Article
Biology
Yu Liu, Chong Xu, Guangxian Zhao, Yanji Wang, Yuanbing Zhu, Yishu Yin, Jiaping Wang, Yongzhi Li
Summary: With the development of space technology, microbial safety has become a research focus. Escherichia coli is a conditional pathogen that can cause infectious diseases, and it is necessary to study the influence of the space environment on E. coli. Through phenotypic experiments and proteomic analysis, we found that the survival rate of E. coli decreased in acidic and high-salt environments in the spaceflight group. Proteomic analysis also revealed changes in proteins related to chemotaxis, intracellular pH elevation, and metabolic processes in the spaceflight group. Our research demonstrates the successful application of proteomics in mechanism research and provides a comprehensive resource for understanding the effect of the space environment on E. coli.
OPEN LIFE SCIENCES
(2023)
Article
Multidisciplinary Sciences
Lei Yu, Xinlei Wang, Quanhua Mu, Sindy Sing Ting Tam, Danson Shek Chun Loi, Aden K. Y. Chan, Wai Sang Poon, Ho-Keung Ng, Danny T. M. Chan, Jiguang Wang, Angela Ruohao Wu
Summary: Single-cell multi-omics provides a unique perspective on tumor cellular heterogeneity. We developed scONE-seq, a versatile method for single-cell whole-genome RNA sequencing that is compatible with frozen biobanked samples. By comparing with existing methods, we demonstrated the performance of scONE-seq in various aspects and identified a unique transcriptionally normal-like tumor clone in a frozen astrocytoma sample, suggesting the potential of scONE-seq in uncovering previously unidentified discoveries in tumor biology.
Article
Microbiology
Peter H. Culviner, Isabel Nocedal, Sarah M. Fortune, Michael T. Laub
Summary: A global analysis of 9 endoribonuclease toxins from E. coli revealed that these toxins use low-information cleavage motifs to cut a significant proportion of mRNAs and inhibit ribosome biogenesis, disrupting translation.
Article
Cell Biology
Estelle Colin, Yannis Duffourd, Martin Chevarin, Emilie Tisserant, Simon Verdez, Julien Paccaud, Ange-Line Bruel, Frederic Tran Mau-Them, Anne-Sophie Denomme-Pichon, Julien Thevenon, Hana Safraou, Thomas Besnard, Alice Goldenberg, Benjamin Cogne, Bertrand Isidor, Julian Delanne, Arthur Sorlin, Sebastien Moutton, Melanie Fradin, Christele Dubourg, Magali Gorce, Dominique Bonneau, Salima El Chehadeh, Francois-Guillaume Debray, Martine Doco-Fenzy, Kevin Uguen, Nicolas Chatron, Bernard Aral, Nathalie Marle, Paul Kuentz, Anne Boland, Robert Olaso, Jean-Francois Deleuze, Damien Sanlaville, Patrick Callier, Christophe Philippe, Christel Thauvin-Robinet, Laurence Faivre, Antonio Vitobello
Summary: Multi-omics technologies provide valuable and increasingly accessible tools for diagnostic laboratories to help patients with unresolved rare diseases, especially those clinically diagnosed with rare OMIM diseases. However, there is currently no consensus on the optimal diagnostic care pathway to follow after negative results with standard approaches.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Engineering, Environmental
Yunhan Jiang, Ying Liu, Jian Zhang
Summary: Mixed antibiotics can stimulate the growth and microcystin synthesis of Microcystis aeruginosa by activating photosynthesis, carbon metabolism, and other pathways to enhance resistance to oxidative stress. This study provides insights into the mechanisms underlying the hormetic stimulation of harmful cyanobacterial blooms by antibiotic contaminants.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Microbiology
Franca Schaefer, Pia Goerner, Sabrina Woltemate, Christina Brandenberger, Robert Geffers, Stefan Ziesing, Dirk Schlueter, Marius Vital
Summary: This study investigated the physiological adaptation of carbapenem-resistant Enterobacteriaceae isolates with different resistance mechanisms during growth with sublethal concentrations of ertapenem. The results showed distinct strategies and gene expression patterns between strains carrying carbapenemase or alterations in porin-encoding genes. The study also observed a survival-like phenotype and reduced growth efficiencies in strains with alterations in porin-encoding genes, indicating costs of resistance.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Panagiotis Moulos
Summary: This article introduces a software package called recoup, which can visualize genomic coverage profiles generated from Next Generation Sequencing data quickly, flexibly, comprehensively, while also considering ease of use and reusability.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, Erica Larschan
Summary: TIMEOR is the first web-based and adaptive time-series multi-omics pipeline method that infers the relationship between gene regulatory events across time, addressing the critical need for determining causal regulatory mechanism networks. It integrates time-series RNA-seq, motif analysis, protein-DNA binding data, and protein-protein interaction networks.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Harshrajsinh. B. B. Joddha, Rafiyuddin. A. A. Mathakiya, Kuldip. V. V. Joshi, Ravindra. B. B. Khant, Akash. V. V. Golaviya, Ankit. T. T. Hinsu, Mansi. R. R. Desai, Subhash. J. J. Jakhesara, Prakash. G. G. Koringa
Summary: This study aimed to investigate antibiotic resistance genes (ARGs) and integrons in Escherichia coli isolated from healthy and diarrhoeic/diseased animals/birds' faecal samples. The E. coli isolates exhibited resistance to several antibiotics, with moxifloxacin being the most common. However, they were sensitive to amikacin and other antibiotics. Whole genome sequencing revealed the presence of 47 ARGs from 12 different antibiotic classes, and class 1 integrons were detected in most isolates.
Article
Microbiology
Maria N. Siniagina, Maria Markelova, Eugenia A. Boulygina, Alexander Laikov, Dilyara R. Khusnutdinova, Sayar R. Abdulkhakov, Natalia A. Danilova, Alfiya H. Odintsova, Rustam A. Abdulkhakov, Tatyana Grigoryeva
Summary: Crohn's disease is characterized by chronic inflammation in the gastrointestinal tract, where an imbalance in gut microbiota, particularly Escherichia coli, plays a significant role in its pathogenesis. Analysis of E. coli strains from CD patients and healthy subjects revealed genetic similarities in virulence and antibiotic resistance, suggesting complex bacterial interactions within the gut that may impact the host's intestinal health.
Article
Biology
Victoria Prudent, Gaelle Demarre, Emilie Vazeille, Maxime Wery, Nicole Quenech'Du, Antinea Ravet, Julie Dauverd - Girault, Erwin van Dijk, Marie-Agnes Bringer, Marc Descrimes, Nicolas Barnich, Sylvie Rimsky, Antonin Morillon, Olivier Espeli
Summary: Patients with Crohn's disease exhibit abnormal colonization of the intestine by adherent invasive E. coli (AIEC), which adapt to phagolysosomal stress and form bacterial communities within macrophages through the production of an extrabacterial matrix. This study provides insights into the strategies that AIECs use to establish their replicative niche within macrophages.
COMMUNICATIONS BIOLOGY
(2021)
Article
Microbiology
Marvin Williams, Alyssa B. Jones, Amanda L. Maxedon, Jennifer E. Tabakh, Cindy B. McCloskey, David E. Bard, Daniel P. Heruth, Susana Chavez-Bueno
Summary: This study investigated the colonization rate of E. coli strains in the cervix of fifty pregnant women with preterm labor, revealing that a minority of women were colonized with E. coli and the colonizing strains were not representative of those causing invasive disease in newborns. Further larger studies are needed to explore the molecular characteristics of E. coli strains colonizing pregnant women that may increase the risk of neonatal septicemia.
Article
Microbiology
Heather M. M. Blankenship, Stephen E. E. Dietrich, Elizabeth Burgess, Jason Wholehan, Marty Soehnlen, Shannon D. D. Manning
Summary: This study conducted a retrospective analysis of 510 clinical STEC isolates using core genome SNP analysis and found that PFGE and MLST could not fully reveal the genetic diversity and relatedness. SNP analysis was able to cluster isolates based on similarity in PFGE and MLST and uncover their phylogenetic relationships. The use of high-quality SNP analysis enabled a more rapid identification of related strains during outbreak investigations. This study demonstrates how public health laboratories can utilize whole-genome sequencing and phylogenetics to identify related strains and uncover important genetic attributes that can guide treatment practices.
Article
Microbiology
Xi Yang, Qian Liu, Hui Sun, Yanwen Xiong, Andreas Matussek, Xiangning Bai
Summary: This study identified Stx2l-STEC strains from raw mutton and beef in China, showing that these strains belonged to the same O8 serogroup with diverse host range and geographical distribution. Genomic analysis revealed genetic relatedness between human-derived and food-derived strains, highlighting the need for further investigation into the epidemiological traits and pathogenic potential of Stx2l-STEC strains.
Article
Biochemistry & Molecular Biology
Juan Xu, Hao Guo, Lirong Li, Fang He
Summary: This study identified 27 carbapenem-resistant Escherichia coli (CREC) strains, of which 17 carried the blaNDM-5 gene. All 23 NDM-producing E. coli strains were resistant to all antibiotics except tigecycline, colistin, and cefiderocol. Furthermore, two copies of the blaNDM-5 gene were found on a single plasmid, highlighting the need for attention.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biology
Patrice Monkam, Wenkai Lu, Songbai Jin, Wenjun Shan, Jing Wu, Xiang Zhou, Bo Tang, Hua Zhao, Hongmin Zhang, Xin Ding, Huan Chen, Longxiang Su
Summary: In this study, we proposed an end-to-end framework called US-Net for simultaneous speckle suppression and texture enhancement in ultrasound images. The US-Net architecture is inspired by U-Net and incorporates a feature refinement attention block (FRAB) to effectively learn multi-level and multi-contextual features. Experimental results demonstrate that using US-Net for image enhancement can improve the accuracy of ultrasound diagnosis.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Public, Environmental & Occupational Health
Jie Chen, Hua Ma, Xiaoming Huang, Yanhui Cui, Wenzhong Peng, Fei Zhu, Shiyang Ma, Minjun Rao, Peipei Zhang, Hang Yang, Longxiang Su, Ruichao Niu, Pinhua Pan
Summary: This retrospective study analyzed the data of adult patients with KP-BSI in Xiangya Hospital, China from 2012 to 2019. The occurrence of CRKP-BSI significantly increased during the study period. Hematologic malignancies and ICU acquired infection were identified as significant risk factors for the development of CRKP BSI. Severe sepsis or septic shock incidents, inadequate empirical antimicrobial therapy, and corticosteroids use preceding infection onset led to increased mortality rates in CRKP-BSI patients, while high dose carbapenem combination therapy was associated with better outcomes.
ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL
(2022)
Editorial Material
Medicine, General & Internal
Zhongheng Zhang, Rahul Kashyap, Longxiang Su, Qinghe Meng
FRONTIERS IN MEDICINE
(2022)
Article
Health Care Sciences & Services
Pan Pan, Lina Li, Fei Xie, Xingshuo Hu, Yinghua Guo, Lixin Xie, Longxiang Su
Summary: This study visualized the hemodynamic effects of pulmonary microcirculation and ventilation/perfusion (V/Q) matching after mechanical ventilation with different cardiac outputs and positive end-expiratory pressures (PEEPs). The results suggested that low tidal volume combined with appropriate PEEP is the best option for ventilation and pulmonary blood flow matching. Increasing PEEP could solve the problem of excessive shunt at high cardiac output and improve V/Q ratio. Understanding the relationship between macrocirculation and pulmonary microcirculation is essential in mechanical ventilation.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Medicine, General & Internal
Y. Yang, H. Li, P. Liu, X. Zhang, Q. Wang, N. Cui, X. Tian, Y. Long, H. He, L. Su
QJM-AN INTERNATIONAL JOURNAL OF MEDICINE
(2023)
Article
Urology & Nephrology
Pan Pan, Yuhong Liu, Fei Xie, Zhimei Duan, Lina Li, Hongjun Gu, Lixin Xie, Xiangyun Lu, Longxiang Su
Summary: This study aims to use a machine learning model to predict acute kidney injury (AKI) in the ICU and identify the related factors. The study used data from the MIMIC-III database and included four machine learning models for AKI assessment. The XGBoost model performed the best in predicting new-onset AKI at different time points.
Article
Multidisciplinary Sciences
Lu Wang, Xudong Ma, Huaiwu He, Longxiang Su, Yanhong Guo, Guangliang Shan, Ye Wang, Xiang Zhou, Dawei Liu, Yun Long
Summary: The study on the relationship between quality control and septic shock caused by intestinal perforation in China found that the ICU patient bed occupancy rate is positively correlated with the incidence of complications and costs. The proportion of ICU patients with APACHE II score >= 15 is not associated with complications and can reduce costs. The microbiology detection rate before antibiotic use is not associated with hospital stays, but increases the incidence of ARDS. Therefore, controlling the ICU patient bed occupancy rate, encouraging admission of severe patients to the ICU, and avoiding unnecessary microbiology detection can improve the treatment outcomes for septic shock patients.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Longxiang Su, Xudong Ma, Sifa Gao, Zhi Yin, Yujie Chen, Wenhu Wang, Huaiwu He, Wei Du, Yaoda Hu, Dandan Ma, Feng Zhang, Wen Zhu, Xiaoyang Meng, Guoqiang Sun, Lian Ma, Huizhen Jiang, Guangliang Shan, Dawei Liu, Xiang Zhou, China-NCCQC
Summary: This study aimed to explore the key quality control factors affecting the prognosis of ICU patients in Chinese mainland over a six-year period. It found that 15 initially established quality control indicators were good predictors of patient prognosis. Based on the weights of these core elements, an integrated quality scoring system was developed to assess the key elements of quality management and optimize the quality control indicator system.
FRONTIERS OF MEDICINE
(2023)
Article
Medicine, General & Internal
Longxiang Su, Yunping Lan, Yi Chi, Fuhong Cai, Zhenfeng Bai, Xianlong Liu, Xiaobo Huang, Song Zhang, Yun Long
Summary: This study proposes a self-developed remote mechanical ventilation visualization network system to solve the problem of patient-ventilator asynchrony (PVA). The algorithm model achieves good results in identifying ineffective triggering and double triggering abnormalities in mechanical ventilation. The system analyzes real-time respiratory data, identifies anomalies, and provides abnormal alarms, data analysis reports, and data visualizations to assist physicians in handling abnormalities.
JOURNAL OF CLINICAL MEDICINE
(2023)
Editorial Material
Medicine, General & Internal
Pan Pan, Matthieu Komorowski, Le Shen, Lgnacio Martin-Loeches, Longxiang Su
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, General & Internal
Longxiang Su, Shu Li, Ran Lou, Ying Liu, Hua Zhang, Li Jiang
Summary: This study investigates the perception of intensivists and the importance of training for analgesia and sedation through the Chinese Analgesia and Sedation Education & Research (CASER) group training program. The findings highlight the need for standardized training to improve the assessment of analgesia and sedation in the ICU. Rating: 8 points.
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, General & Internal
Longxiang Su, Xiaohong Ning
FRONTIERS IN MEDICINE
(2023)
Article
Health Care Sciences & Services
Huiping Wu, Ying Wang, Haiyan Fu, Lili Ji, Na Li, Dan Zhang, Longxiang Su, Zhansheng Hu
Summary: The study aimed to investigate the potential neuroprotective effects of Maresin1 (MaR1) on microglia-induced neuroinflammation in sepsis-induced cognitive impairment and explore its anti-inflammatory mechanism. The results showed that MaR1 significantly ameliorated cognitive dysfunction and inhibited neuroinflammation by suppressing the activations of NLRP3 and TLR4-NF-κB signal pathways.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Pan Pan, Jie Chen, Fei Xie, Yinghua Guo, Xudong Liu, Dong Zhang, Lixin Xie, Longxiang Su
Summary: Platelets play a significant role in inflammation and organ injury. The mitophagy in platelets can control the hyperactivation of the inflammasome and alleviate acute kidney injury. Targeting TREM-1 and NLRP3/BNIP3L in platelets may represent a new therapeutic strategy for treating septic AKI.
Article
Education & Educational Research
Pan Pan, Min Zheng, Hongbo Luo, Jinbang Liu, Lina Li, Longxiang Su
Summary: This study evaluates the training effect of teaching critical care parameters on an online platform and explores teaching methods that can cultivate trainees' clinical thinking and practical ability. The results show that teaching critical care parameters on an online platform is effective in improving trainees' clinical care ability, but the cultivation of clinical thinking still needs to be strengthened.
BMC MEDICAL EDUCATION
(2023)