Molecular insights into the defense of Dioscorea opposita cv. 'Tiegun' callus against pathogenic and endophytic fungal infection through transcriptome analysis.

Dioscorea opposita cv. 'Tiegun' is an economically important crop with high nutritional and medicinal value. Plants can activate complex and diverse defense mechanisms after infection by pathogenic fungi. Moreover, endophytic fungi can also trigger the plant immune system to resist pathogen invasion. However, the study of the effects of endophytic fungi on plant infection lags far behind that of pathogenic fungi, and the underlying mechanism is not fully understood. Here, the black spot pathogen Alternaria alternata and the endophytic fungus Penicillium halotolerans of 'Tiegun' were identified and used to infect calli. The results showed that A. alternata could cause more severe membrane lipid peroxidation, while P. halotolerans could rapidly increase the activity of the plant antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT); thus, the degree of damage caused by P. halotolerans to the callus was weaker than that caused by A. alternata. RNA-seq analysis revealed that various plant defense pathways, such as phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and the MAPK signaling pathway, play important roles in triggering the plant immune response during fungal infection. Furthermore, the tryptophan metabolism, betalain biosynthesis, fatty acid degradation, flavonoid biosynthesis, tyrosine metabolism and isoquinoline alkaloid biosynthesis pathways may accelerate the infection of pathogenic fungi, and the ribosome biogenesis pathway in eukaryotes may retard the damage caused by endophytic fungi. This study lays a foundation for exploring the infection mechanism of yam pathogens and endophytic fungi and provides insight for effective fungal disease control in agriculture.

Comparative Analysis of Structural and Functional Properties of Dietary Fiber from Four Grape Varieties.

Muscadine grapes are characterized by their large and abundant seeds and hard and thick skins that contain significant amounts of dietary fiber (DF). The current study investigated the chemical constituents, molecular architecture, and physicochemical attributes of DF derived from Muscadine grapes (Granny Val and Alachua) and compared them with those derived from Shine Muscat and Kyoho. Using a combined enzymatic method, the total dietary fiber (TDF) was extracted and divided into two parts: soluble dietary fiber (SDF) and insoluble dietary fiber (IDF). TDF (mainly IDF, with a small fraction of SDF) was dominated by cellulose, followed by pectin and hemicellulose. In addition, Granny Val and Alachua had a significantly higher abundance of TDF and IDF compared with Shine Muscat and Kyoho. Moreover, Shine Muscat had significantly the highest abundance of SDF among the four grape varieties. Of note, IDF from Granny Val and Alachua exhibited a complex and dense texture on its surface, and notably outperformed Shine Muscat and Kyoho in terms of cholesterol, fatty acid, heavy metal adsorption, and antioxidant activity. Collectively, Muscadine grapes, i.e., Granny Val and Alachua in the current study, possessed elevated DF levels (predominantly IDF), and their enhanced bioactivity underscored their potential as a potential food ingredient for further use.

Identification of BBX gene family and its function in the regulation of microtuber formation in yam.

BBX proteins play important roles in all of the major light-regulated developmental processes. However, no systematic analysis of BBX gene family regarding the regulation of photoperiodic microtuber formation has been previously performed in yam. In this study, a systematic analysis on the BBX gene family was conducted in three yam species, with the results, indicating that this gene plays a role in regulating photoperiodic microtuber formation. These analyses included identification the BBX gene family in three yam species, their evolutionary relationships, conserved domains, motifs, gene structure, cis-acting elements, and expressional patterns. Based on these analyses, DoBBX2/DoCOL5 and DoBBX8/DoCOL8 showing the most opposite pattern of expression during microtuber formation were selected as candidate genes for further investigation. Gene expression analysis showed DoBBX2/DoCOL5 and DoBBX8/DoCOL8 were highest expressed in leaves and exhibited photoperiod responsive expression patterns. Besides, the overexpression of DoBBX2/DoCOL5 and DoBBX8/DoCOL8 in potato accelerated tuber formation under short-day (SD) conditions, whereas only the overexpression of DoBBX8/DoCOL8 enhanced the accelerating effect of dark conditions on tuber induction. Tuber number was increased in DoBBX8/DoCOL8 overexpressing plants under dark, as well as in DoBBX2/DoCOL5 overexpressing plants under SD. Overall, the data generated in this study may form the basis of future functional characterizations of BBX genes in yam, especially regarding their regulation of microtuber formation via the photoperiodic response pathway.

Comparative prevalence of oral bacteria and protozoa in patients with periodontitis in Taiwan.

OBJECTIVES: Periodontitis is an inflammatory disease caused by bacteria present in the dental biofilm. However, the presence of two oral protozoans, Entamoeba gingivalis and Trichomonas tenax, in patients with the periodontal disease remains largely unknown in Taiwan. Therefore, we investigated the prevalence of oral microbial infections between the sites with mild gingivitis and chronic periodontitis in patients. MATERIALS AND METHODS: We collected 60 dental biofilm samples from sites with mild gingivitis (probing depth <5 mm) and chronic periodontitis (probing depth ≥5 mm) from 30 patients at the National Cheng Kung University Hospital. The samples were analyzed via polymerase chain reaction and gel electrophoresis. RESULTS: Among oral protozoans, E. gingivalis and T. tenax were detected in 44 (74.07%) and 14 (23.33%) of all samples, respectively. Among oral bacteria, Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia were detected in 50 (83.33%), 47 (78.33%), and 48 (80.0%) samples, respectively. CONCLUSIONS: This study, which is the first to analyze E. gingivalis and T. tenax presence among patients with periodontitis in Taiwan, revealed an association between periodontitis and oral microbes.

Families of Patients With Cancer: Responses and Actions to People With Cancer Who Use Complementary and Alternative Medicine: A Qualitative Study in Taiwan.

This study aims to explore how the families of patients with cancer respond to and act toward complementary and alternative medicine (CAM) use. A qualitative research design based on grounded theory was adopted in this study. Semistructured and face-to-face in-depth interviews were conducted. Each participant was involved in a one-to-one individual interview. Five categories emerged regarding how the families of patients with cancer responded to and acted toward CAM use: purposes of using CAM, CAM use between patients and families, role of family caregivers, actions when using CAM, and seeking religious practice. The core category following coding emphasized the paramount importance of patients' comfort. The findings revealed that the families of patients with cancer may respond and act differently regarding patients' use of CAM. During this process, patients may not inform family members that they are using CAM. Health care professionals should consider this in their interactions with family members.

The Diabetic Foot Amputation Decision-Making Process.

OBJECTIVE: Diabetes has been the fourth leading cause of death in Taiwan since 2002 and is one of the top four most prevalent chronic diseases worldwide. Patients who have diabetic foot, as well as their families, are faced with the burden of possible limb amputation. The aim of this study was to explore the amputation decision-making process with patients with diabetic foot and their families. METHODS: Grounded theory was used in this study. Data from 16 participants at a regional hospital in Taiwan were collected using purposive sampling. The data analysis was conducted through open coding, axial coding, selective coding, and memo writing. RESULTS: The study revealed that the core factor in the decision-making process was "amputation in order to survive." Patients and families additionally considered "the devastation of experiencing multiple diseases," "treatment of poorly healing wounds," and "facing the decision of whether to undergo amputation." CONCLUSIONS: After understanding the patients' decision-making process regarding amputation, healthcare providers should be encouraged to empathize with such patients. Further, providers should respect the patients' and families' decision and provide them with necessary care. Future research should explore professional perspective and family members' care process for amputees to understand the decision-making process of patients who require amputation.

Interactome analysis of the EV71 5' untranslated region in differentiated neuronal cells SH-SY5Y and regulatory role of FBP3 in viral replication.

Enterovirus 71 (EV71), a single-stranded RNA virus, is one of the most serious neurotropic pathogens in the Asia-Pacific region. Through interactions with host proteins, the 5' untranslated region (5'UTR) of EV71 is important for viral replication. To gain a protein profile that interact with the EV71 5'UTR in neuronal cells, we performed a biotinylated RNA-protein pull-down assay in conjunction with LC-MS/MS analysis. A total of 109 proteins were detected and subjected to Database for Annotation, Visualization and Integrated Discovery (DAVID) analyses. These proteins were found to be highly correlated with biological processes including RNA processing/splicing, epidermal cell differentiation, and protein folding. A protein-protein interaction network was constructed using the STRING online database to illustrate the interactions of those proteins that are mainly involved in RNA processing/splicing or protein folding. Moreover, we confirmed that the far-upstream element binding protein 3 (FBP3) was able to bind to the EV71 5'UTR. The redistribution of FBP3 in subcellular compartments was observed after EV71 infection, and the decreased expression of FBP3 in host neuronal cells markedly inhibited viral replication. Our results reveal various host proteins that potentially interact with the EV71 5'UTR in neuronal cells, and we found that FBP3 could serve as a positive regulator in host cells.

[Exploring the Primary Adaptation Process of First-Ever Stroke Patients].

BACKGROUND: Stroke is a leading cause of death worldwide and the third leading cause of disease-related mortality in Taiwan. Furthermore, stroke is a major cause of functional disability in adults, causing physiological, psychological, and social impacts. Little qualitative research has been conducted on the primary adaptation process of patients with first-ever stroke in Taiwan. PURPOSE: The present study explored the primary adaptation process of patients with first-ever stroke. METHODS: This qualitative study used purposive sampling to enroll 12 patients with first-ever stroke for interviews, followed by theoretical sampling. Grounded theory guided the methodology and data analysis. Data analysis was performed simultaneously in accordance with the coding process. RESULTS: The primary adaptation process used by the participants involved the two main categories of "impacts of stroke" and "adaptation after stroke", with three subcategories associated, respectively, with the former (loss of physical autonomy, diminishing perceptions of self-value, and stroke-related hardships turning into social isolation) and with the latter (regaining autonomy after rehabilitation, receiving support from family without being a burden, and release from suffering/becoming more positive). The core category that emerged from the present study was: "Facing stroke, hoping for the best, transforming lives." CONCLUSIONS/IMPLICATIONS FOR PRACTICE: The above findings on the primary adaptation process of stroke patients provide an important reference for clinical nurses/healthcare professionals who have responsibilities to care for patients with first-ever stroke. In addition, healthcare professionals should offer more health education and psychological support to stroke patients based on individual patient needs.

The Epidemiological Analysis of COVID-19 Outbreaks in Nursing Homes during the Period of Omicron Variant Predominance.

BACKGROUND: The main purpose of this study was to evaluate the epidemic trend and risk factors associated with COVID-19 outbreaks in nursing homes during the period of Omicron variant predominance. METHODS: The study analyzed the risk factors associated with SARS-CoV-2 infection and death among the 327 residents and 129 healthcare workers (HCWs) in three hospital-affiliated nursing homes through a multivariate Cox regression model. RESULTS: The rates of receiving a COVID-19 booster dose were 70.3% for the residents and 93.0% for the healthcare workers (HCWs), respectively. A number of asymptomatic individuals, including 54 (16.5%) residents and 15 (11.6%) HCWs, were detected through mass screening surveillance tests. The COVID-19 infection rates during the outbreaks were 41.6% among residents and 48.1% among HCWs, respectively. The case fatality rate among residents was 10.3%. None of the HCWs were hospitalized or died. The multivariate Cox regression model showed that the risk of COVID-19 infection increased in males (HR 2.46; 95% CI 1.47-4.11; p = 0.001), Barthel index ≥ 61 (HR 1.93; 95% CI 1.18-3.17; p = 0.009), and dementia (HR 1.61; 95% CI 1.14-2.27; p = 0.007). The risk of COVID-19 death increased with pneumonia (HR 11.03; 95% CI 3.02-40.31; p < 0.001), hospitalization (HR 7.18; 95% CI 1.97-26.25; p = 0.003), and admission to an intensive care unit (HR 8.67; 95% CI 2.79-26.89; p < 0.001). CONCLUSIONS: This study highlighted the high infection rates with a substantial proportion of asymptomatic infections for both residents and HCWs, as well as a high case fatality rate for the residents among nursing homes during the Omicron epidemic period. We suggest implementing mass screening through regular surveillance testing as an effective strategy for early detection of COVID-19 and for preventing transmission during an epidemic period. Pneumonia is the primary risk associated with COVID-19 death. Early detection and prompt treatment of pneumonia for vulnerable residents in nursing homes are crucial to protect them from potential mortality.

Characterization of walnut JrWOX11 and its overexpression provide insights into adventitious root formation and development and abiotic stress tolerance.

The well-developed root system enables plant survival under various environmental stresses. WUSCHEL-RELATED HOMEOBOX GENE 11 (WOX11) plays a critical role in adventitious root formation and development in rice, Arabidopsis, and easy-to-root tree poplar. However, in difficult-to-root trees, the knowledge of WOX11 during adventitious root formation and development remains scarce. In this study, the JrWOX11 gene was isolated from a difficult-to-root tree walnut and heterologously expressed in the "84K" poplar. The results showed that JrWOX11 contained a similar structure and sequence to the homologous genes in rice, Arabidopsis, and poplar, but had different numbers and types of motifs and cis-elements. JrWOX11 lacked the motif GGAIQY compared to that in easy-to-root trees. In addition, JrWOX11 expression was induced by ABA, PEG, and NaCl treatments. Overexpression of JrWOX11 in poplar promoted root initiation and significantly increased adventitious root (ARs) number, lateral roots (LRs) number, and root hair (RH) length. Furthermore, the aboveground biomass was notably increased under NaCl and PEG treatments in transgenic plants. When NaCl and PEG were removed, the survival rate, aerial shoot development, and de novo root organogenesis were also markedly enhanced in transgenic shoot cuttings. The study provides valuable information on the differences between JrWOX11 and the homologous genes in rice, Arabidopsis, and poplar, and supports the critical role of JrWOX11 in the formation of AR and tolerance to salt and osmotic stresses.

Performance evaluation of knowledge management among hospital employees.

PURPOSE: The purpose of this study is to investigate the cognition of knowledge management (KM) among hospital employees and the relationship between KM and the KM enabler activities (financial, customer, internal business processes, learning and growth) in a regional hospital in Taiwan. DESIGN/METHODOLOGY/APPROACH: Both qualitative and quantitative research were used in this study. The instrument was conducted using in-depth interviews of three policy-makers as participants. The quantitative data were collected from a regional hospital in the Northern part of Taiwan with a 77 percent effective response rate (n=154). FINDINGS: The findings in this paper indicate that the cognition and demand for KM in subordinates is close to the expectations of policy-makers. The policy-makers expect subordinates working in the hospital to be brave in taking on new responsibilities and complying with hospital operation norms. KM is emphasized as a powerful and positive asset. Moreover, understanding KM predicts good performance in an organization. RESEARCH LIMITATIONS/IMPLICATIONS: The findings in this paper can be generalized to other regional hospitals. The findings may be applied to a wider population. PRACTICAL IMPLICATIONS: This study can provide insights into the perceptions and cognitions of workers in a hospital about KM and the activities of KM enablers. The responses and perceptions observed in the interviews in this study, as well as the quantitative research results could be useful to other hospitals and individuals who engage KM as a new management trend. ORIGINALITY/VALUE: This study suggested KM guidelines for policy-makers who are experienced managers.

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits.

BACKGROUND: Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored. RESULTS: We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively. CONCLUSIONS: The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

The complete chloroplast genome of paradox (Juglans major × J. regia), an interspecific hybrid in China.

Paradox is one of the most important rootstock resources in USA and China walnut industry. In this study, we characterized the complete chloroplast genome of Paradox (Juglans major × J. regia) based on next generation sequencing. The circular complete chloroplast genome was 160,324 bp in length, containing a large single-copy (LSC) region of 89,852 bp, and a small single-copy (SSC) region of 18,410 bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb) of 26,031 bp each. A total of 131 functional genes were encoded, consisted of 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome was 36.1% and the GC contents of the LSC, SSC, and IR regions were 33.7, 29.9, and 42.6%, respectively. The phylogenetic analysis by Neighbor-Joining showed that Paradox was relatively closely related to J. major compared to other species of Juglans genus. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Juglans species.

Soil Chemical and Microbiological Properties Are Changed by Long-Term Chemical Fertilizers That Limit Ecosystem Functioning.

Although the effects of fertilization and microbiota on plant growth have been widely studied, our understanding of the chemical fertilizers to alter soil chemical and microbiological properties in woody plants is still limited. The aim of the present study is to investigate the impact of long-term application of chemical fertilizers on chemical and microbiological properties of root-associated soils of walnut trees. The results show that soil organic matter (OM), pHkcl, total nitrogen (TN), nitrate-nitrogen (NO3-), and total phosphorus (TP) contents were significantly higher in non-fertilized soil than after chemical fertilization. The long-term fertilization led to excessive ammonium-nitrogen (NH4+) and available phosphorus (AP) residues in the cultivated soil, among which NH4+ resulted in soil acidification and changes in bacterial community structure, while AP reduced fungal diversity. The naturally grown walnut trees led to an enrichment in beneficial bacteria such as Burkholderia, Nitrospira, Pseudomonas, and Candidatus_Solibacter, as well as fungi, including Trichoderma, Lophiostoma, Phomopsis, Ilyonectria, Purpureocillium, Cylindrocladiella, Hyalorbilia, Chaetomium, and Trichoglossum. The presence of these bacterial and fungal genera that have been associated with nutrient mobilization and plant growth was likely related to the higher soil OM, TN, NO3-, and TP contents in the non-fertilized plots. These findings highlight that reduced chemical fertilizers and organic cultivation with beneficial microbiota could be used to improve economic efficiency and benefit the environment in sustainable agriculture.

Overproduction of gentamicin B in industrial strain Micromonospora echinospora CCTCC M 2018898 by cloning of the missing genes genR and genS.

In pharmaceutical industry, isepamicin is mainly manufactured from gentamicin B, which is produced by Micromonospora echinospora as a minor component of the gentamicin complex. Improvement of gentamicin B production through metabolic engineering is therefore important to satisfy the increasing demand for isepamicin. We hypothesized that gentamicin B was generated from gentamicin JI-20A via deamination of the C2' amino group. Using kanJ and kanK as the gene probes, we identified the putative deamination-related genes, genR and genS, through genome mining of the gentamicin B producing strain M. echinospora CCTCC M 2018898. Interestingly, genR and genS constitute a gene cassette located approximately 28.7 kb away from the gentamicin gene cluster. Gene knockout of genR and genS almost abolished the production of gentamicin B in the mutant strain, suggesting that these two genes, which are responsible for the last steps in gentamicin B biosynthesis, constitute the missing part of the known gentamicin biosynthetic pathway. Based on these finding, we successfully constructed a gentamicin B high-yielding strain (798 mg/L), in which an overexpression cassette of genR and genS was introduced. Our work fills the missing piece to solve the puzzle of gentamicin B biosynthesis and may inspire future metabolic engineering efforts to generate gentamycin B high-yielding strains that could eventually satisfy the need for industrial manufacturing of isepamicin.

Global Methylomic and Transcriptomic Analyses Reveal the Broad Participation of DNA Methylation in Daily Gene Expression Regulation of Populus trichocarpa.

Changes in DNA methylation patterns in different tissues, at various developmental stages, and under environmental stimuli have been investigated in plants. However, the involvement of DNA methylation in daily gene expression regulation and the plant circadian clock have not been reported. Here, we investigated DNA methylomes and mRNA transcriptomes from leaves of P. trichocarpa over 24 h by high-throughput sequencing. We found that approximately 15.63-19.50% of the genomic cytosine positions were methylated in mature poplar leaves, with approximately half being in the form of asymmetric CHH sites. Repetitive sequences and transposable elements (TEs) were heavily methylated, and the hAT and CMC-EnSpm transposons were more heavily methylated than other TEs. High methylation levels were observed upstream and downstream of the transcribed region, medium in exon and intron, low in untranslated region (5'-UTR and 3'-UTR) of genic regions. In total, about 53,689 differentially methylated regions (DMRs) were identified and CHH context was the most abundant type among daily DNA methylation changes. The DMRs overlapped with over one third of the total poplar genes, including plant defense genes. In addition, a positive correlation between expression levels and DNA methylation levels in the gene body region were observed in DMR overlapping genes. About 1,895 circadian regulated genes overlapped with DMRs, with 871 hypermethylated genes with down-regulated expression levels and 881 hypomethylated genes with up-regulated expression levels, indicating the possible regulation of DNA methylation on the daily rhythmic expression of these genes. But rhythmic DNA methylation changes were not detected in any oscillator component genes controlling the plant circadian clock. Our results suggest that DNA methylation participates widely in daily gene expression regulation, but is not the main mechanism modulating the plant circadian clock.

Severe Gingival Ulceration and Necrosis Caused by an Antithyroid Drug: One Case Report and Proposed Clinical Approach.

INTRODUCTION: Diffuse gingival ulceration and necrosis is one of the major manifestations of neutropenia or agranulocytosis. Acquired neutropenia can be induced by many medications. Severe oral pain might induce a patient to seek the help of a dentist. It is important for dentists to be familiar with drug-induced neutropenia and its associated oral manifestations. CASE PRESENTATION: An Asian woman was diagnosed with Graves disease (hyperthyroidism) and was treated with methimazole for about 6 weeks when oral symptoms first occurred. Sore throat, fever, and extensive, painful gingival necrosis were her chief complaints when she visited the emergency department. Methimazole-induced neutropenia was diagnosed based on her blood tests and medical history. Methimazole was replaced with a range of treatments, including injections of broad spectrum antibiotics and granulocyte colony stimulating factor. Superficial debridement and a chlorhexidine plus lidocaine mouthwash were used to control her periodontal microbiota. Within 1 week, blood data of the patient had returned to normal, and the severity of oral symptoms began to diminish. Complete healing of the gingival tissues was noted 8 months after she had been discharged from the hospital. CONCLUSIONS: Methimazole induces neutropenia and subsequent gingival ulceration and necrosis in some patients. Early confirmation of the effect of methimazole and early discontinuation of the drug are the first steps to recovery. Reducing bacterial load by chemotherapeutic methods and maintaining acceptable oral hygiene are important to control the disease.

Prognostic factors of health care-associated bloodstream infection in adult patients ≥40 years of age.

We investigated 401 geriatric patients and 453 middle-aged patients with health care-associated bloodstream infection (HABSI) at a medical center during January-December 2014. Compared with middle-aged patients, the geriatric group had higher 30-day mortality (31.2% vs 23.4%, P = .01). Body mass index, serum albumin concentration, Charlson comorbidity index score, vancomycin-resistant Enterococcus bacteremia, and high C-reactive protein levels predict poor outcomes for HABSI among adult patients.