bluuebunny/crossref_metadata_2025 huggingface dataset:
4-4PREVALENCE AND ASSOCIATED RISK FACTORS OF HYPERTENSION: A CROSS-SECTIONAL STUDY IN NORTH JAKARTA PUBLIC HEALTH CENTER
Authors: Putri Lily Raudah , Lumintang Agnesstacia Vania , Handayani Luh Gede Laksmi Rahayu
Published: July 2020

Introduction:

Hypertension remains an important public health challenge around the world because it could increase the incidence of cardiovascular disease, stroke, kidney damage, and other health problem, even death. An estimated 1.13 billion people worldwide have hypertension. Most of them are living in low and middle-income countries. The prevalence of hypertension in Indonesia is increasing from 25.8% in 2013 to 34.1 % in 2018. Meanwhile, the prevalence of hypertension in Jakarta is 33.4%. With one of the global targets for the noncommunicable disease is to reduce the prevalence of hypertension 25% by 2025, it is important to know several factors that could increase the hypertension prevalence. The study's purpose was to acknowledge the prevalence and risk factors of hypertension.

Method:

This research was a cross-sectional study of 789 patients as primary data by measuring BMI and waist circumference with questionnaire encompassed identity and risk factor of hypertension. This research was held in the Public Health Center of Penjaringan District, North Jakarta.

Result:

Research outcome showed that out of 789 respondents, 260 (33%) had pre-hypertension, 265 (33,6%) had hypertension stage 1, and 142 respondents (18%) had hypertension stage 2—only 122 (15,5%) respondents who had normal tension. Based on statistical analysis, there were some factors associated with hypertension, which were smoking, body mass index, and waist circumference. Chi-square test showed p value 0.008 between hypertension and smoking. Kruskal Wallis test showed p value of 0.020 between hypertension and body mass index, and p-value 0.002 between hypertension and waist circumference. The conclusion of this research was most of the respondents had hypertension. It also revealed that smoking, an increase in body mass index, and waist circumference became the risk factors of hypertension. This could be happened due to an unhealthy lifestyle. Therefore, recommendations should be made to enhance the monitoring of blood pressure regularly and improve health promotion of hypertension risk factors.
Hemiarthroplasty Through a Direct Anterior Approach for Femoral Neck Fractures
Authors: Kain Michael S. , Willier Donald
Published: July 2020

This video demonstrates the direct anterior approach (DAA) for placement of an uncemented hemiarthroplasty for a displaced femoral neck fracture. The DAA is an intranervous and intramuscular approach that is believed to allow patients a quicker recovery and decrease the rate of dislocation. Femoral exposure is the most challenging component of the approach. In this video, the approach is performed with the assistance of the fracture table to facilitate exposure of the femur. This step-by-step description demonstrates how to expose the femur, measure for the femoral head size, and place an uncemented femoral stem in for a unipolar hemiarthroplasty. A full capsular closure is performed by reapproximating the iliofemoral ligament after reduction. This DAA video is taken from the surgeon's point of view to facilitate visualization of the anatomy and orientation of implant placement.
Antegrade Nailing for Midshaft Femur Fractures
Authors: Neiman Rafael
Published: July 2020

The standard of care for treatment of midshaft femur fractures is locked intramedullary nailing. Entry point and patient position remain variables without a single universal method agreed as optimum. Morbid obesity poses additional challenges for intramedullary nailing, where special considerations must be taken. This video demonstrates supine antegrade nailing on a fracture table for a morbidly obese patient with a midshaft bisphosphonate femur fracture.
Surgical Hip Dislocation for Small Posterior Wall Fracture After Hip Subluxation
Authors: Shahien Amir A. , Wegrzyn Katarzyna , Tornetta Paul , Kain Michael S.
Published: July 2020

This case demonstrates a recognized association between an acetabular injury pattern and underlying morphology of the hip. In the patient discussed, hyperflexion of the hip results in the engagement of the present CAM lesion, and the resulting subluxation leads to a fracture of the posterior wall and instability of the hip. This combination of pathologies was addressed with a surgical dislocation approach to address both the CAM lesion and fix the posterior wall.
Pancreatoduodenectomy: Perspectives on a Standardized Grossing Protocol for the Practicing Pathologist
Authors: Williams Margaret , Affolter Kajsa
Published: July 2020

The pancreatoduodenectomy or Whipple procedure is a complex oncologic surgical specimen with 2 dominant yet opposing standardized grossing protocols reported in the literature, the Leeds Pathology Protocol (LP) and the bivalving technique. The LP recommends the axial slicing of the pancreatic head perpendicular to the longitudinal axis of the duodenum, whereas the bivalving technique suggests sampling margins separately followed by bisecting the pancreas along the pancreatic and biliary ductal systems. An assessment can then be performed to determine which plane best serves to examine a particular tumor. This review provides a standardized grossing procedure in sufficient stepwise detail to be replicated by the practicing pathologist and is accompanied by an overview of the literature assessing strengths and limitations of both the LP and the bivalving technique. Factors that influence grossing method are discussed with diagnosis, stage, and margin status evaluated in additional detail, given their significant impact on treatment and prognosis. Consideration is given to adenocarcinoma diagnoses being dictated by the often difficult-to-determine tumor epicenter, the American Joint Commission on Cancer having recently changed their staging criteria in the eighth edition to be far more reliant on size and require enumerating lymph nodes, and the definition of a positive margin remaining controversial. An appreciation for the evidence or lack thereof allows an informed prosector to select a particular standardized method as determined by the unique characteristics of each individual tumor, which can best serve the clinician and patient.
Pulmonary Embolus of Benign Liver Tissue Following Partial Hepatectomy
Authors: Lucas Calixto-Hope G. , Kratz Johannes R. , Urisman Anatoly
Published: July 2020

We report the case of a 55-year-old man with metastatic well-differentiated neuroendocrine tumor involving the liver and lung. He underwent a left hepatectomy to resect a large mass in the liver followed by a right lung lower lobectomy 4 months later to resect a smaller mass in the lung. The histologic evaluation of the lung specimen revealed a 0.1-cm nodule of ectopic benign liver tissue within a lumen of a small pulmonary artery. Histochemical and immunohistochemical stains were consistent with benign liver and did not provide support for metastatic well-differentiated hepatocellular carcinoma. To our knowledge, this is the first documented case of pulmonary arterial embolization by benign liver tissue as a complication of hepatectomy.
Lights, Camera, CANCER: Principles of Macroscropic (Gross) Photography for Pathology Specimens
Authors: Song Linda H.
Published: July 2020

Gross photography is used both as a teaching tool for future health care workers and as a tool in a pathologist's diagnostic arsenal. Whereas gross descriptions can often be subjective and nonstandardized (and sometimes too convoluted in complex cases), photographs can play a final role in documentation. Where words might kindle an abstract imagination of a disease process, a photograph can capture both attention and understanding. There are 4 critical principles of good gross photography: (1) background surface, (2) photograph composition, (3) lighting, and (4) extra photography tools. As gross photography plays a pivotal role in both diagnosis and teaching, it is imperative to give pathologists, pathologists in training, and pathology assistants the skills and tools to execute the perfect gross photograph.
The Vanguard Study: Human Performance Evaluation of UK National Organ Retrieval Service Teams Utilizing a Single Scrub Practitioner in Multiorgan Retrieval
Authors: Morozova Gala , Martindale Amanda B. , Richards Hugh , Stirling John , McIntyre Cecelia , Currie Ian S.
Published: July 2020

Background.

The National Organ Retrieval Service (NORS) 2015 review recommended a single scrub practitioner provide support simultaneously to abdominal and cardiothoracic teams in UK multiorgan retrieval. Previously, this model had been used only by the combined abdominal and cardiac team in Scotland. This study reports the impact on performance as part of the Vanguard project, which utilized the single scrub practitioner role with 5 NORS teams, to determine applicability United Kingdom wide.

Methods.

Participants comprised members of abdominal (n = 56) and cardiothoracic (n = 54) teams attending UK thoraco-abdominal retrievals. Data were collected by validated psychometric scales to assess individual workload, anxiety, confidence, demands/coping resources, and teamwork. Additional data were collected through open comments and quantitative data describing context and outcome of retrieval.

Results.

Abdominal and cardiothoracic teams showed different responses when using single (Vanguard) or dual scrub practitioners (Standard). Vanguard configuration was associated with significantly higher anxiety for abdominal but not cardiothoracic teams. Perceived workload increased for abdominal teams during Vanguard but decreased for cardiothoracic teams. Scrub practitioners reported elevated anxiety and decreased confidence in retrievals using Vanguard configuration.

Conclusions.

This is the first large study examining human performance during organ retrieval in the United Kingdom. Despite previous regional success, this study showed a significant negative impact of the single scrub practitioner when extrapolated widely to UK teams. As a result of this study, NORS declined to implement the single scrub model. These data support the use of human performance analysis as an essential part of successful development in organ retrieval practice.
Beneficial effects of low-dose lithium on cognitive ability and pathological alteration of Alzheimer’s disease transgenic mice model
Authors: Liu Meng , Qian Ting , Zhou Wei , Tao Xiaodong , Sang Shaoming , Zhao Lei
Published: July 2020

Lithium has been shown to delay the progression of Alzheimer’s disease to reduce the prevalence of dementia. However, its narrow therapeutic index and numerous toxic effects at conventional dosage limited its long-term use to older subjects. Here, we tested the effect of low-dose lithium on cognitive impairment and pathology alterations in a mouse model of Alzheimer’s disease, the amyloid precursor protein/presenilin-1 (APP/PS1) transgenic mouse. We found that both chronic and acute administration of lithium dose-dependently increased in blood and brain tissues. Long-term administration of low-dose lithium does not affect the body weight of APP/PS1 mice, but can significantly improve spatial memory of APP/PS1 mice. Pathologically, it also reduced β-amyloid plague and p-tau levels. Therefore, our results show that long-term low-dose lithium can ameliorate cognitive dysfunction and pathological alterations of Alzheimer’s disease transgenic mice, and provide a theoretical basis for the further application of low-dose lithium in Alzheimer’s disease clinical treatment.
Naganishia floricola sp. nov., a novel basidiomycetous yeast species isolated from flowers of Sorbaria sorbifolia
Authors: Zhou Yu , Jia Bi-Si , Zhou Yu-Guang , Li Ai-Hua , Xue Lu
Published: July 2020

Two yeast strains representing a novel species in the basidiomycetous yeast genus Naganishia were isolated from flowers of Sorbaria sorbifolia collected in Beijing Olympic Forest Park, PR China. Results of multi-gene phylogenetic analysis indicated that the two strains were closely related to the type strains of Naganishia bhutanensis (CBS 6294T) and Naganishia antarctica (CBS 7687T). However, the new isolates differed from N. bhutanensis CBS 6294T by 1.79 % sequence divergence in the D1/D2 domain (11 nt substitutions and three indels), and 2.42 % (15 nt differences and one indel) to N. antarctica CBS 7687T. In the ITS region, the new isolates showed 1.15 % divergence (7 nt substitutions and one indel) to N. bhutanensis CBS 6294T and 0.92 % divergence (5 nt substitutions and no indels) to N. antarctica CBS 7687T. A phylogenetic analysis employing the sequences of six genes (D1/D2 domain of large subunit rDNA, ITS, small subunit rDNA, two subunits of the RNA polymerase II and elongation factor-1α) indicated that the novel species belonged to the genus Naganishia and formed a well-supported clade with N. bhutanensis, N. antarctica and N. indica. Moreover, the two strains differed from their closest relatives by the ability to grow on distinct carbon and nitrogen sources and ability to grow at 30 °C. On the basis of these findings, we propose a novel species in the genus Naganishia (Filobasidiales), Naganishia floricola sp. nov. (holotype CGMCC 2.5856).
Did the Indian lockdown avert deaths?
Authors: Raju Suvrat
Published: July 2020

Within the context of SEIR models, we consider a lockdown that is both imposed and lifted at an early stage of an epidemic. We show that, in these models, although such a lockdown may delay deaths, it eventually does not avert a significant number of fatalities. Therefore, in these models, the efficacy of a lockdown cannot be gauged by simply comparing figures for the deaths at the end of the lockdown with the projected figure for deaths by the same date without the lockdown. We provide a simple but robust heuristic argument to explain why this conclusion should generalize to more elaborate compartmental models. We qualitatively discuss some important effects of a lockdown, which go beyond the scope of simple models, but could cause it to increase or decrease an epidemic’s final toll. Given the significance of these effects in India, and the limitations of currently available data, we conclude that simple epidemiological models cannot be used to reliably quantify the impact of the Indian lockdown on fatalities caused by the COVID-19 pandemic.
Wolbachiaand host intrinsic reproductive barriers contribute additively to post-mating isolation in spider mites
Authors: Cruz Miguel A. , Magalhães Sara , Sucena Élio , Zélé Flore
Published: July 2020

Abstract

Wolbachiaare widespread maternally-inherited bacteria suggested to play a role in arthropod host speciation through induction of cytoplasmic incompatibility, but this hypothesis remains controversial. Most studies addressingWolbachia-induced incompatibilities concern closely-related populations, which are intrinsically compatible. Here, we used three populations of two genetically differentiated colour forms of the haplodiploid spider miteTetranychus urticaeto dissect the interaction betweenWolbachia-induced and host-associated incompatibilities, and to assess their relative contribution to post-mating isolation. We found that these two sources of incompatibility act through different mechanisms in an additive fashion. Host-associated incompatibility contributes 1.5 times more thanWolbachia-induced incompatibility in reducing hybrid production, the former through an overproduction of haploid sons at the expense of diploid daugters (ca. 75% decrease) and the latter by increasing the embryonic mortality of daughters (byca. 49%). Furthermore, regardless of cross direction, we observed near-complete F1 hybrid sterility and complete F2 hybrid breakdown between populations of the two forms, but thatWolbachiadid not contribute to this outcome. This study identifies the mechanistic independence and additive nature of host-intrinsic andWolbachia-induced sources of isolation. It suggests thatWolbachiacould drive reproductive isolation in this system, thereby potentially affecting host differentiation and distribution in the field.
Who is dying from Covid-19 in the United Kingdom? A review of cremation authorisations from a single South Wales’ crematorium
Authors: Salmon Roland , Monaghan Stephen
Published: July 2020

Background

Covid 19 is pandemic in the UK. To date only studies in the UK on hospital deaths have been published in the peer reviewed literature. Legal requirements for cremation in England and Wales require the collection of information that can be used to improve understanding of Covid 19 deaths in both hospital and community settings.

Aim

To document demographic and clinical characteristics, including likely place of infection, of individuals dying of Covid 19 to inform public health policy

Design

A comprehensive case series of deaths from Covid 19 between 6 April and 30 May.

Setting

A crematorium in South Wales

Participants

Individuals for whom an application was made for cremation.

Main outcome measures

Age, sex, date and place of death, occupation, comorbidities, where infection acquired.

Results

Of 752 cremations, 215(28.6%) were Covid-19 of which 115 (53.5%) were male and 100 (46.5%) female. The median age was 82 years, with the youngest patient being 47 years and the oldest 103 years. Over half the deaths (121/215: 56.3%) were over 80 years. Males odds of dying in hospital, rather than the community were 1.96 times that of females (95% Confidence Intervals (CI) 1.03 −3.74, p=0.054) despite being of similar age and having a similar number of comorbidities. Only 21(9.8%) of 215 patients had no comorbidities recorded. Patients dying in nursing homes were significantly older than those dying in hospital(median 88y (IQ range 82-93y) v 80y (IQ range 71-87y): p<0.0001). Patients dying in hospital had significantly more comorbidities than those dying in nursing homes (median 2: IQ range 1-3 v. 1: IQ range 1-2: p <0.001).

Conclusions

In a representative series, comprising both hospital and community deaths, persons over 80 with an average 2 comorbidities predominated. Although men and women were represented in similar proportions, men were more likely to die in hospital. Over half the infections were acquired in either hospitals or nursing and residential homes with implications for the management of the pandemic, historically and in the future.
“Scentsor”: A Whole-Cell Yeast Biosensor with an Olfactory Reporter for Low-Cost and Equipment-Free Detection of Pharmaceuticals
Authors: Miller Rachel A. , Lee Seryeong , Fridmanski Ethan J. , Barron Elsa , Pence Julia , Lieberman Marya , Goodson Holly V.
Published: July 2020

Portable and inexpensive analytical tools are required to monitor pharmaceutical quality in technology limited settings including low- and middle-income countries (LMICs). Whole cell yeast biosensors have the potential to help meet this need. However, most of the read-outs for yeast biosensors require expensive equipment or reagents. To overcome this challenge, we have designed a yeast biosensor that produces a unique scent as a readout. This inducible scent biosensor, or “scentsor,” does not require the user to administer additional reagents for reporter development and utilizes only the user’s nose to be “read.” In this manuscript, we describe a scentsor that is responsive to the hormone estradiol (E2). The best estimate threshold (BET) for E2 detection with a panel of human volunteers (n = 49) is 39 nM E2 (15 nM when “non-smellers” are excluded). This concentration of E2 is sensitive enough to detect levels of E2 that would be found in dosage forms. This manuscript provides evidence that scent has potential for use in portable yeast biosensors as a read out, particularly for use in technology-limited environments.
Immediate and long-term effects of transcranial direct-current stimulation in the mouse primary somatosensory cortex
Authors: Sánchez-León Carlos A. , Cordones Isabel , Ammann Claudia , Ausín José M. , Gómez-Climent María A. , Carretero-Guillén Alejandro , Campos Guillermo Sánchez-Garrido , Gruart Agnès , Delgado-García José M. , Cheron Guy , Medina Javier F. , Márquez-Ruiz Javier
Published: July 2020

Transcranial direct-current stimulation (tDCS) is a non-invasive brain stimulation technique consisting in the application of weak electric currents on the scalp. Although previous studies have demonstrated the clinical value of tDCS for modulating sensory, motor, and cognitive functions, there are still huge gaps in the knowledge of the underlying physiological mechanisms. To define the immediate impact as well as the after-effects of tDCS on sensory processing, we first performed electrophysiological recordings in primary somatosensory cortex (S1) of alert mice during and after administration of S1-tDCS, and followed up with immunohistochemical analysis of the stimulated brain regions. During the application of cathodal and anodal transcranial currents we observed polarity-specific bidirectional changes in the N1 component of the sensory-evoked potentials (SEPs) and associated gamma oscillations. Regarding the long-term effects observed after 20 min of tDCS, cathodal stimulation produced significant after-effects including a decreased SEP amplitude for up to 30 min, a power reduction in the 20-80 Hz range and a decrease in gamma event related synchronization (ERS). In contrast, no significant long-term changes in SEP amplitude or power analysis were observed after anodal stimulation except for a significant increase in gamma ERS after tDCS cessation. The polarity-specific differences of these long-term effects were corroborated by immunohistochemical analysis, which revealed an unbalance of GAD 65-67 immunoreactivity between the stimulated vs. non-stimulated S1 region only after cathodal tDCS. These results highlight the differences between immediate and long-term effects of tDCS, as well as the asymmetric long-term changes induced by anodal and cathodal stimulation.

Significance Statement

Here we provide a first glimpse at the immediate and long-term impact of tDCS on neural processing in alert animals. The obtained results highlight the complexity of tDCS-associated effects, which include both bidirectional as well as asymmetrical modulation depending on the polarity of the stimulation. This asymmetry suggests the implication of different mechanisms underlying the long-term effects induced by anodal and cathodal transcranial currents. Identifying and defining these effects and its associated mechanisms is crucial to help design effective protocols for clinical applications.
ANTAGONISTIC ROLES FOR ATAXIN-2 STRUCTURED AND DISORDERED DOMAINS IN RNP CONDENSATION
Authors: Singh Amanjot , Huelsmeier Joern , Kandi Arvind Reddy , Pothapragada Sai Shruti , Hillebrand Jens , Petrauskas Arnas , Agrawal Khushboo , Krishnan RT , Thiagarajan Devasena , VijayRaghavan K. , Ramaswami Mani , Bakthavachalu Baskar
Published: July 2020

Ataxin-2 is a conserved translational control protein associated with spinocerebellar ataxia type II (SCA2) and amyotrophic lateral sclerosis (ALS) as well as an important target for ALS therapeutics under development. Despite its clinical and biological significance, Ataxin-2’s activities, mechanisms and functions are not well understood. WhileDrosophilaAtaxin-2 (Atx2) mediates mRNP condensation via a C-terminal intrinsically disordered domain (cIDR), how Ataxin-2 IDRs work with structured (Lsm, Lsm-AD and PAM2) domains to enable positive and negative regulation of target mRNAs remains unclear. Using TRIBE (Targets of RNA-Binding Proteins Identified by Editing) technology, we identified and analysed Atx-2 target mRNAs in theDrosophilabrain. We show that Atx2 preferentially interacts with AU-rich elements (AREs) in 3’UTRs and plays a broad role in stabilization of identified target mRNAs. Strikingly, Atx2 interaction with its targets is dependent on the cIDR domain required for neuronal-granule formation. In contrast, Atx2 lacking its Lsm domain not only interacts more efficiently with the target mRNA identified, but also forms larger RNP granules. Providing an extensive dataset of Atx2-interacting brain mRNAs, our results demonstrate that Atx2: (a) interacts with target mRNAs within RNP granules; (b) modulates the turnover of these target mRNAs; (c) has an additional essential role outside of mRNP granules; and (d) contains distinct protein domains that drive or oppose RNP-granule assembly. These findings increase understanding of neuronal translational control mechanisms and inform Ataxin-2-based interventions in development for SCA2 and ALS.
KDM6B promotes activation of the oncogenic CDK4/6-pRB-E2F pathway by maintaining enhancer activity in MYCN-amplified neuroblastoma
Authors: D’Oto Alexandra , Fang Jie , Jin Hongjian , Xu Beisi , Singh Shivendra , Mullasseril Anoushka , Jones Victoria , Abu-Zaid Ahmed , von Buttlar Xinyu , Cooke Bailey , Hu Dongli , Shohet Jason , Murphy Andrew J , Davidoff Andrew M , Yang Jun
Published: July 2020

The H3K27me2/me3 histone demethylase KDM6B is over-expressed in neuroblastoma and is essential to neuroblastoma cell survival. While the KDM6B inhibitor, GSK-J4, has shown activity inin vitroandin vivopreclinical models, the mechanism of action remains poorly defined. We demonstrate that genetic and pharmacologic inhibition of KDM6B downregulates the pRB-E2F transcriptome andMYCNexpression. Chemical genetic analyses show that high expression of the E2F transcriptome is positively correlated with sensitivity of cancer cells to GSK-J4. Mechanistically, inhibition of KDM6B activity 1) reduces the chromatin accessibility of E2F target genes andMYCN, 2)selectively leads to an increase of H3K27me3 but a decrease of the enhancer mark H3K4me1 at the CTCF and BORIS binding sites, which may, consequently, disrupt the long-range chromatin interaction ofMYCNand E2F target genes, and 3) phenocopies the transcriptome induced by the specific CDK4/6 inhibitor palbociclib. Overexpression of CDK4/6 orRb1knockout confers neuroblastoma cell resistance to both palbociclib and GSK-J4. A gene signature targeted by KDM6B inhibition is associated with poor survival of patients with neuroblastoma regardless of theMYCNstatus. These data indicate that KDM6B activity promotes an oncogenic CDK4/6-pRB-E2F pathway in neuroblastoma cells via H3K27me3-dependent enhancer-promoter interactions, providing a rationale to target KDM6B for high-risk neuroblastoma.
An open-source experimental framework for automation of high-throughput cell biology experiments
Authors: Katunin Pavel , Cadby Ashley , Nikolaev Anton
Published: July 2020

Modern data analysis methods, such as optimisation algorithms or machine and deep learning, have been successfully applied to a number of biological, biotechnological and medical questions. For these methods to be efficient, a large number of high quality experiments need to be conducted, which requires a high degree of automation. Here we report an open-source hardware that allows for automatic high-throughput generation of large amounts of cell biology data. The hardware consists of an automatic XY-stage for moving a multiwell plate containing growing cells; a perfusion manifold allowing application of up to 8 different solutions; and a small epifluorescent microscope. It is extremely cheap (approximately £400 without and £2500 with a fluorescent microscope) and is easily customizable for individual experimental needs. We demonstrate the usability of this platform with high-throughput Ca2+ imaging and large-scale labelling experiments.

Key points

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We present an open source framework for automation of cell biology experiments

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The framework consists of an XY platform, application of up to 8 solutions and a small epifluorescent microscope with autofocusing

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Very cheap (£400 without a fluorescent microscope and £2500 with a fluorescent microscope), customisable,

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Can be used in a variety of biological applications such as imaging of fluorescent reporters, optimisation of treatment conditions and fluorescent labelling
Relationships between macro-fungal dark diversity and habitat parameters using LiDAR
Authors: Valdez Jose W. , Brunbjerg Ane Kirstine , Fløjgaard Camilla , Dalby Lars , Clausen Kevin K. , Pärtel Meelis , Pfeifer Norbert , Hollaus Markus , Wimmer Michael H. , Ejrnæs Rasmus , Moeslund Jesper Erenskjold
Published: July 2020

Despite the important role of fungi for ecosystems, relatively little is known about the factors underlying the dynamics of their diversity. Moreover, studies do not typically consider their dark diversity: the species absent from an otherwise suitable site. Here, we examined potential drivers of local fungal dark diversity in temperate woodland and open habitats using LiDAR and in-situ field measurements, combined with a systematically collected and geographically comprehensive macro-fungi and plant data set. For the first time, we also estimated species pools of fungi by considering both plant and fungi co-occurrences. The most important LiDAR variables for modelling fungal dark diversity were amplitude and echo ratio, which are both thought to represent vegetation structure. These results suggest that the local fungal dark diversity is highest in production forests like plantations and lowest in more open forests and in open habitats with little woody vegetation. Plant species richness was the strongest explanatory factor overall and negatively correlated with local fungal dark diversity. Soil fertility showed a positive relationship with dark diversity in open habitats. These findings may indicate that the local dark diversity of macro-fungi is highest in areas with a relatively high human impact (typically areas with low plant species richness and high soil fertility). Overall, this study brings novel insights into local macro-fungi dark diversity patterns, suggesting that a multitude of drivers related to both soil and vegetation act in concert to determine fungal dark diversity.
Development of a free radical scavenging probiotic to mitigate coral bleaching
Authors: Dungan Ashley M. , Bulach Dieter , Lin Heyu , van Oppen Madeleine J. H. , Blackall Linda L.
Published: July 2020

Corals are colonized by symbiotic microorganisms that exert a profound influence on the animal’s health. One noted symbiont is a single-celled alga (from the familySymbiodiniaceae), which provides the coral with most of its fixed carbon. During thermal stress, hyperactivity of photosynthesis results in a toxic accumulation of reactive oxygen species (ROS). If not scavenged by the antioxidant network, ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating; this process is known as bleaching. Our goal was to construct a probiotic comprised of host-associated bacteria able to neutralize free radicals such as ROS. Using the coral model, the anemoneExaiptasia diaphana, and pure bacterial cultures isolated from the model animal, we identified six strains with high free radical scavenging ability belonging to the familiesAlteromonadaceae, Rhodobacteraceae, Flavobacteriaceae, andMicrococcaceae. In parallel, we established a “negative” probiotic consisting of genetically related strains with poor free radical scavenging capacities. From their whole genome sequences, we explored genes of interest that may contribute to their potential beneficial roles, which may help facilitate the therapeutic application of a bacterial probiotic. In particular, the occurrence of key pathways that are known to influence ROS in each of the strains has been inferred from the genomes sequences and are reported here.

IMPORTANCE

Coral bleaching is tightly linked to the production of reactive oxygen species (ROS), which accumulates to a toxic level in algae-harboring host cells leading to coral-algal dissociation. Interventions targeting ROS accumulation, such as the application of exogenous antioxidants, have shown promise for maintaining the coral-algal partnership. With the feasibility of administering antioxidants directly to corals being low, we aim to develop a probiotic to neutralize toxic ROS during a thermal stress event. This probiotic can be tested with corals or a coral model to assess its efficacy in improving coral resistance to environmental stress.
Efficient and stable metabarcoding sequencing from DNBSEQ-G400 sequencer examined by large fungal community analysis
Authors: Sun Xiaohuan , Wang Jingjing , Fang Chao , Li Jiguang , Han Mo , Wei Xiaofang , Zheng Haotian , Luo Xiaoqing , Gong Meihua , Xiao Liang , Hu Yuehua , Song Zewei
Published: July 2020

Metabarcoding has become the de facto method for characterizing the structure of microbial communities in complex environmental samples. To determine how sequencing platform may influence microbial community characterization, we present a large-scale comparison of two sequencing platforms; Illumina MiSeq and a new platform DNBSEQ-G400 developed by MGI Tech. The accuracy of DNBSEQ-G400 on bacterial and fungal mock samples and compared sequencing consistency and precision between DNBSEQ-G400 and MiSeq platforms by sequencing the fungal ITS2 region from 1144 soil samples with 3 technical replicates. The DNBSEQ-G400 showed a high accuracy in reproducing mock communities containing different proportions of bacteria and fungi, respectively. The taxonomic profiles of the 1144 soil samples generated by the two DNBSEQ-G400 modes closely resembled each other and were highly correlated with those generated by the MiSeq platform. Analyses of technical replicates demonstrated a run bias against certain taxa on the MiSeq but not DNBSEQ-G400 platform. Based on lower cost, greater capacity, and less bias, we conclude that DNBSEQ-G400 is an optimal platform for short-term metabarcoding of microbial communities.

IMPORTANCE

Experimental steps that generate sequencing bias during amplicon sequencing have been intensively evaluated, including the choice of primer pair, polymerase, PCR cycle and technical replication. However, few studies have assessed the accuracy and precision of different sequencing platforms. Here, we compared the performance of newly released DNBSEQ-G400 sequencer with that of the commonly used Illumina MiSeq platform by leveraging amplicon sequencing of a large number of soil samples. Significant sequencing bias among major fungal genera was found in parallel MiSeq runs, which can be easily neglected without the use of sequencing controls. We emphasize the importance of technical controls in large-scale sequencing efforts and provide DNBSEQ-G400 as an alternative with increased sequencing capacity and more stable reproducibility for amplicon sequencing.
Modeling COVID-19 for lifting non-pharmaceutical interventions
Authors: Koehler Matt , Slater David M. , Jacyna Garry , Thompson James R.
Published: July 2020

As a result of the COVID-19 worldwide pandemic, the United States instituted various non-pharmaceutical interventions (NPIs) in an effort to the slow the spread of the disease. Although necessary for public safety, these NPIs can also have deleterious effects on the economy of a nation. State and federal leaders need tools that provide insight into which combination of NPIs will have the greatest impact on slowing the disease and at what point in time it is reasonably safe to start lifting these restrictions to everyday life. In the present work, we outline a modeling process that incorporates the parameters of the disease, the effects of NPIs, and the characteristics of individual communities to offer insight into when and to what degree certain NPIs should be instituted or lifted based on the progression of a given outbreak of COVID-19.
The Ceratodon purpureus genome uncovers structurally complex, gene rich sex chromosomes
Authors: Carey Sarah B. , Jenkins Jerry , Lovell John T. , Maumus Florian , Sreedasyam Avinash , Payton Adam C. , Shu Shenqiang , Tiley George P. , Fernandez-Pozo Noe , Barry Kerrie , Chen Cindy , Wang Mei , Lipzen Anna , Daum Chris , Saski Christopher A. , McBreen Jordan C. , Conrad Roth E. , Kollar Leslie M. , Olsson Sanna , Huttunen Sanna , Landis Jacob B. , Burleigh J. Gordon , Wickett Norman J. , Johnson Matthew G. , Rensing Stefan A. , Grimwood Jane , Schmutz Jeremy , McDaniel Stuart F.
Published: July 2020

Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration1,2. The correlation between suppressed recombination and degeneration is clear in animal XY systems1,2, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions3,4. Here we test for degeneration in the bryophyte UV sex chromosome system through genomic comparisons with new female and male chromosome-scale reference genomes of the mossCeratodon purpureus. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.
Epitope-Based Peptide Vaccine Design Against Fructose Bisphosphate Aldolase of Candida Glabrata: An Immunomics Approach
Authors: Elhasan LM Elamin , Hassan Mohamed B. , Elhassan Reham M. , Abdelrhman Fatima A. , Salih Essam A. , Ibrahim. H Asma , Mohamed Amna A. , Osman Hozaifa S. , Khalil Marwa Saad M. , Alsafi Athar A. , Idris Abeer Babiker , Hassan Mohamed A.
Published: July 2020

Background

Candida glabratais a human opportunistic pathogen that can cause life-threatening systemic infections. Although, there are multiple effective vaccines against fungal infections, and some of these vaccines were engaged in different stages of clinical trials, none of them yet approved by (FDA).

Aim

To predict the most conserved and immunogenic B- and T-cell epitopes from the Fructose Bisphosphate aldolase (Fba1) protein ofC. glabrata.

Materials and Methods

13C. glabrataFructose bisphosphate aldolase protein sequences (361amino acid) were retrieved from NCBI and several in silico tools presented in the IEDB server for predicting peptides were used and homology modeling and molecular docking were performed.

Result

The promising B-cell Epitopes were AYFKPH, VDKESLYTK, and HVDKESLYTK. While, promising peptides which have the high affinity to MHC I binding were: AVHEALAPI, KYFKRMAAM, QTSNGGAAY, RMAAMNQWL and YFKEHGEPL. Two peptides (LFSSHMLDL and YIRSIAPAY) were noted to have the highest affinity to MHC class II that interact with 9 MHC class II alleles. The molecular Docking revealed the epitopes QTSNGGAAY and LFSSHMLDL have the high binding energy to MHC molecules

Conclusion

The epitope-based vaccines predicted by using immunoinformatics tools have remarkable advantages over the conventional vaccines that they are more specific, less time consuming, safe, less allergic and more antigenic. Further in vivo and in vitro experiments are needed to prove the effectiveness of the best candidates epitopes (QTSNGGAAY and LFSSHMLDL). To the best of our knowledge, this is the first study that has predicted B- and T-cells epitopes from Fba1 protein by using in silico tools in order to design an effective epitope-based vaccine againstC. galabrata.
Predicting Tumor Response to Drugs based on Gene-Expression Biomarkers of Sensitivity Learned from Cancer Cell Lines
Authors: Li Yuanyuan , Umbach David M. , Krahn Juno , Shats Igor , Li Xiaoling , Li Leping
Published: July 2020

Human cancer cell line profiling and drug sensitivity studies provide valuable information about the therapeutic potential of drugs and their possible mechanisms of action. The goal of those studies is to translate the findings fromin vitrostudies of cancer cell lines intoin vivotherapeutic relevance and, eventually, patients’ care. Tremendous progress has been made. In this work, we built predictive models for 453 drugs using data on gene expression and drug sensitivity (IC50) from cancer cell lines. We identified many known drug-gene interactions and uncovered several potentially novel drug-gene associations. Importantly, we further applied these predictive models to ∼17,000 bulk RNA-seq samples from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database to predict drug sensitivity for both normal and tumor tissues. We created a web site for users to visualize and download our predicted data (https://edelgene.niehs.nih.gov/cancerRxTissue). Using trametinib as an example, we showed that our approach can faithfully recapitulate the known tumor specificity of the drug. We further demonstrated that our approach can predict drugs that 1) are tumor-type specific; 2) elicit higher sensitivity from tumor compared to corresponding normal tissue; 3) elicit differential sensitivity across breast cancer subtypes. If validated, our predictions could have clinical relevance for patients’ care.
Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile
Authors: Bravo Veronica , Katz Assaf , Porte Lorena , Weitzel Thomas , Varela Carmen , Gonzalez-Escalona Narjol , Blondel Carlos J.
Published: July 2020

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n=81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for over a third of the genome sequences available of clinical strains from South America. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

AUTHOR SUMMARY

Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. In this study, we performed an in-depth analysis of the genome sequences of 69 C. jejuni and 12 C. coli clinical strains isolated from Chile, which account for over a third of the sequences from clinical strains available from South America. We identified a high genetic diversity among C. jejuni strains and the unexpected identification of clade 3 C. coli strains, which are infrequently isolated from humans in other regions of the world. Most strains harbored the virulence factors described for Campylobacter. While ∼40% of strains harbored mutation in the gyrA gene described to confer fluoroquinolone resistance, very few strains encoded the determinants linked to macrolide resistance, currently used for the treatment of campylobacteriosis. Our study contributes to our knowledge of this important foodborne pathogen providing valuable data from South America.
Nucleosomal association and altered interactome underlie the mechanism of cataract caused by the R54C mutation of αA-crystallin
Authors: Ahsan Saad M. , Raman Bakthisaran , Ramakrishna Tangirala , Rao Ch. Mohan
Published: July 2020

The small heat shock protein (sHSP), αA-crystallin, plays an important role in eye lens development. It has three distinct domainsviz. the N-terminal domain, α-crystallin domain and the C-terminal extension. While the α-crystallin domain is conserved across the sHSP family, the N-terminal domain and the C-terminal extension are comparatively less conserved. Nevertheless, certain arginine residues in the N-terminal region of αA-crystallin are conserved across the sHSP family. Interestingly, most of the cataractcausing mutations in αA-crystallin occur in the conserved arginine residues. In order to understand the molecular basis of cataract caused by the R54C mutation in human αA-crystallin, we have compared the structure, chaperone activity, intracellular localization, effect on cell viability and “interactome” of wild-type and mutant αA-crystallin. Although R54CαA-crystallin exhibited slight changes in quaternary structure, its chaperone activity was comparable to that of the wild-type. When expressed in lens epithelial cells, R54CαA-crystallin triggered a stress-like response, resulting in nuclear translocation of αB-crystallin, disassembly of cytoskeletal elements and activation of Caspase 3, leading to apoptosis. Comparison of the “interactome” of the wild-type and mutant proteins revealed a striking increase in the interaction of the mutant protein with nucleosomal histones (H2A, H2B, H3 and H4). Using purified chromatin fractions, we show an increased association of R54CαA-crystallin with these nucleosomal histones, suggesting the potential role of the mutant in transcriptional modulation. Thus, the present study shows that alteration of “interactome” and its nucleosomal association, rather than loss of chaperone activity, is the molecular basis of cataract caused by the R54C mutation in αA-crystallin.
The Linear Element is a Stable Structure Along the Chromosome Axis in Fission Yeast
Authors: Ding Da-Qiao , Matsuda Atsushi , Okamasa Kasumi , Hiraoka Yasushi
Published: July 2020

Chromosomes structure changes dramatically upon entering meiosis to ensure the successful progression of meiosis-specific events. During this process, a multilayer proteinaceous structure called synaptonemal complex (SC) is formed in many eukaryotes. Instead, in the fission yeastSchizosaccharomyces pombe, linear elements (LinEs), which are structures related to an axial element of SC, form on the meiotic cohesin-based chromosome axis and are required for the formation of DNA double-strand breaks. In contrast to the well-organized SC structure, LinE structure had been observed only by silver-stained electron micrographs or in immuno-fluorescence stained spread nuclei. Thus, their fine structure and dynamics in intact living cells remain to be elucidated. In this study, we performed live cell imaging with wide-field fluorescence microscopy as well as 3D structured illumination microscopy (3D-SIM) for the four components of LinE, the Rec10, Rec25, Rec27 and Mug20. We found that LinEs consist of threads formed along the chromosome axes during the meiotic prophase. Rec10 binds to the chromosome itself and shapes into LinEs only in the presence of all the other LinE components. Rec25, Rec27, and Mug20 attach to the chromosome in the presence of Rec10. LinEs are stable in a short-time treatment with 1,6-hexanediol; and fluorescence recovery after photobleaching (FRAP) experiment reveals slow recovery from photobleaching, indicating a stable property of LinEs.