Biology subjects

Tong, J.

Publications and source records attributed to Tong, J..

3 recordsLinked to original sources

bioRxiv2018

Generation of four iPSC lines from peripheral blood mononuclear cells (PBMCs) of an Attention Deficit Hyperactivity Disorder (ADHD) individual and a healthy sibling in an Australia-Caucasian family

Peripheral blood mononuclear cells were donated by a male teenager with clinically diagnosed Attention Deficit Hyperactivity Disorder under the Diagnostic and Statistical Manual of Mental Disorders IV criteria and his unaffected male sibling. Induced pluripotent stem cells were developed using integration-free Sendai Reprogramming factors containing OCT, SOX2, KLF4, and c-MYC. All four iPSC lines displayed pluripotent cell morphology, pluripotency-associated factors at protein level, alkaline phosphatase enzymatic activity, male karyotype of 46, XY, and in vitro differentiation capacity into all the three germ layers and negative for Mycoplasma.

neuroscience↗

bioRxiv2018

Non-driver somatic alteration burden confers good prognosis in non-small cell lung cancer

BackgroundGenomic profiling of patient tumors has linked somatic driver mutations to survival outcomes of non-small cell lung cancer (NSCLC) patients, especially for those receiving targeted therapies. However, it remains unclear whether specific non-driver mutations have any prognostic utility.\n\nMethodsWhole exomes and transcriptomes were measured from NSCLC xenograft models of patients with diverse clinical outcomes. Penalised regression analysis was performed to identify a set of 865 genes associated with patient survival. The number of somatic copy number aberrations, point mutations and associated expression changes within the 865 genes were used to stratify independent NSCLC patient populations, filtered for chemotherapy naive and early-stage. In-depth genomic analysis and functional testing was conducted on the genomic alterations to understand their effect on improving survival.\n\nResultsHigh burden of somatic alterations are associated with longer disease-free survival (HR=0.153, P=1.48x10-4) in NSCLC patients. When somatic alterations burden was integrated with gene expression, we were able to predict prognosis in three independent patient datasets. Patients with high alteration burden could be further stratified based on the presence of immunogenic mutations, revealing another subgroup of patients with even better prognosis (85% with >5 years survival), and associated with cytotoxic T-cell expression. In addition, 95% of these 865 genes lack documented activity relevant to cancer, but are in pathways regulating cell proliferation, motility and immune response were implicated.\n\nConclusionOur results demonstrate that non-driver somatic alterations may influence the outcome of cancer patients by increasing beneficial immune response and inhibiting processes associated to tumorigenesis.

cancer biology↗

bioRxiv2018

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows

In this study, differences in the ruminal bacterial community between high-yield and low-yield lactating dairy cows fed the same diets were investigated. Sixteen lactating dairy cows with similar parity were divided into two groups based on their milk yield: high-yield (HY) and low-yield (LY) groups. On day 21, rumen content samples were collected, and the microbiota composition was determined using Illumina MiSeq sequencing of the 16S rRNA gene. During the study period, dry matter intake (DMI) and milk yield were measured daily, and milk composition was assessed 3 times per week. The results showed that the milk of the LY group tended to have higher fat (P=0.08), protein (P=0.01) and total solid (P=0.04) contents than that of the HY group, though the HY group had higher ruminal acetate (P=0.05), propionate (P=0.02) and volatile fatty acid (VFA) (P=0.02) concentrations. Principal coordinate analysis indicated significant differences in ruminal bacterial community composition and structure between the HY group and LY group. Overall, Bacteroidetes (HY group: 52.91{+/-}3.06%; LY group: 61.88{+/-}3.03%) was the predominant phylum, followed by Firmicutes (HY group: 41.10{+/-}2.74%; LY group: 32.11{+/-}2.97%). The abundances of Ruminococcus 2, Lachnospiraceae and Eubacterium coprostanoligenes were significantly higher in the HY group than in the LY group. In addition, 3 genera--Anaerostipes, Bacteroidales and Anaeroplasma--were identified as biomarker species with the greatest impacts on the ruminal community structure in the LY group. These findings facilitate the understanding of bacterial synthesis within the rumen and reveal an important mechanism underlying differences in milk production in dairy cows.

microbiology↗