Genome-Wide Identification of the CDPK Gene Family and Their Involvement in Taproot Cracking in Radish.

Taproot cracking, a severe and common physiological disorder, markedly reduces radish yield and commercial value. Calcium-dependent protein kinase (CDPK) plays a pivotal role in various plant developmental processes; however, its function in radish taproot cracking remains largely unknown. Here, 37 RsCDPK gene members were identified from the long-read radish genome "QZ-16". Phylogenetic analysis revealed that the CDPK members in radish, tomato, and Arabidopsis were clustered into four groups. Additionally, synteny analysis identified 13 segmental duplication events in the RsCDPK genes. Analysis of paraffin-embedded sections showed that the density and arrangement of fleshy taproot cortex cells are important factors that affect radish cracking. Transcriptome sequencing of the fleshy taproot cortex revealed 5755 differentially expressed genes (DEGs) (3252 upregulated and 2503 downregulated) between non-cracking radish "HongYun" and cracking radish "505". These DEGs were significantly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interaction KEGG pathways. Furthermore, when comparing the 37 RsCDPK gene family members and RNA-seq DEGs, we identified six RsCDPK genes related to taproot cracking in radish. Soybean hairy root transformation experiments showed that RsCDPK21 significantly and positively regulates root length development. These findings provide valuable insights into the relationship between radish taproot cracking and RsCDPK gene function.

The lesser evil: Consumer acceptance of X-ray irradiation compared with alternative phytosanitary treatments.

X-ray irradiation is becoming a mainstream phytosanitary food treatment that is compatible with solving sustainability challenges. However, understanding how consumers respond to X-ray irradiation is still underdeveloped in research. In two studies, the current research sheds light on the acceptance of X-ray irradiation by New Zealand consumers, compared with an existing treatment, methyl bromide. Study 1 used focus groups to provide insights into barriers and opportunities of X-ray irradiation perceived by participants who accept, are passive towards, or reject irradiation. Acceptors of X-ray highlighted familiarity of use, non-residue/lack of chemicals, and environmentally friendly as positive factors, whereas danger of radiation and long-term health concerns were strong themes for rejection. Subsequently, study 2 extended this to provide a snapshot of measures representative of such themes to understand current attitudes towards X-ray irradiation itself, and as a replacement for methyl bromide usage. The results of study 2 indicated that when provided with information on X-ray in isolation, under half the respondents (39%) indicated a willingness to eat foods treated with X-ray. However, when forced to choose between food that had been treated with either X-ray or methyl bromide, the majority of respondents (84%) chose irradiation. Overall, the studies present an overview that whilst consumers may be apprehensive or passive about acceptance of X-ray irradiation (study 1), they overwhelmingly accept X-ray irradiation over the current alternative in New Zealand, methyl bromide (study 2). This was voiced by participants as accepting 'the lesser of two evils'.

Fortifying wellbeing: How Chinese consumers and doctors navigate the role of functional foods.

China's rapidly developing economy has seen an increase in medical problems commonly associated with affluent lifestyles such as increases in metabolic diseases and digestive issues. One response to this problem is an increase in the amount of functional foods currently available, which may take a Western food form, or be more closely associated with traditional Chinese medicine (TCM). This research seeks to understand how functional food and wellbeing intersect in order to better understand how consumers perceive the complex construct of wellbeing, and their agency in its creation. Interviews and Focus Group Interviews were undertaken in Shanghai, China; with consumers who self-identified as having health concerns, and with Doctors trained in Western Medicine and in TCM. Using an iterative process, the primary objective was to holistically examine how consumers navigate the role of functional foods in relation to their wellbeing. Our findings reveal three broad intersecting themes: (1) self-managed therapy using functional foods; (2) building trust with knowledge sharing; and (3) the importance of functional food heuristics. Functional food was not simply considered to be food with an added benefit, but also a cultural symbol of agency over one's wellness. These findings are discussed and implications for both policy makers and marketers are deliberated.

WWC2 is an independent prognostic factor and prevents invasion via Hippo signalling in hepatocellular carcinoma.

WWC family proteins negatively regulate HEK293 cell proliferation and organ growth by suppressing the transcriptional activity of Yes-associated protein (YAP), a major effector of the Hippo pathway. The function of the scaffolding protein WWC1 (also called KIBRA) has been intensively studied in cells and animal models. However, the expression and clinicopathologic significance of WWC2 in cancer are poorly characterized. This study aimed to clarify the biological function and mechanism of action of WWC2 in hepatocellular carcinoma (HCC). Retrospective analysis revealed WWC2 was significantly down-regulated in 95 clinical HCC tissues compared to the paired adjacent non-cancerous tissues. Moreover, loss of WWC2 expression was significantly associated with advanced clinicopathological features, including venous infiltration, larger tumour size and advanced TNM stage. Positive WWC2 expression was associated with significantly better 5-year overall survival, and WWC2 was an independent prognostic factor for overall survival in HCC. Moreover, we confirmed WWC2 inhibits HCC cell invasive ability in vitro. Elevated YAP expression was also observed in the same cohort of HCC tissues. Pearson's correlation coefficient analysis indicated WWC2 expression correlated inversely with nuclear YAP protein expression in HCC. Mechanistically, we confirmed overexpression of WWC2 suppresses the invasive and metastatic potential of HCC cells by activating large tumour suppressor 1 and 2 kinases (LATS1/2), which in turn phosphorylates the transcriptional co-activator YAP. Overall, this study indicates WWC2 functions as a tumour suppressor by negatively regulating the Hippo signalling pathway and may serve as a prognostic marker in HCC.

Identification of Novel Locus RsCr6 Related to Clubroot Resistance in Radish (Raphanus sativus L.).

Clubroot is a devastating disease that causes substantial yield loss worldwide. However, the inheritance and molecular mechanisms of clubroot resistance during pathogen infection in radish remain largely unclear. In this study, we investigated the inheritance of clubroot resistance in the F2 population derived from crossing clubroot-resistant (CR) and clubroot-susceptible inbred lines "GLX" and "XNQ," respectively. Genetic analysis revealed that a single dominant gene controlled the clubroot resistance of "GLX" with a Mendelian ratio of resistance and susceptibility of nearly 3:1. Bulked segregant analysis combined with whole-genome resequencing (BSA-seq) was performed to detect the target region of RsCr6 on chromosome Rs8. Linkage analysis revealed that the RsCr6 locus was located between two markers, HB321 and HB331, with an interval of approximately 92 kb. Based on the outcomes of transcriptome analysis, in the RsCr6 locus, the R120263140 and R120263070 genes with a possible relation to clubroot resistance were considered candidate genes. In addition, three core breeding materials containing the two reported quantitative trait loci (QTLs) and our novel locus RsCr6 targeting clubroot resistance were obtained using marker-assisted selection (MAS) technology. This study reveals a novel locus responsible for clubroot resistance in radishes. Further analysis of new genes may reveal the molecular mechanisms underlying the clubroot resistance of plants and provide a theoretical basis for radish resistance breeding.

Starch content changes and metabolism-related gene regulation of Chinese cabbage synergistically induced by Plasmodiophora brassicae infection.

Clubroot is one of the major diseases adversely affecting Chinese cabbage (Brassica rapa) yield and quality. To precisely characterize the Plasmodiophora brassicae infection on Chinese cabbage, we developed a dual fluorescent staining method for simultaneously examining the pathogen, cell structures, and starch grains. The number of starch (amylopectin) grains increased in B. rapa roots infected by P. brassicae, especially from 14 to 21 days after inoculation. Therefore, the expression levels of 38 core starch metabolism genes were investigated by quantitative real-time PCR. Most genes related to starch synthesis were up-regulated at seven days after the P. brassicae inoculation, whereas the expression levels of the starch degradation-related genes increased at 14 days after the inoculation. Then genes encoding the core enzymes involved in starch metabolism were investigated by assessing their chromosomal distributions, structures, duplication events, and synteny among Brassica species. Genome comparisons indicated that 38 non-redundant genes belonging to six core gene families related to starch metabolism are highly conserved among Arabidopsis thaliana, B. rapa, Brassica nigra, and Brassica oleracea. Genome sequencing projects have revealed that P. brassicae obtained host nutrients by manipulating plant metabolism. Starch may serve as a carbon source for P. brassicae colonization as indicated by the histological observation and transcriptomic analysis. Results of this study may elucidate the evolution and expression of core starch metabolism genes and provide researchers with novel insights into the pathogenesis of clubroot in B. rapa.

Weakly Supervised Deep Learning for Whole Slide Lung Cancer Image Analysis.

Histopathology image analysis serves as the gold standard for cancer diagnosis. Efficient and precise diagnosis is quite critical for the subsequent therapeutic treatment of patients. So far, computer-aided diagnosis has not been widely applied in pathological field yet as currently well-addressed tasks are only the tip of the iceberg. Whole slide image (WSI) classification is a quite challenging problem. First, the scarcity of annotations heavily impedes the pace of developing effective approaches. Pixelwise delineated annotations on WSIs are time consuming and tedious, which poses difficulties in building a large-scale training dataset. In addition, a variety of heterogeneous patterns of tumor existing in high magnification field are actually the major obstacle. Furthermore, a gigapixel scale WSI cannot be directly analyzed due to the immeasurable computational cost. How to design the weakly supervised learning methods to maximize the use of available WSI-level labels that can be readily obtained in clinical practice is quite appealing. To overcome these challenges, we present a weakly supervised approach in this article for fast and effective classification on the whole slide lung cancer images. Our method first takes advantage of a patch-based fully convolutional network (FCN) to retrieve discriminative blocks and provides representative deep features with high efficiency. Then, different context-aware block selection and feature aggregation strategies are explored to generate globally holistic WSI descriptor which is ultimately fed into a random forest (RF) classifier for the image-level prediction. To the best of our knowledge, this is the first study to exploit the potential of image-level labels along with some coarse annotations for weakly supervised learning. A large-scale lung cancer WSI dataset is constructed in this article for evaluation, which validates the effectiveness and feasibility of the proposed method. Extensive experiments demonstrate the superior performance of our method that surpasses the state-of-the-art approaches by a significant margin with an accuracy of 97.3%. In addition, our method also achieves the best performance on the public lung cancer WSIs dataset from The Cancer Genome Atlas (TCGA). We highlight that a small number of coarse annotations can contribute to further accuracy improvement. We believe that weakly supervised learning methods have great potential to assist pathologists in histology image diagnosis in the near future.

LPS­induced downregulation of microRNA­204/211 upregulates and stabilizes Angiopoietin­1 mRNA in EA.hy926 endothelial cells.

Angiopoietin­1 (ANG­1), a ligand of the endothelial cell­specific TIE2 surface receptor, acts in a complementary and coordinated manner with vascular endothelial growth factor during the process of angiogenesis. ANG­1 can be used as a clinically informative biomarker of disease severity and outcome in severe sepsis. The epithelium­specific Ets transcription factor 1 can activate ANG­1 transcription in the setting of inflammation; however, relatively little is known about the regulation of ANG­1 by microRNAs (miRs). It was observed that lipopolysaccharide (LPS) significantly increased ANG­1 mRNA and protein expression in EA.hy926 cells. ANG­1 was identified as a potential target gene of miR­204 and miR­211. Overexpression of miR­204/211 partially reversed the LPS­induced ANG­1 expression in EA.hy926 cells. Furthermore, overexpression of miR­204/211 significantly reduced the activity of a luciferase reporter gene containing the wild­type ANG­1 3'­untranslated region (UTR), but did not influence the activity of a luciferase reporter gene containing the ANG­1 3'­UTR with a mutated miR­204/211 binding site, confirming that miR­204/211 can bind to the ANG­1 3'­UTR and post­transcriptionally regulate ANG­1. Additionally, LPS enhanced the stability of ANG­1 mRNA by reducing the abundance of miR­204/211. Overexpression of miR­204/211 reduced the migration of EA.hy926 cells in vitro. The present study demonstrated that ANG­1 is a novel direct target gene of miR­204 and miR­211; in addition, LPS was able to inhibit this effect by reducing the expression of miR­204 and miR­211.