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HER2, encoded by the ERBB2 gene, is an important druggable driver of human cancer gaining increasing importance as a therapeutic target in urothelial carcinoma (UC). The genomic underpinnings of HER2 overexpression in ERBB2 nonamplified UC are poorly defined. To address this knowledge gap, we investigated 172 UC tumors from patients treated at the University of California San Francisco, using immunohistochemistry and next-generation sequencing. We found that GATA3 and PPARG copy number gains individually predicted HER2 protein expression independently of ERBB2 amplification. To validate these findings, we interrogated the Memorial Sloan Kettering/The Cancer Genome Atlas (MSK/TCGA) dataset and found that GATA3 and PPARG copy number gains individually predicted ERBB2 mRNA expression independently of ERBB2 amplification. Our findings reveal a potential link between the luminal marker HER2 and the key transcription factors GATA3 and PPARG in UC and highlight the utility of examining GATA3 and PPARG copy number states to identify UC tumors that overexpress HER2 in the absence of ERBB2 amplification. In summary, we found that an increase in copy number of GATA3 and PPARG was independently associated with higher ERBB2 expression in patient samples of UC. This finding provides a potential explanation for HER2 overexpression in UC tumors without ERBB2 amplification and a way to identify these tumors for HER2-targeted therapies.

The recently proposed concept of electric chiral magnonic resonator (ECMR) has been extended to include usage of spin–orbit torques (SOT). Unlike the original version of ECMR which was based on voltage controlled magnetic anisotropy (VCMA), the spin wave amplification power by this new version of ECMR (pumped by SOT) no longer depends on the phase of the incident wave, which is highly desirable from an application point of view. The performance of the SOT pumped ECMR has been compared with the case of amplification by applying SOT pumping directly to a waveguide (without any ECMR involved). It is argued that at the expense of narrowing the bandwidth (i.e., slower amplifier response), the advantage of the former configuration (amplification by a SOT pumped ECMR) over the latter (amplification by direct SOT pumping the waveguide) is to offer gain, while at the same time, maintaining system stability (avoidance of auto-oscillations). Non-linear behavior of the SOT pumped ECMR has been analyzed. It is demonstrated that by cascading a SOT ECMR operating in an off-resonance mode together with a VCMA biased passive ECMR, it is possible to produce a magnonic neuron with a transmitted signal magnitude larger than the input in the firing state. [ABSTRACT FROM AUTHOR]

Context.--: Primary thoracic neoplasms are rare in children, whereas nonneoplastic mass lesions or cysts and metastases are more common, and there is a relative paucity of comprehensive histopathologic and molecular data. Objective.--: To define the clinicopathologic spectrum of neoplastic and nonneoplastic diseases observed in resected mass lesions in the chest of pediatric patients, and to identify somatic alterations observed in primary neoplasms. Design.--: Clinicopathologic features of thoracic mass lesions (n = 385) resected from 373 patients aged ≤21 years in a 25-year period (1993-2018) were included. Primary neoplasms having sufficient material were tested by a laboratory-developed comprehensive genomic profiling assay that assesses tumor mutational burden, microsatellite instability, somatic sequence variants, gene amplifications, fusions, and specific transcript variants. Results.--: The most commonly resected space-occupying lesions were nonneoplastic mass lesions and cysts or malformations, resected in 117 (31.4%) and 58 of 373 patients (15.5%) respectively. Metastatic neoplasms were observed in 169 of 373 patients (45.3%; mean age 14.4 years, range 1-21 years); the most common was osteosarcoma (68 of 169; 40.2% of metastases). Primary lung neoplasms occurred in 24 of 373 patients (6.4%; mean age 14.5 years, range 6 months-21 years), and 16 patients had primary extrapulmonary thoracic tumors. Carcinoid tumor was the most common primary lung neoplasm (7 typical, 3 atypical). Molecular testing showed a prevalence of somatic pathogenic or likely pathogenic mutations and copy-number alterations. No fusions or splice variants were identified. Tumors were microsatellite-stable with low tumor mutational burden. Conclusions.--: Resected pediatric thoracic mass lesions are more likely to be metastatic lesions, congenital cysts or malformations, or nonneoplastic lesions compared to primary thoracic neoplasms, which are encountered at a low frequency and tend to have relatively simple genetic profiles. [ABSTRACT FROM AUTHOR]

Polygalacturonases (PG) are the enzymes that cause depolymerization of pectin. In current study, bacterial strain was isolated from rotten sample and then purified. It was screened for endo-polygalacturonase activity using PSAM media. It had shown positive response for endo-PG activity. Bacterial DNA was isolated and 16 S rRNA gene amplification was done using universal primer pair of 8 F and 1492 R. Bacterial strain was also amplified by 16 S rRNA gene for sequencing. BLAST of gene sequence on NCBI database had shown that bacterial isolate was identified as Bacillus pumilus. Endo-polygalacturonase enzyme was produced by submerged fermentation to optimize culture conditions by RSM in JMP-12 software. The optimized parameters had shown maximum endo-polygalacturonase activity of 153.2 U/mL/min after using 3 g of orange peels as substrate, 3 mL of inoculum size, 6.5 pH buffer, 40°C temperature and 3 days of incubation. After optimizing fermentation conditions, endo-polygalacturonase was precipitated using 70 % concentration of ammonium sulfate. This partially precipitated sample was dialyzed with dialysis tube and used to find activity of endo-polygalacturonase (1620.6 U/mL/min). This sample was applied to gel filtration chromatography for further purification. Endo-polygalacturonase activity increased many times 2231.44 U/mL/min after gel filtration. The Molecular weight of endo-polygalacturonase was 46 kDa after SDS PAGE characterization. High Vmax value and alkaliphilic nature of endo-polygalacturonase will make it good candidate for food and feed industry near future. [Display omitted] • A bacterial strain was isolated from rotten sample. • Bacillus pumilus was identified through 16 S rRNA gene sequencing. • Maximum enzyme activity of 153.2 U/mL/min was achieved under optimized conditions. • The characterized endo-polygalacturonase has great potential in industrial applications. • Polygalacturonase had shown maximum activity after column chromatography. [ABSTRACT FROM AUTHOR]

This article reports on two cases of testicular sclerosing stromal tumors (SSTs) that show GLI1 gene alterations. SSTs are neoplasms that were first described in the ovary in 1973 and are characterized by lobulated microscopic appearance. The patients in these cases were aged 35 and 65 years and presented with testicular masses. The tumors demonstrated large areas of hypocellular myxoid/oedematous stroma with scattered hypercellular areas. Both tumors expressed nuclear GLI1. The article suggests that these findings support the existence of rare SSTs in the testis and their potential pathogenesis related to ovarian SSTs. [Extracted from the article]

MicroRNA (miR)-155-5p increases in innate and adaptive immune cells in response to IL-13 and is associated with the severity of asthma. However, little is known about its role in airway structural cells. Bronchial epithelial cells (BECs) isolated from healthy donors and patients with severe asthma were stimulated with IL-13. miR-155-5p expression and release were measured by real-time (RT)-PCR in BECs and in their derived exosomes. Modulation of miR-155-5p in BECs was performed using transfection of miR-155-5p inhibitor and mimic. IL-13 receptor α1 (IL-13Rα1), IL-13Rα2, MUC5AC, IL-8, and eotaxin-1 expression was measured by RT-PCR and Western blot analysis. The BEC repair process was assessed by a wound-healing assay. IL-13Rα1 and IL-13Rα2 expression and downstream pathways were evaluated by Western blot analysis. A dual luciferase assay was used to identify miR-155-5p target genes associated with IL-13R signaling. BECs from patients with severe asthma showed increased expression and exosomal release of miR-155-5p at baseline with amplification by IL-13 stimulation. BECs from patients with asthma expressed more IL-13Rα1 and less IL-13Rα2 than those from healthy donors, and IL-13Rα1 but not IL-13Rα2 induced miR-155-5p expression under IL-13 stimulation. miR-155-5p overexpression favored MUC5AC, IL-8, and Eotaxin-1 through the IL-13Rα1/SOCS1/STAT6 pathway while delaying the repair process by downregulating IL-13Rα2/MAPK14/c-Jun/c-fos signaling. The dual luciferase assay confirmed that miR-155-5p modulates both IL-13R pathways by directly targeting SOCS1, c-fos, and MAPK14. miR-155-5p is overexpressed in BECs from patients with severe asthma and regulates IL-13Rα1 and IL-13Rα2 expression and signaling, favoring expression of mucin- and eosinophil-related genes to the detriment of airway repair. These results show that miR-155-5p may contribute to airway epithelial cell dysfunction in patients with severe asthma. [ABSTRACT FROM AUTHOR]

A portable multisample absorbance detection system for loop-mediated isothermal amplification using a positive temperature coefficient (PTC) heater was developed in this study. The system can simultaneously measure up to four samples and consists of four LEDs, four photodiodes, two PTC heaters, a sample holder, and a short-pass filter. The system successfully differentiated samples with and without human genomic DNA with photodiodes measuring absorbance in real time. We have also demonstrated that the quantitative analysis of human genomic DNA is possible at initial DNA concentrations ranging from 2.11 × 10² to 2.11 × 104 ng/µL. This device has potential use in on-site genetic testing owing to its compact size, portability, and capability to provide rapid results. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION The identification of adulterated sweet potato vermicelli faces significant challenges, seriously hindering the development of the vermicelli industry. Herein, we investigate effects of energy‐gathered ultrasound (EGU) and energy‐divergent ultrasound (EDU) (30, 40 and 50 W  L−1) on structure, DNA extraction and adulterated quantification of sweet potato vermicelli and its starch, thereby exploring their potential in adulteration of sweet potato vermicelli.EGU‐assisted modified cetyltrimethylammonium bromide (CTAB) protocol with β‐mercaptoethanol significantly improved DNA extraction from sweet potato vermicelli (223.7–249.2 ng μL−1) and its starch (133.4–186.4 ng μL−1), followed by EDU‐assisted DNA extraction from sweet potato vermicelli (115.1–209.3 ng μL−1) and its starch (33.4–61.0 ng μL−1). Both EGU and EDU treatments resulted in the destruction of microstructure and crystalline structure, as well as changes in pasting and thermal properties of sweet potato vermicelli and its starch. Real‐time polymerase chain reaction (PCR) amplification results revealed that EGU and EDU enhanced the efficiency of DNA amplification, and EDU showed smaller cycle threshold (Ct) values than EGU. In addition, EDU‐assisted CTAB protocol combined with real‐time PCR could detect levels of less than 1% of cassava and maize starches in sweet potato vermicelli.EDU‐assisted CTAB protocol combined with real‐time PCR shows promise as a sensitive and reliable analytical tool for vermicelli adulteration. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Background: Ghee, known as "roghane heiwâni," or "Kermanshahi oil" is a traditional fermented butter-like product highly esteemed for its nutritional value. Ghee is prepared using traditional methods and has substantial potential as a reservoir of probiotic microorganisms. Previous research delved into isolating and identifying lactic acid bacteria (LAB) in Kermanshahi through culture and PCR sequencing. This study seeks to elucidate the microbial profiles and diversity within Kermanshahi using culture, Denaturing Gradient Gel Electrophoresis (DGGE), and sequencing methodologies. Methods: Twenty samples of Kermanshahi oil were meticulously gathered from diverse locales across Kermanshah province. These samples were cultivated under specialized conditions in MRS and M17 environments spanning 24 to 72 h. Following DNA extraction, amplification of the 16SrRNA gene sequences was performed, culminating in sequencing for conclusive identification of the isolates. Furthermore, the DGGE technique was directly employed to separate and identify various species present in the oil samples utilizing bioinformatics software. Results: Sequencing outcomes revealed a diverse array of microorganisms among the isolates, with Lactobacillus constituting 43%, Streptococcus comprising 27.6%, Enterococcus at 4.61%, and yeasts at 7.6%. Other species exhibited lower frequencies, encompassing Rhizobium, Bacillus coagulans, and Staphylococcus hominis. Conclusions: The isolation of a diverse spectrum of probiotic microorganisms underscores their potential utility in the realm of industrial dairy product production. These findings allude to the possibility of integrating these valuable microorganisms, which have historically been associated with traditional products, into the contemporary dairy industry. As consumer interest in probiotic-enriched products surges, the insights gained from this study pave the way for harnessing the benefits of Kermanshahi-derived probiotics. [ABSTRACT FROM AUTHOR]

Although faster and powerful, polymerase chain reaction (PCR) often failed to amplify targets efficiently. Numerous PCR enhancers have been used to increase the amplification efficiency of difficult DNA targets. However, there is no systematic comparison of their effects in normal and difficult PCR conditions. In this paper, we have selected nine different PCR enhancers that can promote the PCR amplification efficiency. We have compared their effect in Taq DNA polymerase thermostability, inhibitor resistance, and amplification of various DNA targets. Although the PCR enhancers more or less reduced the amplification efficiency of DNA fragments with moderate GC-content, they were able to improve the amplification efficiency and specificity of GC-rich fragments. Betaine outperformed the other enhancers in amplification of GC-rich DNA fragments, thermostabilizing Taq DNA polymerase, and inhibitor tolerance. Sucrose and trehalose showed similar effect in thermostabilizing Taq DNA polymerase and inhibitor tolerance, while they showed mildest inhibitory effect on normal PCR. For GC-rich region-containing long DNA fragment amplification, 1 M betaine, 0.5 M betaine + 0.2 M sucrose, or 1 M betaine + 0.1 M sucrose can be used to effectively promote the amplification, while keep their negative effect in amplification of normal fragment to a minimal level. [ABSTRACT FROM AUTHOR]

Background: Shen-Bai-Jie-Du decoction (SBJDD), a traditional Chinese herb formula developed based on evidence-based medicine, is efficacy to reduce the recurrence and carcinogenesis of colorectal adenoma. However, the mechanism of SBJDD to treat colorectal adenoma remains unclear. The present study aims to investigate the efficacy and mechanism of SBJDD on colorectal adenoma carcinogenesis from the aspects of regulating gut microbiota and short-chain fatty acids (SCFAs). Methods: Twenty-one patients diagnosed with colorectal adenoma were recruited in the study and required to take SBJDD for four consecutive weeks. Analysis of gut microbiota was conducted using 16S rRNA gene amplicon sequencing, while levels of SCFAs in fecal and serum samples were determined through HPLC–MS/MS. Additionally, twenty-four Apcmin/+ mice were randomly assigned to normal diet (ND), high-fat diet (HFD), and SBJDD groups. The pharmacological effects and mechanism of SBJDD on colorectal adenoma carcinogenesis were assessed using RT-qPCR, HE staining, IHC staining, Western blot, IF staining, and Flow cytometry assays. Results: Our clinical study has shown that SBJDD can regulate the gut microbiota composition and enhance SCFAs production in patients with colorectal adenoma. SBJDD alleviated colorectal adenoma formation and carcinogenesis, as well as protected the integrity of the intestinal barrier in the Apcmin/+ mice model compared to the HFD group. Additionally, SBJDD was found to regulate gut microbiota capable of producing SCFAs. G protein-coupled receptors GPR43, GPR41, and GPR109a were effectively activated in the SBJDD group, while HDAC1 and HDAC3 were inhibited. Furthermore, decreased expression levels of interleukin 1 beta (IL-1β) and interleukin 6 (IL-6), along with elevated expression level of interleukin 10 (IL-10), were observed in the colorectal tissue of the SBJDD group. Finally, SBJDD exhibited the ability to reduce the proportion of M1-type macrophages while increasing the proportion of M2-type macrophages. Conclusions: Our study objectively demonstrated the pharmacological effects of SBJDD in inhibiting the progression of colorectal adenoma and investigated its mechanisms in terms of regulating gut microbiota, increasing SCFAs, and reducing colorectal inflammation. [ABSTRACT FROM AUTHOR]

Background: Cervical cancer is the 4th most common cancer in women globally. Determining the prevalence of the high-risk human papillomavirus (HR-HPV) and low-risk (LR-HPV) genotypes and the distribution in abnormal cervical cytologywill be essential in a future population-based cervical cancer prevention program. Method: Primary studies with women with abnormal cervical cytology were systematically searched for in Medline, CINHAL, Google Scholar, African Journal Online, and the University of Antwerp repository from 19-30 May 2023. A weighted inverse-variance random effects model was used. Variations across the studies were checked using a forest plot, I² statistics, and Egger’s test. Group analysis was performed for evidence of heterogeneity. Results: The pooled prevalence of human papillomavirus (HPV) genotypes with abnormal cervical cytology of a precancerous cervical lesion was 38.74% (95% CI: 27.56-49.93). The leading pooled prevalence estimates by subgroup analysis were 18% (95% CI: 13-26), 14% (95% CI: 111-16), and 66% (51-79) for women with retroviral infection (RVI), DNA genotyping with amplification, and central parts of Ethiopia respectively. There were 25 HPV variants identified by genotyping techniques with the five most prevalent HPV genotypes being HPV-16 and HPV-18 coexisting at 54%; HPV-16 alone at 29%; HPV-51 at 16%; HPV-52 at 13%; and HPV-31 and HPV-33 each contributing approximately 12%. Conclusion: The pooled prevalence of HPV genotypes was higher than in other countries. HPV-51, HPV-52, HPV-31, and HPV-33 are the most prevalent genotypes. Hence, the nonavalent vaccine type would be the one that includes all the most prevalent HPV genotypes, but HPV-51in Ethiopia. Additional data on similar DNA test techniques for comparisons with precancerous lesions and invasive cancer are needed. Cervical cancer prevention and control programs in Ethiopia should be aligned with the most prevalent genotypes. [ABSTRACT FROM AUTHOR]

Porcine hemagglutinating encephalomyelitis virus (PHEV) is the only known porcine neurotropic coronavirus, which is prevalent worldwide at present. It is of great significance to understand the genetic and evolutionary characteristics of PHEV in order to perform effective measures for prevention and control of this disease. In this study, a total of 6,986 tissue samples and nasopharyngeal swabs were collected from different regions of Guangxi province in southern China during 2021-2024, and were tested for PHEV using a quadruplex RT-qPCR. The positivity rate of PHEV was 2.81% (196/6,986), of which tissue samples and nasopharyngeal swabs had 2.05% (87/4,246) and 3.98% (109/2,740) positivity rates, respectively. Fifty PHEV positive samples were selected for PCR amplification and gene sequencing. Sequence analysis revealed that the nucleotide homology and amino acid similarities of S, M, and N genes were 94.3%-99.3% and 92.3%-99.2%, 95.0%-99.7% and 94.7%-100.0%, 94.0%-99.5% and 93.5%-99.3%, respectively, indicating M and N genes were more conservative than S gene. Phylogenetic trees based on these three genes revealed that PHEV strains from different countries could be divided into two groups G1 and G2, and the PHEV strains from Guangxi province obtained in this study distributed in subgroups G1c and G2b. Bayesian analysis revealed that the population size of PHEV has been in a relatively stable state since its discovery until it expanded sharply around 2015, and still on the slow rise thereafter. S gene sequences analysis indicated that PHEV strains existed variation of mutation, and recombination. The results indicated that the prevalent PHEV strains in Guangxi province had complex evolutionary trajectories and high genetic diversity. To the best of our knowledge, this is the first report on the genetic and evolutionary characteristics of PHEV in southern China. [ABSTRACT FROM AUTHOR]

Genomic instability is associated with late stage carcinomas and the epithelial mesenchymal transition (EMT). Of note is chromosome 8q24 amplification that has been documented in many epithelial-derived carcinomas. On this amplified region is the potent oncogene, c-myc. Not only does MYC overexpression activate targets that promote cell proliferation, it also activates transcription factors that drive EMT, including ZEB1. Further reinforcing EMT, overexpressed MYC also represses tumor suppressors involved in promoting the epithelial phenotype, including MIZ1. We predict that as carcinomas progress, chromosome 8q24 is amplified leading to high MYC levels that leads to ZEB1 expression and MIZ1 repression driving cells through EMT. To interrogate this clinically, limited cohorts of human epithelial-derived carcinomas were examined for MYC/ZEB1/MIZ1 expression patterns across increasing carcinoma grades. Interestingly, the predicted temporal patterns were only observed in hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinomas. Yet MIZ1 proved to be an excellent marker to assess carcinoma progression across types. We expanded the HCC cohort and determined that c-myc amplification was restricted to grade III/IV HCC that also exhibited increased MYC and ZEB1 nuclear expression whereas cytosolic MIZ1 expression was lost and only nuclear expression retained. These same resections were obtained from only individuals who had histories of alcohol consumption that were also diagnosed with cirrhosis, metastasis and had viral hepatitis suggesting etiology-specific mechanisms of cancer progression. Finally, analysis performed in Hep3B cells determined that alterations in MYC expression promoted the predicted changes in ZEB1 and MIZ1 expression and/or distributions and in markers for EMT further suggesting a relationship among these three transcription factors in HCC and their correlation to driving EMT. [ABSTRACT FROM AUTHOR]

Heat shock protein 70 (HSP70) is one kind of molecular chaperones which are widely found in organisms, and its members are highly conserved among each other, with important roles in plant growth and development. In this study, 56 HSP70 genes were identified from the apple genome database. Analysis of gene duplication events showed that tandem and segmental duplication events play an important role in promoting the amplification of the MdHSP70 gene family. Collinearity analysis showed that HSP70 family members of apple were more closely related to HSP70 family members of Arabidopsis, tomato and soybean. The promoter region of the apple HSP70 genes contains a large number of cis-acting elements in response to hormones and stress. Tissue-specific expression analysis showed that some of the genes were associated with various stages of the apple growth process. Codon preference analysis showed small differences between codon bases 1 and 3 in the apple HSP70 genome, and the codon base composition had a small effect on codon usage preference. The multiple expression patterns of the MdHSP70 gene suggested that MdHSP70 gene members play important roles in growth and development and in response to hormonal and abiotic stresses. The yeast two-hybrid (Y2H) demonstrated that MdHSP70-53 interacts with MdDVH24_032563. The qRT-PCR analysis showed that most MdHSP70 members' hormonal and abiotic stresses (MdHSP70-6, MdHSP70-26 and MdHSP70-45) appeared to be highly expressed. To further elucidate the function of MdHSP70 (6, 26, 45), we introduced them into tobacco to confirm subcellular locations and noted that these genes are located in the cytoplasm and cell membrane. This study serves as a theoretical basis for further studies of the MdHSP70 gene and helps to further investigate the functional characterization of MdHSP70 gene. [ABSTRACT FROM AUTHOR]

Malaria remains a key health and economic problem, particularly in sub-Saharan Africa. The emergence of artemisinin drug resistance (ART-R) parasite strains poses a serious threat to the control and elimination of this scourge. This is because artemisinin-based combination therapies (ACTs) remain the first-line treatment in the majority of malaria-endemic regions in Sub-Saharan Africa. Certain single-nucleotide polymorphisms in the propeller domains of Plasmodium falciparum Kelch 13 protein (K13) have been associated with delayed parasite clearance in vivo and in vitro. These mutations serve as vital molecular markers for tracking the emergence and dispersion of resistance. Recently, there have been increasing reports of the emergence and spread of P. falciparum ART-R parasites in the Eastern Africa region. This necessitates continued surveillance to best inform mitigation efforts. This study investigated the presence of all reported mutations of K13 propeller domains in the parasite population in Busia County, Kenya, a known malaria-endemic region. Two hundred twenty-six participants with microscopically confirmed uncomplicated malaria were recruited for this study. They were treated with artemether–lumefantrine under observation for the first dose, and microscopic examination was repeated 1 day later after ensuring the participants had taken the second and third doses. P. falciparum DNA from all samples underwent targeted amplification of the K13 gene using a semi-nested PCR approach, followed by Sanger sequencing. The recently validated ART-R K13 mutation C469Y was identified in three samples. These three samples were among 63 samples with a low reduction in parasitemia on day 1, suggesting day 1 parasitemia reduction rate is a useful parameter to enrich the ART-R parasites for further analysis. Our findings highlight the need for continuous surveillance of ART-R in western Kenya and the region to determine the spread of ART-R and inform containment. [ABSTRACT FROM AUTHOR]

Simple Summary: Despite the heterogeneity of resistance mechanisms to tyrosine kinase inhibitor (TKI)-targeting Epidermal Growth Factor Receptor (EGFR)-activating mutations, many induce the activation of MAPK signaling in the presence of EGFR-TKIs. ARAF gene amplification is identified as one such mechanism that activates MAPK signaling by directly interacting with RAS, yet its clinicopathologic characteristics remain poorly understood. In this study, we characterized nine cases with ARAF amplification resistant to EGFR-TKIs. Overall, these ARAF-amplified resistant tumors retained their original founder EGFR mutation and lacked secondary alterations. Furthermore, ARAF amplification was predominantly observed in female patients with EGFR exon 19 deletion. We also identified two cases showing a histologic transformation from lung adenocarcinoma to small-cell lung cancer (SCLC). ARAF amplification potentially fosters conditions that promote tumor cell survival and neuroendocrine marker transcription under EGFR-TKIs. Background/Objectives: Although tyrosine kinase inhibitors (TKIs) targeting EGFR-activating mutations significantly improved the outcome of EGFR-mutant NSCLC, resistance inevitably emerges. Despite the heterogeneity of these resistance mechanisms, many induce activation of MAPK signaling in the presence of EGFR-TKIs. While ARAF gene amplification is identified as a resistance mechanism that activates MAPK signaling by directly interacting with RAS, little is known about its clinicopathologic characteristics. Methods: We conducted a single-center retrospective analysis of the presence of ARAF amplification in re-biopsied samples in patients with EGFR-mutant NSCLC resistant to EGFR-TKIs. Demographic data, treatment course, and clinical molecular testing reports were extracted from electronic medical records. ARAF amplification was determined using a gene copy number assay. RNA sequence analysis was performed in patients with ARAF amplification as well as presenting histologic transformations to small-cell lung carcinoma (SCLC). Results: ARAF amplification was identified in five of ninety-seven patients resistant to erlotinib or gefitinib, and four of forty-eight patients resistant to Osimertinib. ARAF amplification was dominantly observed in female patients with EGFR exon 19 deletion. All ARAF-amplified tumors retained their founder EGFR mutation and were absent of secondary mutations. Two cases were found where ARAF amplification correlated with a histological transformation to SCLC. Conclusions: ARAF amplification was identified in 5–8% of EGFR-TKI-resistant tumors. The possible roles of ARAF in SCLC transformation warrant further investigation. [ABSTRACT FROM AUTHOR]

Simple Summary: Intracranial Epidermoid Cysts (IECs) are rare tumors. Despite their benign course, IECs can adhere to critical brain structures resulting in impairment and morbidity. The primary treatment is surgery; however, cyst adherence often complicates complete removal, resulting in notably high progression rates after subtotal resection. Due to the rarity of IECs, there has been limited research focused on understanding the mechanisms of the disease and advancing therapeutic options. As a result, there are currently no effective drug therapies available for treating patients with IECs. Targeted therapy is an effective form of treatment for tumors. It focuses on mutations that turn healthy cells into tumor cells. The mutation profile of IECs has not been investigated. We aimed to investigate the somatic landscape of IECs to gain insights into tumor biology and identify mutations that could potentially serve as targets for additional therapies. Surgery is still the most effective treatment for these patients. Background/Objectives: Intracranial Epidermoid Cysts (IECs) are rare intracranial tumors primarily treated through surgery. Cyst adherence complicates complete removal, leading to high rates of tumor progression after subtotal resection. The molecular drivers of IEC remain unknown. Consequently, advances in treatment have fallen short. Tumor genetic profiling has revealed potential targets for drug development, including FDA-approved options and reshaping treatment. The genetic landscape of IECs has not been explored. We applied Whole Exome Sequencing (WES) to IECs to gain insights into the mechanisms of oncogenesis and identify potential therapeutic targets. Methods: We performed WES on tumor tissue and matched blood samples, when available. Following GATK best practices, we conducted read processing, quality control, somatic variant calling, and copy-number inference. Data analyses and visualization were conducted in R. Results: Top altered genes are associated with the immune system and tumor microenvironment, suggesting a mechanism of immune evasion. Gene and pathway enrichment revealed a high mutation burden in genes associated with Extracellular Matrix (ECM) and PI3K-AKT-mTOR cascades. Recurrent and deleterious alterations in NOTCH2 and USP8 were identified in 50% and 30% of the cohort, respectively. Frequent amplifications in deubiquitinases and beta-defensins strengthened the involvement of immune mechanisms for oncogenic transformation. Conclusions: Top altered genes and recurrent mutations may play a role in shaping the microenvironment and modulating immune evasion in IECs. USP8 and NOTCH2 may serve as clinically relevant target for IECs. Finally, we present evidence that the crosstalk between the PI3K-Akt-mTOR and ECM signaling pathways may play a role in modulating the immune escape mechanism in IECs. [ABSTRACT FROM AUTHOR]

The AP2/ERF family constitutes one of the largest groups of transcription factors in the Solanaceae. AP2/ERF contributes to various plant biological processes, including growth, development, and responses to various stresses. The origins and functional diversification of AP2/ERF within the Solanaceae family remain poorly understood, primarily because of the complex interactions between whole-genome duplications (WGDs) and tandem duplications. In this study, a total of 1282 AP2/ERF proteins are identified from 7 Solanaceae genomes. The amplification of AP2/ERF genes was driven not only by WGDs but also by the presence of clusters of tandem duplicated genes. The conservation of synteny across different chromosomes provides compelling evidence for the impact of the WGD event on the distribution pattern of AP2/ERF genes. Distinct expression patterns suggest that the multiple copies of AP2/ERF genes evolved in different functional directions, catalyzing the diversification of roles among the duplicated genes, which was of great significance for the adaptability of Solanaceae. Gene silencing and overexpression assays suggest that ERF-1 members' role in regulating the timing of floral initiation in C. annuum. Our findings provide insights into the genomic origins, duplication events, and function divergence of the Solanaceae AP2/ERF. [ABSTRACT FROM AUTHOR]

Background Chlamydia trachomatis is the causative agent of the most prevalent bacterial sexually transmitted infections globally. Whole genome sequencing is essential for molecular Chlamydia surveillance; however, its application is hampered by the pathogen's low abundance in clinical specimens and the expensive labor-intensive nature of existing enrichment methodologies for Chlamydia. Methods We developed a targeted whole genome amplification tool termed SWITCH by integrating phi29 DNA polymerase-mediated amplification with meticulously designed primer sets to enrich the C trachomatis genome, followed by whole genome sequencing. This method underwent evaluation through testing synthetic and clinical specimens. Results SWITCH demonstrated robust ability to achieve up to 98.3% genomic coverage of C trachomatis from as few as 26.4 genomic copies present in synthetic specimens, and it exhibited excellent performance across diverse C trachomatis serovars. Utilizing SWITCH, we directly generated 21 Chlamydia genomes from 26 clinical samples, enabling us to gain insights into the genetic relationships and phylogeny of current Chlamydia strains circulating in the country. Remarkably, this study marked the first instance of generating Chinese Chlamydia genomes directly from clinical samples. Conclusions SWITCH represents a practical cost-efficient approach to enrich the Chlamydia genome directly from clinical specimens, offering an efficient avenue for molecular surveillance of Chlamydia. [ABSTRACT FROM AUTHOR]

AbstractIt is very challenging to distinguish between Panax ginseng (P. ginseng) and Panax quinquefolius (P. quinquefolius) based on their physical appearances. Therefore, a molecular test that can be performed in commercial settings is needed to address this challenge. We have selected a locus containing a single nucleotide polymorphism (SNP) site in the Dammarendiol-II Synthase (DS) gene to differentiate between P. ginseng and P. quinquefolius. An isothermal nucleic acid amplification test (NAAT) developed previously was adapted and used on a spot test (ST) format consisting of a sample pad, a nitrocellulose membrane, and an adsorbent pad. An ST with a colorimetric detection method has been developed with visual detection based on 20-nm gold nanoparticles. The presence of the target DNA will generate a red color signal, which is visible to the naked eye. The assay comprises the capture probes, constructed based on the DS gene of ginseng, and the ends of the probe sequences sit on the SNP site for the P. ginseng and P. quinquefolius sequences; the detection probe employed in the assay is tagged with gold. The NAAT amplifies the extracted plant genomic samples and enhances the detection of specific SNPs. This NAAT technique was used to authenticate two ginseng root samples, showing greater specificity ratios than our previous work. [ABSTRACT FROM AUTHOR]

The basic helix–loop–helix (bHLH) gene family is a crucial regulator in plants, orchestrating various developmental processes, particularly flower formation, and mediating responses to hormonal signals. The molecular mechanism of bamboo flowering regulation remains unresolved, limiting bamboo breeding efforts. In this study, we identified 309 bHLH genes and divided them into 23 subfamilies. Structural analysis revealed that proteins in specific DlbHLH subfamilies are highly conserved. Collinearity analysis indicates that the amplification of the DlbHLH gene family primarily occurs through segmental duplications. The structural diversity of these duplicated genes may account for their functional variability. Many DlbHLHs are expressed during flower development, indicating the bHLH gene's significant role in this process. In the promoter region of DlbHLHs, different homeopathic elements involved in light response and hormone response co-exist, indicating that DlbHLHs are related to the regulation of the flower development of D. latiflorus. [ABSTRACT FROM AUTHOR]

Phenylalanine ammonia-lyase (PAL) acts as the rate-limiting enzyme for anthocyanin biosynthesis through the phenylpropanoid pathway, a crucial component of plant secondary metabolism. The PAL gene family plays a crucial role in plants' defense and stress responses, but its in silico identification and expression analyses in Brassica oleracea under different abiotic stresses remain unexplored. In this study, nine BolPAL, seven BrPAL, four AtPAL, and seventeen BnPAL genes were obtained from the genomes of B. oleracea, Brassica rapa, Arabidopsis thaliana, and Brassica napus, respectively. Segmental duplication and purifying selection are the causes of the BolPAL gene's amplification and evolution. The BolPAL genes with comparable intron–exon architectures and motifs were grouped together in the same clade. Three categories comprised the cis-regulatory elements: abiotic stressors, phytohormones, and light. According to the results of the qRT-PCR experiments, the majority of the BolPAL genes were expressed highly under MeJA, a low temperature, and a high temperature, and they were downregulated under ABA. Under white light (100 µmol m−2 s−1) with 50, 100, or 150 µmol m−2 s−1 far-red (FR), only a small number of the PAL genes were expressed at 50 and 100 µmol m−2 s−1 FR, while the majority of the PAL genes were slightly elevated at 150 µmol m−2 s−1 FR. This work offers a theoretical foundation for molecular breeding research to investigate the role of BolPAL genes and their role in anthocyanin biosynthesis. [ABSTRACT FROM AUTHOR]

Objective: Identification of driver mutations in tumors is an extremely important task in oncology for the choice of treatment strategy and assessment of therapy efficacy. In many cases, especially in disease monitoring, there is a need to detect a small number of copies of the mutant allele against the background of excessive content of wild-type DNA. Methods: Genomic DNA was isolated from tumor tissue in paraffine blocks and amplified using polymerase-chain reaction (PCR) with blocking of wild-type DNA amplification via addition of locked-nucleic acid (LNA) oligonucleotides. Fluorescently labelled PCR-product enriched by IDH-mutant alleles was hybridized on a biochip with immobilized oligonucleotide probes which was able to determine 5 mutations in the IDH1 gene and 2 mutations in the IDH2 gene. Results and Discussion: The method was developed and tested on a collection of 26 samples of paraffinized tumor tissue (glioma, glioblastoma, chondrosarcoma). In three cases, R132C, R132L, and R132H mutations in the IDH1 gene were detected in tumor samples with low representation of the mutant allele. The limit of detection of mutant DNA was determined to be 0.1% in the wild-type DNA background. The advantages of the method are simultaneous analysis of multiple targets, simplicity, reliability, and cost-effectiveness. Conclusions: A highly sensitive method for detecting somatic mutations in the IDH1/2 genes by LNA-mediated blocking of amplification of wild-type alleles and hybridization in a biological microchip was developed. We believe that the method may be useful for detecting low-abundance mutations in tumor samples, as well as in circular tumor DNA. [ABSTRACT FROM AUTHOR]

With advancements in DNA amplification research, isothermal amplification technology has emerged as an attractive method for detecting target DNA. Here, we describe primer generation-rolling circle amplification (PG-RCA) as an isothermal amplification method for detecting Escherichia coli O157:H7, Salmonella Typhimurium, Bacillus cereus, and Listeria monocytogenes. To improve PG-RCA sensitivity, the concentrations of the reaction components, dNTPs, phi29 DNA polymerase, and circular probes were optimized; the optimized conditions were applied to detect each target bacterium. A pair of forward and reverse circular probes that hybridized to the sense and anti-sense target genes was used in PG-RCA, exhibiting target selectivity. PG-RCA, which generated additional primers simultaneously with linear RCA and comprised multiple reaction cycles, resulted in higher accumulation of amplified DNA products than did linear RCA within the same reaction period. The threshold time (Tt) for each target gene concentration was determined based on the threshold value set in the amplification plot for PG-RCA, and a linear correlation between the Tt value and genomic DNA concentration was proven for each of the four bacteria. The PG-RCA-based assay could be applied to gene-based detection of various microorganisms and may be a useful isothermal amplification method for replacing traditional PCR methods. [ABSTRACT FROM AUTHOR]

Haemaphysalis longicornis (Neumann), the Asian longhorned tick, is a species native to East Asia, but invasive to Australia, New Zealand, and most recently, the United States. It has spread rapidly across the eastern United States after being established in New Jersey in 2017. Aiding this rapid expansion is the ability of this tick to reproduce parthenogenically and feed on diverse host species. In cattle, this tick can cause heavy burdens and act as a vector for the pathogenic hemoprotozoan parasite Theileria orientalis, genotype Ikeda, creating economic losses that impact the cattle industry. Here, we report Asian longhorned ticks, collected from cattle, a dog, and pastures and morphologically identified at the Oklahoma Animal Disease Diagnostic Laboratory as H. longicornis before molecular confirmation through PCR amplification of the cox1 gene. Blood samples from infested cattle were collected and assessed molecularly for the presence of T. orientalis, with no pathogenic DNA detected. This report describes the first record of H. longicornis in Oklahoma and the farthest westward detection of this tick in the United States to date. [ABSTRACT FROM AUTHOR]

Contamination of soil by spills of crude oil and oilfield brine is known to affect the species composition and functioning of soil microbial communities. However, the effect of such contamination on nitrogen cycling, an important biogeochemical cycle in tallgrass prairie soil, is less well known. Detecting nitrate-reducing (NR) and denitrifying (DN) bacteria via PCR amplification of the genes essential for these processes depends on how well PCR primers match the sequences of these bacteria. In this study, we enriched for NR and DN bacteria from oil/brine tallgrass prairie soil contaminated 5–10 years previously versus those cultured from uncontaminated soil, confirmed the capacity of 75 strains isolated from the enrichments to reduce nitrate and/nitrite, then screened the strains with primers specific to seven nitrogen cycle functional genes. The strains comprised a phylogenetically diverse group of NR and DN bacteria, with proportionately more γ-Proteobacteria in oil-contaminated sites and more Bacilli in brine-contaminated sites, suggesting some residual effect of the contaminants on the NR and DN species distribution. Around 82% of the strains shown to reduce nitrate/nitrite would not be identified as NR and DN bacteria by the battery of NR and DN primers used. Our results indicate an urgent need to expand the NR/DN functional gene primer database by first identifying novel NR/DN strains through their capacity to reduce nitrate/nitrite. [ABSTRACT FROM AUTHOR]

Background: Mosquitoes (Culicidae), as disease vectors, represent a risk for human health worldwide. Repeated introductions of alien mosquito species and the spread of invasive species have been recorded in different countries. Traditionally, identification of mosquitoes relies on morphological observation. However, morphology-based identification is associated with a number of potential disadvantages, such as the high level of specialisation of the operator and its limited applicability to damaged samples. In these cases, species identification is achieved through molecular methods based on DNA amplification. Molecular-based taxonomy has also enabled the development of techniques for the study of environmental DNA (eDNA). Previous studies indicated the 16S mitochondrial ribosomal RNA (rRNA) gene as a promising target for this application; however, 16S rRNA sequences are available for only a limited number of mosquito species. In addition, although primers for the 16S rRNA gene were designed years ago, they are based on limited numbers of mosquito sequences. Thus, the aims of this study were to: (i) design pan-mosquito 16S rRNA gene primers; (ii) using these primers, generate a 16S rRNA gene mosquito reference library (with a focus on mosquitoes present in Italy); and (iii) compare the discriminatory power of the 16S rRNA gene with two widely used molecular markers, cytochrome c oxidase subunit 1 mitochondrial gene (COI) and internal transcribed spacer 2 (ITS2). Methods: A total of six mosquito genera (28 mosquito species) were included in this study: Aedes (n = 16 species), Anopheles (5 species), Coquillettidia (1 species), Culex (3 species), Culiseta (2 species) and Uranotaenia (1 species). DNA was extracted from the whole mosquito body, and more than one specimen for each species was included in the analysis. Sanger sequencing was used to generate DNA sequences that were then analysed through the Barcode of Life Data Systems (BOLD). Phylogenetic analyses were also performed. Results: Novel 16S rDNA gene, COI and ITS2 sequences were generated. The 16S rRNA gene was shown to possess sufficient informativeness for the identification of mosquito species, with a discriminatory power equivalent to that of COI. Conclusions: This study contributes to the generation of DNA barcode libraries, focussed on Italian mosquitoes, with a significant increase in the number of 16S rRNA gene sequences. We hope that these novel sequences will provide a resource for studies on the biodiversity, monitoring and metabarcoding of mosquitoes, including eDNA-based approaches. [ABSTRACT FROM AUTHOR]

p53 gene is one of the most important anticancer genes and has been recognized as a typical biomarker for the early diagnosis of cancers. In this paper, a portable point-of-care testing (POCT) platform was developed for the colorimetric and photothermal dual-modal analysis of the p53 gene. Long concatemer G4 structures with high catalytic activity were formed by a target-driven hybridization chain reaction, and their catalytic properties can further be enhanced with the help of iodide ions. This dual-modal method realized the sensitive multicolor visual point-of-care detection of the p53 gene, where color variations from colourless to blue were easily distinguished by the naked eye. The temperature output was achieved by effective photothermal conversion and regulation guided by the accumulated concatemer G4 complexes in the TMB–H2O2 system, avoiding the need for complex instruments. The proposed dual-modal assay for p53 gene detection is cost-effective, simple, highly sensitive (3.34 pM), stable, and remarkably selective. It was also applied to determine the concentration of the p53 gene in spiked serum samples. [ABSTRACT FROM AUTHOR]

Purpose: To investigate the role of Actin like 6 A (ACTL6A) in cancer and explore the potential mechanism of its function. Methods: Differential expression of ACTL6A was analyzed using Oncomine and TIMER database. Then, we downloaded data sets from TCGA database. The correlation between ACTL6A expression and survival in pan-cancer were analyzed by "survival", "survminer" R package and PrognoScan database. STRING (v 11.0) and stringAPP for Cytoscape v3.7.2 were used to predict ACTL6A associated genes. Copy number and methylation alterations of ACTL6A were analyzed using cBioPortal and GSCALite. Transcription factors were downloaded from The Human Transcription Factors Database and analyzed using "limma" R package, JASPAR and PROMO database. Correlations analysis between ACTL6A and immune cells were performed using TIMER and GEPIA database. Results: In our studies, we found that ACTL6A was widely upregulated in cancers, which might be attributed to its gene amplifications. Moreover, ACTL6A might regulated by transcription factors (TFs), including E2F1, YY1, CDX2 and HOXD10. In addition, high ACTL6A expression was associated with poor prognosis in most cancers. Meanwhile, ACTL6A was associated with the infiltration of immune cells, especially in liver hepatocellular carcinoma and brain lower grade glioma. Conclusion: Amplification of ACTL6A is correlated with poor prognosis and contribute to immune cells infiltration in LIHC and LGG, which may provide immune-related therapeutic targets to guide clinical strategies. [ABSTRACT FROM AUTHOR]

Introduction: Oncogenic-addicted non-small cell lung cancer (NSCLC) has emerged as the most prevalent form of lung cancer, presenting a dynamic landscape in treatment modalities. Among these, epidermal growth factor receptor (EGFR)-mutant NSCLC remains the predominant oncogenic mutation, particularly prevalent in regions such as Asia and Latin America. Case Presentation: This case study highlights the experience of a woman diagnosed with EGFR-sensitive (del exon 19) mutant NSCLC who demonstrated an extended duration of response to third-generation EGFR-tyrosine kinase inhibitor (TKI) therapy. Upon disease progression, detection of MET gene amplification prompted the addition of a selective MET inhibitor to the existing EGFR-TKI regimen, resulting in a complete response for the patient. Discussion: The molecular heterogeneity of this condition has significantly increased in complexity over recent years, marked by the identification of baseline co-alterations and development of a broad spectrum of resistance mechanisms post-EGFR-TKI therapy. This complexity poses a substantial challenge to clinicians. Despite the rapid advancement of targeted therapies and the implementation of treatment escalation through combination strategies, there remains an ongoing debate regarding which patients would benefit most from combination therapies, both in the initial treatment phase and in the setting of disease progression, particularly when off-target resistance mechanisms or co-alterations are identified. [ABSTRACT FROM AUTHOR]

PURPOSE: The National Cancer Institute-Children's Oncology Group Pediatric Molecular Analysis for Therapy Choice trial assigned patients age 1-21 years with relapsed or refractory solid tumors, lymphomas, and histiocytic disorders to phase II treatment arms of molecularly targeted therapies on the basis of genetic alterations detected in their tumor. Patients with tumors that harbored prespecified genomic alterations in the cyclinD-CDK4/6-INK4a-Rb pathway with intact Rb expression were assigned and treated with the cdk4/6 inhibitor palbociclib. METHODS: Patients received palbociclib orally once daily for 21 days of 28-day cycles until disease progression, intolerable toxicity, or up to 2 years. The primary end point was objective response rate; secondary end points included safety/tolerability and progression-free survival. RESULTS: Twenty-three patients (median age, 15 years; range, 8-21) were enrolled; 20 received protocol therapy and were evaluable for toxicity and response. Of the evaluable patients, the most common diagnoses were osteosarcoma (n = 9) and rhabdomyosarcoma (n = 6). A single actionable gene amplification was found in 19 tumors (CDK4 , n = 11, CDK6 , n = 2, CCND3 , n = 6), with one tumor harboring two amplifications (CDK4 and CCND2). Hematologic toxicities were the most common treatment-related events. No objective responses were seen. Two patients with tumors harboring CDK4 amplifications (neuroblastoma and sarcoma) had best response of stable disease for six and three cycles. Six-month progression was 10% (95% CI, 1.7 to 27.2). CONCLUSION: The CDK4/6 inhibitor palbociclib at 75 mg/m2 orally daily was tolerable in this heavily pretreated cohort. No objective responses were observed in this histology-agnostic biomarker-selected population with treatment-refractory solid tumors, demonstrating that pathway alteration alone is insufficient in pediatric cancers to generate a response to palbociclib monotherapy. Study reports on the NCI-COG Pediatric MATCH trial arm I (palbociclib)—no objective responses observed. [ABSTRACT FROM AUTHOR]

Antifreeze proteins (AFPs) are found in a variety of marine cold‐water fishes where they prevent freezing by binding to nascent ice crystals. Their diversity (types I, II, III and antifreeze glycoproteins), as well as their scattered taxonomic distribution hint at their complex evolutionary history. In particular, type I AFPs appear to have arisen in response to the Late Cenozoic Ice Age that began ~ 34 million years ago via convergence in four different groups of fish that diverged from lineages lacking this AFP. The progenitor of the alanine‐rich α‐helical type I AFPs of sculpins has now been identified as lunapark, an integral membrane protein of the endoplasmic reticulum. Following gene duplication and loss of all but three of the 15 exons, the final exon, which encoded a glutamate‐ and glutamine‐rich segment, was converted to an alanine‐rich sequence by a combination of frameshifting and mutation. Subsequent gene duplications produced numerous isoforms falling into four distinct groups. The origin of the flounder type I AFP is quite different. Here, a small segment from the original antiviral protein gene was amplified and the rest of the coding sequence was lost, while the gene structure was largely retained. The independent origins of type I AFPs with up to 83% sequence identity in flounder and sculpin demonstrate strong convergent selection at the level of protein sequence for alanine‐rich single alpha helices that bind to ice. Recent acquisition of these AFPs has allowed sculpins to occupy icy seawater niches with reduced competition and predation from other teleost species. [ABSTRACT FROM AUTHOR]

Simple Summary: Atypical spindle cell/pleomorphic lipomatous tumor (ASCPLT) is a novel entity of benign adipocytic neoplasm that can show variable CD34 immunoreactivity, loss of Rb expression, and RB1 gene deletion. Due to the rarity of the disease, ASCPLT remains poorly understood. This review aims to provide a comprehensive reference, offer valuable insights into the clinicopathological characteristics and pathogenesis, and discuss the differential diagnosis of ASCPLT. Atypical spindle cell/pleomorphic lipomatous tumor (ASCPLT) is a rare and recently described adipocytic neoplasm that primarily occurs in the subcutis of the limbs and limb girdles, particularly of middle-aged adults. It has locally recurrent potential if incompletely excised but no risk for distant metastasis. ASCPLT is histologically similar to spindle cell/pleomorphic lipoma and atypical lipomatous tumor and shows a mixture of atypical spindle cells, adipocytes, lipoblasts, floret-like multinucleated giant cells, and/or pleomorphic cells. It has been recently recognized that ASCPLT can undergo sarcomatous transformation. However, the biological significance of morphological sarcomatous transformation in ASCPLT remains uncertain. Immunohistochemically, the tumor cells show variable expression of CD34, S-100 protein, and desmin. Loss of nuclear Rb expression is observed in the majority of cases. ASCPLT lacks MDM2 gene amplification but can show RB1 gene deletion in a significant subset of cases. Complete surgical excision is the treatment of choice. This review provides an overview of the current knowledge on the clinicoradiological features, pathogenesis, histopathology, and treatment of ASCPLT. In addition, we will discuss the differential diagnosis of this new entity. [ABSTRACT FROM AUTHOR]

Diagnosing the cause of death can be challenging, particularly for patients with no prior history of visits to the treating hospital. We encountered a case involving a 76‐year‐old male who was discovered in a state of cardiopulmonary arrest at his home and subsequently declared deceased in our hospital due to severe pneumonia. He had exhibited symptoms of fever over 37°C and severe coughing for several days. Despite consulting a primary care physician one day prior, his symptoms worsened. Autopsy findings revealed an increase in lung weight and diffuse changes in parenchyma. Histological analysis showed numerous inflammatory cells and exudate within the alveoli. Gram and Periodic acid‐Schiff staining were negative, but slight staining was observed in the cytoplasm of macrophages by Warthin‐starry and Gimenez stains. Tests using a pan bacterial/viral detection kit and qualitative polymerase chain reaction (PCR) for Legionella pneumophila were negative. However, using deoxyribonucleic acid extracted from formalin‐fixed paraffin‐embedded lung tissue, PCR amplification of the ssrA gene of congeneric Legionella species yielded positive results. The results suggest that the cause of death was likely due to bacterial pneumonia caused by Legionella species. [ABSTRACT FROM AUTHOR]

Spectroscopic multiplex bioassay allows the rapid and simultaneous detection of various biomarkers in biomedical applications. The high cost and bulky configuration of conventional spectrometers hinder the decentralization of biomedical instruments for point‐of‐care diagnostics. Here a flat‐field lens grating‐based microspectrometer (FLG‐µSPEC) is reported for continuous detection of multi‐target nucleic acid amplification. FLG‐µSPEC features the vertical integration of microslit, integrated flat‐field lens and transmission grating (FLG), concave mirror, and CMOS line sensor. FLG effectively corrects the field curvature by flattening the focal plane of dispersed wavelengths and also facilitates compact module packaging. FLG‐µSPEC module is precisely assembled into a dimension of 10 mm × 16 mm × 10 mm. The average spectral resolution exhibits 3.4 ± 0.9 nm over an operating range of 500 to 950 nm. A spectral detection system utilizing FLG‐µSPEC demonstrates the amplification of lambda DNA (휆‐DNA) for each target, exhibiting a high correlation with the obtained result from a conventional real‐time PCR (qPCR) machine. Furthermore, multiplex qPCR analysis using FLG‐µSPEC and spectral deconvolution successfully demonstrates simultaneous and accurate quantification of three different targets. The FLG‐µSPEC module offers diverse on‐demand analytical applications, including not only multiplex bioassay but also environmental monitoring. [ABSTRACT FROM AUTHOR]

Introduction: Enterocytozoon bieneusi is one of the most important zoonotic pathogens, responsible for nearly 90% of human infections. Its host spectrum is broad in China, encompassing humans, non-human primates, domestic animals, wildlife, and wastewater. Wild rodents have the potential to act as carriers of E. bieneusi, facilitating the parasite’s transmission to humans and domestic animals. Methods: The present study involved the collection of 344 wild rodents, representing nine species, from three provinces in China. The prevalence and genotypes of E. bieneusi were determined through amplification of the ITS gene. Evolutionary analysis was conducted using Mega 5.0 with the neighborjoining method (Kimura 2-parameter model, 1,000 replicates). Results: Among the sampled wild rodents, 41 (11.92%) were tested positive for E. bieneusi. Rattus flavipectus exhibited the highest prevalence (11/39), while Bandicota indica and Rattus rattus sladeni showed no infections (0/39 and 0/5, respectively), highlighting significant differences. Environmental factors strongly influenced E. bieneusi infection; rodents residing in lake beaches (10.27%, 15/146) and fields (19.95%, 18/95) were more susceptible compared to those in mountainous areas (7.77%, 8/103). The study identified four known genotypes (D, Type IV, SDD5, PigEBITS7) and five novel genotypes (HNRV-1 to HNRV-3, GXRL-1, GXRL-2) in the investigated wild rodents, with Genotype D exhibiting the highest prevalence. Discussion: Remarkably, this study reports the presence of E. bieneusi, R. flavipectus, M. fortis, A. agrarius, R. losea, and N. lotipes for the first time. These findings underscore the common occurrence of E. bieneusi infection in wild rodents in China, highlighting its diverse nature and significant potential for zoonotic transmission. Hence, it is imperative to conduct a comprehensive epidemiological investigation of rodent infection with E. bieneusi, particularly focusing on wild rodents that are closely associated with humans. Additionally, developing appropriate measures and monitoring strategies to minimize the risk of infection is essential. [ABSTRACT FROM AUTHOR]

Phlebotomine sand flies are vectors of the protozoan parasite Leishmania spp. Although the intestinal microbiota is involved in a wide range of biological and physiological processes and has the potential to alter vector competence, little is known about the impact of host species and environment on the gut microbiome. To address this issue, a comparative analysis of the microbiota of sand fly vector populations of Leishmania major and L. tropica in a mixed focus of cutaneous leishmaniasis in Tunisia was performed. Bacterial 16S rRNA gene amplification and Illumina MiSeq sequencing were used to characterize and compare the overall bacterial and fungal composition of field-collected sand flies: Phlebotomus papatasi, Ph. perniciosus, Ph. riouxi, and Ph. sergenti. Thirty-eight bacterial genera belonging to five phyla were identified in 117 female specimens. The similarities and differences between the microbiome data from different samples collected from three collections were determined using principal coordinate analysis (PCoA). Substantial variations in the bacterial composition were found between geographically distinct populations of the same sand fly species, but not between different species at the same location, suggesting that the microbiota content was structured according to environmental factors rather than host species. These findings suggest that host phylogeny may play a minor role in determining the insect gut microbiota, and its potential to affect the transmission of the Leishmania parasite appear to be very low. These results highlight the need for further studies to decode sand fly Leishmania-microbiota interactions, as even the same bacterial species, such as Enterococcus faecalis, can exert completely opposite effects when confronted with different pathogens within various host insects and vice versa. Author summary: Leishmania major and L. tropica are the causative agents of cutaneous leishmaniasis in the Tataouine governorate of southeast Tunisia. In this study, the microbiota of Phlebotomus papatasi, Ph. perniciosus, Ph. riouxi, and Ph. sergenti, which were caught from three diverse ecotypes, were analyzed using 16S rRNA gene amplification and Illumina MiSeq sequencing. In total, 117 Leishmania-free and blood-non-fed female specimens were used individually in this study to avoid any bias caused by pooling samples. We found that the gut microbiota was mainly controlled by environmental habitats and other factors, as remarkable differences in microbiota composition within the same species collected from the same location was revealed. Moreover, the results suggested that host phylogeny may play a minor role in determining the insect gut microbiota, and the potential of the host factor to affect the transmission of the Leishmania parasite appeared to be very low. A better understanding of microorganism-insect-gut bacterial interactions is critical, as the interactions between pathogens and gut microbiota do not adhere to a consistent pattern of synergy or antagonism. Even the same bacterial species, such as Enterococcus faecalis, can exert opposing effects when confronted with different pathogens in various host insects [ABSTRACT FROM AUTHOR]

Genetic variation is one of the important factors leading to the incidence and development of cancer. Copy number variation is an important source of genetic diversity, which can be expressed as gene amplification or deletion in structure, and is related to the occurrence and development of different tumors. High-throughput sequencing and gene chip technology can be adopted to detect the variation of copy number, and provide relevant information about tumor molecular characteristics, prognosis and treatment, which is conducive to more accurate diagnosis and treatment decisions for patients in clinical practice. Ovarian cancer is one of the female reproductive system diseases with the highest mortality rate. Understanding its pathogenesis is of significance for improving the survival rate of ovarian cancer. At present, the specific role and mechanism of copy number variation in ovarian cancer are still unclear. In this article, relevant copy number variation in ovarian cancer was reviewed based on the existing research results, aiming to provide novel ideas and methods for the prevention, diagnosis and treatment of ovarian cancer. [ABSTRACT FROM AUTHOR]

Background and Aim: The sun conure (Aratinga solstitialis), a bird belonging to the Psittaciformes family, is a popular pet because of its bright color and beautiful appearance. The sun conure is a monomorphic bird with similar appearances between males and females, making sex identification difficult by observing the external morphology. Therefore, molecular techniques are utilized. Loop-mediated isothermal amplification (LAMP) is a molecular technique that is often applied for sex identification in birds and is a quick and simple method that can be used in the field. This study used the LAMP technique to improve sex identification in sun conures by observing the color change of hydroxy naphthol blue. Materials and Methods: Two primer sets, SunSpin-W and SunSpin-Z, were designed for sex identification in sun conures using the LAMP technique specific to the spindlin gene. The developed LAMP reaction was tested for optimal conditions, sensitivity, and specificity compared with the polymerase chain reaction (PCR) technique. Results: The SunSpin-W primer set amplified only female birds, whereas the SunSpin-Z primer set amplified DNA from both male and female birds. The primer sets were optimized at 62°C for 45 min. A positive result was visible to the naked eye from the color change of the reaction. In the LAMP assay, the lowest detectable concentration was 10 pg/µL and in the PCR assay, it was 1 ng/µL, while a 100% accuracy rate in sex identification was observed when comparing the LAMP assay results with the PCR assay. Conclusion: This study successfully developed a LAMP technique for sex identification of sun conure, which took 45 min to complete and can be expanded for use in the field. [ABSTRACT FROM AUTHOR]

The Ujung Genteng Beach, located in Sukabumi, is renowned for its extensive seagrass beds and functions as an intertidal area. However, there has been limited scientific investigation into the diversity of microalgae in this ecosystem. This research aimed to identify the diversity of microalgae sourced from the seawater of Ujung Genteng Beach based on morphological characteristics and optimize DNA isolation and amplification techniques. Sampling was conducted three times at predetermined research locations. Morphological identification was performed using a binocular microscope, while DNA isolation and amplification were performed using CTAB methods with modification. The number of species found at Ujung Genteng Beach, Sukabumi is 47 species, 12 of which are often found at the three research locations both morning and afternoon, namely Navicula sp., Frustulia sp., Diploneis parma, Nitzschia sp., Achnanthidium sp., Amphora sp., Oscillatoria teneuis, Achanthes sp., Planothidium sp., Uronema sp., Zygnema sp., and Flagillaria sp.Based on the gel image, genomic DNA of seawater microalgae was successfully isolated, despite the relatively low purity and concentration. Analysis of diversity index and species diversity revealed variations in species abundance and diversity among different locations, particularly in seawater microalgae found within distinct zones: 0-2 meters from the low tide line (location I), seawater within seagrass areas located 2-5 meters away (location II), and seawater near the open sea, situated 5-10 meters away (location III).Therefore, the diversity of microalgae at all sampling locations was in the medium category and the uniformity index between species was low. [ABSTRACT FROM AUTHOR]

Simple Summary: Sexual reproduction in Cordyceps sensu lato is regulated by the mating-type locus, which has two alternate idiomorphs: MAT1-1 and MAT1-2. Ophiocordyceps xuefengensis, a heterothallic Cordyceps used as a traditional tonic by the Yao ethnic group in southern China, produces sterile fruiting bodies regardless of whether it is the MAT1-1 or MAT1-2 strain. However, the impact of mating types on the quality of these fruiting bodies is not well understood. In this study, we developed a loop-mediated isothermal amplification (LAMP) method that quickly and efficiently distinguishes between MAT1-1 and MAT1-2 strains of O. xuefengensis, with advantages including a short duration (1 h or less), visual detection, and the elimination of the need for a thermal cycler and gel electrophoresis. We also systematically compared biochemical contents of the fruiting bodies from MAT1-1 and MAT1-2 strains. Our findings show that the MAT1-1 strain of O. xuefengensis is a promising alternative for natural Cordyceps production, as it contains higher levels of adenosine and essential amino acids, as well as lower levels of toxic elements in the fruiting bodies compared to the MAT1-2 strain. This study provides a new approach to addressing issues related to unstable artificial cultivation, long cultivation periods, and high heavy metal content in Cordyceps. Many Cordyceps sensu lato species are used as traditional Chinese medicines. However, Cordyceps are entomopathogenic fungi in the family Clavicipitaceae of Ascomycota, and excessive harvesting severely disrupts natural habitat ecosystems. Artificial cultivation of Cordyceps fruiting bodies offers a viable strategy to protect the ecological environment and mitigate the depletion of wild resource. In this study, mononucleate hyphae were selected using DAPI fluorescence staining, the MAT1-1 and MAT1-2 strains of O. xuefengensis were successfully distinguished using loop-mediated isothermal amplification (LAMP). The chemical composition and bioactive components of fruiting bodies produced by these strains were compared. Results showed that the levels of adenosine, thymidine, adenine, guanosine, uridine, total amino acids, and total essential amino acids in the fruiting bodies of MAT1-1 strains were 1.31 mg/g, 0.15 mg/g, 0.26 mg/g, 2.40 mg/g, 2.34 mg/g, 270.3 mg/g, and 102.5 mg/g, respectively, which were significantly higher than those in the MAT1-2 sample. Contrastingly, the fruiting bodies of MAT1-2 strains contained higher levels of mannose and polysaccharides, at 11.7% and 12.2%, respectively. The levels of toxic elements such as Al, Pb, As, and Hg in the MAT1-1 fruiting bodies were 1.862 mg/kg, 0.0848 mg/kg, 0.534 mg/kg, and 0.0054 mg/kg, respectively, which were markedly lower than those in the MAT1-2 fruiting bodies. [ABSTRACT FROM AUTHOR]

Shiga toxin-producing Escherichia coli (STEC) is known as a crucial zoonotic food-borne pathogen. The main virulence factor of STEC is the production of Shiga toxins 1 and 2. A total of 400 poultry faecal samples were collected from different poultry farms in and around Tirupathi, Andhra Pradesh. The samples were cultured in selective and differential culture media, and the virulence genes of E. coli isolates were analyzed by PCR assay. Out of 400 poultry faecal samples, 170 isolates were isolated and confirmed as E. coli by different biochemical tests with an overall prevalence of 42.5%. Out of 170 E. coli isolates 154 (90.5%) were found positive by targeting uspA gene with an amplification of 884 bp. All the 154 PCR confirmed E. coli isolates subjected to multiplex PCR for the detection of virulent genes targeting eae A, stx 1 and stx 2 and obtained an amplification products, respectively at 384 bp, 180 bp and 254 bp. Out of 154 E. coli isolates, 54 (35.06%) isolates had eae A gene, 36 (23.37 %) had stx 1 gene, 41 (26.62 %) isolates had stx 2 gene, 16 (3.89 %) isolates had both eae A & stx 2, and 12 (7.79%) isolates had both stx 1 & stx 2. By avoiding contact with contaminated faeces and by maintaining proper hygienic measures at farm, contamination of poultry and poultry products may be avoided which in turn may safeguard the health of public. [ABSTRACT FROM AUTHOR]

In the present study, fowl pox was diagnosed in 129 backyard chicken based on gross and histopathological lesions. Fowl pox is manifested by pock nodular lesions on featherless parts of body (cutaneous form) and purulent, cheesy patches in upper respiratory tract (diphtheritic form). Tissue samples revealed Bollinger bodies in epithelial cells on histopathology. Among these, extraction of DNA was carried out from cutaneous and diphtheretic lesions from 29 fowl pox affected chicken. Molecular diagnosis of fowl pox was performed by amplification of P4b gene of fowl pox virus using specific primers and obtained a desired amplicon of 578 bp. Nucleotide sequencing and phylogenetic analysis of four cutaneous fowl pox samples revealed close relation with the FPV isolates from Singapore, North America and USA (KY464130, MH175285 and KC017961 with an identity of 97.28%, 97.21% and 97.16% respectively) when compared to FPVs isolated from Portugal, Brazil, Jammu and India (KM974727, KX863706, MF496042 and HM481406 respectively with an identity of 96.66% to 96.86%). [ABSTRACT FROM AUTHOR]

Thoracic cancers comprise non-small cell lung cancers (NSCLCs), small cell lung cancers (SCLCs) and malignant pleural mesotheliomas (MPM). Collectively, they account for the highest rate of death from malignancy worldwide. Genomic instability is a universal feature of cancer, which fuels mutations and tumour evolution. Deficiencies in DNA damage response (DDR) genes amplify genomic instability. Homologous recombination deficiency (HRD), resulting from BRCA1/BRCA2 inactivation, is exploited for therapeutic synthetic lethality with poly-ADP ribose polymerase (PARP) inhibitors in breast and ovarian cancers, as well as in prostate and pancreatic cancers. However, DDR deficiency and its therapeutic implications are less well established in thoracic cancers. Emerging evidence suggests that a subset of thoracic cancers may harbour DDR deficiency and may, thus, be effectively targeted with DDR agents. Here, we review the current evidence surrounding DDR in thoracic cancers and discuss the challenges and promise for achieving clinical benefit with such therapeutics. [ABSTRACT FROM AUTHOR]

In this study, we aimed to assess the concordance between HER2 positivity, defined as scores of 2+ or 3+ by immunohistochemistry (IHC), and HER2 gene amplification results obtained by fluorescence in situ hybridization (FISH) and gene panel testing (GPT). A total of 45 breast cancer patients with sufficient biopsy, breast-conserving surgery, or mastectomy specimens collected between 2018 and 2024 at Hokuto Hospital were included in the study. HER2 status was defined as HER2+ in cases with scores of 3+ on IHC staining, HER2-FISHamp in cases with scores of 2+ on IHC staining plus FISH amplification. FISH amplification was defined as a ratio of HER2 to the amplification of the chromosome 17 centromere ≥2.0. Next-generation sequencing (NGS) for these genes was conducted using MiSeq. The criterion for ERBB2 amplification requires gene amplification of more than 2 standard deviations (SD) above the average of the panel genes and CN ≥4. HER2+ correlated with the presence of NGS amplification of ERBB2 (p<0.001). NGS amplification was significantly more detectable in HER2+ than in HER2-FISHamp. HER2-FISHamp correlated with larger tumor size (p=0.009) and the presence of lymph node metastases (p<0.001). No correlations were observed between the HER2 status and other parameters such as age, histological grade, stage histological type, recurrence, treatment response evaluation, and breast cancer mortality. To achieve a comprehensive diagnosis, it is crucial to integrate GPT findings with other diagnostic approaches and to have a though understanding of the characteristics and limitations of each method. [ABSTRACT FROM AUTHOR]

Strengthening the expression level of integrated genes on the genome is crucial for consistently expressing key enzymes in microbial cell factories for efficient bioproduction in synthetic biology. In comparison to plasmidbased multi-copy expression, the utilization of chromosomal multi-copy genes offers increased stability of expression level, diminishes the metabolic burden on host cells, and enhances overall genetic stability. In this study, we developed the “BacAmp”, a stabilized gene integration expression and copy number amplification system for high-level expression in Bacillus subtilis, which was achieved by employing a combination of repressor and non-natural amino acids (ncAA)-dependent expression system to create a reversible switch to control the key gene recA for homologous recombination. When the reversible switch is turned on, genome editing and gene amplification can be achieved. Subsequently, the reversible switch was turned off therefore stabilizing the gene copy number. The stabilized gene amplification system marked by green fluorescent protein, achieved a 3-fold increase in gene expression by gene amplification and maintained the average gene copy number at 10 after 110 generations. When we implemented the gene amplification system for the regulation of N-acetylneuraminic acid (NeuAc) synthesis, the copy number of the critical gene increased to an average of 7.7, which yielded a 1.3-fold NeuAc titer. Our research provides a new avenue for gene expression in synthetic biology and can be applied in metabolic engineering in B. subtilis. [ABSTRACT FROM AUTHOR]

Simple Summary: The continuous evolution of the H3 subtype of avian influenza virus (AIV) poses a constant threat to the poultry industry and human health. This study successfully established a highly specific and rapid detection method for H3 AIV using real-time reverse transcription recombinase-aided isothermal amplification (RT–RAA). This method achieves accurate detection of H3 AIV by designing specific primers and probes without cross-reactivity with other viruses. The results show that the method exhibits high sensitivity and specificity and is highly consistent with the results of real-time quantitative PCR (RT–qPCR). In addition, RT–RAA amplification products can be visually observed by a portable blue light instrument, which is suitable for rapid detection in resource-constrained settings. The continued evolution of H3 subtype avian influenza virus (AIV)—which crosses the interspecific barrier to infect humans—and the potential risk of genetic recombination with other subtypes pose serious threats to the poultry industry and human health. Therefore, rapid and accurate detection of H3 virus is highly important for preventing its spread. In this study, a method based on real-time reverse transcription recombinase-aided isothermal amplification (RT–RAA) was successfully developed for the rapid detection of H3 AIV. Specific primers and probes were designed to target the hemagglutinin (HA) gene of H3 AIV, ensuring highly specific detection of H3 AIV without cross-reactivity with other important avian respiratory viruses. The results showed that the detection limit of the RT–RAA fluorescence reading method was 224 copies/response within the 95% confidence interval, while the detection limit of the RT–RAA visualization method was 1527 copies/response within the same confidence interval. In addition, 68 clinical samples were examined and the results were compared with those of real-time quantitative PCR (RT–qPCR). The results showed that the real-time fluorescence RT–RAA and RT–qPCR results were completely consistent, and the kappa value reached 1, indicating excellent correlation. For visual detection, the sensitivity was 91.43%, the specificity was 100%, and the kappa value was 0.91, which also indicated good correlation. In addition, the amplified products of RT–RAA can be visualized with a portable blue light instrument, which enables rapid detection of H3 AIV even in resource-constrained environments. The H3 AIV RT-RAA rapid detection method established in this study can meet the requirements of basic laboratories and provide a valuable reference for the early diagnosis of H3 AIV. [ABSTRACT FROM AUTHOR]