Molecular Biology Research Articles (Page 1)

17β-trenbolone increases circulating myeloid-derived MMP8 in CSDS-induced mice and drives depressive tendencies to social threat.

Climate change and invasive species are leading drivers of biodiversity loss, with island ecosystems being especially vulnerable. South Georgia, a remote sub-Antarctic island, is 170 km long with approximately 30,000 ha of vegetated coastal areas, as snow and ice dominate the inland regions. Human activities on the island have historically introduced non-native species, resulting in 41 introduced vascular plant species compared with only 24 native ones. To address this imbalance, the South Georgia Non-Native Plant Management Strategy was implemented (2016-2020) to control non-native plant populations. We assessed emergent seedlings from South Georgia soil samples and wind-dispersed seeds to determine which species persist in the soil seed bank and contribute to dispersal. Using a molecular barcoding approach, we evaluated traditional markers (rbcL and matK) and optimized a high-throughput Angiosperms353 sequencing pipeline for accurate seedling identification. We generated a reference library covering all native and non-native species and applied this to 1,498 emergent seedlings and 737 trapped seeds. Molecular barcoding identified 21 species, including 10 non-natives and 11 natives. Strikingly, 84% of emergent seedlings were non-native, with Class III invasive species (Cerastium fontanum, Poa annua, Taraxacum officinale) dominating across most sites and in all wind traps. By contrast, Class I and II species occurred rarely and only at a few sites, indicating that management efforts have substantially reduced their spread, though viable seeds persist in the soil. These findings highlight both the continued threat from persistent seed banks of dominant invaders and the value of molecular barcoding for long-term monitoring. Our approach provides a framework for biosecurity and restoration management in South Georgia and other vulnerable ecosystems under climate change pressures.

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and ion structure to the cryo-EM densities observed around the Tetrahymena ribozyme at 2.2-2.3 Å resolution, collected through target R1260 in the CASP16 competition. Twenty-six groups participated in this solvation "cryo-ensemble" prediction challenge, submitting over 350 million atoms in total, offering the first opportunity to compare blind predictions of dynamic solvent shell ensembles to cryo-EM density. Predicted atomic ensembles were converted to density through local alignment and these densities were compared to the cryo-EM densities using Pearson correlation, Spearman correlation, mutual information, and precision-recall curves. These predictions show that an ensemble representation is able to capture information of transient or dynamic water and ions better than traditional atomic models, but there remains a large accuracy gap to the performance ceiling set by experimental uncertainty. Overall, molecular dynamics approaches best matched the cryo-EM density, with blind predictions from bussilab_plain_md, SoutheRNA, bussilab_replex, coogs2, and coogs3 outperforming the baseline molecular dynamics prediction. This study indicates that simulations of water and ions can be quantitatively evaluated with cryo-EM maps. We propose that further community-wide blind challenges can drive and evaluate progress in modeling water, ions, and other previously hidden components of biomolecular systems.

Whole genome sequencing (WGS) provides complete genetic information in one test, supporting the shift towards individualized metastatic colorectal cancer (mCRC) treatment. Although WGS is validated as a diagnostic test, the potential clinical implications for mCRC remain unknown. We evaluated the clinical consequences of WGS in 96 mCRC patients. Clinically actionable biomarkers were identified by a molecular biologist and medical oncologist, with added value defined as biomarkers undetected by standard diagnostics. We evaluated how these biomarkers informed treatment decisions. We used patient-derived organoids (PDOs) to test drug sensitivity to MET, MEK, and CDK4/6 inhibitors, translating genomic findings into functional evidence. WGS yields biomarkers with clinical implications in 81% of patients, with 49% (N = 47/96) identified by WGS that were not detected by guideline-based diagnostics, and 40% (N = 38/96) not detected by applied diagnostics. The proportion of patients receiving biomarker-based treatment has increased from 11% to at least 24% by WGS. PDOs with actionable biomarkers showed clear differential response to different biomarker-based treatments. WGS enables considerably more personalized therapeutic interventions and represents a promising approach in advancing precision oncology for mCRC patients. PDO pre-screening can refine therapy by identifying (in)effective treatments in a patient-specific context, to accelerate the development of personalized treatment.

Endometrial cancer is the sixth most common cancer in women worldwide and the fourth most common cancer in women in the United States. In the United States, its incidence and mortality rates have continued to increase since the late 1990s. Endometrial cancer comprises most uterine corpus carcinomas and represents a heterogeneous group of cancers varying in pathology, histology, molecular biology, immunogenicity, and prognosis. Recently, the advancement of molecular classification and subsequent clinical trials have led to new FDA approvals for the use of immune checkpoint inhibitors in endometrial cancer. However, recurrent and advanced-stage endometrial cancer continues to demonstrate high morbidity and mortality, denoting an unmet need for innovative immunotherapeutic strategies. This review explores current concepts in the endometrial cancer tumor immune microenvironment, comparing antigenicity, immunosurveillance, and immunoregulation among molecular and histologic subtypes and providing insight into which subtypes may be particularly responsive to immunotherapy. Novel immunotherapeutic strategies targeting cancer antigens, emerging immune checkpoints, immunomodulatory cytokines, and tumor-infiltrating immune cells are described, and corresponding clinical trials are presented. Integrated approaches such as immunogenic modulation, which enhances tumor susceptibility to immune attack, and immune subset conditioning, which modifies suppressive immune components within the tumor immune microenvironment, are presented as promising avenues to render "cold" tumors responsive. Together, the immunotherapies reviewed here offer potential strategies for treating patients with advanced or refractory endometrial cancer.

Molecular methods for high-throughput, multiplexed, and automated genome editing in prokaryotes and eukaryotes.

This article presents data from the analysis of biomass and culture medium concerning the content of sulfur-containing amino acids in mutants designated as “feeders” of Chlorella, utilizing the method of radioactive indicators. The objective of this study is to address the question of the nature of the substances responsible for the “feeding” effect attributed to the extracellular products of the mutant “feeders.” To achieve this, a radiochemical method was employed to determine the relative quantities of the sulfur-containing amino acids methionine and cysteine in the biomass and culture medium of various Chlorella mutants, using radioactive sulfur S35. The method for determining the relative amounts of sulfur-containing amino acids in the biomass and culture medium of Chlorella “feeder” mutants is described. It is demonstrated that mutants 94, U-6, U-7, and 722-2-S accumulate cysteine in their proteins at levels 2-3 times higher than those found in the original strain B, while in the peptide fraction (in the medium), the accumulation is nearly six times greater. Low molecular weight peptides find extensive applications in the food, pharmaceutical, and medical industries. They also serve as foundational models for biochemical, genetic, and molecular-biological research. Specifically, these peptides influence the DNA of aged cells, prompting their activation and thereby rejuvenating them. The application sphere of chlorella and other algae encompasses agriculture, where they serve as fertilizers and growth stimulants; medicine, cosmetology, and sports for detoxification and immune system enhancement; aquaculture for oxygen enrichment of water and improving fish health; as well as in the production of biofuels, bioplastics, and as feed additives.

To date, the gold standard for Pneumocystis jirovecii pneumonia (PjP) diagnosis is direct microscopic examination (ME). However, several studies have shown that the DNA copy number of the P. jirovecii, measured by quantitative real-time PCR (qPCR), is significantly higher in patients with PjP than in colonized individuals. Nevertheless, this approach is not standardized yet and requires further investigation. In this study, we aimed to compare the results obtained using the Pneumocystis ELITe MGB Kit (ELITech Group S.p.a., Italy) with those from ME, evaluating specificity, sensitivity, and the ability to distinguish infection from colonization through the identification of a cut-off value. A total of 163 bronchoalveolar lavage (BAL) or sputum samples, collected and tested with direct ME for P. jirovecii in our Unit over the past 10 years, were also analyzed using a qPCR assay. The results were concordant between the two methods in all 63 ME-positive samples. Among 100 ME-negative samples, 21 (21%) tested positive by qPCR. A receiver operating characteristic curve analysis was performed to assess the qPCR assay's prognostic performance in identifying patients already diagnosed with PjP by ME on BAL or sputum samples. A cut-off value of 150 DNA copies/105 cells yielded a sensitivity of 100% (95% confidence interval [CI]: 94%-100%) and a specificity of 99% (95% CI: 95%-100%) in the diagnosis of the disease. qPCR may be used alongside careful clinical evaluation to ensure accurate diagnosis and appropriate treatment.IMPORTANCERecently, molecular approaches have been proposed for the detection of Pneumocystis jirovecii. Thanks to their high sensitivity, these methods can detect small amounts of fungal DNA. However, it is necessary to establish a cut-off value to distinguish between colonization and infection. Since P. jirovecii is closely related to epithelial cells in the lung environment, normalizing the fungal DNA load on the host cellular DNA content could represent an important step toward standardizing the procedure.

Leptospirosis is one of the most common zoonotic infections in the world and is considered a neglected disease. Development of molecular methods and approaches in gene typing significantly contributed to the discovery of novel Leptospira strains, which require detailed studying and systematization and are an important factor of managing the pathogen and the disease leptospirosis as a classic One Health problem. Characterization of leptospira populations in water, soil and other environmental objects will aid in the development and implementation of prevention and control approaches aimed at reducing the risks of infection, and will contribute to a deeper understanding of the bacteria's ecology. This study aimed to briefly describe the phylogenic history of Leptospira spp., and to conduct a review and retrospective analysis of new strains discovered during the years 2000-2025 impacting the leptospires landscape significantly. The discovery of novel Leptospira strains has been an important development in the research of this pathogen, and has helped to better understand the potential risks associated with its presence. In this review, we analyzed and summarized literature on the detection of new Leptospira strains and their global distribution.

Sorghum is one of the major millet crops globally and is severely affected by various pests and diseases, with the shoot fly (Atherigona soccata) being one of the most damaging pests to sorghum production worldwide. This pest primarily targets sorghum seedlings, causing yield losses of up to 90 %. Despite adopting various management practices, host plant resistance remains the most effective, economical and environment friendly method for controlling this pest. Conventional breeding strategies, which rely exclusively on phenotypic selection, haveencountered significant challenges in developing cultivars with broad-spectrum resistance. In recent decades, significant efforts have been made to address these limitations by leveraging advancements in molecular breeding approaches, including Quantitative Trait Loci (QTL) mapping and Marker-Assisted Selection (MAS). These approaches have led to the identification of several resistant genotypes, QTLs and genes associated with shoot fly resistance in sorghum. However, progress in improving sorghum resistance to the shoot fly through molecular breeding remains limited. This review discusses the biology and impact of the shoot fly on sorghum, evaluates progress and constraints in molecular breeding for resistance, identifies existing research gaps and proposes future directions to enhance efforts in combating shoot fly resistance in sorghum.

One of the characteristic features of the monoraphid genus Planothidium is the structure of the central part of the rapheless valve. Planothidium is divided into three groups based on this feature: with a sinus, a cavum, or with uninterrupted striae. Representatives of all three groups of Planothidium from the Kamchatka Peninsula have been studied using molecular (genetic markers 18S rDNA and rbcL) and morphological approach. Two new genera are separated from Planothidium: Paraplanothidium gen. nov., characterised by a cavum, and Pseudoplanothidium gen. nov., characterised by the absence of a horseshoe-shaped depression on the rapheless valve; this decision is supported by molecular data. Three new species from the new genera are described based on light and scanning electron microscopy as well as molecular analysis: Paraplanothidium laevis, Pseudoplanothidium foliiformis and Pseudoplanothidium minutum. New taxonomic combinations are proposed for previously described Planothidium species. This study contributes to the research of monoraphid diatoms taxonomy.

The teaching of molecular methods through programs designed to answer real-world questions is rare. Here, we use the shark fin trade and take a problem-based approach that introduces students to the molecular methods used in conservation biology and genetics. The teaching of biodiversity loss and the sheer magnitude of the problem can lead to students feeling ecological grief and helplessness. To combat this, here, we describe a semester-long lab class that tackles a contemporary problem in conservation and the associated biodiversity loss. The class takes students from project design and sample collection to the publication of results in reputable peer-reviewed scientific journals. These publications have been picked up by local and international media and have been used in policy documents outlining shark conservation strategies. This gives students a sense of achievement, which helps alleviate the sense of helplessness and despair that frequently manifests when discussing global challenges such as biodiversity loss. Participants came from a wide array of backgrounds, with diverse scientific experiences ranging from no molecular laboratory experience to those who are comfortable and already competent with molecular techniques. Student evaluations and comments over a 5-year period overwhelmingly indicate the successful nature of this problem-based approach to learning.

57th National Congress of the Italian Society of Clinical Biochemistry and Clinical Molecular Biology (SIBioC-Laboratory Medicine).

Abstract With the rise in planting new grape varieties, accurate identification and ensuring plant authenticity are crucial, as mistakes can cause significant financial losses in wine and table grape production. However, traditional morphological methods are often unreliable because they are strongly influenced by environmental conditions, creating a need for robust molecular approaches. Inter-simple sequence repeat (ISSR) markers represent a powerful DNA-based system for diversity analysis and accurate identification of grape varieties. Iran, as a centre of grape domestication, hosts a rich diversity of grape ( Vitis vinifera L.) cultivars. This study aimed to assess the genetic relationships among 20 Iranian and foreign grape cultivars cultivated in Iran using seven ISSR primers. A total of 31 bands were produced, of which 23 (74.19%) were polymorphic. The effective number of alleles (Ae) ranged from 1.22 to 1.70, and the polymorphic information content varied from 0.18 to 0.40. The highest Shannon’s index (0.84) was obtained for the UBC848 primer, indicating strong discriminatory ability. Cluster analysis and principal component analysis (PCA) classified the cultivars into three main groups, regardless of geographic origin. Cultivars from Japan, the USA and Iran showed close genetic relationships, suggesting historical germplasm exchange through human or natural-mediated gene flow. The observed moderate genetic differentiation (Fst = 0.236) and limited gene flow (Nm = 0.81) highlight the impact of geographical and anthropogenic barriers on cultivar divergence. The results also indicated that genetically distant Iranian cultivars, such as ‘Bidaneh Ghermez’ and ‘Dizmari’, offer promising material for breeding programmes aimed at maximizing heterosis. Overall, ISSR markers proved effective in detecting polymorphism and assessing genetic diversity in grape cultivars. Future work should expand the analysis to a broader set of Iranian and international germplasm using complementary molecular markers to strengthen breeding strategies and improve adaptability under climate change. Significance of the study What is already known on this subject? Research has shown that grape cultivars from different geographical origins can exhibit genetic similarities, likely due to historical germplasm exchange facilitated by environmental factors or human activities such as trade and farming. What are the new findings? The greatest genetic distance (0.589) was observed between the Iranian Bidaneh Ghermez and the Uzbek Black Seedless, suggesting limited gene flow between these populations. This finding highlights unique genetic reservoirs that could be valuable for breeding programmes. What are the expected impacts on horticulture? This study’s findings are expected to strengthen grape breeding, conservation, and commercial production by: (1) Enabling targeted cross-breeding for better cultivars; (2) Supporting genetic preservation of rare Iranian varieties; (3) Improving vineyard management through DNA-based identification; and (4) Promoting sustainable viticulture by leveraging natural genetic diversity. ltimately, these impacts will contribute to more resilient, productive, and economically viable grape cultivation systems, benefiting farmers, researchers, and the horticulture industry.

We are pleased to introduce this Special Issue titled ‘New Insight: Enzymes as Targets for Drug Development in Current Issues in Molecular Biology,’ which highlights recent progress and updates in molecular and computational approaches to understanding disease mechanisms and discovering new therapeutics [...]

Robert Haselkorn (1934–2025) began a long and impactful career during the early years of nucleic acids research when the foundations of molecular biology were being laid. Focusing first on plant viruses, and then also bacteriophage, he hit upon a cyanophage—a cyanobacterial virus—that led his group to establish cyanobacterial strains as model organisms for fundamental bacterial research. He established that the specialized cells called heterocysts that are differentiated by multicellular Anabaena (Nostoc) are the sites of biological nitrogen fixation, and went on to reveal mechanisms of prokaryotic development. The Haselkorn lab became a leader more broadly in prokaryotic gene, and later genome, sequencing and annotation. Appreciated for his generosity and unwavering support of his lab members, and his contributions to creating a field of cyanobacterial molecular genetics, his impact continues across molecular biology and microbiology through those whose creativity he encouraged.

Mitochondrial DNA has unique biological characteristics, such as a high mutation rate and clonal inheritance, which make it an appropriate marker in molecular biology. However, exceptionally high mitochondrial divergences have been reported in terrestrial and marine invertebrates, plants, and certain vertebrate lineages, which complicates the interpretation of the results in DNA barcoding and evolutionary studies. The freshwater snails in the genus Semisulcospira have two mitochondrial DNA lineages: a normal mitochondrial lineage (mt-A type) and a highly divergent ‘enigmatic’ lineage (mt-B type). We assembled thirty-two mitogenomes of Semisulcospira to understand the molecular evolution of the mt-B type. We found that the mt-B type evolves faster than the mt-A type, has more non-synonymous mutations, and exhibits structural variations with truncated cob and cox3 genes. Our results showed that the observed molecular evolution of the mt-B type could result from a decreased efficiency of natural selection due to small population size and/or the accumulation of slightly deleterious mutations caused by mitochondrial sex ratio distortion.

Amyloid-β (Aβ) is recognized as a pathological hallmark of Alzheimer's disease, but accumulating evidence suggests that it also serves physiological roles in the healthy brain. Notably, Aβ secretion is tightly linked to neuronal activity and wakefulness, and its clearance is facilitated by sleep, raising the possibility that Aβ regulates sleep homeostasis. We propose that Aβ functions as a cytokine-like somnogen: a molecule whose accumulation during wakefulness promotes sleep onset and maintenance via synaptic and immune mechanisms. This framework reframes Aβ not as a toxic byproduct but as a key intermediary between neural activity and restorative sleep processes. We synthesize findings from molecular biology, electrophysiology, animal models, and human sleep studies, including research on AβPP processing, activity-dependent Aβ release, oligomeric signaling, and the effects of anti-amyloid therapies on sleep. Particular emphasis is placed on evidence that Aβ modulates synaptic excitability, engages glial immune pathways, and fulfills formal criteria for cytokine classification. Across multiple systems, Aβ exhibits properties consistent with homeostatic downscaling: it dampens neurotransmitter release, suppresses excitatory receptor trafficking, and activates sleep-promoting neuronal populations. Disruption of endogenous AβPP cleavage impairs sleep consolidation, while depletion of Aβ can lead to network hyperexcitability and disturbed sleep. Post-marketing reports of insomnia and abnormal dreams with plaque-clearing agents further support a physiological role. Recognizing Aβ as a somnogen offers a unifying model for sleep disruption in AD and raises caution about therapies that neutralize Aβ indiscriminately. Future interventions may benefit from preserving Aβ's homeostatic roles while mitigating its pathological aggregation.

EcoSal Plus (ESP) is the authoritative online review journal that publishes an ever-growing body of expert reviews covering virtually all aspects of Escherichia coli, Salmonella, and other members of the order Enterobacterales and their use as model microbes for biological explorations. This review will cover the history of ESP, starting with its origins as multi-volume printed books entitled Escherichia coli and Salmonella: Cellular and Molecular Biology that became "the Bible" for information on the physiology, metabolism, genetics, and other aspects of E. coli and Salmonella. After two printed editions, this resource moved online as EcoSal in an era when electronic publishing was still in its infancy. Progress in establishing EcoSal was slow due to technical issues of online publishing and difficulties in recruiting authors to produce new material. This venture was relaunched in 2013 as EcoSal Plus in a completely new web platform that was much more user (and author) friendly and with an expanded scope to include other members of the order Enterobacterales. EcoSal Plus will be ending as a standalone publication but will merge with Microbiology and Molecular Biology Reviews to continue providing high-quality, authoritative reviews on E. coli, Salmonella, and related organisms.

I write this interim editorial to record my heartfelt appreciation to all participants and to express sincere gratitude to the authors, reviewers, and editorial staff of Current Issues in Molecular Biology, whose intellectual engagement and professional dedication have been pivotal to the success of my Special Issue “Molecular Mechanisms in Plant Stress Tolerance” [...]