Category Archives: DNA

The world is still not over with the COVID-19 pandemic and now anotherhighly infectious virus is on a surge. Also known as thevomiting bug, Norovirus is highly infectious and causes vomiting and diarrhoea but usually passes in a couple of days. This normally peaks in the winter months.

But cases of the bug have recently been increasing across England.Outbreaks have been particularly concentrated in nursery and childcare facilities with far more than expected in summer months, Public Health England (PHE) said.

In the past five weeks, 154 outbreaks have been notified, compared with an average of 53 outbreaks for the same time period in the previous five years.PHE said while young children were affected, there has also been a rise in infection in all age groups.

The overall number of laboratory-confirmed norovirus reports across all age groups has also recently increased to the levels seen in previous years before the COVID-19 pandemic.

Norovirus is commonly known as the winter vomiting bug.

It is easily transmitted through contact with infected individuals or contaminated surfaces.

Norovirus is highly infectious and causes vomiting and diarrhoea but usually passes in a couple of days.

The increase in outbreaks has been mostly in educational settings, particularly in nursery and childcare facilities.

Symptoms include sudden onset of nausea, projectile vomiting and diarrhoea.

Symptoms can also include a high temperature, abdominal pain and aching limbs.

Norovirus can be spread through food contaminated by the virus when food is handled by symptomatic people or infected individuals.

Stay at home if you are experiencing norovirus symptoms.

Wash your hands frequently and thoroughly with soap and warm water.

Unlike for COVID-19, alcohol gels do not kill off norovirus so soap and water is best.

A bleach-based household cleaner or a combination of bleach and hot water should be used to disinfect potentially contaminated household surfaces.

If you are ill, avoid cooking and helping prepare meals for others until 48 hours after symptoms have stopped.

Wash any contaminated clothing or bedding using detergent and at 60C, and if possible, wear disposable gloves to handle contaminated items.

Go here to read the rest:
DNA Explainer: Know about highly infectious Norovirus and precautions to be taken - DNA India

TACOMA, Wash. - For the first time in federal court, tree DNA has been used to help decide a case.

39-year-old Justin Wilke was put on trialfor his role in an illegal logging operation at Washington's Olympic National Forest. In 2018, Wilke and his accomplice Shawn Williamsillegally felled maple trees and sold the lumber to sawmills. Williams was then sentenced to 30 months in prison.

But that's not all. In August 2018, the two encountered a tree with a wasp's nest at its base. They decided to burn the nest with gasoline to get rid of it.

A blaze soon erupted, which ended up burning 3,300 acres of forest. Many of the destroyed trees were bigleaf maple, a prized species used in higher-end acoustic guitars.

Dubbed the "Maple Fire", officials estimated it cost around $4.2 million to eventually contain.

Now, prosecutors used DNA analysis to determine that the lumber Wilke sold matched the remains of three bigleaf maples taken from the forest. This proved that the trees had not been harvested legally from private lands, as Wilke had said.

The DNA analysis was so precise that it found the probability of the match being coincidental was approximately one in one undecillion (one followed by 36 zeros), saidthe U.S. Attorneys Office for Western Washington.

Wilke was convicted ofconspiracy, theft of public property, depredation of public property, and trafficking and attempted trafficking in unlawfully harvested timber. Wilke could face up to ten years in prison. He will be sentenced in October.

See the full Department of Justice release here.

The rest is here:
Tree DNA helps convict timber thief who started forest fire - woodworkingnetwork.com

Introduction

Obsessive-compulsive disorder (OCD) is a serious and common mental disorder with an estimated prevalence of 1% to 3% in children and adolescents.1 Pediatric OCD is associated with significant distress and marked interpersonal, academic, and occupational impairments,2 which can have a detrimental impact on psychosocial development.3

Treatments for OCD include pharmacological approaches using selective serotonin reuptake inhibitors (SSRI) and psychological approaches involving cognitive behavioral therapy (CBT). The recommended first-line treatment for pediatric OCD is CBT. It has been proven to be more effective than no intervention and while comparable to treatment with SSRIs, CBT has a lower risk-to-benefit ratio compared to medication and a higher acceptability among patients and their families.4 However, there is significant variability in how children and adolescents with OCD respond to CBT, with 39% of patients showing adequate remission of their symptoms.5 Similar variability is observed when patients with early-onset OCD are treated with SSRI monotherapy (22% remission rates) or when CBT is combined with an SSRI (54% remission rates).6

Clinical guidelines recommend CBT as the first-line treatment for patients with mild to moderate symptoms. It can be combined with an SSRI as the initial treatment in more severe cases or when there is no adequate response to CBT alone.7,8 Although the severity of OCD symptoms may help in guiding treatment selection, the observed variability in remission rates highlights the importance of identifying moderators and predictors of response to help clinicians optimize the initial treatment for a particular patient.

Several factors have been proposed as predictors of a poorer outcome to CBT in pediatric OCD, such as an older age, the severity of symptoms and impairment, co-morbidities and a family history of OCD.9 However, their importance and validity as predictors remain controversial. Genetic variants represent a potential source of predictors, with the study of such variants referred to as therapy genetics. The first evidence of the contribution of genetic variants to psychological therapy response came from candidate gene studies; however, these findings have proven to be difficult to replicate.10,11 Recently, genome-wide association studies (GWAS) on outcomes following psychological therapy were published for both children and adults with anxiety disorders.12,13 However, these studies were underpowered to detect the small effect size of single genetic variants with genome-wide significance.

Several investigations have explored the epigenetic process of DNA methylation and differential gene expression in treatment response. Early studies using candidate gene (BDNF, NGF, FKBP5, and MAO-A) approaches have demonstrated that changes in DNA methylation may underlie response to psychological therapies in a variety of disorders including OCD.1421 A small number of studies have examined the role of gene expression and the response to psychological therapy: two studies using FKBP5 as a candidate gene in post-traumatic stress disorder and two studies using genome-wide expression analysis in anxiety disorders.12,2224

Here, we performed a genome-wide methylation analysis using peripheral blood obtained after eight weeks of CBT from a cohort of children and adolescents with a diagnosis of OCD who were drug-nave and never previously treated with psychological interventions. Furthermore, we integrated the methylation and gene expression profiles using samples from the same individuals. The main objective of the present study was to provide new insight into the biological mechanisms of CBT and to identify new candidate biomarkers of CBT response.

Twelve children and adolescents aged between 8 and 16 years who were receiving CBT for the first time participated in the present study. None of the participants had been treated previously with antidepressants or other psychotropic drugs, or with psychological therapies. Patients were diagnosed using the Diagnostic and Statistical Manual of Mental Disorders-V (DSM-V).25 The study was carried out at the Child and Adolescent Psychiatry and Psychology Service of the Institute of Neuroscience at the Hospital Clinic of Barcelona. The study was naturalistic and the treatment was established according to the Clinical Guidelines for the Treatment of Obsessive-Compulsive Disorder of the Child and Adolescent Psychiatry and Psychology Service. All procedures were approved by the Hospital Clnic ethics committee. Written informed consent was obtained from all the parents and verbal informed consent was given by all the participants following explanation of the procedures involved. All experiments were performed in accordance with relevant guidelines and regulations. This study was conducted in accordance with the Declaration of Helsinki.

Cognitive-behavioral therapy counseling consisted of one session that covered the psycho-educational aspects of OCD (nature of OCD, clinical characteristics and principles of behavior therapy) and twelve sessions (two sessions every week during the first month and a weekly session during the second month) based on exposure and response prevention.

Information on illness severity was obtained during the initial phase of the study using the Childrens Yale-Brown Obsessive Compulsive Scale (CYBOCS).26 The same scale was administered after 8 weeks of CBT. Treatment response was evaluated using the percentage of improvement as follows: ((CYBOCS8weeks- CYBOCSbasal)/ CYBOCS basal)*100. Patients were classified as responders or non-responders according to the percentage of improvement after 8 weeks of CBT. Responders were patients with an improvement > 35%, while non-responders were those with an improvement < 25%. Patients with an improvement > 25% and < 35% were classified as partial responders.27

Two blood samples from each participant were collected before the start of CBT: one in EDTA (BD Vacutainer K2EDTA tubes; Becton Dickinson, Franklin Lakes, New Jersey, USA) and another in PAXgene Blood RNA tubes (Qiagen, Valencia, CA). Genomic DNA was extracted using the MagNA Pure LC DNA Isolation Kit and a MagNA Pure LC 2.0 instrument (Roche Diagnostics GmbH, Mannheim, Germany). DNA concentration and quality were measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Surrey, CA). Genome-wide DNA methylation was profiled at the CEGEN-PRB3-ISCIII using the Illumina Infinium MethylationEPIC BeadChip Kit. Total RNA was isolated in accordance with the manufacturers protocol (PAXgene Blood RNA kit). RNA quality and quantity were measured by an Agilent Bioanalyzer 2100 (Santa Clara, CA). 1 g of purified RNA from each of the samples was submitted to the Kompetenzzentrum fur Fluoreszente Bioanalytik Microarray Technology (KFB, BioPark Regensburg GmbH, Regensburg, Germany) for labeling and hybridization using Human Genome U219 array plates (Affymetrix, Santa Clara, CA, USA), following the manufacturers protocols.

Raw intensity data (.IDAT) files were received and bioinformatics processes were conducted in house using the Chip Analysis Methylation Pipeline (ChAMP) Bioconductor package.28 Raw IDAT files were used to load the data into the R environment with the champ.load function, which also allows for the probe QC and removal steps to occur simultaneously. Probes with weak signals (p < 0.01) (n = 3103), cross-reactive probes (n = 11), non-CpG probes (n = 2952), probes with < 3 beads in at least 5% of the samples per probe (n = 10,683), probes that bound to SNP sites (n = 96,500), and sex chromosome probes (n = 61,734) were all considered problematic for the accurate detection of downstream methylation. After removing these probes, 736,109 probes remained for downstream analysis. values were then normalized using the champ.norm function, specifically with the beta-mixture quartile method (BMIQ function). Cell counts were measured using the champ.refbase function. The following cells were counted: CD8+ T cells, CD4+ T cells, natural killer (NK) cells, B cells, monocytes, and granulocytes. Next, the singular value decomposition (SVD) method was performed by champ.SVD to assess the amount and significance of the technical batch components, along with any potential confounding variables (eg, sex, age, and cell count) in our dataset. Using the champ.runCombat function, Combat algorithms were applied to correct for slide and array (significant components detected by the SVD method). No effect of sex, age or cell count was detected.

After filtering, normalization, and the detection of batches and covariates, differentially methylated positions (DMPs) were identified using the champ.DMP function, which implements the limma package to calculate the p-value for differential methylation using a linear model (FDR-adjusted p-values < 0.05). An absolute value of the difference between the -value medians () of responders and non-responders higher than 0.2 was set as the cut-off value to decrease the number of significant CpGs and identify sites with the more biologically relevant methylation differences.

Microarray data preprocessing was performed using the Babelomics 5 suite (http://www.babelomics.org/).29 The data were standardized using robust multichip analysis. Multiple probes mapping to the same gene were merged using the average as the summary of the hybridization values. Co-expression modules were identified using the R software package for weighted gene co-expression network analysis (WGCNA).30 The co-expression analysis involved constructing a matrix of pairwise correlations between all pairs of genes across all selected samples. Next, the matrix was raised to a soft-thresholding power ( = 8 in this study) to obtain an adjacency matrix. To identify modules of co-expressed genes, we constructed the topological overlap-based dissimilarity, which was then used as input to average linkage hierarchical clustering. This step resulted in a clustering tree (dendrogram) whose branches were identified for cutting based on their shape, using the dynamic tree-cutting algorithm. The above steps were performed using the automatic network construction and module detection function (blockwiseModules in WGCNA), with the following parameters: minModuleSize of 30, reassignThreshold of 0, and mergeCutHeight of 0.25. The modules were then tested for their associations with the trait by correlating module eigengenes with trait measurements.

We then used ClueGO v2.1, a Cytoscape plug-in, to perform a gene set enrichment analysis, as described previously.31 Briefly, we selected the unstructured terms of biological processes from Gene Ontology (GO). Only terms with an adjusted p-value < 0.05 and experimental evidence were selected for analysis. Genes involved in significant modules were mapped to their enriched term based on the hypergeometric test (two-sided), with the p-value being corrected by the Benjamini-Hochberg method. ClueGO created a functional module network in which the different GO terms were clustered according to the strength of the association between the terms calculated using chance-corrected kappa statistics.

Data were analyzed using the SPSS 22.0 software (IBM, Chicago, IL, USA). The normality of continuous variables was tested using the KolmogorovSmirnov and ShapiroWilk tests, while the equality of the variance between the groups was assessed using Levenes test. Two-tailed p-values < 0.05 were considered to be of statistical significance. In genes enriched with DMPs significantly associated with CBT response ( > 0.2, FDR-adjusted p-values < 0.05), the values of the most significant DMPs in each gene were tested for correlation, using Spearmans rank correlation coefficient, with the eigengene values of the modules significantly associated with CBT response in the WGCNA.

An overview of the study design is shown in Figure 1. Table 1 shows the demographic and clinical characteristics of the study participants. As can be observed, there were non-significant differences between the responders and non-responders for age, sex, symptom severity at baseline and family history of OCD. Although non-significant, a higher percentage of non-responders (100%) than responders (50%) presented co-morbidities.

Table 1 Demographic and Clinical Characteristics of the Study Participants

Figure 1 Overview of the study.

We classified 55,149 probes as significant DMPs (FDR-adjusted p-values < 0.05). However, this included DMPs with very small differences in methylation between responders and non-responders. Therefore, a cut-off of > 0.2 was applied, which identified 89 DMPs with methylation changes that were more likely to be biologically relevant (Supplementary Table 1).

The 89 significant CpGs mapped to 70 genes. Two of these genes were enriched with significant DMPs (FDR-adjusted p-value < 0.05, > 0.2) and were selected for subsequent analysis: PIWIL1 and MIR886. PIWIL1 was enriched with five CpGs that were significantly hypermethylated in the non-responders. These DMPs were upstream of the transcription start site (from +1500 to +200 bp), in a region that, according to the UCSC browser, includes a CpG island and a DNase hypersensitive site (Figure 2A). The most significant CpG in PIWIL1 (cg13861644) is included in the Blood Brain DNA Methylation Comparison Tool (https://epigenetics.essex.ac.uk/bloodbrain/),32 showing a significant correlation (p < 0.05) between methylation levels in the blood and in the prefrontal cortex (r = 0.76), entorhinal cortex (r = 0.83), superior temporal gyrus (r = 0.77) and cerebellum (r = 0.73) (Supplementary Figure 1).

Figure 2 (A) Distribution of significant DMPs (FDR-adjusted p-value < 0.05, > 0.2) in the PIWIL1 gene and methylation values in responders and non-responders. (B) Distribution of significant DMPs (FDR-adjusted p-value < 0.05, > 0.2) in the MIR886 gene and methylation values in responders and non-responders. (C) Module eigengene values (y-axis) for the yellowgreen module in individual samples (x-axis). Black bars indicate non-responders, while gray bars indicate responders. (D) Scatter plots showing correlations between yellowgreen module eigengene values (x-axis) and methylation values of the cg13861644 in PIWIL1 (y-axis). Black points correspond to non-responders, while gray points correspond to responders. (E) Scatter plots showing correlations between yellowgreen module eigengene values (x-axis) and methylation values of the cg04481923 in MIR886 (y-axis). Black points correspond to non-responders, while gray points correspond to responders.

MIR886 was enriched with four DMPs that were significantly hypomethylated in the responders. These CpGs were upstream of the transcription start site (from +1500 to +200 bp), a region that, according to the UCSC browser, includes a promoter region enriched with H3K27AC marks in all the cell lines considered by ENCODE (Figure 2B). The four CpGs in MIR886 are included in the Blood Brain DNA Methylation Comparison Tool, showing a significant correlation (p < 0.05) between methylation levels in the blood and in the prefrontal cortex (r > 0.89), entorhinal cortex (r = 0.95), superior temporal gyrus (r > 0.92) and cerebellum (r > 0.52) (Supplementary Figure 2).

We applied WGCNA to genome-wide expression data, which identified 70 gene co-expression modules (Supplementary Figure 3). One module, the yellowgreen (197 genes), showed a significant correlation with CBT response (r = 0.85, FDR-corrected p-value = 0.0003). The yellowgreen module contained genes that were upregulated in non-responders to CBT (Figure 2C).

To explore the biological mechanism associated with the genes of the yellowgreen module, we performed a gene set enrichment analysis using the unstructured terms of biological processes from Gene Ontology (GO). We identified five clusters involving ten significant terms (Bonferroni-corrected p-value < 0.05) (Table 2) that were related to DNA replication, chemotaxis, hormone metabolism and catecholamine transport.

Table 2 Gene Set Enrichment Analysis of Biological Processes from Gene Ontology (GO) Obtained for the Yellowgreen Module. The Table Shows the GO Terms Identified, Their Cluster Distribution According to ClueGO, Their Bonferroni-Corrected p-values and the Associated Genes Found in the Yellowgreen Module

We next investigated the possible relationship between the differences in DNA methylation between the responders and non-responders and the gene co-expression modules that were associated with CBT response. We analyzed the correlation between the values of the most significant DMP in the PIWIL1 and MIR886 genes and the module eigengene values. There were significant correlations between the yellowgreen module and the cg13861644 in PIWIL1 (r = 0.74, p = 0.005) and the cg04481923 in MIR886 (r = 0.72, p = 0.008). Patients showing higher methylation in these CpGs showed an upregulation of the genes in the yellowgreen module (Figure 2D and E).

We also analyzed the correlation between the values of the most significant DMP in the PIWIL1 and its expression. The Human Genome U219 array plates only includes probes for the PIWIL1 gene but not for the MIR886. Non-significant correlation between methylation and expression was detected between cg13861644, the most significant DMP in the PIWIL1 gene, and its expression in the microarray. Although non-responders showed lower gene expression of PIWIL1 (4.51.9), in agreement with the observed hypermethylation, than responders (5.30.3), the difference was not significant (p>0.05).

To our knowledge, the present study is the first to analyze and integrate differences in DNA methylation and gene expression in association with CBT response in the peripheral blood of children and adolescents with early-onset OCD. We identified two genes, PIWIL1 and MIR886, that were enriched in significant CpG sites that showed meaningful differences ( > 0.2) in the methylation level between responders and non-responders and also a strong correlation in DNA methylation between the blood and brain. These CpGs showed higher methylation levels in non-responders and were associated with a module of 197 genes that were co-expressed and upregulated in the non-responders. Interestingly, PIWIL1 and MIR886 are involved in the tight control of gene expression with non-coding RNAs (ncRNAs). Small ncRNAs have roles in neuronal function, cognition, learning and memory.33

PIWIL1 encodes a Piwi-like protein that forms an evolutionarily-conserved gene regulatory mechanism together with the Piwi-interacting RNAs (piRNAs), a class of small ncRNAs. Piwi proteins and piRNAs are found primarily within the male germline, where they are necessary for germ cell maintenance and spermatogenesis because they protect the genome by silencing transposon expression at both the epigenetic and post-transcriptional levels.3437 In addition to their role in germline genome defence, there is growing recognition that the Piwi pathway is involved in neuronal development throughout the lifespan and in neuronal gene regulation in the adult brain.3842 Moreover, functional disruption of the Piwi pathway has indicated that it is also involved in learning and memory and in the regulation of behavioral responses to the environment.43 These findings are consistent with the strong association between coding mutations in the Piwi genes in humans and autism.44

MIR886 is a Pol III non-coding RNA 886 gene (nc886), which was previously proposed to encode a pre-miR-886 or an RNA component of the vault complex referred to as vtRNA2-1.45 However, a later study did not find any evidence that nc886 gives rise to microRNAs or that it associates with the vault complex.46 This gene was previously shown to be elevated in Friedreichs ataxia and differentially methylated in Parkinsons disease.4749 nc886 has a CpG island in its upstream region that is maternally imprinted.50 Genomic imprinting is the monoallelic expression of a subset of genes in a conserved, parent-of-origin fashion. The frequency of imprinting of the nc886 CpG island in children has been associated with the genetic background and has also been linked to the mothers age and season of conception, indicating that genetic and environmental factors may affect the establishment of imprinting, which is closely associated with human physiology.50,51 Changes in gene expression of imprinted sites within the placenta, including of MIR886, that are suggestive of an altered imprinting status have been linked to newborn neurobehavioral outcomes.52

The genes in the yellowgreen module are associated with several biological processes such as DNA replication, chemotaxis, hormone metabolism and catecholamine transport. These results agree with those of one of the two studies using genome-wide expression analysis of CBT response in anxiety disorders, which identified similar GO terms of DNA transcription and elongation and positive regulation of chemotaxis.12

Although correlations between DNA methylation in promoter regions and gene expression have been reported,53 in our study we did not observed this effect. This could be due to the small sample size of our study. However, it could also be related to the complex mechanisms implicated in the epigenetic regulation of gene expression. The hypermethylation observed in the promoter region of PIWIL1 could not affect the basal expression of this gene but could modify its regulation by transcription factors that participate in the modulatory effects exerted by CBT therapy.

The findings of this study should be interpreted by bearing in mind several important limitations. The sample size limited the statistical power of the study and made it difficult to detect small or modest effects on DNA methylation or gene expression. Given that the study was hypothesis-driven and due to the small sample size, our results should be seen as preliminary and should be considered as exploratory findings that require further confirmation. However, it should be noted that our sample comprised patients with early-onset OCD. Thus, the sample represented a homogeneous clinical population who had not been previously treated and who were at the initial stages of the illness. Moreover, several potential confounders were controlled for, such as age, smoking status, pharmacological treatment and the course of the disease. We also controlled for blood cell composition, as DNA methylation is cell type-specific and different cell compositions between samples could affect the methylation data obtained.

In conclusion and despite the study limitations, our results provide evidence that the epigenetic regulation of ncRNAs could be a predictor of CBT response and might be related to differences in the expression of genes involved in biological processes associated with CBT response. Our results have to be replicated in large samples before using the methylation level of these specific genes as predictive biomarkers with clinical application.

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Funding sources had no further role in study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the paper for publication.

This work was supported by the Alicia Koplowitz Foundation; Ministerio de Economa y Competitividad- Instituto de Salud Carlos III- Fondo Europeo de Desarrollo Regional (FEDER)-Unin Europea (PI16/01086, PI19/01122). Support was also given by the CERCA Programme/the Government of Catalonia, Secretaria dUniversitats i Recerca del Departament dEconomia i Coneixement to the Child Psychiatry and Psychology Group (2017SGR881) and to the Clinical Pharmacology and Pharmacogenetics Group (2017SGR1562). The authors thank the Language Advisory Service at the University of Barcelona for manuscript revision. The authors also thank all subjects and their families for the time and effort spent on this study.

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

The authors declare no conflicts of interest for this work.

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Excerpt from:
DNA methylation of cognitive therapy | PGPM - Dove Medical Press

By Scott Meacham| Oklahoman

Of the nearly 3 billion base pairs in the human genome, about 99% are the same in every human being however, it is the sequence of these DNA pairs that makes each of us who we are genetically.

Its like that with entrepreneurial DNA every state has it.

Our country was built by entrepreneurs. Its just that from state to state, our DNA is sequenced differently.

In Oklahoma, our entrepreneurial DNA isnt channeled from one dominant industry or from a particular type of entrepreneur. Our state heroes of innovation have impacted industries across the board from human flight to rock and roll. From changing the way that people drive to changing the way the way people exercise. From making it easier to shop to making it easier to park. From digging ditches to accessing the Internet.

Wiley Post, the aviator with the vision of moving people and freight faster over greater distances, envisioned space travel and, in 1934, invented the pressure suit and advanced innovation in airplane design and fuel forever linking our state to the moon and Mars.

While Wiley Post was pushing the limitations of flight, Oklahoma musician and electric guitar pioneer Bob Dunn was doing some soaring of his own. Dunn carved a place in the history of country swing, during a two-day recording session of 30 one-take cuts, making the first recording of music on an electric guitar, which was his self-engineered electric instrument.

Tulsa state patrol officer Clinton Riggs invented a funny-shaped sign with just the word yield that, without changing laws or the construction of intersections and access ramps, reduced accidents and saved lives.

Nautilus inventor Arthur A. Jones built his first exercise machine while living at the Tulsa YMCA.

Grocer Sylvan Goldman created the shopping cart so that his Oklahoma City customers could buy more on each trip to the grocery store the icon in the upper corner of your Amazon page is the icon of Sylvans legacy.

Another icon invention, Carl Magees parking meter, improved traffic flow and access to parking in Oklahoma City and in all other 49 states.

The Malzahn family, of Ditch Witch fame, gave the world a whole new way to install underground utilities safely and efficiently from gas, electric, and plumbing in the 1950s to telecommunications, CATV, and fiber options today.

Edward Roberts in 1974 invented the first personal computer that attractedPaul Allen and Bill Gates, who then wrote Altair BASIC, the first high-level coding language which became the first product of Microsoft, and the foundation upon which Gates and Allen eventually built the largest software company in the world.

DNA was discovered in 1869 when Swiss biologist Friedrich Miescher found an odd substance that didnt match the proteins he expected in his research of white blood cells. It took another 100+ years, extensive Nobel-caliber research, and groundbreaking advances in computer technology and nuclear medicine to gain the understanding we have today of DNA.

Just as human development is built on the hereditary material of DNA, so is Oklahomas path of innovation and construction of the entrepreneurial DNA of our state. With pride and determination, we need to continue to build on our amazing history of commercializing great ideas that happen here.

Scott Meachamis president and CEO of i2E Inc., a nonprofit corporation that mentors many of the states technology-based startup companies. i2E receives state support from the Oklahoma Center for the Advancement of Science and Technology and is an integral part of Oklahomas Innovation Model. Contact Meacham at i2E_Comments@i2E.org.

Originally posted here:
Meacham: Oklahoma has long exhibited the DNA of entrepreneurship - Oklahoman.com

Earlham College researchers have returned to Iceland with a variety of tech tools to help Icelanders learn more about their Nordic past.

Computer scientist Charlie Peck and biologist Emmett Smith have spent a month at the end of a long peninsula on the east coast of Iceland. Peck explains if you were to drop a stick in the ocean in Norway, the currents would likely bring that stick near the sites where they are working with Icelandic archaeologists.

Peck and Smith are doing what they call 21st century science. Examining the past not only requires archaeologists, but computer scientists using drones to locate where to dig and biologists to identify DNA found in the environment, particularly soil.

The National Geographic Society is funding the project looking at some of the earliest Viking settlements in Iceland in the year 875.

Peck, Smith and the archaeologists want to know what was there and what the people were doing there.

According to Smith, "If I take a soil sample, extract DNA, are we going to find things like particular whole species or fish species that we know they would be consuming? Are we going to see sheep we know they were husbanding? Do we have dogs, horses and cattle which are not in Iceland natively?"

Peck pulls up a picture during our Zoom interview that shows very dark soil. That's the fire pit his drone, guided by computer software, picked up in a giant field.

"You'll fly and pick out features through the change in surface plants that tells you to dig here," he says.

They are also creating a 3D map in a river valley to measure erosion. Climate change is more pronounced in Iceland than in the Midwest and the scientists, when comparing their map to a British-made one in 1942, can determine how nature moves in as the glacier recedes. Microbes in the soil are also useful in determining this.

Smith has dozens of soil samples but moving them across international borders isn't easy. They will use a series of techniques and specialized tools to extract the DNA from the soil samples and store it in tubes. "Then we just come back with a hundred 1.5 ml tubes on frozen vegetables - to keep them cold - and bring those back to Indiana to do the sequencing and the analysis on."

What Have They Found?

Archaeologists discovered a Roman coin which could mean the site was once a trading post.

Smith focuses on the DNA found in soil.

"The henbane and the cranberry in particular indicate that we are seeing ancient DNA that was brought to this location in the form of plant material by the settlers. We've not yet found any human DNA. That was our goal. But every year the technology (and) the analysis tools get better."

Yujeong Lee is telling Earlham's story on the Earlham Field Science Instagram account.

Blog:https://fieldscience.cs.earlham.edu/andhttps://fieldscience.cs.earlham.edu/index.php/blog-2021/

Continued here:
How Drones And DNA Can Drill Down To The Past - WVXU

By Maggie Brown, WRAL multiplatform producer

Tampa, Fla. A Florida man was charged with sexual battery in relation to a cold case that happened in 2007. Police used genetic genealogy testing to find Jared Vaughn, 44, after he submitted his DNA to the genealogy website, FamilyTreeDNA.

In 2007, a woman was assaulted after a man offered to drive her home. At that time, a sexual assault kit was done to try and identify the woman's attacker, officials said.

A crime lab used GEDmatch and FamilyTree's DNA databases to identify Vaughn as a possible suspect, according to authorities. A warrant was obtained and officials gathered a swab from Vaughn, to confirm that his DNA matched what was in the kit.

Police have used DNA from online genealogy sites to solve dozens of cold cases, according to Pew Research.

According to a survey from June, 48% of people said they were OK with DNA testing companies sharing data with police. A third said it was unacceptable, and 18% were unsure.

The website officials say Vaughn used, FamilyTree, only allows law enforcement to use its site to solve homicides, sexual assault or abduction cases.

Experts say that even if someone did not use a genealogy website, their DNA could still be retrieved. Someone's third cousin's DNA profile on FamilyTree could be used by law enforcement in an investigation, according to Nia Bala, a senior attorney at the Policing Project at New York University Law School.

"I click the box and say, yes, law enforcement can use my information. That feels above board," she told Slate. "But what about my third cousin? Do they know that their information essentially is out there as well, because my DNA and their DNA are linked?

See the original post here:
Man charged with sexual battery in 14-year-old cold case after entering his DNA into ancestry website - WRAL.com

Headlines about molecular genetics being used to shed new light on old mysteries or even put criminals behind bars have become increasingly more common.

In South Africa DNA is being used to answer important questions about everything from a group of peoples origins to the biological paternity of a child.

But paternity tests arent just applicable to modern cases. Fellow researcher Christoff Erasmus and I considered DNA evidence to understand a divorce case dating back 321 years. The events before and after the divorce case of Maria Kickers had long-term consequences for a family with a surname that, for decades, appeared often among the countrys white leaders. That name is Botha.

The first prime minister of the Union of South Africa, established in 1910, was Louis Botha. There was also PW Botha, the last prime minister to hold that title, and the first to become executive state president of the Republic of South Africa.

Our research shows that Kickers lied in her 1700 divorce case at the Cape of Good Hope. Her lie about the paternity of her children led to a chain of events that affected the Botha lineage, resulting in 38 000 people carrying that name when in fact they were descendants of Ferdinandus Appel.

The genetic evidence, which we gathered using a DNA-based paternity test kit, in combination with the documented testimonies, suggests that Ferdinandus Appel was likely the father of Kickers first son and Frederik Botha the father of the other boys. When we genotyped a random sample of Botha males. We found that almost half of them have the Appel rather than the Botha Y chromosome.

The false paternity claim means that tens of thousands of Bothas more than 76 000 South Africans had this surname in 2013 should in fact be called Appel, a very uncommon name in the country.

If the Kickers divorce case was heard today, DNA evidence would have refuted the lie about paternity outright and the Botha family may well have shattered. Our findings provide another reminder that DNA evidence can clarify events that happened centuries ago, deepening and improving our understanding of history.

One of our sources was a set of records presented by Richard Ball, who is linked to the families at the heart of the divorce case. We also drew information from published genealogical records.

From these we pieced together the following events.

Kickers married Jan Cornelitz in 1683 at the Cape. They had seven children four boys and three girls. Christening records for six of these children have been located; all named Cornelitz as the father. In 1700 Jan filed for divorce, claiming that Maria cheated on him with Ferdinandus Appel as well as a tenant who farmed alongside him, Frederik Botha.

Maria denied any involvement with Ferdinandus Appel, but confessed that Frederik Botha was the biological father of all her children.

In her own defence, she claimed that Jan, her husband, encouraged her relationship with Frederik Botha because Jan was onbequaamd a Dutch word meaning incompetent.

Frederik Botha confirmed before the court Marias claim that all her children were his. While the court did not find Maria to be licentious, they did not give her permission to remarry. As a result, Maria and Frederik Botha had to wait until Jan died, 14 years later, before they could marry. The children then took on the name Botha.

Y chromosomes are inherited like surnames. So, any of Marias sons descendants along an unbroken line of males should carry identical Y chromosomes, bar a few mutations.

With the help of a genealogist we managed to contact and obtain DNA samples from all four of Marias sons along unbroken male lines. In three cases, more than one descendent was found. We genotyped these Bothas Y chromosomes with a kit that is used for paternity tests. The Y chromosomes clearly separated into two groups distinguished by too many mutations to have stemmed from the same Botha ancestor. Within each group, there were a few mutations between individuals, as one would expect for two Y chromosomes with 11 to 19 ancestors between them.

Interestingly, the one group linked to Marias first-born son, whereas the other sons descendants all shared virtually identical genetic profiles. This pattern piqued our curiosity as it suggested that the first sons profile may have stemmed from Ferdinandus Appel.

To test this idea, we genotyped two Appel men: one was a clear match to the first sons descendants. It is 130 times more likely that Marias first son was fathered by Ferdinandus Appel than by a random male that just happened to have the same Y chromosome profile

When we genotyped a random sample of Bothas we found that almost half of them have the Appel rather than the Botha profile. To understand why the first son seems to account for more than a quarter of modern Bothas, we looked at the male descendants as listed in the genealogical records published by the now-closed Genealogical Institute of South Africa.

Just counting the 62 males that were 30 years old or younger in 1780, 45% descended from the first brother while the other three Botha brothers accounted for the remaining 55%. The high number of the first brothers descendants in 1780 could thus explain why so many of our random sample grouped with the Appel profile.

Originally posted here:
Sex, lies and DNA: why many 'Bothas' in South Africa have the wrong surname - The Conversation CA

Identifying the age of animals is fundamental to wildlife management. It helps scientists know if a species is at risk of extinction and the rate at which it reproduces, as well as determining what level of fishing is sustainable.

Determining the age of fish has been difficult in the past primarily involving extracting the inner ear bone, also known as the otolith. Layers of growth in the otolith are counted like rings on a tree to reveal an individuals age. Unless a dead specimen is available, this method requires killing a fish, making it unsuitable for use on endangered populations.

However a non-lethal DNA test developed by the CSIRO enables researchers to determine fish age for three iconic and threatened Australian freshwater species: the Australian lungfish, the Murray cod and the Mary River cod. We outline the technological breakthrough in our research just published.

Our fast, accurate and cost-effective test can be adapted for other fish species. We now hope to share this method to improve the protection of wild fish populations and help promote sustainable fisheries around the world.

Human activity has led to the population declines of the three Australian fish species at the centre of our research.

The threatened Australian lungfish is found in rivers and lakes in southeast Queensland. Its often referred to as a living fossil because its extraordinary evolutionary history stretches back more than 100 million years, before all land animals including dinosaurs.

Man-made barriers in rivers reduce the movement of water, which lowers lungfish breeding rates.

Older lungfish do not have hard otolith structures, which makes determining their age difficult. Bomb radiocarbon, which analyses carbon levels in organic matter, has been used to age Australian lungfish, but this method is too expensive to be widely used.

The threatened Murray cod is Australias largest freshwater fish. The Mary River cod is one of Australias most endangered fish, found in less than 30% of its former range in Queenslands Mary River.

Habitat destruction and overfishing are major threats to Murray cod and Mary River cod populations.

Otoliths can be used to determine age for both these cod species, however this has only been done on a population-wide scale for the more prevalent Murray cod.

Read more: Australia's smallest fish among 22 at risk of extinction within two decades

When cells divide to make new cells, DNA is replicated. This can lead to DNA methylation, which involves the addition or the loss of a methyl group molecule at places along the DNA strand.

Research has found the level of DNA methylation is a reliable predictor of age, particularly in mammals, including humans.

To develop our test, we first worked with zebrafish. This species is useful when studying fish biology because it has a short lifespan and high reproductive rates. We took zebrafish whose ages were known, then removed a tiny clip of their fin. We then examined DNA methylation levels in the fin sample to identify the fishs age.

Following this successful step, we transferred the method to Australian lungfish, Murray cod and Mary River cod. Again, we used fish of known ages, as well as bomb radiocarbon dating of scales and ages determined from otoliths.

We found despite the zebrafish and the study fish species being separated by millions of years of evolution, our method worked in all four species. This suggests the test can be used to predict age in many other fish species.

Read more: Good news from the River Murray: these 2 fish species have bounced back from the Millennium Drought in record numbers

In the same way human population demographers use census data to understand and model human populations, we now have the tools to do this with animals.

We are looking to expand this DNA-based method to determine the age of the endangered eastern freshwater cod and trout cod. We will also continue to test the method across other species including reptiles and crustaceans.

This work is part of CSIROs ongoing efforts to use DNA to measure and monitor the environment. This includes estimating the lifespan of vertebrate species such as long-lived fish and surveying biodiversity in seawater using DNA extracted from the environment.

We envisage that in the not too distant future, these methods may be used by other researchers to better understand and manage wild animal populations.

Read more: A new study shows an animal's lifespan is written in the DNA. For humans, it's 38 years

Continue reading here:
Breakthrough allows scientists to determine the age of endangered native fish using DNA - The Conversation AU

The term DNA at least in the Ultra Boosts case encompasses much more than the design of the shoe itself. And as it joins the 5.0 iteration, the moniker brings along an array of classic, trail-inspired colorways.

We can expect at least three iterations to surface in the next few days, each vivid as it mimics some of the best outdoors gear. The first, which is arguably the most bold of the trio, renders its knits in a dual-tone of light and dark blue; brighter red fixtures dress the branding adjacent, while the sole features a familiar speckling. Opposite, the Wonder White pair is far more muted as it joins alongside cream threads and a warm and cool color combo. Finally, the last rounds us out with a mix replete with Grey Three, Sonic Ink, and Solar Gold pops.

For a closer look at the range, see the official images below. A release, according to adidas AU, is due for June 30th; expect an adidas.com drop in the US to follow.

In other news, the adidas Trae Young 1 is coming soon.

Where to Buy

Make sure to follow @kicksfinder for live tweets during the release date.

Classic Trail-Themed Colorways Appear On The adidas UltraBOOST 5.0 DNA

Mens: $180Style Code: GV7714

Where to Buy

Make sure to follow @kicksfinder for live tweets during the release date.

Mens: $180Style Code: GV7713

Where to Buy

Make sure to follow @kicksfinder for live tweets during the release date.

Mens: $180Style Code: GV7715

See more here:
Classic Trail-Themed Colorways Appear On The adidas UltraBOOST 5.0 DNA - Sneaker News

SALT LAKE CITY, Utah Researchers in Utah are leading the way when it comes to collecting DNA in sexual assault cases. At this moment, Utah is the only state using touch DNA to find answers, and the forensic nurse at the forefront is trying to change that.

Dr. Julie Valentine, a forensic nurse and nursing professor at Brigham Young University in Utah, explains the groundbreaking case that changed the way some DNA evidence is collected.

In 2011, there was a case on a campus where a young woman was violently assaulted and groped," Valentine said When the nurse walked into the room to greet the patient, she was finishing a sandwich and a soda, and anytime you activate the salivary enzymes you destroy the DNA. So, the nurse thought, 'Well, I know that our crime lab has these improved DNA analysis methods."

Valentine is referring to touch DNA, which is DNA from skin cells. Traditionally, it hasnt been used in sexual assault and groping cases.

Well, it turned out we got a full STR DNA profile of the suspect," Valentine said.

That means they were able to identify the assailant. Dr. Valentine says this was a turning point.

"If you are a victim of a groping or a sexual assault and youre thinking oh the person didnt ejaculate or there was no bodily fluid, that does not mean we cant collect evidence," Valentine said.

Monica Garder is a survivor of sexual assault, abuse, and adulthood rape. While she knows who her assailants are, they were never prosecuted for their actions.

"Its dulled me down from the bright light that I used to be to someone thats just barely surviving," Gardner said. And Ive had months and months of being suicidal every day. Ive had times where even in my room with the door locked, Im pacing my room because I feel unsafe.

Gardner knows the pain of sexual assault too well, but technology developed in Utah is giving her hope. She is putting her bravery on display in an effort to help other survivors.

I think there is something that is validating in that to say here is another step, another piece that says Im telling the truth," Gardner said.

Every perpetrator in a sexual assault case leaves behind answers; answers researchers in Utah are helping to find.

I had a case where a victim had been taken by two men and one man held her down on her upper body while she was raped by the other man," Valentine said.

She says both men were identified using Touch DNA.

Dr. Valentine is now working with the National Institute for Justice to create best practice guidelines for touch DNA in sexual assault and groping cases. Throughout the last four years, she has created a series of webinars and presentations to teach professionals in other states and countries about how they too can use touch DNA in these cases.

When DNA tests first came out, you needed about a quarter size of bodily fluid," Valentine said. But thats just not the case; the science has advanced.

They also developed a touch DNA form to help nurse examiners collect evidence, and its the first of its kind. So far, the researchers have found a match in about 21% of cases that utilized Touch DNA.

"It really is this new tool in the toolbox for investigations, but we also have to be cautious and always look at everything in context and look at this as a piece of the investigation and the prosecution," Valentine said.

Unfortunately, touch DNA is only part of the puzzle. Another piece is testing a significantly higher number of rape kits and understanding their scientific value.

The NIJ explains that untested rape kits are a national problem. There is no national system for collecting rape kit data, making it nearly impossible to know how bad the problem really is. There are numerous states where limited reform has been enacted, but there is still much more to do.

Thats why Valentine and the rest of her team are continuing to work behind the scenes to change the future for survivors like Garder. This technology was not around to help in Garder's case, but she's hopeful it will help others get justice.

"This is going to empower the survivor to say, 'No, I can prove you were there. I can prove you touched my body because there is DNA evidence,'" Gardner said.

Read this article:
How researchers in Utah are leading the way in collecting DNA samples to solve sexual assault cases - The Denver Channel