scholarly journals Whole-Genome Resequencing of Twenty Branchiostoma belcheri Individuals Provides a Brand-New Variant Dataset for Branchiostoma

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Changwei Bi ◽  
Na Lu ◽  
Tingyu Han ◽  
Zhen Huang ◽  
J.-Y. Chen ◽  
...  
Keyword(s):  
Rare Variants ◽  
Population Expansion ◽  
Immune Gene ◽  
Illumina Hiseq ◽  
Intracellular Digestion ◽  
New Variant ◽  
Novel Variant ◽  
Food Particles ◽  
Demographic Inference ◽  
Whole Genome Resequencing

As the extant representatives of the basal chordate lineage, amphioxi (including the genera Branchiostoma, Asymmetron and Epigonichthys) play important roles in tracing the state of chordate ancestry. Previous studies have reported that members of the Branchiostoma species have similar morphological phenotypic characteristics, but in contrast, there are high levels of genetic polymorphisms in the populations. Here, we resequenced 20 Branchiostomabelcheri genomes to an average depth of approximately 12.5X using the Illumina HiSeq 2000 platform. In this study, over 52 million variations (~12% of the total genome) were detected in the B. belcheri population, and an average of 12.8 million variations (~3% of the total genome) were detected in each individual, confirming that Branchiostoma is one of the most genetically diverse species sequenced to date. Demographic inference analysis highlighted the role of historical global temperature in the long-term population dynamics of Branchiostoma, and revealed a population expansion at the Greenlandian stage of the current geological epoch. We detected 594 Single nucleotide polymorphism and 148 Indels in the Branchiostoma mitochondrial genome, and further analyzed their genetic mutations. A recent study found that the epithelial cells of the digestive tract in Branchiostoma can directly phagocytize food particles and convert them into absorbable nontoxic nutrients using powerful digestive and immune gene groups. In this study, we predicted all potential mutations in intracellular digestion-associated genes. The results showed that most “probably damaging” mutations were related to rare variants (MAF < 0.05) involved in strengthening or weakening the intracellular digestive capacity of Branchiostoma. Due to the extremely high number of polymorphisms in the Branchiostoma genome, our analysis with a depth of approximately 12.5X can only be considered a preliminary analysis. However, the novel variant dataset provided here is a valuable resource for further investigation of phagocytic intracellular digestion in Branchiostoma and determination of the phenotypic and genotypic features of Branchiostoma.

scholarly journals Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura

2002 ◽  
Vol 80 (3) ◽  
pp. 163-175 ◽  
Author(s):  
STEPHEN W. SCHAEFFER
Keyword(s):  
Negative Selection ◽  
Genome Rearrangement ◽  
Rare Variants ◽  
Natural Populations ◽  
Population Expansion ◽  
Purifying Selection ◽  
Sequence Length ◽  
Nucleotide Sequence Analysis ◽  
Drosophila Pseudoobscura ◽  
Indel Variation

Positive and negative selection on indel variation may explain the correlation between intron length and recombination levels in natural populations of Drosophila. A nucleotide sequence analysis of the 3·5 kilobase sequence of the alcohol dehydrogenase (Adh) region from 139 Drosophila pseudoobscura strains and one D. miranda strain was used to determine whether positive or negative selection acts on indel variation in a gene that experiences high levels of recombination. A total of 30 deletion and 36 insertion polymorphisms were segregating within D. pseudoobscura populations and no indels were fixed between D. pseudoobscura and its two sibling species D. miranda and D. persimilis. The ratio of Tajima's D to its theoretical minimum value (Dmin) was proposed as a metric to assess the heterogeneity in D among D. pseudoobscura loci when the number of segregating sites differs among loci. The magnitude of the D/Dmin ratio was found to increase as the rate of population expansion increases, allowing one to assess which loci have an excess of rare variants due to population expansion versus purifying selection. D. pseudoobscura populations appear to have had modest increases in size accounting for some of the observed excess of rare variants. The D/Dmin ratio rejected a neutral model for deletion polymorphisms. Linkage disequilibrium among pairs of indels was greater than between pairs of segregating nucleotides. These results suggest that purifying selection removes deletion variation from intron sequences, but not insertion polymorphisms. Genome rearrangement and size-dependent intron evolution are proposed as mechanisms that limit runaway intron expansion.

The Ecology and Digestive System of the Struthiolariidae (Gastropoda)

1951 ◽  
Vol s3-92 (17) ◽  
pp. 1-25
Author(s):  
J. E. MORTON
Keyword(s):  
Digestive System ◽  
Structure And Function ◽  
Crystalline Style ◽  
Intracellular Digestion ◽  
Mud Flat ◽  
Food Particles ◽  
Gill Filaments ◽  
And Function ◽  
Deposit Feeding ◽  
Muscular Action

The two neozelanic species Struthiolaria papulosa and Pelicaria vermis have been studied as regards ecology, feeding mechanism, and structure and function of the digestive system. They are dwellers on sand or sand-mud-flat, wit h a feeding position just below the surface, where they construct paired siphonal tubes with the rostrum. A ciliary mode of feeding has been acquired by the modification of the gill filaments and the pallial rejection system. The alimentary canal isadapted for deposit feeding and has developed a crystalline style. Food particles are conducted to the stomach by a functionally reduced mucus-secreting oesophagus, where they are subjected to the action of the rotating style, and a complex system of ciliary currents. Digestible par-ticles are passed into paired diverticula, where absorption and intracellular digestion, takes place, while faecal material is surrounded with mucus and formed into firm pellets by the ciliary and muscular action of the intestine. The relationships of the Struthiolariidae are discussed, and their origin from the Aporrhaidae is postulated.

Evaluation of a Dual Hemoglobin A2/A1c Quantitation Kit on the Bio-Rad Variant II Automated Hemoglobin Analyzer

2002 ◽  
Vol 126 (12) ◽  
pp. 1494-1500 ◽  
Author(s):  
John D. Lafferty ◽  
Andrew G. McFarlane ◽  
David H. K. Chui
Keyword(s):  
Linear Regression ◽  
Rare Variants ◽  
Reference Interval ◽  
Objective Evaluation ◽  
Laboratory Medicine ◽  
Reference Intervals ◽  
Hb A1c ◽  
Regional Laboratory ◽  
New Variant ◽  
Hb S

Abstract Context.—Quantitation of hemoglobin (Hb) A1c and investigation of hemoglobinopathy on the Bio-Rad Variant analyzers require a switch between 2 separate kits that is time consuming and causes errors. Objective.—Evaluation of a new Variant II HbA2/HbA1c Dual kit capable of both Hb A1c quantitation and hemoglobinopathy investigation on a single kit. Design.—We evaluated Hb A1c, Hb A2, and Hb F quantitation for precision, linearity, and correlation with current methodology. We also evaluated detection of Hb variants and correlation of Hb Barts quantitation. Setting.—Hamilton Regional Laboratory Medicine Program, Provincial Hemoglobinopathy Laboratory, St Joseph's Healthcare Site, Hamilton, Ontario. Patients.—Patient blood samples submitted for Hb A1c quantitation or hemoglobinopathy investigation. Main Outcome Measures.—Precision, linearity, linear regression, and reference interval validation. Results.—We provide tables and figures illustrating precision, linearity, linear regression, and quantitation of Hb variants. We validated reference intervals for Hb A1c, Hb A2, and Hb F. Conclusions.—The dual kit provides precise Hb A1c, Hb A2, and Hb F quantitation. The results show good linearity and correlate well with the results of current methods. We detected all clinically important Hb variants and a wide variety of rare variants. The dual kit has several advantages: it eliminates the need for extensive kit switch over; improves utility for newborn screening because of its quantification of Hb Barts; permits quantification of Hb A1c using the β-Thal method; and eliminates the need for separate Hb A2 reference intervals for patients with Hb S because of its accurate quantitation of Hb A2 in the presence of Hb S.

scholarly journals Approximation algorithms for tours of orientation-varying view cones

2020 ◽  
Vol 39 (4) ◽  
pp. 389-401
Author(s):  
Nikolaos Stefas ◽  
Patrick A Plonski ◽  
Volkan Isler
Keyword(s):  
Approximation Algorithm ◽  
Ground Plane ◽  
Orientation Angle ◽  
Apex Angle ◽  
Field Of View ◽  
Plane Normal ◽  
Polynomial Time Approximation Algorithm ◽  
New Variant ◽  
Angle Difference ◽  
Novel Variant

This article considers the problem of finding a shortest tour to visit viewing sets of points on a plane. Each viewing set is represented as an inverted view cone with apex angle [Formula: see text] and height [Formula: see text]. The apex of each cone is restricted to lie on the ground plane. Its orientation angle (tilt) [Formula: see text] is the angle difference between the cone bisector and the ground plane normal. This is a novel variant of the 3D Traveling Salesman Problem with Neighborhoods (TSPN) called Cone-TSPN. One application of Cone-TSPN is to compute a trajectory to observe a given set of locations with a camera: for each location, we can generate a set of cones whose apex and orientation angles [Formula: see text] and [Formula: see text] correspond to the camera’s field of view and tilt. The height of each cone [Formula: see text] corresponds to the desired resolution. Recently, Plonski and Isler presented an approximation algorithm for Cone-TSPN for the case where all cones have a uniform orientation angle of [Formula: see text]. We study a new variant of Cone-TSPN where we relax this constraint and allow the cones to have non-uniform orientations. We call this problem Tilted Cone-TSPN and present a polynomial-time approximation algorithm with ratio [Formula: see text], where [Formula: see text] is the set of all cone heights. We demonstrate through simulations that our algorithm can be implemented in a practical way and that by exploiting the structure of the cones we can achieve shorter tours. Finally, we present experimental results from various agriculture applications that show the benefit of considering view angles for path planning.

scholarly journals Genome resequencing data for Iranian local dogs and wolves

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Zeinab Amiri Ghanatsaman ◽  
Guo-Dong Wang ◽  
Masood Asadi Fozi ◽  
Ya-Ping Zhang ◽  
Ali Esmailizadeh
Keyword(s):  
Evolutionary Biology ◽  
Sequence Data ◽  
Genome Resequencing ◽  
Illumina Hiseq ◽  
Blood Samples ◽  
Animal Domestication ◽  
Hunting Dogs ◽  
Physical Traits ◽  
Whole Genome Resequencing ◽  
Dog Domestication

Abstract Objective The data provided herein represent the whole-genome resequencing data related to three wolves and three Iranian local dogs. The understanding of genome evolution during animal domestication is an interesting subject in genome biology. Dog is an excellent model for understanding of domestication due to its considerable variety of behavioral and physical traits. The Zagros area of current day Iran has been identified as one of the initial centers of animal domestication. The availability of the complete genome sequences of Iranian local canids can be a valuable resource for researchers to address questions and testing hypotheses on the dog domestication process. Data description We collected blood samples from six Iranian local canids including two hunting dogs (Saluki breed), a mastiff dog (Qahderijani ecotype) and three wolves. We extracted genomic DNA from blood samples. Sequence data were produced using the Illumina HiSeq 2500 system. All sequence data are available in the National Genomics Data Center (NGDC), Genome Sequence Archive (GSA) database under the accession of CRA001324 and the National Center for Biotechnology Information (NCBI) under the accession of PRJNA639312. The short-read sequences with the mean depth of 16X were aligned to the dog reference genome (CanFam3.1) and achieved 99% coverage of the reference assembly. The obtained information from this experiment will be useful in evolutionary biology.

SHANK3 mutation in consanguineous schizophrenia family in northwest Algeria

2017 ◽  
Vol 41 (S1) ◽  
pp. S595-S596
Author(s):  
A. Dahdouh ◽  
J. Prados ◽  
M. Guipponi ◽  
F. Bena ◽  
W. Adouan ◽  
...  
Keyword(s):  
Psychotic Disorders ◽  
Rare Variants ◽  
University Hospital ◽  
High Rate ◽  
Common Disease ◽  
Multiplex Family ◽  
Illumina Hiseq ◽  
Genetic Technologies ◽  
Competing Interest ◽  
The University

IntroductionSeveral studies have asserted the existence of a strong and complex genetic component in the determination of psychotic disorders. GWAS studies conducted over the past decade lead to the identification of only a few low effect associations, calling questioning the hypothesis of “common disease – common variants” for a model involving a large number of rare variants.AimsHere, we studied a multigenerational multiplex family with schizophrenia a high rate of consanguinity, located in the northwest of Algeria. This study aims to identify inherited rare variants of schizophrenia using new genetic technologies.MethodsThis family has received complete clinical (DIGS, DSM-IV criteria), genealogical investigations, CNV analysis using CGH Microarray Kit 244 K (Santa Clara, CA) and WES (by GAIIx Illumina/HiSeq 2000) focused in CNV regions, that were performed in the department of genetics in the university hospital of Geneva.ResultsWe identify 11 affected members by psychotic disorders. The main CNVs analysis results found in a schizophrenic member a Del 22q13.33 affecting SHANK3 gene. WES regarding these regions identified a mutation at position 511178000 in SHANK3 gene in all the selected affected relatives.DiscussionSeveral studies have asserted the association of SHANK3 mutations with schizophrenia and autism disorders. This is the first observation of rs511,178,000 in schizophrenia phenotype.ConclusionIn total, this highly informative family have identified new rare genetic variant of schizophrenia. The search for this mutation in wider control population in would be useful to validate these data.Disclosure of interestThe authors have not supplied their declaration of competing interest.

Population differentiation between Australian and Chinese Helicoverpa armigera occurs in distinct blocks on the Z-chromosome

2018 ◽  
Vol 108 (6) ◽  
pp. 817-830 ◽  
Author(s):  
S.V. Song ◽  
C. Anderson ◽  
R.T. Good ◽  
S. Leslie ◽  
Y. Wu ◽  
...  
Keyword(s):  
Population Structure ◽  
Helicoverpa Armigera ◽  
Nucleotide Diversity ◽  
Selective Sweep ◽  
Rare Variants ◽  
Population Expansion ◽  
Z Chromosome ◽  
Chinese Populations ◽  
Continental Population ◽  
Helicoverpa Armígera

AbstractOver the last 40 years, many types of population genetic markers have been used to assess the population structure of the pest moth species Helicoverpa armigera. While this species is highly vagile, there is evidence of inter-continental population structure. Here, we examine Z-chromosome molecular markers within and between Chinese and Australian populations. Using 1352 polymorphic sites from 40 Z-linked loci, we compared two Chinese populations of moths separated by 700 km and found virtually no population structure (n = 41 and n = 54, with <1% of variation discriminating between populations). The levels of nucleotide diversity within these populations were consistent with previous estimates from introns in Z-linked genes of Australian samples (π = 0.028 vs. 0.03). Furthermore, all loci surveyed in these Chinese populations showed a skew toward rare variants, with ten loci having a significant Tajima's D statistic, suggesting that this species could have undergone a population expansion. Eight of the 40 loci had been examined in a previous study of Australian moths, of which six revealed very little inter-continental population structure. However, the two markers associated with the Cyp303a1 locus that has previously been proposed to be a target of a selective sweep, exhibited allele structuring between countries. Using a separate dataset of 19 Australian and four Chinese moths, we scanned the molecular variation distributed across the entire Z-chromosome and found distinct blocks of differentiation that include the region containing Cyp303a1. We recommend some of these loci join those associated with insecticide resistance to form a set of genes best suited to analyzing population structure in this global pest.

scholarly journals A Cluster of Colistin- and Carbapenem-Resistant Klebsiella pneumoniae Carrying blaNDM-1 and mcr-8.2

2019 ◽  
Vol 221 (Supplement_2) ◽  
pp. S237-S242 ◽  
Author(s):  
Ke Ma ◽  
Yu Feng ◽  
Lu Liu ◽  
Zhihong Yao ◽  
Zhiyong Zong
Keyword(s):  
Klebsiella Pneumoniae ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq ◽  
Carbapenem Resistant ◽  
Interhospital Transfer ◽  
Transmissible Plasmid ◽  
New Variant ◽  
Long Read ◽  
Illumina Hiseq Platform ◽  
Resistant Strains

Abstract Background Klebsiella pneumoniae resistant to both carbapenems and colistin imposes severe challenges for management. In this study, we report a cluster of 5 carbapenem-resistant K pneumoniae clinical strains belonging to ST1 and K57 types, 4 of which were also resistant to colistin, from 2 hospitals. Methods The 5 strains were subjected to whole-genome sequencing (WGS) using the short-read Illumina HiSeq platform, and 2 strains were also selected for long-read WGS using MinION. Clonal relatedness of the 5 strains was determined based on single-nucleotide polymorphisms (SNPs). Conjugation experiments were performed to obtain self-transmissible plasmids. Results All 5 strains carried the carbapenemase-encoding gene blaNDM-1, whereas the 4 colistin-resistant strains also harbored a new variant of the mcr-8 colistin resistance gene, namely, mcr-8.2. MCR-8.2 differs from MCR-8.1 by four amino acid substitutions (A51V, A232S, N365Y, and N480K). mcr-8.2 was located on a large, hybrid, nonself-transmissible plasmid containing IncQ, IncR, and IncFII replicons, whereas blaNDM-1 was carried by self-transmissible IncX3 plasmids. Phylogenetic analysis based on SNPs revealed that the 5 strains were likely to have a common origin. Conclusions Both the intra- and interhospital transfer of strains carrying mcr-8 and blaNDM-1 were identified, which represents an emerging threat for clinical management and infection control.

Molecular cloning and characterization of a novel human variant of RIC-3, a putative chaperone of nicotinic acetylcholine receptors

2008 ◽  
Vol 28 (6) ◽  
pp. 299-306 ◽  
Author(s):  
Tamara Seredenina ◽  
Teresa Ferraro ◽  
Georg C. Terstappen ◽  
Andrea Caricasole ◽  
Renza Roncarati
Keyword(s):  
Nicotinic Acetylcholine Receptors ◽  
Acetylcholine Receptors ◽  
Coiled Coil ◽  
Surface Expression ◽  
Protein Product ◽  
Nicotinic Acetylcholine ◽  
Α7 Nachr ◽  
New Variant ◽  
Novel Variant

Recent reports demonstrate that the RIC-3 (resistant to inhibitors of cholinesterase-3) protein is important for the maturation of nAChRs (nicotinic acetylcholine receptors). In the present study RIC-3e, a novel variant of RIC-3, is described. This variant contains a deletion of exons 4 and 5 of RIC-3, resulting in a protein product lacking a conserved coiled-coil domain. Like RIC-3, the new variant is predominantly, but not exclusively, expressed in the brain. The analysis of expression of variant RIC-3 mRNA and of α7-nAChR mRNA in a set of human tissues shows a similar profile. The RIC-3e protein is functionally active and enables surface expression of mature α7-nAChRs in cell lines not otherwise permissive for the expression of this receptor.

scholarly journals A Novel RHCE*ce Variant Allele Is Highly Frequent in Chinese D-Negative Individuals and Results in C-Expression

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2892-2892
Author(s):  
Tamara C Stegmann ◽  
Y L Ji ◽  
Lonneke Haer-Wigman ◽  
L Wei ◽  
Y Zhao ◽  
...  
Keyword(s):  
Conflicts Of Interest ◽  
Lentiviral Vector ◽  
Variant Allele ◽  
The Novel ◽  
Facs Analysis ◽  
Exon 2 ◽  
Chinese Populations ◽  
New Variant ◽  
Novel Variant ◽  
Dependent Probe

Abstract Background: The RHCE allele is highly polymorphic and many variants have been described, especially in individuals of African origin. Donors carrying these variants can be falsely typed and elicit transfusion reactions, and patients carrying such a variant may be at risk to develop allo-antibodies in response to mismatched transfusions. Not much is known about the frequency of RHCE variants in Chinese populations, whereas in China genotyping assays are increasingly applied for typing of blood donors and patients. Methods: Standard column agglutination was used to serologically type for C/c and E/e expression in 200 serologically D-negative and 200 serologically D-positive Chinese donors. The RH Multiplex Ligation-dependent Probe Amplification (MLPA) genotyping assay was used for genotyping the RHCE status (Transfusion 2013;53:1559). In donors with discrepant results of genotyping and phenotyping all 10 exons of RHCE were amplified and directly sequenced. A lentivirus containing the novel RHce variant was created to transduce human erythroblasts cultured from peripheral blood from 3 ccDee and 3 CCDee donors as previously described (Haematologica 2010;95:1594). FACS analysis was used to assess the c- and C-expression caused by the variant. Results: In 6 out of 200 Chinese D-negative donors the results of the RH-MLPA indicated the presence of only one copy of exon 2 of the CE*c-allele, and no copy of exon 2 of the CE*C-allele, whereas these donors were serologically typed as Cc. Sequencing of all 10 RHCE exons revealed a novel RHCE*ce allele defined by 308C>T (p.103Pro>Leu) mutation next to a normal RHCE*ce allele. The variant allele was not found in the 200 Chinese D-positive donors, indicating the linkage of this new variant RHCE*ce allele with the D-negative haplotype. Wild type Rhce cDNA was mutated to create the RHce*308C>T mutation and subsequently cloned into a lentiviral vector. Transduction of human ccDee erythroblasts with this vector resulted in C expression, whereas virtually no c-expression was induced by transduction of human CCDee erythroblasts as assessed by FACS analysis with the monoclonals MS33, MS35 and MS42 to detect c expression and monoclonals MS24 and MS273 to detect C. Discussion: A new RHCE variant (RHCE*ce308T) is identified, which is present in 3% of D-negative Chinese individuals. The 308C>T mutation in the triplet encoding the 103Pro results in the expression of 103Leu. Position 103 is one of the 4 aminoacid differences between the c- and C-carrying polypeptides (Pro and Ser, respectively). The Pro>Leu mutation in the novel variant leads to C-expression and loss or strongly diminished c-expression. Most Rhc-genotyping assays target the c-specific-307C nucleotide and most RhC-genotyping assays target the C-specific-intron 2, which are respectively present and absent in this variant allele. Therefore, when individuals carrying this allele are genotyped, the predictive phenotype will be falsely C-negative. Conclusion: RHC-genotyping assays applied in Chinese populations, should be adapted to recognize the presence of this new RHCE*ce308T allele to prevent C-mismatched transfusions. Disclosures No relevant conflicts of interest to declare.

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