Is the BNT162b2 vaccine still effective against the latest variant: XBB.1.5?

Background: The XBB.1.5 sub-variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron now continues to spread rapidly due to the increased transmission rate as a result of increased affinity of the virus binding over the ACE-2 receptor - a gained property due to the mutation that occurred in spike protein. Aim: The protectivity of BNT162b2 antibodies produced in the serum of patients is an important parameter for preventing transmission. However, the affinity of the antibodies of patients vaccinated with BNT162b2 over the latest SARS-CoV-2 variant, XBB.1.5, is not well established. This study aimed to evaluate the efficacy of the BNT162b2 vaccine-induced antibody on XBB.1.5 by comparing the X-ray crystallographic structures and spike protein mutations of BA.5 and XBB.1.5 using in silico methods. Materials and Methods: Binding points and binding affinity values of the BNT162b2 antibody with BA.5 and XBB.1.5 spike protein were calculated using ClusPro 2.0 protein-protein docking and Discovery Studio 2021 Client software. Mutations in the genetic code of the spike protein for SARS-CoV-2 BA.5 and XBB.1.5 sub-variants were screened using the GISAID database. Results: Binding affinity values showed that BNT162b2 had higher negative values in the XBB.1.5 sub-variant than BA.5 at the mutation sites at the binding region. The results suggested that BNT162b2 may retain its activity despite mutations and conformational changes in the binding site of the XBB.1.5. Conclusion: The findings of this study shed light on the importance and usability of the current BNT162b2 vaccine for XBB.1.5 and future variants of concern.

Clonality inference in multiple tumor samples using phylogeny.

MOTIVATION: Intra-tumor heterogeneity presents itself through the evolution of subclones during cancer progression. Although recent research suggests that this heterogeneity has clinical implications, in silico determination of the clonal subpopulations remains a challenge. RESULTS: We address this problem through a novel combinatorial method, named clonality inference in tumors using phylogeny (CITUP), that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and deep sequencing data from two cancer studies, we show that CITUP predicts clonal frequencies and the underlying phylogeny with high accuracy. AVAILABILITY AND IMPLEMENTATION: CITUP is freely available at: http://sourceforge.net/projects/citup/. CONTACT: cenk@sfu.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A Study on the Identification of Five Arboviruses from Hematophagous Mosquitoes and Midges Captured in Some Parts of Northern Turkey.

BACKGROUND: Whether zoonotic or not, arboviral infections are continuing to be a major threat to human health as well as the livestock industry all around the world. This project presented the results of the identification study on five arboviruses, including West Nile virus (WNV), Bovine ephemeral fever virus, Akabane virus, Bluetongue virus, and Epizootic hemorrhagic disease virus, in mosquitos and midges from eight provinces of the Black Sea Region. METHODS: During 2011 and 2012, 3193 mosquitoes were captured around natural streams, rivers, lakes, and ponds using dry-baited miniature light-traps. Identification studies were concluded by employing molecular methods. RESULTS: According to the morphological identification, blood-sucking mosquitoes and biting-midges belonged to Aedes (44.69%), Anopheles (28.34%), Culex (22.14%) and Culicoides (4.83%) species. Overall, 146 pools were made up of captured mosquitos and midges. None of the five viruses were directly identified by mosquitoes. CONCLUSION: Mosquitoes and midges have got a crucial role in the transmission of arboviruses. The risk of occurrence for the investigated arboviruses will continue depending upon many factors including the presence of these viruses in Turkey and its neighboring countries, uncontrolled livestock movements, global warming and climate changes.

Fasciola gigantica cases in ruminants from Samsun Province, Turkey.

Animal fasciolosis occurs every year as an occasional problem in Samsun Province, especially of grazing animals in the Kizilirmak and Yesilirmak Deltas and surrounding areas. On occasions, dead animals or internal organs, including livers, lungs and hearts, are submitted to the Parasitology Department of the Faculty of Veterinary Medicine at Ondokuz Mayis University for diagnostic purposes. Upon diagnosis of fasciolosis, the owners and veterinarians are informed about prevention measures and treatment of the disease. In that context, the livers and gallbladders of one sheep, one cow and two water buffalo, suspected of having died as a result of fasciolosis, were submitted to the parasitology laboratory of the faculty in 2015 and 2016. All organs were examined thoroughly and 38, 1076, 456 and 714. F. gigantica were collected from the sheep, cow and buffaloes' livers and gallbladders, respectively. In addition to these cases, according to information received from animal breeders and some veterinarians, at least 5 sheep and 3 cattle had also died due to fasciolosis in the previous two years. Because of the re-occurrence of F. gigantica cases in recent years, it is pertinent to discuss the past and current situation surrounding this parasite in Turkey.

Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression.

The androgen receptor (AR) plays a critical role in the development of the normal prostate as well as prostate cancer. Using an integrative transcriptomic analysis of prostate cancer cell lines and tissues, we identified ARLNC1 (AR-regulated long noncoding RNA 1) as an important long noncoding RNA that is strongly associated with AR signaling in prostate cancer progression. Not only was ARLNC1 induced by the AR protein, but ARLNC1 stabilized the AR transcript via RNA-RNA interaction. ARLNC1 knockdown suppressed AR expression, global AR signaling and prostate cancer growth in vitro and in vivo. Taken together, these data support a role for ARLNC1 in maintaining a positive feedback loop that potentiates AR signaling during prostate cancer progression and identify ARLNC1 as a novel therapeutic target.

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression.

Molecular classification of cancers into subtypes has resulted in an advance in our understanding of tumour biology and treatment response across multiple tumour types. However, to date, cancer profiling has largely focused on protein-coding genes, which comprise <1% of the genome. Here we leverage a compendium of 58,648 long noncoding RNAs (lncRNAs) to subtype 947 breast cancer samples. We show that lncRNA-based profiling categorizes breast tumours by their known molecular subtypes in breast cancer. We identify a cohort of breast cancer-associated and oestrogen-regulated lncRNAs, and investigate the role of the top prioritized oestrogen receptor (ER)-regulated lncRNA, DSCAM-AS1. We demonstrate that DSCAM-AS1 mediates tumour progression and tamoxifen resistance and identify hnRNPL as an interacting protein involved in the mechanism of DSCAM-AS1 action. By highlighting the role of DSCAM-AS1 in breast cancer biology and treatment resistance, this study provides insight into the potential clinical implications of lncRNAs in breast cancer.

Thermal properties and optical transition probabilities of Tm3 + doped TeO2-WO3 glass.

Glasses with the composition of (1 - x)TeO2 + (x)WO3, where x = 0.15, 0.25 and 0.3 were prepared and, their thermal and absorption measurements were carried out. Differential thermal analysis (DTA) curves taken in the 23-600 degrees C temperature range with a heating rate of 10 degrees C/min reveal a change in the value of the glass transition temperature, Tg, while crystallization was not observed for the glasses containing a WO3 content of more than 15 mol%. All the glasses were found to be moisture-resistant. The absorption bands corresponding to the absorption of the 1G4, 3F2, 3F3 and 3F4, 3H5 and 3H4 levels from the 3H6 ground level of the Tm3+ ion were observed in the optical absorption spectra. Integrated absorption cross-sections of each band except that of 3H5 level was found to vary with the glass composition. Judd-Ofelt analysis was carried out for the samples doped with 1.0 mol% Tm2O3. The omega2 parameter shows the strongest dependence on the host composition and it increases with the increasing WO3 amount. The value of omega4 increases rather slowly while the value of omega6 is practically independent of the composition. The strong dependence of the parameter omega2 indicates that this parameter is related to the structural change and the symmetry of the local environment of the Tm3+ ions in this glass.

A short history of bladder exstrophy.

The first description of bladder exstrophy was noted on Assyrian tablets nearly 4000 years ago. Since then various papers has been published with an increasing rate. According to the available historical data, almost all operative techniques had been described during the last two centuries. We believe, the pioneers put a lot of work in this field and passed on their theoretic knowledge and surgical experience to the current era. Our duty is keep this treasure and add the benefits of recent new technological developments for the future care of our bladder exstrophy patients.

A therapeutic method for failed bladder augmentation in children: re-augmentation.

OBJECTIVE: To investigate the causes leading to the deterioration of previously successful bladder augmentation and to evaluate the efficacy of re-augmentation. PATIENTS AND METHODS: Between 1988 and 2004, 136 bladder augmentations were performed in two paediatric urological units in Hungary and Turkey. Re-augmentation was necessary in two patients after colocystoplasty and in three after gastrocystoplasty. A secondary augmentation was not required in any patients after ileocystoplasty. The clinical data of these five patients were evaluated. RESULTS: On the basis of the clinical signs and urodynamic studies, re-augmentation was performed 2-7 years after the initial augmentation cystoplasties. Anticholinergic therapy given before re-augmentation did not improve bladder capacity, intravesical pressure and/or bladder compliance. An ileal or sigmoid segment was used for the secondary augmentation. After re-augmentation, all five patients became continent, and showed marked improvement in their urodynamic parameters at a mean (range) follow-up of 6.8 (2-10) years. CONCLUSION: A decreased bladder capacity and/or compliance and increased bladder pressure after successful augmentation cystoplasty might be the result of: (i) impairment of the blood supply to the large bowel or gastric segment used for augmentation; or (ii) bowel mass contractions. Ileocystoplasty seems to be the "first-line" of choice for primary augmentation. Re-augmentation with a bowel segment is a suitable treatment if conservative treatment fails. Regular urodynamic investigations are needed for early detection of malfunction of the augmented bladder, and advising therapy.