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Pancreatic ductal adenocarcinoma (PDA) presents a significant challenge in oncology due to its aggressive nature and limited treatment options. Despite advancements in understanding the genomic landscape of PDA initiation and progression, the mechanisms driving metastasis remain elusive. This doctoral thesis explores the critical role of epigenetic mechanisms, specifically focusing on transcriptional regulation, histone modification, and molecular crowding in PDA metastasis. Through a multidisciplinary approach, encompassing genomic analyses, functional studies, and biophysical investigations, the thesis sheds light on the intricate interplay between genetic and epigenetic factors driving PDA progression. Chapters elucidate the aberrant expression of the homeodomain transcription factor EN1 in PDA, its impact on downstream signaling pathways, and its promotion of PDA transformation and metastasis. Furthermore, the thesis uncovers the influence of nucleoplasmic macromolecular crowding, particularly highlighting the role of nesprin-3, in regulating nuclear dynamics and metastatic potential in PDA. By integrating genetic, epigenetic, and biophysical perspectives, this work not only advances our understanding of PDA pathogenesis but also paves the way for the development of targeted therapeutic interventions. Additionally, the thesis underscores the significance of pancreatic cancer organoid models in recapitulating disease progression, elucidating molecular dynamics, and guiding precision medicine approaches. Overall, this research underscores the importance of a comprehensive approach in deciphering the complexities of PDA and offers valuable insights for future therapeutic strategies aimed at improving patient outcomes.

Aneuploidy, aberrant chromosome numbers, is a chromosome alteration that is associated with poor prognosis and outcome in cancer. However, the exact role aneuploidy plays in cancer progression and local immune cell regulation are a matter of debate. Here we investigate the hypothesis that aneuploidy in cancer cells triggers an ER stress that will be transmitted to T cell, ultimately driving their dysfunction. We found that the conditioned medium (CM) of aneuploid murine B16.F10 and human SKOV3 cancer cells caused diminished Interferon-gamma (IFNG) and Granzyme B (GzmB) expression in T cells activated by anti-CD3/CD28 stimulation. However, the induction of aneuploidy in cancer cells did not result in UPR elevated enough to enable the transmission of UPR phenotype in T cells. T cells with diminished cytokine expression in response to aneuploid CM did not have an increase in UPR gene expression and the addition of UPR inhibitors could not restore IFNG or Granzyme expression. In fact, the induction of UPR, both through chemical means and transmissible ER stress factors, enhanced the function and activation of T cells rather than impairing their function. Finally, accumulating evidence indicates that glucose-restriction can contribute to the loss of T cell effector function by repressing EZH2, a subunit of Polycomb Repressive Complex 2 (PRC2). T cells made dysfunctional by aneuploid CM had significantly lower EZH2 expression which positively correlated with IFNG. However, addition of glucose to reactivate EZH2-mediate glucose metabolism only partially restored IFNG production in T cells. A provisional conclusion is that aneuploidy in cancer cells can cause T cell dysfunction in a cell-nonautonomous manner, but the mechanism behind it does not seem to depend on ER stress and glucose deprivation only provides a partial explanation. Further investigation is still needed to fully understand the molecular mechanism by which aneuploid CM impairs T cell immunity.

Tumor-associated macrophages (TAMs) are heterogenous myeloid populations that dictate the inflammatory tone of the tumor microenvironment (TME). Although TAMs pervade various types of solid tumors, immunotherapies targeting the recruitment or repolarization of TAMs have yielded little success in clinical trials, urging the discovery of novel mechanisms that control the immunosuppressive states of TAMs. As the metabolic landscape of the TME can restrict effector functions of immune cells, in this thesis research, we aimed to understand how specific metabolites, such as lipids, dictate the function of TAMs in cancer. First, we characterized the metabolic heterogeneity within TAM populations using bioinformatics and experimental approaches. Next, we established lipid accumulation as a hallmark of TAM dysfunction in solid tumors. Moreover, we dissected the role of scavenger receptor CD36 in dampening TAM’s anti-tumoral functions through binding to oxidized lipids in the TME. Lastly, we discussed some preliminary data on targeting cholesterol metabolic pathways in TAMs using genetic knockout models. In summary, our findings suggested that lipid metabolic pathways are critical regulators of TAM functions in cancer, providing rationale for therapeutically targeting lipid receptors or selected lipid metabolic processes to rejuvenate anti-tumor innate immunity.

Mutations in DDX3X are associated with autism spectrum disorder, brain malformations, and epilepsy, and account for up to 3% of cases of females with unexplained intellectual disability. However, little is currently known about the molecular mechanism linking DDX3X mutations to neurodevelopmental disease. DDX3X encodes an RNA helicase of the DEAD-box protein family and has been implicated in many aspects of RNA metabolism, yet we still lack a mechanistic understanding of DDX3X’s role in these processes, as well as how patient mutations in DDX3X affect RNA metabolism. To address this gap in knowledge of understanding of how DDX3X mutations perturb cellular function and contribute to neurodevelopmental disease, this study investigated the mechanism of how DDX3X regulates its target transcripts at the level of mRNA nuclear export, and how pathogenic mutations in DDX3X alter these processes. In addition to DDX3X’s role in translation, DDX3X has been implicated in nuclear mRNA processing, and our preliminary data show that the genes in the mRNA export pathway are genetic interaction partners of DDX3X. However, we still do not understand what the function of DDX3X is in the nucleus or mRNA export. This study aimed to gain a greater understanding the precise mechanism of how DDX3X regulates RNA metabolism both at the level of translation initiation as well as mRNA export. This knowledge is critical for advancing our knowledge of RNA metabolism, as well as understanding and developing treatments for patients with DDX3X syndrome.

Drug discovery is a costly and time-consuming process. It has four major stages: early drug discovery, pre-clinical phase, clinical trials, and regulatory approval. Early drug discovery is the steps of target validation, hit identification (hit ID), hit-to-lead, and lead optimization for new chemical entities (NCEs) and therapeutic targets. Basic research identifies and validates disease-relevant targets. Hit ID is the process of testing a group of compounds against a target protein. Thermal shift assay (TSA) can detect slight changes in protein melting point and stability, and, therefore, be used to screen for hit ID. X-ray crystallography studies can determine the binding between target protein and hits. In vitro enzymatic assays can confirm the inhibition of hits and measure IC50 (inhibitory concentration 50%). Hit-to-lead can be done by ‘SAR by catalog’, in which the features of the hits are used to identify commercially available compounds. During the hit-to-lead stage, hits are developed to improve the binding affinity to move along as a final drug.Structural-based drug discovery (SBDD) is one of the early-stage drug discovery approaches and has been wildly used in academic and industrial settings since the 1990s. SBDD uses small molecules that follow Lipinski's Rule of Five that ensures that the small molecules can be administered orally once they become drugs. Fragment-based lead discovery (FBLD) evolved from SBDD. Fragments follow the Rule of Three that helps reduce off-target effects and for a broad search of chemical diversity using smaller libraries in the low thousands of compounds. In silico artificial intelligence-computer-aided drug discovery (AI-CADD) is used to identify hits and develop leads using computer tools and the simulation of human intelligence processed by machines. Post-translational modifications (PTMs) are the last stage in protein biosynthesis, being either reversible or irreversible chemical events occurring after protein translation. One type of PTM is ubiquitin-like protein is the Small-Ubiquitin-Related Modifier (SUMO) modification. SUMOylation of a target protein occurs via an enzyme cascade that involves three steps: First, the SUMO E1 activation enzyme, the Aos1/Uba2 complex, activates matured SUMO protein and form a high-energy thioester bond to the Uba2 subunit. Next, the activated SUMO is transferred to cysteine 93 of Ubc9 (SUMO E2 conjugating enzymes). Ubc9 conjugates SUMO onto the substrates, or SUMO E3 enzyme, such as Pias1, often aids in this conjugation event to increase substrate specificity. SUMOylation has been studied extensively and found involved in cancer as “non-oncogene addiction”. SUMO enzymes are not mutated or classical oncogenes, but cancer cells essentially depend on them for survival. Notably, non-oncogene addiction may provide novel targets for intractable and undruggable cancers. Another target for cancer is the dual-specificity tyrosine phosphorylation-regulated kinase 1A (Dyrk1a). It plays multiple roles in animal development, with critical effects on neuronal cell cycle regulation and cancer development. We hypothesis that targeting the SUMOylation modification and Dyrk1a will impact cancer cells as therapeutic treatments. Utilizing SBDD, FBDD, and AI-CADD, we have identified a small molecule, AW2 F5, targets the ATP binding pocket and inhibits Aos1/Uba2 with an IC50 of 497.7 nM. We have identified a fragment, LC B3, covalently bind to the backside of Ubc9 as a potential degrader. We also have found a small molecule, DTP C1, targets the ATP binding pocket and inhibit Dyrk1a with IC50 of 35.7 nM. In the future, each compound will be optimized and tested in cancer cells for their therapeutic effects.

While the lung is well known for its vital functions of performing gas exchange and supplying oxygen to the whole body, its ability of interrogating environmental stimuli has been neglected. In this dissertation, I am presenting two studies during my Ph.D. training, addressing 1) in vivo sensory functions of pulmonary neuroendocrine cells (PNECs), a rare, innervated epithelial cell type; and 2) underlying mechanisms of how the lung responds to mechanical cues under both developmental and pathological conditions. The former revealed an unanticipated role of PNECs in regulating gas exchange by signaling to endothelial cells through secreted neuropeptides. The latter unveiled underappreciated mechanosensation and signaling functions of alveolar type I (AT1) cells, the cell type performing gas exchange, in promoting lung construction perinatally and reconstruction upon mechanical insults-coupled injury in adult. These findings uncover novel sensory functions of the lung epithelium, where they play a central role in physiological regulations in respond to atmospheric cues.

RNA silencing mediated by 19-to-24 nucleotide-long small RNAs is a central mechanism regulating gene expression. In plants, the two major types of small RNAs are microRNAs (miRNAs) and small interfering RNAs (siRNAs). miRNAs are derived from long hairpin RNA precursors while siRNAs are derived from long double-stranded RNAs. In plants, the majority of miRNAs and certain siRNAs associate with the ARGONAUTE1 (AGO1) protein to exert their regulatory effects by forming an RNA-induced silencing complex (RISC). Even though many studies have been done to characterize Arabidopsis AGO1 and AGO1 activities, little is known about the mechanisms that regulate AGO1 RISC formation. In my dissertation research, two mechanisms that regulate AGO1 RISC formation were identified and reported in chapters two and three. In the second chapter, we found that the long structurally unresolved N-terminal extension (NTE) is essential for the functions of AGO1, as an AGO1 mutant lacking this region is unable to rescue the developmental and molecular phenotypes of an ago1 null allele. RNA sequencing of total small RNAs and AGO1-associated small RNAs showed that amino acids (a.a.) 91-189 of the NTE are required for RISC formation, thus crucial for the activities of AGO1 in gene silencing. Furthermore, a.a. 1-90 and a.a. 91-189 regions of the NTE redundantly promote the activities of AGO1 in the biogenesis of trans-acting siRNAs (ta-siRNAs). This work provides a new understanding of the AGO1 NTE region in RISC assembly and ta-siRNA biogenesis. In the third chapter, through immunoprecipitation-mass spectrometry, we found that AGO1 is phosphorylated in vivo. Analysis of AGO1-associated small RNAs in vivo and RISC formation assays in vitro showed that phospho-mimetic AGO1 is compromised in the loading of both miRNA and siRNA duplexes and in passenger strand ejection of siRNA but not miRNA duplexes. Non-phosphorylatable AGO1 is compromised in target RNA repression. This work revealed a regulatory role of phosphorylation and dephosphorylation in the small RNA association and target repression activities of AGO1. Taken together, my dissertation research provided new insights into mechanisms regulating the activities of plant AGO1 and these insights have implications beyond plant AGO1.

An 8-week feeding trial investigated the optimum dietary vitamin K3 requirements of largemouth bass. A total of 600 healthy fish (12.96 ± 0.07 g) were fed diets containing varying levels of vitamin K3 at 0.78 (K0), 5.80 (K5), 10.82 (K10), 15.84 (K15), and 20.85 (K20) mg/kg with four replicates per level. Results showed that dietary vitamin K3 enhanced growth, with weight gain rate and specific growth rate in K15 trials significantly higher than K0 trials (P 0.05). However, the supplementation of vitamin K3 significantly contributed to calcium accumulation in muscle tissues and vertebrae (P 0.05). The antioxidant capacity was improved with the addition of vitamin K3, which was inconsistent with the changes in malondialdehyde and MK-4 (a form of menaquinone) within liver and serum, suggesting that the toxicity of excessive artificial vitamin K3 may account for this difference. Using regression analysis, the appropriate dietary vitamin K3 levels within a largemouth bass diet was determined to be in the range of 9.93–15.22 mg/kg, which will provide a reference for the preparation of vitamin premix and artificial diet for largemouth bass.

Major histocompatibility complex (MHC) molecules play a critical role in the immune response of vertebrate animals by presenting foreign antigens to T lymphocytes. In this study, we first cloned and identified a classical and a novel nonclassical MHC I α molecules from Japanese eel (Anguilla japonica), named as AjMHC I-UBA and AjMHC I-L, respectively. The full-length cDNA of AjMHC I-UBA contains an open reading frame (ORF) of 1047 bp encoding a predicted protein of 348 amino acids, while AjMHC I-L 1089 bp encodes 362 amino acids. The multiple alignment of the amino acid sequence showed that AjMHC I-UBA and AjMHC I-L consist of an N-terminal MHC I superfamily domain within α1 and α2 helices, an IgC-MHC I α3 domain, and a transmembrane region close to the C-terminal, which are similar to other fish and mammal species. Molecular polymorphism analysis showed that eight different major alleles of AjMHC I-UBA, named as AjMHC I-UBA*0101～1001, were identified from six Japanese eel individuals. Furthermore, a distinguishing signature of the nonclassical L-lineage genes specific motif “HINMTL”, including an N-glycosylation site (NXS/T), was present in the α3 domain of AjMHC I-L sequences. Although the predicted three-dimensional structures of AjMHC I-UBA and AjMHC I-L are similar to that of human MHC I α, phylogenetic analysis showed that these two protein molecules belong to classical MHC I UBA gene of U-lineage and nonclassical MHC I gene of L-lineage, respectively. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the highest expression of AjMHC I-UBA and AjMHC I-L was found in the intestine and the expression level of AjMHC I-UBA in all of the examined tissues was significantly higher than that of AjMHC I-L. The expressions of AjMHC I-UBA and AjMHC I-L in liver, kidney and spleen were significantly induced following injection with the viral mimic poly I:C, LPS, and Aeromonas hydrophila infection. In vitro, the AjMHC I-UBA and AjMHC I-L transcripts of Japanese eel liver cells were significantly enhanced by the treatment of poly I:C or the stimulation of the high concentration of A. hydrophila. Subcellular localization showed that under natural conditions, AjMHC I-UBA and AjMHC I-L were uniformly distributed in the cytoplasm, and aggregated into spots or flakes in the cytoplasm after the stimulation of poly I:C or LPS. These results collectively suggested that AjMHC I-UBA and AjMHC I-L are important components possibly involved in Japanese eel defense against viral and bacterial infection. Taken together, these findings provide valuable insight into the immune function of MHC class I in the immune system of teleost.

Background: Human adipose-derived stem cells (hASCs) play an important role in regenerative medicine. Objective: Exploring the mechanism of Rg1 in the promotion of the proliferation and adipogenic differentiation of hASCs is important in regenerative medicine research. Methods: To observe ginsenoside Rg1 in promoting the proliferation and adipogenic differentiation of hASCs, Rg1 medium at different concentrations was established and tested using the cell counting kit-8 (CCK-8) assay, oil red O staining, alizarin red, and alcian blue. Compared to the control, differentially expressed genes (DEGs) were screened via DEG analysis, which was carried out in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. To explore the relationship among mRNA, long non-coding RNA (lncRNA) and microRNA (miRNA), we constructed a competing endogenous RNA (ceRNA) network. Results: In this study, Rg1 was observed to promote the proliferation and adipogenic differentiation of hASCs. Additionally, enriched BPs and KEGG pathways may be involved in the promotion process, where FXR1 and Lnc-GAS5-AS1 were found to be regulatory factors. The regulatory network suggested that Rg1 could regulate the adipocytokine signaling pathway and IL−17 signaling pathway via FXR1 and Lnc-GAS5-AS1, which served as the mechanism encompassing the promotion of Rg1 on the proliferation and adipogenic differentiation of hASCs. Conclusion: A comprehensive transcriptional regulatory network related to the promotion ability of Rg1 was constructed, revealing mechanisms regarding Rg1’s promotion of the proliferation and adipogenic differentiation of hASCs. The present study provides a theoretical basis for optimizing the function of hASCs.

Pumpkin (Cucurbita moschata) has been widely used as cucumber (Cucumis sativus L.) rootstock to defend against Fusarium wilt (FW) and increase cucumber yields and profits. However, the resistance genes and mechanisms underlying the FW tolerance in pumpkin are poorly understood. Here we analyzed the transcriptome of pumpkin inoculated with the cucumber FW causal agent Fusarium oxysporum f. sp. cucumerinum (Foc), and obtained 3 152 and 4 735 upregulated genes induced by Foc at 24 h after Foc inoculation compared with at 0 h and 24 h non-inoculated control, respectively. Next, 404 common differentially expressed genes (DEGs) were screened using the criterion log2 FPKM (fold change) ≥ 2. In total, 206 of 404 DEGs were predominantly expressed in roots, which is the first tissue that Foc contacts and invades. 140 DEGs were selected and classified into four groups (pathogenesis resistance, secondary metabolism-related, transcription factor and signal binding) based on their functional descriptions. Then, 29 genes having high expression levels were selected to investigate the expression patterns induced by a Foc inoculation. Among them, 16 genes were significantly induced by Foc and showed high expression levels at various treatment time points. These candidate genes may act as positive regulators of FW resistance in pumpkin and provide effective resources for improving cucumber FW resistance through breeding programs.

This study aimed to establish age- and sex-specific reference intervals for serum amylase and lipase in children by prospective investigation. A total of 6466 healthy Han children of 1 month ∼18 years were recruited in communities and schools in five administrative regions of Jilin Province, China. The serum amylase and lipase concentrations were measured on the VITROS 5600 integrated system. The reference intervals were defined by a nonparametric 95% percentile interval. Reference intervals of amylase were divided into four age-specific partitions. It increased rapidly between the ages of 1 month ∼1 year and 1 ∼5 years, slightly decreased between the ages of 5 ∼12 years, and increased slowly between 12 ∼18 years. Lipase concentrations showed sex differences after 1-year-old, with reference intervals in males divided into 2 divisions and 3 divisions in females. The lipase concentrations in both males and females showed an upward trend, and the lipase concentrations in females were higher than those in males. This study established reference intervals for amylase and lipase in healthy Chinese children and provided a more accurate explanation for the diagnosis and prognosis of clinical pediatric diseases.

Tiger pufferfish (Takifugu rubripes) is one of Asia's most economically valuable aquaculture species. However, winter production of this species in North China is limited by low water temperature and unavailability of high-quality feed, resulting in high mortality and low profitability. Therefore, the aim of this study was to evaluate the effect of feeding frequency (F1: one daily meal; F2: two daily meals; F3: four daily meals; F4: continuous diurnal feeding using a belt feeder) on the growth performance, plasma biochemistry, digestive and antioxidant enzyme activities, and expression of appetite-related genes in T. rubripes (initial weight: 266.80 ± 12.32 g) cultured during winter (18.0 ± 1.0 °C) for 60 days. The results showed that fish in the F3 group had the highest final weight, weight gain rate, specific growth rate, survival rate, and best feed conversion ratio. Additionally, daily feed intake increased significantly with increasing feeding frequency. The protein efficiency and lipid efficiency ratios of fish in the F3 group were significantly higher than those of fish in the other groups. Furthermore, total cholesterol, triglycerides, and glucose levels increased with increasing feeding frequency, peaking in the F2 group and decreasing under higher feeding frequencies. The antioxidant (superoxide dismutase, catalase, glutathione, and glutathione peroxidase) and digestive (trypsin, amylase, and lipase) enzyme activities of fish in the F1 group were significantly higher than those of fish in the F3 and F4 groups. Additionally, there was a decrease in orexin expression with increasing feeding frequency. In contrast, the expression levels of tachykinin, cholecystokinin, and leptin increased with increasing feeding frequency, peaking in the F4 group. Overall, the findings of this study indicated that a feeding frequency of four meals per day was optimal for improved growth performance of pufferfish juveniles cultured during winter.

The presence of multiple immunosuppressive targets and insufficient activation and infiltration of cytotoxic T lymphocytes (CTLs) allow tumor cells to escape immune surveillance and disable anti-PD-1/PD-L1 immunotherapy. Nanobiotechnology-engineered autologous tumor vaccines (ATVs) that were camouflaged by tumor cell membrane (TCM) were designed to activate and facilitate CTLs infiltration for killing the unprotected lung tumor cells, consequently realizing the sequential immunotherapy. PDE5 was firstly screened out as a new immunosuppressive target of lung cancer in clinical practice. Immediately afterwards, phosphodiesterase-5 (PDE5) and programmed cell death 1 ligand 1 (PD-L1) dual-target co-inhibition was proposed to unfreeze the immunosuppressive microenvironment of NSCLC. Systematic studies validated that this ATVs-unlocked sequential immunotherapy after co-encapsulating PDE5 inhibitor and NO donor (i.e., l -arginine) exerted robust anti-tumor effects through increasing inducible nitric oxide synthase (iNOS) expression, blockading PDE5 pathway and activating systematic immune responses, which synergistically eradicated local and abscopal lung cancers in either orthotopic or subcutaneous models. The pluripotent ATVs that enable PDE5 inhibition and sequential immunotherapy provide a new avenue to mitigate immunosuppressive microenvironment and magnify anti-PD-1/PD-L1 immunotherapy.

Iridoviruses are emerging pathogens widely spread in diverse environments and hosts. Numerous species of the iridoviridae family are known to cause severe disease in freshwater and marine organisms. Here, we report the complete genome sequence and phylogenetic analysis of the iridovirus strain LPIV-ZS-2021 isolated from a small yellow croaker (Larimichthys polyactis) in China. The genome sequence comprises 110,560 bp with a G+C content of 53.42%, has 104 putative open reading frames (ORFs) and shares highest sequence homology with Red red seabream iridovirus (RSIV) isolated in Japan (98.61%). Phylogenetic analysis revealed that it is clustered within RSIV clade1. This is the first fully sequenced RSIV genomes detected in the small yellow croaker. The host range expansion of Megalocytivirus genus iridovirus warrants further attention to determine its potential economic and ecological impact.

The caspase family is commonly involved in the pathophysiology of acute brain injury (ABI) through complex apoptotic, pyroptotic, and inflammatory pathways. Current translational strategies for caspase modulation in ABI primarily focus on caspase inhibitors. Because there are no caspase-inhibiting drugs approved for clinical use on the market, the development of caspase inhibitors remains an attractive challenge for researchers and clinicians. Therefore, we conducted the present review with the aim of providing a comprehensive introduction of caspases in ABI. In this review, we summarized the available evidence and potential mechanisms regarding the biological function of caspases. We also reviewed the therapeutic effects of caspase inhibitors on ABI and its subsequent complications. However, various important issues remain unclear, prompting further verification of the efficacy and safety regarding clinical application of caspase inhibitors. We believe that our work will be helpful to further understand the critical role of the caspase family and will provide novel therapeutic potential for ABI treatment.

The Hessian fly (HF, Mayetiola destructor) is one of the destructive pests of wheat (Triticum aestivum L.) worldwide. Resistant cultivars can effectively minimize wheat damage due to this insect pest. To identify new quantitative trait loci (QTL) for HF resistance, a population of recombinant inbred lines (RILs) was developed from a cross between the HF-resistant wheat cultivar ‘Chokwang’ and susceptible wheat ‘Ning 7840’, and phenotyped for responses to HF attack. A linkage map was constructed using 1147 single nucleotide polymorphism (SNP) markers generated from genotyping-by-sequencing (GBS). One major QTL, QHf.hwwg-6BS, for HF-resistance was identified on chromosome arm 6BS, which explained up to 84.0% of the phenotypic variation and was contributed by Chokwang. Two RILs showed recombination in the candidate interval of QHf.hwwg-6BS, which delimited QHf.hwwg-6BS to a 4.75 Mb physical interval between 6,028,601 bp and 10,779,424 bp on chromosome arm 6BS of IWGSC Chinese Spring reference genome RefSeq v2.0. Seven GBS-SNPs in the candidate interval were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers. Two of them, KASP-6B112698 and KASP-6B7901215, were validated in a U.S. winter wheat panel. KASP-6B112698 was nearly diagnostic, thus can be used to screen QHf.hwwg-6BS and pyramid it with other resistance genes in breeding programs.

Tauopathies, such as Alzheimer’s Disease (AD) and Progressive Supranuclear Palsy (PSP), are characterized by the central nervous system accumulation of misfolded tau protein. Endoplasmic reticulum (ER) stress and Unfolded Protein Response (UPR) may be cellular mechanisms that cause tauopathies. As one of three major branches of UPR, PERK was identified as a genetic risk factor for AD and PSP in several GWAS studies. Upon activation, PERK attenuates protein translation to restore ER homeostasis but prolonged PERK activation can induce apoptosis. Here, we studied the role of PERK in tau aggregation in human AD and PSP brain tissues and in a cell culture model. We prepared protein lysates from the hippocampus region of advanced AD patient brains (Braak 6) and normal brains (Braak 1). We found more tau aggregated protein in Braak 6 brains in comparison to Braak 1 brains by immunoblotting. We also found a statistically significant increase of phosphorylated PERK in Braak 1 brains in comparison to Braak 6 brains in AD patients. This finding suggests that PERK activity is inversely proportional to insoluble misfolded tau aggregation. We did not find any correlation between PERK-haplotype and PERK functional in AD brains. We also prepared protein lysates from 3 different anatomic regions from PSP patient brains (midbrain, frontal cortex, and occipital cortex). The PSP results were highly variable due to technical problems, and we did not identify any reproducible correlations between tau levels and phosphorylated PERK levels.We further studied how PERK and tau interact utilizing HEK293 cells stably expressing TauRD-YFP (Biosensor cells) developed by Marc Diamond’s group as a cellular model of tau protein aggregation. We activated or inhibited PERK activity in TauRD biosensor cells by treating them with pharmacochemical small molecule modulators (GSK2656157, GSK2606414, salubrinal, ISRIB). We monitored tau aggregation by the formation of YFP fluorescent puncta in the cells. We found an inverse association between PERK pathway activation and tau aggregation. In summary, our brain and cell culture findings implicate PERK as a regulator of tau protein accumulation. PERK pathway activation may have high therapeutic potential for tauopathy treatment.

Wide exposure to endocrine-disrupting chemicals (EDCs) poses a great risk on human health. However, few large-scale cohort studies have comprehensively estimated the association between EDCs exposure and mortality risk. This study aimed to investigate the association of urinary EDCs exposure with mortality risk and quantify attributable mortality and economic loss. Multivariable Cox proportional hazards regression models were performed to investigate the association of 38 representative EDCs exposure with mortality risk in the National Health and Nutrition Examination Survey (NHANES). During a median follow-up of 7.7 years, 47,279 individuals were enrolled. All-cause mortality was positively associated with 1-hydroxynaph-thalene, 2-hydroxynaphthalene, cadmium, antimony, cobalt, and monobenzyl phthalate. Cancer mortality was positively associated with cadmium. Cardiovascular disease (CVD) mortality was positively associated with 1-hydroxynaphthalene, 2-hydroxynaph-thalene, and 2-hydroxyfluorene. Nonlinear U-shaped relationships were found between all-cause mortality and cadmium and cobalt, which was also identified between 2-hydroxyfluorene and CVD mortality. J-shaped association of cadmium exposure with cancer mortality was also determined. EDCs exposure may cause 56.52% of total deaths (1,528,500 deaths) and around 1,897 billion USD in economic costs. Exposure to certain phthalates, polycyclic aromatic hydrocarbons, phytoestrogens, or toxic metals, even at substantially low levels, is significantly associated with mortality and induces high economic costs.

In this paper, we studied the structure, expression and function of black carp insulin gene. The complete Mylopharyngodon piceus insulin (Mp-Ins) gene is 1,965 bp long and includes a 1,499 bp 5ʹ-untranslated region (UTR), a 139 bp 3′-UTR with a poly(A) tail, and an open reading frame (ORF) of 327 bp. The predicted molecular weight of the recombinant Mp-Ins(rMp-Ins) protein is 11.87 kDa. The mRNA expression of Mp-Ins is upregulated in the brain and liver. After the injection of rMp-Ins, Mp-Ins mRNA transcript abundance was significantly upregulated in the liver. The rMp-Ins protein could inhibit the concentration of glycogen phosphorylase (GP), growth hormone (GH), fatty acid synthase (FAS), and insulin-like growth factors-1 (IGF-1), and it also significantly increased the concentration of PI3K. Additionally, the injection of rMp-Ins did not have a significant impact on the glucose-6-phosphatase (G6Pase) content in blood. In situ hybridization results showed that the positive signal of the Mp-Ins gene was mainly concentrated in the cell nucleus of brain tissue and the cell membrane of liver tissue and muscle tissue. Together, these results demonstrated that Mp-Ins plays an important role in growth and metabolism in M. piceus.

The large yellow croaker (Larimichthys crocea) is an economically important marine species with the highest annual production among the farmed marine fishes in China. However, the aquaculture industry of this species is suffering from severe problems that include weakened disease resistance, decreased growth rate, and reduced meat quality due to frequent inbreeding. Genome editing, which has a huge potential for solving those problems by introducing favorable genetic changes, is not yet available for the large yellow croaker. Here, we pioneered the techniques of embryo microinjection and genome editing using the CRISPR/Cas9 system in this species. Recombinant plasmids encoding green fluorescent protein (GFP) were introduced into the fertilized eggs of L. crocea by microinjection before the chorion had hardened. A high survival rate (40%) and GFP-positive larvae rate (81.8%) were achieved, indicating that the microinjection technique in L. crocea was successfully established. On this basis, Cas9 mRNA and sgRNA targeting the tyrosinase a gene in L. crocea (Lc-tyra) were co-injected into fertilized eggs of L. crocea. Mutant individuals with insertion and deletion mutations of Lc-tyra were detected. These results indicated that the CRISPR/Cas9-based genome editing technology established herein could efficiently introduce mutations at a specific site in the L. crocea genome. This method provides the potential for genetic improvement and functional genomic study in this species. This is the first report on effective CRISPR/Cas9-based genome editing in L. crocea.

Ionic liquids (ILs) have been widely used in the pretreatment of biomass. However, the effects of residual ILs on the enzymolysis and fermentation of biomass are still unknown. Therefore, a large quantity of water-washing is usually followed after biomass pretreatment to eliminate the inhibition of residual ILs on subsequent hydrolysis and fermentation steps. In this work, the effect of choline glycine ([Ch][Gly]) concentration on the activity of cellulase and Bacillus sp. strain P38 was systematically investigated to explore the impacts of residual ILs on enzymolysis and fermentation. The results confirmed that the activities of them were almost not inhibited in low concentrations (less than 0.5 wt%) of [Ch][Gly]. Under optimal pretreatment conditions, the maximum cellulose digestibility was 99.23%. Enzymatic hydrolysate was suitable for l -lactic acid fermentation without appreciable inhibition, and the highest sugar-acid conversion rate of 96.33% was obtained by simplified detoxification. This work provides an economic route to produce fermentable sugar and l -lactic acid, which shows an industrial application prospect in lignocellulosic biorefinery.

The demand for accurate estimation of aboveground biomass (AGB) at high spatial resolution is increasing in grassland-related research and management, especially for those regions with complex topography and fragmented landscapes, where grass and shrub are interspersed. In this study, based on 519 field AGB observations, integrating Synthetic Aperture Radar (SAR; Sentinel-1) and high-resolution (Sentinel-2) remote sensing images, environmental and topographical data, we estimated the AGB of mountain grassland in Southwest China (Yunnan Province and Guizhou Province) by using remote sensing algorithms ranging from traditional regression to cutting edge machine learning (ML) and deep learning (DL) models. Four models (i.e., multiple stepwise regression (MSR), random forest (RF), support vector machine (SVM) and convolutional neural network (CNN)) were developed and compared for AGB simulation purposes. The results indicated that the RF model performed the best among the four models (testing dataset: decision co-efficient (R2) was 0.80 for shrubland and 0.75 for grassland, respectively). Among all input variables in the RF model, the vegetation indices played the most important role in grassland AGB estimation, with 6 vegetation indices (EVI, EVI2, NDVI, NIRv, MSR and DVI) in the top 10 of input variables. For shrubland, however, topographical factors (elevation, 12.7% IncMSE (increase in mean squared error)) and SAR data (VH band, 11.3% IncMSE) were the variables which contributed the most in the AGB estimation model. By comparing the input variables to the RF model, we found that integrating SAR data has the potential to improve grassland AGB estimation, especially for shrubland (26.7% improvement in the estimation of shrubland AGB). Regional grassland AGB estimation showed a lower mean AGB in Yunnan Province (443.6 g/m2) than that in Guizhou Province (687.6 g/m2) in 2021. Moreover, the correlation between five consecutive years (2018–2022) of AGB data and climatic factors calculated by partial correlation analysis showed that regional AGB was positively related with mean annual precipitation in more than 70% of the grassland and 60% of the shrubland area, respectively. Also, we found a positive relationship with mean annual temperature in 62.8% of the grassland and 55.6% of the shrubland area, respectively. This study demonstrated that integrating SAR into grassland AGB estimation led to a remote sensing estimation model that greatly improved the accuracy of modeled mountain grassland AGB in southwest China, where the grassland consists of a complex mix of grass and shrubs.