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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]

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]

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]

The study on nucleic acid retention in ion-pair reversed-phase high-performance liquid chromatography mainly focuses on size-dependence, however, other factors influencing retention behaviors have not been comprehensively clarified up to date. In this present work, the retention behaviors of oligonucleotides and double-stranded DNAs were investigated on silica-based C18 stationary phase by ion-pair reversed-phase high-performance liquid chromatography. It is found that the retention of oligonucleotides was influenced by base composition and base sequence as well as size, and oligonucleotides prone to self-dimerization have weaker retention than those not prone to self-dimerization but with the same base composition. However, homo-oligonucleotides are suitable for the size-dependent separation as a special case of oligonucleotides. For double-stranded DNAs, the retention is also influenced by base composition and base sequence, as well as size. This may be attributed to the interaction of exposed bases in major or minor grooves with the hydrophobic alky chains of stationary phase. In addition, no specific influence of guanine and cytosine content was confirmed on retention of double-stranded DNAs. Notably, the space effect resulted from the stereostructure of nucleic acids also influences the retention behavior in ion-pair reversed-phase high-performance liquid chromatography. [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]

Despite substantial eff orts, the cause of a signifi cant proportion of mendelian disorders is still unknown. Recently, signifi cant advances in determination of nucleotide sequence present an opportunity to investigate the genetic material down to a single nucleotide resolution on the whole exome or genome scale. This opens complete possibilities for deciphering genetic etiology of genetic disorders and, most importantly, expanding the fi eld of genetic studies from limited cases of diseases occurring in large families to smaller familial confi gurations, making detection of causative genes possible even in trios of parents with a single aff ected proband. Despite the development in both the technology of next generation sequencing and increases in computational power for complex data analysis, the interpretation of results, making sense of genome-scale information in medical setting and conveying this information to the patient, have been lagging behind. In addition, novel ethical questions have opened, especially those related to reporting of incidental fi ndings. These issues are the key points for discussion prior to setting the protocols and guidelines for implementing the whole exome and genome sequencing into clinical practice. This overview will initially give a brief introduction to the technical background behind the next generation sequencing and methodological steps involved. Basic introduction to some of the key steps in data analysis of the next generation sequencing data and challenges encountered thereby will also be given, based on our experiences at the Centre for Mendelian Genomics in Slovenia. [ABSTRACT FROM AUTHOR]

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]

The development of string theory has opened a completely new chapter and the way of thinking. A tight connection between DNA, water and strings, as well as their properties, lead to the idea that the soul is the shelter of our thoughts. Only 2% of the haploid human genome codes for proteins, while the rest consists of non-coding RNA genes, regulatory sequences, introns. The rest of the DNA, about 2.9 billion of base pairs, represents: cultural heredity of the person's family and a part being formed by the person during his/her lifetime, which gives the answer to what the use of the non-coding sequences is. Water molecules do not stay permanently united with DNA (the connection is not covalent), but they disconnect at every 0.5-1 nsec, forming and leaving the DNA molecule. It is well known that the DNA structure depends on water and that „water remembers thoughts", and depending on the thoughts of a person it carries them to the physical structure of DNA. At the beginning of the physical organization of the water molecule there are strings. When a person dies, the DNA and water molecule are disconnected leaving only strings with an appropriate features being conditioned by three-dimensional structure of DNA shaped by water. Every person has a unique string appearance, as it is the case with the snowflakes (the DNA print in the strings). [ABSTRACT FROM AUTHOR]

This article presents a case of tick infestation of the lower eyelid by a previously unreported species. A 71-year-old male presented with a tick attached to the lower eyelid. The tick was identified morphologically, and then molecularly via polymerase chain reaction (PCR) and sequencing of its DNA. In addition, a review of the literature relevant to the genera of ticks associated with infestation of the human eye is provided. The tick, which was in the nymphal developmental stage, was first identified according to taxonomic keys as Dermacentor sp. For complete species identification, 16s rDNA gene PCR and sequencing were performed, which showed that the tick was D. marginatus. Systematizing tick species could assist physicians in determining the potential for transmission of tick-borne human diseases. [ABSTRACT FROM AUTHOR]

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]