Biology subjects

Jing, H.

Publications and source records attributed to Jing, H..

23 records · Page 2Linked to original sources

bioRxiv2020

Cell phone digital microscopy using an oil droplet

We introduce an accessible imaging method using droplets of microscope immersion and consumer-grade oils and a cell phone camera. We found that oil droplets were more resistant to evaporation than water droplets. We characterized the transverse magnification of oil and water droplets using cell phone screens and a resolution target. We further harnessed the close refractive index of cooking oils to that of the immersion oil and demonstrated their use as lenses for cell phone microscopy. Our method enables stable droplet-based optical imaging without specialized setups or manufacturing processes.

bioengineering↗

bioRxiv2019

Calling differential DNA methylation at cell-type resolution: an objective status-quo

Due to cost and logistical reasons, Epigenome-Wide-Association Studies (EWAS) are normally performed in complex tissues, resulting in average DNA methylation profiles over potentially many different cell-types, which can obscure important cell-type specific associations with disease. Identifying the specific cell-types that are altered is a key hurdle for elucidating causal pathways to disease, and consequently statistical algorithms have recently emerged that aim to address this challenge. Comparisons between these algorithms are of great interest, yet here we find that the main comparative study so far was substantially biased and potentially misleading. By using this study as an example, we highlight some of the key issues that need to be considered to ensure that future assessments between methods are more objective.

bioinformatics↗

bioRxiv2019

Multilocus sequence analysis, a rapid and accurate identification tool for taxonomic classification, evolutionary relationship and population biology of the genus Shewanella.

The genus Shewanella comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA and topA) was established as a rapid and accurate identification tool in fifty-nine type Shewanella strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the Shewanella genus. The split network tree proposed twelve distinct monophyletic clades with identical G+C contents and high genetic similarities. Eighty-six tested strains were investigated to explore the population biology of the Shewanella genus in China. The most prevalent Shewanella species were Shewanella algae, Shewanella xiamenensis, Shewanella chilikensis, Shewanella indica, Shewanella seohaensis and Shewanella carassii. The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of Shewanella species. Combined with the genetic, genomic and phenotypic analyses, Shewanella upenei should be considered a synonym of S. algae, and Shewanella pacifica should be reclassified as a synonym of Shewanella japonica.\n\nIMPORTANCEThe MLSA scheme based on six HKGs (gyrA, gyrB, infB, recN, rpoA and topA) is well established as a reliable tool for taxonomic, evolutionary and epidemiological analyses of the genus Shewanella in this study. The standard MLSA method allows researchers to make rapid, economical and precise identification of Shewanella strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus Shewanella. The population genetics of Shewanella species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further studies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships and ecological status of the genus Shewanella.

microbiology↗

bioRxiv2018

Impact of Premorbid Infection on Onset and Disease Activity of Rheumatoid Arthritis

ObjectiveInfections have been implicated in rheumatoid arthritis (RA) development. However, the impact of premorbid infection on initiation and perpetuation of RA has not been well elucidated. Thus, we sought to conduct a large scale on-site survey to study whether premorbid infection may trigger RA and influence status of the disease.\n\nMethodsPremorbid infectious events were collected in cohort of 902 RA patients from December 2015 to June 2016. Type of infections prior to RA onset and its possible effects on disease status were analyzed.\n\nResultThree hundred and thirty-four out of 902 patients (37.03%) experienced infections within one month preceding RA onset. The most frequent infections were respiratory (16.08%), intestinal (11.09%) and urinary tract (9.87%) infection, respectively. The infection was associated with increased disease activity. Early onset was found in patients with urinary infection. High disease activity risk was increased in patients who pre-exposure to urinary infection (OR=3.813, 95%CI=1.717-12.418) and upper respiratory infection (OR=2.475, 95%CI= 0.971-6.312).\n\nConclusionPre-exposure infections are associated with development of RA. Severe disease status of RA and persistent of active disease status are related to preceding infections.

epidemiology↗

bioRxiv2017

SIRT2 and lysine fatty acylation regulate the oncogenic activity of K-Ras4a

Ras proteins play vital roles in numerous biological processes and Ras mutations are found in many human tumors. Understanding how Ras proteins are regulated is important for elucidating cell signaling pathways and identifying new targets for treating human diseases. Here we report that one of the K-Ras splice variants, K-Ras4a, is subject to lysine fatty acylation, a previously under-studied protein post-translational modification. Sirtuin 2 (SIRT2), one of the mammalian nicotinamide adenine dinucleotide (NAD)-dependent lysine deacylases, catalyzes the removal of fatty acylation from K-Ras4a. We further demonstrate that SIRT2-mediated lysine defatty-acylation promotes endomembrane localization of K-Ras4a, enhances its interaction with A-Raf, and thus promotes cellular transformation. Our study identifies lysine fatty acylation as a previously unknown regulatory mechanism for the Ras family of GTPases that is distinct from cysteine fatty acylation. These findings highlight the biological significance of lysine fatty acylation and sirtuin-catalyzed protein lysine defatty-acylation.

biochemistry↗