bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and functional evidence for gp130/IL6ST-induced transient receptor potential ankyrin 1 upregulation in uninjured but not injured neurons in a mouse model of neuropathic pain
Authors: Kalpachidou Theodora , Malsch Philipp , Qi Yanmei , Mair Norbert , Geley Stephan , Quarta Serena , Kummer Kai K. , Kress Michaela
Published: July 2021

Peripheral nerve injuries result in pronounced alterations in dorsal root ganglia, which can lead to the development of neuropathic pain. Although the polymodal mechanosensitive transient receptor potential ankyrin 1 (TRPA1) ion channel is emerging as a relevant target for potential analgesic therapies, preclinical studies do not provide unequivocal mechanistic insight into its relevance for neuropathic pain pathogenesis. By using a transgenic mouse model with a conditional depletion of the interleukin-6 (IL-6) signal transducer gp130 in Nav1.8 expressing neurons (SNS-gp130−/−), we provide a mechanistic regulatory link between IL-6/gp130 and TRPA1 in the spared nerve injury (SNI) model. Spared nerve injury mice developed profound mechanical hypersensitivity as indicated by decreased withdrawal thresholds in the von Frey behavioral test in vivo, as well as a significant increase in mechanosensitivity of unmyelinated nociceptive primary afferents in ex vivo skin-nerve recordings. In contrast to wild type and control gp130fl/fl animals, SNS-gp130−/− mice did not develop mechanical hypersensitivity after SNI and exhibited low levels of Trpa1 mRNA in sensory neurons, which were partially restored by adenoviral gp130 re-expression in vitro. Importantly, uninjured but not injured neurons developed increased responsiveness to the TRPA1 agonist cinnamaldehyde, and neurons derived from SNS-gp130−/− mice after SNI were significantly less responsive to cinnamaldehyde. Our study shows for the first time that TRPA1 upregulation is attributed specifically to uninjured neurons in the SNI model, and this depended on the IL-6 signal transducer gp130. We provide a solution to the enigma of TRPA1 regulation after nerve injury and stress its significance as an important target for neuropathic pain disorders.
Intersectional identity approach to chronic pain disparities using latent class analysis
Authors: Newman Andrea K. , Thorn Beverly E.
Published: July 2021

Research on intersectionality and chronic pain disparities is very limited. Intersectionality explores the interconnections between multiple aspects of identity and provides a more accurate image of disparities. This study applied a relatively novel statistical approach (ie, Latent Class Analysis) to examine chronic pain disparities with an intersectional identity approach. Cross-sectional data were analyzed using pretreatment data from the Learning About My Pain trial, a randomized comparative effectiveness study of group-based psychosocial interventions (Patient-Centered Outcomes Research Institute Contract #941, Beverly Thorn, PI; clinicaltrials.gov identifier NCT01967342) for patients receiving care for chronic pain at low-income clinics in rural and suburban Alabama. Latent Class Analysis results suggested a 5-class model. To easily identify each class, the following labels were created: older adults, younger adults, severe disparity, older Black or African American, and Working Women. The latent disparity classes varied by pretreatment chronic pain functioning. Overall, the severe disparity group had the lowest levels of functioning, and the Working Women group had the highest levels of functioning. Although younger and with higher literacy levels, the younger adults group had similar levels of pain interference and depressive symptoms to the severe disparity group (P's < 0.05). The younger adults group also had higher pain catastrophizing than the older adults group (P < 0.005). Results highlighted the importance of the interactions between the multiple factors of socioeconomic status, age, and race in the experience of chronic pain. The intersectional identity theory approach through Latent Class Analysis provided an integrated image of chronic pain disparities in a highly understudied and underserved population.
Mental Health, Cognitive, and Neuropsychiatric Needs in Children and Young People With Wilson Disease
Authors: Day Jemma , Samyn Marianne , Proctor Sarah Ellen , Joshi Deepak , Pissas Eleanna , Chanpong Atchariya , Hedderly Tammy , Dhawan Anil
Published: July 2021

Objective:

Wilson disease (WD) is associated with neurological, psychiatric, cognitive, and psychosocial difficulties, but there is little data regarding the nature and prevalence of these problems in children and young people (CYP).

Methods:

A single-center case-note review to establish the incidence and nature of these issues in CYP with WD, managed before and after multidisciplinary team (MDT) clinics, was established.

Results:

Out of 69 (43 males) CYP with WD, 37.8% presented with acute liver failure, 48.6% with chronic liver disease and 13.5% after family screening. Medical treatment was with penicillamine (40), trientene (18), zinc and penicillamine/trientene (11), and zinc monotherapy (2). Twenty-one underwent liver transplantation. After a median follow-up of 9.8 (IQR 6.4–16.9) years, 86% are alive. Six died posttransplantation and 7 grafts were lost. Mental health difficulties were recorded in 49.3%, particularly prevalent in the acute liver failure group (70.8%). Nonadherence was common (50.7%) and associated with greater mental health prevalence. Neurological issues were reported in 36.2% and poor cognition/attainment in 14.5%, consistent across modes of presentation. Four patients had diagnoses of autism spectrum conditions, all diagnosed pre WD. CYP seen within an MDT-clinic had more frequent documentation of all issues examined, but lower levels of late graft loss (94% versus 80%,P= 0.07).

Conclusion:

Our data highlight the need to offer management in WD patients especially as these aspects are underrecognized in CYP presenting with liver involvement. We aim to highlight the importance of multidisciplinary input when looking after this population beyond transition through to adult services.
ARPC1B Mutation Manifesting as Recurrent Hematemesis With Metaplasia
Authors: Antala Swati , Whitehead Bridget , Melin-Aldana Hector , Bass Lee M.
Published: July 2021

ARPC1B is important in the maintenance and assembly of the ARP2/3 complex. Loss of this complex due to ARPC1B mutation results in impairment of actin polymerization and subsequent defects in chemotaxis, cell migration, and DNA repair. Individuals with this rare mutation present in infancy and have abnormal innate and adaptive immune responses. They develop immune-mediated inflammatory disease with associated platelet defects, eosinophilia, rashes, and bowel disease. Recurrent gastrointestinal hemorrhage has been described in known cases. Here, we report a case with endoscopic and histologic findings in a patient with this rare mutation.
Acute Pancreatitis in a Previously Exocrine Pancreatic Insufficient Cystic Fibrosis Patient Who Had Improved Pancreatic Function After Being Treated With Lumacaftor/Ivacaftor
Authors: Redman Alexander W. , Yoo Michelle , Freswick Peter , Thompson Karen
Published: July 2021

Exocrine pancreatic insufficiency (EPI) is a common complication of cystic fibrosis (CF). While previously considered to be irreversible, recent reported cases document improved pancreatic function in CF patients with mild mutations after ivacaftor treatment alone. We report a 12-year-old female with homozygous F508del CF and EPI who developed acute pancreatitis after 3 years on lumacaftor/ivacaftor and subsequently had improved pancreatic function. As CF therapies advance, some EPI CF patients with more severe CF transmembrane conductance regulator mutations may see improved pancreatic function and subsequently develop pancreatitis.
Repeat Biopsy to Assess Duodenal Healing in Children With Celiac Disease and Eosinophilic Gastrointestinal Disorders
Authors: Payne Kaitlin , Ramharack Lydia , Bierly Patricia , Feigenbaum Kara , Steinhoff Janel , Hlywiak Karen , Farrara Ann , Verma Ritu , Singh Arunjot , Fahey Lisa M.
Published: July 2021

Objectives:

The aim of the study was to determine the correlation between duodenal mucosal biopsies and tissue transglutaminase immunoglobulin A (tTG-IgA) levels in pediatric patients with biopsy-confirmed celiac disease (CD) and eosinophilic gastrointestinal disorders (EGID) who have had repeat duodenal biopsies after initiating a gluten-free diet.

Methods:

A retrospective chart review was performed of children with CD and EGID seen at the Children’s Hospital of Philadelphia between 2003 and 2018. Data collected included duodenal biopsy pathology, celiac serology including tTG-IgA, and symptom reports. Duodenal healing was defined as normal villous architecture and no intraepithelial lymphocytes. These data were compared with tTG-IgA level. Data were analyzed with Fisher exact test and t test methods.

Results:

Thirty-nine patients had normal IgA and diagnoses of both CD and EGID. At second biopsy, 44% (17/39) of patients showed no histologic evidence of active CD and 36% (14/39) of patients had negative tTG-IgA values. Sixty percent (9/15) of patients with no evidence of CD on biopsy had abnormal tTG-IgA levels, and 57% (8/14) of patients with normal tTG-IgA levels had evidence of active disease on biopsy.

Conclusions:

The data show that an abnormal tTG-IgA drawn after initiation of a gluten-free diet is not correlated with duodenal mucosal injury in pediatric patients with CD and EGID. This suggests that serologic surveillance with tTG-IgA is not sufficient to monitor CD intestinal healing in this patient cohort. Persistent elevations of tTG-IgA in CD patients with normal duodenal biopsies should prompt investigation into other potential causes.
Sex-chromosome evolution in frogs: what role for sex-antagonistic genes?
Authors: Perrin Nicolas
Published: July 2021

Sex-antagonistic (SA) genes are widely considered to be crucial players in the evolution of sex chromosomes, being instrumental in the arrest of recombination and degeneration of Y chromosomes, as well as important drivers of sex-chromosome turnovers. To test such claims, one needs to focus on systems at the early stages of differentiation, ideally with a high turnover rate. Here, I review recent work on two families of amphibians, Ranidae (true frogs) and Hylidae (tree frogs), to show that results gathered so far from these groups provide no support for a significant role of SA genes in the evolutionary dynamics of their sex chromosomes. The findings support instead a central role for neutral processes and deleterious mutations.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
Sex chromosome degeneration, turnover, and sex-biased expression of sex-linked transcripts in African clawed frogs (
Xenopus
)
Authors: Song Xue-Ying , Furman Benjamin L. S. , Premachandra Tharindu , Knytl Martin , Cauret Caroline M. S. , Wasonga Domnick Victor , Measey John , Dworkin Ian , Evans Ben J.
Published: July 2021

The tempo of sex chromosome evolution—how quickly, in what order, why and how their particular characteristics emerge during evolution—remains poorly understood. To understand this further, we studied three closely related species of African clawed frog (genus
Xenopus
), that each has independently evolved sex chromosomes. We identified population polymorphism in the extent of sex chromosome differentiation in wild-caught
Xenopus borealis
that corresponds to a large, previously identified region of recombination suppression. This large sex-linked region of
X. borealis
has an extreme concentration of genes that encode transcripts with sex-biased expression, and we recovered similar findings in the smaller sex-linked regions of
Xenopus laevis
and
Xenopus tropicalis
. In two of these species, strong skews in expression (mostly female-biased in
X. borealis
, mostly male-biased in
X. tropicalis
) are consistent with expectations associated with recombination suppression, and in
X. borealis
, we hypothesize that a degenerate ancestral Y-chromosome transitioned into its contemporary Z-chromosome. These findings indicate that
Xenopus
species are tolerant of differences between the sexes in dosage of the products of multiple genes, and offer insights into how evolutionary transformations of ancestral sex chromosomes carry forward to affect the function of new sex chromosomes.

This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
Actinomyces turicensis parapharyngeal space infection in an immunocompetent host: first case report and review of literature
Authors: Tabaksert Ayla , Kumar Ravi , Raviprakash Veena , Srinivasan Rajeev
Published: July 2021

Actinomyces

are common commensals of the oral cavity, gastrointestinal tract and urogenital tract. They are anaerobic, Gram-positive, non-acid-fast bacilli, which can cause invasive infection and abscesses. We present the first reported case of supraglottitis and deep neck space abscess formation secondary to

Actinomyces turicensis

infection. The patient was managed with intravenous antibiotics, incision and drainage of a left parapharyngeal abscess and subsequent mediastinal abscess. After 6 weeks in hospital, the patient was successfully discharged to complete a 6-month course of oral amoxicillin.
Characterization of isolates of members of the genus Actinomyces from Marmota himalayana: description of Actinomyces faecalis sp. nov., Actinomyces respiraculi sp. nov., and Actinomyces trachealis sp. nov.
Authors: Zhou Juan , Zhang Sihui , Zhang Gui , Yang Jing , Lai Xin-He , Pu Ji , Jin Dong , Lu Shan , Huang Ying , Zhu Wentao , Huang Yuyuan , Xu Mingchao , Lei Wenjing , Cheng Yanpeng , Liu Liyun , Xu Jianguo
Published: July 2021

Six novel strains (ZJ34T, ZJ561, ZJ750T, ZJ1629, zg-993T and zg-987) isolated from faeces and respiratory tracts of Marmota himalayana from the Qinghai–Tibet Plateau of PR China were characterized comprehensively. The results of analyses of the 16S rRNA gene and genome sequences indicated that the six strains represent three novel species of the genus

Actinomyces

, and are closely related to

Actinomyces urogenitalis

DSM 15434T (16S rRNA gene sequences similarities, 94.9–98.7 %),

Actinomyces weissii

CCUG 61299T (95.6–96.6 %),

Actinomyces bovis

CCTCC AB2010168T (95.7 %) and

Actinomyces bowdenii

DSM 15435T (95.2–96.4 %), with values of digital DNA–DNA hybridization less than 30.1 % when compared with their closest relatives but higher than 70 % within each pair of novel strains (ZJ34T/ZJ561, ZJ750T/ZJ1629 and zg-993T/zg-987). All the novel strains had C18 : 1
ω9c and C16 : 0 as the two most abundant major fatty acids. MK-9(H4) or MK-8(H4) was the sole or predominant respiratory quinone of strains ZJ34T, ZJ750T and zg-993T and their polar lipid profiles differed, but all had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidyl inositol mannoside as major components. ZJ750T shared identical peptidoglycan amino acid profile with ZJ34T (alanine, glutamic acid, lysine and ornithine) and the same whole-cell sugar composition with zg-993T (glucose, rhamnose and ribose). Strain zg-993T contained alanine, aspartic acid, glutamic acid, glycine and lysine in the peptidoglycan, and the only sugar in ZJ34T was ribose. The DNA G+C contents of the novel strains were within the range of 65.8–70.1 mol%. On the basis of the results from the aforementioned analyses, the six novel strains were classified as representing three novel species of genus

Actinomyces

, for which the names Actinomyces faecalis sp. nov. [type strain ZJ34T (=GDMCC 1.1952T=JCM 34355T)], Actinomyces respiraculi sp. nov. [type strain ZJ750T (=GDMCC 1.1950T=JCM 34356T)] and Actinomyces trachealis sp. nov. [type strain zg-993T (=GDMCC 1.1956T=JCM 34357T)] were proposed, respectively.
Performance of a loop-mediated isothermal amplification assay (Isoplex CRE-ART) to detect common carbapenemase-encoding genes in Gram-negative bacteria
Authors: Berneking Laura , Asar Lucia , Both Anna , Berinson Benjamin , Aepfelbacher Martin , Lütgehetmann Marc , Rohde Holger
Published: July 2021

Carbapenem-resistant Gram-negative bacteria (CR-GNB) are a major source of nosocomial infections worldwide. In this study, the ability of a loop-mediated isothermal amplification (LAMP)-based method (Isoplex CRE-ART) to rapidly detect carbapenemase-encoding genes bla
OXA-48-like, bla
OXA-23-like, bla
OXA-24-like, bla
KPC, bla
VIM, bla
NDM and bla
IMP in 231 carbapenem-resistant Enterobacterales, Pseudomonas aeruginosa and

Acinetobacter baumannii

isolates was investigated. The accuracy of the LAMP test was compared to results of molecular isolate characterization using a Laboratory Developed Test multiplex carbapenemase PCR assay. The LAMP test correctly identified the presence of on-panel carbapenemases with a sensitivity of 99.16 % [95 % confidence interval (CI): 95.39–99.96 %] and a specificity of 98.21 % (95 % CI: 93.72–99.68 %) in 60 min. Our findings suggest that the Isoplex CRE-ART assay is able to rapidly identify carbapenemase genes in CR-GNB and improves options for pathogen characterization in the context of clinical microbiological and infection control diagnostics.
Predicted Norovirus Resurgence in 2021-2022 Due to the Relaxation of Nonpharmaceutical Interventions Associated with COVID-19 Restrictions in England: A Mathematical Modelling Study
Authors: O’Reilly Kathleen M , Sandman Frank , Allen David , Jarvis Christopher I , Gimma Amy , Douglas Amy , Larkin Lesley , Wong Kerry LM , Baguelin Marc , Baric Ralph S , Lindesmith Lisa C , Goldstein Richard A , Breuer Judith , Edmunds W John
Published: July 2021

Background

To reduce the coronavirus disease burden in England, along with many other countries, the Government implemented a package of non-pharmaceutical interventions (NPIs) that have also impacted other transmissible infectious diseases such as norovirus. It is unclear what future norovirus disease incidence is likely to look like upon lifting these restrictions.

Methods

Here we use a mathematical model of norovirus fitted to community incidence data in England to project forward expected incidence based on contact surveys that have been collected throughout 2020-2021.

Results

We report that susceptibility to norovirus infection has likely increased between March 2020 to mid-2021. Depending upon assumptions of future contact patterns incidence of norovirus that is similar to pre-pandemic levels or an increase beyond what has been previously reported is likely to occur once restrictions are lifted. Should adult contact patterns return to 80% of pre-pandemic levels the incidence of norovirus will be similar to previous years. If contact patterns return to pre-pandemic levels there is a potential for the expected annual incidence to be up to 2-fold larger than in a typical year. The age-specific incidence is similar across all ages.

Conclusions

Continued national surveillance for endemic diseases such as norovirus will be essential after NPIs are lifted to allow healthcare services to adequately prepare for a potential increase in cases and hospital pressures beyond what is typically experienced.
Gastric Neurons in the Nucleus Tractus Solitarius are Selective to the Orientation of Gastric Electrical Stimulation
Authors: Cao Jiayue , Wang Xiaokai , Powley Terry L. , Liu Zhongming
Published: July 2021

Gastric electrical stimulation (GES) is a bioelectric intervention for gastroparesis, obesity, and other functional gastrointestinal disorders. In a potential mechanism of action, GES activates the nerve endings of vagal afferent neurons and induces the vago-vagal reflex through the nucleus tractus solitarius (NTS) in the brainstem. However, it is unclear where and how to stimulate in order to optimize the vagal afferent responses. To address this question with electrophysiology in rats, we applied mild electrical currents to two serosal targets on the distal forestomach with dense distributions of vagal intramuscular arrays that innervated the circular and longitudinal smooth muscle layers. During stimulation, we recorded single and multi-unit responses from gastric neurons in NTS and evaluated how the recorded responses depended on the stimulus orientation and amplitude. We found that NTS responses were highly selective to the stimulus orientation for a range of stimulus amplitudes. The strongest responses were observed when the applied current flowed in the same direction as the intramuscular arrays in parallel with the underlying smooth muscle fibers. Our results suggest that gastric neurons in NTS may encode the orientation-specific activity of gastric smooth muscles relayed by vagal afferent neurons. This finding suggests that the orientation of GES is critical to effective engagement of vagal afferents and should be considered in light of the structural phenotypes of vagal terminals in the stomach.
Allometry, sexual selection, and evolutionary lines of least resistance shaped the evolution of exaggerated sexual traits within the genus Tyrannus
Authors: Fasanelli MN , Milla Carmona P , Soto IM , Tuero DT
Published: July 2021

Variational properties hold a fundamental role in shaping biological evolution, exerting control over the magnitude and direction of evolutionary change elicited by microevolutionary processes that sort variation, such as selection or drift. We studied the Tyrannus genus, as a model for examining the conditions and drivers that facilitate the repeated evolution of exaggerated, secondary sexual traits in the face of significant functional limitations. We study the role of allometry, sexual selection, and their interaction on the diversification of tail morphology in the genus, assessing whether and how they promoted or constrained phenotypic evolution. The exaggerated and functionally-constrained long feathers of deep-forked species, T. savana and T. forficatus, independently diverged from the rest of the genus following the same direction of main interspecific variation common to the entire cluster of species. However, at a macroevolutionary scale those axes summarising both sexual dimorphism and allometric variation of the deep-forked species were aligned with the between-species maximum variation axis of non deep-forked species. Thus, we are presenting evidence of amplified divergence via the co-option and reorientation of allometric shape variation involved in a sexual selection process that repeatedly drove morphology along a historically favoured direction of cladogenetic evolution.
Analyzing the U.S. Post-marketing safety surveillance of COVID-19 vaccines
Authors: Albalawi Omar M. , Alomran Maha I. , Alsagri Ghada M. , Althunian Turki A. , Alshammari Thamir M.
Published: July 2021

Background

Since December 2020, three COVID-19 vaccines have been authorized in the United States (U.S.) and were proceeded by large immunization programs. The aim of this study was to characterize the U.S. post-marketing safety (PMS) profiles of these vaccines with an in-depth analysis of mortality data.

Methods

This was a retrospective database analysis study. Details of the U.S. PMS reports (15 December 2020 to 19 March 2021) of the three vaccines (Pfizer-BioNTech, Moderna, and Janssen Ad26.COV2.S) were retrieved from the U.S. Vaccine Adverse Event Reporting System (VAERS). A descriptive analysis was conducted to characterize the reported adverse events (AEs). A comparative (Pfizer-BioNTech vs. Moderna) analysis of mortality was conducted. The mean count ratio of death between the two vaccines was estimated using a negative binomial regression model adjusting for the measured confounders.

Results

A total of 44,451 AE reports were retrieved (corresponding to 0.05% of the U.S. population who received at least one dose). The most commonly reported AEs were injection site reactions (30.4% of the reports), pain (reported in 26.7% of the reports), and headache (18.6% of the reports). Serious AEs were reported in only 14.6% of the reports with 4,108 hospitalizations. The total number of deaths was 1,919 with a mean count ratio of Moderna (n=997) vs. Pfizer-BioNTech (n=899) of 1.07 (95% confidence interval 0.86 to 1.33).

Conclusions

The vast majority of PMS AEs in the U.S. were non-serious, and the number of serious AEs is very low given the total number of vaccinated U.S. population.
Enhanced chemotaxis through spatially-regulated absolute concentration robustness
Authors: Biswas Debojyoti , Bhattacharya Sayak , Iglesias Pablo A.
Published: July 2021

Chemotaxis, the directional motility of cells in response to spatial gradients of chemical cues, is a fundamental process behind a wide range of biological events, including the innate immune response and cancer metastasis. Recent advances in cell biology have shown that the protrusions that enable amoeboid cells to move are driven by the stochastic threshold crossings of an underlying excitable system. As a cell encounters a chemoattractant gradient, the size of this threshold is regulated spatially so that the crossings are biased towards the front of the cell. For efficient directional migration, cells must limit undesirable lateral and rear-directed protrusions. The inclusion of a control mechanism to suppress these unwanted firings would enhance chemotactic efficiency. It is known that absolute concentration robustness (ACR) exerts tight control over the mean and variance of species concentration. Here, we demonstrate how the coupling of the ACR mechanism to the cellular signaling machinery reduces the likelihood of threshold crossings in the excitable system. Moreover, we show that using the cell’s innate gradient sensing apparatus to direct the action of ACR to the rear, suppresses the lateral movement of the cells and that this results in improved chemotactic performance.
CADD-SV – a framework to score the effects of structural variants in health and disease
Authors: Kleinert Philip , Kircher Martin
Published: July 2021

While technological advances improved the identification of structural variants (SVs) in the human genome, their interpretation remains challenging. Several methods utilize individual mechanistic principles like the deletion of coding sequence or 3D genome architecture disruptions. However, a comprehensive tool using the broad spectrum of available annotations is missing. Here, we describe CADD-SV, a method to retrieve and integrate a wide set of annotations to predict the effects of SVs.

Previously, supervised learning approaches were limited due to a small number and biased set of annotated pathogenic or benign SVs. We overcome this problem by using a surrogate training-objective, the Combined Annotation Dependent Depletion (CADD) of functional variants. We use human and chimpanzee derived SVs as proxy-neutral and contrast them with matched simulated variants as proxy-pathogenic, an approach that has proven powerful for SNVs.

Our tool computes summary statistics over diverse variant annotations and uses random forest models to prioritize deleterious structural variants. The resulting CADD-SV scores correlate with known pathogenic and rare population variants. We further show that we can prioritize somatic cancer variants as well as non-coding variants known to affect gene expression. We provide a website and offline-scoring tool for easy application of CADD-SV (https://cadd-sv.bihealth.org/).
Power Calculator for Detecting Allelic Imbalance Using Hierarchical Bayesian Model
Authors: Sherbina Katrina , León-Novelo Luis G. , Nuzhdin Sergey V. , McIntyre Lauren M. , Marroni Fabio
Published: July 2021

Allelic imbalance (AI) is the differential expression of the two alleles in a diploid. AI can vary between tissues, treatments, and environments. Statistical methods for testing in this area exist, with impacts of explosive type I error in the presence of bias well understood. However, for study design, the more important and understudied problem is the type II error and power. As the biological questions for this type of study explode, and the costs of the technology plummet, what is more important: reads or replicates? How small of an interaction can be detected while keeping the type I error at bay? Here we present a simulation study that demonstrates that the proper model can control type I error below 5% for most scenarios. We find that a minimum of 2400, 480, and 240 allele specific reads divided equally among 12, 5, and 3 replicates is needed to detect a 10%, 20%, and 30%, respectively, deviation from allelic balance in a condition with power >80%. A minimum of 960 and 240 allele specific reads is needed to detect a 20% or 30% difference in AI between conditions with comparable power but these reads need to be divided amongst 8 replicates. Higher numbers of replicates increase power more than adding coverage without affecting type I error. We provide a Python package that enables simulation of AI scenarios and enables individuals to estimate type I error and power in detecting AI and differences in AI between conditions tailored to their own specific study needs.
A novel non-antibiotic selectable marker GASA6 for plant transformation
Authors: Luo Yuewan , Gu Jiena , Wang Xiaojing , Zhang Shengchun
Published: July 2021

Selectable markers help the transformed cell/tissue to survive in an otherwise lethal exposure of an antibiotic or herbicide. Unfortunately, almost all the traditional selectable markers are antibiotic and herbicide resistance genes, which are controversial on human health concerns and environmental impact. Novel plant-derived, non-antibiotic, and non-herbicide selectable markers are urgently needed in plant transformation. Our previous work showed that the seedlings of overexpression Arabidopsis lines of AtGASA6 survived on medium with a high concentration of sugar, which leads to the hypothesis that AtGASA6 could be a selectable marker on media with high or low sugar content. In this study, leaf explants of AtGASA6 overexpression tobacco lines regenerated shoots on sugar-free shooting medium while those of wild type could not. Moreover, the seeds of AtGASA6 overexpression tobacco lines germinated and grew into normal seedlings on sugar-free MS medium while those of WT could not. Attractively, no developmental defects were observed in AtGASA6 transgenic progenies. Using AtGASA6 as a selectable marker, overexpression tobacco lines of GAI, which restrains plant size, were created on sugar-free media. The GAI overexpression lines had a smaller plant size than that of control. Considering its plant-derived and non-antibiotic nature, GASA6 is promising to be used as a selectable marker in plant transformation.
Independent adoptions of a set of proteins found in the matrix of the mineralized shell-like eggcase of Argonaut octopuses
Authors: Setiamarga Davin H. E. , Hirota Kazuki , Ikai Risa , Imoto Seiji , Sato Noriyoshi , Ono Hiroki , Isowa Yukinobu , Yonemitsu Hiroshi , Sasaki Takenori , Yoshida Masa-aki
Published: July 2021

The Argonaut octopus, commonly called the paper nautilus, has a spiral-coiled shell-like eggcase. As the main characteristics, the eggcase has no internal septum, is composed entirely of calcite with chitosan being the main polycarbonate and is reportedly formed by organic materials secreted from the membranes of the arms. Meanwhile, the biomineralized external “true” shells of the Mollusks, which includes the Cephalopods, are secreted from the mantle tissue. Therefore, the histological origin of the two shells is completely different. The question of how the Argonauts, which phylogenetically diverged from the completely shell-less octopuses, could form a converging shell-like external structure has thus intrigued biologists for a long time. To answer this question, we performed a multi-omics analysis of the transcriptome and proteome of the two congeneric Argonaut species,Argonauta argoandA. hians. Our result indicates that the shell-like eggcase is not a homolog of the shell, even at the protein level, because the Argonauts apparently recruited a different set of protein repertoires to as eggcase matrix proteins (EcMPs). However, we also found the homologs of three shell matrix proteins (SMPs) of the Conchiferan Mollusks, Pif-like, SOD, and TRX, in the eggcase matrix. The proteins were also found in the only surviving shelled Cephalopods, the nautiloidNautilus pompilius. Phylogenetic analysis revealed that homologous genes of the Conchiferan SMPs and EcMPs were found in the draft genome of shell-less octopuses. Our result reported here thus suggests that the SMP-coding genes are conserved in both shelled and shell-less Cephalopods. Meanwhile, the Argonauts adopted some of the SMP-coding genes and other non-SMP-coding genes, to form a convergent, non-homologous biomineralized external structure, the eggcase, which is autapomorphic to the group.
Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs
Authors: Sun Yu H. , Wang Ruoqiao Huiyi , Du Khai , Zheng Jihong , Xie Li Huitong , Pereira Amanda A. , Zhang Chao , Ricci Emiliano P. , Li Xin Zhiguo
Published: July 2021

PIWI-interacting small RNAs (piRNAs) protect the germline genome and are essential for fertility. Previously, we showed that ribosomes guide the biogenesis of piRNAs from long non-coding RNAs (lncRNAs) after translating the short open reading frames (ORFs) near their 5’ cap. It remained unclear, however, how ribosomes proceed downstream of ORFs and how piRNA precursors distinguish from other RNAs. It is thus important to test whether a short ORF length is required for substrate recognition for ribosome guided-piRNA biogenesis. Here, we characterized a poorly understood class of piRNAs that originate from the 3’ untranslated regions (3’UTRs) of protein coding genes in mice and chickens. We demonstrate that their precursors are full-length mRNAs and that post-termination 80S ribosomes guide piRNA production on 3’UTRs after translation of upstream long ORFs. Similar to non-sense mediated decay (NMD), piRNA biogenesis degrades mRNA right after pioneer rounds of translation and fine-tunes protein production from mRNAs. Interestingly, however, we found that NMD, along with other surveillance pathways for ribosome recycling are temporally sequestered during the pachytene stage to allow for robust piRNA production. Although 3’UTR piRNA precursor mRNAs code for distinct proteins in mice and chickens, they all harbor embedded transposable elements (TEs) and produce piRNAs that cleave TEs, suggesting that TE suppression, rather than the function of proteins, is the primary evolutionary force maintaining a subset of mRNAs as piRNA precursors. Altogether, we discover a function of the piRNA pathway in fine-tuning protein production and reveal a conserved, general piRNA biogenesis mechanism that recognizes translating RNAs regardless of their ORF length in amniotes.
Bacterial type 1A topoisomerases maintain the stability of the genome by preventing and dealing with R-loop-and nucleotide excision repair-dependent topological stress
Authors: Brochu Julien , Vlachos-Breton Emilie , Drolet Marc
Published: July 2021

E. coli type 1A topoisomerases (topos), topo I (topA) and topo III (topB) have both relaxation and decatenation activities. B. subtilis and E. coli topA topB null cells can survive owing to DNA amplifications allowing overproduction of topo IV, the main cellular decatenase that can also relax supercoiling. We show that overproducing human topo IB, a relaxase but not a decatenase, can substitute for topo IV in allowing E. coli topA null but not topA topB null cells to survive. Deleting topB exacerbates phenotypes of topA null mutants including hypernegative supercoiling, R-loop formation, and RNase HI-sensitive replication, phenotypes that are not corrected by topo IV overproduction. These phenotypes lead to Ter DNA amplification causing a chromosome segregation defect that is corrected by topo IV overproduction. Furthermore, topA topB null mutants not overproducing topo IV acquire uvrB or uvrC mutations, revealing a nucleotide excision repair (NER)-dependent problem with replication fork progression. Thus, type IA topos maintain the stability of the genome by providing essential relaxase and decatenase activities to prevent and solve topological stress related to R-loops and NER. Moreover, excess R-loop formation is well tolerated in cells that have enough topoisomerase activity to support the subsequent replication-related topological stress.
Pili Expression inGeobacter sulfurreducensLacking the Putative Gene for the PilB Pilus Assembly Motor
Authors: Ueki Toshiyuki , Walker David J.F. , Nevin Kelly P. , Ward Joy E. , Woodard Trevor L. , Nonnenmann Stephen S. , Lovley Derek R.
Published: July 2021

Multiple lines of evidence suggest that electrically conductive pili (e-pili) are an important conduit for long-range electron transport inGeobacter sulfurreducens, a common model microbe for the study of extracellular electron transport mechanisms. One strategy to study the function of e-pili has been to delete the gene for PilB, the pilus assembly motor protein, in order to prevent e-pili expression. However, we found that e-pili are still expressed after the gene for PilB is deleted. Conducting probe atomic force microscopy revealed filaments with the same diameter and similar current-voltage response as e-pili harvested from wild-typeG. sulfurreducensor when e-pili are heterologously expressed from theG. sulfurreducenspilin gene inE. coli. Immunogold labeling demonstrated that aG. sulfurreducensstrain expressing e-pili with a His-tag continued to express His-tag labelled e-pili when the PilB gene was deleted. Strains with the PilB gene deleted produced maximum current densities comparable to wild-type controls. These results demonstrate that deleting the gene for PilB is not an appropriate strategy for constructing strains ofG. sulfurreducenswithout e-pili, necessitating a reinterpretation of the results of previous studies that have employed this approach.

Importance

Geobacter sulfurreducensis a model microbe for the study of biogeochemically and technologically significant processes such as the reduction of Fe(III) oxides in soils and sediments; bioelectrochemical applications that produce electric current from waste organic matter or drive useful processes with the consumption of renewable electricity; direct interspecies electron transfer in anaerobic digestors and methanogenic soils and sediments; and metal corrosion. The phenotypes associated with gene deletions are an important strategy for determining the mechanisms for extracellular electron transfer inG. sulfurreducens. The results reported here demonstrate that a gene deletion previously thought to prevent the expression of electrically conductive pili inG. sulfurreducensdoes not have the intended result. Conductive pili continue to be expressed. This finding is important for interpreting the results of several previous studies on conductive pili function.
Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing
Authors: Wang Yiquan , Lei Ruipeng , Nourmohammad Armita , Wu Nicholas C.
Published: July 2021

As one of the main influenza antigens, neuraminidase (NA) in H3N2 virus has evolved extensively for more than 50 years due to continuous immune pressure. While NA has emerged as an effective vaccine target recently, biophysical constraints on the antigenic evolution of NA remain largely elusive. Here, we apply deep mutational scanning to characterize the local fitness landscape in an antigenic region of NA in six different human H3N2 strains that were isolated around 10 years apart. The local fitness landscape correlates well among strains and the pairwise epistasis is highly conserved. Our analysis further demonstrates that local net charge governs the pairwise epistasis in this antigenic region. In addition, we show that residue coevolution in this antigenic region can be predicted by charge states and pairwise epistasis. Overall, this study demonstrates the importance of quantifying epistasis and the underlying biophysical constraint for building a predictive model of influenza evolution.
Identification of RNA base pairs and complete assignment of nucleobase resonances by proton-detected solid-state NMR spectroscopy at 100 kHz MAS
Authors: Aguion Philipp Innig , Kirkpatrick John , Carlomagno Teresa , Marchanka Alexander
Published: July 2021

Knowledge of RNA structure, either in isolation or in complex, is fundamental to understand the mechanism of cellular processes. Solid-state NMR (ssNMR) is applicable to high molecular-weight complexes and does not require crystallization; thus, it is well-suited to study RNA as part of large multicomponent assemblies. Recently, we solved the first structures of both RNA and an RNA–protein complex by ssNMR using conventional 13C- and 15N-detection. This approach is limited by the severe overlap of the RNA peaks together with the low sensitivity of multidimensional experiments. Here, we overcome the limitations in sensitivity and resolution by using 1H-detection at fast MAS rates. We develop experiments that allow the identification of complete nucleobase spin-systems together with their site-specific base pair pattern using sub-milligram quantities of one uniformly labelled RNA sample. These experiments provide rapid access to RNA secondary structure by ssNMR in protein–RNA complexes of any size.
The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes
Authors: Costello Shawn M. , Shoemaker Sophie R. , Hobbs Helen T. , Nguyen Annalee W. , Hsieh Ching-Lin , Maynard Jennifer A. , McLellan Jason S. , Pak John E. , Marqusee Susan
Published: July 2021

Current COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 spike ectodomain. Using hydrogen deuterium exchange mass spectrometry, we have uncovered that, in addition to the prefusion structure determined by cryo-EM, this protein adopts an alternative conformation that interconverts slowly with the canonical prefusion structure. This new conformation—an open trimer— contains easily accessible RBDs. It exposes the conserved trimer interface buried in the prefusion conformation, thus exposing potential epitopes for pan-coronavirus antibody and ligand recognition. The population of this state and kinetics of interconversion are modulated by temperature, receptor binding, antibody binding, and sequence variants observed in the natural population. Knowledge of the structure and populations of this conformation will help improve existing diagnostics, therapeutics, and vaccines.

One Sentence Summary

An alternative conformation of SARS-CoV-2 spike ectodomain modulated by temperature, binding, and sequence variants.
Circuit motifs and graph properties of connectome development in C. elegans
Authors: Matelsky Jordan K. , Norman-Tenazas Raphael , Davenport Felicia , Reilly Elizabeth P. , Gray-Roncal William
Published: July 2021

Network science is a powerful tool that can be used to better explore the complex structure of brain networks. Leveraging graph and motif analysis tools, we interrogate C. elegans connectomes across multiple developmental time points and compare the resulting graph characteristics and substructures over time. We show the evolution of the networks and highlight stable invariants and patterns as well as those that grow or decay unexpectedly, providing a substrate for additional analysis.
Evolution with private resources reverses some changes from long-term evolution with public resources
Authors: van Raay Katrina , Stolyar Sergey , Sevigny Jordana , Tirado Adamaris Muñiz , Draghi Jeremy A. , Lenski Richard E. , Marx Christopher J. , Kerr Benjamin , Zaman Luis
Published: July 2021

A population under selection to improve one trait may evolve a sub-optimal state for another trait due to tradeoffs and other evolutionary constraints. How this evolution affects the capacity of a population to adapt when conditions change to favor the second trait is an open question. We investigated this question using isolates from a lineage spanning 60,000 generations of the Long-Term Evolution Experiment (LTEE) with Escherichia coli, where cells have access to a shared pool of resources, and have evolved increased competitive ability and a concomitant reduction in numerical yield. Using media-in oil emulsions we shifted the focus of selection to numerical yield, where cells grew in isolated patches with private resources. We found that the time spent evolving under shared resources did not affect the ability to re-evolve toward higher numerical yield. The evolution of numerical yield commonly occurred through mutations in the phosphoenolpyruvate phosphotransferase system. These mutants exhibit slower uptake of glucose, making them poorer competitors for public resources, and produce smaller cells that release less carbon as overflow metabolites. Our results demonstrate that mutations that were not part of adaptation under one selective regime may enable access to ancestral phenotypes when selection changes to favor evolutionary reversion.
Glby, is a PBP with β-lactamase activity and is required for in vivo viability of M. abscessus
Authors: Galanis Christos , Maggioncalda Emily C. , Kumar Gaurav , Lamichhane Gyanu
Published: July 2021

The prevalence of Mycobacteroides abscessus, Mab, (also known as Mycobacterium abscessus) has been increasing steadily globally. Patients with structural lung conditions such as bronchiectasis, cystic fibrosis and chronic obstructive pulmonary disease are at high risk of developing pulmonary Mab disease. The disease is often recurrent as the current treatment regimen is considered sub-efficacious. The cell wall peptidoglycan of bacteria is required for their viability and its biosynthetic pathway is enriched in proteins whose inhibition is the basis for two of the most widely used classes of antibiotics to treat bacterial infections. The peptidoglycan of Mab is distinct from that of most bacteria as its synthesis involves penicillin binding proteins (PBP) and L,D-transpeptidases. Here, we demonstrate that Mab gene locus MAB_3167c encodes a PBP (hereafter referred to as Glby) and is required for normal planktonic growth in liquid broth. Glby exhibits a strong β-lactamase activity and is sensitive to β-lactamase inhibitors. In a mouse model of pulmonary Mab disease, mutant lacking this gene was unable to proliferate, gradually cleared and undetectable after three weeks. In a collection of 1.046 Mab clinical isolates, there is evidence that changes in amino acid sequence that compromise Glby function are not favored. These evidences suggest that an agent that can inhibit Glby in vivo has the potential to be an efficacious treatment against Mab disease.
Chemically Induced Senescence in Human Stem Cell-Derived Neurons Promotes Phenotypic Presentation of Neurodegeneration
Authors: Fathi Ali , Mathivanan Sakthikumar , Kong Linghai , Petersen Andrew J , Harder Cole R. K. , Block Jasper , Miller Julia Marie , Bhattacharyya Anita , Wang Daifeng , Zhang Su-Chun
Published: July 2021

Modeling age-related neurodegenerative disorders with human stem cells is difficult due to the embryonic nature of stem cell derived neurons. We developed a chemical cocktail to induce senescence of iPSC-derived neurons to address this challenge. We first screened small molecules that induce embryonic fibroblasts to exhibit features characteristic of aged fibroblasts. We then optimized a cocktail of small molecules that induced senescence in fibroblasts and cortical neurons without causing DNA damage. The utility of the “senescence cocktail” was validated in motor neurons derived from ALS patient iPSCs which exhibited protein aggregation and axonal degeneration substantially earlier than those without cocktail treatment. Our “senescence cocktail” will likely enhance the manifestation of disease-related phenotypes in neurons derived from iPSCs, enabling the generation of reliable drug discovery platforms.