scholarly journals Both a Nicotinic Single Nucleotide Polymorphism (SNP) and a Noradrenergic SNP Modulate Working Memory Performance when Attention is Manipulated

2009 ◽  
Vol 21 (11) ◽  
pp. 2139-2153 ◽  
Author(s):  
Pamela M. Greenwood ◽  
Ramya Sundararajan ◽  
Ming-Kuan Lin ◽  
Reshma Kumar ◽  
Karl J. Fryxell ◽  
...  
Keyword(s):  
Working Memory ◽  
Cognitive Task ◽  
Memory Performance ◽  
Visuospatial Attention ◽  
Attention And Memory ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Two Systems ◽  
Target Memory

We investigated the relation between the two systems of visuospatial attention and working memory by examining the effect of normal variation in cholinergic and noradrenergic genes on working memory performance under attentional manipulation. We previously reported that working memory for location was impaired following large location precues, indicating the scale of visuospatial attention has a role in forming the mental representation of the target. In one of the first studies to compare effects of two single nucleotide polymorphisms (SNPs) on the same cognitive task, we investigated the neurotransmission systems underlying interactions between attention and memory. Based on our previous report that the CHRNA4 rs#1044396 C/T nicotinic receptor SNP affected visuospatial attention, but not working memory, and the DBH rs#1108580 G/A noradrenergic enzyme SNP affected working memory, but not attention, we predicted that both SNPs would modulate performance when the two systems interacted and working memory was manipulated by attention. We found the scale of visuospatial attention deployed around a target affected memory for location of that target. Memory performance was modulated by the two SNPs. CHRNA4 C/C homozygotes and DBH G allele carriers showed the best memory performance but also the greatest benefit of visuospatial attention on memory. Overall, however, the CHRNA4 SNP exerted a stronger effect than the DBH SNP on memory performance when visuospatial attention was manipulated. This evidence of an integrated cholinergic influence on working memory performance under attentional manipulation is consistent with the view that working memory and visuospatial attention are separate systems which can interact.

Single nucleotide polymorphisms of CBF4 locus region of Arabidopsis thaliana correspond to drought tolerance

2004 ◽  
Vol 1 (3) ◽  
pp. 181-190 ◽  
Author(s):  
Hao Gang-Ping ◽  
Wu Zhong-Yi ◽  
Chen Mao-Sheng ◽  
Cao Ming-Qing ◽  
Dominique Brunel ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Drought Tolerance ◽  
World Wide ◽  
Nucleotide Variation ◽  
Nucleotide Polymorphisms ◽  
Water Deficiency ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Adaptation To Drought

AbstractThe levels of drought tolerance and nucleotide polymorphism at the CBF4 locus were examined in a world-wide sample of 17 core accessions of Arabidopsis thaliana. The results showed that different accessions exhibited considerable differences in adaptation to drought stress. Compared with Columbia accession, the frequency of nucleotide polymorphism at the CBF4 locus of 25av, 203av and 244av accessions, including single nucleotide polymorphism (SNP) and insertion/deletion (Indel), was high, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. No significance in all regions of Tajima's D test indicated that the neutral mutation hypothesis could explain the nucleotide polymorphism in this CBF4 gene region. The higher polymorphism was the result of purification selection. Nucleotide polymorphism in the non-coding region was three times higher than in the coding region. This might indicate a recent relaxation of selection pressures on the non-coding region of CBF4 gene. In the coding region of CBF4, SNP frequency was 1 SNP per 96.4 bp and one non-synonymous mutation was detected from 25av, 203av and 244av accessions: the amino acid variation gly↔val at position 205, caused by the nucleotide variation G↔T at position 1034 (corresponding to the nucleotide at position 19 696 of GenBank accession no. AB015478 as 1). Furthermore, four differential SNPs were discovered in haplotype 6 constituted by 203av, one of them located in the 3′ non-coding region (A↔C at position 1106) and the others in the 5′ non-coding region (A↔G, A↔C and G↔A at positions 27, 129 and 171, respectively). The drought tolerance assay indicated that accession 203av was the best at tolerating water deficiency. We propose that haplotype 6 is consistent with its drought tolerance.

scholarly journals Single Nucleotide Polymorphism in SMAD7 and CHI3L1 and Colorectal Cancer Risk

2018 ◽  
Vol 2018 ◽  
pp. 1-23 ◽  
Author(s):  
Amal Ahmed Abd El-Fattah ◽  
Nermin Abdel Hamid Sadik ◽  
Olfat Gamil Shaker ◽  
Amal Mohamed Kamal
Keyword(s):  
Colorectal Cancer ◽  
Genetic Variation ◽  
Sequence Variation ◽  
Regulatory Protein ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Third ◽  
Common Cancer ◽  
Cancer Initiation

Colorectal cancer (CRC) is one of the leading cancers throughout the world. It represents the third most common cancer and the fourth in mortality. Most of CRC are sporadic, arise with no known high-penetrant genetic variation and with no previous family history. The etiology of sporadic CRC is considered to be multifactorial and arises from the interaction of genetic variants of low-penetrant genes and environmental risk factors. The most common well-studied genetic variation is single nucleotide polymorphisms (SNPs). SNP arises as a point mutation. If the frequency of the sequence variation reaches 1% or more in the population, it is referred to as polymorphism, but if it is lower than 1%, the allele is typically considered as a mutation. Lots of SNPs have been associated with CRC development and progression, for example, genes of TGF-β1 and CHI3L1 pathways. TGF-β1 is a pleiotropic cytokine with a dual role in cancer development and progression. TGF-β1 mediates its actions through canonical and noncanonical pathways. The most important negative regulatory protein for TGF-β1 activity is termed SMAD7. The production of TGF-βcan be controlled by another protein called YKL-40. YKL-40 is a glycoprotein with an important role in cancer initiation and metastasis. YKL-40 is encoded by the CHI3L1 gene. The aim of the present review is to give a brief introduction of CRC, SNP, and examples of some SNPs that have been documented to be associated with CRC. We also discuss two important signaling pathways TGF-β1 and CHI3L1 that influence the incidence and progression of CRC.

scholarly journals Negative Effects of Embodiment in a Visuo-Spatial Working Memory Task in Children, Young Adults, and Older Adults

2021 ◽  
Vol 12 ◽  
Author(s):  
Gianluca Amico ◽  
Sabine Schaefer
Keyword(s):  
Older Adults ◽  
Working Memory ◽  
Young Adults ◽  
Spatial Information ◽  
Spatial Working Memory ◽  
Cognitive Task ◽  
Memory Performance ◽  
Age Groups ◽  
Memory Task ◽  
Negative Effects

Studies examining the effect of embodied cognition have shown that linking one’s body movements to a cognitive task can enhance performance. The current study investigated whether concurrent walking while encoding or recalling spatial information improves working memory performance, and whether 10-year-old children, young adults, or older adults (Mage = 72 years) are affected differently by embodiment. The goal of the Spatial Memory Task was to encode and recall sequences of increasing length by reproducing positions of target fields in the correct order. The nine targets were positioned in a random configuration on a large square carpet (2.5 m × 2.5 m). During encoding and recall, participants either did not move, or they walked into the target fields. In a within-subjects design, all possible combinations of encoding and recall conditions were tested in counterbalanced order. Contrary to our predictions, moving particularly impaired encoding, but also recall. These negative effects were present in all age groups, but older adults’ memory was hampered even more strongly by walking during encoding and recall. Our results indicate that embodiment may not help people to memorize spatial information, but can create a dual-task situation instead.

Association of body mass index-related single nucleotide polymorphisms with psychiatric disease and memory performance in a Japanese population

2016 ◽  
Vol 29 (5) ◽  
pp. 299-308 ◽  
Author(s):  
Midori Ninomiya-Baba ◽  
Junko Matsuo ◽  
Daimei Sasayama ◽  
Hiroaki Hori ◽  
Toshiya Teraishi ◽  
...  
Keyword(s):  
Body Mass Index ◽  
Single Nucleotide Polymorphisms ◽  
Japanese Population ◽  
Memory Performance ◽  
Psychiatric Disease ◽  
Psychiatric Diseases ◽  
Healthy Controls ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Poor Memory

ObjectiveObesity is a risk factor for psychiatric diseases. Recently, a number of single nucleotide polymorphisms (SNPs) have been shown to be related to body mass index (BMI). In this study, we investigated the association of BMI-related SNPs with psychiatric diseases and one of their endophenotypes, memory performance, in a Japanese population.MethodsThe subjects were 1624 patients with one of three psychiatric diseases (799 patients with major depressive disorder, 594 with schizophrenia, and 231 with bipolar disorder) and 1189 healthy controls. Memory performance was assessed using the Wechsler Memory Scale – Revised (WMS-R). Genomic DNA was prepared from venous blood and used to genotype 23 BMI-related SNPs using the TaqMan 5′-exonuclease allelic discrimination assay. We then analysed the relationships between the SNPs and psychiatric disease and various subscales of the WMS-R.ResultsThree SNPs (rs11142387, rs12597579, and rs6548238) showed significant differences in the genotype or allele frequency between patients with any psychiatric diseases and controls. Furthermore, six SNPs (rs11142387, rs12597579, rs2815752, rs2074356, rs4776970, and rs2287019) showed significant differences in at least one subscale of the WMS-R depending on the genotypes of the healthy controls. Interestingly, rs11142387 near the Kruppel-like factor 9 (KLF9) was significantly associated with psychiatric disease and poor memory function.ConclusionsWe identified three and six BMI-related SNPs associated with psychiatric disease and memory performance, respectively. In particular, carrying the A allele of rs11142387 near KLF9 was found to be associated with psychiatric disease and poor memory performance, which warrants further investigations.

Performance Comparison of Massively Parallel Sequencing (MPS) Instruments Using Single-Nucleotide Polymorphism (SNP) Panels for Ancestry

2020 ◽  
pp. 247263032095418
Author(s):  
Ashley M. Cooley ◽  
Kelly A. Meiklejohn ◽  
Natalie Damaso ◽  
James M. Robertson ◽  
Tracey Dawson Cruz
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Performance Metrics ◽  
Massively Parallel Sequencing ◽  
Performance Comparison ◽  
Massively Parallel ◽  
Personal Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Parallel Sequencing ◽  
Two Systems

Thermo Fisher Scientific released the Precision ID Ancestry Panel, a 165-single-nucleotide polymorphism (SNP) panel for ancestry prediction that was initially compatible with the manufacturer’s massively parallel sequencer, the Ion Torrent Personal Genome Machine (PGM). The semiautomated workflow using the panel with the PGM involved several time-consuming manual steps across three instruments, including making templating solutions and loading sequencing chips. In 2014, the manufacturer released the Ion Chef robot, followed by the Ion S5 massively parallel sequencer in late 2015. The robot performs the templating with reagent cartridges and loads the chips, thus creating a fully automated workflow across two instruments. The objective of the work reported here is to compare the performance of two massively parallel sequencing systems and ascertain if the change in the workflow produces different ancestry predictions. For performance comparison of the two systems, forensic-type samples ( n = 16) were used to make libraries. Libraries were templated either with the Ion OneTouch 2 system (for the PGM) or on the Ion Chef robot (for the S5). Sequencing results indicated that the ion sphere particle performance metrics were similar for the two systems. The total coverages per SNP and SNP quality were both higher for the S5 system. Ancestry predictions were concordant for the mock forensic-type samples sequenced on both massively parallel sequencing systems. The results indicated that automating the workflow with the Ion Chef system reduced the labor involved and increased the sequencing quality.

scholarly journals Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 625 ◽  
Author(s):  
Jörg T. Wennmann ◽  
Jiangbin Fan ◽  
Johannes A. Jehle
Keyword(s):  
Nucleotide Polymorphisms ◽  
Downstream Process ◽  
Sequencing Data ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Natural Isolates ◽  
Genotype Composition ◽  
R Programming ◽  
Dsdna Viruses ◽  
Virus Isolates

Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool “bacsnp”, written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample.

scholarly journals Single Nucleotide Polymorphisms in Selected Genes in Inflammatory Bowel Disease

2018 ◽  
Vol 2018 ◽  
pp. 1-5 ◽  
Author(s):  
Ewa Dudzińska ◽  
Magdalena Gryzinska ◽  
Janusz Kocki
Keyword(s):  
Ulcerative Colitis ◽  
Inflammatory Bowel Disease ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Bowel Disease ◽  
Disease Patient ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Inflammatory Bowel

Introduction. Inflammatory bowel disease (IBD) is a complicated, multifunctional disorder characterized by chronic, recurring inflammation of the digestive tract. The two main types of IBD are ulcerative colitis (UC) and Crohn’s disease (CD). The aim of the study was to determine single nucleotide polymorphism in fragments of the genes CARD15/NOD2 and DLG5 in patients from the Lublin Voivodeship. Patients and Methods. The study was carried out in Lublin (Poland) in 2016. 27 individuals participated in the research. The research group comprised 9 patients with a diagnosis of Crohn’s disease and 9 with ulcerative colitis, aged 20 to 48, and 9 healthy volunteers. Results. No SNPs were confirmed for the CARD15/NOD2 gene fragment, but a substitution (T>C) was found in the DLG5 gene in a Crohn’s disease patient. Conclusion. Absence of extraintestinal symptoms in patients with Crohn’s disease may be associated with the absence of CARD15/NOD2 SNPs. The study suggests that SNPs (T>C substitution) affect the function of the DLG5 protein and thus play a role in the development of IBD, in particular Crohn’s disease. The analysis presented is a pilot study due to the small number of samples.

Contributions of cholinergic receptor muscarinic 1 and CYP1A2 gene variants on the effects of plasma ratio of clozapine/N-desmethylclozapine on working memory in schizophrenia

2020 ◽  
Vol 35 (1) ◽  
pp. 31-39
Author(s):  
Farhana Islam ◽  
Malgorzata Maciukiewicz ◽  
Natalie Freeman ◽  
Eric Huang ◽  
Arun Tiwari ◽  
...  
Keyword(s):  
Working Memory ◽  
Smoking Status ◽  
Memory Performance ◽  
Cholinergic Receptor ◽  
Gene Variants ◽  
Nucleotide Polymorphisms ◽  
Cholinergic Mechanism ◽  
M1 Receptor ◽  
The Relationship ◽  
Cyp1a2 Genotype

Background: Clozapine has heterogenous efficacy in enhancing working memory in schizophrenia. We have previously hypothesized that this is due to opposing effects of clozapine and its metabolite, N-desmethylclozapine, at the muscarinic M1 receptor and demonstrated that a lower clozapine/ N-desmethylclozapine ratio is associated with better working memory than clozapine or N-desmethylclozapine levels alone. Aims: In this study, we expanded the above hypothesis to explore whether genetic variation in the cholinergic receptor muscarinic 1 gene, encoding the M1 receptor, affects the relationship between clozapine/ N-desmethylclozapine and working memory. Further, we explored whether CYP1A2 gene variants affect the ratio of clozapine/ N-desmethylclozapine and by this, working memory performance. Methods: We evaluated two functionally significant single nucleotide polymorphisms, rs1942499 and rs2075748, in cholinergic receptor muscarinic 1, with the haplotype T-A associated with lower transcriptional activity than the haplotype C-G. Further, we examined CYP1A2 *1F, with *1F/*1F conferring high inducibility in the presence of smoking. Results: In a sample of 30 patients with schizophrenia on clozapine monotherapy, clozapine/ N-desmethylclozapine was correlated with working memory only in non-carriers of the haplotype T-A of the cholinergic receptor muscarinic 1 gene. Interaction of CYP1A2 genotype and smoking status significantly affected clozapine concentrations, but there were no significant effects of CYP1A2 genotype and smoking status on the relationship between clozapine/ N-desmethylclozapine on working memory. Conclusions: Our finding that the relationship between clozapine/ N-desmethylclozapine and working memory is specific to patients with potentially higher transcription of M1 receptor (i.e. non-carriers of the haplotype T-A of cholinergic receptor muscarinic 1) supports a cholinergic mechanism underlying this relationship.

Promoter region single nucleotide polymorphism of siglec-8 gene associates with susceptibility to allergic asthma

2020 ◽  
Vol 17 (3) ◽  
pp. 195-201 ◽  
Author(s):  
Mohammad Sajay-asbaghi ◽  
Mahnaz Sadeghi-shabestrai ◽  
Amir Monfaredan ◽  
Narges Seyfizadeh ◽  
Alireza Razavi ◽  
...  
Keyword(s):  
Allergic Asthma ◽  
Normal Subjects ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Potential Therapeutic Target ◽  
Single Nucleotide ◽  
Study Materials ◽  
Protective Allele ◽  
Conformation Polymorphism

Aim: Siglec-8 is exclusively expressed on mast cells, eosinophils and basophils. Possible association of six siglec-8 single nucleotide polymorphisms (SNPs) with susceptibility to allergic asthma in the Azeri population of Iran was investigated in this study. Materials & methods: A total of 194 patients and 190 normal subjects were enrolled. PCR single strand conformation polymorphism (PCR-SSCP) was used to determine the genotypes of the studied SNPs. Results: The rs36498 showed significant association with allergic asthma (odds ratio [OR]: 0.65; p = 0.022) and the T allele was found as a protective allele (OR: 0.61; p = 0.008). Also, eosinophil count in the CC genotype was significantly higher than that in the other genotypes (p = 0.026). Conclusion: The rs36498 is thought to influence the expression level of siglec-8. Siglec-8 could be a potential therapeutic target for allergic asthma.

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