bluuebunny/crossref_metadata_2025 huggingface dataset:
Local adaptation contributes to gene expression divergence in maize
Authors: Blanc Jennifer , Kremling Karl A. G. , Buckler Edward , Josephs Emily B.
Published: August 2020

Gene expression links genotypes to phenotypes, so identifying genes whose expression is shaped by selection will be important for understanding the traits and processes underlying local adaptation. However, detecting local adaptation for gene expression will require distinguishing between divergence due to selection and divergence due to genetic drift. Here, we adapt aQST–FSTframework to detect local adaptation for transcriptome-wide gene expression levels in a population of diverse maize genotypes. We compare the number and types of selected genes across a wide range of maize populations and tissues, as well as selection on cold-response genes, drought-response genes, and coexpression clusters. We identify a number of genes whose expression levels are consistent with local adaptation and show that genes involved in stress-response show enrichment for selection. Due to its history of intense selective breeding and domestication, maize evolution has long been of interest to researchers, and our study provides insight into the genes and processes important for in local adaptation of maize.
The role of CLV1, CLV2 and HPAT homologs in nitrogen-regulation of root development
Authors: Wang Chenglei , Reid James B , Foo Eloise
Published: August 2020

Plants use a variety of hormonal and peptide signals to control root development, including in adapting root development to cope with nutrient stress. Nitrogen (N) is a major limiting factor in plant growth and in response to N stress plants dramatically modulate root development, including in legumes influencing the formation of N-fixing nodules in response to external N supply. Recently, specific CLE peptides and/or receptors important for their perception, including CLV1 and CLV2, have been found to play important roles in root development in a limited number of species, including in some cases the response to N. In the legumeMedicago truncatula, this response also appears to be influenced by RDN1, a member of the hydroxyproline O-arabinosyltransferase (HPAT) family which can modify specific CLE peptides. However, it not known if this signalling pathway plays a central role in root development across species, in particular root responses to N. In this study, we sought to systematically examine the role of homologues of these genes in root development of the legume pea (Pisum sativum. L) and non-legume tomato (Solanum lycopersicum) using a mutant based approach. This included a detailed examination of root development in response to N in these mutant series in tomato. We found no evidence for a role of these genes in pea seedling root development. Furthermore, theCLV1-like FABgene did not influence tomato root development, including N response. In contrast, bothCLV2and theHPAT FINappear to positively influence root size in tomato but do not mediate root responses to N. These suggest a relatively species-specific role for these genes in root development, including N regulation of root architecture.
Gender disparities in international COVID-19 clinical trial leadership
Authors: Cevik Muge , Haque Syed Arefinul , Manne-Goehler Jennifer , Kuppalli Krutika , Sax Paul E. , Majumder Maimuna S. , Orkin Chloe
Published: August 2020

The COVID-19 pandemic offers considerable possibilities for research and leadership that might equalize opportunity in a new field; however, our study finds instead that more than two-thirds of investigators leading COVID-19-related clinical studies are predicted to be men. These gender disparities in trial leadership during the pandemic suggest that the structural reproduction of inequalities in research has taken place once again in this new academic field. This indicates that policies are needed to facilitate the identification and implementation of strategies to correct gender bias. The active participation of women, trans and gender-nonconforming individuals are needed in research to drive scientific discovery and innovation as well as to better address health disparities.
Visual Perception in the Periphery: The Role of Covert Attention Vectors in the Extraction of Semantic Information
Authors: Suri Ikaasa , Wilson Patrick McGranor , Doustmohammadi Saba , De Schutter Anna , Chunwatanapong Thida Sandy , Tan Juanyi , Varadharajulu Sara Divija , O’Connell Nicholas Hunter , Lai Archibald , Dureja Sakshi , Govin River Jonathan Phoenix , Arisaka Katsushi , Mills Elizabeth Anne Falcone
Published: August 2020

Under covert attention, our visual perception deteriorates dramatically as eccentricity increases. This reduction of peripheral visual acuity (PVA) is partially due to the coarse sampling of the retinal ganglion cells towards the periphery, but this property cannot be solely responsible. Other factors, such as character crowding, have been studied, yet the origin of the poor PVA is not entirely understood. This gap motivated us to investigate the PVA by varying the crowding conditions systematically. Under completely crowded conditions (i.e. resembling a full page of text), PVA was observed to be eight times worse than the PVA under uncrowded conditions. By partially crowding the periphery, we obtained PVA values between the fully crowded and uncrowded conditions. On the other hand, crowding the fovea center while leaving the periphery uncrowded improved PVA relative to the uncrowded case. These results support a model for a top-down “covert attention vector” that assists the resulting PVA in a manner analogous to saccadic eye movement for overt attention. We speculate that the attention vector instructs the dorsal pathway to transform the peripheral character to the foveal center. Then, the scale-invariant log-polar retinotopy of the ventral pathway can scale the centered visual input to match the prior memory of the specific character shape.
Glucose clearance and uptake is increased in the SOD1G93Amouse model of amyotrophic lateral sclerosis through an insulin-independent mechanism
Authors: McDonald Tanya S. , Kumar Vinod , Fung Jenny N. , Woodruff Trent M. , Lee John D.
Published: August 2020

Metabolic disturbances are associated with the progression of the neurodegenerative disorder, amyotrophic lateral sclerosis (ALS), however the molecular events that drive energy imbalances in ALS are not completely understood. In this study we aimed to elucidate deficits in energy homeostasis in the SOD1G93Amouse model of ALS. We identified that SOD1G93Amice at mid-symptomatic disease stage have increased oxygen consumption and faster exogenous glucose uptake, despite presenting with normal insulin tolerance. Fasting glucose homeostasis was also disturbed, along with increased liver glycogen stores, despite elevated circulating glucagon, suggesting that glucagon signalling is impaired. Metabolic gene expression profiling of livers indicated that glucose cannot be utilised efficiently in SOD1G93Amice. Overall, we demonstrate that glucose homeostasis and uptake are altered in SOD1G93Amice, which is linked to an increase in insulin-independent glucose uptake and a disturbance in glucagon sensitivity, suggesting glucagon secretion and signalling could be potential therapeutic targets for ALS.
scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses
Authors: Wang Juexin , Ma Anjun , Chang Yuzhou , Gong Jianting , Jiang Yuexu , Fu Hongjun , Wang Cankun , Qi Ren , Ma Qin , Xu Dong
Published: August 2020

Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce the scGNN (single-cell graph neural network) to provide a hypothesis-free deep learning framework for scRNA-Seq analyses. This framework formulates and aggregates cell-cell relationships with graph neural networks and models heterogeneous gene expression patterns using a left-truncated mixture Gaussian model. scGNN integrates three iterative multi-modal autoencoders and outperforms existing tools for gene imputation and cell clustering on four benchmark scRNA-Seq datasets. In an Alzheimer’s disease study with 13,214 single nuclei from postmortem brain tissues, scGNN successfully illustrated disease-related neural development and the differential mechanism. scGNN provides an effective representation of gene expression and cell-cell relationships. It is also a novel and powerful framework that can be applied to scRNA-Seq analyses.
Severity Assessment and Progression Prediction of COVID-19 Patients based on the LesionEncoder Framework and Chest CT
Authors: Feng You-Zhen , Liu Sidong , Cheng Zhong-Yuan , Quiroz Juan C. , Rezazadegan Dana , Chen Ping-Kang , Lin Qi-Ting , Qian Long , Liu Xiao-Fang , Berkovsky Shlomo , Coiera Enrico , Song Lei , Qiu Xiao-Ming , Cai Xiang-Ran
Published: August 2020

Automatic severity assessment and progression prediction can facilitate admission, triage, and referral of COVID-19 patients. This study aims to explore the potential use of lung lesion features in the management of COVID-19, based on the assumption that lesion features may carry important diagnostic and prognostic information for quantifying infection severity and forecasting disease progression.

A novel LesionEncoder framework is proposed to detect lesions in chest CT scans and to encode lesion features for automatic severity assessment and progression prediction. The LesionEncoder framework consists of a U-Net module for detecting lesions and extracting features from individual CT slices, and a recurrent neural network (RNN) module for learning the relationship between feature vectors and collectively classifying the sequence of feature vectors.

Chest CT scans of two cohorts of COVID-19 patients from two hospitals in China were used for training and testing the proposed framework. When applied to assessing severity, this framework outperformed baseline methods achieving a sensitivity of 0.818, specificity of 0.952, accuracy of 0.940, and AUC of 0.903. It also outperformed the other tested methods in disease progression prediction with a sensitivity of 0.667, specificity of 0.838, accuracy of 0.829, and AUC of 0.736. The LesionEncoder framework demonstrates a strong potential for clinical application in current COVID-19 management, particularly in automatic severity assessment of COVID-19 patients. This framework also has a potential for other lesion-focused medical image analyses.
Altitude as a protective factor from COVID-19
Authors: Thomson Timothy M. , Casas Fresia , Guerrero Harold Andre , Figueroa-Mujíca Rómulo , Villafuerte Francisco C. , Machicado Claudia
Published: August 2020

The COVID-19 pandemic had a delayed onset in South America compared to Asia (outside of China), Europe or North America. In spite of the presumed time advantage for the implementation of preventive measures to help contain its spread, the pandemic in that region followed growth rates that paralleled, and currently exceed, those observed several weeks before in Europe. Indeed, in early August 2020, many countries in South and Central America presented among the highest rates in the world of COVID-19 confirmed cases and deaths per million inhabitants. Here, we have taken an ecological approach to describe the current state of the pandemic in Peru and its dynamics. Our analysis supports a protective effect of altitude from COVID-19 incidence and mortality. Further, we provide circumstantial evidence that internal migration through a specific land route is a significant factor progressively overriding the protection from COVID-19 afforded by high altitude. Finally, we show that protection by altitude is independent of poverty indexes and is inversely correlated with the prevalence in the population of risk factors associated with severe COVID-19, including hypertension and hypercholesterolemia. We discuss long-term multisystemic adaptive traits to hypobaric hypoxia as possible mechanisms that may explain the observed protective effect of high altitude from death due to COVID-19.
COVID-19 Case Mortality Rates Continue to Decline in Florida
Authors: Harris Jeffrey E.
Published: August 2020

We studied COVID-19 case mortality in Florida among four successive cohorts of persons at least 50 years of age, each of whom we followed for 28 to 48 days from date of diagnosis. The cohorts were separated by date of diagnosis into four nonoverlapping intervals: March 29 - April 18; April 29 - May 19; May 21 - June 10; and June 14 - July 4, 2020. Case mortality rates declined consistently and significantly over the course of the four intervals: 57% among those aged 50-59 years; 62% among those aged 60-69 years; 52% among those aged 70-79 years; and 34% among those aged 80 or more years. These findings were consistent with progressive improvements in the medical care of COVID-19 patients. We further studied case mortality by hospitalization status. The case mortality rate among hospitalized patients aged 60-69 years fell significantly from the first to the third interval. During the fourth interval, an apparent rise in mortality among hospitalized patients in the same age group was mirrored by a significant decline in mortality among those not hospitalized. These findings were consistent with the out-of-hospital treatment of some patients who would have previously been hospitalized.

This study relies exclusively on publicly available, aggregate health data that contain no individual identifiers. The author has no competing interests and no funding sources to declare. This article represents to the sole opinion of its author and does not necessarily represent the opinions of the Massachusetts Institute of Technology, the National Bureau of Economic Research, Eisner Health, or any other organization.
The effect of wildSaccharomyceson composition and aroma of the Sauvignon blanc
Authors: Mendes Sandra D. C. , Arcari Stefany Grützmann , Ramirez-Castrillon Mauricio , Werner Simone Silmara , Valente Patricia
Published: August 2020

Saccharomycesstrains isolated from vineyards in Southern Brazil were used as starter in micro-fermentations of Sauvignon Blanc juice (SB) to study the ability to produce different aromatic profiles. The molecular characterization allowed to differentiate the isolates from vineyards 06 CE, 11CE, 33CE, 01PP, 12M, 13PP, 26PP, 28AD, 41PP from the reference strain (2048SC) used in wine production. Under the same conditions tested, each strain belonging to the genusSaccharomycesproduced metabolites in different concentration and combination, significantly influencing the aroma of the SB must. Volatile compounds such as octanoic acid, diethyl succinate and ethyl lactate were associated with the strains 26PP, 41PP, 01PP and 12M, while the strains 33CE, 28AD, 13PP and 06 CE were associated with the production of ethyl acetate, 1-hexanol, highlighting 06CE for production of 1-hexanol (592.87 ± 17.46 µg/L). In addition, the olfactory activity value (OAV> 1) allowed the evaluation of the range of participation of each compound in the final SB fermented. Finally, the selected wild strains are promising to improve the regional character of the wine.
Extensive Phenomenological Overlap between Induced and Naturally-Occurring Synaesthetic Experiences
Authors: Schwartzman David. J. , Oblak Ales , Rothen Nicolas , Bor Daniel , Seth Anil. K.
Published: August 2020

Grapheme-colour synaesthesia (GCS) is defined by additional perceptual experiences, which are automatically and consistently triggered by specific inducing stimuli. The associative nature of GCS has motivated attempts to induce synaesthesia by means of associative learning. Two recent studies have shown that extensive associative training can generate not only behavioural (consistency and automaticity) and neurophysiological markers of GCS, but also synaesthesia-like phenomenology [1,2]. However, these studies provided only superficial descriptions regarding the training-related changes in subjective experience: they did not directly assess how closely induced synaesthetic experiences mirror those found in natural GCS. Here we report an extended qualitative analysis of the transcripts of the semi-structured interviews obtained following the completion of the associative training protocol used by [2]. In addition, we performed a comparable analysis of responses to an interview with a new population of natural occurring grapheme-colour synaesthetes (NOS), allowing us to directly compare the phenomenological dimensions of induced and naturally occurring synaesthetic experience. Our results provide an extensive addition to the description of the phenomenology of NOS experience, revealing a high degree of heterogeneity both within and across all experiential categories. Capitalising on this unique level of detail, we identified a number of shared experiential categories between NOS and induced synaesthesia-like (ISL) groups, including:stability of experience, location of colour experience, shape of co-occurring colour experience, relative strength of colour experience and automaticity of colour experience. Only the automaticity of colour experience differed significantly between the two groups: NOS experience was reported as being mostly automatic, whereas induced ISL were mostly described as being ‘wilful’. We observed three additional experiential categories relating to the automaticity of synaesthetic experience within the NOS group:contextually varied experience, semi-automatic experienceandreflective association, which suggests that, as with other experiential categories, the automaticity of synaesthetic experience is also highly heterogeneous. Our results provide new evidence that that intensive training of letter-colour associations can alter conscious perceptual experiences in non-synaesthetes, and that such alterations produce synaesthesia-like phenomenology which substantially resembles similarities to natural grapheme-colour synaesthesia.
Genomics of a killifish from the Seychelles islands supports transoceanic island colonization and reveals relaxed selection of developmental genes
Authors: Cui Rongfeng , Tyers Alexandra M , Malubhoy Zahabiya Juzar , Wisotsky Sadie , Valdesalici Stefano , Henriette Elvina , Pond Sergei L Kosakovsky , Valenzano Dario Riccardo
Published: August 2020

How freshwater fish colonize remote islands remains an evolutionary puzzle. Tectonic drift and trans-oceanic dispersal models have been proposed as possible alternative mechanisms. Integrating dating of known tectonic events with population genetics and experimental test of salinity tolerance in the Seychelles islands golden panchax (Pachypanchax playfairii), we found support for trans-oceanic dispersal being the most likely scenario. At the macroevolutionary scale, the non-annual killifish golden panchax shows stronger genome-wide purifying selection compared to annual killifishes from continental Africa. Reconstructing past demographies in isolated golden panchax populations provides support for decline in effective population size, which could have allowed slightly deleterious mutations to segregate in the population. Unlike annual killifishes, where relaxed selection preferentially targets aging-related genes, relaxation of purifying selection in golden panchax affects genes involved in developmental processes, including fgf10.
Induction of core symptoms of autism spectrum disorders by in vivo CRISPR/Cas9-based gene editing in the brain of adolescent rhesus monkeys
Authors: Wu Shi-Hao , Li Xiao , Qin Dong-Dong , Zhang Lin-Heng , Cheng Tian-Lin , Chen Zhi-Fang , Nie Bin-Bin , Ren Xiao-Feng , Wu Jing , Wang Wen-Chao , Hu Ying-Zhou , Gu Yilin , Lv Long-Bao , Yin Yong , Hu Xin-Tian , Qiu Zi-Long
Published: August 2020

Although CRISPR/Cas9-mediated gene editing is widely applied to mimic human disorders, whether acute manipulation of disease-causing genes in the brain leads to behavioral abnormalities in non-human primates remains to be determined. Here we induced genetic mutations in MECP2, a critical gene linked to Rett syndrome (RTT) and autism spectrum disorders (ASDs), in the hippocampus (DG and CA1–4) of adolescent rhesus monkeys (Macaca mulatta) in vivo via adeno-associated virus (AAV)-delivered Staphylococcus aureus Cas9 with sgRNAs targeting MECP2. In comparison to monkeys injected with AAV-SaCas9 alone (n = 4), numerous autistic-like behavioral abnormalities were identified in the AAV-SaCas9-sgMECP2-injected monkeys (n = 7), including social interaction deficits, abnormal sleep patterns, insensitivity to aversive stimuli, abnormal hand motions and defective social reward behaviors. Furthermore, some aspects of ASDs and RTT, such as stereotypic behaviors, did not appear in the MECP2 gene-edited monkeys, suggesting that different brain areas likely contribute to distinct ASD symptoms. This study showed that acute manipulation of disease-causing genes via in vivo gene editing directly led to behavioral changes in adolescent primates, paving the way for the rapid generation of genetically engineered non-human primate models for neurobiological studies and therapeutic development.
The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence
Authors: Zhang Fan , Wang Yuan , Zhang Luyang , Wang Chunjie , Chen Deping , Liu Haibo , Xu Ren , Haynes Cole M. , Shim Jae-Hyuck , Ge Xianpeng
Published: August 2020

The dysfunction of the cellular endolysosomal pathway, such as in lysosomal storage diseases, can cause severe musculoskeletal disorders. However, how endolysosomal dysfunction causes musculoskeletal abnormalities remains poorly understood, limiting therapeutic options. Here, we report that CHMP5, a member of the endosomal sorting complex required for transport (ESCRT)-III protein family, is essential to maintain the endolysosomal pathway and regulate bone formation in osteogenic lineage cells. Genetic ablation ofChmp5in mouse osteogenic cells increases bone formation in vivo and in vitro. Mechanistically,Chmp5deletion causes endolysosomal dysfunction by decreasing the VPS4A protein, and CHMP5 overexpression is sufficient to increase the VPS4A protein. Subsequently, endolysosomal dysfunction disturbs mitochondrial functions and increases mitochondrial ROS, ultimately resulting in skeletal cell senescence. Senescent skeletal cells cause abnormal bone formation by combining cell-autonomous and paracrine actions. Importantly, elimination of senescent cells using senolytic drugs can alleviate musculoskeletal abnormalities inChmp5conditional knockout mice. Therefore, our results show that cell senescence represents an underpinning mechanism and a therapeutic target for musculoskeletal disorders caused by the aberrant endolysosomal pathway. These results also uncover the function and mechanism of CHMP5 in the regulation of cell senescence by affecting the endolysosomal-mitochondrial pathway.
Sex identification in embryos and adults of Darwin’s finches
Authors: Dobreva Mariya P. , Lynton-Jenkins Joshua G. , Chaves Jaime A. , Tokita Masayoshi , Bonneaud Camille , Abzhanov Arkhat
Published: August 2020

Darwin’s finches, endemic to the Galapagos and Cocos islands, are an iconic example of adaptive radiation and evolution under natural selection. Comparative genetic studies using embryos of Darwin’s finches have shed light on the possible evolutionary processes underlying the speciation of this clade. Molecular identification of the sex of embryonic samples is important for such studies, where this information often cannot be inferred otherwise. We tested a fast and simple chicken embryo protocol for extraction of genomic DNA on Darwin’s finch embryos. In addition, we suggest modifications to two of the previously reported PCR primer sets forCHD1, a gene used for sexing in adult passerine birds. The sex of all 29 tested embryos of six species of Darwin’s finches was determined successfully by PCR, using both primer sets. Hatchlings/nestlings and fledglings are also impossible to distinguish visually. This includes juveniles of sexually dimorphic species which are yet to moult in adult-like plumage and beak colouration. Furthermore, four species of Darwin’s finches are monomorphic, males and females looking alike. Therefore, sex assessment in the field can be a source of error, especially with respect to juveniles and mature monomorphic birds outside of the mating season. We caught 567 juveniles and adults belonging to six species of Darwin’s finches and only 44% had unambiguous sex-specific morphology. We sexed 363 birds by PCR, including individuals sexed based on marginal sex specific morphological traits (N=278) and birds which were impossible to classify in the field (N=39). For birds with marginal sex specific traits, PCR results revealed a 13% sexing error rate. This demonstrates that PCR based sexing can improve field studies on Darwin’s finches, especially when individuals with unclear sex-related morphology are involved. The protocols used here provide an easy and reliable way to sex Darwin’s finches throughout ontogeny, from embryos to adults.
Areca catechu-(Betel-nut)-induced whole transcriptome changes associated with diabetes, obesity and metabolic syndrome in a human monocyte cell line
Authors: Cardoso Shirleny , Ogunkolade B. William , Lowe Rob , Savage Emanuel , Mein Charles A , Boucher Barbara J , Hitman Graham A
Published: August 2020

Betel-nut consumption is the fourth most common addictive habit globally and there is good evidence to link it with obesity, type 2 diabetes and the metabolic syndrome. We adopted a genome-wide transcriptomic approach in a human monocyte cell line incubated with arecoline and its nitrosated products to identify gene expression changes relevant to obesity, type 2 diabetes and the metabolic syndrome. The THP1 monocyte cell line was incubated separately with arecoline and 3-methylnitrosaminopropionaldehyde (MNPA) in triplicate for 24 hours and pooled cDNA indexed paired-end libraries were sequenced (Illumina NextSeq 500). After incubation with arecoline and MNPA, 15 and 39 genes respectively had significant changes in their expression (q<0.05, log fold change 1.5). Eighteen of those genes have reported associations with type 2 diabetes and obesity in humans; of these genes there was strong evidence to implicateCLEC10A,MAPK8IP1,NEGR1,NQ01andINHBE. In summary, these pilot studies have identified a large number of genes whose expression was changed significantly in human TPH1 cells following incubation with arecoline or with 3-methylnitrosaminopropionaldehyde. These findings suggest that further investigation of these genes in betel-quid chewers with obesity and/or type 2 diabetes is warranted.
Mutational Survivorship Bias: The case of PNKP
Authors: Bermudez-Guzman Luis , Jimenez-Huezo Gabriel , Arguedas Andrés , Leal Alejandro
Published: August 2020

The molecular function of a protein relies on its structure. Understanding how mutations alter structure and function in multi-domain proteins, is key to elucidate how a pathological phenotype is generated. However, one may fall into the logical bias of assessing protein damage only based on the mutations that are viable (survivorship bias), which can lead to partial conclusions. This is the case of PNKP, an important nuclear and mitochondrial DNA repair enzyme with kinase and phosphatase function. Most mutations in PNKP are confined to the kinase domain, leading to a pathological spectrum of three apparently distinct clinical entities. Since proteins and domains may have a different tolerance to disease causing mutations, we evaluated whether mutations in PNKP are under survivorship bias. Even when all mutations in the kinase domain are deleterious, we found a mayor mutation tolerability landscape in terms of survival. Instead, the phosphatase domain is less tolerant due to its low mutation rates, higher degree of sequence conservation, lower dN/dS ratios, and more disease-propensity hotspots. Thus, in multi-domain proteins, we propose the term “Wald’s domain” for those who are not apparently more associated with disease, but that are less resistant to mutations in terms of survival. Together, our results support previous experimental evidence that demonstrated that the phosphatase domain is functionally more necessary and relevant for DNA repair, especially in the context of the development of the central nervous system. Thus, this bias should be taken into account when analyzing the mutational landscape in protein structure, function, and finally in disease.
Body size and food plants drive local extinction risk in butterflies
Authors: Palash Anwar , Paul Shatabdi , Resha Sabrina Karim , Khan Md Kawsar
Published: August 2020

Lepidoptera, butterflies and moths, are significant pollinators and ecosystem health indicators. Therefore, monitoring their diversity, distribution, and extinction risks are of critical importance. We aim to understand the drivers of the local extinction risks of the butterflies in Bangladesh. We conducted a systematic review to extract the diversity, distribution and local extinction risks of the butterflies of Bangladesh, and possible drivers of their extinction, e.g., body size, host plants and nectar plants. We updated the current checklist, which now consists of 463 species. We provided distribution and extinctions risk atlas showing both the diversity and extinction risks were highest in the eastern region of Bangladesh. We tested whether body size and host plants contribute to the local extinction risks of butterflies. We predicted butterflies with larger body size and fewer host plants and nectar plants would be in greater extinction risk. Accordingly, we showed that extinction risk was higher in larger butterflies than smaller butterflies, and in butterflies with a fewer number of host plants and nectar plants than the butterflies with higher number host plants. Our study highlights the contribution of body size and host plants as potential drivers of the local extinction risks of butterflies.
Extreme ecological specialization in a rainforest mammal, the Bornean tufted ground squirrel,Rheithrosciurus macrotis
Authors: Marshall Andrew J. , Meijaard Erik , Leighton Mark
Published: August 2020

The endemic Bornean tufted ground squirrel,Rheithrosciurus macrotis, has attracted great interest among biologists and the public recently. Nevertheless, we lack information on the most basic aspects of its biology. Here we present the first empirical data on the feeding ecology of tufted ground squirrels, and use data from 81 sympatric mammalian and avian vertebrates to place it within a broad comparative context.R. macrotisis a dedicated seed predator and shows much more extreme ecological specialization than any other vertebrate, feeding on a far smaller subset of available plant foods and demonstrating a greater reliance on a single plant species–Canarium decumanum–than any other vertebrate taxon. Our results suggest thatR. macrotisplays an important, previously unknown role in the ecology of Bornean lowland forests, and highlight how much we have yet to learn about the fauna inhabiting some of the most diverse, and most severely threatened, ecosystems on the planet.
Reconciling fish and farms: Methods for managing California rice fields as salmon habitat
Authors: Holmes Eric J. , Saffarinia Parsa , Rypel Andrew L. , Bell-Tilcock Miranda N. , Katz Jacob V. , Jeffres Carson A.
Published: August 2020

The rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as promising habitat for rearing juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods for rearing fall-run Chinook Salmon on winter-flooded rice fields in the Yolo Bypass, a modified floodplain of the Sacramento River in California. These included: 1) influence of field substrate differences from previous season rice harvest; 2) effects of depth refugia from avian predators (trenches); 3) field drainage methods to promote efficient egress of fish; and 4) in-field salmon survivorship over time. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant when directly compared to the adjacent Sacramento River. Correspondingly, somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater versus fish in the adjacent Sacramento River. Post-harvest field substrate treatments had little effect on the lower trophic food web and had an insignificant effect on growth rates of in-field salmon. Though depth refugia did not directly increase survival, it buffered maximum water temperatures in the trenches and facilitated outmigration from fields during draining. Rapid field drainage methods yielded the highest survival and were preferable to drawn-out drainage methods. High initial mortality immediately after stocking was observed in the survival over time experiment with stable and high survival after the first week. In-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. The abundance of food resources and exceptionally high growth rates observed during these experiments illustrate the benefits associated with reconciling off-season agricultural land use with fish conservation practices. Without any detriment to flood control or agricultural yield, there is great promise for reconciliation ecology between agricultural floodplains and endangered fish conservation where minor alterations to farm management practices could greatly enhance the effectiveness of fish conservation outcomes.
Antidiabetic drug therapy alleviates type 1 diabetes in mice by promoting pancreatic α-cell transdifferentiation
Authors: Sarnobat Dipak , Moffett Charlotte R , Tanday Neil , Reimann Frank , Gribble Fiona M , Flatt Peter R , Tarasov Andrei I
Published: August 2020

Gut incretins, glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic peptide (GIP), enhance secretion of insulin in a glucose-dependent manner, predominantly by elevating cytosolic levels of cAMP in pancreatic β-cells. Successful targeting of the incretin pathway by several drugs, however, suggests the antidiabetic mechanism is likely to span beyond the acute effect on hormone secretion and include, for instance, stimulation of β-cell growth and/or proliferation. Likewise, the antidiabetic action of kidney sodium-glucose linked transporter-2 (SGLT-2) inhibitors exceeds simple increase glucose excretion. Potential reasons for these ‘added benefits’ may lie in the long-term effects of these signals on developmental aspects of pancreatic islet cells. In this work, we explored if the incretin mimetics or SGLT-2 inhibitors can affect the size of the islet α- or β-cell compartments, under the condition of β-cell stress.

To that end, we utilised mice expressing YFP specifically in pancreatic α-cells, in which we modelled type 1 diabetes by injecting streptozotocin, followed by a 10-day administration of liraglutide, sitagliptin or dapagliflozin.

We observed an onset of diabetic phenotype, which was partially reversed by the administration of the antidiabetic drugs. The mechanism for the reversal included induction of β-cell proliferation, due to a decrease in β-cell apoptosis and, for the incretin mimetics, transdifferentiation of α-cells into β-cells.

Our data therefore emphasize the role of chronic incretin signalling in induction of α-/β-cell transdifferentiation. We conclude that incretin peptides may act directly on islet cells, making use of the endogenous local sites of ‘ectopic’ expression, whereas SGLT-2 inhibitors work via protecting β-cells from chronic hyperglycaemia.

Graphical abstract
Esrrbis a cell cycle dependent XEN priming factor balancing between pluripotency and differentiation
Authors: Levi Sapir Herchcovici , Feldman Sharon , Arnon Lee , Lahav Shlomtzion , Awawdy Muhammad , Alajem Adi , Bavli Danny , Sun Xue , Buganim Yosef , Ram Oren
Published: August 2020

Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying retinoic acid, a multi-linage differentiation assay, on G1 and G2/M pre-sorted ESCs, we show that only G2/M ESCs were capable of differentiating into extraembryonic endoderm cells (XENs), whereas cells in the G1 phase predominantly produce Epiblast Stem Cells. We identified ESRRB, a key pluripotency factor that is upregulated during G2/M phase, as a central driver of XEN differentiation. Furthermore, enhancer chromatin states based on WT andEsrrb-KO ESCs show association of ESRRB with XEN poised enhancers. Cells engineered to overexpress Esrrb during G1 allow ESCs to produce XENs, while ESRRB-KO ESCs lost their potential to differentiate into XEN. In addition, Embryonic bodies (EBs) are not affected by deletion of ESRRB but trigger apoptosis upon attempts to apply direct XEN differentiation. Taken together, this study reveals an important functional link between Esrrb and cell-cycle states during the exit from pluripotency. Finally, the experimental scheme of single cell RNA-seq in the context of cell cycle can be further expanded into other cellular systems to better understand differentiation decisions and cancer models.
Non-canonical, potassium-driven cerebrospinal fluid clearance
Authors: Xu Huixin , Fame Ryann M , Sadegh Cameron , Sutin Jason , Naranjo Christopher , Syau Della , Cui Jin , Shipley Frederick B , Vernon Amanda , Gao Fan , Zhang Yong , Holtzman Michael J. , Heiman Myriam , Warf Benjamin C , Lin Pei-Yi , Lehtinen Maria K
Published: August 2020

Cerebrospinal fluid (CSF) provides vital support for the brain. Abnormal CSF accumulation is deleterious for perinatal neurodevelopment, but how CSF leaves the brain during this critical period is unknown. We found in mice a postnatal neurodevelopmental transition phase featuring precipitous CSF K+clearance, accompanied by water, through the choroid plexus (ChP). The period corresponds to a human fetal stage when canonical CSF clearance pathways have yet to form and congenital hydrocephalus begins to manifest. Unbiased ChP metabolic and ribosomal profiling highlighted this transition phase with increased ATP yield and activated energy-dependent K+transporters, in particular the Na+-K+-Cl−and water cotransporter NKCC1. ChP-targeted NKCC1 overexpression enhanced K+-driven CSF clearance and enabled more permissive cerebral hydrodynamics. Moreover, ventriculomegaly in an obstructive hydrocephalus model was improved by ChP-targeted NKCC1 overexpression. Collectively, we identified K+-driven CSF clearance through ChP during a transient but critical neurodevelopmental phase, with translational value for pathologic conditions.
Structural and functional microbial community response to short-term impact of switching between tillage and no-tillage at soil aggregate level
Authors: Frene Juan Pablo , Gabbarini Luciano Andrés , Wall Luis Gabriel
Published: August 2020

An understanding of the distribution of soil microorganisms and enzyme activities at different soil aggregate level could help to understand the mechanisms operating behind different tillage management on soil structure and function. Our objective was to determine if the microbial community structure and soil enzymes activity (EA) associated with different aggregate fractions changed within the transition at switching between no-till and conventional tillage at 30 months after the switch of management on a base line field of 27 years long were no-till (NT) and conventional tillage (CT) were side by side compared. Part of NT plot was turned into new CT (n-CT) while part of CT plot was turned into new NT (n-NT). Aggregate fractions of 2000-250, 250-63, 63-20, 20-2 and 2-0.1μm were obtained from soil samples taken at 30 months after the switch. Specific microbial abundances, measured by qPCR, and EAs were greatest on 2-0.1μm following by 20-2and 2000-250μm. The EAs showed the highest activities in the CT (β-Glucosidase and β-D-cellobiosidase) and in the nCT (Phosphatase and N-acetyl-β-Glucosaminidase) in 2000-250μm. In contrast, in the intermediate fractions (250-63μm and 63-20μm), the highest activities were observed in NT soil. Microbial communities were significantly different among different aggregates. In the 20-2μm fraction, fungi were able to differentiate between current treatments, and bacteria and archaea showed similar trends. In 2000-250μm, the treatments were associated by their historical management, and the abundances in CT samples were superior to those of the NT. In contrast, in the fractions 250-63 and 63-20μm, the NT samples showed greater abundances to those of the CT and the new treatment samples have suffered differences from historical treatments. In conclusion, tillage systems influenced the spatial distribution of soil enzymes as well as the abundances of microbial communities in the different soil aggregate size fractions.

Highlights

Soil microbial structure and functional activity showed a heterogeneous distribution within aggregate soil fraction.

Distribution of functions and microbial structure is shaped by tillage soil management

The greater values of microbial abundance and soil activity appeared at smaller aggregates.

Fungi abundance significantly enhanced under NT than the CT at 20-2 μm.
Photosynthetic resistance and resilience under drought and rewatering in maize plants
Authors: Qi Miao , Liu Xiaodi , Li Yibo , Song He , Zhang Feng , Xu Zhenzhu , Zhou Guangsheng
Published: August 2020

Abnormally altered precipitation patterns induced by climate change have profound global effects on crop production. However, the plant functional responses to various precipitation regimes remain unclear. Here, greenhouse and field experiments were conducted to determine how maize plant functional traits respond to drought, flooding, and rewatering. Drought and flooding hampered photosynthetic capacity, particularly when severe and/or prolonged. Most photosynthetic traits recovered after rewatering, with few compensatory responses. Rewatering often elicited high photosynthetic resilience in plants exposed to severe drought at the end of plant development, with the response strongly depending on the drought severity/duration and plant growth stage. The associations of chlorophyll concentrations with photosynthetically functional activities were stronger during post-tasselling than pre-tasselling, implying an involvement of leaf age/senescence in responses to episodic drought and subsequent rewatering. Coordinated changes in chlorophyll content, gas exchange, fluorescence parameters (PSII quantum efficiency and photochemical/non-photochemical radiative energy dissipation) possibly contributed to the enhanced drought resistance and resilience and suggested a possible regulative trade-off. These findings provide fundamental insights into how plants regulate their functional traits to deal with sporadic alterations in precipitation. Breeding and management of plants with high resistance and resilience traits could help crop production under future climate change.
TheArabidopsis thalianaNIP2;1 Lactic Acid Channel promotes Plant Survival Under Low Oxygen Stress
Authors: Beamer Zachary , Routray Pratyush , Choi Won-Gyu , Spangler Margaret K. , Lokdarshi Ansul , Roberts Daniel M.
Published: August 2020

Under anaerobic stressArabidopsis thalianainduces the expression of a collection of core hypoxia genes that encode proteins associated with an adaptive response. Included in these core hypoxia genes isNIP2;1, which encodes a member of the “Nodulin-like Intrinsic Protein” (NIP) subgroup of the aquaporin superfamily of membrane channel proteins. Under normal growth,NIP2;1expression is limited to the “anoxia core” region of the root stele, but shows substantial induction in response to low oxygen stress (as high as 1000-fold by 2-4 hr of hypoxia challenge), and accumulates in all root tissues. During hypoxia,NIP2;1-GFP, accumulates on the cell surface by 2 hr and then is distributed between the cell surface and internal membranes during sustained hypoxia, and remains elevated in root tissues through 4 hrs of reoxygenation recovery. T-DNA insertional mutantnip2;1plants show elevation of lactic acid within root tissues, and a reduced efflux of lactic acid and acidification of the external medium. Together with previous biochemical evidence demonstrating that NIP2;1 has lactic acid permease activity, the present work supports the hypothesis that the protein facilitates the release of cellular lactate to the rhizosphere to prevent lactic acid toxicity. In support of this,nip2;1plants show poorer survival to argon-induced hypoxia stress.Nip2;1mutant plants also show elevated expression of ethanolic fermentation transcripts, as well as reduced expression the lactate metabolic enzyme GOX3, suggesting that the altered efflux of lactate through NIP2;1 regulates other pyruvate and lactate metabolism pathways.

One-sentence Summary

The NIP2;1 lactic acid permease is necessary for an optimum response to low oxygen stress through the release of lactate from roots during hypoxia stress.
High-precision protein-tracking with interferometric scattering microscopy
Authors: Taylor Richard W. , Holler Cornelia , Mahmoodabadi Reza Gholami , Küppers Michelle , Dastjerdi Houman Mirzaalian , Zaburdaev Vasily , Schambony Alexandra , Sandoghdar Vahid
Published: August 2020

The mobility of proteins and lipids within the cell, sculpted oftentimes by the organisation of the membrane, reveals a great wealth of information on the function and interaction of these molecules as well as the membrane itself. Single particle tracking has proven to be a vital tool to study the mobility of individual molecules and unravel details of their behaviour. Interferometric scattering (iSCAT) microscopy is an emerging technique well suited for visualising the diffusion of gold nanoparticle-labelled membrane proteins to a spatial and temporal resolution beyond the means of traditional fluorescent labels. We discuss the applicability of interferometric single particle tracking (iSPT) microscopy to investigate the minutia in the motion of a protein through measurements visualising the mobility of the epidermal growth factor receptor in various biological scenarios on the live cell.
E-scape: consumer specific landscapes of energetic resources derived from stable isotope analysis and remote sensing
Authors: James W. Ryan , Santos Rolando O. , Rehage Jennifer S. , Doerr Jennifer C. , Nelson James A.
Published: August 2020

Energy and habitat distribution are inherently linked. Energy is a major driver of the distribution of consumers, but estimating how much specific habitats contribute to the energetic needs of a consumer can be problematic. We present a new approach that combines remote sensing information and stable isotope ecology to produce maps of energetic resources (E-scapes).E-scapes project species specific resource use information onto the landscape to classify areas based on energetic importance and successfully predict the biomass and energy density of a consumer in salt marsh habitats in coastal Louisiana, USA. OurE-scape maps can be used alone or in combination with existing models to improve habitat management and restoration practices and have potential to be used to test fundamental movement theory.