Article
Biochemical Research Methods
Jim Shaw, Yun William Yu
Summary: This study investigates the conservation metric for k-mer selection methods, deriving exact expressions for various methods and demonstrating an increase in mapped reads using a more conserved k-mer selection method. However, the trade-off includes the potential for increased runtime due to the repetitive nature of the selected k-mers. The findings provide insights on using new k-mer selection methods to optimize for speed and alignment quality.
Article
Biochemical Research Methods
Johan Nystrom-Persson, Gabriel Keeble-Gagnere, Niamat Zawad
Summary: In this study, a distributed k-mer counting tool called Discount was introduced based on Apache Spark. By investigating the behavior of different Minimizer ordering methods in practice, a universal frequency ordering was introduced, which achieved evenly distributed binning and small bin sizes. This new approach significantly improved efficiency in distributed k-mer counting compared to existing methods.
Article
Mathematics
Sally McClean
Summary: Processes are ubiquitous and process mining helps understand, predict, and improve efficiency in these processes. Markov processes play a key role in evaluating compliance with completion targets, especially in complex scenarios.
Article
Engineering, Mechanical
Ziwei Dai, Xingyi Zhu, Francisco A. Gilabert
Summary: In this study, a generic and multi-material phenomenological-based healing formulation is proposed to investigate and characterize the self-healing effect in the mechanical response of materials exhibiting strong nonlinearities. The proposed formulation integrates objective experimental measures and is incorporated in a combined computational-experimental procedure. The framework is applied to predict the mechanical response influenced by the healing process in a validated material at multiple loading rates and damage levels.
INTERNATIONAL JOURNAL OF MECHANICAL SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Odei Barrenada, Eduardo Larriba, Miguel A. Brieno-Enriquez, Jesus del Mazo
Summary: piRNAs are a diverse and versatile type of small RNA, discovered about two decades ago, with important roles in maintaining genomic integrity in germ cells and potential functions in somatic cells. However, distinguishing them from other sncRNAs has led to challenges in identification and analysis in existing databases.
Article
Biochemical Research Methods
Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
Summary: The research introduces the K-mer File Format as a general framework for storing and manipulating k-mer sets, achieving significant space savings compared to other formats and enabling interoperability across different tools.
Article
Biotechnology & Applied Microbiology
Na Zhao, Lei Jia, Qiuxia Deng, Chunhua Zhu, Bo Zhang
Summary: This study characterized the sperm piwi-interacting RNAs profiles of Cynoglossus semilaevis and identified differential piRNAs associated with sex development and methylation. Five of the piRNAs showed sex bias and could be used as male-specific molecular biomarkers for C. semilaevis. Additionally, the study implied the possibility of transgenerational inheritance of sex-biased piRNAs in sperm.
MARINE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Shaopeng Liu, David Koslicki
Summary: This study introduces a hashing-based technique that leverages KTST and m-sketch to obtain k-mer-based similarity estimates for a range of k values. By truncating k-mers stored in a pre-built KTST with a large k value, they can simultaneously obtain estimates for all k values, making the analysis more efficient. The biases due to truncation are shown to be negligible in practice, resulting in significantly faster running time and less space used when compared to a classic MinHash approach.
Article
Biochemical Research Methods
Cong Feng, Min Dai, Yongjing Liu, Ming Chen
Summary: The study introduces a new computational approach called RepLoc for efficient identification of repetitive sequences in the genome, revealing potential relationships between sequence repetitiveness and genome structures.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Jianan Wang, Su Chen, Lili Dong, Guohua Wang
Summary: The paper proposes a new method called CHTKC to efficiently calculate the frequency of each substring of length k in DNA sequences, using a lock-free hash table and linked lists to resolve collisions and optimize memory usage. Thorough testing on multiple datasets shows that using a hash-table-based method remains a feasible solution for the k-mer counting problem.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Kristen P. Rodgers, Alicia Hulbert, Hamza Khan, Maria Shishikura, Shun Ishiyama, Malcolm V. Brock, Yuping Mei
Summary: A new method called TFP, using TRIzol for the extraction of 30-60 nt sncRNAs from plasma, is reported in this study. The TFP method yields more sncRNAs compared to commercial kits and shows lower CT values in plasma samples from different races.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Neha Periwal, Priya Sharma, Pooja Arora, Saurabh Pandey, Baljeet Kaur, Vikas Sood
Summary: This study proposes a novel method for efficient classification of coding sequences (CDS) and non-coding RNA (ncRNA) sequences using binary frequency. By analyzing complete datasets from fifteen diverse species, the frequency of binary patterns is identified as distinguishing features between CDS and ncRNAs. The proposed approach outperforms the traditional ATGC method in terms of performance metrics and exhibits correlation with the geological evolutionary timeline across diverse species.
Article
Biochemical Research Methods
Yoshihiro Shibuya, Djamal Belazzougui, Gregory Kucherov
Summary: k-mer counting is an important feature in many bioinformatics pipelines. Existing counting methods optimize either time or memory usage, resulting in large count tables. We introduce Set-Min sketch, a sketching technique for representing associative maps, and apply it to the problem of representing k-mer count tables. Set-Min is more accurate and more memory-efficient than other methods.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Medicinal
Gabriele Fumagalli, Rodrigo J. Carbajo, J. Willem M. Nissink, Jonathan Tart, Rongxuan Dou, Andrew P. Thomas, David R. Spring
Summary: The study focused on the identification of pan-mutant RAS inhibitors by designing novel peptides using a binding pharmacophore. Through a chemically divergent approach, the researchers generated a library of small stapled peptides and optimized them to create low-micromolar binders of KRAS that inhibit nucleotide exchange.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Maklin, Simon J. Puglisi
Summary: Themisto is a scalable colored k-mer index that works for large collections of microbial reference genomes. It outperforms competing tools in terms of indexing efficiency and pseudoalignment quality.
Article
Biochemistry & Molecular Biology
Huimin Wang, Feng Jiang, Xiang Liu, Qing Liu, Yunyun Fu, Ran Li, Li Hou, Jie Zhang, Jing He, Le Kang
Summary: This study identifies a novel function of Piwi and piRNAs in regulating food intake in locusts. Knockdown of Piwi1 expression leads to reduced food consumption and body weight, potentially through decreased expression of neuropeptide NPF1. Mechanistically, intronic piRNAs may enhance RNA splicing of NPF1 by preventing hairpin formation at the branch point sites. This discovery reveals a novel nuclear PIWI/piRNA-mediated mechanism that controls food intake in the locust nervous system.
Article
Biology
Dafeng Chen, Li Hou, Jianing Wei, Siyuan Guo, Weichan Cui, Pengcheng Yang, Le Kang, Xianhui Wang
Summary: The migratory locust displays synchronous maturation and oviposition when forming large swarms. Research has found that gregarious female locusts show more synchronous sexual maturation and oviposition than solitarious females. The presence of gregarious male adults is necessary to stimulate the sexual maturation synchrony of female adults.
Article
Multidisciplinary Sciences
Jing Li, Liya Wei, Yongsheng Wang, Haikang Zhang, Pengcheng Yang, Zhangwu Zhao, Le Kang
Summary: The phase transition from solitary to gregarious locusts is important in locust outbreaks, affecting agricultural yield and food security. This study reveals the translational regulatory mechanism of locust phase transition, in which the locusts employ divergent ribosome pathways to cope with changes in population density.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Lijie Zhang, Le Kang, Yan Xu
Summary: This study compared the genome and transcriptome of two industrial koji molds used for soy sauce production in China and Japan, revealing differences in growth, catalytic characteristics, protease secretion ratio, and transcriptional level. By combining comparative phenotypic and transcriptome data, 58 potential important enzymes associated with high protein breakdown efficiency were identified. This work comprehensively analyzed the genome development of three industrial koji molds and provided insights into the study of key proteolytic enzymes during soy sauce production.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Physical
Dexiang Gao, Xingyu Tang, Chunfang Zhang, Yajie Wang, Xin Yang, Peijie Zhang, Xuan Wang, Jingqin Xu, Jie Su, Fuyang Liu, Xiao Dong, Xiaohuan Lin, Bao Yuan, Nozomu Hiraoka, Haiyan Zheng, Le Kang, Kuo Li, Ho-kwang Mao
Summary: By compressing the co-crystal of trans-azobenzene and transperfluoroazobenzene, a high-pressure synthesis strategy was used to achieve the formation of a high-energy density N4-ring structure. The increase in external pressure reduced the kinetic barrier and promoted the formation of the N4-ring structure. This work demonstrates the effectiveness of high pressure as an alternative synthetic strategy for high-tensile structures, with the cooperation of crystal engineering.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Electrochemistry
Mengli Wang, Lele Ma, Le Kang, Mingsan Miao, Huaixia Yang
Summary: In this study, an electrochemical biosensor was developed for the sensitive detection of estrogen receptor alpha (ERa) in breast cancer. The biosensor utilized AuNPs-SWCNT nanocomposites and hemin@HKUST-1 for signal amplification. The biosensor demonstrated a low detection limit of 27.8 fg.ml(-1) and a good linear relationship between current intensity and the logarithm of ERa concentration. It also exhibited excellent selectivity, stability, reproducibility, and interference immunity, making it highly applicable in practical detection.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Hetan Chang, Sina Cassau, Juergen Krieger, Xiaojiao Guo, Markus Knaden, Le Kang, Bill S. Hansson
Summary: Many animals engage in cannibalism for dietary supplementation, and this is also prevalent among dense populations of migratory locusts. This study shows that locusts produce an anticannibalistic pheromone called phenylacetonitrile under crowded conditions. The degree of cannibalism and phenylacetonitrile production are dependent on population density. By identifying the olfactory receptor that detects phenylacetonitrile and inactivating the gene responsible for its production, researchers demonstrate the loss of protection against intraspecific predation in locusts lacking this compound. This research sheds light on the importance of an anticannibalistic feature in locust population ecology and its potential for locust management.
Review
Immunology
Xue Fang, Le Kang, Yi-Fan Qiu, Zhao-Shen Li, Yu Bai
Summary: There is increasing focus on the roles of gut microbes in physiological and pathological processes. Crohn's disease (CD) is a chronic, relapsing, inflammatory disease of the gastrointestinal tract with unknown causes. Gastrointestinal infection, particularly Yersinia enterocolitica, has been suggested as a possible trigger for CD, although its specific role is still debated. This review discusses the current understanding of how Y. enterocolitica and its compounds may be involved in the development of CD, as well as potential interventions for diagnosis and treatment.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yu-Hang Wang, Ming Li, Le Kang, Quan-Jie Jia
Summary: A finite-element method based on a weak formulation of the Takagi-Taupin equations was used to study X-ray diffraction of crystals with surface undulations. The diffraction features caused by the surface undulations were simulated in a general diffraction geometry. The numerical results showed that the effects of surface undulations on Bragg diffraction were local and resulted from the refractive effect caused by the variation of the local asymmetry angle. A formula based on the local perfect flat crystal approximation was introduced to efficiently evaluate the change in the direction of the diffracted wave caused by surface undulations.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2023)
Article
Microbiology
Qing Liu, Feng Cui, Xiang Liu, Yumei Fu, Wenjing Fang, Xun Kang, Hong Lu, Siping Li, Biao Liu, Wei Guo, Qianfeng Xia, Le Kang, Feng Jiang
Summary: This study analyzed RNA viromes of field-caught mosquitoes from Hainan Island, China, and found that virome composition is influenced by mosquito species and food sources. Most RNA viruses remained stable across three years and different locations, indicating species-specific viromes in Hainan Island. However, virome compositions of single mosquito species in different geographic regions worldwide were visibly distinct, consistent with differences in the widespread distribution of mosquito food sources.
Article
Ecology
Siyuan Guo, Li Hou, Liushu Dong, Xin Nie, Le Kang, Xianhui Wang
Summary: Comparative transcriptomic analysis of flight muscles in migratory locusts reveals that plasticity in expression of the lipid metabolism gene PLIN2 regulates differences in ageing-related muscle degeneration between gregarious and solitary phases. The knockdown of the upregulated PLIN2 gene significantly relieved the ageing-related flight impairments in gregarious locusts. Ectopic lipid accumulation led to an ageing-related beta-oxidation decline through limiting fatty acid transport and content.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Jinxin Miao, Le Kang, Tianfeng Lan, Jianyao Wang, Siqing Wu, Yifan Jia, Xia Xue, Haoran Guo, Pengju Wang, Yan Li
Summary: This study investigated the expression stability of several reference genes in a Syrian hamster model of acute pancreatitis (AP). The results showed that Ywhaz and Gapdh were the most stable reference genes for gene expression analysis in this model.
ANIMAL MODELS AND EXPERIMENTAL MEDICINE
(2023)
Review
Biology
Xiaojiao Guo, Helen He, Jianghua Sun, Le Kang
Summary: This article presents a review of research progress regarding pheromone plasticity in three typical aggregative insects: locusts, bark beetles, and cockroaches. The plasticity of aggregation pheromones in these insect species is significantly impacted by various factors, indicating its complexity. The potential application of pheromone plasticity in basic research and pest management is also discussed.
CURRENT OPINION IN INSECT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Xinle Kang, Meiling Yang, Xiaoshuang Cui, Huimin Wang, Le Kang
Summary: Warning coloration is a common defense strategy used by animals to deter predators. Gregarious locusts exhibit a black-brown pattern as a form of warning coloration. However, the mechanisms regulating this distinctive pattern remain largely unknown.
Review
Medicine, General & Internal
Sizhe Liu, Mingsan Miao, Le Kang
Summary: This study conducted a pan-cancer analysis for MAD2L1 prognosis and expression using The Cancer Genome Atlas and Genotype-Tissue Expression data. The results showed that MAD2L1 may act as an oncogene in hepatocellular carcinoma and is regulated by non-coding ribonucleic acids. High expression of MAD2L1 is closely associated with poor prognosis and tumor infiltration.
