Usefulness of Nested PCR Assay for the Molecular Diagnosis of Human Rickettsial Infection: A Study in Bangladesh

Background: Rickettsial infections are re-emerging arthropods born worldwide zoonotic disease caused by Rickettsia, which is responsible for spotted fever and typhus fever. The diagnosis of a rickettsial illness is important for appropriate antibiotic treatment. Aims: The study aimed to determine the diagnostic accuracy and clinical usefulness of using nested polymerase chain reaction (PCR) by comparing nested PCR, ELISA, and Weil-Felix (WF) tests. Methodology: This was a prospective type of cross-sectional study. A total of 135 clinically suspected rickettsial infection cases were enrolled. Peripheral blood was taken to detect gltA, 17 kDa lipoprotein antigen gene (17 kDa), ompA, and ompB gene of Rickettsia by nested PCR. ELISA and Weil-Felix tests were done to compare with nested PCR. Results: Out of 135 cases, we detected Rickettsia in 70(51.85%) cases by nested PCR assay (p<0.01), 33((24.4%) by Weil- Felix test, 34 (25.18%) by ELISA. Only 26.66% of cases were PCR positive, which were negative by both ELISA and Weil-Felix test. Fifteen (11.11%) cases were positive by all three tests. Among 70 PCR positive rickettsia cases most frequently detected gene was ompB 42(60%), followed by 17kDa 34(48.58%); gltA 21(30%), and ompA 3(4.28%). Multiple gene combinations (ompB, 17kDa and gltA) detected in 98.57 % cases. Conclusion: Nested PCR assays showed the highest rate of detection of rickettsia cases than ELISA and Weil-Felix test. Multiple gene combinations (ompB, 17kDa, and gltA) showed the highest positivity. Therefore, diagnosis of rickettsial infection can be confirmed by PCR assay, and clinicians can plan appropriate treatment for these patients.

Tumor Microenvironment Features and Chemoresistance in Pancreatic Ductal Adenocarcinoma: Insights into Targeting Physicochemical Barriers and Metabolism as Therapeutic Approaches

Currently, the median overall survival of PDAC patients rarely exceeds 1 year and has an overall 5-year survival rate of about 9%. These numbers are anticipated to worsen in the future due to the lack of understanding of the factors involved in its strong chemoresistance. Chemotherapy remains the only treatment option for most PDAC patients; however, the available therapeutic strategies are insufficient. The factors involved in chemoresistance include the development of a desmoplastic stroma which reprograms cellular metabolism, and both contribute to an impaired response to therapy. PDAC stroma is composed of immune cells, endothelial cells, and cancer-associated fibroblasts embedded in a prominent, dense extracellular matrix associated with areas of hypoxia and acidic extracellular pH. While multiple gene mutations are involved in PDAC initiation, this desmoplastic stroma plays an important role in driving progression, metastasis, and chemoresistance. Elucidating the mechanisms underlying PDAC resistance are a prerequisite for designing novel approaches to increase patient survival. In this review, we provide an overview of the stromal features and how they contribute to the chemoresistance in PDAC treatment. By highlighting new paradigms in the role of the stromal compartment in PDAC therapy, we hope to stimulate new concepts aimed at improving patient outcomes.

The Utility of Pharmacogenetics Testing in Psychiatric Populations

The implementation of pharmacogenetic tests including multiple gene variants has shown promising potential as a decision-making tool for optimizing psychopharmacological treatment regimens and reducing treatment costs. However, the varying clinical validity of gene variants included in pharmacogenetic test batteries, and inconsistencies in their translation into medical recommendations between commercially available pharmacogenetic tests, complicates their rational implementation. Thus, there is a need for well-designed, reproducible studies documenting the clinical significance of the various genetic variants.

The evolving role of microRNA subtypes 21, 155 and 10b as oncogenes and biomarkers in breast cancer in a decade: A systematic review article

Breast cancer is a malignant disease with a high incidence worldwide in women-and to less extent in men-, thus remains a health burden. miRNA plays a key role in the development and prognosis of breast cancer; as a single miRNA has the ability to regulate multiple gene targets and adversely alter their expression. In this review, we attempt to systematically analyze the rapidly accumulating body of research regarding the role of miRNAs subtypes particularly as oncogenes and biomarkers in breast cancer, and their clinical implications. A total of 11 pertinent articles in the past 10 years were extracted from high-rank reviews, analyzed, and summarized. Amongst many (eight miRNA subtypes), three subtypes (miR21, 155, and 10b) were selected in order to evaluate the validity of their oncogenicity as well as their diagnostic value as biomarkers.

The Evolution of Hemocyanin Genes in Caenogastropoda: Gene Duplications and Intron Accumulation in Highly Diverse Gastropods

Hemocyanin is the oxygen transport protein of most molluscs and represents an important physiological factor that has to be well-adapted to their environments because of the strong influences of abiotic factors on its oxygen affinity. Multiple independent gene duplications and intron gains have been reported for hemocyanin genes of Tectipleura (Heterobranchia) and the caenogastropod species Pomacea canaliculata, which contrast with the uniform gene architectures of hemocyanins in Vetigastropoda. The goal of this study was to analyze hemocyanin gene evolution within the diverse group of Caenogastropoda in more detail. Our findings reveal multiple gene duplications and intron gains and imply that these represent general features of Apogastropoda hemocyanins. Whereas hemocyanin exon–intron structures are identical within different Tectipleura lineages, they differ strongly within Caenogastropoda among phylogenetic groups as well as between paralogous hemocyanin genes of the same species. Thus, intron accumulation took place more gradually within Caenogastropoda but finally led to a similar consequence, namely, a multitude of introns. Since both phenomena occurred independently within Heterobranchia and Caenogastropoda, the results support the hypothesis that introns may contribute to adaptive radiation by offering new opportunities for genetic variability (multiple paralogs that may evolve differently) and regulation (multiple introns). Our study indicates that adaptation of hemocyanin genes may be one of several factors that contributed to the evolution of the large diversity of Apogastropoda. While questions remain, this hypothesis is presented as a starting point for the further study of hemocyanin genes and possible correlations between hemocyanin diversity and adaptive radiation.

Phylogenetic and ecological reevaluation of the order Onygenales

The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous, and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by abilities of keratin- and cellulose-degradation. The present study aimed to investigate whether the ecological trends of the members of the Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigaceae were accepted in the Onygenales, and two new families, Auxarthraceae and Neogymnomycetaceae were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of the Onygenales, supported by multilocus analyses of ITS, LSU, TUB , TEF1 , TEF3 , RPB1 , RPB2, and ribosomal protein 60S L10 (L1) ( RP60S ) sequences, combined with available data on ecology, physiology, morphology, and genomics.

A tensor decomposition-based integrated analysis applicable to multiple gene expression profiles without sample matching

The integrated analysis of multiple gene expression profiles measured in distinct studies is always problematic. Especially, missing sample matching and missing common labeling between distinct studies prevent the integration of multiple studies in fully data-driven and unsupervised manner. In this study, we propose a strategy enabling the integration of multiple gene expression profiles among multiple independent studies without either labeling or sample matching, using tensor decomposition-based unsupervised feature extraction. As an example, we applied this strategy to Alzheimer’s disease (AD)-related gene expression profiles that lack exact correspondence among samples as well as AD single-cell RNA-seq (scRNA-seq) data. We found that we could select biologically reasonable genes with integrated analysis. Overall, integrated gene expression profiles can function analogously to prior learning and/or transfer learning strategies in other machine learning applications. For scRNA-seq, the proposed approach was able to drastically reduce the required computational memory.

Case Report: Complete Response to Nivolumab in a Patient With Programmed Cell Death 1 Ligand 1-Positive and Multiple Gene-Driven Anaplastic Lymphoma Kinase Tyrosine Kinase Inhibitor-Resistant Lung Adenocarcinoma

Multiple gene-driven programmed cell death 1 ligand 1 (PD-L1)-expressing non-small-cell lung cancer (NSCLC) is very rare. Previous studies have shown that patients with NSCLC with anaplastic lymphoma kinase (ALK) gene rearrangement rarely benefit from PD-L1 inhibitors. Besides the secondary mutations in ALK gene, other mechanisms might contribute to tumor resistance to ALK tyrosine kinase inhibitors (ALK-TKIs). Herein, we present a case of PD-L1-overexpressing lung adenocarcinoma that harbors both EML4-ALK gene rearrangement and BRAF mutation. In particular, a second molecular analysis after resistance to first- and second-generation ALK-TKIs revealed a high PD-L1 expression and tumor mutation burden. Therefore, treatment with nivolumab monotherapy, an anti-PD-1 inhibitor, was started and the patient achieved complete remission. This case report suggested that PD-1 inhibitors might be an effective treatment option for patients with multiple gene-driven PD-L1-expressing NSCLC harboring ALK gene rearrangement.