Search Results (281)

This study analyzed the heavy metal tolerance and chromium reduction and the potential of plant growth to promote Rhizobium sp. OS-1. By genetic makeup, the Rhizobium strain is nitrogen-fixing and phosphate-solubilizing in metal-contaminated agricultural soil. Among the Rhizobium group, bacterial strain OS-1 showed a significant tolerance to heavy metals, particularly chromium (900 µg/mL), zinc (700 µg/mL), and copper. In the initial investigation, the bacteria strains were morphologically short-rod, Gram-negative, appeared as light pink colonies on media plates, and were biochemically positive for catalase reaction and the ability to ferment glucose, sucrose, and mannitol. Further, bacterial genomic DNA was isolated and amplified with the 16SrRNA gene and sequencing; the obtained 16S rRNA sequence achieved accession no. HE663761.1 from the NCBI GenBank, and it was confirmed that the strain belongs to the Rhizobium genus by phylogenetic analysis. The strain’s performance was best for high hexavalent chromium [Cr(VI)] reduction at 7–8 pH and a temperature of 30 °C, resulting in a total decrease in 96 h. Additionally, the adsorption isotherm Freundlich and Langmuir models fit best for this study, revealing a large biosorption capacity, with Cr(VI) having the highest affinity. Further bacterial chromium reduction was confirmed by an enzymatic test of nitro reductase and chromate reductase activity in bacterial extract. Further, from the metal biosorption study, an Artificial Neural Network (ANN) model was built to assess the metal reduction capability, considering the variables of pH, temperature, incubation duration, and initial metal concentration. The model attained an excellent expected accuracy (R² > 0.90). With these features, this bacterial strain is excellent for bioremediation and use for industrial purposes and agricultural sustainability in metal-contaminated agricultural fields. Full article

The excessive use of antimicrobials drives the emergence of multidrug resistance (MDR) in bacterial strains, which harbor resistance genes to survive under diverse drug pressures. Such resistance can result in life-threatening infections. The predominance of MDR Pseudomonas spp. poses significant challenges to public health and environmental sustainability, particularly in ecosystems affected by human activities. Characterizing MDR Pseudomonas spp. is crucial for developing effective diagnostic tools and biosecurity protocols, with broader implications for managing other pathogenic bacteria. Strains were diagnosed through 16S rRNA PCR and sequencing, complemented by phylogenetic analysis to evaluate local and global evolutionary connections. Antibiotic susceptibility tests revealed extensive resistance across multiple classes, with MIC values surpassing clinical breakpoints. This study examined the genetic diversity, resistance potential, and phylogenetic relationships among Pseudomonas aeruginosa strain DG2 and Pseudomonas fluorescens strain FM3, which were isolated from solid waste dump sites (n = 30) and dairy farms (n = 22) in West Bengal, India. Phylogenetic analysis reveals distinct clusters that highlight significant geographic linkages and genetic variability among the strains. Significant biofilm production under antibiotic exposure markedly increased resistance levels. RAPD-PCR profiling revealed substantial genetic diversity among the isolates, indicating variations in their genetic makeup. In contrast, SDS-PAGE analysis provided insights into the protein expression patterns that are activated by stress, which are closely linked to MDR. This dual approach offers a clearer perspective on their adaptive responses to environmental stressors. This study underscores the need for vigilant monitoring of MDR Pseudomonas spp. in anthropogenically impacted environments to mitigate risks to human and animal health. Surveillance strategies combining phenotypic and molecular approaches are essential to assess the risks posed by resilient pathogens. Solid waste and dairy farm ecosystems emerge as critical reservoirs for the evolution and dissemination of MDR Pseudomonas spp. Full article

This review addresses the critical conservation challenges faced by Pinna nobilis, the noble pen shell, a keystone umbrella species in Mediterranean marine ecosystems. Since 2016, the species has experienced catastrophic population declines due to mass mortality events likely driven by protozoan, bacterial, and viral infections. Despite these severe circumstances, small resilient populations persist in select estuaries and coastal lagoons across the Mediterranean, offering potential for recovery. We provide a comprehensive overview on research dedicated to Pinna nobilis’ biology, genetic variation, disease dynamics, and environmental factors influencing its survival, with a focus on refugia where populations still endure. Remarkably, recent studies have revealed signs of resistance in certain individuals and the potential for hybridisation with Pinna rudis. In this context, the possible impact of the increasing occurrence of hybridisation between Pinna nobilis and Pinna rudis on the conservation of their genetic diversity should be carefully considered. This review highlights the importance of ongoing conservation efforts including habitat restoration, protection of remaining populations, assessment of past and present genetic variability, and the development of captive breeding programmes. We aim to elucidate the need for continued studies on Pinna nobilis’ biodiversity, particularly its evolutionary dynamics, genetic makeup, and the interplay of environmental variables influencing its survival and persistence. Full article

In acute myeloid leukemia (AML) it is important to elucidate the biological events that lead from remission to relapse, which have a high probability of leading to an adverse disease outcome. The cancer stem cell marker aldehyde dehydrogenase 1 (ALDH1A1) is underexpressed in AML cells when compared to healthy cells, both at the RNA level and at the protein level, and at least in the former, both in the bone marrow and in peripheral blood. Nonetheless, ALDH1A1/ALDH1A2 activity increases in AML cells during disease relapse and is higher in adverse prognosis AML in comparison with favorable prognosis AML. Furthermore, especially in relapsed AML and in unfavorable AML, AML cells rich in ALDH1A1 can contain high levels of reactive oxygen species (ROS), in parallel with high ALDH1A1/2 activity. This metabolic feature is clearly incompatible with normal stem cells. The term “stem-like” therefore is useful to coin malignant cells with a variety of genetic makeups, metabolic programming and biomarkers that converge in the function of survival of clones sufficient to sustain, spread and re-establish neoplastic disease. Therefore, AML “stem-like” cells survive cancer treatment that eradicates other malignant cell clones. This fact differentiates AML “stem-like” cells from normal stem and progenitor cells that function in tissue regeneration as part of a distinct hierarchical order of cell phenotypes. The ODYSSEY clinical trial is a Phase I/II study designed to evaluate the safety, tolerability, pharmacokinetics, and pharmacodynamics of ABD-3001, a novel therapeutic agent, in patients with AML who have relapsed or are refractory to standard treatments. In this context, ABD-3001 is used as an inhibitor of cytosolic ALDH1 enzymes, such as ALDH1A1 and ALDH1A2. Full article

An important historical and cultural region in southern China, the Xiangjiang River Basin, has formed a unique spatial pattern and regional cultural characteristics in its long-term development. In recent years, the acceleration of urbanization has led to the historical texture and cultural elements of Changsha’s suburban blocks facing deconstruction pressure. How to identify and protect their cultural value at the spatial structure level has become an urgent issue. Taking three typical traditional township blocks in the suburbs of Changsha as the research object, this paper constructs a trinity research framework of “spatial gene identification–diversity analysis–strategy optimization.” It systematically discusses the makeup of the types, quantity, distribution, relative importance ranking, and diversity characteristics of their spatial genes. The results show that (1) the distribution and quantity of spatial genes are affected by multiple driving forces such as historical function, geographic environment, and settlement evolution mechanisms, and that architectural spatial genes have significant advantages in type richness and importance indicators; (2) spatial gene diversity shows the structural characteristics of “enriched artificial space and sparse natural space,” and different blocks show clear differences in node space and boundary space; (3) spatial genetic diversity not only reflects the complexity of the spatial evolution of a block but is also directly related to its cultural inheritance and the feasibility of renewal strategies. Based on this, this paper proposes strategies such as building a spatial gene database, improving the diversity evaluation system, and implementing differentiated protection mechanisms. These strategies provide theoretical support and methods for the protection and sustainable development of cultural heritage in traditional blocks. Full article

Background/Objectives: Pharmacogenetic (PGx) testing can predict drug efficacy, toxicity, and risk of adverse drug reactions (ADRs). However, PGx-guided prescribing for pediatric chronic pain is underutilized. Methods: We evaluated the rate of deviance from standard drug dosing regimens in children and adolescents with chronic pain based on PGx testing of drug-metabolizing genes. We also assessed the acceptability and feasibility of PGx testing and implementation of PGx-guided recommendations from patient, caregiver, and prescriber perspectives. Finally, we explored whether PGx results could predict self-reported therapeutic responses and/or ADRs to medications. Results: Forty-eight participants aged 8–17 years with chronic pain provided DNA via buccal swab. Genetic variant data for CYP2D6, CYP2C9, and CYP2C19 metabolism genes and associated metabolizer status were analyzed with respect to clinical PGx guidelines for dosing recommendations of analgesics and psychotropic medications. Participants, their caregivers, and their prescribers also completed quantitative questionnaires evaluating their experience with PGx testing. Twenty-three (50%) participants were predicted to benefit from non-standard dosing for medications with clinical PGx guidelines. Participants expressed satisfaction with the PGx testing process and felt it was safe and worthwhile. Prescribers also reported that PGx results were relevant for medication choices in 42 (91%) participants. Seven (15%) participants had genotyping results which may have predicted their self-reported therapeutic responses and/or ADRs to specific medications. Conclusions: Though further research on pharmacodynamic associations is required to sufficiently address the complexity of interpatient responses to medications for the treatment of pediatric pain and mental health conditions, PGx testing may be used to inform individualized medication choices based on genetic make-up. Full article

Red algae are recognized for their health-promoting bioactive substances and dietary fibers, making them important as functional food. In order to identify species and determine phylogenetic relationships, mitochondrial genes serve as important markers. Thus, this study sequenced the complete mitochondrial genome of Ahnfeltiopsis flabelliformis, compared with Phyllophoraceae species, and performs phylogenetic analysis to reveal its evolutionary position. The genome is 25,992 bp long, has 71.3% of biased AT content, and comprises 24 protein-coding genes (PCGs), 22 tRNA, and three rRNA genes. The overall base composition of its mitochondrial genome was 37.4% for A, 33.9% for T, 14.7% for G, 14.0% for C and 28.7% for GC. The gene content, annotation, and genetic makeup are identical to those of Phyllophoraceae species. Phylogenetic study based on the complete mitochondrial genome and shared mitochondrial genes revealed that the six Phyllophoraceae species form a well-supported clade. Within this clade, A. flabelliformis groups with Gymnogongrus griffithsiae, and together they form a distinct subclade including four species of the Mastocarpus. The results indicate that A. flabelliformis shares a closer evolutionary relationship with G. griffithsiae than with Mastocarpus species. Future research on Ahnfeltiopsis is necessary to comprehend the evolutionary history and phylogenetic relationships among species in this genus. Full article

Sheep farming is a common agricultural practice in Greece, with many sheep populations belonging to Greek breeds. However, their genetic makeup remains relatively unexplored and limited information is available for their genetic variability. Here, we provide the first whole genome sequencing (WGS) data for six Greek sheep breeds, namely Chios, Kalarritiko, Karagouniko, Lesvos, Serres, and Thraki breeds. We performed variant discovery analysis on the data and identified 23,526,500 high-quality variants. The high average variant depth (148.7X ± 28.3) and low Single Nucleotide Polymorphism (SNP) density (1 variant per 111 bases) in the callset demonstrated the high quality of the data. The vast majority of the variants (97.46%) were located in non-coding regions, while a small percentage (1.32%) was positioned in exonic regions. The overall transition to transversion−Ti/Tv (2.449) and heterozygous to non-reference homozygous−Het/Hom (1.49) ratios further confirmed the callset’s high quality. This dataset comprises the first WGS data for six Greek sheep breeds, providing invaluable information to the Greek agricultural sector for the design and implementation of targeted breeding schemes, for traceability purposes, and for the overall enhancement of the sector, in terms of performance and sustainability. Full article

Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin–antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research. Full article

Salmonella Dublin (S. Dublin) and Salmonella Typhimurium (S. Typhimurium) are commonly linked to bovine salmonellosis. S. Dublin is, however, considered a bovine-adapted serovar for primarily infecting and thriving in cattle. Using S. Typhimurium (a generalist serovar) as a benchmark, this study investigates genomic factors contributing to S. Dublin’s adaptation to cattle hosts in the U.S. A total of 1337 S. Dublin and 787 S. Typhimurium whole-genome sequences from bovine sources were analyzed with CARD (version 4.0.0), ARG-NOTT (version 6), and AMRfinderPlus (version 4.0.3) for antimicrobial resistance (AMR) genes; VFDB and AMRfinderPlus for virulence genes; AMRFinderPlus for stress genes; and Plasmidfinder for plasmids. Existing clonal groups among isolates of the two serovars were also investigated using the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) model. The results revealed minimal genomic variation among S. Dublin isolates. Comparatively, the IncX1 plasmid was somewhat exclusively identified in S. Dublin isolates and each carried an average of four plasmids (p-value < 0.05). Furthermore, S. Dublin isolates exhibited a higher prevalence of AMR genes against key antimicrobials, including aminoglycosides, beta-lactams, tetracyclines, and sulfonamides, commonly used in U.S. cattle production. Additionally, Type VI secretion system genes tssJKLM and hcp2/tssD2, essential for colonization, were found exclusively in S. Dublin isolates with over 50% of these isolates possessing genes that confer resistance to heavy metal stressors, like mercury. These findings suggest that S. Dublin’s adaptation to bovine hosts in the U.S. is supported by a conserved genetic makeup enriched with AMR genes, virulence factors, and stress-related genes, enabling it to colonize and persist in the bovine gut. Full article

Neuropsychiatric disorders are complex conditions with multifactorial etiologies, in which genetics play a pivotal role. Despite significant advancements in psychiatric research, traditional treatment options remain largely symptomatic, focusing on clinical signs without fully addressing the underlying biological causes. However, recent developments in precision medicine—an approach that tailors treatments based on genetic, environmental, and lifestyle factors—hold great promise for transforming the treatment of these disorders. By identifying specific genetic markers and understanding gene–environment interactions, precision medicine can offer more personalized and effective treatments, leading to better patient outcomes. Our primary aim was to explore how integrating genetic data with environmental factors could enhance the understanding and treatment of neuropsychiatric conditions such as schizophrenia, bipolar disorder, and depression. The secondary aim was to examine the potential of pharmacogenomics and gene therapy in improving therapeutic strategies. The results indicate that while significant progress has been made, challenges remain, including the complexity of genetic interactions and the need for more granular phenotypic data. In conclusion, precision medicine has the potential to revolutionize neuropsychiatric treatment by providing individualized care that considers genetic makeup, environmental influences, and lifestyle factors, paving the way for more effective therapies and improved patient outcomes. Full article

Background/Objectives: An individual’s genetic makeup influences their organ development, orofacial structures, and overall health. Though many studies have been conducted to determine the inheritance of oral diseases and conditions, there is a lack of comprehensive research classifying these disorders based on the genetic and environmental etiology. Methods: This systematic review aimed to analyze the existing body of literature using the PubMed and Cochrane databases and answer the following question: “What evidence exists supporting the role of genetic factors in oral conditions?” This systematic–narrative review methodically categorizes oral diseases and conditions based on their genetic or environmental linkages. Each classification is rigorously supported by the peer-reviewed articles and evidence strength, affirming the sufficient validity of the identified associations. Results: This study provides an overview of how genetics can influence oral health, from predisposition to susceptibility to various oral diseases, and the impact of genetic alterations on dental and oral conditions. Additionally, this study discusses the importance of understanding the interplay between genetic and environmental factors to improve oral health outcomes. An enhanced understanding of the impact of genetics on oral health will provide a better understanding of the implications of inherited or de novo genetic mutations and their potential interactions with environmental factors. Conclusions: The data collection and analysis indicate 25 oral conditions with strong genetic components and 2 with moderate genetic contributions (fibrous dysplasia and impacted teeth), while 14 oral conditions seem to have weak genetic contributions. Treatment planning that includes genetic testing and counseling as an approach of precision oral healthcare is encouraged to develop appropriate preventative and timely treatment plans to provide the effective management of patients’ symptoms. Full article

Background/Objectives: Pharmacogenomics is an emerging field in precision medicine that aims to improve patient outcomes by tailoring drug selection and dosage to an individual’s genetic makeup. However, patients in rural communities often cannot take advantage of specialized services such as pharmacogenomics due to various barriers that limit access to healthcare. This article aims to identify the barriers to implementing pharmacogenomic initiatives in rural communities and assess strategies for integrating pharmacogenomics into rural healthcare systems. Methods: This article describes the qualitative research that was conducted using semi-structured interviews with various stakeholders in addition to explaining how strategic frameworks were used to synthesize secondary research. Results: The findings of this article indicated mixed awareness of pharmacogenomics as an option amongst stakeholders, highlighting the need for targeted outreach and education intervention. Solutions such as mail-in testing and telemedicine were determined to be feasible solutions to address various geographical and logistical barriers that exist for rural patients. This article determines that successful strategies will leverage existing infrastructure and prioritize patient care, workflow integration, and adoption. Conclusions: Making pharmacogenomics a viable option for rural patients will take a multi-faceted approach that combines outreach, education, and innovative delivery models to overcome the multiple barriers facing rural communities. Full article

Autophagy, a cellular process essential for maintaining homeostasis, plays a fundamental role in recycling damaged components and in adapting to stress. The dysregulation of autophagy is implicated in numerous human diseases, including cancer, where it exhibits a dual role as both a suppressor and a promoter, depending on the context and the stage of tumor development. The significant sex differences observed in autophagic processes are determined by biological factors, such as genetic makeup and sex hormones. Estrogens, through their interaction with specific receptors, modulate autophagy and influence tumor progression, therapy resistance, and the immune response to tumors. In females, the escape from X inactivation and estrogen signaling may be responsible for the advantages, in terms of lower incidence and longer survival, observed in oncology. Women often show better responses to traditional chemotherapy, while men respond better to immunotherapy. The action of sex hormones on the immune system could contribute to these differences. However, women experience more severe adverse reactions to anticancer drugs. The estrogen/autophagy crosstalk—involved in multiple aspects of the tumor, i.e., development, progression and the response to therapy—deserves an in-depth study, as it could highlight sex-specific mechanisms useful for designing innovative and gender-tailored treatments from the perspective of precision medicine. Full article

Background/Objectives: The interaction of bioactive compounds derived from plants with drugs has become a significant area of investigation due to its potential to improve, reduce, or have no effect on therapeutic outcomes. Due to the dual effect of these interactions, elucidating the underlying mechanisms is essential for establishing a therapeutic strategy. This study emphasizes the significant findings, mechanisms, and clinical implications of drug–plant bioactive interactions. It calls for more studies to seek safe and effective incorporation into clinical practice. Methods: To identify relevant studies, we performed a systematic literature search based on various scientific databases from 11 August 2024 to 30 December 2024. The search will be based on relevant keywords such as synergy, antagonism, plant bioactive compounds, and drug interactions supplemented with secondary terms such as phytochemicals, herb-drug interactions, pharmacokinetics, and pharmacodynamics. Results: Plant bioactives, including polyphenols, flavonoids, alkaloids, and terpenoids, display valuable biological activities that can interact with medications in three principal ways: synergy, additive effects, and antagonism. Synergy occurs when the combined effects of plant chemicals and pharmaceuticals outweigh the sum of their separate effects, increasing therapeutic effectiveness or allowing dosage decrease to reduce adverse effects. Additive effects occur when the combined impact equals the total individual effects, resulting in better outcomes without increasing risk. Antagonism occurs when a plant ingredient reduces or counteracts the effects of a medicine, thereby jeopardizing treatment. In addition, specific interactions may have no discernible effect. The chemical makeup of bioactive chemicals, medication pharmacokinetics, and individual patient characteristics such as genetics and metabolism all impact the intricacy of these interactions. Conclusions: Pharmacokinetics and pharmacodynamics of drugs can be considerably modulated through their interactions with plant bioactive components, which may cause a significant decrease in efficacy or increase in toxicity of therapeutic agents. More studies are needed to clarify mechanisms of action, prove clinical relevance, and create guidelines for safe co-administration. This integrative approach can mitigate those risks and allow for therapeutic optimization by introducing pharmacogenomics and personalized medicine approaches. Full article