Article
Biochemical Research Methods
Javier Perez Tobia, Po-Jung Jimmy Huang, Yuzhe Ding, Runjhun Saran Narayan, Apurva Narayan, Juewen Liu
Summary: Computer-aided prediction of aptamer sequences has traditionally focused on primary sequence alignment and motif comparison. However, this study introduces a new algorithm that incorporates secondary structure information, combining conserved primary sequences and secondary structures. This algorithm was successfully used in predicting aptamer sequences from two different selections and showed promise in predicting challenging sequences. It provides a novel approach to pattern discovery in aptamer selection libraries and has the potential to shorten selection time and improve applications in biosensors and chemical biology.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Adriana Arneson, Amin Haghani, Michael J. Thompson, Matteo Pellegrini, Soo Bin Kwon, Ha Vu, Emily Maciejewski, Mingjia Yao, Caesar Z. Li, Ake T. Lu, Marco Morselli, Liudmilla Rubbi, Bret Barnes, Kasper D. Hansen, Wanding Zhou, Charles E. Breeze, Jason Ernst, Steve Horvath
Summary: The authors developed a Mammalian Methylation Array that includes 36k well-conserved CpGs in mammals, facilitating cross-species comparisons. They annotated the conserved CpGs in > 200 species. The array allows one to measure methylation in all mammalian species, including unsequenced ones.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Masaki Tagashira, Kiyoshi Asai
Summary: By detecting homology among RNAs, probabilistic consideration of RNA structural alignments has improved the prediction accuracy of significant RNA prediction problems. ConsAlifold, a dynamic programming-based method, considers RNA structural alignments and achieves moderate running time and the best prediction accuracy of RNA consensus secondary structures among available prediction methods.
Article
Biochemistry & Molecular Biology
Eric Westhof, Bryan Thornlow, Patricia P. Chan, Todd M. Lowe
Summary: Metazoan organisms have highly conserved tRNA sequence motifs, despite the presence of a large number of tRNA genes. Non-Watson-Crick base pairs, especially GoU pairs, play important roles in the structure and function of tRNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Polymer Science
Kazuki Tada, Chiaki Ikegaki, Yuki Fuse, Kazuki Tateishi, Hiromitsu Sogawa, Fumio Sanda
Summary: The polycondensation reaction of N-((3,5-diamino)benzoyl)-L-alanine dodecyl ester (1L) with p-phthalaldehyde (2) resulted in the synthesis of a novel optically active polymer, poly(1L-2), containing Schiff base moieties in the main chain. Similar polymers with Schiff base moieties were also synthesized by varying the feed ratios of N-((3,5-diamino) benzoyl)-D-alanine dodecyl ester (1D) and N-((3,5-diamino)benzoyl)glycine dodecyl ester (1G). These polymers exhibited chiral CD signals in CHCl3 solvent, dependent on the molar ratios of 1L/1D and 1L/1G. Poly(1L-2) showed lyotropic liquid crystallinity in CHCl3 and THF solvents.
Article
Plant Sciences
Tong Li, Liangwei Yin, Claire E. Stoll, Damon Lisch, Meixia Zhao
Summary: Genomic imprinting is a parent-of-origin-dependent epigenetic phenomenon. This study reveals the importance of transposable elements and conserved noncoding sequences in genomic imprinting in maize.
Article
Physics, Fluids & Plasmas
Dilimulati Aierken, Michael Bachmann
Summary: The study shows that a bifurcation of the coil-globule transition line occurs for polymers with a bending stiffness above a threshold value, which is revealed through a systematic microcanonical inflection-point analysis of precise numerical results obtained in extensive generalized-ensemble Monte Carlo simulations. The region between the toroidal and random-coil phases is dominated by structures transitioning from hairpins to loops as the energy decreases. Conventional canonical statistical analysis is unable to identify these separate phases.
Review
Chemistry, Multidisciplinary
Shalakha Hegde, Zhichao Tang, Junxing Zhao, Jingxin Wang
Summary: The ongoing COVID-19 pandemic has had a significant impact on global public health and society, with research on targeting conserved SARS-CoV-2 RNA structures and sequences emerging as a promising new approach to inhibit viral infection. These RNA-targeting molecules could serve as an emerging class of antiviral drug candidates for future viral outbreaks.
FRONTIERS IN CHEMISTRY
(2021)
Article
Computer Science, Information Systems
Liyu Huang, Qingfeng Chen, Yongjie Li, Cheng Luo
Summary: In this paper, a novel RNA secondary structure model called modified adjoining grammars binary tree (BTMGcsp) is proposed to intuitively represent complex RNA secondary structures while preserving structural properties. The method substantially reduces memory and time consumption, with experimental results showing a high AUC value of 0.949 in PseudoBase.
Article
Biochemistry & Molecular Biology
Baoxing Song, Edward S. Buckler, Hai Wang, Yaoyao Wu, Evan Rees, Elizabeth A. Kellogg, Daniel J. Gates, Merritt Khaipho-Burch, Peter J. Bradbury, Jeffrey Ross-Ibarra, Matthew B. Hufford, M. Cinta Romay
Summary: Thousands of species are set to be sequenced in the coming years, and understanding the functionality of their genomes requires molecular and evolutionary approaches. A study focusing on the Andropogoneae tribe, which includes multiple crop species, revealed highly conserved noncoding sequences rich in functional elements. These findings shed light on the evolution and functional significance of CNSs in maize.
Article
Biotechnology & Applied Microbiology
Merve Vural-Ozdeniz, Aslinur Akturk, Mert Demirdizen, Ronaldo Leka, Rana Acar, Ozlen Konu
Summary: CoVrimer is a webserver designed to assist researchers in sensitively and specifically amplifying virus primers. Users can search, align, and assess mutation load of primer pair sequences against the viral genome.
Article
Virology
Nina Aboughanem-Sabanadzovic, Thomas W. Allen, James Frelichowski, Jodi Scheffler, Sead Sabanadzovic
Summary: This study characterized the population of cotton leafroll dwarf virus in Mississippi using Illumina-based high-throughput sequencing data. The analysis identified contigs with similar nucleotide content and similarities to reverse transcriptases of plant pararetroviruses. Further investigation revealed endogenous viral elements (EVEs) integrated into the upland cotton genome, tentatively named endogenous cotton pararetroviral elements (eCPRVE). The study also found similar loci in a newly recognized cotton species, G. ekmanianum, suggesting recent evolution within the cotton family.
Review
Biochemistry & Molecular Biology
Robert J. Schmitz, Erich Grotewold, Maike Stam
Summary: This review discusses the characteristics, identification technologies, and role of cis-regulatory sequences in plant biology. Despite advances in sequence assembly and genome annotation, there are still challenges in identifying and understanding cis-regulatory modules.
Article
Biochemistry & Molecular Biology
Rachel J. Hagey, Menashe Elazar, Edward A. Pham, Siqi Tian, Lily Ben-Avi, Claire Bernardin-Souibgui, Matthew F. Yee, Fernando R. Moreira, Meirav Vilan Rabinovitch, Rita M. Meganck, Benjamin Fram, Aimee Beck, Scott A. Gibson, Grace Lam, Josephine Devera, Wipapat Kladwang, Khanh Nguyen, Anming Xiong, Steven Schaffert, Talia Avisar, Ping Liu, Arjun Rustagi, Carl J. Fichtenbaum, Phillip S. Pang, Purvesh Khatri, Chien-Te Tseng, Jeffery K. Taubenberger, Catherine A. Blish, Brett L. Hurst, Timothy P. Sheahan, Rhiju Das, Jeffrey S. Glenn
Summary: By targeting conserved RNA secondary structures, researchers have discovered a potential therapeutic approach that can effectively treat multiple viruses and has shown good efficacy and resistance in experiments. These findings are important for antiviral prophylaxis and post-exposure therapy.
Article
Chemistry, Medicinal
Shufen He, Peishan Li, Jingxuan Wang, Yanzhu Zhang, Hongmei Lu, Liufei Shi, Tao Huang, Weiyan Zhang, Lijian Ding, Shan He, Liwei Liu
Summary: In this study, the distribution of secondary metabolite biosynthetic gene clusters (SMBGCs) in Hahella was examined, and a potential source of bioactive compounds was identified. A strain named NBU794 was isolated from mangrove soil and found to contain multiple SMBGCs and bioactive compounds, including prodigiosin and a novel compound called 2-methyl-3-heptyl-prodiginine. These compounds showed antimicrobial activity, making NBU794 a promising source for prodigiosin.
Article
Microbiology
Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki Vazquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu
Article
Microbiology
Xiaoquan Su, Gongchao Jing, Zheng Sun, Lu Liu, Zhenjiang Xu, Daniel McDonald, Zengbin Wang, Honglei Wang, Antonio Gonzalez, Yufeng Zhang, Shi Huang, Gavin Huttley, Rob Knight, Jian Xu
Article
Gastroenterology & Hepatology
Mengchen Guo, Huixia Wang, Sixie Xu, Yaoyao Zhuang, Jingang An, Chuan Su, Yankai Xia, Jingyun Chen, Zhenjiang Zech Xu, Qisha Liu, Jianwei Wang, Zhou Dan, Kun Chen, Xiaoting Luan, Zhi Liu, Kangjian Liu, Faming Zhang, Yumin Xia, Xingyin Liu
Article
Genetics & Heredity
Zhi Liu, Kai Mi, Zhenjiang Zech Xu, Qiankun Zhang, Xingyin Liu
Summary: The study introduces a new analysis framework, PM2RA, to identify and quantify microbial relationship alterations (RAs) between health and disease, demonstrating higher specificity and sensitivity than existing methods and robustly quantifying microbial RAs across different datasets in several diseases.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Review
Chemistry, Applied
Ping Li, Shengliang Deng, Zhenjiang Zech Xu
Summary: Substitute-based immunoassay technologies offer an effective solution to the recurring mycotoxins contamination in food, providing high sensitivity and renewability, while posing minimal threats to operators and the environment.
Article
Microbiology
Zhenhua Wu, Shimeng Huang, Tiantian Li, Na Li, Dandan Han, Bing Zhang, Zhenjiang Zech Xu, Shiyi Zhang, Jiaman Pang, Shilan Wang, Guolong Zhang, Jiangchao Zhao, Junjun Wang
Summary: The study found that oral EGCG helps alleviate colonic inflammation by increasing the abundance of Akkermansia, a short-chain fatty acids-producing bacteria, and promoting SCFAs production. Prophylactic supplementation of EGCG also showed beneficial outcomes. FMT experiments confirmed the role of EGCG in attenuating colitis.
Article
Microbiology
Heather Deel, Alexandra L. Emmons, Jennifer Kiely, Franklin E. Damann, David O. Carter, Aaron Lynne, Rob Knight, Zhenjiang Zech Xu, Sibyl Bucheli, Jessica L. Metcalf
Summary: The research on human bone microbial decomposer community identified microbial succession as a marker for postmortem interval (PMI) and revealed significant differences in bone microbial community composition between seasons. The study also developed random forest models that predict PMI with an accuracy of approximately 634 days, providing a quantitative tool for estimating time since death of skeletal remains.
Article
Microbiology
Yichen Hu, Zhiyuan Pan, Zongyu Huang, Yan Li, Ni Han, Xiaomei Zhuang, Hui Peng, Quansheng Gao, Qing Wang, B. J. Yang Lee, Heping Zhang, Ruifu Yang, Yujing Bi, Zhenjiang Zech Xu
Summary: This study investigated the effects of probiotics, prebiotics, and synbiotics on altitude-related cardiac impairment in a rat model. The treatments alleviated cardiac hypertrophy and restored gut microbiota disruptions caused by hypobaric hypoxia. The study suggests that the gut microbiome may play a causal role in high-altitude-related diseases and could be a target for therapeutic interventions.
MICROBIOLOGY SPECTRUM
(2022)
Article
Agriculture, Multidisciplinary
Ya-Shuai Kong, Hong-Yu Ren, Rui Liu, Ricardo R. da Silva, Alexander A. Aksenov, Alexey V. Melnik, Ming Zhao, Miao-Miao Le, Zhi-Wei Ren, Feng-Qing Xu, Xiao-Wei Yan, Li-Jun Yu, Yu Zhou, Zhong-Wen Xie, Da-Xiang Li, Xiao-Chun Wan, Yan-Hua Long, Zhenjiang Zech Xu, Tie-Jun Ling
Summary: Understanding microbial and chemical diversities and their influencing factors is crucial for modern manufacturing of traditional fermented foods. This study focused on Chinese dark teas (CDTs), traditional microbial fermented beverages with high sample diversity. The results showed that the diversity of CDT microbial communities and nonvolatile chemicals is predominantly influenced by geography and manufacturing procedures. Moreover, molecular networking revealed shared metabolites between CDTs and fungi, including important compounds related to nutrition, biofunctions, and flavor.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biology
Zhiyuan Pan, Yichen Hu, Zongyu Huang, Ni Han, Yan Li, Xiaomei Zhuang, Jiye Yin, Hui Peng, Quansheng Gao, Wenpeng Zhang, Yong Huang, Yujun Cui, Yujing Bi, Zhenjiang Zech Xu, Ruifu Yang
Summary: This study investigated the dynamics of gut microbiota and their association with altitude-related illnesses using a rat model of hypobaric hypoxia challenge. The results showed significant changes in gut microbiota composition and metabolic abnormalities of short-chain fatty acids and bile acids in response to hypoxic conditions. Furthermore, fecal microbiota transplantation was found to partially restore the gut microbiota diversity and ameliorate cardiac hypertrophy in hypoxic rats. These findings shed light on the role of gut microbiota in the development of high-altitude heart disease.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Nutrition & Dietetics
Ping Li, Ming Li, Ying Song, Xiaochang Huang, Tao Wu, Zhenjiang Zech Xu, Hui Lu
Summary: Green banana flour, rich in resistant starch, can restore gut microbiota disrupted by antibiotics, improve mucin secretion, and repair the intestinal barrier. Additionally, it accelerates the restoration of balanced gut microbiota.
FRONTIERS IN NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Yichen Hu, Amnon Amir, Xiaochang Huang, Yan Li, Shi Huang, Elaine Wolfe, Sophie Weiss, Rob Knight, Zhenjiang Zech Xu
Summary: This study tracked the dynamic changes of the saliva microbiome during human activities through a dense time series data. The results showed that eating activity significantly affected the salivary microbiota composition, with certain bacteria increasing after each meal. The composition of the microbiome also exhibited diurnal oscillation patterns at different taxonomy levels. This research emphasizes the importance of considering daily activities and diurnal factors in the design of oral microbiome studies.
Article
Biology
Shanwen Chen, Yunfan Jin, Siqi Wang, Shaozhen Xing, Yingchao Wu, Yuhuan Tao, Yongchen Ma, Shuai Zuo, Xiaofan Liu, Yichen Hu, Hongyan Chen, Yuandeng Luo, Feng Xia, Chuanming Xie, Jianhua Yin, Xin Wang, Zhihua Liu, Ning Zhang, Zhenjiang Zech Xu, Zhi John Lu, Pengyuan Wang
Summary: The utility of cell-free nucleic acids in monitoring cancer has been recognized. By profiling cfRNAs in plasma samples, human and microbe-derived plasma cfRNAs were found to have diagnostic value for cancer detection. Adding microbial features improved the accuracy of tumor classification.
Article
Gastroenterology & Hepatology
Yan Li, Yichen Hu, Xiang Zhan, Ying Song, Meng Xu, Shijie Wang, Xiaochang Huang, Zhenjiang Zech Xu
Summary: Accumulating evidence suggests that the gastric bacterial community plays a role in gastric cancer development. However, there is inconsistency in the reported alterations of gastric microbiota. In this meta-analysis, we identified significant changes in gastric microbiome composition during gastric carcinogenesis, particularly when removing Helicobacter pylori (HP) reads to mitigate its compositional effect. Differential microbes such as Fusobacterium, Leptotrichia, and lactic acid bacteria were consistently enriched in gastric cancer patients compared to gastritis, and oral microbes were significantly enriched in gastric cancer compared to precancerous stages. Additionally, we observed mutual exclusivity of different HP species and convergent dysbiosis of gastric fluid and mucosal microbiome during gastric disease progression.
Article
Food Science & Technology
Ping Li, Ming Li, Tao Wu, Ying Song, Yan Li, Xiaochang Huang, Hui Lu, Zhenjiang Zech Xu
Summary: Antimicrobial preservatives (APs) have been found to disrupt gut microbiota and glucose metabolism, regardless of their origin. The biogenic AP nisin had the most significant effects, potentially due to perturbation of glucagon-like peptide 1 related glucoregulatory hormone secretion.
NPJ SCIENCE OF FOOD
(2022)