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PeerJ 2024Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere...
Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' () and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly ( < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).
Topics: Soil Microbiology; Chromium; Rhizosphere; Soil Pollutants; Edible Grain; Stress, Physiological; Fungi; Microbiota; Bacteria
PubMed: 38952992
DOI: 10.7717/peerj.17461 -
PeerJ 2024FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by...
BACKGROUND
FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the genes in maize are not well characterized and their function in drought are unknown.
METHOD
The FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR).
RESULTS
A total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of contain abundant abiotic stress-responsive and hormone-respovensive -elements. Among them, drought-responsive -elements are quite abundant. were expressed in all tissues detected, but the expression level varies widely. The expression of were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most were down-regulated in root after PEG-simulated drought stress.
CONCLUSIONS
We performed a genome-wide and systematic identification of genes in maize. And most were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of in response to drought stress.
Topics: Zea mays; Droughts; Gene Expression Regulation, Plant; Plant Proteins; Stress, Physiological; Transcription Factors
PubMed: 38952979
DOI: 10.7717/peerj.17684 -
PeerJ 2024Mitochondrial creatine kinase (MtCK) plays a pivotal role in cellular energy metabolism, exhibiting enhanced expression in various tumors, including colorectal cancer...
BACKGROUND
Mitochondrial creatine kinase (MtCK) plays a pivotal role in cellular energy metabolism, exhibiting enhanced expression in various tumors, including colorectal cancer (CRC). Creatine kinase mitochondrial 2 (CKMT2) is a subtype of MtCK; however, its clinical significance, biological functions, and underlying molecular mechanisms in CRC remain elusive.
METHODS
We employed immunohistochemical staining to discern the expression of CKMT2 in CRC and adjacent nontumor tissues of patients. The correlation between CKMT2 levels and clinical pathological factors was assessed. Additionally, we evaluated the association between CKMT2 and the prognosis of CRC patients using Kaplan-Meier survival curves and Cox regression analysis. Meanwhile, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect the expression levels of in different CRC cell lines. Finally, we explored the biological functions and potential molecular mechanisms of CKMT2 in CRC cells through various techniques, including qRT-PCR, cell culture, cell transfection, western blot, Transwell chamber assays, flow cytometry, and co-immunoprecipitation.
RESULTS
We found that CKMT2 was significantly overexpressed in CRC tissues compared with adjacent nontumor tissues. The expression of CKMT2 is correlated with pathological types, tumor size, distant metastasis, and survival in CRC patients. Importantly, CKMT2 emerged as an independent prognostic factor through Cox regression analysis. Experimental downregulation of expression in CRC cell lines inhibited the migration and promoted apoptosis of these cells. Furthermore, we identified a novel role for CKMT2 in promoting aerobic glycolysis in CRC cells through interaction with lactate dehydrogenase B (LDHB).
CONCLUSION
In this study, we found the elevated expression of CKMT2 in CRC, and it was a robust prognostic indicator in CRC patients. CKMT2 regulates glucose metabolism amplifying the Warburg effect through interaction with LDHB, which promotes the growth and progression of CRC. These insights unveil a novel regulatory mechanism by which CKMT2 influences CRC and provide promising targets for future CRC therapeutic interventions.
Topics: Humans; Colorectal Neoplasms; Warburg Effect, Oncologic; Male; Female; Cell Line, Tumor; Prognosis; Creatine Kinase, Mitochondrial Form; Disease Progression; L-Lactate Dehydrogenase; Middle Aged; Cell Proliferation; Apoptosis; Gene Expression Regulation, Neoplastic
PubMed: 38952967
DOI: 10.7717/peerj.17672 -
Data in Brief Aug 2024The large-fruited fresh-market tomato cultivated in the U.S. represents a unique fruit market class of contemporary (modern) tomatoes for direct consumption. The genomes...
The large-fruited fresh-market tomato cultivated in the U.S. represents a unique fruit market class of contemporary (modern) tomatoes for direct consumption. The genomes of F plants from crosses between inbred contemporary U.S. large-fruited fresh-market tomatoes were sequenced. 516 F individual plants randomly selected from five different biparental segregating populations were used for DNA extraction. The polymerase chain reaction (PCR)-free, paired-end (2 × 150 bp) sequencing libraries (350 bp DNA fragment length) were prepared, and sequenced on average 5 Gb for each plant using the Illumina next-generation sequencing technologies [1,2]. Raw Illumina reads with adapter contamination and/or uncertain nucleotides constitute (Ns, >10 % of either read; Q-score 5 or lower, >50 % of either read) were removed. This data article will contribute to improving our knowledge of the genetic recombination and variation in tomato.
PubMed: 38952950
DOI: 10.1016/j.dib.2024.110567 -
The Canadian Veterinary Journal = La... Jul 2024A 21-year-old retired polo Argentinian thoroughbred horse from a teaching herd was presented for a routine bronchoalveolar lavage demonstration, during which an...
A 21-year-old retired polo Argentinian thoroughbred horse from a teaching herd was presented for a routine bronchoalveolar lavage demonstration, during which an incidental finding of a granulomatous mass on the dorsal aspect of the epiglottis was made. was suspected from a histological section obtained from an initial biopsy, and the mass was removed laser surgery for cytology and PCR. Sequencing of the PCR amplicons confirmed the diagnosis of A treatment protocol of nebulized voriconazole for 10 d postoperatively was used. Long-term follow-up required 2 more laser surgeries plus oral fluconazole to resolve the remaining fungal spores. However, 2.5 y later, there was no evidence of remaining fungal spores. Key clinical message: Horses from endemic regions can potentially be exposed to Based on its travel history, this horse may have contracted the infection in South America, California, or Alberta. Treatments administered, including diode laser resection, voriconazole antifungal nebulization, and oral fluconazole administration, were successful but required repeated interventions.
Topics: Animals; Horses; Horse Diseases; Voriconazole; Antifungal Agents; Male; Rhinosporidiosis; Nebulizers and Vaporizers; Laser Therapy; Polymerase Chain Reaction; Laryngeal Diseases
PubMed: 38952752
DOI: No ID Found -
International Journal of Nanomedicine 2024Implants are widely used in the field of orthopedics and dental sciences. Titanium (TI) and its alloys have become the most widely used implant materials, but...
BACKGROUND
Implants are widely used in the field of orthopedics and dental sciences. Titanium (TI) and its alloys have become the most widely used implant materials, but implant-associated infection remains a common and serious complication after implant surgery. In addition, titanium exhibits biological inertness, which prevents implants and bone tissue from binding strongly and may cause implants to loosen and fall out. Therefore, preventing implant infection and improving their bone induction ability are important goals.
PURPOSE
To study the antibacterial activity and bone induction ability of titanium-copper alloy implants coated with nanosilver/poly (lactic-co-glycolic acid) (NSPTICU) and provide a new approach for inhibiting implant-associated infection and promoting bone integration.
METHODS
We first examined the in vitro osteogenic ability of NSPTICU implants by studying the proliferation and differentiation of MC3T3-E1 cells. Furthermore, the ability of NSPTICU implants to induce osteogenic activity in SD rats was studied by micro-computed tomography (micro-CT), hematoxylin-eosin (HE) staining, masson staining, immunohistochemistry and van gieson (VG) staining. The antibacterial activity of NSPTICU in vitro was studied with gram-positive and gram-negative bacteria. was used as the test bacterium, and the antibacterial ability of NSPTICU implanted in rats was studied by gross view specimen collection, bacterial colony counting, HE staining and Giemsa staining.
RESULTS
Alizarin red staining, alkaline phosphatase (ALP) staining, quantitative real-time polymerase chain reaction (qRT-PCR) and western blot analysis showed that NSPTICU promoted the osteogenic differentiation of MC3T3-E1 cells. The in vitro antimicrobial results showed that the NSPTICU implants exhibited better antibacterial properties. Animal experiments showed that NSPTICU can inhibit inflammation and promote the repair of bone defects.
CONCLUSION
NSPTICU has excellent antibacterial and bone induction ability, and has broad application prospects in the treatment of bone defects related to orthopedics and dental sciences.
Topics: Animals; Anti-Bacterial Agents; Osteogenesis; Polylactic Acid-Polyglycolic Acid Copolymer; Mice; Staphylococcus aureus; Coated Materials, Biocompatible; Rats, Sprague-Dawley; Escherichia coli; Cell Differentiation; Prostheses and Implants; Alloys; Rats; Titanium; Silver; Cell Proliferation; Copper; Male; X-Ray Microtomography; Cell Line; Metal Nanoparticles
PubMed: 38952675
DOI: 10.2147/IJN.S456906 -
Cureus Jun 2024Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the... (Review)
Review
Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the efficacy of antimicrobial agents. While foundational in microbial identification, traditional cultural methods are often laborious, time-consuming, and limited in their ability to detect AMR markers. In response to these challenges, innovative paradigms have emerged, leveraging advances in molecular biology, genomics, proteomics, nanotechnology, and bioinformatics. This comprehensive review provides an overview of innovative approaches beyond traditional cultural methods for microbial detection and AMR surveillance. Molecular-based techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer enhanced sensitivity and specificity, enabling the rapid identification of microbial pathogens and AMR determinants. Mass spectrometry-based methods provide rapid and accurate detection of microbial biomarkers, including matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and biosensor technologies. Nanotechnology approaches, such as nanoparticle-based assays and nanopore sequencing, offer novel platforms for sensitive and label-free detection of pathogens and AMR markers. Embracing these innovative paradigms holds immense promise for improving disease diagnosis, antibiotic stewardship, and AMR containment efforts. However, challenges such as cost, standardization, and integration with existing healthcare systems must be addressed to realize the full potential of these technologies. By fostering interdisciplinary collaboration and innovation, we can strengthen our ability to detect, monitor, and combat AMR, safeguarding public health for generations.
PubMed: 38952583
DOI: 10.7759/cureus.61476 -
Pakistan Journal of Medical Sciences Jul 2024This case report is of herpes zoster which is caused by Varicella zoster virus (VZV). The patient was presented with acute renal failure associated with intravenous...
This case report is of herpes zoster which is caused by Varicella zoster virus (VZV). The patient was presented with acute renal failure associated with intravenous acyclovir administration for its management. A 50 years old man visited the hospital with rashes on his back. The serum sample was positive for anti-VZV IgM via Enzyme Linked Immunosorbent Assay (ELISA), and vesicular swab for VZV via polymerase chain reaction (PCR). Phylogenetic analysis identified it as M2-genotype. Patient was treated with intravenous acyclovir administration, which led to acute renal failure. Later with shift to oral acyclovir, renal functions were restored. Elderly patients with reactivation of VZV in Pakistan are at risk to contract herpes zoster. Acyclovir is drug of choice via intravenous route was found to be nephrotoxic, however oral acyclovir was safe and effective. This is first report on pathogenic VZV genotype from Pakistan and is presented to highlight that the herpes zoster cases of elderly patients' treatment option need to be revisited.
PubMed: 38952536
DOI: 10.12669/pjms.40.6.8764 -
Pakistan Journal of Medical Sciences Jul 2024To screen gene variants and predict potential role of the identified variants in breast cancer.
OBJECTIVE
To screen gene variants and predict potential role of the identified variants in breast cancer.
METHOD
This case-control study included two hundred and fifty breast cancer patients and equal healthy individuals from the Federal Breast Cancer Screening Centre, Pakistan Institute of Medical Sciences, Islamabad from March 2021- January 2023. Demographic data was collected through questionnaires and clinical data was assessed using mammograms, ultrasound, histopathology and immunohistochemistry reports. Polymerase chain reaction and Sanger sequencing approach were used to detect variants in gene. analyses were carried out to predict mutation effect, miRNA binding site alterations and change in mRNA structure and stability.
RESULTS
Invasive ductal carcinoma was the most prevalent type of breast cancer. Old age [OR: 2.8149 (1.5995 to 4.9538) value = 0.0003] and family history [OR: 4.3186 (1.7336 to 10.7581) value = 0.001] were significant breast cancer risk. Six variants were identified. Two novel missense variants, Chr17:43082553A>T and Chr17:43093710A>T were predicted deleterious as these disrupted interaction with PALB2 and importin alpha's NLS2 site, respectively. analysis predicted the loss of hsa-miR-1179 binding site due to variant Chr17:43093220T>C. Moreover, four variants were predicted to affect the mRNA structure and stability.
CONCLUSION
Two novel variants were predicted to be pathogenic. analysis predicted the loss of miRNA binding site along with change in mRNA secondary structure plus stability, possible mechanisms for oncogenesis. Further, expressional studies are required to confirm gene dysregulation in breast cancer due to these variants.
PubMed: 38952531
DOI: 10.12669/pjms.40.6.8761 -
Journal of Biosciences 2024Owing to the lack of effective vaccines, current control measures and eradication strategies for the African swine fever virus (ASFV) rely on early detection and... (Comparative Study)
Comparative Study
Owing to the lack of effective vaccines, current control measures and eradication strategies for the African swine fever virus (ASFV) rely on early detection and stringent stamping-out procedures. In the present study, we developed two independent isothermal amplification assays, namely, loop-mediated isothermal amplification (LAMP) and polymerase spiral reaction (PSR), for quick visualization of the ASFV genome in clinical samples. Additionally, a quantitative real-time PCR (qRT-PCR)-based hydrolysis probe assay was developed for comparative assessment of sensitivity with the developed isothermal assays. The analytical sensitivity of the LAMP, PSR, and qRT-PCR was found to be 2.64 ×10 copies/µL, 2.64 ×10 copies/µL, and 2.64 ×10 copies/µL, respectively. A total of 165 clinical samples was tested using the developed visual assays. The relative accuracy, relative specificity, and relative diagnostic sensitivity for LAMP vs PSR were found to be 95.37% vs 102.48%, 97.46% vs 101.36%, and 73.33% vs 113.33%, respectively.
Topics: African Swine Fever Virus; Animals; Nucleic Acid Amplification Techniques; Swine; African Swine Fever; Sensitivity and Specificity; Real-Time Polymerase Chain Reaction; Molecular Diagnostic Techniques; Genome, Viral
PubMed: 38952078
DOI: No ID Found