bluuebunny/crossref_metadata_2025 huggingface dataset:
Hindu religion and suicide in India
Authors: Vijayakumar Lakshmi
Published: February 2021

Hinduism is one of the oldest religions in the world. It is estimated that there are approximately 1.1 billion adherents comprising 16% of the world population, living mostly in India and Nepal. As early as 3000 bc, suicides were generally condemned, but religious suicides were condoned. The practice of sati (self-immolation) and jauhar (mass suicide) was also prevalent among the Hindus. Suicide by self-immolation often occurs in Hindus, particularly among young women. Suicidal behaviour was higher among Hindus than that of the native population in the countries to which Hindus had migrated. A case control study in India found that strong faith in Hinduism is a significant protective factor against suicide. Belief in karma and reincarnation probably make a Hindu more concerned that they should have a dignified death: in Hinduism it is ultimately the individual’s decision as to how they live and die.
The role of religion in suicide prevention work in Uganda
Authors: Ovuga Emilio , Boardman Jed
Published: February 2021

Themes of traditional religious practice in Uganda have been the role of a creator, an understanding of life in an integral sense, and maintenance of contact with the spirit world. Christianity was introduced to Uganda in the nineteenth century and was associated with the colonial powers. Present expressions of cosmology mainly involve a strong sense of the collective and its responsibility, the breakdown of which plays a central role in suicide. The recent rise in suicide in Uganda may be the result of substantial social and economic changes, and long-term strife affecting the population. Associated with this have been mass suicide and internal wars, which resulted in mass killings that may have roots in traditional and non-traditional religious beliefs. An understanding of the traditional world view of Ugandans, and how this has changed over time, may help in developing strategies for the management and prevention of suicide in Uganda.
Biological predictors of suicidal behaviour in mood disorders
Authors: Mann J. John , Currier Dianne
Published: February 2021

Predicting suicide is difficult due to its low base rate and the multicausal nature of suicidal behaviour. Retrospective and cross-sectional studies have identified a number of biologic abnormalities associated with suicide and non-fatal suicide attempt. Non-fatal suicidal behaviour shows a big range in terms of degree of intent and medical damage or lethality. High intent more lethal suicide attempts are associated with greater risk of suicide and different demographics and biology compared with impulsive low lethality attempts. Prospective studies of suicide provide estimates of the predictive utility of biologic measures. Here, we review prospective studies of suicidal behaviour and serotonergic, noradrenergic, dopaminergic systems, inflammation, polyunsaturated fatty acids, and the hypothalamic–pituitary–adrenocortical (HPA) axis function in mood disorders. The most promising biologic predictors are low cerebrospinal fluid (CSF), 5-hydroxyindoleacetic acid (5-HIAA), and HPA axis dysfunction, as demonstrated by dexamethasone non-suppression where each are associated with a 4.5-fold greater risk of suicide.
Treatment of suicide attempts and suicidal patients in psychiatric care
Authors: Mehlum Lars
Published: February 2021

No other known risk factor has such a high suicide prevention potential as a psychiatric disorder. However, to release this potential, psychiatric care needs to be made more available to suicidal individuals, and there is a necessity to establish a continuity of care between hospital and outpatient treatment for patients who have been admitted after a suicide attempt. In this chapter, important aspects of the psychiatric treatment of suicidal individuals are described. The importance of conducting systematic and repeated clinical risk assessments, providing treatments targeted at the patient’s needs, and instigating safety measures according to the actual risk level, is reinforced. Treatment standards should be kept high through continuous staff education measures, clinical supervision, adherence to written procedures, and should be improved through suicide review procedures whenever there has been a severe suicidal incident within the context of the clinical unit.
Introduction to the training exercises
Authors: Cookson Richard , Love-Koh James , Angus Colin , Lomas James
Published: February 2021

This chapter introduces the handbook spreadsheet training exercises, which are designed to provide hands-on experience in using the methods of distributional cost-effectiveness analysis (DCEA). Seven of the exercises form a cumulative step-by-step sequence relating to nicotine replacement therapy (NRT) in England, which is a classic example of a preventive healthcare programme designed to improve health and reduce health inequality. This allows us to illustrate all the main steps involved in conducting a DCEA using a single common example. There are also two stand-alone exercises relating to other topics in other countries.
Health by disease categories
Authors: Johansson Kjell Arne , Coates Matthew M. , Økland Jan-Magnus , Tsuchiya Aki , Bukhman Gene , Norheim Ole F. , Haaland Øystein
Published: February 2021

This chapter shows how to quantify and compare the baseline health between and within disease categories using three main health concepts—current health, future health, and lifetime health—and shows how each concept can be measured using three main metrics—absolute health achievement, absolute health shortfall, and relative health shortfall. Different health concepts can have quite different equity implications about which disease group is worse-off in terms of health or has greater ‘severity of illness’. Metrics based on current or future health might be useful for a decision maker who believes that past health is water under the bridge. Metrics based on lifetime health might be useful for a decision maker who believes that priority should be given to people who suffer a greater burden of illness from the perspective of the whole life course from birth until death.
Future challenges
Authors: Cookson Richard , Morton Alec , Schokkaert Erik , Gomez Gabriela B. , Merritt Maria W. , Norheim Ole F. , Griffin Susan , Culyer Anthony J.
Published: February 2021

In this chapter we discuss some of the challenges facing the field of distributional cost-effectiveness analysis (DCEA). We cover four methodological challenges for researchers: (1) modelling complexities such as economies of scale, spillovers, and behavioural responses; (2) ex post DCEA based on distributions of realized outcomes rather than expected outcomes; (3) cross-sectoral DCEA combining information about health and non-health dimensions of well-being; and (4) fair shares DCEA based on distributing in proportion to strength of claim rather than maximizing value. We also discuss the practical challenge of making DCEA more useful to decision makers.
Boundary violations
Authors: Gabbard Glen O.
Published: February 2021

Professional boundaries can be described as the ‘edge’ or limit of appropriate behaviour by the practitioner in the clinical setting. The therapeutic frame comprised of this set of boundaries allows the clinician and the patient to interact in a safe and productive way. These boundaries can be violated by sexual contact between the practitioner and the patient or by nonsexual overinvolvement. The mental health clinicians who transgress boundaries may do so for different reasons, and there are varied characterological and symptomatic clinical pictures that lead to boundary violations. Detailed evaluation of each individual case is necessary to determine if the clinician can be rehabilitated or not. Rehabilitation generally involves psychotherapy, monitoring, practice limitations, continuing education, and supervision. The digital era has brought about new forms of boundary violations involving cyberspace and the relative ease with which information about patients can be accessed.
A photometric and kinematic analysis of UDG1137+16 (dw1137+16): Probing ultradiffuse galaxy formation in a group environment
Authors: Gannon Jonah S , Dullo Bililign T , Forbes Duncan A , Rich R Michael , Román Javier , Couch Warrick J , Brodie Jean P , Ferré-Mateu Anna , Alabi Adebusola , Mould Jeremy
Published: February 2021

The dominant physical formation mechanism(s) for ultradiffuse galaxies (UDGs) is still poorly understood. Here, we combine new, deep imaging from the Jeanne Rich Telescope with deep integral field spectroscopy from the Keck II telescope to investigate the formation of UDG1137+16 (dw1137+16). Our new analyses confirm both its environmental association with the low density UGC 6594 group, along with its large size of 3.3 kpc and status as a UDG. The new imaging reveals two distinct stellar components for UDG1137+16, indicating that a central stellar body is surrounded by an outer stellar envelope undergoing tidal interaction. Both the components have approximately similar stellar masses. From our integral field spectroscopy, we measure a stellar velocity dispersion within the half-light radius (15 ± 4 km s−1) and find that UDG1137+16 is similar to some other UDGs in that it is likely dark matter dominated. Incorporating literature measurements, we also examine the current state of UDG observational kinematics. Placing these data on the central stellar velocity dispersion–stellar mass relation, we suggest there is little evidence for UDG1137+16 being created through a strong tidal interaction. Finally, we investigate the constraining power current dynamical mass estimates (from stellar and globular cluster velocity dispersions) have on the total halo mass of UDGs. As most are measured within the half-light radius, they are unable to accurately constrain UDG total halo masses.
ESTIMATION OF ENTRANCE SURFACE AIR KERMA IN DIGITAL RADIOGRAPHIC EXAMINATIONS
Authors: Kaushik Chanchal , Sandhu Inderjeet Singh , Srivastava A K , Chitkara Mansi
Published: February 2021

Purpose: Contribution of radiation doses from medical X-ray examination to collective dose is significant. Unusually, high doses may increase the risk of stochastic effects of radiations. Therefore, radiation dose assessment was performed in 241 digital X-ray examinations in the study and was compared with published dose reference levels (DRLs). Methods: Entrance surface air kerma (ESAK) was calculated in chest PA, cervical AP/Lat, abdomen AP, lumbar AP/Lat and pelvis AP digital radiographic examinations (119 male and 122 female) following the International Atomic Energy Agency recommended protocol. Initially, 270 digital examinations were selected, reject analysis was performed and final 241 examinations were enrolled in the study for dose calculations. The exposure parameters and X-ray tube output were used for dose calculations. Effective doses were estimated with the help of conversion coefficients from ICRP 103. Results: Median ESAK (mGy) and associated effective doses obtained were cervical spine AP (1.30 mGy, 0.045 mSv), cervical spine Lat (0.25 mGy, 0.005 mSv), chest PA (0.11 mGy, 0.014 mSv), abdomen AP (0.90 mGy, 0.118 mSv), lumbar spine AP (1.52 mGy, 0.177 mSv), lumbar spine Lat (7.76 mGy, 0.209 mSv) and pelvis AP (0.82 mGy, 0.081 mSv). Results were compared with the studies of UK, Oman, India and Canada. Conclusion: The calculated ESAK and effective dose values were less than or close to previously published literature except for cervical spine AP and lumbar spine Lat. The results reinforce the need for radiation protection optimization, improving examination techniques and appropriate use of automatic exposure control in digital radiography. ESAK values reported in this study could further contribute to establishing local DRLs, regional DRLs and national DRLs.
Acerihabitans arboris gen. nov., sp. nov., a new member of the family Pectobacteriaceae isolated from sap drawn from Acer pictum
Authors: Lee Soon Dong , Kim In Seop , Choe Hanna , Kim Ji-Sun
Published: February 2021

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6T belonged to the family

Pectobacteriaceae

and formed a distinct clade between members of the genera

Sodalis

and

Biostraticola

with gene support index of 89. The closest phylogenetic neighbours were

Biostraticola tofi

DSM 19580T (97.3% 16S rRNA gene sequence similarity) and

Sodalis praecaptivus

HS1T (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C16:0, C17:0 cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6T (=KCTC 52622T=DSM 104038T) represents a novel species of a new genus in the family

Pectobacteriaceae

, for which the name Acerihabitans arboris gen. nov., sp. nov. is proposed.
Pseudomonas bijieensis sp. nov., isolated from cornfield soil
Authors: Liang Jingling , Wang Sai , Yiming Ayizekeranmu , Fu Luoyi , Ahmad Iftikhar , Chen Gongyou , Zhu Bo
Published: February 2021

Strain L22-9T, a Gram-stain-negative and rod-shaped bacterium, motile by one polar flagellum, was isolated from cornfield soil in Bijie, Guizhou Province, PR China. Based on 16S rRNA gene sequences, it was identified as aPseudomonasspecies. Multilocus sequence analysis of concatenated 16S rRNA,gyrB,rpoBandrpoDgene sequences showed that strain L22-9Tformed a clearly separated branch, located in a cluster together withPseudomonas brassicacearumLMG 21623T,Pseudomonas kilonensisDSM 13647TandPseudomonas thivervalensisDSM 13194T. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) confirmed that strain L22-9Tshould be classified as a novel species. It was most closely related toP. kilonensisDSM 13647Twith ANI and dDDH values of 91.87 and 46.3 %, respectively. Phenotypic features that can distinguish strain L22-9TfromP. kilonensisDSM 13647Tare the assimilation ability ofN-acetyl-d-glucosamine, poor activity of arginine dihydrolase and failure to ferment ribose andd-fucose. The predominant cellular fatty acids of strain L22-9Tare C16 : 0, summed feature 3 (C16 : 1 ω6cand/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7cand/or C18 : 1 ω6c). The respiratory quinones consist of Q-9 and Q-8. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipids, two unidentified aminophospholipids and an unidentified glycolipid. Based on the evidence, we conclude that strain L22-9Trepresents a novel species, for which the namePseudomonas bijieensissp. nov. is proposed. The type strain is L22-9T(=CGMCC 1.18528T=LMG 31948T), with a DNA G+C content of 60.85 mol%.
Microbispora sitophila sp. nov., a novel actinobacterium isolated from rhizosphere soil of wheat (Triticum aestivum L.)
Authors: Guo Lifeng , Li Zhiqi , Xu Xi , Pang Qiuying , Zhao Junwei
Published: February 2021

A novel actinobacterium, designated strain NEAU-D428T, was isolated from rhizosphere soil of wheat and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the strain coincided with members of the genus

Microbispora

. The 16S rRNA gene sequence analysis showed that the isolate was most closely related to

Microbispora bryophytorum

NEAU-TX2-2T (99.2 %). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain clustered with

Microbispora clausenae

CLES2T (99.1 %), but formed a separate subclade in the phylogenomic tree within the genus

Microbispora

. The menaquinones were identified as MK-9(H4), MK-9(H2) and MK-9(H0). The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, ninhydrin-positive glycophospholipid, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were identified as iso-C16 : 0, C16 : 0, 10-methyl C17 : 0 and C18 : 0. Digital DNA–DNA hybridization and average nucleotide identity values between strain NEAU-D428T and

M. bryophytorum

NEAU-TX2-2T,

Microbispora camponoti

2C-HV3T,

M. clausenae

CLES2T, ‘Microbispora cellulosiformans’ Gxj-6T and

Microbispora fusca

NEAU-HEGS1-5T were 47.6 and 92.2 %, 47.5 and 92.2 %, 55.9 and 94.0 %, 33.1 and 86.8 %, and 33.6 and 87.1 %, respectively. These results and some physiological and biochemical properties demonstrated that the strain could be distinguished from its closest relatives. Therefore, it is proposed that strain NEAU-D428T should be classified as representative of a novel species of the genus

Microbispora

, for which the name Microbispora sitophila sp. nov. is proposed. The type strain is NEAU-D428T (=CGMCC 4.7523T=DSM 109822T).
Going virtual: a report from the sixth Young Microbiologists Symposium on ‘Microbe Signalling, Organisation and Pathogenesis’
Authors: An Shi-qi , Lopes Bruno Silvester , Connolly James P. R. , Sharp Connor , Nguyen Thi Kim Loan , Kirkpatrick Clare Louise
Published: February 2021

The sixth Young Microbiologists Symposium on 'Microbe Signalling, Organisation and Pathogenesis' was scheduled to be held at the University of Southampton, UK, in late August 2020. However, due to the health and safety guidelines and travel restrictions as a response to the COVID-19 pandemic, the symposium was transitioned to a virtual format, a change embraced enthusiastically as the meeting attracted over 200 microbiologists from 40 countries. The event allowed junior scientists to present their work to a broad audience and was supported by the European Molecular Biology Organization, the Federation of European Microbiological Societies, the Society of Applied Microbiology, the Biochemical Society, the Microbiology Society and the National Biofilms Innovation Centre. Sessions covered recent advances in all areas of microbiology including: Secretion and transport across membranes, Gene regulation and signalling, Host–microbe interactions, and Microbial communities and biofilm formation. This report focuses on several of the highlights and exciting developments communicated during the talks and poster presentations.
Genomic deletions in Rhodococcus based on transformation of linear heterologous DNA
Authors: Singhi Divya , Parwin Shabnam , Srivastava Preeti
Published: February 2021

Several genome engineering methods have been developed for

Rhodococcus

. However, they suffer from limitations such as extensive cloning, multiple steps, successful expression of heterologous genes via plasmid etc. Here, we report a rapid method for performing genomic deletions/disruptions in

Rhodococcus

spp. using heterologous linear DNA. The method is cost effective and less labour intensive. The applicability of the method was demonstrated by successful disruption of rodA and orphan parA. None of the disrupted genes were found to be essential for the viability of the cell. Disruption of orphan parA and rodA resulted in elongated cells and short rods, respectively. This is the first report demonstrating disruption of rodA and orphan parA genes by electroporation of heterologous linear DNA in

Rhodococcus

spp.
Persistent COVID-19 symptoms minimally impact the development of SARS-CoV-2 specific cellular immunity
Authors: Fang HengSheng , Wegman Adam D. , Ripich Kianna , Friberg Heather , Currier Jeffrey R. , Thomas Stephen J. , Endy Timothy P. , Waickman Adam T.
Published: February 2021

SARS-CoV-2 represents an unprecedented public health challenge with many unknowns remaining regarding the factors that impact viral pathogenicity and the development of immunity after infection. While the majority of SARS-CoV-2 infected individuals with mild-to-moderate COVID-19 resolve their infection with few complications, a significant number of individuals experienced prolonged symptoms lasting for weeks after initial diagnosis. Persistent viral infections are commonly accompanied by immunologic dysregulation, especially within the cellular immune compartment. However, it is unclear if persistent mild-to-moderate COVID-19 impacts the development of virus-specific cellular immunity. To this end, we analyzed the development of SARS-CoV-2 specific cellular immunity in convalescent COVID-19 patients who experienced eight days or fewer of COVID-19 symptoms, or symptoms persisting for 18 days or more. We observed that the duration of COVID-19 symptoms minimally impacts the magnitude, antigen specificity, and transcriptional profile of SARS-CoV-2 specific cellular immunity within both the CD4+ and CD8+ T cell compartments. Furthermore, we observed that reactivity against the structural N protein from SARS-CoV-2 in convalescent COVID-19 patients correlates with the amount of reactivity against the seasonal human coronaviruses 229E and NL63. These results provide additional insight into the complex processes that regulate the development of cellular immunity against SARS-CoV-2 and related human coronaviruses.
dSCOPE: a software to detect sequences critical for liquid-liquid phase separation
Authors: Li Shihua , Yu Kai , Zhang Qingfeng , Liu Zekun , Liu Jia , Ju Huai-Qiang , Zuo Zhixiang , Li Xiaoxing , Wang Zhenlong , Cheng Han , Liu Ze-Xian
Published: February 2021

Membrane based cells are the fundamental structure and function units of organisms, while evidences were increasing that liquid-liquid phase separation (LLPS) is associated with the formation of membraneless organelles, such as P-bodies, nucleoli and stress granules. Many studies have been undertaken to explore the functions of protein phase separation, but these studies lacked an effective tool to identify the sequence segments that critical for LLPS (SCOPEs). In this study, we presented a novel software called dSCOPE (http://dscope.omicsbio.info) to predict the SCOPEs. To develop the predictor, we curated experimentally identified sequence segments that can drive LLPS from published literature. Then sliding sequence window based physiological, biochemical, structural and coding features were integrated by random forest algorithm to perform prediction. Through rigorous evaluation, dSCOPE was demonstrated to achieve satisfactory performance. Furthermore, large-scale analysis of human proteome based on dSCOPE showed that the predicted SCOPEs enriched various protein post-translational modifications and cancer mutations, and the proteins which contain predicted SCOPEs enriched critical cellular signaling pathways. Taken together, dSCOPE precisely predicted the protein sequence segments critical for LLPS, with various helpful information visualized in the webserver to facilitate LLPS related research.
Identification of a conserved neutralizing epitope present on spike proteins from all highly pathogenic coronaviruses
Authors: Huang Yimin , Nguyen Annalee W. , Hsieh Ching-Lin , Silva Rui , Olaluwoye Oladimeji S. , Wilen Rebecca E. , Kaoud Tamer S. , Azouz Laura R. , Qerqez Ahlam N. , Le Kevin C. , Bohanon Amanda L. , DiVenere Andrea M. , Liu Yutong , Lee Alison G. , Amengor Dzifa , Shoemaker Sophie R. , Costello Shawn M. , Marqusee Susan , Dalby Kevin N. , D’Arcy Sheena , McLellan Jason S. , Maynard Jennifer A.
Published: February 2021

Three pathogenic human coronaviruses have emerged within the last 20 years, with SARS-CoV-2 causing a global pandemic. Although therapeutic antibodies targeting the SARS-CoV-2 spike currently focus on the poorly conserved receptor-binding domain, targeting essential neutralizing epitopes on the more conserved S2 domain may provide broader protection. We report an antibody binding an epitope conserved in the pre-fusion core of MERS-CoV, SARS-CoV and SARS-CoV-2 spike S2 domains. Antibody 3A3 binds a conformational epitope with ~2.5 nM affinity and neutralizes spike from SARS-CoV, SARS-CoV-2 and variants of concern inin vitropseudovirus assays. Hydrogen-deuterium exchange mass spectrometry identified residues 980-1006 in the flexible hinge region at the S2 apex as the 3A3 epitope, suggesting 3A3 prevents the S2 conformational rearrangements required for conversion to the spike post-fusion state and virus-host cell fusion. This work defines a conserved vulnerable site on the SARS-CoV-2 S2 domain and guides the design of pan-protective spike immunogens.
Cell-type specific expression and behavioral impact of galanin and GalR1 in the locus coeruleus during opioid withdrawal
Authors: Foster Stephanie L. , Galaj Ewa , Karne Saumya L. , Ferré Sergi , Weinshenker David
Published: February 2021

The neuropeptide galanin is reported to attenuate opioid withdrawal symptoms, potentially by reducing neuronal hyperactivity in the noradrenergic locus coeruleus (LC) via galanin receptor 1 (GalR1). We evaluated this mechanism by using RNAscopein situhybridization to characterize GalR1 mRNA distribution in the dorsal pons and to compare galanin and GalR1 mRNA expression in tyrosine hydroxylase-positive (TH+) LC cells at baseline and following chronic morphine or precipitated withdrawal. We then used genetically altered mouse lines and pharmacology to test whether noradrenergic galanin (NE-Gal) modulates withdrawal symptoms. RNAscope revealed that, while GalR1 signal was abundant in the dorsal pons, 80.7% of the signal was attributable to TH-neurons outside the LC. Galanin and TH mRNA were abundant in LC cells at baseline and were further increased by withdrawal, whereas low basal GalR1 mRNA expression was unaltered by chronic morphine or withdrawal. Naloxone-precipitated withdrawal symptoms in mice lacking NE-Gal (GalcKO-Dbh) were largely similar to WT littermates, indicating that loss of NE-Gal does not exacerbate withdrawal. Complimentary experiments using NE-Gal overexpressor mice (NE-Gal OX) and systemic administration of the galanin receptor agonist galnon revealed that increasing galanin signaling also failed to alter behavioral withdrawal, while suppressing noradrenergic transmission with the alpha-2 adrenergic receptor agonist clonidine attenuated multiple symptoms. These results indicate that galanin does not acutely attenuate precipitated opioid withdrawal via an LC-specific mechanism, which has important implications for the general role of galanin in regulation of somatic and affective opioid responses and LC activity.
Faecal metabarcoding reveals pervasive long-distance impacts of garden bird feeding
Authors: Shutt Jack D , Trivedi Urmi H , Nicholls James A
Published: February 2021

Supplementary feeding of wildlife is widespread, being undertaken by more than half of households in many countries. However, the impact that these supplemental resources have is unclear, with impacts assumed to be restricted to urban ecosystems. We reveal the pervasiveness of supplementary foodstuffs in the diet of a wild bird using metabarcoding of blue tit (Cyanistes caeruleus) faeces collected in early spring from a 220km transect in Scotland with a large urbanisation gradient. Supplementary foodstuffs were present in the majority of samples, with peanut (Arachis hypogaea) the single commonest (either natural or supplementary) dietary item. Consumption rates exhibited a distance decay from human habitation but remained high at several hundred metres from the nearest household and continued to our study limit of 1.4km distant. Supplementary food consumption was associated with a near quadrupling of blue tit breeding density and a five-day advancement of breeding phenology. We show that woodland bird species using supplementary food have increasing UK population trends, while species that don’t, and/or are outcompeted by blue tits, are likely to be declining. We suggest that the impacts of supplementary feeding are larger and more spatially extensive than currently appreciated and could be disrupting population and ecosystem dynamics.
Viral evolutionary dynamics predict Influenza-Like-Illnesses in patients
Authors: Wallbank Christopher D. , Aris-Brosou Stéphane
Published: February 2021

Viral infections such as those caused by the influenza virus can put a strain on healthcare systems. However, such a burden is typically difficult to predict. In order to improve such predictions, we hypothesize that the severity of epidemics can be linked to viral evolutionary dynamics. More specifically, we posit the existence of a negative association between patients’ health and the stability of coevolutionary networks at key viral proteins. To test this, we performed a thorough evolutionary analysis of influenza viruses circulating in continental US between 2010 and 2019, assessing how measures of the stability of these coevolutionary networks correlate with clinical data based on outpatient healthcare visits showing Influenza-Like Illness (ILI) symptoms. We first show evidence of a significant correlation between viral evolutionary dynamics and increased influenza activity during seasonal epidemics, and then show that these dynamics closely follow the progression of epidemics through each season, providing us with predictive power based on genetic data collected between week 20 and week 40/52, that is one to fifteen weeks prior to peak ILI. Viral evolutionary dynamics may hence be used by health authorities to further guide non-pharmaceutical interventions.
Isolating and Cryo-Preserving Pig Skin Cells for Single Cell RNA Sequencing Study
Authors: Han Li , Jara Carlos P , Wang Ou , Thibivilliers Sandra , Wóycicki Rafał K. , Carlson Mark A. , Velander William H. , Araújo Eliana P. , Libault Marc , Zhang Chi , Lei Yuguo
Published: February 2021

The Pigskin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-Seq has been used to study mouse and human skins. However, studying pigskin with scRNA-Seq is still rare. Here we described a robust method for isolating and cryo-preserving pig single cells for scRNA-Seq. We showed that pigskin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. Also, we showed that the subsequent single cells could be cryopreserved using DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study will be very valuable for the skin research scientific community.
Artificial seawater based long-term culture of colonial ascidians
Authors: Wawrzyniak M. , Matas Serrato L.A. , Blanchoud S.
Published: February 2021

Tunicates are highly diverse marine invertebrate filter-feeders that are vertebrates’ closest relatives. These organisms, despite a drastically different body plan during their adulthood, have a tissue complexity related to that of vertebrates. Ascidians, which compose most of the Tunicata, are benthic sessile hermaphrodites that reproduce sexually through a motile tadpole larval stage. Over half of the known ascidians species are able to reproduce asexually by budding, typically leading to the formation of colonies where animals, called zooids, are interconnected through an external vascular system. In addition, colonial ascidians are established models for important biological processes including allorecognition, immunobiology, aging, angiogenesis and whole-body regeneration. However, the current paucity in breeding infrastructures limits the study of these animals to coastal regions.

To promote a wider scientific spreading and popularity of colonial ascidians, we have developed a flexible recirculating husbandry setup for their long-term in-lab culture. Our system is inspired both by the flow-through aquariums used by coastal ascidian labs, as well as by the recirculating in-lab systems used for zebrafish research. Our hybrid system thus combines colony breeding, water filtering and food culturing in a semi-automated system where specimens develop on hanging microscopy glass slides. Temperature, light/dark cycles, flow speed and feeding rates can be controlled independently in four different breeding environments to provide room for species-specific optimization as well as for running experiments. This setup is complemented with a quarantine for the acclimatization of wild isolates.

Herein we present our success in breedingBotrylloides diegensis, a species of colonial ascidians, for more than 3 years in recirculating artificial seawater over 600 km away from their natural habitat. We show that colonies adapt well to in-lab culturing provided that a suitable marine microbiome is present, and that a specific strain can be isolated, propagated and efficiently used for research over prolonged periods of time. The flexible and modular structure of our system can be scaled and adapted to the needs of specific species, such asBotryllus schlosseri, as well as of particular laboratory spaces. Overall, we show thatBotrylloides diegensiscan be proficiently bred in-land and suggest that our results can be extended to other species of colonial ascidians to promote research on these fascinating animals.

Highlights

First artificial seawater based recirculating aquaculture for colonial ascidians

Over 3 years of continuous breeding

Semi-automated setup with minimized maintenance

Good biomass production for strain propagation

4 different culture conditions for optimized breeding for species of interest
Single cell analysis of population-wide nuclear and cytosolic drug responses using high-content FRET imaging: measuring protein kinase activation in rat primary striatal neurons
Authors: Jones-Tabah Jace , Martin Ryan D. , Tanny Jason C. , Clarke Paul B.S. , Hébert Terence E.
Published: February 2021

Genetically-encoded biosensors are used to track biochemical activities in living cells by measuring changes in fluorescence emitted by one or more fluorescent proteins. In the present article, we describe the application of genetically-encoded FRET biosensors with high content microscopy to image the signaling responses of thousands of neurons in response to drug treatments. We applied this approach to reveal intercellular variation in signaling responses among cultured striatal neurons stimulated with multiple drugs. The striatum is largely composed of medium-spiny GABAergic neurons which are divided into two broad sub-types based in part on their expression of dopamine D1vs.D2 receptors. Using high content FRET imaging and immunofluorescence, we identified neuronal sub-populations with unique responses to pharmacological manipulation. Focusing on dopamine- and glutamate-regulated PKA and ERK1/2 signaling in both the cytoplasm and nucleus, we identified pronounced intercellular differences, in both the magnitude and kinetics of signaling responses to drug application. Importantly, we found that a conventional “bulk” analysis that included all cells in culture yielded a different rank order of drug potency than that revealed by our single-cell analysis. The high degree of heterogeneity that we observed at the single cell level would not have been detectable using common population-level analyses, derived for example from western blotting or plate reader-based measurements. In conclusion, our single-cell analytical approach highlights the limitations of population-level analyses, and provides a novel way to study signaling biology.
Consequences of the Nyquist-Shannon sampling criterion in Mesoscopic Multiphoton Microscopy to avail full-field sub-micron resolution resolvability
Authors: Borah Bhaskar Jyoti , Lee Jye-Chang , Chi Han-Hsiung , Hsiao Yang-Ting , Yen Chen-Tung , Sun Chi-Kuang
Published: February 2021

With a limited effective voxel rate, to date, each laser-scanning mesoscopic multiphoton microscope (MPM), despite securing an ultra-large field of view (FOV) and an ultra-high optical resolution simultaneously, experiences afundamental issue with digitization; i.e., inability to satisfy the Nyquist-Shannon sampling criterion to resolve the optics-limited sub-micron resolution over the whole FOV. Such a system either neglects the criterion degrading the digital resolution to twice the pixel size, or significantly reduces the imaging area and/or the imaging speed to respect the digitization. Here we introduce a Nyquist figure of merit parameter to assess this issue, further to comprehend a maximum aliasing-free FOV and a cross-over excitation wavelength for a laser scanning MPM system. Based on our findings we demonstrate an ultra-high voxel rate acquisition in a custom-builtmesoscopic MPM systemto exceed the Nyquist-rate for a >3800 FOV-resolution ratio while not compromising the imaging speed as well as the photon-budget.
Stimulated oxygen transport in tissue by magnetic needle acupuncture
Authors: Liu Zhu , Wen Chenyu , Zhang Shi-Li
Published: February 2021

Aim

To understand physiology of magnetic needle acupuncture by investigating O2transport in tissue during needle intervention.

Methods

O2transport in tissue is modeled by utilizing COMSOL with magnetic needle inserted into muscle tissue in a 2D porous media. The damaged tissue has been mimicked by an extracted tissue block with 1storder O2consumption rate. The convection-diffusion O2transport in the damaged tissue has been further evaluated by varying magnetic flux densityB0of the needle (0-1 T), myoglobin concentration (0-1 mM), O2tension (5-100 Torr), O2consumption rates, tissue permeability (10−12-10−6m2) and porosity (0.1-0.9).

Results

1) Active O2transport carried by interstitial flow is enhanced with the intervention of a magnetic needle by generating a high gradient magnetic field around the tip, which exerts a strong force (104N/m3) on the diamagnetic interstitial fluid to accelerate the flow. 2) This interstitial flow can reach 30 μm/s atB0= 1T and strongly correlates to the needleB0and tissue permeability. 3) The needle stirs the interstitial flow can pump O2flux by 1-2 orders of magnitude compared to that without magnetic field. 4) The enhancement of active O2transport by magnetic needle is site-specific to the tissue in the vicinity of the tip. This enhancement is more effective in edema condition with a high tissue permeability (>10−9m2).

Conclusions

The dramatic enhancement of O2transport to restore the O2mitochondria metabolism for dysfunctional muscle tissues is the fundamental physiological mechanism of magnetic needle acupuncture.
LoopViz: A uLoop Assembly Clone Verification Tool for Nanopore Sequencing Reads
Authors: Lensink Mariele , Abramson Bradley W. , Hartwick Nolan , Poire Alfonzo , Bielinski Vincent A. , Michael Todd P.
Published: February 2021

Cloning has been an integral part of most laboratory research questions and continues to be an essential tool in defining the genetic elements determining life. Cloning can be difficult and time consuming as each plasmid is unique to a particular project and each sequence must be carefully selected, cloned and sequenced to determine correctness. Loop assembly (uLOOP) is a recursive, Golden Gate-like assembly method that allows rapid cloning of domesticated DNA fragments to robustly refactor novel pathways. With uLOOP methodologies, one can clone several sequences directionally to generate a library of transcriptional units (TUs) in plasmids within a single reaction but analysis of the plasmid population has been impeded by current sequencing and analysis methods. Here we develop LoopViz, a quality control tool that quantifies and visualizes results from assembly reactions using long-read Oxford Nanopore Technologies (ONT) sequencing. LoopViz identifies full length reads originating from a single plasmid in the population, and visualizes them in terms of a user input DNA fragments file, and provides QC statistics. This methodology enables validation and analysis of cloning and sequencing reactions in less than a day, determination of the entire plasmid’s sequence, and sequencing through repetitive meta-regions that cannot be meaningfully assembled. Finally, LoopViz represents a new paradigm in determining plasmid sequences that is rapid, cost-effective and performed in-lab. LoopViz is made publicly available athttps://gitlab.com/marielelensink325/loopseq
Nanotraps for the containment and clearance of SARS-CoV-2
Authors: Chen Min , Rosenberg Jillian , Cai Xiaolei , Lee Andy Chao Hsuan , Shi Jiuyun , Nguyen Mindy , Wignakumar Thirushan , Mirle Vikranth , Edobor Arianna Joy , Fung John , Donington Jessica Scott , Shanmugarajah Kumaran , Chang Eugene , Randall Glenn , Penaloza-MacMaster Pablo , Tian Bozhi , Madariaga Maria Lucia , Huang Jun
Published: February 2021

SARS-CoV-2 enters host cells through its viral spike protein binding to angiotensin-converting enzyme 2 (ACE2) receptors on the host cells. Here we show functionalized nanoparticles, termed “Nanotraps”, completely inhibited SARS-CoV-2 infection by blocking the interaction between the spike protein of SARS-CoV-2 and the ACE2 of host cells. The liposomal-based Nanotrap surfaces were functionalized with either recombinant ACE2 proteins or anti-SARS-CoV-2 neutralizing antibodies and phagocytosis-specific phosphatidylserines. The Nanotraps effectively captured SARS-CoV-2 and completely blocked SARS-CoV-2 infection to ACE2-expressing human cell lines and primary lung cells; the phosphatidylserine triggered subsequent phagocytosis of the virus-bound, biodegradable Nanotraps by macrophages, leading to the clearance of pseudotyped and authentic virus in vitro. Furthermore, the Nanotraps demonstrated excellent biosafety profile in vitro and in vivo. Finally, the Nanotraps inhibited pseudotyped SARS-CoV-2 infection in live human lungs in an ex vivo lung perfusion system. In summary, Nanotraps represent a new nanomedicine for the inhibition of SARS-CoV-2 infection.

Highlights

Nanotraps block interaction between SARS-CoV-2 spike protein and host ACE2 receptors

Nanotraps trigger macrophages to engulf and clear virus without becoming infected

Nanotraps showed excellent biosafety profiles in vitro and in vivo

Nanotraps blocked infection to living human lungs in ex vivo lung perfusion system

Progress and Potential

To address the global challenge of creating treatments for SARS-CoV-2 infection, we devised a nanomedicine termed “Nanotraps” that can completely capture and eliminate the SARS-CoV-2 virus. The Nanotraps integrate protein engineering, immunology, and nanotechnology and are effective, biocompatible, safe, stable, feasible for mass production. The Nanotraps have the potential to be formulated into a nasal spray or inhaler for easy administration and direct delivery to the respiratory system, or as an oral or ocular liquid, or subcutaneous, intramuscular or intravenous injection to target different sites of SARS-CoV-2 exposure, thus offering flexibility in administration and treatment. More broadly, the highly versatile Nanotrap platform could be further developed into new vaccines and therapeutics against a broad range of diseases in infection, autoimmunity and cancer, by incorporating with different small molecule drugs, RNA, DNA, peptides, recombinant proteins, and antibodies.
Telomere maintenance pathway activity analysis enables tissue- and gene-level inferences
Authors: Nersisyan Lilit , Simonyan Arman , Binder Hans , Arakelyan Arsen
Published: February 2021

Telomere maintenance is one of the mechanisms ensuring indefinite divisions of cancer and stem cells. Good understanding of telomere maintenance mechanisms (TMM) is important for studying cancers and designing therapies. However, molecular factors triggering selective activation of either the telomerase dependent (TEL) or the alternative lengthening of telomeres (ALT) pathway are poorly understood. In addition, more accurate and easy-to-use methodologies are required for TMM phenotyping. In this study, we have performed literature based reconstruction of signaling pathways for the ALT and TEL TMMs. Gene expression data were used for computational assessment of TMM pathway activities and compared with experimental assays for TEL and ALT. Explicit consideration of pathway topology makes bioinformatics analysis more informative compared to computational methods based on simple summary measures of gene expression. Application to healthy human tissues showed high ALT and TEL pathway activities in testis, and identified genes and pathways that may trigger TMM activation. Our approach offers a novel option for systematic investigation of TMM activation patterns across cancers and healthy tissues for dissecting pathway-based molecular markers with diagnostic impact.
Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern
Authors: Lu Mingji , Schneider Dominik , Daniel Rolf
Published: February 2021

Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phylaActinobacteria, Proteobacteria, Firmicutes, BacteroidetesandChloroflexi.Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique genes encoding lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integral classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.