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New approach methodologies (NAM), including omics and in vitro approaches, are contributing to the implementation of 3R (reduction, refinement and replacement) strategies in ...regulatory science and risk assessment. In this study, we present an integrative transcriptomics and proteomics analysis workflow for the validation and revision of complex fish genomes and demonstrate how proteogenomics expression matrices can be used to support multi-level omics data integration in non-model species in vivo and in vitro. Using Atlantic salmon as an example, we constructed proteogenomic databases from publicly available transcriptomic data and in-house generated RNA-Seq and LC-MS/MS data. Our analysis identified ∼80,000 peptides, providing direct evidence of translation for over 40,000 RefSeq structures. The data also highlighted 183 co-located peptide groups that supported a single transcript each, and in each case, either corrected a previous annotation, supported Ensembl annotations not present in RefSeq, or identified novel previously unannotated genes. Proteogenomics data-derived expression matrices revealed distinct profiles for the different tissue types analyzed. Focusing on proteins involved in defense against xenobiotics, we detected distinct expression patterns across different salmon tissues and observed homology in the expression of chemical defense proteins between in vivo and in vitro liver systems. Our study demonstrates the potential of proteogenomic analyses in extending our understanding of complex fish genomes and provides an advanced bioinformatic toolkit to support the further development of NAMs and their application in regulatory science and (eco)toxicological studies of non-model species.
We have employed recently developed blind modification search techniques to generate the most comprehensive map of post-translational modifications (PTMs) in human lens constructed to date. Three ...aged lenses, two of which had moderate cataract, and one young control lens were analyzed using multidimensional liquid chromatography mass spectrometry. In total, 491 modification sites in lens proteins were identified. There were 155 in vivo PTM sites in crystallins: 77 previously reported sites and 78 newly detected PTM sites. Several of these sites had modifications previously undetected by mass spectrometry in lens including carboxymethyl lysine (+58 Da), carboxyethyl lysine (+72 Da), and an arginine modification of +55 Da with yet unknown chemical structure. These new modifications were observed in all three aged lenses but were not found in the young lens. Several new sites of cysteine methylation were identified indicating this modification is more extensive in lens than previously thought. The results were used to estimate the extent of modification at specific sites by spectral counting. We tested the long-standing hypothesis that PTMs contribute to age-related loss of crystallin solubility by comparing spectral counts between the water-soluble and water-insoluble fractions of the aged lenses and found that the extent of deamidation was significantly increased in the water-insoluble fractions. On the basis of spectral counting, the most abundant PTMs in aged lenses were deamidations and methylated cysteines with other PTMs present at lower levels. Keywords: proteomics • mass spectrometry • post-translational modification • spectral counting • modification abundance • human lens • crystallin • aging • cataract
Manipulation of the temporalis muscle during pterional and frontotemporal approaches poses major cosmetic and functional issues postoperatively. The temporalis muscle has usually been secured in its ...normal position using implants or by leaving a thin rim of muscle and fascia attached along the superior temporal line. In the present report, we have described a pure tissue-based method of anchoring the intact temporalis muscle precisely along the superior temporal line.
A total of 30 consecutive cases of pterional or frontotemporal craniotomy were performed by single surgeon (SKR). A subfascial dissection technique was used to expose the transition zone of the frontal pericranium with the temporalis fascia. These were then separated by sharp dissection along the superior temporal line at which the muscle is attached. The temporalis muscle and fascia were repositioned during closure, precisely at their original anatomical location by passing multiple anchoring sutures along the free edge of the muscle and fascia lying along the superior temporal line.
Temporalis muscle reattachment was achieved in all 30 cases with good cosmesis and functional outcome without temporalis muscle-related complications at 6 months of follow-up.
The approximation of sutures running through the free edge of the temporalis muscle with intact fascia along the superior temporal line from anteriorly to posteriorly restored the muscle and fascial layer to its original position. Avoidance of the formation of any potential dead space during surgical exposure will prevent periorbital edema and/or subgaleal collection postoperatively. The described inexpensive technique avoids implant-related complications, with good functional and aesthetic outcomes. A comparative study is needed to establish the superiority of this procedure over other techniques.
Searching genomes for noncoding RNA using FastR Shaojie Zhang; Haas, B.; Eskin, E. ...
IEEE/ACM transactions on computational biology and bioinformatics,
2005-Oct.-Dec., 2005 Oct-Dec, 2005-10-00, 20051001, Volume:
2, Issue:
4
Journal Article
Peer reviewed
The discovery of novel noncoding RNAs has been among the most exciting recent developments in biology. It has been hypothesized that there is, in fact, an abundance of functional noncoding RNAs ...(ncRNAs) with various catalytic and regulatory functions. However, the inherent signal for ncRNA is weaker than the signal for protein coding genes, making these harder to identify. We consider the following problem: Given an RNA sequence with a known secondary structure, efficiently detect all structural homologs in a genomic database by computing the sequence and structure similarity to the query. Our approach, based on structural filters that eliminate a large portion of the database while retaining the true homologs, allows us to search a typical bacterial genome in minutes on a standard PC. The results are two orders of magnitude better than the currently available software for the problem. We applied FastR to the discovery of novel riboswitches, which are a class of RNA domains found in the untranslated regions. They are of interest because they regulate metabolite synthesis by directly binding metabolites. We searched all available eubacterial and archaeal genomes for riboswitches from purine, lysine, thiamin, and riboflavin subfamilies. Our results point to a number of novel candidates for each of these subfamilies and include genomes that were not known to contain riboswitches.
We report the clinical efficacy against COVID-19 infection of BBV152, a whole virion inactivated SARS-CoV-2 vaccine formulated with a toll-like receptor 7/8 agonist molecule adsorbed to alum ...(Algel-IMDG) in Indian adults.
We did a randomised, double-blind, placebo-controlled, multicentre, phase 3 clinical trial in 25 Indian hospitals or medical clinics to evaluate the efficacy, safety, and immunological lot consistency of BBV152. Adults (age ≥18 years) who were healthy or had stable chronic medical conditions (not an immunocompromising condition or requiring treatment with immunosuppressive therapy) were randomised 1:1 with a computer-generated randomisation scheme (stratified for the presence or absence of chronic conditions) to receive two intramuscular doses of vaccine or placebo administered 4 weeks apart. Participants, investigators, study coordinators, study-related personnel, the sponsor, and nurses who administered the vaccines were masked to treatment group allocation; an unmasked contract research organisation and a masked expert adjudication panel assessed outcomes. The primary outcome was the efficacy of the BBV152 vaccine in preventing a first occurrence of laboratory-confirmed (RT-PCR-positive) symptomatic COVID-19 (any severity), occurring at least 14 days after the second dose in the per-protocol population. We also assessed safety and reactogenicity throughout the duration of the study in all participants who had received at least one dose of vaccine or placebo. This report contains interim results (data cutoff May 17, 2021) regarding immunogenicity and safety outcomes (captured on days 0 to 56) and efficacy results with a median of 99 days for the study population. The trial was registered on the Indian Clinical Trials Registry India, CTRI/2020/11/028976, and ClinicalTrials.gov, NCT04641481 (active, not recruiting).
Between Nov 16, 2020, and Jan 7, 2021, we recruited 25 798 participants who were randomly assigned to receive BBV152 or placebo; 24 419 received two doses of BBV152 (n=12 221) or placebo (n=12 198). Efficacy analysis was dependent on having 130 cases of symptomatic COVID-19, which occurred when 16 973 initially seronegative participants had at least 14 days follow-up after the second dose. 24 (0·3%) cases occurred among 8471 vaccine recipients and 106 (1·2%) among 8502 placebo recipients, giving an overall estimated vaccine efficacy of 77·8% (95% CI 65·2–86·4). In the safety population (n=25 753), 5959 adverse events occurred in 3194 participants. BBV152 was well tolerated; the same proportion of participants reported adverse events in the vaccine group (1597 12·4% of 12 879) and placebo group (1597 12·4% of 12 874), with no clinically significant differences in the distributions of solicited, unsolicited, or serious adverse events between the groups, and no cases of anaphylaxis or vaccine-related deaths.
BBV152 was highly efficacious against laboratory-confirmed symptomatic COVID-19 disease in adults. Vaccination was well tolerated with no safety concerns raised in this interim analysis.
Bharat Biotech International and Indian Council of Medical Research.
We consider the following problem: Given a set of binary sequences, determine lower bounds on the minimum number of recombinations required to explain the history of the sample, under the ...infinite-sites model of mutation. The problem has implications for finding recombination hotspots and for the Ancestral Recombination Graph reconstruction problem. Hudson and Kaplan gave a lower bound based on the four-gamete test. In practice, their bound R/sub m/ often greatly underestimates the minimum number of recombinations. The problem was recently revisited by Myers and Griffiths, who introduced two new lower bounds R/sub h/ and R/sub s/ which are provably better, and also yield good bounds in practice. However, the worst-case complexities of their procedures for computing R/sub h/ and R/sub s/ are exponential and super-exponential, respectively. In this paper, we show that the number of nontrivial connected components, R/sub c/, in the conflict graph for a given set of sequences, computable in time 0(nm/sup 2/), is also a lower bound on the minimum number of recombination events. We show that in many cases, R/sub c/ is a better bound than R/sub h/. The conflict graph was used by Gusfield et al. to obtain a polynomial time algorithm for the galled tree problem, which is a special case of the Ancestral Recombination Graph (ARG) reconstruction problem. Our results also offer some insight into the structural properties of this graph and are of interest for the general Ancestral Recombination Graph reconstruction problem.
Vacuum vessel inwall shield (IWS) (VV-IWS) which consists of block assemblies will be inserted between the inner and outer shells of the ITER vacuum vessel. The vacuum vessel will be operating at the ...following: 1) 100 ° C and 2) 200 ° C. The temperature of the vacuum vessel will be maintained by flowing water between the shells of the vessel. To achieve the temperature of the vessel, the water will be flowed at two operation phases: 1) normal operation condition (OC1), i.e., 100 ° C temperature and 1.1-MPa pressure, and 2) off-normal condition, i.e., 200 ° C temperature and 2.4-MPa pressure. The water flow rate is locally rather low in the VV-IWS block assemblies, and low flow rates generally promote local attacks on the stainless steel (SS). In addition, local accumulation of the aggressive compounds like chloride and other anions might be higher for ITER condition due to the different operational modes. IWS blocks are not accessible until the life of the machine after closing of the vacuum vessel. Hence, it is necessary to study the susceptibility of IWS materials to general corrosion and crevice corrosion under operations of the ITER vacuum vessel. Corrosion properties of IWS materials were studied by using the following: 1) immersion technique and 2) electrochemical polarization techniques at OC1, baking condition (OC2), and draining and drying operations of the ITER vacuum vessel. Before and after the immersion test, all the sample materials were subjected to a series of examinations, like loss/gain weight measurement, scanning electron microscopy (SEM) analysis, optical stereomicroscopy, and measurement of surface profile and hardness of materials. After the immersion test, SS 304B4 and SS 304B7 showed slight weight gains of 0.0593 and 0.0286 g, respectively, which indicate oxide layer formation on the surface of coupons. The SS 430 material showed a negligible weight loss of 0.0160 g which is equivalent to a corrosion rate of 0.00267 mm/year, indicating mild general corrosion effect. On visual observation with SEM and metallography, all materials showed pitting corrosion attack. During the electrochemical polarization test, all sample materials were subjected to a series of measurements, like open-circuit potential, cyclic polarization, pitting potential, protection potential, critical anodic current, and SEM examination. Under the OC1 condition, the I CC value (critical current density) is found lowest for SS 304B7 and highest for SS 430, and under the OC2 condition, the I CC value is found lowest for XM-19 and highest for SS 304B7 which indicates that SS 430 and SS 304B7 showed the highest general corrosion rates under the OC1 and OC2 conditions, respectively. All materials show a pitting loop in the OC2 operating condition. However, its absence in the OC1 operating condition clearly indicates the activity of chloride ion to penetrate the oxide layer on the sample surface, at higher temperature. The critical pitting temperature of all samples remains between 100 ° and 200 ° C.
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