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Adult stem cells (SCs) are defined by their ability to self-renew to maintain a SC pool while preserving their potential to differentiate, ensuring tissue homeostasis. Yet, how SC fate decisions are dictated and synchronized across a tissue remains poorly understood. SCs are surrounded by and communicate with their supporting microenvironments, or “niches,” for tissue regeneration. Recent evidence has revealed the lymphatic vascular system as a new niche entity for adult SCs across epithelial tissues, including hair follicle stem cells (HFSCs) in the skin. However, whether lymphatic vasculature can instruct SC fate decisions in tissue renewal is unknown. Here, we investigate how HFSC fate decisions and differentiation potential are guided by their spatial proximity to lymphatic niches during homeostatic tissue regeneration. Using deep 3-dimensional imaging of the regenerated hair follicles (HFs), coupled with genetic lineage tracing and conditional lymphatic ablation models, we identify an asymmetric lymphatic architecture surrounding the HFSCs across the horizontal axis of the follicle. Through tracking SC proliferation rates and detailed temporal lineage tracing, our findings reveal a clonal imbalance in the regenerated HF. We demonstrate the most regenerating SCs exhibit earlier cell divisions and originate near lymphatic capillaries. In contrast, SCs from later division waves, which reside farther from the lymphatics, primarily maintain self-renewal rather than contribute to differentiation and tissue regeneration. This study provides a further direction to understand the lymphatic-stem cell duet in tissue regeneration, which could have important clinical implications for stem cell transplantation and therapeutic intervention to advance wound response in degenerative pathologies.

Human retinal vasculopathies commonly result in breakdown of the blood retinal barrier and formation of scars on the retinal surface. The formation of rigid scar tissue creates traction on the retinal layers that can result in tearing, detachment, and complete blindness. Currently, the only treatment option for retinal fibrosis is surgical removal, an invasive procedure that lacks consistent success at treating the condition. Furthermore, an optimized animal model for retinal fibrosis has yet to be developed. The absence of an animal model severely limits the improvement of patient standard of care. This creates a strong need for a model capable of emulating the clinical progression of retinal fibrosis in a laboratory setting. Mouse models have been proven effective at modeling the angiogenic features of retinal vasculopathies. However, current models have yet to produce the long-term scarring that is also present in a variety of ischemic retinal vasculopathies. Therefore, this study focuses on the scarring and leakage induced by the long oxygen induced retinopathy (l-OIR) as it compares to the classical oxygen induced retinopathy model, referred to as the standard-oxygen induced retinopathy (s-OIR) model. This study primarily focuses on how breakdown of the blood retinal barrier contributes to disease pathophysiology. This was accomplished through an extensive set of leakage assays that follow the disease progression in the mice across an array of time points. It was observed that leakage occurs immediately upon completion of the high oxygen treatment in the l-OIR model. This leakage persists for 7 days and was no longer observed at 14 days. While the s-OIR model leads to a greater acute peak in leakage, the l-OIR model produces leakage over a longer duration as well as a defined fibrotic plaque. This difference may be due to the difference in induced disease severity across the models, with l-OIR producing retinas with more damaged vascular structures, often lacking in central veins and arteries. Furthering scientific and clinical understanding of the role that leakage and scarring play in ischemic retinal vasculopathies will allow future research into bettering the standard of care for patients suffering from such diseases.

Gene expression involves multiple layers of regulation to change the amount of proteins produced. The complexity of this phenomenon starts in the nucleus, where various cis-regulatory elements near genes can engage in transcriptional regulation by association with transcription factors that often function in diverse combinations to enhance or silence transcription. In addition, chemical modifications of DNA such as methylation can have varying impacts on the rate of transcription. Furthermore, molecular events that occur to a maturing pre-mRNA synthesized by RNA polymerase II, notably 5’ capping, splicing and 3’ end processing, all contribute to the intricacies of gene regulation. Whereas these processes need to successfully occur to a maturing pre-mRNA to make it competent for export, malfunction in any of these steps can compromise the RNA’s nuclear export, often leading to its sequestration in the nucleus. Despite ongoing research in the nuclear retention of various RNAs, including mRNAs, mechanisms and tissue-specific consequences of this surveillance mechanism are poorly understood. This work aims to better our understanding of the molecular mechanisms leading to chromatin association of RNAs, particularly mRNAs, by RNA binding proteins PTBP1 and NXF1. Our work demonstrates that these proteins play key roles in altering gene expression in mouse embryonic stem cells (mESCs) through manipulation of splicing and subcellular localization of their target RNAs. We discovered that these mechanisms can have direct consequences on the biology of the mESCs, affecting their pluripotency and differentiation.

House Dust Mite (HDM) is a common aeroallergen that can induce asthma and allergic airway inflammation. The effects of acute exposure to HDM have been well studied in various mouse models asthma; however, the effects of chronic exposure have been much less investigated. Our studies identified that chronic exposure to HDM induces chronic lung inflammation and accelerates lung cancer development in two different mouse models of lung cancer. The lung cancer-promoting effect of HDM was mainly due to chronic activation of the NLRP3 inflammasome in lung macrophages and persistent production of IL-1β in the lungs. Based on these findings, we hypothesize that chronic exposure to HDM changes the lung microenvironment and makes it conducive to tumor growth by activating the IL-1β signaling pathway. To further evaluate the mechanisms by which HDM affects the lung microenvironment, we conducted a single-cell RNA sequencing (scRNA-seq) analysis and compared the effect of chronic HDM exposure in the lungs of wild-type (WT) and IL-1β knock out (KO) mice. Our findings suggest that HDM and IL-1β signaling affect various cell types such as macrophage, neutrophils, and T cells and their gene profiles that may contribute to the protumorigenic effects of HDM and IL-1β in the lungs. In conclusion, our study revealed the transcriptomic landscape of the murine lung microenvironment and uncovered the effects of chronic HDM exposure and IL-1β signaling.

Periodontitis is an oral chronic inflammatory disease. Inhibiting tissue destruction and promoting tissue regeneration are important means for the treatment of periodontitis. Metformin not only has hypoglycemic effect but also has anti-inflammatory effect. Metformin has been shown to inhibit oxidative stress and activate autophagy through AMPK/mTOR pathway. High mobility group box 1 (HMGB1) has been implicated in the pathogenesis of many inflammatory diseases including periodontitis, it can participate in the induction of oxidative stress. HMGB1 is an autophagy regulator under oxidative stress, which can activate mTOR pathway. However, it is not clear whether metformin is related to HMGB1 and its mechanism in the process of periodontitis. Cell viability and expression of inflammatory cytokines were clarified by Cell Counting Kit-8, real-time PCR and enzyme-linked immunosorbent assay. Western blot and immunofluorescence were conducted to determine HMGB1 intracellular localization and expression of autophagy-associated proteins in vitro. Experimental periodontitis mice model was induced by administering a ligature. Immunohistochemistry was performed to detect the expression and localization of HMGB1 in vivo. The results of CCK-8, real-time PCR, enzyme-linked immunosorbent assay, Western blot and immunofluorescence showed lipopolysaccharide (LPS) treatment inhibited cell viability, and increased HMGB1 expression at a dose-independent manner. Metformin can reduce the effect of LPS. It also improves autophagy pathway inhibited by LPS and down-regulates mTOR expression. In addition, metformin attenuated alveolar bone resorption induced by ligation. This study provides new evidence for that metformin is a potential drug for the treatment of periodontitis and HMGB1 may be a potential target for periodontal intervention.

Climate change has had large impacts on marine animals, including neon flying squid Ommastrephes bartramii (O. bartramii) in the North Pacific Ocean. O. bartramii statoliths from 2012, 2015, and 2016 were used to evaluate the variations in life cycle events. The relationship between mantle length and body weight showed significant differences between years and gender. The oldest squid was collected in 2016 at 271 days old, further proving that O. bartramii has nearly a 1-year life span. The hatching season ranged from December to May and the peak hatching time in 2015 was one-half month later than in 2012 and 2016. Growth rates varied with environmental factors such as sea surface temperature (SST) and chlorophyll a concentration (chl. a), indicating that higher SST and chl. a concentrations led to faster growth. An extreme El Nino event with lower SST in 2015 also led to younger age class and slower growth rates. The occurrence of differences in body size and growth rates between years, caused by the interannual variations of environmental factors, makes it necessary to use separate growth curves for different years when analyzing North Pacific O. Bartramii populations.

CD8+ tissue-resident memory T cells play a well-established role in host defense againstmicrobial pathogens but have also been recently implicated in playing a role in the pathogenesisof inflammatory and autoimmune diseases. Previous work demonstrated that the T-boxtranscription factor Eomes is extinguished during the formation of skin TRM cells owing to TGF-ꞵ signaling. However, our lab previously observed high expression of Eomes in a pathogenicCD8+ TRM subset enriched in patients with ulcerative colitis, a form of inflammatory boweldisease. Thus, we sought to investigate the role of Eomes in the maintenance of TRM in smallintestine and colon tissue compartments. We adoptively transferred congenically distinct wildtypeand Eomesfl/fl ER-Cre+ CD8+ P14 cells into recipient mice and infected them with LCMV.We administered tamoxifen injections to inducibly delete Eomes at 30 days post-infection afterthe formation of TRM cells. Our results suggest that Eomes plays a previously unappreciatedfunction in intestinal TRM maintenance through a potential role in regulating tissue damage andTGF-ꞵ responsiveness.

Lentivirus is a type of retrovirus that can integrate viral genetic information into the DNA of the host cell. Lentivirus has gone through generations of engineering to become a safe robust gene delivery vehicle for gene and cell therapies, known as the lentiviral vectors (LVs). LVs demonstrate advantages over other gene delivery methods including effective infections of both dividing and non-dividing cells, long-term stable expression of the transgene, and relatively safe integration profile. Autologous hematopoietic stem cell transplant (HSCT) in combination with gene therapy has successfully treated multiple genetic blood diseases, such as sickle cell disease and severe combined immunodeficiency, in clinical trials. In this approach, the patient’s own HSCs are collected from either bone marrow or mobilized peripheral blood, genetically modified with LVs in a cell-culture plate, and transplanted back to the same patient, thereby avoiding many immune complications associated with allogeneic HSCT. The genetically modified HSCs with the therapeutic gene can self-renew and differentiate into different blood cells, therefore providing life-long therapeutic benefits for patients. The success of lentiviral gene therapy relies on several intrinsic properties of the LVs. The first property is the viral titer, the concentration of transduction units (TU) per milliliter (mL). We and others have observed that titer decreases with increasing vector length, making it difficult to produce LVs with high titers for diseases that require large transgenes. Next, infectivity or the gene transfer capacity is a measure of how well the vector can transfer its genome into HSCs at a given dose of TU/mL. Some LVs have limited gene transfer capacity that the copies of the integrated genome do not further increase with additional TU and cannot achieve the minimum copy number required for therapeutic benefits.Although the vector length is a well-known factor that affects titer and infectivity, how the vector genome limits the lentiviral lifecycle remains elusive. In Chapter 2, we compared a “well-behaved” clinical LV, EFS-ADA (4 kb), and a “poorly-performing” β-globin LV, Lenti/βAS3-FB (8.9 kb), at different steps of lentiviral lifecycle and identified several rate-limiting steps. We observed that the viral RNA (vRNA) of Lenti/βAS3-FB, but not vRNA of EFS-ADA, was heavily truncated. These truncated vRNAs failed to be reverse transcribed and subsequently cannot be integrated into the host cell genome. We also demonstrated that virion particle formation, measured by p24 ELISA, was impaired in Lenti/βAS3-FB and other reverse-oriented LVs, as they triggered certain cellular antiviral responses. Our findings uncovered two rate-limiting steps, vRNA truncation and defective virion formation, in the lentiviral lifecycle leading to low titer and infectivity.We then developed strategies to overcome these two roadblocks. In Chapter 3, we focused on overcoming cellular restriction factors (RF) in the packaging cells by conducting a targeted CRISPR Cas9 screen to knock out potential RFs. We created a new packaging cell line CRISPRed HEK293T to Disrupt Antiviral Responses (CHEDAR) by knocking out OAS1, LDLR, and PKR. In Chapter 4, we explored several methods to improve vRNA production, such as shortening the vector length, packaging with Tat, and overexpressing transcription elongation factors. The strategies described in Chapters 3 and 4 worked additively to increase titer and infectivity of different LVs, especially those with low titer or reverse-oriented transgene cassettes.In summary, the work described in this thesis elucidates the rate-limiting steps in lentiviral production and demonstrates multiple strategies to increase titer and infectivity of LVs. We hope this work help to advance the field of gene and cell therapy by improving the production technology and reducing the cost to make the therapy more effective and accessible for patients.

In binocular animals that exhibit stereoscopic visual responses, the axons of retinal ganglion cells (RGCs) connect to brain areas bilaterally by forming a commissure called the optic chiasm (OC). Ventral anterior homeobox 1 (Vax1) contributes to the formation of the OC, acting endogenously in optic pathway cells and exogenously in growing RGC axons. Here, we generated Vax1AA/AA mice expressing the Vax1AA mutant, which is incapable of intercellular transfer. We found that RGC axons cannot take up Vax1AA protein from the Vax1AA/AA mouse optic stalk (OS) and grow slowly to arrive at the hypothalamus at a late stage. The RGC axons of Vax1AA/AA mice connect exclusively to ipsilateral brain areas after failing to access the midline, resulting in reduced visual acuity and abnormal oculomotor responses. Overall, our study provides physiological evidence for the necessity of intercellular transfer of Vax1 and the importance of the bilateral RGC axon projection in proper visuomotor responses.

Congenital factor V (FV) deficiency is a rare hemorrhagic disorder that can cause excessive bleeding during and after surgery in the affected patient. This report is the case of a patient who had FV deficiency with recurrent posthemorrhoidectomy bleeding treated with the hemostatic procedure and fresh frozen plasma (FFP) transfusions. A 45-year-old male patient had previously undergone hemorrhoidectomy for multiple hemorrhoids at a local hospital. Hemorrhoidectomy was successful; however, he was transferred to our hospital for evaluation of the origin of the recurrent posthemorrhoidectomy bleeding and underwent a hemostatic procedure. This bleeding was treated with coagulation using electrocautery, multiple sutures, and FFP transfusion (1,600 mL/day) for 7 consecutive days. The patient’s plasma FV activity was 23%. Early detection of clotting factor deficiency in patients with hemorrhagic events after surgical treatments may prevent unnecessary procedures such as reoperations and minimize the cost of replacement therapy such as large-volume FFP transfusion.

Introduction Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. Objectives Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. Methods We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. Results We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of “QTL-hotspot” identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, ‘Legumepedia’. Conclusion This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.

Background Klebsiella pneumoniae is a gram-negative opportunistic pathogen that causes diseases mostly in immunocompromised individuals. Recently, hypervirulent K. pneumoniae strains also cause severe disease in healthy individuals. Capsular polysaccharide (CPS) is the major virulence determinant in hypervirulent K. pneumoniae and protects the cell against the bactericidal activity of the immune system. Gallic acid (GA), a natural phenolic compound, is known to exhibit wide spectrum antibacterial activity; however, its effect on hypervirulent K. pneumoniae remains largely unresolved. We aimed to identify the effects of GA on CPS biosynthesis in hypervirulent K. pneumoniae. Methods Antibacterial activity of GA was evaluated by counting colonies. CPS amount was determined by glucuronic acid content. The transcriptions of cps gene cluster were measured by quantitative real time PCR (qRT-PCR) and the β-galactosidase activity. The effect of GA on the resistance of K. pneumoniae to streptonigrin (SNG), an iron-activated antibiotic, was evaluated. The effect of GA on the resistance of K. pneumoniae to serum killing and phagocytosis by macrophages was observed. Results GA inhibited the growth and CPS biosynthesis in K. pneumoniae. GA may affect the iron availability in K. pneumoniae, thus possibly repressing the cps transcription. In addition, GA reduced the resistance of K. pneumoniae to serum killing and enhanced its susceptibility to phagocytosis. Conclusion GA possesses bactericidal activity and inhibits the CPS biosynthesis in hypervirulent K. pneumoniae, thereby facilitating pathogen clearance by the host immune system. Therefore, GA may represent a promising strategy for the prevention or treatment of patients with hypervirulent K. pneumoniae infections.

It is necessary to develop a new strategy for treatment of lung cancer since it is the main cause of cancer death. Tanshinone IIA (Tan IIA), an active ingredient of a commonly used traditional Chinese herb Salvia miltiorrhiza, provides a new direction to develop a new strategy for the treatment. It has been found that Tan IIA could inhibit lung cancer in vitro and in vivo by inducing autophagic apoptosis. Tan IIA increased apoptotic cells and the expression of cleaved caspase 3 and cleaved caspase 9, decreased B-cell lymphoma-2 (Bcl-2)/Bcl-2 associated X protein (Bax) ratio in human non-small cell lung cancer (NSCLC) cell lines, which was promoted by an autophagy activator Rapamycin, and weaken by autophagy inhibitor 3-methyladenine (3-MA). In addition, Tan IIA induced more autophagosomes, up-regulated light chain 3β (LC-3B) I and LC-3B II conversion and less sequestosome 1 (SQSTM1/p62) expression, which cannot be weakened by the caspase 3 antagonist. Moreover, overexpression of LC-3B gene (LC3B) and downregulation of autophagic gene 5 (ATG5) further confirmed that Tan IIA induced autophagic apoptosis in NSCLC cell lines. Beclin-1 gene (BECN1) overexpression and silence attenuated the effects of Tan IIA, suggesting autophagic apoptosis that Tan IIA induced was dependent on Beclin-1. Overall, our study demonstrated a new treatment mechanism of Tan IIA and suggested that Tan IIA is a potential new anti-cancer therapeutic option.

Soil microbial diversity is extremely vulnerable to fertilization, which is one of the main anthropogenic activities associated with global changes. Yet we know little about how and why soil microbial diversity responds to fertilization across contrasting local ecological contexts. This knowledge is fundamental for predicting changes in soil microbial diversity in response to ongoing global changes. We analyzed soils from ten 20-year field fertilization (organic and/or inorganic) experiments across China and found that the national-scale responses of soil bacterial diversity to fertilization are dependent on ecological context. In acidic soils from regions with high precipitation and soil fertility, inorganic fertilization can result in further acidification, resulting in negative impacts on soil bacterial diversity. In comparison, organic fertilization causes a smaller disturbance to soil bacterial diversity. Despite the overall role of environmental contexts in driving soil microbial diversity, a small group of bacterial taxa were found to respond to fertilization in a consistent way across contrasting regions throughout China. Taxa such as Nitrosospira and Nitrososphaera, which benefit from nitrogen fertilizer addition, as well as Chitinophagaceae, Bacilli, and phototrophic bacteria, which respond positively to organic fertilization, could be used as bioindicators for soil fertility in response to fertilization at the national scale. Overall, our work provides new insights into the importance of local environmental context in determining the responses of soil microbial diversity to fertilization, and identifies regions with acidic soils wherein soil microbial diversity is more vulnerable to fertilization at the national scale.

Introduction Metagenomic next-generation sequencing (mNGS) assay for detecting infectious agents is now in the stage of being translated into clinical practice. With no approved approaches or guidelines available, laboratories adopt customized mNGS assays to detect clinical samples. However, the accuracy, reliability, and problems of these routinely implemented assays are not clear. Objectives To evaluate the performance of 90 mNGS laboratories under routine testing conditions through analyzing identical samples. Methods Eleven microbial communities were generated using 15 quantitative microbial suspensions. They were used as reference materials to evaluate the false negatives and false positives of participating mNGS protocols, as well as the ability to distinguish genetically similar organisms and to identify true pathogens from other microbes based on fictitious case reports. Results High interlaboratory variability was found in the identification and the quantitative reads per million reads (RPM) values of each microbe in the samples, especially when testing microbes present at low concentrations (1 × 103 cell/ml or less). 42.2% (38/90) of the laboratories reported unexpected microbes (i.e. false positive problem). Only 56.7% (51/90) to 83.3% (75/90) of the laboratories showed a sufficient ability to obtain clear etiological diagnoses for three simulated cases combined with patient information. The analysis of the performance of mNGS in distinguishing genetically similar organisms in three samples revealed that only 56.6% to 63.0% of the laboratories recovered RPM ratios (RPMS. aureus/RPMS. epidermidis) within the range of a 2-fold change of the initial input ratios (indicating a relatively low level of bias). Conclusion The high interlaboratory variability found in both identifying microbes and distinguishing true pathogens emphasizes the urgent need for improving the accuracy and comparability of the results generated across different mNGS laboratories, especially in the detection of low-microbial-biomass samples.

Base editing using CRISPR technologies is an invaluable tool for crop breeding. One of the major base editors, the adenine base editor (ABE), has been successfully used in both model plants and many crops. However, owing to limited editing efficiency, the ABE has been difficult to apply in polyploid crops such as allohexaploid bread wheat that often require simultaneous mutation of multiple alleles for fast breeding. We have designed a wheat high-efficiency ABE (WhieABE), using the newly developed high-activity adenosine deaminase TadA8e. In vivo and in vitro analysis demonstrated the improved applicability of TadA8e over the commonly used TadA7.10. Dinitroaniline is a widely used herbicide with high effectiveness and low toxicity to animals. However, wheat cultivars with tolerance to dinitroaniline are rare, limiting the application of dinitroaniline in wheat planting. Using A-to-G editing with WhieABE, we found that a Met-to-Thr mutation in wheat tubulin alleles located on chromosomes 1A, 1B, 1D, 4A, and 4D increased the resistance of wheat to dinitroaniline, revealing a dosage effect of edited tubulins in resistance. The WhieABE promises to be a valuable editing tool for accelerating crop improvement and developing herbicide-resistant wheat germplasm.

Wenchengia alternifolia C.Y. Wu & S. Chow (Lamiaceae), the sole species of the genus Wenchengia C.Y. Wu & S. Chow, is extremely rare and is currently listed as Critically Endangered (CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island, China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010. Four more populations were later found on Hainan and in Vietnam. In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species, we identified infraspecific molecular markers in the present study, using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively. The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp, and exhibited a typical angiosperm quadripartite structure. Six plastid hotspot regions with the Pi > 0.01 (trnH-psbA, psbA-trnK, rpl22, ndhE, ndhG-ndhI and rps15-ycf1), 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes were identified, thereby providing important information for further genetic studies.

Cucumber is one of the most widely consumed vegetables worldwide, and the fruit spine is an important fruit quality trait. Expansins play critical roles in fruit development; however, the regulation of expansins in cucumber fruit spine development has not been reported. In this study, 33 expansin genes were identified in the cucumber genome V3; additionally, expansin genes in Citrullus lanatus, Cucumis melo, Cucurbita maxima, Lagenaria siceraria, and Benincasa hispida were also identified. Phylogenetic analysis of expansin proteins in Cucurbitaceae and Arabidopsis showed that they evolved separately in each plant species. Phylogenetic analysis showed that C. maxima was derived earlier than the other five Cucurbitaceae species. The expression of CsEXPA2, CsEXPA14, and CsEXLA3 varied in cucumber lines with different fruit spine densities. A yeast two-hybrid assay showed that a putative auxin transporter encoded by numerous spine gene (ns) interacts with CsEXLA2, which may be involved in the development of the numerous spines in cucumber. These results provide novel insights into the expansins related to plant development and fruit spine development in cucumber.

Background: Both microRNA (miR)-205 and GATA Binding Protein 3 (GATA3) were involved in cervical cancer (CC), yet their correlation remained poorly understood. The authors' study aimed to unveil their correlation in CC. Materials and Methods: Clinical cervical tissue samples were collected. Survival rates of CC patients with high or low miR-205 and GATA3 expressions were analyzed using Kaplan-Meier curve. CC cell viability, migration, and tube formation were measured by cell counting kit-8 assay, scratch assay, and tube formation assay, respectively. The potential binding sites between miR-205 and GATA3 were predicted by TargetScan, and confirmed with dual-luciferase reporter assay. Relative expressions of miR-205, GATA3, vascular endothelial growth factor, E-cadherin, N-cadherin, and vimentin were quantified with quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot as needed. Results: MiR-205 was increased, yet GATA3 was decreased in CC, indicating that they were negatively correlated. Upregulating miR-205 increased miR-205 expression and CC cell viability and promoted migration and tube formation, yet decreased GATA3 expression, while downregulating miR-205 exerted the opposite effects. GATA3 was the target gene of miR-205, and reversed the effect of miR-205 on GATA3 expression and cell viability, migration, and tube formation in CC cells by reversing the effects of miR-205 on migration- and tube formation-related protein expressions. Conclusion: MiR-205 promotes CC cell viability, migration, and tube formation in vitro by targeting GATA3, providing new evidence for the implication of miR-205 in CC and a possible therapeutic method for CC. Clinical Trial Registration number: ZLK-20181103-01.

The genus Woodwardia, which together with the genera Anchistea and Lorinseria comprise the subfamily Woodwardioideae of Blechnaceae, has a disjunct distribution across Central and North America, Europe and the temperate to tropical areas of Asia. Fossil records of Woodwardia occur throughout the Paleogene and Neogene of North America, Europe and Asia. However, well-preserved fertile pinna fossils of this genus have not yet been reported in South China. In this paper, a new species, W. changchangensis Naugolnykh et Song, sp. nov. is described from the middle Eocene of the Changchang Basin, Hainan Island, South China. Macromorphological and micromorphological features of the fertile pinna show a straight pinna rachis, alternate, subtriangular pinnules, acute pinnule apices, almost entire or slightly undulate pinnule margins, long-ovoid sori, stalked sporangia and spores with wing-like folds on the surface, which are characterised in detail. Overall, the present fossil is most similar to the extant species Woodwardia japonica, which mostly grows in warm and moist environments. The discovery of this new species from the Changchang Basin of Hainan Island indicates that this genus has been distributed in the low-latitude tropical regions of South China from as early as the middle Eocene. Based on this find, and previous studies of other ferns from the same site, we infer that the climate of the Palaeo-Hainan landscape during deposition of the Changchang Formation was warm and humid, similar to conditions prevailing today across this region.

Background: Desmoid tumor, also known as aggressive fibromatosis, is well-characterized by abnormal Wnt/β-catenin signaling. Various therapeutic options, including imatinib, are available to efficiently treat desmoid tumor. However, molecular mechanism of why imatinib works remains poorly understood. Here, we describe the potential roles of NOTCH2 and HES1 in association with clinical response to imatinib as in genome and transcriptome levels. Methods: We identified all somatic mutations in coding and non-coding regions via whole genome sequencing using desmoid tumor samples. To validate the genetic interaction with expression level in desmoid-tumor condition, we utilized large-scale Whole-genome sequencing (WGS) and transcriptome datasets from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. RNA-sequencing was performed using prospective and retrospective cohort samples to evaluate the expressional relevance with clinical response. Results: Among 20 patients, 4 (20%) had a partial response and 14 (66.7%) had stable disease, 11 of which continued for ≥1 year. With gene-wise functional analyses, we detected significant correlation between recurrent NOTCH2 noncoding mutations and clinical response to imatinib. Based on PCAWG data analyses, NOTCH2 mutations affect its expression levels particularly in the presence of CTNNB1 missense mutations. By analyzing RNA-sequencing with additional desmoid tumor samples, we found that NOTCH2 expression was significantly correlated with HES1 expression. Interestingly, NOTCH2 had no statistical power to discriminate responders and non-responders. Instead, HES1 was differentially expressed with statistical significance between responders and non-responders Conclusions: Imatinib was effective and well tolerated for advanced desmoid tumor treatment. Our results show that HES1, regulated by NOTCH2, as an indicator of sensitivity to imatinib, which provides an important therapeutic consideration for desmoid tumor. Trial Registration: ClinicalTrials.gov, NCT02495519, Registered July 13, 2015- Retrospectively registered, https://www.clinicaltrials.gov/ct2/show/NCT02495519

From urban green space to pristine forest, Collembola is one of the most numerous and species-rich members of the soil fauna around the world. However, due to lack of taxonomic expertise and research, its diversity is poorly understood, especially in tropical and subtropical regions. Collembola biodiversity studies in Taiwan have not seen much progress since 1981, when Hsin Chi reviewed 26 species belonging to 20 genera and eight families. Additionally, reports of new records in Taiwan in the last 40 years are scattered amongst several publications and not easily accessible to most end-users. Thus, a concise summary of related research is urgently needed. In this study, we updated the checklist of Collembola in Taiwan, based on published papers as well as images recorded in 2020–2022. We concluded that 58 species of Collembola belonging to 31 genera and 12 families have been reported in Taiwan, including 13 newly-recorded species. This species richness marks a 123% increase from the 1981 review. The results have been made publicly available in the Catalog of Life in Taiwan database and the images recorded have been used to update species information in collembola.org. We also characterised morphological and genetic variations in the globular springtail species Papirioides jacobsoni Folsom, 1924 using DNA barcodes and highlighted potential research directions.

Background: Breast cancer is a major challenge affecting women's survival. Circular RNAs have been demonstrated to be vital regulators in the pathogenesis of human cancers. The authors' objective was to determine the functional role and mechanism of circKLHL24 in breast cancer development. Materials and Methods: The expression of circKLHL24, miR-1204, and aristaless-like 4 (ALX4) mRNA was measured using quantitative real-time polymerase chain reaction. The effects on cell viability, proliferation, migration/invasion, and glycolysis were identified using the Cell Counting Kit-8 (CCK-8) assay, colony formation assay, Transwell assay, and glycolysis stress test, respectively. For glycolysis progression analysis, glucose consumption and lactate production were assessed using corresponding kits, and the expression of glycolysis-related proteins was detected by western blot. The putative interactions between miR-1204 and circKLHL24 or ALX4 were validated by dual-luciferase reporter assay or RNA pull-down assay. The expression of ALX4 at the protein level was detected by western blot. Animal study was performed to clarify the role of circKLHL24 in vivo. Results: circKLHL24 and ALX4 were downregulated, while miR-1204 was upregulated in breast cancer tissues and cells. circKLHL24 overexpression blocked cell viability, colony formation, migration/invasion, and glycolysis progression. circKLHL24 competitively targeted miR-1204, and miR-1204 reintroduction reversed the effects of circKLHL24 restoration. miR-1204 bound to ALX4, and circKLHL24 sponged miR-1204 to upregulate ALX4. Cell viability, colony formation, migration/invasion, and glycolysis progression suppressed by miR-1204 deficiency were recovered by ALX4 knockdown. Besides, circKLHL24 blocked tumor growth in vivo by regulating miR-1204 and ALX4. Conclusions: circKLHL24 blocked the progression of breast cancer by activating ALX4 through targeting miR-1204, which might be a novel perspective to understand the pathogenesis of breast cancer.

Background: Helicobacter pylori is a major risk factor for gastric cancer. Screening and treatment of H. pylori may reduce the risk of gastric cancer and peptic ulcer disease. Polymerase chain reaction (PCR) of gastric biopsies provides superior sensitivity and specificity for the detection of H. pylori. This study explores whether population-based H. pylori screening with PCR is cost-effective in the US.Methods: A Markov cohort state-transition model was developed to compare three strategies: no screening with opportunistic eradication, 13C-UBT population screening and treating of H. pylori, and PCR population screening and treating of H. pylori. Estimates of risks and costs were obtained from published literature. Since the efficacy of H. pylori therapy in gastric cancer prevention is not certain, we broadly varied the benefit 30-100% in sensitivity analysis.Results: PCR screening was cost-effective and had an incremental-cost effectiveness ratio per quality adjusted life-year (QALY) of $38,591.89 when compared to 13C-UBT strategy with an ICER of $2373.43 per QALY. When compared to no screening, PCR population screening reduced cumulative gastric cancer incidence from 0.84% to 0.74% and reduced peptic ulcer disease risk from 14.8% to 6.0%. The cost-effectiveness of PCR screening was robust to most parameters in the model.Conclusion: Our modeling study finds PCR screening and treating of H. pylori to be cost-effective in the prevention of gastric cancer and peptic ulcer disease. However, the potential negative consequences of H. pylori eradication such as antibiotic resistance could change the balance of benefits of population screening.

Although liverworts are widely distributed around the world with a large number of extant species, reliable fossil records are relatively rare. Here, we report a new species, Ricciopsis baojishanensis Han and Yan, n. sp. (Ricciaceae) and an unnamed species, Hepaticites sp. from the Late Triassic Nanying’er Formation in Baojishan Basin, Baiyin City, Gansu Province, Northwest China. The generic designation is based on detailed comparison of the gross morphology with related fossil and extant species. The new species is characterized by its rosette-forming thallus, dichotomous branching, ribbon-like segments and entire margins. The current fossils represent the first record of liverwort from the Late Triassic in Baojishan Basin, Gansu Province. Based on the different fossil records of the Ricciaceae, we suggest that these taxa were widely distributed during Late Triassic to Oligocene worldwide, mainly in warm temperate and tropical environments, similar with their current distribution. The discovery of the present fossils indicates that the climate of Baojishan Basin in Late Triassic is warmer and more humid than that of today.

Colorectal cancer (CRC) is the third leading cancer globally. Metagenomics has been widely used to analyze the association between the gut microbiota and CRC based on bacterial genus- or species-level comparisons, providing evidence of dysbiosis in CRC development. However, this kind of analysis is unable to provide strain-level information for understanding the individual role of a species in CRC. Here, we used culturomics to isolate CRC mucosal samples and selected 158 Escherichia coli strains to reveal their differences in both genomics and functions by means of phylogenetic analysis and inflammatory induction based on cell and animal experiments. Through genomic comparison, these strains were divided into five phylogroups. The representative strains of each phylogroup significantly induced different levels of cytokine secretion by human leukemic monocyte (THP-1 cell)-based Transwell and animal experiments. Further bioinformatic analysis revealed different profiles of single-nucleotide polymorphisms, genes, and metabolic pathways in the different phylogroups, which can improve the current understanding of the phenotypic differences between these strains. The strain differences revealed in both genomics and functions indicate that the microbiota’s function at the strain level should be investigated in order to understand the interacting mechanisms between hosts and gut bacteria.

Diseases caused by harmful microorganisms pose a serious threat to human health. Safe and environment-friendly disinfectants are, therefore, essential in preventing and controlling such pathogens. This study aimed to investigate the antimicrobial activity and mechanism of a novel hydrogen peroxide and silver (H 2 O 2 -Ag + ) complex (HSC) in combatting Staphylococcus aureus ATCC 29213, Escherichia coli O157:H7 NCTC 12900 and Salmonella typhimurium SL 1344. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values against S. aureus were found to be 0.014 % H 2 O 2 -3.125 mg/L Ag + , while 0.028 % H 2 O 2 -6.25 mg/L Ag + for both E. coli and S. typhimurium . Results of the growth curve assay and time-kill trial suggest that the HSC could inhibit the growth of the tested bacteria, as 99.9 % of viable cells were killed following treatment at the 1 MIC for 3 h. Compared with Oxytech D10 disinfectant (0.25 % H 2 O 2 -5 mg/L Ag + ), the HSC exhibited better antibacterial efficacy at a lower concentration (0.045 % H 2 O 2 -10 mg/L Ag + ). The mechanism of antibacterial action of HSC was found including the disruption of the bacterial cell membrane, followed by entry into the bacteria cell to reduce intracellular adenosine triphosphate (ATP) concentration, and inhibit the activity of antioxidases, superoxide dismutase (SOD) and catalase (CAT). The enhanced bactericidal effect of hydrogen peroxide combined with silver indicates a potential for its application in environmental disinfection, particularly in the food industry.