Weekly Reading List: August 25, 2024

Genetic testing can help people who may have a rare disease. Until public and private insurance covers the costs of this testing, the federal government should support biotech companies’ provision of tests.

Evolutionary tree of angiosperms reveals two major bursts of diversification.

Negotiators from around the world are meeting in Montreal this week to hammer out how to divide the billions of dollars and other benefits derived from using genetic sequences to make new drugs, cosmetics and agricultural products.

Decision by Nice to rule out drug being available on NHS comes despite medicines licensing body giving green light

FDA will host a webinar for industry and other interested stakeholders to discuss how to comply with these requirements.

As teams grow, new Ph.D. graduates are less likely to land tenure-track jobs and more likely to leave science—especially women and international researchers

On August 19, 2024, Association for Molecular Pathology (AMP) filed an 83-page legal case against the FDA and its regulation to govern lab-d…

We find that massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and KRAB-domain protein genes that suppress transposable element expansion, and lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype.

Membraneless coacervate microdroplets have long been proposed as model protocells as they can grow, divide, and concentrate RNA by natural partitioning. However, the rapid exchange of RNA between these compartments, along with their rapid fusion, both within minutes, means that individual droplets would be unable to maintain their separate genetic identities. Hence, Darwinian evolution would not be possible, and the population would be vulnerable to collapse due to the rapid spread of parasitic RNAs.

The completion of the Human Genome Project has provided a foundational blueprint for understanding human life. Nonetheless, understanding the intricate mechanisms through which our genetic blueprint is involved in disease or orchestrates development across temporal and spatial dimensions remains a profound scientific challenge. Recent breakthroughs in cellular omics technologies have paved new pathways for understanding the regulation of genomic elements and the relationship between gene expression, cellular functions, and cell fate determination.

Hundreds of medical algorithms have been approved on basis of limited clinical data. Scientists are debating who should test these tools and how best to do it.

Mpox circulated in Nigeria for 8 years before it sparked a global outbreak. What happened? And could it have been stopped?

Objective Routine use of whole genome sequencing (WGS) has been shown to help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time-intensive. In light of recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource utilization approach capable of providing accurate WGS-based comparisons of HAI pathogens within a time frame allowing for infection prevention and control (IPC) interventions. Methods WGS was prospectively performed on antimicrobial-resistant pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecalling algorithm. Potential transmission was assessed via Ridom SeqSphere+ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cut-off values. The accuracy of our ONT pipeline was determined relative to Illumina-based WGS data generated from the same genomic DNA sample. Results Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold-standard data, our ONT pipeline achieved a Q score of 60 for assembled genomes, even with a coverage rate of as low as 40X. The mean time from initiating DNA extraction to complete genetic analysis was 2 days (IQR 2-3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of all sequenced strains). Combining ONT WGS data with epidemiological data, >70% (15/21) of the isolates originated from patients with potential healthcare transmission links. Conclusions Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in the efficient detection and deployment of preventative measures against HAI transmission. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Core grant CA016672 (Advanced Technology Genomics Core - ATGC) and NIH grant 1S10OD024977-01 provided funding for the ATGC sequencing facility at MDACC. C.-T.W. was supported by a Peter and Cynthia Hu scholarship. W.C.S. was supported through the National Institute of Allergy and Infectious Diseases (NIAID) T32 AI141349 Training Program in Antimicrobial Resistance. Support for this study was also provided by NIAID grants R21AI151536 and P01AI152999 for S.A.S and T.J.T, and provided by the National Science Foundation (NSF: EF-2126387, IIS-2239114) to T.J.T. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the MDACC quality improvement institutional review board I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

Three major startups have faltered over the past year, but smaller firms are finding a niche

First patient in UK gets dose of jab designed to kill most common form of lung cancer – and stop it coming back

FDA approves and authorizes updated mRNA COVID-19 vaccines to better protect against currently circulating variants.

If you don't know anyone who does research on (or using) yeast, you might not have heard about this problem. But for several years now, there's been an annoying and expensive problem for those labs that do depend on yeast cultures: sometimes the yeast die for no apparent reason (or just fail to grow in the first place). Here's an article at Science, and if you look around, you'll see plenty of evidence.

Assessing brain aging heterogeneity in a cohort of 49,482 individuals from 11 studies, a generative model identifies five dominant patterns of brain atrophy, with specific associations with biomedical, lifestyle and genetic factors.

Illumina Ventures is seeking $300 million for a new investment fund, according to filing with the US Securities and Exchange Commission this week.

Abstract. There is an accumulation of evidence that the human gut microbiota plays a role in maintaining health, and that an altered gut microbiota (someti

Predators often search for prey while moving through the environment, but there are important exceptions, including the way sedentary predators sometimes rely on signals for drawing prey to within striking distance. Some spiders, for instance, leave the remnants of previously-captured prey in their webs where they function as static lures that effectively attract a diverse array of additional prey. However, important questions remain concerning how specific the targeted prey may be and how dynamic, instead of static, signalling might be.