Pattern formation in the dipolar Ising model on a two-dimensional honeycomb lattice

We present Monte Carlo simulation results for a two-dimensional Ising model with ferromagnetic nearest-neighbor couplings and a competing long-range dipolar interaction on a honeycomb lattice. Both structural and thermodynamic properties are very similar to the case of a square lattice, with the exception that structures reflect the sixfold rotational symmetry of the underlying honeycomb lattice. To deal with the long-range nature of the dipolar interaction we also present a simple method of evaluating effective interaction coefficients, which can be regarded as a more straightforward alternative to the prevalent Ewald summation techniques.Comment: 5 pages, 5 figure

CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data

Cell-cell communication is essential for tissue development, regeneration and function, and its disruption can lead to diseases and developmental abnormalities. The revolution of single-cell genomics technologies offers unprecedented insights into cellular identities, opening new avenues to resolve the intricate cellular interactions present in tissue niches. CellPhoneDB is a bioinformatics toolkit designed to infer cell-cell communication by combining a curated repository of bona fide ligand-receptor interactions with a set of computational and statistical methods to integrate them with single-cell genomics data. Importantly, CellPhoneDB captures the multimeric nature of molecular complexes, thus representing cell-cell communication biology faithfully. Here we present CellPhoneDB v5, an updated version of the tool, which offers several new features. Firstly, the repository has been expanded by one-third with the addition of new interactions. These encompass interactions mediated by non-protein ligands such as endocrine hormones and GPCR ligands. Secondly, it includes a differentially expression-based methodology for more tailored interaction queries. Thirdly, it incorporates novel computational methods to prioritise specific cell-cell interactions, leveraging other single-cell modalities, such as spatial information or TF activities (i.e. CellSign module). Finally, we provide CellPhoneDBViz, a module to interactively visualise and share results amongst users. Altogether, CellPhoneDB v5 elevates the precision of cell-cell communication inference, ushering in new perspectives to comprehend tissue biology in both healthy and pathological states.Comment: 30 pages, 3 figures and 2 tables. Added previously missing figures and tables; Updated the reference for 'An integrated single-cell reference atlas of the human endometrium' pape

The phase diagram of the square lattice bilayer Hubbard model: a variational Monte Carlo study

We investigate the phase diagram of the square lattice bilayer Hubbard model at half-filling with the variational Monte Carlo method for both the magnetic and the paramagnetic case as a function of the interlayer hopping t\u3c4 and on-site Coulomb repulsion U. With this study we resolve some discrepancies in previous calculations based on the dynamical mean-field theory, and we are able to determine the nature of the phase transitions between metal, Mott insulator and band insulator. In the magnetic case we find only two phases: an antiferromagnetic Mott insulator at small t\u3c4 for any value of U and a band insulator at large t\u3c4 . At large U values we approach the Heisenberg limit. The paramagnetic phase diagram shows at small t\u3c4 a metal to Mott insulator transition at moderate U values and a Mott to band insulator transition at larger U values. We also observe a re-entrant Mott insulator to metal transition and metal to band insulator transition for increasing t\u3c4 in the range of 5.5t < U < 7.5t. Finally, we discuss the phase diagrams obtained in relation to findings from previous studies based on different many-body approaches.\ua9 2014 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft

Rab27a: A key to melanosome transport in human melanocytes

Normal pigmentation depends on the uniform distribution of melanin-containing vesicles, the melanosomes, in the epidermis. Griscelli syndrome (GS) is a rare autosomal recessive disease, characterized by an immune deficiency and a partial albinism that has been ascribed to an abnormal melanosome distribution. GS maps to 15q21 and was first associated with mutations in the myosin-V gene. However, it was demonstrated recently that GS can also be caused by a mutation in the Rab27a gene. These observations prompted us to investigate the role of Rab27a in melanosome transport. Using immunofluorescence and immunoelectron microscopy studies, we show that in normal melanocytes Rab27a colocalizes with melanosomes. In melanocytes isolated from a patient with GS, we show an abnormal melanosome distribution and a lack of Rab27a expression. Finally, reexpression of Rab27a in GS melanocytes restored melanosome transport to dendrite tips, leading to a phenotypic reversion of the diseased cells. These results identify Rab27a as a key component of vesicle transport machinery in melanocytes

Microphthalmia-associated transcription factor regulates RAB27A gene expression and controls melanosome transport.

Melanosomes are lysosome-related organelles specialized in melanin synthesis and transport. In this study, we show that microphthalmia-associated transcription factor (MITF) silencing induces melanosome gathering around the nucleus and causes the relocalization of Rab27A, Slac2a-Mlph, and Myo5a that control the transport of melanosomes on the actin network. In an attempt to elucidate the mechanism by which MITF controls melanosome distribution, we identify RAB27A as a new MITF target gene. Indeed, MITF silencing leads to a dramatic decrease in Rab27A expression and blocks the stimulation of Rab27A expression evoked by cAMP. Further, forced expression of MITF increases Rab27A expression, indicating that MITF is required and sufficient for Rab27A expression in melanoma cells. MITF binds to two E-boxes in the proximal region of the Rab27A promoter and stimulates its transcriptional activity. Finally, re-expression of Rab27A, in MITF-depleted cells, restores the transport of melanosomes to the cell periphery. These results show that RAB27A is a new direct transcriptional target of MITF and link MITF to melanosome transport, another key parameter of melanocyte differentiation and skin pigmentation. Interestingly, Rab27A is involved in other fundamental physiological functions, such as the transport of lytic granules and insulin secretion. Thus our results, deciphering the mechanism of Rab27A transcriptional regulation, have an interest that goes beyond the skin pigmentation field

MiRNA profiling of whole trabecular bone: identification of osteoporosis-related changes in MiRNAs in human hip bones

Background MicroRNAs (miRNAs) are important regulators of gene expression, with documented roles in bone metabolism and osteoporosis, suggesting potential therapeutic targets. Our aim was to identify miRNAs differentially expressed in fractured vs nonfractured bones. Additionally, we performed a miRNA profiling of primary osteoblasts to assess the origin of these differentially expressed miRNAs. Methods Total RNA was extracted from (a) fresh femoral neck trabecular bone from women undergoing hip replacement due to either osteoporotic fracture (OP group, n = 6) or osteoarthritis in the absence of osteoporosis (Control group, n = 6), matching the two groups by age and body mass index, and (b) primary osteoblasts obtained from knee replacement due to osteoarthritis (n = 4). Samples were hybridized to a microRNA array containing more than 1900 miRNAs. Principal component analysis (PCA) plots and heat map hierarchical clustering were performed. For comparison of expression levels, the threshold was set at log fold change > 1.5 and a p-value < 0.05 (corrected for multiple testing). Results Both PCA and heat map analyses showed that the samples clustered according to the presence or absence of fracture. Overall, 790 and 315 different miRNAs were detected in fresh bone samples and in primary osteoblasts, respectively, 293 of which were common to both groups. A subset of 82 miRNAs was differentially expressed (p < 0.05) between osteoporotic and control osteoarthritic samples. The eight miRNAs with the lowest p-values (and for which a validated miRNA qPCR assay was available) were assayed, and two were confirmed: miR-320a and miR-483-5p. Both were over-expressed in the osteoporotic samples and expressed in primary osteoblasts. miR-320a is known to target CTNNB1 and predicted to regulate RUNX2 and LEPR, while miR-483-5p down-regulates IGF2. We observed a reduction trend for this target gene in the osteoporotic bone. Conclusions We identified two osteoblast miRNAs over-expressed in osteoporotic fractures, which opens novel prospects for research and therapy