bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship between osteoporosis, sarcopenia, vertebral fracture, and osteosarcopenia in patients with primary biliary cholangitis
Authors: Saeki Chisato , Oikawa Tsunekazu , Kanai Tomoya , Nakano Masanori , Torisu Yuichi , Sasaki Nobuyuki , Abo Masahiro , Saruta Masayuki , Tsubota Akihito
Published: June 2020

Aim

Bone disorders are serious complications in patients with primary biliary cholangitis (PBC), especially in postmenopausal female patients. Given that osteoporosis interrelates closely with sarcopenia, the concept of osteosarcopenia (coexistence of the two complications) has been established. This study aimed to investigate the relationship between osteoporosis, sarcopenia, vertebral fracture, and osteosarcopenia in PBC patients.

Methods

This study involved 117 consecutive PBC patients (21 males and 96 females). Bone mineral density (BMD) was measured with dual-energy X-ray absorptiometry. Sarcopenia was diagnosed according to the Japan Society of Hepatology assessment criteria.

Results

Of the 117 patients, 33 (28.2%), 27 (23.1%), 21 (17.9%), and 18 (15.4%) had osteoporosis, sarcopenia, vertebral fracture, and osteosarcopenia, respectively. Multivariate analysis identified sarcopenia as a significant, independent risk factor associated with osteoporosis in all and female patients [odds ratio (OR) = 4.126, P = 0.018; OR = 6.510, P = 0.001, respectively], and vice versa (OR = 3.420, P = 0.040; OR = 4.012, P = 0.026, respectively). The skeletal muscle mass index and handgrip strength were significantly correlated with the BMD of the lumbar spine, femoral neck, and total hip (r = 0.46–0.59, P < 0.001). Patients with osteosarcopenia had significantly higher prevalence of vertebral fracture (10/18; 55.6%) than those without both osteoporosis and sarcopenia (5/75; 6.7%).

Conclusion

We demonstrated the prevalence of osteoporosis, sarcopenia, vertebral fracture, and osteosarcopenia in PBC, and noted that these complications interrelated closely with each other. Comprehensive assessment and treatment strategies for bone and muscle disorders are essential for PBC patients.
Case series and review of liver dysfunction in COVID-19 patients
Authors: Kudaravalli Pujitha , Saleem Sheikh A , Ibeche Bashar , John Savio
Published: June 2020

Coronoviraus disease 2019 (COVID-19) has infected over two million people worldwide and the number keeps growing every day. While the pulmonary complications of COVID-19 are obvious, the effect of the virus on the other organs and the chronicity of the organ dysfunction remain unknown. The virus causes a debilitating infection with multiorgan injury and has a high mortality rate estimated to be around 3.70%. Several hypotheses are formulated to explain the liver dysfunction in COVID-19 patients which include collateral damage from cytokine storm, drug-induced liver injury, viral-induced hepatitis and hypoxia-induced damage. Through this case series, we would like to highlight that liver enzyme abnormalities are often seen in COVID-19 patients and would like to highlight that physicians need to serially monitor biochemical testing until the liver enzymes return to baseline. Physicians also need to be vigilant of liver enzyme abnormalities in these patients, especially before starting new medications.
Protocol Optimization and Implementation of Dual-Energy and Dual-Source Computed Tomography in Clinical Practice: Field of View, Speed, or Material Separation?
Authors: Pedersen Christian K. , Mackey Justin E. , Teytelboym Oleg M.
Published: June 2020

Clinical use of dual-energy computed tomography (DECT) and dual-source computed tomography (DSCT) has been well established for more than a decade. Improved software and decreased postprocessing time have increased the advantages and availability of DECT and DSCT imaging. In this article, we will provide a practical guide for implementation of DECT and DSCT in clinical practice and discuss automated processing and selection of CT protocols in neurologic, cardiothoracic, vascular, body, and musculoskeletal imaging.
Thai Patients With Antineutrophil Cytoplasmic Antibody–Associated Vasculitis: Outcomes and Risk Factors for Mortality
Authors: Intapiboon Porntip , Siripaitoon Boonjing
Published: June 2020

Background/Objective

Patients with antineutrophil cytoplasmic antibody–associated vasculitis (AAV) have an increased risk of premature death. Different subtypes, predictors, and ethnicities may affect the overall survival. However, the overall survival of Thai AAV patients has not been reported. We examined the mortality and prognosis of these patients.

Methods

This medical record review study included adult AAV patients, admitted to Songklanagarind Hospital from 2007 to 2017. Antineutrophil cytoplasmic antibody–associated vasculitis was diagnosed according to the 1990 American College of Rheumatology criteria or 2012 revised International Chapel Hill Consensus Conference Nomenclature of Vasculitides. Follow-up data were collected until June 2018. Prognostic factors and overall survival were analyzed.

Results

Among 57 AAV patients, mean (SD) age was 49.3 (16.1) years. Microscopic polyangiitis was the predominant diagnosis (42%). Kidneys (67%) and lungs (65%) were the 2 most affected organs. Initial Birmingham Vasculitis Activity Score (BVAS) greater than 20 was found in 61% of patients. Corticosteroids were the main drugs, and 58% received cyclophosphamide during the induction phase. Overall mean survival time was 38.8 (42.2) months. Patient survival was 91% and 82% at 1 and 6 months, respectively. One-year and 5-year survival rates were 78% and 63%, respectively. Univariate analysis showed that initial BVAS of greater than 20, neutrophil-to-lymphocyte ratio greater than 5.8, and need for invasive ventilator were significant predictors of mortality. Initial BVAS of greater than 20 was the only predictor of death in multivariate analyses (odds ratio, 4.22; 95% confidence interval, 1.01–17.63; p = 0.048).

Conclusions

The mortality rate of Thai AAV patients is high and strongly related to high disease activity. An early recognition and referral system are warranted to improve outcomes.
Detection of Unsuspected Coronavirus Disease 2019 Cases by Computed Tomography and Retrospective Implementation of the Radiological Society of North America/Society of Thoracic Radiology/American College of Radiology Consensus Guidelines
Authors: Lang Min , Som Avik , Mendoza Dexter P. , Flores Efren J. , Li Matthew D. , Shepard Jo-Anne O. , Little Brent P.
Published: June 2020

Purpose:

The purpose of this article was to report the utility of computed tomography (CT) for detecting unsuspected cases of Coronavirus disease 2019 (COVID-19) and the utility of the Radiological Society of North America (RSNA)/Society of Thoracic Radiology (STR)/American College of Radiology (ACR) consensus guidelines for COVID-19 reporting.

Materials and Methods:

A total of 22 patients of the 156 reverse transcriptase polymerase chain reaction confirmed COVID-19 patients who were hospitalized between March 27, 2020 and March 31, 2020 at our quaternary care academic medical center and who underwent CT imaging within 1 week of admission were included in this retrospective study. Demographics and clinical data were extracted from the electronic medical record system. Two thoracic radiologists independently categorized each CT study on the basis of RSNA/STR/ACR consensus guidelines. Disagreement in categorization was resolved by consensus discussion with a third thoracic radiologist.

Results:

At the time of imaging, 16 patients (73%) were suspected of COVID-19, and 6 patients (27%) were not. Common symptoms at presentation were fever (73%), cough (77%), and gastrointestinal symptoms (59%). An overall 63% of suspected COVID-19 patients exhibited shortness of breath, whereas 0 unsuspected COVID-19 patients did (P=0.02). On the basis of the RSNA consensus guidelines, 68%, 18%, 9%, and 5% of studies were categorized as “typical appearance,” “indeterminate appearance,” “atypical appearance,” and “negative for pneumonia,” respectively. There was no difference of category distribution between suspected and unsuspected COVID-19 patients (P=0.20), with “typical appearance” being the most prevalent in both (69% vs. 67%, respectively).

Conclusions:

It is important to recognize imaging features of COVID-19 pneumonia even in unsuspected patients. Implementation of the RSNA/STR/ACR consensus guidelines may increase consistency of reporting and convey the level of suspicion for COVID-19 to other health care providers, with “typical appearance” especially warranting further attention.
Role of alpha-synuclein phosphorylation at Serine 129 in methamphetamine-induced neurotoxicity in vitro and in vivo
Authors: Ding Jiuyang , Wang Yue , Huang Jian , Lian Yongling , Meng Yunle , Li Chen , He Yitong , Qiu Pingming
Published: June 2020

The phosphorylation and aggregation of alpha-synuclein (α-Syn) play a key role in methamphetamine (METH)-induced dopaminergic neurotoxicity. The exact mechanism underlying the interaction between METH-induced neurotoxicity and α-Syn was poorly clarified. We aimed to figure out the role of serine 129 phosphorylation (pS129) of α-Syn on its aggregation and neurotoxicity in vitro and in vivo. In this study, we examined pS129 α-Syn expression in vitro and in vivo at the protein phosphorylation and genetic levels and evaluated its effect on METH-induced neurotoxicity. Here, we found that pS129 α-Syn was significantly increased after METH treatment; moreover, the neuronal α-Syn aggregation and apoptosis caused by METH exposure were significantly attenuated after inhibiting α-Syn phosphorylation. We demonstrate that pS129 α-Syn contributes to the aggregation of α-Syn, and that phosphorylated and aggregated forms of α-Syn play an important role in METH-induced neurotoxicity in dopaminergic neurons and SH-SY5Y cells, supporting a potential insight into the treatment of METH-induced neurotoxicity.
Recurrence After Stopping Maintenance Electroconvulsive Therapy
Authors: Cabelguen Clémence , Caillet Pascal , Poulet Emmanuel , Szekely David , Desmidt Thomas , Pichot Anne , Vanelle Jean-Marie , Sauvaget Anne , Bulteau Samuel
Published: June 2020

Objectives

Relapses and recurrence remain the greatest risks posed by patients with severe mood disorders after discontinuation of electroconvulsive therapy (ECT). To date, despite a wide range of literature on ECT, little is known about the rate of recurrence of depression after maintenance ECT (mECT) discontinuation specifically. This study sought to address this lacuna, confronting literature data to the results of a retrospective case study.

Methods

A comprehensive review was conducted, followed by a retrospective analysis of 18 cases of mECT discontinuation between January 2011 and June 2016 involving patients with affective disorders.

Results

The comprehensive review revealed that only 3 studies have assessed recurrence rate after c/mECT discontinuation. In our retrospective analysis, mean (SD) mECT duration was 12.69 (12.16) months. A new mood event (usually a depressive state) was observed in 50% of the cases, and 44% of those recurrences occurred during the first 6 months after discontinuation.

Discussion

Given that high recurrence rates are observed after mECT discontinuation, the authors discuss the advantages of long-term mECT and the choice of concomitant pharmacotherapy for severe and complex affective disorders.
Building memories on prior knowledge: behavioral and fMRI evidence of impairment in early Alzheimer’s Disease
Authors: Jonin Pierre-Yves , Duché Quentin , Bannier Elise , Corouge Isabelle , Ferré Jean-Christophe , Belliard Serge , Barillot Christian , Barbeau Emmanuel J.
Published: June 2020

Impaired memory is a hallmark of prodromal Alzheimer’s Disease (AD). Prior knowledge associated with the memoranda has proved to have a powerful effect on memory in healthy subjects. Yet, barely nothing is known about its effect in early AD. We used functional MRI to ask whether prior knowledge enhanced memory encoding in early AD and whether the nature of prior knowledge mattered. Early AD patients and healthy controls underwent a task-based fMRI experiment, being scanned while learning face-scene associations. Famous faces carried Pre-Experimental Knowledge (PEK) while unknown faces repeatedly familiarized prior to learning carried Experimental Knowledge (EK). As expected, PEK increased subsequent memory in healthy elderly. However, patients did not benefit from PEK. Partly non-overlapping brain networks supported PEK vs. EK encoding in healthy controls. Patients displayed impaired activation in a right subhippocampal region where activity predicted successful associative memory formation of PEK stimuli. These findings call for a thorough consideration of how prior knowledge impacts learning and suggest a possible underestimation of the extent of associative memory impairment in early AD.

Highlights

Learning is impaired in prodromal AD, but we currently ignore whether prior knowledge available at encoding promotes learning in AD as it does in healthy controls.

Patients with AD failed to benefit from pre-experimental prior knowledge (famous faces) by comparison with experimental knowledge (unknown but familiarized faces).

fMRI responses at study revealed distinct networks underlying associative encoding for both pre-experimental and experimental knowledge.

A subsequent memory effect found in control subjects for associations carrying pre-experimental knowledge in the right subhippocampal structures, including the perirhinal cortex, was absent in patients.

Pre-experimental knowledge-based associative encoding relies on brain regions specifically targeted by early tau pathology.

Using unfamiliar materials to probe memory in early AD might underestimate learning impairment.
The MRi-Share database: brain imaging in a cross-sectional cohort of 1,870 university students
Authors: Tsuchida Ami , Laurent Alexandre , Crivello Fabrice , Petit Laurent , Joliot Marc , Pepe Antonietta , Beguedou Naka , Gueye Marie-Fateye , Verrecchia Violaine , Nozais Victor , Zago Laure , Tzourio-Mazoyer Nathalie , Mellet Emmanuel , Debette Stephanie , Tzourio Christophe , Mazoyer Bernard
Published: June 2020

We report on MRi-Share, a multi-modal brain MRI database acquired in a unique sample of 1,870 young healthy adults, aged 18 to 35 years, while undergoing university-level education. MRi-Share contains structural (T1 and FLAIR), diffusion (multispectral), susceptibility weighted (SWI), and resting-state functional imaging modalities. Here, we described the contents of these different neuroimaging datasets and the processing pipelines used to derive brain phenotypes, as well as how quality control was assessed. In addition, we present preliminary results on associations of some of these brain image-derived phenotypes at the whole brain level with both age and sex, in the subsample of 1,722 individuals aged less than 26 years. We demonstrate that the post-adolescence period is characterized by changes in both structural and microstructural brain phenotypes. Grey matter cortical thickness, surface area and volume were found to decrease with age, while white matter volume shows increase. Diffusivity, either radial or axial, was found to robustly decrease with age whereas fractional anisotropy only slightly increased. As for the neurite orientation dispersion and densities, both were found to increase with age. The isotropic volume fraction also showed a slight increase with age. These preliminary findings emphasize the complexity of changes in brain structure and function occurring in this critical period at the interface of late maturation and early aging.
Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes
Authors: Lin Zongtao , Wang Xie , Bustin Katelyn A , He Lin , Suciu Radu M , Schek Nancy , Ahmadi Mina , Hu Kai , Olson Erika J , Parsons Will H , Witze Eric S , Morton Paul D , Gregus Ann M , Buczynski Matthew W , Matthews Megan L
Published: June 2020

Known chemoproteomic probes generally use warheads that tag a single type of amino acid or modified form thereof to identify cases in which its hyper-reactivity underpins function. Much important biochemistry derives from electron-poor enzyme cofactors, transient intermediates and chemically-labile regulatory modifications, but probes for such species are underdeveloped. Here, we have innovated a versatile class of chemoproteomic probes for this less charted hemisphere of the proteome by using hydrazine as the common chemical warhead. Its electron-rich nature allows it to react by both polar and radicaloid mechanisms and to target multiple, pharmacologically important functional classes of enzymes bearing diverse organic and inorganic cofactors. Probe attachment can be blocked by active-site-directed inhibitors, and elaboration of the warhead supports connection of a target to a lead compound. The capacity of substituted hydrazines to profile, discover and inhibit diverse cofactor-dependent enzymes enables cell and tissue imaging and makes this platform useful for enzyme and drug discovery.
Polypeptide collapse modulation and folding stimulation by GroEL-ES
Authors: Naqvi Mohsin M. , Avellaneda Mario J. , Roth Andrew , Koers Eline J. , Sunderlikova Vanda , Kramer Günter , Rye Hays S. , Tans Sander J.
Published: June 2020

Unfolded proteins ubiquitously collapse into a compact yet dynamic state1,2. While this compaction is pivotal to protein folding3, aggregation4,5, intrinsic disorder6, and phase separation7, its role in protein quality control mechanisms remains obscure8. Collapse has been characterized mainly for polypeptides that are free in solution, in terms of kinetics, chain expansion, and effect on folding9,10. Yet, theory suggests that the solvent-mediated forces driving collapse can be altered near hydrophobic and charged surfaces, which are observed for many proteins including GroEL-ES11,12. Notably, while GroEL-ES is the archetypal protein-folding chaperone, its folding mechanism remains unresolved13,14. GroEL-ES is proposed to sterically confine polypeptides within its closed chamber15, unfold misfolded states16,17, or promote folding indirectly by suppressing aggregation18,19. Here, using integrated protein manipulation and imaging, we show that GroEL-ES can strengthen the collapse of polypeptide substrates, and hence stimulate folding directly. Strikingly, attractive forces pull substrate chains into the open GroEL cavity -unclosed by GroES-, and hence trigger a gradual compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL, and is aided by GroES binding to the cavity rim, and by the amphiphilic C-terminal tails at the cavity bottom. Peptides corresponding to these C-termini alone are sufficient to strengthen the collapse. The results show a mechanism that allows folding to be stimulated: by strengthening the collapse, residues are brought together that must contact to fold. The notion that one protein can modulate the collapse of another may be generally important in protein conformation and coacervation control, for systems ranging from the GroEL-ES homologue TRiC/CCT20, to the oncogenic c-Myc/Max complex21, and the nuclear pore transporter transportin22.
Prefusion spike protein stabilization through computational mutagenesis
Authors: Zhang Dong Yan , Wang Jian , Dokholyan Nikolay V.
Published: June 2020

A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) has emerged as a human pathogen, causing global pandemic and resulting in over 400,000 deaths worldwide. The surface spike protein of SARS-CoV-2 mediates the process of coronavirus entry into human cells by binding angiotensin-converting enzyme 2 (ACE2). Due to the critical role in viral-host interaction and the exposure of spike protein, it has been a focus of most vaccines’ developments. However, the structural and biochemical studies of the spike protein are challenging because it is thermodynamically metastable1. Here, we develop a new pipeline that automatically identifies mutants that thermodynamically stabilize the spike protein. Our pipeline integrates bioinformatics analysis of conserved residues, motion dynamics from molecular dynamics simulations, and other structural analysis to identify residues that significantly contribute to the thermodynamic stability of the spike protein. We then utilize our previously developed protein design tool, Eris, to predict thermodynamically stabilizing mutations in proteins. We validate the ability of our pipeline to identify protein stabilization mutants through known prefusion spike protein mutants. We finally utilize the pipeline to identify new prefusion spike protein stabilization mutants.
HNRNPM controls circRNA biogenesis and splicing fidelity to sustain prostate cancer cell fitness
Authors: Ho Jessica SY , Low Diana , Schwarz Megan , Incarnato Danny , Gay Florence , Tabaglio Tommaso , Zhang Jingxian , Wollman Heike , Chen Leilei , An Omer , Chan Tim Hon Man , Hickman Alexander Hall , Zheng Simin , Roudko Vladimir , Chen Sujun , Ahmed Musaddeque , He Housheng Hansen , Greenbaum Benjamin D. , Marazzi Ivan , Serresi Michela , Gargiulo Gaetano , Oliviero Salvatore , Wee Dave Keng Boon , Guccione Ernesto
Published: June 2020

Cancer cells are differentially dependent on the splicing machinery compared to normal untransformed cells. The splicing machinery thus represents a potential therapeutic target in cancer. To identify splicing factors important for prostate cancer cell (PCa) cell growth, we performed a parallel pooled shRNA screen onin vitropassaged cells andin vivoxenografted PCa tumor lines. Our screen revealed HNRNPM as a potential regulator of PCa cell growth. RNA- and eCLIP-sequencing data suggest that HNRNPM is bound to transcripts of key homeostatic genes and that loss of HNRNPM binding in a subset of these genes results in aberrant exon inclusion and exon back-splicing events in target transcripts. In both linear and circular mis-spliced transcripts, HNRNPM appears to preferentially bind to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM dependent linear splicing events using splice-switching antisense oligonucleotides (SSOs) was sufficient to inhibit cell growth in HNRNPM expressing cells. This suggests that prostate cancer cell dependence on HNRNPM is likely a result of mis-splicing of key homeostatic coding and non-coding genes. Taken together, our data reveal a role for HNRNPM in supporting prostate cancer cell fitness, and also as a potential therapeutic target in PCa.
Mechanical control of tissue shape and morphogenetic flows during vertebrate body axis elongation
Authors: Banavar Samhita P. , Carn Emmet K. , Rowghanian Payam , Stooke-Vaughan Georgina , Kim Sangwoo , Campàs Otger
Published: June 2020

Shaping embryonic tissues into their functional morphologies requires cells to control the physical state of the tissue in space and time. While regional variations in cellular forces or cell proliferation have been typically assumed to be the main physical factors controlling tissue morphogenesis, recent experiments have revealed that spatial variations in the tissue physical (fluid/solid) state play a key role in shaping embryonic tissues. Here we theoretically study how the regional control of fluid and solid tissue states guides morphogenetic flows to shape the extending vertebrate body axis. Our results show that both the existence of a fluid-to-solid tissue transition along the anteroposterior axis and the tissue surface tension determine the shape of the tissue and its ability to elongate unidirectionally, with large tissue tensions preventing unidirectional elongation and promoting blob-like tissue expansions. We predict both the tissue morphogenetic flows and stresses that enable unidirectional axis elongation. Our results show the existence of a sharp transition in the structure of morphogenetic flows, from a flow with no vortices to a flow with two counter-rotating vortices, caused by a transition in the number and location of topological defects in the flow field. Finally, comparing the theoretical predictions to quantitative measurements of both tissue flows and shape during zebrafish body axis elongation, we show that the observed morphogenetic events can be explained by the mere existence of a fluid-to-solid tissue transition along the anteroposterior axis. These results highlight the role of spatiotemporally-controlled fluid-to-solid transitions in the tissue state as a physical mechanism of embryonic morphogenesis.
Low Dose Hyperoxia Primes Airways for Fibrosis in Mice after Influenza A Infection
Authors: Dylag Andrew M. , Haak Jeannie , Warren Rachel , Yee Min , Pryhuber Gloria S. , O’Reilly Michael A.
Published: June 2020

It is well known that supplemental oxygen used to treat preterm infants in respiratory distress is associated with permanently disrupting lung development and the host response to influenza A virus (IAV). However, many infants who go home with normally functioning lungs are also at risk for hyperreactivity after a respiratory viral infection suggesting neonatal oxygen may have induced hidden molecular changes that may prime to the lung for disease. We discovered that thrombospondin-1 (TSP-1) is elevated in adult mice exposed to high-dose neonatal hyperoxia that is known to cause alveolar simplification and fibrotic lung disease following IAV infection. TSP-1 was also elevated in a new, low-dose hyperoxia mouse model (40% for 8 days; 40×8) that we recently reported causes a transient change in lung function that resolves by 8 weeks of age. Elevated TSP-1 was also identified in human autopsy samples of BPD-affected former preterm infants. Consistent with TSP-1 being a master TGFβ regulator, an early transient activation of TGFβ signaling, increased airway hyperreactivity, and peribronchial inflammation and fibrosis were seen when 40×8 mice were infected with IAV, which was not seen in infected room air controls. These findings reveal low dose of neonatal hyperoxia that does not affect lung function or structure may still change expression of genes, such as TSP-1, that may prime the lung for disease following respiratory viral infections, and may help explain why former preterm infants who have normal lung function are susceptible to airway obstruction and increased morbidity after viral infection.
Conclusive Identification of Senescent T Cells Reveals Their Abundance in Aging Humans
Authors: Martínez-Zamudio Ricardo Iván , Dewald Hannah K. , Vasilopoulos Themistoklis , Gittens-Williams Lisa , Fitzgerald-Bocarsly Patricia , Herbig Utz
Published: June 2020

Aging leads to a progressive functional decline of the immune system, which renders the elderly increasingly susceptible to disease and infection. The degree to which immune cell senescence contributes to this functional decline, however, remains unclear since methods to accurately identify and isolate senescent immune cells are missing. By measuring senescence-associated ß-galactosidase activity, a hallmark of senescent cells, we demonstrate here that healthy humans develop senescent T lymphocytes in peripheral blood with advancing age. Particularly senescent CD8+ T cells increased in abundance with age, ranging from 30% of the total CD8+ T cell population in donors in their 20s and reaching levels of 64% in donors in their 60s. Senescent CD8+ T cell populations displayed features of telomere dysfunction-induced senescence as well as p16-mediated senescence, developed in various T cell differentiation states and established gene expression signatures consistent with the senescence state observed in other cell types. On the basis of our results we propose that cellular senescence of T lymphocytes is a major contributing factor to the observed decline of immune cell function with advancing age and that immune cell senescence, therefore, plays a significant role in the increased susceptibility of the elderly to age-associated diseases and infection.
Mutatorfoci are regulated by developmental stage, RNA, and the germline cell cycle inCaenorhabditis elegans
Authors: Uebel Celja J. , Agbede Dana , Wallis Dylan C. , Phillips Carolyn M.
Published: June 2020

RNA interference is a crucial gene regulatory mechanism inCaenorhabditis elegans. Phase-separated perinuclear germline compartments calledMutatorfoci are a key element of RNAi, ensuring robust gene silencing and transgenerational epigenetic inheritance. Despite their importance,Mutatorfoci regulation is not well understood, and observations ofMutatorfoci have been largely limited to adult hermaphrodite germlines. Here we reveal that punctateMutatorfoci arise in the progenitor germ cells of early embryos and persist throughout all larval stages. They are additionally present throughout the male germline and in the cytoplasm of post-meiotic spermatids, suggestive of a role in paternal epigenetic inheritance. In the adult germline, transcriptional inhibition results in a pachytene-specific loss ofMutatorfoci, indicating thatMutatorfoci are partially reliant on RNA for their stability. Finally, we demonstrate thatMutatorfoci intensity is modulated by the stage of the germline cell cycle and specifically, thatMutatorfoci are brightest and most robust in the mitotic cells, transition zone, and late pachytene of adult germlines. Thus, our data defines several new factors that modulateMutatorfoci morphology which may ultimately have implications for efficacy of RNAi in certain cell stages or environments.
Fluorescence Microscopy Datasets for Training Deep Neural Networks
Authors: Hagen Guy M. , Bendesky Justin , Machado Rosa , Nguyen Tram-Anh , Kumar Tanmay , Ventura Jonathan
Published: June 2020

Background

Fluorescence microscopy is an important technique in many areas of biological research. Two factors which limit the usefulness and performance of fluorescence microscopy are photobleaching of fluorescent probes during imaging, and, when imaging live cells, phototoxicity caused by light exposure. Recently developed methods in machine learning are able to greatly improve the signal to noise ratio of acquired images. This allows researchers to record images with much shorter exposure times, which in turn minimizes photobleaching and phototoxicity by reducing the dose of light reaching the sample.

Findings

To employ deep learning methods, a large amount of data is needed to train the underlying convolutional neural network. One way to do this involves use of pairs of fluorescence microscopy images acquired with long and short exposure times. We provide high quality data sets which can be used to train and evaluate deep learning methods under development.

Conclusion

The availability of high quality data is vital for training convolutional neural networks which are used in current machine learning approaches.
The novel, recurrent mutation in theTOP2Agene results in the enhanced topoisomerase activity and transcription deregulation in glioblastoma
Authors: Gielniewski Bartlomiej , Poleszak Katarzyna , Roura Adria-Jaume , Szadkowska Paulina , Krol Sylwia K. , Guzik Rafal , Wiechecka Paulina , Maleszewska Marta , Kaza Beata , Marchel Andrzej , Czernicki Tomasz , Koziarski Andrzej , Zielinski Grzegorz , Styk Andrzej , Kawecki Maciej , Szczylik Cezary , Czepko Ryszard , Banach Mariusz , Kaspera Wojciech , Szopa Wojciech , Bujko Mateusz , Czapski Bartosz , Zabek Miroslaw , Izycka-Swieszewska Ewa , Kloc Wojciech , Nauman Pawel , Cieslewicz Joanna , Wojtas Bartosz , Kaminska Bozena
Published: June 2020

Background

High grade gliomas (HGGs) are aggressive, primary brain tumors with poor clinical outcomes. We aim to better understand glioma pathobiology and find potential therapeutic susceptibilities.

Methods

We designed a custom panel of 664 cancer- and epigenetics-related genes, and employed targeted next generation sequencing to study the genomic landscape of somatic and germline variants in 182 gliomas of different malignancy grades. mRNA sequencing was performed to detect transcriptomic abnormalities.

Results

In addition to known alterations inTP53,IDH1,ATRX,EGFRgenes found in this cohort, we identified a novel, recurrent mutation in theTOP2Agene coding for Topoisomerase 2A occurring only in glioblastomas (GBM, WHO grade IV gliomas). Biochemical assays with recombinant proteins demonstrated stronger DNA binding and DNA supercoil relaxation activities of the variant proteins. GBM patients carrying the mutatedTOP2Ahad shorter overall survival than those with the wild typeTOP2A. Computational analyses of transcriptomic data showed that GBMs with the mutatedTOP2Ahave different transcriptomic patterns suggesting higher transcriptomic activity.

Conclusion

We identified a novel TOP2A E948Q variant that strongly binds to DNA and is more active than the wild type protein. Our findings suggest that the discoveredTOP2Avariant is gain–of-function mutation.

Key points

The most frequent genetic alterations in high grade gliomas are reported.

A new mutation in theTOP2Agene was found in 4 patients from Polish population.

A E948Q substitution changes TOP2A activities towards DNA.

The recurrentTOP2Avariant is a gain-of-function mutation.

Importance of the study

Glioblastoma is a deadly disease. Despite recent advancements in genomics and innovative targeted therapies, glioblastoma therapy has not shown improvements. Insights into glioblastoma biology may improve diagnosis, prognosis, and treatment prediction, directing to a better outcome. We performed targeted sequencing of 664 cancer genes, and identified a new variant of theTOP2Agene encoding topoisomerase 2A in glioblastomas. The TOP2A protein variant shows a higher affinity towards DNA and causes transcriptional alterations, suggesting a higherde novotranscription rate.
Investigation of Compatibility of SARS-CoV-2 RT-PCR Kits Containing Different Gene Targets During COVID-19 Pandemic
Authors: Sarıgul Figen , Doluca Osman , Akhan Sıla , Sayan Murat
Published: June 2020

Aim

In the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reverse transcriptase-polymerase chain reaction (RT-PCR) technique is often used. We evaluated the compatibility of SARS-CoV-2 RT-PCR kits containing different gene targets during the pandemic.

Materials & methods

Samples were tested by Bio-Speddy® (RdRp gene) and Diagnovital® (RdRp+E genes). The correlation between two assays were determined by Deming regression and chi-square heatmap analyses.

Results

Diagnovital PCR kit showed in a constricted range and conveniently exponential amplification curves than Bio-Speedy PCR kit. While the correlation increased when a secondary biomarker was added to the kit.

Conclusion

In an unknown sample, using together different PCR kits that target different genes during the pandemic situation may provide a more accurate diagnosis of SARS-CoV-2.
Variant analysis of SARS-CoV-2 strains in Middle Eastern countries
Authors: Bindayna Khalid Mubarak , Crinion Shane
Published: June 2020

Background

SARS-CoV-2 is diverging from the initial Wuhan serotype, and different variants of the virus are reported. Mapping the variant strains and studying their pattern of evolution will provide better insights into the pandemic spread

Methods

Data on different SARS-CoV2 for WHO EMRO countries were obtained from the Chinese National Genomics Data Center (NGDC), Genbank and the Global Initiative on Sharing All Influenza Data (GISAID). Multiple sequence alignments (MSA) was performed to study the evolutionary relationship between the genomes. Variant calling, genome and variant alignment were performed to track the strains in each country. Evolutionary and phylogenetic analysis is used to explore the evolutionary hypothesis.

Findings

Of the total 50 samples, 4 samples did not contain any variants. Variant calling identified 379 variants. Earliest strains are found in Iranian samples. Variant alignment indicates Iran samples have a low variant frequency. Saudi Arabia has formed an outgroup. Saudi Arabia, Qatar and Kuwait were the most evolved genomes and are the countries with the highest number of cases per million.

Interpretation

Iran was exposed to the virus earlier than other countries in the Eastern Mediterranean Region.

Funding

None
Low-Pass Whole Genome Bisulfite Sequencing of Neonatal Dried Blood Spots Identifies a Role for RUNX1 in Down Syndrome DNA Methylation Profiles
Authors: Laufer Benjamin I. , Hwang Hyeyeon , Jianu Julia M. , Mordaunt Charles E. , Korf Ian F. , Hertz-Picciotto Irva , LaSalle Janine M.
Published: June 2020

Neonatal dried blood spots (NDBS) are a widely banked sample source that enable retrospective investigation into early-life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early-life Down syndrome (DS) DNA methylation profiles. DS represents an example of genetics shaping epigenetics, as multiple array-based studies have demonstrated that trisomy 21 is characterized by genome-wide alterations to DNA methylation. By assaying over 24 million CpG sites, thousands of genome-wide significant (q< 0.05) DMRs that distinguished DS from typical development (TD) and idiopathic developmental delay (DD) were identified. Machine learning feature selection refined these DMRs to 22 loci. The DS DMRs mapped to genes involved in neurodevelopment, metabolism, and transcriptional regulation. Based on comparisons to previous DS methylation studies and reference epigenomes, the hypermethylated DS DMRs were significantly (q< 0.05) enriched across tissues while the hypomethylated DS DMRs were significantly (q< 0.05) enriched for blood-specific chromatin states. A ∼28 kb block of hypermethylation was observed on chromosome 21 in theRUNX1locus, which encodes a hematopoietic transcription factor whose binding motif was the most significantly enriched (q< 0.05) overall and specifically within the hypomethylated DMRs. Finally, we also identified DMRs that distinguished DS NDBS based on the presence or absence of congenital heart disease (CHD). Together, these results not only demonstrate the utility of low-pass WGBS on NDBS samples for epigenome-wide association studies, but also provide new insights into the early-life mechanisms of epigenomic dysregulation resulting from trisomy 21.
Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses
Authors: Banerjee Arinjay , El-Sayes Nader , Budylowski Patrick , Richard Daniel , Maan Hassaan , Aguiar Jennifer A. , Baid Kaushal , D’Agostino Michael R. , Ang Jann Catherine , Tremblay Benjamin J.-M. , Afkhami Sam , Karimzadeh Mehran , Irving Aaron T. , Yip Lily , Ostrowski Mario , Hirota Jeremy A. , Kozak Robert , Capellini Terence D. , Miller Matthew S. , Wang Bo , Mubareka Samira , McGeer Allison J. , McArthur Andrew G. , Doxey Andrew C. , Mossman Karen
Published: June 2020

Type I interferons (IFNs) are our first line of defence against a virus. Protein over-expression studies have suggested the ability of SARS-CoV-2 proteins to block IFN responses. Emerging data also suggest that timing and extent of IFN production is associated with manifestation of COVID-19 severity. In spite of progress in understanding how SARS-CoV-2 activates antiviral responses, mechanistic studies into wildtype SARS-CoV-2-mediated induction and inhibition of human type I IFN responses are lacking. Here we demonstrate that SARS-CoV-2 infection induces a mild type I IFN responsein vitroand in moderate cases of COVID-19.In vitrostimulation of type I IFN expression and signaling in human airway epithelial cells is associated with activation of canonical transcriptions factors, and SARS-CoV-2 is unable to inhibit exogenous induction of these responses. Our data demonstrate that SARS-CoV-2 is not adept in blocking type I IFN responses and provide support for ongoing IFN clinical trials.
Reconstitution of an intact clock that generates circadian DNA binding in vitro
Authors: Chavan Archana G. , Ernst Dustin C. , Fang Mingxu , Sancar Cigdem , Partch Carrie L. , Golden Susan S. , LiWang Andy
Published: June 2020

Circadian clocks control gene expression in the complex milieu of cells. Here, we reconstituted under defined conditions in vitro the cyanobacterial circadian clock system which includes an oscillator, signal-transduction pathways, transcription factor, and promoter DNA. The system oscillates autonomously with a near 24 h period, remains phase coherent for many days, and allows real-time observation of each component simultaneously without user intervention. This reassembled clock system provides new insights into how a circadian clock exerts control over gene expression and can serve in the area of synthetic biology as a new platform upon which to build even more complexity.

One Sentence Summary

An autonomously oscillating circadian clock-controlled gene regulatory circuit is studied in vitro using a real-time high-throughput assay.
Structure-based modelling and dynamics of MurM, aStreptococcus pneumoniaepenicillin resistance determinant that functions at the cytoplasmic membrane interface
Authors: York Anna , Lloyd Adrian. J. , del Genio Charo I. , Shearer Jonathan , Hinxman Karen. J. , Fritz Konstantin , Fulop Vilmos , Khalid Syma , Dowson Christopher. G. , Roper David. I.
Published: June 2020

MurM is an aminoacyl-tRNA dependant ligase that aminoacylates the Lipid II peptidoglycan precursor, in the human pathogenStreptococcus pneumoniae. MurM is required for the generation of branched peptidoglycan precursors enabling indirect cross-links in the peptidoglycan and is found to be essential for penicillin resistance. In this study we have solved the X-ray crystal structure ofStaphylococcus aureusFemX, an isofunctional homologue of MurM, and used this as a template to generate a homology model of MurM. Using this model, we perform molecular docking and molecular dynamics to examine the interaction of the protein with the phospholipid bilayer and the membrane embedded Lipid II substrate of MurM. Our model suggests that MurM is associated with the major membrane phospholipid cardiolipin, and we confirm this with experimental evidence that the activity of MurM is enhanced by this phospholipid and inhibited by its direct precursor phosphatidylglycerol. This suggests that the spatial association of pneumococcal membrane phospholipids and their impact on MurM activity may be a critical to the final architecture of the peptidoglycan and the expression of clinically relevant penicillin resistance in this pathogen.
Microscope-AOtools: A generalised adaptive optics implementation
Authors: Hall Nicholas , Titlow Josh , Booth Martin J. , Dobbie Ian M.
Published: June 2020

Microscope-AOtools is a software package which allows for a simple, robust and generalised implementation of adaptive optics (AO) elements. It contains all the necessary methods for set-up, calibration, and aberration correction which are simple to use and function in a robust manner. Aberrations arising from sources such as sample hetero-geneity and refractive index mismatches are constant problems in biological imaging. These aberrations reduce image quality and the achievable depth of imaging, particularly in super-resolution microscopy techniques. AO technology has been proven to be effective in correcting for these aberrations and thereby improving the image quality. However, it has not been widely adopted by the biological imaging community due, in part, to difficulty in set-up and operation of AO, particularly by non-specialist users. Microscope-AOtools offers a robust, easy-to-use implementation of the essential methods for set-up and use of AO techniques. These methods are constructed in a generalised manner that can utilise a range of adaptive optics elements, wavefront sensing techniques and sensorless AO correction methods. Furthermore, the methods are designed to be easily extensible as new techniques arise, leading to a streamlined pipeline for new AO technology and techniques to be adopted by the wider microscopy community.
Beyond Plug and Pray: Context Sensitivity andin silicoDesign of Artificial Neomycin Riboswitches
Authors: Günzel Christian , Kühnl Felix , Arnold Katharina , Findeiß Sven , Weinberg Christina , Stadler Peter F , Mörl Mario
Published: June 2020

Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5’ untranslated region of mRNA. Rearrangements of the RNA structure in response, e. g., to the binding of small molecules or ions control translational initiation or premature termination of transcription and thus mRNA expression. Such structural responses are amenable to computational modeling, making it possible to rationally design synthetic riboswitches for a given aptamer. Starting from an artificial aptamer, we construct the first synthetic transcriptional riboswitches that respond to the antibiotic neomycin. We show that the switching behaviorin vivocritically depends not only on the sequence of the riboswitch itself, but also on its sequence context. We therefore developedin silicomethods to predict the impact of the context, making it possible to adapt the design and to rescue non-functional riboswitches. We furthermore analyze the influence of 5’ hairpins with varying stability on neomycin riboswitch activity. Our data highlight the limitations of a simple plug-and-play approach in the design of complex genetic circuits and demonstrate that detailed computational models significantly simplify, improve, and automate the design of transcriptional circuits. Our design software is available under a free license on Github.1
Rub1/NEDD8, a ubiquitin-like modifier, is also a ubiquitin modifier
Authors: Gurevich Sylvia Zerath , Sinha Abhishek , Longworth Joseph , Singh Rajesh K. , Lemma Betsegaw E. , Thakur Anita , Popp Oliver , Kornitzer Daniel , Reis Noa , Scheffner Martin , Dittmar Gunnar , Pick Elah , Fushman David , Glickman Michael H.
Published: June 2020

Of all ubiquitin-like small protein modifiers, Rub1/NEDD8 is the closest kin of ubiquitin in sequence and in structure. Despite their profound similarities, prevalence of ubiquitin and of Rub1 is starkly different: targets of ubiquitin modification reach into the thousands, whereas unique targets of Rub1/NEDD8 appear limited to one family of proteins, Cullins. This distinction is likely due to dedicated E1 activating enzymes that select either one or the other and relay the modifier until it is covalently attached to a target. To convert typical neddylation targets for modification by ubiquitin, and vice versa, we designed reciprocal substitutions at position 72 of Rub1 and of ubiquitin to render them substrates for activation by their non-cognate E1 activating enzymes. We found that this single amino acid is sufficient to distinguish between Ub and Rub1 in living cells, and determine their targets. Thus, modification of Cullins by UbR72Tcould compensate for loss of Rub1, even as it maintained its ability to polymerize and direct conjugates for degradation. Conversely, Rub1T72Ractivated by ubiquitin-activating enzyme entered into the ubiquitination cascade, however was not efficiently polymerized, essentially capping polyubiquitin chains. Upon shortage of free ubiquitin under stress, even native Rub1 spilled-over into the ubiquitinome suppressing polyubiquitination. By contrast, the need to maintain monomeric modifications on unique targets is a likely explanation for why the Rub1-activating enzyme strictly discriminates against ubiquitin. Swapping Rub1 and ubiquitin signals uncovered a reason for maintaining two separate pathways across eukaryotic kingdom.