Diagnostic yield of next-generation sequencing in suspect primary immunodeficiencies diseases: a systematic review and meta-analysis.

To determine the diagnostic yield of Next-generation sequencing (NGS) in suspect Primary Immunodeficiencies Diseases (PIDs). This systematic review was conducted following PRISMA criteria. Searching Pubmed and Web of Science databases, the following keywords were used in the search: ("Next-generation sequencing") OR "whole exome sequencing" OR "whole genome sequencing") AND ("primary immunodeficiency disease" OR "PIDs"). We used STARD items to assess the risk of bias in the included studies. The meta-analysis included 29 studies with 5847 patients, revealing a pooled positive detection rate of 42% (95% CI 0.29-0.54, P < 0.001) for NGS in suspected PID cases. Subgroup analyses based on family history demonstrated a higher detection rate of 58% (95% CI 0.43-0.71) in patients with a family history compared to 33% (95% CI 0.21-0.46) in those without (P < 0.001). Stratification by disease types showed varied detection rates, with Severe Combined Immunodeficiency leading at 58% (P < 0.001). Among 253 PID-related genes, RAG1, ATM, BTK, and others constituted major contributors, with 34 genes not included in the 2022 IUIS gene list. The application of NGS in suspected PID patients can provide significant diagnostic results, especially in patients with a family history. Meanwhile, NGS performs excellently in accurately diagnosing disease types, and early identification of disease types can benefit patients in treatment.

Development and validation of outcome prediction model for reperfusion therapy in acute ischemic stroke using nomogram and machine learning.

OBJECTIVE: To develop logistic regression nomogram and machine learning (ML)-based models to predict 3-month unfavorable functional outcome for acute ischemic stroke (AIS) patients undergoing reperfusion therapy. METHODS: Patients undergoing reperfusion therapy (intravenous thrombolysis and/or endovascular treatment) were prospectively recruited. Unfavorable outcome was defined as 3-month modified Rankin Scale (mRS) score 3-6. The independent risk factors associated with unfavorable outcome were obtained by regression analysis and included in the prediction model. The performance of nomogram was assessed by the area under the curve (AUC), calibration curve, and decision curve analysis (DCA). ML models were compared with nomogram using AUC; the generalizability of all models was ascertained in an external cohort. RESULTS: A total of 505 patients were enrolled, with 256 in the model construction, and 249 in the external validation. Five variables were identified as prognostic factors: baseline NIHSS, D-dimer level, random blood glucose (RBG), blood urea nitrogen (BUN), and systolic blood pressure (SBP) before reperfusion. The AUC values of nomogram were 0.865, 0.818, and 0.779 in the training set, test set, and external validation, respectively. The calibration curve and DCA indicated appreciable reliability and good net benefits. The best three ML models were extra trees (ET), CatBoost, and random forest (RF) models; all of them showed favorable discrimination in the training cohort, and confirmed in the test and external sets. CONCLUSION: Baseline NIHSS, D-dimer, RBG, BUN, and SBP before reperfusion were independent predictors for 3-month unfavorable outcome after reperfusion therapy in AIS patients. Both nomogram and ML models showed good discrimination and generalizability.

Effects of Quercetin on the Intestinal Microflora of Freshwater Dark Sleeper Odontobutis potamophila.

Flavonoids have antimicrobial and anti-oxidation properties. The effects of the flavonoid quercetin on the intestinal microflora of freshwater dark sleeper Odontobutis potamophila were tested for the first time. Odontobutis potamophila juveniles were treated with quercetin for 21 days at one of three concentrations (2.5, 5.0, or 10.0 mg/L) and compared with a control group that was not treated with quercetin. Quercetin improved the stability of the intestinal flora in O. potamophila and the probiotic bacteria Bacillus spp. and Lactobacillus spp. increased in species abundance after the low concentration quercetin treatments. Furthermore, the abundance of pathogenic bacteria Plesiomonas spp., Aeromonas spp., and Shewanella spp. decreased after the fish had been exposed to quercetin. Activity of hepatic antioxidant enzymes (superoxide dismutase, SOD), (glutathione S-transferase, GST), (glutathione peroxidase, GSH-Px), and (total antioxidant capacity, T-AOC) increased in the livers of O. potamophila treated with quercetin, thereby increasing their hepatic antioxidant capacity and their ability to scavenge free radicals.

Detection of EGFR gene with a droplet digital PCR chip integrating a double-layer glass reservoir.

The lack of reliable and practical method for detecting rare hot mutation of epidermal growth factor receptor (EGFR) in circulating tumor DNA (ctDNA) for lung cancer has remained a challenge for general clinical application due to excess wild type DNA in clinical samples. In this study, we developed a droplet digital PCR (ddPCR) platform, integrating a PDMS chip and double-layer glass reservoir. The duplex T-junction droplet generators in PDMS chip can produce about one million uniform droplets of 4.187 pL within ∼10 min, which were then stored in the glass reservoir. The double-layer glass reservoir can protect droplets from evaporation and breaking, solving the problem of instability during thermal-cycling. The quantitative capabilities of the ddPCR chip were evaluated by testing EGFR exon gene 21, with a good linear correlation in the wide range of 101 to 106 copies/µL (R2 = 0.9998). We then demonstrated that the proposed ddPCR device can recognize rare EGFR L858R mutation under a background of 106 copies/µL wild-type DNA at a sensitivity of 0.0001%. Finally, we demonstrated this ddPCR platform could identify low amount of EGFR L858R mutation in ctDNA and CTCs of patients with lung cancer.

Effect of quercetin on muscle growth and antioxidant status of the dark sleeper Odontobutis potamophila.

Quercetin is a flavanol beneficial in reducing fat, promoting muscle growth, and Anti-oxidation. To study its effects in freshwater fish, the full-length cDNA of the follistatin (FST) and myostatin (MSTN) genes of the dark sleeper Odontobutis potamophila were cloned for the first time. Juvenile individual O. potamophila was exposed to quercetin at one of four concentrations (0, 2.5, 5, and 10 mg/L) for 21 days. The expression level of MSTN which inhibits muscle growth in the quercetin solution was lower than in the unexposed control group. The genes that promote muscle growth are in TGF-ß superfamily like FST, TGF-ß1 (transforming growth factor-beta 1), and Myogenic regulatory factors (MRFs) like Myf5 (myogenic factor 5), MyoD (myogenic differentiation), MyoG (myogenin), were higher than in the control group. Apolipoprotein and growth hormone receptor transcription levels in the quercetin-treated fish were significantly lower than in the control group. The concentrations of triglyceride, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol in the muscle tissue decreased, and the lipid-lowering function of quercetin was also demonstrated at the biochemical level. In this study, we analyzed the mRNA levels of AKT, Keap1 (kelch-like ECH-associated protein 1), Nrf2 (NF-E2-related factor 2) oxidation-related genes in the Nrf2/ARE antioxidant pathway, and Malondialdehyde (MDA), catalase (CAT) activity and glutathione (GSH) content in the hepatopancreas of O. potamophila after quercetin treatment, the mRNA expression of AKT, Nrf2 and CAT activity and GSH content are higher than in the control group. Quercetin enhances antioxidant properties and positively affects muscle growth. The results showed that quercetin has no significant effects on the growth performance of O. potamophila, but is effective in increasing muscle growth rate and lowering muscle fat content.

A Novel Perspective on Ischemic Stroke: A Review of Exosome and Noncoding RNA Studies.

Ischemic stroke is a life-threatening condition that also frequently results in long-term disability. Currently, intravenous thrombolysis with tissue plasminogen activator and mechanical thrombectomy is the most popular treatment. However, the narrow time window and related complications limit the treatment benefits. Exosomes have recently emerged as ideal therapeutic candidates for ischemic stroke with the ability to pass through the blood_brain barrier and mediate intercellular communication, in addition, exosomes and their contents can be bioengineered to implement targeted delivery. In the last two decades, exosomes and exosomal noncoding RNAs have been found to be involved in the pathophysiological progression of ischemic stroke, including atherosclerosis, apoptosis, inflammation, oxidative stress, and neurovascular remodeling. In this review, we describe the latest progress regarding the role of exosomal long noncoding RNAs and circular RNAs in the occurrence, progression, and recovery of ischemic stroke. Exploration of exosomal noncoding RNAs and their correlated effects in ischemic stroke may facilitate accurate diagnosis, and they may serve as new therapeutic targets for the disease.

Changes in life-history traits, antioxidant defense, energy metabolism and molecular outcomes in the cladoceran Daphnia pulex after exposure to polystyrene microplastics.

Ubiquitous plastic pollution is a threat to the organisms' survival and ecosystem functions, especially in aquatic environments. Although there is increasing concern about the toxicity of microplastics, knowledge about the effects of microplastics of diverse sizes and adverse impacts on freshwater organisms is still limited. In the present study, the alteration in life-history traits, antioxidant defense and energy metabolism of the model freshwater zooplankton Daphnia pulex were assessed after chronic exposure to gradient concentrations (0.5, 1, 2 and 4 mg/L) of 500-nm polystyrene microplastics (PS-MPs). Changes in protein abundance were analyzed using proteomics after exposure to 1 mg/L of PS-MPs for 14 days. The results showed that ingested PS-MPs accumulated in the digestive tract of D. pulex. 2 and 4 mg/L of PS-MPs inhibited the survival function and 4 mg/L of PS-MPs reduced the body length of D. pulex after 14 or 21 days of exposure. The exposure did not decrease the fecundity of D. pulex. After 14 days of exposure, PS-MPs changed the antioxidant capacity in a dose-dependent way and all concentrations of PS-MPs induced lipid oxidative damage. Exposure to 500-nm PS-MPs for 14 days decreased glucose and fructose contents and disturbed the lipid transport and utilization in D. pulex. Meanwhile, PS-MPs activated DNA repair and transcription regulation but inhibited lipid metabolism and response to unfolded or misfolded proteins. These results indicated that chronic exposure to 500-nm PS-MPs negatively affected D. pulex and showed similar toxic mechanisms to smaller nano-sized microplastics. Exposure to 500-nm PS-MPs resulted in restricted resources such as inhibited antioxidant capacity or energy metabolisms and D. pulex showed a potential trade-off among life-history traits to maintain fecundity at the cost of self-maintenance. The present study offers perspectives for understanding the differences in ecological effects caused by microplastics of different sizes.

A batch microfabrication of a self-cleaning, ultradurable electrochemical sensor employing a BDD film for the online monitoring of free chlorine in tap water.

Free chlorine is one of the key water quality parameters in tap water. However, a free chlorine sensor with the characteristics of batch processing, durability, antibiofouling/antiorganic passivation and in situ monitoring of free chlorine in tap water continues to be a challenging issue. In this paper, a novel silicon-based electrochemical sensor for free chlorine that can self-clean and be mass produced via microfabrication technique/MEMS (Micro-Electro-Mechanical System) is proposed. A liquid-conjugated Ag/AgCl reference electrode is fabricated, and electrochemically stable BDD/Pt is employed as the working/counter electrode to verify the effectiveness of the as-fabricated sensor for free chlorine detection. The sensor demonstrates an acceptable limit of detection (0.056 mg/L) and desirable linearity (R 2 = 0.998). Particularly, at a potential of +2.5 V, hydroxyl radicals are generated on the BBD electrode by electrolyzing water, which then remove the organic matter attached to the surface of the sensor though an electrochemical digestion process. The performance of the fouled sensor recovers from 50.2 to 94.1% compared with the initial state after self-cleaning for 30 min. In addition, by employing the MEMS technique, favorable response consistency and high reproducibility (RSD < 4.05%) are observed, offering the opportunity to mass produce the proposed sensor in the future. A desirable linear dependency between the pH, temperature, and flow rate and the detection of free chlorine is observed, ensuring the accuracy of the sensor with any hydrologic parameter. The interesting sensing and self-cleaning behavior of the as-proposed sensor indicate that this study of the mass production of free chlorine sensors by MEMS is successful in developing a competitive device for the online monitoring of free chlorine in tap water.

A novel gene order and remolded tRNAs revealed in the mitogenome of Asian gecarcinucid freshwater crabs (Brachyura, Gecarcinucidae).

Here we report the first mitochondrial genomes (mitogenomes) of four species of gecarcinucid freshwater crabs (FWCs) in two genera, two from China (Somanniathelphusa hainanensis and S. yangshanensis), one from Laos (Esanthelphusa dugasti), and one from Myanmar (Esanthelphusa keyini). A novel gecarcinucid mitochondrial gene order (GMGO2) that was only found in E. dugasti that contains a total of 42 genes, including one pseudogene, two remolded tRNAs and two duplicated tRNAs. The GMGO2 of E. dugasti was compared with the brachyuran ground-pattern mitochondrial gene order (BMGO), revealing the rearrangements of the positions of 10 tRNAs, two PCGs, and one mNCR. The three other gecarcinucids in this study were all found to possess a previously reported gecarcinucid mitochondrial gene order (GMGO1). The phylogenetic tree reconstructed using the secondary structures of 22 tRNAs of the mitogenomes of 41 species of FWCs provides insights into the evolution of the mitogenome of E. dugasti (GMGO2) which includes remolded and duplicated tRNAs.

Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea).

The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

Microfluidic sensor integrated with nanochannel liquid conjunct Ag/AgCl reference electrode for trace Pb(II) measurement.

Pollution due to heavy metals is becoming increasingly hazardous; therefore, demand for the large-scale deployment of sensor nodes for water quality monitoring has increased. The development of integrated and miniaturised sensors for detecting heavy metals is necessary. Herein, an integrated microfluidic sensor based on a "glass-silicon-glass" sandwich structure is proposed for Pb2+ detection. This micro-sensor consists of a nanochannel liquid conjunct Ag/AgCl reference electrode(RE), a working electrode with a three-dimensional Au micropillar array, and a detection chamber for sample measurement. The potential fluctuation of the RE in this sensor was only 0.62% over seven days, remaining relatively stable. Under optimal conditions, the limit of detection and sensitivity for lead were 0.13 µg L-1 (S/N = 3) and 52.30 nA (µg L-1)-1, respectively. The linearity of the sensor for detecting lead was good in the concentration range of 0.50-150 µg L-1 (R2 = 0.9989). Moreover, the proposed microsensor showed high selectivity for Pb2+ and achieved sensitive detection of trace Pb2+ in different water samples. Therefore, this integrated and miniaturised sensor is a practical tool for trace lead detection, allowing the development of large scale sensor network for water monitoring.

The complete mitogenome of freshwater gammarid Grandidierella taihuensis (Crustacea: Amphipoda).

The freshwater gammarid Grandidierella taihuensis is an important composition of benthic community. In this study, the complete mitogenome sequences of G. taihuensis are determined using next-generation and PacBio long-read sequencing. The mitogenome of G. taihuensis is 15,099 bp in size, and consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and a putative control region. Gene arrangement is as same as that of G. rubroantennata. The base composition of the entire mitogenome showed a conspicuous A + T bias of 69.4%. The mitogenome data produced in this study provides a useful resource for future evolutionary and ecological studies.

A high-precision thermometry microfluidic chip for real-time monitoring of the physiological process of live tumour cells.

Temperature changes in cells are generally accompanied by physiological processes. Cellular temperature measurements can provide important information to fully understand cellular mechanisms. However, temperature measurements with conventional methods, such as fluorescent polymeric thermometers and thermocouples, have limitations of low sensitivity or cell state disturbance. We developed a microfluidic chip integrating a high-precision platinum (Pt) thermo-sensor that can culture cells and monitor the cellular temperature in situ. During detection, a constant temperature system with a stability of 0.015 °C was applied. The temperature coefficient of resistance of the Pt thermo-sensor was 2090 ppm/°C, giving a temperature resolution of the sensor of less than 0.008 °C. This microchip showed a good linear correlation between the temperature and resistance of the Pt sensor at 20-40 °C (R2 = 0.999). Lung and liver cancer cells on the microchip grew normally and continuously. The maximum temperature fluctuation of H1975 (0.924 °C) was larger than that of HepG2 (0.250 °C). However, the temperature of adherent HepG2 cells changed over time, showing susceptibility to the environment most of the time compared to H1975. Moreover, the temperature increment of non-cancerous cells, such as hepatic stellate cells, was monitored in response to the stimulus of paraformaldehyde, showing the process of cell death. Therefore, this thermometric microchip integrated with cell culture could be a non-disposable and label-free tool for monitoring cellular temperature applied to the study of physiology and pathology.

Single-cell genetic analysis of lung tumor cells based on self-driving micro-cavity array chip.

Lung cancer is one of the common malignant tumors with a high incidence and mortality rate. Targeted therapies are efficient on lung cancer patients with specific gene mutations. Circulating tumor cells (CTCs) are used for liquid biopsy, providing genetic information for lung cancer treatment selection and prognosis. We developed a less costly self-driving micro-cavity array for simple molecular analysis at a single cell level to examine the genetic make-up of CTCs. This chip integrated sample detection structure and vacuum driving system to achieve cell loading, lysing, isothermal amplification (LAMP), and signal read-out on one chip. We used the "film-polydimethylsiloxane (PDMS) chip-film" structure and oil sealing method during amplification reaction to minimize water loss. We then conducted a LAMP assay using the self-driving device to detect epidermal growth factor receptor (EGFR) L858R mutation and identified an excellent linear in the range between 101-104 copies/µL (R2 = 0.997). We finally assessed the EGFR L858R gene expression of lung tumor cells (H1975 cells) as putative CTCs using the proposed detection platform. We discovered its ability to perform genetic analysis at the single-cell level. The EGFR L858R mutational gene expression levels were different in H1975 cells. In conclusion, the self-driving micro-cavity array is a less costly and simple tool for mutational gene profiling of single lung CTC. Besides, it can be used in personalized therapy and efficacy monitoring.

The complete mitochondrial genome of Callionymus olidus (Perciformes Callionymidae).

In this study, we present the complete mitogenome and a phylogenetic analysis of Callionymus olidus, determined by long PCR and primer walking methods. The complete mitochondrial genome is a circular molecule of 16,491 bp in length and contains the same set of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. The base composition of the entire mitogenome showed a slight excess of AT bias. The entire mitogenome data produced in this study provides the genomic resources available for future evolutionary studies.

Establishment of an induced pluripotent stem cell line (SAHGMUi001-A) from a patient with Netherton syndrome carrying SPINK5 mutation.

Netherton syndrome (NS) is a rare, autosomal recessive hereditary skin disease caused by mutations in SPINK5 gene, characterized with severe skin barrier damage. A human induced pluripotent stem cell (iPSC) line has been established with electroporation method from urine-derived cells of a NS patient carrying a compound heterozygous mutation c.2260A > T (p.K754X) and c.2423C > T(p.T808I) in SPINK5 gene. This iPSC line may serve as a valuable model for the research of pathogenesis of NS, and the mechanisms and therapeutics for skin barrier damage.

A batch microfabrication of a microfluidic electrochemical sensor for rapid chemical oxygen demand measurement.

Chemical oxygen demand (COD) is one of the key water quality parameters in environmental monitoring. However, fabricating a COD sensor with the characteristic of batch-processing and rapid measurement is always a challenging issue. This paper reports a microfluidic electrochemical sensor for the organic matter measurement based on advanced oxidization within a fixed microvolume detection chamber by a microfabrication technique/MEMS. By fabricating a silicon-based Ag/AgCl reference electrode and employing PbO2 as the working electrode with Pt as the counter electrode, we verified the superiority of the as-fabricated sensor by continuous potassium acid phthalate detection; an acceptable limit of detection (4.17 mg L-1-200 mg L-1), a low limit of detection (2.05 mg L-1), a desirable linearity (R2 = 0.982) and relative stability at different pH values and Cl- concentrations was witnessed. Particularly, a shorter detection time (2 s) was witnessed for the as-proposed sensor compared with traditional organic matter measurement methods. Each sensing process takes only 2 seconds for sensing because a micro-cavity with a volume of 2.5 µL was fabricated and used as a detection pool. Moreover, as the sensor was fabricated by a mass-production technique, potential response consistency of multiple sensors was expected and was verified via a series of parallel experiments. In this paper, a miniaturized (8 mm × 10 mm), low-cost and reliable COD sensor was designed and fabricated by MEMS, and it provided a core sensor component for construction of an online water environment monitoring network to meet the substantial demand for COD sensors in the Internet of Things (IOT) era.

Programmed cell death of Chlamydomonas reinhardtii induced by three cyanobacterial volatiles ß-ionone, limonene and longifolene.

ß-Ionone, limonene and longifolene are 3 main components in cyanobacterial volatile organic compounds, which are formed through different pathways and can poison and even kill other algae. To uncover their toxic mechanism from programmed cell death (PCD), the photosynthetic pigments, chlorophyll fluorescence, caspase-like activities, cell size, nuclear variations and DNA ladders were investigated in Chlamydomonas reinhardtii treated with ß-ionone (0.2 mM), limonene (0.2 mM) and longifolene (0.4 mM) at lethal concentration during 24 h. In the treatments with the 3 compounds, the photosynthetic pigments in C. reinhardtii cells gradually degraded, and Fv/Fm gradually decreased and disappeared at 24 h, suggesting that the cell death might be a PCD, due to the physiological activities gradually disappearing. During the cell death, the activities of caspase-9-like and caspase-3-like significantly increased, with the highest at 1 h. With prolonging the treatment time, C. reinhardtii cells gradually shrank, and the nuclei concentrated firstly following by a broken process, with moving to the cell edge. For DNA, obvious ladders were detected at 1 h, and then they gradually degraded to fragments of 100-250 bp at 24 h. These hallmarks suggested that ß-ionone, limonene and longifolene may poison other algae by inducing PCD.