bluuebunny/crossref_metadata_2025 huggingface dataset:
When does hepatitis B virus meet long-stranded noncoding RNAs?
Authors: Lei Bingxin , Song Hongxiao , Xu Fengchao , Wei Qi , Wang Fei , Tan Guangyun , Ma Haichun
Published: September 2022

Hepatitis B virus (HBV) infection in humans and its associated diseases are long-standing problems. HBV can produce a large number of non-self-molecules during its life cycle, which acts as targets for innate immune recognition and initiation. Among these, interferon and its large number of downstream interferon-stimulated gene molecules are important early antiviral factors. However, the development of an effective antiviral immune response is not simple and depends not only on the delicate regulation of the immune response but also on the various mechanisms of virus-related immune escape and immune tolerance. Therefore, despite there being a relatively well-established consensus on the major pathways of the antiviral response and their component molecules, the complete clearance of HBV remains a challenge in both basic and clinical research. Long-noncoding RNAs (lncRNAs) are generally >200 bp in length and perform different functions in the RNA strand encoding the protein. As an important part of the IFN-inducible genes, interferon-stimulated lncRNAs are involved in the regulation of several HBV infection-related pathways. This review traces the basic elements of such pathways and characterizes the various recent targets of lncRNAs, which not only complement the regulatory mechanisms of pathways related to chronic HBV infection, fibrosis, and cancer promotion but also present with new potential therapeutic targets for controlling HBV infection and the malignant transformation of hepatocytes.
Sigma factor RpoS positively affects the spoilage activity of Shewanella baltica and negatively regulates its adhesion effect
Authors: Zhang Caili , Chen Jiaqi , Pan Xiaoming , Liu Haimei , Liu Yanlong
Published: September 2022

Shewanella baltica is the dominant bacterium that causes spoilage of seafood. RpoS is an alternative sigma factor regulating stress adaptation in many bacteria. However, the detailed regulatory mechanism of RpoS in S. baltica remains unclear. This study aims to investigate the regulatory function of RpoS on spoilage activity and adhesion ability in S. baltica. Results revealed that RpoS had no effect on the growth of S. baltica, but positively regulated the spoilage potential of S. baltica accompanied by a slower decline of total volatile basic nitrogen, lightness, and the sensory score of fish fillets inoculated with rpoS mutant. RpoS negatively regulated the adhesion ability, which was manifested in that the bacterial number of rpoS mutant adhered to stainless steel coupon was higher than that of the S. baltica in the early stage, and the biofilm formed on glass slide by rpoS mutant was thicker and tighter compared with S. baltica. Transcriptomic analysis showed that a total of 397 differentially expressed genes were regulated by RpoS. These genes were mainly enrichment in flagellar assembly, fatty acid metabolism/degradation, and RNA degradation pathways, which were associated with motility, biofilm formation and cold adaptation. This study demonstrated that RpoS is a primary regulator involved in flagellar assembly mediated biofilm formation and cold adaptation-related spoilage activity of S. baltica. Our research will provide significant insights into the control of microbiological spoilage in seafood.
RNA-sequencing analysis of the Diquat-degrading yeast strain Meyerozyma guilliermondii Wyslmt and the discovery of Diquat degrading genes
Authors: Wang Fangyuan , Kong Lingwei , Guo Jing , Song Xiuli , Tao Bo , Han Yujun
Published: September 2022

Diquat is used in agricultural contexts to control the growth of broadleaf and grassy weeds in both terrestrial and aquatic areas. Diquat can be readily absorbed by the soil and can remain therein for extended periods of time, altering the local microenvironment. In this study, the Meyerozyma guilliermondii Wyslmt yeast strain, which has the capacity to degrade Diquat, was isolated from soil exposed to long-term Diquat treatment. Over a 7-day incubation period, this strain was able to remove 42.51% of available Diquat (100 mg/L). RNA-Seq was performed to assess changes in gene expression in this yeast strain over the course of Diquat degradation, revealing 63 and 151 upregulated and downregulated genes, respectively. KEGG pathway enrichment analysis revealed these genes to be most highly enriched in the carbohydrate metabolism pathway. Through functional annotation and gene expression analyses, we identified seven genes were predicted to be involved in Diquat biodegradation. Results of qRT-PCR assays indicated that the relative mRNA expression levels of these seven genes were significantly higher relative to the control group. Together these analyses led to the identification of DN676 as a candidate Diquat-degrading gene. When a pET-DN676 vector was expressed in E. coli BL21, this strain was able to remove 12.49% of provided Diquat (100 mg/L) over the course of a 7-day incubation. These results thus confirmed that the DN676 gene can promote Diquat degradation, with these studies having yielded an engineered BL21-pET-DN676 bacterial strain capable of degrading Diquat.
CASP6 predicts poor prognosis in glioma and correlates with tumor immune microenvironment
Authors: Guo Kai , Zhao Jiahui , Jin Qianxu , Yan Hongshan , Shi Yunpeng , Zhao Zongmao
Published: September 2022

Background

Glioma is an aggressive tumor of the central nervous system. Caspase-6 (CASP6) plays a crucial role in cell pyroptosis and is a central protein involved in many cellular signaling pathways. However, the association between CASP6 and prognosis of glioma patients remains unclear.

Methods

Four bioinformatic databases were analyzed to identify differentially expressed genes (DEGs) between glioma and healthy tissues. Eighty-one protein-coding pyroptosis-related genes (PRGs) were obtained from the GeneCards database. The pyroptosis-related DEGs (PRDEGs) were extracted from each dataset, and CASP6 was found to be aberrantly expressed in glioma. We then investigated the biological functions of CASP6 and the relationship between CASP6 expression and the tumor microenvironment and immunocyte infiltration. The half maximal inhibitory concentration of temozolomide and the response to immune checkpoint blockade in the high- and low-CASP6 expression groups were estimated using relevant bioinformatic algorithms. Quantitative real-time reverse transcription PCR and western blotting were carried out to confirm the different expression levels of CASP6 between human astrocytes and glioma cell lines (U251 and T98G). We determined the role of CASP6 in the tumorigenesis of glioma by knocking down CASP6 in U251 and T98G cell lines.

Results

We found that CASP6 was overexpressed in glioma samples and in glioma cell lines. CASP6 expression in patients with glioma correlated negatively with overall survival. In addition, CASP6 expression correlated positively with the degree of glioma progression. Functional analysis indicated that CASP6 was primarily involved in the immune response and antigen processing and presentation. Patients with high CASP6 levels responded more favorably to temozolomide, while patients with low expression of CASP6 had a better response to immunotherapy. Finally, in vitro experiments showed that CASP6 knockdown inhibited glioma proliferation.

Conclusions

The pyroptosis-related gene CASP6 might represent a sensitive prognostic marker for patients with glioma and might predict their response of immunotherapy and temozolomide therapy. Our results might lead to more precise immunotherapeutic strategies for patients with glioma.
Prognostic value of dysadherin in cancer: A systematic review and meta-analysis
Authors: Niinivirta Aino , Salo Tuula , Åström Pirjo , Juurikka Krista , Risteli Maija
Published: September 2022

Cancer is a leading cause of death worldwide and novel prognostic factors are reported with increasing numbers. Systematic reviews and meta-analyses on cumulative research data are crucial in estimating the true prognostic value of proposed factors. Dysadherin (FXYD Domain Containing Ion Transport Regulator 5; FXYD5) is a cell membrane glycoprotein that modulates Na+, K+-ATPase activity and cell-cell adhesion. It is abundantly expressed in a variety of cancer cells, but only in a limited number of normal cells and its levels are increased in many different tumor types. The expression or level of dysadherin has been suggested as an independent predictor for metastasis and poor prognosis by number of studies, yet we lack a definitive answer. In this study, we systematically evaluated the prognostic value of dysadherin in cancer and summarized the current knowledge on the subject. PubMed, Scopus, Web of Science and relevant clinical trial and preprint databases were searched for relevant publications and PRISMA and REMARK guidelines were applied in the process. After a careful review, a total of 23 original research articles were included. In each study, dysadherin was pointed as a marker for poor prognosis. Meta-analyses revealed 3- and 1.5-fold increases in the risk of death (fixed effects HR 3.08, 95% CI 1.88-5.06, RR 1.47, 95% CI 1.06-2.05 on overall survival, respectively) for patients with high (>50%) tumoral FXYD5 level. In many studies, a connection between dysadherin expression or level and metastatic behavior of the cancer as well as inverse correlation with E-cadherin level were reported. Thus, we conclude that dysadherin might be a useful prognostic biomarker in the assessment of disease survival of patients with solid tumors.
Comparison between three age-stratified cohorts reveals poor prognosis of young patients with tongue carcinoma
Authors: Baba Daisuke , Matsuura Kazuto , Wakabayashi Masashi , Morishita Yohei , Nishiya Yukio , Okano Wataru , Tomioka Toshifumi , Shinozaki Takeshi , Hayashi Ryuichi
Published: September 2022

Objectives

Investigation of the prognosis of young patients with tongue carcinoma has been the focus of several recent studies aimed at improving future precision treatment. Most studies have been two-cohort investigations comparing young and older patients, who have wide discrepancies in prognosis. Older patients, especially those aged >70 years, often have a poor general condition. This affects the prognosis of the older cohort and accounts for the discrepancies observed in two-cohort studies. Accordingly, in this study, older patients (aged ≥71 years) were separated and compared to young and middle-aged patients.

Methods

A total of 257 patients with oral tongue carcinoma referred during 2011–2017 were analyzed. Patients were sorted into young (aged ≤40 years), middle-aged (aged ≥41 and ≤70 years), and older (aged ≥71 years) groups. Overall survival (OS) and disease-free survival (DFS) were compared among the groups. Furthermore, patterns of recurrence rates were compared.

Results

Compared with young patients, there was no difference in OS or DFS for older patients (hazard ratio [HR]: 1.2, 95% confidence interval [CI]: 0.5–2.7 and HR: 0.7, 95% CI: 0.4–1.2, respectively) in a multivariate analysis. There was also no difference in OS (HR: 0.6, 95% CI: 0.3–1.3) for middle-aged patients. However, middle-aged patients had low recurrence rates (HR: 0.5, 95% CI: 0.3–0.8). With respect to the recurrence type, middle-aged patients had a low local recurrence rate (HR: 0.3, 95% CI: 0.1–0.7).

Conclusion

Three-cohort studies should be conducted to evaluate whether the prognosis of young patients with tongue carcinoma is truly poor in terms of future precision treatment.
Lymph node ratio is a superior predictor in surgically treated early-onset pancreatic cancer
Authors: Zheng Yangyang , Lu Zhenhua , Shi Xiaolei , Tan Tianhua , Xing Cheng , Xu Jingyong , Cui Hongyuan , Song Jinghai
Published: September 2022

Background

The prognostic performance of four lymph node classifications, the 8th American Joint Committee on Cancer (AJCC) Tumor Node Metastasis (TNM) N stage, lymph node ratio (LNR), log odds of positive lymph nodes (LODDS), and examined lymph nodes (ELN) in early-onset pancreatic cancer (EOPC) remains unclear.

Methods

The Surveillance, Epidemiology, and End Results (SEER) database was searched for patients with EOPC from 2004 to 2016. 1048 patients were randomly divided into training (n = 733) and validation sets (n = 315). The predictive abilities of the four lymph node staging systems were compared using the Akaike information criteria (AIC), receiver operating characteristic area under the curve (AUC), and C-index. Multivariate Cox analysis was performed to identify independent risk factors. A nomogram based on lymph node classification with the strongest predictive ability was established. The nomogram’s precision was verified by the C-index, calibration curves, and AUC. Kaplan–Meier analysis and log-rank tests were used to compare differences in survival at each stage of the nomogram.

Results

Compared with the 8th N stage, LODDS, and ELN, LNR had the highest C-index and AUC and the lowest AIC. Multivariate analysis showed that N stage, LODDS, LNR were independent risk factors associated with cancer specific survival (CSS), but not ELN. In the training set, the AUC values for the 1-, 3-, and 5-year CSS of the nomogram were 0.663, 0.728, and 0.760, respectively and similar results were observed in the validation set. In addition, Kaplan–Meier survival analysis showed that the nomogram was also an important factor in the risk stratification of EOPC.

Conclusion

We analyzed the predictive power of the four lymph node staging systems and found that LNR had the strongest predictive ability. Furthermore, the novel nomogram prognostic staging mode based on LNR was also an important factor in the risk stratification of EOPC.
Incidence of venous thromboembolism after surgery for adenocarcinoma in situ and the validity of the modified Caprini score: A propensity score-matched study
Authors: Cai Yong-sheng , Dong Hong-hong , Li Xin-yang , Ye Xin , Chen Shuo , Hu Bin , Li Hui , Miao Jin-bai , Chen Qi-rui
Published: September 2022

Background

Recently, the new World Health Organization (WHO) tumor classification removed adenocarcinoma in situ (AIS) from the diagnosis of lung cancer. However, it remains unclear whether the “malignancy” item should be assessed when the modified Caprini Risk Assessment Model (RAM) is used to assess venous thromboembolism (VTE) risk in AIS. The purpose of our study is to assess differences between AIS and stage IA adenocarcinoma (AD) from a VTE perspective.

Methods

A retrospective study was performed on AIS and IA adenocarcinoma in our hospital from January 2018 to December 2021, and divided into AIS group and AD group. Propensity score matching (PSM) was used to compare the incidence of VTE and coagulation function, and to analyze whether the RAM is more effective when the “malignancy” item is not evaluated in AIS.

Results

491 patients were included after screening, including 104 patients in the AIS group and 387 patients in the AD group. After PSM, 83 patients were matched. The incidence of VTE and D-dimer in the AIS group was significantly lower than that in the AD group (P<0.05).When using the RAM to score AIS, compared with retaining the “malignancy” item, the incidence of VTE in the intermediate-high-risk group was significantly higher after removing the item (7.9% vs. 36.4%, P=0.018), which significantly improved the stratification effect of the model.

Conclusions

The incidence of postoperative VTE in AIS was significantly lower than that in stage IA adenocarcinoma. The stratification effect was more favorable when the “malignancy” item was not evaluated in AIS using the RAM.
The mechanism of branched-chain amino acid transferases in different diseases: Research progress and future prospects
Authors: Nong Xiazhen , Zhang Caiyun , Wang Junmin , Ding Peilun , Ji Guang , Wu Tao
Published: September 2022

It is well known that the enzyme catalyzes the first step of branched-chain amino acid (BCAA) catabolism is branched-chain amino transferase (BCAT), which is involved in the synthesis and degradation of leucine, isoleucine and valine. There are two main subtypes of human branched chain amino transferase (hBCAT), including cytoplasmic BCAT (BCAT1) and mitochondrial BCAT (BCAT2). In recent years, the role of BCAT in tumors has attracted the attention of scientists, and there have been continuous research reports that BCAT plays a role in the tumor, Alzheimer’s disease, myeloid leukaemia and other diseases. It plays a significant role in the growth and development of diseases, and new discoveries about this gene in some diseases are made every year. BCAT usually promotes cancer proliferation and invasion by activating the phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin pathway and activating Wnt/β-catenin signal transduction. This article reviews the role and mechanism of BCAT in different diseases, as well as the recent biomedical research progress. This review aims to make a comprehensive summary of the role and mechanism of BCAT in different diseases and to provide new research ideas for the treatment, prognosis and prevention of certain diseases.
Ultrasomics prediction for cytokeratin 19 expression in hepatocellular carcinoma: A multicenter study
Authors: Zhang Linlin , Qi Qinghua , Li Qian , Ren Shanshan , Liu Shunhua , Mao Bing , Li Xin , Wu Yuejin , Yang Lanling , Liu Luwen , Li Yaqiong , Duan Shaobo , Zhang Lianzhong
Published: September 2022

Objective

The purpose of this study was to investigate the preoperative prediction of Cytokeratin (CK) 19 expression in patients with hepatocellular carcinoma (HCC) by machine learning-based ultrasomics.

Methods

We retrospectively analyzed 214 patients with pathologically confirmed HCC who received CK19 immunohistochemical staining. Through random stratified sampling (ratio, 8:2), patients from institutions I and II were divided into training dataset (n = 143) and test dataset (n = 36), and patients from institution III served as external validation dataset (n = 35). All gray-scale ultrasound images were preprocessed, and then the regions of interest were then manually segmented by two sonographers. A total of 1409 ultrasomics features were extracted from the original and derived images. Next, the intraclass correlation coefficient, variance threshold, mutual information, and embedded method were applied to feature dimension reduction. Finally, the clinical model, ultrasonics model, and combined model were constructed by eXtreme Gradient Boosting algorithm. Model performance was assessed by area under the receiver operating characteristic curve (AUC), sensitivity, specificity, and accuracy.

Results

A total of 12 ultrasomics signatures were used to construct the ultrasomics models. In addition, 21 clinical features were used to construct the clinical model, including gender, age, Child-Pugh classification, hepatitis B surface antigen/hepatitis C virus antibody (positive/negative), cirrhosis (yes/no), splenomegaly (yes/no), tumor location, tumor maximum diameter, tumor number, alpha-fetoprotein, alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, glutamyl-transpeptidase, albumin, total bilirubin, conjugated bilirubin, creatinine, prothrombin time, fibrinogen, and international normalized ratio. The AUC of the ultrasomics model was 0.789 (0.621 – 0.907) and 0.787 (0.616 – 0.907) in the test and validation datasets, respectively. However, the performance of the combined model covering clinical features and ultrasomics signatures improved significantly. Additionally, the AUC (95% CI), sensitivity, specificity, and accuracy were 0.867 (0.712 – 0.957), 0.750, 0.875, 0.861, and 0.862 (0.703 – 0.955), 0.833, 0.862, and 0.857 in the test dataset and external validation dataset, respectively.

Conclusion

Ultrasomics signatures could be used to predict the expression of CK19 in HCC patients. The combination of clinical features and ultrasomics signatures showed excellent effects, which significantly improved prediction accuracy and robustness.
The Wnt signaling cascade in the pathogenesis of osteoarthritis and related promising treatment strategies
Authors: Cheng Jinchao , Li Min , Bai Ruijun
Published: September 2022

Osteoarthritis (OA) is the most prevalent joint disease, characterized by the degradation of articular cartilage, synovial inflammation, and changes in periarticular and subchondral bone. Recent studies have reported that Wnt signaling cascades play an important role in the development, growth, and homeostasis of joints. The Wnt signaling cascade should be tightly regulated to maintain the homeostasis of cartilage in either the over-activation or the suppression of Wnt/β-catenin, as this could lead to OA. This review summarizes the role and mechanism of canonical Wnt cascade and noncanonical Wnt cascade experimentsin vivoandin vitro. The Wnt cascade is controlled by several agonists and antagonists in the extracellular medium and the cytoplasm. These antagonists and agonists serve as key molecules in drug intervention into the Wnt pathway and may provide potential approaches for the treatment of OA. However, the complexity of the Wnt signaling cascade and the pharmaceutical effects on its mechanism are still not fully understood, which forces us to conduct further research and develop efficient therapeutic approaches to treat OA.
Evaluation of in ovo feeding of low or high mixtures of cysteine and lysine on performance, intestinal morphology and physiological responses of thermal-challenged broiler embryos
Authors: Ajayi O. I. , Smith O. F. , Oso A. O. , Oke O. E.
Published: September 2022

The objective of this study was to evaluate the effect of in ovo feeding cysteine, lysine or their combinations on the perinatal and post-hatch physiological responses of broiler embryos exposed to heat stress during incubation. A total of two thousand fertile eggs of broiler breeders (Ross 308) flock (at 38 weeks of age) were used for this study. In the first 10 days, the eggs were incubated using the conventional protocol of relative humidity and temperature of 55% and 37.8°C respectively. From day ten onward, the temperature was increased to 39.6°C for 6 h per day. On day 17.5, 1,500 eggs with the evidence of living embryos were randomly selected and assigned to 6 treatments having five replicates of 50 eggs each. The treatments were: un-injected eggs (UI), eggs injected with only 0.5 ml distilled water (DW), 3.5 mg/egg cysteine (CY), 2mg/egg lysine (LY), 3.4 mg cysteine+2 mg lysine (CLH) and 1.7 mg cysteine+1 mg lysine (CLL). On day 21, the hatchability, anatomical characteristics, chick quality and the antioxidant status of the chicks were evaluated. During the post-hatch phase, data were collected on the haematology, biochemical parameters, growth performance and intestinal morphology of the birds. The results revealed that the hatchability of CY chicks was higher (p< 0.05) than in the other treatments, while the lowest values were recorded in CLH. The hatching muscle of the chicks of CLL was similar to those of CY but higher (p< 0.05) than the others. The MDA of DW and UI chickens was similar and higher than birds in the other treatment groups. The serum SOD of CLL birds was comparable to that of CY but higher than the values recorded in the other treatments. The final weights of CLL chickens were similar to those of LY but significantly higher (p< 0.05) than those of the other treatments. The duodenal villus heights of the birds of CLL were higher than those of the other treatment groups, whereas the villus height of the birds of CLH was higher than those of UI, DW and CY. Overall,in ovofeeding of cysteine alone improved the hatchability of thermally-challenged broiler embryos. In contrast, a low-dose mixture of cysteine plus lysine improved the post-hatch growth performance.
Disentangling the effects of jasmonate and tissue loss on the sex allocation of an annual plant
Authors: Villamil Nora , Sommervogel Benoit , Pannell John R.
Published: September 2022

Selection through pollinators plays a major role in the evolution of reproductive traits. However, herbivory can also induce changes in plant sexual expression and sexual systems, potentially influencing conditions governing transitions between sexual systems. Previous work has shown that herbivory has a strong effect on sex allocation in the wind-pollinated annual plant Mercurialis annua, likely via responses to resource loss. It is also known that many plants respond to herbivory by inducing signaling, and endogenous responses to it, via the plant hormone jasmonate. Here, we attempt to uncouple the effects of herbivory on sex allocation in M. annua through resource limitation (tissue loss) versus plant responses to jasmonate hormone signaling. We used a two-factorial experiment with four treatment combinations: control, herbivory (25% chronic tissue loss), jasmonate, and combined herbivory and jasmonate. We estimated the effects of tissue loss and defense-inducing hormones on reproductive allocation, male reproductive effort, and sex allocation. Tissue loss caused plants to reduce their male reproductive effort, resulting in changes in total sex allocation. However, application of jasmonate after herbivory reversed its effect on male investment. Our results show that herbivory has consequences on plant sex expression and sex allocation, and that defense-related hormones such as jasmonate can buffer the impacts. We discuss the physiological mechanisms that might underpin the effects of herbivory on sex allocation, and their potential implications for the evolution of plant sexual systems.
Alternative splicing of Arabidopsis G6PD5 recruits NADPH-producing OPPP reactions to the endoplasmic reticulum
Authors: Linnenbrügger Loreen , Doering Lennart , Lansing Hannes , Fischer Kerstin , Eirich Jürgen , Finkemeier Iris , von Schaewen Antje
Published: September 2022

Glucose-6-phosphate dehydrogenase is the rate-limiting enzyme of the oxidative pentose-phosphate pathway (OPPP). The OPPP mainly provides NADPH and sugar-phosphate building blocks for anabolic pathways and is present in all eukaryotes. In plant cells, the irreversible part of the OPPP is found in several compartments. Among the isoforms catalyzing the first OPPP step in Arabidopsis, G6PD1 to G6PD4 target plastids (with G6PD1 being also directed to peroxisomes), whereas G6PD5 and G6PD6 operate in the cytosol. We noticed that alternative splice forms G6PD5.4 and G6PD5.5 encode N-terminally extended proteoforms. Compared to G6PD5.1, RT-PCR signals differed and fluorescent reporter fusions expressed in Arabidopsis protoplasts accumulated in distinct intracellular sites. Co-expression with organelle-specific markers revealed that the G6PD5.4 and G6PD5.5 proteoforms label different subdomains of the endoplasmic reticulum (ER), and analysis of C-terminal roGFP fusions showed that their catalytic domains face the cytosol. In g6pd5-1 g6pd6-2 mutant protoplasts lacking cytosolic G6PDH activity, the ER-bound proteoforms were both active and thus able to form homomers. Among the Arabidopsis 6-phosphogluconolactonases (catalyzing the second OPPP step), we noticed that isoform PGL2 carries a C-terminal CaaX motif that may be prenylated for membrane attachment. Reporter-PGL2 fusions co-localized with G6PD5.4 in ER subdomains, which was abolished by Cys-to-Ser exchange in the 256CSIL motif. Among the Arabidopsis 6-phosphogluconate dehydrogenases (catalyzing the third OPPP step), S-acylated peptides were detected for all three isoforms in a recent palmitoylome, with dual cytosolic/peroxisomal PGD2 displaying three sites. Co-expression of GFP-PGD2 diminished crowding of OFP-G6PD5.4 at the ER, independent of PGL2's presence. Upon pull-down of GFP-G6PD5.4, not only unlabeled PGD2 and PGL2 were enriched, but also enzymes that depend on NADPH provision at the ER, indicative of physical interaction with the OPPP enzymes. When membrane-bound G6PD5.5 and 5.4 variants were co-expressed with KCR1 (ketoacyl-CoA reductase, involved in fatty acid elongation), ATR1 (NADPH:cytochrome-P450 oxidoreductase), or pulled C4H/CYP73A5 (cinnamate 4-hydroxylase) as indirectly (via ATR) NADPH-dependent cytochrome P450 enzyme, co-localization in ER subdomains was observed. Thus, alternative splicing of G6PD5 can direct the NADPH-producing OPPP reactions to the cytosolic face of the ER, where they may operate as membrane-bound metabolon to support several important biosynthetic pathways of plant cells.
An automatic fluorescence phenotyping platform to evaluate dynamic infection process of Tobacco mosaic virus-green fluorescent protein in tobacco leaves
Authors: Ye Junli , Song Jingyan , Gao Yuan , Lu Xu , Pei Wenyue , Li Feng , Feng Hui , Yang Wanneng
Published: September 2022

Tobacco is one of the important economic crops all over the world. Tobacco mosaic virus (TMV) seriously affects the yield and quality of tobacco leaves. The expression of TMV in tobacco leaves can be analyzed by detecting green fluorescence-related traits after inoculation with the infectious clone of TMV-GFP (Tobacco mosaic virus - green fluorescent protein). However, traditional methods for detecting TMV-GFP are time-consuming and laborious, and mostly require a lot of manual procedures. In this study, we develop a low-cost machine-vision-based phenotyping platform for the automatic evaluation of fluorescence-related traits in tobacco leaf based on digital camera and image processing. A dynamic monitoring experiment lasting 7 days was conducted to evaluate the efficiency of this platform using Nicotiana tabacum L. with a total of 14 samples, including the wild-type strain SR1 and 4 mutant lines generated by RNA interference technology. As a result, we found that green fluorescence area and brightness generally showed an increasing trend over time, and the trends were different among these SR1 and 4 mutant lines samples, where the maximum and minimum of green fluorescence area and brightness were mutant-4 and mutant-1 respectively. In conclusion, the platform can full-automatically extract fluorescence-related traits with the advantage of low-cost and high accuracy, which could be used in detecting dynamic changes of TMV-GFP in tobacco leaves.
Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice
Authors: Ma Yamei , Wang Jian , Yang Tifeng , Dong Jingfang , Yang Wu , Chen Luo , Zhou Lian , Chen Jiansong , Liu Bin , Zhang Shaohong , Edwards David , Zhao Junliang
Published: September 2022

High seedling vigor can improve the ability to compete against weeds and flooding at the seedling stage and is essential for the direct seeding of rice. Early shoot length is an important performance index in seedling vigor evaluation. However, information on the identity of rice germplasm with high seedling vigor, and the genetic basis of seedling vigor are not well understood. In this study, we have conducted a genome-wide association study using 302 international diverse rice accessions from the Rice Diversity Panel 2. Six quantitative trait loci (QTLs) were found to associate with shoot length (SL). The locus qSL2 was further analyzed for candidate gene characterization. We identified OsCPS1, which encodes CDP synthase and functions in GA (Gibberellins) biosynthesis in rice, exhibits differential expression between long and short SL accessions. Using the Nipponbare genome sequence as the reference, we identified a 36 bp deletion in the 5’ UTR of OsCPS1 in long SL accessions, which is absent in short SL accessions. GA content analysis showed that the levels of bioactive GA1 and GA4 are considerably higher in long SL accessions than in short SL accessions. Genome-wide gene expression analysis indicated the expression of some photosynthesis genes is higher in long SL accessions than in short SL accessions. In contrast, genes involved in ABA (Abscisic Acid)-activated signal pathway showed lower expression in long SL accessions. Population analysis across wild rice, indica and japonica, suggested that OsCPS1 may be under selection in japonica during domestication. The results suggest that OsCPS1 is a candidate gene underlying qSL2. These data provide a promising source for candidate genetic variation associated with seedling vigor, with practical applications in rice breeding.
LANet: Stereo matching network based on linear-attention mechanism for depth estimation optimization in 3D reconstruction of inter-forest scene
Authors: Liu Lina , Liu Yaqiu , Lv Yunlei , Xing Jian
Published: September 2022

The 3D reconstruction of forests provides a strong basis for scientific regulation of tree growth and fine survey of forest resources. Depth estimation is the key to the 3D reconstruction of inter-forest scene, which directly determines the effect of digital stereo reproduction. In order to solve the problem that the existing stereo matching methods lack the ability to use environmental information to find the consistency of ill-posed regions, resulting in poor matching effect in regions with weak texture, occlusion and other inconspicuous features, LANet, a stereo matching network based on Linear-Attention mechanism is proposed, which improves the stereo matching accuracy by effectively utilizing the global and local information of the environment, thereby optimizing the depth estimation effect. An AM attention module including a spatial attention module (SAM) and a channel attention module (CAM) is designed to model the semantic relevance of inter-forest scenes from the spatial and channel dimensions. The linear-attention mechanism proposed in SAM reduces the overall complexity of Self-Attention from O(n2) to O(n), and selectively aggregates the features of each position by weighted summation of all positions, so as to learn rich contextual relations to capture long-range dependencies. The Self-Attention mechanism used in CAM selectively emphasizes interdependent channel maps by learning the associated features between different channels. A 3D CNN module is optimized to adjust the matching cost volume by combining multiple stacked hourglass networks with intermediate supervision, which further improves the speed of the model while reducing the cost of inferential calculation. The proposed LANet is tested on the SceneFlow dataset with EPE of 0.82 and three-pixel-error of 2.31%, and tested on the Forest dataset with EPE of 0.68 and D1-all of 2.15% both of which outperform some state-of-the-art methods, and the comprehensive performance is very competitive. LANet can obtain high-precision disparity values of the inter-forest scene, which can be converted to obtain depth information, thus providing key data for high-quality 3D reconstruction of the forest.
Organic acid metabolism in Chinese dwarf cherry [Cerasus humilis (Bge.) Sok.] is controlled by a complex gene regulatory network
Authors: Guo Caizhen , Wang Pengfei , Zhang Jiancheng , Guo Xiwen , Mu Xiaopeng , Du Junjie
Published: September 2022

The acidity of Chinese dwarf cherry [Cerasus humilis (Bge.) Sok.] fruits is a key factor affecting the sensory quality of fruits, and it undergoes great changes during development. The molecular mechanisms of these changes are still unclear. In this study, fruits of high-acid ‘Nongda4’ and low-acid ‘DS-1’ varieties of Chinese dwarf cherry were used to determine the acid content at different developmental stages. We used transcriptome profiles to identify key genes related to organic acid metabolism and construct their co-expression networks, and we studied the expression patterns of key genes in 36 Chinese dwarf cherry accessions. The titratable acid content of both ‘DS-1’ and ‘Nongda4’ fruits first increased and then decreased during fruit development; however, the titratable acid content of ‘DS-1’ fruits changed to a minor extent. The organic acid content of ‘Nongda4’ was significantly higher than that of ‘DS-1’. The organic acids in mature fruits were mainly malic acid and citric acid. Analysis of the differentially expressed genes related to organic acid metabolism revealed six key genes, including two MDH genes, one tDT gene, one ME gene, one PEPCK gene, and one VHA gene. Weighted gene co-expression network association analysis revealed four modules that were significantly correlated with organic acid content, and 10 key genes with high connectivity among these four modules were screened, including two PK genes, two MDH genes, two ME genes, one PEPCK gene, one VHA gene, one PEPC gene, and one tDT gene. According to the expression patterns of genes in different Chinese dwarf cherry accessions, seven genes were confirmed to represent key genes related to the regulation of organic acids during Chinese dwarf cherry fruit development. These results provide a foundation for further studies on the molecular mechanism of organic acid accumulation in Chinese dwarf cherry fruit.
Exploiting the miniature inverted-repeat transposable elements insertion polymorphisms as an efficient DNA marker system for genome analysis and evolutionary studies in wheat and related species
Authors: Ubi Benjamin Ewa , Gorafi Yasir Serag Alnor , Yaakov Beery , Monden Yuki , Kashkush Khalil , Tsujimoto Hisashi
Published: September 2022

Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of “full site” insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 “full sites,” respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.
A moderated mediation mechanism underlying the impact of website telepresence on purchase intention — Evidence from Chinese female college student customers
Authors: Zhu Guiqin , Jiang Shuaihe , Li Kai
Published: September 2022

Telepresence in e-commerce, the feeling of resembling shopping in a physical store, plays a critical role in determining online purchase intention. However, the cognitive mechanism and boundary conditions about its effect still need further investigation. The current study construed flow experience and socioeconomic status as important variables and developed a moderated mediation model for their roles in the effect of telepresence. The model was supported by our study where a group of Chinese female college students participated in simulated online apparel shopping and completes relevant questionnaire surveys. The results show that: (1) website telepresence predicts positively the purchase intention of females, (2) flow experience mediates the impact of website telepresence on purchase intention, and (3) the relationship between website telepresence and flow experience could be moderated by socioeconomic status, namely, females with higher socioeconomic status demonstrate stronger mediation of flow experience. These findings can help researchers and online retailers understand the flow concept in e-commerce and formulate marketing strategies to retain consumers with different socioeconomic statuses.
Effects of social experience on abstract concepts in semantic priming
Authors: Yao Zhao , Chai Yu , Yang Peiying , Zhao Rong , Wang Fei
Published: September 2022

Humans can understand thousands of abstract words, even when they do not have clearly perceivable referents. Recent views highlight an important role of social experience in grounding of abstract concepts and sub-kinds of abstract concepts, but empirical work in this area is still in its early stages. In the present study, a picture-word semantic priming paradigm was employed to investigate the contribution effect of social experience that is provided by real-life pictures to social abstract (SA, e.g., friendship, betrayal) concepts and emotional abstract (EA, e.g., happiness, anger) concepts. Using a lexical decision task, we examined responses to picture-SA word pairs (Experiment 1) and picture-EA word pairs (Experiment 2) in social/emotional semantically related and unrelated conditions. All pairs shared either positive or negative valence. The results showed quicker responses to positive SA and EA words that were preceded by related vs. unrelated prime pictures. Specifically, positive SA words were facilitated by the corresponding social scene pictures, whereas positive EA words were facilitated by pictures depict the corresponding facial expressions and gestures. However, such facilitatory effect was not observed in negative picture-SA/EA word conditions. This pattern of results suggests that a facilitatory effect of social experience on abstract concepts varies with different sub-kinds of abstract concepts, that seems to be limited to positive SA concepts. Overall, our findings confirm the crucial role of social experience for abstract concepts and further suggest that not all abstract concepts can benefit from social experience, at least in the semantic priming.
The effects of social participation on social integration
Authors: Xie Peng , Cao Qinwei , Li Xue , Yang Yurong , Yu Lianchao
Published: September 2022

With the fast expansion of urbanization, temporary migrants have become a large demographic in Chinese cities. Therefore, in order to enhance the social integration of the migrant population, scholars and policymakers have an urgency to investigate the influencing factors of the integration progress. Prior studies regarding social integration have neglected to examine this topic from the perspective of social participation. Empirical research is conducted based on the data of 15,997 migrants across eight cities in the 2014 wave of National Migrant Population Dynamic Monitoring Survey (MDMS) in China. Hierarchical linear models were used to test the hypotheses regarding the impacts of formal social participation (FSP) and informal social participation (ISP) on social integration. Community type, neighbor composition, hometown pressure, withdrawal guarantee, and constraints of hukou were examined as moderators. FSP and ISP possess different features such as operating with distinct modes, providing different services. Members within the organizations also entail different rights and responsibilities, providing them with different types of social capital and psychological perceptions. Hence, this study strived to identify the effects of social participation behaviors on social integration from a social capital perspective. The results revealed that social participation is positively linked to social integration. We also distinguished between FSP and ISP of migrants to investigate the boundary effects of different types of social participation on social integration. The findings provide both theoretical and practical implications for scholars as well as policymakers on issues regarding the social integration of migrants.
Anhedonia in endometriosis: An unexplored symptom
Authors: Mallorquí Aida , Martínez-Zamora María-Angeles , Carmona Francisco
Published: September 2022

Anhedonia is the diminished motivation and sensitivity to pleasurable stimuli. It has been reported to be more prevalent in patients with chronic pain as compared to healthy controls. Endometriosis is a chronic inflammatory systemic disease with a significant psychosocial impact that compromises wellbeing and the day-to-day life of patients. Women with endometriosis show significant psychological distress, even more pervasive when chronic pelvic pain is present. In the current review we will discuss the role of anhedonia in endometriotic chronic pelvic pain. We will also present new lines of research that could lead to more fully clarifying the psychological impact of endometriosis and its detrimental repercussions to quality of life and mental health.
Influence of co-creation signals on observers’ co-creation willingness: A self-determination theory perspective
Authors: Zhang Li , Zhu Na , Wang Hui
Published: September 2022

With the service-dominant logic gradually replacing the traditional commodity-dominant reason, co-creating value with consumers has become an essential marketing practice for enterprises. As a critical information carrier in enterprise marketing communication, the co-creation signal impacts co-creation observers. Enterprises are now exploring how to effectively release co-creation signals to attract most observers to participate in value creation activities actively. Based on self-determination theory, this study investigates the influence mechanism of co-creation signals on observers’ willingness to co-create and the moderating role of mental simulation through the experimental method. The conclusions are as follows: (a) The co-creation signal has a significant positive effect on the co-creation intention of observers. Self-designed co-creation signals generate more important co-creation willingness than self-produced co-creation signals; (b) Self-determination and its dimensions mediate the relationship between co-creation signals and the observer’s co-creation willingness; and (c) Mental simulation moderates the relationship between co-creation signal and self-determination. This study has important theoretical significance in enriching co-creation signals and mental simulation research. It also provides management implications for enterprises to release co-creation signals and optimize co-creation marketing practices effectively.
Video fingerprinting: Past, present, and future
Authors: Allouche Mohamed , Mitrea Mihai
Published: September 2022

The last decades have seen video production and consumption rise significantly: TV/cinematography, social networking, digital marketing, and video surveillance incrementally and cumulatively turned video content into the predilection type of data to be exchanged, stored, and processed. Belonging to video processing realm,video fingerprinting(also referred to ascontent-based copy detectionornear duplicate detection) regroups research efforts devoted to identifying duplicated and/or replicated versions of a given video sequence (query) in a reference video dataset. The present paper reports on a state-of-the-art study on the past and present of video fingerprinting, while attempting to identify trends for its development. First, the conceptual basis and evaluation frameworks are set. This way, the methodological approaches (situated at the cross-roads of image processing, machine learning, and neural networks) can be structured and discussed. Finally, fingerprinting is confronted to the challenges raised by the emerging video applications (e.g., unmanned vehicles or fake news) and to the constraints they set in terms of content traceability and computational complexity. The relationship with other technologies for content tracking (e.g.,DLT - Distributed Ledger Technologies) are also presented and discussed.