scholarly journals Identification of the Ovine Keratin-Associated Protein 2-1 Gene and Its Sequence Variation in Four Chinese Sheep Breeds

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 604
Author(s):  
Jianqing Wang ◽  
Huitong Zhou ◽  
Jon G. H. Hickford ◽  
Yuzhu Luo ◽  
Hua Gong ◽  
...  
Keyword(s):  
Single Strand Conformation Polymorphism ◽  
Local Alignment ◽  
Polymorphism Analysis ◽  
Chromosome 11 ◽  
Gene Encoding ◽  
Reading Frame ◽  
Sheep Breeds ◽  
Wool Fibers ◽  
Associated Proteins ◽  
Search Tool

Keratin-associated proteins are important components of wool fibers. The gene encoding the high-sulfur keratin-associated protein 2-1 has been described in humans, but it has not been described in sheep. A basic local alignment search tool nucleotide search of the Ovine Genome Assembly version 4.0 using a human keratin-associated protein 2-1 gene sequence revealed a 399-base pair open reading frame, which was clustered among nine previously identified keratin-associated protein genes on chromosome 11. Polymerase chain reaction–single strand conformation polymorphism analysis revealed four different banding patterns, with these representing four different sequences (A–D) in Chinese sheep breeds. These sequences had the highest similarity to human keratin-associated protein 2-1 gene, suggesting that they represent variants of ovine keratin-associated protein 2-1 gene. Nine single nucleotide variations were detected in the gene, including one non-synonymous nucleotide substitution. Differences in variant frequencies between fine-wool sheep breeds and coarse-wool sheep breeds were detected. The gene was found to be expressed in various tissues, with the highest expression level in skin, and moderate expression levels in heart and lung tissue. These results reveal that the ovine keratin-associated protein 2-1 gene is variable and suggest the gene might affect variation in mean fiber diameter.

scholarly journals Identification of Caprine KRTAP28-1 and Its Effect on Cashmere Fiber Diameter

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 121 ◽  
Author(s):  
Jiqing Wang ◽  
Huitong Zhou ◽  
Jon G. H. Hickford ◽  
Mengli Zhao ◽  
Hua Gong ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Fiber Diameter ◽  
Single Strand Conformation Polymorphism ◽  
Chromosome 1 ◽  
Polymorphism Analysis ◽  
Gene Encoding ◽  
Banding Patterns ◽  
Reading Frame ◽  
Associated Proteins ◽  
Cashmere Goats

The keratin-associated proteins (KAPs) are constituents of cashmere fibers and variation in many KAP genes (KRTAPs) has been found to be associated with fiber traits. The gene encoding the high-sulphur KAP28-1 has been described in sheep, but it has not been identified in the goat genome. In this study, a 255-bp open reading frame on goat chromosome 1 was identified using a search of similar sequence to ovine KRTAP28-1, and that would if transcribed and translated encode a high sulphur KAP. Based on the analysis of polymerase chain reaction amplicons for the goat nucleotide sequences in 385 Longdong cashmere goats in China, five unique banding patterns were detected using single strand conformation polymorphism analysis. These represented five DNA sequences (named variants A to E) and they had the highest resemblance to KRTAP28-1 sequences from sheep, suggesting A–E are variants of caprine KRTAP28-1. DNA sequencing revealed a 2 or 4-bp deletion and eleven nucleotide sequence differences, including four non-synonymous substitutions. Of the four common variants (A, B, C and D) found in these goats, the presence of variant A was associated with decreased mean fiber diameter and this effect appeared to be additive. These results indicate that caprine KRTAP28-1 variation might have value as a molecular marker for reducing cashmere mean fiber diameter.

scholarly journals Analysis of Loss of Heterozygosity on Chromosome 11 and Infrequent Inactivation of the MEN1 Gene in Sporadic Pituitary Adenomas1

1998 ◽  
Vol 83 (8) ◽  
pp. 2631-2634 ◽  
Author(s):  
Chisato Tanaka ◽  
Takehiko Kimura ◽  
Peng Yang ◽  
Maki Moritani ◽  
Takashi Yamaoka ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Pituitary Adenomas ◽  
Single Strand Conformation Polymorphism ◽  
Polymorphism Analysis ◽  
Chromosome 11 ◽  
Gene Encoding ◽  
Men1 Gene

abstract To investigate the role of tumor suppressor genes in sporadic pituitary adenomas, we first analyzed loss of heterozygosity on 11q13 with microsatellite analysis in 31 tumors. Loss of heterozygosity on 11q13 was detected in 1 mixed GH/PRL adenoma, and the somatic 22-bp deletion of the multiple endocrine neoplasia type 1 (MEN1) gene encoding menin was detected in this tumor. Trisomy 11 suggested by the decreased mean allelic ratios of 66% or 65% for 16 or 13 microsatellite markers, respectively, in 2 of 31 pituitary adenomas was confirmed by interphase fluorescence in situ hybridization. Screening for mutations of the MEN1 gene did not find mutations with PCR-single strand conformation polymorphism analysis in other pituitary adenomas retaining heterozygosity on 11q13. Based on these, it is concluded that inactivation of the MEN1 gene comprises a rare etiology for tumorigenesis of the pituitary gland, and that trisomy 11 or another gene(s) may contribute to the pathogenesis of sporadic pituitary adenomas.

scholarly journals Kelch 13-propeller polymorphisms in Plasmodium falciparum from Jazan region, southwest Saudi Arabia

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Ommer Mohammed Dafalla ◽  
Mohammed Alzahrani ◽  
Ahmed Sahli ◽  
Mohammed Abdulla Al Helal ◽  
Mohammad Mohammad Alhazmi ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Saudi Arabia ◽  
Parasite Clearance ◽  
Sub Saharan Africa ◽  
Local Alignment ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Synonymous Mutations ◽  
Search Tool ◽  
Sub Saharan

Abstract Background Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. Methods One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). Results This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) ‘11.8%’ in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). Conclusions Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.

scholarly journals The Mean Staple Length of Wool Fibre Is Associated with Variation in the Ovine Keratin-Associated Protein 21-2 Gene

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 148
Author(s):  
Shaobin Li ◽  
Huitong Zhou ◽  
Hua Gong ◽  
Fangfang Zhao ◽  
Jiqing Wang ◽  
...  
Keyword(s):  
Fibre Diameter ◽  
Single Strand Conformation Polymorphism ◽  
Amino Acid Sequences ◽  
Chromosome 1 ◽  
Wool Fibre ◽  
Gene Marker ◽  
Reading Frame ◽  
Associated Proteins ◽  
Fleece Weight ◽  
Staple Length

Wool and hair fibres consist of a variety of proteins, including the keratin-associated proteins (KAPs). In this study, a putative ovine homologue of the human KAP21-2 gene (KRTAP21-2) was identified. It was located on chromosome 1 as a 201-bp open reading frame (ORF) in the ovine genome assembly from a Texel sheep (v.4 NC_019458.2: nt122932727 to 122932927). A polymerase chain reaction- single strand conformation polymorphism (PCR-SSCP) analysis of this ORF, and subsequent DNA sequencing, identified five sequences (named A-E). The putative amino acid sequences that would be produced, shared some identity with each other and with other KAPs, but they were most similar to ovine KAP21-1, and phylogenetically related to human KAP21-2. The location of the ovine KRTAP21-2 sequence was consistent with the location of human KRTAP21-2, and this suggests they represent different variant forms of ovine KRTAP21-2. Variation in this gene was investigated in 389 Merino (sire) × Southdown-cross (ewe) lambs. These were derived from four independent sire-lines. The sequence variation was found to be associated with variation in five wool traits: including mean staple length (MSL), mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), prickle factor (PF), and greasy fleece weight (GFW). The most persistent effect of KRTAP21-2 variation was with variation in MSL; with the MSL of sheep of genotype AC being 12.5% greater than those of genotype CE. A similar effect was observed from individual variant absence/presence models. This suggests that KRTAP21-2 should be further investigated as a possible gene-marker for improving MSL.

scholarly journals First Report of Virus and Phytoplasma Pathogens Associated with Yellow Leaf Syndrome of Sugarcane in Cuba

Plant Disease ◽  
1999 ◽  
Vol 83 (12) ◽  
pp. 1177-1177 ◽  
Author(s):  
Y. Arocha ◽  
L. Gonzalez ◽  
E. L. Peralta ◽  
P. Jones
Keyword(s):  
Enzyme Linked Immunosorbent Assay ◽  
Local Alignment ◽  
Polymorphism Analysis ◽  
Yellow Leaf ◽  
Nested Polymerase Chain Reaction ◽  
Aster Yellows ◽  
First Report ◽  
Pcr Products ◽  
Search Tool ◽  
Saccharum Sp

Yellow leaf syndrome (YLS) has been seen recently in sugarcane (Saccharum sp.) in Cuba. The primary symptom is a yellow discoloration of the midrib that may spread from the midrib to the lamina in cane 6 months and older. In certain cultivars, such as CP 5243, EPC 17-395, and F31-156, a reddish coloration has been observed. In severe cases, plants are stunted and can be pulled easily. YLS was first reported from Hawaii, followed by Brazil, Florida, and Australia, where it is associated with a luteovirus: sugarcane yellow leaf virus (ScYLV). However, in South Africa, YLS is associated with a phytoplasma: sugarcane yellow leaf phytoplasma (ScYLP) (1). A survey performed in Jovellanos, Matanzas, Cuba, for ScYLV, using enzyme-linked immunosorbent assay with antiserum provided by B. E. L. Lockhart, showed that only a small percentage of canes with YLS carried the virus. A nested polymerase chain reaction (PCR) (1) was used to amplify phytoplasma 16S/23S rDNA from sugarcane leaves with YLS symptoms, also collected from Jovellanos. Restriction fragment length polymorphism analysis with HaeIII, RsaI, and AluI produced patterns similar to those of members of the aster yellows group for 260 of 277 samples tested. Sequencing of the 16S/23S intergenic rDNA PCR products, followed by BLAST (basic local alignment search tool) analysis, confirmed the high homology (97%) of these amplimers to the DNA of phytoplasmas belonging to the aster yellows I-A subgroup. This is the first report of ScYLV and ScYLP from Cuba, and it demonstrates the difficulty of determining the identity of the YLS pathogen based on symptoms alone. Reference: (1) C. P. R. Cronjé et al. Ann. Appl. Biol. 133:177, 1998.

scholarly journals A Novel Lectin, DltA, Is Required for Expression of a Full Serum Resistance Phenotype in Haemophilus ducreyi

2004 ◽  
Vol 72 (6) ◽  
pp. 3418-3428 ◽  
Author(s):  
Isabelle Leduc ◽  
Patricia Richards ◽  
Crystal Davis ◽  
Birgit Schilling ◽  
Christopher Elkins
Keyword(s):  
Lectin Binding ◽  
Haemophilus Ducreyi ◽  
Local Alignment ◽  
Serum Resistance ◽  
Reading Frame ◽  
Resistance Phenotype ◽  
Binding Domains ◽  
Bactericidal Effects ◽  
Search Tool ◽  
Β Chain

ABSTRACT Haemophilus ducreyi, the causative agent of chancroid, is highly resistant to the complement-mediated bactericidal activity of normal human serum (NHS). Previously, we identified DsrA (for ducreyi serum resistance A), a major factor required for expression of the serum resistance phenotype in H. ducreyi. We describe here a second outer membrane protein, DltA (for ducreyi lectin A), which also contributes to serum resistance in H. ducreyi. Isogenic dltA mutants, constructed in 35000HP wild-type and FX517 dsrA backgrounds, were more susceptible to the bactericidal effects of NHS than each respective parent, demonstrating the additive effect of the mutations. Furthermore, expression of dltA in H. influenzae strain Rd rendered this highly susceptible strain partially resistant to 5% NHS compared to a vector-control strain. Although primary basic local alignment search tool analysis of the dltA open reading frame revealed no close bacterial homologue, similarity to the β-chain of the eukaryotic lectin ricin was noted. DltA shares highly conserved structural motifs with the ricin β chain, such as cysteines and lectin-binding domains. To determine whether dltA was a lectin, ligand blots and affinity chromatography experiments were performed. DltA was affinity purified on immobilized lactose and N-acetylgalactosamine, and N-glycosylated but not glycosidase-treated model glycoproteins bound DltA. These data indicate that DltA is a lectin with specificity for lactose-related carbohydrates (CHO) and is important for H. ducreyi serum resistance.

scholarly journals Identification, Expression, and Characterization of Escherichia coli Guanine Deaminase

2000 ◽  
Vol 182 (16) ◽  
pp. 4658-4660 ◽  
Author(s):  
Jason T. Maynes ◽  
Richard G. Yuan ◽  
Floyd F. Snyder
Keyword(s):  
Escherichia Coli ◽  
Metal Binding ◽  
Open Reading Frame ◽  
Local Alignment ◽  
Purine Base ◽  
Putative Gene ◽  
Reading Frame ◽  
Guanine Deaminase ◽  
Bacterial Enzyme ◽  
Search Tool

ABSTRACT Using the human cDNA sequence corresponding to guanine deaminase, the Escherichia coli genome was scanned using the Basic Local Alignment Search Tool (BLAST), and a corresponding 439-residue open reading frame of unknown function was identified as having 36% identity to the human protein. The putative gene was amplified, subcloned into the pMAL-c2 vector, expressed, purified, and characterized enzymatically. The 50.2-kDa protein catalyzed the conversion of guanine to xanthine, having a Km of 15 μM with guanine and a k cat of 3.2 s−1. The bacterial enzyme shares a nine-residue heavy metal binding site with human guanine deaminase, PG[FL]VDTHIH, and was found to contain approximately 1 mol of zinc per mol of subunit of protein. The E. coli guanine deaminase locus is 3′ from an open reading frame which shows homology to a bacterial purine base permease.

The Influence of Memory-Aware Computation on Distributed BLAST

2019 ◽  
Vol 14 (2) ◽  
pp. 157-163
Author(s):  
Majid Hajibaba ◽  
Mohsen Sharifi ◽  
Saeid Gorgin
Keyword(s):  
Search Time ◽  
Genomic Research ◽  
Local Alignment ◽  
Negative Effects ◽  
Sequencing Technologies ◽  
Percent Improvement ◽  
Fast Processing ◽  
Search Tool ◽  
Memory Awareness ◽  
Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

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