Metabolic fingerprinting of Angelica sinensis during growth using UPLC-TOFMS and chemometrics data analysis

BACKGROUND: The radix of Angelica sinensis is widely used as a medicinal herbal and metabolomics research of this plant during growth is necessary. RESULTS: Principal component analysis of the UPLC-QTOFMS data showed that these 27 samples could be separated into 4 different groups. The chemical markers accounting for these separations were identified from the PCA loadings plot. These markers were further verified by accurate mass tandem mass and retention times of available reference standards. The study has shown that accumulation of secondary metabolites of Angelica sinensis is closely related to the growth periods. CONCLUSIONS: The UPLC-QTOFMS based metabolomics approach has great potential for analysis of the alterations of secondary metabolites of Angelica sinensis during growth

Transcriptome dataset of sago palm in peat soil

Sago palm (Metroxylon sagu Rottb.) is an important agricultural starch-producing palm that contributes to Malaysia's economics, especially in the State of Sarawak, Malaysian Borneo. In this palm tree, the central part of the plant storage-starch. Under normal condition, sago palm develop its trunk after 4-5 years being planted. However, sago palms planted on deep-peat soil failed to develop their trunk even after 17 years of being planted. This phenomenon is known as ‘non-trunking’, which eliminates the economic value of the palms. Numerous research has been done to address the phenomenon, but the molecular mechanisms of sago palm responding toward the responsible stresses are still lacking. Therefore, in this study, leaf samples were collected from trunking (normal) and non-trunking sago palms planted on peat soil for total RNA extraction, followed by next-generation sequencing using the BGISEQ-500 platform. The raw reads were cleaned, and de novo assembled using TRINITY software package. A total of 40.11 Gb bases were sequenced from the sago palm leaf samples. The assembled sequence produced 102,447 unigenes, with N50 score 1809 bp and GC ratio of 44.34%. The alignment of unigenes with seven functional databases (NR, NT, GO, KOG, KEGG, SwissProt and InterPro) resulted in the annotation of 65,523 (63.96%) unigenes. Functional annotation results in the detection of 46,335 coding DNA sequences by Transdecoder. A total of 30,039 simple-sequence repeats distributed on 21,676 unigenes were detected using Primer3 software, and 2355 transcription factor coding unigenes were predicted using getorf and hmmseach software. This work is registered under NCBI BioProject PRJNA781491. The raw RNA sequencing data are available in Sequence Read Archive (SRA) database with accession numbers SRX13165895, SRX13165896, SRX13165897, SRX13165898, SRX13165899, and SRX13165900. Gene expression and annotation information are accessible in public functional genomics data repository Gene Expression Omnibus (GEO) with accession number GSE189085

Perspectives on decision making amongst older people with end‐stage renal disease and caregivers in Singapore: a qualitative study

Background End‐stage renal disease (ESRD) is increasing both globally and in Asia. Singapore has the fifth highest incidence of ESRD worldwide, a trend that is predicted to rise. Older patients with ESRD are faced with a choice of haemodialysis, peritoneal dialysis or conservative management, all of which have their risks and benefits. Objective This study seeks to explore perspectives on decision making amongst older (≥70) Singaporean ESRD patients and their caregivers to undergo (or not to undergo) dialysis. Design Qualitative study design using semi‐structured interviews. Setting and participants Twenty‐three participants were recruited from the largest tertiary hospital in Singapore: seven peritoneal dialysis patients, five haemodialysis patients, four patients on conservative management and seven caregivers. Results While some patients believed that they had made an independent treatment decision, others reported feeling like they had no choice in the matter or that they were strongly persuaded by their doctors and/or family members to undergo dialysis. Patients reported decision‐making factors including loss of autonomy in daily life, financial burden (on themselves or on their families), caregiving burden, alternative medicine, symptoms and disease progression. Caregivers also reported concerns about financial and caregiving burden. Discussion and conclusion This study has identified several factors that should be considered in the design and implementation of decision aids to help older ESRD patients in Singapore make informed treatment decisions, including patients' and caregivers' decision‐making factors as well as the relational dynamics between patients, caregivers and doctors.This research was supported by the National Medical Research Council of Singapore (Grant Number: NMRC/HSRG/0080/2017), the Lien Centre for Palliative Care at Duke NUS Medical School and the National University Health System (NUHS) Singapore Population Health Improvement Centre (SPHERiC)(Grant Number: NMRC/CG/C026/2017_NUHS)

Associations of Tissue Tumor Mutational Burden and Mutational Status With Clinical Outcomes With Pembrolizumab Plus Chemotherapy Versus Chemotherapy For Metastatic NSCLC

INTRODUCTION: We evaluated tissue tumor mutational burden (tTMB) and mutations in STK11, KEAP1, and KRAS as biomarkers for outcomes with pembrolizumab plus platinum-based chemotherapy (pembrolizumab-combination) for NSCLC among patients in the phase 3 KEYNOTE-189 (ClinicalTrials.gov, NCT02578680; nonsquamous) and KEYNOTE-407 (ClinicalTrials.gov, NCT02775435; squamous) trials. METHODS: This retrospective exploratory analysis evaluated prevalence of high tTMB and STK11, KEAP1, and KRAS mutations in patients enrolled in KEYNOTE-189 and KEYNOTE-407 and the relationship between these potential biomarkers and clinical outcomes. tTMB and STK11, KEAP1, and KRAS mutation status was assessed using whole-exome sequencing in patients with available tumor and matched normal DNA. The clinical utility of tTMB was assessed using a prespecified cutpoint of 175 mutations/exome. RESULTS: Among patients with evaluable data from whole-exome sequencing for evaluation of tTMB (KEYNOTE-189, n = 293; KEYNOTE-407, n = 312) and matched normal DNA, no association was found between continuous tTMB score and overall survival (OS) or progression-free survival for pembrolizumab-combination (Wald test, one-sided p \u3e 0.05) or placebo-combination (Wald test, two-sided p \u3e 0.05) in patients with squamous or nonsquamous histology. Pembrolizumab-combination improved outcomes for patients with tTMB greater than or equal to 175 compared with tTMB less than 175 mutations/exome in KEYNOTE-189 (OS, hazard ratio = 0.64 [95% confidence interval (CI): 0.38‒1.07] and 0.64 [95% CI: 0.42‒0.97], respectively) and KEYNOTE-407 (OS, hazard ratio = 0.74 [95% CI: 0.50‒1.08 and 0.86 [95% CI: 0.57‒1.28], respectively) versus placebo-combination. Treatment outcomes were similar regardless of KEAP1, STK11, or KRAS mutation status. CONCLUSIONS: These findings support pembrolizumab-combination as first-line treatment in patients with metastatic NSCLC and do not suggest the utility of tTMB, STK11, KEAP1, or KRAS mutation status as a biomarker for this regimen

Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX

Although picornaviruses are conventionally considered ‘nonenveloped’, members of multiple picornaviral genera are released nonlytically from infected cells in extracellular vesicles. The mechanisms underlying this process are poorly understood. Here, we describe interactions of the hepatitis A virus (HAV) capsid with components of host endosomal sorting complexes required for transport (ESCRT) that play an essential role in release. We show release of quasi-enveloped virus (eHAV) in exosome-like vesicles requires a conserved export signal located within the 8 kDa C-terminal VP1 pX extension that functions in a manner analogous to late domains of canonical enveloped viruses. Fusing pX to a self-assembling engineered protein nanocage (EPN-pX) resulted in its ESCRT-dependent release in extracellular vesicles. Mutational analysis identified a 24 amino acid peptide sequence located within the center of pX that was both necessary and sufficient for nanocage release. Deleting a YxxL motif within this sequence ablated eHAV release, resulting in virus accumulating intracellularly. The pX export signal is conserved in non-human hepatoviruses from a wide range of mammalian species, and functional in pX sequences from bat hepatoviruses when fused to the nanocage protein, suggesting these viruses are released as quasi-enveloped virions. Quantitative proteomics identified multiple ESCRT-related proteins associating with EPN-pX, including ALG2-interacting protein X (ALIX), and its paralog, tyrosine-protein phosphatase non-receptor type 23 (HD-PTP), a second Bro1 domain protein linked to sorting of ubiquitylated cargo into multivesicular endosomes. RNAi-mediated depletion of either Bro1 domain protein impeded eHAV release. Super-resolution fluorescence microscopy demonstrated colocalization of viral capsids with endogenous ALIX and HD-PTP. Co-immunoprecipitation assays using biotin-tagged peptides and recombinant proteins revealed pX interacts directly through the export signal with N-terminal Bro1 domains of both HD-PTP and ALIX. Our study identifies an exceptionally potent viral export signal mediating extracellular release of virus-sized protein assemblies and shows release requires non-redundant activities of both HD-PTP and ALIX

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

NTU undergraduates perceptions of depression and gender stereotypes.

This paper aims to study on how Nanyang Technological University (NTU) undergraduate students perceive depression in relation to gender stereotypes. In my study, I focus on the kinds of gender attributes linked to students’ perception of depression. First, I examine how undergraduates perceive biological differences between genders as females’ hormonal changes contribute to their proneness to depression. Second, I examine the aspect of students’ perceptions of gender differences in coping strategies. Students usually think that males are better at externalizing or concealing their negative emotions through explicit means or externalization of emotions unlike females who engage in internalization of emotions, resulting in them being more depression-prone. Third, I examine how students perceive that the egalitarian gender ideology of modern day women which requires them to strike a balance between the dual spheres of the household and workplace thereby contributing to their depression.Bachelor of Art

Patient adherence to aromatase inhibitor treatment in early stage breast cancer - local experience from Western Sydney hospitals

Background: Aromatase inhibitor (AI) is effective in various clinical setting for breast cancer, ranging from chemoprevention to treating in both adjuvant setting and metastatic disease. Each year Medicare Australia spends $50,000,000 on AI prescriptions, compared to$3,000,000 on tamoxifen prescriptions. The reported adherence rate to oral antineoplastic agents varied between 20 to 100%. Adherence to AI was evaluated to be suboptimal in America, but no local data is available in Australian. This study aimed to evaluate adherence rate and the factors affecting adherence in Western Sydney early breast cancer population. Method: The adherence rate was recalled by participants as the percentage of days they took AI. A Breast Cancer Hormonal Treatment Questionnaire was developed to evaluate factors affecting adherence. Non-adherence is identified if participants take AI in less than 80% of eligible days. Association between non-adherence and clinical characteristics were assessed using Pearson-χ2. Results: The study recruited 82 early breast cancer women on AI between June 2012 and June 2014 from Westmead, Nepean and Norwest Private Hospitals. The median age was 62.5 years (range 38 to 83 years). The median time on AI was 4 years (range 1 to more than 5 years). 22.2% participants were non-adherent to AI treatment. Higher educational status (p = 0.0088), good general health (p = 0.0502) and higher stage disease (p = 0.0451) were associated with non-adherence to AI treatment. The most common adverse reactions reported were muscles and joint aches (65.9%) which were higher than reported literature (25%). Regarding provision of information by healthcare professionals, only 28% of participant recalled receiving information before starting AI treatment. Conclusions: Our study found non-adherence to AI is relatively common in Western Sydney early breast cancer population. We also identified potential factors associated with non-adherence. Due to the small sample size and limitation of patient self-recall, further validation in a large cohort is warranted.1 page(s