Unveiling the underappreciated: The bonding features of C-H⋯S-S interactions observed from rotational spectroscopy

The C-H⋯S-S interactions are fundamentally important to understand the stability of biomacromolecules and their binding with small molecules, but they are still underappreciated. Herein, we characterized the C-H⋯S-S interactions in model molecular complexes. The rotational spectra of the complexes of diethyl disulfide with CH2CH2 and CH2CHF were measured and analyzed. All the detected structures are mainly stabilized by a C-H⋯S-S hydrogen bond, providing stabilization energies of 2.3-7.2 kJ mol-1. Incidental C-H⋯π or C-H⋯F interactions enhance the stabilization of the complexes. London dispersion, which accounts for 54%-68% of the total attractions, is the main driving force of stabilization. The provided bonding features of C-H⋯S-S are crucial for understanding the stabilizing role of this type of interaction in diverse processes such as supramolecular recognition, protein stability, and enzyme activity.

Intestinal Translocation of Live Porphyromonas gingivalis Drives Insulin Resistance

Periodontitis has been emphasized as a risk factor of insulin resistance-related systemic diseases. Accumulating evidence has suggested a possible "oral-gut axis" linking oral infection and extraoral diseases, but it remains unclear whether periodontal pathogens can survive the barriers of the digestive tract and how they play their pathogenic roles. The present study established a periodontitis mouse model through oral ligature plus Porphyromonas gingivalis inoculation and demonstrated that periodontitis aggravated diet-induced obesity and insulin resistance, while also causing P. gingivalis enrichment in the intestine. Metabolic labeling strategy validated that P. gingivalis could translocate to the gastrointestinal tract in a viable state. Oral administration of living P. gingivalis elicited insulin resistance, while administration of pasteurized P. gingivalis had no such effect. Combination analysis of metagenome sequencing and nontargeted metabolomics suggested that the tryptophan metabolism pathway, specifically indole and its derivatives, was involved in the pathogenesis of insulin resistance caused by oral administration of living P. gingivalis. Moreover, liquid chromatography-high-resolution mass spectrometry analysis confirmed that the aryl hydrocarbon receptor (AhR) ligands, mainly indole acetic acid, tryptamine, and indole-3-aldehyde, were reduced in diet-induced obese mice with periodontitis, leading to inactivation of AhR signaling. Supplementation with Ficz (6-formylindolo (3,2-b) carbazole), an AhR agonist, alleviated periodontitis-associated insulin resistance, in which the restoration of gut barrier function might play an important role. Collectively, these findings reveal that the oral-gut translocation of viable P. gingivalis works as a fuel linking periodontitis and insulin resistance, in which reduction of AhR ligands and inactivation of AhR signaling are involved. This study provides novel insight into the role of the oral-gut axis in the pathogenesis of periodontitis-associated comorbidities.

Evaluation of air quality changes in a Chinese megacity over a 15-year period (2006-2021) using PM2.5 receptor modelling

Air quality impairment has a massive impact on human health, with atmospheric particulate matter (PM) playing a major role. The People's Republic of China experienced a trend of increasing PM2.5 concentrations from 2000 to 2013. However, after the application of the Air Pollution Prevention and Control Action Plan and other related control measures, sharp decreases in air pollutant concentrations were particularly evident in the city of Wuhan (central China). This study analysed major changes in PM2.5 concentrations, composition and source apportionment (using receptor modelling) based on Wuhan's PM2.5 chemical speciation datasets from 2006 to 2007, 2019-2021 and contemporaneous gaseous pollutant values. Average SO2 concentrations decreased by 88%, from the first to the second period, mostly due to measures that reduced coal combustion. However, NO2 only declined by 25%, with policy measures likely being undermined by an increased number of vehicles. PM2.5 concentrations decreased by 65%, with the PM constituents each being affected differently. Coal combustion-related element concentrations, OC, SO42-, NH4+, EC, Cl-, Al, Ca, Cu, Fe, Co and NO3- decreased by 22-90%. Secondary inorganic aerosol (SIA) was initially dominated by (NH4)2SO4 (73%) in 2006, but later dominated by NH4NO3 (52%) in 2021. Receptor modelling identified major sources contributing to PM2.5: Mineral, road and desert dust (MRDD), Secondary sulphate (SECS), Secondary nitrate (SECN), Tungsten industry (W), Toxic Elements of Coal (TEC), Iron and Steel (IRONS), Coal Combustion (CC), Residential Heating (RH), Refinery (REF) and Traffic (TRF). In relative proportions, TEC (-83%), SECS (-64%) and SECN (-48%) reduced their contributions to PM2.5 whilst MRDD increased (+62.5%). Thus, the results indicate not only a drastic abatement of PM pollution in Wuhan but also a change in the sources of pollution, which requires further actions to reduce PM2.5 concentrations to health protective values. Secondary PM and fugitive emissions are key components to abate.

Loop-Mediated Isothermal Amplification (LAMP): Potential Point-of-Care Testing for Vulvovaginal Candidiasis

PURPOSE

The aim of this study is to establish a loop-mediated isothermal amplification (LAMP) method for the rapid detection of vulvovaginal candidiasis (VVC).

METHODS

We developed and validated a loop-mediated isothermal amplification (LAMP) method for detecting the most common Candida species associated with VVC, including C. albicans, N. glabratus, C. tropicalis, and C. parapsilosis. We evaluated the specificity, sensitivity, positive predictive value (PPV), negative predictive value (NPV), and Kappa value of the LAMP method to detect different Candida species, using the conventional culture method and internal transcribed spacer (ITS) sequencing as gold standards and smear Gram staining and real-time Rolymerase Chain Reaction (PCR) as controls.

RESULTS

A total of 202 cases were enrolled, of which 88 were VVC-positive and 114 were negative. Among the 88 positive patients, the fungal culture and ITS sequencing results showed that 67 cases (76.14%) were associated with C. albicans, 13 (14.77%) with N. glabratus, 5 (5.68%) with C. tropicalis, and 3 (3.41%) with other species. Regarding the overall detection rate, the LAMP method presented sensitivity, specificity, PPV, NPV, and Kappa values of 90.91%, 100%, 100%, 93.4%, and 0.919, respectively. Moreover, the LAMP had a specificity of 100% for C. albicans, N. glabratus, and C. tropicalis, with a sensitivity of 94.03%, 100%, and 80%, respectively. Moreover, the microscopy evaluation had the highest sensitivity, while the real-time PCR was less specific for C. albicans than LAMP. In addition, CHROMagar Candida was inferior to LAMP in detecting non-albicans Candida (NAC) species.

CONCLUSIONS

Based on the cost-effective, rapid, and inexpensive characteristics of LAMP, coupled with the high sensitivity and specificity of our VVC-associated Candida detection method, we provided a possibility for the point-of-care testing (POCT) of VVC, especially in developing countries and some laboratories with limited resources.

A microfluidic-chip-based system with loop-mediated isothermal amplification for rapid and parallel detection of Trichomonas vaginalis and human papillomavirus

Cervical cancer is a significant global health issue primarily caused by high-risk types of human papillomavirus (HPV). Recent studies have reported an association between Trichomonas vaginalis (T. vaginalis) infections and HPV infections, highlighting the importance of simultaneously detecting these pathogens for effective cervical cancer risk management. However, current methods for detecting both T. vaginalis and HPV are limited. In this study, we present a novel approach using a microfluidic-chip-based system with loop-mediated isothermal amplification (LAMP) for the rapid and parallel detection of T. vaginalis, HPV16, HPV18, and HPV52 in a reagent-efficient and user-friendly manner. Compared to conventional LAMP assays in tubes, our system exhibits enhanced sensitivity with values of 2.43 × 101, 3.00 × 102, 3.57 × 101, and 3.60 × 102 copies per reaction for T. vaginalis, HPV16, HPV18, and HPV52, respectively. Additionally, we validated the performance of our chip by testing 47 clinical samples, yielding results consistent with the diagnostic methods used by the hospital. Therefore, our system not only offers a promising solution for concurrent diagnosis of T. vaginalis and HPV infections, particularly in resource-limited areas, due to its cost-effectiveness, ease of use, and rapid and accurate detection performance, but can also contribute to future research on the co-infection of these two pathogens. Moreover, the system possesses the capability to simultaneously detect up to 22 different types of pathogens, making it applicable across a wide range of domains such as diagnostics, food safety, and water monitoring.

Meta-analysis of the effect of whole-body vibration training on the improvement of limb function in patients with Parkinson's disease

OBJECTIVE

This study aimed to systematically evaluate the effect of whole-body vibration (WBV) training on the improvement of limb function in patients with Parkinson's disease (PD).

MATERIALS AND METHODS

An electronic search was performed on the databases, including PubMed, Web of Science, Scopus, SCI-hub, ScienceDirect, Embase, IEEE, Medline, Wiley, ClinicaIKey, CNKI, Wanfang, VIP database, Chinese Medical Association, and CBM Database from inception to May 2022 to collect randomized controlled studies on whole-body vibration training for patients with Parkinson's disease. Two researchers independently screened the literature, extracted the data, and evaluated the quality of the literature, then used ReviewManager 5.4 software for quantitative statistical analysis, including heterogeneity test, sensitivity analysis, risk of bias assessment, combined outcome index effect size and effect size inspection.

RESULTS

A total of 9 studies were included in the meta-analysis, including 346 patients, 174 patients in the control group and 172 patients in the observation group. Meta-analysis results showed that, compared with conventional physical therapy or drug therapy alone, whole-body vibration reduced the Unified Parkinson's Disease Rating Scale (UPDRSIII) score and significantly improved the motor function of patients with Parkinson's disease [MD=-2.39, 95% CI (-4.41, -0.37), Z=2.14 (p=0.23)]. Moreover, whole-body vibration significantly improved the walking stability of Parkinson's patients [MD=-1.96, 95% CI (-2.71-1.21), Z=1.17 (p=0.03)]. However, its improvement in balance ability [MD=-0.06, 95% CI (-0.77, 0.65), Z=1.07 (p=0.19)] and daily living ability [MD=0.03, 95% CI (-1.68, 0.74), Z=0.24 (p=0.87)] of patients, it was not t statistically significant.

CONCLUSIONS

Compared with conventional therapy, WBV has certain advantages in improving the balance function and gait performance of PD patients, but the effect on balance ability and daily living ability is not significant. Thus, more high-quality research is required for further verification.

An Integrated and Multi-Target Nucleic Acid Isothermal Analysis System for Rapid Diagnosis of Vulvovaginal Candidiasis

Rapid identification of Candida species is significant for the diagnosis of vulvovaginal candidiasis (VVC). An integrated and multi-target system for the rapid, high-specificity, and high-sensitivity detection of four Candida species was developed. The system consists of a rapid sample processing cassette and a rapid nucleic acid analysis device. The cassette could process the Candida species to release nucleic acids in 15 min. The released nucleic acids were analyzed by the device as fast as within 30 min, using the loop-mediated isothermal amplification method. The four Candida species could be simultaneously identified, with each reaction using only 1.41 µL of reaction mixture, which was low cost. The RPT (rapid sample processing and testing) system could detect the four Candida species with high sensitivity (<2 CFU/reaction) and high specificity. The system also processed and analyzed 32 clinical samples, giving the results with high clinical sensitivity and specificity. Hence, the system was a significant and effective platform for the diagnosis of VVC. Furthermore, the period of validity of the reagents and chips used in the system was >90 days, and the system could also be used for the detection of bacteria.

First-in-human, phase I study of AK109, an anti-VEGFR2 antibody in patients with advanced or metastatic solid tumors

BACKGROUND

Vascular endothelial growth factor receptor 2 (VEGFR2) plays a key role in antiangiogenesis which has been an essential strategy for cancer treatment. We report the first-in-human study of AK109, a novel anti-VEGFR2 monoclonal antibody, to characterize the safety profile and pharmacokinetics/pharmacodynamics (PK/PD) properties, and explore the preliminary antitumor efficacy in patients with solid tumors.

PATIENTS AND METHODS

This was a multicenter, open-label, phase I study, including dose escalation and dose expansion (NCT04547205). Patients with advanced cancers were treated 2 and 3 weekly with escalating doses of AK109. A 3 + 3 design was used to determine the maximum tolerated dose. Blood was sampled for PK/PD analysis. The primary endpoint was safety and recommended phase II dose (RP2D).

RESULTS

A total of 40 patients were enrolled. No dose-limiting toxicity was observed. However, 38 patients reported treatment-related adverse events (TRAEs); grade ≥3 TRAEs occurred in 10 patients. The most common TRAEs were proteinuria (n = 24, 60%), hypertension (n = 13, 32.5%), increased aspartate transaminase (n = 11, 27.5%), thrombopenia (n = 10, 25%), and anemia (n = 10, 25%). A total of 28 patients (70%) reported adverse events of special interest (AESIs). The most common AESIs were proteinuria (60%), hypertension (32.5%), and hemorrhage (32.5%), mainly including gum bleeding and urethrorrhagia. AK109 exhibited an approximately linear PK exposure with dose escalation at 2-12 mg/kg. PD analyses showed rapid target engagement. Among the 40 patients, 4 achieved partial response and 21 achieved stable disease with an objective response rate of 10% and a disease control rate of 62.5%. Based on the safety profile, the PK/PD profile, and preliminary antitumor activities, 12 mg/kg Q2W and 15 mg/kg Q3W were selected as RP2D.

CONCLUSIONS

AK109 showed manageable safety profile and promising antitumor activity, supporting further clinical development in a large population.

Multi-omics Investigation of Freeze Tolerance in the Amur Sleeper, an Aquatic Ectothermic Vertebrate

Freeze tolerance, the ability of an organism to survive internal ice formation, is a striking survival strategy employed by some ectotherms living in cold environments. However, the genetic bases of this remarkable adaptation are largely unknown. The Amur sleeper (Perccottus glenii), the only known freeze-tolerant fish species, can overwinter with its entire body frozen in ice. Here, we sequenced the chromosome-level genome of the Amur sleeper and performed comparative genomic, transcriptomic, and metabolomic analyses to investigate its strategies for surviving freezing. Evolutionary analysis suggested that the Amur sleeper diverged from its closest non-cold-hardy relative about 15.07 million years ago and has experienced a high rate of protein evolution. Transcriptomic and metabolomic data identified a coordinated and tissue-specific regulation of genes and metabolites involved in hypometabolism, cellular stress response, and cryoprotectant accumulation involved in freezing and thawing. Several genes show evidence of accelerated protein sequence evolution or family size expansion were found as adaptive responses to freezing-induced stresses. Specifically, genetic changes associated with cytoskeleton stability, cryoprotectant synthesis, transmembrane transport, and neuroprotective adaptations were identified as potentially key innovations that aid in freezing survival. Our work provides valuable resources and opportunities to unveil the molecular adaptations supporting freeze tolerance in ectothermic vertebrates.

High prevalence of vertebral deformity in tumor-induced osteomalacia associated with impaired bone microstructure

PURPOSE

Patients with tumor-induced osteomalacia (TIO) often suffer from irreversible height loss due to vertebral deformity. However, the prevalence of vertebral deformity in TIO patients varies among limited studies. In addition, the distribution and type of vertebral deformity, as well as its risk factors, remain unknown. This study aimed to identify the prevalence, distribution, type and risk factors for vertebral deformity in a large cohort of TIO patients.

METHODS

A total of 164 TIO patients were enrolled in this retrospective study. Deformity in vertebrae T4-L4 by lateral thoracolumbar spine radiographs was evaluated according to the semiquantitative method of Genant. Bone microstructure was evaluated by trabecular bone score (TBS) and high-resolution peripheral QCT (HR-pQCT).

RESULTS

Ninety-nine (99/164, 60.4%) patients had 517 deformed vertebrae with a bimodal pattern of distribution (T7-9 and T11-L1), and biconcave deformity was the most common type (267/517, 51.6%). Compared with patients without vertebral deformity, those with vertebral deformity had a higher male/female ratio, longer disease duration, more height loss, lower serum phosphate, higher bone turnover markers, lower TBS, lower areal bone mineral density (aBMD), lower peripheral volumetric BMD (vBMD) and worse microstructure. Lower trabecular vBMD and worse trabecular microstructure in the peripheral bone and lower spine TBS were associated with an increased risk of vertebral deformity independently of aBMD. After adjusting for the number of deformed vertebrae, we found little difference in clinical indexes among the patients with different types of vertebral deformity. However, we found significant correlations of clinical indexes with the number of deformed vertebrae and the spinal deformity index.

CONCLUSION

We reported a high prevalence of vertebral deformity in the largest cohort of TIO patients and described the vertebral deformity in detail for the first time. Risk factors for vertebral deformity included male sex, long disease duration, height loss, abnormal biochemical indexes and bone impairment. Clinical manifestation, biochemical indexes and bone impairment were correlated with the number of deformed vertebrae and degree of deformity, but not the type of deformity.

Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation

High hydrostatic pressure, low temperature, and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments. Here, we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel (MAE, Ilyophis brunneus, captured below a depth of 3,500 m) by using Illumina, PacBio, and Hi-C sequencing. We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes. The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes. Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species, European eel, ∼111.9 Mya and experienced a rapid evolution. The genome evolutionary analyses primarily revealed the following: (i) under high hydrostatic pressure, the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability; ACOX1 may enhance the fluidity of cell membrane and maintain transport activity; the expansion of ABCC12 gene family may enhance the integrity of DNA; (ii) positively selected HARS likely maintain the transcription ability at low temperatures; and (iii) energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and mTOR signaling pathways.

Sympatric or micro-allopatric speciation in a glacial lake? Genomic islands support neither

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation. One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence, wherein divergent DNA segments are interspersed with low-divergence segments. Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow. Sympatric divergence of endemic fishes is known from isolated saline, crater, postglacial, and ancient lakes. Two morphologically distinct cyprinid fishes, Gymnocypris eckloni scoliostomus (GS) and G. eckloni eckloni (GE), in a small glacial lake on the Qinghai-Tibet Plateau, Lake Sunmcuo, match the biogeographic criteria of sympatric speciation. In this study, we examined genome-wide variation in 46 individuals from these two groups. The divergence time between the GS and GE lineages was estimated to be 20-60 Kya. We identified 54 large genomic islands (≥100 kb) of speciation, which accounted for 89.4% of the total length of all genomic islands. These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes. Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation, they were too large to support the hypothesis of sympatric speciation. Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands (as small as a few kilobases in size). Thus, the observed pattern is consistent with the extensive evidence on parapatric speciation, in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation. We suggest that many, if not most, of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

Miniaturized microfluidic-based nucleic acid analyzer to identify new biomarkers of biopsy lung cancer samples for subtyping

Identifying new biomarkers is necessary and important to diagnose and treat malignant lung cancer. However, existing protein marker detection methods usually require complex operation steps, leading to a lag time for diagnosis. Herein, we developed a rapid, minimally invasive, and convenient nucleic acid biomarker recognition method, which enabled the combined specific detection of 11 lung cancer typing markers in a microliter reaction system after only one sampling. The primers for the combined specific detection of 11 lung cancer typing markers were designed and screened, and the microfluidic chip for parallel detection of the multiple markers was designed and developed. Furthermore, a miniaturized microfluidic-based analyzer was also constructed. By developing a microfluidic chip and a miniaturized nucleic acid analyzer, we enabled the detection of the mRNA expression levels of multiple biomarkers in rice-sized tissue samples. The miniaturized nucleic acid analyzer could detect ≥10 copies of nucleic acids. The cell volume of the typing reaction on the microfluidic chip was only 0.94 μL, less than 1/25 of that of the conventional 25-μL Eppendorf tube PCR method, which significantly reduced the testing cost and significantly simplified the analysis of multiple biomarkers in parallel. With a simple injection operation and reverse transcription loop-mediated isothermal amplification (RT-LAMP), real-time detection of 11 lung cancer nucleic acid biomarkers was performed within 45 min. Given these compelling features, 86 clinical samples were tested using the miniaturized nucleic acid analyzer and classified according to the cutoff values of the 11 biomarkers. Furthermore, multi-biomarker analysis was conducted by a machine learning model to classify different subtypes of lung cancer, with an average area under the curve (AUC) of 0.934. This method shows great potential for the identification of new nucleic acid biomarkers and the accurate diagnosis of lung cancer.

Molecular Mechanisms of the Convergent Adaptation of Bathypelagic and Abyssopelagic Fishes

Harsh environments provide opportunities to study how different species adapt, at the molecular level, to similar environmental stressors. High hydrostatic pressure, low temperature, and absence of sunlight in the deep-sea environment are challenging conditions for gene expression, cell morphology and vision. Adaptation of fish to this environment appears independently in at least 22 orders of fish, but it remains uncertain whether these adaptations represent convergent evolution. In this study, we performed comparative genomic analysis of 80 fish species to determine genetic evidences for adaptations to the deep-sea environment. The 80 fishes were divided into six groups according to their order. Positive selection and convergent evolutionary analysis were performed and functional enrichment analysis of candidate genes was performed. Positively selected genes (pik3ca, pik3cg, vcl and sphk2) were identified to be associated with the cytoskeletal response to mechanical forces and gene expression. Consistent signs of molecular convergence genes (grk1, ednrb, and nox1) in dark vision, skin color, and bone rarefaction were revealed. Functional assays of Grk1 showed that the convergent sites improved dark vision in deep-sea fish. By identifying candidate genes and functional profiles potentially involved in cold, dark, and high-pressure responses, the results of this study further enrich the understanding of fish adaptations to deep-sea environments.

Rapid, Highly Sensitive, and Label-Free Pathogen Assay System Using a Solid-Phase Self-Interference Recombinase Polymerase Amplification Chip and Hyperspectral Interferometry

Recombinase polymerase amplification (RPA) is a useful pathogen identification method. Several label-free detection methods for RPA amplicons have been developed in recent years. However, these methods still lack sensitivity, specificity, efficiency, or simplicity. In this study, we propose a rapid, highly sensitive, and label-free pathogen assay system based on a solid-phase self-interference RPA chip (SiSA-chip) and hyperspectral interferometry. The SiSA-chips amplify and capture RPA amplicons on the chips, rather than irrelevant amplicons such as primer dimers, and the SiSA-chips are then analysed by hyperspectral interferometry. Optical length increases of SiSA-chips are used to demonstrate RPA detection results, with a limit of detection of 1.90 nm. This assay system can detect as few as six copies of the target 18S rRNA gene of Plasmodium falciparum within 20 min, with a good linear relationship between the detection results and the concentration of target genes (R² = 0.9903). Single nucleotide polymorphism (SNP) genotyping of the dhfr gene of Plasmodium falciparum is also possible using the SiSA-chip, with as little as 1% of mutant gene distinguished from wild-type loci (m/wt). This system offers a high-efficiency (20 min), high-sensitivity (6 copies/reaction), high-specificity (1% m/wt), and low-cost (∼1/50 of fluorescence assays for RPA) diagnosis method for pathogen DNA identification. Therefore, this system is promising for fast identification of pathogens to help diagnose infectious diseases, including SNP genotyping.

A nature-inspired hierarchical branching structure pressure sensor with high sensitivity and wide dynamic range for versatile medical wearables

Pressure-sensing capability is essential for flexible electronic devices, which require high sensitivity and a wide detection range to simplify the system. However, the template-based pressure sensor is powerless to detect high pressure due to the rapid deformation saturation of microstructures. Herein, we demonstrated that a nature-inspired hierarchical branching (HB) structure can effectively address this problem. Finite element analysis demonstrates that the HB structure permits a step-by-step mobilization of microstructure deformation, resulting in a dramatically improved sensitivity (up to 2 orders of magnitude) when compared with the traditional monolayer structure. Experiments show that the HB structure enables pressure sensors to have a lower elastic modulus (1/3 of that of monolayer sensors), a high sensitivity of 13.1 kPa^-1 (almost 14 times higher than the monolayer sensor), and a wide dynamic range (0-800 kPa, the minimum detection pressure is 1.6 Pa). The maximum frequency that the sensor can detect is 250 Hz. The response/recovery time is 0.675/0.55 ms respectively. Given this performance, the HB sensor enables high-resolution detection of the weak radial artery pulse wave characteristics in different states, indicating its potential to noninvasively reveal cardiovascular status and the effectiveness of related interventions, such as exercise and drug intervention. As a proof of concept, we also verified that the HB sensor can serve as a versatile platform to support diverse applications from low to high pressure.

Microfluidic Chip with Two-Stage Isothermal Amplification Method for Highly Sensitive Parallel Detection of SARS-CoV-2 and Measles Virus

A two-stage isothermal amplification method, which consists of a first-stage basic recombinase polymerase amplification (RPA) and a second-stage fluorescence loop-mediated isothermal amplification (LAMP), as well as a microfluidic-chip-based portable system, were developed in this study; these enabled parallel detection of multiplex targets in real time in around one hour, with high sensitivity and specificity, without cross-contamination. The consumption of the sample and the reagent was 2.1 μL and 10.6 μL per reaction for RPA and LAMP, respectively. The lowest detection limit (LOD) was about 10 copies. The clinical amplification of about 40 nasopharyngeal swab samples, containing 17 SARS-CoV-2 (severe acute respiratory syndrome coronavirus) and 23 measles viruses (MV), were parallel tested by using the microfluidic chip. Both clinical specificity and sensitivity were 100% for MV, and the clinical specificity and sensitivity were 94.12% and 95.83% for SARS-CoV-2, respectively. This two-stage isothermal amplification method based on the microfluidic chip format offers a convenient, clinically parallel molecular diagnostic method, which can identify different nucleic acid samples simultaneously and in a timely manner, and with a low cost of the reaction reagent. It is especially suitable for resource-limited areas and point-of-care testing (POCT).

Microfluidic Biosensor for Rapid Nucleic Acid Quantitation Based on Hyperspectral Interferometric Amplicon-Complex Analysis

Nucleic acid detection plays a vital role in both biomedical research and clinical medicine. The temperature circulation changes of the widely used polymerase chain reaction technique are time-consuming and technically challenging for system development. Recombinase polymerase amplification (RPA) is an isothermal method for rapid nucleic acid detection. However, current RPA amplicon detection methods are complicated and expensive and easily generate false positives, restricting the promotion of RPA techniques. In this work, a hyperspectral interferometric amplicon-complex quantitation method is presented, combined with asymmetric dipole complex strategy optical scattering analysis. GelRed dye was utilized to form amplicon-complex particles, and the Fourier domain spectrum computation contributed to complex scattering quantitation. With this method, a supporting microfluidic chip and automatic system were developed to achieve integrated, rapid, quantitative, and miniscule nucleic acid detection. The Plasmodium falciparum dhfr gene was utilized as an example for targeted nucleic acid quantitation and single nucleotide polymorphism detection. The total reaction time was decreased to merely 20 min, and the limit of detection was only 3.17 ng/μL. The minimum measurable concentration of target was 1.68 copies/μL, 31.67 times more sensitive than turbidity detection, and the single reaction chamber was only 9.33 μL. No scattering increase occurred for template-free control, and thus, false positives caused by primer dimers and nonspecific products could be avoided. The experimental results prove that the provided method and system can detect single-base mutations in the dhfr gene and is a reasonable technique for rapid, automatic, and low-cost nucleic acid detection.

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

Background

The order Oedogoniales within the single family Oedogoniaceae comprised of three genera, Oedogonium, Oedocladium, and Bulbochaete based on traditional morphological criteria. While several molecular phylogenetic studies have suggested that both Oedogonium and Oedocladium may not be monophyletic, broader taxon sampling and large amounts of molecular data acquisition could help to resolve the phylogeny and evolutionary problems of this order. This study determined five chloroplast (cp) genomes of Oedogonium species and aimed to provide further information on cp genome for a better understanding of the phylogenetic and evolutionary relationships of the order Oedogoniales.

Results

The five Oedogonium cp genomes showed typical quadripartite and circular structures, and were relatively conserved in their structure, gene synteny, and inverted repeats boundaries in general, except for small variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses based on 54 cp protein-coding genes examined by maximum likelihood and Bayesian analyses using amino acid and nucleotide datasets indicated that both Oedocladium and Oedogonium are polyphyletic groups. A positively selected gene (psbA) was identified in the two Oedocladium species and the terrestrial Oedogonium species, indicating that terrestrial Oedogoniales taxa may have undergone adaptive evolution to adjust to the difference in light intensity between aquatic and terrestrial habitats.

Conclusions

Our results enrich the data on cp genomes of the genus Oedogonium. The availability of these cp genomes can help in understanding the cp genome characteristics and resolve phylogenetic and evolutionary relationships of the order Oedogoniales.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08006-1.

Quantitative and specific detection of viable pathogens on a portable microfluidic chip system by combining improved propidium monoazide (PMAxx) and loop-mediated isothermal amplification (LAMP)

An accurate and specific detection of viable Candida albicans (C. albicans) in vaginal discharge is crucial for the diagnosis of vulvovaginal candidiasis (VVC) and assessment of antifungal effects. In this study, improved propidium monoazide (PMAxx) and loop-mediated isothermal amplification (LAMP) were used for the first time to distinguish between viable and dead C. albicans. A portable microfluidic chip system was developed to detect multiple viable pathogens in parallel. The consumption of samples and reagents in per reaction cell were only 0.94 μL, less than 1/25 of the conventional 25 μL Eppendorf tubular test method, both significantly reducing testing cost and greatly simplifying the detection of multiple viable pathogens. The concentration of PMAxx was optimized against C. albicans at 4.0 log CFU mL^-1 to 5.0 log CFU mL^-1, and 1 μM PMAxx was proven to be suitable for the detection of C. albicans in clinical samples. When testing mixtures containing different ratios of viable to dead C. albicans, PMAxx-LAMP could circumvent the signal arising from dead cells and, therefore, reflected the abundance of viable cells precisely. Furthermore, the suitability of this technique to evaluate the effects of antifungal agents, including clotrimazole, miconazole, and tioconazole, was assessed. Finally, the viability of Escherichia coli (E. coli) and C. albicans were detected on the portable microfluidic chip system. PMAxx-LAMP based portable microfluidic chip system was determined to be a feasible technique for assessing the viability of multiple pathogens in gynecology and might provide insights into new VVC treatment strategies.

Hb adaptation to hypoxia in high-altitude fishes: Fresh evidence from schizothoracinae fishes in the Qinghai-Tibetan Plateau

Uncovering the genetic basis of hypoxic adaptation is one of the most active research areas in evolutionary biology. Among air-breathing vertebrates, modifications of hemoglobin (Hb) play a pivotal role in mediating an adaptive response to high-altitude hypoxia. However, the relative contributions in water-breathing organisms are still unclear. Here, we tested the Hb concentration of fish at different altitudes. All species showed species-specific Hb concentration, which has a non-positive correlation with altitude. Moreover, we investigated the expression of Hb genes by the RNA-seq and quantitative real-time PCR (qRT-PCR), and Hb composition by two-dimensional electrophoresis (2-DE). The results showed that the multiple Hb genes and isoforms are co-expressed in schizothoracinae fishes endemic to the Qinghai-Tibetan Plateau (QTP). Phylogenetic analyses of Hb genes indicated that the evolutionary relationships are not easily reconciled with the organismal phylogeny. Furthermore, evidence of positive selection was found in the Hb genes of schizothoracinae fishes through the selection pressure analysis. We demonstrated that positively selected sites likely facilitated the functional divergence of Hb isoforms. Taken together, this study indicated that the long-term maintenance of high Hb concentration may be a disadvantage for physiologically acclimating to high altitude hypoxia. Meanwhile, the genetically based modification of Hb-O₂ affinity in schizothoracinae fishes might facilitate the evolutionary adaptation to Tibetan aqueous environments.

Label-Free and Quantitative Dry Mass Monitoring for Single Cells during In Situ Culture

Quantitative measurement of single cells can provide in-depth information about cell morphology and metabolism. However, current live-cell imaging techniques have a lack of quantitative detection ability. Herein, we proposed a label-free and quantitative multichannel wide-field interferometric imaging (MWII) technique with femtogram dry mass sensitivity to monitor single-cell metabolism long-term in situ culture. We demonstrated that MWII could reveal the intrinsic status of cells despite fluctuating culture conditions with 3.48 nm optical path difference sensitivity, 0.97 fg dry mass sensitivity and 2.4% average maximum relative change (maximum change/average) in dry mass. Utilizing the MWII system, different intrinsic cell growth characteristics of dry mass between HeLa cells and Human Cervical Epithelial Cells (HCerEpiC) were studied. The dry mass of HeLa cells consistently increased before the M phase, whereas that of HCerEpiC increased and then decreased. The maximum growth rate of HeLa cells was 11.7% higher than that of HCerEpiC. Furthermore, HeLa cells were treated with Gemcitabine to reveal the relationship between single-cell heterogeneity and chemotherapeutic efficacy. The results show that cells with higher nuclear dry mass and nuclear density standard deviations were more likely to survive the chemotherapy. In conclusion, MWII was presented as a technique for single-cell dry mass quantitative measurement, which had significant potential applications for cell growth dynamics research, cell subtype analysis, cell health characterization, medication guidance and adjuvant drug development.

Standardization in Quantitative Imaging: A Multicenter Comparison of Radiomic Features from Different Software Packages on Digital Reference Objects and Patient Data Sets

Radiomic features are being increasingly studied for clinical applications. We aimed to assess the agreement among radiomic features when computed by several groups by using different software packages under very tightly controlled conditions, which included standardized feature definitions and common image data sets. Ten sites (9 from the NCI's Quantitative Imaging Network] positron emission tomography–computed tomography working group plus one site from outside that group) participated in this project. Nine common quantitative imaging features were selected for comparison including features that describe morphology, intensity, shape, and texture. The common image data sets were: three 3D digital reference objects (DROs) and 10 patient image scans from the Lung Image Database Consortium data set using a specific lesion in each scan. Each object (DRO or lesion) was accompanied by an already-defined volume of interest, from which the features were calculated. Feature values for each object (DRO or lesion) were reported. The coefficient of variation (CV), expressed as a percentage, was calculated across software packages for each feature on each object. Thirteen sets of results were obtained for the DROs and patient data sets. Five of the 9 features showed excellent agreement with CV < 1%; 1 feature had moderate agreement (CV < 10%), and 3 features had larger variations (CV ≥ 10%) even after attempts at harmonization of feature calculations. This work highlights the value of feature definition standardization as well as the need to further clarify definitions for some features.

Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life

Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448.52-Mb genome assembly with contig N50 length of 5.53 Mb by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin map. Demographic history reconstruction of the butterfly hillstream loach reveals that the population dynamics is correlated with the different stages of uplifting of the Tibetan Plateau. Comparative genomic analysis finds evidence of six keratin genes in butterfly hillstream loach evolving under positive selection. Within these genes, two keratin genes exhibit species-specific and divergent amino acid changes, suggesting a role in the formation of the unculi. Additionally, a series of positively selected genes, rapid evolving genes, specific variant genes and expanded gene families are found, including genes related to Hedgehog, Notch and BMP pathways, which may be involved in craniofacial development. These findings may have important implications for understanding the genetic basis of phenotypic adaptation to torrential mountain stream life.

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

BACKGROUND

Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.

METHODS

We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.

RESULTS

Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.

CONCLUSIONS

Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19. Video Abstract.

Single cell capture, isolation, and long-term in-situ imaging using quantitative self-interference spectroscopy

Single cell research with microfluidic chip is of vital importance in biomedical studies and clinical medicine. Simultaneous microfluidic cell manipulations and long-term cell monitoring needs further investigations due to the lack of label-free quantitative imaging techniques and systems. In this work, single cell capture, isolation and long-term in-situ monitoring was realized with a microfluidic cell chip, compact cell incubator and quantitative self-interference spectroscopy. The proposed imaging method could obtain quantitative and dynamic refractive index distribution in living cells. And the designed microfluidic chip could capture and isolate single cells. The customized incubator could support cell growth conditions when single cell was captured in microfluidic chip. According to the results, single cells could be trapped, transferred and pushed into the culture chamber with the microfluidic chip. The incubator could culture single cells in the chip for 120 h. The refractive index sensitivity of the proposed quantitative imaging method was 0.0282 and the relative error was merely 0.04%.

Deep Learning Algorithm for Automated Detection of Polycystic Ovary Syndrome Using Scleral Images

The high prevalence of polycystic ovary syndrome (PCOS) among reproductive-aged women has attracted more and more attention. As a common disorder that is likely to threaten women's health physically and mentally, the detection of PCOS is a growing public health concern worldwide. In this paper, we proposed an automated deep learning algorithm for the auxiliary detection of PCOS, which explores the potential of scleral changes in PCOS detection. The algorithm was applied to the dataset that contains the full-eye images of 721 Chinese women, among which 388 are PCOS patients. Inputs of the proposed algorithm are scleral images segmented from full-eye images using an improved U-Net, and then a Resnet model was applied to extract deep features from scleral images. Finally, a multi-instance model was developed to achieve classification. Various performance indices such as AUC, classification accuracy, precision, recall, precision, and F1-score were adopted to assess the performance of our algorithm. Results show that our method achieves an average AUC of 0.979 and a classification accuracy of 0.929, which indicates the great potential of deep learning in the detection of PCOS.

Efficacy and safety of endothelin receptor antagonists in type 2 diabetic kidney disease: A systematic review and meta-analysis of randomized controlled trials

AIM

To analyse the efficacy and safety of endothelin receptor antagonists for people with diabetic kidney disease.

METHODS

Randomized controlled trials comparing endothelin receptor antagonists with placebo in people with diabetic kidney disease were identified through PubMed, Embase and the Cochrane Library. We used a random-effect model to calculate the mean difference or risk ratio with the 95% CI.

RESULTS

Seven studies with a total of 4730 participants were included. Overall, endothelin receptor antagonists significantly reduced albuminuria compared with placebo (standardized mean difference -0.48, 95% CI -0.64 to -0.33). Atrasentan, in particular, effectively reduced albuminuria (standardized mean difference -0.58, 95% CI -1.00 to -0.17) and the risk of composite renal endpoints (risk ratio 0.65; 95% CI 0.49 to 0.88), with insignificant change in the rate of congestive heart failure (risk ratio 1.40, 95% CI 0.76 to 2.56) and mortality (risk ratio 1.11, 95% CI 0.77 to 1.61). In contrast, although avosentan reduced albuminuria (standardized mean difference -0.47, 95% CI -0.57 to -0.36) and the risk of composite renal endpoints (risk ratio 0.63, 95% CI 0.42 to 0.94), it was associated with a significant increase in congestive heart failure risk (risk ratio 2.61, 95% CI 1.36 to 5.00) and an insignificant increase in mortality risk (risk ratio 1.50, 95% CI 0.81, 2.78). No significant change in efficacy or safety outcomes with bosentan was detected. Dose-response analysis indicated that 0.75 mg/day atrasentan is expected to be optimal for renoprotection, with maximal albuminuria reduction and minimal fluid retention events.

CONCLUSIONS

Among the endothelin receptor antagonists, atrasentan and avosentan, but not bosentan, are effective for renoprotection in people with diabetic kidney disease. Compared with other types and doses, atrasentan 0.75 mg/day is the most promising, with maximal albuminuria reduction and minimal fluid retention. Vigilant monitoring of congestive heart failure risk is needed in future clinical practice. (PROSPERO registration no. CRD42020169840).

Focus on autonomic dysfunctions in anti-NMDAR encephalitis: a case report

OBJECTIVE

We hope it will provide a reference for early detection, early diagnosis, and early treatment of atypical Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis with non-typical autonomic dysfunctions as the first symptom.

PATIENTS AND METHODS

We present a 15-year-old girl with the repetition of conscious disturbance at different levels, but no abnormal movements. Initially, there were no positive findings on routine electroencephalography (EEG) and dynamic video-electroencephalography (V-EEG), but the head-up tilt test (HTT) suggested neurocardiogenic syncope (vascular rejection type), which seemed to be the final diagnosis. However, the patient later experienced several episodes of disturbance of consciousness with unexplained abdominal pain. Abnormalities were discovered on EEG, which indicated the possibility of "epileptic seizures with autonomic-gastrointestinal features". Based on these findings, we finally tested the autoimmune encephalitis-related antibodies for the patient after the literature search and review.

RESULTS

The patient was finally diagnosed with anti-NMDAR encephalitis. Her symptoms were fully controlled after glucocorticoid and gamma globulin treatment, and she left the hospital with complete recovery.

CONCLUSIONS

Although autonomic nervous dysfunction occurred in our patient, her prognosis was good because she did not have respiratory or (and) circulatory failure. Exclusive diagnosis and early treatment are important in patients with anti-NMDAR encephalitis. Abdominal pain with positive HTT may be a manifestation of autonomic dysfunction in this disease.

LncRNA NEAT1/miR-1224/KLF3 contributes to cell proliferation, apoptosis and invasion in lung cancer

OBJECTIVE

The aim of this study was to detect the relationship between long-chain non-coding RNA (lncRNA) NEAT1 and microRNA-1224 (miR-1224) in lung cancer and to explore its underlying mechanism.

MATERIALS AND METHODS

The expression levels of lncRNA NEAT1 and miR-1224 in lung cancer tissues and cells were detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). The interaction between lncRNA NEAT1 with miR-1224, miR-1224, and KLF3 was detected by Dual-Luciferase Reporter Gene Assay. MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide and flow cytometry were used to detect the changes in the proliferative and apoptosis abilities of lung cancer cells after silencing lncRNA NEAT1 or up-regulating miR-1224, respectively.

RESULTS

Compared with adjacent normal tissues, lncRNA NEAT1 was significantly up-regulated, while miR-1224 was significantly down-regulated in lung cancer tissues. LncRNA NEAT1 could specifically bind to the 3'UTR of miR-1224 and regulate its expression. The inhibition of lncRNA NEAT1 remarkably reduced the proliferation and enhanced the apoptosis of lung cancer cells. However, the upregulation of the expression of miR-1224 level could significantly inhibit proliferation and promote the apoptosis rate of lung cancer cells. Furthermore, miR-1224 could downregulate KLF3 expression by directly binding to its 3'UTR.

CONCLUSIONS

LncRNA NEAT1 can sponge the expression of miR-1224, thereby affecting the proliferation and apoptosis of lung cancer.

Nasal fluid cytology and cytokine profiles of eosinophilic and non-eosinophilic chronic rhinosinusitis with nasal polyps

BACKGROUND

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a heterogeneous disease with different clinical characteristics and different treatment responsiveness. The aims of this study were to compare the nasal fluid cytology and cytokines between eosinophilic CRSwNP (eCRSwNP) and non-eosinophilic CRSwNP (neCRSwNP) and establish a new multivariate model to predict eCRSwNP before surgery to improve personalized treatment for CRSwNP patients.

METHODS

Eighty-six consecutive patients with CRSwNP and sixteen healthy controls were recruited in this study. Nasal fluid (NF) was collected from all subjects and nasal polyp tissue was collected during the surgery. The differential cell counts and concentrations of IL-6, IL-8, TNF-77; and IL-10 in NF were measured. Univariate and multivariate logistic regression were used to identify predictors for eCRSwNP.

RESULTS

There were more inflammatory cells in NF of CRSwNP than controls. The eosinophil percentage was significantly higher in eCRSwNP than neCRSwNP and controls. The level of IL-8 was significantly higher in neCRSwNP than in eCRSwNP and controls. Blood eosinophilia, nasal fluid eosinophilia, higher total ethmoid score / total maxillary score (E/M ratio) and higher visual analogue scale (VAS) score of CRS were associated with eCRSwNP, the area under receiver operating characteristic curve (AUC) was 0.800, 0.755, 0.703 and 0.648, respectively. Using the coefficients of multivariate regression, we set up a scoring system to predict eCRSwNP with three of the variates and the AUC was 0.883.

CONCLUSION

ECRSwNP, neCRSwNP and healthy controls demonstrated different cytology and cytokine profiles in NF. A new preoperational multivariate prediction model for eCRSwNP with NF eosinophilia, blood eosinophilia and higher E/M ratio was established.

Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae

Whole-genome duplications (WGDs) are an important contributor to phenotypic innovations in evolutionary history. The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates. In this study, the evolutionary changes of hemoglobin (Hb) repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish, including eight diploid and four tetraploid species. Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species. Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes. Data were integrated with the expression profiles of the genes during ontogeny. Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family; each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications. This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression. Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.

Transcriptome-Wide Patterns of the Genetic and Expression Variations in Two Sympatric Schizothoracine Fishes in a Tibetan Plateau Glacier Lake

Sympatric speciation remains a central focus of evolutionary biology. Although some evidence shows speciation occurring in this way, little is known about the gene expression evolution and the characteristics of population genetics as species diverge. Two closely related Gymnocypris fish (Gymnocypris chui and Gymnocypris scleracanthus), which come from a small glacier lake in the Tibetan Plateau, Lake Langcuo, exist a possible incipient sympatric adaptive ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and tissues from each of the two species and compared gene expression patterns and genetic polymorphisms between them. Ordination analysis separated samples by organ rather than by species. The degree of expression difference between organs within and between species was different. Phylogenetic analyses indicated that the two closely related taxa formed a monophyletic complex. Population structure analysis displayed two distinctly divergent clusters of G. chui and G. scleracanthus populations. By contrast, G. scleracanthus population genetic diversity is higher than that of G. chui. Considerable sites of the two populations were differentiated with a coefficient of F_ST = 0.25–0.50, implying that a small proportion of loci nevertheless exhibited deep divergence in two comparisons. Concomitantly, putatively selected genes during speciation revealed functional categories are enriched in bone morphogenesis, cell growth, neurogenetics, enzyme activity, and binding activity in G. chui population. In contrast, nutrition and localization were highlighted in G. scleracanthus. Collectively, morphological traits and dietary preference combine with genetic variation and expression variation, probably contributed to the incipient speciation of two sympatric populations.

Analysis of Multiplicity of Hypoxia-Inducible Factors in the Evolution of Triplophysa Fish (Osteichthyes: Nemacheilinae) Reveals Hypoxic Environments Adaptation to Tibetan Plateau

HIF (Hypoxia-inducible factor) gene family members function as master regulators of cellular and systemic oxygen homeostasis during changes in oxygen availability. Qinghai-Tibet Plateau is a natural laboratory for for long-term hypoxia and cold adaptation. In this context, T. scleroptera that is restricted to >3500 m high-altitude freshwater rivers was selected as the model to compare with a representative species from the plain, P. dabryanus. We cloned different HIF-α and carried out a phylogenetic analysis from invertebrates to vertebrates for identifying HIF-α genes and analyzing their evolutionary history. Intriguingly, the HIF-α has undergone gene duplications might be due to whole-genome duplication (WGD) events during evolution. PAML analysis indicated that HIF-1αA was subjected to positive selection acted on specific sites in Triplophysa lineages. To investigate the relationship between hypoxia adaptation and the regulation of HIF-α stability by pVHL in plateau and plain fish, a series of experiments were carried out. Comparison the luciferase transcriptional activity and protein levels of HIF-αs and the differing interactions of HIF-αs with pVHL, show clear differences between plateau and plain fish. T. scleroptera pVHL could enhance HIF-α transcriptional activity under hypoxia, and functional validation through pVHL protein mutagenesis showed that these mutations increased the stability of HIF-α and its hetero dimerization affinity to ARNT. Our research shows that missense mutations of pVHL induced evolutionary molecular adaptation in Triplophysa fishes living in high altitude hypoxic environments.

Noninvasive prenatal diagnosis for pregnancies at risk for β-thalassaemia: a retrospective study

OBJECTIVE

To evaluate the clinical feasibility of noninvasive prenatal diagnosis (NIPD) for β-thalassaemia using circulating single molecule amplification and re-sequencing technology (cSMART).

DESIGN

Through carrier screening, 102 pregnant Chinese couples carrying pathogenic HBB gene variants were recruited to the study. Pregnancies were managed using traditional invasive prenatal diagnosis (IPD). Retrospectively, we evaluated the archived pregnancy plasma DNA by NIPD to evaluate the performance of our cSMART assay for fetal genotyping.

SETTING

Chinese prenatal diagnostic centres specialising in thalassaemia testing.

POPULATION

Chinese carrier couples at high genetic risk for β-thalassaemia.

METHODS

Fetal cell sampling was performed by amniocentesis and HBB genotypes were determined by reverse dot blot. NIPD was performed by a newly designed HBB cSMART assay and fetal genotypes were called by measuring the allelic ratios in the maternal cell-free DNA.

MAIN OUTCOME MEASURES

Concordance of HBB fetal genotyping between IPD and NIPD and the sensitivity and specificity of NIPD.

RESULTS

Invasive prenatal diagnosis identified 29 affected homozygotes or compound heterozygotes, 54 heterozygotes and 19 normal homozygotes. Compared with IPD results, 99 of 102 fetuses (97%) were correctly genotyped by our NIPD assay. Two of three discordant samples were false positives and the other sample involved an incorrect call of a heterozygote carrier as a homozygote normal. Overall, the sensitivity and specificity of our NIPD assay was 100% (95% CI 88.06-100.00%) and 97.26% (95% CI 90.45-99.67%), respectively.

CONCLUSIONS

This study demonstrates that our cSMART-based NIPD assay for β-thalassaemia has potential clinical utility as an alternative to IPD for pregnant HBB carrier couples.

TWEETABLE ABSTRACT

A new noninvasive test for pregnancies at risk for β-thalassaemia.

Comparative Genomics Reveals Accelerated Evolution of Fright Reaction Genes in Ostariophysan Fishes

The ostariophysian fishes are the most species-rich clade in freshwaters. This diversification has been suggested to be associated with the fright reaction presented in most ostariophysians. However, the genetic forces that underlie fright reaction remains poorly understood. In the present study, through integrating behavioral, physiological, transcriptomic, and evolutionary genomic analyses, we found that the fright reaction has a broad impact on zebrafish at multiple levels, including changes in swimming behaviors, cortisol levels, and gene expression patterns. In total, 1,555 and 1,599 differentially expressed genes were identified in olfactory mucosae and brain of zebrafish, respectively, with a greater number upregulated after the fright reaction. Functional annotation showed that response to stress and signal transduction were strongly represented, which is directly associated with the fright reaction. These differentially expressed genes were shown to be evolved accelerated under the influence of positive selection, indicating that protein-coding evolution has played a major role in fright reaction. We found the basal vomeronasal type 2 receptors (v2r) gene, v2rl1, displayed significantly decrease expression after fright reaction, which suggests that v2rs may be important to detect the alarm substance and induce the fright reaction. Collectively, based on our transcriptome and evolutionary genomics analyses, we suggest that transcriptional plasticity of gene may play an important role in fright reaction in ostariophysian fishes.

Serum sclerostin as a potential novel biomarker for heart valve calcification in patients with chronic kidney disease

OBJECTIVE

To explore the correlation between change in sclerostin level and heart valve calcification in patients with chronic kidney disease (CKD) in stages 3-5, as well as the possible underlying mechanism, which could provide a clinical reference for the diagnosis and treatment of cardiovascular disease (CVD).

PATIENTS AND METHODS

110 patients were divided into a healthy control group and three groups of patients with CKD stages 3, 4, and 5 according to CKD staging guidelines. Scr, BUN, AKP, TC, TG, HDL, LDL, Ca, Pi, and CRP were measured, and calcium-phosphate product (Ca×Pi) calculated. ELISA was used to measure the sclerostin level, and the estimated glomerular filtration rate (eGFR) was calculated by MDRD. Heart valve calcification was measured by a physician in the Cardiac Department of our hospital. The correlations between sclerostin-level change and heart valve calcification, as well as each index in CKD patients in stages 3-5, were analyzed.

RESULTS

Compared with the healthy control group, the serum Ca in CKD stage-3, stage-4, and stage-5 groups (p < 0.05) was reduced, and PTH was increased (p < 0.05). Blood Pi and Ca×Pi in the stage-4 and stage-5 groups were increased (p < 0.05). The serum sclerostin level increased with renal hypofunction in stage-3 CKD patients, and was significantly increased compared with that of the control group, reaching the highest level in the terminal stage (p < 0.01). Pearson correlation analysis indicated that serum sclerostin was negatively correlated with eGFR (r = -0.91, p < 0.001) and blood Ca (r= -0.271, p < 0.001), and positively correlated with SCr (r = 0.608, p < 0.001), blood Pi level (r = 0.295, p < 0.001), PTH (r = 0.334, p < 0.001), and Ca×Pi (r = 0.275, p < 0.001). The rate of heart valve calcification in the CKD patients in stage 5 was relatively high (11/30, 36.67%), and significantly higher than that in healthy controls (1/20, 5%; p < 0.01). Logistic regression analysis of heart valve calcification indicated that sclerostin was a risk factor for heart valve calcification in CKD patients in stages 3-5.

CONCLUSIONS

The sclerostin level gradually increased with renal hypofunction in CKD patients in stages 3-5, and the increase in serum sclerostin level in the CKD patients occurred earlier than the change in Pi and Ca×Pi. The risk of heart valve calcification in stage-5 CKD patients was significantly increased. Sclerostin is an independent risk factor for heart valve calcification in CKD patients.

Long non-coding RNA LINC00675 inhibits tumorigenesis and EMT via repressing Wnt/β-catenin signaling in esophageal squamous cell carcinoma

OBJECTIVE

Long noncoding RNA LINC00675 (LINC00675) seems to play an anti-oncogenic role in cancers, though its exact function remains unknown. Up to date, little is known about the role of LINC00675 in esophageal squamous cell carcinoma (ESCC). In this study, we aimed to explore the expression pattern, clinical significance and biological function of LINC00675 in ESCC.

PATIENTS AND METHODS

RT-PCR was performed to detect the expression levels of LINC00675 in both ESCC tissue and cell lines. The association of LINC00675 expression with clinicopathological factors and prognosis was statistically analyzed. Cell growth was detected by MTT assay and colony formation assay. Cell apoptosis was evaluated with flow cytometry. Migration and invasion ability of ESCC cells were detected wound healing assay and transwell assays. The expressions of EMT-related proteins and Wnt/β-catenin-related proteins by Western blot were investigated.

RESULTS

LINC00675 expression was significantly downregulated in both ESCC tissues and cell lines. Decreased LINC00675 expression was correlated with histological grade, lymph nodes metastasis and advanced clinical stage. Furthermore, LINC00675 could serve as an independent predictor for overall survival in ESCC. Importantly, in vitro experiments indicated that that forced LINC00675 expression significantly suppressed inhibited ESCC cell proliferation, colony formation, migration, invasion and EMT, and promoted cell apoptosis through suppressing Wnt/β-catenin signaling pathway.

CONCLUSIONS

We suggested that LINC00675 acted as a tumor suppressor in ESCC via regulation of Wnt/β-catenin signaling pathway and may be a new prognostic biomarker and potential therapeutic target for ESCC intervention.

Circular circ_0000885 promotes hepatocellular carcinoma proliferation by epigenetically upregulating Caprin1

OBJECTIVE

Recently, the vital role of circular RNAs is discovered in many diseases, including tumor progression. Hepatocellular carcinoma (HCC) is one of the most ordinary malignant tumors. The purpose of our study is to detect the potential function of circ_0000885 in HCC to offer new biomarkers and targets.

PATIENTS AND METHODS

The expression level of circ_0000885 in HCC tissues and cell lines was monitored by Real Time-quantitative Polymerase Chain Reaction (RT-qPCR). Pearson's Chi-square test was used to determine the association of circ_0000885 expression with several clinicopathological factors. Then knockdown of circ_0000885 was constructed to uncover its function in HCC. The cell growth ability was measured through the cell counting kit-8 (CCK-8) assay, colony formation assay, and cell cycle assay. The Western blot assay was performed to analyze the protein level of Caprin1.

RESULTS

Circ_0000885 was highly expressed in HCC tissues than that in adjacent samples. The miR-532-5p expression was associated with lymphatic metastasis and TNM stage. The expression of circ_0000885 was also higher in HCC cell lines. The cell growth ability of HCC cells was inhibited after circ_0000885 was silenced. Furthermore, Caprin1 was inhibited via knockdown of circ_0000885.

CONCLUSIONS

Circ_0000885 could enhance cell proliferation and regulate cell cycle of HCC by promoting Caprin1.