Recently Published Documents
Attenuation of Mycoplasma hyopneumoniae Strain ES-2 and Comparative Genomic Analysis of ES-2 and Its Attenuated Form ES-2L
Mycoplasma hyopneumoniae causes swine respiratory disease worldwide. Due to the difficulty of isolating and cultivating M. hyopneumoniae, very few attenuated strains have been successfully isolated, which hampers the development of attenuated vaccines. In order to produce an attenuated M. hyopneumoniae strain, we used the highly virulent M. hyopneumoniae strain ES-2, which was serially passaged in vitro 200 times to produce the attenuated strain ES-2L, and its virulence was evidenced to be low in an animal experiment. In order to elucidate the mechanisms underlying virulence attenuation, we performed whole-genome sequencing of both strains and conducted comparative genomic analyses of strain ES-2 and its attenuated form ES-2L. Strain ES-2L showed three large fragment deletion regions including a total of 18 deleted genes, compared with strain ES-2. Analysis of single-nucleotide polymorphisms (SNPs) and indels indicated that 22 dels were located in 19 predicted coding sequences. In addition to these indels, 348 single-nucleotide variations (SNVs) were identified between strains ES-2L and ES-2. These SNVs mapped to 99 genes where they appeared to induce amino acid substitutions and translation stops. The deleted genes and SNVs may be associated with decreased virulence of strain ES-2L. Our work provides a foundation for further examining virulence factors of M. hyopneumoniae and for the development of attenuated vaccines.
Evaluation of Body Composition, Physical Activity, and Food Intake in Patients with Inborn Errors of Intermediary Metabolism
Children with inborn errors of intermediary metabolism (IEiM) must follow special diets that restrict their intake of essential nutrients and may compromise normal growth and development. We evaluated body composition, bone mineral density, physical activity, and food intake in IEiM patients undergoing dietary treatment. IEiM patients (n = 99) aged 5–19 years and healthy age- and sex-matched controls (n = 98) were recruited and underwent dual-energy X-ray absorptiometry to evaluate anthropometric characteristics and body composition. Data on food intake and physical activity were also collected using validated questionnaires. The height z-score was significantly lower in IEiM patients than controls (−0.28 vs. 0.15; p = 0.008), particularly in those with carbohydrate and amino acid metabolism disorders. Significant differences in adiposity were observed between patients and controls for the waist circumference z-score (−0.08 vs. −0.58; p = 0.005), but not the body mass index z-score (0.56 vs. 0.42; p = 0.279). IEiM patients had a significantly lower total bone mineral density (BMD) than controls (0.89 vs. 1.6; p = 0.001) and a higher risk of osteopenia (z-score < −2, 33.3% vs. 20.4%) and osteoporosis (z-score < −2.5, 7.1% vs. 0%), but none presented fractures. There was a significant positive correlation between natural protein intake and BMD. Our results indicate that patients with IEiM undergoing dietary treatment, especially those with amino acid and carbohydrate metabolism disorders, present alterations in body composition, including a reduced height, a tendency towards overweight and obesity, and a reduced BMD.
Interleukin-2 (IL-2) based immunotherapy has been already approved to treat certain type of cancers as it plays vital role in immune system. Thus it is important to discover new peptides or epitopes that can induce IL-2 with high efficiency. We analyzed experimentally validated IL-2 inducing and non-inducing peptides and observed differ in average amino acid composition, motifs, length, and positional preference of amino acid residues at the N- and C-terminus. In this study, 2528 IL-2 inducing and 2104 non-IL-2 inducing peptides have been used for traning, testing, traing and validation of our models. A large number of machine learning techniques and around 10,000 peptide features have been used for developing prediction models. The Random Forest-based model using hybrid features achieved a maximum accuracy of 73.25%, with AUC of 0.73 on the training set; accuracy of 72.89% with AUC of 0.72 on validation dataset. A web-server IL2pred has been developed for predicting IL-2 inducing peptides, scanning IL-inducing regions in a protein and designing IL-2 specific epitopes by ranking peptide analogs ( https://webs.iiitd.edu.in/raghava/il2pred/ ).
Comparative Genomics of Prophages Sato and Sole Expands the Genetic Diversity Found in the Genus Betatectivirus
Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the “gene regulation-genome replication” module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus.
Characterization and biological properties of peptides isolated from dried fermented cow milk products by RP‐HPLC: Amino acid composition, antioxidant, antihypertensive, and antidiabetic properties
Measles fusion complexes from central nervous system clinical isolates: decreased interaction between hemagglutinin and fusion proteins
Measles virus (MeV) viral entry is mediated by a fusion complex comprised of a receptor-binding protein (hemagglutinin, H) and a fusion protein (F). The wild-type H/F complex requires interaction with specific proteinaceous receptors (CD150/SLAM and nectin-4) in order to be activated. In contrast, the H/F complexes isolated from viruses infecting the central nervous system (CNS) do not require a specific receptor. A single amino acid change in the F protein (L454W) was previously identified in two patients with lethal sequelae of MeV CNS infection, and the F bearing this mutation mediates fusion even without the H protein. We show here that viruses bearing the L454W fusion complex are less efficient than wt virus at targeting receptor-expressing cells and that this defect is associated with a decreased interaction between the H and the F proteins.
Define protein variant functions with high-complexity mutagenesis libraries and enhanced mutation detection software
Open reading frame (ORF) variant libraries have advanced our ability to query the functions of a large number of variants of a protein simultaneously. A variant library targeting a full-length ORF typically consists of all possible single-amino-acid substitutions and a stop codon at each amino-acid position. Because a single codon variation separates a variant from the template ORF, variant quantification presents the most profound challenge. Efforts such as dividing a library into sub-libraries for direct sequencing or using a tag-directed subassembly approach are practical only with small ORFs. Our approach, on the other hand, features single-pool libraries for all genes up to 3600bp (EGFR), and an enhanced variant-detecting toolkit. Having succeeded in processing screens of ~20 ORF variant libraries, this tool calls variants reliably, and also presents variant annotations in datafiles to enable analyses that have in turn reshaped our strategies governing library design, screen deconvolution, sequencing and its analysis.
AbstractExpression of the cellular prion protein (PrPC) is crucial for the development of prion diseases. Amino acid changes in PrPC or a reduced amount of PrPC may modulate disease resistance. The relative abundance of C1, a natural α-cleavage fragment of PrPC, was previously found to be associated with a resistant PRNP genotype in sheep. Goats are another small ruminant where classical scrapie susceptibility is under strong genetic control. In this study, we assessed PrPC in goats for the existence of similar associations between PrPC fragments and genotype. Brain tissue homogenates from scrapie-free goats with wild type PRNP or polymorphisms (I142M, H143R, N146S, or Q222K) were deglycosylated prior to immunoblot for assessment of the relative abundance of the C1 fragment of PrPC. The presence of K222 or S146 alleles demonstrated significantly different relative levels of C1 compared to that observed in wild type goats, which suggests that the genotype association with C1 is neither unique to sheep nor exclusive to the ovine Q171R dimorphism.
The genetic code has been proposed to be a "frozen accident", but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force which likely helped drive these codons to low frequency and enable their reassignment.
This study has the main purpose of testing natural carriers as more sustainable alternatives to polymeric coating. New clay-based hybrid organic–inorganic materials have been prepared. An innovative procedure for the intercalation of the bioactive molecule is proposed. The synthesis process implies the use of mild operating conditions and does not require the use of organic reactants or solvents. Moreover, the use of natural carriers, and milder environmentally friendly process conditions, fulfill the requirement of a mostly safe, greener production. The capture and the release properties of the final material mainly depend on the carrier morphology. Large zeolite content in the mineral clays can favor the capture of very large methionine loadings, but due to the trapping mechanism, typical of these structures, zeolites prevent a satisfactory release in mild condition and physiological condition. The Freundlich adsorption model has been found to be able to predict the capture behavior. Once the proper carrier is selected, the preparation procedure guarantees the protection of the amino acid in the right form. Neither the structure of the inorganic matrix nor the amino acid structure was changed in the preparation process. Methionine was detected in its zwitterionic form, showing the main IR bands only slightly affected by the interaction. Further studies on methionine bioaccessibility and intestinal absorption from methionine–Adsorbene (MET–ADS) are required to optimize the application of natural clay in in-field animal nutrition.