bluuebunny/crossref_metadata_2025 huggingface dataset:
Mother's social status is associated with child health in a horticulturalist population
Authors: Alami Sarah , von Rueden Christopher , Seabright Edmond , Kraft Thomas S. , Blackwell Aaron D. , Stieglitz Jonathan , Kaplan Hillard , Gurven Michael
Published: March 2020

High social status is often associated with greater mating opportunities and fertility for men, but do women also obtain fitness benefits of high status? Greater resource access and child survivorship may be principal pathways through which social status increases women's fitness. Here, we examine whether peer-rankings of women's social status (indicated by political influence, project leadership, and respect) positively covaries with child nutritional status and health in a community of Amazonian horticulturalists. We find that maternal political influence is associated with improved child health outcomes in models adjusting for maternal age, parental height and weight, level of schooling, household income, family size, and number of kin in the community. Children of politically influential women have higher weight-for-age (
B
= 0.33; 95% CI = 0.12–0.54), height-for-age (
B
= 0.32; 95% CI = 0.10–0.54), and weight-for-height (
B
= 0.24; 95% CI = 0.04–0.44), and they are less likely to be diagnosed with common illnesses (OR = 0.48; 95% CI = 0.31–0.76). These results are consistent with women leveraging their social status to enhance reproductive success through improvements in child health. We discuss these results in light of parental investment theory and the implications for the evolution of female social status in humans.
Marine subsidies mediate patterns in avian island biogeography
Authors: Obrist Debora S. , Hanly Patrick J. , Kennedy Jeremiah C. , Fitzpatrick Owen T. , Wickham Sara B. , Ernst Christopher M. , Nijland Wiebe , Reshitnyk Luba Y. , Darimont Chris T. , Starzomski Brian M. , Reynolds John D.
Published: March 2020

The classical
theory of island biogeography
, which predicts species richness using island area and isolation, has been expanded to include contributions from marine subsidies, i.e.
subsidized island biogeography
(SIB)
theory
. We tested the effects of marine subsidies on species diversity and population density on productive temperate islands, evaluating SIB predictions previously untested at comparable scales and subsidy levels. We found that the diversity of terrestrial breeding bird communities on 91 small islands (approx. 0.0001–3 km
2
) along the Central Coast of British Columbia, Canada were correlated most strongly with island area, but also with marine subsidies. Species richness increased and population density decreased with island area, but isolation had no measurable influence. Species richness was negatively correlated with marine subsidy, measured as forest-edge soil δ
15
N. Density, however, was higher on islands with higher marine subsidy, and a negative interaction between area and subsidy indicates that this effect is stronger on smaller islands, offering some support for SIB. Our study emphasizes how subsidies from the sea can shape diversity patterns on islands and can even exceed the importance of isolation in determining species richness and densities of terrestrial biota.
Yersinia canariae sp. nov., isolated from a human yersiniosis case
Authors: Nguyen Scott V. , Greig David R. , Hurley Daniel , Donoghue Orla , Cao Yu , McCabe Evonne , Mitchell Molly , Schaffer Kirsten , Jenkins Claire , Fanning Séamus
Published: March 2020

A Gram-negative rod from the

Yersinia

genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technologies (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within

Yersinia

, despite biochemical similarities to

Yersinia enterocolitica

. The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is SRR7544370T (=NCTC 14382T/=LMG 31573T).
Cohnella fermenti sp. nov., isolated from a fermentation process
Authors: Lin Shih-Yao , Chen Wen-Ming , Hameed Asif , Huang Guan-Hua , Hung Mei-Hua , Young Chiu-Chung
Published: March 2020

A novel Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CC-MHH1044T, was isolated from a preserved vegetable sample. A polyphasic taxonomic approach was applied to the isolates in order to clarify its taxonomic position. Growth of the strain CC-MHH1044T occurred at 15–50 °C (optimum, 30 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–2.0 % (w/v) NaCl (optimum, 1 %, w/v). The genome of strain CC-MHH1044T consisted of 8.5 Mb and the genomic DNA G+C content was 58.5 mol%. Comparison of the 16S rRNA gene sequences showed that CC-MHH1044T belonged to the genus

Cohnella

and showed a close relationship with the type strains of

Cohnella damuensis

(96.2 %) and

Cohnella panacarvi

(95.9 %), and lower sequence similarity to other species. Average nucleotide identity values calculated from whole-genome sequencing data proved that CC-MHH1044T represents a distinct

Cohnella

species. The dominant cellular fatty acids (>5 %) included iso-C14 : 0(7.4 %), iso-C15 : 0 (6.4 %), anteiso-C15 : 0(40.3 %), C16 : 0 (6.6 %) and iso-C16 : 0 (27.0 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid and glycolipid. The major polyamine was spermidine. The predominant isoprenoid quinone was menaqinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits, together with results of comparative 16S rRNA gene sequence, average nucleotide identity and digital DNA–DNA hybridization analyses, we conclude that strain CC-MHH1044T represents a novel member of the genus

Cohnella

, for which the name Cohnella fermenti sp. nov. is proposed. The type strain is CC-MHH1044T (=BCRC 81147T=JCM 32834T).
Single Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis
Authors: Schupp Jonas C. , Khanal Sara , Gomez Jose L. , Sauler Maor , Adams Taylor S. , Chupp Geoffrey L. , Yan Xiting , Poli Sergio , Montgomery Ruth R. , Rosas Ivan O. , Cruz Charles S. Dela , Bruscia Emanuela M. , Egan Marie E. , Kaminski Naftali , Britto Clemente J.
Published: March 2020

Cystic fibrosis (CF) is a life-shortening multisystem hereditary disease caused by abnormal chloride transport. CF lung disease is driven by innate immune dysfunction that perpetuates inflammation. The airways provide a window into CF pathogenesis, as immune cells display exaggerated inflammatory responses and impaired phagocytic function, contributing to tissue injury. In order to define the transcriptional profile of this airway immune dysfunction, we performed the first single-cell transcriptome characterization of CF sputum. We show that the airway immune cell repertoire shifted from alveolar macrophages in HC to a predominance of recruited monocytes and neutrophils in CF. Recruited lung mononuclear phagocytes were abundant in CF, separated into three archetypes: activated monocytes, monocyte-derived macrophages, and heat-shock activated monocytes. Neutrophils were most prevalent in CF, with a dominant immature proinflammatory archetype. While CF monocytes exhibited proinflammatory features, both monocytes and neutrophils showed transcriptional evidence of abnormal phagocytic and cell-survival programs. Our findings offer an opportunity to understand subject-specific immune dysfunction and its contribution to divergent clinical courses in CF. As we progress towards personalized applications of therapeutic and genomic developments, we hope this inflammation profiling approach will enable further discoveries that change the natural history of CF lung disease.
Clinical Characteristics of Coronavirus Disease 2019 (COVID-19): An Updated Systematic Review
Authors: Fang Zhangfu , Yi Fang , Wu Kang , Lai Kefang , Sun Xizhuo , Zhong Nanshan , Liu Zhigang
Published: March 2020

OBJECTIVE

Clinical characteristics of novel coronavirus disease (COVID-19) have been described in numerous studies but yielded varying results. We aimed to conduct a systematic review on scientific literatures and to synthesize critical data on clinical traits of COVID-19 from its initial outbreak to pandemic.

METHODS

Systematic searches were conducted to identify retrospective observational study that contained clinical characteristics on COVID-19 through multiple databases. Two reviewers independently evaluated eligible publications. Data on clinical characteristics of COVID-19 were extracted and analyzed.

RESULTS

Seventy-two retrospective studies demonstrating the clinical characteristics of COVID-19 were included. A total of 3470 COVID-19 patients were synthesized to the final analysis in an unbiased manner. The most common symptom was fever (2878 [83.0%]), and 63.4% of the patients presented fever as onset symptom. There were 2528 [88.2%] of 2866 cases had abnormal lung findings on chest CT scan. Laboratory findings showed that 1498 [62.8%] of 2387 cases had lymphopenia, and 1354 [64.8%] of 2091 cases had an increased level of C-reactive protein (CRP). A total of 185 [11.5%] patients were admitted to intensive care unit (ICU) while the overall case fatality rate (CFR) was 3.7%. Compared to patients admitted outside of Hubei, China, those from Hubei had a significant higher ICU admission rate (21.9% vs. 2.5%, p<0.001). Also, CFR attributed to COVID-19 was significantly higher in Hubei than that of non-Hubei admissions (10.4% vs. 0.6%, p<0.001).

INTERPRETATION

This large patient-based systematic review presents a more precise profiling of the COVID-19 from its outbreak to current pandemic. Dynamic evolvements of COVID-19 are needed to be characterized in future studies.
Analysis of early renal injury in COVID-19 and diagnostic value of multi-index combined detection
Authors: Hong Xu-wei , Chi Ze-pai , Liu Guo-yuan , Huang Hong , Guo Shun-qi , Fan Jing-ru , Lin Xian-wei , Qu Liao-zhun , Chen Rui-lie , Wu Ling-jie , Wang Liang-yu , Zhang Qi-chuan , Wu Su-wu , Pan Ze-qun , Lin Hao , Zhou Yu-hua , Zhang Yong-hai
Published: March 2020

Objectives

The aim of the study was to analyze the incidence of COVID-19 with early renal injury, and to explore the value of multi-index combined detection in diagnosis of early renal injury in COVID-19.

Design

The study was an observational, descriptive study.

Setting

This study was carried out in a tertiary hospital in Guangdong, China.

Participants

12 patients diagnosed with COVID-19 from January 20, 2020 to February 20, 2020.

Primary and secondary outcome measures

The primary outcome was to evaluate the incidence of early renal injury in COVID-19. In this study, the estimated glomerular filtration rate (eGFR), endogenous creatinine clearance (Ccr) and urine microalbumin / urinary creatinine ratio (UACR) were calculated to assess the incidence of early renal injury. Secondary outcomes were the diagnostic value of urine microalbumin (UMA), α1-microglobulin (A1M), urine immunoglobulin-G (IGU), urine transferring (TRU) alone and in combination in diagnosis of COVID-19 with early renal injury.

Results

While all patients had no significant abnormalities in serum creatinine (Scr) and blood urea nitrogen (BUN), the abnormal rates of eGFR, Ccr, and UACR were 66.7%, 41.7%, and 41.7%, respectively. Urinary microprotein detection indicated that the area under curve (AUC) of multi-index combined to diagnose early renal injury in COVID-19 was 0.875, which was higher than UMA (0,813), A1M (0.813), IGU (0.750) and TRU (0.750) alone. Spearman analysis showed that the degree of early renal injury was significantly related to C-reactive protein (CRP) and neutrophil ratio (NER), suggesting that the more severe the infection, the more obvious the early renal injury. Hypokalemia and hyponatremia were common in patients with COVID-19, and there was a correlation with the degree of renal injury.

Conclusions

Early renal injury was common in patients with COVID-19. Combined detection of UMA, A1M, IGU, and TRU was helpful for the diagnosis of early renal injury in COVID-19.
Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak
Authors: Liu Yuan , Ning Zhi , Chen Yu , Guo Ming , Liu Yingle , Gali Nirmal Kumar , Sun Li , Duan Yusen , Cai Jing , Westerdahl Dane , Liu Xinjin , Ho Kin-fai , Kan Haidong , Fu Qingyan , Lan Ke
Published: March 2020

Background

The ongoing outbreak of COVID-19 has spread rapidly and sparked global concern. While the transmission of SARS-CoV-2 through human respiratory droplets and contact with infected persons is clear, the aerosol transmission of SARS-CoV-2 has been little studied.

Methods

Thirty-five aerosol samples of three different types (total suspended particle, size segregated and deposition aerosol) were collected in Patient Areas (PAA) and Medical Staff Areas (MSA) of Renmin Hospital of Wuhan University (Renmin) and Wuchang Fangcang Field Hospital (Fangcang), and Public Areas (PUA) in Wuhan, China during COVID-19 outbreak. A robust droplet digital polymerase chain reaction (ddPCR) method was employed to quantitate the viral SARS-CoV-2 RNA genome and determine aerosol RNA concentration.

Results

The ICU, CCU and general patient rooms inside Renmin, patient hall inside Fangcang had undetectable or low airborne SARS-CoV-2 concentration but deposition samples inside ICU and air sample in Fangcang patient toilet tested positive. The airborne SARS-CoV-2 in Fangcang MSA had bimodal distribution with higher concentration than those in Renmin during the outbreak but turned negative after patients number reduced and rigorous sanitization implemented. PUA had undetectable airborne SARS-CoV-2 concentration but obviously increased with accumulating crowd flow.

Conclusions

Room ventilation, open space, proper use and disinfection of toilet can effectively limit aerosol transmission of SARS-CoV-2. Gathering of crowds with asymptomatic carriers is a potential source of airborne SARS-CoV-2. The virus aerosol deposition on protective apparel or floor surface and their subsequent resuspension is a potential transmission pathway and effective sanitization is critical in minimizing aerosol transmission of SARS-CoV-2.
Comparison of Radiologist-Assigned Categories and Quantitative Measures of Background Parenchymal Enhancement on Breast MRI
Authors: Niell Bethany L , Abdalah Mahmoud , Stringfield Olya , Pereira Malesa , Ataya Dana , Balagurunathan Yoga , Gillies Robert , Raghunand Natarajan
Published: March 2020

Background parenchymal enhancement (BPE) on multi-parametric breast magnetic resonance imaging (mpMRI) reflects the volume and intensity of gadolinium uptake. We developed a semi-automated segmentation algorithm to extract and quantify measures of BPE and investigated the agreement of computed measures of BPE with radiologist-assigned categories. We retrospectively identified 123 high risk patients with breast mpMRI performed for screening indications. Pre- and post-gadolinium T1-weighted series with and without fat suppression were co-registered. Using Otsu’s method and an active contours method, the breast tissue was segmented from the chest wall and non-fat voxels were clustered to identify the amount of fibroglandular tissue. Median and inter-quartile ranges for the absolute volume of BPE (BPE cm3) and the percentage of BPE (BPE%) using a threshold PE of 30% were computed within the segmented FGT on the first post-contrast phase. Student’s t-test was used to evaluate BPE volume and BPE% by radiologist-assigned categories. Both BPE volume and BPE% differed significantly between minimal/mild and moderate/marked radiologist assigned categories (p=0.030 and 0.004, respectively). Using our newly developed semi-automated segmentation pipeline, we quantified fibroglandular tissue and BPE. The overlapping ranges of quantitative BPE corresponding to the radiologist-assigned BPE categories showcases the inter-reader variability with visual estimation of BPE.
Data-driven discovery of a clinical route for severity detection of COVID-19 pediatric cases
Authors: Yu Hui , Shao Jianbo , Guo Yuqi , Xiang Yun , Sun Chuan , Yuan Ye
Published: March 2020

The outbreak of COVID-19 epidemic has caused worldwide health concerns since Nov., 2019. A previous study described the demographic, epidemiologic, and clinical features for infected infants. However, compared with adult cases, little attention has been paid to the infected pediatric cases. Severity detection is challenging for children since most of children patients have mild symptoms no matter they are moderately or critically ill therein.
Ascertainment rate of novel coronavirus disease (COVID-19) in Japan
Authors: Omori Ryosuke , Mizumoto Kenji , Nishiura Hiroshi
Published: March 2020

Objective

To estimate the ascertainment rate of novel coronavirus (COVID-19).

Methods

We analyzed the epidemiological dataset of confirmed cases with COVID-19 in Japan as of 28 February 2020. A statistical model was constructed to describe the heterogeneity of reporting rate by age and severity. We estimated the number of severe and non-severe cases, accounting for under-ascertainment.

Results

The ascertainment rate of non-severe cases was estimated at 0.44 (95% confidence interval: 0.37, 0.50), indicating that unbiased number of non-cases would be more than twice the reported count.

Conclusions

Severe cases are twice more likely diagnosed and reported than other cases. Considering that reported cases are usually dominated by non-severe cases, the adjusted total number of cases is also about a double of observed count. Our finding is critical in interpreting the reported data, and it is advised to interpret mild case data of COVID-19 as always under-ascertained.

Highlights

-

Epidemiological dataset of COVID-19 in Japan was analyzed.

-

The ascertainment rate of non-severe cases was estimated at 0.44 (95% confidence interval: 0.37, 0.50).

-

Severe cases are twice more likely diagnosed and reported than other cases.

-

Mild cases of COVID-19 are under-ascertained.
A TgfβRI/Snai1-dependent developmental module at the core of vertebrate axial elongation
Authors: Dias André , Lozovska Anastasiia , Wymeersch Filip J. , Nóvoa Ana , Binagui-Casas Anahi , Sobral Daniel , Martins Gabriel G. , Wilson Valerie , Mallo Moisés
Published: March 2020

Formation of the vertebrate postcranial body axis follows two sequential but distinct phases. The first phase generates pre-sacral structures (the so-called primary body) through the activity of the primitive streak (PS) on axial progenitors within the epiblast. The embryo then switches to generate the secondary body (post-sacral structures), which depends on axial progenitors in the tail bud. Here we show that the mammalian tail bud is generated through an independent developmental module, concurrent but functionally different to that generating the primary body. This module is triggered by convergent TgfβRI and Snai1 activities that promote an incomplete epithelial to mesenchymal transition (EMT) on a subset of epiblast axial progenitors. This EMT is functionally different to that coordinated by the PS, as it does not lead to mesodermal differentiation but brings axial progenitors into a transitory state, keeping their progenitor activity to drive further axial body extension.
IncreasedAPOEε4expression is associated with reactive A1 astrocytes and the difference in Alzheimer Disease risk from diverse ancestral backgrounds
Authors: Griswold A. J. , Celis K. , Bussies P. , Rajabli F. , Whitehead P. , Hamilton-Nelson K. , Beecham G. W. , Dykxhoorn D. M. , Nuytemans K. , Wang L. , Gardner O. K. , Dorfsman D. , Bigio E.H. , Mesulam M. , Weintraub S. , Geula C. , Gearing M. , Martinez-McGrath E. , Dalgard C.L. , Scott W. K. , Haines J. L. , Pericak-Vance M.A. , Young J. I. , Vance J. M.
Published: March 2020

APOEε4African local genomic ancestry (LA) confers less risk for Alzheimer disease (AD) relative to European LA (LA) carriers. Single nucleus RNA sequencing from AD-APOEε4/4frontal cortex found European LA carriers have a 1.45-fold greaterAPOEε4expression (p< 1.8 E10−313) and are associated with a unique A1 reactive astrocyte cluster. This suggests a potential mechanism for the increased risk for AD seen in European LA carriers ofAPOEε4.
Robust inference of positive selection on regulatory sequences in human brain
Authors: Liu Jialin , Robinson-Rechavi Marc
Published: March 2020

A long standing hypothesis is that divergence between humans and chimpanzees might have been driven more by regulatory level adaptions than by protein sequence adaptations. This has especially been suggested for regulatory adaptions in the evolution of the human brain. There is some support for this hypothesis, but it has been limited by the lack of a reliable and powerful way to detect positive selection on regulatory sequences. We present a new method to detect positive selection on transcription factor binding sites, based on Orr’s sign test applied to a machine learning model of binding. Unlike other methods, this requires neither defining a priori neutral sites, nor detecting accelerated evolution, thus removing major sources of bias. The method is validated in flies, mice, and primates, by a McDonald-Kreitman-like measure of polymorphism vs. divergence, by experimental binding site gains and losses, and by changes in expression levels. We scanned the signals of positive selection for CTCF binding sites in 29 human and 11 mouse tissues or cell types. We found that human brain related cell types have the highest proportion of positive selection. This is consistent with the importance of adaptive evolution on gene regulation in the evolution of the human brain.
Benchmark of lasso-like penalties in the Cox model for TCGA datasets reveal improved performance with pre-filtering and wide differences between cancers
Authors: Jardillier Rémy , Chatelain Florent , Guyon Laurent
Published: March 2020

Motivation

Prediction of patient survival from tumor molecular ‘omics’ data is a key step toward personalized medicine. With this aim, the databases available are growing, with the collection of various ‘omics’ characterizations of patient tumors, together with their associated clinical outcomes for weeks to years of follow-up. Cox models with variable selection used with RNA profiling datasets are popular for identification of prognostic biomarkers and for clinical predictions. However, these models are confronted with the ‘curse of dimensionality’, as the numberpof covariates (genes) can greatly exceed the numbernof patients. To tackle this problem, variance-based pre-filtering and penalization methods are popular for dimension reduction. In the present paper, we study the impact of a pre-filtering step based on gene variability, and we evaluate the performance of the lasso penalization of the Cox model and four variants (i.e., elastic net, adaptive elastic net, ridge, univariate Cox) in terms of prediction, selection and stability.

Results

First, we show that the prediction capacity with the Cox penalties method is cancer dependent. Second, we develop a methodology to fix a threshold to filter out genes with low variability without losing prediction capacity. Third, we show that it is best not to use the Cox model to select prognostic biomarkers, as its false discovery proportion is always ≥ 50%. Finally, to predict overall survival, we can suggest the use of the ridge penalty, or the elastic net if a more parsimonious model is needed, after the pre-filtering step.

Availability

We provide the R script generated to reproduce all of the figures presented in this article.

Supplementary information

Supplementary Figures and R scripts are available.
Ecological consequences of intraspecific variation in coevolutionary systems
Authors: Senthilnathan Athmanathan , Gavrilets Sergey
Published: March 2020

The patterns and outcomes of coevolution are expected to depend on intraspecific trait variation. Various evolutionary factors can change this variation in time. As a result, modeling coevolutionary processes solely in terms of mean trait values may not be sufficient; one may need to study the dynamics of the whole trait distribution. Here, we develop a theoretical framework for studying the effects of evolving intraspecific variation in two-species coevolutionary systems. In particular, we build and study mathematical models of competition, exploiter-victim interactions, and mutualism in which the strength of within- and between-species interactions depends on the difference in continuously varying traits. We use analytical approximations based on the invasion analysis and supplement it with a numerical method. We find that intraspecific variation can be maintained if stabilizing selection is weak in at least one species. When intraspecific variation is maintained, stable coexistence is promoted by small ranges of interspecific interaction in two-species competition and mutualism, and large ranges in exploiter-victim interactions. We show that trait distributions can become multimodal. Our approach and results contribute to the understanding of the ecological consequences of intraspecific variation in coevolutionary systems by exploring its effects on population densities and trait distributions.
Massively parallel encapsulation of single cells with structured microparticles and secretion-based flow sorting
Authors: de Rutte Joseph , Dimatteo Robert , Archang Maani M , van Zee Mark , Koo Doyeon , Lee Sohyung , Sharrow Allison C. , Krohl Patrick J. , Mellody Michael P. , Zhu Sheldon , Eichenbaum James , Kizerwetter Monika , Udani Shreya , Ha Kyung , Bertozzi Andrea L. , Spangler Jamie B. , Damoiseaux Robert , Carlo Dino Di
Published: March 2020

Techniques to analyze and sort single cells based on functional outputs, such as secreted products, have the potential to transform our understanding of cellular biology, as well as accelerate the development of next generation cell and antibody therapies. However, secreted molecules rapidly diffuse away from cells, and analysis of these products requires specialized equipment and expertise to compartmentalize individual cells and capture their secretions. Herein we demonstrate the use of suspendable microcontainers to sort single viable cells based on their secreted products at high-throughput using only commonly accessible laboratory infrastructure. Our microparticles act as solid supports which facilitate cell attachment, partition uniform aqueous compartments, and capture secreted proteins. Using this platform, we demonstrate high-throughput screening of stably- and transiently-transfected producer cells based on relative IgG production as well as screening of B lymphocytes and hybridomas based on antigen-specific antibody production using commercially available flow sorters. Leveraging the high-speed sorting capabilities of standard sorters, we sorted >1,000,000 events in less than an hour. The reported microparticles can be easily stored, and distributed as a consumable reagent amongst researchers, democratizing access to high-throughput functional cell screening.
Evolutionary variation in MADS-box dimerization affects floral development and protein stability
Authors: Juarez Maria Jazmin Abraham , Schrager-Lavelle Amanda , Man Jarrett , Whipple Clinton , Handakumbura Pubudu , Babbitt Courtney , Bartlett Madelaine
Published: March 2020

Shifting interactions between MADS-box transcription factors may have been critical in the emergence of the flower, and in floral diversification. However, how evolutionary variation in MADS-box interactions affects the development and evolution of floral form remains unknown. Interactions between B-class MADS-box proteins are variable across the grass family. Here, we test the functional consequences of this evolutionary variability using maize as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to protein complex composition and downstream gene expression. Differential dimerization also affected B-class complex abundance, independent of RNA levels. Thus, differential dimerization may affect protein stability. This reveals an important consequence for evolutionary variability in MADS-box interactions, adding complexity to the evolution of developmental gene networks. Our results show that floral development is robust to molecular change, even coding change in a master regulator of development. This robustness may contribute to the evolvability of floral form.
Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to theMethanomassiliicoccales
Authors: Zinke Laura A. , Evans Paul N. , Schroeder Alena L. , Parks Donovan H. , Varner Ruth K. , Rich Virginia I. , Tyson Gene W. , Emerson Joanne B.
Published: March 2020

Recent discoveries ofmcrandmcr-like complexes in genomes from diverse archaeal lineages suggest that methane (and more broadly alkane) metabolism is an ancient pathway with complicated evolutionary histories. The conventional view is that methanogenesis is an ancestral metabolism of the archaeal classThermoplasmata. Through comparative genomic analysis of 12Thermoplasmatametagenome-assembled genomes (MAGs), we show that these microorganisms do not encode the genes required for methanogenesis, which suggests that this metabolism may have been laterally acquired by an ancestor of the orderMethanomassiliicoccales. These MAGs include representatives from four orders basal to theMethanomassiliicoccales, including a high-quality MAG (95% complete) that likely represents a new order,Ca.Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, such as heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two of these lineages are globally widespread among anoxic, sedimentary environments, with the exception ofCa.Lunaplasma lacustris, which has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of theThermoplasmataand provide new insights into the evolutionary history of methanogenesis within theThermoplasmata.
The demographic decline of a sea lion population followed multi-decadal sea surface warming
Authors: Adame Karen , Elorriaga-Verplancken Fernando R. , Beier Emilio , Acevedo-Whitehouse Karina , Pardo Mario A.
Published: March 2020

Background

The population growth of top predators depends largely on environmental conditions suitable for aggregating sufficient and high-quality prey. We reconstructed numerically the population size dynamics of a resident population of California sea lions in the Gulf of California during 1978 – 2019, and its relation with the gulf’s multi-decadal sea surface temperature trend. This are the first long-term insights to the oceanic environment of the Gulf of California and to the population trend of one of its major predators.

Results

Our results indicate that a three-decade sustained warming explains statistically the population’s trend, including a ∼65% decline between 1991 – 2019, accounting for 92% of the variance. Long-term warming conditions started in the late 80’s, followed by the population’s decline, from a peak of 43,834 animals (range: 34,080 - 58,274) in 1991 to only 15,291 (range: range: 11,861 - 20,316) in 2019. The models suggested a century-scale optimum sea surface habitat for the population occurring in mildly temperate waters, from 0.18 to 0.39°C above the 100- year mean of 22.24°C.

Conclusions

The negative relation of the population size with warming sea surface conditions was evident, and the predictability of the former from the sea surface temperature 100-year anomalies was high. The mechanistic links of this relation are still untested, but an apparent diversification of pelagic fish catches suggests a reduction of high quality prey. We propose that this sea lion population should be considered as vulnerable to any disturbance that could add to the negative effects of the current sea surface warming conditions in the Gulf of California.
Effects of muscarinic M1receptor stimulation on reinforcing and neurochemical effects of cocaine in rats
Authors: Weikop Pia , Jensen Kathrine L. , Thomsen Morgane
Published: March 2020

Cocaine addiction is a chronic illness characterized by maladaptive drug-induced neuroplastic changes that confer lasting vulnerability to relapse. Over several weeks we observed the effects of the M1receptor-selective agonist VU0364572 in adult male rats that self-administer cocaine in a cocaine vs. natural reinforcer choice procedure. The drug showed unusual long-lasting effects, as rats gradually stopped self-administering cocaine, reallocating behavior towards the food reinforcer. The effect lasted as long as tested and at least four weeks. To begin to elucidate how VU0364572 modulates cocaine self-administration, we then examined its long-term effects using dual-probe in vivo dopamine and glutamate microdialysis in nucleus accumbens and medial prefrontal cortex, and ex vivo striatal dopamine reuptake. Microdialysis revealed dramatic decreases in cocaine-induced dopamine and glutamate outflow four weeks after VU0364572 treatment, without significant changes in dopamine uptake function. These lasting and dramatic effects of M1receptor stimulation reinforce our interest in this target as potential treatment of cocaine addiction. M1receptors are known to modulate medium spiny neuron responses to corticostriatal glutamatergic signaling acutely, and we hypothesize that VU0364572 may oppose the addiction-related effects of cocaine by causing lasting changes in this system.
Engineered Heterochronic Parabiosis in 3D Microphysiological System for Identification of Muscle Rejuvenating Factors
Authors: Lee Yunki , Choi Jeongmoon J. , Ahn Song Ih , Leea Nan Hee , Han Woojin M. , Mohiuddin Mahir , Shin Eun Jung , Wood Levi , Park Ki Dong , Kim YongTae , Jang Young C.
Published: March 2020

Exposure of aged mice to a young systemic milieu revealed remarkable rejuvenation effects on aged tissues, including skeletal muscle. Although some candidate factors have been identified, the exact identity and the underlying mechanisms of putative rejuvenating factors remain elusive, mainly due to the complexity ofin vivoparabiosis. Here, we present anin vitromuscle parabiosis system that integrates young- and old-muscle stem cell vascular niche on a three-dimensional microfluidic platform designed to recapitulate key features of native muscle stem cell microenvironment. This innovative system enables mechanistic studies of cellular dynamics and molecular interactions within the muscle stem cell niche, especially in response to conditional extrinsic stimuli of local and systemic factors. We demonstrate that vascular endothelial growth factor (VEGF) signaling from endothelial cells and myotubes synergistically contribute to the rejuvenation of the aged muscle stem cell function. Moreover, with the adjustable on-chip system, we can mimic both blood transfusion and parabiosis and detect the time-varying effects of anti-geronic and pro-geronic factors in a single organ or multi-organ systems. Our unique approach presents a complementaryin vitromodel to supplementin vivoparabiosis for identifying potential anti-geronic factors responsible for revitalizing aging organs.
Dopamine pathway characterization during the reproductive mode switch in the pea aphid
Authors: Le Trionnaire Gaël , Hudaverdian Sylvie , Richard Gautier , Tanguy Sylvie , Gleonnec Florence , Prunier-Leterme Nathalie , Gauthier Jean-Pierre , Tagu Denis
Published: March 2020

Abstract

Aphids are major pests of most of the crops worldwide. Such a success is largely explained by the remarkable plasticity of their reproductive mode. They reproduce efficiently by viviparous parthenogenesis during spring and summer generating important damage on crops. At the end of the summer, viviparous parthenogenetic females perceive the photoperiod shortening and transduce this signal to their embryos that change their reproductive fate to produce sexual individuals: oviparous females and males. After mating, those females lay cold-resistant eggs. Earlier studies showed that some transcripts coding for key components of dopamine pathway were regulated between long days and short days conditions suggesting that dopamine might be involved in the transduction of seasonal cues prior to reproductive mode switch. In this study, we aimed at going deeper into the characterization of the expression dynamics of this pathway but also in the analysis of its functional role in this context in the pea aphidAcyrthosiphon pisum. We first analysed the level of expression of ten genes of this pathway in embryos and larval heads of aphids reared under long days (asexual producers) or short days (sexual producers) conditions. We then performed in situ hybridization experiments to localize in embryos theddcandpaletranscripts that are coding for two key enzymes in dopamine synthesis. Finally, Using CRISPR-Cas9 mutagenesis in eggs produced after the mating of sexual individuals, we targeted theddcgene. We could observe strong melanization defaults inddcmutated eggs, which confidently mimicked the Drosophiladdcphenotype. Nevertheless, such a lethal phenotype did not allow us to validate the involvement of dopamine as a signaling pathway necessary to trigger the reproductive mode switch in embryos.
In vivocorneal and lenticular microscopy with asymmetric fundus retroillumination
Authors: Weber Timothy D. , Mertz Jerome
Published: March 2020

We describe a new technique for non-contactin vivocorneal and lenticular microscopy. It is based on fundus retro-reflection and back-illumination of the crystalline lens and cornea. To enhance phase-gradient contrast, we apply asymmetric illumination by illuminating one side of the fundus. The technique produces micron-scale lateral resolution across a 1-mm diagonal field of view. We show representative images of the epithelium, the subbasal nerve plexus, large stromal nerves, dendritic immune cells, endothelial nuclei, and the anterior crystalline lens, demonstrating the potential of this instrument for clinical applications.
Assessment of Potential Health and Genetic Impacts in Releasing ConfiscatedParoaria coronataandSaltator similis
Authors: Cruz Cláudio E. F. , Funkler Gustavo R. , Zani André L. S. , Wagner Paulo G. C. , Segura Luciano N. , Andretta Inês , Fagundes Nelson J. R.
Published: March 2020

Illegal capture and trade of wild birds has long been a threat to biodiversity. Translocation—the release of individuals from one location into another—is a useful conservation tool in the management of species. However, both health (such as different pathogens) and adaptive (such as local adaptation), differences among populations must be taken into account, as both can impact the recipient population negatively. Here, we provide health and genetic information to support release planning for two of the most trafficked Brazilian wild bird species (Paroaria coronataandSaltator similis). We focused on two fundamental questions: Are there significant differences in pathogen load between wild and captive populations? Is there significant genetic structure among populations? In total, 223 free-living birds were captured, sampled, and released at the same site. Devices and live decoys characteristics were top factors influencing captures. We tested blood, feces, and oropharyngeal swabs from free-ranging (n=101) and confiscated (n=92) birds for Newcastle disease virus,Salmonellaspp., andMycoplasma gallisepticum. Genetic structure among populations was investigated using mtDNA in a subsample of these birds. We found no evidence for Newcastle disease virus andSalmonellaspp. in seized and free-living birds from both species. However, seizedP. coronataandS. similismay be potential sources ofM. gallisepticum. We found significant but low genetic structure among populations occurring in different Biomes (ΦCT=0.26 forP. coronata;ΦCT=0.13 forS. similis) and no significant structure among populations occurring in the Pampa Biome. These results suggest that while it may be important to screen seized birds for avian pathogens, genetic structure among populations seems to be of lesser concern when planning the release of seized songbirds in the wild.
Causal relationship between the right auditory cortex and speech-evoked envelope-following response: Evidence from combined transcranial stimulation and electroencephalography
Authors: Mai Guangting , Howell Peter
Published: March 2020

Speech-evoked envelope-following response (EFR) reflects brain encoding of speech periodicity that serves as a biomarker for pitch and speech perception and various auditory and language disorders. While EFR is thought to originate from the subcortex, recent research illustrated a right-hemispheric cortical contribution to EFR. However, it is unclear whether this contribution is causal. This study aimed to establish this causality by combining transcranial direct current stimulation (tDCS) and measurement of EFR (pre- and post-tDCS) via scalp-recorded electroencephalography (EEG). We applied tDCS over the left and right auditory cortices in right-handed normal-hearing participants and examined whether altering cortical excitability via tDCS causes changes in EFR during monaural listening to speech syllables. We showed significant changes in EFR magnitude when tDCS was applied over the right auditory cortex compared to sham stimulation for the listening ear contralateral to the stimulation site. No such effect was found when tDCS was applied over the left auditory cortex. Crucially, we further observed a hemispheric laterality where after-effect was significantly greater for tDCS applied over the right than the left auditory cortex in the contralateral ear condition. Our finding thus provides the first evidence that validates the causal relationship between the right auditory cortex and EFR.
Coevolutionary dynamics of genetic traits and their long-term extended effects under non-random interactions
Authors: Mullon Charles , Wakano Joe Yuichiro , Ohtsuki Hisashi
Published: March 2020

Organisms continuously modify their living conditions via extended genetic effects on their envi-ronment, microbiome, and in some species culture. These effects can impact the fitness of current but also future conspecifics due to non-genetic transmission via ecological or cultural inheritance. In this case, selection on a gene with extended effects depends on the degree to which current and future genetic relatives are exposed to modified conditions. Here, we detail the selection gradient on a quantitative trait with extended effects in a patch-structured population, when gene flow between patches is limited and ecological inheritance within patches can be biased towards offspring. Such a situation is relevant to understand evolutionary driven changes in individual condition that can be preferentially transmitted from parent to offspring, such as cellular state, micro-environments (e.g., nests), pathogens, microbiome, or culture. Our analysis quantifies how the interaction between limited gene flow and biased ecological inheritance influences the joint evolutionary dynamics of traits together with the conditions they modify, helping understand adaptation via non-genetic modifications. As an illustration, we apply our analysis to a gene-culture coevolution scenario in which genetically-determined learning strategies coevolve with adaptive knowledge. In particular, we show that when social learning is synergistic, selection can favour strategies that generate remarkable levels of knowledge under intermediate levels of both vertical cultural transmission and limited dispersal. More broadly, our theory yields insights into the interplay between genetic and non-genetic inheritance, with implications for how organisms evolve to transform their environments.
High-Throughput Image Analysis of Lipid-Droplet-Bound Mitochondria
Authors: Miller Nathanael , Wolf Dane , Alsabeeh Nour , Mahdaviani Kiana , Segawa Mayuko , Liesa Marc , Shirihai Orian
Published: March 2020

Changes to mitochondrial architecture are associated with various adaptive and pathogenic processes. However, quantification of changes to mitochondrial structures are limited by the yet unmet challenge of defining the borders of each individual mitochondrion within an image.. Here, we describe a novel method for segmenting Brown Adipose Tissue (BAT) images. We describe a granular approach to quantifying subcellular structures, particularly mitochondria in close proximity to lipid droplets, peri-droplet mitochondria. In addition, we lay out a novel machine-learning-based mitochondrial segmentation method that eliminates the bias of manual mitochondrial segmentation and improves object recognition compared to conventional thresholding analyses. By applying these methods, we discovered a significant difference between cytosolic and peridroplet BAT mitochondrial H2O2production, and validated the machine learning algorithm in BAT via norepinephrine-induced mitochondrial fragmentation and comparing manual analyses to the automated analysis. This approach provides a higher-throughput analysis protocol to quantify ratiometric probes in subpopulations of mitochondria in adipocytes.
γ-H2AX is present at mouse meiotic kinetochores
Authors: Guajardo Andrea , Viera Alberto , Parra María Teresa , Valdivia Manuel M. , Rufas Julio S. , Suja José A.
Published: March 2020

The histone variant H2AX phosphorylated on serine 139, named γ-H2AX, is a canonical DNA double-strand breaks marker. During mammalian meiotic prophase I, γ-H2AX participates in meiotic recombination, meiotic sex chromosome inactivation and meiotic silencing of unsynapsed chromatin. In this study, we have analyzed the distribution of γ-H2AX during male mouse meiosis by immunofluorescence on spread and squashed spermatocytes. We have found that γ-H2AX locates at the inner kinetochore plate of meiotic kinetochores in both meiotic divisions. Therefore our results, for the first time, uncover a novel role for γ-H2AX at mammalian meiotic kinetochores.
Energy harvesting wireless sensor for achieving self-powered structural health monitoring system
Authors: Srinivasan Revathy , Hyder Ali Umma Habiba
Published: March 2020

Purpose

On average, a medium-sized satellite consist of almost 500 sensors where powering these sensors in space in such an unreachable environment is critical. Backing this, a compact energy harvester for powering up distant sensors is discussed here is the purpose of this paper. This is in line with the geostationary satellite-powered using the available electromagnetic energy on the satellite panels in space.

Design/methodology/approach

The designed rectenna makes use of a compact wideband receiving antenna operating at the targeted frequency band from 8 to 18 GHz. It also consists of a simple dual diode rectifier topology with a matching circuit, bandpass filter and a resistive load to convert the received radio frequency energy into usable direct current (DC) voltage.

Findings

The rectenna measurement is performed using three different configuration setups. This shows that a maximum DC voltage of 1.8 V and 5-10 mV is harvested from rectifier and rectenna (includes antenna and rectifier) when 20 dBm power is transmitted from the transmitting antenna operating at X and Ku band. This makes the rectenna feasible to power wireless sensors in a structural health monitoring system.

Originality/value

The measurements are performed by considering a real-time environment in space in terms of the distance between the transmitting and receiving antenna, which depends on the far-field of the transmitting antenna in a satellite.