A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.

The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components.

A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation.

Evolution by natural selection is expected to be a slow and gradual process. In particular, the mutations that drive evolution are predicted to be small and modular, incrementally improving a small number of traits. However, adaptive mutations identified early in microbial evolution experiments, cancer, and other systems often provide substantial fitness gains and pleiotropically improve multiple traits at once.

A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.

Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics.

Navigated Osteosynthesis for Unstable Atlas Fractures: Technical Note and Case Series.

Objective: Fractures of the atlas are typically considered stable or unstable based on the integrity of the transverse ligament. Whereas stable Jefferson burst fractures can be treated nonoperatively, unstable fractures with disruption of the transverse ligament often require surgical intervention. Atlas osteosynthesis has been proposed as a motion-preserving alternative to atlantoaxial fusion.

Cancers adapt to their mutational load by buffering protein misfolding stress.

In asexual populations that don't undergo recombination, such as cancer, deleterious mutations are expected to accrue readily due to genome-wide linkage between mutations. Despite this mutational load of often thousands of deleterious mutations, many tumors thrive. How tumors survive the damaging consequences of this mutational load is not well understood.

Genomics of a sexually selected sperm ornament and female preference in Drosophila.

Our understanding of animal ornaments and the mating preferences driving their exaggeration is limited by knowledge of their genetics. Post-copulatory sexual selection is credited with the rapid evolution of female sperm-storage organ morphology and corresponding sperm quality traits across diverse taxa. In Drosophila, the mechanisms by which longer flagella convey an advantage in the competition among sperm for limited storage space in the female, and by which female sperm-storage organ morphology biases fertilization in favour of longer sperm have been resolved.

Pervasive fitness trade-offs revealed by rapid adaptation in large experimental populations of .

Life-history trade-offs are an inherent feature of organismal biology that evolutionary theory posits play a key role in patterns of divergence within and between species. Efforts to quantify trade-offs are largely confined to phenotypic measurements and the identification of negative genetic-correlations among fitness-relevant traits. Here, we use time-series genomic data collected during experimental evolution in large, genetically diverse populations of to directly measure the manifestation of trade-offs in response to temporally fluctuating selection pressures on ecological timescales.

Dominance reversal protects large-effect resistance polymorphisms in temporally varying environments.

A central challenge in evolutionary biology is to uncover mechanisms maintaining functional genetic variation in heterogeneous environments . Population genetics theory suggests that beneficial reversal of dominance, where alleles are dominant when beneficial and recessive when deleterious, can help maintain such variation in temporally varying environments . However, empirical examples are scarce due to difficulties in measuring dominance in fitness in field experiments .

Massively parallel experimental interrogation of natural variants in ancient signaling pathways reveals both purifying selection and local adaptation.

The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are mostly neutral or have functional effects. We address this question by directly mapping the fitness effects of over 9,000 natural variants in the Ras/PKA and TOR/Sch9 pathways-key regulators of cell proliferation in eukaryotes-across four conditions in . While many variants are neutral in our assay, on the order of 3,500 exhibited significant fitness effects.

Implementing verifiable oncological imaging by quality assurance and optimization (i‑Violin) : Protocol for a European multicenter study.

Background: Advanced imaging techniques play a pivotal role in oncology. A large variety of computed tomography (CT) scanners, scan protocols, and acquisition techniques have led to a wide range in image quality and radiation exposure. This study aims at implementing verifiable oncological imaging by quality assurance and optimization (i-Violin) through harmonizing image quality and radiation dose across Europe.

Helium Detection in Natural Gas Using Raman Spectroscopy.

Raman spectroscopy has great potential for quantitative analysis of natural gas. Helium is one of the components of natural gas and has a wide range of applications. It was believed that noble gases could not be detected using this technique due to the absence of their vibrational spectra.

A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.

Unlabelled: The cohesin complex is a critical regulator of gene expression. is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and show that STAG2 is uniquely tumor suppressive among all core and auxiliary cohesin components.

Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.

, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes.

Functional mapping of epigenetic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes.

Epigenetic dysregulation is widespread in cancer. However, the specific epigenetic regulators and the processes they control to drive cancer phenotypes are poorly understood. Here, we employed a novel, scalable and high-throughput method to perform iterative functional screens of over 250 epigenetic regulatory genes within autochthonous oncogenic KRAS-driven lung tumors.

pigmentation demonstrates adaptive phenotypic parallelism but genomic unpredictability over multiple timescales.

Unlabelled: Populations are capable of responding to environmental change over ecological timescales via adaptive tracking. However, the translation from patterns of allele frequency change to rapid adaptation of complex traits remains unresolved. We used abdominal pigmentation in as a model phenotype to address the nature, genetic architecture, and repeatability of rapid adaptation in the field.

The visible magneto-optical response of REAMnOmanganites: relationship with the charge component of the material.

Magnetic circular dichroism (MCD) spectroscopy for manganite films of various compositions and morphologies has been studied in the range of 1.2-3.7 eV.

Continuously fluctuating selection reveals fine granularity of adaptation.

Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown. Here we generated genome-wide allele frequency data every 1-2 generations from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December (a period of approximately 12 total generations).

Antiferromagnetic liquid-crystal suspensions of goethite nanorods: three mechanisms of magnetic field influence on orientational structure.

The study looks into magnetically induced orientational transitions in suspensions of goethite nanorods based on a nematic liquid crystal. The study considers magnetically compensated suspension, which is a liquid-crystal analogue of an antiferromagnet. Unlike conventional magnetic particles, goethite nanorods have a remanent magnetic moment directed along the long axis of the particle and also they have negative diamagnetic anisotropy.

Return of intracranial beta oscillations and traveling waves with recovery from traumatic brain injury.

Traumatic brain injury (TBI) remains a pervasive clinical problem associated with significant morbidity and mortality. However, TBI remains clinically and biophysically ill-defined, and prognosis remains difficult even with the standardization of clinical guidelines and advent of multimodality monitoring. Here we leverage a unique data set from TBI patients implanted with either intracranial strip electrodes during craniotomy or quad-lumen intracranial bolts with depth electrodes as part of routine clinical practice.

Improving the Accuracy of Bulk Fitness Assays by Correcting Barcode Processing Biases.

Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce nonuniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples.

Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab.

Environmental memory alters the fitness effects of adaptive mutations in fluctuating environments.

Evolution in a static laboratory environment often proceeds via large-effect beneficial mutations that may become maladaptive in other environments. Conversely, natural settings require populations to endure environmental fluctuations. A sensible assumption is that the fitness of a lineage in a fluctuating environment is the time average of its fitness over the sequence of static conditions it encounters.

Highly pure DNA-encoded chemical libraries by dual-linker solid-phase synthesis.

The first drugs discovered using DNA-encoded chemical library (DEL) screens have entered late-stage clinical development. However, DEL technology as a whole still suffers from poor chemical purity resulting in suboptimal performance. In this work, we report a technique to overcome this issue through self-purifying release of the DEL after magnetic bead-based synthesis.