bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in external, internal oral and chondrocranial morphology of the tadpole ofCorythomantis greeningiBoulenger, 1896 (Anura: Hylidae)
Authors: Uchôa Lucas Rafael , Costa Claylton A. , Santos Antonia Joyce S. , Silva Rayone A. , Sena Felipe P. , Andrade Etielle B. 
Published: October 2020

ABSTRACTThe genusCorythomantiscurrently comprises a single species,Corythomantis greeningi, a hylid widely distributed in xerophilic and subhumid morphoclimatic regions of Brazil, mainly in the Northeast region. Recently the external morphology, internal oral anatomy, and chondrocranium ofC. greeningitadpoles were described from specimens collected in the state of Bahia, however, we observed some differences in morphology of individuals from the state of Piauí, northeastern Brazil. The tadpoles were collected during the 2019 rainy season and 14 individuals were used to describe and compare the larval characters. We observed differences in external, internal oral and chondrocranial morphology in relation to specimens previously described, especially in oral disc, number and shape of oral cavity papillae, and some chondrocranium structures, as:cartilago suprarostralis,cornua trabeculae,fontanella frontoparietalis,cartilago orbitaliseplanum hypobranchiale. Our results point to the occurrence of heterochrony inC. greeningi, but we do not rule out the possibility that tadpoles belong to different species. Further studies involving a greater number of tadpoles at different stages, combined with genetic, acoustic, and morphological factors of adult specimens may establish the variation degree ofC. greeningiin different regions of northeastern Brazil.RESUMOO gêneroCorythomantiscompreende atualmente uma única espécie,Corythomantis greeningi, um hilídeo amplamente distribuído nas regiões morfoclimáticas xerofílicas e subúmidas do Brasil, principalmente na região Nordeste. Recentimente foram descritas a morfologia externa, anatomia oral interna e condrocrânio do girino deC. greeningia partir de espécimes coletados no estado da Bahia, no entanto, observamos algumas diferenças na morfologia dos indivíduos coletados na região norte do estado do Piauí, Nordeste do Brasil. Os girinos foram coletados durante o período chuvoso de 2019 e 14 indivíduos foram utilizados para descrição e comparação dos caracteres larvais. Observamos diferenças na morfologia externa, oral interna e no condrocranio do girino em relação ao descrito anteriormente, sobretudo no disco oral, no número e formato de papilas cavidade oral e algumas estruturas do condrocrânio, como:cartilago suprarostralis,cornua trabeculae,fontanella frontoparietalis,cartilago orbitaliseplanum hypobranchiale. Nossos resultados apontam a ocorrência de heterocronia emC. greeningi, porém não descartamos a possibilidade dos girinos pertencerem a espécies diferentes. Estudos futuros envolvendo uma maior área de distribuição e maior número de indivíduos em estágios diferentes, aliados a fatores genéticos, acústico e morfológicos dos espécimes adultos poderão estabelecer o grau de variação deC. greeningiem diferentes regiões do Nordeste brasileiro.
Proteomic analysis of microtubule inner proteins (MIPs) in Rib72 nullTetrahymenacells reveals functional MIPs
Authors: Fabritius Amy S. , Bayless Brian A. , Li Sam , Stoddard Daniel , Heydeck Westley , Ebmeier Christopher C. , Anderson Lauren , Gunnels Tess , Nachiappan Chidambaram , Whittall Justen B. , Old William , Agard David A. , Nicastro Daniela , Winey Mark 
Published: October 2020

AbstractMotile cilia and flagella are built from stable populations of doublet microtubules that comprise their axonemes. Their unique stability is brought about, at least in part, by a network ofMicrotubuleInnerProteins (MIPs) found in the lumen of their doublet microtubules. Rib72A and Rib72B were identified as microtubule inner proteins (MIPs) in the motile cilia ofTetrahymena thermophila. Loss of these proteins leads to ciliary defects and loss of multiple MIPs. We performed mass spectrometry coupled with proteomic analysis and bioinformatics to identify the MIPs lost inRIB72A/Bknockout (KO)Tetrahymenacells. From this analysis we identified a number of candidate MIPs and pursued one, Fap115, for functional characterization. We find that loss of Fap115 results in disrupted cell swimming and aberrant ciliary beating. Cryo-electron tomography reveals that Fap115 localizes to MIP6a in the A-tubule of the doublet microtubules. Overall, our results highlight the complex relationship between MIPs, ciliary structure, and ciliary function.
Combined analysis of the time-resolved transcriptome and proteome of plant pathogenXanthomonas oryzaepv.oryzae
Authors: Kim Seunghwan , Jang Wooyoung Eric , Kim Min-Sik , Kim Jeong-Gu , Kang Lin-Woo 
Published: October 2020

AbstractXanthomonas oryzaepv.oryzae(Xoo) is a plant pathogen responsible for causing bacterial blight in rice. The immediate alterations in Xoo upon initial contact with rice are essential for pathogenesis. We studied time-resolved genome-wide gene expression in pathogenicity-activated Xoo cells at the transcriptome and proteome levels. The early response genes of Xoo include genes related to cell motility, inorganic ion transport, and effectors. The alteration of gene expression is initiated as early as few minutes after the initial interaction and changes with time. The time-resolved comparison of the transcriptome and proteome shows the differences between transcriptional and translational expression peaks in many genes, although the overall expression pattern of mRNAs and proteins is conserved. The discrepancy suggests an important role of translational regulation in Xoo at the early stages of pathogenesis. The gene expression analysis using time-resolved transcriptome and proteome provides unprecedented valuable information regarding Xoo pathogenesis.
Evolution of co-regulatory network of C4metabolic genes and TFs in the genus Flaveria: go anear or away in the intermediate species?
Authors: Lyu Ming-Ju Amy , Essemine Jemaa , Chen Faming , Chen Genyun , Zhu Xin-Guang 
Published: October 2020

AbstractC4photosynthesis evolved from the ancestral C3photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4photosynthesis have been intensively studied; however, the transcription factors (TFs) regulating these C4metabolic genes are not well understood. In particular, how the TF regulatory network of C4metabolic genes was rewired during the evolution is unclear. Here, we constructed TFs co-regulatory networks for core C4metabolic genes (C4GRN) for four evolutionarily closely related species from the genus Flaveria, which represent four different evolutionary stages of the C4photosynthesis, namely, C3, type I C3-C4, type II C3-C4and C4. Our results show that more than half of the co-regulations of TFs and C4core metabolic genes were species specific. The counterparts of C4genes in C3species were already co-regulated with the photosynthesis-related genes; whereas the required TFs for the C4photosynthesis were recruited later. The type I C3-C4species recruited 40% of C4required TFs which co-regulated all core C4metabolic genes but PEPC; nevertheless, the type II C3-C4species took on a high divergent C4GRN with C4species itself. In C4species, PEPC and PPDK-RP possessed much more co-regulated TFs than other C4metabolic genes. This study provides for the first time the TFs profiles of the C4metabolic genes in species with different photosynthetic types and reveal the dynamic of C4genes-TFs co-regulations along the evolutionary process, providing thereby new insights into the evolution of C4photosynthesis.
Postharvest properties of ultra-late maturing peach cultivars and their attributions toMelting Flesh(M) locus: Re-evaluation ofMlocus in association with flesh texture
Authors: Nakano Ryohei , Kawai Takashi , Fukamatsu Yosuke , Akita Kagari , Watanabe Sakine , Asano Takahiro , Takata Daisuke , Sato Mamoru , Fukuda Fumio , Ushijima Koichiro 
Published: October 2020

AbstractThe postharvest properties of two ultra-late maturing peach cultivars, ‘Tobihaku’ (TH) and ‘Daijumitsuto’ (DJ), were investigated. Fruit were harvested at commercial maturity and held at 25°C. TH exhibited the characteristics of normal melting flesh (MF) peach, including rapid fruit softening associated with an increase in endogenous ethylene production In contrast, DJ did not soften at all during three-week experimental period even though substantial ethylene production was observed. Fruit of TH and DJ were treated with 5000 ppm of propylene, an ethylene analog, continuously for seven days. TH softened rapidly whereas DJ maintained high flesh firmness in spite of an increase in endogenous ethylene production, suggesting that DJ but not TH lacked the ability to be softened in response to endogenous and exogenous ethylene/propylene. DNA-seq analysis showed that tandem endo-polygalacturonase (endoPG) genes located atmelting flesh(M) locus,Pp-endoPGM(PGM) andPp-endoPGF(PGF), were deleted in DJ. TheendoPGgenes atMlocus are known to control flesh texture of peach fruit, and it was suggested that the non-softening property of DJ is due to the lack ofendoPGgenes. On the other hand, TH possessed an unidentifiedMhaplotype that is involved in determination of MF phenotype. Structural identification of the unknownMhaplotype, designated asM0, through comparison with previously reportedMhaplotypes revealed distinct differences betweenPGMonM0haplotype (PGM-M0) andPGMon other haplotypes (PGM-M1). PeachMhaplotypes were classified into four main haplotypes:M0withPGM-M0;M1with bothPGM-M1andPGF;M2withPGM-M1; andM3lacking bothPGMandPGF. Re-evaluation ofMlocus in association with MF/non-melting flesh (NMF) phenotypes in more than 400 accessions by using whole genome shotgun sequencing data on database and/or by PCR genotyping demonstrated thatM0haplotype was the common haplotype in MF accessions, andM0andM1haplotypes were dominant overM2andM3haplotypes and co-dominantly determined the MF trait. It was also assumed on the basis of structural comparison ofMhaplotypes amongPrunusspecies that the ancestral haplotype ofM0diverged from those of the other haplotypes before the speciation ofPrunus persica.
Spermidine and spermine are the natural substrates of theAcinetobacter baumanniiAmvA multidrug efflux pump
Authors: Short Francesca L. , Liu Qi , Ashwood Heather E. , Naidu Varsha , Li Liping , Mabbutt Bridget C. , Hassan Karl A. , Paulsen Ian T. 
Published: October 2020

AbstractMultidrug efflux pumps are important drivers of antibiotic resistance inAcinetobacter baumanniiand other pathogens, however their ‘natural’ roles beyond transport of clinical antimicrobials are poorly described. Polyamines are an ancient class of molecules with broad roles in all three kingdoms of life, and are the likely natural substrate of at least one efflux pump family. We have defined the transcriptome ofA. baumanniifollowing treatment with high levels of the polyamines putrescine, cadaverine, spermidine and spermine. These molecules influenced expression of multiple gene classes inA. baumanniiincluding those associated with virulence, and the four polyamines induced distinct but overlapping transcriptional responses. Polyamine shock also induced expression of the MFS-family efflux pump geneamvAand its repressor geneamvR. Loss ofamvAdramatically reduced tolerance to the long-chain triaamine spermidine, but caused only modest changes in resistance to known AmvA substrates such as acriflavine. We confirmed reduced accumulation of spermidine inamvA-deficientA. baumannii, and showed that its expression is induced by long-chain polyamines through its cognate regulator AmvR. Our findings suggest that the conservedA. baumanniiefflux pump AmvA has evolved to export spermidine from the cell, but that its substrate recognition promiscuity also allows activity against clinically-important biocides and antibiotics.ImportanceAMR genes, including multidrug efflux pumps, evolved long before the ubiquitous use of antimicrobials in medicine and infection control. Multidrug efflux pumps often transport metabolites, signals and host-derived molecules in addition to antibiotics or biocides. Understanding the ancestral physiological roles of multidrug efflux pumps could help to inform the development of strategies to subvert their activity. In this study, we investigated the response ofAcinetobacter baumanniito polyamines, a widespread, abundant class of amino acid-derived metabolites, which led us to identify long-chain polyamines as natural substrates of the disinfectant efflux pump AmvA. A second clinically-important efflux pump, AdeABC, also contributed to polyamine tolerance. Our results suggest that the disinfectant resistance capability that allowsA. baumanniito survive in hospitals may have evolutionary origins in the transport of polyamine metabolites.
Effects of various carbohydrates on the in vitro pollen germination ofVinca roseaandCucumis melo var. utilissimus
Authors: Sharma S , Marni A D , Sharma V , Manchanda P 
Published: October 2020

AbstractPollen germination is crucial for the process of plant development which strongly depends on the presence of carbohydrates as a primary source of energy. In this study, we analyzed the differential effects of four sugars with varying concentrations on the pollen germination ofVinca rosea Linn. andCucumis melo var. utilissimus(Duth. & Fuller) using Brewbaker and Kwack’s medium as germination medium and hanging drop method after an incubation period of 1 hour. Sucrose and glucose supported the pollen germination but galactose and fructose did not support and even considerably inhibited the pollen germination ofVinca rosea. However in pollen germination ofCucumis melo var. utilissimus, all the four sugars supported the pollen germination. The study suggests that 15% sucrose, forVinca rosea, and 12% galactose, forCucumis melo var. utilissimus, supports in achieving the highest pollen germination percentage when added to the pollen germination medium.
Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture
Authors: Bashirzadeh Yashar , Redford Steven A. , Lorpaiboon Chatipat , Groaz Alessandro , Litschel Thomas , Schwille Petra , Hocky Glen M. , Dinner Aaron R. , Liu Allen P. 
Published: October 2020

SummaryHow complex actin network architectures arise and coexist in membrane-enclosed cell environment remains unknown. By encapsulating actin and crosslinking proteins α-actinin and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement and its size can lead to formation of complex actin structures, including rings and asters at GUV peripheries and centers. Strikingly, we find that the materials properties of the aster structures depend on the ratio of the relative concentrations of α-actinin and fascin, and we demonstrate that this results from α-actinin and fascin sorting into separate domains in the structures. We complement our experiments with molecular simulations that capture the spontaneous formation of competing network architectures; these provide a microscopic view of the dynamics and delineate the molecular features that promote sorting. We propose that the observed boundary-imposed effect on protein sorting is a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers.
Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation
Authors: Wyckelsma VL , Venckunas T , Houweling PJ , Schlittler M , Lauschke VM , Tiong CF , Wood H , Ivarsson N , Paulauskas H , Eimantas N , Andersson DC , North KN , Brazaitis M , Westerblad H 
Published: October 2020

ABSTRACTThe fast skeletal muscle protein α-actinin-3 is absent in 1.5 billion people worldwide due to homozygosity for a nonsense polymorphism in theACTN3gene (R577X)1. The prevalence of the 577X allele increased as modern humans moved to colder climates, suggesting a link between α-actinin-3 deficiency and improved cold tolerance1,2. Here, we show that humans lacking α-actinin-3 (XX) are superior in maintaining core body temperature during cold-water immersion due to changes in skeletal muscle thermogenesis. Muscles of XX individuals displayed a shift towards more slow-twitch isoforms of myosin heavy chain (MyHC) and sarcoplasmic reticulum (SR) proteins, accompanied by altered neuronal muscle activation resulting in increased tone rather than overt shivering3,4. Experiments onActn3knockout mice showed no alterations in brown adipose tissue (BAT) properties that could explain the improved cold tolerance in XX individuals. Thus, this study provides a clear mechanism for the positive selection of theACTN3X-allele in cold climates and supports a key thermogenic role of skeletal muscle during cold exposure in humans.
Scaffolded Learning of Bipedal Walkers: Bootstrapping Ontogenetic Development
Authors: Zhu Jiahui , Rong Chunyan , Iida Fumiya , Rosendo Andre 
Published: October 2020

AbstractBipedal locomotion has several key challenges, such as balancing, foot placement, and gait optimization. We reach optimality from a very early age by using natural supports, such as our parent’s hands, chairs, and training wheels, and bootstrap a new knowledge from the recently acquired one. In this paper, we propose a scaffolded learning method from an evolutionary robotics perspective, where a biped creature achieves stable and independent bipedal walking while exploiting the natural scaffold of its changing morphology to create a third limb. Hence, we compare three conditions of scaffolded learning to reach bipedalism, and we prove that a performance-based scaffold is the most conducive to accelerate the learning of ontogenetic bipedal walking. Beyond a pedagogical experiment, this work presents a powerful tool to accelerate learning on robots.
Impaired dynamic profile of brain recurring functional connectivity states in Alzheimer’s disease
Authors: Maleki-Balajoo Somayeh , Asemani Davud , Khadem Ali , Soltanian-Zadeh Hamid 
Published: October 2020

AbstractUp to now, disrupted functional organization of the brain in Alzheimer’s disease (AD) has mostly been examined by assessing “static” functional connectivity (FC). However, recent studies have provided clear evidence that brain FC exhibits intrinsic spatiotemporal “dynamic” organization also being significantly affected in AD. However, inconsistency in former studies is a motivation for further investigation of impaired dynamic profile of brain FC networks in Alzheimer’s disease._In this work, we identified recurring FC states during rest (eyes-open) in 24 AD patients and 37 healthy controls (HC) by combining sliding window-based method (examining dynamic FC) and k-means clustering algorithm (identifying recurring FC states over time). To define the optimum number of recurring FC states in k-means algorithm, we employed non-supervised validity criteria such as silhouette value and Dunn index over bootstrap samples. Then, we examined differences in dynamic properties of recurring FC states including probability of occurrence, lifetime and switching profile between groups. Afterward, association between impaired dynamic profile of recurring FC states and cognitive performance was assessed in AD patients. Our findings revealed three recurring FC states and among them, FC state with the most significant differences in probability of occurrence (corrected p-value < 0.0001) included brain regions involved in default mode, frontoparietal and salience networks. This recurring FC state occurred significantly less and lasted shorter in patients with AD than in the HC. Further, the probability of occurrence in this recurring FC state significantly correlated positively with cognitive decline in patients with AD. Our findings suggest more decreased in cognitive performance in patients with AD associated with more reduced ability of AD patients to access clinically relevant impaired brain FC networks. Impaired dynamic profile of recurring FC states in AD provide greater understanding of AD’s pathophysiology.
Phenomenon of music-induced opening of the blood-brain barrier in healthy mice
Authors: Semyachkina-Glushkovskaya O. , Esmat A. , Bragin D. , Bragina O. , Shirokov A. A. , Navolokin N. , Yang Y. , Abdurashitov A. , Khorovodov A. , Terskov A. , Klimova M. , Mamedova A. , Fedosov I. , Tuchin V. , Kurths J. 
Published: October 2020

Music plays a more important role in our life than just being an entertainment. It is an even anti-anxiety therapy of human and animals. However, the unsafe listening of loud music triggers hearing loss in millions of young people and professional musicians (rock, jazz, and symphony orchestra) due to exposure to damaging levels of sound using personal audio devices or at noisy entertainment venues including nightclubs, discotheques, bars, and concerts. Therefore, it is important to understand how loud music affects us.In this pioneering study on healthy mice, we discover that loud rock music below the safety threshold causes opening of the blood-brain barrier (OBBB), which plays an important role in protecting the brain from viruses, bacteria and toxins. We clearly demonstrate that listening loud music during 2 hrs in an intermittent adaptive regime is accompanied by delayed (1h after music exposure) and short-lasting (during 1-4 hrs) OBBB to low and high molecular weight compounds without cochlear and brain impairments. We present the systemic and molecular mechanisms responsible for music-induced OBBB. Finally, a revision of our traditional knowledge about the BBB nature and the novel strategies in optimization of sound-mediated methods for brain drug delivery are discussed.
Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals
Authors: Liu Jianheng , Huang Tao , Zhang Yusen , Zhao Tianxuan , Zhao Xueni , Chen Wanying , Zhang Rui 
Published: October 2020

AbstractmRNA m5C, which has recently been implicated in the regulation of mRNA mobility, metabolism, and translation, plays important regulatory roles in various biological events. Two types of m5C sites are found in mRNAs. Type I m5C sites, which contain a downstream G-rich triplet motif and are computationally predicted to locate in the 5’ end of putative hairpin structures, are methylated by NSUN2. Type II m5C sites contain a downstream UCCA motif and are computationally predicted to locate in the loops of putative hairpin structures. However, their biogenesis remains unknown. Here we identified NSUN6, a methyltransferase that is known to methylate C72 of tRNAThrand tRNACys, as an mRNA methyltransferase that targets Type II m5C sites. Combining the RNA secondary structure prediction, miCLIP, and results from a high-throughput mutagenesis analysis, we determined the RNA sequence and structural features governing the specificity of NSUN6-mediated mRNA methylation. Integrating these features into an NSUN6-RNA structural model, we identified an NSUN6 variant that largely loses tRNA methylation but retains mRNA methylation ability. Finally, we revealed a negative correlation between m5C methylation and translation efficiency. Our findings uncover that mRNA m5C is tightly controlled by an elaborate two-enzyme system, and the protein-RNA structure analysis strategy established may be applied to other RNA modification writers to distinguish the functions of different RNA substrates of a writer protein.