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Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open-source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating and organising sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity. The primer module designs universal primers for downstream applications. Finally, a visualisation pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we identified 30 plastid intergenic spacers. These spacers exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, highlighting the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilisation of organelle genomic data and broaden the prospects for related research endeavours., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

To systematically characterize the loss of tissue integrity and organ dysfunction resulting from aging, we produced an in-depth spatial transcriptomic profile of nine tissues in male mice during aging. We showed that senescence-sensitive spots (SSSs) colocalized with elevated entropy in organizational structure and that the aggregation of immunoglobulin-expressing cells is a characteristic feature of the microenvironment surrounding SSSs. Immunoglobulin G (IgG) accumulated across the aged tissues in both male and female mice, and a similar phenomenon was observed in human tissues, suggesting the potential of the abnormal elevation of immunoglobulins as an evolutionarily conserved feature in aging. Furthermore, we observed that IgG could induce a pro-senescent state in macrophages and microglia, thereby exacerbating tissue aging, and that targeted reduction of IgG mitigated aging across various tissues in male mice. This study provides a high-resolution spatial depiction of aging and indicates the pivotal role of immunoglobulin-associated senescence during the aging process., Competing Interests: Declaration of interests Y.G., C.N., Y.S., Z.L., H.D., and F.W. are employees of BGI. J.C.I.B. and C.R.E. are employees of Altos Labs., (Copyright © 2024 Elsevier Inc. All rights reserved.)

In this study, we aim to investigate the role of enolase 1 (ENO1) in osteoarthritis (OA) pathogenic process and to uncover the underlying mechanism. To this end, we used IL-1β to induce an in vitro OA‑like chondrocyte model in human immortalized chondrocyte C-28/I2 cells. We manipulated the expression of ENO1 and cytokine receptor-like factor 1 (CRLF1) in IL-1β-induced C-28/I2 cells using siRNA and/or overexpression and tested their effects on IL-1β-induced pathologies including cell viability, apoptosis and inflammatory cytokine levels (IL-6 and TNF-α), and the expression of extracellular matrix-related enzymes and major mediators in the NF-κB signaling pathway (p-p65, p65, p-IκBα and IκBα). We used co-immunoprecipitation and immunofluorescence imaging to study a possible binding between ENO1 and CRLF1. Our data showed that IL-1β induction elevated ENO1 and CRLF1 expression in C-28/I2 cells. Silencing ENO1 or CRLF1 inhibited the IL-1β-induced cell viability damage, apoptosis, inflammation, and extracellular matrix degradation. The inhibitory effect of silencing ENO1 was reversed by CRLF1 overexpression, suggesting a functional connection between ENO1 and CRLF1, which could be attributed to a binding between these two partners. Our study could help validate the role of ENO1 in OA pathogenies and identify novel therapeutic targets for OA treatment., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Bayesian tensor decomposition has been widely applied in channel parameter estimations, particularly in cases with the presence of interference. However, the types of interference are not considered in Bayesian tensor decomposition, making it difficult to accurately estimate the interference parameters. In this paper, we present a robust tensor variational method using a CANDECOMP/PARAFAC (CP)-based additive interference model for multiple input-multiple output (MIMO) with orthogonal frequency division multiplexing (OFDM) systems. A more realistic interference model compared to traditional colored noise is considered in terms of co-channel interference (CCI) and front-end interference (FEI). In contrast to conventional algorithms that filter out interference, the proposed method jointly estimates the channel and interference parameters in the time-frequency domain. Simulation results validate the correctness of the proposed method by the evidence lower bound (ELBO) and reveal the fact that the proposed method outperforms traditional information-theoretic methods, tensor decomposition models, and robust model based on CP (RCP) in terms of estimation accuracy. Further, the interference parameter estimation technique has profound implications for anti-interference applications and dynamic spectrum allocation.

Neuroligin-3 (Nlgn3) is an autism-associated cell-adhesion molecule that interacts with neurexins and is robustly expressed in both neurons and astrocytes. Neuronal Nlgn3 is an essential regulator of synaptic transmission but the function of astrocytic Nlgn3 is largely unknown. Given the high penetrance of Nlgn3 mutations in autism and the emerging role of astrocytes in neuropsychiatric disorders, we here asked whether astrocytic Nlgn3 might shape neural circuit properties in the cerebellum similar to neuronal Nlgn3. Imaging of tagged Nlgn3 protein produced by CRISPR/Cas9-mediated genome editing showed that Nlgn3 is enriched in the cell body but not the fine processes of cerebellar astrocytes (Bergmann glia). Astrocyte-specific knockout of Nlgn3 did not detectably alter the number of synapses, synaptic transmission, or astrocyte morphology in mouse cerebellum. However, spatial transcriptomic analyses revealed a significant shift in gene expression among multiple cerebellar cell types after the deletion of astrocytic Nlgn3. Hence, in contrast to neuronal Nlgn3, astrocytic Nlgn3 in the cerebellum is not involved in shaping synapses but may modulate gene expression in specific brain areas., (© 2024. The Author(s).)

Background: Ferroptosis is a type of cell death characterized by the accumulation of iron-dependent lethal lipid peroxides, which is associated with various pathophysiological processes. Psoriasis is a chronic autoimmune skin disease accompanied by abnormal immune cell infiltration and excessive production of lipid reactive oxygen species (ROS). Currently, its pathogenesis remains elusive, especially the potential role of ferroptosis in its pathophysiological process., Methods: The microarrays GSE13355 (58 psoriatic skin specimens versus 122 healthy skin specimens) and the ferroptosis database were employed to identify the common differentially expressed genes (DEGs) associated with psoriasis and ferroptosis. The functions of common DEGs were investigated through functional enrichment analysis and protein-protein interaction analysis. The potential diagnostic markers for psoriasis among the common DEGs were identified using four machine-learning algorithms. DGIdb was utilized to explore potential therapeutic agents for psoriasis. Additionally, CIBERSORT was employed to investigate immune infiltration in psoriasis., Results: A total of 8 common DEGs associated with psoriasis and ferroptosis were identified, which are involved in intercellular signaling and affect pathways of cell response to stress and stimulation. Four machine-learning algorithms were employed to identify poly (ADP-ribose) polymerase 12 (PARP12), frizzled homolog 7 (FZD7), and arachidonate 15-lipoxygenase (ALOX15B) among the eight common DEGs as potential diagnostic markers for psoriasis. A total of 18 drugs targeting the five common DEGs were identified as potential candidates for treating psoriasis. Additionally, significant changes were observed in the immune microenvironment of patients with psoriasis., Conclusion: This study has contributed to our enhanced comprehension of ferroptosis-related genes as potential biomarkers for psoriasis diagnosis, as well as the alterations in the immune microenvironment associated with psoriasis. Our findings offer valuable insights into the diagnosis and treatment of psoriasis., Competing Interests: The authors declare that they have no competing interests in this work., (© 2024 Wu et al.)

Rationale: Systemic sclerosis (SSc) is a chronic and incurable autoimmune disease with high mortality rates, and skin fibrosis is one of distinguishing hallmarks in the pathogenesis. However, macrophage heterogeneity regulating skin fibrosis remain largely unknown. Methods: We established mouse disease model and performed single-cell RNA-sequencing (scRNA-seq) to resolve the dynamic and heterogenous characteristics of macrophages in skin fibrosis, and the role of TREM2-dependent macrophages in the pathological process was investigated using knockout mice and intraperitoneal transferring TREM2 + macrophages combining with functional assays. Results: We show that TREM2-expressing macrophages (TREM2 + MФs) accumulate in injured skin of mice treated by bleomycin (BLM) and human SSc, and their gene signatures and functional pathways are identified in the course of disease. Genetic ablation of Trem2 in mice globally accelerates and aggravates skin fibrosis, whereas transferring TREM2 hi macrophages improves and alleviates skin fibrosis. Amazingly, we found that disease-associated TREM2 + MФs in skin fibrosis exhibit overlapping signatures with fetal skin counterparts in mice and human to maintain skin homeostasis, but each has merits in skin remodeling and development respectively. Conclusion: This study identifies that TREM2 acts as a functional molecule and a major signaling by which macrophage subpopulations play a protective role against fibrosis, and disease-associated TREM2 + MФs in skin fibrosis might undergo a fetal-like reprogramming similar to fetal skin counterparts., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Objective: The study's objective was to explore whether early time-restricted eating (eTRE) and late time-restricted eating (lTRE) have different impacts on intrahepatic fat and metabolic health among patients with nonalcoholic fatty liver disease (NAFLD)., Methods: This is an 8-week, randomized, parallel-arm, open-label trial. Forty eligible patients were randomly assigned to eTRE (eating between 8:00 a.m. and 4:00 p.m.) or lTRE (eating between 12:00 p.m. and 8:00 p.m.). The primary outcome was the change of intrahepatic fat measured by magnetic resonance image-derived proton density fat fraction. Secondary outcomes included changes in weight, body composition, liver function, and cardiometabolic factors., Results: Forty participants who underwent randomization completed the trial (mean age: 38.25 years). The eTRE group had a -3.24% absolute reduction of intrahepatic fat (95% CI: -4.55% to -1.92%) and there was a -3.51% absolute reduction for the lTRE group (95% CI: -5.10% to -1.92%). Changes in intrahepatic fat were not statistically different between the two groups. Both the eTRE and lTRE groups had similar and significant reductions in weight, visceral fat, subcutaneous fat, liver enzymes, and glucose regulatory indicators., Conclusions: Among patients with NAFLD, both eTRE and lTRE induced significant reductions in intrahepatic fat and improvements in body composition, liver function, and metabolic health with similar magnitude. These findings suggest that eTRE and lTRE are comparable and feasible strategies for NAFLD management., (© 2024 The Obesity Society.)

Objective: To investigate the differences and similarities of parameters associated with anemia of inflammation between patients with stage Ⅲ periodontitis and periodontally healthy volunteers, and to explore the influence of periodontal initial therapy on those indicators., Methods: Patients with stage Ⅲ periodontitis and periodontally healthy volunteers seeking periodontal treatment or prophylaxis at Department of Periodontology, Peking University School and Hospital of Stomatology from February 2020 to February 2023 were enrolled. Their demographic characteristics, periodontal parameters (including probing depth, clinical attachment loss, bleeding index), and fasting blood were gathered before periodontal initial therapy. Three months after periodontal initial therapy, the periodontal parameters of the patients with stage Ⅲ periodontitis were re-evaluated and their fasting blood was collected again. Blood routine examinations (including white blood cells, red blood cells, hemoglobin, packed cell volume, mean corpuscular volume of erythrocytes, and mean corpuscular hemoglobin concentration) were performed. And ferritin, hepcidin, erythropoietin (EPO) were detected with enzyme-linked immunosorbent assay (ELISA). All data analysis was done with SPSS 21.0, independent sample t test, paired t test, and analysis of covariance were used for comparison between the groups., Results: A total of 25 patients with stage Ⅲ periodontitis and 25 periodontally healthy volunteers were included in this study. The patients with stage Ⅲ periodontitis were significantly older than those in periodontally healthy status [(36.72±7.64) years vs. (31.44±7.52) years, P =0.017]. The patients with stage Ⅲ periodontitis showed lower serum hemoglobin [(134.92±12.71) g/L vs. (146.52±12.51) g/L, P =0.002] and higher serum ferritin [(225.08±103.36) μg/L vs. (155.19±115.38) μg/L, P =0.029], EPO [(41.28±12.58) IU/L vs. (28.38±10.52) IU/L, P < 0.001], and hepcidin [(48.03±34.44) μg/L vs. (27.42±15.00) μg/L, P =0.009] compared with periodontally healthy volunteers. After adjusting the age with the covariance analysis, these parameters (hemoglobin, ferritin, EPO, and hepcidin) showed the same trends as independent-sample t test with statistical significance. Three months after periodontal initial therapy, all the periodontal parameters showed statistically significant improvement. The serum hemoglobin raised [(146.05±15.48) g/L vs. (133.77± 13.15) g/L, P < 0.001], while the serum ferritin [(128.52±90.95) μg/L vs. (221.22±102.15) μg/L, P < 0.001], EPO [(27.66±19.67) IU/L vs. (39.63± 12.48) IU/L, P =0.004], and hepcidin [(32.54±18.67) μg/L vs. (48.18±36.74) μg/L, P =0.033] decreased compared with baseline., Conclusion: Tendency of iron metabolism disorder and anemia of inflammation was observed in patients with stage Ⅲ periodontitis, which can be attenuated by periodontal initial therapy.

Human aging is invariably accompanied by a decline in renal function, a process potentially exacerbated by uremic toxins originating from gut microbes. Based on a registered household Chinese Guangxi longevity cohort (n = 151), we conducted comprehensive profiling of the gut microbiota and serum metabolome of individuals from 22 to 111 years of age and validated the findings in two independent East Asian aging cohorts (Japan aging cohort n = 330, Yunnan aging cohort n = 80), identifying unique age-dependent differences in the microbiota and serum metabolome. We discovered that the influence of the gut microbiota on serum metabolites intensifies with advancing age. Furthermore, mediation analyses unveiled putative causal relationships between the gut microbiota (Escherichia coli, Odoribacter splanchnicus, and Desulfovibrio piger) and serum metabolite markers related to impaired renal function (p-cresol, N-phenylacetylglutamine, 2-oxindole, and 4-aminohippuric acid) and aging. The fecal microbiota transplantation experiment demonstrated that the feces of elderly individuals could influence markers related to impaired renal function in the serum. Our findings reveal novel links between age-dependent alterations in the gut microbiota and serum metabolite markers of impaired renal function, providing novel insights into the effects of microbiota-metabolite interplay on renal function and healthy aging., (© 2023 The Authors. Aging Cell published by Anatomical Society and John Wiley & Sons Ltd.)

The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro-ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this study, deep-shotgun sequencing (average 21.5 Gigabyte (Gb)) from 450 facial samples and publicly available skin metagenomic datasets of 2069 samples to assemble a Unified Human Skin Genome (UHSG) catalog is integrated. The UHSG encompasses 813 prokaryotic species derived from 5779 metagenome-assembled genomes, among which 470 are novel species covering 20 phyla with 1385 novel assembled genomes. Based on the UHSG, the core functions of the skin microbiome are described and the differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla are identified. Furthermore, analysis of secondary metabolites of the near-complete genomes further find 1220 putative novel secondary metabolites, several of which are found in previously unknown genomes. Single nucleotide variant (SNV) reveals a possible skin protection mechanism: the negative selection process of the skin environment to conditional pathogens. UHSG offers a convenient reference database that will facilitate a more in-depth understanding of the role of skin microorganisms in the skin., (© 2023 The Authors. Advanced Science published by Wiley-VCH GmbH.)

Silver chalcogenides demonstrate great potential as flexible thermoelectric materials due to their excellent ductility and tunable electrical and thermal transport properties. In this work, we report that the amorphous/crystalline phase ratio and thermoelectric properties of the Ag 2 S x Te 1- x ( x = 0.55-0.75) samples can be modified by altering the S content. The room-temperature power factor of the Ag 2 S 0.55 Te 0.45 sample is 4.9 μW cm -1 K -2 , and a higher power factor can be achieved by decreasing the carrier concentration as predicted by the single parabolic band model. The addition of a small amount of excessive Te into Ag 2 S 0.55 Te 0.45 (Ag 2 S 0.55 Te 0.45+ y ) not only enhances the power factor by decreasing the carrier concentration but also reduces the total thermal conductivity due to decreased electronic thermal conductivity. Owing to the effectively optimized carrier concentration, the thermoelectric power factor and dimensionless figure of merit zT of the sample with y = 0.007 reaches, respectively, 6.2 μW cm -1 K -2 and 0.39, while the excellent plastic deformability is well maintained, demonstrating its promising potential as a flexible thermoelectric material at room temperature.

Coronavirus 2019 (COVID-19) is a complex disease that affects billions of people worldwide. Currently, effective etiological treatment of COVID-19 is still lacking; COVID-19 also causes damages to various organs that affects therapeutics and mortality of the patients. Surveillance of the treatment responses and organ injury assessment of COVID-19 patients are of high clinical value. In this study, we investigated the characteristic fragmentation patterns and explored the potential in tissue injury assessment of plasma cell-free DNA in COVID-19 patients. Through recruitment of 37 COVID-19 patients, 32 controls and analysis of 208 blood samples upon diagnosis and during treatment, we report gross abnormalities in cfDNA of COVID-19 patients, including elevated GC content, altered molecule size and end motif patterns. More importantly, such cfDNA fragmentation characteristics reflect patient-specific physiological changes during treatment. Further analysis on cfDNA tissue-of-origin tracing reveals frequent tissue injuries in COVID-19 patients, which is supported by clinical diagnoses. Hence, our work demonstrates and extends the translational merit of cfDNA fragmentation pattern as valuable analyte for effective treatment monitoring, as well as tissue injury assessment in COVID-19., (© 2023. The Author(s).)

Small extracellular vesicle (sEV) is an emerging source of potential biomarkers of Alzheimer's disease (AD), but the role of microRNAs (miRNAs) in sEV is not well understood. In this study, we conducted a comprehensive analysis of sEV-derived miRNAs in AD using small RNA sequencing and coexpression network analysis. We examined a total of 158 samples, including 48 from AD patients, 48 from patients with mild cognitive impairment (MCI), and 62 from healthy controls. We identified an miRNA network module (M1) that was strongly linked to neural function and showed the strongest association with AD diagnosis and cognitive impairment. The expression of miRNAs in the module was decreased in both AD and MCI patients compared to controls. Conservation analysis revealed that M1 was highly preserved in the healthy control group but dysfunctional in the AD and MCI groups, suggesting that changes in the expression of miRNAs in this module may be an early response to cognitive decline prior to the appearance of AD pathology. We further validated the expression levels of the hub miRNAs in M1 in an independent population. The functional enrichment analysis showed that 4 hub miRNAs might interact with a GDF11-centered network and play a critical role in the neuropathology of AD. In summary, our study provides new insights into the role of sEV-derived miRNAs in AD and suggests that M1 miRNAs may serve as potential biomarkers for the early diagnosis and monitoring of AD., (Copyright © 2023 Yuzhe Sun et al.)

A multi-wavelength bandstop filter is proposed and numerically demonstrated using the sum-frequency generation (SFG) process in a waveguide of periodically poled lithium niobate (PPLN). This proposed device achieves channels number reconfigurable, central filtering wavelength of each filtering channel independently tunable and extinction ratios (ERs) equalized via all-optical methods., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

Background and Objectives: Local hyperthermia at 44°C can clear multiple human papillomavirus (HPV)-infected skin lesions (warts) by targeting a single lesion, which is considered as a success of inducing antiviral immunity in the human body. However, approximately 30% of the patients had a lower response to this intervention. To identify novel molecular targets for anti-HPV immunity induction to improve local hyperthermia efficacy, we conducted a lysine succinylome assay in HaCaT cells (subjected to 44°C and 37°C water baths for 30 min)., Methods: The succinylome analysis was conducted on HaCaT subjected to 44°C and 37°C water bath for 30 min using antibody affinity enrichment together with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results were validated by western blot (WB), immunoprecipitation (IP), and co-immunoprecipitation (Co-IP). Then, bioinformatic analysis including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, motif characterization, secondary structure, and protein-protein interaction (PPI) was performed., Results: A total of 119 proteins with 197 succinylated sites were upregulated in 44°C-treated HaCaT cells. GO annotation demonstrated that differential proteins were involved in the immune system process and viral transcription. Succinylation was significantly upregulated in annexin A2. We found that hyperthermia upregulated the succinylated level of global proteins in HaCaT cells by downregulating the desuccinylase sirtuin7 (SIRT7), which can interact with annexin A2., Conclusions: Taken together, these data indicated that succinylation of annexin A2 may serve as a new drug target, which could be intervened in combination with local hyperthermia for better treatment of cutaneous warts., Competing Interests: Conflict of Interest None declared., (© 2023 Xueli Niu, Yiping Zhao, Tao Zhang, Yuzhe Su, Zhendong Wei, Kangle Fu, Jingyi Li, Mingsui Tang, Wenyu Wan, Xinghua Gao, Hongduo Chen, Ruiqun Qi, Bing Song, published by De Gruyter on behalf of Scholar Media Publishing.)

Competing Interests: Conflicts of interest The medical instrument for infrared thermotherapy is a patented device (Patent No: US 8,246,668 B2) owned by The First Hospital of China Medical University; Rui-Qun Qi, Xing-Hua Gao, and Hong-Duo Chen are original patent holders. The patent was transferred to and manufactured by Liaoning Yanyang Medical Instrument Co Ltd.

As primary producers, plants provide food, oxygen, and other resources for global ecosystems, and should therefore be given priority in biodiversity protection. Most biodiversity research focuses on biodiversity hotspots, while biodiversity coldspots, such as deserts, are largely ignored. We propose that the factors shaping plant species diversity differ between biodiversity hot spots and cold spots, especially for desert ecosystems. To test this hypothesis, we investigated plant species diversity along the Modern Silk Road in the Northwest China desert, an area characterized by low precipitation, scarce vegetation, a limited number of species, and variable human activities. Surface soil was sampled from 144 plots, environmental DNA (eDNA) was extracted from soil samples, and seed plant species were identified using DNA metabarcoding technology. A total of 671 seed plant species were detected, which was more diverse than indicated by plot survey data. Plant species diversity gradually decreased from east to west along the Silk Road. In this area, temperature determines plant species diversity more than precipitation. Additionally, human activity has altered plant species diversity by introducing crops and invasive plants and eliminating environmentally adapted indigenous plants. Our results demonstrate the potential of eDNA metabarcoding technology for plant species diversity surveying. Desert plants have adapted to dry environments by relying on underground water or utilizing occasional rainfall as ephemerals, which are often not visible during surface surveys because of their short aboveground life cycle but can be detected with eDNA metabarcoding technology. Groundwater maintenance and human activity control are recommended for plant species diversity conservation and desertification control., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors. iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.)

Recent technological advances in multi-omics and bioinformatics provide an opportunity to develop precision health assessments, which require big data and relevant bioinformatic methods. Here we collect multi-omics data from 4,277 individuals. We calculate the correlations between pairwise features from cross-sectional data and then generate 11 biological functional modules (BFMs) in males and 12 BFMs in females using a community detection algorithm. Using the features in the BFM associated with cardiometabolic health, carotid plaques can be predicted accurately in an independent dataset. We developed a model by comparing individual data with the health baseline in BFMs to assess health status (BFM-ash). Then we apply the model to chronic patients and modify the BFM-ash model to assess the effects of consuming grape seed extract as a dietary supplement. Finally, anomalous BFMs are identified for each subject. Our BFMs and BFM-ash model have huge prospects for application in precision health assessment., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

Competing Interests: Conflicts of interest The medical instrument for infrared thermotherapy is a patented device (Patent No: US 8,246,668 B2) owned by The First Hospital of China Medical University; Rui-Qun Qi, Xing-Hua Gao, and Hong-Duo Chen are original patent holders. The patent was transferred to and manufactured by Liaoning Yanyang Medical Instrument Co Ltd.

Background: 2019 Coronavirus disease (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic has already had a serious influence on human existence, causing a huge public health concern for countries all around the world. Because SARS-CoV-2 infection can be spread by contact with the oral cavity, the link between oral illness and COVID-19 is gaining traction. Through bioinformatics approaches, we explored the possible molecular mechanisms linking the COVID-19 and periodontitis to provide the basis and direction for future research., Methods: Transcriptomic data from blood samples of patients with COVID-19 and periodontitis was downloaded from the Gene Expression Omnibus database. The shared differentially expressed genes were identified. The analysis of Gene Ontology, Kyoto Encyclopedia of Genesand Genomes pathway, and protein-protein interaction network was conducted for the shared differentially expressed genes. Top 5 hub genes were selected through Maximal Clique Centrality algorithm. Then mRNA-miRNA network of the hub genes was established based on miRDB database, miRTarbase database and Targetscan database. The Least absolute shrinkage and selection operator regression analysis was used to discover possible biomarkers, which were then investigated in relation to immune-related genes., Results: Fifty-six shared genes were identified through differential expression analysis in COVID-19 and periodontitis. The function of these genes was enriched in regulation of hormone secretion, regulation of secretion by cell. Myozenin 2 was identified through Least absolute shrinkage and selection operator regression Analysis, which was down-regulated in both COVID-19 and periodontitis. There was a positive correlation between Myozenin 2 and the biomarker of activated B cell, memory B cell, effector memory CD4 T cell, Type 17 helper cell, T follicular helper cell and Type 2 helper cell., Conclusion: By bioinformatics analysis, Myozenin 2 is predicted to correlate to the pathogenesis and immune infiltrating of COVID-19 and periodontitis. However, more clinical and experimental researches are needed to validate the function of Myozenin 2., (© 2022. The Author(s).)

Numerous studies have investigated the risk factors of Alzheimer's disease (AD); however, AD-risk factors related miRNAs were rarely reported. In this study, AD-risk factor related miRNAs of 105 Chinese individuals (45 AD patients and 60 cognitively normal controls) were investigated. The results showed that Hsa-miR-185-5p, Hsa-miR-20a-5p, and Hsa-miR-497-5p were related to AD and education, Hsa-miR-185-5p, Hsa-miR-181c-5p, Hsa-miR-664a-3p, Hsa-miR-27a-3p, Hsa-miR-451a, and Hsa-miR-320a were related to AD and depression. Target prediction of above miRNAs showed that these miRNAs were involved in the generation and clearance of amyloid-beta (Aβ), important molecules related to cognition, and disease-activated microglia response to AD. It is worth noting that Hsa-miR-185-5p was related to both education and depression, whose decreased expression pattern in AD patients was alleviated by education and enhanced by depression, and participates in Aβ generation and accumulation. Our results indicated that certain education and depression factors can contribute to AD progression by modulating miRNA expression, implying that preventive interventions might alter AD progression in Chinese patients., (© 2022. The Author(s).)

The intricate processes of microbiota-gut-brain communication in modulating human cognition and emotion, especially in the context of mood disorders, have remained elusive. Here we performed faecal metagenomic, serum metabolomics and neuroimaging studies on a cohort of 109 unmedicated patients with depressed bipolar disorder (BD) patients and 40 healthy controls (HCs) to characterise the microbial-gut-brain axis in BD. Across over 12,000 measured metabolic features, we observed a large discrepancy (73.54%) in the serum metabolome between BD patients and HCs, spotting differentially abundant microbial-derived neuroactive metabolites including multiple B-vitamins, kynurenic acid, gamma-aminobutyric acid and short-chain fatty acids. These metabolites could be linked to the abundance of gut microbiota presented with corresponding biosynthetic potentials, including Akkermansia muciniphila, Citrobacter spp. (Citrobacter freundii and Citrobacter werkmanii), Phascolarctobacterium spp., Yersinia spp. (Yersinia frederiksenii and Yersinia aleksiciae), Enterobacter spp. (Enterobacter cloacae and Enterobacter kobei) and Flavobacterium spp. Based on functional neuroimaging, BD-related neuroactive microbes and metabolites were discovered as potential markers associated with BD-typical features of functional connectivity of brain networks, hinting at aberrant cognitive function, emotion regulation, and interoception. Our study combines gut microbiota and neuroactive metabolites with brain functional connectivity, thereby revealing potential signalling pathways from the microbiota to the gut and the brain, which may have a role in the pathophysiology of BD., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

A tubular-shaped Janus nanoparticle based on polydopamine that responds to near-infrared, magnetic, and pH stimuli is reported. The robust tubular polydopamine structure was obtained by optimizing the halloysite template-to-dopamine ratio during synthesis. The inner and outer surfaces of the tube were exposed at different steps of the template-sonication--etching process, enabling the differential surface modification of these surfaces. Poly(ethylene glycol) (PEG) and poly( N -isopropylacrylamide) (PNIPAM) were grafted to the outer and inner surface of the nanotube, respectively. The PEG-coated surface limited aggregation of the nanoparticles at elevated temperatures. The PNIPAM-coated interior enhanced doxorubicin loading and endowed the nanoparticle with temperature-responsive behavior. The deposition of precipitated Fe 3 O 4 nanoparticles further modified the nanoparticles. The resulting magnetic Janus nanoparticles responded to pH, temperature, and magnetic fields. Temperature changes could be induced by near-infrared laser, and all three stimuli were found to influence release rates of adsorbed doxorubicin from the nanoparticles. The interaction of the stimuli on release kinetics was elucidated using a linear mixed model; reduced pH and NIR irradiation enhanced release while applying a static magnetic field retarded release. Furthermore, the mechanism was shifted toward Fickian behavior by applying a static magnetic field and low pH conditions. However, NIR irradiation only shifted the behavior toward Fickian behavior at low pH.

Hepatocellular carcinoma (HCC) is the fourth main reason of cancer-related death. Codonopsis pilosula is a commonly used traditional Chinese medicine (TCM) for patients with HCC. However, its potential mechanism for treatment of HCC remains unclear. Here, we used transcriptomics and network pharmacology to explore the potential molecular mechanisms of Codonopsis pilosula . In our study, twelve differentially expressed genes (DEGs) (5 upregulated and 7 downregulated) of Codonopsis pilosula treating HepG2 cells (a kind of HCC cell) were identified. Among the 12 DEGs, HMOX1 may play an essential role. Codonopsis pilosula mainly affects the mineral absorption pathway in HCC. We acquired 2957, 1877, and 255 targets from TCMID, SymMap, and TCMSP, respectively. Codonopsis pilosula could upregulate HMOX1 via luteolin, capsaicin, and sulforaphane. Our study provided new understanding of the potential pharmacological mechanisms of Codonopsis pilosula in treating HCC and pointed out a direction for further experimental research., Competing Interests: There are no conflicts of interest., (Copyright © 2022 Zhili Liu et al.)

Biological age (BA) has been proposed to evaluate the aging status instead of chronological age (CA). Our study shows evidence that there might be multiple "clocks" within the whole-body system: systemic aging drivers/clocks overlaid with organ/tissue-specific counterparts. We utilize multi-omics data, including clinical tests, immune repertoire, targeted metabolomic molecules, gut microbiomes, physical fitness examinations, and facial skin examinations, to estimate the BA of different organs (e.g., liver, kidney) and systems (immune and metabolic system). The aging rates of organs/systems are diverse. People's aging patterns are different. We also demonstrate several applications of organs/systems BA in two independent datasets. Mortality predictions are compared among organs' BA in the dataset of the United States National Health and Nutrition Examination Survey. Polygenic risk score of BAs constructed in the Chinese Longitudinal Healthy Longevity Survey cohort can predict the possibility of becoming centenarian., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

The pathogenesis of COVID-19 is still elusive, which impedes disease progression prediction, differential diagnosis, and targeted therapy. Plasma cell-free RNAs (cfRNAs) carry unique information from human tissue and thus could point to resourceful solutions for pathogenesis and host-pathogen interactions. Here, we performed a comparative analysis of cfRNA profiles between COVID-19 patients and healthy donors using serial plasma. Analyses of the cfRNA landscape, potential gene regulatory mechanisms, dynamic changes in tRNA pools upon infection, and microbial communities were performed. A total of 380 cfRNA molecules were up-regulated in all COVID-19 patients, of which seven could serve as potential biomarkers (AUC > 0.85) with great sensitivity and specificity. Antiviral ( NFKB1A , IFITM3 , and IFI27 ) and neutrophil activation ( S100A8 , CD68 , and CD63 )-related genes exhibited decreased expression levels during treatment in COVID-19 patients, which is in accordance with the dynamically enhanced inflammatory response in COVID-19 patients. Noncoding RNAs, including some microRNAs (let 7 family) and long noncoding RNAs ( GJA9 - MYCBP ) targeting interleukin (IL6/IL6R), were differentially expressed between COVID-19 patients and healthy donors, which accounts for the potential core mechanism of cytokine storm syndromes; the tRNA pools change significantly between the COVID-19 and healthy group, leading to the accumulation of SARS-CoV-2 biased codons, which facilitate SARS-CoV-2 replication. Finally, several pneumonia-related microorganisms were detected in the plasma of COVID-19 patients, raising the possibility of simultaneously monitoring immune response regulation and microbial communities using cfRNA analysis. This study fills the knowledge gap in the plasma cfRNA landscape of COVID-19 patients and offers insight into the potential mechanisms of cfRNAs to explain COVID-19 pathogenesis., (© 2022 Wang et al.; Published by Cold Spring Harbor Laboratory Press.)

Quinoa ( Chenopodium quinoa Willd.) with a history of 5000 years as food is extremely rich in nutrients and bioactive compounds, including γ-aminobutyric acid (GABA), a natural four-carbon non-protein amino acid with great benefits to human health. In quinoa, GABA generally increases with the germination time, but the underlying molecular mechanism is unclear. Here, we found that the GABA content in quinoa varied significantly among 25 varieties using an automatic amino acid analyzer. Next, six varieties (three low-GABA and three high-GABA varieties) were used for further analyses. The content of GABA in six varieties all showed an increasing trend after germination. In addition, Pearson's correlation analysis showed that the changes in GABA content were closely related to the transcript level or enzyme activity of three key enzymes including glutamate decarboxylase (GAD), GABA transaminase (GABA-T), and succinate-semialdehyde dehydrogenase (SSADH) in the GABA shunt, especially GAD. Based on RNA-sequencing analysis, eight GAD genes, two GABA - T genes, one SSADH gene, nine polyamine oxidase ( PAO ) genes, five diamine oxidase ( DAO ) genes, four 4-aminobutyraldehyde dehydrogenase ( BADH ) genes, and three thermospermine synthase ACAULIS5 ( ACL 5) genes were identified. Among these, CqGAD 8 and CqGABA - T 2 may make a greater contribution to GABA accumulation during quinoa germination.

The immune system of skin develops in stages in mice. However, the developmental dynamics of immune cells in human skin remains elusive. Here, we perform transcriptome profiling of CD45 + hematopoietic cells in human fetal skin at an estimated gestational age of 10-17 weeks by single-cell RNA sequencing. A total of 13 immune cell types are identified. Skin macrophages show dynamic heterogeneity over the course of skin development. A major shift in lymphoid cell developmental states occurs from the first to the second trimester that implies an in situ differentiation process. Gene expression analysis reveals a typical developmental program in immune cells in accordance with their functional maturation, possibly involving metabolic reprogramming. Finally, we identify transcription factors (TFs) that potentially regulate cellular transitions by comparing TFs and TF target gene networks. These findings provide detailed insight into how the immune system of the human skin is established during development., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

DNA barcoding has become one of the most important techniques in plant species identification. Successful application of this technology is dependent on the availability of reference database of high species coverage. Unfortunately, there are experimental and data processing challenges to construct such a library within a short time. Here, we present our solutions to these challenges. We sequenced six conventional DNA barcode fragments (ITS1, ITS2, matK 1, matK 2, rbcL 1, and rbcL 2) of 380 flowering plants on next-generation sequencing (NGS) platforms (Illumina Hiseq 2500 and Ion Torrent S5) and the Sanger sequencing platform. After comparing the sequencing depths, read lengths, base qualities, and base accuracies, we conclude that Illumina Hiseq2500 PE250 run is suitable for conventional DNA barcoding. We developed a new "Cotu" method to create consensus sequences from NGS reads for longer output sequences and more reliable bases than the other three methods. Step-by-step instructions to our method are provided. By using high-throughput machines (PCR and NGS), labeling PCR, and the Cotu method, it is possible to significantly reduce the cost and labor investments for DNA barcoding. A regional or even global DNA barcoding reference library with high species coverage is likely to be constructed in a few years., Competing Interests: The authors declare no conflict of interest., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

The outbreak of coronavirus disease 2019 (COVID-19) is a global health emergency. Various omics results have been reported for COVID-19, but the molecular hallmarks of COVID-19, especially in those patients without comorbidities, have not been fully investigated. Here we collect blood samples from 231 COVID-19 patients, prefiltered to exclude those with selected comorbidities, yet with symptoms ranging from asymptomatic to critically ill. Using integrative analysis of genomic, transcriptomic, proteomic, metabolomic and lipidomic profiles, we report a trans-omics landscape for COVID-19. Our analyses find neutrophils heterogeneity between asymptomatic and critically ill patients. Meanwhile, neutrophils over-activation, arginine depletion and tryptophan metabolites accumulation correlate with T cell dysfunction in critical patients. Our multi-omics data and characterization of peripheral blood from COVID-19 patients may thus help provide clues regarding pathophysiology of and potential therapeutic strategies for COVID-19., (© 2021. The Author(s).)

To achieve the promise of stimuli-responsive drug delivery systems for the treatment of cancer, they should (1) avoid premature clearance; (2) accumulate in tumors and undergo endocytosis by cancer cells; and (3) exhibit appropriate stimuli-responsive release of the payload. It is challenging to address all of these requirements simultaneously. However, the numerous proof-of-concept studies addressing one or more of these requirements reported every year have dramatically expanded the toolbox available for the design of drug delivery systems. This review highlights recent advances in the targeting and stimuli-responsiveness of drug delivery systems. It begins with a discussion of nanocarrier types and an overview of the factors influencing nanocarrier biodistribution. On-demand release strategies and their application to each type of nanocarrier are reviewed, including both endogenous and exogenous stimuli. Recent developments in stimuli-responsive targeting strategies are also discussed. The remaining challenges and prospective solutions in the field are discussed throughout the review, which is intended to assist researchers in overcoming interdisciplinary knowledge barriers and increase the speed of development. This review presents a nanocarrier-based drug delivery systems toolbox that enables the application of techniques across platforms and inspires researchers with interdisciplinary information to boost the development of multifunctional therapeutic nanoplatforms for cancer therapy.

Purpose: Critically ill COVID-19 patients have significantly increased risk of death. Although several circulating biomarkers are thought to be related to COVID-19 severity, few studies have focused on the characteristics of critically ill patients with different outcomes. The objective of this study was to perform a longitudinal investigation of the potential mechanisms affecting the prognosis of critically ill COVID-19 patients., Methods: In addition to clinical data, 113 whole blood samples and 85 serum samples were collected from 33 severe and critical COVID-19 patients without selected comorbidities. Multi-omics analysis was then performed using longitudinal samples., Results: Obvious transcriptional transitions were more frequent in critical survivors than in critical non-survivors, indicating that phase transition may be related to survival. Based on analysis of differentially expressed genes during transition, the erythrocyte differentiation pathway was significantly enriched. Furthermore, clinical data indicated that red blood cell counts showed greater fluctuation in survivors than in non-survivors. Moreover, declining red blood cell counts and hemoglobin levels were validated as prognostic markers of poor outcome in an independent cohort of 114 critical COVID-19 patients. Protein-metabolite-lipid network analysis indicated that tryptophan metabolism and melatonin may contribute to molecular transitions in critical COVID-19 patients with different outcomes., Conclusions: This study systematically and comprehensively depicted the longitudinal hallmarks of critical COVID-19 patients and indicated that multi-omics transition may impact the prognosis., Take Home Message: Frequent transcriptional phase transitions may contribute to outcome in critically ill COVID-19 patients. Furthermore, fluctuation in red blood cell and hemoglobin levels may relate to poor prognosis. The biological function of melatonin was suppressed in COVID-19 non-survivors, which may provide a potential theoretical basis for clinical administration.

Key Message: We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.

Background: Lysine succinylation is a newly identified posttranslational modification (PTM), which exists widely from prokaryotes to eukaryotes and participates in various cellular processes, especially in the metabolic processes. Staphylococcus epidermidis is a commensal bacterium in the skin, which attracts more attention as a pathogen, especially in immunocompromised patients and neonates by attaching to medical devices and forming biofilms. However, the significance of lysine succinylation in S. epidermidis proteins has not been investigated., Objectives: The purpose of this study was to investigate the physiological and pathological processes of S. epidermidis at the level of PTM. Moreover, by analyzing previous succinylome datasets in various organisms, we tried to provide an in-depth understanding of lysine succinylation., Methods: Using antibody affinity enrichment followed by LC-MS/MS analysis, we examined the succinylome of S. epidermidis (ATCC 12228). Then, bioinformatics analysis was performed, including Gene Ontology (GO), KEGG enrichment, motif characterization, secondary structure, protein-protein interaction, and BLAST analysis., Results: A total of 1557 succinylated lysine sites in 649 proteins were identified in S. epidermidis (ATCC 12228). Among these succinylation proteins, GO annotation showed that proteins related to metabolic processes accounted for the most. KEGG pathway characterization indicated that proteins associated with the glycolysis/gluconeogenesis and citrate cycle (TCA cycle) pathway were more likely to be succinylated. Moreover, 13 conserved motifs were identified. The specific motif KsuD was conserved in model prokaryotes and eukaryotes. Succinylated proteins with this motif were highly enriched in the glycolysis/gluconeogenesis pathway. One succinylation site (K144) was identified in S-ribosylhomocysteine lyase, a key enzyme in the quorum sensing system, indicating the regulatory role succinylation may play in bacterial processes. Furthermore, 15 succinyltransferases and 18 desuccinylases (erasers) were predicted in S. epidermidis by BLAST analysis., Conclusion: We performed the first comprehensive profile of succinylation in S. epidermidis and illustrated the significant role succinylation may play in energy metabolism, QS system, and other bacterial behaviors. This study may be a fundamental basis to investigate the underlying mechanisms of colonization, virulence, and infection of S. epidermidis , as well as provide a new insight into regulatory effects succinylation may lay on metabolic processes (Data are available via ProteomeXchange with identifier PXD022866)., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zhao, Han, Sun, Wei, Chen, Niu, An, Zhang, Qi and Gao.)

Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the matR transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include nad1 introns 2/3/4, nad4 intron 3, nad5 introns 2/3, cox2 intron 1, and ccmFc intron 1. A greater splicing efficiency of nad4 intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III 2 were also observed in nodules, although the causal relationship between these observations requires further investigation.

In the field of criminal investigations, in the event that a body is found in water, the ability to differentiate whether the cause of death was drowning or the body was murdered then dumped into water elsewhere is difficult but important for case detection. Detecting diatoms in human organs can be used to effectively identify if the cause of death was drowning. At present, diatom detection methods are roughly divided into morphological and molecular detection methods, but both methods have different limitations. In this study, a total of 79 samples from 23 victims in 19 known drowning deaths were collected. The diatom morphological identification combined with DNA metabarcoding technology was used to compare the reliability of the diatom detection method. Microscopic observations revealed that the positive detection rate of diatoms was 52.6 %, 26.3 % and 58.8 % respectively in the kidney, liver and lung samples. DNA metabarcoding analysis found that the positive detection rate of diatoms was 31.6 %, 31.6 % and 35.3 % respectively in kidney, liver and lung samples. When compared with barcode BacirbcL, barcode 18S605 detected more diatoms, while diatoms in BacirbcL were more consistent with environmental samples. The comparative analysis found that microscopic observations were not highly correlated with the identification results of DNA barcoding technology. There were no obvious differences in the effect of internal organs on diatom enrichment, and different organs should be tested at the same time. At present, the DNA barcode reference sequence is gravely insufficient and has many errors, which leads to restrictions in the application of this technology, resulting in many OTU not being accurately identified. This explains why the success rate of molecular identification is not higher than that of microscopic identification. Construction of a reliable diatom DNA barcode reference sequence database is an urgent task for drowning forensics., Competing Interests: Declaration of Competing Interest The authors declare no conflicts of interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)

The presence of diatoms in victim's internal organs has been regarded as a gold biological evidence of drowning. The idea becomes true at the advent of DNA metabarcoding. Unfortunately, the DNA barcode of diatoms are far from being applicable due to neither consensus on the barcode and nor reliable reference library.In this study we tested 23 pairs of primers, including two new primer pairs, Baci18S (V4 of 18S) and BacirbcL (central region of rbcL), for amplifying fragments of 16S/18S, 23S/28S, COI, ITS and rbcL. A total of five pairs of primers performed satisfactory for diatoms. We used three of them, 18S605 (V2 + V3 of 18S), Baci18S and BacirbcL, to barcode four water samples using next generation sequencing platform. The results showed that these primers worked well for NGS metabarcoding of diatoms. We suggest that 18S605, Baci18S and BacirbcL be barcodes of diatoms and the corresponding primer pairs be used. Considering a quite high proportion of sequences deposited in GenBank were mislabeled, the most urgent task for DNA barcoding of diatoms is to create standard sequences using correctly identified specimens, ideally type specimens., (© FEMS 2020.)

Synthesis of hollow polydopamine bowl-shaped nanoparticles (nanobowls), as small as 80 nm in diameter, via a one-pot template-free rapid method is reported. Addition of dopamine to a solution of 0.606 mg/mL tris(hydroxymethyl)aminomethane in an ethanol/water mixed solvent resulted in the formation of hollow spherical nanocapsules within 2 h. At longer reaction times, the formation of conventional solid nanospheres dominated the reaction. The wall thickness of the nanocapsules increased with increasing dopamine concentration in the reaction medium. Wall thickness was also influenced by oxygen availability during the reaction. Nanocapsules with thin walls were prone to collapse. When dried, over 90% of the nanocapsules with wall thickness on the order of 11 nm collapsed. Also, the degree of collapse of individual nanoparticles changed from complete to partial to no collapse as the wall thickness was increased. Varying the ethanol content affected the cavity size and overall dimension of the nanocapsules produced but did not result in a significant change to the wall thickness. A mechanism describing the formation of the nanocapsules and their subsequent collapse into nanobowls is presented. The shape-tunable nanobowls prepared through this green, rapid, and affordable method are expected to have applications in the biomedical, electrochemical, and catalytic fields.

Neurodegenerative diseases encompass a wide variety of pathological conditions caused by a loss of neurons in the central nervous system (CNS) and are severely debilitating. Exosome contains bio-signatures of great diagnostic and therapeutic value. There is proof that exosomal proteins can be biomarkers for Alzheimer's disease (AD) and Parkinson's disease (PD). MicroRNAs in exosome has potential to be an important source of biomarkers for neurodegenerative diseases. Here, we report exosomal microRNA performance of human plasma in neurodegenerative diseases by small RNA sequencing. A wide range of altered exo-miRNA expression levels were detected in both AD and PD patients. Down-regulated miRNAs in AD samples were enriched in ECM-receptor interaction pathway and both up-/down-regulated miRNAs in PD samples were enriched in fatty acid biosynthesis pathway. Compared to the control, 8 miRNAs were found to be significantly elevated/declined in AD and PD samples, of which 4 miRNAs were newly identified. Additionally, two exosome isolating methods were compared and the reproducibility of plasma exo-miRNA expression was confirmed, suggesting the feasibility of large-scale clinical application of this method. This study revealed exo-miRNA expression levels in neurodegenerative diseases, proposed new biomarkers and their potential functional pathway for AD and PD, confirmed the reproductivity of exo-miRNA profiles by using a different exosome isolating method, and compared the results with plasma miRNA expression. Therefore, this study also provides a precedent for identifying exosomal biomarkers of neurodegenerative diseases in plasma by high-throughput sequencing and it could extend the therapeutic repertoire of exosomal biomarkers., (Copyright © 2020 Nie, Sun, Zhen, Guo, Ye, Liu, Yang and Zhang.)

Background: Multimorbidity not only affects the quality of patients' lives, but can also bring a heavy economic burden to individuals, families and society. The purpose of this study was to reveal the connections between diseases, especially the important role each disease played in the entire multimorbidity network., Methods: A total of 1,155,734 inpatients were enrolled through multistage stratified random sampling in Jilin Province in 2017. Categorical variables were compared using the Rao-Scott-χ2 test. Weighted networks were adopted to present the complex relationships of multimorbidity., Results: The distributions of the number of diseases differed significantly by gender, age and health insurance scheme ( P < 0.001). Diseases of the respiratory system had the highest weight in multimorbidity in young people. Endocrine, nutritional and metabolic diseases and circulatory system diseases were often associated with other systemic diseases in middle aged and old people., Conclusions: Multimorbidity with respiratory system diseases in young people should not be overlooked. Additionally, effective prevention efforts that target endocrine, nutritional and metabolic diseases and circulatory system diseases are needed in middle aged and old people.

We report a novel synthesis scheme to produce polydopamine (PDA) nanotubes using halloysite clay nanotubes (HNT) as a sacrificial template. Polydopamine nanotubes were fabricated via the formation of a polydopamine coating on HNT from a dopamine solution followed by template removal. Michael Addition was used to decorate the outer surface with polyethylene glycol. Removal of the template material resulted in a bilayered organic nanotube consisting of an inner layer of polydopamine adjacent to the lumen and an outer polyethylene glycol surface. The tubes had an aspect ratio of 5.3 ± 0.6, a diameter on the order of 70 nm, and wall thicknesses on the order of 15 nm. The PDA nanotubes exhibited photothermal conversion upon irradiation at near infrared wavelengths; a temperature increase of 30 °C was observed when a 250 μg ml -1 sample was subjected to 1 W cm -2 density irradiation at 808 nm wavelength. Analysis indicated that the prepared tubes had slightly higher photothermal conversion efficiency than PDA nanospheres. An antitumor drug, doxorubicin, was used as a model to test the potential for drug delivery of the organic nanotubes. The nanotubes exhibited higher loading capacities than PDA nanospheres and were capable of controlled release at pHs relevant to human serum and tumors (pH 7.4 and 5.0 respectively). Drug release rates varied as a function of system pH and application of near infrared irradiation. Release of doxorubicin was enhanced at a pH of 5.0, and retarded at a pH of 7.4. Irradiation with 808 nm wavelength light also increased the release of doxorubicin.

Whispering-gallery-mode (WGM) microresonators have shown their potential in high-precision gyroscopes because of their small volume and high-quality factors. However, Kerr noise can always be the limit of accuracy. Angular-rate sensing based on mode splitting treats backscattering as a measured signal, which can induce mode splitting, while it is considered as a main source of noise in conventional resonator optical gyroscopes. Meanwhile, mode splitting also provides superior noise suppression owing to its self-reference scheme. Kerr noise in this scheme has not been defined and solved yet. Here, the mechanism of the Kerr noise in the measurement is analyzed and the mathematical expressions are derived, indicating the relationship between the Kerr noise and the output of the system. The influence caused by Kerr noise on the output is simulated and discussed. Simulations show that the deviation of the splitting caused by Kerr noise is 1.913 × 10 -5 Hz at an angular rate of 5 × 10⁶ °/s and the corresponding deviation of the angular rate is 9.26 × 10 -9 °/s. It has been proven that angular-rate sensing based on mode splitting offers good suppression of Kerr noise.

Matching ATP:NADPH provision and consumption in the chloroplast is a prerequisite for efficient photosynthesis. In terms of ATP:NADPH ratio, the amount of ATP generated from the linear electron flow does not meet the demand of the Calvin-Benson-Bassham (CBB) cycle. Several different mechanisms to increase ATP availability have evolved, including cyclic electron flow in higher plants and the direct import of mitochondrial-derived ATP in diatoms. By imaging a fluorescent ATP sensor protein expressed in living Arabidopsis thaliana seedlings, we found that MgATP 2- concentrations were lower in the stroma of mature chloroplasts than in the cytosol, and exogenous ATP was able to enter chloroplasts isolated from 4- and 5-day-old seedlings, but not chloroplasts isolated from 10- or 20-day-old photosynthetic tissues. This observation is in line with the previous finding that the expression of chloroplast nucleotide transporters (NTTs) in Arabidopsis mesophyll is limited to very young seedlings. Employing a combination of photosynthetic and respiratory inhibitors with compartment-specific imaging of ATP, we corroborate the dependency of stromal ATP production on mitochondrial dissipation of photosynthetic reductant. Our data suggest that, during illumination, the provision and consumption of ATP:NADPH in chloroplasts can be balanced by exporting excess reductants rather than importing ATP from the cytosol., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

An interpolation computational ghost imaging (ICGI) method is proposed and demonstrated that is able to reduce the noise interference from a fluctuating source and background. The noise is estimated through periodic illuminations by a specific assay pattern during sampling, which is then used to correct the bucket detector signal. To validate this method simulations and experiments were conducted. Light source intensity and background lighting were randomly varied to modulate the noise. The results show that good quality images can be obtained, while with conventional computational ghost imaging (CGI) the reconstructed object is barely recognizable. The ICGI method offers a general approach applicable to all CGI techniques, which can attenuate the interference from source fluctuations, background light noise, dynamic scattering, and so on.

Phosphorylation of the transit peptides of nuclear-encoded preprotein is a well-known regulatory process of protein import in plant chloroplasts. In the Arabidopsis Protein Phosphorylation Site Database, 103 out of 802 mitochondrial proteins were found to contain one or more experimentally proven phosphorylation sites in their first 60 amino acid residues. Analysis of the N-terminal sequences of selected mitochondrial preproteins and their homologs from 64 plant species showed high conservation among phosphorylation sites. The ability of kinases from various sources including leaf extract (LE), root extract (RE), wheat germ lysate (WGL), and STY kinases to phosphorylate N-terminal sequences of several respiratory chain proteins were examined by in vitro kinase assays. The three STY kinases were shown to phosphorylate the N-terminal sequences of some proteins we tested but exhibited different specificities. Interestingly, the N-terminal sequences of two mitochondrial ATP synthase beta subunit 1/3 (pF1β-1/3) could be phosphorylated by LE and RE but not by STY kinases, suggesting that there are uncharacterized presequence-phosphorylating kinases other than STY kinases present in RE and LE. Mitochondrial import studies showed that the import of RRL-synthesized pF1βs was impeded by the treatment of LE, and the addition of a short SSU transit peptide containing a phosphorylatable 14-3-3 binding site could enhance the import of LE-treated pF1βs. Our results suggested that the transit peptide of pSSU can compete with the presequences of pF1βs for an uncharacterized kinase(s) in leaf. Altogether, our data showed that phosphorylation of transit peptides/presequences are not uncommon for chloroplast-targeted and mitochondria-targeted proteins, albeit possibly differentially regulated.

Overexpression of AtPAP2, a phosphatase located on the outer membranes of chloroplasts and mitochondria, leads to higher energy outputs from these organelles. AtPAP2 interacts with seven MORF proteins of the editosome complex. RNA-sequencing analysis showed that the editing degrees of most sites did not differ significantly between OE and WT, except some sites on the transcripts of several cytochrome c maturation (Ccm) genes. Western blotting of 2D BN-PAGE showed that the patterns of CcmF N1 polypeptides were different between the lines. We proposed that AtPAP2 may influence cytochrome c biogenesis by modulating RNA editing through its interaction with MORF proteins., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)

Disease resistance exerts a fitness cost on plants, presumably due to the extra consumption of energy and carbon. In this study, we examined whether transgenic Arabidopsis thaliana with increased levels of ATP and sucrose is more resistant or susceptible to pathogen infection. Lines of A. thaliana over-expressing purple acid phosphatase 2 (AtPAP2) (OE lines) contain increased levels of ATP and sucrose, with improved growth rate and seed production. Compared to wild type (WT) and pap2 lines, the OE lines were more susceptible to several Pseudomonas syringae pv. tomato (Pst) strains carrying AvrRpm1, AvrRpt2 AvrRps4, AvrPtoB, HrcC and WT strain DC3000. The increased susceptibility of the OE lines to Pst strains cannot solely be attributed to the suppressed expression of R-genes but must also be attributed to the suppression of downstream signaling components, such as MOS2, EDS1 and EDS5. Before infection, the levels of salicylic acid (SA) and jasmonic acid (JA) precursor OPDA were similar in the leaves of OE, pap2 and WT plants, whereas the levels of JA and its derivative JA-Ile were significantly lower in the leaves of OE lines and higher in the pap2 line. The expression of JA marker defense gene PDF1.2 was up-regulated in the OE lines compared to the WT prior to Pst DC3000 infection, but its expression was lower in the OE lines after infection. In summary, high fitness Arabidopsis thaliana exhibited altered JA metabolism and broad suppression of R-genes and downstream genes as well as a higher susceptibility to Pst infections., Competing Interests: I would like to declare that AtPAP2 is the subject of the US patent number 9,476,058 “Method for Speeding Up Plant Growth and Improving Yield by Introducing Phosphatases in Transgenic Plant” and this does not alter our adherence to all PLOS ONE policies on sharing data and materials. We do not have other competing interests.