Genome Sequence and Transcriptome Analysis of the Radioresistant Bacterium Deinococcus gobiensis: Insights into the Extreme Environmental Adaptations

The desert is an excellent model for studying evolution under extreme environments. We present here the complete genome and ultraviolet (UV) radiation-induced transcriptome of Deinococcus gobiensis I-0, which was isolated from the cold Gobi desert and shows higher tolerance to gamma radiation and UV light than all other known microorganisms. Nearly half of the genes in the genome encode proteins of unknown function, suggesting that the extreme resistance phenotype may be attributed to unknown genes and pathways. D. gobiensis also contains a surprisingly large number of horizontally acquired genes and predicted mobile elements of different classes, which is indicative of adaptation to extreme environments through genomic plasticity. High-resolution RNA-Seq transcriptome analyses indicated that 30 regulatory proteins, including several well-known regulators and uncharacterized protein kinases, and 13 noncoding RNAs were induced immediately after UV irradiation. Particularly interesting is the UV irradiation induction of the phrB and recB genes involved in photoreactivation and recombinational repair, respectively. These proteins likely include key players in the immediate global transcriptional response to UV irradiation. Our results help to explain the exceptional ability of D. gobiensis to withstand environmental extremes of the Gobi desert, and highlight the metabolic features of this organism that have biotechnological potential

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Otoendoscope combined with ablation electrodes for treatment of benign tracheal stenosis caused by granulation tissue hyperplasia after tracheotomy

Benign tracheal stenosis mainly appears due to tracheotomy, tuberculosis, trauma, benign tumor, or ventilation. With the increase in the number of tracheotomies and the prolongation of the life span of patients after incision, the long-term complications after tracheotomy gradually increase, among which intratracheal granulation hyperplasia is a more serious complication. The present case describes a 59-year-old male with granulation tissue hyperplasia induced by tracheotomy. He underwent tracheal resection to remove the granulation tissue and he remained well after the follow-up. Even though the endoscopic intervention and tracheal resection are readily accessible, they usually quite challenging. Here we summarize the present details on this condition

The Pollution Characteristics and Risk Assessment of Microplastics in Mollusks Collected from the Bohai Sea

Microplastic (MP) pollution in the marine environment has become a global problem. In this study, a number of 21 mollusk species (n = 2006) with different feeding habits were collected from 11 sites along the Bohai Sea for MP uptake analysis. The MPs in mollusk samples were isolated and identified by micro-Fourier Transform Infrared Spectroscopy (μ-FTIR). Approximately 91.9% of the individuals among all the collected species ingested MPs, and there was an average abundance of 3.30 items·individual-1 or 1.04 items·g-1 of wet weight. The shape of MPs was mainly fiber, and a total of 8 polymers were detected, of which rayon had the highest detection rate (58.3%). The highest abundance, uptake rate and polymer composition of MPs was observed in creeping types, suggesting that they might ingest these MPs from their food. The gastropod Siphonalia subdilatata contains the highest levels of MPs, which may increase the risk of human exposure if consumed whole without removing the digestive gland. The polymer risk level of MPs in these mollusks was Level III (H = 299), presenting harmful MPs such as polyvinyl chloride. In terms of human exposure risk, the average exposure of the Bohai Sea residents to MPs through the consumption of mollusks is estimated to be 3399 items·(capita·year)-1. Overall, this study provides a basis for the ecological and health risk assessment of MPs in mollusks collected from the coastline of China. © 2023, The Authors. All rights reserved

Seasonal change of microplastics uptake in the Pacific oysters Crassostrea gigas cultured in the Yellow Sea and Bohai Sea, China

This study investigated seasonal microplastics (MPs) pollution characteristics in oysters and surrounding surface seawater from five aquaculture farms located at the Yellow Sea and Bohai Sea. MPs abundances in oysters were 2.40 +/- 0.14 (winter) to 3.28 +/- 0.19 (autumn) items/individual, and 0.22 +/- 0.02 (spring) to 0.45 +/- 0.06 (summer) items/g (ww). In surface seawater, average seasonal MPs abundances were 3.41 +/- 1.06-8.86 +/- 2.48 items/L. Fibers were dominant shape, and cellophane and polyethylene terephthalate (PET) were dominant polymers in oysters and surface seawater. Positive correlation was found between oysters' MPs abundance (items/individual) and environmental factors (NO2-N (r = 0.466), and temperature (r = 0.485)) by Spearman correlation analysis in four seasons. Main environmental factor affecting seasonal MPs abundance of oysters and surface seawater was NH3-N and SiO3-Si in summer and winter respectively. In conclusion, seasonal change of MPs uptake in cultured oysters was relatively small