M2 macrophages independently promote beige adipogenesis via blocking adipocyte Ets1.

Adipose tissue macrophages can promote beige adipose thermogenesis by altering local sympathetic activity. Here, we perform sympathectomy in mice and further eradicate subcutaneous adipose macrophages and discover that these macrophages have a direct beige-promoting function that is independent of sympathetic system. We further identify adipocyte Ets1 as a vital mediator in this process. The anti-inflammatory M2 macrophages suppress Ets1 expression in adipocytes, transcriptionally activate mitochondrial biogenesis, as well as suppress mitochondrial clearance, thereby increasing the mitochondrial numbers and promoting the beiging process. Male adipocyte Ets1 knock-in mice are completely cold intolerant, whereas male mice lacking Ets1 in adipocytes show enhanced energy expenditure and are resistant to metabolic disorders caused by high-fat-diet. Our findings elucidate a direct communication between M2 macrophages and adipocytes, and uncover a function for Ets1 in responding to macrophages and negatively governing mitochondrial content and beige adipocyte formation.

An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data.

High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures, greatly promoting biological studies involving large amounts of complex samples, especially those involving environmental and pathogen-monitoring ones. Commercial library preparation kits for amplicon sequencing, which generally require multiple steps, including adapter ligation and indexing, are expensive and time-consuming, especially for applications at a large scale. To overcome these limitations, a "one-step PCR approach" has been previously proposed for constructions of amplicon libraries using long fusion primers. However, efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed. To tackle these, we present an integrative protocol for one-step PCR amplicon library construction (OSPALC). High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples. With this protocol, the amplicon library is constructed through one regular PCR with long primers, and the total cost per DNA/cDNA sample decreases to just 7% of the typical cost via the multi-step PCR approach. Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study. Tools to design primers targeting at any genomic regions are also presented. In principle, OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples, and will facilitate research in numerous fields. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-023-00182-1.

Duodenal-Jejunal bypass improves metabolism and re-models extra cellular matrix through modulating ceRNA network.

BACKGROUND: Bariatric surgery (BS) is an effective approach in treating obesity and ameliorating T2DM with obesity. Our previous studies demonstrated that duodenal-jejunal bypass (DJB) altered long non-coding RNAs (lncRNAs) in the gastrointestinal system, which is associated with modulation of lipid metabolism, and glycemic control through entero-pancreatic axis and gut-brain axis. The adipose non-coding RNA expression profile and the underlying competing endogenous RNA (ceRNA) regulatory network pattern post DJB needs further research and investigation. RESULTS: In this study, we compared the lncRNAs, circular RNAs (circRNAs) and messenger RNAs (mRNAs) expression in adipose tissues between the sham group and the DJB group. 2219 differentially expressed mRNAs (DEmRNAs), 722 differential expression of lncRNAs (DElncRNAs) and 425 differential expression of circRNAs (DEcircRNAs) were identified. GO terms and KEGG pathways analysis of the DEmRNAs implied that the dysregulated adipose mRNAs were associated with lipid, amino acid metabolism, insulin resistance, and extra cellular matrix (ECM)-related pathways. Moreover, via analyzing ceRNA regulatory networks of DElncRNAs and DEcircRNAs, 31 hub DE mRNAs, especially Mpp7, 9330159F19Rik, Trhde. Trdn, Sorbs2, were found on these pathways. CONCLUSIONS: The role of DJB in adipose tends to remodel ECM and improve the energy metabolism through the ceRNA regulatory network.

Paramecium Genetics, Genomics, and Evolution.

The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.

The divergence of mutation rates and spectra across the Tree of Life.

Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several-fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift-barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population-genetic analysis and raises challenges for future applications in these areas.

Dual-Mode Porous Polymeric Films with Coral-like Hierarchical Structure for All-Day Radiative Cooling and Heating.

Passive radiative cooling (PRC) and passive radiative heating (PRH) have drawn increasing attention as green and sustainable cooling and heating approaches, respectively. Existing material designs for PRC/PRH are usually static and unsuitable for dynamic seasonal and weather changes. Herein, we demonstrate an all-day dual-mode film fabricated by decorating MXene nanosheets on porous poly(vinylidene fluoride) with abundant coral-like hierarchical structures obtained via phase inversion. The cooling side of the dual-mode film exhibits high solar reflectivity (96.7%) and high infrared emissivity (96.1%). Consequently, daytime subambient radiative cooling of 9.8 °C is achieved with a theoretical cooling power of 107.5 W/m2 and nighttime subambient cooling of 11.7 °C is achieved with a theoretical cooling power of 140.7 W/m2. Meanwhile, the heating side of the dual-mode film exhibits low infrared emissivity (11.6%) and high solar absorptivity (75.7%), contributing to a PRH capability of 8.1 °C, and excellent active solar and Joule heating as effective compensation for PRH. The dual-mode film could be easily switched between cooling and heating modes by flipping it to adapt to dynamic cooling and heating scenarios, which is important for alleviating the energy crisis and reducing greenhouse emissions.

Amomum longiligulare polysaccharide 1- PLGA nanoparticle promotes the immune activities of T lymphocytes and dendritic cells.

Amomum longiligulare polysaccharide 1 (ALP1) was extracted from Amomum longiligulare T.L. Wu fruits and the poly (lactic-co-glycolic acid) nanoparticle enveloping ALP1 (ALPP) showed a good promoting effect on the activation of macrophages in our previous study. To further understand the immunomodulatory property of ALPP, the effect of ALPP on T lymphocytes and dendritic cells was investigated in the present study. The proliferation rates of chicken T lymphocytes and chicken bone marrow dendritic cells (chBM-DCs) that were treated with ALP1 or ALPP were determined by using MTT method. Meanwhile, the relative mRNA levels of cytokines from T lymphocytes and surface molecules of chBM-DCs were determined by using qRT-PCR method. In addition, the drug uptake capacity of chBM-DCs was also tested. As a result, the promoting effect on the proliferation of T lymphocytes and the Th1-type immune response of ALPP was better than that of ALP1. In addition, ALPP was much more effectively swallowed by chBM-DCs so that its promoting effect on the proliferation and maturation of chBM-DCs was higher than that of ALP1. To conclude, ALPP had a stronger immunomodulatory activity than ALP1, and showed the potential to become a new type of immune booster.

Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica.

Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.

Characterization of Alpinia officinarum Hance polysaccharide and its immune modulatory activity in mice.

This study aimed to characterize the structural features of a novel water-soluble polysaccharide (AOHP) extracted from Alpinia officinarum Hance and to verify its regulating effect on mouse immunity. Cellulose DEAE-52 and Sephadex G-100 columns were used to obtain purified AOHP. Techniques including NMR, methylation, monosaccharide composition, FT-IR, and molecular weight determination were applied to investigate the physicochemical properties and structural characterization of AOHP. Then, the influence of AOHP on mice was studied. After oral administration of AOHP, organ indexes, serum biochemistry indexes, and cytokines in the spleens of the mice were analysed. The results showed that AOHP was composed of T-α-D-Glcp, (1,4)-α-D-Glcp and (1,4,6)-α-D-Glcp with a number-average molecular weight of 26.0 kDa and a weight-average molecular weight of 52.8 kDa. Additionally, the innate immune statuses of the mice were improved by treatment with AOHP, while no obvious damage was identified. To conclude, the immunomodulatory activity and biological safety make AOHP a viable candidate as an ingredient for healthcare drugs.

Extracellular and Intracellular Skeletons: How Do They Involve in Apoptosis.

Apoptosis plays a key role in removing abnormal or senescent cells, maintaining the overall health of the tissue, and coordinating individual development. Recently, it has been discovered that the intracellular cytoskeleton plays a role in the apoptotic process. In addition, the regulatory role of extracellular matrix (ECM) fibrous proteins, which can be considered as the extracellular skeleton, in the process of apoptosis is rarely summarized. In this review, we collect the latest knowledge about how fibrous proteins inside and outside cells regulate apoptosis. We describe how ECM fibrous proteins participate in the regulation of death receptor and mitochondrial pathways through various signaling cascades mediated by integrins. We then explore the molecular mechanisms by which intracellular intermediate filaments regulate cell apoptosis by regulating death receptors on the cell membrane surface. Similarly, we report on novel supporting functions of microtubules in the execution phase of apoptosis and discuss their formation mechanisms. Finally, we discuss that the polypeptide fragments formed by caspase degradation of ECM fibrous proteins and intracellular intermediate filament act as local regulatory signals to play different regulatory roles in apoptosis.

PIWIs maintain testis apoptosis to remove abnormal germ cells in Eriocheir sinensis.

PIWI proteins play important roles in germline development in the mammals. However, the functions of PIWIs in crustaceans remain unknown. In the present study, we identified three Piwis from the testis of Eriocheir sinensis (E. sinensis). Three Piwi genes encoded proteins with typical features of PIWI subfamilies and were highly expressed in the testis. Three PIWIs could be detected in the cytoplasm of spermatocytes and spermatids, while in spermatozoa, we could only detect PIWI1 and PIWI3 in the nucleus. The knockdown of PIWIs by dsRNA significantly affected the formation of the nuclei in spermatozoa, which resulted in deviant and irregular nuclei. PIWI defects significantly inhibited the apoptosis of abnormal germ cells through the caspase-dependent apoptosis pathway and p53 pathway. Knockdown of PIWIs inhibited the expression of caspase (Casp) 3, 7, 8, and p53 without affecting Bcl2 (B-cell lymphoma gene 2), Bax (B-cell lymphoma-2-associated X), and BaxI (B-cell lymphoma-2-associated X inhibitor), which further significantly increased abnormal spermatozoa in the knockdown-group crabs. These results show a new role of PIWI proteins in crustaceans that is different from that in mammals. In summary, PIWIs play roles in the formation of the germline nucleus and can maintain apoptosis in abnormal germ cells to remove abnormal germ cells in E. sinensis.

Characterizations of glucose-rich polysaccharides from Amomum longiligulare T.L. Wu fruits and their effects on immunogenicities of infectious bursal disease virus VP2 protein.

The aim of this study is to explore the characterization of Amomum longiligulare T.L. Wu fruits polysaccharide (ALP) and their immune enhancement effects. Two homogeneous polysaccharides (ALP1 and ALP2) were isolated from the fruits. The structural characterization results showed that ALP1 (26.10 kDa) and ALP2 (64.10 kDa) were both mainly composed of glucose. Furthermore, ALP1 was consisted of (1,2)-α-D-Glcp, (1,2,3)-α-D-Glcp and T-α-D-Glcp, while ALP2 was consisted of T-α-D-Glcp, (1,3)-α-D-Glcp and (1,3,6)-α-D-Glcp. Afterwards, the immune enhancement effects of two polysaccharides were evaluated by determining their effects on immunogenicities of infectious bursal disease virus (IBDV) VP2 protein. Chickens were immunized with IBDV VP2 protein accompanied with ALP1/ALP2. And the results indicated both ALP1 and ALP2 promoted the weights and bursa of fabricius indexes of chickens. In addition, both two polysaccharides increased specific IBDV antibody levels, while ALP1 possessed higher immune enhancement ability and was expected to be an adjuvant for IBDV VP2 protein.

KIF3A regulates the Wnt/ß-catenin pathway via transporting ß-catenin during spermatogenesis in Eriocheir sinensis.

The Wnt/ß-catenin pathway participates in many important physiological events such as cell proliferation and differentiation in the male reproductive system. We found that Kinesin-2 motor KIF3A is highly expressed during spermatogenesis in Eriocheir sinensis; it may potentially promote the intracellular transport of cargoes in this process. However, only a few studies have focused on the relationship between KIF3A and the Wnt/ß-catenin pathway in the male reproductive system of decapod crustaceans. In this study, we cloned and characterized the CDS of ß-catenin in E. sinensis for the first time. Fluorescence in situ hybridization and immunofluorescence results showed the colocalization of Es-KIF3A and Es-ß-catenin at the mRNA and the protein level respectively. To further explore the regulatory function of Es-KIF3A to the Wnt/ß-catenin pathway, the es-kif3a was knocked down by double-stranded RNA (dsRNA) in vivo and in primary cultured cells in testes of E. sinensis. Results showed that the expression of es-ß-catenin and es-dvl were decreased in the es-kif3a knockdown group. The protein expression level of Es-ß-catenin was also reduced and the location of Es-ß-catenin was changed from nucleus to cytoplasm in the late stage of spermatogenesis when es-kif3a was knocked down. Besides, the co-IP result demonstrated that Es-KIF3A could bind with Es-ß-catenin. In summary, this study indicates that Es-KIF3A can positively regulate the Wnt/ß-catenin pathway during spermatogenesis and Es-KIF3A can bind with Es-ß-catenin to facilitate the nuclear translocation of Es-ß-catenin.