RetroSeeker reveals the characteristics, expression, and evolution of a large set of novel retrotransposons.

Retrotransposons are highly prevalent in most animals and account for more than 35% of the human genome. However, the prevalence, biogenesis mechanism and function of retrotransposons remain largely unknown. Here, we developed retroSeeker, a novel computational software that identifies novel retrotransposons from pairwise alignments of genomes and decodes their biogenesis, expression, evolution and potential functions.

Variation in cancer risk between organs can not be explained by the degree of somatic clonal expansion.

Somatic clonal expansion refers to the proliferation and expansion of a cell clone within a multicellular organism. Since cancer also results from the uncontrolled proliferation of few cell clones, it is generally believed that aging-associated somatic clonal expansion observed in normal tissues represents a precancerous condition. For instance, hematological malignancy is often preceded by clonal hematopoiesis.

Importance of pre-mRNA splicing and its study tools in plants.

Alternative splicing (AS) significantly enriches the diversity of transcriptomes and proteomes, playing a pivotal role in the physiology and development of eukaryotic organisms. With the continuous advancement of high-throughput sequencing technologies, an increasing number of novel transcript isoforms, along with factors related to splicing and their associated functions, are being unveiled. In this review, we succinctly summarize and compare the different splicing mechanisms across prokaryotes and eukaryotes.

Acetylation modification in the regulation of macroautophagy.

Macroautophagy, commonly referred to as autophagy, is an evolutionarily conserved cellular process that plays a crucial role in maintaining cellular homeostasis. It orchestrates the delivery of dysfunctional or surplus cellular materials to the vacuole or lysosome for degradation and recycling, particularly during adverse conditions. Over the past few decades, research has unveiled intricate regulatory mechanisms governing autophagy through various post-translational modifications (PTMs).

Advancements in delivery strategies and non-tissue culture regeneration systems for plant genetic transformation.

Plant genetic transformation is a pivotal and essential step in modifying important agronomic traits using biotechnological tools, which primarily depend on the efficacy of transgene delivery and the plant regeneration system. Over the years, advancements in the development of delivery methods and regeneration systems have contributed to plant engineering and molecular breeding. Recent studies have demonstrated that the efficiency of plant transformation can be improved by simultaneously delivering meristem-developmental regulators, utilizing virus-mediated gene editing, and executing non-sterile in planta manipulations.

Abscission in plants: from mechanism to applications.

Abscission refers to the natural separation of plant structures from their parent plants, regulated by external environmental signals or internal factors such as stress and aging. It is an advantageous process as it enables plants to shed unwanted organs, thereby regulating nutrient allocation and ensuring the dispersal of fruits and seeds from the parent. However, in agriculture and horticulture, abscission can severely reduce crop quality and yield.

Roots to the rescue: how plants harness hydraulic redistribution to survive drought across contrasting soil textures.

Hydraulic redistribution (HR) is a critical ecological process whereby plant roots transfer water from wetter to drier soil layers, significantly impacting soil moisture dynamics and plant water and nutrient uptake. Yet a comprehensive understanding of the mechanism triggering HR and its influencing factors remains elusive. Here, we conducted a systematic meta-analysis to discuss the influence of soil conditions and plant species characteristics on HR occurrence.

Development of a CRISPR-Cas12a based assay for the detection of swine enteric coronaviruses in pig herds in China.

Porcine epidemic diarrhea virus (PEDV), Transmissible gastroenteritis virus (TGEV), Porcine deltacoronavirus (PDCoV) and Swine acute diarrhea syndrome coronavirus (SADS-CoV) rank among the most frequently encountered swine enteric coronaviruses (SECoVs), leading to substantial economic losses to the swine industry. The availability of a rapid and highly sensitive detection method proves beneficial for the monitoring and surveillance of SECoVs. Based on the N genes of four distinct SECoVs, a novel detection method was developed in this study by combining recombinant enzyme polymerase isothermal amplification (RPA) with clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) 12a.

Multi-omics sequencing of gastroesophageal junction adenocarcinoma reveals prognosis-relevant key factors and a novel immunogenomic classification.

Background: Gastroesophageal junction adenocarcinoma (GEJAC) exhibits distinct molecular characteristics due to its unique anatomical location. We sought to investigate effective and reliable molecular classification of GEJAC to guide personalized treatment.

Methods: We analyzed the whole genomic, transcriptomic, T-cell receptor repertoires, and immunohistochemical data in 92 GEJAC patients and delineated the landscape of genetic and immune alterations.

The role of granulocyte-macrophage colony-stimulating factor in female assisted reproductive technology treatment: a systematic review and meta-analysis.

The objective of this study is to explore the impact of the use of granulocyte-macrophage colony-stimulating factor (GM-CSF) in female undergoing assisted reproductive technology (ART) on reproductive outcomes. A literature search was performed using electronic databases (PubMed, EMBASE, Web of Science, CNKI, Wanfang data, Geen Medical, and Cochrane Library). Risk ratio (RR), odds ratio (OR), and mean difference (MD) with 95% confidence intervals (CI) for various outcomes were presented.

Mechanisms underlying the interactions and adaptability of nitrogen removal microorganisms in freshwater sediments.

Microorganisms in eutrophic water play a vital role in nitrogen (N) removal, which contributes significantly to the nutrient cycling and sustainability of eutrophic ecosystems. However, the mechanisms underlying the interactions and adaptation strategies of the N removal microorganisms in eutrophic ecosystems remain unclear. We thus analyzed field sediments collected from a eutrophic freshwater ecosystem, enriched the N removal microorganisms, examined their function and adaptability through amplicon, metagenome and metatranscriptome sequencing.

A simple and effective method to remove pigments from heterologous secretory proteins expressed in Pichia pastoris.

Pichia pastoris is a popular yeast host for high-level heterologous expression of proteins on an industrial scale owing to its reliable expression, robust growth, high fermentation density, and easy genetic manipulation and cultivation at a relatively low cost. Of particular interest is its high secretion efficiency for small proteins including insulin, human serum albumin, vaccines, enzymes, and llama-derived heavy-chain only antibodies (nanobodies) for pharmaceutical and research applications. However, a recurring challenge in using P.

Hydrogen Sulfide (HS) Generated in the Colon Induces Neuropathic Pain by Activating Spinal NMDA Receptors in a Rodent Model of Chronic Constriction Injury.

Neuropathic pain (NP) imposes a significant burden on individuals, manifesting as nociceptive anaphylaxis, hypersensitivity, and spontaneous pain. Previous studies have shown that traumatic stress in the nervous system can lead to excessive production of hydrogen sulfide (HS) in the gut. As a toxic gas, it can damage the nervous system through the gut-brain axis.

Advances in biotechnology and breeding innovations in China's marine aquaculture.

Biotechnology is the key driving force behind the sustainable development of aquaculture, as biological innovation would significantly improve the capabilities of aquatic breeding and achieve independent and controllable seeding sources to ensure food safety. In this article, we have analyzed the current status and existing problems of marine aquaculture in China. Based on these data, we have summarized the recent (especially the last 10 years) biotechnological innovation and breeding progress of marine aquaculture in China, including whole genome sequencing, sex-related marker screening, genomic selection, and genome editing, as well as progress of improved marine fish varieties in China.

Cardiovascular Outcomes in Patients with Complex Type 2 Diabetes Mellitus Treated with the Dual SGLT Inhibitor Sotagliflozin: A Meta-analysis.

Introduction: Scientific publications have shown sodium-glucose co-transporter-2 (SGLT2) inhibitors to have several beneficial effects in patients with complex type 2 diabetes mellitus (T2DM). However, sodium-glucose co-transporter-1 (SGLT-1) inhibitor is still under investigation in clinical trials. Recently, a dual inhibitor of sodium-glucose co-transporter (SGLT1/2), sotagliflozin, has been approved for use in patients with T2DM.

Technologies for studying phase-separated biomolecular condensates.

Biomolecular condensates, also referred to as membrane-less organelles, function as fundamental organizational units within cells. These structures primarily form through liquid-liquid phase separation, a process in which proteins and nucleic acids segregate from the surrounding milieu to assemble into micron-scale structures. By concentrating functionally related proteins and nucleic acids, these biomolecular condensates regulate a myriad of essential cellular processes.

The ability of CD4CD8 T cells to distinguish between Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis and pediatric infectious mononucleosis.

Epstein-Barr virus (EBV)-related hemophagocytic lymphohistiocytosis (EBV-HLH) and infectious mononucleosis (IM) are characterized by fever, hepatomegaly, and splenomegaly, but HLH has a 50% lethality rate. Therefore, this study aimed to compare the laboratory findings in differentiating EBV-HLH children from IM children who have fever, hepatomegaly, or splenomegaly. A total of 131 IM patients and 29 EBV-HLH pediatric patients with fever, hepatomegaly, or splenomegaly were enrolled in our study.

Role of glycosylation in bacterial resistance to carbapenems.

Carbapenems are a class of β-lactam antibacterial drugs with a broad antibacterial spectrum and strong activity, commonly used to treat serious bacterial infections. However, improper or excessive use of carbapenems can lead to increased bacterial resistance, which is a significant concern as they are often used as last resort for treating multidrug-resistant (MDR) gram-negative bacteria. Confronted with this challenge, it is crucial to comprehensively understand the mechanism of carbapenem resistance to develop effective therapeutic strategies and innovative drugs.

Growth trajectory of Yiling sheep and its related genetic parameters.

Growth traits are one of the focuses of sheep breeding, and growth curve is an effective method to describe growth traits. The body weight of Yiling sheep at 0, 120, 180, 360 and 540 days of age were fitted with five common nonlinear growth models: Logistic, Gompertz, Von Bertalanffy, Brody and Negative exponential, and the growth models were evaluated by goodness of fit standard. The results showed that the Von Bertalanffy model was suitable for characterizing the growth of Yiling sheep.

Applications of mass spectrometry imaging in botanical research.

Mass spectrometry imaging (MSI) serves as a valuable tool enabling researchers to scrutinize various compounds, peptides, and proteins within a sample, providing detailed insights at both elemental and molecular levels. This innovative technology transforms information obtained from a mass spectrometer- encompassing ionic strength, mass-to-charge ratio, and ionized molecule coordinates-within a defined region into a pixel-based model. Consequently, it reconstructs the spatial distribution of ions, allowing for a comprehensive understanding of molecular landscapes.

RNA structure: implications in viral infections and neurodegenerative diseases.

RNA is an intermediary between DNA and protein, a catalyzer of biochemical reactions, and a regulator of genes and transcripts. RNA structures are essential for complicated functions. Recent years have witnessed rapid advancements in RNA secondary structure probing techniques.

Metabolic engineering for single-cell protein production from renewable feedstocks and its applications.

Proteins are indispensable for maintaining a healthy diet and performing crucial functions in a multitude of physiological processes. The growth of the global population and the emergence of environmental concerns have significantly increased the demand for protein-rich foods such as meat and dairy products, exerting considerable pressure on global food supplies. Single-cell proteins (SCP) have emerged as a promising alternative source, characterized by their high protein content and essential amino acids, lipids, carbohydrates, nucleic acids, inorganic salts, vitamins, and trace elements.