Bif­1 inhibits activation of inflammasome through autophagy regulatory mechanism.

Inflammasome activation is a crucial mechanism in inflammatory responses. Bax­interacting factor 1 (Bif­1) is required for the normal formation of autophagosomes, but its ability to exert an inflammatory regulatory effect remains unclear. The aim of the present study was to explore the role of Bif­1 in inflammation, possibly mediated through autophagy regulation. Using a lipopolysaccharide (LPS)/adenosine triphosphate (ATP)­induced inflammatory model in J774A.1 cells, the effect of Bif­1 on inflammasome activation and the underlying mechanisms involving autophagy regulation were investigated. Elevated levels of NLR family pyrin domain containing protein 3 inflammasome and interleukin­1ß (IL­1ß) proteins were observed in J774A.1 cells after LPS/ATP induction. Furthermore, Bif­1 and autophagy activity were significantly upregulated in inflammatory cells. Inhibition of autophagy resulted in inflammasome activation. Silencing Bif­1 expression significantly upregulated IL­1ß levels and inhibited autophagy activity, suggesting a potential anti­inflammatory role of Bif­1 mediated by autophagy. Additionally, inhibition of the nuclear factor­κB (NF­κB) signaling pathway downregulated Bif­1 and inhibited autophagy activity, highlighting the importance of NF­κB in the regulation of Bif­1 and autophagy. In summary, the current study revealed that Bif­1 is a critical anti­inflammatory factor against inflammasome activation mediated by a mechanism of autophagy regulation, indicating its potential as a therapeutic target for inflammatory regulation.

Evolution of schooling drives changes in neuroanatomy and motion characteristics across predation contexts in guppies.

One of the most spectacular displays of social behavior is the synchronized movements that many animal groups perform to travel, forage and escape from predators. However, elucidating the neural mechanisms underlying the evolution of collective behaviors, as well as their fitness effects, remains challenging. Here, we study collective motion patterns with and without predation threat and predator inspection behavior in guppies experimentally selected for divergence in polarization, an important ecological driver of coordinated movement in fish. We find that groups from artificially selected lines remain more polarized than control groups in the presence of a threat. Neuroanatomical measurements of polarization-selected individuals indicate changes in brain regions previously suggested to be important regulators of perception, fear and attention, and motor response. Additional visual acuity and temporal resolution tests performed in polarization-selected and control individuals indicate that observed differences in predator inspection and schooling behavior should not be attributable to changes in visual perception, but rather are more likely the result of the more efficient relay of sensory input in the brain of polarization-selected fish. Our findings highlight that brain morphology may play a fundamental role in the evolution of coordinated movement and anti-predator behavior.

Glucolipid metabolism improvement in impaired glucose tolerance subjects consuming a Quinoa-based diet: a randomized parallel clinical trial.

Purpose: To investigate the effects of quinoa on glucose and lipid metabolism, and the prognosis in people with impaired glucose tolerance. Methods: One hundred and thirty-eight patients diagnosed with impaired glucose tolerance following a glucose tolerance test in Guangzhou Cadre Health Management Center were selected and randomly divided into quinoa intervention and control groups, according to the digital table method. After 1 year of follow-up, the differences in blood glucose, blood lipid, glycosylated hemoglobin and other indicators were compared. The disease prognosis between the two groups was also compared. Results: The 2 h postprandial blood glucose, glycosylated hemoglobin, insulin resistance index, total cholesterol, low-density lipoprotein cholesterol, body mass index, waist circumference, systolic and diastolic blood pressure after intervention in the quinoa group were significantly lower than before intervention. In contrast, high-density lipoprotein cholesterol was higher than before intervention and is statistically significant (p < 0.05). After 1 year of follow-up, the control group's glycosylated hemoglobin and body mass index are higher than before intervention, and are statistically significant (p < 0.05). The 2 h postprandial blood glucose, glycosylated hemoglobin, insulin resistance index, body mass index, and mean diastolic blood pressure in the quinoa group are statistically significantly lower than in the control group, while high-density lipoprotein cholesterol is higher (p < 0.05). The rate of conversion to diabetes for participants in the quinoa group (7.8%) is statistically significantly lower than in the control group (20.3%) (χ2 = 12.760, p = 0.002). Logistic regression analysis showed that quinoa consumption is a protective factor against delaying the progression of diabetes (p < 0.05). Conclusion: Adding quinoa to staple food intake can reduce postprandial blood glucose, and improve lipid metabolism and insulin resistance, delaying the progression of diabetes in people with impaired glucose tolerance.

Statistical genetics in and out of quasi-linkage equilibrium.

This review is about statistical genetics, an interdisciplinary topic between statistical physics and population biology. The focus is on the phase ofquasi-linkage equilibrium(QLE). Our goals here are to clarify under which conditions the QLE phase can be expected to hold in population biology and how the stability of the QLE phase is lost. The QLE state, which has many similarities to a thermal equilibrium state in statistical mechanics, was discovered by M Kimura for a two-locus two-allele model, and was extended and generalized to the global genome scale byNeher&Shraiman (2011). What we will refer to as the Kimura-Neher-Shraiman theory describes a population evolving due to the mutations, recombination, natural selection and possibly genetic drift. A QLE phase exists at sufficiently high recombination rate (r) and/or mutation ratesµwith respect to selection strength. We show how in QLE it is possible to infer the epistatic parameters of the fitness function from the knowledge of the (dynamical) distribution of genotypes in a population. We further consider the breakdown of the QLE regime for high enough selection strength. We review recent results for the selection-mutation and selection-recombination dynamics. Finally, we identify and characterize a new phase which we call the non-random coexistence where variability persists in the population without either fixating or disappearing.

Variation of glomalin-metal binding capacity in 1 m soil profiles from mangrove forests to mudflat and affected factor analysis.

Glomalin-related soil protein (GRSP) plays an important role in soil metal sequestration in coastal wetlands. Additionally, it can release dissolved organic matter (GDOM) in water-soaked condition. The purpose of this study was to clarify the variation of GRSP's heavy metal immobilisation capacity at soil profiles of coastal wetland, and explore the compositional characteristics of GDOM and its influence on the heavy metals' environmental behaviour. The results indicated that the metal immobilisation capacity of GRSP decreased with increasing burial depth. The contributions of GRSP to soil Cr, As, and Pb were higher in both mangrove soils (K. obovata and A. marina forests) than in the mudflat. Oxygen-containing functional groups of GRSP (CO, -COO-, etc.) played a positive role in heavy metals accumulation. Redundancy analysis (RDA) showed that high soil pH was not conducive to the enrichment of heavy metals by GRSP. Besides, the concentrations of GRSP-Fe showed a significant positive correlation with the concentrations of other metals (Cu, As, and Pb) in GRSP. It is speculated that the Fe minerals in GRSP contributed the enrichment of heavy metals. Based on PARAFAC modelling, four fluorescent components of GDOM were identified, including three humic-like fluorescent components and one tyrosine-like fluorescent component. The contributions of GDOM to GRSP-bound heavy metals fluctuated between 4.05 % and 88.80 %, which could enhance the fluidity of heavy metals in water and weaken the soil heavy metal immobilisation capacity of GRSP. High salinity exerted an inhibitory effect on the heavy metal content of the GDOM. This study comprehensively explored the potential of GRSP to immobilise heavy metals in wetland soils and highlighted the potential heavy metal risks associated with the GDOM component in water, which could contribute to the multidimensional assessment and control of heavy metal pollution in coastal wetlands.

Temporal epistasis inference from more than 3 500 000 SARS-CoV-2 genomic sequences.

We use direct coupling analysis (DCA) to determine epistatic interactions between loci of variability of the SARS-CoV-2 virus, segmenting genomes by month of sampling. We use full-length, high-quality genomes from the GISAID repository up to October 2021 for a total of over 3 500 000 genomes. We find that DCA terms are more stable over time than correlations but nevertheless change over time as mutations disappear from the global population or reach fixation. Correlations are enriched for phylogenetic effects, and in particularly statistical dependencies at short genomic distances, while DCA brings out links at longer genomic distance. We discuss the validity of a DCA analysis under these conditions in terms of a transient auasilinkage equilibrium state. We identify putative epistatic interaction mutations involving loci in spike.

Exogenous Betaine Enhances the Protrusion Vigor of Rice Seeds under Heat Stress by Regulating Plant Hormone Signal Transduction and Its Interaction Network.

Rice is an important food crop. Rice seedlings are mainly composed of root, coleoptile, mesocotyl and euphylla. The elongation of coleoptile and mesocotyl promotes the emergence of rice seedlings. Therefore, analyzing the mechanism of coleoptile and mesocotyl elongation is important for the cultivation of rice varieties. Due to global warming, heat stress is threatening rice yields. Betaine plays an important role in plant resistance to heat stress; however, we lack research on its regulation mechanism of rice seed germination under heat stress. Therefore, we explored the effects of soaking seeds with betaine at different concentrations on rice seed germination under heat stress. According to the results, soaking seeds with 10 mM of betaine could effectively improve the seeds' germination potential and rate under heat stress to promote the germination of rice seeds. To clarify the mitigation mechanism of betaine in heat stress, we measured the antioxidant enzyme activity, malondialdehyde content, soluble protein content and endogenous hormone content of seed protrusion under heat stress. We constructed the cDNA library for transcriptome sequencing. According to the results, 10 mM of betaine improved the activities of the superoxide dismutase, peroxidase and catalase of seed protrusion under heat stress to reduce the malondialdehyde content and increase the soluble protein content to alleviate the effect of heat stress on rice seed germination. The detection of the endogenous hormone content showed that soaking seeds with 10 mM of betaine increased the content of gibberellin and decreased the contents of auxin and abscisic acid of seed protrusion under heat stress. According to the transcriptome analysis, betaine can induce the expressions of key genes in the biosynthesis and metabolism of auxin, abscisic acid and gibberellins in the seed coleoptile and mesocotyl elongation stage, regulate the signal transduction of three hormones and promote the germination of rice seeds under heat stress. This study revealed, for the first time, the physiological and molecular regulation mechanism of betaine promotion of seed germination under heat stress.

Extrachromosomal Circular DNA: A New Target in Cancer.

Genomic instability and amplification are intrinsically important traits determining the development and heterogeneity of tumors. The role of extrachromosomal circular DNA (eccDNA) in tumors has recently been highlighted. EccDNAs are unique genetic materials located off the chromosomal DNA. They have been detected in a variety of tumors. This review analyzes the mechanisms involved in the formation of eccDNAs and their genetic characteristics. In addition, the high-copy number and transcriptional levels of oncogenes located in eccDNA molecules contribute to the acceleration of tumor evolution and drug resistance and drive the development of genetic heterogeneity. Understanding the specific genomic forms of eccDNAs and characterizing their potential functions will provide new strategies for tumor therapy. Further research may yield new targets and molecular markers for the early diagnosis and treatment of human cancer.

Switchable Interlayer Magnetic Coupling of Bilayer CrI3.

Due to the weak van der Waals (vdW) interlayer interaction, interfacial geometry of two-dimensional (2D) magnetic vdW materials can be freely assembled, and the stacking order between layers can be readily controlled, such as laterally shifting or rotating, which may trigger the variation of magnetic order. We investigate the H-type bilayer CrI3 where the two layers are aligned in anti-parallel directions. Based on first-principles calculations, we propose two states with different interlayer magnetic couplings, i.e., ferromagnetic and antiferromagnetic, and analyze the superexchange mechanism inside. It is found that the two magnetic coupling states are stacking-dependent, and could be switched by applying out-of-plane axial strain and electron doping. Our findings show great application potential in the design of heterostructural and spintronic devices based on 2D magnetic vdW materials.

Electrically controlled spin reversal and spin polarization of electronic transport in nanoporous graphene nanoribbons.

Based on first-principles calculations, the spin-dependent electronic transport of nanoporous graphene nanoribbons is investigated. A three-terminal configuration is proposed, which can electronically control the spin polarization of transmission, instead of magnetic methods. By modulating the gate voltage, not only could the transmission be switched between completely spin up and spin down polarized states to realize a dual-spin filter, but also the spin polarization could be finely tuned between 100% and -100%. Any ratio of spin up to spin down transport electrons can be realized, providing more possibilities for the design of nanoelectronic devices. Further analysis shows that the transmission spectra, with two distinct transmission peaks with opposite spins around EF, are the key point, which are contributed by p orbitals. And such a phenomenon is robust to the width and length of the nanoporous graphene nanoribbons, suggesting that it is an intrinsic feature of these systems. The electrical control on spin polarization is realized in pure-carbon systems, showing great application potential.

Rapid evolution of coordinated and collective movement in response to artificial selection.

Collective motion occurs when individuals use social interaction rules to respond to the movements and positions of their neighbors. How readily these social decisions are shaped by selection remains unknown. Through artificial selection on fish (guppies, Poecilia reticulata) for increased group polarization, we demonstrate rapid evolution in how individuals use social interaction rules. Within only three generations, groups of polarization-selected females showed a 15% increase in polarization, coupled with increased cohesiveness, compared to fish from control lines. Although lines did not differ in their physical swimming ability or exploratory behavior, polarization-selected fish adopted faster speeds, particularly in social contexts, and showed stronger alignment and attraction responses to multiple neighbors. Our results reveal the social interaction rules that change when collective behavior evolves.

Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes.

Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to deeper understanding of microbial pathogenesis. We have considered all complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes deposited in the Global Initiative on Sharing All Influenza Data (GISAID) repository until four different cutoff dates, and used direct coupling analysis together with an assumption of quasi-linkage equilibrium to infer epistatic contributions to fitness from polymorphic loci. We find eight interactions, of which three are between pairs where one locus lies in gene ORF3a, both loci holding nonsynonymous mutations. We also find interactions between two loci in gene nsp13, both holding nonsynonymous mutations, and four interactions involving one locus holding a synonymous mutation. Altogether, we infer interactions between loci in viral genes ORF3a and nsp2, nsp12, and nsp6, between ORF8 and nsp4, and between loci in genes nsp2, nsp13, and nsp14. The paper opens the prospect to use prominent epistatically linked pairs as a starting point to search for combinatorial weaknesses of recombinant viral pathogens.

Sustained Release of Magnesium Ions Mediated by a Dynamic Mechanical Hydrogel to Enhance BMSC Proliferation and Differentiation.

Hydrogel scaffolds are promising and widely applicable platforms for various therapeutic agents to facilitate bone tissue regeneration due to their biocompatibility and low immunogenicity. Nevertheless, the improvement of local administration efficiency and on-demand release of drugs from a hydrogel system is still an obstacle. In this work, we reported that a novel injectable hydrogel system was fabricated based on coordination of multiarm thiolated polyethylene glycol (PEG-SH) and magnesium ions for bone marrow-derived mesenchymal stem cell (BMSC) proliferation and differentiation. The dynamic nature coordination bond of Mg-S and the dynamic disulfide bond of S-S provide hydrogels with good mechanical performance and typical rheological behavior and thus endow the hydrogels with a satisfactory swelling rate and degradation property. Mg2+ was incorporated in the system not only to act as an effective cross-linker to enhance the hydrogel network structure but also to mediate the sustained release of Mg2+. Due to the controlled release of Mg2+, the PEG-SH/Mg2+ hydrogel can effectively improve BMSC proliferation and osteoblastic activity via the PI3K/Akt/GSK3ß/ß-catenin signal pathway in vitro. These findings indicated that the novel hydrogel controlled release of a Mg2+ ion is viewed as a promising and flexible platform for bone regeneration clinically.

Electrically precise control of the spin polarization of electronic transport at the single-molecule level.

Compared with the conventional magnetic means (such as ferromagnetic contacts), controlling a spin current by electrical methods could largely reduce the energy consumption and dimensions of nano-devices, which has become a focus of research in spintronics. Inspired by recent progress in the synthesis of an iron-based metal-organic nanostructure, we investigate the spin-dependent electronic transport of the molecule of Fe3-terpyridine-phenyl-phenyl-terpyridine-Fe3 (Fe3-TPPT-Fe3) through first-principles calculations, and propose a three-terminal device without ferromagnetics. By applying a gate voltage, not only the spin polarization can be switched between 100% and -100% to achieve a dual-spin filter, but also its fine regulation can be realized, where the transmission with any ratio of spin-up to spin-down electron numbers is achievable. Analysis shows that the particular transmission spectra are the key mechanism, where two peaks reside discretely on both sides of the Fermi level with opposite spins. Such a feature is found to be robust to the number of Fe atoms and TPPT chain length, suggesting that it is an intrinsic feature of such systems and very conducive to practical applications. The electrical control (such as an electric field) of spin polarization is realized at the single-molecule level, showing great application potential.

Inferring genetic fitness from genomic data.

The genetic composition of a naturally developing population is considered as due to mutation, selection, genetic drift, and recombination. Selection is modeled as single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). The problem is posed to infer epistatic fitness from population-wide whole-genome data from a time series of a developing population. We generate such data in silico and show that in the quasilinkage equilibrium phase of Kimura, Neher, and Shraiman, which pertains at high enough recombination rates and low enough mutation rates, epistatic fitness can be quantitatively correctly inferred using inverse Ising-Potts methods.

Edge-modulated dual spin-filter effect in zigzag-shaped buckling Ag2S nanoribbons.

Unlike MoS2, single-layered Ag2S nanoribbons (Ag2SNRs) exhibit a nonmetal-shrouded and a zigzag-shaped buckling structure and possess two distinct edges, S- or Ag-terminated ones. By performing first principle calculations, the spin-dependent electron transport of Ag2SNRs in a ferromagnetic state has been investigated. It is found that the SS- and AgAg-terminated Ag2SNRs exhibit semi-metallic characteristics, but with opposite spin-polarized directions. And AgS-terminated ones show metallic characteristics, but with completely spin-unpolarized transmission. That is to say, all three states, i.e., spin up polarized, spin down polarized and spin unpolarized ones, could be achieved by modulating the edge geometry. Further analysis shows that, the spatial separation on edges of the energy states with different spins around EF is responsible for the switch in the three states. The system could operate as a dual spin-filter, and the direction of the spin polarization can be switched by the edge morphology. Furthermore, calculations show that such a phenomenon is robust to the width of the ribbon and strain, showing great application potential.

Edge morphology induced rectifier diode effect in C3N nanoribbon.

The two-dimensional material C3N has a honeycomb structure similar to graphene, but its heterogeneity of carbon and nitrogen elements makes it multifunctional. By performing a first-principles study, we find that edge morphology induces interesting electronic transport properties in step-like heterojunction devices composed of width-variable zigzag C3N nanoribbons. As long as the right part has an edge of all-carbon morphology, negative differential resistance and rectification effects will occur. If both edges are not of all-carbon morphology due to the presence of N atoms, a forward-conducting and reverse-blocking rectifier diode behavior will appear. These phenomena originate from the peculiar electronic structure of the zigzag C3N nanoribbons. The number of energy bands crossing the Fermi level gradually decreases from 2 to 0 as the number of all-carbon edges decreases, realizing a transition from metal to semiconductor. The band gap determines the cut-off region at low bias and the presence of an interface barrier causes the cut-off state to continue under high reverse bias. Diverse edge morphologies, simple cutting methods and rich electronic transport properties make C3N materials competitive in nanodevice applications.

A progressive metal-semiconductor transition in two-faced Janus monolayer transition-metal chalcogenides.

Breaking the symmetry in the out-of-plane direction in two-dimensional materials to trigger distinctive electronic properties has long been predicted. Inspired by the recent progress in the experimental synthesis of a sandwiched S-Mo-Se structure (Janus SMoSe) at the monolayer limit [Zhang et al., ACS Nano, 2017, 11, 8192-8198], we investigate the transport and electronic structure of two-faced XMoY monolayers (X, Y = O, S, Se and Te) through first-principles calculations. It is found that all the monolayers are semiconductors except OMoTe, which is metallic. Interestingly, the "parents" of OMoTe (MoO2 and MoTe2) are both semiconductors. Further analysis shows that it is the out-of-plane asymmetry-induced strain that results in the metal-semiconductor transition between Janus OMoTe and its parents. By increasing the ratio of O atoms in one face of MoTe2, a progressive decreasing trend of the bandgap, as well as the transition to metallic, is found. In addition, a transition from the direct band gap semiconductor to the indirect one is also observed in the process. This could be used as an effective way to precisely control electronic structures, e.g., the bandgap. Different from other methods, this method uses the intrinsic features of the material, which can persist without the need of additional equipment. Moreover, such a modulating method is expected to be extended to many other transition-metal chalcogenides, showing great application potential.

Edge defect switched dual spin filter in zigzag hexagonal boron nitride nanoribbons.

Unlike graphene nanoribbons, zigzag monolayer hexagonal boron nitride nanoribbons (ZBNNRs) possess two distinct edges (B and N edges). Using first-principles calculations, we investigate the spin-dependent electronic transport of ZBNNRs with edge defects. It is found that the defects could make the system operate as a dual spin filter, where the direction of spin polarization is switched by the defect. Further analysis shows that the transmission eigenchannels for the opposite spins reside spatially separated on opposite edges. The defect on one edge could suppress the transmission for only one spin component, but preserve that for the other spin, resulting in a dual spin filter effect. This effect is found to be unaffected by the width of the ribbon and the length of the defect. Moreover, by constructing defects on both edges, the system exhibits two transmission peaks with opposite spins residing discretely on both sides of the Fermi level, suggesting that an electrically controlled dual spin filter based on ZBNNRs is also realizable. As controllable defects have been experimentally fabricated on monolayer boron nitride [T. Pham, A. L. Gibb, Z. Li, S. M. Gilbert, C. Song, S. G. Louie and A. Zettl, Nano Lett., 2016, 16, 7142-7147], our results may shed light on the development of B/N-based spintronic devices.

Brain size does not impact shoaling dynamics in unfamiliar groups of guppies (Poecilia reticulata).

Collective movement is achieved when individuals adopt local rules to interact with their neighbours. How the brain processes information about neighbours' positions and movements may affect how individuals interact in groups. As brain size can determine such information processing it should impact collective animal movement. Here we investigate whether brain size affects the structure and organisation of newly forming fish shoals by quantifying the collective movement of guppies (Poecilia reticulata) from large- and small-brained selection lines, with known differences in learning and memory. We used automated tracking software to determine shoaling behaviour of single-sex groups of eight or two fish and found no evidence that brain size affected the speed, group size, or spatial and directional organisation of fish shoals. Our results suggest that brain size does not play an important role in how fish interact with each other in these types of moving groups of unfamiliar individuals. Based on these results, we propose that shoal dynamics are likely to be governed by relatively basic cognitive processes that do not differ in these brain size selected lines of guppies.