Biology subjects

Luo, C.

Publications and source records attributed to Luo, C..

130 records · Page 8Linked to original sources

bioRxiv2017

Transcriptome analysis of the quantitative distribution of the Cyrtotrachelus buqueti population in two cities in China

Background: Cyrtotrachelus buqueti is a forest pest that severely damages bamboo shoots. Reducing the population of this insect involves complex mechanisms and is dependent on diverse gene expression influenced by environmental factors.\n\nMethods: In this study, samples from two regions of China, Muchuan in Sichuan Province and Chishui in Guizhou Province, were investigated through RNA-seq to explore the causes and molecular mechanisms underlying the population reduction of this species. Environmental factors, such as temperature, heavy metal content, and pH, may affect the reduced population of C. buqueti in Chishui.\n\nResults: Approximately 44 million high-quality reads were generated, and 94.2% of the data were mapped to the transcriptome. A total of 15,641 out of the 29,406 identified genes were predicted. Moreover, 348 genes were differentially expressed between the two groups of imagoes and included 77 upregulated and 271 downregulated UniGenes. The functional analysis showed that these genes were significantly enriched in ribosome and metabolic pathway categories. The candidate genes, which contributed to C. Buqueti reduction, included 41 genes involved in the ribosome constitution category, five genes in the one-carbon pool pathway by folate category, and five heat shock protein genes.\n\nConclusions: Downregulation of these candidate genes seems to have impaired metabolic processes, such as protein, DNA, RNA, and purine synthesis, as well as carbon and folate metabolism, and finally resulted in the observed reduced population of C. buqueti. Furthermore, temperature, heavy metal content, and pH might influence the population by altering the expressions of genes involved in these metabolic processes.

genomics↗

bioRxiv2017

Attention is required for knowledge-based sequential grouping of syllables into words

How the brain sequentially groups sensory events into temporal chunks and how this process is modulated by attention are fundamental questions in cognitive neuroscience. Sequential grouping includes bottom-up primitive grouping and top-down knowledge-based grouping. In speech perception, grouping acoustic features into syllables can rely on bottom-up acoustic continuity cues but grouping syllables into words critically relies on the listeners lexical knowledge. This study investigates whether top-down attention is required to apply lexical knowledge to group syllables into words, by concurrently monitoring neural entrainment to syllables and words using electroencephalography (EEG). When attention is directed to a competing speech stream or cross-modally to a silent movie, neural entrainment to syllables is weakened but neural entrainment to words largely diminishes. These results strongly suggest that knowledge-based grouping of syllables into words requires top-down attention and is a bottleneck for the neural processing of unattended speech.

neuroscience↗

bioRxiv2017

Worldwide Population Structure Of Escherichia coli Reveals Two Major Subspecies

Recombination is one of the most important mechanisms of prokaryotic species evolution but its exact roles are still in debate. Here we try to infer genome-wide recombination events within a species uti-lizing a dataset of 104 complete genomes of Escherichia coli from diverse origins, among which 45 from world-wide animal-hosts are in-house sequenced using SMRT (single-molecular real time) technology.Two major clades are identified based on evidences of ecological and physiological characteristics, as well as distinct genomic features implying scarce inter-clade genetic exchange. By comparing the synteny of identical fragments genome-widely searched for each genome pair, we achieve a fine-scale map of re-combination within the population. The recombination is rather extensive within clade, which is able to break linkages between genes but does not interrupt core genome framework and primary metabolic port-folios possibly due to natural selection for physiological compatibility and ecological fitness. Meanwhile,the recombination between clades declines drastically as the phylogenetic distance increases, generally 10-fold reduced than those of the intra-clade, which establishes genetic barrier between clades. These empirical data of recombination suggest its critical role in the early stage of speciation, where recombina-tion rate differs according to phylogentic distance. The extensive intra-clade recombination coheres sister strains into a quasi-sexual group and optimizes genes or alleles to streamline physiological activities,whereas shapely declined inter-clade recombination split the population into clades adaptive to divergent ecological niches.\n\nSignificance StatementRoles of recombination in species evolution have been debated for decades due to difficulties in inferring recombination events during the early stage of speciation, especially when recombination is always complicated by frequent gene transfer events of bacterial genomes. Based on 104 high-quality complete E. coli genomes, we infer gene-centric dynamics of recombination in the formation of two E. coli clades or subpopulations, and recombination is found to be rather intensive in a within-clade fashion, which forces them to be quasi-sexual. The recombination events can be mapped among individual genomes in the context of genes and their variations; decreased between-clade and increased intra-claderecombination engender a genetic barrier that further encourages clade-specific secondary metabolic portfolios for better environmental adaptation. Recombination is thus a major force that accelerates bacterial evolution to fit ecological diversity.

microbiology↗

bioRxiv2017

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital syndromes1,2. In July 2016, mosquito-borne ZIKV transmission was first reported in the continental United States and since then, hundreds of locally-acquired infections have been reported in Florida3. To gain insights into the timing, source, and likely route(s) of introduction of ZIKV into the continental United States, we tracked the virus from its first detection in Miami, Florida by direct sequencing of ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least four distinct ZIKV introductions contributed to the outbreak in Florida and that local transmission likely started in the spring of 2016 - several months before its initial detection. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions are phylogenetically linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. By comparing mosquito abundance and travel flows, we describe the areas of southern Florida that are especially vulnerable to ZIKV introductions. Our study provides a deeper understanding of how ZIKV initiates and sustains transmission in new regions.

epidemiology↗