bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent advances in chemical ecology: complex interactions mediated by molecules
Authors: Mori Naoki , Noge Koji 
Published: January 2021

Abstract
Chemical ecology is the highly interdisciplinary study of biochemicals that mediate the behavior of organisms and the regulation of physiological changes that alter intraspecific and/or interspecific interactions. Significant advances are often achieved through the collaboration of chemists and biologists working to understand organismal survival strategies with an eye on the development of targeted technologies for controlling agricultural, forestry, medical, and veterinary pests in a sustainable world. We highlight recent advances in chemical ecology from multiple viewpoints and discuss future prospects for applications.
Controlling the production of phytotoxin pyriculol in Pyricularia oryzae by aldehyde reductase
Authors: Furuyama Yuuki , Motoyama Takayuki , Nogawa Toshihiko , Hayashi Toshiaki , Hirota Hiroshi , Kiyota Hiromasa , Kamakura Takashi , Osada Hiroyuki 
Published: January 2021

Abstract
Pyricularia oryzae is one of the most devastating plant pathogens in the world. This fungus produces several secondary metabolites including the phytotoxin pyriculols, which are classified into 2 types: aldehyde form (pyriculol and pyriculariol) and alcohol form (dihydropyriculol and dihydropyriculariol). Although interconversion between the aldehyde form and alcohol form has been predicted, and the PYC10 gene for the oxidation of alcohol form to aldehyde is known, the gene responsible for the reduction of aldehyde to alcohol form is unknown. Furthermore, previous studies have predicted that alcohol analogs are biosynthesized via aldehyde analogs. Herein, we demonstrated that an aldo/keto reductase PYC7 is responsible for the reduction of aldehyde to alcohol congeners. The results indicate that aldehyde analogs are biosynthesized via alcohol analogs, contradicting the previous prediction. The results suggest that P. oryzae controls the amount of pyriculol analogs using two oxidoreductases, PYC7 and PYC10, thereby controlling the bioactivity of the phytotoxin.
A new peptaibol, RK-026A, from the soil fungusTrichodermasp. RK10-F026 by culture condition-dependent screening
Authors: Rawa Mira Syahfriena Amir , Nogawa Toshihiko , Okano Akiko , Futamura Yushi , Nakamura Takemichi , Wahab Habibah A , Osada Hiroyuki 
Published: January 2021

AbstractA new peptaibol, RK-026A (1) was isolated from a fungus, Trichoderma sp. RK10-F026, along with atroviridin B (2), alamethicin II (3), and polysporin B (4) as a cytotoxic compound, which was selected by principal component analysis of the MS data from 5 different culture conditions. The structure of 1 was determined as a new atroviridin B derivative containing Glu at the 18th residue instead of Gln by NMR and HR-MS analyses including the investigation of detailed MS/MS fragmentations. 1 showed cytotoxicity toward K562 leukemia cells at an IC50 value of 4.1 µm.
A novel translation inhibitor, mersicarpine, inhibits S-phase progression and induces apoptosis in HL60 cells
Authors: Shiobara Tomoko , Nagumo Yoko , Nakajima Rie , Fukuyama Tohru , Yokoshima Satoshi , Usui Takeo 
Published: January 2021

Abstract
Mersicarpine is an aspidosperma alkaloid isolated from the Kopsia genus of plants. Its intriguing structural features have attracted much attention in synthetic organic chemistry, but no biological activity has been reported. Here, we report the effects of mersicarpine on human leukemia cell line HL60. At concentrations above 30 µm, mersicarpine reversibly arrested cell cycle progression in S-phase. At higher concentrations, it induced not only production of reactive oxygen species, but also apoptosis. Macromolecular synthesis assay revealed that mersicarpine specifically inhibits protein synthesis. These results suggest that mersicarpine is a novel translation inhibitor that induces apoptosis.
Complex effects of helper relatedness on female extrapair reproduction in a cooperative breeder
Authors: Hajduk Gabriela K , Cockburn Andrew , Osmond Helen L , Kruuk Loeske E B 
Published: January 2021

AbstractIn cooperatively breeding species, the presence of male helpers in a group often reduces the breeding female’s fidelity to her social partner, possibly because there is more than one potential sire in the group. Using a long-term study of cooperatively breeding superb fairy-wrens (Malurus cyaneus) and records of paternity in 1936 broods, we show that the effect of helpers on rates of extrapair paternity varied according to the helpers’ relatedness to the breeding female. The presence of unrelated male helpers in a group increased average rates of extrapair paternity, from 57% for groups with no unrelated helpers, to 74% with one unrelated helper, to 86% with 2+ unrelated helpers. However, this increase was due in equal part to helpers within the group and males in other groups achieving increased paternity. In contrast, helpers who were sons of the breeding female did not gain paternity, nor did they affect the level of extra-group paternity (which occurred at rates of 60%, 58%, 61% in the presence of 0, 1, 2+ helper sons, respectively). There was no evidence of effects of helpers’ relatedness to the female on nest productivity or nestling performance. Because the presence of helpers per se did not elevate extrapair reproduction rates, our results undermine the “constrained female hypothesis” explanation for an increase in extrapair paternity with helper number in cooperative breeders. However, they indicate that dominant males are disadvantaged by breeding in “cooperative” groups. The reasons why the presence of unrelated helpers, but not of helper-sons, results in higher rates of extra-group reproduction are not clear.
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases
Authors: Mayer Gerhard , Müller Wolfgang , Schork Karin , Uszkoreit Julian , Weidemann Andreas , Wittig Ulrike , Rey Maja , Quast Christian , Felden Janine , Glöckner Frank Oliver , Lange Matthias , Arend Daniel , Beier Sebastian , Junker Astrid , Scholz Uwe , Schüler Danuta , Kestler Hans A , Wibberg Daniel , Pühler Alfred , Twardziok Sven , Eils Jürgen , Eils Roland , Hoffmann Steve , Eisenacher Martin , Turewicz Michael 
Published: January 2021

Abstract
This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.
Bayesian biclustering for microbial metagenomic sequencing data via multinomial matrix factorization
Authors: Zhou Fangting , He Kejun , Li Qiwei , Chapkin Robert S , Ni Yang 
Published: January 2021

Summary
High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious challenges for statistical modeling. We propose an identifiable Bayesian multinomial matrix factorization model to infer overlapping clusters on both microbes and hosts. The proposed method represents the observed over-dispersed zero-inflated count matrix as Dirichlet-multinomial mixtures on which latent cluster structures are built hierarchically. Under the Bayesian framework, the number of clusters is automatically determined and available information from a taxonomic rank tree of microbes is naturally incorporated, which greatly improves the interpretability of our findings. We demonstrate the utility of the proposed approach by comparing to alternative methods in simulations. An application to a human gut microbiome data set involving patients with inflammatory bowel disease reveals interesting clusters, which contain bacteria families Bacteroidaceae, Bifidobacteriaceae, Enterobacteriaceae, Fusobacteriaceae, Lachnospiraceae, Ruminococcaceae, Pasteurellaceae, and Porphyromonadaceae that are known to be related to the inflammatory bowel disease and its subtypes according to biological literature. Our findings can help generate potential hypotheses for future investigation of the heterogeneity of the human gut microbiome.
Prioritizing Genetic Contributors to Cortical Alterations in 22q11.2 Deletion Syndrome Using Imaging Transcriptomics
Authors: Forsyth Jennifer K , Mennigen Eva , Lin Amy , Sun Daqiang , Vajdi Ariana , Kushan-Wells Leila , Ching Christopher R K , Villalon-Reina Julio E , Thompson Paul M ,   22q11.2 ENIGMA Consortium, Jonas Rachel K , Pacheco-Hansen Laura , Bakker Geor , van Amelsvoort Therese , Antshel Kevin M , Fremont Wanda , Kates Wendy R , Campbell Linda E , McCabe Kathryn L , Craig Michael C , Daly Eileen , Gudbrandsen Maria , Murphy Clodagh M , Murphy Declan G , Murphy Kieran C , Fiksinski Ania , Koops Sanne , Vorstman Jacob , Crowley T Blaine , Emanuel Beverly S , Gur Raquel E , McDonald-McGinn Donna M , Roalf David R , Ruparel Kosha , Schmitt J Eric , Zackai Elaine H , Durdle Courtney A , Goodrich-Hunsaker Naomi J , Simon Tony J , Bassett Anne S , Butcher Nancy J , Chow Eva W C , Vila-Rodriguez Fidel , Cunningham Adam , Doherty Joanne L , Linden David E , Moss Hayley , Owen Michael J , van den Bree Marianne , Crossley Nicolas A , Repetto Gabriela M , Bearden Carrie E 
Published: January 2021

Abstract
22q11.2 deletion syndrome (22q11DS) results from a hemizygous deletion that typically spans 46 protein-coding genes and is associated with widespread alterations in brain morphology. The specific genetic mechanisms underlying these alterations remain unclear. In the 22q11.2 ENIGMA Working Group, we characterized cortical alterations in individuals with 22q11DS (n = 232) versus healthy individuals (n = 290) and conducted spatial convergence analyses using gene expression data from the Allen Human Brain Atlas to prioritize individual genes that may contribute to altered surface area (SA) and cortical thickness (CT) in 22q11DS. Total SA was reduced in 22q11DS (Z-score deviance = −1.04), with prominent reductions in midline posterior and lateral association regions. Mean CT was thicker in 22q11DS (Z-score deviance = +0.64), with focal thinning in a subset of regions. Regional expression of DGCR8 was robustly associated with regional severity of SA deviance in 22q11DS; AIFM3 was also associated with SA deviance. Conversely, P2RX6 was associated with CT deviance. Exploratory analysis of gene targets of microRNAs previously identified as down-regulated due to DGCR8 deficiency suggested that DGCR8 haploinsufficiency may contribute to altered corticogenesis in 22q11DS by disrupting cell cycle modulation. These findings demonstrate the utility of combining neuroanatomic and transcriptomic datasets to derive molecular insights into complex, multigene copy number variants.
Adaptive Reconfiguration of Intrinsic Community Structure in Children with 5-Year Abacus Training
Authors: Zhang Yi , Wang Chunjie , Yao Yuzhao , Zhou Changsong , Chen Feiyan 
Published: January 2021

ABSTRACT
Human learning can be understood as a network phenomenon, underpinned by the adaptive reconfiguration of modular organization. However, the plasticity of community structure (CS) in resting-state network induced by cognitive intervention has never been investigated. Here, we explored the individual difference of intrinsic CS between children with 5-year abacus-based mental calculation (AMC) training (35 subjects) and their peers without prior experience in AMC (31 subjects). Using permutation-based analysis between subjects in the two groups, we found the significant alteration of intrinsic CS, with training-attenuated individual difference. The alteration of CS focused on selective subsets of cortical regions (“core areas”), predominantly affiliated to the visual, somatomotor, and default-mode subsystems. These subsystems exhibited training-promoted cohesion with attenuated interaction between them, from the perspective of individuals’ CS. Moreover, the cohesion of visual network could predict training-improved math ability in the AMC group, but not in the control group. Finally, the whole network displayed enhanced segregation in the AMC group, including higher modularity index, more provincial hubs, lower participation coefficient, and fewer between-module links, largely due to the segregation of “core areas.” Collectively, our findings suggested that the intrinsic CS could get reconfigured toward more localized processing and segregated architecture after long-term cognitive training.
Adding a Natural Enemy to Respond to Pest Immigration and Delayed Natural Enemy Releases in Augmentative Biological Control
Authors: Vafaie Erfan K , Pemberton H Brent , Gu Mengmeng , Kerns David , Eubanks Micky D , Heinz Kevin M 
Published: January 2021

AbstractWhether increased natural enemy density or adding a second natural enemy species will provide superior pest suppression in greenhouse augmentative biological control is unknown for many commercially available natural enemy species. In this study, we use sweetpotato whiteflies, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), on poinsettias, Euphorbia pulcherrima Willd. ex Klotzsch (Malpighiales: Euphorbiaceae), to determine whether adding Amblyseius swirskii (Athias-Henriot) (Acari: Phytoseiidae) to Eretmocerus eremicus Rose and Zolnerowich (Hymenoptera: Aphelinidae) is better for B. tabaci suppression compared with either natural enemy alone, both with and without challenges with whitefly immigration or delayed natural enemy releases. The number of whiteflies on caged poinsettias treated with different natural enemy release rates (single or double rate), natural enemy species (one or two species), natural enemy delayed release (weeks 4 and 8), and whitefly immigration treatments (introduced at week 4 or week 8) was censused biweekly for 16 wk. Both species used in combination provided similar or better suppression of whiteflies compared with either natural enemy alone. Both species combined also provided superior suppression of whiteflies when challenged with whitefly immigration or delays in natural enemy releases compared with E. eremicus alone. Whitefly immigration or delays in E. eremicus releases did not increase whitefly populations, suggesting that suppression of whiteflies by E. eremicus alone is relatively robust. This study found no evidence for negative interactions between E. eremicus and A. swirskii for suppressing B. tabaci.
The hydroxychloroquine debate: a therapeutic dilemma for general practitioners
Authors: Lutaud Romain , Scronias Dimiti , Ward Jeremy , Verger Pierre 
Published: January 2021

AbstractFrance has been at the epicenter of the worldwide debate about hydroxychloroquine, as the main advocacy for its use to treat COVID-19 comes from a research unit led by Didier Raoult in Marseille. Among a national panel of 2940 general practitioners, we found that physicians in the areas most strongly affected by the epidemic or closest to the epicenter of the controversy reported that the hydroxychloroquine debate had made it difficult for them to deal with patients' treatment requests. Their adherence to official recommendations was also lower. It will be necessary to examine the conditions producing so strong a conflict.
Transcriptomics analysis of the metabolic mechanisms of iron reduction induced by sulfate reduction mediated by sulfate-reducing bacteria
Authors: Li Guo-Xiang , Bao Peng 
Published: January 2021

ABSTRACT
Sulfate-reducing bacteria (SRB) play an important role in sulfur, iron and carbon cycling. The majority of studies have illustrated the role of SRB in biogeochemical cycling in pure cultures. In this study, we established three SRB enrichment cultures (designated HL, NB and WC) from different paddy soils and conducted a transcriptomic analysis of their metabolic characteristics under sulfate and sulfate-free conditions. In the HL cultures, there was no sulfate consumption but ferrihydrite was reduced. This indicated that bacteria in the HL samples can reduce ferrihydrite and preferentially utilize ferrihydrite as the electron acceptor in the absence of both ferrihydrite and sulfate. Sulfate consumption was equal in the NB and the WC cultures, although more ferrihydrite was reduced in the NB cultures. Transcriptomics analysis showed that (i) upregulation of O-acetylserine sulfhydrylase gene expression indicating sulfate assimilation in the WC samples; (ii) the energy conservation trithionate pathway is commonly employed by SRB and (iii) sulfate not only enhanced iron reduction by its conversion to sulfide but also promoted enzymatic electron transfer via c-type cytochromes.
Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas
Authors: Fernandez-Gnecco Gabriela , Smalla Kornelia , Maccario Lorrie , Sørensen Søren J , Barbieri Pablo , Consolo Veronica F , Covacevich Fernanda , Babin Doreen 
Published: January 2021

ABSTRACT
Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.
Yeast mer1 mutants display reduced levels of meiotic recombination.
Authors: Engebrecht J , Roeder G S 
Published: January 2021

Abstract
Mutations at the MER1 locus were identified in a search for meiotic mutants defective in chromosome segregation. mer1 strains show decreased levels of inter- and intrachromosomal meiotic recombination and produce inviable spores. The MER1 gene was cloned by complementation of the spore inviability phenotype. Strains carrying disruptions of the MER1 gene are mitotically viable. The epistatic relationships between MER1 and previously characterized meiotic genes are described.
Genetic variation in an inbred plant: variation in tissue cultures of soybean [Glycine max (L.) Merrill].
Authors: Roth E J , Frazier B L , Apuya N R , Lark K G 
Published: January 2021

Abstract
Although soybean [Glycine max (L.) Merrill] grows as an inbreeding, generally homozygous, plant, the germplasm of the species contains large amounts of genetic variation. Analysis of soybean DNA has indicated that variation of RFLP (restriction fragment length polymorphism) markers within the species usually entails only two alleles at any one locus and that mixtures of such dimorphic loci account for virtually all of the restriction fragment variation seen in soybean (G. max), and in its ancestors, G. soja and G. gracilis. We report here that tissue cultures prepared from root tissue of individual soybean plants develop RFLP allelic differences at various loci. However, these newly generated alleles are almost always the same as ones previously found and characterized in other varieties of cultivated soybean (cultivars). This repeated generation of particular alleles suggests that much of the genetic variation seen in soybean could be the consequence of specific, relatively frequently employed, recombinational events. Such a mechanism would allow inbred cultivars to generate genetic variation (in the form of alternative alleles) in a controlled manner, perhaps in response to stress.
Role of recBC function in formation of chromosomal rearrangements: a two-step model for recombination.
Authors: Mahan M J , Roth J R 
Published: January 2021

Abstract
The role of recBC functions has been tested for three types of chromosomal recombination events: (1) recombination between direct repeats to generate a deletion, (2) recombination between a small circular fragment and the chromosome, and (3) recombination between inversely oriented repeats to form an inversion. Deletion formation by recombination between direct repeats, which does not require a fully reciprocal exchange, is independent of recBC function. Circle integration and inversion formation are both stimulated by the recBC function; these events require full reciprocality. The results suggest that half-reciprocal exchanges can occur without recBC, but recBC functions greatly stimulate completion of a fully reciprocal exchange. We propose that chromosomal recombination is a two-step process, and recBC functions are primarily required for the second step.
New mutants of Paramecium tetraurelia defective in a calcium control mechanism: genetic and behavioral characterizations.
Authors: Evans T C , Nelson D L 
Published: January 2021

Abstract
The k-shy mutants of Paramecium tetraurelia are altered in several Ca2+-dependent functions which regulate ciliary motility. The isolation, genetics, and phenotypes of these mutants are described. Of six independent isolates, all contained recessive single-factor mutations and comprise two unlinked loci, ksA and ksB. All k-shy strains showed prolonged backward swimming responses to depolarizing stimuli, but gave infrequent responses to some stimuli. At least four k-shy strains displayed temperature sensitivity. Neither ksA nor ksB was allelic or linked to dancer, a mutation causing weak Ca2+ current inactivation and prolonged backward swimming. Analysis of ks+; Dn double mutants revealed synergism between the two mutations. The ksA mutant survived Ba2+ solutions longer than wild type, but was more sensitive to K+. Together with previous studies, these results are consistent with a defect in reducing intracellular Ca2+ causing both prolonged ciliary reversal and reduced Ca2+ channel activity due to more active Ca2+-dependent feedback mechanisms. The integration of the Ca2+-dependent stimulatory and inhibitory functions is therefore dependent on ks+ gene functions. The ksA mutant was rescued by microinjection of wild-type cytoplasm, suggesting a possible behavioral assay for factors related to the ksA+ gene product.