to buckling failure in case of large network deformation. The presented method and the specific in silico findings from its application may allow in the future to reproduce mechanical cell responses in engineered environments.
Spatio-temporal analysis at landscape scale of the Iberian oak decline epidemic caused by Phytophthora cinnamomi
Authors: Cardillo Enrique , Abad Enrique , Meyer Sebastian
Published: March 2020

Phytophthora cinnamomiRands is considered a main factor behind the Iberian oak decline (IOD). This epidemic is decimating Holm oaks (Quercus ilexL.) and cork oaks (Quercus suberL.) which are the keystone trees of a multipurpose, silvo-pastoral and semi-natural ecosystem of 3.1 million hectares in the south west of Europe. Forest diseases are characterized by pronounced spatial patterns, since many of the underlying ecological processes are inherently spatial. To improve the current understanding of such processes, we carried out a complete census of diseased sites via aerial imagery at landscape scale at four different dates over a period of 35 years. We validated our photographic interpretation ofP. cinnamomipresence in-situ by subsampling soil and roots of diseased sites. To analyse the role of host population heterogeneities in shaping the spread of IOD, we used a ‘self-exciting’ spatio-temporal point process model. Its so-called epidemic component represents the inoculum pressure arising from nearby foci whereas its background component allows for sporadic infections from unobserved sources or disease transmission over larger distances. The best fit was obtained with a lagged power-law for the spatial dispersal kernel, where 49% of the infections triggered by an infected site occur within a distance of 250 meters. Both risk components were found to increase over time. The rate of sporadic infections appeared to be significantly lower in silvo-pastoral systems (dehesas) than in forests and higher in mixed stands and shrub encroached oak-lands. These results may have direct implications for IOD management, for example, the estimated spatial dispersal function helps to define a suitable target area for more efficient control measures. Our results also suggest that silviculture treatments aimed at controlling the density and species composition of oak stands, as well as the abundance of shrubs, could play a key role for disease management
Comprehensive proteomics analyses identify PIM kinases as key regulators of IL-15 driven activation of intestinal intraepithelial lymphocytes
Authors: James Olivia J. , Vanderyken Maud , Marchingo Julia M. , Singh Francois , Love Andrew G. , Swamy Mahima
Published: March 2020

Intestinal intraepithelial lymphocytes (IEL) are an abundant population of tissue-resident T cells that protect the gut from pathogens and maintain intestinal homeostasis. The cytokine IL-15 is transpresented by epithelial cells to IEL in complex with the IL-15 receptor α chain (IL-15Rα). It plays essential roles both in maintaining IEL homeostasis, and in inducing IEL activation in response to epithelial stress. IL-15 overexpression also drives the gluten-induced enteropathy Coeliac disease, through cytotoxic activation of IEL. In order to better understand how IL-15 directly regulates both homeostatic and inflammatory functions of IEL, we set up quantitative proteomics of IL-15/Rα stimulated IEL. We reveal that high IL-15/Rα stimulation licenses cell cycle activation, upregulates the biosynthetic machinery in IEL, increases mitochondrial respiratory capacity and induces expression of cell surface immune receptors and adhesion proteins that potentially drive IEL activation. We find that high IL-15/Rα selectively upregulated the Ser/Thr kinases PIM1 and PIM2 and demonstrate that PIM1/2 are essential for IEL to proliferate, grow, and upregulate Granzyme B in response to high IL-15. Significantly, IEL from Coeliac disease patients express high levels of PIM kinases. These unexpected findings reveal PIM kinases to be key determinants of IEL responses to elevated levels of IL-15.
Chromatin-based mechanisms to coordinate convergent overlapping transcription
Authors: Inagaki Soichi , Takahashi Mayumi , Takashima Kazuya , Oya Satoyo , Kakutani Tetsuji
Published: March 2020

In eukaryotic genomes, transcription units of genes often overlap with other protein-coding and/or noncoding transcription units1,2. In such intertwined genomes, coordinated transcription of nearby or overlapping genes would be important to ensure integrity of genome function; however, the mechanisms underlying this coordination are largely unknown3-6. Here, we show inArabidopsis thalianathat genes with convergent orientation of transcription are major sources of overlapping bidirectional transcripts and that these bidirectionally transcribed genes are regulated by a putative LSD1 family histone demethylase, FLD7,8. Our genome-wide chromatin profiling revealed that FLD downregulated histone H3K4me1 in regions with convergent overlapping transcription. FLD localizes to actively transcribed genes where it colocalizes with elongating RNA polymerase II phosphorylated at Ser-2 or Ser-5 sites. Genome-wide transcription analyses suggest that FLD-mediated H3K4me1 removal negatively regulates bidirectional transcription by retaining the elongating transcription machinery. Furthermore, this effect of FLD on transcription dynamics is mediated by DNA topoisomerase I. Our study has revealed chromatin-based mechanisms to cope with overlapping bidirectional transcription, likely by modulating DNA topology. This global mechanism to cope with bidirectional transcription could be co-opted for specific epigenetic processes, such as cellular memory of responses to environment9.
Loss of Activating Transcription Factor 3 prevents KRAS-mediated pancreatic cancer
Authors: Azizi Nawab , Toma Jelena , Martin Mickenzie , Khalid Muhammad Faran , Steele Nina , Shi Jiaqi , Pasca di Magliano Marina , Pin Christopher L.
Published: March 2020

The unfolded protein response (UPR) is activated in pancreatic pathologies and suggested as a target for therapeutic intervention. In this study, wxe examined Activating Transcription Factor 3 (ATF3), a mediator of the UPR which promotes acinar-to-ductal metaplasia (ADM) in response to pancreatic injury. Since ADM is an initial step in the progression to pancreatic ductal adenocarcinoma (PDAC), we hypothesized ATF3 is required for initiation and progression of PDAC. We generated mice carrying a germ line mutation ofAtf3(Atf3-/-) combined with acinar-specific induction of oncogenic KRAS (Ptf1acreERT/+KrasLSL-G12D).Atf3-/-mice with (termedAPK) and without KRASG12Dwere exposed to cerulein-induced pancreatitis. In response to recurrent pancreatitis,Atf3-/-mice showed decreased ADM and enhanced regeneration based on morphological and biochemical analysis. Similarly, an absence of ATF3 reduced spontaneous pancreatic intraepithelial neoplasia formation and PDAC inPtf1acreERT/+KrasLSL-G12Dmice. In response to injury, KRASG12Dbipassed the requirement for ATF3 with a dramatic loss in acinar tissue and PanIN formation observed regardless of ATF3 status. However, unlikePtf1acreERT/+KrasLSL-G12Dmice,APKmice exhibited a cachexia-like phenotype, did not progress through to PDAC, and showed altered pancreatic fibrosis and immune cell infiltration. These findings suggest a complex, multifaceted role for ATF3 in pancreatic cancer pathology.
Abiotic drivers of protein abundance variation among natural populations
Authors: Ebner Joshua Niklas , Ritz Danilo , Fumetti Stefanie von
Published: March 2020

Identifying when and where environmental change induces molecular responses in natural populations is an important goal in contemporary ecology. It can aid in identifying molecular signatures of populations experiencing stressful conditions and potentially inform if species are approaching the limits of their tolerance niches. Achieving this goal is hampered by our limited understanding of the influence of environmental variation on the molecular systems of most ecologically relevant species as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms under controlled laboratory conditions. In this study, we establish relationships between protein abundance patterns and the abiotic environment by profiling the proteomes of 24 natural populations of the caddisflyCrunoecia irrorata.We subsequently relate these profiles to natural variations in the abiotic characteristics of their freshwater spring habitats which shows that protein abundances and networks respond to abiotic variation according to the functional roles these proteins have. We provide evidence that geographic and past and present environmental differences between sites affect protein abundances and identifications, and that baseline reaction norms are ubiquitous and can be used as information rather than noise in comparative field studies. Taking this natural variation into account is a prerequisite if we are to identify the effects environmental change has on natural populations.