bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Characterization oflncRNA152as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers
Authors: Kim Dae-Seok , Gadad Shrikanth S. , Setlem Rohit , Kim Kangsan , Malladi Srinivas , Hou Tim Y. , Nandu Tulip , Camacho Cristel V. , Kraus W. Lee 
Published: February 2022

AbstractLong non-coding RNAs have been implicated in many of the hallmarks of cancer. Herein, we found that the expression oflncRNA152(lnc152; a.k.a.DRAIC), which we annotated previously, is highly upregulated in luminal breast cancer (LBC) and downregulated in triple-negative breast cancer (TNBC). Knockdown oflnc152promotes cell migration and invasion in LBC cell lines. In contrast, ectopic expression oflnc152inhibits growth, migration, invasion, and angiogenesis in TNBC cell lines. In mice,lnc152inhibited the growth of TNBC cell xenografts, as well as metastasis of TNBC cells in an intracardiac injection model. Transcriptome analysis of the xenografts indicated thatlnc152downregulates genes controlling angiogenesis. Using pull down assays coupled with LC-MS/MS, we identified RBM47, a known tumor suppressor in breast cancer, as alnc152-interacting protein. The effects oflnc152in TNBC cells are mediated, in part, by regulating the expression of RBM47. Collectively, our results demonstrate thatlnc152is an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC.Statement ofSignificanceThis study identifieslncRNA152as an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC by upregulating the expression of the tumor suppressor RBM47. As such,lncRNA152may serve as a biomarker to track aggressiveness of breast cancer, as well as therapeutic target for treating TNBC.
Plants cope with fluctuating light by frequency-dependent non-photochemical quenching and cyclic electron transport
Authors: Niu Yuxi , Lazár Dušan , Holzwarth Alfred R. , Kramer David M. , Matsubara Shizue , Fiorani Fabio , Poorter Hendrik , Schrey Silvia D. , Nedbal Ladislav 
Published: February 2022

SummaryIn natural environments, plants are exposed to rapidly changing light. Maintaining photosynthetic efficiency while avoiding photodamage requires equally rapid regulation of photoprotective mechanisms. We asked what the operation frequency range of regulation is in which plants can efficiently respond to varying light.Chlorophyll fluorescence, P700, plastocyanin, and ferredoxin responses of wild-typeArabidopsis thalianawere measured in oscillating light of various frequencies. We also investigated thenpq1mutant lacking violaxanthin de-epoxidase, thenpq4mutant lacking PsbS-protein, and the mutantscrr2-2, andpgrl1abimpaired in different pathways of the cyclic electron transport.The fastest was the PsbS-regulation responding to oscillation periods longer than 10s. Processes involving violaxanthin de-epoxidase dampened changes of chlorophyll fluorescence in oscillation periods of 2min or longer. Knocking out the PGRL1-PGR5 pathway strongly reduced variations of all monitored parameters, probably due to congestion in the electron transport. Incapacitating the NDH-like pathway only slightly changed the photosynthetic dynamics.Our observations are consistent with the assumption that non-photochemical quenching in slow light oscillations involves violaxanthin de-epoxidase to produce, presumably, a stationary, non-oscillating level of zeaxanthin. We interpret the observed dynamics of Photosystem I components as being formed in slow light oscillations partially by thylakoid remodeling that modulates the redox rates.
A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding
Authors: Xu Gen , Lyu Jing , Obata Toshihiro , Liu Sanzhen , Ge Yufeng , Schnable James C. , Yang Jinliang 
Published: February 2022

ABSTRACTUnderstanding the patterns of selection during plant evolution and recent crop improvement processes is the central topic in plant breeding and genetics. As an essential macronutrient for plant growth and development, nitrogen (N) is a key factor in affecting plant adaptation and crop improvement. The widespread adoption of less expensive industrial N fixation has dramatically reshaped plant morphology by favoring compact maize plants to tolerant crowding stress. The associated genetic changes, however, have not been systematically studied. Here, we investigated maize inbred lines developed before and after the 1960s — the time point when inorganic N fertilizer started to be widely used for maize production. We identified a strong selective sweep exhibiting pronounced genomic differentiation between Old-Era (pre-1960s) and New-Era (post-1960s) inbred lines. Further study revealed population genetics statistics in the sweep exhibited patterns consistent with historical balancing selection. This balanced genomic interval is associated with a number of morphological, physiological, and metabolite traits related to vegetative N responses. A cluster of three glutamate receptor-like (GLR) genes is located within the region targeted by selection. Functional characterizations suggested differences in transcriptional activity of the GLR genes between the haplotypes carried by Old-Era and New-Era inbred lines likely play an essential role in mediating distinct N responses. The identification of both targets of selection and changes in the regulation of N responsive genes between maize lines developed in different eras sheds light on the N sensing and regulation pathways and paves the way to developing N resilient crops.
Targeting fatty acid beta-oxidation impairs monocyte differentiation and prolongs heart allograft survival
Authors: Zhu Yuehui , Dun Hao , Ye Li , Terada Yuriko , Shriver Leah P. , Patti Gary J. , Kreisel Daniel , Gelman Andrew E. , Wong Brian W. 
Published: February 2022

AbstractMonocytes play an important role in the regulation of alloimmune responses after heart transplantation (HTx). Recent studies have highlighted the importance of immunometabolism in the differentiation and function of myeloid cells. While the importance of glucose metabolism in monocyte differentiation and function has been reported, a role for fatty acid β-oxidation (FAO) has not been explored. Heterotopic HTx was performed using hearts from Balb/c donor mice implanted into C57Bl/6 recipient mice and treated with etomoxir (eto), an irreversible inhibitor of carnitine palmitoyltransferase 1 (Cpt1), a rate-limiting step of FAO, or vehicle control. FAO inhibition prolonged HTx survival, reduced early T cell infiltration/ activation and reduced dendritic cell (DC) and macrophage infiltration to heart allografts of eto-treated HTx recipients. ELISPOT demonstrated eto-treated HTx were less reactive to activated donor antigen presenting cells. FAO inhibition reduced monocyte-to-DC and monocyte-to-macrophage differentiation in vitro and in vivo. Further, FAO inhibition did not alter the survival of heart allografts when transplanted into Ccr2-deficient recipients, suggesting the effects of FAO inhibition on reduced immune cell infiltration and increased heart allograft survival were dependent on monocyte mobilization. Finally, we confirmed the importance of FAO on monocyte differentiation in vivo using conditional deletion of Cpt1a. Our findings demonstrate that targeting FAO attenuates alloimmunity after HTx, in part through impairing monocyte differentiation.
MraZ is a transcriptional inhibitor of cell division in Bacillus subtilis
Authors: White Maria L. , Hough-Neidig Abigail , Khan Sebastian J. , Eswara Prahathees J. 
Published: February 2022

AbstractThe bacterial division and cell wall (dcw) cluster is a highly conserved region of the genome which encodes several essential cell division factors including the central divisome protein FtsZ. Understanding the regulation of this region is key to our overall understanding of the division process. mraZ is found at the 5’ end of the dcw cluster and previous studies have described MraZ as a sequence-specific DNA binding protein. In this article, we investigate MraZ to elucidate its role in Bacillus subtilis. Through our investigation, we demonstrate that increased levels of MraZ result in lethal filamentation due to repression of its own operon (mraZ-mraW-ftsL-pbpB). We observe rescue of filamentation upon decoupling ftsL expression, but not other genes in the operon, from MraZ control. Furthermore, through timelapse microscopy we were able to identify that overexpression of mraZ, results in de-condensation of the FtsZ ring (Z-ring). This is likely due to depletion of FtsL, and thus, we believe the precise role of FtsL is likely in Z-ring maturation and promotion of subsequent treadmilling. Our data suggests that regulation of the mra operon may be an alternative way for cells to quickly arrest cytokinesis potentially during entry into stationary phase and in the event of DNA replication arrest.
Arginine-rich C9ORF72 ALS Proteins Stall Ribosomes in a Manner Distinct From a Canonical Ribosome-Associated Quality Control Substrate
Authors: Kriachkov Viacheslav , McWilliam Hamish E G , Mintern Justine D , Amarasinghe Shanika L , Ritchie Matt , Furic Luc , Hatters Danny M 
Published: February 2022

ABSTRACTHexanucleotide expansion mutations inC9ORF72are a cause of familial amyotrophic lateral sclerosis. We previously reported that long arginine-rich dipeptide repeats (DPR), mimicking abnormal proteins expressed from the hexanucleotide expansion, caused translation stalling when expressed in cell culture models. Whether this stalling provides a mechanism of pathogenicity remains to be determined. Here we explored the molecular features of DPR-induced stalling and examined whether known regulatory mechanisms of ribosome quality control (RQC) are involved to sense and resolve the stalls. We demonstrate that arginine-containing DPRs lead to stalling in a length dependent manner, with lengths longer than 40 repeats invoking severe translation arrest. Mutational screening of 40×Gly-Xxx DPRs shows that stalling is most pronounced where Xxx are positively charged amino acids (Arg or Lys). Through a genome-wide knockout screen we find that genes regulating stalling on polyadenosine mRNA coding for poly-Lys, a canonical RQC substrate, respond differently to the readthrough of arginine-rich DPRs. Indeed, we find evidence that DPR-mediated stalling has no natural regulatory responses even though the stalls may be sensed, as evidenced by an upregulation of RQC gene expression. These findings therefore implicate arginine-rich DPR-mediated stalled ribosomes as posing a particular danger to cellular health and viability.
Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses
Authors: Liu Qing , Yuan Hongyu , Li Mingzhi , Wang Ziwei , Cui Dongli , Ye Yushi , Sun Zongyi , Tan Xukai , Schwarzacher Trude , Heslop-Harrison John Seymour 
Published: February 2022

AbstractBackgroundOat (Avena sativa, 2n=6x=42) is an important crop, and with its wild relatives including A. longiglumis (ALO, 2n=6x=14), has advantageous agronomic and nutritional traits. A de-novo chromosome-level ALO genome assembly was made to investigate diversity and structural genome variation between Avena species and other Poaceae in an evolutionary context, and develop genomic resources to identify the pangenome and economic traits within Pooideae.ResultsThe 3.85 gigabase ALO genome (seven pseudo-chromosomes), contained 40,845 protein-coding genes and 87% repetitive sequences (84.21% transposable elements). An LTR retrotransposon family was abundant at all chromosome centromeres, and genes were distributed without major terminal clusters. Comparisons of synteny with A. eriantha and A. strigosa showed evolutionary translocations of terminal segments including many genes. Comparison with rice (x=12) and the ancestral grass karyotype showed synteny and features of chromosome evolution including fusions, translocations and insertions of syntenic blocks across Pooideae species. With a genome size 10 times larger than rice, ALO showed relatively uniform expansion along the chromosome arms, with few gene-poor regions along arms, and no major duplications nor deletions. Linked gene networks were identified (mixed-linkage glucans and cellulose synthase genes), and CYP450 genes may be related to salt-tolerance.ConclusionsThe high-continuity genome assembly shows gene, chromosomal structural and copy number variation, providing a reference for the Avena pangenome, defining the full spectrum of diversity. Chromosomal rearrangements and genome expansion demonstrate features of evolution across the genus and grass BOP-clade, contributing to exploitation of gene and genome diversity through precision breeding.
Eukaryotic Plankton Community Assembly and Influencing Factors Between Continental Shelf and Slope Sites in the Northern South China Sea
Authors: Li Tangcheng , Liu Guilin , Yuan Huatao , Chen Jianwei , Lin Xin , Li Hongfei , Yu Liying , Wang Cong , Li Ling , Zhuang Yunyun , Lin Senjie 
Published: February 2022

AbstractEukaryotic plankton are pivotal members of marine ecosystems playing crucial roles in food webs and biogeochemical cycles. However, understanding the patterns and drivers of their community assembly remains a grand challenge. A study was conducted in the northern South China Sea (SCS) to address this issue. Here, 49 samples were collected and size-fractionated from discrete depths at continental shelf and continental slope in the northern South China Sea over a diel cycle. From high throughput sequencing of the 18S rDNA gene V4 region, 2,463 operational taxonomic units (OTUs) were retrieved. Alveolata and Opisthokonta overwhelmingly dominated the assemblages in relative abundance (44.76%, 31.08%) and species richness (59%, 12%). Biodiversity was higher in the slope than the shelf and increased with depth. Temperature and salinity were found as the major deterministic drivers of taxon composition. Community structure was influenced by multiple factors in the importance order of: environmental factors (temperature + salinity) > spatial factor > water depth > sampling time. Furthermore, the neutral model explained more variations in the smaller-sized (0.22-3μm) community (24%) than larger-sized (3-200 μm) community (16%) but generally explained less variations than did deterministic processes. Additionally, our data indicated that the larger plankton might be more environmentally filtered and less plastic whereas the smaller plankton had stronger dispersal ability. This study provides novel insights into differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community assembly of micro-nano and pico-eukaryotic biospheres in a subtropical ocean.ImportanceEukaryotic plankton are essential to the biogeochemical processes in the ocean. Understanding the plankton community and influence factors is rapidly increasing with the advances in high-throughput sequencing in recent years, especially the microbe. Our study documented the biodiversity and drivers of community assembly of eukaryotic plankton in the subtropic northern SCS. We found the community structure was influenced by multiple factors and the deterministic process was more important than the stochastic process in the assembly of the eukaryotic plankton communities. Temperture is the most important factors in deterministic factors rather the nutrients which were previously thought important in shaping the eukaryotic plankton community in this oceanic province. Furthermore, we found smaller-sized miceukaryotic plankton are less environment filtered and more plastic than the larger-sized plankton. This insight revealed the differential contributions of the deterministic process and stochastic process and complexities of assembly mechanisms in shaping the community of eukaryotic biospheres.
Differential CO2-fixation potentials and supporting roles of phagotrophy and proton pump among plankton lineages in a subtropical marginal sea
Authors: Li Hongfei , Chen Jianwei , Yu Liying , Fan Guangyi , Li Tangcheng , Li Ling , Yuan Huatao , Wang Jingtian , Wang Cong , Lin Senjie 
Published: February 2022

AbstractLineage-wise physiological activities of plankton communities in the ocean are important but challenging to characterize. Here we conducted whole-assemblage metatranscriptomic profiling at continental shelf and slope sites of South China Sea to investigate carbon fixation in different lineages. We catalogued 4.4 million unique genes, ∼37% being annotatable and mainly involved in microbial metabolism, photosynthesis, amino acid synthesis, oxidative phosphorylation, and two-component systems. With RuBisCO expression as proxy, Calvin carbon fixation (CCF) was mainly contributed by Bacillariophyta, Chlorophyta, Cyanobacteria, Haptophyta and non-diatom Stramenopiles, which was differentially affected by environmental factors among lineages. CCF exhibited positive or negative correlations with phagotrophy gene expression depending on lineages, suggesting phagotrophy enhances (Bacillariophyta, Haptophyta, and Chlorophyta) or complements (Dinophyta) CCF. Our data reveal significant potential of non-Calvin carbon fixation (NCF), mainly contributed by Flavobacteriales, Alteromonadales, Oceanospirillales and Rhodobacterales. Furthermore, in Flavobacteriales, Alteromonadales, Pelagibacterales and Rhodobacterales, NCF potential was positively correlated with proteorhodopsin expression, suggesting that NCF is energetically supported by proteorhodopsin. The novel insights into lineage-dependent potential of carbon fixation, widespread mixotrophy, and proteorhodopsin as energy source for NCF lay a methodological and informational foundation for further research to understand the carbon fixation and trophic landscape in the ocean.ImportanceLineage-dependent physiologies are very important for understanding the contributions of different lineages to the biogeochemical processes in the oceanic plankton, but it is hardly possible using classical ecological methods. Even though metatranscriptomic methods have now been increasingly used to investigate physiologies of marine plankton, lineage-specific contribution to carbon fixation and phagotrophy has not received due research effort. Using whole-assemblage (prokaryotes + eukaryotes) plankton metatranscriptomic approach, with RNA quantity-based calibration to allow comparison across separately sequenced samples, this study reveals differential capacities of carbon fixation among lineages, widespread mixotrophy, and the potential of proteorhodopsin as energy source for non-photosynthetic carbon fixation. With these novel insights this study lays a methodological and informational foundation for further research to understand the carbon fixation and trophic landscape in the ocean.
HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota
Authors: Kim Chan Yeong , Ma Junyeong , Lee Insuk 
Published: February 2022

AbstractAdvances in metagenomic assembly have led to the discovery of genomes belonging to unculturable microorganisms. Metagenome-assembled genomes (MAGs) often suffer from discontinuity and chimerism. Recently, nanopore metagenomic sequencing assembled 20 complete MAGs (cMAGs) from 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were filtered for authentic prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was similar to that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely unculturable RF39 and TANB77 orders, whose genomes have not been characterized yet. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes of human gut microbiota, including unculturable species.
Staphylococcus aureus nt5 gene contributes to bacterial infection ability to form kidney abscess
Authors: Ye Yang , Liu Xinpeng , Xia Zijing , Tang Min , Zhang Dan , He Fuqiang , Zhang Peng , Liang Shufang 
Published: February 2022

AbstractStaphylococcus aureus (S. aureus) is a commonly conditional infection pathogen, in which several key virulence genes are responsible for bacterial infection ability. The S. aureus nt5 gene, encoding 5’-nucleotidase, mediates bacterial nucleic acid pathway, yet it is nearly unknown of nt5 function for staphylococcal infection ability. Herein we have constructed S. aureus mutant with the gene nt5C166T silence (S. aureus Δnt5) by a CRISPR RNA-guided base editing system to investigate bacterial infection ability in vitro and in vivo. As expected, several nt5-related genes are disturbed in S. aureus Δnt5, in which gene transcription level of py is decreased compared with the wild-type S. aureus. Bacterial gene nt5 is downregulated and py/adk are upregulated when S. aureus is exposed to antibiotics daptomycin, which indicates nt5-mediated nucleic acid pathway is interfered upon with daptomycin treatment. Furthermore, the mutant Δnt5 displays about a 40-fold reduction of bacterial loading in mouse kidney on a mouse sepsis model, and the infection ability of Δnt5 is reduced than the wild-type bacteria. The gene nt5 contributes to S. aureus-infected abscess formation in mouse kidney, and the silence of nt5 gene promotes phagocytosis of S. aureus by mouse and human immunocytes. In general, our findings reveal nt5 silence impedes bacterial loading in kidney to form abscess but enhances S. aureus to be phagocytosed by host cell immune system in vitro and in vivo, which indicates that nt5 gene plays an important role in bacterial infection and immune evasion.