Category Archives: Transhuman News

Genomic features

The quadripartite structure of 22 samples of 17 species in Amaranthus consists of a large single-copy region (LSC with 83, 38284, 062bp), a small single-copy region (SSC with 17, 937 18, 124bp), and a pair of inverted repeat regions (IRs with 23, 96424, 357bp). The full length of the 22 cp genomes ranges from 149,949bp in A. polygonoides to 150, 756bp in A. albus (Table 1). The chloroplast genome sequences were deposited in GenBank (Table 1).

The total GC content was 36.5% to 36.6%, only A. albus, A. blitoides and A. polygonoides have a GC content of 36.5% (Table 1). The chloroplast genome contains a total of 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, 18 of which were duplicated in the inverted repeat regions (see Supplementary Table S1 online). The gene rps12 was trans-spliced; the 50-end exon was located in the LSC region, whereas the 30- intron and exon were duplicated and located in the inverted repeat regions. The partial duplicate of rps19 and ycf1 genes appeared as pseudogenes as they lost their protein-coding ability. 16 genes have introns.

The length of the SSC region was conserved among the subgenera by comparing the length of the chloroplast genomes of 22 individuals from 17 species. A. palmeri, A. tuberculatus and A. arenicola in subgen. Acnida were 18,02718,042bp in length, the SSC length of 5 species of subgen. Amaranthus was 17,93717,948bp, and the SSC length of 8 species of subgen. Albersia was 18,05718,124bp (Tables 1, 2). There were about 77bp InDels in ndhE-G and 180bp InDels in ndhG-I, which induced the variation of SSC length among subgenera (Table 2; see Supplementary Fig. S1 online). The frequencies of SNPs and InDels in the chloroplast genomes of the 17 species were 1.79% and 2.86%, respectively (Table 3). The frequencies of SNPs and InDels in the genes were 1.22% and 1.14%, and the frequencies of SNPs and InDels in the intergenic spacer were 3.25% and 7.32%, respectively (Table 3). In general, the variation mainly occurred in the intergenic spacer region, and InDels mainly occurred in the non-coding region (Table 3). The longest InDel was 387bp, which occurred on ycf2, followed by 384bp InDel on psbM-trnD.

Each species has 28 to 38 repeats, distributed in 30 locations, including 11 to 14 forward repeats, 11 to 17 palindromic repeats, and 6 to 8 reverse repeats ranging from 30 to 64bp in length. There were 19 common repeats locations, of which 11 had no variation and 8 had variation in length. The R3, R8, R11 and R13 had the most abundant variation (Fig.2). The R12 (forward and reverse repeats) was distributed in LSC, IRa, SSC and IRb. The R12 on SSC is almost opposite to R12 on LSC, dividing the entire circular genome into two parts of nearly equal length. The repeats on LSC were mainly concentrated near Repeat 12 (loci 29,57246,282), loci 81668327, loci 29,572 and loci 75,230. The repeats on IRs are constant within the genus. There were two common repeats in SSC, and one was a palindrome sequence shared by subgen. Acnida, subgen. Amaranthus, and A. albus.

The distribution of repeat sequences at 30 loci in Amaranthus. R is short for repeat. The red line segment R12 and the black line segments are repeats in all 17 species, the orange line segment represents a repeating sequence in some species. A repeat with only one line segment indicates that there is only one repeat at the site, and vice versa indicates that there are several different repeats at the site. The chloroplast genome figure was generated by the Geneious Prime v. 2020.1.2 software.

MISA analysis showed that each cp genome of Amaranthus contained 2939 SSRs (see Supplementary Table S4 online). On average, the number of SSR types from more to less was mono-, tetra-, di-, tri-, penta- and hexa-nucleotides in order (see Supplementary Table S4 online). About 55.56% of those SSRs were composed of A or T bases. Among all SSRs, most loci located in LSC (77.78%) and IGS (71.91%). About 12 repeat motifs were shared by all species in the genus while the remaining motifs were species-specific or subgenus-specific (see Supplementary Table S4 online). Different combinations of SSR markers could distinguish all species except A. standleynaus and A. crispus, A. dubius and A. spinosus (see Supplementary Table S4 online).

The topologies of the phylogenetic trees constructed by maximum likelihood and Bayesian methods were the same basically. A. palmeri, A. arenicola and A. tuberculatus clustered together (BS/PP=100/1) to form subgen. Acnida, or the Dioecious Clade (Fig.3). A. hybridus, A. hypochondriacus, A. dubius, A. spinosus, A. retroflexus clustered together (BS/PP=100/1) to represent subgen. Amaranthus, or the Hyridus Clade (Fig.3). And the above two clades were very close (BS/PP=100/1) (Fig.3). A. albus and A. blitoides were clustered with low/moderate value (BS/PP=35/0.84) and separated from subgen. Albersia and were closely related to subgen. Amaranthus and subgen. Acnida (BS/PP=58/0.99) (Fig.3). Among the three species of subgen. Albersia distributed in Galpagos, A. polygonoides became a single basal branch. The other two species, A. albus and A. blitoides, formed a separate clade (Galpagos Clade). The rest of subgen. Albersia were clustered into one branch, namely the ESA+South American Clade (BS/PP=100/1) (Fig.3).

A maximum likelihood topological tree based on chloroplast genome of Amaranthus and three outgroups. Values at each node indicate maximum likelihood bootstrap support (BS)/Bayesian inference posterior probability (PP) value. Individuals marked with grey backgrounds represent major monophyletic branches in the genus. The newick format files are imported into MEGA version 6 to generate the final topology tree.

The partially qualified fragment regions searched by exhaustive method were overlapped, and the overlapped regions were combined together as a hotspot region. Finally, 16 hotspot fragments with a length of 737 to 2818bp were obtained, and the SNP variation frequency ranged from 0.78 to 1.49% (see Supplementary Table S3 online). The topological trees constructed by the alignments of these 17 hot fragments and the topological trees constructed by the alignment sequences of each gene and intergenic spacer were consistent with the chloroplast genome topological tree, namely, the hotspots with more than 90% bootstrap value support for the subgen. Amaranthus, subgen. Acnida and subgen. Albersia branch (excluding A. albus, A. polygonoides, and A. blitoides) were ndhF-rpl32, ycf1 and rpoC2 (Fig.4).

Three maximum likelihood topological trees based on rpoC2, ndhF-rpl32 and ycf1 of Amaranthus and three outgroups. Values at each node indicate maximum likelihood bootstrap support (BS)/Bayesian inference posterior probability (PP) value. AMA represented the subgen. Amaranthus, ACN represented the subgen. Acnida, ALB represented the subgen. Albersia. The newick format files are imported into MEGA version 6 to generate the final topology tree.

In several similar taxa, there were 25 InDels and 11 SNPs between A. tunetanus and A. standleyanus. A. crispus and A. standleyanus had no difference. There are 46 SNPs and 144 InDels between A. arenicola and A. tuberculatus. By sequence alignment and variation analysis, it was found that trnK-UUU-atpF, trnT-UGU-atpB, psbE-clpP, rpl14-rps19, ndhF-D could be used to distinguish A. tunetanus from A. standleyanus, A. crispus, and A. arenicola from A. tuberculatus.

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Genetic variation and structure of complete chloroplast genome in alien monoecious and dioecious Amaranthus weeds | Scientific Reports - Nature.com

Sequencing the genome of cancer tumours is often used to help identify the type of cancer a person has and the best treatment for it.

Although cancer genomics has been used for a few years now, scientists are still learning about the best way to use genomic information to grade and categorize cancers.

One area that has received little attention until now is the methylation status of the cancer genome around specific genes. Methylation refers to the presence or absence of a methyl group on a base molecule within a gene that can affect whether or not a gene is expressed. This control of genetic expression is referred to as epigenetics.

Levels of expression of certain genes can also be affected by copy number variants (CNVs). CNVs arise because some sections of DNA are repeated, and the number of repeats varies between individuals due to deletions or duplications of DNA.

This leaves some people with many copies of a particular DNA sequence, whilst others have far fewer. These variations between individuals can be normal and harmless however, they can also underpin disease.

A type of brain cancer called meningioma is known for the diversity of CNVs that occur between the genomes of different tumors. CNVs can also affect methylation, which further affects gene expression.

In a study by researchers at Northwestern University in Evanston, IL, the scientists decided to look at both the level of methylation in the meningioma genomes and the number of repeats in different CNVs. They included certain genes in the cancer genome known to control growth and repair to see if this provided any insight into outcomes.

The findings are published in the journal Nature Genetics.

Using genomic data from 565 tumors taken from two cohorts of patients who had been followed up for 56 years, researchers profiled the DNA methylation of the cancer genomes. They then analyzed this alongside the presence of DNA repeats at certain points in the genome and also looked at the RNA present in the tumors to determine which genes had and hadnt been expressed.

They found that looking at the number of repeats within certain genes alone did not predict patient outcomes accurately, but looking at the number of repeats of genes alongside the level of methylation revealed three different grades of tumor.

Just over one-third of the tumors in the cohort were designated merlin intact meningiomas, where patients had the best outcomes. These tumors did not involve abnormal numbers of repeats on the gene that codes for a protein called merlin, which acts as a tumor suppressor. There was also normal methylation around this gene, allowing it to be expressed normally.

Conversely, 38% had immune-enriched meningiomas where patients had intermediate outcomes. These tumors were characterized by loss of the gene that codes for merlin and downregulation of other tumor-suppressing genes due to methylation.

This allowed them to overcome normal responses from the immune system.

A further 28% had hypermitotic meningiomas where the patient not only had fewer repeats of the gene that codes for merlin but a number of other gene repeats that caused either increased growth or decreased tumor suppression.

They also had methylation that allowed the increased expression of a gene known to promote cell growth. These patients had the least favorable outcomes.

Using this information, the researchers then tested the drug abemaciclib, a cancer drug already used for breast cancer, on tumor cells in cell lines, organoids, and xenografts in mice.

Results from these experiments indicated the drug could be used to treat individuals who had been identified as having either immune-enriched tumors or hypermitotic tumors.

Previously trials have failed to identify drugs that could reliably treat meningioma, but the identification of a biomarker could help identify patients who could benefit from certain treatments, said lead study author Dr. Stephen Magill.

Dr. Magill is an assistant professor of neurological surgery at Northwestern University Feinberg School of Medicine. He told Medical News Today in an interview: Some of our findings are really raising the possibility that the more we know about the biology, [the more] we can then say: this isnt just a meningioma, you have a hypermitotic meningioma.

So we can really use that as a biomarker to stratify who would go into a clinical trial.

Cancer researcher professor Noam Shomron from the Sackler Faculty of Medicine from Tel Aviv University, Israel, who was not involved in the research told Medical News Today:

I think its a wonderful study, because its so comprehensive, and it spans molecular and clinical findings and structural variations and methylation which is epigenetics [and something that] doesnt often take center stage.

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Brain tumor growth may be halted with breast cancer drug - Medical News Today

From UF/IFAS

New research led by a University of Florida scientist shows a development regulator can help plants grow. In the bigger picture, the studys results also may help genome editing and as a result, plant breeding.

Development regulators are genes that regulate plant development and growth. UF/IFAS scientists have discovered that one such gene can help deliver DNA into a plant to promote shoot growth from either a stem of a whole plant or young leaves cultured in a petri dish.

Results from the study show that injection of a plant developmental regulator known as PLT5 into the stem helps some snapdragons and tomatoes grow into new shoots. In addition, scientists found that the PLT5 can help young leaves or petioles of cabbages grow into a whole plant after culturing them in the petri dish.

Generally, it is extremely difficult for cells from some plants to grow into whole plants from a tissue culture, said Alfred Huo, an assistant professor of horticultural sciences at the UF/IFAS Mid-Florida Research and Education Center. By applying PLT5, scientists can more effectively deliver genes or DNA fragments into plant cells, which means plants can grow from the cellular level to adulthood more efficiently.

This research can help scientists address some questions in basic plant breeding, including how to get certain genes into plants, Huo said. It can also help scientists as they apply genome editing to many plant species.

This finding can accelerate a breeding program, Huo said. You want to use genome editing for plant breeding. But you need to deliver a genome editing toolbox to plants to make the editing happen. With this process, scientists can eventually create some desirable traits in plants and develop new cultivars. In this case, the PLT5 regulator can help deliver this toolbox and help grow young leaves or stems into new plants carrying these desirable traits.

More than 20 scientists across Florida including Huo are part of the UF/IFAS Plant Breeding team. They develop new varieties of citrus, tomatoes, strawberries, blueberries, cattle forages, peanuts, sugarcane, ornamental plants, and more.

The mission of the University of Florida Institute of Food and Agricultural Sciencesis to develop knowledge relevant to agricultural, human, and natural resources and to make that knowledge available to sustain and enhance the quality of human life. With more than a dozen research facilities, 67 county Extension offices, and award-winning students and faculty in the UF College of Agricultural and Life Sciences, UF/IFAS brings science-based solutions to the states agricultural and natural resources industries and all Florida residents. ifas.ufl.edu.

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UF scientist based in Apopka may have found a way to more efficiently apply genome editing to plant breeding - The Apopka Voice

New York, May 19, 2022 (GLOBE NEWSWIRE) -- Reportlinker.com announces the release of the report "Synthetic Biology Market Forecast to 2028 - COVID-19 Impact and Global Analysis By Products, Technology, and Application" - https://www.reportlinker.com/p06279470/?utm_source=GNW The increasing investments in synthetic biology and the rising number of start-ups are driving the market growth. However, the renewed regulations for biotechnology hamper the market growth.

Synthetic biology is the science of designing, altering, and building simple organisms to perform specific therapeutic or industrial utilities. The organisms created are genetically modified organisms (GMOs), which do not require a definition that distinguishes them from genetic modifications.

The rising number of start-ups is expected to support market growth during the forecast period.Biotechnology entrepreneurs easily raise funds and procure equipment and space from governments of the respective countries.

Indie Bio (California, US) and EU (Ireland) are among the first synthetic biology accelerators.The start-ups are emerging in Asia Pacific, as governments in this region are providing funds for the domestic development of synthetic biology.

For instance, the Government of India funded IITM Bioincubator, a department of the Indian Institute of Technology Madras, to start a state-of-the-art research facility for cancer biology and a Bioinformatics Infrastructure Facility.The funds were provided by agencies such as the Council of Scientific and Industrial Research (CSIR), the Department of Biotechnology (DBT), and the Department of Science and Technology (DST).

The Indian Institute of Technology Madras raised US$ 7.86 million (550 million rupees) in the fiscal year 20162017. In China, Chinaccelerator is a financer that provides mentorship programs for helping start-ups. It is also associated with SOSV, a venture capital and investment management firm,, which helps establish start-ups by providing funds under programs such as RebelBio and Indie Bio. The easy availability of funds for ideas is motivating entrepreneurs in the world to establish synthetic biology businesses.

Siolta Therapeutics, a US-based firm founded in 2016, produces therapeutic microbial consortia to prevent and treat inflammatory illnesses. It evaluates clinical data and develops mixed-species therapies for oral supplementation. Unlike existing medications for allergies, the microbiome-based approach operates before the onset of the immune dysfunction cascade. STMC-103H, a flagship therapeutic candidate of Siolta Therapeutics, is being studied for the treatment of allergic asthma as well as other chronic inflammatory illnesses, including atopic dermatitis and allergic rhinitis.

Kinnva Ltd., established in 2017, is a synthetic biology start-up catering to biotech, cleantech, and Agri-tech segments. Using a unique fermentation technology and sophisticated processing methods, Kinnva produces high-value biochemicals for applications in the food, feed, nutraceuticals, and cosmetics industries.

Genecis, a Canadian firm established in 2016, employs synthetic biology techniques to convert the trash into high-value commodities. The company used bacterial culture to treat food waste from landfills into compostable polyhydroxyalkanoate (PHA) bioplastics. These bioplastics are suitable for the food, agriculture, and textiles businesses, among others, willing to replace plastics with more sustainable alternatives. PHA polymers, unlike ordinary plastics, disintegrate within a year.

Thus, start-ups are contributing significantly to the synthetic biology market expansion.

Based on product, the synthetic biology market is segmented into oligonucleotides, chassis organisms, enzymes, and xeno-nucleic acid.The oligonucleotides segment is likely to hold the largest share of the market in 2021.

Moreover, the same segment is anticipated to register the highest CAGR in the market during the forecast period of 2021 to 2028.Based on technology, the synthetic biology market is segmented into, gene synthesis, genome engineering, measurement & modeling, cloning & sequencing, nanotechnology, and others.

In 2021, the gene synthesis segment is likely to hold the largest share of the market.However, the genome engineering segment is expected to register highest CAGR during 2021 to 2028.

The growth of genome engineering segment is owing to the rising applications of genetic engineering and gene therapy. Further, based on application, the synthetic biology market is segmented into medical applications, industrial applications, enviornmental applications, food and agriculture, and others. The medical applications segment is further segmented as, drug discovery & therapeutics and pharmaceuticals. In 2021, the medical applications segment held the largest market share, and it is expected to register the highest CAGR during 20212028.

Various organic and inorganic strategies are adopted by companies operating in the synthetic biology market.The organic strategies mainly include product launches and product approvals.

Inorganic growth strategies witnessed in the market are acquisitions, collaboration, and partnerships.These growth strategies have allowed the synthetic biology market players in expanding their business and enhancing their geographic presence, along with contributing to the overall market growth.

Additionally, growth strategies such as acquisitions and partnerships helped them strengthen their customer base and extend their product portfolios. A few of the significant developments by key players in the synthetic biology market are listed below.

In February 2022, Thermo Fisher Scientific announced the launch of GeneMapper Software, a flexible genotyping software package that provides DNA sizing and quality allele calls for all Thermo Fisher Scientific electrophoresis-based genotyping.

In January 2022, Thermo Fisher Scientific announced the launch of Oncomine BRCA Assay GX. It is a targeted next-generation sequencing (NGS) assay designed to provide comprehensive amplification of all coding regions of the human BRCA1 and BRCA2 genes, enabling accurate and sensitive detection of various mutation classes.

In April 2022, Merck KGaA Acquisition of MAST Platform from Lonza, a Leading Automated Bioreactor Sampling System. The acquisition of the MAST platform is another milestone to accelerate innovation in Mercks Process Solutions business unit.

In February 2022, Merck announced the transaction closing to acquire Exelead, following regulatory clearances and the fulfillment of other customary closing conditions, for approximately USD 780 million in cash.

A few of the key primary and secondary sources referred to while preparing the report on the synthetic biology market are the World Health Organization (WHO), the National Institute of Health (NIH), and the National Center for Biotechnology Information (NCBI).Read the full report: https://www.reportlinker.com/p06279470/?utm_source=GNW

About ReportlinkerReportLinker is an award-winning market research solution. Reportlinker finds and organizes the latest industry data so you get all the market research you need - instantly, in one place.

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In 2021, the gene synthesis segment is likely to hold the largest share of the market.However, the genome engineering segment is expected to register...

DUBLIN--(BUSINESS WIRE)--The "Metagenomic Sequencing Market by Product & Services (Reagent, Consumables, Instrument), Workflow (Sample Preparation, Sequencing), Technology (16S rRNA, Shotgun, Whole-genome), Application (Drug Discovery, Diagnostic) - Global Forecast to 2027" report has been added to ResearchAndMarkets.com's offering.

The metagenomic sequencing market is expected to reach USD 4.3 billion by 2027 from USD 1.9 billion in 2022, at a CAGR of 18.4% during the forecast period.

Growth in the metagenomic sequencing market is mainly driven by continuous technological innovations in NGS platforms, increasing initiatives and funding from government & private bodies for large-scale sequencing projects, declining costs of genome sequencing, and the significant applications of metagenomics in various fields.

Market Dynamics

Based on technology, the metagenomic sequencing market is segmented into 16S rRNA sequencing, shotgun metagenomic sequencing, whole-genome sequencing & de novo assembly, and metatranscriptomics. The shotgun metagenomic sequencing segment is estimated to grow at the highest CAGR during the forecast period. This can be attributed to its advantages over other techniques, the growing adoption of shotgun metagenomic sequencing among researchers and healthcare professionals, and the increasing number of metagenomic sequencing-based research activities.

Based on workflow, the market has been segmented into sample processing & library preparation, sequencing, and data processing & analysis. The sample processing & library preparation segment accounted for the largest share of the metagenomic sequencing market in 2021. The large share of this segment can be attributed to the growing number of metagenome sequencing research projects being conducted, the availability of technologically advanced and robust sample processing and library preparation assay kits, and the demand for efficient library preparation products.

The market in Asia Pacific is expected to register the highest growth rate during the forecast period, primarily due to the increasing financial support from public as well as private agencies, the increasing number of NGS-based research projects, increasing awareness about precision medicine, and the rising prevalence of chronic diseases.

North America accounted for the largest share of the metagenomic sequencing market in 2021. Factors such as the increasing applications of metagenomics in diagnostics and genomics research, the availability of research funding, and the development of NGS data analysis solutions are driving the growth of the metagenomic sequencing market in North America.

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Technological Innovations in NGS Platforms - A Key Factor Driving Growth in the Metagenomic Sequencing Market - ResearchAndMarkets.com - Business Wire

Trinity scientists, along with international colleagues, have explored the importance of sea travel in prehistory by examining the genomes of ancient Maltese humans and comparing these with the genomes of this period from across Europe. Previous findings from the archaeological team had suggested that towards the end of the third millennium BC the use of the Maltese temples declined. Now, using genetic data from ancient Maltese individuals the current interdisciplinary research team has suggested a potential contributing cause. Researchers found that these ancient humans lacked some of the signatures of genetic changes that swept across Europe in this period, because of their island separation. Scientists concluded that physical topography, in particular seascapes played a central role as barriers to genetic exchange.

The study is published today [Thursday 19th May 2022] in the journal Current Biology.

Researchers found these Mediterranean islanders were unusual for their time. They showed evidence of inbreeding in their family history, a sign of small, restricted population size indicating genetic isolation. Interestingly researchers found that one of the ancient individuals analysed was the offspring of second-degree relatives. This was an outstanding find as the number of highly inbred individuals is very low even in ancient times, and this is the second most inbred individual yet detected from the Neolithic world.

Scientists in the ancient DNA laboratory in Trinity sequenced the genomes of ancient (4500-5000 yrs old) Maltese humans from the collective cave burials at the Xaghra Circle and compared these with genomes of contemporary groups from around Europe. Trinity collaborated with colleagues from Queens University Belfast, the University of Cambridge, the Superintendence of Cultural Heritage Malta and others on the study (See full list of collaborators in Editors Notes below).

Scientists recreated the genetic geography across the whole of Europe at the time of the earliest farmers. They found evidence that it was fundamentally shaped by its seascapes which include barriers distinguishing Ireland and Britain from the continental mainland, and especially distinguishing the populations from the Scottish Orkney islands. These examples are powerful illustrations of genomic insularity. For genes at least, the seaways were more retardant than accelerant of connection.

The first settlers in the Maltese islands were Neolithic, dated by Queens University from the sixth millennium BC. Communities developed through a series of cultural phases, with some material indications of external connectivity. Maltese culture flourished from 3600 BC with distinctive craft and architecture only found on the islands. One example was the development of elaborate mortuary structures, such as the Xagra circle, Gozo. This monumentalized underground tomb yielded the remains of hundreds of individuals and underwent remodelling and enlargement until around 2500 BC when it was abandoned, possibly as part of a wider population decline or replacement.

To examine the demography of Late Neolithic Malta, scientists sequenced genomes from this burial site. The elucidation of fine structure among closely related groups such as European Neolithic populations is challenging, and requires a fine scale genetic analysis. Therefore, to examine these in a wider context, the team additionally imputed genome wide diploid genotypes from published ancient genomes and assessed long chunks of genomes shared within and between genomes to estimate genetic geography and demographies across Neolithic Europe.

A high resolution picture of the genetic background of ancient human populations allowed scholars to unveil their history, relatedness and migration. For example, it was discovered that ancient Neolithic people from Malta experienced an unusual drop in their size perhaps because of external factors such as the deterioration of the local environment and economy. Moreover, the genetic structure of modern human populations in Europe was mostly already present in the ancient communities that lived thousands of years ago. This discovery will surely open new questions about seafaring in ancient times.

Bruno Ariano, PhD student at Trinity College Dublin, now also Senior Bioinformatician at Open Target and first author of the study said:

"Was the sea a barrier or a highway in connecting regions during ancient times? Our research shows that seafaring increased the differentiation between populations from islands and mainland Europe. Thanks to the analysis of hundreds of ancient genomes we discovered a level of structure among populations that correlates with their geographic location. This unprecedented level of resolution will most likely lead to new theories about migration and seafaring."

Caroline Malone, Professor of Prehistory, School of Natural and Built Environment, Queens University Belfast and co-author, said:

The builders of the temples of prehistoric Malta showed enormous resilience and creativity for over a thousand years, as confirmed by a detailed dating programme at Queens Belfast. The new biological evidence demonstrates that they were also challenged by the maritime distance of their island home.

Simon Stoddart, Professor of Prehistory, Department of Archaeology, University of Cambridge, and co-author said:

"For the first time, we have a scientific understanding of the scale of prehistoric society in Malta. These results suggest that small communities were closely associated with the guardianship of the famous temples"

Funding for this research came from, the Wellcome Trust, Science Foundation Ireland, Health Research Board and the European Research Council (FRAGSUS Advanced grant).

You can read a full copy of the paper: Ancient Maltese genomes and the genetic

geography of Neolithic Europe, in the journal Current Biology, here: https://www.cell.com/current-biology/fulltext/S0960-9822(22)00705-9

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Scientists reveal how seascapes of the ancient world shaped genetic structure of European populations - EurekAlert

This article was originally published here

mSystems. 2022 May 18:e0017922. doi: 10.1128/msystems.00179-22. Online ahead of print.

ABSTRACT

Insertions in the SARS-CoV-2 genome have the potential to drive viral evolution, but the source of the insertions is often unknown. Recent proposals have suggested that human RNAs could be a source of some insertions, but the small size of many insertions makes this difficult to confirm. Through an analysis of available direct RNA sequencing data from SARS-CoV-2-infected cells, we show that viral-host chimeric RNAs are formed through what are likely stochastic RNA-dependent RNA polymerase template-switching events. Through an analysis of the publicly available GISAID SARS-CoV-2 genome collection, we identified two genomic insertions in circulating SARS-CoV-2 variants that are identical to regions of the human 18S and 28S rRNAs. These results provide direct evidence of the formation of viral-host chimeric sequences and the integration of host genetic material into the SARS-CoV-2 genome, highlighting the potential importance of host-derived insertions in viral evolution. IMPORTANCE Throughout the COVID-19 pandemic, the sequencing of SARS-CoV-2 genomes has revealed the presence of insertions in multiple globally circulating lineages of SARS-CoV-2, including the Omicron variant. The human genome has been suggested to be the source of some of the larger insertions, but evidence for this kind of event occurring is still lacking. Here, we leverage direct RNA sequencing data and SARS-CoV-2 genomes to show that host-viral chimeric RNAs are generated in infected cells and two large genomic insertions have likely been formed through the incorporation of host rRNA fragments into the SARS-CoV-2 genome. These host-derived insertions may increase the genetic diversity of SARS-CoV-2 and expand its strategies to acquire genetic material, potentially enhancing its adaptability, virulence, and spread.

PMID:35582907 | DOI:10.1128/msystems.00179-22

Continued here:
Putative Host-Derived Insertions in the Genomes of Circulating SARS-CoV-2 Variants - DocWire News

Prime Minister Narendra Modi announced on Thursday (May 12) that the Indian SARS-CoV-2 Genomics Consortium (INSACOG) would be extended to Indias neighbouring countries.

India has developed low-cost mitigation technologies for testing, treating, and data management. We have offered these capabilities to other countries. Indias genomic consortium has contributed significantly to the global database on the virus. I am happy to share that we will extend this network to countries in our neighbourhood, Modi said at the opening session of the second global Covid virtual summit.

The network

INSACOG was established in December 2020 as a joint initiative of the Union Health Ministry of Health and Department of Biotechnology (DBT) (under the Ministry of Science and Technology) with the Council for Scientific & Industrial Research (CSIR) and Indian Council of Medical Research (ICMR) to expand the whole-genome sequencing of SARS-CoV-2, the coronavirus that causes the Covid-19 disease, across India with the aim of understanding how the virus spreads and evolves.

INSACOG started out with the participation of 10 national research laboratories of the central government, and gradually expanded to a network of 38 labs, including private labs, operating on a hub-and-spoke model.

The 10 INSACOG Genome Sequencing Laboratories handhold the new laboratories, and the pan-India consortium works to monitor genomic variations in SARS-CoV-2 by a sentinel sequencing effort which is facilitated by the National Centre for Disease Control (NCDC), involving the Central Surveillance Unit (CSU) under the central governments Integrated Disease Surveillance Programme (IDSP).

How it helps

The data from the genome sequencing laboratories is analysed as per the field data trends to study the linkages, if any, between the genomic variants and epidemiological trends. This, the INSACOG website says, helps to understand super spreader events and outbreaks, and strengthen public health interventions across the country to help break chains of transmission.

Linking this data with IDSP data and the patients symptoms helps to better understand viral infection dynamics, and trends of morbidity and mortality. The data can be linked with host genomics, immunology, clinical outcomes, and risk factors for a more comprehensive outlook. Sequencing assumes added significance as the incidence of reinfections and vaccine breakthroughs increases.

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INSACOG is also working to establish a systematic correlation between genome sequencing and clinical outcomes. The consortium is working towards establishing a hospital network across the country with the aim to study clinical correlations in mild vs severe cases of Covid-19, and to carry out a longitudinal study to understand long-term post-Covid complications and change in immunity. INSACOG is also looking to expand to sewage surveillance as an early detection tool, and to assess the spread of variants in hotspot localities.

See the article here:
Explained: What is INSACOG, Indias network of labs to sequence the genome of the Covid-19 coronavirus? - The Indian Express