The Impossible Man by Patchen Barss salutes Roger Penrose's groundbreaking work in physics and mathematics while challenging the idea that a genius should be exempt from ordinary obligations

A genetic study of nearly 2700 individuals has revealed the ancestry of Indian people, and gets scientists closer to reconstructing the genomes of ancient Neanderthals

Lake sediments reveal the ancient history of Aboriginal people’s use of fire to manage the landscape, a tradition that has benefits for biodiversity

An excavation on an island in the Coral Sea shows that Indigenous Australians were producing ceramics long before the arrival of Europeans

Historians have claimed the people of Easter Island overexploited natural resources, causing a population crash, but new evidence suggests they lived sustainably for centuries

Analysis of DNA from a Neanderthal fossil found in a French cave indicates that it belonged to a group that was isolated for more than 50,000 years

Title: Infant Car Seats May Lower Oxygen Levels
Category: Health News
Created: 8/24/2009 12:00:00 AM
Last Editorial Review: 8/24/2009 12:00:00 AM

Title: Benji, Marley or Bo: Three Genes Dictate Dog's Coat
Category: Health News
Created: 8/27/2009 4:10:00 PM
Last Editorial Review: 8/28/2009 12:00:00 AM

Title: Inner Workings of Gene Tied to Breast, Ovarian Cancer Revealed
Category: Health News
Created: 8/22/2010 2:10:00 PM
Last Editorial Review: 8/23/2010 12:00:00 AM

Title: Study Links Gene to Serious Eye Disease
Category: Health News
Created: 8/25/2010 6:10:00 PM
Last Editorial Review: 8/26/2010 12:00:00 AM

Title: Blood Oxygen Test Finds Heart Defects in Newborns
Category: Health News
Created: 8/22/2011 11:00:00 AM
Last Editorial Review: 8/22/2011 12:00:00 AM

Title: Risk for Mental Illness Varies by Gender
Category: Health News
Created: 8/23/2011 11:00:00 AM
Last Editorial Review: 8/23/2011 12:00:00 AM

Title: Report: Vaccines Generally Safe, Cause Few Health Problems
Category: Health News
Created: 8/26/2011 11:01:00 AM
Last Editorial Review: 8/26/2011 12:00:00 AM

Title: Gene Mutation Found in Uterine Fibroids
Category: Health News
Created: 8/26/2011 11:01:00 AM
Last Editorial Review: 8/26/2011 12:00:00 AM

Title: Gene Might Predict Brain Tumors' Aggressiveness
Category: Health News
Created: 8/27/2012 10:05:00 AM
Last Editorial Review: 8/27/2012 12:00:00 AM

Title: Could Your Genes Influence How You Vote?
Category: Health News
Created: 8/27/2012 4:05:00 PM
Last Editorial Review: 8/28/2012 12:00:00 AM

Title: Scientists ID 'Happy' Gene in Women
Category: Health News
Created: 8/29/2012 4:05:00 PM
Last Editorial Review: 8/30/2012 12:00:00 AM

Title: Ancient Genome Appears to Have Links to Modern Humans
Category: Health News
Created: 8/30/2012 4:05:00 PM
Last Editorial Review: 8/31/2012 12:00:00 AM

Title: Gene Study Helps Advance Diagnosis of Cystic Fibrosis
Category: Health News
Created: 8/26/2013 2:36:00 PM
Last Editorial Review: 8/27/2013 12:00:00 AM

Title: Gene May Raise Diabetics' Chances of Heart Disease
Category: Health News
Created: 8/27/2013 4:35:00 PM
Last Editorial Review: 8/28/2013 12:00:00 AM

Title: Experimental Drug Shows Promise for Rare Genetic Disorder
Category: Health News
Created: 8/29/2013 12:35:00 PM
Last Editorial Review: 8/30/2013 12:00:00 AM

Title: Gene Tweak Boosts Lifespan by 20 Percent in Mice
Category: Health News
Created: 8/29/2013 12:35:00 PM
Last Editorial Review: 8/30/2013 12:00:00 AM

Title: Scientists Spot Genetic Clues to Crohn's Disease
Category: Health News
Created: 8/27/2014 9:35:00 AM
Last Editorial Review: 8/27/2014 12:00:00 AM

Title: Ban Indoor Use of E-Cigarettes, U.N. Health Agency Says
Category: Health News
Created: 8/26/2014 12:35:00 PM
Last Editorial Review: 8/27/2014 12:00:00 AM

Title: Gene Research Yields Insights Into Ebola Virus
Category: Health News
Created: 8/28/2014 2:36:00 PM
Last Editorial Review: 8/29/2014 12:00:00 AM

Title: Young Driver's Gender May Play Role in Timing, Type of Crash
Category: Health News
Created: 8/28/2014 12:36:00 PM
Last Editorial Review: 8/29/2014 12:00:00 AM

Title: Black Women at Raised Risk of Carrying Breast Cancer Genes
Category: Health News
Created: 8/27/2015 12:00:00 AM
Last Editorial Review: 8/28/2015 12:00:00 AM

Title: Genes Might Explain Hispanics' Added Longevity
Category: Health News
Created: 8/19/2016 12:00:00 AM
Last Editorial Review: 8/22/2016 12:00:00 AM

Title: Gene Test Might Quickly ID Baby's Infection
Category: Health News
Created: 8/23/2016 12:00:00 AM
Last Editorial Review: 8/24/2016 12:00:00 AM

Title: Autism-Linked Genes Often Differ Between Siblings
Category: Health News
Created: 8/25/2016 12:00:00 AM
Last Editorial Review: 8/26/2016 12:00:00 AM

Title: Could an Estrogen Patch Boost Women's Sex Lives in Menopause?
Category: Health News
Created: 8/28/2017 12:00:00 AM
Last Editorial Review: 8/29/2017 12:00:00 AM

Title: First Gene Therapy Approved in U.S.
Category: Health News
Created: 8/30/2017 12:00:00 AM
Last Editorial Review: 8/31/2017 12:00:00 AM

Title: Oxygen Therapy Doesn't Boost Heart Attack Survival
Category: Health News
Created: 8/30/2017 12:00:00 AM
Last Editorial Review: 8/31/2017 12:00:00 AM

Title: FDA Warns of Serious Genital Infection With Diabetes Meds
Category: Health News
Created: 8/30/2018 12:00:00 AM
Last Editorial Review: 8/30/2018 12:00:00 AM

Title: Gene 'Editing' in Dog Study Shows Promise for Kids With Muscular Dystrophy
Category: Health News
Created: 8/30/2018 12:00:00 AM
Last Editorial Review: 8/31/2018 12:00:00 AM

Title: 'Dramatic Resurgence' of Measles in Europe: WHO
Category: Health News
Created: 8/29/2019 12:00:00 AM
Last Editorial Review: 8/29/2019 12:00:00 AM

Title: There Is No 'Gay Gene,' Major Study Concludes
Category: Health News
Created: 8/29/2019 12:00:00 AM
Last Editorial Review: 8/30/2019 12:00:00 AM

Title: Gene Therapy Makes Inroads Against a Form of Hemophilia
Category: Health News
Created: 7/22/2022 12:00:00 AM
Last Editorial Review: 7/22/2022 12:00:00 AM

Title: Gene Tests Could Spot 1 Million Americans at Risk of High Cholesterol
Category: Health News
Created: 5/18/2022 12:00:00 AM
Last Editorial Review: 5/18/2022 12:00:00 AM

Title: Common Diabetes Drug May Contain Traces of Carcinogen
Category: Health News
Created: 8/12/2022 12:00:00 AM
Last Editorial Review: 8/12/2022 12:00:00 AM

Title: Use of Pot, Hallucinogens Soaring Among Young Americans
Category: Health News
Created: 8/23/2022 12:00:00 AM
Last Editorial Review: 8/23/2022 12:00:00 AM

Title: Magic Mushroom Hallucinogen May Treat Problem Drinking
Category: Health News
Created: 8/24/2022 12:00:00 AM
Last Editorial Review: 8/25/2022 12:00:00 AM

Title: Major Gene Study Spots DNA Tied to Autism, Other Disorders
Category: Health News
Created: 8/19/2022 12:00:00 AM
Last Editorial Review: 8/19/2022 12:00:00 AM

Title: Kidneys' Resilience May Depend on Your Gender, Study Finds
Category: Health News
Created: 8/22/2022 12:00:00 AM
Last Editorial Review: 8/22/2022 12:00:00 AM

Retrotransposable elements (RTEs) are common mobile genetic elements comprising ~42% of the human genome. RTEs play critical roles in gene regulation and function, but how they are specifically involved in complex diseases is largely unknown. Here, we investigate the cellular heterogeneity of RTEs using 12 single-cell transcriptome profiles covering three neurodegenerative diseases, Alzheimer's disease (AD), Parkinson's disease, and multiple sclerosis. We identify cell type marker RTEs in neurons, astrocytes, oligodendrocytes, and oligodendrocyte precursor cells that are related to these diseases. The differential expression analysis reveals the landscape of dysregulated RTE expression, especially L1s, in excitatory neurons of multiple neurodegenerative diseases. Machine learning algorithms for predicting cell disease stage using a combination of RTE and gene expression features suggests dynamic regulation of RTEs in AD. Furthermore, we construct a single-cell atlas of retrotransposable elements in neurodegenerative disease (scARE) using these data sets and features. scARE has six feature analysis modules to explore RTE dynamics in a user-defined condition. To our knowledge, scARE represents the first systematic investigation of RTE dynamics at the single-cell level within the context of neurodegenerative diseases.

PWAS (proteome-wide association study) is an innovative genetic association approach that complements widely used methods like GWAS (genome-wide association study). The PWAS approach involves consecutive phases. Initially, machine learning modeling and probabilistic considerations quantify the impact of genetic variants on protein-coding genes’ biochemical functions. Secondly, for each individual, aggregating the variants per gene determines a gene-damaging score. Finally, standard statistical tests are activated in the case-control setting to yield statistically significant genes per phenotype. The PWAS Hub offers a user-friendly interface for an in-depth exploration of gene–disease associations from the UK Biobank (UKB). Results from PWAS cover 99 common diseases and conditions, each with over 10,000 diagnosed individuals per phenotype. Users can explore genes associated with these diseases, with separate analyses conducted for males and females. For each phenotype, the analyses account for sex-based genetic effects, inheritance modes (dominant and recessive), and the pleiotropic nature of associated genes. The PWAS Hub showcases its usefulness for asthma by navigating through proteomic-genetic analyses. Inspecting PWAS asthma-listed genes (a total of 27) provide insights into the underlying cellular and molecular mechanisms. Comparison of PWAS-statistically significant genes for common diseases to the Open Targets benchmark shows partial but significant overlap in gene associations for most phenotypes. Graphical tools facilitate comparing genetic effects between PWAS and coding GWAS results, aiding in understanding the sex-specific genetic impact on common diseases. This adaptable platform is attractive to clinicians, researchers, and individuals interested in delving into gene–disease associations and sex-specific genetic effects.

Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. There is a need for tools that can process this growing volume of bacterial genome data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split k-mer analysis (SKA2), a method that supports both reference-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or genome assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can also accurately map variants to a reference and be used with recombination detection methods to rapidly reconstruct vertical evolutionary history. SKA2 is many times faster than comparable methods and can be used to add new genomes to an existing call set, allowing sequential use without the need to reanalyze entire collections. With an inherent absence of reference bias, high accuracy, and a robust implementation, SKA2 has the potential to become the tool of choice for genotyping bacteria. SKA2 is implemented in Rust and is freely available as open-source software.

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2n = 66) and Staurotypus triporcatus (XX/XY, 2n = 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling in Apalone (Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions in Staurotypus (Kinosternidae) and Trachemys scripta (Emydidae). Furthermore, we identified a chromosome folding pattern that enables "centromere–telomere interactions" previously undetected in turtles. The combined turtle pattern of "centromere–telomere interactions" (discovered here) plus "centromere clustering" (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome.

As a major type of structural variants, tandem duplication plays a critical role in tumorigenesis by increasing oncogene dosage. Recent work has revealed that noncoding enhancers are also affected by duplications leading to the activation of oncogenes that are inside or outside of the duplicated regions. However, the prevalence of enhancer duplication and the identity of their target genes remains largely unknown in the cancer genome. Here, by analyzing whole-genome sequencing data in a non-gene-centric manner, we identify 881 duplication hotspots in 13 major cancer types, most of which do not contain protein-coding genes. We show that the hotspots are enriched with distal enhancer elements and are highly lineage-specific. We develop a HiChIP-based methodology that navigates enhancer–promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63, and VEGFA, as well as potentially novel oncogenes such as GRHL2, IRF2BP2, and CREB3L1. In particular, we identify a duplication hotspot on Chromosome 10p15 harboring a cluster of enhancers, which skips over two genes, through a long-range chromatin interaction, to activate an oncogenic isoform of the NET1 gene to promote migration of gastric cancer cells. Focusing on tandem duplications, our study substantially extends the catalog of noncoding driver alterations in multiple cancer types, revealing attractive targets for functional characterization and therapeutic intervention.