Collective behaviors of animal groups may stem from visual lateralization-Tending to obtain information through one eye.

Animal groups exhibit various captivating movement patterns, which manifest as intricate interactions among group members. Several models have been proposed to elucidate collective behaviors in animal groups. These models achieve a certain degree of efficacy; however, inconsistent experimental findings suggest insufficient accuracy. Experiments have shown that some organisms employ a single information channel and visual lateralization to glean knowledge from other individuals in collective movements. In this study, we consider individuals' visual lateralization and a single information channel and develop a self-propelled particle model to describe the collective behavior of large groups. The results suggest that homogeneous visual lateralization gives the group a strong sense of cohesiveness, thereby enabling diverse collective behaviors. As the overlapping field grows, the cohesiveness gradually dissipates. Inconsistent visual lateralization among group members can reduce the cohesiveness of the group, and when there is a high degree of heterogeneity in visual lateralization, the group loses their cohesiveness. This study also examines the influence of visual lateralization heterogeneity on specific formations, and the results indicate that the directional migration formation is responsive to such heterogeneity. We propose an information network to portray the transmission of information within groups, which explains the cohesiveness of groups and the sensitivity of the directional migration formation.

Skeletal abnormalities in mice with Dnmt3a missense mutations.

Overgrowth and intellectual disability disorders in humans are typified by length/height and/or head circumference ≥ 2 standard deviations above the mean as well as intellectual disability and behavioral comorbidities, including autism and anxiety. Tatton-Brown-Rahman Syndrome is one type of overgrowth and intellectual disability disorder caused by heterozygous missense mutations in the DNA methyltransferase 3A (DNMT3A) gene. Numerous DNMT3A mutations have been identified in Tatton-Brown-Rahman Syndrome patients and may be associated with varying phenotype severities of clinical presentation. Two such mutations are the R882H and P904L mutations which result in severe and mild phenotypes, respectively. Mice with paralogous mutations (Dnmt3aP900L/+ and Dnmt3aR878H/+) exhibit overgrowth in their long bones (e.g., femur, humerus), but the mechanisms responsible for their skeletal overgrowth remain unknown. The goal of this study is to characterize skeletal phenotypes in mouse models of Tatton-Brown-Rahman Syndrome and identify potential cellular mechanisms involved in the skeletal overgrowth phenotype. We report that mature mice with the Dnmt3aP900L/+ or Dnmt3aR878H/+ mutation exhibit tibial overgrowth, cortical bone thinning, and weakened bone mechanical properties. Dnmt3aR878H/+ mutants also contain larger bone marrow adipocytes while Dnmt3aP900L/+ mutants show no adipocyte phenotype compared to control animals. To understand the potential cellular mechanisms regulating these phenotypes, growth plate chondrocytes, osteoblasts, and osteoclasts were assessed in juvenile mutant mice using quantitative static histomorphometry and dynamic histomorphometry. Tibial growth plates appeared thicker in mutant juvenile mice, but no changes were observed in osteoblast activity or osteoclast number in the femoral mid-diaphysis. These studies reveal new skeletal phenotypes associated with Tatton-Brown-Rahman Syndrome in mice and provide a rationale to extend clinical assessments of patients with this condition to include bone density and quality testing. These findings may be also informative for skeletal characterization of other mouse models presenting with overgrowth and intellectual disability phenotypes.

Programmable RNA 5-methylcytosine (m5C) modification of cellular RNAs by dCasRx conjugated methyltransferase and demethylase.

5-Methylcytosine (m5C), an abundant RNA modification, plays a crucial role in regulating RNA fate and gene expression. While recent progress has been made in understanding the biological roles of m5C, the inability to introduce m5C at specific sites within transcripts has hindered efforts to elucidate direct links between specific m5C and phenotypic outcomes. Here, we developed a CRISPR-Cas13d-based tool, named reengineered m5C modification system (termed 'RCMS'), for targeted m5C methylation and demethylation in specific transcripts. The RCMS editors consist of a nuclear-localized dCasRx conjugated to either a methyltransferase, NSUN2/NSUN6, or a demethylase, the catalytic domain of mouse Tet2 (ten-eleven translocation 2), enabling the manipulation of methylation events at precise m5C sites. We demonstrate that the RCMS editors can direct site-specific m5C incorporation and demethylation. Furthermore, we confirm their effectiveness in modulating m5C levels within transfer RNAs and their ability to induce changes in transcript abundance and cell proliferation through m5C-mediated mechanisms. These findings collectively establish RCMS editors as a focused epitranscriptome engineering tool, facilitating the identification of individual m5C alterations and their consequential effects.

Mechanisms by which sheep milk consumption ameliorates insulin resistance in high-fat diet-fed mice.

Sheep milk is rich in fat, protein, vitamins and minerals and is also one of the most important sources of natural bioactives. Several biopeptides in sheep milk have been reported to possess antibacterial, antiviral and anti-inflammatory properties, and they may prevent type 2 diabetes (T2D), disease and cancer. However, the precise mechanism(s) underlying the protective role of sheep milk against T2D development remains unclear. Therefore, in the current study, we investigated the effect of sheep milk on insulin resistance and glucose intolerance in high-fat diet (HFD)-fed mice, by conducting intraperitoneal glucose tolerance tests, metabolic cage studies, genomic sequencing, polymerase chain reaction, and biochemical assays. Hyperinsulinemic-euglycemic clamp-based experiments revealed that mice consuming sheep milk exhibited lower hepatic glucose production than mice in the control group. These findings further elucidate the mechanism by which dietary supplementation with sheep milk alleviates HFD-induced systemic glucose intolerance.

Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits.

Phenotypic heterogeneity in monogenic neurodevelopmental disorders can arise from differential severity of variants underlying disease, but how distinct alleles drive variable disease presentation is not well understood. Here, we investigate missense mutations in DNA methyltransferase 3A (DNMT3A), a DNA methyltransferase associated with overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity. We generate a Dnmt3aP900L/+ mouse mimicking a mutation with mild to moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. P900L mutants exhibit core growth and behavioral phenotypes shared across models but show subtle epigenomic changes, while R878H mutants display extensive disruptions. We identify mutation-specific dysregulated genes that may contribute to variable disease severity. Shared transcriptomic disruption identified across mutations overlaps dysregulation observed in other developmental disorder models and likely drives common phenotypes. Together, our findings define central drivers of DNMT3A disorders and illustrate how variable epigenomic disruption contributes to phenotypic heterogeneity in neurodevelopmental disease.

Correction: A spatial vaccination strategy to reduce the risk of vaccine-resistant variants.

[This corrects the article DOI: 10.1371/journal.pcbi.1010391.].

A strategy for Cas13 miniaturization based on the structure and AlphaFold.

The small size of the Cas nuclease fused with various effector domains enables a broad range of function. Although there are several ways of reducing the size of the Cas nuclease complex, no efficient or generalizable method has been demonstrated to achieve protein miniaturization. In this study, we establish an Interaction, Dynamics and Conservation (IDC) strategy for protein miniaturization and generate five compact variants of Cas13 with full RNA binding and cleavage activity comparable the wild-type enzymes based on a combination of IDC strategy and AlphaFold2. In addition, we construct an RNA base editor, mini-Vx, and a single AAV (adeno-associated virus) carrying a mini-RfxCas13d and crRNA expression cassette, which individually shows efficient conversion rate and RNA-knockdown activity. In summary, these findings highlight a feasible strategy for generating downsized CRISPR/Cas13 systems based on structure predicted by AlphaFold2, enabling targeted degradation of RNAs and RNA editing for basic research and therapeutic applications.

CircUTRN24/miR-483-3p/IGF-1 Regulates Autophagy Mediated Liver Fibrosis in Biliary Atresia.

Biliary atresia (BA) is a rare neonatal cholestatic disease that presents with a marked bile duct reaction and rapid fibrotic development. Our earlier research has shown that circUTRN24 is highly elevated in BA, but the exact molecular mechanism is still unknown. This study attempted to investigate whether circUTRN24 induces BA liver fibrosis through regulation of autophagy and to elucidate its molecular mechanism. Using TGF-ß-treated hepatic stellate cells (HSC) LX-2, we created a liver fibrosis model. qRT-PCR was used to analyze the expression of circUTRN24, miR-483-3p, and IGF-1. Western blot analysis was used to assess the expression of IGF-1, HSC activation-related proteins, and autophagy-related proteins. The TGF-ß-induced LX-2 cell fibrosis model was then supplemented with circUTRN24 siRNA, miR-483-3p mimics, and the autophagy activator Rapamycin, and functional rescue tests were carried out to investigate the role of circUTRN24, miR-483-3p, and autophagy in BA liver fibrosis. Using a luciferase reporter assay, a direct interaction between miR-483-3p and circUTRN24 or IGF-1 was discovered. With the increase of TGF-ß treatment concentration, circUTRN24 expression also gradually increased, as did HSC activation and autophagy-related protein. si-circUTRN24 significantly decreased circUTRN24 expression and inhibited HSC activation and autophagy, which was reversed by Rapamycin. Through bioinformatics prediction and validation, we found circUTRN24 might act through miR-483-3p targeting IGF-1 in the autophagy-related mTOR pathway. Furthermore, miR-483-3p mimics significantly increased miR-483-3p expression and inhibited HSC activation and autophagy, which were reversed by Rapamycin. Functional rescue experiments showed that si-circUTRN24 inhibited circUTRN24 and IGF-1 expressions and promoted miR-483-3p expression, while the miR-483-3p inhibitor abolished these effects. These findings imply that circUTRN24/miR-483-3p/IGF-1 axis mediated LX-2 cell fibrosis by regulating autophagy.

Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits.

Phenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.

Optimizing human α-galactosidase for treatment of Fabry disease.

Fabry disease is caused by a deficiency of α-galactosidase A (GLA) leading to the lysosomal accumulation of globotriaosylceramide (Gb3) and other glycosphingolipids. Fabry patients experience significant damage to the heart, kidney, and blood vessels that can be fatal. Here we apply directed evolution to generate more stable GLA variants as potential next generation treatments for Fabry disease. GLAv05 and GLAv09 were identified after screening more than 12,000 GLA variants through 8 rounds of directed evolution. Both GLAv05 and GLAv09 exhibit increased stability at both lysosomal and blood pH, stability to serum, and elevated enzyme activity in treated Fabry fibroblasts (19-fold) and GLA-/- podocytes (10-fold). GLAv05 and GLAv09 show improved pharmacokinetics in mouse and non-human primates. In a Fabry mouse model, the optimized variants showed prolonged half-lives in serum and relevant tissues, and a decrease of accumulated Gb3 in heart and kidney. To explore the possibility of diminishing the immunogenic potential of rhGLA, amino acid residues in sequences predicted to bind MHC II were targeted in late rounds of GLAv09 directed evolution. An MHC II-associated peptide proteomics assay confirmed a reduction in displayed peptides for GLAv09. Collectively, our findings highlight the promise of using directed evolution to generate enzyme variants for more effective treatment of lysosomal storage diseases.

Lilly's Technique for Delayed Hemorrhage After Choledochal Cyst Radical Surgery.

Background: Choledochal cysts (CCs) are characterized by dilations of the extra- and/or intrahepatic bile ducts. Surgery (cyst excision and Roux-en-Y hepaticojejunostomy) remains the gold standard for treatment. However, delayed hemorrhage can occur postoperatively, and although rare, it can be life-threatening. This study aimed to determine the risk factors and corresponding prevention of delayed hemorrhage after radical CC surgery, and to apply a technique to lower its incidence. Materials and Methods: This retrospective study enrolled 267 patients who received CC surgery between June 2016 and December 2020 at Shenzhen Children's Hospital. Univariate and multivariate logistic regression analyses were performed to identify risk factors for delayed hemorrhage. Results: Eleven (4.1%) patients had delayed hemorrhage after laparoscopic radical surgery. The most common hemorrhage site was the dissected surface between the cyst and adjacent structures with chronic severe adhesions, postoperatively. The occurrence of recurrent CC-associated complication and excessive total blood loss during surgery were risk factors for delayed hemorrhage after CC radical surgery. Length of disease course, operation when cholangitis/pancreatitis still existed, cyst diameter, and application of trypsin inhibitor after the surgery were not significantly different between the two groups. Conclusion: For patients without adhesions, complete cyst resection is the gold standard. However, for those with intensive adhesions, in cases of delayed hemorrhage on the dissection surface and malignancy transformation risk, the Lilly's technique with Roux-en-Y hepaticojejunostomy could be an alternative.

Interaction between human leukocyte antigen (HLA-C) and killer cell Ig-like receptors (KIR2DL) inhibits the cytotoxicity of natural killer cells in patients with hepatoblastoma.

Background: Hepatoblastoma (HB) is the most common liver malignancy in childhood with poor prognosis and lack of effective therapeutic targets. Single-cell transcriptome sequencing technology has been widely used in the study of malignant tumors, which can understand the tumor microenvironment and tumor heterogeneity. Materials and methods: Two children with HB and a healthy child were selected as the research subjects. Peripheral blood and tumor tissue were collected for single-cell transcriptome sequencing, and the sequencing data were compared and analyzed to describe the differences in the immune microenvironment between children with HB and normal children. Results: There were significant differences in the number and gene expression levels of natural killer cells (NK cells) between children with HB and normal children. More natural killer cells were seen in children with HB compared to normal control. KIR2DL were highly expressed in children with HB. Conclusion: Single-cell transcriptome sequencing of peripheral blood mononuclear cells (PBMC) and tumor tissue from children with HB revealed that KIR2DL was significantly up-regulated in NK cells from children with HB. HLA-C molecules on the surface of tumor cells interact with inhibitory receptor KIR2DL on the surface of NK cells, inhibiting the cytotoxicity of NK cells, resulting in immune escape of tumors. Inhibitors of related immune checkpoints to block the interaction between HLA-C and KIR2DL and enhance the cytotoxicity of NK cells, which may be a new strategy for HB treatment.

Maize Lodging Resistance with Plastic Film Removal, Increased Planting Density, and Cultivars with Different Maturity Periods.

While plastic film mulching and proper high-density planting are important methods that can improve maize yield, years of accumulated residual film have created soil pollution and degraded soil, and thus has impeded sustainable agriculture development. Here, we compared the stalk and root lodging resistances of three maize cultivars grown at two planting densities both with (FM) and without (NM) plastic film mulch. Our aim was to provide a theoretical basis that may help assure a future of successful no-film planting with increased planting density. The results showed that, compared with FM, the average dry weight per unit length and bending strength of basal internode decreased for all cultivars at both planting densities in the NM treatment. At 9.0 × 104 plants ha-1, the stalk breaking force (SFC) of Xinyu77, KWS9384, and KWS2030 in the NM treatment decreased by 4%, 21%, and 22%, respectively. At 12.0 × 104 plants ha-1, SFC of Xinyu77 and KWS2030 increased by 14% and 1%, respectively, while KWS9384 decreased by 10%. Additionally, the root diameter, length, volume, width, depth, and the vertical root-pulling force of maize decreased. Although the lodging resistance of maize grown without film mulch was lower than that of maize grown with it, those adverse effects can be mitigated by selecting suitable cultivars and by using proper high-density planting and appropriate cultivation measures.

Epidemic spreading under mutually independent intra- and inter-host pathogen evolution.

The dynamics of epidemic spreading is often reduced to the single control parameter R0 (reproduction-rate), whose value, above or below unity, determines the state of the contagion. If, however, the pathogen evolves as it spreads, R0 may change over time, potentially leading to a mutation-driven spread, in which an initially sub-pandemic pathogen undergoes a breakthrough mutation. To predict the boundaries of this pandemic phase, we introduce here a modeling framework to couple the inter-host network spreading patterns with the intra-host evolutionary dynamics. We find that even in the extreme case when these two process are driven by mutually independent selection forces, mutations can still fundamentally alter the pandemic phase-diagram. The pandemic transitions, we show, are now shaped, not just by R0, but also by the balance between the epidemic and the evolutionary timescales. If mutations are too slow, the pathogen prevalence decays prior to the appearance of a critical mutation. On the other hand, if mutations are too rapid, the pathogen evolution becomes volatile and, once again, it fails to spread. Between these two extremes, however, we identify a broad range of conditions in which an initially sub-pandemic pathogen can breakthrough to gain widespread prevalence.

Distinct spreading patterns induced by coexisting channels in information spreading dynamics.

In modern society, new communication channels and social platforms remarkably change the way of people receiving and sharing information, but the influences of these channels on information spreading dynamics have not been fully explored, especially in the aspects of outbreak patterns. To this end, based on a susceptible-accepted-recovered model, we examined the outbreak patterns of information spreading in a two-layered network with two coexisting channels: the intra-links within a layer and the inter-links across layers. Depending on the inter-layer coupling strength, i.e., average node degree and transmission probability between the two layers, we observed three different spreading patterns: (i) a localized outbreak with weak inter-layer coupling, (ii) two peaks with a time-delay outbreak appear for an intermediate coupling, and (iii) a synchronized outbreak for a strong coupling. Moreover, we showed that even though the average degree between the two layers is small, a large transmission probability still can compensate and promote the information spread from one layer to another, indicating by that the critical average degree decreases as a power law with transmission probability between the two layers. Additionally, we found that a large gap closed to the critical inter-layer average degree appears in the phase space of theoretical analysis, which indicates the emergence of a global large-scope outbreak. Our findings may, therefore, be of significance for understanding the outbreak behaviors of information spreading in real world.

A spatial vaccination strategy to reduce the risk of vaccine-resistant variants.

The COVID-19 pandemic demonstrated that the process of global vaccination against a novel virus can be a prolonged one. Social distancing measures, that are initially adopted to control the pandemic, are gradually relaxed as vaccination progresses and population immunity increases. The result is a prolonged period of high disease prevalence combined with a fitness advantage for vaccine-resistant variants, which together lead to a considerably increased probability for vaccine escape. A spatial vaccination strategy is proposed that has the potential to dramatically reduce this risk. Rather than dispersing the vaccination effort evenly throughout a country, distinct geographic regions of the country are sequentially vaccinated, quickly bringing each to effective herd immunity. Regions with high vaccination rates will then have low infection rates and vice versa. Since people primarily interact within their own region, spatial vaccination reduces the number of encounters between infected individuals (the source of mutations) and vaccinated individuals (who facilitate the spread of vaccine-resistant strains). Thus, spatial vaccination may help mitigate the global risk of vaccine-resistant variants.

Fucosyltransferase 2: A Genetic Risk Factor for Intestinal Diseases.

The fucosyltransferase 2 gene (FUT2) mediates the synthesis of histoblood group antigens (HBGA) that occur in vivo from multiple organs, particularly on the surface of intestinal epithelial cells and body fluids. To date, many studies have demonstrated that the interaction of HBGA with the host microbiota is the cause of pathogenesis of intestinal diseases, making FUT2 non-secretor a risk factor for inflammatory bowel disease (IBD) due to the lack of HBGA. As HBGA also acts as an attachment site for norovirus (NoV) and rotavirus (RV), the non-secretor becomes a protective factor for both viral infections. In addition, the interaction of norovirus and rotavirus with symbiotic bacteria has been found to play an important role in regulating enteroviral infection in IBD. Given the current incomplete understanding of the complex phenomenon and the underlying pathogenesis of intestinal diseases such as IBD, it has recently been hypothesized that the FUT2 gene regulates intestinal bacteria through attachment sites, may help to unravel the role of FUT2 and intestinal flora in the mechanism of intestinal diseases in the future, and provide new ideas for the prevention and treatment of intestinal diseases through more in-depth studies.

A chemoenzymatic strategy for site-selective functionalization of native peptides and proteins.

The emergence of new therapeutic modalities requires complementary tools for their efficient syntheses. Availability of methodologies for site-selective modification of biomolecules remains a long-standing challenge, given the inherent complexity and the presence of repeating residues that bear functional groups with similar reactivity profiles. We describe a bioconjugation strategy for modification of native peptides relying on high site selectivity conveyed by enzymes. We engineered penicillin G acylases to distinguish among free amino moieties of insulin (two at amino termini and an internal lysine) and manipulate cleavable phenylacetamide groups in a programmable manner to form protected insulin derivatives. This enables selective and specific chemical ligation to synthesize homogeneous bioconjugates, improving yield and purity compared to the existing methods, and generally opens avenues in the functionalization of native proteins to access biological probes or drugs.

Amplified signal response by cluster synchronization competition in rings with short-distance couplings.

Topological resonance has been revealed in degree-heterogeneous scale-free networks for weak signal amplification, but not in degree-homogeneous all-to-all networks [Acebrón et al., Phys. Rev. Lett. 99, 128701 (2007)0031-900710.1103/PhysRevLett.99.128701]. Here, we show that when the coupling distance of the all-to-all networks is reduced from global to local, i.e., converting all-to-all networks into rings, we can observe a resonant response to a weak signal similar to scale-free networks. We find that such a resonance effect induced by ring topology is robust across a wide range of ring sizes and signal frequencies. We further show that at intermediate coupling strength, oscillators in the rings can form separate synchronous clusters that compete with each other, resulting in large amplitude oscillations of boundary nodes between clusters and thus giving rise to the resonant signal amplification. Finally, we propose a structure of a three-node feed-forward motif simplified from the observed cluster synchronization competition to analyze the mechanism underlying the resonance behavior, which corresponds well with the numerical results.

Role of lurkers in threshold-driven information spreading dynamics.

The threshold model as a classical paradigm for studying information spreading processes has been well studied. The main focuses are on how the underlying social network structure or the size of initial seeds can affect the cascading dynamics. However, the influence of node characteristics has been largely ignored. Here, inspired by empirical observations, we extend the threshold model by taking into account lurking nodes, who rarely interact with their neighbors. In particular, we consider two different scenarios: (i) Lurkers are absolutely silent and never interact with others and (ii) lurkers intermittently interact with their neighborhood with an activity rate p. In the first case, we demonstrate that lurkers may reduce the effective average degree of the underlying network, playing a dual role in spreading dynamics. In the latter case, we find that the stochastic dynamic behavior of lurkers could significantly promote the spread of information. Concretely, slightly raising the activity rate p of lurkers may result in a remarkable increase in the final cascade size. Further increasing p could make nodes become more stable on average, while it is still easy to observe global cascades due to the fluctuations of the effective degree of nodes.