ELUCIDATING GENE SIGNATURES THAT CONTROL THE CIRCADIAN RHYTHM IN CYANOBACTERIA USING BIOINFORMATICS METHODS

poster abstractBackground: The daily light-dark cycle govern rhythmic changes in the behavior and physiology of most species. This circadian rhythm, or bi-ological “clock,” allows the organism to anticipate and prepare for the changes in the physical environment that are associated with day and night, thereby ensuring that the organism carry our specific processes at the right time of the day. Studies have found that the internal clock con-sists of an array of genes and the protein products they encode, which regulate various physiological processes throughout the body. Cyanothece sp. ATCC 51142 is an organism that has both photosynthetic (producing oxygen) and nitrogen fixing ability. The N2-fixing enzyme, nitrogenase, is highly sensitive to oxygen for which it has developed a temporal regula-tion in which N2 fixation and photosynthesis occur at different times throughout a diurnal cycle with very high levels of CO2 fixation during the light and high levels of N2 fixation in the dark. The mechanisms underly-ing the circadian rhythm and the signature genes elucidating this mecha-nism are addressed in this research. Objective: The objective is to integrate gene expression data with da-ta and knowledge from prior studies using bibliomics techniques, in the de novo construction of quasi-complete transcriptional regulatory networks to identify gene signatures in functional motifs and elucidate their role in circadian rhythms in cyanothece sp. ATCC 51142. Methodology: The sequence data of Transcription profiling time se-ries of cyanothece sp. ATCC 51142 grown in 12-hour light/12 hour dark then 24 h light from Array Express was used to construct the initial global regulatory network. Different network topological features (degree, betweeness and eccentricity) are used to identify the signature pathways during the day and night. The genes of the global regulatory network were used to construct networks of homologous species. The functions of the already known genes in well-studied homologous species were mapped to the function of the unannotated genes of cynaothece sp. ATCC 51142. Results: We have identified significant (p<0.05) signature pathways like photosynthesis, pantothenate and CoA biosynthesis and Glyoxylate and dicarboxylate metabolism that operate during the day. And during the night, pathways such as ribosome, riboflavin metabolism, and fatty acid biosynthesis sulfur metabolism were found to be significant (p<0.05). We will further investigate the genes that were already known to be significant using cyanobase database in a particular biological path-way and the novel genes that are identified by bibliomics approach

Teachers observing classroom communication: An application of the Communicating Supporting Classroom Observation Tool for children aged 4-7 years

The nature of ‘Teacher talk’ is likely to have a considerable bearing on the child’s learning but measuring the communication environment in the classroom can present challenges. One tool which does this is the Communication Supporting Classroom Observation Tool (CSCOT). Initial use suggested that it was valid and reliably used by specialists (psychologists and speech and language therapists) and special educational needs coordinators (SENCOs). A key question is whether it can be used routinely by classroom teachers and whether results coincide with those in earlier studies. CSCOT observations were carried out by teachers in 33 schools (32 Reception classrooms, 25 in Year 1 and 25 in Year 2) in two local authorities in the North East of England and teachers were asked afterwards to reflect on their experiences using the tool. Scores were in line with those in earlier studies and were consistently higher on all dimensions for reception compared to Year 2, but there was no difference between other year groups. Results were mostly consistent with the original studies. Language learning environment was higher relative to both language learning opportunities and interactions across all years (which again did not differ). There was a moderate interaction between language learning environment where scores were significantly higher in the Reception group and lower in the Year 2 group. Teachers supported the use of the CSCOT in their feedback, suggesting that CSCOT was easy to use and useful in informing practice. The CSCOT clearly has utility as a starting point in auditing classroom communication. It allows teachers to compare between classrooms and year groups and potentially fosters collaboration between teachers and specialist practitioners who focus on communication such as speech and language therapists. Further work could link the observation tool into an intervention program co-constructed with teachers

Ab initio dynamics study of poly-para-phenylene vinylene

We present an ab initio dynamics investigation within a density-functional perturbation theory framework of the properties of the conjugated polymer poly-para-phenylene vinylene (PPV) in both the isolated chain and crystalline states. The calculated results show that for an isolated chain, most of the vibrational modes correspond to experimentally observed modes in crystalline PPV. However, additional hitherto unidentified modes have been observed in experiment and our calculations on crystalline material have allowed us to assign these. We also present the results of calculations of the polarizability and permittivity tensors of the material, which are in reasonable agreement with the typical values for conjugated polymers. Dynamical Born effective charges [ S. Baroni, S. de Gironcoli, A. Dal Corso, and P. Giannozzi, Rev. Mod. Phys. 73, 515 (2001) ] are calculated and compared with atomic charges obtained from Mulliken population analysis [ M. D. Segall, C. J. Pickard, R. Shah, and M. C. Payne, Mol. Phys. 89, 571 (1996) ] and we conclude that effective charges are more appropriate for use in the study of the dynamics of the system. Notable differences are found in the infrared-absorption spectra obtained for the isolated chain and crystalline states, which can be attributed to the differences in the crystalline packing effects, which clearly play a key role in influencing the lattice dynamics of PPV

Diagnostic Performance Assessment of Saliva RT-PCR and Nasopharyngeal Antigen for the Detection of SARS-CoV-2 in Peru

Widely available and reliable testing for SARS-CoV-2 is essential for the public health response to the COVID-19 pandemic. We estimated the diagnostic performance of reverse transcription PCR (RT-PCR) performed on saliva and the SD Biosensor STANDARD Q antigen test performed on nasopharyngeal swab compared to the reference standard, nasopharyngeal swab (NP) RT-PCR. We enrolled participants living and/or seeking care in health facilities in North Lima, Peru from November 2020 to January 2021. Consenting participants underwent same-day RT-PCR on both saliva and nasopharyngeal swab specimens, antigen testing on a nasopharyngeal swab specimen, pulse oximetry, and standardized symptom assessment. We calculated sensitivity, specificity, and predictive values for the nasopharyngeal antigen and saliva RT-PCR compared to nasopharyngeal RT-PCR. Of 896 participants analyzed, 567 (63.3%) had acute signs/symptoms of COVID-19. The overall sensitivity and specificity of saliva RT-PCR were 85.8% and 98.1%, respectively. Among participants with and without acute signs/symptoms of COVID-19, saliva sensitivity was 87.3% and 37.5%, respectively. Saliva sensitivity was 97.4% and 56.0% among participants with cycle threshold (CT) values of #30 and .30 on nasopharyngeal RT-PCR, respectively. The overall sensitivity and specificity of nasopharyngeal antigen were 73.2% and 99.4%, respectively. The sensitivity of the nasopharyngeal antigen test was 75.1% and 12.5% among participants with and without acute signs/symptoms of COVID-19, and 91.2% and 26.7% among participants with CT values of #30 and .30 on nasopharyngeal RT-PCR, respectively. Saliva RT-PCR achieved the WHO-recommended threshold of .80% for sensitivity for the detection of SARS-CoV-2, while the SD Biosensor nasopharyngeal antigen test did not. IMPORTANCE In this diagnostic validation study of 896 participants in Peru, saliva reverse transcription PCR (RT-PCR) had .80% sensitivity for the detection of SARS-CoV-2 among all-comers and symptomatic individuals, while the SD Biosensor STANDARD Q antigen test performed on nasopharyngeal swab had,80% sensitivity, except for participants whose same-day nasopharyngeal RT-PCR results showed cycle threshold values of,30, consistent with a high viral load in the nasopharynx. The specificity was high for both tests. Our results demonstrate that saliva sampling could serve as an alternative noninvasive technique for RT-PCR diagnosis of SARS-CoV-2. The role of nasopharyngeal antigen testing is more limited; when community transmission is low, it may be used for mass screenings among asymptomatic individuals with high testing frequency. Among symptomatic individuals, the nasopharyngeal antigen test may be relied upon for 4 to 8 days after symptom onset, or in those likely to have high viral load, whereupon it showed .80% sensitivity.Revisión por pare

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering. When a crystallographic structure of a complex is unavailable, the structure must be predicted using computational tools. In this work, we illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the relative orientation of the antibody light and heavy chains, and the conformations of the six complementarity determining region loops. This approach is especially useful when the crystal structure of the antibody is not available, requiring allowances for inaccuracies in an antibody homology model which would otherwise frustrate rigid-backbone docking predictions. Local docking using SnugDock with the lowest-energy RosettaAntibody homology model produced more accurate predictions than standard rigid-body docking. SnugDock can be combined with ensemble docking to mimic conformer selection and induced fit resulting in increased sampling of diverse antibody conformations. The combined algorithm produced four medium (Critical Assessment of PRediction of Interactions-CAPRI rating) and seven acceptable lowest-interface-energy predictions in a test set of fifteen complexes. Structural analysis shows that diverse paratope conformations are sampled, but docked paratope backbones are not necessarily closer to the crystal structure conformations than the starting homology models. The accuracy of SnugDock predictions suggests a new genre of general docking algorithms with flexible binding interfaces targeted towards making homology models useful for further high-resolution predictions

Complexes Formed in Solution Between Vanadium(IV)/(V) and the Cyclic Dihydroxamic Acid Putrebactin or Linear Suberodihydroxamic Acid

The ability of microbial siderophores to coordinate metal ions, particularly Fe(III), continues to generate interest in the poten-tial applications of these bioligands in the environment and medicine.13 Siderophores produced by terrestrial and marin

Cost-effectiveness of replacing versus discarding the nail in children with nail bed injury

Every year in the UK, around 10 000 children need to have operations to mend injuries to the bed of their fingernails. Currently, most children have their fingernail placed back on the injured nail bed after the operation. The NINJA trial found that children were slightly less likely to have an infection if the nail was thrown away rather than being put back, but the difference between groups was small and could have be due to chance. This study looked at whether replacing the nail is cost-effective compared with throwing it away. Using data from the NINJA trial, we compared costs, healthcare use, and quality of life and assessed the cost-effectiveness of replacing the nail. It was found that throwing the nail away after surgery would save the National Health Service (NHS) £75 (€85) per operation compared with placing the nail back on the nail bed. Changing clinical practice could save the NHS in England £720 000 (€819 000) per year