bluuebunny/crossref_metadata_2025_split huggingface dataset:
Al-induced proteomics changes in tomato plants over-expressing a glyoxalase I gene
Authors: Sun Xudong , Li Hui , Thapa Santosh , Reddy Sangireddy Sasikiran , Pei Xiaobo , Liu Wei , Jiang Yuping , Yang Shaolan , Hui Dafeng , Bhatti Sarabjit , Zhou Suping , Yang Yong , Fish Tara , Thannhauser Theodore W. 
Published: March 2020

AbstractGlyoxalase I (Gly I) is the first enzyme in the glutathionine-dependent glyoxalase pathway for detoxification of methylglyoxal (MG) under stress conditions. Transgenic tomato ‘Money Maker’ plants overexpressing tomato SlGlyI gene (tomato unigene accession SGN-U582631/Solyc09g082120.3.1) were generated and homozygous lines were obtained after four generations of self-pollination. In this study, SlGlyI-overepxressing line (GlyI), wild type (WT, negative control) and plants transformed with empty vector (ECtr, positive control), were subjected to Al-treatment by growing in Magnavaca’s nutrient solution (pH 4.5) supplemented with 20 µM Al3+ ion activity. After 30 days of treatments, the fresh and dry weight of shoots and roots of plants from Al-treated conditions decreased significantly compared to the non-treated conditions for all the three lines. When compared across the three lines, root fresh and dry weight of GlyI was significant higher than WT and ECtr, whereas there was no difference in shoot tissues. The basal 5 mm root-tips of GlyI plants expressed a significantly higher level of glyoxalase activity under both non-Al-treated and Al-treated conditions compared to the two control lines. Under Al-treated condition, there was a significant increase in MG content in ECtr and WT lines, but not in GlyI line. Quantitative proteomics analysis using tandem mass tags mass spectrometry identified 4080 quantifiable proteins and 201 Al-induced differentially expressed proteins (DEPs) in root-tip tissues from GlyI, and 4273 proteins and 230 DEPs from ECtr. The Al-down-regulated DEPs were classified into molecular pathways of gene transcription, RNA splicing and protein biosynthesis in both GlyI and ECtr lines. The Al-induced DEPs in GlyI associated with tolerance to Al3+ and MG toxicity are involved in callose degradation, cell wall components (xylan acetylation and pectin degradation), oxidative stress (antioxidants) and turnover of Al-damaged epidermal cells, repair of damaged DNA, epigenetics, gene transcription, and protein translation. A protein–protein association network was constructed to aid the selection of proteins in the same pathway but differentially regulated in GlyI or ECtr lines. Proteomics data are available via ProteomeXchange with identifiers PXD009456 under project title ‘25Dec2017_Suping_XSexp2_ITAG3.2’ for SlGlyI-overexpressing tomato plants and PXD009848 under project title ‘25Dec2017_Suping_XSexp3_ITAG3.2’ for positive control ECtr line transformed with empty vector.
A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)
Authors: Xue Ting , Zheng Xuehai , Chen Duo , Liang Limin , Chen Nan , Huang Zhen , Fan Wenfang , Chen Jiannan , Cen Wan , Chen Shuai , Zhu Jinmao , Chen Binghua , Zhang Xingtan , Chen Youqiang 
Published: March 2020

AbstractThe Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly forCladopus chinensisof Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes. The assembled genome size was close to the estimated size, and 659.42 Mb of the assembly was assigned to 29 superscaffolds (scaffold N50 21.22 Mb). A total of 59.20% repetitive sequences were identified, among which long terminal repeats (LTRs) were the most abundant class (28.97% of the genome). Genome evolution analysis suggested that the divergence time ofCladopus chinensis(106 Mya) was earlier than that of Malpighiales (82 Mya) and that this taxon diverged into an independent branch of Podestemales. A recent whole-genome duplication (WGD) event occurred 4.43 million years ago. Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation, photosynthesis and isoflavonoid metabolism genes inCladopus chinensisare probably related to the genomic characteristics of this growing submerged species. Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses, including WUSCHEL (WUS), ASYMMETRIC LEAVES (ASL), SHOOT MERISTEMLESS (STM), NAC2, NAC8, NAC29, NAC47, NAC73, NAC83 and NAC102. These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae.
Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus
Authors: Li Shu-Fen , Wang Jin , Dong Ran , Zhu Hong-Wei , Lan Li-Na , Zhang Yu-Lan , Li Ning , Deng Chuan-Liang , Gao Wu-Jun 
Published: March 2020

AbstractAsparagus setaceusis a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome ofA. setaceusto facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly ofA. setaceuscovering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome ofA. setaceuswas predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time ofA. setaceusfrom its close relativeA. officinalisof ~9.66 million years ago, andA. setaceusunderwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted inA. setaceus. These findings provide new knowledge about the characteristics and evolution of theA. setaceusgenome, and will facilitate comparative genetic and genomic research on the genusAsparagus.
Investigation of the transcriptomic and metabolic changes associated with superficial scald physiology impaired by lovastatin and 1-methylcyclopropene in pear fruit (cv. “Blanquilla”)
Authors: Giné-Bordonaba Jordi , Busatto Nicola , Larrigaudière Christian , Lindo-García Violeta , Echeverria Gemma , Vrhovsek Urska , Farneti Brian , Biasioli Franco , De Quattro Concetta , Rossato Marzia , Delledonne Massimo , Costa Fabrizio 
Published: March 2020

AbstractTo elucidate the physiology underlying the development of superficial scald in pears, susceptible “Blanquilla” fruit was treated with different compounds that either promoted (ethylene) or repressed (1-methylcyclopropene and lovastatin) the incidence of this disorder after 4 months of cold storage. Our data show that scald was negligible for the fruit treated with 1-methylcyclopropene or lovastatin, but highly manifested in untreated (78% incidence) or ethylene-treated fruit (97% incidence). The comparison between the fruit metabolomic profile and transcriptome evidenced a distinct reprogramming associated with each treatment. In all treated samples, cold storage led to an activation of a cold-acclimation-resistance mechanism, including the biosynthesis of very-long-chain fatty acids, which was especially evident in 1-methylcyclopropane-treated fruit. Among the treatments applied, only 1-methylcyclopropene inhibited ethylene production, hence supporting the involvement of this hormone in the development of scald. However, a common repression effect on thePPOgene combined with higher sorbitol content was found for both lovastatin and 1-methylcyclopropene-treated samples, suggesting also a non-ethylene-mediated process preventing the development of this disorder. The results presented in this work represent a step forward to better understand the physiological mechanisms governing the etiology of superficial scald in pears.
(E)-Nerolidol is a volatile signal that induces defenses against insects and pathogens in tea plants
Authors: Chen Shenglong , Zhang Liping , Cai Xiaoming , Li Xin , Bian Lei , Luo Zongxiu , Li Zhaoqun , Chen Zongmao , Xin Zhaojun 
Published: March 2020

AbstractPlants release large amounts of volatile organic compounds (VOCs) in response to attackers. Several VOCs can serve as volatile signals to elicit defense responses in undamaged tissues and neighboring plants, but many questions about the ecological functions of VOCs remain unanswered. Tea plants are impacted by two harmful invaders, the piercing herbivore Empoasca (Matsumurasca) onukii Matsuda and the pathogen Colletotrichum fructicola. To determine the VOC signals in tea, we confirmed CsOPR3 as a marker gene and set up a rapid screening method based on a 1.51 kb CsOPR3 promoter fused with a β-glucuronidase (GUS) reporter construct (OPR3p::GUS) in Arabidopsis. Using this screening system, a terpenoid volatile (E)-nerolidol was identified as a potent signal that elicits plant defenses. The early responses triggered by (E)-nerolidol included the activation of a mitogen-activated protein kinase and WRKY, an H2O2 burst, and the induction of jasmonic acid and abscisic acid signaling. The induced plants accumulated high levels of defense-related chemicals, which possessed broad-spectrum anti-herbivore or anti-pathogen properties, and ultimately triggered resistance against Empoasca onukii and Colletotrichum fructicola in tea. We propose that these findings can supply an environmentally friendly management strategy for controlling an insect pest and a disease of tea plants.
Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6
Authors: Garcia-Doval Carmela , Schwede Frank , Berk Christian , Rostøl Jakob T. , Niewoehner Ole , Tejero Oliver , Hall Jonathan , Marraffini Luciano A. , Jinek Martin 
Published: March 2020

AbstractBacterial and archaeal CRISPR-Cas systems provide RNA-guided immunity against genetic invaders such as bacteriophages and plasmids. Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic-oligoadenylate second messengers that activate downstream effectors, including Csm6 ribonucleases, via their CARF domains. Here, we show that Enteroccocus italicus Csm6 (EiCsm6) degrades its cognate cyclic hexa-AMP (cA6) activator, and report the crystal structure of EiCsm6 bound to a cA6 mimic. Our structural, biochemical, and in vivo functional assays reveal how cA6 recognition by the CARF domain activates the Csm6 HEPN domains for collateral RNA degradation, and how CARF domain-mediated cA6 cleavage provides an intrinsic off-switch to limit Csm6 activity in the absence of ring nucleases. These mechanisms facilitate rapid invader clearance and ensure termination of CRISPR interference to limit self-toxicity.
Synthetic antibodies against BRIL as universal fiducial marks for single−particle cryoEM structure determination of membrane proteins
Authors: Mukherjee Somnath , Erramilli Satchal K. , Ammirati Mark , Alvarez Frances J. D. , Fennell Kimberly F. , Purdy Michael D. , Skrobek Blazej M. , Radziwon Katarzyna , Coukos John , Kang Yanyong , Dutka Przemysław , Gao Xiang , Qiu Xiayang , Yeager Mark , Eric Xu H. , Han Seungil , Kossiakoff Anthony A. 
Published: March 2020

AbstractWe propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins.
Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric mouse brain
Authors: Xu Ranjie , Li Xiaoxi , Boreland Andrew J. , Posyton Anthony , Kwan Kelvin , Hart Ronald P. , Jiang Peng 
Published: March 2020

AbstractMicroglia, the brain-resident macrophages, exhibit highly dynamic functions in neurodevelopment and neurodegeneration. Human microglia possess unique features as compared to mouse microglia, but our understanding of human microglial functions is largely limited by an inability to obtain human microglia under homeostatic states. Here, we develop a human pluripotent stem cell (hPSC)-based microglial chimeric mouse brain model by transplanting hPSC-derived primitive macrophage progenitors into neonatal mouse brains. Single-cell RNA-sequencing of the microglial chimeric mouse brains reveals that xenografted hPSC-derived microglia largely retain human microglial identity, as they exhibit signature gene expression patterns consistent with physiological human microglia and recapitulate heterogeneity of adult human microglia. Importantly, the engrafted hPSC-derived microglia exhibit dynamic response to cuprizone-induced demyelination and species-specific transcriptomic differences in the expression of neurological disease-risk genes in microglia. This model will serve as a tool to study the role of human microglia in brain development and degeneration.
Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum)
Authors: Aw Wanping , Jia Huijuan , Lyu Weida , Fukuda Shinji , Tomita Masaru , Otani Lila , Kato Hisanori 
Published: March 2020

AbstractWe used a multi-omics profiling approach to investigate the suppressive effects of 2% Wolfberry (WOL)-enriched diets on dextran sodium sulfate (DSS)-induced colitis in mice. It was observed that in mice fed the WOL diet, the disease activity index, colon shortening, plasma concentrations of matrix metalloproteinase-3 and relative mesenteric fat weight were significantly improved as compared to the DSS group. Results from colon transcriptome and proteome profiles showed that WOL supplementation significantly ameliorated the expression of genes and proteins associated with the integrity of the colonic mucosal wall and colonic inflammation. Based on the hepatic transcriptome, proteome and metabolome data, genes involved in fatty acid metabolism, proteins involved in inflammation and metabolites related to glycolysis were downregulated in WOL mice, leading to lowered inflammation and changes in these molecules may have led to improvement in body weight loss. The integrated nutrigenomic approach thus revealed the molecular mechanisms underlying the ameliorative effect of whole WOL fruit consumption on inflammatory bowel disease.
A systematic study of hexavalent chromium adsorption and removal from aqueous environments using chemically functionalized amorphous and mesoporous silica nanoparticles
Authors: Jang Eun-Hye , Pack Seung Pil , Kim Il , Chung Sungwook 
Published: March 2020

AbstractWe report on the synthesis and characterization of highly monodisperse amorphous silica nanoparticles (ASNs) and mesoporous silica nanoparticles (MSNs) with particle sizes of 15–60 nm. We demonstrate adsorption of Cr(VI) ions on amino-functionalized ASNs (NH2–ASNs) and MSNs (NH2–MSNs) and their removal from aqueous environments and show the specific surface area (SSA) of NH2–MSNs is four times as larger as that of NH2–ASNs and that more than 70% of the total SSA of NH2–MSNs is due to the presence of nanopores. Analyses of Cr(VI) adsorption kinetics on NH2–ASNs and NH2–MSNs exhibited relatively rapid adsorption behavior following pseudo-second order kinetics as determined by nonlinear fitting. NH2–ASNs and NH2–MSNs exhibited significantly higher Cr(VI) adsorption capacities of 34.0 and 42.2 mg·g−1 and removal efficiencies of 61.9 and 76.8% than those of unfunctionalized ASNs and MSNs, respectively. The Langmuir model resulted in best fits to the adsorption isotherms of NH2–ASNs and NH2–MSNs. The adsorption of Cr(VI) on NH2–ASNs and NH2–MSNs was an endothermic and spontaneous process according to the thermodynamic analyses of temperature-dependent adsorption isotherms. The removal efficiencies of NH2–ASNs and NH2–MSNs exhibited a moderate reduction of less than 25% of the maximum values after five regeneration cycles. Furthermore, NH2–MSNs were also found to reduce adsorbed Cr(VI) into less harmful Cr(III).
Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment
Authors: Mandakovic Dinka , Cintolesi Ángela , Maldonado Jonathan , Mendoza Sebastián N. , Aïte Méziane , Gaete Alexis , Saitua Francisco , Allende Miguel , Cambiazo Verónica , Siegel Anne , Maass Alejandro , González Mauricio , Latorre Mauricio 
Published: March 2020

AbstractThe Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO2 production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (β-carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.
Polymorphic Aβ42 fibrils adopt similar secondary structure but differ in cross-strand side chain stacking interactions within the same β-sheet
Authors: Wang Hongsu , Duo Lan , Hsu Frederick , Xue Christine , Lee Yoon Kyung , Guo Zhefeng 
Published: March 2020

AbstractFormation of polymorphic amyloid fibrils is a common feature in neurodegenerative diseases involving protein aggregation. In Alzheimer’s disease, different fibril structures may be associated with different clinical sub-types. Structural basis of fibril polymorphism is thus important for understanding the role of amyloid fibrils in the pathogenesis and progression of these diseases. Here we studied two types of Aβ42 fibrils prepared under quiescent and agitated conditions. Quiescent Aβ42 fibrils adopt a long and twisted morphology, while agitated fibrils are short and straight, forming large bundles via lateral association. EPR studies of these two types of Aβ42 fibrils show that the secondary structure is similar in both fibril polymorphs. At the same time, agitated Aβ42 fibrils show stronger interactions between spin labels across the full range of the Aβ42 sequence, suggesting a more tightly packed structure. Our data suggest that cross-strand side chain packing interactions within the same β-sheet may play a critical role in the formation of polymorphic fibrils.
Host density and habitat structure influence host contact rates and Batrachochytrium salamandrivorans transmission
Authors: Malagon Daniel A. , Melara Luis A. , Prosper Olivia F. , Lenhart Suzanne , Carter Edward Davis , Fordyce J. A. , Peterson Anna C. , Miller Debra L. , Gray Matthew J. 
Published: March 2020

AbstractBatrachochytrium salamandrivorans(Bsal) is an emerging invasive pathogen that is highly pathogenic to salamander species. Modeling infection dynamics in this system can facilitate proactive efforts to mitigate this pathogen's impact on North American species. Given its widespread distribution and high abundance, the eastern newt (Notophthalmus viridescens) has the potential to significantly influenceBsalepidemiology. We designed experiments to 1) estimate contact rates given different host densities and habitat structure and 2) estimate the probability of transmission from infected to susceptible individuals. Using parameter estimates from data generated during these experiments, we modeled infection and disease outcomes for a population of newts using a system of differential equations. We found that host contact rates were density-dependent, and that adding habitat structure reduced contacts. The probability ofBsaltransmission given contact between newts was very high (>90%) even at early stages of infection. Our simulations show rapid transmission ofBsalamong individuals following pathogen introduction, with infection prevalence exceeding 90% within one month and >80% mortality of newts in three months. Estimates of basic reproductive rate (R0) ofBsalfor eastern newts were 1.9 and 3.2 for complex and simple habitats, respectively. Although reducing host density and increasing habitat complexity might decrease transmission, these management strategies may be ineffective at stoppingBsalinvasion in eastern newt populations due to this species’ hyper-susceptibility.