Biology (ISSN 2079-7737) is an international, peer-reviewed, quick-refereeing open access journal of Biological Science published by MDPI online. It publishes reviews, research papers and communications in all areas of biology and at the interface of related disciplines. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. There is no restriction on the length of the papers. The full experimental details must be provided so that the results can be reproduced. Electronic files regarding the full details of the experimental procedure, if unable to be published in a normal way, can be deposited as supplementary material.

Biology is an international, peer-reviewed, quick-refereeing open access journal of Biological Science published online by MDPI. It covers all areas of biology and related disciplines, publishing reviews, research papers, and communications. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. There are no restrictions on the length of the papers, and full experimental details must be provided to ensure reproducibility of results. If the full details of the experimental procedure cannot be published in the usual manner, electronic files can be deposited as supplementary material.

《Biology》是一本国际性的、经过同行评审的快速审稿开放获取期刊，专注于生物科学，由MDPI在线出版。期刊涵盖生物学及相关学科的所有领域，发表综述、研究论文和通讯。我们的目标是鼓励科学家尽可能详细地发布他们的实验和理论结果。对论文的长度没有限制，必须提供完整的实验细节，以便结果可以被复现。如果实验程序的完整细节无法以正常方式发布，可以将电子文件作为补充材料提交。

Biology

The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.

Heena Satam

Kandarp Joshi

Upasana Mangrolia

Sanober Waghoo

Gulnaz Zaidi

Shravani Rawool

Ritesh P. Thakare

Shahid Banday

Alok K. Mishra

Gautam Das

Sunil K. Malonia

Next-Generation Sequencing Technology: Current Trends and Advancements

Glycolipid metabolic disorders (GLMDs) are various metabolic disorders resulting from dysregulation in glycolipid levels, consequently leading to an increased risk of obesity, diabetes, liver dysfunction, neuromuscular complications, and cardiorenal vascular diseases (CRVDs). In patients with GLMDs, excess caloric intake and a lack of physical activity may contribute to oxidative stress (OxS) and systemic inflammation. This study aimed to review the connection between GLMD, OxS, metainflammation, and the onset of CRVD. GLMD is due to various metabolic disorders causing dysfunction in the synthesis, breakdown, and absorption of glucose and lipids in the body, resulting in excessive ectopic accumulation of these molecules. This is mainly due to neuroendocrine dysregulation, insulin resistance, OxS, and metainflammation. In GLMD, many inflammatory markers and defense cells play a vital role in related tissues and organs, such as blood vessels, pancreatic islets, the liver, muscle, the kidneys, and adipocytes, promoting inflammatory lesions that affect various interconnected organs through their signaling pathways. Advanced glycation end products, ATP-binding cassette transporter 1, Glucagon-like peptide-1, Toll-like receptor-4, and sphingosine-1-phosphate (S1P) play a crucial role in GLMD since they are related to glucolipid metabolism. The consequences of this is system organ damage and increased morbidity and mortality.

Enzo Pereira de Lima

Renato Cesar Moretti

Karina Torres Pomini

Lucas Fornari Laurindo

Kátia Portero Sloan

Lance Alan Sloan

Marcela Vialogo Marques de Castro

Edgar Baldi

Bruna Fidencio Rahal Ferraz

Eliana de Souza Bastos Mazuqueli Pereira

Virgínia Maria Cavallari Strozze Catharin

Carolina Haber Mellen

Flávia Cristina Castilho Caracio

Caio Sérgio Galina Spilla

Jesselina F. S. Haber

Sandra Maria Barbalho

Glycolipid Metabolic Disorders, Metainflammation, Oxidative Stress, and Cardiovascular Diseases: Unraveling Pathways

糖脂代谢紊乱、元炎症、氧化应激与心血管疾病：解析相关通路

A facilitative transport system exists on the blood–brain barrier (BBB) that has been tacitly assumed to be a path for glutamate entry to the brain. However, glutamate is a non-essential amino acid whose brain content is much greater than plasma, and studies in vivo show that glutamate does not enter the brain in appreciable quantities except in those small regions with fenestrated capillaries (circumventricular organs). The situation became understandable when luminal (blood facing) and abluminal (brain facing) membranes were isolated and studied separately. Facilitative transport of glutamate and glutamine exists only on the luminal membranes, whereas Na+-dependent transport systems for glutamate, glutamine, and some other amino acids are present only on the abluminal membrane. The Na+-dependent cotransporters of the abluminal membrane are in a position to actively transport amino acids from the extracellular fluid (ECF) into the endothelial cells of the BBB. These powerful secondary active transporters couple with the energy of the Na+-gradient to move glutamate and glutamine into endothelial cells, whereupon glutamate can exit to the blood on the luminal facilitative glutamate transporter. Glutamine may also exit the brain via separate facilitative transport system that exists on the luminal membranes, or glutamine can be hydrolyzed to glutamate within the BBB, thereby releasing ammonia that is freely diffusible. The γ-glutamyl cycle participates indirectly by producing oxoproline (pyroglutamate), which stimulates almost all secondary active transporters yet discovered in the abluminal membranes of the BBB.

Richard Hawkins

Juan Viña

How Glutamate Is Managed by the Blood–Brain Barrier

In China, rice is one of the most important cereal crops. Rice bacterial brown leaf spot caused by P. s. pv. syringae is among the most damaging rice diseases in the Heilongjiang Province of China and results in substantial yield losses. In this study, a comprehensive analysis of the pathogen, population structure, and genetic diversity within the species was performed. For this purpose, 176 bacterial isolates of P. s. pv. syringae collected from 15 locations were characterized by using biochemical tests such as the LOPAT test, and genetic characterizations such as multilocus sequence analysis (MLSA) and repetitive PCR, using BOX, REP and ERIC primers. Biochemical testing and detection of syrB genes confirm the presence of P. s. pv. syringae, genetic characterization by MLSA and genetic fingerprinting by repetitive PCR confirmed that high genetic heterogeneity exists in the P. s. pv. syringae isolates, and clustering of the tested isolates and reference strains are related with the same genomospecies 1. This work contributes to the physiological classification of the P. s. pv. syringae isolated from Heilongjiang Province, China, and the results present new data concerning the phylogeny and genetic diversity. This type of study about P. s. pv. syringae has been not reported from this region until now.

Lili Peng

Songrun Yang

Yao Zhang

Haseeb Haseeb

Shuang Song

Xiaofeng Xu

Mingxiu Yang

Junhua Zhang

Characterization and Genetic Diversity of Pseudomonas syringae pv. syringae Isolates Associated with Rice Bacterial Leaf Spot in Heilongjiang, China

水稻细菌性叶斑病相关丁香假单胞菌丁香致病变种在黑龙江的特性与遗传多样性研究

Acute respiratory distress syndrome (ARDS) remains an important clinical challenge with a mortality rate of 35–45%. It is being increasingly demonstrated that the improvement of outcomes requires a tailored, individualized approach to therapy, guided by a detailed understanding of each patient’s pathophysiology. In patients with ARDS, disturbances in the physiological matching of alveolar ventilation (V) and pulmonary perfusion (Q) (V/Q mismatch) are a hallmark derangement. The perfusion of collapsed or consolidated lung units gives rise to intrapulmonary shunting and arterial hypoxemia, whereas the ventilation of non-perfused lung zones increases physiological dead-space, which potentially necessitates increased ventilation to avoid hypercapnia. Beyond its impact on gas exchange, V/Q mismatch is a predictor of adverse outcomes in patients with ARDS; more recently, its role in ventilation-induced lung injury and worsening lung edema has been described. Innovations in bedside imaging technologies such as electrical impedance tomography readily allow clinicians to determine the regional distributions of V and Q, as well as the adequacy of their matching, providing new insights into the phenotyping, prognostication, and clinical management of patients with ARDS. The purpose of this review is to discuss the pathophysiology, identification, consequences, and treatment of V/Q mismatch in the setting of ARDS, employing experimental data from clinical and preclinical studies as support.

Douglas Slobod

Anna Damia

Marco Leali

Elena Spinelli

Tommaso Mauri

Pathophysiology and Clinical Meaning of Ventilation-Perfusion Mismatch in the Acute Respiratory Distress Syndrome

急性呼吸窘迫综合征中通气-灌注失衡的病理生理学及临床意义

The ongoing rise in global temperatures poses significant challenges to ecosystems, particularly impacting bacterial communities that are central to biogeochemical cycles. The resilience of wild mesophilic bacteria to temperature increases of 2–4 °C remains poorly understood. In this study, we conducted experimental evolution on six wild Bacillus strains from two lineages (Bacillus cereus and Bacillus subtilis) to examine their thermal adaptation strategies. We exposed the bacteria to gradually increasing temperatures to assess their thermal plasticity, focusing on the genetic mechanisms underlying adaptation. While B. subtilis lineages improved growth at highly critical temperatures, only one increased its thermal niche to 4 °C above their natural range. This finding is concerning given climate change projections. B. cereus strains exhibited higher mutation rates but were not able to grow at increasing temperatures, while B. subtilis required fewer genetic changes to increase heat tolerance, indicating distinct adaptive strategies. We observed convergent evolution in five evolved lines, with mutations in genes involved in c-di-AMP synthesis, which is crucial for potassium transport, implicating this chemical messenger for the first time in heat tolerance. These insights highlight the vulnerability of bacteria to climate change and underscore the importance of genetic background in shaping thermal adaptation.

Enrique Hurtado-Bautista

Africa Islas-Robles

Gabriel Moreno-Hagelsieb

Gabriela Olmedo-Alvarez

Thermal Plasticity and Evolutionary Constraints in Bacillus: Implications for Climate Change Adaptation

枯草芽孢杆菌中的热可塑性与进化约束：对气候变化适应的启示

This paper presents the results of microbial corrosion tests on M0-grade copper under conditions simulating a geological repository for radioactive waste at the Yeniseisky site (Krasnoyarsk Krai, Russia). The work used a microbial community sampled from a depth of 450 m and stimulated with glucose, hydrogen and sulfate under anaerobic conditions. It was shown that the maximum corrosion rate, reaching 9.8 µm/y, was achieved with the addition of sulfate (1 g/L) with the participation of microorganisms from the families Desulfomicrobiaceae, Desulfovibrionaceae and Desulfuromonadaceae. It was noted that the most important factor leading to copper corrosion was the accumulation of hydrogen sulfide during the activation of sulfate-reducing microorganisms of the genera Desulfomicrobium, Desulfovibrio and Desulfuromonas. During the development of the microbial community under these conditions, the content of copper can have a significant toxic effect at a concentration of more than 250 mg/L.

Elena Abramova

Natalia Shapagina

Grigoriy Artemiev

Alexey Safonov

Microbial Corrosion of Copper Under Conditions Simulating Deep Radioactive Waste Disposal

模拟深层放射性废物处置条件下铜的微生物腐蚀

Lipizzan is a famous horse breed dating back to 1580 when the original stud of Lipica was established by the Hasburg Archduke Charles II. Currently, the Italian State Stud of Lipizzan Horses (ASCAL) is a conservation nucleus managed through strict mating rules where mitochondrial DNA sequences are used to verify the correct assignment of mares to a historical pedigree maternal lineage. Here, we analyzed the D-loop sequences of Lipizzan horses from the ASCAL in Monterotondo (Rome, Italy) in order to confirm their pedigree assignment to known female founder families. The concurrent investigation of the paternal counterpart based on variation in the male-specific region of the Y chromosome (MSY) showed a prevalence of HT02 (80%), typical of the Neapolitan/Oriental wave. The mtDNA polymorphisms identified shaped nine haplotypes that were unequivocally assigned to each of nine classical mare families of the stud (Africa, Almerina, Argentina, Deflorata, Djebrin, Fistula, Ivanka, Sardinia, Spadiglia), while the Europa and Theodorosta families shared a tenth haplotype. New polymorphisms were identified in a not previously studied region (np 16100–16350). The mtDNA phylogenetic analysis revealed that the Lipizzans of the Monterotondo stud belong to six haplogroups (B, C, G, L, M, Q), out of the 18 recorded for the equine species. This work enabled us to identify and preserve ten haplotypes from the historical maternal lines in a small stud kept in genetic segregation for over 100 years.

Alessandra Crisà

Irene Cardinali

Andrea Giontella

Maurizio Silvestrelli

Hovirag Lancioni

Luca Buttazzoni

A Genetic Make Up of Italian Lipizzan Horse Through Uniparental Markers to Preserve Historical Pedigrees

意大利利皮扎马的遗传构成通过单亲标记以保护历史血统

The dramatic changes in precipitation patterns on the Tibetan Plateau affected the carbon-sequestering microbial communities within wetland ecosystems, which were closely related to the responses and adaptation mechanisms of alpine wetland ecosystems to climate change. This study focused on wetland soils subjected to different precipitation gradient treatments and employed high-throughput sequencing technology to analyze the soil cbbM carbon-sequestering microbial communities. The results indicated that Proteobacteria were the dominant microbial community responsible for carbon sequestration in the Wayan Mountain wetland. A 50% increase in precipitation significantly raised the soil moisture content, while a 50% reduction and a 25% increase in precipitation notably enhanced the total soil carbon content. The 25% reduction in precipitation increased the differences in microbial community composition, whereas both the 50% increase and the 50% reduction in precipitation decreased these differences. The soil pH and temperature had the most significant impact on the carbon-sequestering microbial communities. In conclusion, changes in precipitation affect the cbbM carbon sequestration characteristics of soil microbial communities, and a moderate reduction in water input benefited carbon sequestration in wetlands.

Lin Li

Xia Wang

Yanli Yang

Siyu Wang

Kelong Chen

Ni Zhang

The Response Mechanism of the cbbM Carbon Sequestration Microbial Community in the Alpine Wetlands of Qinghai Lake to Changes in Precipitation

青海湖高山湿地cbbM固碳微生物群落对降水变化的响应机制

Sinonasal squamous cell carcinoma (SNSCC) is a rare tumor with high mortality and recurrence rates. However, SNSCC carcinogenesis mechanisms and potential therapeutic drugs have not been fully elucidated. This study investigated the key molecular mechanisms and hub proteins involved in SNSCC carcinogenesis using proteomics and bioinformatic analysis. Dysregulated proteins were validated by RT-qPCR in SNSCC and nasal polyp (NP) tissues. Proteomic analysis revealed that differentially expressed proteins were clustered using MCODE scores ≥ 4 into three modules. The specific hub proteins in each module were analyzed in carcinogenesis pathways using STRING, highlighting potential mechanisms of histone modification and spliceosome dysregulation. Spliceosome components SNRNP200 and SF3A3 were significantly downregulated in SNSCC by RT-qPCR. Web-based applications L1000CDS2 and iLINCS were applied to identify 10 potential repurposable drugs that could reverse the gene expression pattern associated with SNSCC. Docking studies of TAF1, a protein in histone modification, with these 10 small molecule inhibitors indicated OSI-027 to be the most promising due to its strong binding interactions with key residues. These findings suggest that hub proteins involved in the underlying mechanism of SNSCC carcinogenesis may serve as valuable targets for drug development, with OSI-027 emerging as a novel candidate against TAF1 in SNSCC.

Watcharapong Panthong

Chamsai Pientong

Thawaree Nukpook

Chukkris Heawchaiyaphum

Sirinart Aromseree

Tipaya Ekalaksananan

OSI-027 as a Potential Drug Candidate Targeting Upregulated Hub Protein TAF1 in Potential Mechanism of Sinonasal Squamous Cell Carcinoma: Insights from Proteomics and Molecular Docking

OSI-027作为靶向鼻咽鳞状细胞癌潜在机制中上调枢纽蛋白TAF1的潜在药物候选：基于蛋白质组学和分子对接的见解

Abbreviation
Journal Impact	3.75
Quartiles(Global)	BIOLOGY(Q1)

Publication Information	Publisher: Multidisciplinary Digital Publishing Institute (MDPI)，Publishing cycle: Monthly，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 2012，Proportion of original research papers: 87.93%，Self Citation Rate:5.60%， Gold OA Rate: 99.59%
Journal Fees	$Details
Average review cycle	网友分享经验：first decision to authors ~17.5 days after submission; acceptance to publication ~3.1 days
Average recruitment ratio	网友分享经验：quick review and publication, high-level EBM board

Biology

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