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Abstract Sea cucumbers are predominant deposit feeders in benthic ecosystems, providing protective benefits to coral reefs by reducing disease prevalence. However, how they receive sufficient nutrition from seabed sediments remains poorly understood. Here, we investigate Holothuria leucospilota, an ecologically significant tropical sea cucumber, to elucidate digestive mechanisms underlying marine deposit-feeding. Genomic analysis reveals intriguing evolutionary adaptation characterized by an expansion of digestive carbohydrase genes and a contraction of digestive protease genes, suggesting specialization in digesting microalgae. Developmentally, two pivotal dietary shifts, namely, from endogenous nutrition to planktonic feeding, and from planktonic feeding to deposit feeding, induce changes in digestive tract enzyme profiles, with adults mainly expressing carbohydrases and lipases. A nuanced symbiotic relationship exists between gut microbiota and the host, namely, specific resident bacteria supply crucial enzymes for food digestion, while other bacteria are digested and provide assimilable nutrients. Our study further identifies Holothuroidea lineage-specific lysozymes that are restrictedly expressed in the intestines to support bacterial digestion. Overall, this work advances our knowledge of the evolutionary innovations in the sea cucumber digestive system which enable them to efficiently utilize nutrients from seabed sediments and promote food recycling within marine ecosystems.

Abstract Background Cross‐sectional evidence suggests a possible link between frailty and atrial fibrillation (AF). It remains unclear whether frailty and incident arrhythmias are longitudinally associated. This study aimed to determine whether the frailty phenotype is longitudinally associated with incident arrhythmias, especially AF. Methods In this prospective cohort of UK Biobank, individuals with arrhythmias at baseline, those without data for frailty phenotype, and no genetic data were excluded. Five domains of physical frailty, including weight loss, exhaustion, low physical activity, low grip strength, and slow gait speed, were assessed. A total of 142 single‐nucleotide polymorphisms was used to calculate the polygenic risk score (PRS) for AF. Hospital inpatient records and death records were used to identify incident arrhythmias. Results This study included 464 154 middle‐aged and older adults (mean age 56.4 ± 8.1 years, 54.7% female) without arrhythmia at baseline. During a median follow‐up of 13.4 years (over 5.9 million person‐years), 46 454 new‐onset arrhythmias cases were recorded. In comparison with non‐frailty, the multivariable‐adjusted hazard ratios (HRs) of AF were 1.12 (95% CI: 1.09, 1.15, P

Abstract Cellular senescence is characterized by a decrease in protein synthesis, although the underlying processes are mostly unclear. Chemical modifications to transfer RNAs (tRNAs) frequently influence tRNA activity, which is crucial for translation. We describe how tRNA N7-methylguanosine (m7G46) methylation, catalyzed by METTL1-WDR4, regulates translation and influences senescence phenotypes. Mettl1/Wdr4 and m7G gradually diminish with senescence and aging. A decrease in METTL1 causes a reduction in tRNAs, especially those with the m7G modification, via the rapid tRNA degradation (RTD) pathway. The decreases cause ribosomes to stall at certain codons, impeding the translation of mRNA that is essential in pathways such as Wnt signaling and ribosome biogenesis. Furthermore, chronic ribosome stalling stimulates the ribotoxic and integrative stress responses, which induce senescence-associated secretory phenotype. Moreover, restoring eEF1A protein mitigates senescence phenotypes caused by METTL1 deficiency by reducing RTD. Our findings demonstrate that tRNA m7G modification is essential for preventing premature senescence and aging by enabling efficient mRNA translation.

Brassinosteroid (BR), a plant hormone regulating growth, development, and stress responses, emerges as a promising tool for maintaining agricultural production under abiotic stress conditions. In this study, we conducted RNA-seq profiling and morpho-physiological analysis to investigate the molecular cross-talk involved in 24-epibrassinolide (EBR) mediating alleviation of chromium (Cr) stress. EBR inhibited Cr accumulation and reversed Cr-induced phytotoxicity, thereby promoting plant growth. The photosynthetic pigments, chlorophyll fluorescence a, electron transport rate (ETR) and non-photochemical quenching (NPQ) were significantly higher in EBR+Cr treated plants compared to Cr alone. EBR application facilitated the recovery from Cr-induced structural deformities, including the disintegration of cell walls and membranes. Furthermore, under Cr stress, EBR application reduced malondialdehyde (MDA) and reactive oxygen species (ROS) production and accumulation. The levels of glutathione reductase (GR) and the activities of antioxidant enzymes were notably higher in plants subjected to EBR application following Cr stress. In addition, we established a transcriptomic database comprising 2345 differentially expressed genes (DEGs) (1255 upregulated and 1090 downregulated) as a result of EBR application under Cr stress. The transcriptome analysis unveiled key DEGs and the associated pathways, emphasizing the importance of defense responses, genes encoding photosystem I and II, jasmonate signaling, aquaporins, ABC transporters, and cell wall biogenesis-related genes in the response of EBR to Cr stress.

Noroviruses (NoVs) are a leading cause of viral gastroenteritis. Despite global clinical relevance, our understanding of how host factors, such as antiviral cytokines interferons (IFNs), modulate NoV population dynamics is limited. Murine NoV (MNoV) is a tractable in vivo model for the study of host regulation of NoV. A persistent strain of MNoV, CR6, establishes a reservoir in intestinal tuft cells for chronic viral shedding in stool. However, the influence of host innate immunity and permissive cell numbers on viral population dynamics is an open question. We generated a pool of 20 different barcoded viruses (CR6BC) by inserting 6-nucleotide barcodes at the 3' position of the NS4 gene and used this pool as our viral inoculum for in vivo infections of different mouse lines. We found that over the course of persistent CR6 infection, shed virus was predominantly colon-derived, and viral barcode richness decreased over time irrespective of host immune status, suggesting that persistent infection involves a series of reinfection events. In mice lacking the IFN-λ receptor, intestinal barcode richness was enhanced, correlating with increased viral intestinal replication. IL-4 treatment, which increases tuft cell numbers, also increased barcode richness, indicating the abundance of permissive tuft cells to be a bottleneck during CR6 infection. In mice lacking type I IFN signaling (Ifnar1-/-) or all IFN signaling (Stat1-/-), barcode diversity at extraintestinal sites was dramatically increased, implicating different IFNs as critical bottlenecks at specific tissue sites. Of interest, extraintestinal barcodes were overlapping but distinct from intestinal barcodes, indicating that disseminated virus represents a distinct viral population than that replicating in the intestine. Barcoded viruses are a valuable tool to explore the influence of host factors on viral diversity in the context of establishment and maintenance of infection as well as dissemination and have provided important insights into how NoV infection proceeds in immunocompetent and immunocompromised hosts.

Abstract This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

Abstract Background Oral squamous cell carcinoma (OSCC) is a common malignant tumor associated with poor prognosis. MicroRNAs (miRNAs) play crucial regulatory roles in the cancer development. However, the role of miRNAs in OSCC development and progression is not well understood. Methods We sought to establish a dynamic Chinese hamster OSCC animal model, construct miRNA differential expression profiles of its occurrence and development, predict its targets, and perform functional analysis and validation in vitro. Results Using expression and functional analyses, the key candidate miRNA (miR-181a-5p) was selected for further functional research, and the expression of miR-181a-5p in OSCC tissues and cell lines was detected. Subsequently, transfection technology and a nude mouse tumorigenic model were used to explore potential molecular mechanisms. miR-181a-5p was significantly downregulated in human OSCC specimens and cell lines, and decreased miR-181a-5p expression was observed in multiple stages of the Chinese hamster OSCC animal model. Moreover, upregulated miR-181a-5p significantly inhibited OSCC cell proliferation, colony formation, invasion, and migration; blocked the cell cycle; and promoted apoptosis. BCL2 was identified as a target of miR-181a-5p. BCL2 may interact with apoptosis- (BAX), invasion- and migration- (TIMP1, MMP2, and MMP9), and cell cycle-related genes (KI67, E2F1, CYCLIND1, and CDK6) to further regulate biological behavior. Tumor xenograft analysis indicated that tumor growth was significantly inhibited in the high miR-181a-5p expression group. Conclusion Our findings indicate that miR-181a-5p can be used as a potential biomarker and provide a novel animal model for mechanistic research on oral cancer.

Abstract Aim To develop and validate a questionnaire on knowledge, attitude, behaviour and care preference of family members of Chinese older adults related to palliative care. Design A descriptive study design and STROBE checklist were applied in this research. Methods The theoretical framework of the questionnaire was knowledge–attitude–behaviour model. An additional dimension of palliative care preference of family members was set up in the questionnaire. Items were generated from a rapid review of international literature and interviews with 61 family members of the older adults living either in an aged care service organization or the community. The content validity was examined by five experts. A preliminary questionnaire with 69 items was then set up, and its psychometric property was assessed. Results A final version of questionnaire with 42 items under four dimensions was constructed. The content validity index of the overall questionnaire was 0.93 and of each item ranged 0.80–1.00. The factor loading of all items was higher than 0.50 as per exploratory and confirmatory factor analysis; the average variance extracted for each dimension was higher than 0.50; the composite reliability was higher than 0.90; and the absolute value of the correlation coefficient of each dimension was

To date, studies on apoptosis in echinoderms mainly focus on the caspase-dependent extrinsic apoptotic pathway, while knowledges regarding the intrinsic apoptotic pathway is still limited. In this study, 55 genes belong to 7 families of the intrinsic apoptotic pathway, namely, Bcl-2, caspase, AIF, Cyt c, Apaf-1, Smac, HTRA2 and Endo G, were identified by screening of the genomic database of the tropical sea cucumber Holothuria leucospilota. The Bcl-2 family showed significant gene expansion in H. leucospilota but not in other echinoderms, while the pro-apoptotic factor Endo G is generally lost in echinoderms. Transcriptomic data showed that the genes of the intrinsic apoptotic pathway were ubiquitously expressed in all tissues, and all embryonic and larval developmental stages of H. leucospilota. The gene numbers and functional domains of the caspase family and AIF family were further clarified and showed conserved with their counterparts in vertebrates. In primary coelomocytes, the transcript expression of different caspases showed different responses to pathogenic challenges of vibrio and pathogen-associated molecular patterns, and environmental challenges of heave metal and reactive oxygen species. Overall, this study indicates that the intrinsic apoptotic pathway is conserved between vertebrates and echinoderms by using the sea cucumber H. leucospilota as a model. This study may contribute in increasing the knowledge of development and innate immunity in ancestral deuterostomia species.

Considering the risk of a sudden degeneration caused by the oxidation of MXenes in dielectric and microwave absorption properties, to enhance the oxidation resistance of multilayer MXenes can make them more applicable as microwave absorbers than those with few-layer. However, there remains disadvantage in optimizing the poor impedance matching and inherent aggregation of multilayer MXenes via rational assembling. In the present study, a facile self-assembly process is conducted to obtain 2D MXenes/1D MnO2/0D NiCo2S4 assembled low-dimensional aggregate with hierarchical structure and interlaminar electromagnetic synergy network. In addition to bridging adjacent MXenes lamellas for the enhancement of internal electron transport, high-density MnO2 can also combine with NiCo2S4 to form an electromagnetic synergy network between lamellas, thus improving microwave attenuation. Though the modulation of components and assembled structures, it is achievable to effectively adjust and optimize the performance in impedance matching and microwave absorption. Given the thickness of 2.17 ​mm, the optimal reflection loss of −59.23 ​dB, and the effective absorption bandwidth of 5.8 ​GHz are achieved. Moreover, the RCS simulations is performed to demonstrate its excellent performance. Thus, the present work contributes a facile method to the development of multi-layer MXenes based-MAs via interlaminar electromagnetic network design.

RIPK1 is critical for normal development and cell death. Here, the authors identify a metabolic role for RIPK1 in aspartate homeostasis, as increased aspartate levels in RIPK1-deficient cells inhibits starvation-induced autophagy by ULK1.

IntroductionEarly breast carcinomas can be effectively diagnosed and controlled. However, it demands extra work and radiologist in China often suffer from overtime working due to too many patients, even experienced ones could make mistakes after overloaded work. To improve the efficiency and reduce the rate of misdiagnosis, automatic breast diagnosis on Magnetic Resonance Imaging (MRI) images is vital yet challenging for breast disease screening and successful treatment planning. There are some obstacles that hinder the development of automatic approaches, such as class-imbalance of samples, hard mimics of lesions, etc. In this paper, we propose a coarse-to-fine algorithm to address those problems of automatic breast diagnosis on multi-series MRI images. The algorithm utilizes deep learning techniques to provide breast segmentation, tumor segmentation and tumor classification functions, thus supporting doctors' decisions in clinical practice.MethodsIn proposed algorithm, a DenseUNet is firstly employed to extract breast-related regions by removing irrelevant parts in the thoracic cavity. Then, by taking advantage of the attention mechanism and the focal loss, a novel network named Attention Dense UNet (ADUNet) is designed for the tumor segmentation. Particularly, the focal loss in ADUNet addresses class-imbalance and model overwhelmed problems. Finally, a customized network is developed for the tumor classification. Besides, while most approaches only consider one or two series, the proposed algorithm takes in account multiple series of MRI images.ResultsExtensive experiments are carried out to evaluate its performance on 435 multi-series MRI volumes from 87 patients collected from Tongji Hospital. In the dataset, all cases are with benign, malignant, or both type of tumors, the category of which covers carcinoma, fibroadenoma, cyst and abscess. The ground truths of tumors are labeled by two radiologists with 3 years of experience on breast MRI reporting by drawing contours of tumor slice by slice. ADUNet is compared with other prevalent deep-learning methods on the tumor segmentation and quantitative results, and achieves the best performance on both Case Dice Score and Global Dice Score by 0.748 and 0.801 respectively. Moreover, the customized classification network outperforms two CNN-M based models and achieves tumor-level and case-level AUC by 0.831 and 0.918 respectively.DiscussionAll data in this paper are collected from the same MRI device, thus it is reasonable to assume that they are from the same domain and independent identically distributed. Whether the proposed algorithm is robust enough in a multi-source case still remains an open question. Each stage of the proposed algorithm is trained separately, which makes each stage more robust and converge faster. Such training strategy considers each stage as a separate task and does not take into account the relationships between tasks.

Heavy-metal pollution has increasingly jeopardized the habitats of marine organisms including the sea cucumber, a seafloor scavenger vital to seawater bio-decontamination, ocean de-acidification and coral-reef protection. Normal physiology including immune functions of sea cucumbers is toxicologically modulated by marine metal pollutants such as cadmium (Cd). The processes underpinning Cd’s toxic effects on immune systems in the sea cucumber, Holothuria leucospilota, are still poorly understood. To this end, we cloned and characterized a full-length caspase-9 (Hl-CASP9) cDNA in the sea cucumber, Holothuria leucospilota. Hl-CASP9 mRNA levels evolved dynamically during embryonic development. Coelomocytes, a type of phagocytic immune effectors central to H. leucospilota immunity, were found to express Hl-CASP9 mRNA most abundantly. Hl-CASP9 protein structurally resembles caspases-2 and -9 in both invertebrate and vertebrate species, comprising a CARD domain and a CASc domain. Remarkably, Hl-CASP9 was transcriptionally sensitive to abiotic oxidative stress inducers including hydrogen peroxide (H2O2), nitric oxide (•NO) and cadmium (Cd), but insensitive to immunostimulants including lipopolysaccharide (LPS), and poly(I:C). Overexpression of Hl-CASP9 augmented mitochondria-dependent apoptosis in HEK293T cells, while knock-down of Hl-CASP9 blunted Cd-induced coelomocyte apoptosis in vivo. Overall, we illustrate that an evolutionarily ancient caspase-9-dependent pathway exists to sensitize coelomocytes to premature cell death precipitated by heavy metal pollutants, with important implications for negative modulation of organismal immune response in marine invertebrates.

Karin Holmfeldt et al. sequence metagenomes and metatranscriptomes of viruses in deep groundwaters down to 448 m below the surface. The results reveal ecological dynamics of viruses including slow motion ‘boom and burst’ cycles and a ‘kill the winner’ model potentially driven by viral predation.

Abstract Our aims were to determine the accuracy of an improved formula for determining the minimum occlusive force (MOF) of a vascular clamp on rats’ abdominal aortas, compare our findings with the calculated theoretical MOF, and provide reference data for clinical research and development of medical instruments that cause minimal damage. We created a vessel closure model and developed a formula for calculating the theoretical MOF of arterial vessels when they are occluded. This formula utilises the blood pressure in the blood vessel, its diameter, and the width of the vascular clamp. We then measured the actual MOF in 24 rat abdominal aortic segments with different diameters and different blood pressures and compared the theoretical and actual MOFs. Analysis of the experimental data showed a probability of 0.315, which means that, under the condition of normal distribution, the difference between the theoretical and actual MOF is not significant at the α = 0.05 level. Thus, the actual measured MOF tended to be consistent with the theoretical MOF calculated by the formula we developed. The improved formula will provide a reference for clinical research and development of medical instruments that cause minimal injury, thus contributing to the development of microsurgery.

Abstract Background Dyslipidemia contributes to the development and progression of arterial stiffness. We aimed to identify the most informative measures of serum lipids and their calculated ratios in terms of arterial stiffness progression risk. Methods Total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and brachial-ankle pulse wave velocity (baPWV) of 659 healthy males (47.4 ± 10.7 years) were measured at baseline. Values for non-HDL-C, TC/HDL-C, TG/HDL-C, LDL-C/HDL-C, and non-HDL-C/HDL-C were calculated. BaPWV was re-performed after 4.1 years follow-up. Elevated baPWV was defined as baPWV ≥ 1400 cm/s. Results Over the follow-up period, the mean baPWV value increased from 1340 cm/s to 1410 cm/s, and 331 individuals increased/persisted with high baPWV (outcome 1). Among the 448 subjects who had normal baseline baPWV, 100 incident elevated baPWV occurred (outcome 2). Only baseline logTG (OR 1.64 [95% CI: 1.14–2.37] for outcome 1; 1.89 [1.14–3.17] for outcome 2) and logTG/HDL-C (1.54 [1.15–2.10] for outcome 1; 1.60 [1.05–2.45] for outcome 2) were significantly associated with arterial stiffness progression after adjusting for confounding factors. Adding logTG or logTG/HDL-C to age and blood pressure improved the accuracy of risk predictions for arterial stiffness progression. These associations remained significant when lipids were analyzed as categorical variables. Conclusions Baseline serum TG and TG/HDL-C were independently associated with increases in/persistently high baPWV and incident elevated baPWV, and they performed more effectively than other lipid variables in identifying healthy men at high risk of arterial stiffness progression.

Abstract Background The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is filled with fluid and suspended coelomic cells similar to blood cells. The humoral immune response of the sea cucumber is based on the secretion of various immune factors from coelomocytes into the coelomic cavity. The aim of this study is to lay out a foundation for the immune mechanisms in echinoderms and their origins in chordates by using RNA-seq. Results Sea cucumber primary coelomocytes were isolated from healthy H. leucospilota and incubated with lipopolysaccharide (LPS, 10 μg/ml), polyinosinic-polycytidylic acid [Poly (I:C), 10 μg/ml] and heat-inactived Vibrio harveyi (107 cell/ml) for 24 h, respectively. After high-throughput mRNA sequencing on an Illumina HiSeq2500, a de novo transcriptome was assembled and the Unigenes were annotated. Thirteen differentially expressed genes (DEGs) were selected randomly from our data and subsequently verified by using RT-qPCR. The results of RT-qPCR were consistent with those of the RNA-seq (R 2 = 0.61). The top 10 significantly enriched signaling pathways and immune-related pathways of the common and unique DEGs were screened from the transcriptome data. Twenty-one cytokine candidate DEGs were identified, which belong to 4 cytokine families, namely, BCL/CLL, EPRF1, IL-17 and TSP/TPO. Gene expression in response to LPS dose-increased treatment (0, 10, 20 and 50 μg/ml) showed that IL-17 family cytokines were significantly upregulated after 10 μg/ml LPS challenge for 24 h. Conclusion A de novo transcriptome was sequenced and assembled to generate the gene expression profiling across the sea cucumber coelomocytes treated with LPS, Poly (I:C) and V. harveyi. The cytokine genes identified in DEGs could be classified into 4 cytokine families, in which the expression of IL-17 family cytokines was most significantly induced after 10 μg/ml LPS challenge for 24 h. Our findings have laid the foundation not only for the research of molecular mechanisms related to the immune response in echinoderms but also for their origins in chordates, particularly in higher vertebrates.

Objective Arterial stiffness may be an intermediary biological pathway involved in the association between cardiovascular health (CVH) and cardiovascular disease. We aimed to evaluate the effect of CVH on progression of brachial–ankle pulse wave velocity (baPWV) over approximately 4 years. Methods We included 1315 cardiovascular disease-free adults (49±12 years) who had two checkups from 2010 to 2019. CVH metrics (current smoking, body mass index, total cholesterol, blood pressure, and fasting plasma glucose) were assessed at baseline, and the number of ideal CVH metrics and CVH score were calculated. Additionally, baPWV was examined at baseline and follow-up. Results Median baPWV increased from 1340 cm/s to 1400 cm/s, with an average annual change in baPWV of 15 cm/s. More ideal CVH metrics and a higher CVH score were associated with lower baseline and follow-up baPWV, and the annual change in baPWV, even after adjustment for confounding variables. Associations between CVH parameters and baseline and follow-up baPWV remained robust in different sex and age subgroups, but they were only able to predict the annual change in baPWV in men and individuals older than 50 years. Conclusions Our findings highlight the benefit of a better baseline CVH profile for progression of arterial stiffness.

Oocyte maturation and ovarian development are sequentially coordinated events critical to reproduction. In the ovaries of adult oviparous animals such as birds, bony fish, insects, and crustaceans, vitellogenin receptor (VgR) is a plasma membrane receptor that specifically mediates vitellogenin (Vg) transport into oocytes. Accumulation of Vg drives sexual maturation of the female crustaceans by acting as a pivotal regulator of nutritional accumulation within oocytes, a process known as vitellogenesis. However, the mechanisms by which VgR mediates vitellogenesis are still not fully understood. In this study, we first identified a unique VgR (Lv-VgR) and characterized its genomic organization and protein structural domains in Litopenaeus vannamei, a predominant cultured shrimp species worldwide. This newly identified Lv-VgR phylogenetically forms a group with VgRs from other crustacean species within the arthropod cluster. Duplicated LBD/EGFD regions are found exclusively among arthropod VgRs but not in paralogs from vertebrates and nematodes. In terms of expression patterns, Lv-VgR transcripts are specifically expressed in ovaries of female shrimps, which increases progressively during ovarian development, and rapidly declines toward embryonic development. The cellular and subcellular locations were For analyzed by in situ hybridization and immunofluorescence, respectively. The Lv-VgR mRNA was found to be expressed in the oocytes of ovaries, and Lv-VgR protein was found to localize in the cell membrane of maturing oocytes while accumulation of the ligand Vg protein assumed an even cytoplasmic distribution. Silencing of VgR transcript expression by RNAi was effective for stunting ovarian development. This present study has thus provided new insights into the regulatory roles of VgR in crustacean ovarian development.

In this study, the functions of Holothuria leucospilota Fas-associated death domain (HLFADD) in the innate immune-related signalling pathways were investigated. The results showed that over-expression of HLFADD in HEK293T cells could activate the transcription factors NF-κB and activator protein-1 (AP-1), and induce the secretion of downstream pro-inflammatory cytokines IL-6, IL-8 and IL-18, suggesting the involvement of the sea cucumber FADD in activating the NF-κB and c-Jun NH 2 -terminal kinase-dependent pathways. On the other hand, HLFADD could down-regulate the activations of NF-κB and AP-1 that induced by over-expression of H. leucospilota myeloid differentiation factor 88 (HLMyD88), which is supposed to be mediated through its interaction with HLMyD88 to keep the MyD88-dependent TLR signalling at a proper magnitude. The interaction of HLFADD and HLMyD88 were further supported by a co-immunoprecipitation assay. Moreover, HLFADD could activate transcription factor IFN regulatory factor-3 and induced the secretion of downstream IFN-α and IFN-β, indicating that the sea cucumber FADD may also activate the antiviral IFN signalling pathway. In summary, our study may give new insights on the functions of sea cucumber FADD in the innate immune-related signalling pathways.

Holothuria leucospilota (Echinodermata: Holothuroidea) is a widespread tropical sea cucumber with strong value for the ecological restoration of coral reefs. Therefore, some studies regarding the artificial breeding and cultivation of H. leucospilota have been undertaken recently. However, the biological functions of the digestive system of this species have not been elucidated. In this study, a cDNA coding for α-amylase, an indicator of digestive maturity in animals, was identified from H. leucospilota and designated Hl-Amy. The full-length cDNA of the Hl-Amy gene, which is 1734 bp in length with an open reading frame (ORF) of 1578 bp, encodes a 525 amino acid (a.a.) protein with a deduced molecular weight of 59.34 kDa. According to the CaZy database annotation, Hl-Amy belongs to the class of GH-H with the official nomenclature of α-amylase (EC 3.2.1.1) or 4-α-D-glucan glucanohydrolase. The Hl-Amy protein contains a signal peptide at the N-terminal followed by a functional amylase domain, which includes the catalytic activity site. The mRNA expression of Hl-Amy was abundantly exhibited in the intestine, followed by the transverse vessel with a low level, but was hardly detected in other selected tissues. During embryonic and larval development, Hl-Amy was constitutively expressed in all stages, and the highest expression level was observed in the blastula. By in situ hybridization (ISH), positive Hl-Amy signals were observed in different parts of the three different intestinal segments (foregut, midgut and hindgut). The Hl-Amy recombinant protein was generated in an E. coli system with codon optimization, which is necessary for Hl-Amy successfully expressed in this heterogenous system. The Hl-Amy recombinant protein was purified by immobilized metal ion affinity chromatography (IMAC), and its activity of starch hydrolysis was further detected. The optimal temperatures and pH for Hl-Amy recombinant protein were 55°C and 6.0, respectively, with an activity of 62.2 U/mg. In summary, this current study has filled a knowledge gap on the biological function and expression profiles of an essential digestive enzyme in sea cucumber, which may encourage future investigation toward rationalized diets for H. leucospilota in artificial cultivation, and optimized heterogenous prokaryotic systems for producing recombinant enzymes of marine origins.

In this study, the mitochondrial genome (mitogenome) of Holothuria fuscocinerea was unraveled to be 15,890 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The PCGs were initiated by four initiation codons (ATG, TAC, ATC, and ATA). Only one PCG (nad6) and five tRNA genes (tRNASer(UCN), tRNAGln, tRNAAla, tRNAVal, and tRNAAsp) were encoded on the light chain, and the other genes were encoded on the heavy chain. A phylogenetic tree constructed with 16S rRNA sequences showed that H. fuscocinerea is most closely related to H. leucospilota.

FOXO transcription factors have long been associated with longevity control and tissue homeostasis. Although the transcriptional regulation of FOXO have been previously characterized (especially in long-lived insulin mutants and under stress conditions), how normal aging impacts the transcriptional activity of FOXO is poorly understood. Here, we conducted a chromatin immunoprecipitation sequencing (ChIP-Seq) analysis in both young (2-week-old) and aged (5-week-old) wild-type female fruit flies, Drosophila melanogaster, to evaluate the dynamics of FOXO gene targeting during aging. Intriguingly, the number of FOXO-bound genes dramatically decreases with age (from 2617 to 224). Consistent to the reduction of FOXO binding activity, many genes targeted by FOXO in young flies are transcriptionally altered with age, either up-regulated (FOXO-repressing genes) or down-regulated (FOXO-activating genes) in adult head tissue. In addition, we show that many FOXO-bound genes in wild-type flies are unique from those in insulin receptor substrate chico mutants. Distinct from chico mutants, FOXO targets specific cellular processes (e.g., actin cytoskeleton) and signaling pathways (e.g., Hippo, MAPK) in young wild-type female flies. FOXO targeting on these pathways decreases with age. Interestingly, FOXO targets in aged flies are enriched in cellular processes like chromatin organization and nucleosome assembly. Furthermore, FOXO binding to core histone genes is well maintained at aged flies. Together, our findings provide new insights into dynamic FOXO targeting under normal aging and highlight the diverse and understudied regulatory mechanisms for FOXO transcriptional activity.

ABSTRACT The continental subsurface is suggested to contain a significant part of the earth’s total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Äspö Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of

Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed ‘acid mine drainage (AMD)’] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe–mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.

Epigenetic alteration has been implicated in aging. However, the mechanism by which epigenetic change impacts aging remains to be understood. H3K27me3, a highly conserved histone modification signifying transcriptional repression, is marked and maintained by Polycomb Repressive Complexes (PRCs). Here, we explore the mechanism by which age-modulated increase of H3K27me3 impacts adult lifespan. Using Drosophila, we reveal that aging leads to loss of fidelity in epigenetic marking and drift of H3K27me3 and consequential reduction in the expression of glycolytic genes with negative effects on energy production and redox state. We show that a reduction of H3K27me3 by PRCs-deficiency promotes glycolysis and healthy lifespan. While perturbing glycolysis diminishes the pro-lifespan benefits mediated by PRCs-deficiency, transgenic increase of glycolytic genes in wild-type animals extends longevity. Together, we propose that epigenetic drift of H3K27me3 is one of the molecular mechanisms that contribute to aging and that stimulation of glycolysis promotes metabolic health and longevity.

The mitochondrial genome of Holothuria leucospilota was 15,906 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. There were four initiation codons (ATG, ATT, ATC, and ATA) for the PCGs, and the termination codon of most PCGs was TAA, except for nad4 (TAG) and nad6 (TAG). Only one PCG (nad6) and five tRNA genes (tRNASer(UCN), tRNAGln, tRNAAla, RNAVal, and tRNAAsp) were encoded on the light chain; the other genes were encoded on the heavy chain. H. leucospilota was most closely related to Holothuria scabra in a phylogenetic tree.

Abstract Background This study aimed to investigate the gene expression changes associated with carcinoma-associated fibroblasts (CAFs) involving in non-small cell lung carcinoma (NSCLC). Methods We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and normal fibroblasts samples, and series GSE27289 containing SNP genotyping for four matched NSCLC samples. The differentially expressed genes in CAF samples were identified using the limma package in R. Then we performed gene ontology (GO) and pathway enrichment analysis and protein–protein interaction (PPI) network construction using the identified DEGs. Moreover, aberrant cell fraction, ploidy, allele-specific copy number, and loss of heterozygosity (LOH) within CAF cells were analyzed using the allele-specific copy number analysis. Results We obtained 545 differentially expressed genes between CAF and normal fibroblasts samples. The up-regulated genes are mainly involved in GO terms such as positive regulation of cell migration and extracellular region, while the down-regulated genes participate in the lung development and extracellular region. Multiple genes including bone morphogenetic protein 4 (BMP4) and transforming growth factor, beta 3 (TGFB3) are involved in the TGF-β signaling pathway. Genes including BMP4, TGFBI and matrix Gla protein (MGP) were hub genes. Moreover, no LOH event for BMP4 and MGP was found, that for sphingosine kinase 1 (SPHK1) was 70%, and for TGFBI was 40%. Conclusion Our data suggested that BMP4, MGP, TGFBI, and SPHK1 may be important in CAFs-associated NSCLC, and the abnormal expression and high LOH frequency of them may be used as the diagnosis targets of CAFs in NSCLC.

In response to the population aging, on May 31, 2021, the Political Bureau of the Central Committee of the Communist Party of China (CPC) proposed the policy that a couple can have three children and rolled out more supportive measures to further optimize fertility policies, which is another major initiative following the universal two-child policy introduced in November 2015. Currently, a series of population policy innovations have aroused great attractions among the public and triggered a hot debating on the Internet. People’s fertility attitude tendency under different related policies can reflect their current fertility intentions. Based on the fact, this paper firstly classifies the sentiment of online comment data on the three-child policy and analyzes people’s sentiment tendency toward the three-child policy from the spatio-temporal perspectives. Secondly, people’s points of view on the three-child policy are summarized by using Latent Dirichlet Allocation (LDA) thematic clustering. The reasons for the change in people’s fertility attitude tendency under different fertility policies are analyzed by comparing the change in people’s fertility attitude tendency with the change in people’s attentions. Finally, a multiple regression equation is constructed to analyze the key factors influencing people’s intention to have three children by using public opinion data and its extension data. The findings demonstrate: (1) people’s fertility attitudes toward the three-child policy are negative and similar among different regions; (2) compared to the two-child policy, the percentage of negative and neutral attitudes toward the three-child policy increases, while the percentage of positive attitudes decreases; (3) the increase in fertility costs, the deterioration of women’s employment environment, and the change in the concept of marriage and childbirth become important reasons for the negative change in people’s fertility attitudes toward different policies. Therefore, the government should take measures to reduce the burden of childbirth and guide the correct concept of marriage and childbirth to improve people’s fertility intentions. [ABSTRACT FROM AUTHOR]