bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining chemogenomic and gene-dose assays to investigate drug synergy
Authors: Gaikani Hamid , Smith Andrew M. , Lee Anna Y. , Giaever Guri , Nislow Corey
Published: February 2021

From the earliest days of using natural remedies to modern applications of clinically tested medications, combining therapies for disease treatment has been standard practice. Combination treatments can exhibit synergistic effects, broadly defined as a greater-than-additive effect of two or more therapeutic agents. Indeed, clinicians often use their experience and expertise to tailor such combinations in the hopes of maximizing the therapeutic effect. Alongside these efforts, computational studies into understanding and predicting the biophysical underpinnings of how synergy is achieved have benefitted from high-throughput screening and computational biology. One challenge is how to best design and analyze the results of synergy studies performed at scale, especially because the number of possible combinations to test quickly becomes unmanageable, and the tools to analyze the resulting data are quite new. Nevertheless, the benefits of such studies are clear — by combining multiple drugs in the treatment of infectious disease and cancer, for instance, one can lessen host toxicity and simultaneously reduce the likelihood of resistance to treatment. In this study, we extend the widely validated chemogenomic HIPHOP assay to drug combinations. We identify a class of “combination-specific sensitive strains” that suggest mechanisms for the synergies we observe and further suggest focused follow-up studies.
Efficient CRISPR/Cas9 mutagenesis for neurobehavioral screening in adult zebrafish
Authors: Shaw Dana Klatt , Mokalled Mayssa H.
Published: February 2021

Adult zebrafish are increasingly used to interrogate mechanisms of disease development and tissue regeneration. Yet, the prospect of large-scale genetics in adult zebrafish has traditionally faced a host of biological and technical challenges. Here, we describe an experimental pipeline that combines high-efficiency CRISPR/Cas9 mutagenesis with functional phenotypic screening to identify genes required for spinal cord repair in adult zebrafish. Using CRISPR/Cas9 dual-guide ribonucleic proteins, we show selective and combinatorial mutagenesis of 17 genes at 28 target sites with efficiencies exceeding 85% in adult F0‘crispants’. We find that capillary electrophoresis is a reliable method to measure indel frequencies, while avoiding the limitations of restriction enzyme-based genotyping. Using a quantifiable behavioral assay, we identify 7 single- or duplicate-gene crispants with reduced functional recovery after spinal cord injury. To rule out off-target effects, we generate germline mutations that recapitulate the crispant regeneration phenotypes. This study provides a platform that combines high-efficiency somatic mutagenesis with a functional phenotypic readout to perform medium- to large-scale genetic studies in adult zebrafish.
A Thermostable, Flexible RNA Vaccine Delivery Platform for Pandemic Response
Authors: Gerhardt Alana , Voigt Emily , Archer Michelle , Reed Sierra , Larson Elise , Van Hoeven Neal , Kramer Ryan , Fox Christopher , Casper Corey
Published: February 2021

Current RNA vaccines against SARS-CoV-2 are limited by instability of both the RNA and the lipid nanoparticle delivery system, requiring storage at −20°C or −70°C and compromising universally accessible vaccine distribution. This study demonstrates the thermostability and adaptability of a nanostructured lipid carrier (NLC) RNA vaccine delivery system for use in pandemic preparedness and pandemic response. Liquid NLC is stable at refrigerated temperatures for ≥ 1 year, enabling stockpiling and rapid deployment by point-of-care mixing with any vaccine RNA. Alternatively, NLC complexed with RNA may be readily lyophilized and stored at room temperature for ≥ 8 months or refrigerated temperature for ≥ 21 months. This thermostable RNA vaccine platform could significantly improve distribution of current and future pandemic response vaccines, particularly in low-resource settings.

One Sentence Summary

An RNA vaccine delivery system stable at room temperature for 8+ months and refrigerated for 21+ months.
Evaluation of Depression, Anxiety and Sleep Quality in the Brazilian Population During Social Isolation Due to the New Coronavirus (SARS-CoV-2) pandemic: the DEGAS-CoV Study
Authors: Mei Paulo Afonso , Sasse Amanda , Fernandez Ana Lara Navarrete , Perri Barbara Neiva , Bispo Breno Alexander , Santana Giselly Brito , Munhos Gabriela Sakita , Verghetti Giovanni Giuliani , Martins Guilherme Barbosa de Almeida Olivei , Rocha Jennifer Pereira da , Mendonca Jessyca Rosa Lopes , Lebl Julia Patel , Rolt Valdemiro Da , Ruivo Lais Grabner , Loeb Laura , Isepon Marielly , Pachecco Marina Joseane , Baptista Cintia Zonta , Nespoli Fabio Soares , Castro Paloma Ricciardi de , Castro Paola Ricciardi de , Brustolin Rafaela Dotta , Silva Taysa Maria Pimentel Goncalves Gome , Andreata Victoria Gomes , Santos Amilton , Cardoso Tania Marchiori de Oliveira
Published: February 2021

Introduction: The new coronavirus infection (COVID-19) has caused distress and repercussions in mental and physical health of individuals. Depression, anxiety and worsening of sleep quality have been reported in several recent articles that surveyed populations all over the globe. Our work meant to access, through a cross-sectional study, these disorders in the Brazilian population, through the application of an online questionnaire conducted on the second trimester of 2020.

Materials and Methods: We applied an online questionnaire, filled with questions regarding social, economic, financial, educational and health status, as well as questions from the Hospital Anxiety and Depression Scale (HAD), and from the Pittsburgh Sleep Quality Index (PSQI).

Results: We collected 2,695 valid answers, from April 24th to May 31st, 2020. Age ranged from 18 to 79 years, mean of 31.3. Women were 76.3%, men 23.7%. Symptoms of Anxiety were found in 56.5%, of depression in 46.1%, and of bad sleep in 49.2%. Some groups were more prone than others to one or more of those conditions, such as: younger people, women, mestizos, Northeasterners, people with lesser years of education, of lower income or whose income dropped significantly during the pandemic, caregivers, students, sedentary or people practicing less physical activity, people who followed more hours of news of COVID-19 and those less engaged in social and instrumental activities.

Conclusion: anxiety, depression and bad sleep quality were significantly high in our survey. Mental and sleep health is heterogeneously affected among individuals, depending on social, economic, financial, educational and health status.
A novel biomechanical injury risk score demonstrates correlation with lower limb posterior chain injury in fifty elite level rugby union athletes
Authors: Hughes Rhys , Cross Matt , Stokes Keith
Published: February 2021

Objectives

Lower limb posterior chain injury (PCI) is common amongst athletic populations, with multi-factorial risk factors including age, previous injury, strength measurements, range of motion and training load. Biomechanics are commonly considered in the prevention and rehabilitation of PCI by performance staff. However, there is no documented testing method to assess for associations between biomechanics and PCI. The aim of this study was to investigate whether there is an association between an easily applicable, novel biomechanical assessment tool and PCI.

Methods

Fifty male elite-level rugby union athletes (age 22.83±5.08) participating in the highest tier of England were tested at the start of the 2019 pre-season period and PCIs (N=48) were recorded over the 2019/20 playing season. Participants’ biomechanics were analysed using two-dimensional video analysis against an Injury Risk Score (IRS) system in the performance of the combined movement – prone hip extension and knee flexion. Participants’ biomechanics in carrying out this movement were scored against the 10-point IRS, where the more compensatory movement recorded sees an increase in an individual’s IRS. Participants’ IRS were then compared against the number of PCI sustained and Spearman’s correlation coefficient was utilised for analysis.

Results

There is a good significant association between IRS and PCI (R=0.573, p<0.001). Linear Regression demonstrated that an increase of 1 in IRS was associated with a 35% increase in PCI incidence (R2=0.346).

Conclusion

A good significance between the IRS and PCI provides preliminary support for its use as an injury risk assessment tool.
Muscle strength is associated with COVID-19 hospitalization in adults 50 years of age or older
Authors: Cheval Boris , Sieber Stefan , Maltagliati Silvio , P. Millet Grégoire , Formánek Tomáš , Chalabaev Aïna , Cullati Stéphane , Boisgontier Matthieu P.
Published: February 2021

Background

Weak muscle strength has been associated with a wide range of adverse health outcomes. Yet, whether individuals with weaker muscle strength are more at risk for hospitalization due to severe COVID-19 is still unclear. The objective of this study was to investigate the independent association between muscle strength and COVID-19 hospitalization.

Methods

Data from adults 50 years of age or older were analyzed using logistic models adjusted for several chronic conditions, body-mass index, age, and sex. Hand-grip strength was repeatedly measured between 2004 and 2017 using a handheld dynamometer. COVID-19 hospitalization during the lockdown was self reported in summer 2020 and was used as an indicator of COVID-19 severity.

Results

The study was based on the Survey of Health, Ageing and Retirement in Europe (SHARE) and included 3600 older adults (68.8 ± 8.8 years, 2044 females), amongst whom 316 were tested positive for the severe acute respiratory syndrome coronavirus 2 (8.8%) and 83 (2.3 %) were hospitalized due to COVID-19. Results showed that higher grip strength was associated with a lower risk of COVID-19 hospitalization (adjusted odds ratio [OR] per increase of 1 standard deviation in grip strength = .64, 95% confidence interval [95% CI] = .45–.87,p= .015). Results also showed that age (OR for a 10-year period = 1.70, 95% CI = 1.32–2.20,p< .001) and obesity (OR = 2.01, 95% CI = 1.00–3.69,p= .025) were associated with higher risk of COVID-19 hospitalization. Sensitivity analyses using different measurements of grip strength as well as robustness analyses based on rare-events logistic regression and a different sample of participants (i.e., COVID-19 patients) were consistent with the main results.

Conclusion

Muscle strength is an independent risk factor for COVID-19 severity in adults 50 years of age or older.
Elevated mucosal antibody responses against SARS-CoV-2 are correlated with lower viral load and faster decrease in systemic COVID-19 symptoms
Authors: Fröberg Janeri , Gillard Joshua , Philipsen Ria , Lanke Kjerstin , Rust Joyce , van Tuijl Diana , Bousema Teun , Simonetti Elles , van der Gaast – de Jongh Christa E. , Bos Mariska , van Kuppeveld Frank J. , Bosch Berend-Jan , Nabuurs-Franssen Marrigje , van der Geest-Blankert Nannet , van Daal Charlotte , Huynen Martijn A. , de Jonge Marien I. , Diavatopoulos Dimitri A.
Published: February 2021

Mucosal antibodies play a key role in protection against SARS-CoV-2 exposure, but their role during primary infection is not well understood. We assessed mucosal antibody responses during primary infection with SARS-CoV-2 and examined their relationship with viral load and clinical symptoms. Elevated mucosal IgM was associated with lower viral load. RBD and viral spike protein-specific mucosal antibodies were correlated with decreases in systemic symptoms, while older age was associated with an increase in respiratory symptoms. Up to 42% of household contacts developed SARS-CoV-2-specific mucosal antibodies, including children, indicating high transmission rates within households in which children might play an important role.
Colchicine use in patients with COVID-19: a systematic review and meta-analysis
Authors: Chiu Leonard , Lo Chun-Han , Shen Max , Chiu Nicholas , Aggarwal Rahul , Lee Jihui , Choi Young-Geun , Lam Henry , Prsic Elizabeth Horn , Chow Ronald , Shin Hyun Joon
Published: February 2021

Introduction

Colchicine may inhibit inflammasome signaling and reduce proinflammatory cytokines, a purported mechanism of COVID-19 pneumonia. The aim of this systematic review and meta-analysis is to report on the state of the current literature on the use of colchicine in COVID-19 and to investigate the reported clinical outcomes in COVID-19 patients by colchicine usage.

Methods

The literature was searched from January 2019 through January 28, 2021. References were screened to identify studies that reported the effect of colchicine usage on COVID-19 outcomes including mortality, intensive care unit (ICU) admissions, or mechanical ventilation. Studies were meta-analyzed for mortality by the subgroup of trial design (RCT vs observational) and ICU status. Studies reporting an risk ratio (RR), odds ratio (OR) and hazard ratio (HR) were analyzed separately.

Results

Eight studies, reporting on 16,248 patients, were included in this review. The Recovery trial reported equivalent mortality between colchicine and non-colchicine users. Across the other studies, patients who received colchicine had a lower risk of mortality - HR of 0.25 (95% CI: 0.09, 0.66) and OR of 0.22 (95% CI: 0.09, 0.57). There was no statistical difference in risk of ICU admissions between patients with COVID-19 who received colchicine and those who did not – OR of 0.26 (95% CI: 0.06, 1.09).

Conclusion

Colchicine may reduce the risk of mortality in individuals with COVID-19. Further prospective investigation may further determine the efficacy of colchicine as treatment in COVID-19 patients in various care settings of the disease, including post-hospitalization and long-term care.
Associations between total MRI-visible small vessel disease burden and domain-specific cognitive abilities in a community-dwelling older-age cohort
Authors: Hamilton OKL , Cox SR , Ballerini L , Bastin ME , Corley J , Gow AJ , Muñoz Maniega S , Redmond P , M del C Valdés-Hernández , Wardlaw JM , Deary IJ
Published: February 2021

Cerebral small vessel disease (SVD) is a leading cause of vascular cognitive impairment, however the precise nature of SVD-related cognitive deficits, and their associations with structural brain changes, remain unclear. We combined computational volumes and visually-rated MRI markers of SVD to quantify total SVD burden, using data from the Lothian Birth Cohort 1936 (n=540; age:72.6±0.7 years). We found negative associations between total SVD burden and general cognitive ability (standardised β: −0.363; 95%CI: [−0.49, −0.23]; p(FDR)<0.001), processing speed (−0.371 [−0.50, −0.24]; p(FDR)<0.001), verbal memory (−0.265; [−0.42, −0.11]; p(FDR)=0.002), and visuospatial ability (−0.170; [−0.32, −0.02]; p(FDR)=0.029). Only the association between SVD burden and processing speed remained after accounting for covariance with general cognitive ability (−0.325; [−0.61, −0.04]; p(FDR)=0.029). This suggests that SVD’s association with poorer processing speed is not driven by, but isindependentof its association with poorer general cognitive ability. Tests of processing speed may be particularly sensitive to the cognitive impact of SVD, but all major cognitive domains should be tested to determine the full range of SVD-related cognitive characteristics.
SEVERE COVID-19 IS MARKED BY DYSREGULATED SERUM LEVELS OF CARBOXYPEPTIDASE A3 AND SEROTONIN
Authors: Soria-Castro Rodolfo , Meneses-Preza Yatsiri G. , Rodríguez López Gloria M. , Romero-Ramírez Sandra , Sosa-Hernandez Víctor A. , Cervantes-Díaz Rodrigo , Pérez-Fragoso Alfredo , Torres-Ruíz José J. , Gómez-Martín Diana , Campillo-Navarro Marcia , Álvarez-Jiménez Violeta D. , Pérez-Tapia Sonia M. , Chávez-Blanco Alma D. , Estrada-Parra Sergio , Maravillas-Montero José L. , Chacón Salinas Rommel
Published: February 2021

The immune response plays a critical role in the pathophysiology of SARS-CoV-2 infection ranging from protection to tissue damage. This is observed in the development of acute respiratory distress syndrome when elevated levels of inflammatory cytokines are detected. Several cells of the immune response are implied in this dysregulated immune response including innate immune cells and T and B cell lymphocytes. Mast cells are abundant resident cells of the respiratory tract, able to rapidly release different inflammatory mediators following stimulation. Recently, mast cells have been associated with tissue damage during viral infections, but little is known about their role in SARS-CoV-2 infection. In this study we examined the profile of mast cell activation markers in the serum of COVID-19 patients. We noticed that SARS-CoV-2 infected patients showed increased carboxypeptidase A3 (CPA3), and decreased serotonin levels in their serum. CPA3 levels correlated with C-reactive protein, the number of circulating neutrophils and quick SOFA. CPA3 in serum was a good biomarker for identifying severe COVID-19 patients, while serotonin was a good predictor of SARS-CoV-2 infection. In summary, our results show that serum CPA3 and serotonin levels are relevant biomarkers during SARS-CoV-2 infection, suggesting that mast cells are relevant players in the inflammatory response in COVID-19, might represent targets for therapeutic intervention.
Quantifying meaningful usage of a SARS-CoV-2 exposure notification app on the campus of the University of Arizona
Authors: Masel Joanna , Shilen Alexandra , Helming Bruce , Rutschman Jenna , Windham Gary , Pogreba-Brown Kristen , Ernst Kacey
Published: February 2021

Objective

To measure meaningful, local exposure notification usage without in-app analytics.

Methods

We surveyed app usage via case investigation interviews at the University of Arizona, with a focus on the period from September 9 to November 28, 2020, after automating the issuance of secure codes to verify positive test results. As independent validation, we compared the number of verification codes issued to the number of local cases.

Results

Forty six percent (286/628) of infected persons interviewed by university case investigators reported having the app, and 55% (157/286) of these app users shared their positive SARS-CoV-2 test result in the app prior to the case investigation interview, comprising 25% (157/628) of those interviewed. This is corroborated by a 33% (565/1,713) ratio of code issuance (inflated by some unclaimed codes) to cases. Combining the 25% probability that those who test positive rapidly share their test result with a 46% probability that a person they infected can receive exposure notifications, an estimated 11.4% of transmission pairs exhibit meaningful app usage. High usage was achieved without the use of “push” notifications, in the context of a marketing campaign that leveraged social influencers.

Conclusions

Usage can be assessed, without in-app analytics, within a defined local community such as a college campus rather than an entire jurisdiction. With marketing, high uptake in dense social networks like universities makes exposure notification an impactful complement to traditional contact tracing. Integrating verification code delivery into patient results portals was successful in making the exposure notification process rapid.

3 question summary box

1)

What is the current understanding of this subject?

The extent to which exposure notification technology reduces SARS-CoV-2 transmission depends on usage among infected persons.

2)

What does this report add to the literature?

A novel metric estimates meaningful usage, and demonstrates potential transmission reduction on a college campus. Clear benefit was seen from simplifying verification of positive test results with automation.

3)

What are the implications for public health practice?

Defined communities can benefit from local deployment and marketing even in the absence of statewide deployment. Lifting current restrictions on deployment would allow more entities such as campuses to copy the model shown here to be successful.
Spatial-proteomics revealin-vivophospho-signaling dynamics at subcellular resolution
Authors: Martinez-Val Ana , Bekker-Jensen Dorte B. , Steigerwald Sophia , Mehta Adi , Tran Trung , Sikorski Krzysztof , Torres-Vega Estefanía , Kwasniewicz Ewa , Brynjólfsdóttir Sólveig Hlín , Frankel Lisa B. , Kjøbsted Rasmus , Krogh Nicolai , Lundby Alicia , Bekker-Jensen Simon , Lund-Johansen Fridtjof , Olsen Jesper V.
Published: February 2021

Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for eliciting a coordinated response to stimuli. Mass spectrometry (MS)-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of cells, but involves laborious workflows that does not cover the phospho-proteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. We benchmarked the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in-vitro in HeLa cells and in-vivo in mouse tissues. Finally, we investigated the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction. Proteomics data generated in this study can be explored throughhttps://SpatialProteoDynamics.github.io.
Therapeutic antibodies, targeting the SARS-CoV-2 spike N-terminal domain, protect lethally infected K18-hACE2 mice
Authors: Noy-Porat Tal , Mechaly Adva , Levy Yinon , Makdasi Efi , Alcalay Ron , Gur David , Aftalion Moshe , Falach Reut , Ben-Arye Shani Leviatan , Lazar Shirley , Zauberman Ayelet , Epstein Eyal , Chitlaru Theodor , Weiss Shay , Achdout Hagit , Edgeworth Jonathan D. , Kikkeri Raghavendra , Yu Hai , Chen Xi , Yitzhaki Shmuel , Shapira Shmuel C. , Padler-Karavani Vered , Mazor Ohad , Rosenfeld Ronit
Published: February 2021

Since the onset of the current COVID-19 pandemic, high priority is given to the development of neutralizing antibodies, as a key approach for the design of therapeutic strategies to countermeasure and eradicate the disease. Previously, we reported the development of human therapeutic monoclonal antibodies (mAbs) exhibiting very high protective ability. These mAbs recognize epitopes on the spike receptor binding domain (RBD) of SARS-CoV-2 that is considered to represent the main rout of receptor engagement by the SARS-CoV-2 virus. The recent emergence of viral variants emphasizes the notion that efficient antibody treatments need to rely on mAbs against several distinct key epitopes in order to circumvent the occurrence of therapy escape-mutants. Here we report the isolation and characterization of 12 neutralizing mAbs, identified by screening a phage-display library constructed from lymphatic cells collected from severe COVID-19 patients. The antibodies target three distinct epitopes on the spike N-terminal domain (NTD) of SARS-CoV-2, one of them defining a major site of vulnerability of the virus. Extensive characterization of these mAbs suggests a neutralization mechanism which relies both on amino-acid and N-glycan recognition on the virus, and involvement of receptors other than the hACE2 on the target cell. Two of the selected mAbs, which demonstrated superior neutralization potency in vitro, were further evaluated in vivo, demonstrating their ability to fully protect K18-hACE2 transgenic mice even when administered at low doses and late after infection. The study demonstrates the high potential of the mAbs for therapy of SARS-CoV-2 infection and underlines the possible role of the NTD in mediating infection of host cells via alternative cellular portals other than the canonical ACE2 receptor.
Predicting Epigenomic Functions of Genetic Variants in the Context of Neurodevelopment via Deep Transfer Learning
Authors: Lai Boqiao , Qian Sheng , Zhang Hanwen , Zhang Siwei , Kozlova Alena , Duan Jubao , He Xin , Xu Jinbo
Published: February 2021

Decoding the regulatory effects of non-coding variants is a key challenge in understanding the mechanisms of gene regulation as well as the genetics of common diseases. Recently, deep learning models have been introduced to predict genome-wide epigenomic profiles and effects of DNA variants, in various cellular contexts, but they were often trained in cell lines or bulk tissues that may not be related to phenotypes of interest. This is particularly a challenge for neuropsychiatric disorders, since the most relevant cell and tissue types are often missing in the training data of such models.

To address this issue, we introduce a deep transfer learning framework termed MetaChrom that takes advantage of both a reference dataset - an extensive compendium of publicly available epigenomic data, and epigenomic profiles of cell types related to specific phenotypes of interest. We trained and evaluated our model on a comprehensive set of epigenomic profiles from fetal and adult brain, and cellular models representing early neurodevelopment. MetaChrom predicts these epigenomic features with much higher accuracy than previous methods, and than models without the use of reference epigenomic data for transfer learning. Using experimentally determined regulatory variants from iPS cell-derived neurons, we show that MetaChrom predicts functional variants more accurately than existing non-coding variant scoring tools. By combining genome-wide association study (GWAS) data with MetaChrom predictions, we prioritized 31 SNPs for Schizophrenia (SCZ). These candidate SNPs suggest potential risk genes of SCZ and the biological contexts where they act.

In summary, MetaChrom is a general transfer learning framework that can be applied to the study of regulatory functions of DNA sequences and variants in any disease-related cell or tissue types. The software tool is available at https://github.com/bl-2633/MetaChrom and a prediction web server is accessible at https://metachrom.ttic.edu/.
Lateral Undulation Aids Biological and Robotic Earthworm Anchoring and Locomotion
Authors: Ozkan-Aydin Yasemin , Liu Bangyuan , Ferrero Alexandra Carruthers , Seidel Max , Hammond Frank L. , Goldman Daniel I.
Published: February 2021

Earthworms (Lumbricus terrestris) are characterized by soft, highly flexible and extensible bodies, and are capable of locomoting in most terrestrial environments. Previous studies of earthworm movement have focused on the use of retrograde peristaltic gaits in which controlled contraction of longitudinal and circular muscles results in waves of shortening/thickening and thinning/lengthening of the hydrostatic skeleton. These waves can propel the animal across ground as well as into soil. However, worms can also benefit from axial body bends during locomotion. Such lateral undulation dynamics can aid locomotor function via hooking/anchoring (to provide propulsion), modify travel orientation (to avoid obstacles and generate turns) and even generate snake-like undulatory locomotion in environments where peristaltic locomotion results in poor performance. To the best of our knowledge, the important aspects of locomotion associated with the lateral undulation of an earthworm body are yet to be systematically investigated. In this study, we observed that within confined environments, the worm uses lateral undulation to anchor its body to the walls of their burrows and tip (nose) bending to search the environment. This relatively simple locomotion strategy drastically improved the performance of our soft bodied robophysical model of the earthworm both in a confined (in an acrylic tube) and above-ground heterogeneous environment (rigid pegs), where the peristaltic gait often fails. In summary, lateral undulation facilitates the mobility of earthworm locomotion in diverse environments and can play an important role in the creation of low cost soft robotic devices capable of traversing a variety of environments.
Semi-quantitative detection for L-asparaginase producing fungi and the impact of carbon and nitrogen sources on enzyme activity
Authors: Hamed Mahdi , Osman Ahmed A , Ateş Mustafa
Published: February 2021

Objective

To semi-quantitively screen filamentous fungi isolated from different habitats for L-asparaginase production by three indicators; phenol red, cresol red and bromothymol blue and to examine the impact of different carbon and nitrogen sources on the enzyme production using different fungal isolates.

Materials and methods

Fifty-five fungal isolates were tested for L-asparaginase production by plate assay using Modified Czapek-Dox (MCD) medium. The enzyme activity was estimated using the Nessler method which measures the concentration of ammonia formed owing to the enzyme action on the substrate. The impact of nitrogen and carbon sources on the enzyme production was done by using the best three L-asparaginase producers from the semi-quantitative screening.

Results and conclusions

A total of 53/55 (96.36%) fungal isolates were L-asparaginase producing strains, of them, Cladosporium tenuissimum, Penicillium camembertii and Aspergillus carneus showed high enzyme production. Production of L-asparaginase was higher with the glucose and urea as carbon and nitrogen sources, respectively. The highest enzyme level (5,558 U/ml) was produced by C. tenuissimum in a glucose-containing medium. This study shows that P. camemberti, A. carneus, and C. tenuissimum are good L-asparaginase producers and thus could be used for L-asparaginase production
Akr1d1-/- mice have a sexually dimorphic metabolic phenotype with reduced fat mass, increased insulin sensitivity and hypertriglyceridemia in males
Authors: Gathercole Laura L , Nikolaou Nikolaos , Arvaniti Anastasia , Harris Shelley E , Poolman Toryn M , Hazlehurst Jonathan M , Kratschmar Denise V , Todorčević Marijana , Moolla Ahmad , Dempster Niall , Pink Ryan C , Saikali Michael F , Bentley Liz , Penning Trevor M , Ohlsson Claes , Cummins Carolyn L , Poutanen Matti , Odermatt Alex , Cox Roger D , Tomlinson Jeremy W
Published: February 2021

Background

Steroid 5β-reductase (AKR1D1) plays important roles in hepatic glucocorticoid clearance and bile acid synthesis. Glucocorticoids and bile acids are potent metabolic regulators, but whether AKR1D1 controls metabolic phenotype in vivo is unknown.

Methods

Akr1d1-/-mice were generated on a C57BL/6 background. Liquid chromatography / mass spectrometry, metabolomic and transcriptomic approaches were used to determine effects on glucocorticoid and bile acid homeostasis. Metabolic phenotypes including body weight and composition, lipid homeostasis, glucose tolerance and insulin sensitivity were evaluated. Molecular changes were assessed by RNASeq and western blotting. Male Akr1d1-/-mice were challenged with a 60% high fat diet.

Results

Akr1d1-/-mice had a sex specific metabolic phenotype. At 30-weeks of age male, but not female, Akr1d1-/-mice were more insulin sensitive and had reduced lipid accumulation in the liver and adipose tissue, concomitant with hypertriglyceridemia and increased intramuscular triacylglycerol. This phenotype was underpinned by sexually dimorphic changes in bile acid metabolism and composition, but without overt effects on glucocorticoid action. Male Akr1d1-/-mice were not protected against diet induced obesity and insulin resistance.

Conclusion

This study shows that AKR1D1 controls bile acid homeostasis in vivo and that altering its activity can affect insulin sensitivity and lipid homeostasis in a sex dependent manner.
Defining a Connectome-Based Predictive Model of Attentional Control in Aging
Authors: Fountain-Zaragoza Stephanie , Manglani Heena R. , Rosenberg Monica D. , Andridge Rebecca , Prakash Ruchika Shaurya
Published: February 2021

With advancing age, declines in the executive control of attention are accompanied by shifts in the functional topology of brain networks. However, there is increasing recognition of the considerable individual variability in the extent and types of attentional deficits that older adults exhibit, with results from neuroimaging investigations paralleling behavioral heterogeneity. Emerging computational methods leverage whole-brain functional connectivity to predict individual-level behaviors. These approaches are well-suited to the cognitive aging context, as they may elucidate configurations of functional connections that best explain group- and individual-level differences across older adults. Two independent samples of neurologically and psychiatrically healthy older adults were used to separately derive a predictive model of attentional control and test the model’s external validity. Here we show that despite challenges posed by heterogeneity in these aging samples, select functional connections carried meaningful variance, allowing for successful prediction of attention in a novel sample of older individuals.
In vivo amyloid-like fibrils produced under stress
Authors: Fontana Natália A. , Rosse Ariane D. , Watts Anthony , Coelho Paulo S. R. , Costa-Filho Antonio J.
Published: February 2021

The participation of amyloids in neurodegenerative diseases and functional processes has triggered the quest for methods allowing their direct detection in vivo. Despite the plethora of data, those methods are still lacking. The autofluorescence from the extended β-sheets of amyloids is here used to follow fibrillation of S. cerevisiae Golgi Reassembly and Stacking Protein (Grh1). Grh1 has been implicated in starvation-triggered unconventional protein secretion (UPS), and here its participation also in heat shock response (HSR) is suggested. Fluorescence Lifetime Imaging (FLIM) is used to detect fibril autofluorescence in cells (E. coli and yeast) under stress (starvation and higher temperature). The formation of Grh1 large complexes under stress is further supported by size exclusion chromatography and ultracentrifugation. The data show for the first time in vivo detection of amyloids without the use of extrinsic probes as well as bring new perspectives on the participation of Grh1 in UPS and HSR.
Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes
Authors: Quan Hui , Tian Hao , Liu Sirui , Xue Yue , Zhang Yu , Xie Wei , Gao Yi Qin
Published: February 2021

The author has withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2019/521401. Therefore, the author does not wish this work to be cited as a reference for the project. Please cite and refer to the preprint BIORXIV/2019/521401 if necessary. If you have any questions, please contact the corresponding author (gaoyq@pku.edu.cn).
Nascent polypeptide within the exit tunnel ensures continuous translation elongation by stabilizing the translating ribosome
Authors: Chadani Yuhei , Sugata Nobuyuki , Niwa Tatsuya , Ito Yosuke , Iwasaki Shintaro , Taguchi Hideki
Published: February 2021

Continuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, the risk of elongation abortion is concealed within nascent polypeptide products. Negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, destabilizes the translating ribosomal complex. Thus, some nascent chain sequences lead to premature translation cessation. Here, we show that the risk of IRD is maximal at the N-terminal regions of proteins encoded by dozens of Escherichia coli genes. In contrast, most potential IRD sequences in the middle of open reading frames remain cryptic. We found two elements in nascent chains that counteract IRD: the nascent polypeptide itself that spans the exit tunnel and its bulky amino acid residues that occupy the tunnel entrance region. Thus, nascent polypeptide products have a built-in ability to ensure elongation continuity by serving as a bridge and thus by protecting the large and small ribosomal subunits from dissociation.
dcHiC: differential compartment analysis of Hi-C datasets
Authors: Chakraborty Abhijit , Wang Jeffrey , Ay Ferhat
Published: February 2021

The compartmental organization of chromatin and its changes play important roles in distinct biological processes carried out by mammalian genomes. However, differential compartment analyses have been mostly limited to pairwise comparisons and with a main focus on only the compartment flips (e.g., A-to-B). Here, we introduce dcHiC, which utilizes quantile normalized compartment scores and a multivariate distance measure to identify significant changes in compartmentalization among multiple contact maps. Evaluating dcHiC on three collections of Hi-C contact maps from mouse neural differentiation (n=3), mouse hematopoiesis (n=10) and human LCL cell lines (n=20), we show its effectiveness and sensitivity in detecting biologically relevant differences, including those validated by orthogonal experiments. Across these experiments, dcHiC reported regions with dynamically regulated genes associated with cell identity, along with correlated changes in chromatin states, replication timing and lamin B1 association. With its efficient implementation, dcHiC not only enables high-resolution compartment analysis but also includes a suite of additional features, including standalone browser visualization, differential interaction identification, and time-series clustering. As such, it is an essential addition to the Hi-C analysis toolbox for the ever-growing number of contact maps being generated. dcHiC is freely available at https://github.com/ay-lab/dcHiC, and examples from this paper can be seen at https://ay-lab.github.io/dcHiC.
Genetic autonomy and low singlet oxygen yield support kleptoplast functionality in photosynthetic sea slugs
Authors: Havurinne Vesa , Handrich Maria , Antinluoma Mikko , Khorobrykh Sergey , Gould Sven B. , Tyystjärvi Esa
Published: February 2021

Elysia chlorotica is a kleptoplastic sea slug that preys on Vaucheria litorea, stealing its plastids which then continue to photosynthesize for months inside the animal cells. We investigated the native properties of V. litorea plastids to understand how they withstand the rigors of photosynthesis in isolation. Transcription of specific genes in laboratory-isolated V. litorea plastids was monitored up to seven days. The involvement of plastid-encoded FtsH, a key plastid maintenance protease, in recovery from photoinhibition in V. litorea was estimated in cycloheximide-treated cells. In vitro comparison of V. litorea and spinach thylakoids was applied to investigate ROS formation in V. litorea. Isolating V. litorea plastids triggered upregulation of ftsH and translation elongation factor EF-Tu (tufA). Upregulation of FtsH was also evident in cycloheximide-treated cells during recovery from photoinhibition. Charge recombination in PSII of V. litorea was found to be fine-tuned to produce only small quantities of singlet oxygen (1O2). Our results support the view that the genetic characteristics of the plastids themselves are crucial in creating a photosynthetic sea slug. The plastid’s autonomous repair machinery is likely enhanced by low 1O2 production and by upregulation of FtsH in the plastids.

Highlight

Isolated Vaucheria litorea plastids exhibit upregulation of tufA and ftsH, key plastid maintenance genes, and produce only little singlet oxygen. These factors likely contribute to plastid longevity in kleptoplastic slugs.
Increased levels of the mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol
Authors: Schlagowski Anna M. , Knöringer Katharina , Morlot Sandrine , Sáchez Vicente Ana , Boos Felix , Khalid Nabeel , Ahmed Sheraz , Schramm Jana , Murschall Lena Maria , Haberkant Per , Stein Frank , Riemer Jan , Westermann Benedikt , Braun Ralf J. , Winklhofer Konstanze F. , Charvin Gilles , Herrmann Johannes M.
Published: February 2021

The formation of protein aggregates is a hallmark of neurodegenerative diseases. Observations on patient material and model systems demonstrated links between aggregate formation and declining mitochondrial functionality, but the causalities remained unclear. We used yeast as model system to analyze the relevance of mitochondrial processes for the behavior of an aggregation-prone polyQ protein derived from human huntingtin. Induction of Q97-GFP rapidly leads to insoluble cytosolic aggregates and cell death. Although this aggregation impairs mitochondrial respiration only slightly, it interferes with efficient import of mitochondrial precursor proteins. Mutants in the import component Mia40 are hypersensitive to Q97-GFP. Even more surprisingly, Mia40 overexpression strongly suppresses the formation of toxic Q97-GFP aggregates both in yeast and in human cells. Based on these observations, we propose that the posttranslational import into mitochondria competes with aggregation-prone cytosolic proteins for chaperones and proteasome capacity. Owing to its rate-limiting role for mitochondrial protein import, Mia40 acts as a regulatory component in this competition. This role of Mia40 as dynamic regulator in mitochondrial biogenesis can apparently be exploited to stabilize cytosolic proteostasis. (174/175 words)
Impact of central complex lesions on visual orientation in ants: Turning behaviour, but not the overall movement direction, is disrupted
Authors: Dell-Cronin Scarlett , Buehlmann Cornelia , Pathirannahelage Angela Diyalagoda , Goulard Roman , Webb Barbara , Niven Jeremy , Graham Paul
Published: February 2021

Wood ants are excellent navigators using a combination of innate and learnt navigational strategies to travel between their nest and feeding sites. Visual navigation in ants has been studied extensively, however, we only know little about the underlying neural mechanisms. The central complex (CX) is located at the midline of the insect brain. It receives sensory input that allows an insect to keep track of the direction of sensory cues relative to its own orientation and to control movement. We show here direct evidence for the involvement of the central complex in the innate visual orientation response of freely moving wood ants. Lesions in the CX disrupted the control of turning in a lateralised manner, but had no effect on the overall heading direction, walking speed or path straightness.
Super-resolved local recruitment of CLDN5 to filtration slits implicates a direct relationship with podocyte foot process effacement
Authors: Tesch Florian , Siegerist Florian , Hay Eleonora , Artelt Nadine , Daniel Christoph , Amann Kerstin , Zimmermann Uwe , Kavvadas Panagiotis , Grisk Olaf , Chadjichristos Christos , Endlich Karlhans , Chatziantoniou Christos , Endlich Nicole
Published: February 2021

Under healthy conditions, foot processes of neighboring podocytes are interdigitating and connected by an electron-dense slit diaphragm. Beside slit diaphragm proteins, typical adherens junction proteins are also found to be expressed at this cell-cell junction. It is therefore considered as a highly specialized type of adherens junction.

During podocyte injury, podocyte foot processes lose their characteristic 3D structure and the filtration slits typical meandering structure gets linearized. It is still under debate how this change of structure leads to the phenomenon of proteinuria. Using super-resolution 3D structured illumination microscopy, we observed a spatially restricted up-regulation of the tight junction protein claudin 5 (CLDN5) in areas where podocyte processes of patients suffering from minimal change disease (MCD), focal and segmental glomerulosclerosis (FSGS) as well as in murine nephrotoxic serum (NTS) nephritis and uninephrectomy DOCA-salt hypertension models, were locally injured. CLDN5/nephrin ratios in human glomerulopathies and NTS-treated mice were significantly higher compared to controls. In patients, the CLDN5/nephrin ratio is significantly correlated with the filtration slit density as a foot process effacement marker, confirming a direct association of local CLDN5 up-regulation in injured foot processes. Moreover, CLDN5 up-regulation was observed in some areas of high filtration slit density, suggesting that CLND5 up-regulation preceded the changes of foot processes. Therefore, CLDN5 could serve as a biomarker predicting early foot process effacement.
Chromatin Bridges, not Micronuclei, Activate cGAS after Drug-induced Mitotic Errors in Human Cells
Authors: Flynn Patrick J. , Koch Peter D. , Mitchison Timothy J.
Published: February 2021

Mitotic errors can activate cGAS and induce type-I interferon (IFN) signaling. Current models propose that chromosome segregation errors generate micronuclei whose rupture activates cGAS. We used a panel of anti-mitotic drugs to perturb mitosis in fibroblasts and measured abnormal nuclear morphologies, cGAS localization and IFN signaling in the subsequent interphase. Micronuclei consistently recruited cGAS without activating it. Instead, IFN signaling correlated with formation of cGAS-coated chromatin bridges that were selectively generated by microtubule stabilizers and MPS1 inhibitors. cGAS activation by chromatin bridges was suppressed by drugs that prevented cytokinesis. We confirmed cGAS activation by chromatin bridges in cancer lines that are unable to secrete IFN by measuring paracrine transfer of 2′3-cGAMP to fibroblasts. We propose that cGAS is selectively activated by self-chromatin when it is stretched in chromatin bridges. Immunosurveillance of cells that fail mitosis, and anti-tumor actions of taxanes and MPS1 inhibitors, may depend on this effect.
A novel positive feedback mechanism of ABI5 phosphorylation by mitogen activated protein kinase-3 regulates ABA signaling inArabidopsis
Authors: Bhagat Prakash Kumar , Verma Deepanjali , Verma Neetu , Sinha Alok Krishna
Published: February 2021

Seed germination is the crucial physiological process regulated by both environmental and endogenous phytohormones. ABA negatively regulates seed germination, post-germination growth and floral transition, however, the cross talk between multiple regulatory pathways are still unclear. Here, we show that ABA activates two MAP kinases, AtMPK3/AtMPK6 and selectively regulates the transcript of AtMPK3 through ABI5, a master regulator of ABA signaling. As a feedback loop, AtMPK3 interacts and phosphorylates ABI5 at the serine-314 position. ABI5 phosphorylation by MAP kinases positively regulates ABI5 nuclear localization and negatively regulates its dimerization. Subcellular localization of ABI5 phospho-null protein further suggests the role of phosphorylation in regulation of its cytoplasmic stability and its nuclear dimerization. Overexpression of phosphor-null ABI5 inabi5-8mutant restored the ABA sensitivity during seed germination and delayed the floral transition as compared to phospho-mimic ABI5. Additionally, overexpression of constitutive phosphorylated ABI5 inabi5-8mutants suggest that phosphorylation makes ABI5 partially inactive. Furthermore, phospho-null ABI5 plants showed drought sensitive phenotype whereas,mpk3,mkk4,mkk5,abi5-8and phosphor-mimic plants showed drought tolerant phenotype. Our findings present a new insight between MAP kinase cascade and ABA signaling which collectively regulates the ABA response through ABI5 phosphorylation.