bluuebunny/crossref_metadata_2025 huggingface dataset:
Synergistic degradation of a biodegradable plastic film by a marine microbial community
Authors: Meyer-Cifuentes Ingrid , Werner Johannes , Heuer Anja , Jehmlich Nico , Öztürk Basak
Published: July 2020

Background: The need for replacing conventional plastics has led to an increase of the use biodegradable plastics. Most biodegradable plastic materials are certified for compostability, and their degradation mechanisms by marine bacterial communities, is still largely unknown.

Methods: Bacterial communities that degrade a PBAT-based biodegradable film (PF) were enriched from marine samples collected from the Mediterranean (Greece and Italy) and North Sea (Germany). DNA, RNA and proteins were extracted simultaneously from cultures that were starved and induced with biodegradable films, for metagenomic, transcriptomic and proteomic analyses. Mineralization of the films was assessed by CO2 evolution and film disintegration was physicochemically assessed.

Results: Within the enriched marine communities, Alphaproteobacteria and Gammaproteobacteria were the most abundant classes. Among these groups, Marinobacter was the most predominant genus on the PF film. Hydrolases similar to PETases, MHETases and terephthalic acid dioxygenases, the enzymes needed for polyethylene terephthalate (PET) degradation, were expressed when communities were exposed to the biodegradable PF film. The PETases-like hydrolases (Ple) belonged to Marinobacter, MHETases-like hydrolases (Mle) to Marinobacter and Pseudooceanicola species, and the putative terephtalate dioxygenases (Tph) to Saccharospirillum and to a α-proteobacterium candidate. Ple proteins were mainly abundant and upregulated on the PF film while Mle and Tph were abundant in the free-living fraction. Around 60% of the tested biodegradable plastic was converted to CO2 and no traces of the film were detected after the mineralization was complete.

Conclusion: Biodegradable plastics degradation is achieved synergistically by labour division among specialized film-attached and free-living bacteria. Ultimately, their complex interaction leads to the complete mineralization of a biodegradable plastic.
Impact of Amoxicillin treatment on E. coli in dairy cow faeces
Authors: Marsh Caleb , Whigham Imogen , Sherwin Ginny , Jones Michael
Published: July 2020

Introduction: There has been a global drive for increased antimicrobial stewardship. In the UK, this drive has focused on decreased usage of antimicrobials, specifically HP-CIAs. It is well known that antimicrobials are selection drivers for antimicrobial resistance. How a given dose will impact the prevalence of resistance in a microbiome, and therefore the associated risk of a resistant infection is less understood. Questions also remain around the impact of antimicrobial therapy on resistance across a herd, if selection occurs within an animal receiving treatment, what is the potential risk of this resistance spreading throughout other animals?

Methods:
E. COLI ISOLATION Tryptone Bile X-Glucuronide (TBX) media was used for selective growth of non – toxigenic E. coli from dairy cow faeces. SUSCEPTIBILITY TESTING EUCAST Disk Diffusion testing guidelines were followed to determine susceptibility of faecal isolates to a panel of 8 antimicrobials from 5 different classes. ISOLATE FINGERPRINTING To determine clonality of faecal isolates ERIC-PCR was used as an efficient method to provide a genomic fingerprint.

Results This work is ongoing. Current work suggests that low frequency Amoxicillin treatment has no significant selection for resistance. However, there appears to be some instances of co-selection for Streptomycin, Tetracycline and Sulphonamide resistance, and several multi drug resistance isolates have been identified. More work needs to be done to confirm the impact of low frequency Amoxicillin treatment on E. coli resistance and identify the mechanism behind suspected co-selection and multi drug resistance.
Assessment of Recycling-derived Fertilizers as an Alternative to Mineral Fertilizers – Effects on the Soil Microbiome
Authors: Deinert Lea , Ikoyi Israel , Schmalenberger Achim
Published: July 2020

Phosphorus (P) is an essential macronutrient for all living organisms and is applied as fertilizer in agroecosystems to improve crop growth. Recycling-derived fertilizers (RDFs) have been developed for nutrient recovery from Europe’s largest waste streams as a sustainable alternative to this finite resource. The impact of four RDFs (two ashes, two struvites) on the soil microbiome in comparison with a P-free control and triple super phosphate (TSP) as mineral fertilizer was investigated in a pot trial and a subsequent microcosm trial (subset of samples). For both experiments perennial ryegrass was cultivated for 54 days. The pot trial was conducted at P fertilization rates of 20 and 60 kg P ha-1 in quadruplicates. After the pot harvest the bulk soil was stored until the microcosm trial was conducted, using the control, TSP and the two ashes at 60 kg P ha-1 in six replicates. Pot trial results showed highest P bioavailability from struvites at high P rates, also resulting in higher biomass yield on average. Furthermore, P solubilization capabilities from tri-calcium phosphate was enhanced in the RDFs treatments, while the TSP treatments were negatively affected. For the microcosm trial, most probable number (MPN) analysis showed that phytate-utilizing bacterial abundance was significantly increased in one of the ashes and had also remained higher in the RDF treatments after storage. Understanding the effects of recycling-derived fertilizer application on the soil P cycle is vital for developing a more sustainable agriculture.
Structural investigation of cyclic nucleotide binding proteins from Trypanosoma cruzi
Authors: Ferri Gabriel , Edreira Martin , Campeotto Ivan
Published: July 2020

Fora targeted therapy of Trypanosomiasis, new antiparasitic drugs should be specifically directed against essential pathways in the parasite life cycle. Among these potential targets are signal transduction pathways, which have remained largely unexplored in Trypanosoma species. Of special interest is cAMP-mediated signaling, since cAMP has been shown to play critical roles in the life cycle of T. cruzi and in host cell during invasion. The presented research focuses on the identification and characterisation of novel cAMP response proteins (CARPs) in T. cruzi by using a multi disciplinary approach involving the parasitology group of Dr Martin Edreira (University of Buenos Aires, Argentina) and the structural biology group of Dr Ivan Campeotto (University of Leicester, UK). The aim of the project is not only to increase our knowledge about T. cruzi biology but also to target CARPs for the design and development of novel therapeutic agents against Chagas disease. To date, protein crystals of one of the members of the CARP family have been obtained, paving the way for structure determination and for a structure-based drug design approach.
Antimicrobial resistance: Transdisciplinary research on humans, antimicrobials and microbes
Authors: de Lima Hutchison Coll , Núñez Andrea
Published: July 2020

Calls for action on antimicrobial resistance (AMR) have existed almost as early as the discovery of penicillin and the sulpha drugs. Since then solutions to AMR have circled around the development of new antimicrobials and the rationalisation of their use via various configurations of regulation of access and distribution, promotion of diagnostics and education of prescribers and consumers. Research by historians and social scientists (HSS) are increasingly demonstrating the various limitations and unintended consequences of many of these approaches, while also seeking to propose not only different ways to study AMR as a problem, but also address it. Part of this, involves serious engagement with microbiological insights (i.e. related to the microbiome) and methods to move beyond the impasses of outdated concepts (e.g. germ theory), methodological reductionism and disciplinary boundaries. Based on our empirical research on AMR and human microbiome science, we demonstrate how AMR is a transdisciplinary problem requiring contributions from HSS’s research and expertise in order to devise socially meaningful and microbiologically effective solutions. We have identified four areas where such contributions would be beneficial: (1) policies (e.g. AMR policies still assume germ theory and operate within silos); (2) AMR solutions are human centred (i.e. neglect of the microbiome and pay limited attention to other nonhumans) vs one health; (3) epidemiological variables and microbiological discourse (i.e. often employ outdated anthropological and philosophical concepts, such as westernised, modern, traditional); (4) Rhetorics and lexicon (i.e. can be morally and conceptually simplistic, like ‘war’, ‘sweets’, ‘good’/’bad’ bugs, ‘irrational’).
Phenotypic characterization and ecological succession of microorganisms during the fermentation of Cassava and Maize
Authors: Ukwuru Michael , Kalu Achi Ome , Nnambuihe Ekwenye Uchechi
Published: July 2020

Fermented foods are consumed by a very large population in Africa but the products have many drawbacks ranging from shelf life instability to contamination and toxicity. These foods therefore require an upgrade through improved fermentation processes. This work determined the phenotypic characteristics of the fermenting microorganisms and microbial ecological succession during fermentation of cassava and maize to determine the predominant fermenting microorganisms. Cassava roots and maize grains were fermented using the traditional method of processing them into fufu and ogi for 72 h and 48 h respectively. Samples were drawn every 12 h for analysis. Enumeration and characterization of lactic acid bacteria were carried out on MRS medium with subsequent microscopic examination, physiological, biochemical reaction tests and API 50 CH gallery. Yeast isolates were identified by their morphological characteristics. Thirteen lactic acid bacteria were isolated from the fermenting cassava and 6 from the fermenting maize. The Isolates were Gram positive and catalase negative. Lactobacillus plantarum, L. fermentum and L. pentusus predominated in both fermentations while Candida tropicalis, C. krusei and Saccharomyces cerevisae also predominated in both fermentations. Candida inconspicuo was found only in cassava fermentation. The results of this work revealed the microbial ecology of fermented cassava and maize which is a prerequisite to the understanding needed to develop a multifunctional starter culture for these fermentations for their upgrade.

Keywords: Cassava, Maize, Fermentation, lactic acid bacteria, Yeasts.
Galleria mellonella – a novel infection model for the study of Neisseria gonorrhoeae virulence and pathogenicity”
Authors: Dijokaite Aiste , Humbert Victoria-Maria , Christodoulides Myron
Published: July 2020

Gonorrhea is the second most commonly reported notifiable sexually transmitted disease in the world. Neisseria gonorrhoeae causes 78 million cases annually of gonorrhoea worldwide. There are no vaccines and antibiotic-resistant organisms are circulating rapidly. The estradiol-treated female mouse model is the only animal model available for studying the host response against gonococci and biological significance of host-restricted bacterial-host cell interactions observed in vitro. However, mouse models have limitations such as cost, time and ethics. Therefore, there is an urgent need for the development of new alternative in vivo models. The Galleria mellonella larval model is a simple, widely available, cost-effective, and powerful tool for studying microbial infections prior to any vertebrate animal testing. Here we report, for the first time, that G. mellonella can be used as an infection model for Neisseria spp., focusing particularly on N. gonorrhoeae. We demonstrated dose-dependent larval death and recovery of viable gonococci from the host, visualised host-pathogen interactions using histopathology and confirmed the importance of insect haemocytes as an innate immune cell during infection. The model was also used to test the efficacy of antibiotics used to treat gonorrhoea. Our results demonstrate that G. mellonella can be used as a model to study pathogenesis and virulence of gonococcal infection in addition to rapid in vivo testing of antimicrobials.
Reversal of Epigenetic Age with Diet and Lifestyle in a Pilot Randomized Clinical Trial
Authors: Fitzgerald Kara N. , Hodges Romilly , Hanes Douglas , Stack Emily , Cheishvili David , Szyf Moshe , Henkel Janine , Twedt Melissa W. , Giannopoulou Despina , Herdell Josette , Logan Sally , Bradley Ryan
Published: July 2020

Manipulations to set back biological age and extend lifespan in animal models are well established, and translation to humans has begun. The length of human life makes it impractical to evaluate results by plotting mortality curves, so surrogate markers of age have been suggested and, at present, the best established surrogates are DNA methylation clocks. Herein we report on a randomized, controlled clinical trial designed to be a first step in evaluating the effect of a diet and lifestyle intervention on biological age. Compared to participants in the control group (n=20), participants in the treatment group tested an average 3.23 years younger at the end of the eight-week program according to the Horvath DNAmAge clock (p=0.018). Those in the treatment group (n=18) tested an average 1.96 years younger at the end of the program compared to the same individuals at the beginning with a strong trend towards significance (p=0.066 for within group change). This is the first such trial to demonstrate a potential reversal of biological age. In this study, the intervention was confined to diet and lifestyle changes previously identified as safe to use. The prescribed program included multiple components with documented mechanistic activity on epigenetic pathways, including moderate exercise, breathing exercises for stress, and a diet rich in methyl donor nutrients and polyphenols.
Feasibility and sociopsychological impact of video consultations in medical oncology - a randomized controlled open label trial
Authors: Walle Thomas , Erdal Erkin , Mühlsteffen Leon , Singh Hans Martin , Gnutzmann Editha , Grün Barbara , Hofmann Helene , Ivanova Alexandra , Köhler Bruno , Korell Felix , Mavratzas Athanasios , Mock Andreas , Pixberg Constantin Frederic , Schult David , Starke Helen , Steinebrunner Niels , Woydack Lena , Schneeweiss Andreas , Dietrich Mareike , Jäger Dirk , Krisam Johannes , Kather Jakob N. , Winkler Eva C.
Published: July 2020

Background

Mobile phone video call applications generally did not undergo testing in randomized controlled clinical trials prior to their implementation in patient care regarding the rate of successful patient visits and impact on the physician-patient relationship.

Methods

The NCT MOBILE trial was a monocentric open-label randomized controlled clinical trial of patients with solid tumors undergoing systemic cancer therapy with need of a follow-up visit with their consulting physician at outpatient clinics. 66 patients were 1:1 randomized to receive either a standard in-person follow-up visit at outpatient clinics or a video callviaa mobile phone application. The primary outcome was feasibility defined as the number of successful appointments at the first follow up visit. Secondary outcomes included success rate of further video calls, time spent by patient and physician, patient satisfaction, and quality of physician-patient relationship.

Findings

Success rate of the first follow up visit in the intention-to-treat cohort was 87.8% for in-person visits and 78.7% for video calls (p=0.51, RR=0.88-1.43 95%CI). The most common reasons for failure were software incompatibility (12%) in the video call and no-show (6%) in the in-person visit arm. The success rate for further video visits was 91.6% (11 of 12 calls). Standardized patient questionnaires showed significantly decreased total time spent and less direct costs for patients (Δ95 to 246min 95%CI, Δ4.8 to 23.9€ 95%CI) and comparable time spent for physicians in the video call arm (Δ-6.4 to 5.4min, 95%CI). Doctor-patient relationship quality mean scores assessed by the validated standardized “questionnaire on quality of physician-patient interaction”(QQPPI) were higher in the video call arm (video call/in-person = 1.12 fold, p=0.02).

Interpretation

Follow-up visits with the tested mobile phone video call application were feasible but software compatibility should be critically evaluated.

Trial registration

Retrospectively registered in the German Clinical Trials Register DRKS00015788, 26thOctober 2018
A simplified SARS-CoV-2 detection protocol for research laboratories
Authors: Paz Sean , Mauer Christopher , Ritchie Anastasia , Robishaw Janet D. , Caputi Massimo
Published: July 2020

Widespread testing is required to limit the current public health crisis caused by the COVID-19 pandemic. Multiple tests protocols have been authorized by the food and drugs administration under an emergency use authorization (EUA). The majority of these protocols are based on the gold-standard RT-qPCR test pioneered by the U.S. Centers for Disease Control and Prevention. However, there is still a widespread lack of testing in the US and many of the clinical diagnostics protocols require extensive human labor and materials, such as RNA extraction kits, that could face supply shortages and present biosafety concerns. Given the need to develop alternative reagents and approaches to allow nucleic-acid testing in the face of heightened demand and potential shortages, we have developed a simplified SARS-CoV-2 testing protocol adapted for its use in laboratory research with minimal molecular biology equipment and expertise. The protocol requires minimal BSL1 biosafety level precautions and facilities.
Decontamination of N95 masks against coronavirus: a scoping review
Authors: Sarkis-Onofre Rafael , do Carmo Borges Rafaela , Demarco Giulia , Dotto Lara , Schwendicke Falk , Demarco Flávio Fernando
Published: July 2020

Background

At present, it remains uncertain which method to decontaminate N95 is most suitable and should be recommended to healthcare professionals worldwide.

Objectives

The aim of this scoping review was to map and compile the available evidence about the effectiveness of decontaminating N95 masks against coronavirus.

Methods

We selected studies written in English assessing or discussing decontamination strategies of N95 masks against coronavirus. The search and study screening were performed in PubMed and SCOPUS by two independent researchers. A descriptive analysis was performed considering the study design of included studies.

Results

We included nineteen studies. Eight articles were letter to the editors, five were in vitro studies, three were literature reviews, and three were classified as other study designs. The use of vaporized hydrogen peroxide and ultraviolet irradiation were the strategies most cited. However, there is a lack of evidence and consensus related to the best method of N95 masks decontamination.

Conclusion

The evidence towards decontamination strategies of N95 masks against coronavirus remains scarce. Vaporized hydrogen peroxide and ultraviolet irradiation seem the current standard for N95 masks decontamination.
Neonatal death: supporting bereaved mothers
Authors: Embaireeg Alia , Ayed Amal KA , Ayed Mariam Khader
Published: July 2020

Background

Death of a child is a devastating experience for parents, owing to which parents may show dissatisfaction towards medical care or suffer from intense and prolonged grief. The objective of the present study was to explore the needs of bereaved mothers after the death of their infant.

Methods

The present study was a descriptive qualitative design that consisted of 10 mothers who have been bereaved in the past year. All mothers were recruited from the registry. Data were obtained through an unstructured single interview and analyzed using conventional content analysis.

Results

The current study demonstrated that parents had the same needs despite their different backgrounds, socioeconomic standards, and religious beliefs. Their needs were based on several main points; 1) Lack of sensitivity/method in delivering the news, 2) Bonding with the child; 3) Safety and family support; 4) Providing understanding and meaning; 5) Ability to express emotions.

Conclusions

The key components that should be considered to support the bereaved parents include honesty, information, choices, and timing. The present study provided a comprehensive view of the overall experiences of the parents with neonatal death and the ability to give guidance to the healthcare providers.
Multidisciplinary approach to COVID-19 risk communication: A framework and tool for individual and regional risk assessment
Authors: Parajuli Rishi Ram , Mishra Bhogendra , Banstola Amrit , Ghimire Bhoj Raj , Poudel Shobha , Sharma Kusum , Dixit Sameer Mani , Sah Sunil Kumar , Simkhada Padam , Van Teijlingen Edwin
Published: July 2020

The COVID-19 pandemic has exceeded over ten million cases globallywith no vaccine available yet. Different approaches are followed to mitigate its impact and reduce its spreading in different countries, but limiting mobility and exposure have been de-facto precaution to reduce transmission. However, a full lockdown cannot be sustained for a prolonged period. Evidence-based, multidisciplinary approach on risk zoning, personal and transmission risk assessment on a near real-time, and risk communication would support the optimized decisions to minimize the impact of coronavirus on our lives. This paper presents a framework to assess the individual and regional risk of COVID-19 along with risk communication tools and mechanisms. Relative risk scores on a scale of 100 represent the integrated risk of influential factors. The personal risk model incorporates: age, exposure history, symptoms, local risk and existing health condition, whereas regional risk is computed through the actual cases of COVID-19, public health risk factors, socioeconomic condition of the region, and immigration statistics. A web application tool (www.covira.info) has been developed, where anyone can assess their risk and find the guided information links primarily for Nepal. This study provides regional risk for Nepal, but the framework is scalable across the world. However, personal risk can be assessed immediately from anywhere.
Quantification of the South African Lockdown Regimes, for the SARS-CoV-2 Pandemic, and the Levels of Immunity They Require to Work
Authors: Childs S. J.
Published: July 2020

This research quantifies the various South African lockdown regimes, for the SARS-CoV-2 pandemic, in terms of the basic reproduction number, r0. It further calculates the levels of immunity required for these selfsame lockdown regimes to begin to work, then predicts their perceived values, should infections have been underestimated by a factor of 10. The first, level-5 lockdown was a valiant attempt to contain the highly infectious, SARS-CoV-2 virus, based on a limited knowledge. Its basic reproduction number (r0= 1.93) never came anywhere close to the requirement of being less than unity. Obviously, it could be anticipated that the same would apply for subsequent, lower levels of lockdown. The basic reproduction number for the level-3 lockdown was found to be 2.34 and that of the level-4 lockdown, 1.69. The suggestion is therefore that the level-4 lockdown might have been marginally ‘smarter’ than the ‘harder’, level-5 lockdown, although its basic reproduction number may merely reflect an adjustment by the public to the new normal, or the ever-present error associated with data sets, in general. The pandemic’s basic reproduction number was calculated to be 3.16, in the Swedish context. The lockdowns therefore served to ensure that the medical system was not overwhelmed, bought it valuable time to prepare and provided useful data. The lockdowns nonetheless failed significantly in meeting any objective to curtail the pandemic.
Development of Magnetic Particle Imaging (MPI) for Cell Tracking and Detection
Authors: Melo Kierstin P , Makela Ashley V , Knier Natasha N , Hamilton Amanda M , Foster Paula J
Published: July 2020

Introduction

Magnetic particle imaging (MPI) is a new imaging modality that sensitively and specifically detects superparamagnetic iron oxide nanoparticles (SPIONs) within a sample. SPION-based MRI cell tracking has very high sensitivity, but low specificity and quantification of iron labeled cells is difficult. MPI cell tracking could overcome these challenges.

Methods

MDM-AB-231BR cells labeled with MPIO, mice were intracardially injected with either 2.5 × 105or 5.0 × 105cells. MRI was performed in vivo the same day at 3T using a bSSFP sequence. After mice were imaged ex vivo with MPI. In a second experiment Mice received an intracardiac injection of either 2.5 × 105or 5 × 104MPIO-labeled 231BR cells. In a third experiment, mice were injected with 5 × 1044T1BR cells, labelled with either MPIO or the SPION Vivotrax. MRI and MPI was performed in vivo.

Results

Signal from MPI and signal voids from MRI both showed more iron content in mice receiving an injection of 5.0 × 105cells than the 2.5 × 105injection. In the second experiment, Day 0 MRI showed signal voids and MPI signal was detected in all mouse brains. The MPI signal and iron content measured in the brains of mice that were injected with 2.5 × 105cells were approximately four times greater than in brains injected with 5 × 104cells. In the third experiment, in vivo MRI was able to detect signal voids in the brains of mice injected with Vivotrax and MPIO, although voids were fainter in Vivotrax labeled cells. In vivo MPI signal was only detectable in mice injected with MPIO-labeled cells.

Conclusion

This is the first example of the use of MPIO for cell tracking with MPI. With an intracardiac cell injection, approximately 15% of the injected cells are expected to arrest in the brain vasculature. For our lowest cell injection of 5.0 × 104cells this is ∼10000 cells.
Unbiased placental secretome characterization identifies candidates for pregnancy complications
Authors: Napso T , Zhao X , Ibañez Lligoña M , Sandovici I , Kay RG , Gribble FM , Reimann F , Meek CL , Hamilton RS , Sferruzzi-Perri AN
Published: July 2020

Pregnancy requires adaptation of maternal physiology to enable normal fetal development. These adaptations are driven, in part, by the production of placental hormones. Failures in maternal adaptation and placental function lead to pregnancy complications including abnormal birthweight and gestational diabetes. However, we lack information on the full identity of hormones secreted by the placenta that mediate changes in maternal physiology. This study used an unbiased approach to characterise the secretory output of mouse placental endocrine cells and examined whether these data could identify placental hormones that are important for determining pregnancy outcome in humans. Secretome and cell peptidome analyses were performed using mass spectrometry on cultured primary trophoblast and fluorescence-activated sorted endocrine cells from pregnant mouse dams, and a placenta secretome map containing 319 proteins was generated. Gene ontology analyses showed that a high proportion of placental secretome proteins are involved in metabolic and immune modulation, signalling and growth. The majority of proteins identified are also expressed by human placenta and several have been reported to be dysregulated in pregnancy complications. Moreover, in proof of concept studies, we found that the relative abundance of secreted placental proteins (sFLT1/MIF and ANGPT2/MIF ratios) was increased in women at 12 weeks of pregnancy, prior to diagnosis of gestational diabetes. Finally, we identified several transcription factors that may be important for controlling hormone production by the placenta and associate with pregnancy outcome. Thus, our observations suggest that analysis of the placental secretome could lead to the identification of new placental biomarkers of pregnancy complications.
C4 photosynthesis with Kranz anatomy evolved in the Oryza coarctata Roxb
Authors: Chowrasia Soni , Mondal Tapan Kumar
Published: July 2020

The C4 cycle is a complex biochemical pathway that has been evolved in plants to deal with the adverse environmental conditions. Mostly C4 plants grow in arid, water-logged area or poor nutrient habitats. Wild species, Oryza coarctata (genome type KKLL; chromosome number (4x) =48, genome size 665 Mb) belongs to the genus of Oryza which thrives well under high saline as well as submerged conditions. Here, we report for the first time that O. coarctata is a C4 plant by observing the increased biomass growth, morphological features such as vein density, anatomical features including ultrastuctural characteristics as well as expression patterns of C4 related genes. Leaves of O. coarctata have higher vein density and possess Kranz anatomy. The ultrastructural observation showed chloroplast dimorphism i.e. presence of agranal chloroplasts in bundle sheath cells whereas, mesophyll cells contain granal chloroplasts. The cell walls of bundle sheath cells contain tangential suberin lamella. The transcript level of C4 specific genes such as phosphoenolpyruvate carboxylase, pyruvate orthophosphate dikinase, NADP-dependent malic enzyme and malate dehydrogenase was higher in leaves of O. coarctata compare to high yielding rice cultivar (IR-29). These anatomical, ultra structural as well as molecular changes in O. coarctata for C4 photosynthesis adaptation might be might be due to its survival in wide diverse condition from aquatic to saline submerged condition. Being in the genus of Oryza, this plant could be potential donor for production of C4 rice in future through conventional breeding, as successful cross with rice has already been reported.
The role of syndapin-2 mediated transcytosis across the blood-brain barrier on amyloid-β accumulation in the brain
Authors: Leite Diana M. , Seifi Mohsen , Ruiz-Perez Lorena , Nguemo Filomain , Plomann Markus , Swinny Jerome D. , Battaglia Giuseppe
Published: July 2020

A deficient transport of amyloid-(Aβ) across the blood-brain barrier (BBB), and its diminished clearance from the brain, contributes to neurodegenerative and vascular pathologies, including Alzheimer’s (AD) and cerebral angiopathy, respectively. At the BBB, Aβ efflux transport is associated with the low-density receptor-related protein 1 (LRP1). However, the precise mechanisms governing Aβ transport across the BBB, in health and disease, remain to be fully understood. Recent evidence indicates that the LRP1 transcytosis occurs through a tubulation-mediated mechanism stabilised by syndapin-2. Here, we show that syndapin-2 is associated with Aβ clearance via LRP1 across the BBB. We further demonstrate that risk factors for AD, Aβ expression and ageing, are associated with a decline in the native expression of syndapin-2 within brain endothelium. Our data reveal that the syndapin-2-mediated pathway, and its balance with the endosomal sorting, are important for Aβ clearance proposing a measure to evaluate AD and ageing, as well as a target for counteracting Aβ build-up. Moreover, we provide evidence for the impact of the avidity of Aβ assemblies in their trafficking across the brain endothelium and in LRP1 expression levels, which may affect the overall clearance of Aβ across the BBB.
Potential silencing of gene expression by PIWI-interacting RNAs (piRNAs) in somatic tissues in mollusk
Authors: Huang Songqian , Ichikawa Yuki , Yoshitake Kazutoshi , Igarashi Yoji , Mariom  , Kinoshita Shigeharu , Asaduzzaman Md , Omori Fumito , Maeyama Kaoru , Nagai Kiyohito , Watabe Shugo , Asakawa Shuichi
Published: July 2020

PIWI/piRNA suppress transposon activity in animals, thereby safeguarding the genome from detrimental insertion mutagenesis. Recently, evidence revealed additional piRNA targets and functions in various animals. Although piRNAs are ubiquitously expressed in somatic tissues of the pearl oysterPinctada fucata, their role is not well-characterized. Here, we report a PIWI/piRNA pathway, including piRNA biogenesis and piRNA-mediated gene regulation inP. fucata. A locked-nucleic-acid modified oligonucleotide (LNA-antagonist) was used to silence a single piRNA (piRNA0001) expression inP. fucata, which resulted in the differential expression of hundreds of endogenous genes. Target prediction analysis revealed that, following silencing, tens of endogenous genes were targeted by piRNA0001, including twelve up-regulated and nine down-regulated genes. Bioinformatic analyses suggested that different piRNA populations participate in the ping-pong amplification loop in a tissue-specific manner. These findings have improved our knowledge of the role of piRNA in mollusks, and provided evidence to understand the regulatory function of the PIWI/piRNA pathway on protein-coding genes outside of germline cells.
Antibody responses to SARS-CoV2 are distinct in children with MIS-C compared to adults with COVID-19
Authors: Weisberg Stuart P. , Connors Thomas , Zhu Yun , Baldwin Matthew , Lin Wen-hsuan , Wontakal Sandeep , Szabo Peter A. , Wells Steven B. , Dogra Pranay , Gray Joshua , Idzikowski Emma , Bovier Francesca T. , Davis-Porada Julia , Matsumoto Rei , Li Poon Maya Meimei , Chait Michael , Mathieu Cyrille , Horvat Branka , Decimo Didier , Bitan Zachary C. , La Carpia Francesca , Ferrara Stephen A. , Mace Emily , Milner Joshua , Moscona Anne , Hod Eldad , Porotto Matteo , Farber Donna L.
Published: July 2020

Clinical manifestations of COVID-19 caused by the novel coronavirus SARS-CoV-2 are associated with age. While children are largely spared from severe respiratory disease, they can present with a SARS-CoV-2-associated multisystem inflammatory syndrome (MIS-C) similar to Kawasaki’s disease. Here, we show distinct antibody (Ab) responses in children with MIS-C compared to adults with severe COVID-19 causing acute respiratory distress syndrome (ARDS), and those who recovered from mild disease. There was a reduced breadth and specificity of anti-SARS-CoV-2-specific antibodies in MIS-C patients compared to the COVID patient groups; MIS-C predominantly generated IgG Abs specific for the Spike (S) protein but not for the nucleocapsid (N) protein, while the COVID-19 cohorts had anti-S IgG, IgM and IgA Abs, as well as anti-N IgG Abs. Moreover, MIS-C patients had reduced neutralizing activity compared to both COVID-19 cohorts, indicating a reduced protective serological response. These results suggest a distinct infection course and immune response in children and adults who develop severe disease, with implications for optimizing treatments based on symptom and age.
Prehospitalization Proton Pump Inhibitor (PPI) use and Clinical Outcomes in COVID-19
Authors: Ramachandran Preethi , Perisetti Abhilash , Gajendran Mahesh , Jean-Louis Farla , Bansal Pardeep , Dwivedi Alok Kumar , Goyal Hemant
Published: July 2020

Background and Aim

Gastric acid has shown to neutralize many viruses. The working receptor of SARS-CoV-2 is angiotensin-converting enzyme-2 (ACE-2), which has shown to be omnipresent in the gastrointestinal tract. There is a theoretical concern that SARS-CoV-2 can escape the neutralization by gastric acid because of hypochlorhydria caused by the use of proton pump inhibitors (PPI) and can predispose the patients for severe COVID-19.

Methods

We studied the association between prehospitalization PPI use and clinical outcomes among hospitalized COVID-19 patients.

Results

In our study, 15.6% of hospitalized COVID-19 patients were on PPIs at home. Mortality among PPI-users was 2.3 times higher than non-users, along with 2.5 times higher risk of mechanical ventilation. This relationship existed even after adjusting for confounding variables.

Conclusion

These results warrant further investigation in prospective studies to evaluate if PPI-induced hypochlorhydria is associated with worse outcomes, including mortality because of the omnipresence of ACE-2 in the gastrointestinal tract.
COVID-19 scenarios for the United States
Authors:   IHME COVID-19 Forecasting Team, Hay Simon I
Published: July 2020

The United States (US) has not been spared in the ongoing pandemic of novel coronavirus disease1,2. COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to cause death and disease in all 50 states, as well as significant economic damage wrought by the non-pharmaceutical interventions (NPI) adopted in attempts to control transmission3. We use a deterministic, Susceptible, Exposed, Infectious, Recovered (SEIR) compartmental framework4,5 to model possible trajectories of SARS-CoV-2 infections and the impact of NPI6 at the state level. Model performance was tested against reported deaths from 01 February to 04 July 2020. Using this SEIR model and projections of critical driving covariates (pneumonia seasonality, mobility, testing rates, and mask use per capita), we assessed some possible futures of the COVID-19 pandemic from 05 July through 31 December 2020. We explored future scenarios that included feasible assumptions about NPIs including social distancing mandates (SDMs) and levels of mask use. The range of infection, death, and hospital demand outcomes revealed by these scenarios show that action taken during the summer of 2020 will have profound public health impacts through to the year end. Encouragingly, we find that an emphasis on universal mask use may be sufficient to ameliorate the worst effects of epidemic resurgences in many states. Masks may save as many as 102,795 (55,898–183,374) lives, when compared to a plausible reference scenario in December. In addition, widespread mask use may markedly reduce the need for more socially and economically deleterious SDMs.
Patient and programmatic characteristics, retention and predictors of attrition among patients starting antiretroviral therapy (ART) before and after the implementation of HIV “Treat All” in Zimbabwe
Authors: Makurumidze Richard , Buyze Jozefien , Decroo Tom , Lynen Lutgarde , de Rooij Madelon , Mataranyika Trevor , Sithole Ngwarai , Takarinda Kudakwashe C. , Apollo Tsitsi , Hakim James , Van Damme Wim , Rusakaniko Simbarashe
Published: July 2020

Background

Since scale-up of the HIV “Treat All”, evidence on its real-world effect on known predictors of attrition (either death or lost to follow-up) is lacking. We conducted a retrospective study using Zimbabwe ART program data to assess the association between “Treat All” and, patient and programmatic characteristics, retention and predictors of attrition.

Methods

We used patient-level data from the electronic patient monitoring system (ePMS) from the nine districts which piloted “Treat All”. We compared patient and programme characteristics, retention and predictors of attrition (lost to follow-up, death or stopping ART) in two cohorts; before (April/May 2016) and after (January/February 2017) “Treat All”. Retention was estimated using survival analysis. Predictors of attrition were determined using a multivariable Cox regression model. Interactions were used to assess the change in predictors.

Results

We analysed 3787 patients, 1738 (45.9%) and 2049 (54.1%) started ART before and after “Treat All”, respectively. The proportion of men was higher after “Treat All” (39.4.% vs 36.2%, p=0.044). Same-day ART initiation was more frequent after “Treat All” (43.2% vs 16.4%; p<0.001) than before. Retention on ART was higher before “Treat All” (p<0.001). Among non-pregnant women and men, the adjusted hazard ratio (aHR) of attrition after “Treat All” compared to before “Treat All” was 1.73 (95%CI: 1.30 - 2.31). The observed hazard of attrition for women being pregnant at ART initiation decreased by 17% (aHR: 1.73*0.48 = 0.83). Being male (vs female; aHR: 1.45; 95%CI: 1.12 - 1.87) and WHO Stage IV (vs WHO Stage I-III; aHR: 2.89; 95%CI: 1.16 - 7.11) predicted attrition both before and after “Treat All” implementation.

Conclusion

Attrition was higher after “Treat All”; being male, WHO Stage 4, and pregnancy predicted attrition in both before and after Treat All. However, pregnancy became a less strong risk factor for attrition after “Treat All” implementation.”
Quantifying Respiratory Airborne Particle Dispersion Control Through Improvised Reusable Masks: The Physics of Non-Pharmaceuptical Interventions for Reducing SARS-COV-2 (COVID-19) Airborne Transmision
Authors: Edwards Nathan J. , Widrick Rebecca , Potember Richard , Gerschefske Mike
Published: July 2020

Background

For much of the SARS-CoV-2 (COVID-19) pandemic, many countries have struggled to offer definitive guidance on the wearing of masks or face coverings to reduce the highly infectious disease transmission resulting from a lack of compelling evidence on the effectiveness of communities wearing masks, and slow acceptance that aerosols are a primary SARS-CoV-2 disease transmission mechanism. Recent studies have shown that masks have been effective in several countries and populations, leaving only a lack of quantitative data on the control of airborne dispersion from human exhalation. This current study specifically has the objective to quantify the effectiveness of non-medical grade washable masks or face coverings in controlling airborne dispersion from exhalation (both droplet and aerosol) by measuring changes in direction, particle cloud velocities, and concentration.

Design

This randomized effectiveness study used a 10% NaCl nebulized polydisperse particle solution (0.3 μm up to 10 μm in size) delivered by an exhalation simulator to conduct 94 experiment runs with combinations of 8 different fabrics, 5 mask designs, and airflows for both talking and coughing. Multiple particle sensors were instrumented to measure reduction in aerosol dispersion.

Results

Three-way multivariate analysis of variance establishes that fabric, mask design, and exhalation breath level have a statistically significant effect on changing direction, reducing velocity, or concentrations of airborne particles (Fabric: P = < .001, Wilks’ Λ = .000; Mask design: P = < .001, Wilks' Λ = .000; Breath level: P = < .001, Wilks' Λ = .004). There were also statistically significant interaction effects between combinations of all primary factors.

Conclusions and Relevance

The application of facial coverings or masks can significantly reduce the airborne dispersion of aerosolized particles from exhalation by diffusing the particle cloud direction and slow down its travel speed. Consequently, the results indicate that wearing masks when coupled with social distance can decrease the potentially inhaled dose of SARS-CoV-2 aerosols or droplets especially where infectious contaminants may exist in shared air spaces. The conclusion is well aligned with the concept of “time-distance-shielding” from hazardous materials emergency response. However, the effectiveness varies greatly between the specific fabrics and mask designs used.
Evaluation of consensus strategies for haplotype phasing
Authors: Al Bkhetan Ziad , Chana Gursharan , Ramamohanarao Kotagiri , Verspoor Karin , Goudey Benjamin
Published: July 2020

Motivation

Haplotype phasing is a critical step for many genetic applications but incorrect estimates of phase can negatively impact downstream analyses. One proposed strategy to improve phasing accuracy is to combine multiple independent phasing estimates to overcome the limitations of any individual estimate. As such a strategy is yet to be thoroughly explored, this study provides a comprehensive evaluation of consensus strategies for haplotype phasing, exploring their performance, along with their constituent tools, across a range of real and simulated datasets with different data characteristics and on the downstream task of genotype imputation.

Results

Based on the outputs of existing phasing tools, we explore two different strategies to construct haplotype consensus estimators: voting across outputs from multiple phasing tools and multiple outputs of a single non-deterministic tool. We find the consensus approach from multiple tools reduces switch error by an average of 10% compared to any constituent tool when applied to European populations and has the highest accuracy regardless of population ethnicity, sample size, SNP-density or SNP frequency. Furthermore, a consensus provides a small improvement indirectly the downstream task of genotype imputation regardless of which genotype imputation tools were used. Our results provide guidance on how to produce the most accurate phasing estimates and the tradeoffs that a consensus approach may have.

Availability

Our implementation of consensus haplotype phasing, consHap, is available freely athttps://github.com/ziadbkh/consHap.
STARCH: Copy number and clone inference from spatial transcriptomics data
Authors: Elyanow Rebecca , Zeira Ron , Land Max , Raphael Benjamin J.
Published: July 2020

Tumors are highly heterogeneous, consisting of cell populations with both transcriptional and genetic diversity. These diverse cell populations are spatially organized within a tumor, creating a distinct tumor microenvironment. A new technology calledspatial transcriptomicscan measure spatial patterns of gene expression within a tissue by sequencing RNA transcripts from a grid of spots, each containing a small number of cells. In tumor cells, these gene expression patterns represent the combined contribution of regulatory mechanisms, which alter the rate at which a gene is transcribed, and genetic diversity, particularly copy number aberrations (CNAs) which alter the number of copies of a gene in the genome. CNAs are common in tumors and often promote cancer growth through upregulation of oncogenes or downregulation of tumor-suppressor genes. We introduce a new method STARCH (Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity) to infer CNAs from spatial transcriptomics data. STARCH overcomes challenges in inferring CNAs from RNA-sequencing data by leveraging the observation that cells located nearby in a tumor are likely to share similar CNAs. We find that STARCH outperforms existing methods for inferring CNAs from RNA-sequencing data without incorporating spatial information.
Callosal anisotropy predicts attentional network changes after parietal inhibitory stimulation
Authors: Schintu Selene , Cunningham Catherine A. , Freedberg Michael , Taylor Paul , Gotts Stephen J. , Shomstein Sarah , Wassermann Eric M.
Published: July 2020

Hemispatial neglect is thought to result from disruption of interhemispheric equilibrium. Right hemisphere lesions deactivate the right frontoparietal network and hyperactivate the left via release from interhemispheric inhibition. Support for this theory comes from neuropsychological evidence as well as transcranial magnetic stimulation (TMS) studies in healthy subjects, in whom right posterior parietal cortex (PPC) inhibition causes neglect-like, rightward, visuospatial bias. Concurrent TMS and fMRI after right PPC TMS show task-dependent changes but may fail to identify effects of stimulation in areas not directly activated by the specific task, complicating interpretations. We used resting-state functional connectivity (RSFC) after inhibitory TMS over the right PPC to examine changes in the networks underlying visuospatial attention.

In a crossover experiment in healthy individuals, we delivered continuous theta burst TMS to the right PPC and vertex as control condition. We hypothesized that PPC inhibitory stimulation would cause a rightward visuospatial bias, decrease PPC connectivity with frontal areas, and increase PPC connectivity with the attentional network in the left hemisphere. We also expected that individual differences in fractional anisotropy (FA) in white matter connections between the PPCs would account for variability in TMS-induced RSFC changes.

As expected, TMS over the right PPC caused a rightward shift in line bisection judgment and increased RSFC between the right PPC and the left superior temporal gyrus. This effect was inversely related to FA in the posterior corpus callosum. Local inhibition of the right PPC reshapes connectivity in the attentional network and depends on interhemispheric connections.