bluuebunny/crossref_metadata_2025 huggingface dataset:
Developingin vivoassays for investigation of p75NTRand NRH1 transmembrane domain cleavage events using zebrafish embryos
Authors: Jayne Tanya , Newman Morgan , Lardelli Michael
Published: May 2020

γ-secretase is an important protease complex responsible for the cleavage of over 100 substrates within their transmembrane domains. γ-secretase acts in Alzheimer’s disease by cleavage of AMYLOID BETA (A4) PRECURSOR PROTEIN to produce aggregation-prone Amyloid beta peptide. Other γ-secretase substrates such as p75NTRare also relevant to Alzheimer’s disease. How γ-secretase cleavage site specificity is determined is still unclear. A previous study usingXenopus laevisto investigate the proteolytic processing of p75NTRand its homolog NRH1 found that transmembrane cleavage of NRH1 was not sensitive to the γ-secretase inhibitor DAPT, suggesting that it is not processed by γ-secretase. To investigate this further, we identified zebrafish orthologues of the genes p75NTRand NRH1 and developedin vivoassays to assess cleavage of the resultant p75NTRand Nrh1 proteins. Our observations from these assays in zebrafish are consistent with theXenopus laevisstudy. Inhibition of γ-secretase by DAPT treatment results in accumulation of uncleaved p75NTRsubstrate, while cleavage of Nrh1 is not affected. This supports that p75NTRis cleaved by γ-secretase while Nrh1 is cleaved by a separate γ-secretase-like activity. We extended our approach by generating a chimeric Nrh1 protein in which the Nrh1 transmembrane domain was replaced by that of p75NTR, in an attempt to determine whether it is the p75NTRTMD that confers susceptibility for γ-secretase cleavage. Our results from analysis of this chimeric protein revealed that the p75NTRtransmembrane domain alone is insufficient to confer γ-secretase cleavage susceptibility. This is not completely unexpected, as there is evidence to suggest that other factors are crucial for selection/cleavage by the γ-secretase complex. We have established a system in which we can now attempt to dissect the structural basis for γ-secretase cleavage specificity and evolution.
Circumstances and factors of sleep-related sudden infancy deaths in Japan
Authors: Osawa Motoki , Ueno Yasuhiro , Ikeda Noriaki , Ikematsu Kazuya , Yamamoto Takuma , Irie Wataru , Kozawa Shuji , Kotani Hirokazu , Hamayasu Hideki , Murase Takehiko , Shingu Keita , Sugimoto Marie , Nagao Ryoko , Kakimoto Yu
Published: May 2020

Background

Sudden unexpected death in infancy (SUDI) comprises both natural and unnatural causes of death. However, a few epidemiological surveys have investigated SUDI in Japan.

Objective

This retrospective study was conducted to investigate the recent trends of circumstances and risk factors of sleep-related SUDI cases.

Methods

Forensic pathology sections from eight universities participated in the selection of subjects from 2013 to 2018. Data obtained from the checklist form were analyzed based on information at postmortem.

Results

There were 259 SUDI cases consisting of 145 male infants and 114 female infants with a mean birth weight of 2888 ± 553 and 2750 ± 370 g, respectively. Deaths most frequently occurred among infants at 1 month of age (18%). According to population-based analyses, the odds ratio (95% confidence interval) of mother’s age ≤19 years was 11.1 (6.9–17.7) compared with ages 30–39. The odds ratio for the fourth- and later born infants was 5.2 (3.4–7.9) compared with the frequency of first-born infants. The most frequent time of day for discovery was between 7 and 8 o’clock. Co-sleeping was recorded for 61%, and the prone position was found for 40% of cases at discovery. Mother’s smoking habit exhibited an adds ratio of 4.5 (2.9–5.8).

Conclusion

This study confirmed the trends that have been observed for sudden infant death syndrome; particularly, very high odds ratios were evident for teenage mothers and later birth order in comparison with those in other developed countries. The child of a young mother tended to die within 2 months of age. To our knowledge, this is the first report of an extensive survey of sleep-related SUDI in Japan.
Genetic variation associated with PPO-inhibiting herbicide tolerance in sorghum
Authors: Adhikari Pragya , Goodrich Emma , Fernandes Samuel B. , Lipka Alexander E. , Tranel Patrick , Brown Patrick , Jamann Tiffany M.
Published: May 2020

Herbicide application is crucial for weed management in most crop production systems, but for sorghum herbicide options are limited. Sorghum is sensitive to residual protoporphyrinogen oxidase (PPO)- inhibiting herbicides, such as fomesafen, and a long re-entry period is required before sorghum can be planted after its application. Improving sorghum for tolerance to such residual herbicides would allow for increased sorghum production and the expansion of herbicide options for growers. To investigate the underlying mechanism of tolerance to residual fomesafen, a genome-wide association mapping study was conducted using the sorghum biomass panel (SBP) and field-collected data, and a greenhouse assay was developed to confirm the field phenotypes. A total of 26 significant SNPs (FDR<0.05), spanning a 215.3 kb region, were detected on chromosome 3. The ten most significant SNPs included two in genic regions (Sobic.003G136800, and Sobic.003G136900) and eight SNPs in the intergenic region encompassing the genes Sobic.003G136700, Sobic.003G136800, Sobic.003G137000, Sobic.003G136900, and Sobic.003G137100. The gene Sobic.003G137100 (PPXI), which encodes the PPO1 enzyme, one of the targets of PPO-inhibiting herbicides, was located 12kb downstream of the significant SNP S03_13152838. We found thatPPXIis highly conserved in sorghum and expression does not significantly differ between tolerant and sensitive sorghum lines. Our results suggest thatPPXImost likely does not underlie the observed herbicide tolerance. Instead, the mechanism underlying herbicide tolerance in the SBP is likely metabolism-based resistance, possibly regulated by the action of multiple genes. Further research is necessary to confirm candidate genes and their functions.
Network-based atrophy modelling in the common epilepsies: a worldwide ENIGMA study
Authors: Larivière Sara , Rodríguez-Cruces Raúl , Royer Jessica , Caligiuri Maria Eugenia , Gambardella Antonio , Concha Luis , Keller Simon S. , Cendes Fernando , Yasuda Clarissa , Bonilha Leonardo , Gleichgerrcht Ezequiel , Focke Niels K. , Domin Martin , Podewills Felix von , Langner Soenke , Rummel Christian , Wiest Roland , Martin Pascal , Kotikalapudi Raviteja , O’Brien Terence J. , Sinclair Benjamin , Vivash Lucy , Desmond Patricia M. , Alhusaini Saud , Doherty Colin P. , Cavalleri Gianpiero L. , Delanty Norman , Kälviäinen Reetta , Jackson Graeme D. , Kowalczyk Magdalena , Mascalchi Mario , Semmelroch Mira , Thomas Rhys H. , Soltanian-Zadeh Hamid , Davoodi-Bojd Esmaeil , Zhang Junsong , Lenge Matteo , Guerrini Renzo , Bartolini Emanuele , Hamandi Khalid , Foley Sonya , Weber Bernd , Depondt Chantal , Absil Julie , Carr Sarah J. A. , Abela Eugenio , Richardson Mark P. , Devinsky Orrin , Severino Mariasavina , Striano Pasquale , Tortora Domenico , Hatton Sean N. , Vos Sjoerd B. , Duncan John S. , Whelan Christopher D. , Thompson Paul M. , Sisodiya Sanjay M. , Bernasconi Andrea , Labate Angelo , McDonald Carrie R. , Bernasconi Neda , Bernhardt Boris C.
Published: May 2020

Epilepsy is increasingly conceptualized as a network disorder. In this cross-sectional mega-analysis, we integrated neuroimaging and connectome analysis to identify network associations with atrophy patterns in 1,021 adults with epilepsy compared to 1,564 healthy controls from 19 international sites. In temporal lobe epilepsy, areas of atrophy co-localized with highly interconnected cortical hub regions, whereas idiopathic generalized epilepsy showed preferential subcortical hub involvement. These morphological abnormalities were anchored to the connectivity profiles of distinct disease epicenters, pointing to temporo-limbic cortices in temporal lobe epilepsy and fronto-central cortices in idiopathic generalized epilepsy. Indices of progressive atrophy further revealed a strong influence of connectome architecture on disease progression in temporal lobe, but not idiopathic generalized, epilepsy. Our findings were reproduced across individual sites and single patients, and were robust across different analytical methods. Through worldwide collaboration in ENIGMA-Epilepsy, we provided novel insights into the macroscale features that shape the pathophysiology of common epilepsies.
Chromatin Regulates Bipartite-Classified Small RNA Expression to Maintain Epigenome Homeostasis in Arabidopsis
Authors: Papareddy Ranjith K. , Páldi Katalin , Paulraj Subramanian , Kao Ping , Nodine Michael D.
Published: May 2020

Eukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development, and must be properly re-established after its decondensation. Small interfering RNAs (siRNAs) promote heterochromatin formation in eukaryotes, but little is known about how chromatin regulates siRNA transcription. We demonstrated that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs inArabidopsis thalianaembryos. Depending on whether they are located in euchromatic or heterochromatic regions of the genome, bipartite-classified TEs generate siRNAs throughout embryogenesis according to two distinct patterns. siRNAs are transcribed in embryos and required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation. Decondensed chromatin also permits the production of 24-nt siRNAs from heterochromatic TEs during post-embryogenesis, and siRNA production from bipartite-classified TEs is controlled by their chromatin states. Decondensation of heterochromatin in response to developmental, and perhaps environmental, cues promotes the transcription and function of siRNAs in plants. Our results indicate that chromatin-mediated siRNA transcription provides a cell-autonomous homeostatic control mechanism to reconstitute pre-existing chromatin states during growth and development including those that ensure silencing of TEs in the future germ line.
A pan-cancer atlas of transcriptional dependence on DNA methylation and copy number aberrations
Authors: Fougner Christian , Höglander Elen K. , Lien Tonje G. , Sørlie Therese , Nord Silje , Lingjærde Ole Christian
Published: May 2020

Cancer transcriptomes are shaped by genetic and epigenetic features, such as DNA methylation and copy number aberrations. Knowledge of the relationships between gene expression and such features is fundamental to understanding the basis of tumor phenotypes. Here, we present a pan-cancer atlas of transcriptional dependence on DNA methylation and copy number aberrations (PANORAMA). Our analyses suggest that copy number alterations are a central driver of inter-tumor heterogeneity, while the majority of expression-methylation associations found in cancer are a reflection of cell-of-origin and normal cell admixture. The atlas is made available through an online tool athttps://pancancer.app.
Cognitive and Motor Correlates of Grey and White Matter Pathology in Parkinson’s Disease
Authors: Dadar Mahsa , Gee Myrlene , Shuaib Ashfaq , Duchesne Simon , Camicioli Richard
Published: May 2020

Introduction

Previous studies have found associations between grey matter atrophy and white matter hyperintensities (WMH) of vascular origin with cognitive and motor deficits in Parkinson’s disease (PD). Here we investigate these relationships in a sample of PD patients and age-matched healthy controls.

Methods

Data included 50 PD patients and 45 age-matched controls with T1-weighted and FLAIR scans at baseline, 18-months, and 36-months follow-up. Deformation-based morphometry was used to measure grey matter atrophy. SNIPE (Scoring by Nonlocal Image Patch Estimator) was used to measure Alzheimer’s disease-like textural patterns in the hippocampi. WMHs were segmented using T1-weighted and FLAIR images. The relationship between MRI features and clinical scores was assessed using mixed-effects models. The motor subscore of the Unified Parkinson’s Disease Rating Scale (UPDRSIII), number of steps in a walking trial, and Dementia Rating Scale (DRS) were used respectively as measures of motor function, gait, and cognition.

Results

Substantia nigra atrophy was significantly associated with motor deficits, with a greater impact in PDs (p<0.05). Hippocampal SNIPE scores were associated with cognitve decline in both PD and controls (p<0.01). WMH burden was significantly associated with cognitive decline and increased motor deficits in the PD group, and gait deficits in both PD and controls (p<0.03).

Conclusion

While substantia nigra atrophy and WMH burden were significantly associated with additional motor deficits, WMH burden and hippocampal atrophy were associated with cognitive deficits in PD patients. These results suggest an additive contribution of both grey and white matter damage to the motor and cognitive deficits in PD.
Pathologic α-Synuclein Species Activate LRRK2 in Pro-Inflammatory Monocyte and Macrophage Responses
Authors: Xu Enquan , Boddu Ravindra , Abdelmotilib Hisham A. , Kelly Kaela , Sokratian Arpine , Harms Ashley S. , Schonhoff Aubrey M. , Bryant Nicole , Harmsen Irene E. , Schlossmacher Michael G. , Chandra Sidhanth , Krendelshchikova Valentina , Liu Zhiyong , West Andrew B.
Published: May 2020

Missense mutations in theLRRK2gene that lead to LRRK2 kinase hyperactivity can cause Parkinson’s disease (PD). The link between LRRK2 and α-synuclein aggregation in PD remains enigmatic. Numerous reports suggest critical LRRK2 functions in microglial responses. Herein, we find that LRRK2-positive immune cells in the brain represent CD68-positive pro-inflammatory, monocyte-derived macrophages, distinct from microglia. Rod α-synuclein fibrils stimulate LRRK2 kinase activity in monocyte-derived macrophages, and LRRK2 mutations lead to enhanced recruitment of classical monocytes into the midbrain in response to α-synuclein. LRRK2 kinase inhibition blocks α-synuclein fibril induction of LRRK2 protein in both human and murine macrophages, with human cells demonstrating much higher LRRK2 levels and kinase activity than equivalent murine cells. Further, interferon-γ strongly induces LRRK2 kinase activity in primary human macrophages in comparison to weak effects observed in murine cells. These results highlight peripheral immune responses in LRRK2-linked paradigms that further connect two central proteins in PD.
Highly accurate long-read HiFi sequencing data for five complex genomes
Authors: Hon Ting , Mars Kristin , Young Greg , Tsai Yu-Chih , Karalius Joseph W. , Landolin Jane M. , Maurer Nicholas , Kudrna David , Hardigan Michael A. , Steiner Cynthia C. , Knapp Steven J. , Ware Doreen , Shapiro Beth , Peluso Paul , Rank David R.
Published: May 2020

The PacBio®HiFi sequencing method yields highly accurate long-read sequencing datasets with read lengths averaging 10-25 kb and accuracies greater than 99.5%. These accurate long reads can be used to improve results for complex applications such as single nucleotide and structural variant detection, genome assembly, assembly of difficult polyploid or highly repetitive genomes, and assembly of metagenomes. Currently, there is a need for sample data sets to both evaluate the benefits of these long accurate reads as well as for development of bioinformatic tools including genome assemblers, variant callers, and haplotyping algorithms. We present deep coverage HiFi datasets for five complex samples including the two inbred model genomesMus musculusandZea mays, as well as two complex genomes, octoploidFragaria×ananassaand the diploid anuranRana muscosa. Additionally, we release sequence data from a mock metagenome community. The datasets reported here can be used without restriction to develop new algorithms and explore complex genome structure and evolution. Data were generated on the PacBio Sequel II System.
Yeast Rgd3 is a phospho-regulated F-BAR-containing RhoGAP involved in the regulation of Rho3 distribution and cell morphology
Authors: Gingras Robert M. , Lwin Kyaw Myo , Miller Abigail M. , Bretscher Anthony
Published: May 2020

Polarized growth requires the integration of polarity pathways with the delivery of exocytic vesicles for cell expansion and counterbalancing endocytic uptake. In budding yeast, the myosin-V Myo2 is aided by the kinesin-related protein Smy1 in carrying out the essential Sec4-dependent transport of secretory vesicles to sites of polarized growth. Over-expression suppressors of a conditionalmyo2 smy1mutant identified a novel F-BAR-containing RhoGAP, Rgd3, that has activity primarily on Rho3, but also Cdc42. Internally tagged Rho3 is restricted to the plasma membrane in a gradient corresponding to cell polarity that is altered upon Rgd3 over-expression. Rgd3 itself is localized to dynamic polarized vesicles that, while distinct from constitutive secretory vesicles, are dependent on actin and Myo2 function.In vitroRgd3 associates with liposomes in a PIP2-enhanced manner. Further, the Rgd3 C-terminal region contains several phosphorylatable residues within a reported SH3-binding motif. An unphosphorylated mimetic construct is active and highly polarized, while the phospho-mimetic form is not. Rgd3 is capable of activating Myo2, dependent on its phospho-state and Rgd3 overexpression rescues aberrant Rho3 localization and cell morphologies seen at the restrictive temperature in themyo2 smy1mutant. We propose a model where Rgd3 functions to modulate and maintain Rho3 polarity during growth.
Progress in quickly finding orthologs as reciprocal best hits
Authors: Hernández-Salmerón Julie E , Moreno-Hagelsieb Gabriel
Published: May 2020

Introduction

Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). Here we compared RBH results, between prokaryotic genomes, obtained using software that runs faster than blastp. Namely, lastal, diamond, and MMseqs2.

Results

We found that lastal required the least time to produce results. However, it yielded fewer results than any other program when comparing evolutionarily distant genomes. The program producing the most similar number of RBH as blastp was MMseqs2. This program also resulted in the lowest error estimates among the programs tested. The results with diamond were very close to those obtained with MMseqs2, with diamond running faster. Our results suggest that the best of the programs tested was diamond, ran with the “sensitive” option, which took 7% of the time as blastp to run, and produced results with lower error rates than blastp.

Availability

A program to obtain reciprocal best hits using the software we tested is maintained athttps://github.com/Computational-conSequences/SequenceTools
Breeding success of Eleonora’s falcon (Falco eleonorae) in Cyprus revisited using survey techniques for cliff-nesting species
Authors: Hadjikyriakou Thomas G. , Kassinis Nikolaos , Skarlatos Dimitrios , Charilaou Pantelis , Kirschel Alexander N. G.
Published: May 2020

The global breeding population of Eleonora’s falcon is distributed from the Canary Islands in the west, across the Mediterranean Sea, to Cyprus in the east. The remoteness of nesting colonies, which are predominantly located on sea cliffs and islets, renders breeding success estimation a challenging task, requiring a composite approach to assess each of the breeding stages. Early estimates of the breeding success of Eleonora’s falcon suggested that Akrotiri colony in Cyprus had the lowest breeding success among all the colonies throughout the species’ breeding range, at a level seemingly unsustainable, suggesting the colony might have been in danger of gradual extinction. Here we use a diversity of survey methods using boat, ground and aerial surveys, with the incorporation of photography and photogrammetry, to reassess the breeding success and the effect of nest characteristics on the Eleonora’s falcon breeding population in Cyprus. During a six-year study, we found that Cyprus hosts ~138 ± 8 breeding pairs and that breeding success equals 1.54 ± 0.85 fledglings per breeding pair, thus considerably higher than previous estimates. In addition, by analyzing temporal variation in breeding and nest characteristics, we found that early breeding and reuse of nests positively influence breeding success, but physical nest characteristics have a limited effect on colony productivity. The range of survey methods employed, as well as the array of photography techniques utilized, highly enhanced the efficiency and accuracy of this study, allowing us to overcome the challenge of inaccessibility of nesting cliffs.
Decomposition of transcriptional responses provides insights into differential antibiotic susceptibility
Authors: Sastry Anand , Dillon Nick , Poudel Saugat , Hefner Ying , Xu Sibei , Szubin Richard , Feist Adam , Nizet Victor , Palsson Bernhard
Published: May 2020

Responses of bacteria to antibiotic treatments depend on their environments. Differences betweenin vitrotesting conditions and the physiological environments inside patients have resulted in poor antibiotic susceptibility predictions, contributing to treatment failures in the clinic. Here, we investigate how media composition affects antibiotic susceptibility in the laboratory strainE. coliK-12 MG1655, and contextualize these changes through machine learning of transcriptomics data. We show that complex transcriptional changes induced by different media or antibiotic treatment can be traced back to a few key regulators. Integration of results from machine learning with biochemical knowledge reveals fundamental shifts in respiration and iron availability that may explain media-dependent differential susceptibility to antibiotics. The data generation and analytical workflow used here can interrogate the regulatory state of a pathogen under any condition, and can be extended to additional strains and organisms for which data is available.
ALKBH7 mediates necrosis via rewiring of glyoxal metabolism
Authors: Kulkarni Chaitanya A. , Nadtochiy Sergiy M. , Kennedy Leslie , Zhang Jimmy , Chhim Sophea , Alwaseem Hanan , Murphy Elizabeth , Fu Dragony , Brookes Paul S.
Published: May 2020

Alkb homolog 7 (ALKBH7) is a mitochondrial α-ketoglutarate dioxygenase required for necrotic cell death in response to DNA alkylating agents, but its physiologic role within tissues remains unclear. Herein, we show that ALKBH7 plays a key role in the regulation of dialdehyde metabolism, which impacts cardiac survival in response to ischemia-reperfusion (IR) injury. Using a multi-omics approach, we do not find evidence that ALKBH7 functions as a prolyl-hydroxylase. However, we do find that mice lacking ALKBH7 exhibit a significant increase in glyoxalase I (GLO-1), a dialdehyde detoxifying enzyme. Consistent with increased dialdehyde production, metabolomics analysis reveals rewiring of metabolic pathways related to the toxic glycolytic by-product methylglyoxal (MGO), as well as accelerated glycolysis and elevated levels of MGO protein adducts, in mice lacking ALKBH7. Consistent with roles for both necrosis and glycative stress in cardiac IR injury, hearts from male but not femaleAlkbh7-/-mice are protected against IR, although somewhat unexpectedly this protection does not appear to involve modulation of the mitochondrial permeability transition pore. Highlighting the importance of MGO metabolism for the observed protection, removal of glucose as a metabolic substrate or pharmacologic inhibition of GLO-1 both abrogate cardioprotection in ALKBH7 deficient mice. Integrating these observations, we propose that ALKBH7 plays a role in the regulation of glyoxal metabolism, and that protection against necrosis and IR injury bought on by ALKBH7 deficiency originates from hormetic signaling in response to elevated MGO stress.
Dual-located WHIRLY1 affects salicylic acid homeostasisviacoordination of ICS1, PAL1 and BSMT1 duringArabidopsisplant aging
Authors: Lin Wenfang , Zhang Hong , Huang Dongmei , Schenke Dirk , Cai Daguang , Wu Binghua , Miao Ying
Published: May 2020

Salicylic acid (SA) homeostasis determines also developmental senescence and is spatiotemporally controlled by various mechanisms, including biosynthesis, transport and conjugate formation. The alteration of WHIRLY1 (WHY1), a repressor of leaf natural senescence, with respect to allocation in the nucleus or chloroplast causes a perturbation in SA homeostasis, resulting in adverse plant senescence phenotypes. Loss ofWHY1resulted in a 5 days earlier SA peak compared to wild type plants which accumulated SA at 42 days after germination. SA accumulation coincided with an early leaf senescence phenotype, which could be prevented by ectopic expression of the nuclear WHY1 isoform (nWHY1). However, expressing the plastid WHY1 isoform (pWHY1) greatly enhanced cellular SA levels. A global transcriptional analysis in WHY1 loss-of-function background by expressing either pWHY1 or nWHY1 indicated that hormone metabolism related genes were most significantly altered. The pWHY1 isoform predominantly affected stress related gene expression, while the nWHY1 controlled rather developmental gene expression. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) assays indicated that nWHY1 directly binds to the promoter region of isochorismate synthase (ICS1)to activateitsexpression at later stage, but indirectly activated S-adenosyl-L-methionine-dependent methyltransferase (BSMT1)gene expressionviaethylene response factor 109 (ERF109), while repressing phenylalanine ammonia lyase (PAL1)expressionviaR2R3-MYB member 15 (MYB15) at the early stage of development. Interestingly, rising SA levels exerted a feedback effect by inducing nWHY1 modification and pWHY1 accumulation. Thus, the alteration of WHY1 organelle isoforms and the feedback of SA intervened in a circularly integrated regulatory network during developmental or stress-induced senescence inArabidopsis.
A lectin that targets specific bacteria for killing on DNA-based extracellular traps
Authors: Farinholt Timothy , Dinh Christopher , Kuspa Adam
Published: May 2020

Animal defenses directed against bacteria include DNA-based extracellular traps (ETs) that are produced by innate immune cells. ET-bound bacteria are prevented from further tissue dissemination and are eventually killed by ET-bound antibacterial proteins. It is unclear how bacteria bind to ETs, though it has been proposed that the negatively-charged DNA scaffold of the ETs is involved. We have found that the bacterial-binding lectin CadA is a component of the ETs produced by the innate immune cells ofDictyostelium discoideumand is required for the binding and killing of twoEnterobacteriaceaeby ETs, but not other bacteria. Our results suggest that ETs selectively sequester bacteria and that lectins can facilitate bacterial killing by acting as ET-bacteria binding proteins.
Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization
Authors: Escorcia-Rodríguez Juan M. , Tauch Andreas , Freyre-González Julio A.
Published: May 2020

Some organism-specific databases about regulation in bacteria have become larger, accelerated by high-throughput methodologies, while others are no longer updated or accessible. Each database homogenize its datasets, giving rise to heterogeneity across databases. Such heterogeneity mainly encompasses different names for a gene and different network representations, generating duplicated interactions that could bias network analyses. Abasy (Across-bacteriasystems) Atlas consolidates information from different sources into meta-curated regulatory networks in bacteria. The high-quality networks in Abasy Atlas enable cross-organisms analyses, such as benchmarking studies where gold standards are required. Nevertheless, network incompleteness still casts doubts on the conclusions of network analyses, and available sampling methods cannot reflect the curation process. To tackle this problem, the updated version of Abasy Atlas presented in this work provides historical snapshots of regulatory networks. Thus, network analyses can be performed at different completeness levels, making possible to identify potential bias and to predict future results. We leverage the recently found constraint in the complexity of regulatory networks to develop a novel model to quantify the total number of regulatory interactions as a function of the genome size. This completeness estimation is a valuable insight that may aid in the daunting task of network curation, prediction, and validation. The new version of Abasy Atlas provides 76 networks (204,282 regulatory interactions) covering 42 bacteria (64% Gram-positive and 36% Gram-negative) distributed in 9 species (Mycobacterium tuberculosis, Bacillus subtilis, Escherichia coli, Corynebacterium glutamicum, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pyogenes, Streptococcus pneumoniae, andStreptomyces coelicolor), containing 8,459 regulons and 4,335 modules.

Database URL

https://abasy.ccg.unam.mx/
Complexity in SARS-CoV-2 genome data: Price theory of mutant isolates
Authors: Mandal Saurav , Singh R.K. Sanayaima , Sharma Saurabh Kumar , Malik Md. Zubbair , Singh R.K. Brojen
Published: May 2020

SARS-CoV-2 is a highly virulent and deadly RNA virus causing the Covid-19 pandemic and several deaths across the world. The pandemic is so fast that any concrete theory of sudden widespread of this disease is still not known. In this work, we studied and analyzed a large number of publicly available SARS-CoV-2 genomes across the world using the multifractal approach. The mutation events in the isolates obey the Markov process and exhibit very high mutational rates, which occur in six specific genes and highest inorf1abgene, leading to virulent nature.f(α) analysis indicated that the isolates are highly asymmetric (left-skewed), revealing the richness of complexity and dominance by large fluctuations in genome structure organization. The values ofHqandDqare found to be significantly large, showing heterogeneous genome structure self-organization, strong positive correlation in organizing the isolates, and quite sensitive to fluctuations in and around it. We then present multiple-isolates hosts-virus interaction models, and derived Price equation for the model. The phase plane analysis of the model showedasymptotic stabilitytype bifurcation. The competition among the mutant isolates drives the trade-off of the dominant mutant isolates, otherwise confined to the present hosts.
Pro-inflammatory response of non-inflammatory Classical monocytes stimulated with LPSin vitro
Authors: Karsulovic Claudio , Tempio Fabian , Lopez Mercedes , Guerrero Julia , Goecke Annelise
Published: May 2020

BACKGROUND

CD14 (Monocyte identifying Toll-Like Receptor) and CD16 (FcyRIII co-receptor, marker of inflammatory monocytes) were used to define 3 subpopulations of circulating monocytes with different attributes in terms of inflammatory and phagocytic capabilities. There are contradictory reports regarding response of circulating monocytes to pro-inflammatory or non-inflammatory stimuliin vitro. Here we aimed to analyze the phenotypic changes in circulating monocytes when stimulated with pro and non-inflammatory stimuli.

METHODS

Whole blood from 9 healthy donors was extracted and studied. Monocyte subpopulations were directly measured using flow cytometry with PBMC Ficoll extraction method. Pro-inflammatory interleukin IL-1β was measured by intracellular cytometry. Whole blood-extracted monocytes were stimulated using LPS and IL-4 as previously described. Changes against non-stimulated (N-S) populations were statistically analyzed.

RESULTS

Compared to N-S, LPS-stimulated monocytes display a singular milieu of markers, with higher levels of intracellular IL-1β in parallel raise of CD14+CD163-/CD14+CD163+ ratio. CD163 shows positive correlation with levels of IL-1β. In t-SNE (T-distributed Stochastic Neighbor Embedding) analysis, after LPS stimulation, subpopulation CD14+CD16-CD163-, containing mainly classical monocytes, show a higher number of IL-1β+ cells.

CONCLUSION

Classical monocytes, the non-inflammatory subset, show higher levels of IL-1β in response to LPS narrowing down to a new subpopulation of monocytes CD14+CD16-CD163-, which correlates better with this interleukin response than widely used monocytes classification. Using CD163 in addition to CD16, we were able to show that classical monocytes display the most intense response to LPS. Additionally, CD163 appears to be a suitable addition to CD14-CD16 classification to improve its performance.
The structural basis for kinetochore stabilization by Cnn1/CENP-T
Authors: Hinshaw Stephen M. , Harrison Stephen C.
Published: May 2020

Chromosome segregation depends on a regulated connection between spindle microtubules and centromeric DNA. The kinetochore, a massive modular protein assembly, mediates this connection and also serves as a signaling hub that integrates and responds to changing cues during the cell cycle. Kinetochore functions evolve as the cell cycle progresses, culminating in the assurance of a persistent chromosome-microtubule connection during anaphase, when sister chromatids must transit into daughter cells uninterrupted. We previously determined the structure of the Ctf19 complex, a group of kinetochore proteins at the centromeric base of the kinetochore. We now present a high-resolution structure of a Ctf19 complex sub-assembly involved in centromere-microtubule contact: the Ctf3 complex bound to the Cnn1-Wip1 heterodimer. The resulting composite model of the Ctf19 complex and live-cell imaging experiments provide a mechanism for Cnn1-Wip1 recruitment to the kinetochore. The mechanism suggests feedback regulation of Ctf19 complex assembly and unanticipated similarities in kinetochore organization between yeast and vertebrates.
Activation of FAM111A Protease Induces Defects in Nuclear Function that Likely Underlie its Roles in Disease and Viral Restriction
Authors: Nie Minghua , Oravcová Martina , Jami-Alahmadi Yasaman , Wohlschlegel James A. , Lazzerini-Denchi Eros , Boddy Michael N.
Published: May 2020

Mutations in the nuclear trypsin-like serine protease FAM111A cause Kenny-Caffey syndrome (KCS2) with hypoparathyroidism and skeletal dysplasia, or perinatally lethal osteocraniostenosis (OCS). In addition, FAM111A was identified as a restriction factor for certain host range mutants of the SV40 polyomavirus and VACV orthopoxvirus. However, because FAM111A function is poorly characterized, its roles in restricting viral replication and the etiology of KCS2 and OCS remain undefined. We find that the FAM111A KCS2 and OCS patient mutants are hyperactive, inducing apoptosis-like phenotypes in a protease-dependent manner. Similarly, in response to the attempted replication of SV40 host range mutants in restrictive cells, FAM111A activity induces the loss of nuclear barrier function and structure. Interestingly, pan-caspase inhibitors do not block FAM111A-dependent phenotypes such as nuclear “leakiness”, shrinkage and pore redistribution, implying it acts independently or upstream of caspases. In this regard, we identified nucleoporins and the associated GANP transcription factor as FAM111A interactors and candidate targets. Together our data provide key insight into how FAM111A activation can restrict viral replication, and how its deregulated activity could cause KCS2 and OCS.
Antagonistic control of DDK binding to licensed replication origins by Mcm2 and Rad53
Authors: Wahab Syafiq Abd , Remus Dirk
Published: May 2020

Eukaryotic replication origins are licensed by the loading of the replicative DNA helicase, Mcm2-7, in inactive double hexameric form around DNA. Subsequent origin activation is under control of multiple protein kinases that either promote or inhibit origin activation, which is important for genome maintenance. Using the reconstituted budding yeast DNA replication system, we find that the flexible N-terminal tail of Mcm2 promotes the stable recruitment of Dbf4-dependent kinase (DDK) to Mcm2-7 double hexamers, which in turn promotes DDK phosphorylation of Mcm4 and -6 and subsequent origin activation. Conversely, we demonstrate that the checkpoint kinase, Rad53, inhibits DDK binding to Mcm2-7 double hexamers. Unexpectedly, this function is not dependent on Rad53 kinase activity, but requires Rad53 activation by trans-autophosphorylation, suggesting steric inhibition of DDK by activated Rad53. These findings identify critical determinants of the origin activation reaction and uncover a novel mechanism for checkpoint-dependent origin inhibition.
Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree
Authors: Tripathi Anupriya , Vázquez-Baeza Yoshiki , Gauglitz Julia M. , Wang Mingxun , Dührkop Kai , Nothias-Esposito Mélissa , Acharya Deepa D. , Ernst Madeleine , van der Hooft Justin J.J. , Zhu Qiyun , McDonald Daniel , Gonzalez Antonio , Handelsman Jo , Fleischauer Markus , Ludwig Marcus , Böcker Sebastian , Nothias Louis-Félix , Knight Rob , Dorrestein Pieter C.
Published: May 2020

Untargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on hierarchical organization of molecular fingerprints predicted from fragmentation spectra, represented in the context of sample metadata and chemical ontologies. By expressing molecular relationships as a tree, we can apply ecological tools, designed around the relatedness of DNA sequences, to study chemical composition.
JavaDL: a Java-based Deep Learning Tool to Predict Drug Responses
Authors: Huang Beibei , Fong Lon W. R. , Chaudhari Rajan , Tan Zhi , Zhang Shuxing
Published: May 2020

Motivation

Accurate prediction of drug response in each patient is the holy grail in personalized medicine. Recently, deep learning techniques have been witnessed with revival in a variety of areas such as image processing and genomic data analysis, and they will be useful for the coming age of big data analysis in pharmaceutical research and chemogenomic applications. This provides us an impetus to develop a novel deep learning platform to accurately and reliably predict the response of cancer to different drug treatments.

Results

In this study, we describe a Java-based implementation of deep neural network (DNN) method, termed JavaDL, to predict cancer responses to drugs solely based on their chemical features. To this end, we devised a novel cost function by adding a regularization term which suppresses overfitting. We also adopted an “early stopping” strategy to further reduce overfit and improve the accuracy and robustness of our models. Currently the software has been integrated with a genetic algorithm-based variable selection approach and implemented as part of our JavaDL package. To evaluate our program, we compared it with several machine learning programs including SVM and kNN. We observed that JavaDL either significantly outperforms other methods in model building and prediction or obtains better results in handling big data analysis. Finally, JavaDL was employed to predict drug responses of several highly aggressive triple-negative breast cancer cell lines, and the results showed robust and accurate predictions with r2as high as 0.80.

Availability

The program is freely available athttps://imdlab.mdanderson.org/JavaDL/JavaDL.php.
Cholesterol Sequestration by Xenon Leads to Lipid Raft Destabilization
Authors: Reyes-Figueroa A.D. , Karttunen Mikko , Ruiz-Suárez J.C.
Published: May 2020

Combined coarse-grained (CG) and atomistic molecular dynamics (MD) simulations were performed to study the interactions of xenon with model lipid rafts consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and cholesterol (Chol). At a concentration of 2 Xe/lipid we observed an unexpected result: Spontaneous nucleation of Xe nanoclusters which then rapidly plunged into the bilayer. In this process Chol, essential for raft stabilization, was pulled out from the raft into the hydrophobic zone. When concentration was further increased (3 Xe/lipid), the clusters disrupted both the membrane and raft. We computed the radial distribution functions, pair-wise potentials, second virial coefficients and Schlit-ter entropy to scrutinize the nature of the interactions. Our findings suggest that the well-known anaesthetic effect of Xe could be mediated by sequestration of Chol, which, in turn, compromises the stability of rafts where specialized proteins needed to produce the nervous signal are anchored.
PrimeDesign software for rapid and simplified design of prime editing guide RNAs
Authors: Hsu Jonathan Y. , Anzalone Andrew V. , Grünewald Julian , Lam Kin Chung , Shen Max W. , Liu David R. , Joung J. Keith , Pinello Luca
Published: May 2020

Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we also constructed PrimeVar, the first comprehensive and searchable database for prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations to install or correct >68,500 pathogenic human genetic variants from the ClinVar database.
Stable gene expression for normalisation and single-sample scoring
Authors: Bhuva Dharmesh D. , Cursons Joseph , Davis Melissa J.
Published: May 2020

Background

Transcriptomic signatures are useful in defining the molecular phenotypes of cells, tissues, and patient samples. Their most successful and widespread clinical application is the stratification of breast cancer patients into molecular (PAM50) subtypes. In most cases, gene expression signatures are developed using transcriptome-wide measurements, thus methods that match signatures to samples typically require a similar degree of measurements. The cost and relatively large amounts of fresh starting material required for whole-transcriptome sequencing has limited clinical applications, and accordingly thousands of existing gene signatures are unexplored in a clinical context.

Results

Genes in a molecular signature can provide information about molecular phenotypes and their underlying transcriptional programs from tissue samples, however determining the transcriptional state of these genes typically requires the measurement of all genes across multiple samples to allow for comparison. An efficient assay and scoring method should quantify the relative abundance of signature genes with a minimal number of additional measurements. We identified genes with stable expression across a range of abundances, and with a preserved relative ordering across large numbers (thousands) of samples, allowing signature scoring, and supporting general data normalisation for transcriptomic data. Based on singscore, we have developed a new method,stingscore, which quantifies and summarises relative expression levels of signature genes from individual samples through the inclusion of these “stably-expressed genes”.

Conclusion

We show that our proposed list of stable genes has better stability across cancer and normal tissue data than previously proposed stable or housekeeping genes. Additionally, we show that signature scores computed from whole-transcriptome data are comparable to those calculated using only values for signature genes and our panel of stable genes. This new approach to gene expression signature analysis may facilitate the development of panel-type tests for gene expression signatures, thus supporting clinical translation of the powerful insights gained from cancer transcriptomic studies.
Improved growth and morphological plasticity ofHaloferax volcanii
Authors: de Silva Roshali T. , Abdul-Halim Mohd F. , Pittrich Dorothea A. , Brown Hannah J. , Pohlschroder Mechthild , Duggin Iain G.
Published: May 2020

Some microbes display pleomorphism, showing variable cell shapes in a single culture, whereas others differentiate to adapt to changed environmental conditions. The pleomorphic archaeonHaloferax volcaniicommonly forms discoid-shaped (‘plate’) cells in culture, but may also be present as rods, and can develop into motile rods in soft agar, or longer filaments in certain biofilms. Here we report improvement ofH. volcaniigrowth in both semi-defined and complex media by supplementing with eight trace-element micronutrients. With these supplemented media, transient development of plate cells into uniformly-shaped rods was clearly observed during the early log phase of growth; cells then reverted to plates for the late log and stationary phases. In media prepared with high-purity water and reagents, without supplemental trace elements, rods and other complex elongated morphologies (‘pleomorphic rods’) were observed at all growth stages of the culture; the highly-elongated cells sometimes displayed a substantial tubule at one or less frequently both poles, as well as unusual tapered and highly-curved forms. Polar tubules were observed forming by initial mid-cell narrowing or tubulation, causing a dumbbell-like shape, followed by cell division towards one end. Formation of the uniform early-log rods, as well as the pleomorphic rods and tubules were dependent on the function of the tubulin-like cytoskeletal protein, CetZ1. Our results have revealed the remarkable morphological plasticity ofH. volcaniicells in response to multiple culture conditions, and should facilitate the use of this species in further studies of archaeal biology.