A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity.

Background: In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).

Results: We achieved a haploid size of 940 megabase pairs (Mbp) for haplome 1 and 929 Mbp for haplome 2 with high scaffold N50 values of 36.

Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.

Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.

Tubulin tyrosination/detyrosination regulate the affinity and sorting of intraflagellar transport trains on axonemal microtubule doublets.

Cilia assembly and function rely on the bidirectional transport of components between the cell body and ciliary tip via Intraflagellar Transport (IFT) trains. Anterograde and retrograde IFT trains travel along the B- and A-tubules of microtubule doublets, respectively, ensuring smooth traffic flow. However, the mechanism underlying this segregation remains unclear.

Metabolic activities are selective modulators for individual segmentation clock processes.

Numerous cellular and molecular processes during embryonic development prompt the fundamental question of how their tempos are coordinated and whether a common global modulator exists. While the segmentation clock tempo scales with the kinetics of gene expression and degradation processes of the core clock gene Hes7 across mammals, the coordination of these processes remains unclear. This study examines whether metabolic activities serve as a global modulator for the segmentation clock, finding them to be selective instead.

Sciatic nerve analysis in thyroid hormone transporter Mct8 and Oatp1c1 knockout mice.

Objective: Mutations in the thyroid hormone (TH) transporter monocarboxylate transporter 8 (MCT8) cause Allan-Herndon-Dudley syndrome (AHDS), a severe form of psychomotor retardation with muscle hypoplasia and spastic paraplegia as key symptoms. These abnormalities have been attributed to an impaired TH transport across brain barriers and into neural cells thereby affecting brain development and function. Likewise, Mct8/Oatp1c1 (organic anion transporting polypeptide 1c1) double knockout (M/Odko) mice, a well-established murine AHDS model, display a strongly reduced TH passage into the brain as well as locomotor abnormalities.

Validation of a hypomorphic variant in CDK13 as the cause of CHDFIDD with autosomal recessive inheritance through determination of an episignature.

Autosomal dominant CDK13-related disease is characterized by congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (CHDFIDD). Heterozygous pathogenic variants, particularly missense variants in the kinase domain, have previously been described as disease causing. Using the determination of a methylation pattern and comparison with an established episignature, we reveal the first hypomorphic variant in the kinase domain of CDK13, leading to a never before described autosomal recessive form of CHDFIDD in a boy with characteristic features.

Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology.

Precision oncology offers new cancer treatment options, yet sequencing methods vary in type and scope. In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tissue DNA for germline assessment, from 20 patients with rare or advanced tumors, who were originally sequenced by WES/WGS ± TS within the DKFZ/NCT/DKTK MASTER program from 2015 to 2020. Molecular analyses resulted in a median number of 2.

The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos.

Anaphase is tightly controlled spatiotemporally to ensure proper separation of chromosomes. The mitotic spindle, the self-organized microtubule structure driving chromosome segregation, scales in size with the available cytoplasm. Yet, the relationship between spindle size and chromosome movement remains poorly understood.

Assembly of tight junction belts by ZO1 surface condensation and local actin polymerization.

Tight junctions play an essential role in sealing tissues, by forming belts of adhesion strands around cellular perimeters. Recent work has shown that the condensation of ZO1 scaffold proteins is required for tight junction assembly. However, the mechanisms by which junctional condensates initiate at cell-cell contacts and elongate around cell perimeters remain unknown.

RNA encodes physical information.

Most amino acids are encoded by multiple codons, making the genetic code degenerate. Synonymous mutations affect protein translation and folding, but their impact on RNA itself is often neglected. We developed a genetic algorithm that introduces synonymous mutations to control the diversity of structures sampled by an mRNA.

Motor Function of the Two-Component EEA1-Rab5 Revealed by dcFCCS.

Fluorescence correlation spectroscopy (FCS) enables the measurement of fluctuations at fast timescales (typically few nanoseconds) and with high spatial resolution (tens of nanometers). This single-molecule measurement has been used to characterize single-molecule transport and flexibility of polymers and biomolecules such as DNA and RNA. Here, we apply this technique as dual-color fluorescence cross-correlation spectroscopy (dcFCCS) to identify the motor function of the tethering protein EEA1 and the small GTPase Rab5 by probing the flexibility changes through end-monomer fluctuations.

Buckling by disordered growth.

Buckling instabilities driven by tissue growth underpin key developmental events such as the folding of the brain. Tissue growth is disordered due to cell-to-cell variability, but the effects of this variability on buckling are unknown. Here, we analyze what is perhaps the simplest setup of this problem: the buckling of an elastic rod with fixed ends driven by spatially varying, yet highly symmetric growth.

Loss of bimolecular reactions in reaction-diffusion master equations is consistent with diffusion limited reaction kinetics in the mean field limit.

We show that the resolution-dependent loss of bimolecular reactions in spatiotemporal Reaction-Diffusion Master Equations (RDMEs) is in agreement with the mean-field Collins-Kimball (C-K) theory of diffusion-limited reaction kinetics. The RDME is a spatial generalization of the chemical master equation, which enables studying stochastic reaction dynamics in spatially heterogeneous systems. It uses a regular Cartesian grid to partition space into locally well-mixed reaction compartments and treats diffusion as a jump reaction between neighboring grid cells.

PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms.

Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards proteins with high structural disorder content with focus on self-phase separating (driver) proteins. Here, we present a machine learning algorithm, PICNIC (Proteins Involved in CoNdensates In Cells) to classify proteins that localize to biomolecular condensates regardless of their role in condensate formation.

Empirical methods that provide physical descriptions of dynamic cellular processes.

We review empirical methods that can be used to provide physical descriptions of dynamic cellular processes during development and disease. Our focus will be nonspatial descriptions and the inference of underlying interaction networks including cell-state lineages, gene regulatory networks, and molecular interactions in living cells. Our overarching questions are: How much can we learn from just observing? To what degree is it possible to infer causal and/or precise mathematical relationships from observations? We restrict ourselves to data sets arising from only observations, or experiments in which minimal perturbations have taken place to facilitate observation of the systems as they naturally occur.

A Photo-Caged Cross-Linker for Identifying Protein-Protein Interactions.

Cross-linking mass spectrometry (XL-MS) has seen significant improvements which have enhanced its utility for studying protein-protein interactions (PPIs), primarily due to the emergence of novel crosslinkers and the development of streamlined analysis workflows. Nevertheless, poor membrane permeability and side reactions with water limit the extent of productive intracellular crosslinking events that can be achieved with current crosslinkers. To address these problems, we have synthesized a novel crosslinker with o-nitrobenzyl-based photoresponsive groups.

Optical characterization of molecular interaction strength in protein condensates.

Biomolecular condensates have been identified as a ubiquitous means of intracellular organization, exhibiting very diverse material properties. However, techniques to characterize these material properties and their underlying molecular interactions are scarce. Here, we introduce two optical techniques-Brillouin microscopy and quantitative phase imaging (QPI)-to address this scarcity.

A tuneable minimal cell membrane reveals that two lipid species suffice for life.

All cells are encapsulated by a lipid membrane that facilitates their interactions with the environment. How cells manage diverse mixtures of lipids, which dictate membrane property and function, is experimentally challenging to address. Here, we present an approach to tune and minimize membrane lipid composition in the bacterium Mycoplasma mycoides and its derived 'minimal cell' (JCVI-Syn3A), revealing that a two-component lipidome can support life.