Identification Of Single Nucleotide Polymorphisms Research Articles

Proteomic Characterization of Damaged Single Hairs Recovered after an Explosion for Protein-Based Human Identification.

Evidence recovery is challenging where an explosion has occurred. Though hair evidence may be sufficiently robust to be recovered at the site, forensic analysis underutilizes the matrix by relying on morphological analysis. Where DNA is compromised, particularly in hair, protein-based human identification presents a promising alternative. Detection of amino acid polymorphisms in hair proteins as genetically variant peptides (GVPs) permits the inference of individualizing single nucleotide polymorphisms for identification. However, an explosive blast may damage hair proteins and compromise GVP identification. This work assesses effects of an explosive blast on the hair proteome and GVP identification, investigates microscopy as a predictor of proteome profiling success in recovered hairs to improve analysis throughput, and quantifies discriminative power in damaged hairs. The proteomics dataset has been deposited into the ProteomeXchange Consortium (PXD017427). With the exception of degradation in keratins K75, K80, K40, and keratin-associated protein KAP10-11 as markers of hair cuticular damage, corroborated by scanning electron microscopic analysis, minimal hair proteome degradation following explosion allowed successful proteome profiling of single hairs regardless of morphological damage. Finally, GVP identification remained independent of explosion conditions, permitting similar discriminative power between exploded and undamaged hairs. These findings lend greater confidence to GVP analysis in one-inch hairs for forensic identification and provide information about hair protein localization.

Loop-Primer Endonuclease Cleavage–Loop-Mediated Isothermal Amplification Technology for Multiplex Pathogen Detection and Single-Nucleotide Polymorphism Identification

Loop-mediated isothermal amplification (LAMP) provides effective diagnostic technology for infectious disease pathogen identification and is compatible with inexpensive instrumentation for use in disease-prevalent developing regions. However, simultaneous multiple-target detection and single-nucleotide polymorphism (SNP) identification, essential properties of nucleic acid diagnostics, are difficult to achieve using LAMP. This study introduces loop-primer endonuclease cleavage (LEC)-LAMP, a singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification. We developed a singleplex LEC-LAMP Neisseria meningitidis assay that demonstrated complete analytical specificity and a limit of detection of 3.1 genome copies per reaction. Small-scale clinical testing of this assay demonstrated 100% diagnostic specificity and sensitivity when assessed with anonymized DNA extracts from confirmed cases of bacterial meningitis infection. The single-base specificity of this assay indicated effective SNP identification properties when challenged with DNA templates containing SNPs located within a specific six-base region. This assay was modified to generate an allele-specific LEC-LAMP N. meningitidis assay that successfully demonstrated single-tube differentiation of wild-type and mutant allele templates. The singleplex assay was further modified to generate a multiplex LEC-LAMP assay that successfully demonstrated simultaneous multiple-target detection of three bacterial targets, N. meningitidis, Streptococcus pneumonia, and Hemophilus influenzae. LEC-LAMP is the first report of single-tube, real-time, singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification.

SNP Data Science for Classification of Bipolar Disorder I and Bipolar Disorder II.

Bipolar disorder I (BD-I) and bipolar disorder II (BD-II) have specific characteristics and clear diagnostic criteria, but quite different treatment guidelines. In clinical practice, BD-II is commonly mistaken as a mild form of BD-I. This study uses data science technique to identify the important Single Nucleotide Polymorphisms (SNPs) significantly affecting the classifications of BD-I and BD-II, and develops a set of complementary diagnostic classifiers to enhance the diagnostic process. Screening assessments and SNP genotypes of 316 Han Chinese were performed with the Affymetrix Axiom Genome-Wide TWB Array Plate. The results show that the classifier constructed by 23 SNPs reached the area under curve of ROC (AUC) level of 0.939, while the classifier constructed by 42 SNPs reached the AUC level of 0.9574, which is a mere addition of 1.84 percent. The accuracy rate of classification increased by 3.46 percent. This study also uses Gene Ontology (GO) and Pathway to conduct a functional analysis and identify significant items, including calcium ion binding, GABA-A receptor activity, Rap1 signaling pathway, ECM proteoglycans, IL12-mediated signaling events, Nicotine addiction), and PI3K-Akt signaling pathway. The study can address time-consuming SNPs identification and also quantify the effect of SNP-SNP interactions.

Identification and characterization of trait-specific SNPs using ddRAD sequencing in water buffalo

Single Nucleotide Polymorphism (SNP) is one of the important molecular markers widely used in animal breeding program for improvement of any desirable genetic traits. Considering this, the present study was carried out to identify, annotate and analyze the SNPs related to four important traits of buffalo viz. milk volume, age at first calving, post-partum cyclicity and feed conversion efficiency. We identified 246,495, 168,202, 74,136 and 194,747 genome-wide SNPs related to mentioned traits, respectively using ddRAD sequencing technique based on 85 samples of Murrah Buffaloes. Distribution of these SNPs were highest (61.69%) and lowest (1.78%) in intron and exon regions, respectively. Under coding regions, the SNPs for the four traits were further classified as synonymous (4697) and non-synonymous (3827). Moreover, Gene Ontology (GO) terms of identified genes assigned to various traits. These characterized SNPs will enhance the knowledge of cellular mechanism for enhancing productivity of water buffalo through molecular breeding.

Genetic determinants of lipid aberrations in patents with essential hypertension

Aim. To reveal the relationship between apolipoprotein E gene polymorphism and lipid spectrum modification in patients with essential hypertension. Materials and methods. The lipid spectrum components and apolipoprotein E gene polymorphism were analyzed in 310 patients with essential hypertension. Results. The mean plasma levels of total cholesterol, high and low density lipoproteins, triglycerides and the atherogenic index were 5.18 ± 0.08 mmol/l, 1.32 ± 0.03 mmol/l, 3.06 ± 0.07 mmol/l, 1.74 ± 0.05 mmol/l and 3.21 ± 0.08, respectively. In patients with essential hypertension, the genetic polymorphism of apolipoprotein E was characterized by the alleles E2 (13.26 %), E3 (93.87 %) and E4 (30.65 %) presence. Based on single nucleotide polymorphism identification, there were defined the following genotypes: E2/E2 (0.65 %), E2/E3 (10.97 %), E2/E4 (1.61 %), E3/E3 (57.74 %), E3/E4 (25.16 %) and E4/E4 (3.87 %). Individuals with E2/E4 genotype had higher levels of total cholesterol (+17.56 %, P < 0.05) and low density lipoproteins (+25.7 %, P < 0.01), and atherogenic index was increased (+38.18 %, P < 0.05) in E4/E4 carriers in comparison with E2/E3. Hypertonic E4/E4 carriers were found to have elevated plasma triglycerides (+20.23 %, P < 0.05) in comparison with E3/E3, as well as increased triglycerides (+25.3 %, p < 0.05) and very low density lipoproteins (+25.33 %, P < 0.05) in comparison with E3/E4 carriers. E3/E3 and E3/E4 carriers demonstrated decrease in total cholesterol (-12.9 %, P < 0.05) and (-11.04 %, P < 0.05), respectively, as well as low density lipoproteins (-15.69 %, P < 0.001) and (-11.48 %, P < 0.05), respectively, as compared to E2/E4. The plasma content of high density lipoproteins was not dependent on ApoE genotype. Conclusions. In patients with essential hypertension, the most common allele is E3 (93.87 %) and the E3/E3 genotype (57.74 %), while the E3/E4 genotype is 25.16 %. Presence of the E2/E4 genotype is significantly associated with the elevated total cholesterol and low density lipoproteins plasma levels, whereas the E4/E4 genotype is accompanied by the increased triglycerides, low density lipoproteins levels and atherogenic index.

Exploring SNPs (Single Nucleotide Polymorphisms) of Myostatin gene in coding region in Bali cattle

The gene MSTN is a member of the superfamily growth gene transforming growth factor β (TGF-β) that functions to suppress muscle growth. The purpose of this study was to analyze the polymorphisms of MSTN genes in the coding region (exon 1, 2, and 3) in Bali cattle kept at the Breeding Center for Bali cattle (BPTU-HPT) in Denpasar. The number of samples used was 52 heads male of Bali cattle aged 2-3 years. SNP identification was done by amplifying the coding region, exon 1, exon 2 and exon 3 MSTN genes using direct sequencing method. Analysis of MSTN gene sequences in Bali cattle was carried out by using the BioEdit and MEGA7 programs. The present study found a total of 18 SNP mutations namely point mutation that are 4 SNP (g.313 C>A, g.324 T>A, g.330 T>G, g.400 G>A) in exon 1, 1 SNP (g.2609 G>A) in exon 2, and 13 SNP (g.4821 C>A, g.4838 C>T, g.4842 A>C, g.4849 T>C, g.4868 C>A, g.4873 C>G, g.4900 T>G, 4905 C>G, g.4957 C>G, g.4959 C>A, g.4969 T>A, g.4974 T>C, g.5044 C>A) in exon 3. SNPs found in the MSTN gene in Bali cattle might be used as candidates for Marker Assisted Selection, especially in Bali cattle.

Identification of Single-Nucleotide Polymorphisms in Mitochondria-Associated Genes Capable of Affecting the Development of Hypertrophic Cardiomyopathy in Senescence-Accelerated OXYS Rats

Hypertrophic cardiomyopathy (HC) is a heterogeneous myocardial disease with a wide range of clinical manifestations, and the risk of its development increases with age against the background of myocardial changes that are characteristic of aging. The contribution of the genetic component to the development of HC is obvious; however, the etiology and pathogenesis of this disease remain unclear in 50% of cases. The goal of the study was to search for single-nucleotide polymorphisms in mitochondria-associated genes, which can contribute to the development of myocardial hypertrophy in senescence-accelerated OXYS rats, based on the results of RNA-Seq. Polymorphisms with a potential negative effect on the function of the protein product in the mitochondria-associated genes Fbxl4 and Slc25a32, mutations in which were not previously associated with HC, were revealed. Changes in the expression of these genes in the myocardium of OXYS rats at different stages of the development of pathological changes indicate that the identified polymorphisms can contribute to the development of HC. Thus, polymorphisms in the genes Fbxl4 and Slc25a32, as well as the genes themselves, can be considered promising molecular targets in the study of the contribution of mitochondrial dysfunction to the development of myocardial hypertrophy.

Identifying Diagnostic Genetic Markers for a Cryptic Invasive Agricultural Pest: A Test Case Using the Apple Maggot Fly (Diptera: Tephritidae)

AbstractInsect pests destroy ~15% of all U.S. crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick, and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella, is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest United States. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks noncommercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double-digest restriction site-associated DNA markers. We identified five informative single-nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme-digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, 1-d species identification by scoring apple- and snowberry-infesting flies from known hosts, reared from fruit collected at 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification, can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.

Identification of Whole-Genome Significant Single Nucleotide Polymorphisms in Candidate Genes Associated With Serum Biochemical Traits in Chinese Holstein Cattle.

A genome-wide association study (GWAS) was conducted on 23 serum biochemical traits in Chinese Holstein cattle. The experimental population consisted of 399 cattle, each genotyped by a commercial bovine 50K SNP chip, which had 49,663 SNPs. After data cleaning, 41,092 SNPs from 361 Holstein cattle were retained for GWAS. The phenotypes were measured values of serum measurements of these animals that were taken at 11 days after parturition. Two statistical models, a fixed-effect linear regression model (FLM) and a mixed-effect linear model (MLM), were used to estimate the association effects of SNPs. Genome-wide significant and suggestive thresholds were set up to be 1.22E−06 and 2.43E−06, respectively. In the Chinese Holstein population, FLM identified 81 genome-wide significant (0.05/41,092 = 1.22E−06) SNPs associated with 11 serum traits. Among these SNPs, five SNPs (BovineHD0100005950, ARS-BFGL-NGS-115158, BovineHD1500021175, BovineHD0800028900, and BTB-00442438) were also identified by the MLM to have genome-wide suggestive effects on CHE, DBIL, and LDL. Both statistical models pinpointed two SNPs that had significant effects on the Holstein population. The SNP BovineHD0800028900 (located near the gene LOC101903458 on chromosome 8) was identified to be significantly associated with serum high- and low-density lipoprotein (HDL and LDL), whereas BovineHD1500021175 (located in 73.4Mb on chromosome 15) was an SNP significantly associated with total bilirubin and direct bilirubin (TBIL and DBIL). Further analyses are needed to identify the causal mutations affecting serum traits and to investigate the correlation of effects for loci associated with fatty liver disease in dairy cattle.

Developing Single Nucleotide Polymorphisms for Identification of Cod Products by RAD-Seq.

Simple SummaryAs high-value fishery products, cod species are frequently faked by non-cod ones. Genetic fingerprinting is important for both certifying authenticity and traceability of fish species. In this study, we developed a method that combines DNA barcoding and restriction-site associated DNA sequencing (RAD-Seq) approach for the identification of cod products. Two sequences that contain single nucleotide polymorphism (SNP)s were identified and these SNPs can be used to distinguish three different cod species, which are Atlantic cod (Gadus morhua), Greenland turbot (Reinhardtius hippoglossoides), and Patagonian toothfish (Dissostichus eleginoides). This SNP-based method will help us to identify the products, which are sold under the name of “Xue Yu” (Cod) in China, and works in parallel with existing fish identification techniques to establish an efficient framework to detect and prevent fraud at all points of the cod commercialization.The increase in the rate of seafood fraud, particularly in the expensive fishes, forces us to verify the identity of marine products. Meanwhile, the definition of cod lacks consistency at the international level, as few standards and effective application methods are capable of accurately detecting cod species. Genetic fingerprinting is important for both certifying authenticity and traceability of fish species. In this study, we developed a method that combines DNA barcoding and the restriction-site associated DNA sequencing (RAD-Seq) approach for the identification of cod products. We first obtained 6941 high-quality single nucleotide polymorphism (SNP)s from 65.6 gigabases (Gb) of RAD-Seq raw data, and two sequences that contain SNPs were finally used to successfully identify three different cod product species, which are Atlantic cod (Gadus morhua), Greenland turbot (Reinhardtius hippoglossoides), and Patagonian toothfish (Dissostichus eleginoides). This SNP-based method will help us to identify the products, which are sold under the name of “Xue Yu” (Cod) in China, and works in parallel with existing fish identification techniques to establish an efficient framework to detect and prevent fraud at all points of the seafood supply chain.

Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants

Catechins are the predominant products in tea plants and have essential functions for both plants and humans. Several genes encoding the enzymes regulating catechin biosynthesis have been identified, and the identification of single nucleotide polymorphisms (SNPs) resulting in nonsynonymous mutations within these genes can be used to establish a functional link to catechin content. Therefore, the transcriptomes of two parents and four filial offspring were sequenced using next-generation sequencing technology and aligned to the reference genome to enable SNP mining. Subsequently, 176 tea plant accessions were genotyped based on candidate SNPs using kompetitive allele-specific polymerase chain reaction (KASP). The catechin contents of these samples were characterized by high-performance liquid chromatography (HPLC), and analysis of variance (ANOVA) was subsequently performed to determine the relationship between genotypes and catechin content. As a result of these efforts, a SNP within the chalcone synthase (CHS) gene was shown to be functionally associated with catechin content. Furthermore, the geographical and interspecific distribution of this SNP was investigated. Collectively, these results will contribute to the early evaluation of tea plants and serve as a rapid tool for accelerating targeted efforts in tea breeding.

In-silico analysis of deleterious missense SNPs of human TYR gene associated with oculocutaneous albinism type 1 (OCA1)

Single Nucleotide Polymorphisms (SNPs) are among the major genetic anomalies behind genetically rare disorders. The human TYR gene encodes a key regulatory enzyme, tyrosinase for melanin biosynthesis. Missense mutations in the TYR gene may disrupt the normal function of tyrosinase and cause oculocutaneous Albinism type 1 (OCA1). The present study involves the use of multiple computational tools based on different algorithms for the identification of potential deleterious missense SNPs from the TYR gene. In this study, we identified ten deleterious missense mutations which may be contributing factors for OCA1. The 3D modeling analysis of mutant models of tyrosinase also strengthen the hypothesis that these mutations may induce significant structural and conformational changes on the native tyrosinase enzyme.

SNPector: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence

Due to the ability to diagnose diseases early and evaluate the effectiveness of medicinal drugs, single nucleotide polymorphism (SNP) identification receives significant interest. Detection and diagnosis of genetic variation through skill-less computational tools would help researchers reducing the severity of such health complications and improving well-tailored therapies using discovered and previously known information. We introduce SNPector, which is a standalone SNP inspection software, which can be used to diagnose gene pathogenicity and drug reaction in naked genomic sequences. It identifies and extracts gene-related SNPs, and reports their genomic position, associated phenotype disorder, associated diseases, linkage disequilibrium, in addition to various drug reaction information. SNPector detects and verifies the existence of an SNP in a given DNA sequence without the reference based on different clinically relevant SNP databases, such as NCBI ClinVar, AWESOME, and PharmGKB, and generates highly informative visualizations of the recovered information.

Abstract P5-06-30: Identification of novel single nucleotide polymorphisms located in MAP3K1 and ABCB1 genes as markers for poor overall survival in early-stage hormone receptor-positive breast cancer using next-generation sequencing

Abstract Background: We previously revealed that single nucleotide polymorphisms (SNPs) of CYP19A1, MAP3K1 rs889312, and ABCB1 rs2032582 were associated with overall survival (OS) in early-stage hormone receptor (HR)-positive breast cancer patients. Previous studies also showed that FGFR2 rs1219468 and TOX3 rs8051542 influenced OS in early-stage breast cancer patients. In this study, we assessed whether undiscovered SNPs of CYP19A1, MAP3K1, ABCB1, FGFR2, and TOX3 are associated with clinical outcome of patients with early-stage HR-positive breast cancer. Patients and Methods: We used next-generation sequencing (NGS) methods to explore unidentified SNPs of CYP19A1, MAP3K1, ABCB1, FGFR2, and TOX3 in 80 patients who had HR+, T1 to T2, and N0 to N1 breast cancer and had matched clinicopathological features and clinical outcomes (experimental cohort). The mapping selected SNPs identified from NGS were located in different chromosomes, such as chromosome 5 (MAP3K), 7 (ABCB1), 10 (FGFR2), 15 (CYP19A1), and 16 (TOX3), were analyzed. The multivariate-adjusted hazard ratio (aHR) of OS associated with the individual genotypes of the experimental cohort was assessed after adjusting for age, tumor size, tumor grade, HER2 status, menopausal status, and chemotherapy using Cox regression analyses. We further correlated identified significant novel SNPs with disease-free survival (DFS) and OS in 195 patients with HR-positive, T1-T2, and N0-1 breast cancer (validation cohort) using stepwise selection multiple Cox model analyses. Results: Through target region re-sequencing, we identified 69 novel SNPs, including 18 CYP19A1 SNPs, 16 MAP3K SNPs, 18 ABCB1 SNPs, 12 FGFR2 SNPs, and 5 TOX3 SNPs in the experimental cohort (n = 80). After multivariate-adjusted analyzing, FGFR2 rs2981460(C/C) (p = 0.0115), and MAP3K1 rs3822625 (A/A) (p = 0.0475), rs702689 (G/G) (p = 0.0312), rs832567 (C/C) (p = 0.0312), and rs9687226 (C/C) (p = 0.0475), and ABCB1 rs2032582 (T/T+T/C) (p = 0.0061) were significantly associated with the poorer OS of the experimental cohort. In a validated cohort (n =195) (Table 1), we found that MAP3K1 rs702689 (G/G) was significantly associated with poorer DFS (aHR = 2.3; 95% confidence interval [CI] = 1.1 to 5.1; p = 0.03) and OS (aHR = 4.9; 95% CI = 1.3 to 18.7; p = 0.02). In addition, MAP3K1 rs832567 (C/C) was significantly associated with poorer DFS (aHR = 2.5; 95% CI = 1.1 to 5.5; p = 0.02) and OS (aHR = 5.4; 95% CI = 1.4 to 21.6; p = 0.02). In premenopausal women of validation cohort (n = 108), ABCB1 rs2032582 (T/T+T/C) was significantly associated with a poor OS (aHR = 62.3; 95% CI = 2.0 to 1911.7; p = 0.02). Conclusions: Our results indicate that 3 novel SNPs, MAP3K1 rs702689, MAP3K1 rs832567, and ABCB1 rs2032582, may affect the prognosis of early-stage HR-positive breast cancer. Further validation of these SNPs in a large series of patients with early-stage HR-positive breast cancer who received adjuvant endocrine therapy alone is warranted. Table 1. The Associations of Hormone Receptor-Positive Breast Cancer Patients with Various Genotypes in multiple Cox model (validation cohort)Disease-free survivalOverall survivalGenotypeaHR (95%CI)PaHR (95%CI)PTotal (n = 195)FGFR2_ rs2981460 (C/C vs.C/T+T/T)0.4 (0.1-1.8)0.220.6 (0.1-5.4)0.68MAP3K1_ rs3822625 (A/A vs. G/A+GG)2.0 (0.7-5.3)0.192.7 (0.6-12.9)0.20MAP3K1_ rs702689 (G/G vs. A/A+A/G)2.3 (1.1-5.1)0.034.9 (1.3-18.7)0.02MAP3K1_rs832567 (C/C vs. A/A+A/C)2.5 (1.1-5.5)0.025.4 (1.4-21.6)0.02MAP3K1_rs9687226 (C/C vs. T/T+T/C)2.0 (0.7-5.3)0.192.7 (0.6-12.9)0.20Premenopausal (n=108)ABCB1_rs2032582 (T/T+T/C vs. C/C)2.0 (0.8-5.0)0.1562.3 (2.0-1911.7)0.02aHR: adjusted by age, estrogen receptor and progesterone receptor status, number of lymph nodes, menopausal status, adjuvant chemotherapy, lymphovascular invasion, and tumor size. Citation Format: Sung-Hsin Kuo, Shi-Yi Yang, Po-Han Lin, Chen-Hsin Chen, Hsin-Chou Yang, Chih-Yuan Hsu, Chiun-Sheng Huang. Identification of novel single nucleotide polymorphisms located in MAP3K1 and ABCB1 genes as markers for poor overall survival in early-stage hormone receptor-positive breast cancer using next-generation sequencing [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-06-30.

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit

We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference.

Genome-wide and SNP network analyses reveal genetic control of spikelet sterility and yield-related traits in wheat

Revealing the genetic factors underlying yield and agronomic traits in wheat are an imperative need for covering the global food demand. Yield boosting requires a deep understanding of the genetic basis of grain yield-related traits (e.g., spikelet fertility and sterility). Here, we have detected much natural variation among ancient hexaploid wheat accessions in twenty-two agronomic traits collected over eight years of field experiments. A genome-wide association study (GWAS) using 15 K single nucleotide polymorphisms (SNPs) was applied to detect the genetic basis of studied traits. Subsequently, the GWAS output was reinforced via other statistical and bioinformatics analyses to detect putative candidate genes. Applying the genome-wide SNP-phenotype network defined the most decisive SNPs underlying the traits. Six pivotal SNPs, co-located physically within the genes encoding enzymes, hormone response, metal ion transport, and response to oxidative stress have been identified. Of these, metal ion transport and Gibberellin 2-oxidases (GA2oxs) genes showed strong involvement in controlling the spikelet sterility, which had not been reported previously in wheat. SNP-gene haplotype analysis confirmed that these SNPs influence spikelet sterility, especially the SNP co-located on the exon of the GA2ox gene. Interestingly, these genes were highly expressed in the grain and spike, demonstrating their pivotal role in controlling the trait. The integrative analysis strategy applied in this study, including GWAS, SNP-phenotype network, SNP-gene haplotype, expression analysis, and genome-wide prediction (GP), empower the identification of functional SNPs and causal genes. GP outputs obtained in this study are encouraging for the implementation of the traits to accelerate yield improvement by making an early prediction of complex yield-related traits in wheat. Our findings demonstrate the usefulness of the ancient wheat material as a valuable resource for yield-boosting. This is the first comprehensive genome-wide analysis for spikelet sterility in wheat, and the results provide insights into yield improvement.

Identification of SNPs involved in Zn and Cu accumulation in the Pacific oyster (Crassostrea gigas) by genome-wide association analysis.

Oysters accumulate high concentrations of zinc (Zn) and copper (Cu), which can be transferred to human due to sea food consumption. Breeding new oyster varieties with low Zn and Cu accumulations is one important way to improve food safety. However, the genetic basis for metal accumulation in mollusks is not well understood. To address this issue, oysters collected in the field were used for genome-wide association study (GWAS) and then the identified genes were used for mRNA expressions analysis in laboratory. First, GWAS were conducted for Zn and Cu accumulation in 288 wild Pacific oysters (Crassostrea gigas) farmed in the same ocean environment. The oysters did not show obvious population structure or kinship but exhibited 8.43- and 10.0- fold changes of Zn and Cu contents respectively. GWAS have identified 11 and 12 single nucleotide polymorphisms (SNPs) associated with Zn and Cu, respectively, as well as 16 genes, which were Zn-containing proteins or participated in caveolae-dependent endocytosis. Second, the mRNA expressions of these 16 genes were observed under Zn and Cu exposure. After 9 days of Zn exposure, Zn contents increased 3.1-fold, while the mRNA expression of cell number regulator 3 increased 1.65-fold. Under 9 days of Cu exposure, Cu contents increased 1.97-fold, while the mRNA expression of caveolin-1 decreased 0.61-fold. These provide the evidence for their roles in regulating physiological levels of these two metals. The findings advance our understanding of the genetic basis of Zn and Cu accumulation in mollusks, which can be useful for breeding new, less toxic varieties of oysters.

ACAA2 and FASN polymorphisms affect the fatty acid profile of Chios sheep milk.

The objective of the research reported in this research communication was the identification and association of single nucleotide polymorphisms (SNP) in the ovine DGAT1, FASN, SCD1 and ACAA2 genes with milk fat percentage and fatty acid (FA) content. Three consecutive monthly milk samplings were obtained from a total of 429 purebred Chios ewes during mid-lactation. Genotypic data were jointly analyzed with 1184 fat content and 37 718 FA percentage records using mixed models. The 3' untranslated region (UTR) of the DGAT1 gene and the 5' and 3'UTRs of the SCD1 gene appeared to be monomorphic. The FASN g.14777C>T SNP on exon 31 was associated with C13:0 and the ACAA2 g.2982T>C SNP on the 3'UTR was associated with C9:0, C11:0, C12:1 cis-9, C13:0 and the ω6/ω3 index, while fat percentage was not affected by the identified SNPs. The results could be useful for breeding programs aiming to improve the quality and nutritional value of ovine milk.

Simple workflow for genome and methylation analyses of ejaculated bovine spermatozoa with low sperm input.

We developed a simplified workflow of gDNA extraction from ejaculated bovine sperm using a low total number of sperm and a short time frame that yields high-quality DNA suitable for downstream methylation and genome analyses. These techniques have broad implications in human biomedical sciences and agriculture, including clinical diagnoses of infertility, the identification of single-nucleotide polymorphisms and aberrant methylation patterns that can impact fertility, lower embryo development and contribute to heritable disease. The methods described here provide a reliable, simplistic approach for analyzing both the genomic and epigenomic status of whole sperm ejaculates that can be adapted for laboratory diagnostics, clinical reproductive practice and basic research.

Colorimetric Detection of Nucleic Acids through Triplex-Hybridization Chain Reaction and DNA-Controlled Growth of Platinum Nanoparticles on Graphene Oxide.

The controllable growth of metal nanoparticles on nanomaterials is becoming a useful strategy for developing nanocomposites with designated performance. Here, a DNA-controlled strategy for growth of Pt nanoparticles on graphene oxide (GO-PtNPs) to regulate the nanozyme activity and a triplex-hybridization chain reaction (tHCR) for triggering the assembly of DNA probes to amplify the target-induced nanozyme catalytic signal were designed. The tHCR with one linear and two hairpin probes could be specially triggered by a tHCR trigger to form a long double-stranded DNA structure in the presence of target nucleic acid, which hindered the adsorption of these probes on a GO surface, and thus accelerated the growth of PtNPs. The formed GO-PtNPs showed strong catalytic activity toward the oxidation of 3,3,5,5-tetramethylbenzidine, thereby producing an amplified "turn-on" detection signal. The proposed method showed very high sensitivity with the detection limits down to 14.6 pM for mutant KRAS DNA and 21.7 pM for let-7a microRNA. This method was validated with better analytical performance than a general HCR system and could be effectively used for the identification of single-nucleotide polymorphisms, thus providing a novel approach for simple and sensitive detection of nucleic acids.