Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae)

Snails in the closely related trochid genera Phorcus Risso, 1826 and Osilinus Philippi, 1847 are ecologically important algal grazers in the intertidal zone of the northeastern Atlantic Ocean and Mediterranean Sea. Here we present the first complete molecular phylogeny for these genera, based on the nuclear 28S rRNA gene and the mitochondrial 16S rRNA and COI genes, and show that the current classification is erroneous. We recognize nine species in a single genus, Phorcus: estimated by BEAST analysis, this arose 30 (±10) Ma; it consists of two subgenera, Phorcus and Osilinus, which we estimate diverged 14 (±4.5) Ma. Osilinus kotschyi, from the Arabian and Red Seas, is not closely related and is tentatively referred to Priotrochus Fischer, 1879. Our phylogeny allows us to address biogeographical questions concerning the origins of the Mediterranean and Macaronesian species of this group. The former appear to have evolved from Atlantic ancestors that invaded the Mediterranean on several occasions after the Zanclean Flood, which ended the Messinian Salinity Crisis 5.3 Ma; whereas the latter arose from several colonizations of mainland Atlantic ancestors within the last 3 (±1.5) Ma.     

Expression Patterns of ABC Transporter Genes in Fluconazole-Resistant <Emphasis Type="Italic">Candida glabrata</Emphasis>

Clinical management of fungal diseases is compromised by the emergence of antifungal drug resistance in fungi, which leads to elimination of available drug classes as treatment options. An understanding of antifungal resistance at molecular level is, therefore, essential for the development of strategies to combat the resistance. This study presents the assessment of molecular mechanisms associated with fluconazole resistance in clinical Candida glabrata isolates originated from Iran. Taking seven distinct fluconazole-resistant C. glabrata isolates, real-time PCRs were performed to evaluate the alternations in the regulation of the genes involved in drug efflux including CgCDR1, CgCDR2, CgSNQ2, and CgERG11. Gain-of-function (GOF) mutations in CgPDR1 alleles were determined by DNA sequencing. Cross-resistance to fluconazole, itraconazole, and voriconazole was observed in 2.5 % of the isolates. In the present study, six amino acid substitutions were identified in CgPdr1, among which W297R, T588A, and F575L were previously reported, whereas D243N, H576Y, and P915R are novel. CgCDR1 overexpression was observed in 57.1 % of resistant isolates. However, CgCDR2 was not co-expressed with CgCDR1. CgSNQ2 was upregulated in 71.4 % of the cases. CgERG11 overexpression does not seem to be associated with azole resistance, except for isolates that exhibited azole cross-resistance. The pattern of efflux pump gene upregulation was associated with GOF mutations observed in CgPDR1. These results showed that drug efflux mediated by adenosine-5-triphosphate (ATP)-binding cassette transporters, especially CgSNQ2 and CgCDR1, is the predominant mechanism of fluconazole resistance in Iranian isolates of C. glabrata. Since some novel GOF mutations were found here, this study also calls for research aimed at investigating other new GOF mutations to reveal the comprehensive understanding about efflux-mediated resistance to azole antifungal agents.     

Detection and molecular characterisation of Potato virus S of weed reservoirs in Iran

Potato virus S causes destructive disease on the plants. In this research, 44 weed samples symptomless were collected during 2015 from Fars, Razavi Khorasan and Kerman provinces of Iran. The coat protein (CP) and 11 K genes from eight PVS isolates were amplified, cloned and sequenced. PVS was detected in eight weed samples including: one sample of Solanum nigrum, two samples of Chenopodium botrytis, three samples of Chenopodium album and two samples of Amaranthus hybridus. Phylogenetic analysis showed that seven Iranian isolates fell into group I, II near to European isolates and one Iranian isolate formed a separate group. Comparison of coat protein and 11 k nucleotide indicated that all Iranian isolates belonged to Ordinary strain and there were 79–100% identity among the eight Iranian isolates and the world isolates of PVS. The highest identity was between Iranian and Ukraine isolates. Recombination analysis identified four recombinant isolates among eight new Iranian isolates.     

Novel structurally designed vaccine for S. aureus α-hemolysin: protection against bacteremia and pneumonia

Staphylococcus aureus (S. aureus) is a human pathogen associated with skin and soft tissue infections (SSTI) and life threatening sepsis and pneumonia. Efforts to develop effective vaccines against S. aureus have been largely unsuccessful, in part due to the variety of virulence factors produced by this organism. S. aureus alpha-hemolysin (Hla) is a pore-forming toxin expressed by most S. aureus strains and reported to play a key role in the pathogenesis of SSTI and pneumonia. Here we report a novel recombinant subunit vaccine candidate for Hla, rationally designed based on the heptameric crystal structure. This vaccine candidate, denoted AT-62aa, was tested in pneumonia and bacteremia infection models using S. aureus strain Newman and the pandemic strain USA300 (LAC). Significant protection from lethal bacteremia/sepsis and pneumonia was observed upon vaccination with AT-62aa along with a Glucopyranosyl Lipid Adjuvant-Stable Emulsion (GLA-SE) that is currently in clinical trials. Passive transfer of rabbit immunoglobulin against AT-62aa (AT62-IgG) protected mice against intraperitoneal and intranasal challenge with USA300 and produced significant reduction in bacterial burden in blood, spleen, kidney, and lungs. Our Hla-based vaccine is the first to be reported to reduce bacterial dissemination and to provide protection in a sepsis model of S. aureus infection. AT62-IgG and sera from vaccinated mice effectively neutralized the toxin in vitro and AT62-IgG inhibited the formation of Hla heptamers, suggesting antibody-mediated neutralization as the primary mechanism of action. This remarkable efficacy makes this Hla-based vaccine a prime candidate for inclusion in future multivalent S. aureus vaccine. Furthermore, identification of protective epitopes within AT-62aa could lead to novel immunotherapy for S. aureus infection.     

The role of S477N mutation in the molecular behavior of SARS-CoV-2 spike protein: An in-silico perspective

The attachment of SARA-CoV-2 happens between ACE2 and the receptor binding domain (RBD) on the spike protein. Mutations in this domain can affect the binding affinity of the spike protein for ACE2. S477N, one of the most common mutations reported in the recent variants, is located in the RBD. Today's computational approaches in biology, especially during the SARS-CoV-2 pandemic, assist researchers in predicting a protein's behavior in contact with other proteins in more detail. In this study, we investigated the interactions of the S477N-hACE2 in silico to find the impact of this mutation on its binding affinity for ACE2 and immunity responses using dynamics simulation, protein–protein docking, and immunoinformatics methods. Our computational analysis revealed an increased binding affinity of N477 for ACE2. Four new hydrogen and hydrophobic bonds in the mutant RBD-ACE2 were formed (with S19 and Q24 of ACE2), which do not exist in the wild type. Also, the protein spike structure in this mutation was associated with an increase in stabilization and a decrease in its fluctuations at the atomic level. N477 mutation can be considered as the cause of increased escape from the immune system through MHC-II.     

Protocol for constructing subject-specific biomechanical models of knee joint

A robust protocol for building subject-specific biomechanical models of the human knee joint is proposed which uses magnetic resonance imaging, motion analysis and force platform data in conjunction with detailed 3D finite element models. The proposed protocol can be used for determining stress and strain distributions and contact kinetics in different knee elements at different body postures during various physical activities. Several examples are provided to highlight the capabilities and potential applications of the proposed protocol. This includes preliminary results on the role of body weight on the stresses and strains induced in the knee articular cartilages and meniscus during single-leg stance and calculations of the induced stresses and ligament forces during the gait cycle.     

Identification of glucose response proteins in two biological models of beta-cell adaptation to chronic high glucose exposure.

High resolution 2-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) combined with computerized analysis of gel images was used to search for proteins whose biosynthesis was induced or repressed in pancreatic islet cells chronically exposed to high glucose in an in situ and a tissue culture model of islet cell adaptation to excessive fuel load. The in situ model involved a 4-day intravenous infusion of either 50% glucose or 0.45% saline solution, followed by islet isolation, [35S]methionine labeling at 3 and 18 mM glucose for both groups, and protein analysis by 2-dimensional SDS-PAGE. The tissue culture model involved a 7-day culture of isolated rat islets in RPMI 1640 with 10% fetal calf serum containing either 3 or 30 mM glucose, followed by radiolabeling and 2-dimensional PAGE of proteins as in the in situ model. A small fraction of about 1.5% of the approximately 2000 identifiable proteins can be characterized as adaptive proteins. Of these altogether 58 proteins in the two models, 5 proteins were demonstrable in both models and two of these (proteins 1526 and 7622) are particularly noteworthy. Protein 1526 (Mr 57,000; pI 5.09) showed the same response pattern in both models and its expression was most enhanced when islets from chronically glucose-infused animals or those cultured for 7 days at 30 mM were radiolabeled at 18 mM glucose. Protein 7622 (Mr 68,000; pI 6.50) (also known as GSP-65; Collins, H.W., Buettger, C., and Matschinsky, F.M. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 5494-5498) showed a different labeling pattern in the two models: stimulation of [35S]methionine incorporation by 18 mM glucose both in control and experimental islets from the infusion study, but lack of such stimulation of radiolabeling in islets cultured for 7 days at 30 mM glucose in contrast to islets cultured at 3 mM. The experimental strategy and the methodology are evaluated and the significance of the results is discussed. Potentials of the approach and plans for future experiments are considered.