Reconstruction of the East Asian monsoon variability since the mid-Holocene from the Pearl River estuary, southern China

The principal aim of this thesis is to reconstruct East Asian Monsoon (EAM) variability during the mid-Holocene, developing a relatively new proxy of bulk organic carbon isotopic signature (δ13C). C/N ratios and trace elements are also employed to conduct a multi-proxy case study from the Pearl River estuary, southern China. Sources of sediments within an estuary include river-derived terrestrial/freshwater input, in situ brackish-water suspended sediment and tide-derived marine input. This study assumes the three proxies can help differentiate sources of sediments relating to monsoon-driven freshwater flux and help reconstruct monsoonal precipitation history during the mid-Holocene when the sea level was relatively stable. To achieve the aims of this thesis a range of modern samples were collected from terrestrial areas, including plants and soil samples, through to estuarine areas, including seasonal estuarine suspended organic matter (SOM) and surface sediment. Results suggest that bulk organic δ13C and C/N ratios can successfully identify sources of the organic component of the estuarine sediment, and thus can be used to infer relative changes in monsoon-driven freshwater flux to the estuary. For example, more negative δ13C values reflect a greater level of contribution of freshwater organic carbon, i.e. stronger monsoonal freshwater discharge. Results also show that a combination of selected metals, such as the terrigenous metals (Fe, Mn, Co and As), can be useful for indicating sediment sources and sedimentary environment. Analysis of an estuarine core (UV1) shows that freshwater discharge from the Pearl River catchment gradually declined from 6400 to 2000 cal. years BP, suggesting a gradual weakening of summer monsoon precipitation, responding to the weakening insolation controlled by the orbital-driven precession cycle. Superimposed on this are wet/dry intervals, ranging from centennial- to millennial- scale, driven by solar activity. Changes in ENSO and high-latitude cooling events might be responsible for dry/wet events at centennial- to decadal- scale, identified during the mid-Holocene. This study also suggests that the coupling of thermal and moist conditions of the EAM might only have become stable after 4500 cal. yr BP. A sudden shift in the geochemical signature indicates agricultural activity in the Pearl River delta intensified from 2000 cal. yr BP

Observational study of tidal mixing asymmetry and eddy viscosity-shear covariance – induced residual flow in the Jiulong River estuary

Abstract(#br)An observation study was conducted at three stations in the inner regime of the Jiulong River estuary to examine the tidal mixing asymmetry and its associated residual flow induced by eddy viscosity-shear covariance (ESCO). The water columns at the observation stations were approximately well-mixed during the later flood and were stratified during the early ebb, a typical tidal mixing asymmetry. Corresponding to the tidal variation of stratification, the Reynolds stress and vertical eddy viscosity, which were obtained using the ADCP variance method, exhibited distinct differences in the magnitude and vertical structure between flood and ebb tides. The ESCO flow was calculated using the decomposition method for estuarine circulation, revealing a two-layer vertical structure similar to density-driven flow but with a much greater magnitude, confirming the findings of previous generic model studies that the ESCO flow dominates the density-driven flow in periodically stratified estuaries. The drivers of tidal mixing asymmetry were explored using the potential energy anomaly method. Longitudinal straining reduced stratification during flood tides and reinforced stratification during ebb tides, whereas longitudinal advection acted in the opposite manner. Although the contribution of lateral circulation to stratification was neglected due to the lack of lateral observation data, scaling analysis revealed that lateral advection was important in the longitudinal dynamics and tidal evolution of stratification and warrants further study

Three strategies of transgenic manipulation for crop improvement

Heterologous expression of exogenous genes, overexpression of endogenous genes, and suppressed expression of undesirable genes are the three strategies of transgenic manipulation for crop improvement. Up to 2020, most (227) of the singular transgenic events (265) of crops approved for commercial release worldwide have been developed by the first strategy. Thirty-eight of them have been transformed by synthetic sequences transcribing antisense or double-stranded RNAs and three by mutated copies for suppressed expression of undesirable genes (the third strategy). By the first and the third strategies, hundreds of transgenic events and thousands of varieties with significant improvement of resistance to herbicides and pesticides, as well as nutritional quality, have been developed and approved for commercial release. Their application has significantly decreased the use of synthetic pesticides and the cost of crop production and increased the yield of crops and the benefits to farmers. However, almost all the events overexpressing endogenous genes remain at the testing stage, except one for fertility restoration and another for pyramiding herbicide tolerance. The novel functions conferred by the heterologously expressing exogenous genes under the control of constitutive promoters are usually absent in the recipient crops themselves or perform in different pathways. However, the endogenous proteins encoded by the overexpressing endogenous genes are regulated in complex networks with functionally redundant and replaceable pathways and are difficult to confer the desirable phenotypes significantly. It is concluded that heterologous expression of exogenous genes and suppressed expression by RNA interference and clustered regularly interspaced short palindromic repeats-cas (CRISPR/Cas) of undesirable genes are superior to the overexpression of endogenous genes for transgenic improvement of crops

A numerical study of residual flow induced by eddy viscosity-shear covariance in a tidally energetic estuary

Abstract(#br)The inner regime of an estuary has unique tidal mixing processes but received relatively less attention. A numerical model was developed to investigate the tidal variability of vertical mixing and the residual flow induced by eddy viscosity–shear covariance (ESCO) in the inner regime of a tidally energetic estuary in Southeastern China. Because of migration of the saltwater/freshwater interface, the water column in the inner regime undergoes a saltwater-dominant high-water period and a freshwater-dominant low-water period during a tidal cycle. The different mixing processes of high- and low-water periods led to typical (reverse) internal tidal asymmetry, i.e. stronger (weaker) mixing during flood tides than ebb tides when the tidal range was large (small). Tidal straining was the main driver of internal tidal asymmetry during the high-water period, while the asymmetries of duration and current velocity between flood and ebb were the main drivers during the low-water period. For typical internal tidal asymmetry, the ESCO stress was negative and the ESCO flow had a two-layer structure with landward flow near the bottom and seaward flow near the surface. For reverse internal tidal asymmetry, the ESCO stress was positive and the vertical pattern of the ESCO flow was reversed. The magnitude of the ESCO flow was several times greater than that of the density-driven flow. The reverse internal tidal asymmetry occurred in the freshwater-dominant low-water period indicates that the ESCO stress could be an important driver of tidal rectification flow in homogeneous coastal waters

Immunomodulatory effect of Bifidobacterium breve on experimental allergic rhinitis in BALB/c mice

Bifidobacterium breve (B. breve) may have a beneficial effect on allergic rhinitis (AR). The aim of the present study was to investigate whether microbial induction of regulatory T cells (Tregs) and adjustment of Th1 and Th2 responses by B. breve are associated with protection against allergic inflammation, and to identify a dose-response association in a murine AR model. Ovalbumin (OVA)-sensitized BALB/c mice were orally treated with different doses of B. breve [10(10), 10(9), 10(7) and 10(5) colony forming units (CFU)]. Following nasal challenge with OVA, sneeze frequency, serum OVA-specific immunoglobulin E (IgE) and cytokine concentrations [interleukin (IL)-4, IL-10, IL-13 and interferon-gamma], splenic percentage of cluster of differentiation (CD)4+CD25+ Tregs, and morphology of the nasal mucosa were examined. Oral treatment with live B. breve at doses of 10(7) CFU or higher alleviated nasal mucosal injury and suppressed sneezing upon repeated administration over a 6-week period. Furthermore, treatment with B. breve at these higher doses reduced the concentrations of serum OVA-specific IgE, IL-4 and IL-10, and increased the splenic percentage of CD4+CD25+ Tregs in rhinitic mice compared with those who did not receive probiotics. In contrast, treatment with B. breve at a lower dose did not indicate any effect on sneezing frequency or mucosal morphology in this animal model, even though the splenic percentage of CD4+CD25+ Tregs increased and the concentrations of serum OVA-specific IgE and IL-10 declined. B. breve exerts its anti-allergic effects by inhibiting type 2 helper T cell immune responses and enhancing CD4+CD25+ Treg activity. Sneezing was also reduced at a dose of 10(7) CFU or higher. The current study investigated the role of B. breve and aided in identifying the optimal dose of B. breve administration in the treatment of AR

Characterization of the microRNA408-LACCASE5 module as a regulatory axis for photosynthetic efficiency in Medicago ruthenica: implications for forage yield enhancement

Medicago ruthenica is closely related to Medicago sativa, a commonly cultivated forage. Characterized by its high tolerance to environmental stress, M. ruthenica is a valuable genetic resource. However, low yield limits its large-scale utilization. Leaf morphology, an important agronomic trait, is closely related to forage yield and photosynthetic efficiency. In the presented study, “Correlation of Leaf Morphology and Photosynthetic Performance with Forage Yield in Medicago ruthenica: The Underlying Molecular Mechanisms,” comprehensive data analysis revealed a significant positive association between leaf width and leaf area with forage yield in Medicago ruthenica (p < 0.05). The specific cultivar “Mengnong No.1 (MN No.1) had a large leaf area, and its physiological parameters related to photosynthetic characteristics were superior. Anatomical examination revealed that the leaves of MN No.1 had strong palisade tissue and compact cell structure. Subsequent investigations, utilizing small RNA and transcriptome sequencing, discerned critical miRNA-target gene networks that underpin the high photosynthetic efficiency in M. ruthenica. A total of 63 differentially expressed miRNAs (DEMs) were identified, inclusive of several well-characterized miRNAs such as miR408, miR171, and miR398. These miRNAs were predicted to target 55 genes (mRNAs), of which 6 miRNA-target gene pairs, particularly those involving miR408and miR171, exhibited inverse expression patterns. Among the six postulated miRNA-target gene pairs, the targeted cleavage of LACCASE5 (LAC5) by miR408 was conclusively validated through degradome sequencing, with the cleavage site pinpointed between the 9th and 10th nucleotides from the 5′end of miR408 via the 5′-RLM-RACE assay. Therefore, it is posited that the miR408-MrLAC5 module constitutes a central mechanism in fostering high photosynthetic efficiency in M. ruthenica. Moreover, these findings also provide valuable information for further study of the regulatory genes and miRNA functions of forage yield in legume forage

A humification-based method toward refining Holocene radiocarbon chronologies: Wetland records from southeastern China

Holocene paleoclimate reconstructions and comparisons largely rely on accurate age-depth modeling. However, uncertainties in chronology, such as those caused by sparse radiocarbon dates, will hamper inter-core comparisons and correlations, and might result in misleading “cause and consequence” conclusions. This study aimed to find a solution to increase the comparability and minimize the uncertainty of wetland chronology as much as possible. Sediment cores were recovered and radiocarbon dated from the Lianhuachi wetland located in Southeastern China. Humification degree and loss-on-ignition (LOI) were determined using colorimetric and combustion methods respectively. Our data were compared with previously published datasets obtained in the same wetland. The results show that independent humification profiles from the Lianhuachi wetland displayed high similarities. This high similarity between the humification profiles allowed us to transfer radiocarbon ages from one core to another using sequence slotting correlation. Applying the humification-based chronology refinement method to all sediment cores resulted in an improvement in the correlation coefficients between the same but independently measured proxy sequences from the wetland, which suggests both the inter- and intra-core comparability was improved. Because determining peat humification degree is easy, inexpensive, and time-saving, we suggest that humification can serve as a tool that can be used to correlate different cores and to transfer published radiocarbon ages within the same wetland (peatland) or in a comparable geological setting, to establish a more robust chronology of these comparable cores. The degree of peat humification can thus serve as a relative dating technique to refine the chronology of wetland (including peatland) records

Diagnostic application of exome sequencing in Chinese children with suspected inherited kidney diseases

Background: Inherited kidney diseases (IKDs) are a group of kidney diseases characterized by abnormal kidney structure or function caused by genetic factors, but they are not easily diagnosed in childhood due to either nonspecific symptoms and signs or clinically silent symptoms in the early stages until the progressive stages, even end-stages. Early diagnosis of IKDs is very urgent for timely treatment and improving outcomes of patients. So far, the etiological diagnosis has been accelerated with the advance of clinical genetic technology, particularly the advent of next-generation sequencing (NGS) that is not only a powerful tool for prompt and accurate diagnosis of IKDs but also gives therapy guidance to decrease the risk of unnecessary and harmful interventions.Methods: The patients presenting with urinalysis abnormalities or structural abnormalities from 149 Chinese families were enrolled in this study. The clinical features of the patients were collected, and the potentially causative gene variants were detected using exome sequencing. The clinical diagnostic utility of the genetic testing was assessed after more detailed clinical data were analyzed.Result: In total, 55 patients identified having causative variants by exome sequencing were genetically diagnosed, encompassing 16 (29.1%) autosomal dominant IKDs, 16 (29.1%) autosomal recessive IKDs, and 23 (41.8%) X-linked IKDs, with 25 unreported and 45 reported variants. The diagnostic yield was 36.9%. The utility of the exome sequencing was accessed, 12 patients (21.8%) were confirmed to have suspected IKDs, 26 patients (47.3%) discerned the specific sub-types of clinical category, and 17 patients (30.9%) with unknown etiology or lack of typical manifestations were reclassified.Conclusion: Our study supported that genetic testing plays a crucial role in the early diagnosis for children with IKDs, which affected follow-up treatment and prognostic assessment in clinical practice. Moreover, the variant spectrum associated with IKDs was expanded

Mechanism of Regulation of Big-Conductance Ca2+-Activated K+ Channels by mTOR Complex 2 in Podocytes

Podocytes, dynamic polarized cells wrapped around glomerular capillaries, are an essential component of the glomerular filtration barrier. BK channels consist of one of the slit diaphragm (SD) proteins in podocytes, interact with the actin cytoskeleton, and play vital roles in glomerular filtration. Mechanistic target of rapamycin (mTOR) complexes regulate expression of SD proteins, as well as cytoskeleton structure, in podocytes. However, whether mTOR complexes regulate podocyte BK channels is still unclear. Here, we investigated the mechanism of mTOR complex regulation of BK channels via real-time PCR, western blot, immunofluorescence, and patch clamping. Inhibiting mTORC1 with rapamycin or downregulating Raptor had no significant effect on BK channel mRNA and protein levels and bioactivity. However, the dual inhibitor of mTORC1 and mTORC2 AZD8055 and short hairpin RNA targeting Rictor downregulated BK channel mRNA and protein levels and bioactivity. In addition, MK2206, GF109203X, and GSK650394, which are inhibitors of Akt, PKCα, and SGK1, respectively, were employed to test the downstream signaling pathway of mTORC2. MK2206 and GF109203X had no effect on BK channel protein levels. MK2206 caused an obvious decrease in the current density of the BK channels. Moreover, GSK650394 downregulated the BK channel protein and mRNA levels. These results indicate mTORC2 not only regulates the distribution of BK channels through Akt, but also modulates BK channel protein expression via SGK1 in podocytes

Low-density reference fingerprinting SNP dataset of CIMMYT maize lines for quality control and genetic diversity analyses

CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally