Daily Archives: August 14, 2021

Denisovans are an elusive bunch, known mainly from ancient DNA samples and traces of that DNA that the ancient hominids shared when they interbred with Homo sapiens. They left their biggest genetic imprint on people who now live in Southeast Asian islands, nearby Papua New Guinea and Australia. Genetic evidence now shows that a Philippine Negrito ethnic group has inherited the most Denisovan ancestry of all. Indigenous people known as the Ayta Magbukon get around 5 percent of their DNA from Denisovans, a new study finds.

This finding fits an evolutionary scenario in which two or more Stone Age Denisovan populations independently reached various Southeast Asian islands, including the Philippines and a landmass that consisted of whats now Papua New Guinea, Australia and Tasmania. Exact arrival dates are unknown, but nearly 200,000-year-old stone tools found on the Indonesian island of Sulawesi may have been made by Denisovans (SN: 1/13/16). H. sapiens groups that started arriving around 50,000 years ago or more then interbred with resident Denisovans.

Evolutionary geneticists Maximilian Larena and Mattias Jakobsson, both at Uppsala University in Sweden, and their team describe the new evidence August 12 in Current Biology.

Even as the complexities of ancient interbreeding in Southeast Asia become clearer, Denisovans remain a mysterious crowd. Its unclear how the different Denisovan groups on the mainland and on Southeast Asian islands were related [to each other] and how genetically diverse they were, Jakobsson says.

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Papua New Guinea highlanders estimated to carry close to 4 percent Denisovan DNA in the new study were previously thought to be the modern record holders for Denisovan ancestry. But the Ayta Magbukon display roughly 30 percent to 40 percent more Denisovan ancestry than Papua New Guinea highlanders and Indigenous Australians, Jakobsson says. That calculation accounts for recent mating of East Asians with Philippine Negrito groups, including the Ayta Magbukon, that diluted Denisovan inheritance to varying degrees.

Genetic analyses suggest that Ayta Magbukon people retain slightly more Denisovan ancestry than other Philippine Negrito groups due to having mated less often with East Asian migrants to the island around 2,281 years ago, the scientists say. Their genetic analyses compared ancient DNA from Denisovans and Neandertals with that of 1,107 individuals from 118 ethnic groups in the Philippines, including 25 Negrito populations. Comparisons were then made to previously collected DNA from present-day Papua New Guinea highlanders and Indigenous Australians.

The new report underscores that still today there are populations that have not been fully genetically described and that Denisovans were geographically widespread, says paleogeneticist Cosimo Posth of the University of Tbingen in Germany, who was not part of the new research.

But its too early to say whether Stone Age Homo fossils found on Southeast Asian islands come from Denisovans, populations that interbred with Denisovans or other Homo lineages, Posth says. Only DNA extracted from those fossils can resolve that issue, he adds. Unfortunately, ancient DNA preserves poorly in fossils from tropical climates.

Only a handful of confirmed Denisovan fossils exist. Those consist of a few fragmentary specimens from a Siberian cave where Denisovans lived from around 300,000 to 50,000 years ago (SN: 1/30/19), and a roughly 160,000-year-old partial jaw found on the Tibetan Plateau (SN: 5/1/19).

Fossils from the Philippines initially classed as H. luzonensis, dating to 50,000 years ago or more (SN: 4/10/19), might actually represent Denisovans. But a lack of consensus on what Denisovans looked like leaves the evolutionary identity of those fossils uncertain.

Larena and Jakobssons findings further increase my suspicions that Denisovan fossils are hiding in plain sight among previously excavated discoveries on Southeast Asian islands, says population geneticist Joo Teixeira of the University of Adelaide in Australia, who did not participate in the new study.

Denisovans may have genetically encompassed H. luzonensis and two other fossil hominids found on different Southeast Asian islands, H. floresiensis on Flores and H. erectus on Java, Teixeira suspects. H. floresiensis, or hobbits, survived from at least 100,000 years ago to around 60,000 years ago (SN: 6/8/16). H. erectus arrived on Java about 1.6 million years ago and died out between 117,000 and 108,000 years ago (SN: 12/18/19).

Geographic ancestry patterns on Southeastern Asian islands and in Australia suggest that this region was settled by a genetically distinct Denisovan population from southern parts of mainland East Asia, Teixeira and his colleagues reported in the May Nature Ecology & Evolution.

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An Indigenous people in the Philippines have the most Denisovan DNA - Science News Magazine

DNA is in the air literally. It is wafted around by all the Earths creatures, and now scientists have found a way to detect these invisible traces of genetic material so they can identify the animals that released them.

The discovery made independently by British and Danish research groups earlier this year opens up a powerful way to pinpoint the presence of rare wildlife in deserts, rainforests and other hostile environments.

This could transform the way we study biodiversity, said Professor Elizabeth Clare of York University. Every other technique we have for tracing animals camera traps, say, or acoustic monitoring relies on the animals being physically present near or in front of you.

Trapping their DNA from the air is much less invasive, and much more flexible. You could detect the presence of creatures in caves without disturbing them, for example.

In their experiments, Clare then at Queen Mary University of London and her colleagues used sensitive filters fitted to vacuum pumps placed at 20 locations across Hamerton Zoo Park in Cambridgeshire last December. We realised a zoo would be an excellent place to test a technique like this because animals there are non-native and are spatially confined in enclosures, said Clare. It meant that if we were successful and could detect DNA in the air, we would know exactly where it was coming from and how far it had travelled.

A total of 72 air samples were collected by the team, who used polymerase chain reaction (PCR) to amplify the tiny fragments of DNA isolated in their filters. They sequenced this genetic material and compared the results with known sequences of animals and identified 17 species of zoo animal from invisible traces of their DNA released into the air.

We found tiger DNA, dingo DNA and, most of all, DNA from black and white ruffed lemurs, said Clare. Their DNA was the most widely distributed. We are not sure why but lemurs are certainly very active compared with other animals. They were bouncing around their cages, taking great interest in the people wandering past them. By contrast, a lot of other animals were lying low as it was winter.

Intriguingly, similar discoveries were made at the same time by researchers led by Christina Lynggaard and Kristine Bohmann of Copenhagen University. In their research, they sucked up air from several sites in Copenhagen Zoo and detected a total of 49 species from the DNA found in their filters.

We were astonished, said Bohmann. We got DNA from mammals, fish, birds and reptiles, from big animals and small animals, from creatures with feathers and others with scales. We even detected the DNA of guppy fish that swim in a pond in the zoos tropical house.

For good measure, both teams found they could also pinpoint the presence of local wildlife, neighbourhood pets and the animals that were there as feed for the zoo animals.

We realised we were detecting DNA from animals that were being fed to zoo animals, for instance fish, said Bohmann. We were also picking up the DNA of local cats and dogs and local wild animals. It was astonishing what we were able to detect.

Both the Danish and British projects were funded as part of high-risk, high-reward strategies set up to back speculative research projects considered to be worth financing for their widespread potential benefits.

There are all sorts of things we have to clear up now about tracking airborne DNA but the practical benefits are very exciting, added Bohmann.

Future uses of airborne DNA detectors could include tracing insect pests from air samples and pinpointing animals living in burrows without disturbing them. However, both sets of scientists acknowledge there are hurdles to be overcome before the technology becomes a standard method for studying biodiversity.

You might detect a piece of tiger DNA but at present we are not sure when it might have been released by the animal. It could be minutes or hours or days ago, said Clare. At present, we have no way of working out how long DNA survives in the air. That is one of the many aspects of this technique that we have to work out.

However, we have already got a head start. If we were the only team to come up with this, we would have to wait for others to replicate our work. Our colleagues in Denmark have already done that independently so we both know that this technology works, and it should have a really exciting future.

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DNA from thin air: a new way to detect rare wildlife in hostile environments - The Guardian

STONY BROOK, N.Y.--(BUSINESS WIRE)--Applied DNA Sciences, Inc. (NASDAQ: APDN) (the Company), a leader in Polymerase Chain Reaction (PCR)-based DNA manufacturing and nucleic acid-based technologies, today announced consolidated financial results for the three and nine months ended June 30, 2021.

We delivered excellent year-over-year revenue growth in the fiscal third quarter while laying the groundwork to secure a recently awarded COVID-19 testing services contract that has potential to be the largest contract in the Companys history, said Dr. James A. Hayward, president and CEO of Applied DNA. Demand for safeCircle, our pooled COVID-19 testing program, experienced a seasonal decline from the fiscal second quarter, reflecting the start of the summer recess months for our academic clients and progressively higher vaccination rates and lower positivity rates in our operating area. Our recent award from the City University of New York for large-scale turnkey COVID-19 testing services should continue to drive strong year-over-year revenue growth over the period of the contract.

Continued Dr. Hayward, Our operating activities during the quarter were distinguished by an expansion of our COVID-19 offerings to drive incremental revenue and to drive adoption of LinearDNA as an alternative to plasmids for nucleic acid-based therapies. Following constructive interactions with the U.S. Food and Drug Administration (FDA) as part of a preliminary Emergency Use Authorization application process and the evolving nature of the pandemic, we revised our Linea SARS-CoV-2 Mutation (the Linea Mutation Panel) (formerly SGS Mutation Panel) to target three SARS-CoV-2 mutations (E48K, L452R, N501Y) that have been designated substitutions (mutations) of therapeutic concern by the Centers for Disease Control and Prevention.

Should the FDA grant an EUA for the Linea Mutation Panel, we believe that it will offer clinical utility to healthcare systems by enabling precision COVID-19 treatment and commercial utility to monoclonal antibody manufacturers by better characterizing patients before treatments. In recent months, several monoclonal antibody treatments have had their EUA revoked or have demonstrated a reduction in efficacy on a standalone or in combination with other treatments due to mutational impact. Use of the Linea Mutation Panel is tied to our Linea COVID-19 Assay Kit to determine positivity in clinical samples that would drive additional Assay demand if the EUA is granted for our Mutation Panel. We believe that an EUA-authorized Linea Mutation Panel will also provide additional value to our existing COVID-19 testing customers and, when combined with our Whole Genome Sequencing assets, provide data of interest to epidemiologists.

Concurrently, the launch of our veterinary LinearDNA COVID-19 vaccine trial and the subsequently reported strong immune response that the vaccine candidate elicited, further reinforce the value proposition of LinearDNA, and, longer-term, generates invaluable preclinical data supporting the eventual application of LinearDNA to nucleic acid-based therapies in humans.

Concluded Dr. Hayward, Looking ahead, the confluence of increasing positivity rates due to the Delta variant, the commingling of vaccinated, partially vaccinated, and unvaccinated individuals, and new mandatory testing requirements for local and state-level employees in our operating area affirm the need for ongoing and consistent COVID-19 screening available through safeCircle. Subject to FDA's evolving EUA request review priorities, we expect to file shortly our formal request for EUA for our Linea Mutation Panel. In addition, in the coming weeks we intend to launch our COVID-19 veterinary vaccine candidate challenge trial in furtherance of a commercial animal health opportunity.

Regarding our supply chain security business, we have cautious optimism within the cotton supply chains we serve as we approach the start of the cotton ginning season in the U.S. However, with Asia-Pacific beset by the Delta variant, man-made fiber opportunities remain static. With the tailwind of COVID-19 testing at our back supplemented by continued execution on business development initiatives, we believe we are laying the foundation for sustainable growth.

Fiscal Third Quarter 2021 Financial Highlights:

Nine-Month Financial Highlights:

Fiscal Third Quarter 2021 Conference Call Information

The Company will hold a conference call and webcast to discuss its fiscal third quarter-end 2021 results on Thursday, August 12, 2021, at 4:30 PM ET. To participate on the conference call, please follow the instructions below. While every attempt will be made to answer investors questions on the Q&A portion of the call, not all questions may be answered.

To Participate:

Live webcast: https://services.choruscall.com/mediaframe/webcast.html?webcastid=Bin1qa3n

Telephonic replay (available 1 hour following the conclusion of the live call through August 19, 2021):

The webcast and accompanying PowerPoint presentation will be archived on the IR Calendar and Corporate Presentations page listed under the Investor Relations drop-down menu on the Companys website.

About safeCircle

ADCLs high throughput pooled testing program, known as safeCircle, utilizes frequent, high-sensitivity pooled testing to help prevent virus spread by quickly identifying infections within a community, school, or workplace. safeCircle provides rapid results using real-time PCR (RT-PCR) testing.

Click through to learn more about how safeCircle can help your community, school, and workplace: safeCircle

About Linea COVID-19 Assay Kit and Linea SARS-CoV-2 Mutation Panel

The Linea COVID-19 Assay Kit is a real-time RT-PCR test intended for the qualitative detection of nucleic acid from SARS-CoV-2 in respiratory specimens including anterior nasal swabs, self-collected at a healthcare location or collected by a healthcare worker, and nasopharyngeal and oropharyngeal swabs, mid-turbinate nasal swabs, nasopharyngeal washes/aspirates or nasal aspirates, and bronchoalveolar lavage (BAL) specimens collected by a healthcare worker from individuals who are suspected of COVID-19 by their healthcare provider (HCP). The test is also intended for use with anterior nasal swab specimens that are self-collected in the presence of an HCP from individuals without symptoms or other reasons to suspect COVID-19 when tested at least weekly and with no more than 168 hours between serially collected specimens.

The scope of the Linea COVID-19 Assay Kit EUA, as amended, is expressly limited to use consistent with the Instructions for Use by authorized laboratories, certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) to perform high complexity tests. The EUA will be effective until the declaration that circumstances exist justifying the authorization of the emergency use of in vitro diagnostics for detection and/or diagnosis of COVID-19 is terminated or until the EUAs prior termination or revocation. The diagnostic kit has not been FDA cleared or approved, and the EUAs limited authorization is only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens.

The Linea SARS-CoV-2 Mutation Panel (formally SGS Mutation Panel) (the Linea Mutation Panel) is for Research Use Only (RUO) and shall not be used for clinical diagnostic purposes. The Linea Mutation Panel has not been approved or authorized to diagnose, ameliorate and/or detect any disease by any U.S. or international regulatory authority.

Information about Non-GAAP Financial Measures

As used herein, GAAP refers to accounting principles generally accepted in the United States of America. To supplement our condensed consolidated financial statements prepared and presented in accordance with GAAP, this earnings release includes Adjusted EBITDA, which is a non-GAAP financial measure as defined in Rule 101 of Regulation G promulgated by the Securities and Exchange Commission. Generally, a non-GAAP financial measure is a numerical measure of a companys historical or future performance, financial position, or cash flows that either excludes or includes amounts that are not normally excluded or included in the most directly comparable measure calculated and presented in accordance with GAAP. The presentation of this non-GAAP financial information is not intended to be considered in isolation or as a substitute for, or superior to, the financial information presented in accordance with GAAP. We use this non-GAAP financial measure for internal financial and operational decision-making purposes and as a means to evaluate period-to-period comparisons of the performance and results of operations of our core business. Our management believes that these non-GAAP financial measures provide meaningful supplemental information regarding the performance of our business by excluding non-cash expenses that may not be indicative of our recurring operating results. We believe this non-GAAP financial measure is useful to investors as they allow for greater transparency with respect to key metrics used by management in its financial and operational decision making.

EBITDA- is defined as earnings (loss) before interest expense, income tax expense and depreciation and amortization expense.

Adjusted EBITDA- is defined as EBITDA adjusted to exclude (i) stock-based compensation and (ii) other non-cash expenses.

About Applied DNA Sciences

Applied DNA is commercializing LinearDNA, its proprietary, large-scale polymerase chain reaction (PCR)-based manufacturing platform that allows for the large-scale production of specific DNA sequences.

The LinearDNA platform has utility in the nucleic acid-based in vitro diagnostics and preclinical nucleic acid-based drug development and manufacturing market. The platform is used to manufacture DNA for customers as components of in vitro diagnostic tests and for preclinical nucleic acid-based drug development in the fields of adoptive cell therapies (CAR T and TCR therapies), DNA vaccines (anti-viral and cancer), RNA therapies, clustered regularly interspaced short palindromic repeats (CRISPR) based therapies, and gene therapies.

The LinearDNA platform also has non-biologic applications, such as supply chain security, anti-counterfeiting and anti-theft technology. Key end-markets include textiles, pharmaceuticals and nutraceuticals, and cannabis, among others.

Leveraging its deep expertise in nucleic acid-based technologies, the Company has also established safeCircle, a pooled COVID-19 testing program that is grounded in the Companys EUA-authorized Linea COVID-19 Assay Kit. safeCircle is designed to look for infection within defined populations or communities utilizing pooled testing methodologies that increase testing efficiencies. The Company has also developed and plans to seek EUA-authorization for its Linea SARS-CoV-2 Mutation Panel, an assay-based panel for the detection of certain SARS-CoV-2 genetic mutations.

Visit adnas.com for more information. Follow us on Twitter and LinkedIn. Join our mailing list.

The Companys common stock is listed on NASDAQ under ticker symbol APDN, and its publicly traded warrants are listed on OTC under ticker symbol APPDW.

Applied DNA is a member of the Russell Microcap Index.

Forward-Looking Statements

The statements made by Applied DNA in this press release may be forward-looking in nature within the meaning of Section 27A of the Securities Act of 1933, Section 21E of the Securities Exchange Act of 1934 and the Private Securities Litigation Reform Act of 1995. Forward-looking statements describe Applied DNAs future plans, projections, strategies, and expectations, and are based on assumptions and involve a number of risks and uncertainties, many of which are beyond the control of Applied DNA. Actual results could differ materially from those projected due to its history of net losses, limited financial resources, the unknown amount of revenues and profits that will result from any COVID-19 testing contract (including the testing contract with the City University of New York), limited market acceptance, the uncertainties inherent in research and development, future clinical data and analysis, including whether any of Applied DNAs or its partners diagnostic or therapeutic candidates will advance further in the preclinical research or clinical trial process, including receiving clearance from the U.S. Food and Drug Administration (U.S. FDA), the U.S. Department of Agriculture (USDA) or equivalent foreign regulatory agencies to conduct clinical trials and whether and when, if at all, they will receive final approval from the U.S. FDA, the USDA or equivalent foreign regulatory agencies, the unknown outcome of any applications or requests to U.S. FDA, USDA, equivalent foreign regulatory agencies and/or the New York State Department of Health, the unknown limited duration of any Emergency Use Authorization (EUA) approval from U.S. FDA, changes in guidance promulgated by the CDC, FDA and/or CMS relating to COVID-19 testing, disruptions in the supply of raw materials and supplies, the unknown ability to manufacture the vaccine candidates in large quantities, the fact that the safety and efficacy of the vaccine candidates has not yet been established, the unknown ability of the vaccine candidates to generate revenue or profit for Applied DNA, the fact that there has never been a commercial drug product utilizing PCR-produced DNA technology approved for therapeutic use, and various other factors detailed from time to time in Applied DNAs SEC reports and filings, including our Annual Report on Form 10-K filed on December 17, 2020, Quarterly Reports on Form 10-Q filed on February 11, 2021, May 13, 2021, and August 12, 2021 and other reports we file with the SEC, which are available at http://www.sec.gov. Applied DNA undertakes no obligation to update publicly any forward-looking statements to reflect new information, events, or circumstances after the date hereof or to reflect the occurrence of unanticipated events, unless otherwise required by law.

APPLIED DNA SCIENCES, INC.CONSOLIDATED BALANCE SHEETS

June 30,

September 30,

2021

2020

ASSETS

(unaudited)

$

12,173,443

$

7,786,743

737,347

194,319

429,116

497,367

356,414

599,296

13,696,320

9,077,725

2,576,616

1,277,655

95,053

95,083

285,386

285,386

536,354

605,330

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Applied DNA Announces Third Quarter Fiscal 2021 - Business Wire

The Ayta Magbukon people of the Bataan peninsula on Luzon Island, the Philippines, have the worlds highest proportion of Denisovan genes a new study has discovered, despite centuries of interbreeding with later arrivals to Luzon. The discovery reveals a fourth known encounter between Denisovans and modern humans. It also suggests the ancient humans who inhabited the islands of South East Asia may have been descendants of the Denisovans, and at least some of them may have also bred with modern humans.

Ancient humans such as Neanderthals and Denisovans have shaped the human genome through what geneticists call admixture, changing our immune systems and teeth.Indeed these genes are so common in modern humans as to created debate about whether these archaic humans should be considered subgroups of Homo Sapiens, rather than their original designation as different species. Homo floresiensis (nicknamed hobbits) and the recently discovered Homo luzonensis, on the other hand, have been considered more remote relations, most likely unconnected to us for hundreds of thousands of years.

Neanderthal genes are widespread outside Africa, but the Denisovan contribution to the genome is concentrated in South East Asia and Australia. Past studies have found allele (gene varieties) inherited from Denisovans are most common among Papuan Highlanders in what is now New Guinea and Indigenous Australians. However, a new paper in Current Biology reports something other researchers overlooked: an even higher Denisovan inheritance among the Ayta Magbukon, a Philippine Negrito ethnic group.

Philippine Negritos are thought to be the earliest human population to migrate to the Philippines. There are at least 30 self-identified Negrito groups, 25 of which were involved in this study. The researchers found the higher the Negrito ancestry a person had, the higher their Denisovan ancestry.

This discovery is surprising, and significant, because the Ayta Magbukon have had much more contact, and interbreeding, with the rest of the world than Papuan highlanders, who were largely isolated until very recently.

Philippine Negritos were recently admixed with East Asian-related groups who carry little Denisovan ancestry, and which consequently diluted their levels of Denisovan ancestry,said Dr Maximillian Larena of Uppsala University. Once Larena and co-authors accounted for such dilution they found theAyta Magbukononce had 30-40 percent more Denisovan ancestry than Papuans or Indigenous Australians. Admixture almost certainly occurred in the Philippines, in addition to the three previously identified encounters; two on the Asian mainland before people fanned out through the islands, and a more recent one in New Guinea or nearby.

Some other Luzon Indigenous populations also exceed Papuan levels of Denisovan DNA, but the Ayta Magbukon stand out.

Geneticists estimate the timing of admixture events from the length of DNA tracts left behind. The Ayta Magbukons Denisovan tracts are of similar length to those of Australasian peoples, indicating the admixture was not substantially more recent.

The paper notes no Denisovan fossils have been found in the Philippines (or indeed anywhere outside Siberia and Tibet). However, we know almost nothing about the ancestry of H. luzonensis. Perhaps, the authors suggest, the two were genetically related, and H. luzonensis were still present in Luzon when modern humans arrived.

This then raises the question of whether H. floresiensis, who appear to share many characteristics with H. luzonensis, might also have been of Denisovan descent. A people known to us only from four bones, and the DNA inside, may have adapted to many island environments and survived there for hundreds of thousands of years.

Earlier this year Larena and colleagues were accused of not complying with Philippine guidelines on informed consent from the people whose DNA they studied for previous work and not gaining proper ethical clearance. Larena and a colleague responded that independent investigations have cleared them of these allegations, but this has not satisfied some critics.

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Indigenous Group In The Philippines Has Most Denisovan DNA in the World - IFLScience