Dictyostelium development shows a novel pattern of evolutionary conservation

von Baer\u27s law states that early stages of animal development are the most conserved. More recent evidence supports a modified hourglass pattern in which an early but somewhat later stage is most conserved. Both patterns have been explained by the relative complexity of either temporal or spatial interactions; the greatest conservation and lowest evolvability occur at the time of the most complex interactions, because these cause larger effects that are harder for selection to alter. This general kind of explanation might apply universally across independent multicellular systems, as supported by the recent finding of the hourglass pattern in plants. We use RNA-seq expression data from the development of the slime mold Dictyostelium to demonstrate that it does not follow either of the two canonical patterns but instead tends to show the strongest conservation and weakest evolvability late in development. We propose that this is consistent with a version of the spatial constraints model, modified for organisms that never achieve a high degree of developmental modularity

miRAS: a data processing system for miRNA expression profiling study

<p>Abstract</p> <p>Background</p> <p>The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studies try to discover new miRNAs and reveal the miRNA expression profile in cancer using a SAGE-based total RNA clone method. However, the data processing of this method is labor-intensive with several different biological databases and more than ten data processing steps involved.</p> <p>Results</p> <p>With miRAS, miRNAs and possible miRNA candidates contained in the submitted sequencing data were obtained together with their expression profile. The functions of known and predicted miRNAs were then analyzed by miRNA target prediction followed by target gene annotations. Finally, to extract the biological significance of the miRNAs in the samples, further annotations of the known miRNA and target genes were performed by collecting the public expression datasets of miRNA and target genes in normal and cancer tissues.</p> <p>Conclusion</p> <p>We introduce a web-based analysis platform called miRNA Analysis System (miRAS), for processing and analyzing of the sequence data obtained from the total RNA clone method. The system was built on generalizing the study of a liver cancer cell line total RNA sequencing project. miRAS is freely available on the web.</p

HiFi-123: Towards High-fidelity One Image to 3D Content Generation

Recent advances in text-to-image diffusion models have enabled 3D generation from a single image. However, current image-to-3D methods often produce suboptimal results for novel views, with blurred textures and deviations from the reference image, limiting their practical applications. In this paper, we introduce HiFi-123, a method designed for high-fidelity and multi-view consistent 3D generation. Our contributions are twofold: First, we propose a reference-guided novel view enhancement technique that substantially reduces the quality gap between synthesized and reference views. Second, capitalizing on the novel view enhancement, we present a novel reference-guided state distillation loss. When incorporated into the optimization-based image-to-3D pipeline, our method significantly improves 3D generation quality, achieving state-of-the-art performance. Comprehensive evaluations demonstrate the effectiveness of our approach over existing methods, both qualitatively and quantitatively

A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene

Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria\u27s host is a farmer clone of the social amoeba Dictyostelium discoideum that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of Pseudomonas fluorescens, only one of which serves as a food source. The other strain produces diffusible small molecules: pyrrolnitrin, a known antifungal agent, and a chromene that potently enhances the farmer\u27s spore production and depresses a nonfarmer\u27s spore production. Genome sequence and phylogenetic analyses identify a derived point mutation in the food strain that generates a premature stop codon in a global activator (gacA), encoding the response regulator of a two-component regulatory system. Generation of a knockout mutant of this regulatory gene in the nonfood bacterial strain altered its secondary metabolite profile to match that of the food strain, and also, independently, converted it into a food source. These results suggest that a single mutation in an inedible ancestral strain that served a protective role converted it to a domesticated food source

Amino Acid Repeats Cause Extraordinary Coding Sequence Variation in the Social Amoeba Dictyostelium discoideum

Protein sequences are normally the most conserved elements of genomes owing to purifying selection to maintain their functions. We document an extraordinary amount of within-species protein sequence variation in the model eukaryote Dictyostelium discoideum stemming from triplet DNA repeats coding for long strings of single amino acids. D. discoideum has a very large number of such strings, many of which are polyglutamine repeats, the same sequence that causes various human neurological disorders in humans, like Huntington's disease. We show here that D. discoideum coding repeat loci are highly variable among individuals, making D. discoideum a candidate for the most variable proteome. The coding repeat loci are not significantly less variable than similar non-coding triplet repeats. This pattern is consistent with these amino-acid repeats being largely non-functional sequences evolving primarily by mutation and drift

Robust Super-Resolution Imaging Based on a Ring Core Fiber with Orbital Angular Momentum

Single fiber imaging technology offers unique insights for research and inspection in difficult to reach and narrow spaces. In particular, ultra-compact multimode fiber (MMF) imaging, has received increasing interest over the past decade. However, MMF imaging will be seriously distorted when subjected to dynamic perturbations due to time-varying mode coupling, and the imaging of space objects via Gaussian beam will be relatively degraded at the edge due to insufficient contrast. Here, a robust super-resolution imaging method based on a ring core fiber (RCF) with orbital angular momentum (OAM) has been proposed and experimentally demonstrated. The OAM modes propagating in the RCF form a series of weakly-coupled mode groups, making our imaging system robust to external perturbations. In addition, a spiral phase plate is used as a vortex filter to produce OAM for edge enhancement, thus improving the image resolution. Furthermore, a few-shot U-Transformer neural network is proposed to enhance the resilience of the developed RCF-OAM imaging system against environmental perturbations. Finally, the developed RCF-OAM imaging system achieves biological image transmission, demonstrating the practicality of our scheme. This pioneering RCF OAM imaging system may have broad applications, potentially revolutionising fields such as biological imaging and industrial non-destructive testing

The Protective Effects of Ivabradine in Preventing Progression from Viral Myocarditis to Dilated Cardiomyopathy

To study the beneficial effects of ivabradine in dilated cardiomyopathy mice, which evolved from coxsackievirus B3-induced chronic viral myocarditis. Four-to-five-week-old male balb/c mice were inoculated intraperitoneally with coxsackievirus B3 (Strain Nancy) on day 1, day 14 and day 28. The day of the first virus inoculation was defined as day 1. Thirty-five days later, the surviving chronic viral myocarditis mice were divided randomly into two groups, a treatment group and an untreated group. Ivabradine was administered by gavage for 30 consecutive days in the treatment group, and the untreated group was administered normal saline. Masson’s trichrome stain was used to evaluate the fibrosis degree in myocardial tissue. The expression levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), Collagen I, Collagen III and p38-MAPK signaling pathway proteins were detected by western blot. Electrocardiogram was used to investigate the heart rate and rhythm. The thickness of the ventricular septum and left ventricular posterior wall, left ventricular end diastolic dimension, left ventricular end systolic dimension, left ventricular ejection fractions and fractional shortening were studied by echocardiography. Compared with the untreated chronic viral myocarditis mice, ivabradine significantly increased the survival rate, attenuated the myocardial lesions and fibrosis, improved the impairment of the left ventricular function, diminished the heart dimension, decreased the production of collagen I and collagen III, reduced the expression of the proinflammatory cytokines TNF-α, IL-1β, and IL-6, and lowered the production of phospho-p38MAPK. The findings indicate the therapeutic effect of ivabradine in preventing the progression from viral myocarditis to dilated cardiomyopathy in mice with chronic viral myocarditis induced by coxsackievirus B3, is associated with inhibition of the p38MAPK pathway, downregulated inflammatory responses and decreased collagen expression. Ivabradine appears a promising approach for the treatment of patients with viral myocarditis