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Background: The question of whether the coronavirus genome contain as-yetununderstood genetic component. Purpose (Objective): Elucidate the novel functions of the discovered tRNA-like base sequence and lead to the development of novel therapeutic agents. Methods: A novel tRNA-like base sequence was found in the sequences complementary to the genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-CoV. By comparing mutations in the tRNA-like base sequences of these two viruses, it was found that base pairing in the cloverleaf model of SARS-CoV-2 was more robust than that of SARS-CoV. Results: The results of homology search between a short sequence of the coronavirus tRNA-like base sequence and human genes suggest that the molecule produced by this novel tRNA-like sequence may be involved in the splicing of human messenger RNA. Conclusions: Experimental molecular evidence of the tRNA-like base sequence discovered in this study is urgently needed. [ABSTRACT FROM AUTHOR]

Objectives: To characterize the structure of a variant of Acinetobacter genomic island 1 (AGI1) in the Enterobacter cloacae clinical isolate EclC2185 responsible for an 8 year outbreak in Dijon University Hospital.Methods: The genome was sequenced (Miseq) and de novo assembled (Velvet). PCR and Sanger sequencing were performed to determine the sequence of the genomic island.Results: The new variant of AGI1 named AGI1-A (41.7 kb), located at the 3' end of the chromosomal trmE, was detected in an E. cloacae complex isolate identified as Enterobacter hormaechei subsp. oharae. The backbone of AGI1-A lacked A008, part of A025, A026 and the resolvase gene. Its MDR region (19.7 kb) contained two integrons followed by a hybrid transposon Tn502/Tn5053. The former integron was a typical In4-type class 1 integron carrying aadA1 and the latter integron carrying dfrA1 did not belong to a class described to date. The nucleotide sequence intI-dfrA1 was surrounded by a 78 bp imperfect repeat sequence in inverse orientation. An external circular form of AGI1-A was detected, suggesting potential mobility. AGI1-A was also detected in 15 isolates from the outbreak selected at random. They belonged to the ST114 high-risk clone.Conclusions: AGI1-A, a variant of AGI1 described in Acinetobacter baumannii, is the first genomic resistance island belonging to the Salmonella genomic island/Proteus genomic island/Acinetobacter genomic island family detected in E. cloacae. One might, therefore, fear for interspecies dissemination of genomic islands from this family. [ABSTRACT FROM AUTHOR]

Objectives To characterize the structure of a variant of Acinetobacter genomic island 1 (AGI1) in the Enterobacter cloacae clinical isolate EclC2185 responsible for an 8 year outbreak in Dijon University Hospital. Methods The genome was sequenced (Miseq) and de novo assembled (Velvet). PCR and Sanger sequencing were performed to determine the sequence of the genomic island. Results The new variant of AGI1 named AGI1-A (41.7 kb), located at the 3′ end of the chromosomal trmE, was detected in an E. cloacae complex isolate identified as Enterobacter hormaechei subsp. oharae. The backbone of AGI1-A lacked A008, part of A025, A026 and the resolvase gene. Its MDR region (19.7 kb) contained two integrons followed by a hybrid transposon Tn 502 /Tn 5053. The former integron was a typical In4-type class 1 integron carrying aadA1 and the latter integron carrying dfrA1 did not belong to a class described to date. The nucleotide sequence intI-dfrA1 was surrounded by a 78 bp imperfect repeat sequence in inverse orientation. An external circular form of AGI1-A was detected, suggesting potential mobility. AGI1-A was also detected in 15 isolates from the outbreak selected at random. They belonged to the ST114 high-risk clone. Conclusions AGI1-A, a variant of AGI1 described in Acinetobacter baumannii, is the first genomic resistance island belonging to the Salmonella genomic island/ Proteus genomic island/ Acinetobacter genomic island family detected in E. cloacae. One might, therefore, fear for interspecies dissemination of genomic islands from this family. [ABSTRACT FROM AUTHOR]

Objectives: To provide detailed genetic characterization of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp.Methods: P. aeruginosa 60512, K. pneumoniae 447, P. aeruginosa 12939 and Enterobacter sp. A1137 were subjected to genome sequencing. The complete nucleotide sequences of two plasmids (p60512-IMP from the 60512 isolate and p447-IMP from the 447 isolate) and two chromosomes (the 12939 and A1137 isolates) were determined, then a genomic comparison of p60512-IMP, p447-IMP and four novel blaIMP-carrying transposons (Tn6394, Tn6375, Tn6411 and Tn6397) with related sequences was performed. Transferability of the blaIMP gene and bacterial antimicrobial susceptibility were tested.Results: Tn6394 and Tn6375 were located in p60512-IMP and p447-IMP, respectively, while Tn6411 and Tn6397 were integrated into the 12939 and A1137 chromosomes, respectively. Tn6394 was an ISPa17-based transposition unit that harboured the integron In992 (carrying blaIMP-1). In73 (carrying blaIMP-8), In73 and In992, together with the ISEcp1:IS1R-blaCTX-M-14-IS903D unit, the macAB-tolC region and the truncated aacC2-tmrB region, respectively, were integrated into the prototype transposons Tn1722, Tn1696 and Tn7, respectively, generating the Tn3-family unit transposons, Tn6375 and Tn6378, and the Tn7-family unit transposon Tn6411, respectively. Tn6397 was a large integrative and conjugative element carrying Tn6378.Conclusions: Complex events of transposition and homologous recombination have occurred during the original formation and further plasmid and chromosomal integration of these four transposons, promoting accumulation and spread of antimicrobial resistance genes. [ABSTRACT FROM AUTHOR]

Background: Despite the clear role of the Nkx2-5 gene mutations as the trigger for Congenital Heart Disease (CHD) in different populations, the condition of these mutations in our population remains obscure. Objectives: The present study aimed to assess different Nkx2-5 gene mutations in a sample of Iranian patients with CHD. Patients and Methods: This cross-sectional study was conducted on 79 consecutive suspected non-syndromic CHD patients at Rajaie Cardiovascular Medical and Research Center between 2016 and 2017. Detailed clinical evaluations were performed and CHD was confirmed by echocardiography. The exons of the Nkx2-5 gene were sequenced. In silico analysis was done using Mutation taster, SNP nexus, and Vienna RNA package. In addition, statistical analysis was performed using the SPSS statistical software, version 16.0. P ≤ 0.05 was considered to be statistically significant. Results: The study results revealed four synonymous polymorphisms; i.e., rs2277923, rs703752, rs3729753, and c.217C > T, the last of which was novel. Regarding the frequency of different Single Nucleotide Polymorphism (SNP) genotypes, the overall frequency of wild, heterozygous, and mutant genotypes was respectively 65.8%, 31.6%, and 2.5% for rs2277923, 54.4%, 0.0%, and 45.6% for rs703752, 96.2%, 3.8%, and 0.0% for rs3729753, and 93.7%, 6.3%, and 0.0% for c.217 C > T. Bioinformatics analysis demonstrated that the detected novel variants were not pathogens. Moreover, the genotypic variants of all SNPs were independent of gender, type of heart defect, and hereditary form of the disease. Conclusions: The results could not show any major roles for different exon-related SNPs on the Nkx2-5 gene as the candidate risk profile for CHD. The results also demonstrated no significant associations between such mutations and increased likelihood of specific heart defects. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) negatively regulate mRNAs at post-transcriptional level and thus can regulate different biological processes. Here we analyze the sequence characteristics and length distribution of miRNA sequences of six monocot and six dicot plants. We observe a species specific nucleotide preference of miRNAs. Although the first position of 5' end of mature miRNAs is U rich, there exists a wide variation. While the GC% of monocot mature miRNAs in general is nearly equal to the AU%, the GC% of stress induced miRNAs is significantly higher than AU%. Thus, higher content of GC% can be used as a signature of stress induced miRNAs in monocot. The length distribution of mature miRNAs shows the highest peak at 21 nucleotides with some other minor peaks at 20, 22 and 24 nucleotides. The synthesis of some miRNAs has positional preference either to 5' or to 3' arm of their precursors, but they are different in monocot and dicot. [ABSTRACT FROM AUTHOR]

Objectives: To characterize the mobile colistin resistance gene mcr-5 in Aeromonas hydrophila from backyard pigs in rural areas of China.Methods: Pig faecal samples from 194 households were directly tested for the presence of mcr-5 by PCR assay and the phenotypic antimicrobial susceptibility profiles of the mcr-5-positive isolates were determined using the broth dilution method. The genomic location and transferability of mcr-5 were analysed by S1-PFGE with Southern blotting and DNA hybridization, and natural transformation, respectively. One strain isolated from an mcr-5-positive sample was subjected to WGS and the stability of the mcr-5-harbouring plasmid over successive generations was examined by subculturing.Results: One mcr-5-positive A. hydrophila isolate showing resistance, with a colistin MIC of 4 mg/L, was isolated from a backyard pig faecal sample. mcr-5 was located on a 7915 bp plasmid designated pI064-2, which could naturally transform into a colistin-susceptible A. hydrophila strain of porcine origin and mediated colistin resistance in both the original isolate and its transformants. The plasmid backbone (3790 bp) of pI064-2 showed 81% nucleotide sequence identity to the corresponding region of the ColE2-type plasmid pAsa1 from Aeromonas salmonicida, while similar replication primases are widely distributed among aeromonads, Enterobacteriaceae and Pseudomonas species.Conclusions: To the best of our knowledge, this is the first identification of the novel colistin resistance gene mcr-5 in an A. hydrophila isolate from the faeces of a backyard pig. mcr-5 is expected to be able to disseminate among different bacterial species and genera. [ABSTRACT FROM AUTHOR]

Copyright of Rechtsmedizin is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Laribacter hongkongensis is a facultative anaerobic, non-fermentative, Gram-negative bacillus associated with community-acquired gastroenteritis and traveller's diarrhoea. No clinical MDR L. hongkongensis isolate has been reported yet.Methods: We performed WGS (PacBio and Illumina) on a clinical L. hongkongensis strain HLGZ1 with an MDR phenotype.Results: HLGZ1 was resistant to eight classes of commonly used antibiotics. Its complete genome was a single circular chromosome of 3 424 272 bp with a G + C content of 62.29%. In comparison with the reference strain HLHK9, HLGZ1 had a higher abundance of genes associated with DNA metabolism and recombination. Several inserts including two acquired resistance gene clusters (RC1 and RC2) were also identified. RC1 carried two resistance gene cassette arrays, aac(6')-Ib-cr-aadA2-Δqac-Δsul1-floR-tetR-tetG and arr-3-dfrA32-ereA2-Δqac-sul1, which shared significant nucleotide sequence identities with the MDR region of Salmonella Genomic Island 1 from Salmonella enterica serovar Typhimurium DT104. There was also an integron-like structure, intl1-arr3-dfrA27-Δqac-sul1-aph(3')-Ic, and a tetR-tetA operon located on RC2. MLST analysis identified HLGZ1 as ST167, a novel ST clustered with two strains previously isolated from frogs.Conclusions: This study provides insight into the genomic characteristics of MDR L. hongkongensis and highlights the possibilities of horizontal resistance gene transfer in this bacterium with other pathogens. [ABSTRACT FROM AUTHOR]

The aim of the present study was to determine characteristics of Rheb gene and protein in Raini Cashmere goat. Comparative analyses of the nucleotide sequences were performed. Open reading frames (ORFs), theoretical molecular weights of deduced polypeptides, the protein isoelectric point, protein characteristics and three-dimensional structures was predicted using online standard softwares. The full cDNA nucleotide sequence shares 99%, 99%, 99% and 94% identity with Inner Mongolia Cashmere goat, cattle, horse and human, respectively. The deduced Rheb protein of Raini Cashmere goat consist of 184 amino acid residues and its predicted molecular weight was 20478 g/mol for the unmodified protein and the estimated isoelectric point (pI) was 5.59. Results showed that Rheb has a RAS domain starting at the amino acid 4 and ending at the amino acid 170. In conclusion, our data shows the Rheb cDNA is 555 bp in length, including a complete ORF corresponding to a polypeptide of 184 amino acids. Our results in Raini Cashmere goat showed that there are 1 N-glycosylation sites, 3 protein kinase C phosphorylation sites, 2 casein kinase II phosphorylation sites, 4 microbodies C-terminal targeting signals, 2 ATP/GTP binding sites motif A (Ploop) and a prenyl group binding site for predicted Psites of Rheb. Raini Cashmere goat Rheb protein also had an interaction with other predicted proteins. Hence, can suggest that Rheb has probably role in goat cells and must detect in future investigations. [ABSTRACT FROM AUTHOR]

Panfacial bone fracture is challenging. Even experienced surgeons find restoration of original facial architecture difficult because of the severe degree of fragmentation and loss of reference segments that could guide the start of facial reconstruction. To restore the facial contour, surgeons usually follow a general sequence for panfacial bone reduction. Among the sequences, the bottom-to-top and outside-in sequence is reported to be the most widely used in recent publications. However, a single sequence cannot be applied to all cases of panfacial fractures because of the variations in panfacial bone fracture patterns. In this article, we intend to find the reference and discuss the efficacy of inside-out sequence in facial bone fracture reconstruction. [ABSTRACT FROM AUTHOR]

ABSTRACT Stacking interaction between the aromatic heterocyclic bases plays an important role in the double helical structures of nucleic acids. Considering the base as rigid body, there are total of 18 degrees of freedom of a dinucleotide step. Some of these parameters show sequence preferences, indicating that the detailed atomic interactions are important in the stacking. Large variants of non-canonical base pairs have been seen in the crystallographic structures of RNA. However, their stacking preferences are not thoroughly deciphered yet from experimental results. The current theoretical approaches use either the rigid body degrees of freedom where the atomic information are lost or computationally expensive all atom simulations. We have used a hybrid simulation approach incorporating Monte-Carlo Metropolis sampling in the hyperspace of 18 stacking parameters where the interaction energies using AMBER-parm99bsc0 and CHARMM-36 force-fields were calculated from atomic positions. We have also performed stacking energy calculations for structures from Monte-Carlo ensemble by Dispersion corrected density functional theory. The available experimental data with Watson-Crick base pairs are compared to establish the validity of the method. Stacking interaction involving A:U and G:C base pairs with non-canonical G:U base pairs also were calculated and showed that these structures were also sequence dependent. This approach could be useful to generate multiscale modeling of nucleic acids in terms of coarse-grained parameters where the atomic interactions are preserved. This method would also be useful to predict structure and dynamics of different base pair steps containing non Watson-Crick base pairs, as found often in the non-coding RNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 212-226, 2016. [ABSTRACT FROM AUTHOR]

Lophophora williamsii (peyote) is a small, spineless, greenish-blue cactus found in Mexico and the southwestern United States. Ingestion of the cactus can result in hallucinations due to its content of mescaline. In the United States, L. williamsii is classified as a Schedule I controlled substance. In this study, we use DNA analysis of the chloroplast trnL/ trnF region and chloroplast rbcL gene to identify the individuals of Lophophora. Using the rbcL gene, Lophophora specimens could be distinguished from outgroups, but species within the genus could not be distinguished. The trnL/ trnF region split the Lophophora genus into several groups based on the length and substructure of an AT-rich segment of the sequence. Our results indicate that the genetic variability at the trnL/ trnF locus is greater than previously recognized. Although DNA structures at the trnL/ trnF region and rbcL gene do not align with the classification of Lophophora species, they can be used to aid in forensic analysis. [ABSTRACT FROM AUTHOR]

Copyright of Paediatria Croatica is the property of Paediatria Croatica and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We perform the conventional band structure and local density of states (LDOS) calculations in the vicinity of the Fermi level at ab initio molecular orbital level with 6-31G base set for one DNA duplex with repeated mononucleotide sequences and four DNA duplexes with repeated dinucleotide sequences in B form neutralized by Na+. The LDOS of six other DNA duplexes with repeated trinucleotide sequences in the same states are analyzed. The obtained results are compared with those by the band calculations based on periodic boundary condition using screw axis symmetry. The investigations focused on the influence of the base composition and base sequence on the DNA conductivity. The band structure and LDOS calculation results indicated that base guanine is more important for DNA conductivity than the other bases, and DNA conductivity varies with base sequence of DNA. Moreover, poly (dG) • poly (dC) shows the best conductor in our DNA duplex models. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Copyright of Revista Brasileira de Oftalmologia is the property of Sociedade Brasileira de Oftalmologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

When rope is found at a crime scene, the type of fiber is currently identified through its microscopic characteristics. However, these characteristics may not always unambiguously distinguish some types of rope from others. If rope samples contain cells from the plants of origin, then DNA analysis may prove to be a better way to identify the type of rope obtained from a crime scene. The objective of this project was to develop techniques of DNA analysis that can be used to differentiate between ropes made from Cannabis sativa L. (hemp), Agave sisalana Perrine (sisal), Musa textilis Née (abaca, “Manila hemp”), Linum usitatissimum L. (flax), and Corchorus olitorus L. (jute). The procedures included extracting the DNA from the rope, performing polymerase chain reaction (PCR) using the extracted DNA as a template, and analyzing the DNA products. A primer pair for PCR, chosen from within a chloroplast gene for the large subunit of ribulose bisphosphate carboxylase/oxygenase, was designed to be specific for plant DNA and complementary to the genes from all five plants. The resulting PCR fragments were approximately 771 base pairs long. The PCR fragments, distinguished through base sequence analysis or restriction enzyme analysis, could be used to identify the five different rope types. The procedure provides a useful addition to visual methods of comparing rope samples. [ABSTRACT FROM AUTHOR]

Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it is demonstrated, via an example, the modified model offers better solutions than previous model does. [ABSTRACT FROM AUTHOR]

A multi-copy plasmid containing the SNQ3 gene confers hyper-resistance to 4-nitroquinoline-N-oxide (4NQO), Trenimon, MNNG, cycloheximide, and to sulfometuron methyl in yeast transformants. Restriction analysis, subcloning, and DNA sequencing revealed an open reading frame of 1950 bp on the SNQ3-containing insert DNA. Gene disruption and transplacement into chromosomal DNA yielded 4NQO-sensitive null mutants which were also more sensitive than the wild-type to Trenimon, cycloheximide, sulfometuron methyl, and MNNG. Hydropathic analysis showed that the SNQ3-encoded protein is most likely not membrane-bound, while the codon bias index points to low expression of the gene. [ABSTRACT FROM AUTHOR]

Gonadotropin-releasing hormone (GnRH) has been shown to play a role in the regulation of human chorionic gonadotropin (hCG) secretion by the human placenta. Molecular studies have demonstrated that human placental trophoblast cells synthesize a progonadotropin-releasing hormone (pro-GnRH) identical to its human hypothalamic counterpart. However, far less is known about nonhuman primates. To determine whether pro-GnRH exists in the rhesus placenta, pro-GnRH mRNA was cloned, sequenced, and shown to be 97.6% homologous to its human placental counterpart. A single base difference (base 1167) in the domain encoding GnRH results in the same amino acid, arginine, in position 8, whereas four base differences (bases 1200, 1253, 1268, 1292) in the domain encoding GnRH-associated peptide (GAP) result in four different amino acids in positions 19, 37, 42, and 50. The absence of a basic amino acid in position 50 suggests the rhesus sequence may be cleaved to yield GAP peptides different from the human placenta. Thus, these data justify the use of mammalian GnRH in studies of rhesus placental function, but indicate the need to investigate the roles unique GAP peptides may play in placental/uterine function. [ABSTRACT FROM AUTHOR]

The composition of nuclear DNA in 3 Vicia species are compared. The species V. eriocarpa, V. johannis and V. melanops are from three separate subgeneric sections of Vicia and show a fourfold variation in their amounts of nuclear DNA. DNA melting experiments, buoyant density gradient analysis and Cot reassociation experiments show that the quantitiative change in nuclear DNA between the three species is achieved by changes in the amounts of both repetitive and nonrepetitive DNA sequences. It is suggested that while the increase in the repetitive fraction is achieved by the proliferation of repetitive base sequences the increase in the nonrepetitive fraction is due to the steady accretion of highly diverged base sequences resulting from mutations, deletions, insertions and base sequence rearrangements among families of repetitive sequences. [ABSTRACT FROM AUTHOR]

Rapid advances in molecular technology have led to the identification of many genes responsible for inherited disease in ophthalmology. These discoveries also portend an understanding of the pathogenesis of more common ophthalmic disorders which have a genetic component, such as open-angle glaucoma and age-related macular degeneration. This review comprises a summary of these advances in molecular genetics, particularly the contribution of the Human Genome Project; a tabulation of the genes recently proven to be mutated in hereditary ocular conditions; and a discussion of the implications for the practising ophthalmologist. [ABSTRACT FROM AUTHOR]

The complete nucleotide sequence of a nitrogenase ( nifH) gene was determined from a second strain (HRN18a) of Frankia, an aerobic soil bacterium. The open reading frame is 870 bp long and encodes a polypeptide of 290 amino acids. The amino acid and nucleotide sequences were compared with 21 other published sequences. The two Frankia strains were 96% similar at the amino acid level and 93% similar at the nucleotide level. A number of methods were used to infer phylogenies of these nitrogen fixers, based on nifH amino acid and nucleotide sequences. The results obtained do not agree completely with other phylogenies for these bacteria and thus make probable occurrences of lateral transfer of the nif genes. The time of divergence of the two Frankia strains could be estimated at about 100 million years. The vanadium-dependent (Type 2) nitrogenase present in Azotobacter spp. appears to be a recent derivation from the conventional molybdenum-dependent (Type 1) enzyme, whereas the iron-dependent (Type 3) alternative nitrogenase would have a much older origin. [ABSTRACT FROM AUTHOR]