bluuebunny/crossref_metadata_2025 huggingface dataset:
The Genealogy of Sequences Containing Multiple Sites Subject to Strong Selection in a Subdivided Population
Authors: Nordborg Magnus , Innan Hideki
Published: April 2021

A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.
Nonrandom Homolog Segregation at Meiosis I in Schizosaccharomyces pombe Mutants Lacking Recombination
Authors: Davis Luther , Smith Gerald R
Published: April 2021

Physical connection between homologous chromosomes is normally required for their proper segregation to opposite poles at the first meiotic division (MI). This connection is generally provided by the combination of reciprocal recombination and sister-chromatid cohesion. In the absence of meiotic recombination, homologs are predicted to segregate randomly at MI. Here we demonstrate that in rec12 mutants of the fission yeast Schizosaccharomyces pombe, which are devoid of meiosis-induced recombination, homologs segregate to opposite poles at MI 63% of the time. Residual, Rec12-independent recombination appears insufficient to account for the observed nonrandom homolog segregation. Dyad asci are frequently produced by rec12 mutants. More than half of these dyad asci contain two viable homozygous-diploid spores, the products of a single reductional division. This set of phenotypes is shared by other S. pombe mutants that lack meiotic recombination, suggesting that nonrandom MI segregation and dyad formation are a general feature of meiosis in the absence of recombination and are not peculiar to rec12 mutants. Rec8, a meiosis-specific sister-chromatid cohesin, is required for the segregation phenotypes displayed by rec12 mutants. We propose that S. pombe possesses a system independent of recombination that promotes homolog segregation and discuss possible mechanisms.
Evidence for Inversion Polymorphism Related to Sympatric Host Race Formation in the Apple Maggot Fly,Rhagoletis pomonella
Authors: Feder Jeffrey L , Roethele Joseph B , Filchak Kenneth , Niedbalski Julie , Romero-Severson Jeanne
Published: April 2021

Evidence suggests that the apple maggot, Rhagoletis pomonella (Diptera: Tephritidae) is undergoing sympatric speciation (i.e., divergence without geographic isolation) in the process of shifting and adapting to a new host plant. Prior to the introduction of cultivated apples (Malus pumila) in North America, R. pomonella infested the fruit of native hawthorns (Crataegus spp.). However, sometime in the mid-1800s the fly formed a sympatric race on apple. The recently derived apple-infesting race shows consistent allele frequency differences from the hawthorn host race for six allozyme loci mapping to three different chromosomes. Alleles at all six of these allozymes correlate with the timing of adult eclosion, an event dependent on the duration of the overwintering pupal diapause. This timing difference differentially adapts the univoltine fly races to an ∼3- to 4-week difference in the peak fruiting times of apple and hawthorn trees, partially reproductively isolating the host races. Here, we report finding substantial gametic disequilibrium among allozyme and complementary DNA (cDNA) markers encompassing the three chromosomal regions differentiating apple and hawthorn flies. The regions of disequilibrium extend well beyond the previously characterized six allozyme loci, covering substantial portions of chromosomes 1, 2, and 3 (haploid n = 6 in R. pomonella). Moreover, significant recombination heterogeneity and variation in gene order were observed among single-pair crosses for each of the three genomic regions, implying the existence of inversion polymorphism. We therefore have evidence that genes affecting diapause traits involved in host race formation reside within large complexes of rearranged genes. We explore whether these genomic regions (inversions) constitute coadapted gene complexes and discuss the implications of our findings for sympatric speciation in Rhagoletis.
Experimental Prediction of the Natural Evolution of Antibiotic Resistance
Authors: Barlow Miriam , Hall Barry G
Published: April 2021

The TEM family of β-lactamases has evolved to confer resistance to most of the β-lactam antibiotics, but not to cefepime. To determine whether the TEM β-lactamases have the potential to evolve cefepime resistance, we evolved the ancestral TEM allele, TEM-1, in vitro and selected for cefepime resistance. After four rounds of mutagenesis and selection for increased cefepime resistance each of eight independent populations reached a level equivalent to clinical resistance. All eight evolved alleles increased the level of cefepime resistance by a factor of at least 32, and the best allele improved by a factor of 512. Sequencing showed that alleles contained from two to six amino acid substitutions, many of which were shared among alleles, and that the best allele contained only three substitutions.
Conjugational Hyperrecombination Achieved by Derepressing the LexA Regulon, Altering the Properties of RecA Protein and Inactivating Mismatch Repair in Escherichia coli K-12
Authors: Lanzov Vladislav A , Bakhlanova Irina V , Clark Alvin J
Published: April 2021

The frequency of recombinational exchanges (FRE) that disrupt co-inheritance of transferred donor markers in Escherichia coli Hfr by F- crosses differs by up to a factor of two depending on physiological factors and culture conditions. Under standard conditions we found FRE to be 5.01 ± 0.43 exchanges per 100-min units of DNA length for wild-type strains of the AB1157 line. Using these conditions we showed a cumulative effect of various mutations on FRE. Constitutive SOS expression by lexA gene inactivation (lexA71::Tn5) and recA gene mutation (recA730) showed, respectively, ∼4- and 7-fold increases of FRE. The double lexA71 recA730 combination gave an ∼17-fold increase in FRE. Addition of mutS215::Tn10, inactivating the mismatch repair system, to the double lexA recA mutant increased FRE to ∼26-fold above wild-type FRE. Finally, we showed that another recA mutation produced as much SOS expression as recA730 but increased FRE only 3-fold. We conclude that three factors contribute to normally low FRE under standard conditions: repression of the LexA regulon, the properties of wild-type RecA protein, and a functioning MutSHL mismatch repair system. We discuss mechanisms by which the lexA, recA, and mutS mutations may elevate FRE cumulatively to obtain hyperrecombination.
Crossover Interference in Saccharomyces cerevisiae Requires a TID1/RDH54- and DMC1-Dependent Pathway
Authors: Shinohara Miki , Sakai Kazuko , Shinohara Akira , Bishop Douglas K
Published: April 2021

Two RecA-like recombinases, Rad51 and Dmc1, function together during double-strand break (DSB)-mediated meiotic recombination to promote homologous strand invasion in the budding yeast Saccharomyces cerevisiae. Two partially redundant proteins, Rad54 and Tid1/Rdh54, act as recombinase accessory factors. Here, tetrad analysis shows that mutants lacking Tid1 form four-viable-spore tetrads with levels of interhomolog crossover (CO) and noncrossover recombination similar to, or slightly greater than, those in wild type. Importantly, tid1 mutants show a marked defect in crossover interference, a mechanism that distributes crossover events nonrandomly along chromosomes during meiosis. Previous work showed that dmc1Δ mutants are strongly defective in strand invasion and meiotic progression and that these defects can be partially suppressed by increasing the copy number of RAD54. Tetrad analysis is used to show that meiotic recombination in RAD54-suppressed dmc1Δ cells is similar to that in tid1; the frequency of COs and gene conversions is near normal, but crossover interference is defective. These results support the proposal that crossover interference acts at the strand invasion stage of recombination.
Normal Synaptonemal Complex and Abnormal Recombination Nodules in Two Alleles of the Drosophila Meiotic Mutant mei-W68
Authors: Carpenter Adelaide T C
Published: April 2021

The meiotic phenotypes of two mutant alleles of the mei-W68 gene, 1 and L1, were studied by genetics and by serial-section electron microscopy. Despite no or reduced exchange, both mutant alleles have normal synaptonemal complex. However, neither has any early recombination nodules; instead, both exhibit high numbers of very long (up to 2 μm) structures here named “noodles.” These are hypothesized to be formed by the unchecked extension of identical but much shorter structures ephemerally seen in wild type, which may be precursors of early recombination nodules. Although the mei-W68L1 allele is identical to the mei-W681 allele in both the absence of early recombination nodules and a high frequency of noodles (i.e., it is amorphic for the noodle phene), it is hypomorphic in its effects on exchange and late recombination nodules. The differential effects of this allele on early and late recombination nodules are consistent with the hypothesis that Drosophila females have two separate recombination pathways—one for simple gene conversion, the other for exchange.
Dominance of Mutations Affecting Viability inDrosophila melanogaster
Authors: Fry James D , Nuzhdin Sergey V
Published: April 2021

There have been several attempts to estimate the average dominance (ratio of heterozygous to homozygous effects) of spontaneous deleterious mutations in Drosophila melanogaster, but these have given inconsistent results. We investigated whether transposable element (TE) insertions have higher average dominance for egg-to-adult viability than do point mutations, a possibility suggested by the types of fitness-depressing effects that TEs are believed to have. If so, then variation in dominance estimates among strains and crosses would be expected as a consequence of variation in TE activity. As a first test, we estimated the average dominance of all mutations and of copia insertions in a set of lines that had accumulated spontaneous mutations for 33 generations. A traditional regression method gave a dominance estimate for all mutations of 0.17, whereas average dominance of copia insertions was 0.51; the difference between these two estimates approached significance (P = 0.08). As a second test, we reanalyzed Ohnishi’s (1974) data on dominance of spontaneous and EMS-induced mutations. Because a considerable fraction of spontaneous mutations are caused by TE insertions, whereas EMS induces mainly point mutations, we predicted that average dominance would decline with increasing EMS concentration. This pattern was observed, but again fell short of formal significance (P = 0.07). Taken together, however, the two results give modest support for the hypothesis that TE insertions have greater average dominance in their viability effects than do point mutations, possibly as a result of deleterious effects of expression of TE-encoded genes.
Strand Invasion and DNA Synthesis From the Two 3′ Ends of a Double-Strand Break in Mammalian Cells
Authors: McCulloch Richard D , Read Leah R , Baker Mark D
Published: April 2021

Analysis of the crossover products recovered following transformation of mammalian cells with a sequence insertion (“ends-in”) gene-targeting vector revealed a novel class of recombinant. In this class of recombinants, a single vector copy has integrated into an ectopic genomic position, leaving the structure of the cognate chromosomal locus unaltered. Thus, in this respect, the recombinants resemble simple cases of random vector integration. However, the important difference is that the two paired 3′ vector ends have acquired endogenous, chromosomal sequences flanking both sides of the vector-borne double-strand break (DSB). In some cases, copying was extensive, extending >16 kb into nonhomologous flanking DNA. The results suggest that mammalian homologous recombination events can involve strand invasion and DNA synthesis by both 3′ ends of the DSB. These DNA interactions are a central, predicted feature of the DSBR model of recombination.
The Distribution of Fitness Effects Among Beneficial Mutations
Authors: Orr H Allen
Published: April 2021

We know little about the distribution of fitness effects among new beneficial mutations, a problem that partly reflects the rarity of these changes. Surprisingly, though, population genetic theory allows us to predict what this distribution should look like under fairly general assumptions. Using extreme value theory, I derive this distribution and show that it has two unexpected properties. First, the distribution of beneficial fitness effects at a gene is exponential. Second, the distribution of beneficial effects at a gene has the same mean regardless of the fitness of the present wild-type allele. Adaptation from new mutations is thus characterized by a kind of invariance: natural selection chooses from the same spectrum of beneficial effects at a locus independent of the fitness rank of the present wild type. I show that these findings are reasonably robust to deviations from several assumptions. I further show that one can back calculate the mean size of new beneficial mutations from the observed mean size of fixed beneficial mutations.
Patterns of Cell Division and the Risk of Cancer
Authors: Frank Steven A , Iwasa Yoh , Nowak Martin A
Published: April 2021

Epidermal and intestinal tissues divide throughout life to replace lost surface cells. These renewing tissues have long-lived basal stem cell lineages that divide many times, each division producing one stem cell and one transit cell. The transit cell divides a limited number of times, producing cells that move up from the basal layer and eventually slough off from the surface. If mutation rates are the same in stem and transit divisions, we show that minimal cancer risk is obtained by using the fewest possible stem divisions subject to the constraints imposed by the need to renew the tissue. In this case, stem cells are a necessary risk imposed by the constraints of tissue architecture. Cairns suggested that stem cells may have lower mutation rates than transit cells do. We develop a mathematical model to study the consequences of different stem and transit mutation rates. Our model shows that stem cell mutation rates two or three orders of magnitude less than transit mutation rates may favor relatively more stem divisions and fewer transit divisions, perhaps explaining how renewing tissues allocate cell divisions between long stem and short transit lineages.
Social Determinants of Shingles Vaccination in the United States
Authors: Vogelsang Eric M , Polonijo Andrea N
Published: April 2021

Objective

Only about one-third of older adults in the United States are vaccinated against shingles, contributing to approximately 1 million shingles cases annually. This study examines how sociodemographic characteristics, health behaviors, and self-rated health are associated with shingles vaccine uptake.

Method

Data come from the 2017 wave of the Behavioral Risk Factor Surveillance System survey, using a subset of older adults aged 60-plus (N = 208,301). Logistic regression models test (a) for associations between individual-level sociodemographic characteristics and vaccine uptake and (b) whether health behaviors and self-rated health moderate these associations.

Results

Black and Hispanic older adults have almost 50% lower odds of shingles vaccination, compared to non-Hispanic Whites. Abstaining from alcohol, being employed, living with children, and having poor self-rated health are also associated with lower uptake. Unmarried (vs married) individuals have lower odds of vaccination that are explained by broad differences in health behavior.

Discussion

Our study contributes to understanding how shingles vaccination coverage systematically differs among social groups. In doing so, it provides guidance for public health interventions to increase uptake. This line of research is increasingly salient in a world facing novel virus threats and antivaccine social movements.
Modelling quasi-periodic signals in geodetic time-series using Gaussian processes
Authors: Koulali A , Clarke P J
Published: April 2021

Seasonal signals in geodetic time-series have long been recognized to be associated with environmental phenomena such as polar motion, atmospheric loading, groundwater loading and other hydrological processes. Modelling these periodic signals is crucial for the geophysical interpretation of these time-series. The most common approach used for resolving seasonal (annual and semi-annual) signals is their approximation by sinusoidal functions with constant amplitudes. However, because of their environmental source, seasonal signals are likely to be quasi-periodic. In this study, we investigate a Gaussian process (GP) to model quasi-periodic signals in geodetic time-series, a flexible method that allows capturing the variability structure in the data using covariance functions. We use the Markov Chain Monte Carlo method to evaluate the posterior probability density function. To test its effectiveness, we apply this method to a synthetic time-series in the presence of time-correlated noise. We find that the GP model provides a better fit to the time-series, resulting in time-series residuals with fewer systematic effects. We use the GP model to estimate the secular velocity of selected GPS sites from Antarctica and Alaska, as well as an example of Gravity Recovery and Climate Experiment time-series. The Bayesian aspect of the GP model allows inferring the linear velocity ensemble in the vicinity of the true solution while taking into account the quasi-periodic systematics in the time-series.
Early cusp tear of the second-generation Trifecta valve with Glide Technology
Authors: Morisaki Akimasa , Takahashi Yosuke , Nishimura Shinsuke , Shibata Toshihiko
Published: April 2021

We herein report a case of early cusp tear of the second-generation Trifecta valve with Glide Technology. A 69-year-old woman underwent aortic valve replacement with a Trifecta valve with Glide Technology and partial arch replacement for severe aortic valve stenosis caused by a bicuspid valve and ascending aortic and aortic arch aneurysms 2 years previously. During follow-up, she suddenly developed dyspnoea and a heart murmur. Echocardiography revealed severe aortic valve regurgitation caused by structural valve deterioration. We performed re-aortic valve replacement with a mechanical valve through re-median sternotomy. Intraoperative examination revealed a bottom tear of the left coronary cusp without infection or pannus formation.
Potential Aphid Population Regulation by Aphidius colemani (Hymenoptera: Aphidiidae) in Response to Host Density, Parasitoid Density, and Age
Authors: Khatri Diwas , He Xiong Z , Wang Qiao
Published: April 2021

Aphidius colemani Viereck is an important parasitoid of green peach aphid [Myzus persicae (Sulzer)], a serious pest of greenhouse crops. Augmentation of natural enemies is the most used approach to biological control of greenhouse pests. Yet, the optimal release time, rate, and age of natural enemies are often unclear. Here we tested the influence of population density of both A. colemani and M. persicae, as well as parasitoid age, on parasitism and sex allocation. We aim is to provide information for cost-effective aphid biological control programs. We show that 1) parasitoid females increased parasitism and produced more female-biased offspring with an increase of aphid density, 2) a moderate increase of parasitoid release rate elevated parasitism and daughter production when aphid density was high, 3) parasitism rate declined with an increase of aphid density but the moderate increase of parasitoid release rate eased the decline rate, and 4) 3-d-old parasitoids parasitized more aphids than younger ones but parasitoid age had no effect on daughter production. These findings suggest that A. colemani females can adjust their ability to regulate the aphid population in response to aphid population dynamics. In augmentative programs, a moderate increase of parasitoid release when aphid density is high could achieve effective control and a release of 3-d-old parasitoids could lead to a better control outcome.
Production of D-lactic acid containing polyhydroxyalkanoate polymers in yeast Saccharomyces cerevisiae
Authors: Ylinen Anna , Maaheimo Hannu , Anghelescu-Hakala Adina , Penttilä Merja , Salusjärvi Laura , Toivari Mervi
Published: April 2021

Polyhydroxyalkanoates (PHAs) provide biodegradable and bio-based alternatives to conventional plastics. Incorporation of 2-hydroxy acid monomers into polymer, in addition to 3-hydroxy acids, offers possibility to tailor the polymer properties. In this study, poly(D-lactic acid) (PDLA) and copolymer P(LA-3HB) were produced and characterized for the first time in the yeast Saccharomyces cerevisiae. Expression of engineered PHA synthase PhaC1437Ps6–19, propionyl-CoA transferase Pct540Cp, acetyl-CoA acetyltransferase PhaA, and acetoacetyl-CoA reductase PhaB1 resulted in accumulation of 3.6% P(LA-3HB) and expression of engineered enzymes PhaC1Pre and PctMe resulted in accumulation of 0.73% PDLA of the cell dry weight (CDW). According to NMR, P(LA-3HB) contained D-lactic acid repeating sequences. For reference, expression of PhaA, PhaB1, and PHA synthase PhaC1 resulted in accumulation 11% poly(hydroxybutyrate) (PHB) of the CDW. Weight average molecular weights of these polymers were comparable to similar polymers produced by bacterial strains, 24.6, 6.3, and 1 130 kDa for P(LA-3HB), PDLA, and PHB, respectively. The results suggest that yeast, as a robust and acid tolerant industrial production organism, could be suitable for production of 2-hydroxy acid containing PHAs from sugars or from 2-hydroxy acid containing raw materials. Moreover, the wide substrate specificity of PHA synthase enzymes employed increases the possibilities for modifying copolymer properties in yeast in the future.
Revised points and disputed matters in the eighth edition of the TNM staging system for gastric cancer
Authors: Kumagai Koshi , Sano Takeshi
Published: April 2021

The American Joint Committee on Cancer and the Union for International Cancer Control have now released the eighth edition of the cancer staging system, which incorporates some major revisions concerning gastric cancer. First, grouping of pathological stages has been revised in accordance with a proposal from the International Gastric Cancer Association. That revision was based on analysis of survival of more than 25 000 patients worldwide who had undergone curative gastrectomy without neoadjuvant therapy. Stratification of survival in Stage III subgroups has been improved by subdividing N3 into N3a and N3b. Second, a simplified grouping of clinical stages that differs completely from grouping of pathological stages has been proposed. Pre-treatment depth of tumour invasion is now categorized as T1/T2, T3/T4a or T4b, and lymph node status is simply categorized as N0 or N+. Additionally, a ‘yp-stage’ for specimens resected after neoadjuvant therapy has been newly proposed. These clinical and post-neoadjuvant stages were considered useful now that neoadjuvant chemotherapy is increasingly being administered to patients with potentially resectable gastric cancer. Third, staging of oesophagogastric junction tumours has been modified; Siewert type 3 tumours are now classified as gastric tumours and are staged according to the gastric, rather than the oesophageal, system. More appropriate staging of gastric cancers treated with neoadjuvant therapy, and/or new staging systems incorporating variables other than T/N/M, such as biological or genomic markers, are likely future developments.
Environmental and behavioral factors influencing individual variation in spatial use by Guiana dolphins (Sotalia guianensis)
Authors: de Moura Stephane P G , Cantor Mauricio , Broadhurst Matt K , Domit Camila
Published: April 2021

Marine apex predators, such as coastal dolphins, are key components of ecosystem function and dynamics; understanding their spatial use therefore is important for conservation planning. Here, we describe spatial use of the threatened Guiana dolphin, Sotalia guianensis, within a mosaic of protected areas at their southern range in the Paranaguá estuarine complex (PEC), Brazil. Based on environmental characteristics and S. guianensis population densities, individual photo-identification surveys were focused on two sectors of the northern mouth of the PEC between 2013 and 2015. We photo-identified 107 individuals and recorded 351 groups of Guiana dolphins; nearly 50% of which contained calves. Group sizes were small (mean ± SD: Sector 1 = 3.4 ± 2.7; Sector 2 = 3.6 ± 2.0) and ranged from 1 to 30 individuals. Clustering algorithms were applied to resighted, photo-identified Guiana dolphins to classify individuals as “residents” (sighted in 87% of surveys, n = 11) and “transients” (two clusters; 62%, n = 22; 95%, n = 72). All individuals predominantly were observed foraging (90% in Sector 1 and 76% in Sector 2), but spatial use by transient individuals differed from the residents in terms of environmental (slope, water depth, and rainfall) and behavioral factors (presence of calves and foraging behavior). Compared to transients, resident dolphins ranged over smaller areas, typically more suitable for feeding, calf caring, and more protected from predators and vessels. Because resident Guiana dolphins exhibit small home ranges, they are particularly vulnerable to local anthropogenic activities and habitat loss. These characteristics imply a strong need for regionalized management plans to reduce negative impacts and to maintain the ecological functionality of the species.
Thanks, but No Thanks: Preferences towards Teleworking Colleagues in Public Organizations
Authors: Mele Valentina , Bellé Nicola , Cucciniello Maria
Published: April 2021

Over the last decades, one of the most significant changes in the workplaces of government agencies around the world has been the introduction of telework. The relatively scant public administration research on this innovation and on its semantic or substantive variations such as telecommuting, home-work, remote work, and smart work has examined its effects on teleworkers and only recently on non-teleworkers. However, scholars have overlooked the relational dynamics triggered by telework. This is the focus of our study. We start by connecting telework with specific features of public bureaucracies, such as control, modularity, and the separation of professional and personal life. Next, we explore through a mixed-methods design a relational dynamic overlooked by previous studies, that is, the preferences of non-teleworkers towards teleworking colleagues and the motives behind them. Results from a discrete choice experiment with over 1,000 non-teleworking public employees revealed a remarkably strong preference toward non-teleworkers. A qualitative follow-up based on semi-structured interviews found the workplace collective as the locus of the tensions caused by telework and illuminated critical issues perceived by non-teleworkers, ensuring a more fine-grained understanding of the impacts of flexible work arrangements on the functioning of public organizations.
Recent greening of grasslands in northern China driven by increasing precipitation
Authors: Di Kai , Hu Zhongmin , Wang Mei , Cao Ruochen , Liang Minqi , Wu Genan , Chen Ruru , Hao Guangcun , Zhao Yaolong
Published: April 2021

Aims

Recent warmer and wetter climate in northern China remains a hot topic in recent years, yet its effect on vegetation growth has not been fully understood. This study investigated the temporal change of vegetation cover and its correlations with climatic variables from 1982 to 2018 for grasslands in northern China. Our aim is to clarify whether the warmer and wetter climate in recent years drives the greening of the vegetation in this region.

Methods

We investigated the temporal dynamic of vegetation normalized difference vegetation index (NDVI) and its driving forces based on long time-series data. Piecewise regression was used to examine whether there was a turning point of the trend of NDVI and climatic variables. Pearson correlation analyses were conducted to quantify the relationship between NDVI and climatic factors. Stepwise multivariable regression was used to quantify the contributions of climate variables to the temporal variations in NDVI.

Important Findings

We found a turning point of NDVI trend in 2008, with GIMMS NDVI indicating a slight increase of 0.00022 yr−1 during 1982–2008 to an increase of 0.002 yr−1 for GIMMS NDVI during 2008–2015 and 0.0018 yr−1 for MODIS NDVI during 2008–2018. Precipitation was the predominant driver, and air temperature and vapor pressure deficit exerted a minor impact on the temporal dynamics of NDVI. Overall, our results suggest a turning point of NDVI trend, and that recent warmer and wetter climate has caused vegetation greening, which provides insights for better predicting the vegetation cover in this region under changing climate.
Bacilluspromotes invasiveness of exoticFlaveria bidentisby increasing its nitrogen and phosphorus uptake
Authors: Chen Xue , Li Qiao , Wang Yan , Chen Fengxin , Zhang Xiaoya , Zhang Fengjuan
Published: April 2021

The effect of exotic plants on Bacillus diversity in the rhizosphere and the role of Bacilli in exotic or native plant species remain poorly understood. Flaveria bidentis is an invasive grass in China. Setaria viridis is a native grass and occurs in areas invaded by F. bidentis. Our objectives were (i) to examine the differences in the Bacillus communities between F. bidentis and S. viridis rhizospheres soil, and (ii) to compare the effects of Bacilli from F. bidentis and S. viridis rhizospheres on the competitiveness of the invasive species. Flaveria bidentis monoculture, mixture of F. bidentis and S. viridis and S. viridis monoculture were designed in the field experiment. Bacillus diversity in their rhizosphere was analyzed using 16S rRNA. One of the dominant Bacilli in the rhizosphere soil of F. bidentis was selected to test its effect on the competitive growth of F. bidentis in a greenhouse experiment. Bacillus diversity differed in F. bidentis and S. viridis rhizosphere. Brevibacterium frigoritolerans was the dominant Bacilli in the rhizosphere of both F. bidentis and S. viridis; however, its relative abundance in the F. bidentis rhizosphere was much higher than that in the S. viridis rhizosphere. In addition, B. frigoritolerans in the F. bidentis rhizosphere enhanced the growth of the plant compared with that of S. viridis by improving the nitrogen and phosphorus levels. This study showed that F. bidentis invasion influenced Bacillus communities, especially B. frigoritolerans, which, in turn, facilitated F. bidentis growth by increasing the levels of available nitrogen and phosphorus.
SARS-CoV-2 genomic surveillance in Northeast Brazil: timing of emergence of the Brazilian variant of concern P1
Authors: dos Santos Cliomar Alves , Bezerra Gabriela Vasconcelos Brito , de Azevedo Marinho Aline Rafaelle Rocha Almeida , Alves Juliana Cardoso , Tanajura Diego Moura , Martins-Filho Paulo Ricardo
Published: April 2021

Since March 2020, 11 lineages of severe acute respiratory syndrome coronavirus 2 have been identified in Sergipe state, Northeast Brazil. During the first 6 months of coronavirus disease 2019 (COVID-19) outbreak, there was a higher frequency of B.1 (58.5%) and B.1.1.33 (17.1%) lineages. During the second wave of COVID-19, there was an increased frequency of P.1 (55.6%), the new Brazilian variant of concern.
Identification and characterization of novel QTL conferring internal detoxification of aluminium in soybean
Authors: Li Yang , Ye Heng , Song Li , Vuong Tri D , Song Qijian , Zhao Lijuan , Shannon J Grover , Li Yan , Nguyen Henry T
Published: April 2021

Aluminium (Al) toxicity inhibits soybean root growth, leading to insufficient water and nutrient uptake. Two soybean lines (‘Magellan’ and PI 567731) were identified differing in Al tolerance, as determined by primary root length ratio, total root length ratio, and root tip number ratio under Al stress. Serious root necrosis was observed in PI 567731, but not in Magellan under Al stress. An F8 recombinant inbred line population derived from a cross between Magellan and PI 567731 was used to map the quantitative trait loci (QTL) for Al tolerance. Three QTL on chromosomes 3, 13, and 20, with tolerant alleles from Magellan, were identified. qAl_Gm13 and qAl_Gm20 explained large phenotypic variations (13–27%) and helped maintain root elongation and initiation under Al stress. In addition, qAl_Gm13 and qAl_Gm20 were confirmed in near-isogenic backgrounds and were identified to epistatically regulate Al tolerance via internal detoxification instead of Al3+ exclusion. Phylogenetic and pedigree analysis identified the tolerant alleles of both loci derived from the US ancestral line, A.K.[FC30761], originally from China. Our results provide novel genetic resources for breeding Al-tolerant soybean and suggest that internal detoxification contributes to soybean tolerance to excessive soil Al.
Structural dynamics and determinants of abscisic acid–receptor binding preference in different aggregation states
Authors: Yang Jing-Fang , Chen Mo-Xian , Zhang Jianhua , Hao Ge-Fei , Yang Guang-Fu
Published: April 2021

In the 21st century, drought has been the main cause of shortages in world grain production and has created problems with food security. Abscisic acid (ABA) is a key plant hormone involved in the response to abiotic stress, especially drought. The pyrabactin resistance (PYR)/PYR1-like (PYL)/regulatory component of abscisic acid receptor (RCAR) family of proteins (simplified as PYLs) is a well-known ABA receptor family, which can be divided into dimeric and monomeric forms. PYLs can recognize ABA and activate downstream plant drought-resistance signals. However, the difference between monomeric and dimeric receptors in the mechanism of the response to ABA is unclear. Here, we reveal that monomeric receptors have a competitive advantage over dimeric receptors for binding to ABA, driven by the energy penalty resulting from dimer dissociation. ABA also plays different roles with the monomer and the dimer: in the monomer, it acts as a ‘conformational stabilizer’ for stabilizing the closed gate, whereas for the dimer, it serves as an ‘allosteric promoter’ for promoting gate closure, which leads to dissociation of the two subunits. This work illustrates how receptor oligomerization could modulate hormonal responses and provides a new concept for novel engineered plants based on ABA binding of monomers.
An upper observable black hole mass scale for tidal destruction events with thermal X-ray spectra
Authors: Mummery Andrew , Balbus Steven A
Published: April 2021

We comprehensively model the X-ray luminosity emergent from time-dependent relativistic accretion discs, developing analytical models of the X-ray luminosity of thermal disc systems as a function of black hole mass M, disc mass Md, and disc α-parameter. The X-ray properties of these solutions will be directly relevant for understanding tidal disruption event (TDE) observations. We demonstrate an extremely strong suppression of thermal X-ray luminosity from large mass black holes, LX ∼ exp (− m7/6), where m is a dimensionless mass, roughly the black hole mass in unity of 106M⊙. This strong suppression results in upper observable black hole mass limits, which we demonstrate to be of order Mlim ≃ 3 × 107M⊙, above which thermal X-ray emission will not be observable. This upper observable black hole mass limit is a function of the remaining disc parameters, and the full dependence can be described analytically (equation 82). We demonstrate that the current population of observed X-ray TDEs is indeed consistent with an upper black hole mass limit of order M ∼ 107M⊙, consistent with our analysis.
Forecasting solar cycle 25 using comprehensive precursor combination and multiple regression technique
Authors: Xiong Yating , Lu Jianyong , Zhao Kai , Sun Meng , Gao Yang
Published: April 2021

In this paper, we propose a new model to predict the complete sunspot cycle based on the comprehensive precursor information (peak, skewness, maximum geomagnetic index aa of the previous cycle, and start value of predicted cycle). The monthly average sunspot original data are processed by Gaussian smoothing and the new model is validated by the observed sunspots of cycle 24. Compared with the traditional 13-month moving average, the Gaussian filter has less missing information and is better to describe the overall trend of the raw data. Through the permutation and combination of multiple parameters in precursor methods of solar cycle forecasting, the multiple regression technique is used to successfully achieve the peak prediction. The regression coefficient (R) of the empirical model established in this paper can reach 0.95. By adding a new parameter to the original HWR function, we provide a complete solar cycle profile showing unimodal structure. It shows that the peak value of cycle 25 will come in March 2024, with a peak of 140.2.
Characterization of 92 southern TESS candidate planet hosts and a new photometric [Fe/H] relation for cool dwarfs
Authors: Rains Adam D , Žerjal Maruša , Ireland Michael J , Nordlander Thomas , Bessell Michael S , Casagrande Luca , Onken Christopher A , Joyce Meridith , Kammerer Jens , Abbot Harrison
Published: April 2021

We present the results of a medium-resolution optical spectroscopic survey of 92 cool ($3000 \,\mathrm{ K}\lesssim T_{\rm eff} \lesssim 4500\,$K) southern TESS candidate planet hosts, and describe our spectral fitting methodology used to recover stellar parameters. We quantify model deficiencies at predicting optical fluxes, and while our technique works well for Teff, further improvements are needed for [Fe/H]. To this end, we developed an updated photometric [Fe/H] calibration for isolated main-sequence stars built upon a calibration sample of 69 cool dwarfs in binary systems, precise to $\pm 0.19\,$dex, from supersolar to metal poor, over 1.51 < Gaia (BP − RP) < 3.3. Our fitted Teff and R⋆ have median precisions of 0.8 per cent and 1.7 per cent, respectively, and are consistent with our sample of standard stars. We use these to model the transit light curves and determine exoplanet radii for 100 candidate planets to 3.5 per cent precision and see evidence that the planet radius gap is also present for cool dwarfs. Our results are consistent with the sample of confirmed TESS planets, with this survey representing one of the largest uniform analyses of cool TESS candidate planet hosts to date.
Hard X-ray emission from a Compton scattering corona in large black hole mass tidal disruption events
Authors: Mummery Andrew , Balbus Steven A
Published: April 2021

We extend the relativistic time-dependent thin-disc TDE model to describe non-thermal (2−10 keV) X-ray emission produced by the Compton up-scattering of thermal disc photons by a compact electron corona, developing analytical and numerical models of the evolving non-thermal X-ray light curves. In the simplest cases, these X-ray light curves follow power-law profiles in time. We suggest that TDE discs act in many respects as scaled-up versions of XRB discs, and that such discs should undergo state transitions into harder accretion states. XRB state transitions typically occur when the disc luminosity becomes roughly one per cent of its Eddington value. We show that if the same is true for TDE discs then this, in turn, implies that TDEs with non-thermal X-ray spectra should come preferentially from large-mass black holes. The characteristic hard-state transition mass is MHS ≃ 2 × 107M⊙. Hence, subpopulations of thermal and non-thermal X-ray TDEs should come from systematically different black hole masses. We demonstrate that the known populations of thermal and non-thermal X-ray TDEs do indeed come from different distributions of black hole masses. The null-hypothesis of identical black hole mass distributions is rejected by a two-sample Anderson-Darling test with a p-value <0.01. Finally, we present a model for the X-ray rebrightening of TDEs at late times as they transition into the hard state. These models of evolving TDE light curves are the first to join both thermal and non-thermal X-ray components in a unified scenario.
Globally visible singularity in an astrophysical setup
Authors: Mosani Karim , Dey Dipanjan , Joshi Pankaj S
Published: April 2021

The global visibility of a singularity as an end state of the gravitational collapse of a spherically symmetric pressureless cloud is investigated. We show the existence of a non-zero measured set of parameters: the total mass and the initial mean density of the collapsing cloud, giving rise to a physically strong globally visible singularity as the end state for a fixed velocity function. The existence of such a set indicates that such singularity is stable under small perturbation in the initial data causing its existence. This is true for marginally as well as non-marginally bound cases. The possibility of the presence of such suitable parameters in the astrophysical setup is then studied: (1) The singularities’ requirements at the centre of the M87 galaxy and at the centre of our galaxy (SgrA*) to be globally visible are discussed in terms of the initial size of the collapsing cloud forming them, presuming that such singularities are formed due to gravitational collapse. (2) The requirement for the primordial singularities formed due to a collapsing configuration after getting detached from the background universe at the time of matter-dominated era just after the time of matter-radiation equality, to be globally visible, is discussed. (3) The scenario of the collapse of a neutron star after reaching a critical mass, which is achieved by accreting the supernova ejecta expelled by its binary companion core progenitor, is considered. The primary aim of this paper is to show that globally visible singularities can form in astrophysical setups under appropriate circumstances.
Oocyte-secreted factors strongly stimulate sFRP4 expression in human cumulus cells
Authors: Esfandyari Sahar , Winston Nicola J , Fierro Michelle A , Scoccia Humberto , Stocco Carlos
Published: April 2021

Secreted frizzled-related protein-4 (SFRP4) belongs to a family of soluble ovarian-expressed proteins that participate in female reproduction, particularly in rodents. In humans, SFRP4 is highly expressed in cumulus cells (CCs). However, the mechanisms that stimulate SFRP4 in CCs have not been examined. We hypothesise that oocyte-secreted factors such as growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are involved in the regulation of SFRP4. Human CCs were collected from patients undergoing fertility treatments and treated with GDF9 or BMP15 or their combination in the presence of FSH or vehicle. FSH treatment significantly decreased SFRP4 mRNA levels when compared with nontreated cells. However, SFRP4 mRNA levels were increased significantly by GDF9 plus BMP15 in a concentration-dependent manner in the presence or absence of FSH. The combination of GDF9 plus BMP15 also increased SFRP4 protein levels and decreased the activity of the β-catenin/T cell factor-responsive promoter significantly. GDF9 plus BMP15 inhibited steroidogenic acute regulatory protein and LH/hCG receptor stimulation by FSH, while treatment with SFRP4 blocked the stimulatory effect of FSH on these genes. The evidence demonstrates that GDF9 and BMP15 act in coordination to stimulate SFRP4 expression and suggests that SFRP4 mediates the anti-luteinising effects of the oocyte in human CCs.
Short DNA/RNA heteroduplex oligonucleotide interacting proteins are key regulators of target gene silencing
Authors: Asada Ken , Sakaue Fumika , Nagata Tetsuya , Zhang Ji-chun , Yoshida-Tanaka Kie , Abe Aya , Nawa Makiko , Nishina Kazutaka , Yokota Takanori
Published: April 2021

Antisense oligonucleotide (ASO)-based therapy is one of the next-generation therapy, especially targeting neurological disorders. Many cases of ASO-dependent gene expression suppression have been reported. Recently, we developed a tocopherol conjugated DNA/RNA heteroduplex oligonucleotide (Toc-HDO) as a new type of drug. Toc-HDO is more potent, stable, and efficiently taken up by the target tissues compared to the parental ASO. However, the detailed mechanisms of Toc-HDO, including its binding proteins, are unknown. Here, we developed native gel shift assays with fluorescence-labeled nucleic acids samples extracted from mice livers. These assays revealed two Toc-HDO binding proteins, annexin A5 (ANXA5) and carbonic anhydrase 8 (CA8). Later, we identified two more proteins, apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) and flap structure-specific endonuclease 1 (FEN1) by data mining. shRNA knockdown studies demonstrated that all four proteins regulated Toc-HDO activity in Hepa1–6, mouse hepatocellular cells. In vitro binding assays and fluorescence polarization assays with purified recombinant proteins characterized the identified proteins and pull-down assays with cell lysates demonstrated the protein binding to the Toc-HDO and ASO in a biological environment. Taken together, our findings provide a brand new molecular biological insight as well as future directions for HDO-based disease therapy.
DeepRefiner: high-accuracy protein structure refinement by deep network calibration
Authors: Shuvo Md Hossain , Gulfam Muhammad , Bhattacharya Debswapna
Published: April 2021

The DeepRefiner webserver, freely available at http://watson.cse.eng.auburn.edu/DeepRefiner/, is an interactive and fully configurable online system for high-accuracy protein structure refinement. Fuelled by deep learning, DeepRefiner offers the ability to leverage cutting-edge deep neural network architectures which can be calibrated for on-demand selection of adventurous or conservative refinement modes targeted at degree or consistency of refinement. The method has been extensively tested in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments under the group name ‘Bhattacharya-Server’ and was officially ranked as the No. 2 refinement server in CASP13 (second only to ‘Seok-server’ and outperforming all other refinement servers) and No. 2 refinement server in CASP14 (second only to ‘FEIG-S’ and outperforming all other refinement servers including ‘Seok-server’). The DeepRefiner web interface offers a number of convenient features, including (i) fully customizable refinement job submission and validation; (ii) automated job status update, tracking, and notifications; (ii) interactive and interpretable web-based results retrieval with quantitative and visual analysis and (iv) extensive help information on job submission and results interpretation via web-based tutorial and help tooltips.