Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.

Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality.

Integrated analysis of non‑coding RNAs (HOTAIR and miR‑130a) and their cross‑talk with TGF‑β1, SIRT1 and E‑cadherin as potential biomarkers in colorectal cancer.

Molecular changes have a substantial impact on the onset of colorectal cancer (CRC). Complexes of HOTAIR and miRNAs disrupt several cellular functions during carcinogenesis, primarily by disrupting several carcinogenic signaling pathways. In the present study, the relationships between the serum levels of transforming growth factor-β1 (TGF-β1), sirtuin-1 (SIRT1) and E-cadherin and those of HOX transcript antisense intergenic RNA (HOTAIR) and microRNA-130a (miR-130a) in individuals with CRC were analyzed, including their correlations and diagnostic potential.

External quality assessment in African clinical laboratories: A systematic review and meta-analysis.

Objectives: External quality assessment (EQA) helps evaluate and improve the quality of laboratory testing by providing unbiased reviews. The study aimed to synthesize pooled EQA performance of clinical laboratories across the African region.

Methods: The review was registered in PROSPERO (CRD42024562987) and reported based on the 2020 Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist.

Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing.

Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation.

Morphometrics and First Ultrastructural Characterizations of Intra-Erythrocytic Stages of So-Called Haemogregarina damiettae Ramadan et al. (1996) With Special Reference to Its Cytopathological Effects on the Infected Erythrocytes.

The current study provides the first ultrastructural observations on the intraerythrocytic stages of so-called Haemogregarina damiettae and their cytopathological effects on the infected erythrocytes (IEs) in addition to the recording of new morphometric data. The intraerythrocytic stages are attributed to the immature forms or trophozoites (Ts), and mature gamonts (Gs). Ts are typically bowling-bottle shaped with nucleus (TN) occupying its globose part, while Gs are typically banana- shaped.

Mannose Promotes β-Amyloid Pathology by Regulating BACE1 Glycosylation in Alzheimer's Disease.

Hyperglycemia accelerates Alzheimer's disease (AD) progression, yet the role of monosaccharides remains unclear. Here, it is demonstrated that mannose, a hexose, closely correlates with the pathological characteristics of AD, as confirmed by measuring mannose levels in the brains and serum of AD mice, as well as in the serum of AD patients. AD mice are given mannose by intra-cerebroventricular injection (ICV) or in drinking water to investigate the effects of mannose on cognition and AD pathological progression.

The Type III Secretion System (T3SS) of Escherichia Coli Promotes Atherosclerosis in Type 2 Diabetes Mellitus.

Large-scale studies indicate a strong relationship between the gut microbiome, type 2 diabetes mellitus (T2DM), and atherosclerotic cardiovascular disease (ASCVD). Here, a higher abundance of the type III secretion system (T3SS) virulence factors of Enterobacteriaceae/Escherichia-Shigella in patients with T2DM-related-ASCVD, which correlates with their atherosclerotic stenosis is reported. Overexpression of T3SS via Citrobacter rodentium (CR) infection in Apoe-/- T2DM mice exacerbated atherosclerotic lesion formation and increased gut permeability.

Chrysin: A Potential Antiandrogen Ligand to Mutated Androgen Receptors in Prostate Cancer.

Background: Androgen receptor mutations, particularly T877A and W741L, promote prostate cancer (PCa). The main therapies against PCa use androgen receptor (AR) antagonists, including Bicalutamide; but these drugs lose their effectiveness over time. Chrysin is a flavonoid with several biological activities, including antitumoral properties; however, its potential as an antiandrogen must be explored.

Contribution of Type 2 Diabetes Susceptible Gene GCKR Polymorphisms Rs780094 and Rs1260326 to Gestational Diabetes Mellitus: A Meta-Analysis.

Background: There is still no conclusive understanding of whether the glucokinase regulator (GCKR) gene rs780094 and rs1260326 polymorphisms predispose to gestational diabetes mellitus (GDM).

Objective: This systematic review and meta-analysis aimed to determine the effect of the GCKR polymorphisms on GDM susceptibility.

Methods: Seven literature databases were searched (from inception to February 17, 2024) to locate relevant studies included in further meta-analysis.

Royal Jelly's Strong Selective Cytotoxicity Against Lung Malignant Cells and Macromolecular Alterations in Cells Observed by FTIR Spectroscopy.

Introduction/objective: Several nutraceuticals, food, and cosmetic products can be developed using royal jelly. It is known for its potential health benefits, including its ability to boost the immune system and reduce inflammation. It is rich in vitamins, minerals, and antioxidants, which can improve general health.

Origanum syriacum Induces Apoptosis in Lung Cancer Cells by Altering the Ratio of Bax/Bcl2.

Background: The lung cancer is the leading cause of death worldwide. Although methods such as surgery, chemotherapy, radiotherapy, and immunotherapy are used for treatment, these treatments are sometimes inadequate. In addition, the number of chemotherapeutic agents used is very limited, and it is very important to use new natural agents that can increase the effect of these methods used in treatment.

Current Scenario in Associating Clinical COVID-19 Biomarkers for Developing Surveillance Platforms.

The novel coronavirus that caused the epidemic and pandemic resulting in the acute respiratory illness known as coronavirus disease 2019 (COVID-19) has plagued the world. This is unlike other coronavirus outbreaks that have occurred in the past, such as Middle East respiratory syndrome (MERS) or severe acute respiratory syndrome (SARS). COVID-19 has spread more quickly and posed special challenges due to the lack of appropriate treatments and vaccines.

The Multi-targeted Effect of Fascaplysin on the Proliferation and Dedifferentiation of Schwann Cells Inhibits Peripheral Nerve Degeneration by Blocking CDK4/6 and Androgen Receptor.

Peripheral neurodegenerative diseases induced by irreversible peripheral nerve degeneration (PND), such as diabetic peripheral neuropathy, have a high prevalence worldwide and reduce the quality of life. However, there is no agent effective against the irreversible PND. After peripheral nerve injury, Schwann cells play an important role in regulating PND.

In a Different Light: Irradiation-Induced Cuticular Wax Accumulation Fails to Reduce Cuticular Transpiration.

The cuticle, an extracellular hydrophobic layer impregnated with waxy lipids, serves as the primary interface between plant leaves and their environment and is thus subject to external cues. A previous study on poplar leaves revealed that environmental conditions outdoors promoted the deposition of about 10-fold more cuticular wax compared to the highly artificial climate of a growth chamber. Given that light was the most significant variable distinguishing the two locations, we hypothesized that the quantity of light might serve as a key driver of foliar wax accumulation.

Pollen Morphology of Gentiana L. (Gentianaceae) in Türkiye.

This study investigates the pollen morphology of 13 taxa of Turkish Gentiana using a statistical approach, contributing to their taxonomy. The aim is to elucidate the palynological characteristics of the taxa and to reveal their contributions to the systematic understanding of the genus Gentiana. The pollen grains are monad, radially symmetrical, isopolar, and tricolporate.

Early Initiation of Bundle Sheath Cells During Leaf Development as Visualised by SCARECROW Expression in Dicotyledonous C Plants.

The C type of dicotyledonous plants exhibit a higher density of reticulate veins than the C type, with a nearly 1:1 ratio of mesophyll cells (MCs) to bundle sheath cells (BSCs). To understand how this C-type cell pattern is formed, we identified two SCARECROW (SCR) genes in C Flaveria bidentis, FbSCR1 and FbSCR2, that fully or partially complement the endodermal cell layer-defective phenotype of Arabidopsis scr mutant. We then created FbSCRs promoter β-glucuronidase reporter (GUS) lines of F.

Tumor Vaccine Exploiting Membranes with Influenza Virus-Induced Immunogenic Cell Death to Decorate Polylactic Coglycolic Acid Nanoparticles.

Immunogenic cell death (ICD) of tumor cells, which is characterized by releasing immunostimulatory "find me" and "eat me" signals, expressing proinflammatory cytokines and providing personalized and broad-spectrum tumor antigens draws increasing attention in developing a tumor vaccine. In this study, we aimed to investigate whether the influenza virus (IAV) is efficient enough to induce ICD in tumor cells and an extra modification of IAV components such as hemeagglutinin (HA) will be helpful for the ICD-induced cells to elicit robust antitumor effects; in addition, to evaluate whether the membrane-engineering polylactic coglycolic acid nanoparticles (PLGA NPs) simulating ICD immune stimulation mechanisms hold the potential to be a promising vaccine candidate, a mouse melanoma cell line (B16-F10 cell) was infected with IAV rescued by the reverse genetic system, and the prepared cells and membrane-modified PLGA NPs were used separately to immunize the melanoma-bearing mice. IAV-infected tumor cells exhibit dying status, releasing high mobility group box-1 (HMGB1) and adenosine triphosphate (ATP), and exposing calreticulin (CRT), IAV hemeagglutinin (HA), and tumor antigens like tyrosinase-related protein 2 (TRP2).

Surface-Enhanced Raman Spectroscopy for Nitrite Detection.

Nitrite is an important chemical intermediate in the nitrogen cycle and is ubiquitously present in environmental and biological systems as a metabolite or additive in the agricultural and food industries. However, nitrite can also be toxic in excessive concentrations. As such, the development of quick, sensitive, and portable assays for its measurement is desirable.

Molecular mechanisms of the GABA type A receptor function.

The GABA type A receptor (GABAR) belongs to the family of pentameric ligand-gated ion channels and plays a key role in inhibition in adult mammalian brains. Dysfunction of this macromolecule may lead to epilepsy, anxiety disorders, autism, depression, and schizophrenia. GABAR is also a target for multiple physiologically and clinically relevant modulators, such as benzodiazepines (BDZs), general anesthetics, and neurosteroids.

Viroporins: discovery, methods of study, and mechanisms of host-membrane permeabilization.

The 'Viroporin' family comprises a number of mostly small-sized, integral membrane proteins encoded by animal and plant viruses. Despite their sequence and structural diversity, viroporins share a common functional trend: their capacity to assemble transmembrane channels during the replication cycle of the virus. Their selectivity spectrum ranges from low-pH-activated, unidirectional proton transporters, to size-limited permeating pores allowing passive diffusion of metabolites.

Comparative Evaluation of the Dimensional Accuracy of Silicone-Based Putty Reline Impressions with Different Spacer Acquisition Techniques in Fixed Partial Dentures.

BACKGROUND A tooth preparation's clinical requirements and geometric configurations should take precedence over material characteristics when advocating for putty reline impression techniques for permanent restorations, since they require a technically sensitive spacer for light body elastomer. We evaluated the linear dimensional accuracy of vinyl polysiloxane-based putty reline impressions with different spacer acquisition techniques in short-span and long-span fixed partial dentures (FPD). MATERIAL AND METHODS A typodont tooth set simulated a 3-unit (short-span) and a 5-unit (long-span) FPD.

Recent advances in HPV biotechnology: understanding host-virus interactions and cancer progression - a review.

Cervical cancer ranks as the fourth most common cancer among women globally, posing a significant mortality risk. Persistent infection with high-risk human papillomavirus (HPV) is the primary instigator of cervical cancer development, often alongside coinfection with other viruses, precipitating various malignancies. This study aimed to explore recent biotechnological advances in understanding HPV infection dynamics, host interactions, and its role in oncogenesis.