Deficient cell-cell cohesion is linked with lobular localization in simplified models of lobular carcinoma in situ (LCIS).

Lobular carcinoma in situ (LCIS) is a precursor of invasive lobular carcinoma of the breast. LCIS cells lack cell-cell cohesion due to the loss of E-cadherin. LCIS cells grow in mammary lobules rather than in ducts.

Evolution of sympatric host-specialized lineages of the fungal plant pathogen Zymoseptoria passerinii in natural ecosystems.

The barley disease Septoria Speckled Leaf Blotch, caused by the fungus Zymoseptoria passerinii, last appeared in North America in the early 2000s. Although rare in crops, field sampling of wild grasses in the Middle East revealed the disease persistence in wild barley. Identification of Z.

The social leverage effect: Institutions transform weak reputation effects into strong incentives for cooperation.

Institutions allow cooperation to persist when reciprocity and reputation provide insufficient incentives. Yet how they do so remains unclear, especially given that institutions are themselves a form of cooperation. To solve this puzzle, we develop a mathematical model of reputation-based cooperation in which two social dilemmas are nested within one another.

Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity.

Proteins that emerge de novo from noncoding DNA could negatively or positively influence cellular physiology in the sense of providing a possible adaptive advantage. Here, we employ two approaches to study such effects in a human cell line by expressing random sequences and mouse de novo genes that lack homologs in the human genome. We show that both approaches lead to differential growth effects of the cell clones dependent on the sequences they express.

Individuality Through Ecology: Rethinking the Evolution of Complex Life From an Externalist Perspective.

The evolution of complex life forms, exemplified by multicellular organisms, can be traced through a series of evolutionary transitions in individuality, beginning with the origin of life, followed by the emergence of the eukaryotic cell, and, among other transitions, culminating in the shift from unicellularity to multicellularity. Several attempts have been made to explain the origins of such transitions, many of which have been internalist (i.e.

Conditional cooperation with longer memory.

Direct reciprocity is a wide-spread mechanism for the evolution of cooperation. In repeated interactions, players can condition their behavior on previous outcomes. A well-known approach is given by reactive strategies, which respond to the coplayer's previous move.

The rate and spectrum of new mutations in mice inferred by long-read sequencing.

All forms of genetic variation originate from new mutations, making it crucial to understand their rates and mechanisms. Here, we use long-read PacBio sequencing to investigate de novo mutations that accumulated in 12 inbred mouse lines derived from three commonly used inbred strains (C3H, C57BL/6, and FVB) maintained for 8-15 generations in a mutation accumulation (MA) experiment. We built chromosome-level genome assemblies based on the MA line founders' genomes, and then employed a combination of read and assembly-based methods to call the complete spectrum of new mutations.

Stochastic models allow improved inference of microbiome interactions from time series data.

How can we figure out how the different microbes interact within microbiomes? To combine theoretical models and experimental data, we often fit a deterministic model for the mean dynamics of a system to averaged data. However, in the averaging procedure a lot of information from the data is lost-and a deterministic model may be a poor representation of a stochastic reality. Here, we develop an inference method for microbiomes based on the idea that both the experiment and the model are stochastic.

Indirect reciprocity under opinion synchronization.

Indirect reciprocity is a key explanation for the exceptional magnitude of cooperation among humans. This literature suggests that a large proportion of human cooperation is driven by social norms and individuals' incentives to maintain a good reputation. This intuition has been formalized with two types of models.

Spatiotemporal distribution of neural crest cells in the common wall lizard Podarcis muralis.

Background: Neural crest cells (NCCs) are migratory embryonic stem cells that give rise to a diverse set of cell types. Here we describe the dynamic distribution of NCCs in developing embryos of the common wall lizard Podarcis muralis inferred from 10 markers. Our aim is to provide insights into the NCC development of lacertid lizards and to infer evolutionary modifications by comparisons to other tetrapods.

Unanticipated specificity in effector-triggered immunity.

Effector-triggered immunity (ETI) enables hosts to react to pathogens by monitoring few key cellular processes. ETI responses are assumed to be similar toward related pathogen effectors. However, recent evidence from the invertebrate model Caenorhabditis elegans and pore-forming toxins indicates a much more complex and specific ETI than previously anticipated.

How Light at Night Sets the Circalunar Clock in the Marine Midge .

Many organisms inhabiting the interface between land and sea have evolved biological clocks corresponding to the period of the semilunar (14.77 days) or the lunar (29.53 days) cycle.

Combined transcriptome and proteome profiling reveal cell-type-specific functions of Drosophila garland and pericardial nephrocytes.

Drosophila nephrocytes are specialised cells that share critical functional, morphological, and molecular features with mammalian podocytes. Accordingly, nephrocytes represent a preferred invertebrate model for human glomerular disease. Here, we established a method for cell-specific isolation of the two types of Drosophila nephrocytes, garland and pericardial cells, from animals of different developmental stages and ages.

pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.

The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the incomplete and fragmented genetic information typical of metagenome-assembled genomes (MAGs). While existing tools leverage sequence homology from single genomes, this study introduces pan-Draft, a pan-reactome-based approach exploiting recurrent genetic evidence to determine the solid core structure of species-level GEMs. By comparing MAGs clustered at the species-level, pan-Draft addresses the issues due to the incompleteness and contamination of individual genomes, providing high-quality draft models and an accessory reactions catalog supporting the gapfilling step.

Optical genome mapping of structural variants in Parkinson's disease-related induced pluripotent stem cells.

Background: Certain structural variants (SVs) including large-scale genetic copy number variants, as well as copy number-neutral inversions and translocations may not all be resolved by chromosome karyotype studies. The identification of genetic risk factors for Parkinson's disease (PD) has been primarily focused on the gene-disruptive single nucleotide variants. In contrast, larger SVs, which may significantly influence human phenotypes, have been largely underexplored.

Pathogen non-planktonic phases within the urinary tract impact early infection and resistance evolution.

Treatment of urinary tract infections and the prevention of their recurrence is a pressing global health problem. In a urinary infection, pathogenic bacteria not only reside in the bladder lumen but also attach to and invade the bladder tissue. Planktonic, attached, and intracellular bacteria face different selection pressures from physiological processes such as micturition, immune response, and antibiotic treatment.

Assembly and Evaluation of a Confocal Microscopy Image Analysis Pipeline Useful in Revealing the Secrets of Plant-Fungal Interactions.

The ability of laser scanning confocal microscopy to generate high-contrast 2D and 3D images has become essential in studying plant-fungal interactions. Techniques such as visualization of native fluorescence, fluorescent protein tagging of microbes, green fluorescent protein (GFP)/red fluorescent protein (RFP)-fusion proteins, and fluorescent labeling of plant and fungal proteins have been widely used to aid in these investigations. Use of fluorescent proteins has several pitfalls, including variability of expression in planta and the requirement of gene transformation.

Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations.

The ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full-length transcript enrichment protocol with 5' CAP selection, we sequenced full-length RNA transcripts of 48 individuals from outbred populations and subspecies of , and from the closely related sister species and as outgroups.

Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.

Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited.