PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs.

To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models for human biology and disease, a comprehensive understanding of molecular and cellular mechanisms underlying various complex phenotypes in pigs and how the findings can be translated to other species, especially humans, are urgently needed. Here, within the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build the PigBiobank (http://pigbiobank.farmgtex.org) to systematically investigate the relationships among genomic variants, regulatory elements, genes, molecular networks, tissues and complex traits in pigs. This first version of the PigBiobank curates 71 885 pigs with both genotypes and phenotypes from over 100 pig breeds worldwide, covering 264 distinct complex traits. The PigBiobank has the following functions: (i) imputed sequence-based genotype-phenotype associations via a standardized and uniform pipeline, (ii) molecular and cellular mechanisms underlying trait-associations via integrating multi-omics data, (iii) cross-species gene mapping of complex traits via transcriptome-wide association studies, and (iv) high-quality results display and visualization. The PigBiobank will be updated timely with the development of the FarmGTEx-PigGTEx project, serving as an open-access and easy-to-use resource for genetically and biologically dissecting complex traits in pigs and translating the findings to other species.

Point-of-care detection of Monkeypox virus clades using high-performance upconversion nanoparticle-based lateral flow assay.

There is an urgent need for a point-of-care testing (POCT) method in developing and underserved regions to distinguish between two Monkeypox virus (MPXV) clades, given their varying transmissibility and clinical manifestations. In this paper, we target the specific complement protein gene fragment of two MPXV clades and construct a high-performance upconversion nanoparticles-based lateral flow assay (UCNPs-based LFA) with double T-lines and a shared C-line. This enables qualitative and quantitative dual-mode detection when combined with a smartphone and a benchtop fluorescence analyzer. The developed LFA exhibits stable performance, convenient operation, rapid readout (within 8 min), and a much lower limit of detection (LOD) (~ pM level) compared to existing POCT methods. The proposed detection platform demonstrates significant potential for pathogen diagnosis using a POCT approach.

Long-wave opsin involved in body color plastic development in Nilaparvata lugens.

BACKGROUND: As one of the components of visual photopigments in photoreceptor cells, opsin exhibits different spectral peaks and plays crucial roles in visual function. Besides, it is discovered to evolve other functions despite color vision. However, research on its unconventional function is limited nowadays. With the increase in genome database numbers, various numbers and types of opsins have been identified in insects due to gene duplications or losses. The Nilaparvata lugens (Hemiptera) is a rice pest known for its long-distance migration capability. In this study, opsins were identified in N. lugens and characterized by genome and transcriptome analyses. Meanwhile, RNA interference (RNAi) was carried out to investigate the functions of opsins, and then the Illumina Novaseq 6000 platform-based transcriptome sequencing was performed to reveal gene expression patterns. RESULTS: Four opsins belonging to G protein-coupled receptors were identified in the N. lugens genome, including one long-sensitive opsin (Nllw) together with two ultraviolet-sensitive opsins (NlUV1/2) and an additional new opsin with hypothesized UV peak sensitivity (NlUV3-like). A tandem array of NlUV1/2 on the chromosome suggested the presence of a gene duplication event, with similar exons distribution. Moreover, as revealed by spatiotemporal expression, the four opsins were highly expressed in eyes with age-different expression levels. Besides, RNAi targeting each of the four opsins did not significantly affect the survival of N. lugens in phytotron, but the silencing of Nllw resulted in the melanization of body color. Further transcriptome analysis revealed that silencing of Nllw resulted in up-regulation of a tyrosine hydroxylase gene (NlTH) and down-regulation of an arylalkylamine-N-acetyltransferases gene (NlaaNAT) in N. lugens, demonstrating that Nllw is involved in body color plastic development via the tyrosine-mediated melanism pathway. CONCLUSIONS: This study provides the first evidence in a Hemipteran insect that an opsin (Nllw) takes part in the regulation of cuticle melanization, confirming a cross-talk between the gene pathways underlying the visual system and the morphological differentiation in insects.

Anxiety and depression in the post-pandemic era: concerns about viral mutation and re-outbreak.

BACKGROUND: The 2020 coronavirus pandemic (COVID-19) has been raging for more than 20 months, putting significant strain on public health systems around the world. Despite the fact that the pandemic has been effectively managed in certain countries, regional outbreaks and viral mutations continue to pose a threat to people's lives. The likelihood of post-pandemic changes in people's psychological situations warrants more investigation. DESIGN AND PARTICIPANTS: This study was conducted in the context of another outbreak in Zhangjiajie, China, respondents (infected patients, healthy population) were required to complete self-administered questions and standardized questionnaires, including the patient health questionnaire-9 (PHQ-9), the generalized anxiety disorder-7 (GAD-7), and the Brief Illness Perception Questionnaire (BIPQ). MEASURES: We conducted an anonymous questionnaire survey of infected patients (excluding critically ill patients) in the confirmed COVID-19 ward of Zhangjiajie City People's Hospital's East Hospital from August 14 to 24, 2021, and used convenience sampling to survey medical staff and the general public to assess the psychological reactions of different populations during the delta variant outbreak pandemic. Differences in anxiety and depression severity were compared between groups, with logistic regression models constructed to explore potential factors associated with scoring clinical significant levels of depression and/or anxiety. RESULTS: There is no significant difference (p value = 0.228) between anxiety and depression in patients (n = 53), general public (n = 97), medical personnel (n = 103), and support workers (n = 65). Females reported higher scores on the GAD-7 and the BIPQ, reduced communication with family and friends appeared to be a risk factor for clinically significant anxiety and depression. CONCLUSIONS: There were no significant differences in anxiety and depression across populations explored in this study, but females had higher anxiety and illness perception than males, and effective communication may help improve mental health.

Comparison of paper-based nucleic acid extraction materials for point-of-care testing applications.

Cheap, rapid, simple and equipment-free nucleic acid extraction (NAE) is highly preferred for implementing nucleic acid detection at point-of-care (POC). Paper-based NAE materials have been extensively utilized due to their low cost, abundance, portability, biocompatibility and ease of chemical modification. However, it is challenging for users to choose the proper one from existing paper-based NAE materials for specific POC applications, which is determined by their physical and chemical properties. Additionally, building the relationship between the physical and chemical properties and the NAE efficiency of paper-based materials is instructive for development of new paper-based NAE materials. In this study, we first systematically compared the physical and chemical properties of six widely used paper-based NAE materials (namely Whatman filter paper #1, FTA card, FTA elute card, Fusion 5, silica membrane and polyethersulfone (PES) membrane), and then evaluated their NAE efficiency. The obtained results indicated that pore uniformity, wet strength, porosity and functional groups are key parameters to affect the efficiency of NAE. The NAE performance of FTA card is the best with high concentration and purity. Finally, we envision that more cost-effective paper-based NAE materials will be developed for POCT application in the future. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10570-022-04444-6.

DHFR silence alleviated the development of liver fibrosis by affecting the crosstalk between hepatic stellate cells and macrophages.

Liver fibrogenesis is a dynamic cellular and tissue process which has the potential to progress into cirrhosis of even liver cancer and liver failure. The activation of hepatic stellate cells (HSCs) is the central event underlying liver fibrosis. Besides, hepatic macrophages have been proposed as potential targets in combatting fibrosis. As for the relationship between HSCs and hepatic macrophages in liver fibrosis, it is generally considered that macrophages promoted liver fibrosis via activating HSCs. However, whether activated HSCs could in turn affect macrophage polarization has rarely been studied. In this study, mRNAs with significant differences were explored using exosomal RNA-sequencing of activated Lx-2 cells and normal RNA-sequencing of DHFR loss-of-function Lx-2 cell models. Cell functional experiments in both Lx-2 cells and macrophages animal model experiments were performed. The results basically confirmed exosomes secreted from activated HSCs could promote M1 polarization of macrophages further. Exosome harbouring DHFR played an important role in this process. DHFR silence in HSCs could decrease Lx-2 activation and M1 polarization of M0 macrophages and then alleviate the development of liver fibrosis both in vitro and vivo. Our work brought a new insight that exosomal DHFR derived from HSCs had a crucial role in crosstalk between HSCs activation and macrophage polarization, which may be a potential therapeutic target in liver fibrosis.

A digitalized isothermal nucleic acid testing platform based on a pump-free open droplet array microfluidic chip.

Digital PCR has shown great potential for quantitative nucleic acid testing (NAT), but most existing platforms are dependent on large auxiliary equipment (e.g., vacuum pump, amplification instrument, fluorescence microscope) to achieve target dispersion, amplification, signal capture and result analysis. Such complex, expensive and bulky NAT platforms have limited their applications in resource-limited areas, especially for point-of-care testing (POCT). In this work, we designed a digital isothermal NAT platform based on a pump-free open droplet array microfluidic chip. A pump-free microfluidic chip was developed based on an open microdroplet array in the form of thousands of independent microdroplets for spontaneous sample dispersion, without the need for external power. Combined with a handheld fluorescent signal reader based on a smartphone, this digital NAT platform can accurately quantify as low as 1 copy per µL of λDNA. Therefore, our integrated NAT platform, as a potable, robust and low-cost tool for highly accurate NA quantitative analysis, holds great potential for POCT applications.

Real-Time Visualization of Solid-Phase Ion Migration Kinetics on Nanowire Monolayer.

Ion migration has been recognized as a critical step in determining the performance of numerous devices in chemistry, biology, and material science. However, direct visualization and quantitative investigation of solid-phase ion migration among anisotropic nanostructures have been a challenging task. Here, we report an in-situ ChemTEM method to quantitatively investigate the solid-phase ion migration process among coassembled nanowires (NWs). This complicated process was tracked within a NW and between NWs with an obvious nanogap, which was revealed by both phase field simulation and ab initio modeling theoretical evaluation. A migration "bridge" between neighboring NWs was observed. Furthermore, these new observations could be applied to migration of other metal ions on semiconductor NWs. These findings provide critical insights into the solid-phase ion migration kinetics occurring in nanoscale systems with generality and offer an efficient tool to explore other ion migration processes, which will facilitate fabrication of customized and new heteronanostructures in the future.

Phosphate transporters, PnPht1;1 and PnPht1;2 from Panax notoginseng enhance phosphate and arsenate acquisition.

BACKGROUND: Panax notoginseng is a medicinally important Chinese herb with a long history of cultivation and clinical application. The planting area is mainly distributed in Wenshan Prefecture, where the quality and safety of P. notoginseng have been threatened by high concentration of arsenic (As) from the soil. The roles of phosphate (Pi) transporters involved in Pi acquisition and arsenate (AsV) tolerance were still unclear in this species. RESULTS: In this study, two open reading frames (ORFs) of PnPht1;1 and PnPht1;2 separated from P. notoginseng were cloned based on RNA-seq, which encoded 527 and 541 amino acids, respectively. The results of relative expression levels showed that both genes responded to the Pi deficiency or As exposure, and were highly upregulated. Heterologous expression in Saccharomyces cerevisiae MB192 revealed that PnPht1;1 and PnPht1;2 performed optimally in complementing the yeast Pi-transport defect, particularly in PnPht1;2. Cells expressing PnPht1;2 had a stronger AsV tolerance than PnPht1;1-expressing cells, and accumulated less As in cells under a high-Pi concentration. Combining with the result of plasma membrane localization, these data confirmed that transporters PnPht1;1 and PnPht1;2 were putative high-affinity H+/H2PO4- symporters, mediating the uptake of Pi and AsV. CONCLUSION: PnPht1;1 and PnPht1;2 encoded functional plasma membrane-localized transporter proteins that mediated a putative high-affinity Pi/H+ symport activity. Expression of PnPht1;1 or PnPht1;2 in mutant strains could enhance the uptake of Pi and AsV, that is probably responsible for the As accumulation in the roots of P. notoginseng.

Identification of immune cells and mRNA associated with prognosis of gastric cancer.

BACKGROUND: The clinical success demonstrates the enormous potential of immunotherapy in cancer treatment. METHODS: This article presented research linking gastric cancer to immune cells, based on RNA-seq data of Stomach adenocarcinoma (STAD) and gene expression profile of GSE84437, 24 kinds of tumor-infiltrating immune cells were quantified by single-sample gene set enrichment analysis. RESULTS: Th2 cells, T helper cells, and Mast cells were identified as prognostic immune cells in both TCGA and GEO groups. Then SUPV3L1 and SLC22A17 were identified as hub genes which may affect immune cell infiltration by correlation analysis. Survival analysis further proved that hub genes and prognostic immune cells are associated with the prognosis of gastric cancer. In gastrointestinal tumors, hub genes and prognostic immune cells also found differences in non-tumor and tumor tissues. CONCLUSIONS: We found that three immune cells infiltration are associated with the prognosis of gastric cancer and further identify two hub genes. These two key genes may affect immune cell infiltration, result in the different prognosis of patients.

Transcriptional Regulation of Early Growth Response Gene-1 (EGR1) is Associated with Progression of Nonalcoholic Fatty Liver Disease (NAFLD) in Patients with Insulin Resistance.

BACKGROUND The occurrence of nonalcoholic fatty liver disease (NAFLD) is closely related to type 2 diabetes, especially in patients with insulin resistance. The purpose of this research was to elucidate the major genes and transcriptional regulation of insulin resistance in the progression of NAFLD. MATERIAL AND METHODS We downloaded the gene expression matrix of GSE89632 from Gene Expression Omnibus. Then the principal component analysis was used to identify whether the samples were clustered. Differentially expressed genes were identified by limma R package. Enrichment analysis and protein­protein interaction network was used to find potential function and screening hub genes. We further used ChIP-seq data from ENCODE to predict the transcriptional regulation of hub genes. Finally, we verified the functions of hub genes with clinical information. RESULTS These hub genes were significantly enriched in "response to insulin", "response to glucose", and "fat cell differentiation". ChIP-seq data showed that EGR1 (early growth response gene-1) may play an important role in the transcriptional regulation of SOCS1 (suppressor of cytokine signaling 1), SOCS3 (suppressor of cytokine signaling 3), and Fos gene family in the liver, as the low expression of EGR1 in patients with insulin resistance may promote the occurrence and development of NAFLD. Similarly, correlation analysis showed that EGR1 was positively correlated with the expression of SOCS1, SOCS3, and the genes of Fos gene family, and EGR1 was negatively correlated with the degree of steatosis. CONCLUSIONS Newly identified hub genes and their transcriptional regulation may promote understanding of the molecular mechanisms underlying insulin resistance related to the progression of NAFLD and provide a new therapy target and biomarkers.

Modification of a nitrocellulose membrane with cellulose nanofibers for enhanced sensitivity of lateral flow assays: application to the determination of Staphylococcus aureus.

Lateral flow assays, as a low-cost, simple, portable and disposable product of vitro diagnostic, are being widely used for point-of-care testing. However, the poor sensitivity of LFAs is the main challenge for commercialization. In order to enhance the sensitivity of LFAs, cellulose nanofibers (CNFs) have been integrated into LFAs to enhance the sensitivity of protein LFAs. A simple method is also presented to modify the properties of paper substrate by incorporating CNFs into a nitrocellulose membrane to enhance the sensitivity of nucleic acid LFAs. This method changes the pore size, porosity, surface groups and surface area of paper substrate and then increases the adsorption ability of biomolecules on paper substrate. The results indicate that the sensitivity of nucleic acid LFAs in Staphylococcus aureus testing achieves a 20-fold enhancement. Hence, we anticipate that this simple method has the potential for other paper-based devices to improve the performance. Graphical abstractA simple method is used to modify the properties of paper substrate by incorporating cellulose nanofibers (CNFs) into nitrocellulose (NC) membrane to enhance the sensitivity of nucleic acid LFAs.

Direct writing electrodes using a ball pen for paper-based point-of-care testing.

The integration of paper with an electrochemical device has attracted growing attention for point-of-care testing, where it is of great importance to fabricate electrodes on paper in a low-cost, easy and versatile way. In this work, we report a simple strategy for directly writing electrodes on paper using a pressure-assisted ball pen to form a paper-based electrochemical device (PED). This method is demonstrated to be capable of fabricating electrodes on paper with good electrical conductivity and electrochemical performance, holding great potential to be employed in point-of-care applications, such as in human health diagnostics and food safety detection. As examples, the PEDs fabricated using the developed method are applied for detection of glucose in artificial urine and melamine in sample solutions. Furthermore, our developed strategy is also extended to fabricate PEDs with multi-electrode arrays and write electrodes on non-planar surfaces (e.g., paper cup, human skin), indicating the potential application of our method in other fields, such as fabricating biosensors, paper electronics etc.

Development and validation of a nomogram for Siewert II esophagogastric junction adenocarcinoma: a retrospective analysis.

Background: Due to the complex histological type and anatomical structures, there has been considerable debate on the classification of adenocarcinoma of the esophagogastric junction (AEG), especially Siewert II AEG. Furthermore, neither the American Joint Committee on Cancer (AJCC) 7th tumor-node-metastasis (TNM) [esophageal adenocarcinoma (E) or gastric cancer (G)] nor the AJCC 8th TNM (E or G) accurately predicted the prognosis of patients with Siewert II AEG. Objective: This study aimed to investigate the factors influencing the survival and prognosis of patients with Siewert II AEG and establish a new and better prognostic predictive model. Design: A retrospective study. Methods: Patients with Siewert II AEG, retrieved from the Surveillance, Epidemiology, and End Results (SEER) databases, were assigned to the training set. Patients retrieved from a single tertiary medical center were assigned to the external validation set. Significant variables were selected using univariate and multivariate Cox regression analyses to construct the nomogram. Nomogram models were assessed using the concordance index (C-index), a calibration plot, decision curve analysis (DCA), and external validation. Results: Age, tumor grade, and size, as well as the T, N, and M stages, were included in the nomograms. For the SEER training set, the C-index of the nomogram was 0.683 (0.665-0.701). The C-index of the nomogram for the external validation set was 0.690 (0.653-0.727). The calibration curve showed good agreement between the nomogram estimations and actual observations in both the training and external validation sets. The DCA showed that the nomogram was clinically useful. Conclusion: The new predictive model showed significant accuracy in predicting the prognosis of Siewert II AEG.

Incidence of cancer for patients after bariatric surgery: evidence from 33 cohort studies.

BACKGROUND: With the rising prevalence of severe obesity, bariatric surgery has emerged as a crucial treatment option. As the number of surgeries performed worldwide increases, there has been growing interest in the impact of bariatric surgery on cancer incidence. While several studies have examined this relationship, the topic remains controversial. OBJECTIVES: We conducted this systematic review of cohort studies with meta-analysis to evaluate the effect of bariatric surgery versus nonsurgical treatment on overall cancer incidence. However, the effects may vary when focusing on specific cancer types, surgical procedures, or gender, so we conducted additional subgroup analyses. SETTING: A meta-analysis. University hospital. METHODS: The Cochrane, Embase, PubMed, and Web of Science databases were searched for studies from 1 January 2000 to 1 December 2022. Meta-analysis was conducted to evaluate the pooled effect and further implemented subgroup analysis stratified by cancer type, operation type, and sex. RESULTS: All cohort studies were included in this meta-analysis from 18,216 studies. The overall cancer incidence demonstrated a significant decrease in the group with bariatric surgery (odds ratios [OR] = .56, P = .000, 95% CI .46 to .68). In subgroup analysis, similar decrease effect was found in 9 cancers. Furthermore, the incidence of cancer decreased significantly in male (OR = .66, P = .001, 95% CI .51 to .85) and female patients (OR = .63, P = .000, 95% CI .57 to .69) and patients undergoing gastric bypass (OR = .46, P = .000, 95% CI .33 to .63) or sleeve gastrectomy (OR = .44, P = .001, 95% CI .27 to .70). CONCLUSIONS: In the overall analysis, bariatric surgery could reduce the incidence of cancer significantly. Further large-scale well-matched studies are needed to verify the protective effect of bariatric surgery on cancer incidence.

X chromosomal recombination--a family study analyzing 26 X-STR Loci in Chinese Han three-generation pedigrees.

The aim of this study is to investigate genetic linkage and recombination fractions of 26 X chromosomal (X-STR) loci with two multiplex PCR systems (MX15-STR and MX12-STR). MX15-STR (including DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079) and MX12-STR (including DXS6854, DXS9902, DXS6800, GATA172D05, DXS7423, HPRTB, DXS6807, DXS6803, DXS6804, DXS6799, DXS8378, and DXS8377) were successful analyzed on 206 two-generation families with two or more children and 33 three-generation families with 72 grandsons. Segregation analysis and calculation of recombination fractions between pairs of markers were performed. Linkage analysis of pairs of markers showed that there existed significant linkage (maximum LOD scores >2.0) within the physical distance of 48.5 Mb. Recombination events could be observed within the clusters of closed linked makers spanning <1.0 Mb. These results indicate that close cluster X-STRs used and recombination fractions of the selected loci will be very useful for biostatistical calculations in complex kinship analysis.

Modularized synthetic biology enabled intelligent biosensors.

Biosensors that sense the concentration of a specified target and produce a specific signal output have become important technology for biological analysis. Recently, intelligent biosensors have received great interest due to their adaptability to meet sophisticated demands. Advances in developing standard modules and carriers in synthetic biology have shed light on intelligent biosensors that can implement advanced analytical processing to better accommodate practical applications. This review focuses on intelligent synthetic biology-enabled biosensors (SBBs). First, we illustrate recent progress in intelligent SBBs with the capability of computation, memory storage, and self-calibration. Then, we discuss emerging applications of SBBs in point-of-care testing (POCT) and wearable monitoring. Finally, future perspectives on intelligent SBBs are proposed.

A three-in-one microfluidic droplet digital PCR platform for absolute quantitative analysis of DNA.

Droplet digital polymerase chain reaction (ddPCR) technology has found widespread applications in the ultrasensitive analysis of nucleic acids, where integrated ddPCR platforms with the capability of sample dispersion, followed by in situ amplification and data analysis, are highly expected. However, current integrated ddPCR platforms are usually limited by either difficultly mass-produced materials or lack of integrated control instruments, restricting their practical application. This paper proposes an integrated three-in-one ddPCR platform with high user-friendliness and practicability, which is composed of an easy-to-use chip and a matching control instrument. The chip was made of thermally resistant and easily mass-produced polycarbonate (PC) material, and the benchtop control instrument was designed to perform droplet generation, in situ amplification, and fluorescence reading. The droplet generation and in situ heating on the chip were well characterized. Finally, the performance of the platform was validated through the analysis of the EGFR L858R mutation in lung cancer. The proposed three-in-one ddPCR platform shows great practicability in ultrasensitive nucleic acid testing. By virtue of its sensitivity, practicability, and cost-effectiveness, the ddPCR can serve as a universal detection platform for monitoring nucleic acid in the fields of tumor diagnosis, pathogen detection, and prenatal diagnosis.

Regulation of probe density on upconversion nanoparticles enabling high-performance lateral flow assays.

Upconversion nanoparticles (UCNPs)-based fluorescence probes have shown great potential in point-of-care testing (POCT) applications, due to UCNPs' features of high photostability and background-free fluorescence. Ceaseless improvements of UCNPs-probes have been carried out to increase detection sensitivity and to broaden detection range of UCNPs-based POCT. In this paper, we optimized UCNPs-probes by regulating probe density. The optimization was verified by a traditional lateral flow assay (LFA) platform for C-reactive protein (CRP) detection. Further, the optimized UCNPs-LFA integrating with a home-made benchtop fluorescence analyzer holds the capability to achieve high-performance POCT. Finally, nearly a 20 times sensitivity enhancement with a limit of detection of 0.046 ng/mL and a broad detection range of 0.2-300 ng/mL for CRP detection was obtained. Moreover, the optimized UCNPs-LFA was applied to detecting CRP in clinical serum samples and the detection results were consistent with the clinical test, validating its clinical practicability. The proposed optimization method is also expected to optimize other nanoparticles-based bio-probes for wider POCT application.