Characterization of GPX1 and DIO1 Genes in Bubalus Bubalis

Selenoprotein genes contain selenium in the form of selenocysteine which is involved in protecting the cells from oxidative stress. Soils in India differ greatly in selenium concentrations affecting feed stuffs for selenium availability. Selenoproteins have recently been identified in variety of living organisms including humans which have 25 selenoprotein genes. Among these families of selenoprotein genes, we sequenced Gpx1 gene (Glutathione peroxidases1) and Dio1 gene (Iodothyronine deiodinases) in Bubalus bubalis. Gpx1 is most abundant and ubiquitously expressed selenoprotein which helps to protect against the damaging effects of hydrogen peroxide and oxygen rich free radicals whereas Dio1 is expressed mainly in liver, thyroid gland and adipose tissue, its main function is to convert tetraiodothyronine (T4) to its active form thyroxine (T3) in the presence of deiodinases enzyme. The main aim of the study was to characterize these two genes and to find out the buffalo specific SNPs. This was accomplished by designing primers using cattle database and sequencing a panel of 24 samples consisting of 6 diverse breeds of buffalo. Gpx1 consisted of 2 exons (Accession ID: JQ031269) while Dio1 comprised 4 exons (Accession ID: JQ791197). In Gpx1 gene, 9 SNPs were recorded and 4 were non synonymous, changing amino acid were distributed equally in both exon. In exon 1, A141G (aa Q5R) and G161A (aa A12T); and in exon 2 C785T (aa R132W) and A808T (aa S139R). In Dio1 gene, 3 non synonymous SNPs were identified at A188G (aa H22R), C215G (aa T31R) and G941A (aa V146I). These SNPs are novel and reported for the first time in Indian buffalo and has a potential for their use in diversity analysis and association with various selenium related traits.

Download Full-text

The mouse carbonic anhydrase I gene contains two tissue-specific promoters

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3308-3313.1989 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3308-3313

Author(s):

P Fraser ◽

P Cummings ◽

P Curtis

Keyword(s):

Carbonic Anhydrase ◽

Splice Acceptor Site ◽

Acceptor Site ◽

Exon 2 ◽

Tissue Specific ◽

Isolation And Characterization ◽

Carbonic Anhydrase I ◽

Erythroleukemia Cells ◽

Exon 1

We report the isolation and characterization of the mouse carbonic anhydrase I (CAI) gene. Direct RNA sequence analysis of the 5' nontranslated regions of CAI mRNA from mouse colon and mouse erythroleukemia cells demonstrated tissue specificity in the lengths and sequences of CAI transcripts. Analysis of several mouse CAI genomic clones showed that the transcripts arose from a single CAI gene with two tissue-specific promoters and eight exons. CAI transcripts in the colon were found to initiate just upstream of the erythroid exon 2 of the CAI gene region sequence. Erythroid transcripts originated from a novel promoter upstream of exon 1, which was located more than 10 but less than 250 kilobases upstream of exon 2. Erythroid exon 1 contained only a nontranslated sequence, which was spliced to exon 2 via a cryptic splice acceptor site located in the region that encoded the colon mRNA 5' nontranslated sequence. The remaining exon-intron junctions were conserved in comparison with those of the CAII and CAIII genes.

Download Full-text

Characterization of NRG1 gene fusion events in solid tumors.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.3113 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 3113-3113

Author(s):

Sushma Jonna ◽

Rebecca Feldman ◽

Sai-Hong Ignatius Ou ◽

Misako Nagasaka ◽

Jeffrey Swensen ◽

...

Keyword(s):

Transmembrane Domain ◽

Fusion Partner ◽

Exon 2 ◽

Downstream Signaling ◽

Chimeric Transcripts ◽

Exon 1 ◽

Tumor Types ◽

Fusion Products ◽

Ig Domain

3113 Background: NRG1 fusions are actionable genomic alterations detected across tumor types. The NRG1 gene encode for neuregulin, which serves as a ligand for ERBB3 and ERBB4 receptors and activates downstream signaling through the MAPK and PI3K pathways. Here, we update the detection of NRG1 gene fusions across tumor types and further describe fusion characteristics. Methods: Samples submitted for clinical molecular profiling that included RNA-sequencing (Archer Dx or Caris MI transcriptome) were retrospectively analyzed for NRG1 fusion events. All NRG1 fusions with ≥ 3 junction reads were identified for manual review and for characterization of fusion class, intact functional domains, domain prediction, breakpoints, frame retention and co-occurring alterations by NGS. Results: A total of 82 NRG1 fusion events (0.2% of 44,570) were identified. Among the fusions identified, the distribution across tumor types was as follows: non-small cell lung cancer (NSCLC, 54%), breast cancer (11%), ovarian cancer (7%), pancreatic cancer (7%), cholangiocarcinoma (6%), colorectal cancer (5%), and other (10%). Forty-two unique fusion partners were identified, the most common being CD74 (23%), ATP1B1 (9%), SLC3A2 (7%), RBPMS (6%) and SDC4 (4%). Almost half (47%) of all fusion events are expected to include the transmembrane domain contributed by the NRG1 fusion partner. Lung and pancreatobilliary cancers had the highest rates of transmembrane domain retention from their fusion partners (63.6% and 54.5%, respectively). In all other tumor groups, most fusion partners lacked transmembrane domains. In 15% of cases, the chimeric transcripts are predicted to lead to increased expression of NRG1. The most commonly reported breakpoints in NRG1 occur in exon 6 and exon 2. While fusions with the NRG1 breakpoint at exon 2 retain the immunoglobulin (Ig) domain and all downstream portions (including EGF-like domain), those at exon 6 do not contain the Ig portion and result in shorter chimeric proteins. The breakpoints in all CD74:NRG1 fusions, the most common fusions in NSCLC, occur at exon 5 or 6 and cause truncation of domains upstream of the EGF-like domain. In ATP1B1:NRG1 fusions, the most common fusions in pancreatobilliary cancers, the breakpoints are at exon 1 or 2 and retain the Ig domain. Conclusions: NRG1 fusion products are diverse across tumor types, but the significance of these variations is not clear. The biological and clinical implications of retaining certain domains of NRG1 (such as the Ig domain) and of fusion partners warrants further investigation.

Download Full-text

DISPERSIVE FRACTAL CHARACTERIZATION OF KIDNEY ARTERIES BY THREE-DIMENSIONAL MASS-RADIUS-ANALYSIS

Fractals ◽

10.1142/s0218348x95000771 ◽

1995 ◽

Vol 03 (04) ◽

pp. 879-891 ◽

Cited By ~ 7

Author(s):

M. SERNETZ ◽

M. JUSTEN ◽

F. JESTCZEMSKI

Keyword(s):

Fractal Structure ◽

Three Dimensional ◽

Arterial System ◽

Data Sets ◽

Scaling Properties ◽

Local Scaling ◽

Living Organisms ◽

Global And Local ◽

First Time

Three-dimensional data sets of kidney arterial vessels were obtained from resin casts by serial sectioning and by micro-NMR-tomography, and were analyzed by the mass-radius-relation both for global and local scaling properties. We present for the first time the spatial resolution of local scaling and thus the dispersion of the fractal dimension within the organs. The arterial system is characterized as a non-homogeneous fractal. We discuss and relate the fractal structure to the scaling and allometry of metabolic rates in living organisms.

Download Full-text

Molecular characterization of universal Mycoplasma and Acholeplasma laidlawii from buffaloes (Bubalus bubalis) at Karachi, Pakistan.

Indian Journal of Animal Research ◽

10.18805/ijar.b-737 ◽

2017 ◽

Author(s):

Syed Khurram Fareed ◽

Faiz Muhammad ◽

Javed Muhammad ◽

Masood Rabbani ◽

Taseer Ahmed Khan ◽

...

Keyword(s):

Respiratory Distress ◽

Bubalus Bubalis ◽

Nasal Discharge ◽

Specific Primers ◽

Tissue Samples ◽

Acholeplasma Laidlawii ◽

Precautionary Measures ◽

First Time ◽

Culture Positive

The present study was conducted to identify and characterize the bovine Acholeplasma laidlawii from 1120 clinically ill buffaloes and 470 lungs collected from buffaloes at abattoir of Karachi. All buffaloes were clinically examined and around 467 (13.48%) buffaloes had signs of respiratory distress including sticky nasal discharge, sunken eyes, dyspnea and fever. All the culture positive samples were further evaluated by PCR using specific primers of A. laidlawii and the amplified product to re-validate the sequence of the specie. This revealed that suspected buffaloes, 92 (2.66%) from nasal discharge and 44 (4.03%) from lung tissue samples respectively were positive for A. laidlawii. Rests of the samples were still under investigation. However it is first time proclaimed on research basis that A. laidlawii was infecting the buffaloes in Pakistan and precautionary measures should be taken to prevent losses from this specie in the months of October and April.

Download Full-text

Molecular characterization of novel germline deletions affecting SDHD and SDHC in pheochromocytoma and paraganglioma patients

Endocrine Related Cancer ◽

10.1677/erc-09-0084 ◽

2009 ◽

Vol 16 (3) ◽

pp. 929-937 ◽

Cited By ~ 13

Author(s):

Jean-Pierre Bayley ◽

Marjan M Weiss ◽

Anneliese Grimbergen ◽

Bernadette T J van Brussel ◽

Frederik J Hes ◽

...

Keyword(s):

Nonsense Mutations ◽

Gene Deletions ◽

Exon 2 ◽

Gene Insertion ◽

Large Deletions ◽

Exon 1 ◽

Long Range Pcr ◽

Intron 2 ◽

Dependent Probe

A major cause of paraganglioma and pheochromocytoma is germline mutation of the tumor suppressor genes SDHB, SDHC, and SDHD, encoding subunits of succinate dehydrogenase (SDH). While many SDH missense/nonsense mutations have been identified, few large deletions have been described. We performed multiplex ligation-dependent probe amplification deletion analysis in 126 point mutation-negative patients, and here we describe four novel deletions of SDHD and SDHC. Long-range PCR was used for the fine mapping of deletions. One patient had a 10 kb AluSg–AluSx-mediated deletion including SDHD exons 1 and 2, the entire TIMM8B gene, and deletion of exons of C11orf57. A second patient had a deletion of SDHD exons 1 and 2 and exon 1 of the TIMM8B gene. A third patient showed a deletion of exon 2 of SDHD, together with a 235 bp MIRb–Tensin gene insertion. In a fourth patient, a deletion of exons 5 and 6 of the SDHC gene was found, only the second SDHC deletion currently known. The deletions of the TIMM8B and C11orf57 genes are the first to be described, but do not appear to result in an additional phenotype in these patients. Four of the eight breakpoints occurred in Alu sequences and all three SDHD deletions showed an intron 2 breakpoint. This study underlines the fact that clinically relevant deletions may encompass neighboring genes, with the potential to modify phenotype. Gene deletions of SDHD and SDHC represent a substantial proportion of all mutations, and must be considered in paraganglioma patients shown to be negative for mutations by sequencing.

Download Full-text

Molecular characterization of erythrocyte glycophorin C variants

Blood ◽

10.1182/blood.v77.3.644.bloodjournal773644 ◽

1991 ◽

Vol 77 (3) ◽

pp. 644-648

Author(s):

S Chang ◽

ME Reid ◽

J Conboy ◽

YW Kan ◽

N Mohandas

Keyword(s):

Molecular Characterization ◽

Mechanical Stability ◽

Exon 2 ◽

Mrna Sequencing ◽

Erythrocyte Shape ◽

Altered Glycosylation ◽

Exon 1 ◽

Dna Fragment ◽

Glycophorin C

Human erythrocyte glycophorin C plays a functionally important role in maintaining erythrocyte shape and regulating membrane mechanical stability. Immunochemical and serologic studies have identified a number of glycophorin C variants that include the Yus, Gerbich, and Webb phenotypes. We report here the molecular characterization of these variants. Amplification of glycophorin C mRNA from the Yus phenotype, using two oligonucleotide primers that span the coding domain, generated a 338-bp fragment compared with a 395-bp fragment generated by amplification of normal glycophorin C mRNA. Sequencing of the mutant 338-bp fragment identified a 57-bp deletion that corresponds to exon 2 of the glycophorin C gene. Similar analysis showed deletion of 84-bp exon 3 in the Gerbich phenotype. In contrast to the generation of shorter than normal DNA fragments from mRNA amplification in the Yus and Gerbich phenotypes, amplification of mRNA from the Webb phenotype generated a normal-sized fragment. Sequencing of this DNA fragment showed an A----G substitution at nucleotide 23 of the coding sequence, resulting in the substitution of asparagine by serine. This modification accounts for the altered glycosylation of glycophorin C seen in this phenotype. These results have enabled us to characterize glycophorin C variants in three different phenotypes that involve deletions of exons 2 and 3 of the glycophorin C gene, as well as a point mutation in exon 1 that results in altered glycosylation of this protein.

Download Full-text

Biomacromolecules in recent phosphate-shelled brachiopods: identification and characterization of chitin matrix

Journal of Materials Science ◽

10.1007/s10853-021-06487-9 ◽

2021 ◽

Author(s):

Oluwatoosin B. A. Agbaje ◽

Glenn A. Brock ◽

Zhifei Zhang ◽

Kingsley C. Duru ◽

Yue Liang ◽

...

Keyword(s):

Organic Matrix ◽

Gravimetric Analysis ◽

Thermal Gravimetric ◽

Shallow Marine ◽

The Core ◽

Spectroscopic Analyses ◽

Living Organisms ◽

First Time ◽

Identification And Characterization

Abstract Phosphate-shelled brachiopods differ in filter-feeding lifestyle, with Lingula anatina an active infaunal burrower, and Discinisca tenuis a shallow marine epibenthic animal. The shells of these animals are built of organophosphatic constituents, the organic fibres/sheets reinforced with calcium phosphate to provide a sophisticated ultrastructural robustness. This investigation examined the nature of the organic fibres in order to improve understanding of how living organisms produce hierarchically structured biomaterials. Unlike powdered samples commonly used in previous studies, organic fibres were isolated for the first time and the shell fractions were purified, in order to study the content and nature of the biopolymer fibres. Biochemical methods including Calcofluor staining revealed a chitin matrix. Ultrastructural analysis, thermal gravimetric analysis, and spectroscopic analyses show that the core polysaccharide framework is composed of layers of β-chitin sheets and/or fibrils that are coated with a fibrous organic matrix. There is more chitin matrix in the L. anatina shells (26.6 wt.%) compared to the D. tenuis shells (12.9 wt.%). Taken together, the data show that the chitin matrix contributes to increased skeletal strength, making L. anatina highly adapted for life as an active burrower. In comparison, D. tenuis contains less chitin and lives as attached epibenthos in a shallow marine environment. Graphical abstract First spectroscopic evidence of β-chitin sheets in recent organophosphatic brachiopods

Download Full-text

Characterization of the oligomeric states of the CK2 α2β2 holoenzyme in solution

Biochemical Journal ◽

10.1042/bcj20170189 ◽

2017 ◽

Vol 474 (14) ◽

pp. 2405-2416 ◽

Cited By ~ 8

Author(s):

Graziano Lolli ◽

Denise Naressi ◽

Stefania Sarno ◽

Roberto Battistutta

Keyword(s):

Active Form ◽

Mass Spectrometry Data ◽

Size Exclusion ◽

Saxs Data ◽

Deconvolution Analysis ◽

Exclusion Chromatography ◽

Kinase Ck2 ◽

First Time

The regulatory mechanism of protein kinase CK2 has still to be fully clarified. The prevailing hypothesis is that CK2 is controlled by a self-polymerisation mechanism leading to inactive supramolecular assemblies that, when needed, can be disassembled into the α2β2 monomer, the active form of the holoenzyme. In vitro, monomeric α2β2 seems present only at high ionic strengths, typically 0.35–0.50 M NaCl, while at lower salt concentrations oligomers are formed. In the present study, size-exclusion chromatography (SEC), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS) and mutagenesis have been employed for the characterization of the oligomeric states of CK2 in solution. SAXS measurements at 0.35 M NaCl show for the first time the shape of the α2β2 active monomer in solution. At 0.25 M salt, despite single average properties indicating an aggregated holoenzyme, deconvolution analysis of SAXS data reveals an equilibrium involving not only circular trimeric and linear oligomeric (3–4 units) forms of α2β2, but also considerable amounts of the monomer. Together SAXS and mutagenesis confirm the presence in solution of the oligomers deduced by crystal structures. The lack of intermediate species such as αβ2, α or β2 indicates that the holoenzyme is a strong complex that does not spontaneously dissociate, challenging what was recently proposed on the basis of mass spectrometry data. A significant novel finding is that a considerable amount of monomer, the active form of CK2, is present also at low salt. The solution properties of CK2 shown in the present study complement the model of regulation by polymerization.

Download Full-text

First cloning and characterization of aspartate aminotransferase from river buffalo (Bubalus bubalis)

Biologia ◽

10.2478/s11756-011-0125-z ◽

2011 ◽

Vol 66 (6) ◽

Cited By ~ 1

Author(s):

Muhammad Shahid Nadeem ◽

Naeem Rashid ◽

Muzaffar Iqbal ◽

Qurra-tul-Ann Afza Gardner ◽

Muhammad Akhtar

Keyword(s):

Aspartate Aminotransferase ◽

Pyridoxal Phosphate ◽

Specific Activity ◽

Active Form ◽

Bubalus Bubalis ◽

Recombinant Enzyme ◽

Ionization Mass ◽

River Buffalo ◽

Apparent Homogeneity

AbstractAspartate aminotransferase catalyzes the transfer of an amino group from L-aspartate to α-oxoglutarate. We have purified cytosolic isozyme, to apparent homogeneity, from the heart of river buffalo. In order to clone the enzyme total RNA was isolated and the cDNA encoding complete polypeptide of 413 amino acids was amplified by reverse transcriptase polymerase chain reaction. The cDNA and the deduced amino acid sequence exhibited 98.2% and 99.5% identities, respectively, with that of cow. The cDNA was overexpressed in Escherichia coli and the gene product was obtained in enzymologically active form. The recombinant enzyme was about 40% of the total cell proteins. The purified recombinant enzyme displayed specific activity, Km, temperature and pH stability values similar to that of the native enzyme. Edman degradation and electrospray ionization mass spectra showed that the recombinant enzyme consisted of three species having N-terminal sequences of MAPPSIF, APPSIF and PPSIF, although the second one was the predominant species. Conditions are also described, which in the mass spectral analysis give either the three species corresponding to the apo- or the holo-enzyme; the latter retaining pyridoxal phosphate bound to the protein. To our knowledge this is the first report on sequence determination, cloning and characterization of aspartate aminotransferase from river buffalo.

Download Full-text