Next-Generation DNA Barcoding for Fish Identification Using High-Throughput Sequencing in Tai Lake, China

Tai Lake, an important biodiversity hotspot of the lower reaches of the Yangtze River in China, possesses its characteristic fish fauna. Barcoding on native species is important for species identification and biodiversity assessment with molecular-based methods, such as environmental DNA (eDNA) metabarcoding. Here, DNA-barcoding coupled with high-throughput sequencing (HTS) and traditional Sanger sequencing was introduced to barcoding 180 specimens belonging to 33 prior morphological species, including the most majority of fish fauna in Tai Lake. HTS technology, on the one hand, significantly enhances the capture of barcode sequences of fish. The successful rate of fish barcoding was 74% and 91% in Sanger and HTS, respectively. On the other hand, the HTS output has a large number (64%) of insertions and deletions, which require strict bioinformatics processing to ensure that the ‘‘true’’ barcode sequence is captured. Cross-contamination and parasites were the primary error sources that compromised attempts at the DNA barcoding of fish species. The barcode gap analysis was 100% successful at delimiting species in all specimens. The automatic barcode gap discovery (ABGD) method grouped barcode sequences into 34 OTUs, and some deep divergence and closed species failed to obtain corresponding OTUs. Overall, the local species barcode library established by HTS barcoding here is anticipated to shed new light on conserving fish diversity in Tai Lake

Unsupervised biological integrity assessment by eDNA biomonitoring of multi-trophic aquatic taxa

The biological integrity of global freshwater ecosystems is threatened by ever-increasing environmental stressors due to increased human activities, such as land-use change, eutrophication, toxic pollutants, overfishing, and exploitation. Traditional ecological assessments of lake or riverine ecosystems often require human supervision of a pre-selected reference area, using the current state of the reference area as the expected state. However, selecting an appropriate reference area has become increasingly difficult with the expansion of human activities. Here, an unsupervised biological integrity assessment framework based on environmental DNA metabarcoding without a prior reference area is proposed. Taxon richness, species dominance, co-occurrence network density, and phylogenetic distance were used to assess the aquatic communities in the Taihu Lake basin. Multi-gene metabarcoding revealed comprehensive biodiversity at multiple trophic levels including algae, protists, zooplankton, and fish. Fish sequences were mainly derived from 12S, zooplankton mainly from mitochondrial cytochrome C oxidase subunit I, and algae and protists mainly from 18S. There were significant differences in community composition among lakes, rivers, and reservoirs but no significant differences in the four fundamental biological indicators. The algal and zooplankton integrities were positively correlated with protist and fish integrities, respectively. Additionally, the algal integrity of lakes was found to be significantly lower than that of rivers. The unsupervised assessment framework proposed in this study allows different ecosystems, including the same ecosystem in different seasons, to adopt the same indicators and assessment methods, which is more convenient for environmental management and decision-making

Distinct roles for histone chaperones in the deposition of Htz1 in chromatin

Histone variant Htz1 substitution for H2A plays important roles in diverse DNA transactions. Histone chaperones Chz1 and Nap1 (nucleosome assembly protein 1) are important for the deposition Htz1 into nucleosomes. In literatures, it was suggested that Chz1 is a Htz1–H2B-specific chaperone, and it is relatively unstructured in solution but it becomes structured in complex with the Htz1–H2B histone dimer. Nap1 (nucleosome assembly protein 1) can bind (H3–H4)2 tetramers, H2A–H2B dimers and Htz1–H2B dimers. Nap1 can bind H2A–H2B dimer in the cytoplasm and shuttles the dimer into the nucleus. Moreover, Nap1 functions in nucleosome assembly by competitively interacting with non-nucleosomal histone–DNA. However, the exact roles of these chaperones in assembling Htz1-containing nucleosome remain largely unknown. In this paper, we revealed that Chz1 does not show a physical interaction with chromatin. In contrast, Nap1 binds exactly at the genomic DNA that contains Htz1. Nap1 and Htz1 show a preferential interaction with AG-rich DNA sequences. Deletion of chz1 results in a significantly decreased binding of Htz1 in chromatin, whereas deletion of nap1 dramatically increases the association of Htz1 with chromatin. Furthermore, genome-wide nucleosome-mapping analysis revealed that nucleosome occupancy for Htz1p-bound genes decreases upon deleting htz1 or chz1, suggesting that Htz1 is required for nucleosome structure at the specific genome loci. All together, these results define the distinct roles for histone chaperones Chz1 and Nap1 to regulate Htz1 incorporation into chromatin

Bridge the gap caused by public health crises: medical humanization and communication skills build a psychological bond that satisfies patients

Abstract Background Patient satisfaction is an important outcome domain of patient-centered care. Medical humanization follows the patient-centered principle and provides a more holistic view to treat patients. The COVID-19 pandemic posed significant barriers to maintaining medical humanization. However, empirical study on the relationship between medical humanization and patient satisfaction is clearly absent. Objectives We examined the mediation effects of communication on the relationship between medical humanization and patient satisfaction when faced with a huge public health crisis like the COVID-19 pandemic, and the moderation effect of medical institutional trust on the mediation models. Methods A cross-sectional survey study was performed. A final sample size of 1445 patients was surveyed on medical humanization, communication, patient satisfaction and medical institutional trust. Results All correlations were significantly positive across the main variables (r = 0.35–0.67, p < 0.001 for all) except for medical institutional trust, which was negatively correlated with the medical humanization (r=-0.14, p < 0.001). Moderated mediation analysis showed that the indirect effect of medical humanization on patient satisfaction through communication was significant (b = 0.22, 95% CI: 0.18 ~ 0.25). Medical institutional trust significantly moderated the effect of medical humanization on patient satisfaction (b=-0.09, p < 0.001) and the effect of medical humanization on communication (b= -0.14, p < 0.001). Conclusion Medical humanization positively influence patient satisfaction, communication mediated the association between medical humanization and patient satisfaction, and medical institutional trust negatively moderated the effects of medical humanization on patient satisfaction and communication. These findings suggest that humanistic communication contributes to patient satisfaction in the face of a huge public health crisis, and patients’ evaluation of satisfaction is also regulated by rational cognition

Exploring the association between rosacea and acne by integrated bioinformatics analysis

Abstract Clinically, rosacea occurs frequently in acne patients, which hints the existence of shared signals. However, the connection between the pathophysiology of rosacea and acne are not yet fully understood. This study aims to unveil molecular mechanism in the pathogenesis of rosacea and acne. We identified differentially expressed genes (DEGs) by limma and weighted gene co-expression network analysis and screened hub genes by constructing a protein–protein interaction network. The hub genes were verified in different datasets. Then, we performed a correlation analysis between the hub genes and the pathways. Finally, we predicted and verified transcription factors of hub genes, performed the immune cell infiltration analysis using CIBERSORT, and calculated the correlation between hub genes and immune cells. A total of 169 common DEGs were identified, which were mainly enriched in immune-related pathways. Finally, hub genes were identified as IL1B, PTPRC, CXCL8, MMP9, CCL4, CXCL10, CD163, CCR5, CXCR4, and TLR8. 9 transcription factors that regulated the expression of hub genes were identified. The infiltration of γδT cells was significantly increased in rosacea and acne lesions and positively linked with almost all hub genes. These identified hub genes and immune cells may play a crucial role in the development of rosacea and acne

Label-Free Photoelectrochemical Immunosensor for Neutrophil Gelatinase-Associated Lipocalin Based on the Use of Nanobodies

Acute renal failure (ARF) represents a very important and potentially devastating disorder in clinical nephrology. Neutrophil gelatinase-associated lipocalin (NGAL) is an early biomarker for ARF in a wide range of different disease processes, which is frequently detected in clinical diagnosis. Herein, we present a label-free and sensitive photoelectrochemical (PEC) immunosensor for NGAL by utilizing a biotinylated anti-NGAL Nanobody (Nb) orientedly immobilized to streptavidin-coated cobalt 2,9,16,23-tetraaminophthalocyanine (CoPc)-sensitized TiO₂ electrode. The Nb was biotinylated at the C-terminus, which is situated at the opposite site of the antigen binding region. Using highly oriented Nb as receptor molecules, a label-free PEC immunosensor for NGAL was developed by monitoring the changes in the photocurrent signals of the electrode resulting from immunoreaction. Immobilization of Nb to streptavidin-coated CoPc-sensitized TiO₂ electrode surface provides high binding capacity to NGAL; thus, it can lead to a high sensitivity. The limit of detection (LOD) of the proposed immunosensor has been significantly lowered to 0.6 pg mL^–1. This proposed immunosensor reveals high specificity to detect NGAL, with acceptable intra-assay precision and excellent stability. In addition, the present work provides a new approach to design Nb-based PEC immunosensor and increases versatility of Nbs

Active Site Synergy of Rh and Co Derived from ZrO₂‑Supported LaRh_<i>x</i>Co_1–<i>x</i>O₃ Perovskite Nanostructures for the Direct Synthesis of Ethanol from Syngas

The catalytic synthesis of ethanol directly from syngas is one of the most attractive routes due to its cost-effectiveness and the high demand for ethanol. However, progress is critically stagnant due to the limited activity and ethanol selectivity of the catalysts. Here, La–Rh–Co/ZrO2 nanoscaled catalysts derived from ZrO2-supported LaRhxCo1–xO3 perovskite nanostructures were prepared by citric acid complexing followed by calcination and reduction. Rh and Co species derived from the precursors can increase the amount of interfacial species and construct the active sites for the direct synthesis of ethanol from syngas. Co species were proven to be confined in the ZrO2 matrix, with high-valent Coδ+ derived from LaCoOx. These Co species can decorate Rh species by forming an interface, Rh0–Rh+–O–Coδ+, as confirmed by extended X-ray absorption fine structure, resulting in a higher molar fraction of Rh+. The formed intimate Rh0–Rh+–O–Coδ+ active sites originating from the interfaces are conducive to CO dissociation and CO insertion, leading to an impressive ethanol selectivity of 55.7% and a high CO conversion of 33.5% with good stability over the La–Rh–Co/ZrO2 nanoscaled catalysts. The results show that the strategy of interfacial construction enables the design of robust catalysts to break the scale relationship between conversion and selectivity