bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bivalves are NO different: nitric oxide as negative regulator of metamorphosis in the Pacific oyster, Crassostrea gigas
Authors: Vogeler Susanne , Carboni Stefano , Li Xiaoxu , Nevejan Nancy , Monaghan Sean J. , Ireland Jacqueline H. , Joyce Alyssa 
Published: November 2020

AbstractBackgroundNitric oxide (NO) is presumed to be a regulator of metamorphosis in many invertebrate species, and although NO pathways have been comparatively well-investigated in gastropods, annelids and crustaceans, there has been very limited research on the effects of NO on metamorphosis in bivalve shellfish.ResultsIn this paper, we investigate the effects of NO pathway inhibitors and NO donors on metamorphosis induction in larvae of the Pacific oyster,Crassostrea gigas.The nitric oxides synthase (NOS) inhibitors s-methylisothiourea hemisulfate salt (SMIS), aminoguanidine hemisulfate salt (AGH) and 7-nitroindazole (7-NI) induced metamorphosis at 75, 76 and 83% respectively, and operating in a concentration-dependent manner. Additional induction of up to 54% resulted from exposures to 1H-[1,2,4]Oxadiazole[4,3-a]quinoxalin-1-one (ODQ), an inhibitor of soluble guanylyl cyclase, with which NO interacts to catalyse the synthesis of cyclic guanosine monophosphate (cGMP). Conversely, high concentrations of the NO donor sodium nitroprusside dihydrate in combination with metamorphosis inducers epinephrine, MK-801 or SMIS, significantly decreased metamorphosis, although a potential harmful effect of excessive NO unrelated to metamorphosis pathway cannot be excluded. Expression ofCgNOSalso decreased in larvae after metamorphosis regardless of the inducers used, but intensified again post-metamorphosis in spat. Fluorescent detection of NO in competent larvae with DAF-FM diacetate and localisation of the oyster nitric oxide synthaseCgNOSexpression by in-situ hybridisation showed that NO occurs primarily in two key larval structures, the velum and foot. cGMP was also detected in the foot using immunofluorescent assays, and is potentially involved in the foot’s smooth muscle relaxation.ConclusionTogether, these results suggest that the NO pathway acts as a negative regulator of metamorphosis in Pacific oyster larvae, and that NO reduction induces metamorphosis by inhibiting swimming or crawling behaviour, in conjunction with a cascade of additional neuroendocrine downstream responses.
Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps
Authors: Blaimer Bonnie B. , Gotzek Dietrich , Brady Seán G. , Buffington Matthew L. 
Published: November 2020

AbstractBackgroundParasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior known as galling. Less commonly, cynipoid wasps exhibit inquilinism, a strategy where some species have adapted to usurp other species’ galls instead of inducing their own. Using a phylogenomic data set of ultraconserved elements from nearly all lineages of Cynipoidea, we here generate a robust phylogenetic framework and timescale to understand cynipoid systematics and the evolution of these life histories.ResultsOur reconstructed evolutionary history for Cynipoidea differs considerably from previous hypotheses. Rooting our analyses with non-cynipoid outgroups, the Paraulacini, a group of inquilines, emerged as sister-group to the rest of Cynipoidea, rendering the gall wasp family Cynipidae paraphyletic. The families Ibaliidae and Liopteridae, long considered archaic and early-branching parasitoid lineages, were found nested well within the Cynipoidea as sister-group to the parasitoid Figitidae. Cynipoidea originated in the early Jurassic around 190 Ma. Either inquilinism or parasitoidism is suggested as the ancestral and dominant strategy throughout the early evolution of cynipoids, depending on whether a simple (three states: parasitoidism, inquilinism and galling) or more complex (seven states: parasitoidism, inquilinism and galling split by host use) model is employed.ConclusionsOur study has significant impact on understanding cynipoid evolution and highlights the importance of adequate outgroup sampling. We discuss the evolutionary timescale of the superfamily in relation to their insect hosts and host plants, and outline how phytophagous galling behavior may have evolved from entomophagous, parasitoid cynipoids. Our study has established the framework for further physiological and comparative genomic work between gall-making, inquiline and parasitoid lineages, which could also have significant implications for the evolution of diverse life histories in other Hymenoptera.
Near-chromosome level genome assembly reveals ploidy diversity and plasticity in the intestinal protozoan parasite Entamoeba histolytica
Authors: Kawano-Sugaya Tetsuro , Izumiyama Shinji , Yanagawa Yasuaki , Saito-Nakano Yumiko , Watanabe Koji , Kobayashi Seiki , Nakada-Tsukui Kumiko , Nozaki Tomoyoshi 
Published: November 2020

Abstract
Background
Amoebozoa is a eukaryotic supergroup composed of unicellular and multicellular amoebic protozoa (e.g. Acanthamoeba, Dictyostelium, and Entamoeba). They are model organisms for studies in cellular and evolutionary biology and are of medical and veterinary importance. Despite their importance, Amoebozoan genome organization and genetic diversity remain poorly studied due to a lack of high-quality reference genomes. The slime mold Dictyostelium discoideum is the only Amoebozoan species whose genome is available at the chromosome-level.

Results
Here, we provide a near-chromosome-level assembly of the Entamoeba histolytica genome, the second semi-completed Amoebozoan genome. The availability of this improved genome allowed us to discover inter-strain heterogeneity in ploidy at the near-chromosome or sub-chromosome level among 11 clinical isolates and the reference strain. Furthermore, we observed ploidy-independent regulation of gene expression, contrary to what is observed in other organisms, where RNA levels are affected by ploidy.

Conclusions
Our findings offer new insights into Entamoeba chromosome organization, ploidy, transcriptional regulation, and inter-strain variation, which will help to further decipher observed spectrums of virulence, disease symptoms, and drug sensitivity of E. histolytica isolates.
Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions
Authors: Koul Vatsala , Srivastava Divya , Singh Pushplata Prasad , Kochar Mandira 
Published: November 2020

AbstractBackgroundSmall RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacteriumAzospirillum brasilenseSp245 to date.ResultsExpression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes inA. brasilenseSp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data.ConclusionsDifferential expression of 468A. brasilensesRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.
Variation under domestication in animal models: the case of the Mexican axolotl
Authors: Torres-Sánchez María 
Published: November 2020

AbstractBackgroundSpecies adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864.ResultsUsing gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations.ConclusionsAwareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.
Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line
Authors: Zhang Meng , Liu Ji , Ma Qiang , Qin Yuan , Wang Hantao , Chen Pengyun , Ma Liang , Fu Xiaokang , Zhu Longfu , Wei Hengling , Yu Shuxun 
Published: November 2020

AbstractBackgroundMale sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CCRI040029, was reported of great advantages to cotton heterosis. However, little information concerning the male sterility of CCRI9106 is known. Here, comparative transcriptome analysis of CCRI9106 (the mutant, MT) and CCRI040029 (the wild type, WT) anthers in Anyang (long-day, male sterile condition to CCRI9106) was performed to reveal the potential male sterile mechanism of CCRI9106.ResultsLight and electron microscopy revealed that the male sterility phenotype of MT was mainly attributed to irregularly exine, lacking tryphine and immature anther cuticle. Based on the cytological characteristics of MT anthers, anther RNA libraries (18 in total) of tetrad (TTP), late uninucleate (lUNP) and binucleate (BNP) stages in MT and WT were constructed for transcriptomic analysis, therefore revealing a total of 870,4 differentially expressed genes (DEGs). By performing gene expression pattern analysis and protein-protein interaction (PPI) networks construction, we found down-regulation of DEGs, which enriched by the lipid biosynthetic process and the synthesis pathways of several types of secondary metabolites such as terpenoids, flavonoids and steroids, may crucial to the male sterility phenotype of MT, and resulting in the defects of anther cuticle and tryphine, even the irregularly exine. Furthermore, several lipid-related genes together with ABA-related genes and MYB transcription factors were identified as hub genes via weighted gene co-expression network analysis (WGCNA). Additionally, the ABA content of MT anthers was reduced across all stages when compared with WT anthers. At last, genes related to the formation of anther cuticle and tryphine could activated in MT under short-day condition.ConclusionsWe propose that the down-regulation of genes related to the assembly of anther cuticle and tryphine may lead to the male sterile phenotype of MT, and MYB transcription factors together with ABA played key regulatory roles in these processes. The conversion of fertility in different photoperiods may closely relate to the functional expression of these genes. These findings contribute to elucidate the mechanism of male sterility in upland cotton.
Indole-3-lactic acid associated with Bifidobacterium-dominated microbiota significantly decreases inflammation in intestinal epithelial cells
Authors: Ehrlich Amy M. , Pacheco Alline R. , Henrick Bethany M. , Taft Diana , Xu Gege , Huda M. Nazmul , Mishchuk Darya , Goodson Michael L. , Slupsky Carolyn , Barile Daniela , Lebrilla Carlito B. , Stephensen Charles B. , Mills David A. , Raybould Helen E. 
Published: November 2020

Abstract
Background
Bifidobacterium longum subsp. infantis (B. infantis) is a commensal bacterium that colonizes the gastrointestinal tract of breast-fed infants. B. infantis can efficiently utilize the abundant supply of oligosaccharides found in human milk (HMO) to help establish residence. We hypothesized that metabolites from B. infantis grown on HMO produce a beneficial effect on the host.

Results
In a previous study, we demonstrated that B. infantis routinely dominated the fecal microbiota of a breast fed Bangladeshi infant cohort (1). Characterization of the fecal metabolome of binned samples representing high and low B. infantis populations from this cohort revealed higher amounts of the tryptophan metabolite indole-3-lactic acid (ILA) in feces with high levels of B. infantis. Further in vitro analysis confirmed that B. infantis produced significantly greater quantities of the ILA when grown on HMO versus lactose, suggesting a growth substrate relationship to ILA production. The direct effects of ILA were assessed in a macrophage cell line and intestinal epithelial cell lines. ILA (1-10 mM) significantly attenuated lipopolysaccharide (LPS)-induced activation of NF-kB in macrophages. ILA significantly attenuated TNF-α- and LPS-induced increase in the pro-inflammatory cytokine IL-8 in intestinal epithelial cells. ILA increased mRNA expression of the aryl hydrogen receptor (AhR)-target gene CYP1A1 and nuclear factor erythroid 2–related factor 2 (Nrf2)-targeted genes glutathione reductase 2 (GPX2), superoxide dismutase 2 (SOD2), and NAD(P) H dehydrogenase (NQO1). Pretreatment with either the AhR antagonist or Nrf-2 antagonist inhibited the response of ILA on downstream effectors.

Conclusions
These findings suggest that ILA, a predominant metabolite from B. infantis grown on HMO and elevated in infant stool high in B. infantis, and protects gut epithelial cells in culture via activation of the AhR and Nrf2 pathway.
Emotion regulation through bifocal processing of fear inducing and disgust inducing stimuli
Authors: Wittfoth Dina , Pfeiffer Antonia , Bohne Michael , Lanfermann Heinrich , Wittfoth Matthias 
Published: November 2020

AbstractBackgroundWe present first-time evidence for the immediate neural and behavioral effects of bifocal emotional processing via visualized tapping for two different types of negative emotions (fear and disgust) in a sample of healthy participants.ResultsIndependent of stimulus type, neural activation in the amygdala is increased during regulation, while activation in the ventral anterior cingulate cortex is decreased. Behavioral responses, as well as lateral and medial occipital regions and the dorsolateral prefrontal cortex show differential regulatory effects with respect to stimulus type.ConclusionsOur findings suggest that emotion regulation through bifocal processing has a neural and behavioral signature that is distinct from previously investigated emotion regulation strategies. They support theoretical models of facilitated access to and processing of emotions during bifocal processing and suggest differential neural and behavioral effects for various types of negative emotions.
Occipital repetitive transcranial magnetic stimulation does not affect multifocal visual evoked potentials
Authors: Kolbe Robert , Aytulun Aykut , Müller Ann-Kristin , Ringelstein Marius , Aktas Orhan , Schnitzler Alfons , Hartung Hans-Peter , Groiss Stefan Jun , Albrecht Philipp 
Published: November 2020

Abstract
Background
To identify mechanisms of cortical plasticity of the visual cortex and to quantify their significance, sensitive parameters are warranted. In this context, multifocal visual evoked potentials (mfVEPs) can make a valuable contribution as they are not associated with cancellation artifacts and include also the peripheral visual field.

Objective
To investigate if occipital repetitive transcranial magnetic stimulation (rTMS) can induce mfVEP changes.

Methods
18 healthy participants were included in a single-blind crossover-study receiving sessions of excitatory, occipital 10 Hz rTMS and sham stimulation. MfVEP was performed before and after each rTMS session and changes in amplitude and latency between both sessions were compared using generalized estimation equation models.

Results
There was no significant difference in amplitude or latency between verum and sham group.

Conclusion
We conclude that occipital 10 Hz rTMS has no effect on mfVEP measures, which is in line with previous studies using full field VEP.
Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm
Authors: Khadka Kamal , Torkamaneh Davoud , Kaviani Mina , Belzile Francois , Raizada Manish N. , Navabi Alireza 
Published: November 2020

Abstract
Background
Appropriate information about genetic diversity and population structure of germplasm improves the efficiency of plant breeding. The low productivity of Nepali bread wheat (Triticum aestivum L.) is a major concern particularly since Nepal is ranked the 4th most vulnerable nation globally to climate change. The genetic diversity and population structure of Nepali spring wheat have not been reported. This study aims to improve the exploitation of more diverse and under-utilized genetic resources to contribute to current and future breeding efforts for global food security.

Results
We used genotyping-by-sequencing (GBS) to characterize a panel of 318 spring wheat accessions from Nepal including 166 landraces, 115 CIMMYT advanced lines, and 34 Nepali released varieties. We identified 95 K high-quality SNPs. The greatest genetic diversity was observed among the landraces, followed by CIMMYT lines, and released varieties. Though we expected only 3 groupings corresponding to these 3 seed origins, the population structure revealed two large, distinct subpopulations along with two smaller and scattered subpopulations in between, with significant admixture. This result was confirmed by principal component analysis (PCA) and UPGMA distance-based clustering. The pattern of LD decay differed between subpopulations, ranging from 60 to 150 Kb. We discuss the possibility that germplasm explorations during the 1970s–1990s may have mistakenly collected exotic germplasm instead of local landraces and/or collected materials that had already cross-hybridized since exotic germplasm was introduced starting in the 1950s.

Conclusion
We suggest that only a subset of wheat “landraces” in Nepal are authentic which this study has identified. Targeting these authentic landraces may accelerate local breeding programs to improve the food security of this climate-vulnerable nation. Overall, this study provides a novel understanding of the genetic diversity of wheat in Nepal and this may contribute to global wheat breeding initiatives.
A full-length transcriptome and gene expression analysis reveal genes and molecular elements expressed during seed development in Gnetum luofuense
Authors: Deng Nan , Hou Chen , He Boxiang , Ma Fengfeng , Song Qingan , Shi Shengqing , Liu Caixia , Tian Yuxin 
Published: November 2020

AbstractBackgroundGnetumis an economically important tropical and subtropical gymnosperm genus with various dietary, industrial and medicinal uses. Many carbohydrates, proteins and fibers accumulate during the ripening ofGnetumseeds. However, the molecular mechanisms related to this process remain unknown.ResultsWe therefore assembled a full-length transcriptome from immature and matureG. luofuenseseeds using PacBio sequencing reads. We identified a total of 5726 novel genes, 9061 alternative splicing events, 3551 lncRNAs, 2160 transcription factors, and we found that 8512 genes possessed at least one poly(A) site. In addition, gene expression comparisons of six transcriptomes generated by Illumina sequencing showed that 14,323 genes were differentially expressed from an immature stage to a mature stage with 7891 genes upregulated and 6432 genes downregulated. The expression of 14 differentially expressed transcription factors from the MADS-box, Aux/IAA and bHLH families was validated by qRT-PCR, suggesting that they may have important roles in seed ripening ofG. luofuense.ConclusionsThese findings provide a valuable molecular resource for understanding seed development of gymnosperms.