Category Archives: DNA

Published 9:43 pm Friday, October 13, 2023

You might have noticed the Co-Lin alums and fans in your life carrying themselves with an extra amount of bounce in their steps on Friday.

Thursday night the Wolves went on the road to face the No. 4 ranked Mississippi Gulf Coast Bulldogs and knocked the home team from the ranks of the unbeaten with a 28-23 win.

It was a classic performance from a Glenn Davis coached team in his 20th year leading the football program in Wesson.

Gulf Coast plays football in Perkinston, which is located in Stone County, but the school has campuses and facilities up and down the coastline of our state with a combined enrollment that tops 16,000 students.

By comparison, Co-Lin has somewhere north of 5,000 students combined enrolled in either Wesson, Natchez or Mendenhall.

As one would expect, the resources afforded to Gulf Coast in the areas of athletics are among the top of the MACCC.

In Wesson, Davis has built a program that competes as one of the best teams in the state on a year in and out basis with his teams always having talent, but more importantly, cohesion and toughness.

He and his coaches pitch it in recruiting as a blue-collar program.

That cohesiveness, playing as a band of brothers, was needed by every man on the roster to hold off a Gulf Coast comeback attempt in the late going on Thursday.

And in typical Co-Lin fashion, it was some of the student-athletes that grew up closest to the school that made some of the biggest plays of the night.

The first one was made by sophomore linebacker Collin McGowen. A three-time Daily Leader All-Area selection while playing for the Wesson Cobras, McGowen returned a Gulf Coast fumble 38-yards for a touchdown to put CLCC up 7-0 with 6:22 left in the first quarter.

When Gulf Coast did score on Thursday, they did it in dramatic fashion. The first of those long scoring plays was a 57-yard touchdown run by Trey Hall that tied the game up just over a minute after Co-Lin got on the board.

The Wolves led 14-10 at halftime as the first offensive score of the game for Co-Lin came with 7:15 left until the break. Thats when Crystal Springs High alum Johnnie Daniels ripped off a 65-yard touchdown run.

Daniels was highly sought-after out of Crystal Springs and Co-Lin won a recruiting coup when they inked both he and his high school teammate, defensive back Navarion Benson. Benson finished the game with four tackles and had a fumble return that covered 29 yards.

The most successful Co-Lin teams during the Davis era have been ones that were balanced offensively as being able to generate yards on the ground is a Wolf Pack trademark.

This season, Daniels, and freshman Tray Minor (Natchez High) have been a formidable running back duo whove worked behind an offensive line thats overcome injuries all year.

Co-Lin opened the second half at Gulf Coast with its best drive of the night. The Wolves covered 75 yards in 10 plays and ran 4:54 off the clock.

The possession ended with sophomore tight end Tyler Fortenberry catching his first career touchdown on a 25-yard throw from quarterback DeVon Tott.

Fortenberry was a highly decorated quarterback during this high school career at Brookhaven Academy. Included in those honors was being named Daily Leader All-Area MVP and last season he was Totts backup as a freshman.

After the 2022 campaign wrapped up, Fortenberry made the move to tight end and has thrived in that new role. Last week, Fortenberry gave his verbal pledge to continue his career at the University of Southern Mississippi.

The next drive for MGCCC ended with the fumble that Benson recovered, and it only took three plays for Co-Lin to go ahead 28-10 as Tott connected with Jaylen Smith on a 4-yard touchdown pass to put CLCC up 28-10.

The Wolves had a chance to add to that lead as they had an offensive possession that ended the third quarter and started the final frame deep in Bulldog territory.

The Gulf Coast defense buckled though, and Co-Lin ended the series by missing a long field goal attempt.

One play later, Hall hit on one of those aforementioned, explosive plays as he scored on a 70-yard touchdown run that made the score 28-17 with 10:53 left in the game.

Co-Lin and Gulf Coast have had some wild and wacky matchups over the years. Gulf Coast won 31-28 last season at CLCC in a game that was on full tilt.

A refresher, that one featured a touchdown scored by the Bulldogs on a terribly botched call. A Gulf Coast running back crossed the line of scrimmage with the ball and fumbled it, which bounced backwards to his quarterback, who then threw the ball down field to an open receiver for a score.

You cant do that, FYI.

A year prior, Gulf Coast scored in the closing seconds and converted the PAT kick to beat Co-Lin 14-13, again in Wesson.

There was a sense of dread all through the second half of that one-point loss amongst Co-Lin fans as the games results felt as predictable as a movie that gives too much info away in its previews.

Some of that dread crept back into the hearts of the CLCC diehards on Thursday when Gulf Coast cut the lead to 28-23 with a 65-yard interception returned for a touchdown.

At that point, 6:08 remained in the game and Co-Lin faced a hold em or fold em type of moment.

The feeling of dread began to intensify as the Wolves were held to 3-and-out on their next series as just 50 seconds ran off the clock.

Gulf Coast took its last possession of the game with 4:19 remaining and the ball on the Co-Lin 39-yard line after a short punt and long return.

The Bulldogs got down to the 13-yard line, but facing 1st-and-10 from there, the Co-Lin defense showed they still had some tough left in the tank.

The Wolves stopped a rush for no gain on first down as freshman linebacker Malachi Williams, another local guy from Brookhaven High, didnt think twice before knifing through a gap to make a huge tackle at the line of scrimmage.

Gulf Coast quarterback Eli Anderson went to the end zone on second down and his throw was just past the hands of receiver Dayan Bilbo on a play where CLCC defensive back Jahron Manning provided great coverage.

Manning, a sophomore from New Orleans, has been playing at an outstanding level of late and again led Co-Lin in tackles on Thursday with 11 total stops.

On third down, Co-Lin linebacker Dedric Hicks (West Jones), hit Anderson in the midsection while he was throwing to his right.

As he lay on the field being attended to by trainers, Anderson had his helmet off and his arms spread out as it appeared that the wind had been knocked out of him by Hicks.

After being looked at, he tried to return to the field, but was forced to the sideline by the officials. Gulf Coast then called a timeout and Anderson wanted to go in again, but he was once again ushered back by the refs.

On fourth down, backup quarterback Kason Linke came in without warming up and threw his first pass of the night, a ball that skipped on the turf behind its intended receiver.

With that, Co-Lin was content to kneel out the clock and head for the bus in a literal sense.

Last season there were some post-game antics between the schools in the handshake line, Davis and his staff decided to send their team to the locker room rather than have the chance of that happening again.

It was a memorable win in Perkinston, a place where Co-Lin won 41-37 in the 2012 MACCC state championship game in a similarly exciting type of game.

Now Co-Lin finishes the regular season with straight games, two at home, against schools that badly want to spoil a potential playoff spot for the Wolves.

On Thursday, theyll host Pearl River (0-6) and the next week will be homecoming in Wesson with a matchup on Oct. 26 against an East Central (3-3) team that knocked off an unbeaten Northeast Mississippi team on Thursday.

The regular season ends on Nov. 2 at Hinds (3-3) for the Wolves. Gulf Coast and CLCC are now both 2-1 in the MACCC South Division with Jones (5-1, 4-0) leading the division. Jones and Gulf Coast (5-1, 2-1) close the regular season on Nov. 2 in Ellisville.

Lots of football left, but the Wolves always savor a win against Gulf Coast, because the Bulldogs are usually favored when the teams meet.

And being victorious as an underdog is one of lifes great joys, a feeling the Co-Lin football program has in its DNA.

Cliff Furr is the sports editor at The Daily Leader. He can be reached via email at sports@dailyleader.com

Continued here:
Co-Lin football's blue-collar DNA on display in huge road win at Gulf ... - Dailyleader

image:

Experimental setup and phenotypic responses under common garden-conditions in Fragaria vesca plants after propagation at different temperatures for up to three asexual generations.

Credit: Horticulture Research

As global warming continues to redefine ecosystems, plants are increasingly tasked with swift adaptation to ensure their survival. One primary mechanism facilitating such rapid adaptation is epigenetic memory, specifically DNA methylation. DNA methylation, a form of epigenetic modification, involves the addition of a methyl group to the cytosine bases of the DNA, altering its accessibility in chromatin and modulating gene expression. In the context of a warming climate, changes in DNA methylation can be triggered by environmental factors like increased temperature. Such epigenetic adaptations play an instrumental role in allowing plants to synchronize their growth with evolving environmental cues. However, a comprehensive understanding of how these DNA methylation changes affect plant phenotypes, especially in response to warmer temperatures, remains unclear.

In July 2023, Horticulture Researchpublished a research paper entitled by Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vescaecotypes.

To examine the influence of temperature on phenotypic and epigenetic variations, an experiment was conducted across three asexual generations on four European F. vescaecotypes (ES12, ICE2, NOR2, IT4), exposing them to 18 and 28. At the phenotypic level, the ES12ecotype had an increased stolon production at 28 during the first asexual generation (AS1) but not by the third (AS3). Conversely, the IT4ecotype displayed decreased stolon production at 28 in both AS1and AS3. The ICE2and NOR2ecotypes showed significant delays in flowering time at 28 by AS3, with statistical significance at 0.05 > p > 0.001. For petiole length, plants from the ES12, ICE2, and NOR2ecotypes had longer lengths when grown at 28 during AS1. By AS3, the increased petiole length remained only for the NOR2ecotype.The results showed a statistically significant difference between theall phenotypic traits investigated and growth temperature in the experiment, which can be preserved during asexual reproduction. Further in-depth studies at the molecular level, bisulfite-sequencing of the genomic DNA samples from the ecotypes revealed discernible differences in DNA methylation patterns between the two temperature conditions, especially in the CHG and CHH contexts. NOR2exhibited the most pronounced difference in methylation levels between the temperature conditions. Principal Component Analysis (PCA) of methylation profiles showed clear differences between ecotypes grown at 18 and 28. Significant changes in both hypo- and hypermethylation occurred across all ecotypes with the largest temperature-specific methylation increases observed for the CHH context.Notably, methylation changes were identified to be correlated with genomic features such as transcription start sites (TSS) and transcription termination sites (TTS). Regions with differential CHG and CHH methylation typically exhibited hypermethylation.At the same time, transcriptome changes related to temperature increase were observed in approximately 3,500 to 5,000 differentially expressed genes (DEGs) in different ecotypes. In addition, this study also explored the ecotype specific methylation and expression patterns of genes related to gibberellin metabolism, flowering time, and epigenetic mechanisms. It was found that among three or fewer ecotypes, the absolute multiple change of 1,318 related differentially expressed and differentially methylated genes (DEDMGs) was>1.5.

In summary, the research indicates that temperature variations during asexual propagation induce considerable hereditary epigenetic and phenotypic modifications, underscoring the existence of a temperature-related epigenetic memory effect in F. vescaecotypes. This groundbreaking study not only deepens our understanding of plant adaptation but also opens the door for leveraging epigenetic memory to develop crops better suited to the warming world.

###

References

Authors

YuPeng Zhang()1,2, Guangxun Fan3, Tuomas Toivainen3, Torstein Tengs2, Igor Yakovlev2, Paal Krokene2, Timo Hytnen3, Carl Gunnar Fossdal2,*, Paul E. Grini1,*

Affiliations

1. EVOGENE, Department of Biosciences, University of Oslo, 0313 Oslo, Norway

2. Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 s, Norway

3. Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland

AboutCarl Gunnar Fossdal & Paul E. Grini

Carl Gunnar Fossdal: He is currently head of Department Dept. Forest Health, Division for Biotechnology and Plant Health, NIBIO, Norway. His research areas are epigenetics, genomics, plant-pathogen interactions, phytobiome, forest health, wood decay, and fungal enzymes.

Paul E. Grini: He is a professor at the Department of Biological Sciences, University of Oslo. His research focuses on the biology of plant reproductive development.

Horticulture Research

Experimental study

Not applicable

Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes

31-Jul-2023

The authors declare that they have no competing interests.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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DNA methylation: The hidden mechanism enabling plants to adapt ... - EurekAlert

Modern humans migrated to Eurasia 75,000 years ago, where they encountered and interbred with Neanderthals. A new study published in the journal Current Biology shows that at this time Neanderthals were already carrying human DNA from a much older encounter with modern humans. The Penn-led research team, including collaborators from Addis Ababa University, the University of Botswana, Fudan University, Hubert Kairuki Memorial University, and the University of Yaound, showed that an ancient lineage of modern humans migrated to Eurasia over 250,000 years ago where they interbred with Neanderthals. Over time, these humans died out, leaving a population with predominantly Neanderthal ancestry.

We found this reflection of ancient interbreeding where genes flowed from ancient modern humans into Neanderthals, says Alexander Platt, a senior research scientist in the Perelman School of Medicine and one of the studys first authors. This group of individuals left Africa between 250,000 and 270,000 years ago. They were sort of the cousins to all humans alive today, and they were much more like us than Neanderthals.

The team arrived at this conclusion by comparing a Neanderthal genome with a diverse set of genomes from modern indigenous populations in sub-Saharan Africa.

This study highlights the importance of including ethnically and geographically diverse populations in human genetics and genomic studies, says Sarah Tishkoff, a Penn Integrates Knowledge University professor at Penn and senior author on the work.

Because most Neanderthal-human interbreeding is thought to have occurred in Eurasia, not in Africa, Neanderthal ancestry is expected to be limited in sub-Saharan Africa; however, a recent study made the puzzling observation that several sub-Saharan populations contain chunks of DNA that resemble Neanderthal DNA. The study was unable to determine how this Neanderthal-like DNA entered these populations, whether it originated from modern humans who had migrated from Africa, interbred with Neanderthals in Eurasia, and then returned, or whether it was the result of an earlier encounter between Neanderthals and humans. Because the study relied on a limited number of genomes from the 1,000 Genomes Project, all of which share a relatively recent common ancestry in Central and Western Africa, it was also unclear whether Neanderthal-like DNA is widespread among sub-Saharan populations.

To better understand how widespread these Neanderthal-like DNA regions are across sub-Saharan Africa and to elucidate their origins, Tishkoffs team leveraged a genetically diverse set of genomes of 180 individuals from 12 different populations in Cameroon, Botswana, Tanzania, and Ethiopia. For each genome, the researchers identified regions of Neanderthal-like DNA and looked for evidence of Neanderthal ancestry.

Then, they compared the modern human genomes to a genome belonging to a Neanderthal who lived approximately 120,000 years ago. For this comparison, the team developed a novel statistical method that allowed them to determine the origins of the Neanderthal-like DNA in these modern sub-Saharan populations, whether they were regions that Neanderthals inherited from modern humans or regions that modern humans inherited from Neanderthals and then brought back to Africa.

They found that all of the sub-Saharan populations contained Neanderthal-like DNA, indicating that this phenomenon is widespread. In most cases, this Neanderthal-like DNA originated from an ancient lineage of modern humans that passed their DNA on to Neanderthals when they migrated from Africa to Eurasia around 250,000 years ago. As a result of this modern human-Neanderthal interbreeding, approximately 6% of the Neanderthal genome was inherited from modern humans.

In some specific sub-Saharan populations, the researchers also found evidence of Neanderthal ancestry that was introduced to these populations when humans bearing Neanderthal genes migrated back into Africa. Neanderthal ancestry in these sub-Saharan populations ranged from 0 to 1.5%, and the highest levels were observed in the Amhara from Ethiopia and Fulani from Cameroon.

To try to understand whether carrying modern human DNA was helpful or harmful when introduced into the Neanderthal genome, the researchers also investigated where these chunks of modern human DNA were located.To try to understand whether carrying modern human DNA was helpful or harmful, the researchers also investigated where these chunks of modern human DNA were located within the Neanderthal genome. They found that most of the modern human DNA was in noncoding regions of the Neanderthal genome, indicating that modern human gene variants were being preferentially lost from coding sections of the genome, which suggests that having modern human genes in a Neanderthal background is detrimental to fitness.

This is similar to what is seen in modern humans, where natural selection has slowly been removing Neanderthal genes from modern human populations.

This research opens new avenues for exploring human evolution by identifying a genetic reference of a population that occupies a part of the human family tree that had previously been lacking from the genomic and fossil record.

Discovering this ancient lineage of modern humans is really exciting for future research because it gives us a different lens to look at human evolution, says Daniel Harris, a postdoctoral research fellow in the Perelman School of Medicine and the studys other first author. Because we don't have DNA sequences from modern human fossils from that long ago, identifying these sequences will shed light on very early modern human evolution in Africa.

Sarah Tishkoff is the David and Lyn Silfen University Professor in Genetics and Biology and a Penn Integrates Knowledge University Professor with appointments in the Perelman School of Medicines Department of Genetics and Department of Medicine and in the School of Arts & Sciences Department of Biology at the University of Pennsylvania.

Daniel Harris is a postdoctoral research fellow in the Perelman School of Medicine at Penn.

Alexander Platt is a senior research scientist in Penns Perelman School of Medicine.

In addition to Tishkoff, Harris, and Platt, the study authors were Penn Medicines Matthew E.B. Hansen and Michael McQuillan; Fudan Universitys Shaohua Fan; the Hubert Kairuki Memorial Universitys Thomas Nyambo;the University of Botswanas SunungukoWata Mpoloka, and Gaonyadiwe George Mokone; Addis Ababa Universitys Gurja Belay; and the University of Yaounds Charles Fokunang and Alfred K. Njamnshi.

The study was supported by the National Institutes of Health (grants 1R35GM134957, R01AR076241, and 5T32DK007314-39) and the American Diabetes Association (Grant 1-19-VSN-02.

Originally posted here:
Neanderthals carried genes acquired from ancient interactions with ... - Penn Today

The Journal Club returns on Friday October 27th at 11:30 am Eastern time on the Lifespan.io Facebook page. We will be discussing the new paper from Conboy et al. which examines current DNA meythlation clocks and their limitations in the context of aging. They also developed a noise baraometer to measure the epigenetic impact of aging. We will be joined on this episode of the Journal Club by two of the authors of the paper, Drs. Irina and Michael Conboy.

To do this, we need your support. Your charitable contribution tranforms into rejuvenation research, news, shows, and more. Will you help?

This study shows that Elastic Net (EN) DNA methylation (DNAme) clocks have low accuracy of predictions for individuals of the same age and a low resolution between healthy and disease cohorts; caveats inherent in applying linear model to non-linear processes. We found that change in methylation of cytosines with age is, interestingly, not the determinant for their selection into the clocks. Moreover, an EN clocks selected cytosines change when non-clock cytosines are removed from the training data; as expected from optimization in a machine learning (ML) context, but inconsistently with the identification of health markers in a biological context. To address these limitations, we moved from predictions to measurement of biological age, focusing on the cytosines that on average remain invariable in their methylation through lifespan, postulated to be homeostatically vital. We established that dysregulation of such cytosines, measured as the sums of standard deviations of their methylation values, quantifies biological noise, which in our hypothesis is a biomarker of aging and disease. We term this approach a noise barometer the pressure of aging and disease on an organism. These noise-detecting cytosines are particularly important as sums of SD on the entire 450K DNAme array data yield a random pattern through chronology. Testing how many cytosines of the 450K arrays become noisier with age, we found that the paradigm of DNAme noise as a biomarker of aging and disease remarkably manifests in ~1/4 of the total. In that large set even the cytosines that have on average constant methylation through age show increased SDs and can be used as noise detectors of the barometer.

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DNA meythlation clocks and their limitations - Lifespan.io News

Neanderthal gene variants may boost the pain sensitivity of people who carry them and may be most common in populations with prevalent Native American ancestry, a new study finds.

The research, published Tuesday (Oct. 10) in the journal Communications Biology, focused on three versions of the SCN9A gene, which codes for a protein that shuttles sodium into cells and helps pain-detecting nerves send signals. People with any of the three variants are more sensitive to pain caused by being prodded with a sharp object, but not pain caused by heat or pressure.

"In 2020, another group of researchers studied people of European ancestry and linked these Neanderthal gene variants to increased pain sensitivity," first study author Pierre Faux, a geneticist at the French National institute for Agriculture, Food and Environment, told Live Science.

"We extend these findings by studying Latin Americans and showing that these Neanderthal genetic variants are much more common in people with Native American ancestry," Faux said. "We also show the type of pain these variants affect, which wasn't known before."

Related: Mysterious 'Viking disease' linked to Neanderthal DNA

In the new study, the scientists analyzed genetic samples collected from more than 5,900 people living in Brazil, Chile, Colombia, Mexico and Peru. On average, the participants had 46% Native American ancestry, 49.6% European ancestry and 4.4% African ancestry, but these proportions varied significantly between individuals.

The analysis revealed that around 30% of the participants had one of the SCN9A gene variants, called D1908G, while roughly 13% of participants had the other two gene variants, known as V991L and M932L, which tend to be inherited together.

The participants living in Peru, who had the highest proportion of Native American ancestry among the countries studied, were most likely to carry these Neanderthal gene variants. Conversely, participants recruited from Brazil had the lowest proportion of Native American ancestry and were least likely to carry the variants.

"We know that modern humans and Neanderthals interbred something like 50,000 to 70,000 years ago, and that modern humans first crossed over from Eurasia into the Americas by 15- to 20,000 years ago," Faux said.

"The high frequency of the Neanderthal variants in people with Native American ancestry could potentially be explained by a scenario where the Neanderthals carrying these variants happened to breed with the modern humans who eventually migrated into the Americas," he said.

Related: The 1st Americans were not who we thought they were

Following the genetic analysis, the researchers carried out pain threshold tests on more than 1,600 volunteers in Colombia, 56% of whom were women, who had on average 31% Native American ancestry, 59% European ancestry and 9.7% African ancestry. In these tests, participants were asked to tell the researchers to stop as soon as they felt discomfort. The team also analyzed the gene variants carried by each of these tested participants.

In one of the tests, the team applied mustard oil, which irritates the skin, to the forearm skin of participants before pushing plastic filaments of increasing widths onto the same area of skin. In this test, wider filaments exerted a stronger force on the already-irritated skin. Participants who had any of the Neanderthal gene variants tapped out after being prodded with filaments that were significantly smaller than those who did not carry the gene variants.

"When we tested the participants' pain threshold by applying pressure, heat or cold, the gene variants did not affect pain sensitivity, so the Neanderthal variants only affected their response to pinprick pressure," Faux noted.

It is possible that carrying these gene variants gave Neanderthals, and the modern humans who first settled the Americas, some sort of survival benefit, Faux said. But that survival benefit wasn't necessarily related to pain sensitivity, he added.

"The modern humans who first reached North America would have had to bear harsh and cold conditions, so it could be that these variants have other effects beyond pain for example, they could have somehow helped humans to cope with the cold," he said. In other words, the heightened sensitivity to sharp objects might have been just a side effect of another evolutionary change.

However, the evolutionary pressures that acted on SCN9A were likely complex, and "why Neanderthals might have had a greater pain sensitivity and whether introgression in SCN9A represented an advantage during human evolution remains to be determined," the authors wrote..

Nevertheless, it is interesting to know these gene variants, which have previously been linked to small fiber neuropathy a painful nerve condition would have also caused pain in our Neanderthal ancestors, Sulayman Dib-Hajj, a professor of Neurology at the Yale School of Medicine who was not involved in the study, told Live Science in an email.

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Neanderthal DNA may shape how sensitive you are to pain, genetic ... - Livescience.com

Purpose High-grade serous ovarian carcinoma (HGSOC) is the most lethal epithelial ovarian cancer (EOC) and is often diagnosed at late stage. In women with a known pelvic mass, surgery followed by pathological assessment is the most reliable way to diagnose EOC and there are still no effective screening tools in asymptomatic women. In the current study we developed a cfDNA methylation liquid biopsy for the risk assessment of early-stage HGSOC. Experimental Design We performed reduced representation bisulfite sequencing to identify differentially methylated regions (DMRs) between HGSOC and normal ovarian and fallopian tube tissue. Next, we performed hybridization probe capture for 1677 DMRs and constructed a classifier (OvaPrint) on an independent set of cfDNA samples to discriminate HGSOC from benign masses. We also analyzed a series of non-HGSOC EOC, including low-grade, and borderline samples to assess the generalizability of OvaPrint. A total of 372 samples (tissue n=59, plasma n=313) were analyzed in this study. Results OvaPrint achieved a positive predictive value of 95% and a negative predictive value of 88% for discriminating HGSOC from benign masses, surpassing other commercial tests. OvaPrint was less sensitive for non-HGSOC EOC, albeit it may have potential utility for identifying low-grade and borderline tumors with higher malignant potential. Conclusions OvaPrint is a highly sensitive and specific test that can be used for the risk assessment of HGSOC in symptomatic women. Prospective studies are warranted to validate OvaPrint for HGSOC and further develop it for non-HGSOC EOC histotypes in both symptomatic and asymptomatic women with adnexal masses.

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OvaPrint a cell-free DNA methylation liquid biopsy for the risk ... - Cancer Discovery

Tony Apanovitch and his supporters are adamant: Hes innocent and theres DNA evidence to prove it.That evidence is in addition to doubts about Apanovitchs conviction raised by a state Supreme Court Justice before the existence of the DNA came to light.

In fact, doubts about his conviction are so compelling that a trial court judge freed Apanovitch in 2015, only to see the Ohio Supreme Court send him back to death row on a technicality in 2018. The courts rationale for re-incarcerating Apanovitch was that he didnt request the DNA testing that he says exonerates him.

Now Apanovitchs lawyers and his advocates are demanding a clemency hearing from the Ohio Parole Board. But Gov. Mike DeWines spokesman said this week that the governor wont request one because Apanovitch hasnt exhausted his appeals or had an execution date set.

In Ohio, there have been 11 people who have been sent to death row only to be exonerated. Apanovitchs supporters argue that he should be the 12th.

Now 68, he was convicted in the 1984 rape and murder in Cuyahoga County of Mary Anne Flynn, who was found dead in her home after she hadnt shown up for her job as a nurse at Cleveland General Hospital. Apanovitch received the death penalty.

Even before the DNA evidence came to light, the Ohio Supreme Court in 1987 nearly overturned the conviction, with three dissents to four justices voting to uphold it.

That was before the court adopted the doctrine of residual doubt overturning convictions because of a lingering fear that the defendant might not be guilty. Had that doctrine been in place, Apanovitchs appeal would have turned out differently, Justice Craig Wright wrote to the Parole Board in 1996.

There is no question that there is some residual doubt in this case and had we had that doctrine, this case would have gone the other way, said Wright, who wrote the ruling denying Apanovitchs appeal. Mr. Apanovitch would not have to face the death penalty. I think it of some interest that I have discussed this case with my now-colleague, Justice (Francis Edward) Sweeney, who was the trial judge in this case. He has indicated to me that he came close to granting a Rule 29 motion (that the evidence was insufficient for a conviction) following the states case.

Then, in 1991, an employee of the Cuyahoga County Coroners office found slides containing fluids from the victims mouth and pelvis that were previously believed to be lost, the Cleveland Plain Dealer reported last year. Any DNA evidence gathered from them would be crucial, because there were no eyewitnesses to the crime; only testimony that Flynn had complained that Apanovitch had made sexually suggestive comments to her while he was painting her house that summer.

There was too little fluid to do DNA testing, given the technology at the time the slides were discovered.

But in 2000 and 2006, prosecutors asked for additional testing using more advanced technology. Crucially, however, they didnt tell Apanovitchs lawyers that they had done so, the Plain Dealer reported.

The prosecutors tests claimed to find that Apanovitchs DNA matched fluid taken from Flynns mouth, and that there wasnt enough fluid from her pelvis to test. However, they declined to present that evidence in a 2015 court proceeding, Dale Baich, one of Apanovitchs attorneys, told the Capital Journal last year.

Testing ordered up by Apanovitchs team claimed to find the DNA of two people in the samples taken from Flynns mouth and pelvis and that Apanovitchs DNA was found in neither sample. Defense attorneys also raised questions about the integrity of samples that lay undiscovered in a desk for so many years.

The events were emblematic of the slipshod nature of Apanovitchs prosecution, Tiana Bohnanon, another of his attorneys, said last week at a press conference urging the Parole Board to schedule a clemency hearing for her client.

Prosecutors said the evidence had been destroyed, Bohanon said. And then they turned around years later and tested those slides and it turns out that it wasnt Tonys DNA. Their case was that Tony was the one that raped her and murdered her, but there was no witness that Tony murdered her and his DNA wasnt on that slide.

Cuyahoga County Common Pleas Judge Robert McClelland in 2015 overturned Apanovitchs conviction and freed him after three decades on death row.

While free, Apanovitch held a job and got married. But in 2018, the Ohio Supreme Court sent him back to death row on the rationale that the DNA evidence can only be considered if Apanovitch requested the initial testing of samples he didnt know were available and that prosecutors waited years to disclose.

According to the court, the DNA statute in Ohio applies only where the prisoner makes the request to test the DNA, the group Justice 4 Apanovich said in a written statement last week. Tony didnt ask for the testing to be done indeed he never had the opportunity to make that request because the state did the testing itself in secret

As Apanovitch continues to languish on death row, his lawyers and other supporters are calling on DeWine to grant clemency. But to do that, he needs a recommendation from the parole board, which is appointed by the director of the Ohio Department of Rehabilitation and Correction who is appointed by the governor, DeWine.

So far at least, neither board nor governor is inclined to act.

The board has an unwritten policy of not scheduling clemency hearings until an execution date is set for a defendant. But those dates keep moving back as DeWine has delayed every execution since he took office nearly four years ago, citing the unavailability of the necessary drugs.

The governors office was asked whether DeWine would heed calls from state Reps. Jean Schmidt, Josh Williams and Bill Seitz all fellow Republicans as well as many others and call on the Parole board to schedule a clemency hearing for Apanovitch.

Without getting into the evidentiary disputes in this case, it is correct that the Parole Board could schedule a hearing if it so chose, Dan Tierney, DeWines press secretary, replied in an email. However, we are aware the Parole Board generally only does so if all appeals have been exhausted OR an execution date has been set. Our understanding is appeals have not been exhausted, so that remains the current avenue to argue actual innocence.'

Former Ohio Supreme Court Justice Herbert Brown said the Parole Board has a duty to act.

The 2018 Ohio Supreme Court decision sent a man back to death row, and effectively narrowed any legal options in the courts for Mr. Apanovitch, Brown wrote in a March 11, 2022 letter to the Parole Board. This board has the authority, even the duty, to right a wrong and correct an injustice that has now lasted almost 38 years.

He added, Although the death penalty remains a punishment accepted by the courts, legislature and the public, nobody should countenance the execution of an innocent man. Certainly not on the technical point of whether it was the state or Mr. Apanovitch who requested the exculpatory DNA evidence. Considering all of the above, I believe this Board should release Mr. Apanovitch from prison.

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After being freed once, Ohio man languishes on death row - Ohio Capital Journal

This is Tim Hammerich of the Ag Information Network with your Farm of the Future Report.

The United States is known as a world leader in beef production in terms of quality, volume, and efficiency. But, for many American ranchers, it took decades of trial and error to select and perfect these desired traits in their breeding program. Lee Leachman says DNA testing commercial herds can speed up this process, and is something more ranchers could be taking advantage of.

Leachman... "You have to be DNA testing your commercial replacement heifers today and using that genomic selection based on a good index to keep your cows right but to also maximize the value of those calves. And I don't really think it's hard to balance the maternal and the post-weaning traits, but you've got to measure it all and youve got to use indexes to balance them appropriately. So, you know, I think DNA is a great tool to do that in the beef cow segment. Were a long way from a place where a rancher buys in his replacement heifers and terminal processes them. That may be where we end up. When you study the economics of it, there are huge financial incentives that can come out of that system but until then, because we're a decade or more often that, I think until then it's going to be genomically testing heifers within your commercial herd to make sure that you produced enough really good replacements and then make sure you're maximizing the calf value on the rest of your calves."

Leachman says DNA sampling of replacement heifers can result in 3 to 5 times increased ROI, depending on the sampling technique.

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Maximizing ROI With Cattle DNA Testing - AG INFORMATION ... - AGInfo Ag Information Network

Every new member of this roster fills a role that fits into how the Penguins want to play, with guys listing their team identity as fast and assertive. And while the Penguins are skilled, they also want to be hard-working and tough to play against.

Kind of an always on type of game, Letang said. Were not a type of team that necessarily wants to come up slow with the puck. We want to make sure the pace is really high during the game.

We try to play fast and smart, Malkin echoed. We watch lots of video and we understand were not happy from last year, and we want to start the season pretty well. We start at home, new guys, great experience in this locker room. I think weve had a great training camp. Were ready to go against Chicago.

Dubas knows that based on the fact Pittsburghs 16-year playoff streak ended last season, people outside of the room dont have the same belief thats inside of the room - which is to win each day and stack those days one on top of the other, which will lead to contending for a Stanley Cup.

For me, it's been great to be a part of that group and try to help as best as I possibly can, learn from them and what's got them to hold that as their standard, and try to supplement and add to the group as best we possibly can across everything roster, staff, systems to try to help the team get its way back to winning the Stanley Cup again, he said.

Here is the projected opening-night lineup for Tuesday versus the Blackhawks, with the puck dropping at 8 PM:

FORWARDS

Jake Guentzel-Sidney Crosby-Bryan Rust

Reilly Smith-Evgeni Malkin-Rickard Rakell

Drew OConnor-Lars Eller-Jansen Harkins

Matt Nieto-Noel Acciari-Jeff Carter

DEFENSEMEN

Ryan Graves-Kris Letang

Marcus Pettersson-Erik Karlsson

P.O Joseph-Chad Ruhwedel

(Ryan Shea, John Ludvig)

GOALTENDERS

Tristan Jarry

Alex Nedeljkovic

A few notes on the roster:

- While theres only a finite amount of players who can make the opening-night roster, the Penguins are expecting the guys who have already gone down to Wilkes-Barre/Scranton to continue to push and keep the pressure on. I think the players who are here know the level of competition that it was, and thatll help us as a team throughout the year in continuing to foster that type of competition, and push everyone to be at their absolute best, Dubas said.

- While Guentzel is officially listed as a game-time decision, it looks like he'll most likely be in, as the Penguins currently aren't carrying an extra forward. Hes been practicing with the team in a full capacity since Oct. 3 after undergoing ankle surgery in early August. With the level of competitor that he is, its not a true surprise that he's at this point and trying to push his way to be ready to go for tomorrow. We'll see how it goes, Dubas said this morning.

- This feels like its going to be a good year for OConnor. The 25-year-old is entering his fourth season in the Penguins organization, and his comfortability is evident, saying he feels more established at this level. He stood out in the exhibition games, creating plenty of scoring chances and scoring three goals, as OConnor has a better understanding of how he needs to play to set himself up for success. He also seems more confident and outgoing around the locker room. Dubas said they were looking forward to seeing which young guys stepped up, and OConnor certainly did so this training camp. I think hes ready to take the next step, Sullivan said. That certainly is our hope.

- The bottom six has truly gotten a complete overhaul, as only a couple of familiar faces remain from last year, with OConnor and Carter. Dubas filled it with players who are the right fit for what the Penguins believe in. It'll be our job to support (the top six) with secondary scoring and being very hard to play against, Lars Eller said.

Dubas also tried to build out the group deep enough so that they dont have to rely on every single person to be firing on all cylinders at all times. There are a number of solid players who performed well at training camp that got re-assigned to Wilkes-Barre/Scranton for now, with Dubas specifically mentioning Alex Nylander, Vinnie Hinostroza, Andreas Johnsson, Sam Poulin, and Valtteri Puustinen. I'm happy with (the bottom six) now, but I'm also very happy with the depth that's there and what's available, Dubas said.

And while Radim Zohorna was also among the group that got sent down, Sullivan called that part of the games business aspect and having flexibility in the roster. The Penguins were pleased with his training camp, and feel like he played extremely well. We'll see where it goes, but it doesn't for one minute change or diminish what we think of Z, Sullivan said.

- As for the top six 10/10, no notes. Its absolutely loaded.

- A reminder that a big reason the Penguins targeted Erik Karlsson was because they wanted to improve their ability to move the puck from their own zone, and hes one of the NHLs elite players in that regard.

- There was essentially one spot open on the third pairing, with P.O Joseph taking the other after coming into camp with a full season of NHL experience. Sullivan said the 24-year-old defenseman looked like he picked up a step, along with more confidence in his overall game. It looks like Chad Ruhwedel, a terrific teammate who defines professionalism, will start alongside Joseph. The dependable veteran is able to log a lot of PK minutes.

That being said, the Penguins are currently carrying eight defensemen, including John Ludvig, claimed off of waivers from the Florida Panthers just this afternoon. He is signed through next season, with the 23-year-old playing parts of three seasons in the AHL with the Charlotte Checkers and Syracuse Crunch.

Also in the mix is Ryan Shea, an under-the-radar signing from this summer. The young blueliner brings a different dimension than others in the group, as he can defend well, but has good puck skills. Hes not just an off-the-glass and out guy, Sullivan said. Shea, who has yet to make his NHL debut, has done what he can to make the most of his opportunity.

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Pittsburgh's Opening Night Roster Stays True to Its DNA | Pittsburgh ... - NHL.com

Millions of organisms contribute to global marine biodiversity, and most of them are in need of protection. Unfortunately, the planet has lost about 70% of its animal diversity in the last five decades.Indonesia, known for its rich marine diversity, is at the heart of this challenge. Researchers have discovered that Indonesian sharks and manta ray populations are vanishing at an alarming rate.

Sharks and rays are some of the biggest victims of declining marine biodiversity. Once considered apex predators, these elasmobranchs have become vulnerable ocean inhabitants fighting for survival. The biological characteristics of sharks and rays also put them at a significant disadvantage. They grow relatively slowly, mature late, and reproduce at very low rates.

While this is a global crisis, Indonesia is taking a bigger hit than most countries worldwide. The country is home to over 220 shark and ray species, translating to one-fifth of the global population. Having such a rich diversity of sharks and rays comes with a few economic benefits. For example, shark tourism in the country contributes at least $22 million annually to the national coffers.

Despite their economic value, only six species are protected from all forms of catch and trade in Indonesia. These include whale sharks (Rhincodon typus), giant manta rays (Mobula birostris), reef manta rays (Mobula alfredi), and three sawfish species.

The country also does not allow the export of four globally endangered species: three hammerhead shark species and oceanic white-tip sharks (Carcharhinus longimanus).

From 2007-2017, Indonesias shark and ray fishery recorded an annual average catch of 110,737 metric tons. This is the largest in the world.

Interestingly, the larger part of this weight comes from unintentional bycatch rather than intentional or active fishing. This aligns with the Wildlife Conservation Societys 2018 observation that up to 86% of Indonesian fisheries incidentally capture sharks and rays.

This situation leaves Indonesia with a crucial but tricky choice to make between conservation and the socioeconomic benefits of shark fishing.

The recent efforts of Indonesian authorities indicate the readiness of the country to protect these endangered marine species from extinction.

According to a newly published study, the recent advancements in science and technology may offer the country a solution. New DNA-based diagnostic tools, such as the FASTFISH-ID method, have advanced the process of wildlife identification.

FASTFISH-ID is an advanced real-time polymerase chain reaction (PCR) technique that supports rapid and reliable species identification. It uses fluorescent probes to create unique genetic signatures for each species, offering precise identification.

Initially designed for bony fishes, FASTFISH-ID has shown promise for elasmobranchs. Hence, researchers used it to generate fluorescent signatures for 28 frequently traded elasmobranch species found below the surface of Indonesian waters.

These signatures allowed for accurate species identification, although with a few misclassifications. The deep machine learning approach achieved an impressive 79.41% accuracy in species identification.

Andhika P. Prasetyo, a researcher at the University of Salford, led this vital work. Based on their findings, the experts believe the FASTFISH-ID could be a game-changer offering speed, portability, universality, and single nucleotide resolution when identifying elasmobranch species.

While limitations like misassignments and inconsistencies in hybridizations have been observed, the scientists hope the ongoing improvements and database expansions will improve the technology.

With further refinement, this method can improve monitoring of the elasmobranch trade worldwide, without a lab or species-specific assays, they noted.

The findings of this study were first published in the journal iScience.

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Indonesia turns to DNA technology to save their sharks - Earth.com