Search Results (68)

To dissect the molecular mechanisms underlying chicken cecal development, this study used Liangshan Yanying chickens (a local slow-growing breed) and Arbor Acres (AA) chickens (a fast-growing breed) as experimental models. Cecal tissues were collected from healthy chickens at 1, 14, and 28 days of age (n = 10 per breed per day of age) to measure cecal length and perform transcriptome sequencing. Through the screening of differentially expressed genes (DEGs), functional enrichment analysis, construction of protein–protein interaction (PPI) networks, and qRT-PCR validation, temporal changes in cecal development between the two breeds were systematically compared. Results showed that cecal length of both breeds increased significantly with age (p < 0.05), with significant differences between breeds. A total of 18 high-quality samples were obtained from transcriptome analysis (Q30 ≥ 93%), with a mapping efficiency of 86.2–90.5%. The number of DEGs was highest between 1 and 28 days of age (1844 DEGs in Liangshan Yanying chickens and 1747 DEGs in AA chickens), and the number of inter-breed DEGs reached 2133 at 28 days of age. A total of 70 DEGs with consistent expression trends were identified (22 upregulated and 48 downregulated), which were enriched in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways such as “B cell activation”, “peptide transport”, and “bile acid metabolism”. qRT-PCR validation indicated that the expression trends of genes (e.g., CD79B, IRF4) were highly consistent with sequencing results (R² = 0.91). PPI network analysis suggested that SLC15A1, ACE, and ENPEP were key hub genes, forming a “transport–metabolism” synergistic module. This study reveals the temporal dynamics of chicken cecal development and the molecular basis of inter-breed differences, providing a theoretical foundation for broiler genetic improvement. Full article

The Na⁺/K⁺-ATPase (NKA) gene encodes a critical membrane transporter that maintains cellular ion homeostasis and plays a pivotal role in osmoregulation and salinity adaptation of aquatic organisms. In this study, we identified and validated SNP markers in the NKA gene associated with low-salinity tolerance in Scylla paramamosain. Four candidate SNPs (g.72037G>T, g.72122G>C, g.74293G>T, and g.74433G>T) were screened and genotyped in low-salinity tolerant and intolerant groups. Association analysis revealed that mutant genotypes at all four loci were significantly enriched in the tolerant group (p < 0.05), with odds ratios (OR) > 1. The tolerant group exhibited higher genetic diversity parameters than the intolerant group. Haplotype analysis showed the GGGG haplotype was dominant in the intolerant group, whereas the other haplotypes were mainly enriched in the tolerant group. The NKA expression in the mutant genotypes was significantly higher than that in the wild genotypes by qRT-PCR. For tolerant individuals, the fast-growing group exhibited higher mutation frequencies than the slow-growing group. Multi-locus analysis achieved substantially more discrimination accuracy than single-locus analysis. These findings demonstrated that these SNPs could be candidate molecular markers for breeding programs in S. paramamosain in low-salinity environments, helping to identify individuals with enhanced salinity tolerance and supporting sustainable aquaculture practices. Full article

Foodborne pathogens remain a global public health concern, and antimicrobial resistance increases their impact. In mass-gathering cities such as Al-Madinah Al-Munawarah, contaminated ready-to-eat (RTE) fast foods can contribute to both local transmission and international spread. In this study, 300 RTE fast food samples, including shawarma, burgers, fried chicken, sandwiches, and salads, were collected from international franchises, local restaurants, and street vendors. Pathogens were identified using conventional culture combined with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing followed CLSI guidelines, and real-time PCR confirmed species identity and screened resistance determinants. Principal component analysis (PCA) and dendrogram clustering were used to assess diagnostic discrimination. Among the 300 samples, 129 (43.0%) were culture positive. The most common pathogens were Staphylococcus aureus (14.3%) and Escherichia coli (13.0%), followed by Salmonella spp. (9.0%) and Acinetobacter baumannii (6.7%). About 35% of S. aureus isolates were methicillin resistant (MRSA), and 85% of A. baumannii carried OXA-type carbapenemase genes. MALDI-TOF MS achieved 96.1% score-based identification and, with PCA, showed strong interspecies separation. PCR confirmed species identity and detected widespread resistance genes, with genotype–phenotype concordance of at least 80%. Overall, 60.5% of isolates were multidrug resistant. RTE fast foods in Al-Madinah represent reservoirs of MDR pathogens, including carbapenemase-producing A. baumannii. The combined use of MALDI-TOF MS and real-time PCR established a rapid and scalable workflow that provided reliable identification and resistance profiling in less than 24 h, compared with 48 to 72 h for conventional methods. This approach supports One Health surveillance in high-risk food settings and strengthens preparedness for mass gatherings. Full article

Current gene-based PCR diagnostics involving reverse-transcription polymerase chain reaction (RT-PCR) require at least several hours, expensive tools, and complicated sample collection methods to obtain results. A test for detecting volatile organic compounds (VOCs) in exhaled breath is advantageous as a simple, non-invasive, and fast screening method. In this study, a VOC detection system of array sensors was applied for the classification of breath control and COVID-19 virus infection. The ability to classify VOCs in the breath with COVID-19 virus infection has been studied with two metal-oxide (MOX) gas sensor arrays, commercially available sensors, and in-house sensors. The dataset of gas response signals from the array-type semiconductive gas sensors of the VOC detection system was analyzed using machine learning; principal component analysis (PCA) was used as a dimensionality-reduction method, and random forest (RF) and a convolutional neural network (CNN) were used as classification methods for the VOC concentration patterns in each breath. For the RF model, the accuracy results for the classification by two gas sensor arrays was 0.917 and this was improved by CO₂ calibration to 0.967, and the feature importance analysis revealed the importance of specific gas sensors. For the CNN, an input layer of a transformed gray-scale image with the shape of 12 data points × 8 sensors was used, and its accuracy reached 100% within a relatively small number of epochs, demonstrating a short training time, which is beneficial for breath detectors or e-nose devices. Full article

In recent decades, the problem of resistant strains, which present resistance to different types of antimicrobials, has increased. Klebsiella pneumoniae is one of the most important species that exhibits an acquired resistance phenotype to at least one agent in three or more classes of antimicrobials and is thus characterized as a multidrug-resistant bacterium (MDR). 98 nosocomial strains of K. pneumoniae were isolated during the pre-COVID-19 period, and more specifically, from February 2015 to March 2019, were analyzed for the detection of class A, D, and B carbapenemase genes. The existence of KPC, OXA-48 like, IMP, VIM, and NDM carbapenemases has been examined. The immunochromatography showed that NDM carbapenemases are more frequently detected in the samples, reaching a percentage of 30.7%, while correspondingly the percentage for VIM carbapenemases was 7.68% among the strains with resistant phenotypes. No strain with carbapenemase IMP was found. Real-time multiplex polymerase chain reaction (PCR) showed, in contrast to immunochromatography kits, that a high percentage of bacterial isolates (94.26%) carry NDM and VIM carbapenemase genes, while no IMP carbapenemase genes were detected. Regarding the KPC enzymes, the immunochromatography kits showed that KPC positive strains are reaching 53.1%, and OXA-48 positive strains are reaching 3.1% among the strains with resistant phenotypes. Real-time multiplex polymerase chain reaction revealed a much higher percentage of 89.6% KPC positive isolates and a percentage of 14.6% OXA-48 carbapenemase producers. The aforementioned results indicate the dominance of the Multiplex Real-Time PCR as a “gold standard” method. This study could not fully support the usefulness of rapid immunochromatographic tests as a fast and useful diagnostic tool in the laboratory daily routine, as per the results of previous studies. Thus, more studies need to be conducted in this field to introduce these rapid tests safely into the daily laboratory workflow as a screening tool. Additionally, this study underlines the predominance of KPC enzymes from clinical isolates of ICUs and a significant shift over the OXA-48 like enzymes that are not limited to the ICU environment. Full article

The pathogenesis of temporomandibular joint osteoarthritis (TMJOA) is poorly understood. This study aims to identify key biomarkers involved in TMJOA progression and explore potential therapeutic drugs through transcriptome analysis. A rat TMJOA model was established by bilateral injection of monosodium iodoacetate (MIA) into the TMJ cavities. Model validation was conducted using hematoxylin-eosin (HE) and Safranin O-Fast Green (SO-FG) staining. Differentially expressed genes (DEGs) were identified through RNA sequencing. Key pathways were explored using Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Reactome pathway analyses. DEGs were clustered using MCODE analysis, and Hexokinase 3 (HK3) was identified as a key gene, which was further validated by qPCR. Potential drugs targeting HK3 were selected using the DGIdb database, and molecular docking was conducted to confirm drug-HK3 binding affinity. The TMJOA model was successfully established. RNA-seq analysis revealed 160 upregulated and 97 downregulated DEGs. KEGG, GO, and Reactome pathways analysis identified dysregulated pathways. The top five clusters of DEGs were identified, with HK3 emerging as the key gene. qPCR validation confirmed upregulated HK3 mRNA expression in TMJOA cartilage compared to the control group. Three drugs (MK8719, LY3372689, and Thiamet-G) targeting HK3 were identified through the Drug-Gene Interaction Database (DGIdb) screening, and molecular docking demonstrated high binding affinity between these drugs and HK3. This study suggests that HK3 may play a role in TMJOA progression and could serve as a potential biomarker for inflammatory progression in TMJOA. Targeting HK3 may offer new diagnostic and therapeutic strategies for TMJOA management. Full article

Objectives: Sex-based disparities in COVID-19 outcomes are well-documented, with men experiencing greater acute severity and women showing increased vulnerability to post-viral syndromes. However, longitudinal immunometabolic trajectories in vaccinated individuals remain underexplored. In this study, sex-based differences in long-term metabolic, endocrine, renal, cardiovascular, and inflammatory responses were investigated among vaccinated individuals recovering from SARS-CoV-2 infection. Methods: This retrospective single-center cohort study included 426 adults (199 females, 227 males) with PCR-confirmed symptomatic COVID-19 and at least two vaccine doses. Serial assessments were conducted at baseline, 18-, 24-, and 30-month post-infection. Parameters included fasting glucose, HbA1c, lipid profile, thyroid function, renal markers, CRP, D-dimer, fibrinogen, troponin, and hematologic indices. Statistical analyses assessed longitudinal changes and sex-stratified correlations. Results: Fasting glucose and HbA1c levels significantly declined over time, more prominently in males. Glucose correlated with age and BMI only in females. Lipid levels remained largely unchanged, although males had higher baseline triglycerides. Females showed rising TSH levels and persistently lower free T3; males exhibited higher creatinine, urea, and troponin levels throughout. Inflammatory markers declined significantly in both sexes, with males displaying higher CRP and troponin, and females showing sustained fibrinogen elevation and a temporary lymphocyte surge. D-dimer was elevated in females at the 30-month point. Conclusions: Sex-specific physiological recovery patterns were evident among vaccinated COVID-19 survivors. Males exhibited earlier metabolic and cardiac alterations, while females had more persistent endocrine and inflammatory shifts. These findings underscore the need for sex-tailored long-term monitoring strategies prioritizing early metabolic and cardiac screening in men and prolonged immunoendocrine surveillance in women. Full article

(1) Background: Epidemiological studies link ozone (O₃) exposure to diabetes risk, but mechanisms and early biomarkers remain unclear. (2) Methods: Female mice exposed to 0.5/1.0 ppm O₃ were assessed for glucose tolerance and HOMA (homeostasis model assessment) index. Genes related to impaired glucose tolerance and insulin resistance were screened through the Comparative Toxicogenomics Database (CTD), and verified using quantitative real-time PCR. In addition, liver histopathological observations and the determination of basic biochemical indicators were conducted, and targeted metabolomics analysis was performed on the liver to verify glycogen levels and gene expression. In vitro validation was conducted with HepG2 and Min6 cell lines. (3) Results: Fasting blood glucose and insulin resistance were elevated following O₃ exposure. Given that the liver plays a critical role in glucose metabolism, we further investigated hepatocyte apoptosis and alterations in glycogen metabolism, including reduced glycogen levels and genetic dysregulation. Metabolomics analysis revealed abnormalities in fructose metabolism and glycogen synthesis in the livers of the O₃-exposed group. In vitro studies demonstrated that oxidative stress enhances both liver cell apoptosis and insulin resistance in pancreatic islet β cells. (4) Conclusions: O₃ triggers prediabetes symptoms via hepatic metabolic dysfunction and hepatocyte apoptosis. The identified metabolites and genes offer potential as early biomarkers and therapeutic targets. Full article

Background: Effective early risk stratification in COVID-19 remains a critical challenge in emergency care, particularly due to the limitations of RT-PCR testing, including delayed processing and false negatives. There is an unmet need for imaging tools that are fast, reliable, and safe for repeated use in acute clinical settings. Methods: In this prospective, multicenter study, over 1000 patients hospitalized with suspected or confirmed COVID-19 were initially screened. A total of 555 patients with PCR-confirmed infection were ultimately included for analysis. All participants underwent low-dose chest CT (LDCT) at admission. Pulmonary involvement was assessed using the chest CT severity score (CTSS) based on a unified protocol. CTSS values were analyzed in relation to ICU admission, in-hospital mortality, demographic data, oxygen saturation, dyspnea scores, and laboratory markers (CRP, LDH, lymphocyte, and neutrophil counts). Imaging was interpreted by board-certified radiologists under harmonized reporting standards. Results: CTSS values ≥13 and ≥15 were significantly associated with ICU admission and in-hospital mortality, respectively (p < 0.01). Strong correlations were observed between the CTSS and CRP, LDH, and dyspnea scores, with negative correlations to oxygen saturation and lymphocyte count. The standardized LDCT protocol ensured consistent image quality and minimized radiation exposure. Conclusions: LDCT combined with the CTSS provides a robust, reproducible, and radiation-sparing method for emergency risk stratification in COVID-19. Its high clinical utility supports deployment in frontline triage systems and future AI-enhanced diagnostic workflows. Full article

Talaromycosis (TM) is an invasive fungal infection caused by Talaromyces marneffei (T. marneffei). It has high morbidity and mortality rates, particularly among immunocompromised people. Globally, approximately 17,300 cases and 4900 deaths are reported annually. TM often has vague clinical signs with limited current tests, leading to misdiagnosis, incorrect treatments, or the long-term use of expensive antifungal drugs, which raises healthcare costs and patient risks. Although accurate diagnosis is key for starting the right antifungal therapy and improving outcomes, there are not enough reliable and fast tests. Recent progress with monoclonal antibodies (mAbs) that have high specificity for antigens may boost diagnostic accuracy and cut misdiagnosis rates. This review explores current ways to diagnose TM, including culture, histopathology, and molecular methods such as polymerase chain reaction (PCR) and antigen detection. We also discuss the merits and weaknesses of each method and highlight how mAbs may help diagnose TM. We searched PubMed, Web of Science, and Google Scholar for English-language papers (1990—1 January 2025) using “Talaromycosis” OR “Talaromyces marneffei” plus diagnostic terms (‘diagnosis’, ‘molecular diagnostics’, ‘monoclonal antibody’, ‘lateral flow’, ‘antigen detection’, and ‘fungal diagnosis’). After deduplication and relevance screening, studies with original data or substantive discussion on T. marneffei diagnostics or mAb development were retained to inform this narrative review. Full article

Background/Objectives: Vancomycin-resistant enterococci (VRE) are one of the leading causes of antibiotic-resistant infections in the hospital setting worldwide, and this has become a major issue, because most patients infected with this strain are difficult to treat. Multiplex real-time polymerase chain reaction (RT PCR) is an advantageous technique that can amplify multiple targets in a single reaction, and can be used to quickly detect specific targets in VRE within two hours, starting from suspected colonies of bacterial cultures, without sample preparation. Methods: In this study, we selected the glycopeptide/vancomycin resistance genes that are most common in clinical settings, vanA and vanB, in combination with the species markers ddl_faecium and ddl_faecalis for the most common VRE species—Enterococcus faecium and Enterococcus faecalis. Results: DNA from forty clinical VRE strains was prepared using a fast and economic heat lysis method, and a multiplex real-time PCR assay was optimized and carried out subsequently. The results were in concordance with the results from recombinase polymerase amplification (RPA) of the same VRE samples. Conclusions: Multiplex RT PCR and RPA for VRE detection proffers a second method for the confirmation of vancomycin resistance, and it can be developed as a fast screening assay for patients before admission into high-risk settings. Full article

Spinal muscular atrophy (SMA) and severe T- and/or B-cell lymphopenias (STBCL) in the form of severe combined immunodeficiencies (SCID) or X-linked agammaglobulinemia (XLA) are rare but potentially fatal pathologies. In January 2021, we initiated the first pilot study in Spain to evaluate the efficacy of a very early detection technique for SMA and SCID. RT–PCR was performed on prospectively collected dried blood spots (DBSs) from newborns in Western Andalusia (Spain). Internal and external controls (SCID, XLA and SMA) were included. The determination of SMA was relative (positive/negative) and that of TRECs and KRECs was quantitative (copies/punch). A total of 14.035 prospective samples were analysed. All controls were correctly identified while no cases of SMA or SCID/XLA were prospectively identified. DBS analysis of infants with suspected SMA or STBCL that presented to our centre showed pathological values in two cases each for SMA and SCID and one for XLA, all of them being subsequently confirmed genetically. In this prospective pilot study, no infants with SMA or STBCL were detected; however, the technique applied here was shown to be reliable and fast, further supporting the benefits and need to include SMA and SCID in national newborn screening (NBS) programs, as it will allow early supportive and curative therapy. Full article

The substitution of ingredients with Salmonidae, particularly Salmo salar, has led to widespread reports of financial losses and health risks globally, emphasizing the urgent need for the development of a rapid and precise method for species identification. The aim of the present study was to develop a novel method for the rapid screening of Salmonidae ingredients and the accurate detection of S. salar simultaneously using multiplex real-time PCR coupled with melting curve analysis. Specifically, primer sets specific for S. salar and Salmonidae were cross-confirmed. Moreover, the reaction system and conditions of a real-time duplex PCR were optimized, and the proposed methodology was verified, proving that the assay has good specificity and sensitivity. Clear and distinguishable melting peaks, with expected Tm values of around 80 °C (S. salar) and 84 °C (Salmonidae), were observed for twelve products, proving the presence of S. salar. However, four products were not derived from S. salar, but they could have belonged to another species within the Salmonidae family due to the presence of only one specific melting peak at a Tm value of about 84 °C. Therefore, the novel assay in the present study allows for the fast and accurate screening of Salmonidae ingredients and the detection of S. salar simultaneously. Full article

Spinibarbus sinensis, also known as Qingbo, is an important economic fish in China. However, the detailed mechanisms underlying its growth are still unknown. To excavate the genes and signaling pathways related to its growth, we compared the transcriptome profiles of the hepatopancreas tissues of S. sinensis, with two groups of growth rate for evaluation. An average of 66,304,909 and 68,739,585 clean reads were obtained in the fast growth (FG) and slow growth (SG) group, respectively. The differential gene expression analysis results showed that 272 differentially expressed genes (DEGs) were screened between the FG and SG groups, including 101 up-regulated genes and 171 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results showed that GO terms related to metabolic process, organic substance metabolic process, and catalytic activity were enriched, pathway signals related to steroid biosynthesis and protein digestion and absorption were also detected. Meanwhile, the potential key regulatory genes sst2, fndc4, and cckra related to the growth of S. sinensis were screened. Reverse transcript fluorescence quantitative PCR (RT-qPCR) validation of 18 DEGs associated with growth differences showed that the RT-qPCR results were consistent with RNA-seq analysis, and nine genes, stk31, gpr149, angptl1, fstl1, sik1, ror2, nlrc3, pdlim2, and nav2 were significantly expressed in the FG group. bmp1, stc1, gpatch8, sstrt2, s100a1, ktf6, cckar6, sync1, bhlha15, a total of nine genes were significantly expressed in the SG group. This study provides basic information for improving the growth characteristics of S. sinensis and the functional research of candidate genes. Full article

Given the proven zoonotic potential of the intestinal protozoan Blastocystis sp., a fast-growing number of surveys are being conducted to identify potential animal reservoirs for transmission of the parasite. Nevertheless, few epidemiological studies have been conducted on farmed animals in Egypt. Therefore, a total of 1089 fecal samples were collected from herbivores (sheep, goats, camels, horses, and rabbits) in six Egyptian governorates (Dakahlia, Gharbia, Kafr El Sheikh, Giza, Aswan, and Sharqia). Samples were screened for the presence of Blastocystis sp. by real-time PCR followed by sequencing of positive PCR products and phylogenetic analysis for subtyping of the isolates. Overall, Blastocystis sp. was identified in 37.6% of the samples, with significant differences in frequency between animal groups (sheep, 65.5%; camels, 62.2%; goats, 36.0%; rabbits, 10.1%; horses, 3.3%). Mixed infections were reported in 35.7% of the Blastocystis sp.-positive samples. A wide range of subtypes (STs) with varying frequency were identified from single infections in ruminants including sheep (ST1–ST3, ST5, ST10, ST14, ST21, ST24, ST26, and ST40), goats (ST1, ST3, ST5, ST10, ST26, ST40, ST43, and ST44), and camels (ST3, ST10, ST21, ST24–ST26, ST30, and ST44). Most of them overlapped across these animal groups, highlighting their adaptation to ruminant hosts. In other herbivores, only three and two STs were evidenced in rabbits (ST1–ST3) and horses (ST3 and ST44), respectively. The greater occurrence and wider genetic diversity of parasite isolates among ruminants, in contrast to other herbivores, strongly suggested that dietary habits likely played a significant role in influencing both the colonization rates of Blastocystis sp. and ST preference. Of all the isolates subtyped herein, 66.3% were reported as potentially zoonotic, emphasizing the significant role these animal groups may play in transmitting the parasite to humans. These findings also expand our knowledge on the prevalence, genetic diversity, host specificity, and zoonotic potential of Blastocystis sp. in herbivores. Full article