scholarly journals Molecular Characterization of a New Variant of Toxin-Coregulated Pilus Protein (TcpA) in a Toxigenic Non-O1/Non-O139 Strain ofVibrio cholerae

2000 ◽  
Vol 68 (2) ◽  
pp. 948-952 ◽  
Author(s):  
Bisweswar Nandi ◽  
Ranjan K. Nandy ◽  
Ana C. P. Vicente ◽  
Asoke C. Ghose
Keyword(s):  
Southern Hybridization ◽  
Analysis Data ◽  
Nucleotide Sequence Analysis ◽  
Predicted Amino Acid Sequence ◽  
Ancestral Gene ◽  
Hypervariable Regions ◽  
New Variant ◽  
Toxin Coregulated Pilus ◽  
El Tor

ABSTRACT A toxigenic non-O1/non-O139 strain of Vibrio cholerae(10259) was found to contain a new variant of the toxin-coregulated pilus (TCP) protein gene (tcpA) as determined by PCR and Southern hybridization experiments. Nucleotide sequence analysis data of the new tcpA gene in strain 10259 (O53) showed it to be about 74 and 72% identical to those of O1 classical and El Tor biotype strains, respectively. The predicted amino acid sequence of the 10259 TcpA protein shared about 81 and 78% identity with the corresponding sequences of classical and El Tor TcpA strains, respectively. An antiserum raised against the TCP of a classical strain, O395, although it recognized the TcpA protein of strain 10259 in an immunoblotting experiment, exhibited considerably less protection against 10259 challenge compared to that observed against the parent strain. Incidentally, the tcpA sequences of two other toxigenic non-O1/non-O139 strains (V2 and S7, both belonging to the serogroup O37) were determined to be almost identical to that of classicaltcpA. Further, tcpA of another toxigenic non-O1/non-O139 strain V315-1 (O nontypeable) was closely related to that of El Tor tcpA. Analysis of these results with those already available in the literature suggests that there are at least four major variants of the tcpA gene in V. cholerae which probably evolved in parallel from a common ancestral gene. Existence of highly conserved as well as hypervariable regions within the sequence of the TcpA protein would also predict that such evolution is under the control of considerable selection pressure.

scholarly journals Genetic characterization of a new variant within the ET-37 complex of Neisseria meningitidis associated with outbreaks in various parts of the world

2000 ◽  
Vol 125 (2) ◽  
pp. 285-298 ◽  
Author(s):  
J. JELFS ◽  
R. MUNRO ◽  
F. E. ASHTON ◽  
D. A. CAUGANT
Keyword(s):  
Neisseria Meningitidis ◽  
Genetic Markers ◽  
Southern Hybridization ◽  
Genetic Characterization ◽  
Mortality Rates ◽  
Pulsed Field Gel Electrophoresis ◽  
Additional Restriction ◽  
New Variant ◽  
Genetic Rearrangements

A new variant within the electrophoretic type (ET)-37 complex of Neisseria meningitidis, ET-15, first detected in Canada in 1986, has been associated with severe clinical infections and high mortality rates in several European countries, Israel and Australia. To ascertain the genetic and epidemiological relationships of ET-15 strains from different geographical areas, 72 ET-15 isolates from 10 countries were compared to 13 isolates representing other clones of the ET-37 complex. The 85 strains were analysed by pulsed-field gel electrophoresis (PFGE) using 2 restriction endonucleases and Southern hybridization with 10 genetic markers. Four ET-15 strains and 4 other strains of the ET-37 complex were further examined using an additional restriction enzyme and a total of 18 genetic markers. PFGE fingerprints of the ET-15 strains were closely related. Strains within each country were even more closely related, suggesting single introductions of the clone. Physical mapping of genes in ET-15 and other strains of the ET-37 complex demonstrated that large genetic rearrangements of the genome have occurred in association with the appearance of the ET-15 variant.

scholarly journals Cloning and structural characterization of the genes coding for adenosylcobalamin-dependent methylmalonyl-CoA mutase from Propionibacterium shermanii

1989 ◽  
Vol 260 (2) ◽  
pp. 345-352 ◽  
Author(s):  
E N Marsh ◽  
N McKie ◽  
N K Davis ◽  
P F Leadlay
Keyword(s):  
Amino Acid ◽  
Alpha Subunit ◽  
Nucleotide Sequence Analysis ◽  
Homologous Region ◽  
Amino Acid Residues ◽  
Upstream Gene ◽  
Ancestral Gene ◽  
Propionibacterium Shermanii ◽  
Hybridization Probes

The structural genes coding for both subunits of adenosylcobalamin-dependent methylmalonyl-CoA mutase from the Gram-positive bacterium Propionibacterium shermanii have been cloned, with the use of synthetic oligonucleotides as primary hybridization probes. The genes are closely linked and are transcribed in the same direction. Nucleotide sequence analysis of 4.5 kb of DNA encompassing both genes allowed us to infer the complete amino acid sequence of the two subunits: the beta-subunit is the product of the upstream gene, and consists of 638 amino acid residues (Mr 69465) and the alpha-subunit consists of 728 amino acid residues (Mr 80,147). There is a very close structural homology between the two subunits, reflecting the probable duplication of a common ancestral gene. A sequence present only in the alpha-subunit is significantly homologous to a portion of the sequence of the methylmalonyl-CoA-binding subunit of transcarboxylase from P. shermanii [Samols, Thornton, Murtif, Kumar, Haase & Wood (1988) J. Biol. Chem. 263, 6461-6464], and this homologous region may form part of the CoA ester-binding site in both enzymes.

scholarly journals Detection of a New Variant in Outbreak of Bovine Ephemeral Fever in Turkey, 2020

2022 ◽  
Author(s):  
Neval Berrin Arserim ◽  
Metin Gürçay ◽  
Ahmed Sait ◽  
Mustafa Türkdoğan
Keyword(s):  
Phylogenetic Analysis ◽  
Respiratory Symptoms ◽  
Nucleotide Sequences ◽  
Nucleotide Sequence Analysis ◽  
Bovine Ephemeral Fever Virus ◽  
Partial Nucleotide Sequence ◽  
Bovine Ephemeral Fever ◽  
New Variant ◽  
Indian Isolates

Background: In this study, partial nucleotide sequence analysis of the G gene was performed for the molecular characterization of the virus that caused the bovine ephemeral fever virus (BEFV) epidemic in Turkey in 2020. Phylogenetic analysis of these nucleotide sequences was performed with the virus nucleotide sequences of the epidemics seen in 2008 and 2012. These sequences were announced in GenBank. Phylogenetic analysis of these nucleotide sequences was performed with the virus nucleotide sequences of the epidemics seen in 2008 and 2012. Methods: The study was conducted in dairy cattle holdings located in Diyarbakır Sur, Çınar and Dicle regions in South-eastern Turkey in August-November 2020. The number of animals in the holdings consisted of 750 (n=750), 150 (n=150) and 200 (n=200) cattle, respectively. Result: Severe respiratory symptoms and high mortality in the affected animals were notable symptoms. As a result of the phylogenetic analysis, it was determined that the virus that caused the epidemic in Turkey in 2020 was formed by a new variant in the Turkey-2 group, which was similar to the Indian isolates, unlike the Turkey-1 group, which was close to the Middle East variants in 2008 and 2012 isolates.

scholarly journals Cloning and Characterization of a Chromosomal Class C β-Lactamase and Its Regulatory Gene in Laribacter hongkongensis

2005 ◽  
Vol 49 (5) ◽  
pp. 1957-1964 ◽  
Author(s):  
Susanna K. P. Lau ◽  
Pak-leung Ho ◽  
Maria W. S. Li ◽  
Hoi-wah Tsoi ◽  
Raymond W. H. Yung ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Southern Hybridization ◽  
Regulatory Gene ◽  
Kinetic Properties ◽  
Restriction Fragments ◽  
Regulatory Systems ◽  
Laribacter Hongkongensis ◽  
Consensus Motifs ◽  
Class C

ABSTRACT Laribacter hongkongensis, a newly discovered bacterium recently shown to be associated with community-acquired gastroenteritis, is generally resistant to most β-lactams except the carbapenems. We describe the cloning and characterization of a novel chromosomal class C β-lactamase and its regulatory gene in L. hongkongensis. Two genes, ampC and ampR, were cloned by inserting restriction fragments of genomic DNA from L. hongkongensis strain HLHK5 into pBK-CMV to give the recombinant plasmid pBK-LHK-5. The ampR and ampC genes and their promoters were divergently oriented, with the ampR gene immediately upstream of the ampC gene and an intercistronic Lys-R motif, typical of inducible ampC-ampR regulatory systems. The deduced amino acid sequence of the cloned AmpC β-lactamase (pI 8.1) contained consensus motifs characteristic of class C β-lactamases but had identities no greater than 46% to known class C β-lactamases. The kinetic properties of this AmpC were also compatible with those of a class C β-lactamase. PCR of 20 clinical isolates of L. hongkongensis, including HLHK5, showed the presence of both ampC and ampR genes in all isolates. Southern hybridization suggested that the ampC gene of HLHK5 was chromosomally encoded. Subcloning experiments showed that the expression of the ampC gene of HLHK5 was regulated by its ampR gene, which acts as a repressor. The β-lactamase characterized from strain HLHK5 was named LHK-5 (gene, bla LHK-5) and represents the first example of AmpC β-lactamase in the β subdivision of proteobacteria.

scholarly journals Isolation and characterization of the new SARS-CoV-2 variant in travellers from the United Kingdom to India: VUI-202012/01 of the B.1.1.7 lineage

2021 ◽  
Vol 28 (2) ◽  
Author(s):  
Pragya D Yadav ◽  
Dimpal A Nyayanit ◽  
Rima R Sahay ◽  
Prasad Sarkale ◽  
Jayshri Pethani ◽  
...  
Keyword(s):  
United Kingdom ◽  
Severe Acute Respiratory Syndrome ◽  
Surveillance System ◽  
The United Kingdom ◽  
Isolation And Characterization ◽  
New Variant ◽  
The Uk ◽  
Local Transmission

We have isolated the new severe acute respiratory syndrome coronavirus-2 variant of concern 202 012/01 from the positive coronavirus disease 2019 cases that travelled from the UK to India in the month of December 2020. This emphasizes the need for the strengthened surveillance system to limit the local transmission of this new variant.

scholarly journals Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1556
Author(s):  
Monika J. Hjortaas ◽  
Elena Fringuelli ◽  
Adérito L. Monjane ◽  
Aase B. Mikalsen ◽  
Christine M. Jonassen ◽  
...  
Keyword(s):  
Full Length ◽  
Genomic Diversity ◽  
Last Common Ancestor ◽  
Source Of Infection ◽  
New Variant ◽  
Genotype 2 ◽  
Boat Traffic ◽  
Horizontal Spread ◽  
Full Length Genome

Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.

Cloning and characterization of an electrogenic Na/HCO3− cotransporter from the squid giant fiber lobe

2007 ◽  
Vol 292 (6) ◽  
pp. C2032-C2045 ◽  
Author(s):  
Peter M. Piermarini ◽  
Inyeong Choi ◽  
Walter F. Boron
Keyword(s):  
Giant Axon ◽  
Predicted Amino Acid Sequence ◽  
Giant Fiber ◽  
Reading Frame ◽  
Excitable Membranes ◽  
Current Voltage ◽  
Partial Cdna ◽  
Partial Cdna Clone ◽  
Current Voltage Relationship

The squid giant axon is a classic model system for understanding both excitable membranes and ion transport. To date, a Na+-driven Cl-HCO3− exchanger, sqNDCBE—related to the SLC4 superfamily and cloned from giant fiber lobe cDNA—is the only HCO3−-transporting protein cloned and characterized from a squid. The goal of our study was to clone and characterize another SLC4-like cDNA. We used degenerate PCR to obtain a partial cDNA clone (squid fiber clone 3, SF3), which we extended in both the 5′ and 3′ directions to obtain the full-length open-reading frame. The predicted amino-acid sequence of SF3 is similar to sqNDCBE, and a phylogenetic analysis of the membrane domains indicates that SF3 clusters with electroneutral Na+-coupled SLC4 transporters. However, when we measure pHi and membrane potential—or use two-electrode voltage clamping to measure currents—on Xenopus oocytes expressing SF3, the oocytes exhibit the characteristics of an electrogenic Na/HCO3− cotransporter, NBCe. That is, exposure to extracellular CO2/HCO3− not only causes a fall in pHi, followed by a robust recovery, but also causes a rapid hyperpolarization. The current-voltage relationship is also characteristic of an electrogenic NBC. The pHi recovery and current require HCO3− and Na+, and are blocked by DIDS. Furthermore, neither K+ nor Li+ can fully replace Na+ in supporting the pHi recovery. Extracellular Cl− is not necessary for the transporter to operate. Therefore, SF3 is an NBCe, representing the first NBCe characterized from an invertebrate.

Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution

1990 ◽  
Vol 10 (6) ◽  
pp. 2513-2520
Author(s):  
L C Samuelson ◽  
K Wiebauer ◽  
C M Snow ◽  
M H Meisler
Keyword(s):  
Gene Family ◽  
Single Gene ◽  
Primate Evolution ◽  
Endogenous Retrovirus ◽  
Gene Copy ◽  
Nucleotide Sequence Analysis ◽  
Ancestral Gene ◽  
Molecular Events ◽  
Amylase Genes ◽  
History Of

We have analyzed the junction regions of inserted elements within the human amylase gene complex. This complex contains five genes which are expressed at high levels either in the pancreas or in the parotid gland. The proximal 5'-flanking regions of these genes contain two inserted elements. A gamma-actin pseudogene is located at a position 200 base pairs upstream of the first coding exon. All of the amylase genes contain this insert. The subsequent insertion of an endogenous retrovirus interrupted the gamma-actin pseudogene within its 3'-untranslated region. Nucleotide sequence analysis of the inserted elements associated with each of the five human amylase genes has revealed a series of molecular events during the recent history of this gene family. The data indicate that the entire gene family was generated during primate evolution from one ancestral gene copy and that the retroviral insertion activated a cryptic promoter.

Tx1: a transposable element from Xenopus laevis with some unusual properties

1986 ◽  
Vol 6 (3) ◽  
pp. 933-941
Author(s):  
J E Garrett ◽  
D Carroll
Keyword(s):  
Xenopus Laevis ◽  
Germ Line ◽  
Variable Number ◽  
Target Site ◽  
Nucleotide Sequence Analysis ◽  
Chromosomal Locus ◽  
Stem Loop ◽  
Left Handed ◽  
Transposable Genetic Elements

A family of transposable genetic elements in the genome of the frog, Xenopus laevis, is described. They are designated Tx1. Transposability of the elements was deduced by characterization of a chromosomal locus which is polymorphic for the presence or absence of a Tx1 element. Nucleotide sequence analysis suggested that Tx1 elements show target site specificity, as they are inserted at the pentanucleotide TTTAA in all four cases that were examined. The elements appear to have 19-base-pair (bp) inverted terminal repeats, and they are flanked by 4-bp target duplications (TTAA), although the possibility that they do not create target site duplications is discussed. Tx1 elements have several unusual characteristics: the central portion of each element is comprised of a variable number of two types of 393-bp repeating units; the rightmost 1,000 bp of the element contains separate regions potentially capable of forming bends, left-handed Z-form DNA, and alternative stem-loop structures. Comparisons among single frogs suggest that germ line transposition is relatively infrequent and that variations in numbers of internal repeats accumulate quite slowly at any locus.

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