Daily Archives: July 11, 2024

New research shows that recurrent episodes of gene flow, beginning 250,000 to 200,000 years ago, affected the genomes and biology of both modern humans and Neanderthals, and estimates that Neanderthals have 2.5 to 3.7% human ancestry.

Li et al. provide insights into the history of admixture between modern humans and Neanderthals, show that gene flow had substantial impacts on patterns of modern human and Neanderthal genomic variation, and show that accounting for human-introgressed sequences in Neanderthals enables more-accurate inferences of admixture and its consequences in both Neanderthals and modern humans. Image credit: Neanderthal Museum.

This is the first time that geneticists have identified multiple waves of modern human-Neanderthal admixture, said Southeast Universitys Professor Liming Li.

We now know that for the vast majority of human history, weve had a history of contact between modern humans and Neanderthals, added Princeton Universitys Professor Joshua Akey.

The hominins who are our most direct ancestors split from the Neanderthal family tree about 600,000 years ago, then evolved our modern physical characteristics about 250,000 years ago.

From then until the Neanderthals disappeared that is, for about 200,000 years modern humans have been interacting with Neanderthal populations.

Using genomes from 2,000 living humans as well as three Neanderthals and one Denisovan, the researchers mapped the gene flow between the hominin groups over the past quarter-million years.

They used a genetic tool they designed a few years ago called IBDmix, which uses machine learning techniques to decode the genome.

Scientists previously depended on comparing human genomes against a reference population of modern humans believed to have little or no Neanderthal or Denisovan DNA.

The study authors have established that even those referenced groups, who live thousands of miles south of the Neanderthal caves, have trace amounts of Neanderthal DNA, probably carried south by voyagers (or their descendants).

With IBDmix, they identified a first wave of contact about 200,000-250,000 years ago, another wave 100,000-120,000 years ago, and the largest one about 50,000-60,000 years ago. That contrasts sharply with previous genetic data.

To date, most genetic data suggests that modern humans evolved in Africa 250,000 years ago, stayed put for the next 200,000 years, and then decided to disperse out of Africa 50,000 years ago and go on to people the rest of the world, Professor Akey said.

Our models show that there wasnt a long period of stasis, but that shortly after modern humans arose, weve been migrating out of Africa and coming back to Africa, too.

To me, this story is about dispersal, that modern humans have been moving around and encountering Neanderthals and Denisovans much more than we previously recognized.

That vision of humanity on the move coincides with the archaeological and paleoanthropological research suggesting cultural and tool exchange between the hominin groups.

The key insight was to look for modern-human DNA in the genomes of the Neanderthals, instead of the other way around.

The vast majority of genetic work over the last decade has really focused on how mating with Neanderthals impacted modern human phenotypes and our evolutionary history but these questions are relevant and interesting in the reverse case, too, Professor Akey said.

They realized that the offspring of those first waves of Neanderthal-modern matings must have stayed with the Neanderthals, therefore leaving no record in living humans.

Because we can now incorporate the Neanderthal component into our genetic studies, we are seeing these earlier dispersals in ways that we werent able to before, Professor Akey said.

The final piece of the puzzle was discovering that the Neanderthal population was even smaller than previously believed.

Genetic modeling has traditionally used variation diversity as a proxy for population size. The more diverse the genes, the larger the population.

But using IBDmix, the team showed that a significant amount of that apparent diversity came from DNA sequences that had been lifted from modern humans, with their much larger population.

As a result, the effective population of Neanderthals was revised down from about 3,400 breeding individuals down to about 2,400.

Put together, the new findings paint a picture of how the Neanderthals vanished from the record, some 30,000 years ago.

I dont like to say extinction, because I think Neanderthals were largely absorbed, Professor Akey said.

The idea is that Neanderthal populations slowly shrank until the last survivors were folded into modern human communities.

This assimilation model was first articulated by Fred Smith, an anthropology professor at Illinois State University, in 1989. Our results provide strong genetic data consistent with Freds hypothesis, and I think thats really interesting, Professor Akey said.

Neanderthals were teetering on the edge of extinction, probably for a very long time.

If you reduce their numbers by 10 or 20%, which our estimates do, thats a substantial reduction to an already at-risk population.

Modern humans were essentially like waves crashing on a beach, slowly but steadily eroding the beach away.

Eventually we just demographically overwhelmed Neanderthals and incorporated them into modern human populations.

The findings were published in the journal Science.

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Liming Li et al. 2024. Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years. Science 385 (6705); doi: 10.1126/science.adi1768

Originally posted here:
Homo sapiens and Neanderthals Interacted Over 200,000-Year Period, Study Reveals - Sci.News

SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany

Abdoallah Sharaf

Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt

Abdoallah Sharaf&Asmaa Mohammed Abushady

College of Agriculture and Environmental Sciences, University of South Africa, Florida, South Africa

Lucky Tendani Nesengani,Sinebongo Mdyogolo,Rae Marvin Smith,Appolinaire Djikeng&Ntanganedzeni Mapholi

Laboratory of Biodiversity, Ecology, and Genome, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco

Ichrak Hayah&Bouabid Badaoui

Washington State University, Global Health, Nairobi, Kenya

Josiah Ochieng Kuja

Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria

Taiwo Crossby Omotoriogun

A. P. Leventis Ornithological Research Institute, University of Jos, Jos, Nigeria

Taiwo Crossby Omotoriogun

Regional Centre for Biotechnology and Bioresources Research, University of Port Harcourt, Port Harcourt, Nigeria

Blessing Adanta Odogwu,Victor Ezebuiro&Julian O. Osuji

SouthSouth Zonal Centre of Excellence, National Biotechnology Development Agency, Port Harcourt, Nigeria

Blessing Adanta Odogwu,Victor Ezebuiro&Julian O. Osuji

Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, UK

Girish Beedessee

Research Department, Institut Pasteur du Maroc, Casablanca, Morocco

Abdelhamid Barakat,Adil El Hamouchi,Fouzia Radouani,Hicham Charoute,Ichrak Benamri&Meriem Khyatti

Inqaba Biotec, Pretoria, South Africa

Acclaim M. Moila&Hamilton Ganesan

Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, Universit de Tunis El Manar, Tunis, Tunisia

Alia Benkahla,Mariem Hanachi,Melek Chaouch&Oussema Souiai

Field Crops Laboratory, National Institute of Agricultural Research of Tunisia (INRAT), University of Carthage, Tunis, Tunisia

Amal Boukteb

Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco

Amine Elmouhtadi,Driss Iraqi,Rachid Mentag&Slimane Khayi

Laboratory of Molecular Biology, Department of Basic Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo

Antoine Lusala Mafwila&Georges Lelo Mvumbi

Biotechnology School, Nile University, Giza, Egypt

Asmaa Mohammed Abushady,Assem Kadry Elsherif&Shaimaa Roshdy Abdullah Reda

African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir, Morocco

Bulbul Ahmed,Khaoula Errafii&Mohamed Hijri

Separations (Pty) Ltd, Johannesburg, South Africa

Charles Wairuri,Maritte Kilian&Marija Kvas

University of Lagos, Lagos, Nigeria

Charlotte C. Ndiribe

Finima Nature Park, Port Harcourt, Nigeria

Chukwuike Ebuzome

South African Medical Research Council Genomics Platform, Cape Town, South Africa

Craig J. Kinnear

Science for Africa Foundation, Nairobi, Kenya

Deborah-Fay Ndlovu,Fatu Badiane Markey,Judy Omumbo&Thomas Kariuki

National Center for Scientific and Technical Research, Rabat, Morocco

Elmostafa El Fahime&Marouane Melloul

Bio and Emerging Technology Institute, Addis Ababa, Ethiopia

Ermias Assefa&Yonas Geberemichael

Faculty of Sciences, Mohammed V University, Rabat, Morocco

Faissal Ouardi

Applied Genetics in Agriculture, Ecology and Public Health Laboratory, University of Abou Bekr Belkaid Tlemcen, Tlemcen, Algeria

Fatima Zohra Belharfi,Ikram Mkedder,Imane Haddadi,Mohammed Rida Mediouni,Sarra Selka,Semir Bechir Suheil Gaouar&Soumia Ayed

Megaflex, Casablanca, Morocco

Fatim Zohra Tmimi&Mossaab Maaloum

Rutgers University-Newark, Newark, NJ, USA

Fatu Badiane Markey

Biotechnology Centre, University of Yaound 1, Yaound, Cameroon

Francis Zeukeng,Jude Bigoga Daiga,Libert Brice Tonfack,Pierre Franois Djocgoue&Rosette Megnekou

Department of Microbial Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia

Helen Nigussie

Plant and Microbial Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research, University Mohammed VI Polytechnic, Ben Guerir, Morocco

Issam Meftah-Kadmiri

Department of Breeding and Reproduction, National Animal Genetic Resources Centre and Data Bank, Entebbe, Uganda

Jackson Franco Mubiru,Joan Bayowa Rokani&Joel Ogwang

International Livestock Research Institute, Nairobi, Kenya

Jean-Baka Kodjo Domelevo Entfellner,Cathrine Ziyomo&Appolinaire Djikeng

AbbVie Inc., North Chicago, IL, USA

Justin Eze Ideozu

Foundational Biodiversity Science, South African National Biodiversity Institute, Pretoria, South Africa

Kim Labuschagne,Mamohale Chaisi,Monica Mwale&Mudzuli Mavhunga

Laboratoire des Sciences Biomdicales, Alimentaires et de Sant Environnementale (LaSBASE), Dpartement des Analyses Biomdicales (AMB), Ecole Suprieure des Techniques Biologiques et Alimentaires (ESTBA), Universit de Lom, Lom, Togo

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Illumina, Inc., Evry, France

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Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa

Madeleine Ramantswana&Thabang Madisha

Division of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa

Marietjie W. Botes

MGI-Tech, Pretoria, South Africa

Mmatshepho Phasha-Muchemenye

Lakes and Fish Resources Protection and Development Agency (LFRPDA), Cairo, Egypt

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Veterinary Genetic Analysis Laboratory, Hassan II Agronomy and Veterinary Institute (IAV), Rabat, Morocco

Mohammed Piro,Oumaima Aminou&Siham Fellahi

Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa

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Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa

Nicholas Abraham Olivier&Renate Dorothea Zipfel

Department of Veterinary Pathology and Public Health, Hassan II Agronomy and Veterinary Institute (IAV), Rabat, Morocco

Oumayma Arbani

Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa

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Inqaba Biotec Central Africa, Yaound, Cameroon

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University of Warwick, Coventry, UK

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Department of Neurogenetics of Language, Rockefeller University, New York, NY, USA

Sadye Paez

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Establishing African genomics and bioinformatics programs through annual regional workshops - Nature.com

Researchers have assembled the genome and 3D structures of a 52,000-year-old woolly mammoth. It is the first time cell-specific gene activity has been measured in ancient DNA.

The researchers say they discovered an entirely new type of fossil which has superbly preserved ancient remains which led to the first ever 3D assembly of a chromosome.

This was possible because the mammoths remains freeze-dried shortly after it died. Its DNA was preserved in a glass-like state.

The woolly mammoth was discovered in Siberia in 2018. The research is published in the journal Cell.

This is a new type of fossil, and its scale dwarfs that of individual ancient DNA fragmentsa million times more sequence, says corresponding author Erez Lieberman Aiden, Director of the Center for Genome Architecture at Baylor College of Medicine.

Being able to reconstruct the fossilised chromosomes provides insight into how the mammoths genome was organised in its living cells and which genes were active in the skin tissue.

Using modern elephants as a baseline, the scientists were able to put the giant DNA puzzle together. It led them to create the first ever ancient karyotype an individuals complete set of chromosomes. It revealed woolly mammoths have the same number of chromosomes as todays African and Asian elephants 28.

The mammoths genomic structure was reconstructed using DNA extracted from the skin on the animals ear.

A method called Hi-C was used to detect sections of DNA likely to be in close proximity to and interact with each other.

Imagine you have a puzzle that has 3 billion pieces, but you dont have the picture of the final puzzle to work from, says corresponding author Marc A. Marti-Renom, a Catalan Institution for Research and Advanced Studies research professor. Hi-C allows you to have an approximation of that picture before you start putting the puzzle pieces together.

Bringing the DNA together allowed the researchers to see which genes were active and which were turned off in the skin cells.

The mammoths skin showed unique gene activation patterns compared to its closest living relative, the Asian elephant. It is possible these genes control its woolly-ness and cold tolerance.

These results have obvious consequences for contemporary efforts aimed at woolly mammoth de-extinction, says corresponding author M. Thomas Gilbert from the University of Copenhagen and the Norwegian University of Science and Technology.

The method used could also be applied to other ancient DNA specimens including other mammoths and mummified people from Egypt and other parts of the world.

View original post here:
First 3D assembly of woolly mammoth chromosome thanks to freeze-dried skin - Cosmos

A team of researchers has used cut-and-paste mobile genetic elements (MGEs) from the insert sequence (IS)110 family and clues from noncoding (nc)RNA to determine that large-scale genome design could be a possibility through a new class of guide RNAs.

The potential breakthrough came from asking whether ncRNA might assist recombinase in recognizing the target DNA site or the donor DNA (that is, the IS110 element itself), according to Drs. Matthew Durrant and Nicholas Perry of the Arc Institute in Palo Alto, CA. Together, Durrant, a computational biologist and senior scientist at Arc, and Perry, a PhD graduate student at the University of California (UC), Berkeley, led the experimental study with Dr. Patrick Hsu at Arc's Patrick Hsu lab.

Aided by cryo-electron microscopy analysis and nanopore sequencing, the study used Escherichia coli (E. coli) for its large, circular molecule of DNA chromosome and small, circular molecule plasmids.

In June, researchers confirmed a mechanism for a programmable target loop that allows the user to specify any desired genomic target sequence and any donor DNA molecule to be inserted. The development, detailed in the journal Nature, could eventually lead to a new genome editing method that sidesteps CRISPR DNA-cutting techniques, according to Arc.

The key, researchers discovered, lies in a new class of guide RNA, called "bridge RNA," that connects target and donor DNA and enables recombination by the IS621 recombinase. IS621, which resides in the IS110 family and is native to some strains of E. coli, as well as five closely related orthologues, was a central focus of this research, according to Durrant and colleagues.

"The bridge RNA system is a fundamentally new mechanism for genome design," said Hsu, senior author of the study and an Arc Institute core investigator and UC Berkeley assistant professor of bioengineering, in "Genomes by Design," an Arc blog post. "Bridge recombination can universally modify genetic material through sequence-specific insertion, excision, inversion, and more, enabling a word processor for the living genome beyond CRISPR."

Arc describes the discovery as a compact and entirely new type of programmable molecular system.

First, the team constructed a custom sequence database of bacterial isolate and metagenomic sequences by aggregating publicly available sequence databases.

As explained in Nature, the work investigated the potential presence of an IS110-encoded ncRNA by focusing on IS621. Researchers also evaluated the ncRNA consensus secondary structure across 103 diverse orthologues.

Durrant and colleagues found that ncRNA is necessary for in vitro recombination, and that the four components (ncRNA, recombinase, target DNA, and donor DNA) are sufficient to produce the expected recombination product. In addition, the base-pairing mechanism of target and donor recognition by the bridge RNA suggested programmability.

To assess programmability, the team designed an E. coli selection screen linking thousands of barcoded pairs of DNA targets and bridge RNAs on a single plasmid. This step helped to assess mismatch tolerance and reprogramming rules of bridge RNAs. They reprogrammed bridge RNAs to target sequences found only once in the E. coli genome.

"Altogether, these experiments provide evidence of the robust capability of IS621 to specifically insert multi-kilobase cargos into the genome, and offer further insights into the mechanisms of recombination," Durrant and colleagues wrote.

"The system can go far beyond its natural role that inserts the IS110 element itself, instead enabling insertion of any desirable genetic cargo like a functional copy of a faulty, disease-causing gene into any genomic location," Arc explained, adding that Hsu and colleagues demonstrated over 60% insertion efficiency of a desired gene in E. coli with over 94% specificity for the correct genomic location.

According to Arc, the Hsu lab found that when IS110 excises itself from a genome, the non-coding DNA ends are joined together to produce an RNA molecule the bridge RNA that folds into two loops. One loop binds to the IS110 element itself, while the other loop binds to the target DNA where the element will be inserted.

"We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules," the researchers explained in Nature. "The bridge RNA that we discovered in this work is the first example, to our knowledge, of a bispecific guide molecule that encodes modular regions of specificity for both the target and the donor DNA, coordinating these two DNA sequences in close proximity to catalyse efficient recombination."

Arc Institute operates in collaboration with Stanford University, UC Berkeley, and the University of California, San Francisco, according to information on the institute's website. The bridge RNA study included collaborators Hiroshi Nishimasu and Masahiro Hiraizumi at the University of Tokyo.

Continued here:
Researchers discover new class of guide RNA for genome editing - LabPulse

Crowdfund Capital Advisors (CCA) has distributed its new Crowdfunding Genome, an ecosystem report and visualization of the crowdfunding industry. The report includes the hot spots in the US, and the Phoenix/Scottsdale region is in the top spot, beating out the traditional startup ecosystem of the San Francisco Bay area.

The Arizona community earned the leading position due to metrics such asgrowth in valuation, repeat issuers, robust investment climate, supportive community, and innovative spirit.

CCA explains that entrepreneurs in Phoenix/Scottsdale have successfully leveraged crowdfunding (Reg CF) to fund their ventures, which the firm believes makes it a model for other regions to emulate.

Calling Phoenix/Scottsdale the top startup ecosystem, Sherwood Neiss, Principal at CCA, believes the regions success is a testament to its vibrant entrepreneurial community.

It is another proof point that startups need not be located in Silicon Valley to prosper, said Neiss.

Neiss told CI that Phoenix/Scottsdales continuous use of investment crowdfunding is a key factor in its rise to the top of the list.

Local issuers dont just use it for one or two rounds; they see it as an ongoing tool for capital formation. Startups in the region are adept at raising capital, achieving their goals such as increasing revenues and hitting key milestones, and then returning for follow-on capital at higher valuations. This strategic approach, combined with Phoenix/Scottsdales leading number of deals per population, has made it a standout ecosystem for pre-IPO startups.

Recent challenges in San Francisco have led to the exit of both established and early-stage firms, and Arizona has emerged as one of the beneficiaries of this exodus. Apparently, these entrepreneurs are also tapping into online capital formation to fund their firms.

At this same time, California is no slouch and continues to reign as the top state when it comes to innovation and access to capital.

Neiss says the states ecosystem enables unparalleled opportunities for entrepreneurs to scale and succeed.

It is exciting to see the broad application of investment crowdfunding for California entrepreneurs.

Other trends gleaned from the data include a biotech boom as more ventures in the biotechnology sector raise funds. There is also a sustainability surge. Tech, including Fintech and AI, continues to be a popular sector of investment crowdfunding.

Neiss said the Crowdfunding Genome helps provide a data-driven understanding of the diverse startup ecosystem in the US.

Traditional metrics often overlook the unique dynamics of crowdfunding and its impact on early-stage ventures. By leveraging our proprietary investment crowdfunding data and advanced analytics, our goal is to offer valuable insights that empower entrepreneurs, investors, and policymakers to make informed decisions and continue to foster innovation.

The report is available on the CCA website.

Read more:
Crowdfund Capital Advisors Reveals "Crowdfunding Genome" - Phoenix/Scottsdale Top Hub, Beats Bay Area - Crowdfund Insider

Reuters file photo Corn plants affected by leafhoppers are seen in a National Institute of Agricultural Technology experimental field, in Marcos Juarez, Cordoba, Argentina on April 20.

Reuters

16:36 JST,July 11, 2024

BUENOS AIRES (Reuters) An Argentine scientific institute has cracked the genome of the leafhopper, the insect which carries the bacteria responsible for wiping out vast swathes of the South American nations latest corn crop, the government said on June 25.

The development, which determined the Dalbulus maidis genetic makeup, will serve future efforts to fight off the leafhopper, according to the government statement.

Experts argue that the leafhopper population has surged in recent months largely due to the lack of frosts during last years Southern Hemisphere winter, which likely would have killed off the insect.

The tiny bug, which sucks sap out of plants, transmits bacteria that produce stunt disease in corn, causing the key grains crop to grow ears with loose or missing kernels.

In the 2023-24 season, the Rosario Grains Exchange expects local farmers to harvest 47.5 million metric tons of corn, about a fifth less than originally estimated due to losses caused by the leafhopper.

This research will help us understand the biology and evolution of the insect, which in turn will help predict and mitigate future outbreaks, the statement said, adding that the scientific advance could also lead to the development of new varieties of leafhopper-resistant genetically modified corn.

Agricultural analysts have said that farmers will likely plant smaller corn fields in the 2024-25 season due to the pest, although fall and winter frosts should improve prospects for the crop.

Continued here:
Argentina Cracks Genome of Leafhopper to Defend Crop - The Japan News