bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutation of NEKL-4/NEK10 and TTLL genes opposes loss of the CCPP-1 deglutamylase and prevents neuronal ciliary degeneration
Authors: Power Kade M. , Akella Jyothi S. , Gu Amanda , Walsh Jonathon D. , Bellotti Sebastian , Morash Margaret , Zhang Winne , Ross N. , Golden Andy , Smith Harold E. , Barr Maureen M. , O’Hagan Robert
Published: May 2020

Ciliary microtubules are subject to post-translational modifications that act as a “Tubulin Code” to regulate motor traffic, binding proteins and stability. In humans, loss of CCP1, acytosoliccarboxypeptidase and tubulin deglutamylating enzyme, causes infantile-onset neurodegeneration. InC. elegans,mutations inccpp-1, the homolog of CCP1, result in progressive degeneration of neuronal cilia and loss of neuronal function. To identify genes that regulate microtubule glutamylation and ciliary integrity, we performed a forward genetic screen for suppressors of ciliary degeneration inccpp-1mutants. We isolated thettll-5(my38)suppressor, a mutation in thetubulintyrosineligase-like glutamylase gene. We show that mutation inttll-4, ttll-5,orttll-11gene suppressed the hyperglutamylation-induced loss of microtubules and kinesin-2 mislocalization inccpp-1cilia. We also identified thenekl-4(my31)suppressor, an allele affecting the NIMA (Never in Mitosis A)-related kinase NEKL-4/NEK10. In humans, NEK10 mutation causes bronchiectasis, an airway and mucociliary transport disorder caused by defective motile cilia.C. elegansNEKL-4 does not localize to cilia yet plays a role in regulating axonemal microtubule stability. This work defines a pathway in which glutamylation, a component of the Tubulin Code, is written by TTLL-4, TTLL-5, and TTLL-11; is erased by CCPP-1; is read by ciliary kinesins; and its downstream effects are modulated by NEKL-4 activity. Identification of regulators of microtubule glutamylation in diverse cellular contexts is important to the development of effective therapies for disorders characterized by changes in microtubule glutamylation. By identifyingC. elegansgenes important for neuronal and ciliary stability, our work may inform research into human ciliopathies and neurodegenerative diseases.
SARS-CoV-2 mutations and where to find them: An in silico perspective of structural changes and antigenicity of the Spike protein
Authors: Gonçalves Ricardo Lemes , Rodrigues Leite Túlio César , de Paula Dias Bruna , da Silva Caetano Camila Carla , de Souza Ana Clara Gomes , da Silva Batista Ubiratan , Barbosa Camila Cavadas , Reyes-Sandoval Arturo , Leomil Coelho Luiz Felipe , de Mello Silva Breno
Published: May 2020

The recent emergence of a novel coronavirus (SARS-CoV-2) is causing a severe global health threat characterized by severe acute respiratory syndrome (Covid-19). At the moment, there is no specific treatment for this disease, and vaccines are still under development. The structural protein Spike is essential for virus infection and has been used as the main target for vaccine and serological diagnosis test development. We analysed 2363 sequences of the Spike protein from SARS-CoV-2 isolates and identified variability in 44 amino acid residues and their worldwide distribution in all continents. We used the three-dimensional structure of the homo-trimer model to predict conformational epitopes of B-cell, and sequence of Spike protein Wuhan-Hu-1 to predict linear epitopes of T-Cytotoxic and T-Helper cells. We identified 45 epitopes with amino acid variations. Finally, we showed the distribution of mutations within the epitopes. Our findings can help researches to identify more efficient strategies for the development of vaccines, therapies, and serological diagnostic tests based on the Spike protein of Sars-Cov-2.
Utilizing Temporal Measurements from UAVs to Assess Root Lodging in Maize and its Impact on Productivity
Authors: Tirado Sara B. , Hirsch Candice N. , Springer Nathan M.
Published: May 2020

Both stalk and root lodging can cause significant yield losses in maize; however, maize plants are often able to recover from root lodging. There is potential among breeding programs for developing lines that are more tolerant and can more rapidly recover from root lodging. We assessed the incidence of root lodging utilizing end-of-season lodging scores collected among the Genomes 2 Fields (G2F) initiative trials and found a large yet variable incidence of lodging across states, years, and genotypes. Lodging in this dataset was scored manually at the end of the season, and little is known about the drivers of lodging and lodging recovery. We therefore developed an approach for utilizing temporal plant height measurements collected from unmanned aerial vehicles to capture in-season lodging and recovery in a yield trial consisting of 24 maize hybrids planted in replicate under two dates and three planting densities in St Paul, MN in the summers of 2018 and 2019. We found that growth rates during vegetative development as well as the developmental timing of plants when exposed to a storm are predictive of the amount of lodging maize plots will experience. We also found that utilizing temporal height measurements can help in not just estimating lodging and early vegetative growth rates, but that utilizing these estimates can also aid in assessing end of season yield.
Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping
Authors: Jegouic Sophie M. , Loureiro Silvia , Thom Michelle , Paliwal Deepa , Jones Ian M.
Published: May 2020

The newly emergent SARS-CoV-2 coronavirus is closely related to SARS-CoV which emerged in 2002. Studies on coronaviruses in general, and SARS in particular, have identified the virus spike protein (S) as being central to virus tropism, to the generation of a protective antibody response and to the unambiguous detection of past infections. As a result of this centrality SARS-CoV-2 S protein has a role in many aspects of research from vaccines to diagnostic tests. We describe a number of recombinant forms of SARS-CoV-2 S expressed in commonly available expression systems and their preliminary use in diagnostics and epitope mapping. These sources may find use in the current and future analysis of the virus and the Covid-19 disease it causes.
Ultra-high field (10.5 T) resting state fMRI in the macaque
Authors: Yacoub Essa , Grier Mark D. , Auerbach Edward J. , Lagore Russell L. , Harel Noam , Ugurbil Kamil , Adriany Gregor , Zilverstand Anna , Hayden Benjamin Y. , Heilbronner Sarah R. , Zimmermann Jan
Published: May 2020

Resting state functional connectivity refers to the temporal correlations between spontaneous hemodynamic signals obtained using functional magnetic resonance imaging. This technique has demonstrated that the structure and dynamics of identifiable networks are altered in psychiatric and neurological disease states. Thus, resting state network organizations can be used as a diagnostic, or prognostic recovery indicator. However, much about the physiological basis of this technique is unknown. Thus, providing a translational bridge to an optimal animal model, the macaque, in which invasive circuit manipulations are possible, is of utmost importance. Current approaches to resting state measurements in macaques face unique challenges associated with signal-to-noise, the need for invasive contrast agents, and within-subject designs. These limitations can, in principle, be overcome through ultra-high magnetic fields. However, ultra-high field imaging has yet to be adapted for fMRI in macaques. Here, we demonstrate that the combination of high channel count transmitter and receiver arrays, optimized pulse sequences, and careful anesthesia regimens, allows for detailed within-subject resting state analysis at ultra-high resolutions. In this study, we uncover thirty spatially detailed resting state components that are highly robust across individual macaques and closely resemble the quality and findings of connectomes from large human datasets. This detailed map of the rsfMRI ‘macaque connectome’ will be the basis for future neurobiological circuit manipulation work, providing valuable biological insights into human connectomics.
Electric-field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2
Authors: Ramachandran Ashwin , Huyke Diego A. , Sharma Eesha , Sahoo Malaya K. , Banaei Niaz , Pinsky Benjamin A. , Santiago Juan G.
Published: May 2020

The rapid spread of COVID-19 across the world has revealed major gaps in our ability to respond to new virulent pathogens. Rapid, accurate, and easily configurable molecular diagnostic tests are imperative to prevent global spread of new diseases. CRISPR-based diagnostic approaches are proving to be useful as field-deployable solutions. In a basic form of this assay, the CRISPR-Cas12 enzyme complexes with a synthetic guide RNA (gRNA). This complex is activated when it highly specifically binds to target DNA, and the activated complex non-specifically cleaves single-stranded DNA reporter probes labeled with a fluorophore-quencher pair. We recently discovered that electric field gradients can be used to control and accelerate this CRISPR assay by co-focusing Cas12-gRNA, reporters, and target. We achieve an appropriate electric field gradient using a selective ionic focusing technique known as isotachophoresis (ITP) implemented on a microfluidic chip. Unlike previous CRISPR diagnostic assays, we also use ITP for automated purification of target RNA from raw nasopharyngeal swab sample. We here combine this ITP purification with loop-mediated isothermal amplification, and the ITP-enhanced CRISPR assay to achieve detection of SARS-CoV-2 RNA (from raw sample to result) in 30 min for both contrived and clinical nasopharyngeal swab samples. This electric field control enables a new modality for a suite of microfluidic CRISPR-based diagnostic assays.

Significance statement

Rapid, early-stage screening is especially crucial during pandemics for early identification of infected patients and control of disease spread. CRISPR biology offers new methods for rapid and accurate pathogen detection. Despite their versatility and specificity, existing CRISPR-diagnostic methods suffer from the requirements of up-front nucleic acid extraction, large reagent volumes, and several manual steps—factors which prolong the process and impede use in low resource settings. We here combine on-chip electric-field control in combination with CRIPSR biology to directly address these limitations of current CRISPR-diagnostic methods. We apply our method to the rapid detection of SARS-CoV-2 RNA in clinical samples. Our method takes 30 min from raw sample to result, a significant improvement over existing diagnostic methods for COVID-19.
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
Authors: Crisp Peter A , Marand Alexandre P , Noshay Jaclyn M , Zhou Peng , Lu Zefu , Schmitz Robert J , Springer Nathan M
Published: May 2020

The genomic sequences of crops continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. UMRs provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.

Significance Statement

Crop genomes can be very large with many repetitive elements and pseudogenes. Distilling a genome down to the relatively small fraction of regions that are functionally valuable for trait variation can be like looking for needles in a haystack. The unmethylated regions in a genome are highly stable during vegetative development and can reveal the locations of potentially expressed genes or cis-regulatory elements. This approach provides a framework towards complete annotation of genes and discovery of cis-regulatory elements using methylation profiles from only a single tissue.
Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Authors: Miller Danielle , Martin Michael A , Harel Noam , Kustin Talia , Tirosh Omer , Meir Moran , Sorek Nadav , Gefen-Halevi Shiraz , Amit Sharon , Vorontsov Olesya , Wolf Dana , Peretz Avi , Shemer-Avni Yonat , Roif-Kaminsky Diana , Kopelman Na'ama , Huppert Amit , Koelle Katia , Stern Adi
Published: May 2020

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequenced 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. A phylogenetic analysis including thousands of globally sampled sequences allowed us to infer multiple independent introductions into Israel, followed by local transmission. Returning travelers from the U.S. contributed dramatically more to viral spread relative to their proportion in incoming infected travelers. Using phylodynamic analysis, we estimated that the basic reproduction number of the virus was initially around ~2.0-2.6, dropping by two-thirds following the implementation of social distancing measures. A comparison between reported and model-estimated case numbers indicated high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 1-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings underscore the ability of this virus to efficiently transmit between and within countries, as well as demonstrate the effectiveness of social distancing measures for reducing its spread.
Validation of the Kuwait Progression Indicator Score for predicting progression of severity in COVID19
Authors: Al Youha Sarah , Doi Suhail A. , Jamal Mohammad H. , Almazeedi Sulaiman , Al Haddad Mohannad , AlSeaidan Mohammad , Al-Muhaini Ali Y. , Al-Ghimlas Fahad , Al-Sabah Salman K.
Published: May 2020

Introduction:
Identifying patients with COVID19, at risk of having a severe clinical course during their hospitalization is important for appropriate allocation of clinical resources. We recently described the Kuwait Progression Indicator based on laboratory findings, in an initial training cohort derived from the first series of 1096 consecutive patients admitted to Jaber AlAhmad AlSabah Hospital in Kuwait. The aim of this study was to validate the KPI scoring system in an independent cohort of patients with COVID19.

Methodology:
Data was collected prospectively for consecutive patients admitted to Jaber AlAhmad AlSabah Hospital in Kuwait between 24th February till 28th April 2020. Patients were grouped according to the severity of their clinical course as their main outcome, based on clinical and radiological parameters, with ICU admission and death as secondary outcomes. Model discrimination was assessed through the area under the receiver operating characteristic curve (AUC) while model calibration was assessed through a calibration plot and measures of slope and calibration in the large (CITL).

Results:
Of 752 patients not used in model development previously, 414 met the criteria for inclusion in this validation study. The baseline characteristics for these 752 patients were similar to the patients that were included in our validation cohort. The area under the curve was equal to 0.904 (95% CI, between 0.867 to 0.942), indicating good model discrimination. The calibration plot and CITL confirmed reasonably good model calibration. Sensitivity and specificity were above 90% for the low and high risk levels respectively.

Conclusions:
We were able to validate our previously described laboratory based prognostic scoring system for COVID19 patients, to predict which patients progressed to a severe clinical course.
Examining the bidirectional association between emotion recognition and autistic traits using observational and genetic analyses
Authors: Reed Zoe E. , Mahedy Liam , Jackson Abigail , Smith George Davey , Penton-Voak Ian , Attwood Angela S , Munafò Marcus R
Published: May 2020

Background

There is mixed evidence for an association between autism spectrum disorder (ASD) and emotion recognition deficits. We sought to assess the bidirectionality of this association using phenotypic and genetic data in a large community sample.

Methods

Analyses were conducted in three stages. First, we examined the bidirectional association between autistic traits at age 8 years and emotion recognition task (ERT) responses at age 24 years (Study 1; N=3,562); and between Diagnostic Analysis of Non-Verbal Accuracy (DANVA) emotion recognition responses at age 8 years and autistic traits at age 10 years (Study 2; N=9,071). Next, we used genetic analyses (Study 3) to examine the association between polygenic risk scores for ASD and these phenotypes. The genetic correlation between ASD and ERT responses at age 24 was also estimated. Analyses were conducted in the Avon Longitudinal Study of Parents and Children.

Results

Autistic traits at age 8 years were negatively associated with later total correct responses on ERT in Study 1 (b=-0.18; 95% CI: −0.27 to −0.09). We also found evidence of an association in Study 2 (b=-0.04; 95% CI: −0.05 to −0.03). We found the opposite association i.e., positive, between the ASD polygenic risk score and ERT (b=0.40; 95% CI: 0.10 to 0.70); however, this association varied across different p-value thresholds so should be interpreted with caution. We did not find evidence of a genetic correlation between ASD and ERT.

Conclusion

We found an observational association between poorer emotion recognition and increased autistic traits. Our genetic analyses revealed an association between ASD polygenic risk and the ERT outcome, which may suggest a shared genetic aetiology between these or a potential causal pathway. Our results may inform interventions targeting emotion recognition.
Effective Screening of SARS-CoV-2 Neutralizing Antibodies in Patient Serum using Lentivirus Particles Pseudotyped with SARS-CoV-2 Spike Glycoprotein
Authors: Tandon Ritesh , Mitra Dipanwita , Sharma Poonam , Stray Stephan J , Bates John T , Marshall Gailen D
Published: May 2020

Pseuodotyped particles have significant importance and use in virology as tools for studying the biology of highly pathogenic viruses in a lower biosafety environment. The biological, chemical, and serological studies of the recently emerged SARS-CoV-2 will be greatly aided by the development and optimization of a suitable pseudotyping system. Here, we pseudotyped the SARS-CoV-2 Spike glycoprotein (SPG) on a retroviral (MMLV) as well as a third generation lentiviral (pLV) vector and tested the transduction efficiency in several mammalian cell lines expressing SARS-CoV-2 receptor hACE2. While MMLV pseudotyped the vesicular stomatitis virus G glycoprotein (VSV-G) efficiently, it could not pseudotype SPG. In contrast, pLV pseudotyped both glycoproteins efficiently; however, much higher titers of pLV-G particles were produced. Among all the tested mammalian cells, 293Ts expressing hACE2 were most efficiently transduced using the pLV-S system. The pLV-S particles were efficiently neutralized by diluted serum (>:640) from a recently recovered COVID-19 patient who showed high SARS-CoV-2 specific IgM and IgG levels. In summary, pLV-S pseudotyped virus provides a valid screening tool for the presence of anti SARS-CoV-2 specific neutralizing antibodies in convalescent patient serum.
Predictors of severe or lethal COVID-19, including Angiotensin Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers, in a sample of infected Italian citizens
Authors: Bravi Francesca , Flacco Maria Elena , Carradori Tiziano , Volta Carlo Alberto , Cosenza Giuseppe , De Togni Aldo , Acuti Martellucci Cecilia , Parruti Giustino , Mantovani Lorenzo , Manzoli Lamberto
Published: May 2020

Aims: This retrospective case-control study was aimed at identifying potential independent predictors of severe/lethal COVID-19, including the treatment with Angiotensin-Converting Enzyme inhibitors (ACEi) and/or Angiotensin II Receptor Blockers (ARBs).
Methods and Results: All adults with SARS-CoV-2 infection in two Italian provinces were followed for a median of 24 days. ARBs and/or ACEi treatments, and hypertension, diabetes, cancer, COPD, renal and major cardiovascular diseases (CVD) were extracted from clinical charts and electronic health records, up to two years before infection. The sample consisted of 1603 subjects (mean age 58.0y; 47.3% males): 454 (28.3%) had severe symptoms, 192 (12.0%) very severe or lethal disease (154 deaths; mean age 79.3 years; 70.8% hypertensive, 42.2% with CVD). The youngest deceased person aged 44 years. Among hypertensive subjects (n=543), the proportion of those treated with ARBs or ACEi were 88.4%, 78.7% and 80.6% among patients with mild, severe and very severe/lethal disease, respectively. At multivariate analysis, no association was observed between therapy and disease severity (Adjusted OR for very severe/lethal COVID-19: 0.87; 95% CI: 0.50-1.49). Significant predictors of severe disease were older age (with AORs largely increasing after 70 years of age), male gender (AOR: 1.76; 1.40-2.23), diabetes (AOR: 1.52; 1.05-2.18), CVD (AOR: 1.88; 1.32-2.70) and COPD (1.88; 1.11-3.20). Only gender, age and diabetes also predicted very severe/lethal disease.
Conclusion: No association was found between COVID-19 severity and treatment with ARBs and/or ACEi, supporting the recommendation to continue medication for all patients unless otherwise advised by their physicians.
Improved measurement of racial/ethnic disparities in COVID-19 mortality in the United States
Authors: Goldstein Joshua R. , Atherwood Serge
Published: May 2020

Different estimation methods produce diverging accounts of racial/ethnic disparities in COVID-19 mortality in the United States. The CDC’s decision to present the racial/ethnic distribution of COVID-19 deaths at the state level alongside re-weighted racial/ethnic population distributions—in effect, a geographic adjustment—makes it seem that Whites have the highest death rates. Age adjustment procedures used by others, including the New York City Department of Health and Mental Hygiene, lead to the opposite conclusion that Blacks and Hispanics are dying from COVID-19 at higher rates than Whites. In this paper, we use indirect standardization methods to adjust per-capita death rates for both age and geography simultaneously, avoiding the one-sided adjustment procedures currently in use. Using CDC data, we find age-and-place-adjusted COVID-19 death rates are 80% higher for Blacks and more than 50% higher for Hispanics, relative to Whites, on a national level, while there is almost no disparity for Asians. State-specific estimates show wide variation in mortality disparities. Comparison with non-epidemic mortality reveals potential roles for pre-existing health disparities and differential rates of infection and care.
A DNA translocase operates by cycling between planar and lock-washer structures
Authors: Castillo Juan P. , Tong Alexander , Tafoya Sara , Jardine Paul J. , Bustamante Carlos
Published: May 2020

Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via ahand-over-handmechanism. Here, we investigate the operation of ring motors that transport substrates possessing a preexisting helical structure, such as the bacteriophage ϕ29 dsDNA packaging motor. During each cycle, this pentameric motor tracks one helix strand (the ‘tracking strand’), and alternates between two segregated phases: adwellin which it exchanges ADP for ATP and aburstin which it packages a full turn of DNA in four steps. We challenge this motor with DNA-RNA hybrids and dsRNA substrates and find that it adapts the size of its burst to the corresponding shorter helical pitches by keeping three of its power strokes invariant while shortening the fourth. Intermittently, the motor loses grip when the tracking strand is RNA, indicating that it makes load-bearing contacts with the substrate that are optimal with dsDNA. The motor possesses weaker grip when ADP-bound at the end of the burst. To rationalize all these observations, we propose ahelical inchwormtranslocation mechanism in which the motor increasingly adopts a lock-washer structure during the ATP loading dwell and successively regains its planar form with each power stroke during the burst.
Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses
Authors: Yu Xi , Zhang Liming , Tong Liangqin , Zhang Nana , Wang Han , Yang Yun , Shi Mingyu , Xiao Xiaoping , Zhu Yibin , Wang Penghua , Ding Qiang , Zhang Linqi , Qin Chengfeng , Cheng Gong
Published: May 2020

Viruses are the major aetiological agents of acute and chronic severe human diseases that place a tremendous burden on global public health and economy; however, for most viruses, effective prophylactics and therapeutics are lacking, in particular, broad-spectrum antiviral agents. Herein, we identified 2 secreted bacterial lipases from aChromobacteriumbacterium, namedChromobacteriumantiviral effector-1 (CbAE-1) andCbAE-2, with a broad-spectrum virucidal activity against dengue virus (DENV), Zika virus (ZIKV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV) and herpes simplex virus (HSV). TheCbAEs potently blocked viral infection in the extracellular milieu through their lipase activity. Mechanistic studies showed that this lipase activity directly disrupted the viral envelope structure, thus inactivating infectivity. A mutation ofCbAE-1 in its lipase motif fully abrogated the virucidal ability. Furthermore,CbAE-2 presented low toxicityin vivoandin vitro, highlighting its potential as a broad-spectrum antiviral drug.
A clinically validated human capillary blood transcriptome test for global systems biology studies
Authors: Toma Ryan , Pelle Ben , Duval Nathan , Parks Matthew M , Gopu Vishakh , Tily Hal , Hatch Andrew , Perlina Ally , Banavar Guruduth , Vuyisich Momchilo
Published: May 2020

Chronic diseases are the leading cause of morbidity and mortality globally. Yet, the majority of them have unknown etiologies, and genetic contribution is weak. In addition, many of the chronic diseases go through the cycles of relapse and remission, during which the genomic DNA does not change. This strongly suggests that human gene expression is the main driver of chronic disease onset and relapses. To identify the etiology of chronic diseases and develop more effective preventative measures, a comprehensive gene expression analysis of the human body is needed. Blood tissue is easy to access and contains a large number of expressed genes involved in many fundamental aspects of our physiology.

We report here the development of a whole blood transcriptome clinical test that is high throughput, automated, inexpensive, and clinically validated. The test requires only 50 microliters of blood from a finger prick, enabling access by diverse populations that have been traditionally under-represented in clinical research. The transcripts in the samples are preserved at the time of collection and can be stored and/or transported at ambient temperatures for up to 28 days. The sample preservative protects integrity, while also inactivating all pathogens (bacteria, fungi, and viruses), enabling safe transportation globally. Given its unique set of usability features and clinical performance, this test should be integrated into longitudinal, population-scale, systems biology studies.
Effect of nanocarbon molecules on theArabidopsis thalianatranscriptome
Authors: Nakamichi Norihito , Sato Ayato , Aihara Yusuke , Kinoshita Toshinori , Segawa Yasutomo , Amaike Kazuma , Itami Kenichiro
Published: May 2020

Nanocarbons, such as fullerenes, carbon nanotubes, and graphene have attracted a great deal of attention as next-generation materials because of their unprecedented structures and unique physicochemical properties; however, almost all nanocarbons reported previously were used as mixtures. Thus, there are still many unsolved issues about their biological functions at the molecular level. Our synthetic campaign in the last decade has synthesized structurally uniform and atomically precise nanocarbons, leading to the preparation of a library consisting of eighty structurally diverse nanocarbon molecules. This resource motivated us to explore the as yet uncovered biological functions of these nanocarbon molecules in organisms. Recently, nanotubes were used to deliver genes to plants; however, the effects of the molecules on plants are not well known. To monitor the effects of nanocarbon molecules on plants, we analyzed the transcriptome ofArabidopsis thalianaseedlings treated with [9]cycloparaphenylene (CPP), decaborylated warped nanographene (WNG), and dimethoxyhexabenzotetracene (HBT). Clustering analysis indicated few effects of nanocarbon molecules on the transcriptome, perhaps suggesting a low toxicity of nanocarbon molecules on plants. We found thatAT1G05880(ARIADNE 12) gene, categorized into ‘response to hypoxia’ genes, was up-regulated by nanocarbon molecules, suggesting that this gene is usable as maker for treatment of nanocarbon molecules.
Integrated cross-study datasets of genetic dependencies in cancer
Authors: Pacini Clare , Dempster Joshua M. , Boyle Isabella , Gonçalves Emanuel , Najgebauer Hanna , Karakoc Emre , van der Meer Dieudonne , Barthorpe Andrew , Lightfoot Howard , Jaaks Patricia , McFarland James M. , Garnett Mathew J. , Tsherniak Aviad , Iorio Francesco
Published: May 2020

CRISPR-Cas9 viability screens are increasingly performed at a genome-wide scale across large panels of cell lines to identify new therapeutic targets for precision cancer therapy. Integrating the datasets resulting from these studies is necessary to adequately represent the heterogeneity of human cancers and to assemble a comprehensive map of cancer genetic vulnerabilities. Here, we integrated the two largest public independent CRISPR-Cas9 screens performed to date (at the Broad and Sanger institutes) by assessing, comparing, and selecting methods for correcting biases due to heterogeneous single guide RNA efficiency, gene-independent responses to CRISPR-Cas9 targeting originated from copy number alterations, and experimental batch effects. Our integrated datasets recapitulate findings from the individual datasets, provide greater statistical power to cancer- and subtype-specific analyses, unveil additional biomarkers of gene dependency, and improve the detection of common essential genes. We provide the largest integrated resources of CRISPR-Cas9 screens to date and the basis for harmonizing existing and future functional genetics datasets.
Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements
Authors: Pinilla-Redondo Rafael , Shehreen Saadlee , Marino Nicole D. , Fagerlund Robert D. , Brown Chris M. , Sørensen Søren J. , Fineran Peter C. , Bondy-Denomy Joseph
Published: May 2020

Many prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have evolved Anti-CRISPR (Acr) proteins to bypass this immunity, yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we uncover 11 new type I anti-CRISPR genes encoded on numerous chromosomal and extrachromosomal mobile genetic elements withinEnterobacteriaceaeandPseudomonas. Candidate genes were identified adjacent to anti-CRISPR associated gene 5 (aca5)and assayed against a panel of six type I systems: I-F (Pseudomonas,Pectobacterium, andSerratia), I-E (PseudomonasandSerratia), and I-C (Pseudomonas), revealing the type I-F and/or I-Eacrgenes and a newaca(aca9). We find thatacrgenes not only associate with otheracrgenes, but also with inhibitors of distinct bacterial defense systems. These genomic regions appear to be “anti-defense islands”, reminiscent of the clustered arrangement of “defense islands” in prokaryotic genomes. Our findings expand on the diversity of CRISPR-Cas inhibitors and reveal the potential exploitation ofacrloci neighborhoods for identifying new anti-defense systems.
Synaptic polarity and sign-balance prediction using gene expression data in theCaenorhabditis eleganschemical synapse neuronal connectome network
Authors: Fenyves Bánk G. , Szilágyi Gábor S. , Vassy Zsolt , Sőti Csaba , Csermely Péter
Published: May 2020

Graph theoretical analyses of nervous systems usually omit the aspect of connection polarity, due to data insufficiency. The chemical synapse network ofCaenorhabditis elegansis a well-reconstructed directed network, but the signs of its connections are yet to be elucidated. Here, we present the gene expression-based sign prediction of theC. elegansconnectome, incorporating presynaptic neurotransmitter and postsynaptic receptor gene expression data (3,638 connections and 20,589 synapses total). We made successful predictions for more than two-thirds of all chemical synapses and determined a ratio of excitatory-inhibitory (E:I) interneuronal ionotropic chemical connections close to 4:1 which was found similar to that observed in many real-world networks. Our open source tool (http://EleganSign.linkgroup.hu) is simple but efficient in predicting polarities by integrating neuronal connectome and gene expression data.

Author Summary

The fundamental way neurons communicate is by activating or inhibiting each other via synapses. The balance between the two is crucial for the optimal functioning of a nervous system. However, whole-brain synaptic polarity information is unavailable for any species and experimental validation is challenging. The roundworm Caenorhabditis elegans possesses a fully mapped connectome with a comprehensive gene expression profile of its 302 neurons. Based on the consideration that the polarity of a synapse must be determined by the neurotransmitter(s) expressed in the presynaptic neuron and the receptors expressed in the postsynaptic neuron, we conceptualized and created a tool that predicts synaptic polarities based on connectivity and gene expression information. We were able to show for the first time that the ratio of excitatory and inhibitory synapses inC. elegansis around 4 to 1 which is in line with the balance observed in many natural systems. Our method opens a way to include spatial and temporal dynamics of synaptic polarity that would add a new dimension of plasticity in the excitatory:inhibitory balance. Our tool is freely available to be used on any network accompanied by any expression atlas.
Modelling the response of the PIF plantain seedlings toTithonia diversifoliaand clam shells treatments in the nursery
Authors: Ewané Cécile Annie , Boudjeko Thaddée
Published: May 2020

The seeds availability is the main constraint for the agricultural explosion in sub-Saharan Africa countries. In the case of plantain, there is a lack of seedlings in quantity, but also in quality. The advent of the PIF method was an excellent opportunity to improve the availability of plantain seeds, although the quality is not fully guaranteed. Indeed, the PIF plants produced have posed many problems during the acclimation period indicating a need for solutions to improve their quality. Recent researches done with five treatments usingTithonia diversifoliaand clam shells have highlighted the improvement of the PIF seedlings quality in terms of growth promotion (biofertilizer action) and protection against black Sigatoka disease (biofungicide action). It seemed essential to determine the best model for robust PIF seedlings. The aim of this study was to analyse the different models that have enabled the production of improved PIF seedlings and to determine the best one. We have modelized the response of PIF seedlings to the different treatment’s protocols. It turns out that the best treatment to apply is T5 (T. diversifolialiquid extract), followed by T4 (T. diversifoliamulch). However, depending on the expected response in the PIF seedlings, all these treatments have proven to be impactful.Tithonia diversifolialiquid extract model is the best and in combination with clams, could be useful to boost the production at low cost and without chemical inputs of large amount of improved vigorous (clean and less susceptible) planting material, impacting thus the food security and poverty alleviation.
Effects of Old Age on Knee Extensor Fatigue and Recovery From High-Velocity Muscle Contractions
Authors: Fitzgerald Liam F. , Ryan Margaret M. , Bartlett Miles F. , Miehm Jules D. , Kent Jane A.
Published: May 2020

Purpose

Although high-velocity contractions elicit greater muscle fatigue in older than young adults, the cause of this difference is unclear. We examined the potential roles of resting muscle architecture and baseline contractile properties, as well as changes in voluntary activation and low-frequency fatigue in response to high-velocity knee extensor work.

Methods

Vastus lateralis muscle architecture was determined in quiescent muscle by ultrasonography in 8 young (23.4±1.8 yrs) and 8 older women (69.6±1.1). Maximal voluntary dynamic (MVDC) and isometric (MVIC), and stimulated (80Hz and 10Hz, 500ms) isometric contractions were performed before and immediately after 120 MVDCs (240°·s−1, one every 2s).

Results

Architecture variables did not differ between groups (p≥0.209), but the half-time of torque relaxation (T1/2) was longer in older than young women at baseline (151.9±6.0 vs. 118.8±4.4 ms, respectively, p=0.001). Older women fatigued more than young (to 33.6±4.7% vs. 55.2±4.2% initial torque, respectively; p=0.004), with no evidence of voluntary activation failure (ΔMVIC:80Hz torque) in either group (p≥0.317). Low-frequency fatigue (Δ10:80Hz torque) occurred in both groups (p<0.001), as did slowing of T1/2(p=0.001), with no differences between groups. Baseline T1/2was inversely associated with fatigue in older (r2=0.584, p=0.045), but not young women (r2=0.147, p=0.348).

Conclusions

These results indicate that differences in muscle architecture, voluntary activation, and low-frequency fatigue do not explain the greater fatigue of older compared with young women during high-velocity contractions. The inverse association between baseline T1/2and fatigue in older women suggests that factors related to slower muscle contractile properties may be protective against fatigue during fast, repetitive contractions in aging.
PD-L1 expression in equine malignant melanoma and functional effects of PD-L1 blockade
Authors: Ganbaatar Otgontuya , Konnai Satoru , Okagawa Tomohiro , Nojima Yutaro , Maekawa Naoya , Minato Erina , Kobayashi Atsushi , Ando Ryo , Sasaki Nobuya , Miyakosi Daisuke , Ichi Osamu , Kato Yukinari , Suzuki Yasuhiko , Murata Shiro , Ohashi Kazuhiko
Published: May 2020

Programmed death-1 (PD-1) is an immunoinhibitory receptor expressed on exhausted T cells during chronic illness. Interaction of PD-1 with its ligand PD-ligand 1 (PD-L1) delivers inhibitory signals and impairs proliferation, cytokine production, and cytotoxicity of T cells. We reported that the PD-1/PD-L1 pathway is closely associated with T-cell exhaustion and disease progression in bovine chronic infections and canine tumors. Moreover, we found that blocking antibodies targeting PD-1 and PD-L1 restore T-cell functions and may be used in immunotherapy in cattle and dogs. However, the immunological role of the PD-1/PD-L1 pathway remains unclear for chronic equine diseases, including tumors. In this study, we identified nucleotide sequences of equine PD-1 (EqPD-1) and PD-L1 (EqPD-L1) and investigated the role of anti-bovine PD-L1 monoclonal antibodies (mAbs) against EqPD-L1 usingin vitroassays. We also evaluated the expression of PD-L1 in tumor tissues of equine malignant melanoma (EMM).

The amino acid sequences of EqPD-1 and EqPD-L1 share a high identity and similarity with homologs from other mammalian species. Two clones of the anti-bovine PD-L1 mAbs recognized EqPD-L1 in flow cytometry, and one of these cross-reactive mAbs blocked the binding of equine PD-1/PD-L1. Importantly, PD-L1 expression was confirmed in EMM tumor tissues by immunohistochemistry. A cultivation assay revealed that PD-L1 blockade enhanced the production of Th1 cytokines in equine immune cells.

These results suggest that our anti-PD-L1 mAbs may be useful for investigating the expression and role of the equine PD-1/PD-L1 pathway. Further research is required to discover the immunological role of PD-1/PD-L1 in chronic equine diseases and elucidate a future application in immunotherapy for horse.
Methodological Issues with Search in MEDLINE: A Longitudinal Query Analysis
Authors: Burns C. Sean , Nix Tyler , Shapiro Robert M. , Huber Jeffrey T.
Published: May 2020

This study compares the results of data collected from a longitudinal query analysis of the MEDLINE database hosted on multiple platforms that include PubMed, EBSCOHost, Ovid, ProQuest, and Web of Science in order to identify variations among the search results on the platforms after controlling for search query syntax. We devised twenty-nine sets of search queries comprised of five queries per set to search against the five MEDLINE database platforms. We ran our queries monthly for a year and collected search result count data to observe changes. We found that search results vary considerably depending on MEDLINE platform, both within sets and across time. The variation is due to trends in scholarly publication that include publishing online first versus publishing in journal issues, which leads to metadata differences in the bibliographic record; to differences in the level of specificity among search fields provided by the platforms; to database integrity issues that lead to large fluctuations in monthly search results based on the same query; and to database currency issues that arise due to when each platform updates its MEDLINE file. Specific bibliographic databases, like PubMed and MEDLINE, are used to inform clinical decision-making, create systematic reviews, and construct knowledge bases for clinical decision support systems. Since they serve as essential information retrieval and discovery tools that help identify and collect research data and are used in a broad range of fields and as the basis of multiple research designs, this study should help clinicians, researcher, librarians, informationalists, and others understand how these platforms differ and inform future work in their standardization.
Genome and transcriptome analysis of the mealybugMaconellicoccus hirsutus: A model for genomic Imprinting
Authors: Kohli Surbhi , Gulati Parul , Maini Jayant , KV Shamsudheen , Pandey Rajesh , Scaria Vinod , Sivasubbu Sridhar , Narang Ankita , Brahmachari Vani
Published: May 2020

In mealybugs, transcriptional inactivation of the entire paternal genome in males, due to genomic imprinting, is closely correlated with sex determination. The sequencing,de-novoassembly and annotation of the mealybug,Maconellicoccus hirsutusgenome and its comparison withPlanococcus citrigenome strengthened our gene identification. The expanded gene classes, in both genomes relate to the high pesticide and radiation resistance; the phenotypes correlating with increased gene copy number rather than the acquisition of novel genes. The complete repertoire of genes for epigenetic regulation and multiple copies of genes for the core members of polycomb and trithorax complexes and the canonical chromatin remodelling complexes are present in both the genomes. Phylogenetic analysis withDrosophilashows high conservation of most genes, while a few have diverged outside the functional domain. The proteins involved in mammalian X-chromosome inactivation are identified in mealybugs, thus demonstrating the evolutionary conservation of factors for facultative heterochromatization. The transcriptome analysis of adult male and femaleM.hirsutusindicates the expression of the epigenetic regulators and the differential expression of metabolic pathway genes and the genes for sexual dimorphism. The depletion of endosymbionts in males during development is reflected in the significantly lower expression of endosymbiont genes in them.

Author summary

The mealybug system offers a unique model for genomic imprinting and differential regulation of homologous chromosomes that pre-dates the discovery of dosage compensation of X chromosomes in female mammals. In the absence of robust genetics for mealybugs, we generated and analysed the genome and transcriptome profile as primary resources for effective exploration. The expanded gene classes in the mealybugs relate to their unique biology; the expansion of pesticide genes, trehalose transporter, SETMAR and retrotransposons correlate with pesticide, desiccation and radiation resistance, respectively. The similarity in the genomic profile of two species of mealybugs strengthens our gene prediction. All the known epigenetic modifiers and proteins of the primary complexes like the PRC1,2 and the trithorax are conserved in mealybugs, so also the homologues of mammalian proteins involved in X chromosome inactivation. The high copy number of genes for many partners in these complexes could facilitate the inactivation of a large part of the genome and raise the possibility of formation of additional non-canonical complexes for sex specific chromosome inactivation. In adult males and females, the status of epigenetic regulation is likely to be in a maintenance state; therefore, it is of interest to analyze the expression of epigenetic regulators during development.
gEL DNA, a cloning- and PCR-free method for CRISPR-based multiplexed genome editing
Authors: Randazzo Paola , Daran Jean-Marc , Daran-Lapujade Pascale
Published: May 2020

Even for the genetically accessible yeastSaccharomyces cerevisiae, the CRISPR/Cas DNA editing technology has strongly accelerated and facilitated strain construction. Several methods have been validated for fast and highly efficient single editing events and diverse approaches for multiplex genome editing have been described in literature by means of Cas9 or Cas12a endonucleases and their associated gRNAs. The gRNAs used to guide the Cas endonuclease to the editing site are typically expressed from plasmids using native PolII or PolIII RNA polymerases. These gRNA-expression plasmids require laborious, time-consuming cloning steps, which hampers their implementation for academic and applied purposes. In this study, we explore the potential of expressing gRNA from linear DNA fragments using the T7 RNA polymerase (T7RNAP) for single and multiplex genome editing inS. cerevisiae. Using Cas12a, this work demonstrates that transforming short, linear DNA fragments encoding gRNAs in yeast strains expressing T7RNAP promotes highly efficient single DNA editing. These DNA fragments can be custom-ordered, which makes this approach highly suitable for high-throughput strain construction. This work expands the CRISPR-toolbox for large-scale strain construction programs inS. cerevisiaeand promises to be relevant for other, less genetically accessible yeast species.