Application of advanced fluorescence microscopy to the structure of meiotic chromosomes

Chromosomes undergoing meiosis are defined by a macromolecular protein assembly called the synaptonemal complex which holds homologs together and carries out important meiotic functions. By retaining the molecular specificity, multiplexing ability, and in situ imaging capabilities of fluorescence microscopy, but with vastly increased resolution, 3D-SIM and other superresolution techniques are poised to make significant discoveries about the structure and function of the synaptonemal complex. This review discusses recent developments in this field and poses questions approachable with current and future technolog

The evolution of the star forming sequence in hierarchical galaxy formation models

It has been argued that the specific star formation rates of star forming galaxies inferred from observational data decline more rapidly below z = 2 than is predicted by hierarchical galaxy formation models. We present a detailed analysis of this problem by comparing predictions from the GALFORM semi-analytic model with an extensive compilation of data on the average star formation rates of star-forming galaxies. We also use this data to infer the form of the stellar mass assembly histories of star forming galaxies. Our analysis reveals that the currently available data favour a scenario where the stellar mass assembly histories of star forming galaxies rise at early times and then fall towards the present day. In contrast, our model predicts stellar mass assembly histories that are almost flat below z = 2 for star forming galaxies, such that the predicted star formation rates can be offset with respect to the observational data by factors of up to 2-3. This disagreement can be explained by the level of coevolution between stellar and halo mass assembly that exists in contemporary galaxy formation models. In turn, this arises because the standard implementations of star formation and supernova feedback used in the models result in the efficiencies of these process remaining approximately constant over the lifetime of a given star forming galaxy. We demonstrate how a modification to the timescale for gas ejected by feedback to be reincorporated into galaxy haloes can help to reconcile the model predictions with the data.Comment: 30 Pages, 16 Figures, MNRAS accepte

Telomeres act autonomously in maize to organize the meiotic bouquet from a semipolarized chromosome orientation

During meiosis, chromosomes undergo large-scale reorganization to allow pairing between homologues, which is necessary for recombination and segregation. In many organisms, pairing of homologous chromosomes is accompanied, and possibly facilitated, by the bouquet, the clustering of telomeres in a small region of the nuclear periphery. Taking advantage of the cytological accessibility of meiosis in maize, we have characterized the organization of centromeres and telomeres throughout meiotic prophase. Our results demonstrate that meiotic centromeres are polarized prior to the bouquet stage, but that this polarization does not contribute to bouquet formation. By examining telocentric and ring chromosomes, we have tested the cis-acting requirements for participation in the bouquet. We find that: (a) the healed ends of broken chromosomes, which contain telomere repeats, can enter the bouquet; (b) ring chromosomes enter the bouquet, indicating that terminal position on a chromosome is not necessary for telomere sequences to localize to the bouquet; and (c) beginning at zygotene, the behavior of telomeres is dominant over any centromere-mediated chromosome behavior. The results of this study indicate that specific chromosome regions are acted upon to determine the organization of meiotic chromosomes, enabling the bouquet to form despite large-scale changes in chromosome architecture

Nematode chromosomes

The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed

A machine learning approach to mapping baryons on to dark matter haloes using the eagle and C-EAGLE simulations

High-resolution cosmological hydrodynamic simulations are currently limited to relatively small volumes due to their computational expense. However, much larger volumes are required to probe rare, overdense environments, and measure clustering statistics of the large scale structure. Typically, zoom simulations of individual regions are used to study rare environments, and semi-analytic models and halo occupation models applied to dark matter only (DMO) simulations are used to study the Universe in the large-volume regime. We propose a new approach, using a machine learning framework to explore the halo-galaxy relationship in the periodic EAGLE simulations, and zoom C-EAGLE simulations of galaxy clusters. We train a tree based machine learning method to predict the baryonic properties of galaxies based on their host dark matter halo properties. The trained model successfully reproduces a number of key distribution functions for an infinitesimal fraction of the computational cost of a full hydrodynamic simulation. By training on both periodic simulations as well as zooms of overdense environments, we learn the bias of galaxy evolution in differing environments. This allows us to apply the trained model to a larger DMO volume than would be possible if we only trained on a periodic simulation. We demonstrate this application using the (800 Mpc)3 P-Millennium simulation, and present predictions for key baryonic distribution functions and clustering statistics from the EAGLE model in this large volume

Antibiotic resistant Shigella is a major cause of diarrhoea in the Highlands of Papua New Guinea

Introduction: Diarrhoea remains a major cause of illness in Papua New Guinea (PNG); however, little is known about its aetiology. As a result of the cholera outbreak that spread throughout PNG in 2009-2011, we conducted diarrhoeal surveillance in Eastern Highlands Province. Methodology: Following informed consent and a brief questionnaire, participants provided a stool sample or duplicate rectal swabs. Samples were tested for common bacterial pathogens Salmonella spp., Shigella spp., Vibrio spp., Campylobacter spp. and Yersinia enterocolitica using established culture methods. Enteric parasites were detected using microscopy. Results: A total of 216 participants were enrolled; where age was recorded, 42% were under 5 years of age, 6.7% were 5 to 17 years of age and 51.3% ≥18 years of age. One or more pathogens were detected in 68 (31.5%) participants, with Shigella (primarily S. flexneri) being the most commonly isolated (47 of 216 participants). Enteric parasites were detected in 23 of the 216 participants, occurring as a co-infection with another pathogen in 12 of 23 cases. No Vibrio cholerae was detected. Shigella isolates were commonly resistant to ampicillin, tetracycline, co-trimoxazole and chloramphenicol. Conclusions: Shigellae, specifically S. flexneri, are important pathogens in the highlands of PNG. While most studies in low-income settings focus on childhood aetiology, we have demonstrated the importance of Shigella in both children and adults. Enteric parasites remain present and presumably contribute to the burden of gastrointestinal illness. While improvements in sanitation and hygiene would help lower the burden of all aetiologies of infectious diarrhoea, additional control strategies targeting Shigella may also be warranted

Entanglement-enhanced probing of a delicate material system

Quantum metrology uses entanglement and other quantum effects to improve the sensitivity of demanding measurements. Probing of delicate systems demands high sensitivity from limited probe energy and has motivated the field's key benchmark-the standard quantum limit. Here we report the first entanglement-enhanced measurement of a delicate material system. We non-destructively probe an atomic spin ensemble by means of near-resonant Faraday rotation, a measurement that is limited by probe-induced scattering in quantum-memory and spin-squeezing applications. We use narrowband, atom-resonant NOON states to beat the standard quantum limit of sensitivity by more than five standard deviations, both on a per-photon and per-damage basis. This demonstrates quantum enhancement with fully realistic loss and noise, including variable-loss effects. The experiment opens the way to ultra-gentle probing of single atoms, single molecules, quantum gases and living cells.Comment: 7 pages, 8 figures; Nature Photonics, advance online publication, 16 December 201

Sequential peripheral enrichment of H2A.Zac and H3K9me2 during trophoblast differentiation in human embryonic stem cells

ES細胞分化過程において継時的に分布変化するヒストン修飾を同定 --ヒト幹細胞が分化する時、核では何が起こっているのか--. 京都大学プレスリリース. 2021-01-06.During the transition from pluripotency to a lineage-committed state, chromatin undergoes large-scale changes in structure, involving covalent modification of histone tails, use of histone variants and gene position changes with respect to the nuclear periphery. Here, using high-resolution microscopy and quantitative image analysis, we surveyed a panel of histone modifications for changes in nuclear peripheral enrichment during differentiation of human embryonic stem cells to a trophoblast-like lineage. We found two dynamic modifications at the nuclear periphery, acetylation of histone H2A.Z (H2A.Zac), and dimethylation of histone H3 at lysine 9 (H3K9me2). We demonstrate successive peripheral enrichment of these markers, with H2A.Zac followed by H3K9me2, over the course of 4 days. We find that H3K9me2 increases concomitantly with, but independently of, expression of lamin A, since deletion of lamin A did not affect H3K9me2 enrichment. We further show that inhibition of histone deacetylases causes persistent and increased H2A.Z acetylation at the periphery, delayed H3K9me2 enrichment and failure to differentiate. Our results show a concerted change in the nature of peripheral chromatin occurs upon differentiation into the trophoblast state

A unified multiwavelength model of galaxy formation

We present a new version of the GALFORM semi-analytical model of galaxy formation. This brings together several previous developments of GALFORM into a single unified model, including a different initial mass function (IMF) in quiescent star formation and in starbursts, feedback from active galactic nuclei supressing gas cooling in massive halos, and a new empirical star formation law in galaxy disks based on their molecular gas content. In addition, we have updated the cosmology, introduced a more accurate treatment of dynamical friction acting on satellite galaxies, and updated the stellar population model. The new model is able to simultaneously explain both the observed evolution of the K-band luminosity function and stellar mass function, and the number counts and redshift distribution of sub-mm galaxies selected at 850μm. This was not previously achieved by a single physical model within the ΛCDM framework, but requires having an IMF in starbursts that is somewhat top-heavy. The new model is tested against a wide variety of observational data covering wavelengths from the far-UV to sub-mm, and redshifts from z = 0 to z = 6, and is found to be generally successful. These observations include the optical and near-IR luminosity functions, HI mass function, fraction of early type galaxies, Tully-Fisher, metallicity-luminosity and size-luminosity relations at z = 0, as well as far-IR number counts, and far-UV luminosity functions at z ∼ 3 − 6. Discrepancies are however found in galaxy sizes and metallicities at low luminosities, and in the abundance of low mass galaxies at high-z, suggesting the need for a more sophisticated model of supernova feedback