Publications by authors named "Jianing Geng"
Article Synopsis
- The text discusses a rare wild edible mushroom from northwest China that thrives in unusual saline-alkali soil, potentially serving as a model for studying how organisms tolerate such environments.
- Comparative genomic analyses indicate significant evolutionary changes in the mushroom's genome, including gene family contractions and the rapid evolution of genes related to adaptability.
- The research highlights specific metabolic pathways and stress responses activated under mildly alkaline conditions, contributing to a better understanding of the mushroom's genomic evolution and its mechanisms for tolerating saline-alkali environments.
Article Synopsis
- SARS-CoV-2 has led to a global pandemic with significant fatalities, and the role of RNA interference (RNAi) in combating it, particularly in mammals, remains controversial due to interference from interferon (IFN) signaling.
- In studies using Vero cells, an IFN-deficient line, it was found that SARS-CoV-2 infection caused dysregulation of host microRNAs, which negatively impacted antiviral responses by downregulating protective miRNAs and upregulating those that facilitate viral replication.
- The analysis revealed that SARS-CoV-2-derived small RNAs (vsRNAs) had specific characteristics and similar patterns were noted in other virus infections, suggesting that targeting the RNAi pathway could provide alternative antiviral strategies for IFN
Article Synopsis
- CodY is a key regulator found in low G + C, Gram-positive Firmicutes, which controls various metabolic pathways and processes.
- Bioinformatics and DNA affinity precipitation assay confirmed that CodY orthologues and their regulatory networks also exist in Gram-negative Synergistetes.
- The study identified a novel palindromic sequence in the promoters of certain operons in Synergistetes that resembles the CodY binding site in Firmicutes, suggesting they may serve a similar regulatory function.
Article Synopsis
- In 2002, the first crop genome of the rice cultivar 93-11 was published, serving as a reference for super-hybrid rice, but it wasn't updated until now.
- The study utilized advanced sequencing techniques to create a more complete and accurate genome assembly for 93-11, enabling better analysis of its genetic features compared to the Nipponbare genome.
- The improved genome data revealed important gene expression patterns during seed development and variations that can aid in targeted breeding efforts for rice.
Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea.
Genomics Proteomics Bioinformatics
June 2020
Article Synopsis
- Agrocybe cylindracea is a nutritionally rich edible mushroom with potential medicinal benefits, but its genomic data has been limited.
- A new genome assembly reveals a 56.5 Mb sequence with 15,384 predicted genes, showcasing its complex reproductive systems and various enzymes for carbon source degradation.
- Pathway analyses indicate distinct functions in its fruiting body, with stipes focusing on carbohydrate synthesis and energy storage, and pilei emphasizing carbon utilization and fatty acid production, enhancing understanding of its nutritional and medicinal properties.
Cardiac arrhythmias and cardiac arrest related to mushroom poisoning: A case report.
World J Clin Cases
August 2019
Article Synopsis
- Mushroom poisoning (MP) can lead to various health issues, including severe liver or kidney failure, cardiac injuries, and neurological symptoms like delirium and seizures.
- A case study of a 68-year-old woman demonstrated severe cardiac arrhythmias and long QT syndrome following her mushroom exposure, although her kidney and liver functions remained normal.
- This case highlights the need for careful monitoring of cardiac function in MP patients, as toxic mushrooms can also affect the heart, necessitating further research into the underlying mechanisms.
Article Synopsis
- This study examines the role of CodY, a regulator in Streptococcus salivarius, in response to changes in pH and glucose availability within the oral environment.
- Findings show that CodY is most active at neutral pH with limited glucose, affecting the bacterium’s transcriptome through both direct and indirect mechanisms.
- The research indicates that CodY is crucial for the bacteria's metabolism, virulence, and ability to evade the immune system, while also influencing biofilm formation and cell wall metabolism.
Article Synopsis
- Mitochondria are crucial for ATP production in eukaryotes, and studying the mitochondrial genome of Upland Cotton can further our understanding of plant evolution.
- The complete mitochondrial genome of Gossypium hirsutum was sequenced, revealing a length of 621,884 bp with 68 genes, including those for proteins, rRNA, and tRNA; specific gene clusters were noted in both monocots and dicots.
- The findings indicate that while the mitochondrial genome of G. hirsutum shares common traits with other higher plants, the evolution of these genomes aligns with plant taxonomy yet varies independently across different species.
Article Synopsis
- S. zooepidemicus is a significant pathogen responsible for swine streptococcosis in China, with its pathogenicity enhanced through gene transfer among bacteria.
- Comparative genomic analysis revealed that the S. zooepidemicus strain ATCC35246 (Sz35246) has specific genes and pathogenicity islands that may elevate its virulence and adaptability to different hosts.
- The study identified novel virulence genes and mechanisms that could help inform future diagnostic and therapeutic approaches targeting this pathogen.
Article Synopsis
- The ocean harbors antibiotic-producing bacteria and is influenced by antibiotics used in marine aquaculture, leading to a complex landscape of antibiotic resistance.
- Studies reveal that there is a significant presence of antibiotic resistance genes in ocean environments, yet their clinical relevance remains poorly understood.
- Through advanced sequencing techniques, researchers discovered that marine sediment bacteria possess resistance genes similar to those found in human pathogens, suggesting a potential exchange of antibiotic resistance between marine and clinical bacteria.
The association between H3K4me3 and antisense transcription.
Genomics Proteomics Bioinformatics
April 2012
Article Synopsis
- H3K4me3, traditionally associated with transcription activation at gene promoters, is also enriched at the 3' ends of many actively transcribed genes in mouse cerebrum and testis, revealing a novel modification termed 3'-H3K4me3.
- This modification correlates with the initiation and expression of antisense transcription, suggesting that it plays a role in regulating this process.
- Additionally, the presence of 3'-H3K4me3 is conserved across various species, indicating it may function as a universal epigenetic feature that could act as a promoter for antisense transcription in eukaryotes.
Article Synopsis
- Streptococcus parasanguinis is a key bacterium in dental health that can lead to subacute endocarditis, and its genome was sequenced to understand its features and behavior better.
- The study identified various transcripts including hypothetical proteins and small RNAs, as well as five genomic islands that may enhance its pathogenic abilities and survival strategies in the mouth.
- Comparative analysis of multiple strains showed that while they share a highly conserved genome, differences exist that could impact their potential to cause disease.
Article Synopsis
- Streptococcus salivarius 57.I is a common bacteria in the human mouth that can break down urea for nitrogen.
- The bacteria's urease enzyme allows it to use urea as its only nitrogen source.
- Genome sequencing showed that S. salivarius 57.I has unique genetic components, including a chromosome and a phage, that are not present in another strain called SK126.
Article Synopsis
- S. equi subsp. zooepidemicus is an opportunistic pathogen linked to significant economic losses in China's swine industry and poses a risk to human health.
- The complete genome sequence of the strain ATCC 35246 has been announced, offering insights into its behavior and potential risks.
- This genomic data can help researchers understand how the bacteria cause disease and its genetic features.
Article Synopsis
- Agrobacterium tumefaciens F2 is a bacterium known for its ability to produce bioflocculants effectively.
- The specific genes involved in the metabolic pathway for bioflocculant synthesis in this strain are currently not understood.
- This research presents the draft genome of A. tumefaciens F2, which may help reveal the biosynthetic mechanisms behind its polysaccharide-like bioflocculant production.
Article Synopsis
- The plateau pika, an underground mammal from the Tibetan plateau, has been studied using a set of 10 genetic markers (microsatellites) to determine parentage.
- Validation tests showed extremely low error rates in identifying parentage, with high power of discrimination and exclusion, indicating that the markers are very reliable.
- This genetic tool allows researchers to accurately assign offspring to mothers and identify fathers or relatives, making it useful for various studies on plateau pika populations.
To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in intergenic and intronic regions, respectively, as compared to 23% and 15% from the mRNA-seq dataset. Further analysis made an additional discovery of transcripts of protein-coding genes (such as Histone, Heg1, and Dux), ncRNAs, snoRNAs, snRNAs, and novel ncRNAs as well as repeat elements in rmRNA-seq dataset.
View Article and Find Full Text PDFA modified enrichment method to construct microsatellite library from plateau pika genome (Ochotona curzoniae).
Genomics Proteomics Bioinformatics
March 2010
Article Synopsis
- A microsatellite-enriched library for plateau pika was developed using a new method based on the strong bond between biotin and streptavidin.
- The process involved fragmenting DNA through ultrasonication, hybridizing with biotinylated probes, and using magnetic beads for purification, followed by PCR amplification.
- The optimized protocol yielded a high percentage of clones with microsatellite repeats and proved effective for creating similar libraries in other species, showing its efficiency and reliability.
Article Synopsis
- The paper reports improved whole-genome sequences for rice varieties, indica and japonica, showing a significant enhancement in quality compared to previous drafts from 2002.
- The gene identification process introduced allows for accurate predictions, estimating at least 38,000-40,000 genes, with only 2%-3% unique to each subspecies.
- There is substantial variation in intergenic regions and ongoing gene duplications, suggesting a complex evolutionary history and the potential for new gene development within the grass family.
Article Synopsis
- Researchers sequenced 11,712 ESTs from the thymus of 100-day-old pigs, resulting in 7,071 cleaned ESTs for further analysis.
- Of these ESTs, 806 contigs and 1,669 singlets were found to have homologues in GenBank, while 1,629 ESTs were identified as novel.
- The study indicates that the thymus is still developing at this age, with 36.99% of ESTs linked to gene expression and a similarity in gene expression patterns compared to human infant thymus.
Article Synopsis
- A draft sequence of the genome for the rice subspecies Oryza sativa L. ssp. indica has been created using whole-genome shotgun sequencing, revealing a size of 466 megabases and estimating between 46,022 and 55,615 genes.
- About 92% of the assembled genome has functional coverage, with a significant portion (42.2%) consisting of exact 20-nucleotide repeats and most transposons found in intergenic regions.
- While around 80.6% of genes in Arabidopsis thaliana (another plant) have homologs in rice, only 49.4% of rice genes have identifiable homologs in A. thaliana, which may be attributed to variations in