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김한해,조안나,이무영,양순모,Xiaozhi Ma,Pamela C. Ronald,이인석 한국분자세포생물학회 2019 Molecules and cells Vol.42 No.2
Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.
Chronic Kidney Disease and Associated Cardiovascular Risk Factors in Chinese with Type 2 Diabetes
Qing-Lin Lou,Xiao-Jun Ouyang,Liu-Bao Gu,Yong-Zhen Mo,Ronald Ma,Jennifer Nan,Alice Kong,Wing-Yee So,Gary Ko,Juliana Chan,Chun-Chung Chow,Rong-Wen Bian 대한당뇨병학회 2012 Diabetes and Metabolism Journal Vol.36 No.6
Background: To determine the frequency of chronic kidney disease (CKD) and its associated risk factors in Chinese type 2 diabetic patients, we conducted a cross-sectional study in Nanjing, China, in the period between January 2008 and December 2009. Methods: Patients with type 2 diabetes under the care by Jiangsu Province Official Hospital, Nanjing, China were invited for assessment. CKD was defined as the presence of albuminuria or estimated glomerular filtration rate <60 mL/min/1.73 m2. Albuminuria was defined as urinary albumin-to-creatinine ratio ≥30 mg/g. Results: We recruited 1,521 urban Chinese patients with type 2 diabetes (mean age, 63.9±12.0 years). The frequency of CKD and albuminuria was 31.0% and 28.9%, respectively. After adjusted by age and sex, hypertension, anemia and duration of diabetes were significantly associated with CKD with odds ratio (95% confidence interval) being 1.93 (1.28 to 2.93), 1.70 (1.09 to 2.64), and 1.03 (1.00 to 1.06), respectively. Conclusion: In conclusion, CKD was common in the urban Nanjing Chinese with type 2 diabetes. Strategies to prevent or delay progression of kidney disease in diabetes should be carried out at the early disease course of type 2 diabetes.
Kim, Hanhae,Joe, Anna,Lee, Muyoung,Yang, Sunmo,Ma, Xiaozhi,Ronald, Pamela C.,Lee, Insuk Korean Society for Molecular and Cellular Biology 2019 Molecules and cells Vol.42 No.2
Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.
Ng, Maggie C.Y.,Park, Kyong Soo,Oh, Bermseok,Tam, Claudia H.T.,Cho, Young Min,Shin, Hyoung Doo,Lam, Vincent K.L.,Ma, Ronald C.W.,So, Wing Yee,Cho, Yoon Shin,Kim, Hyung-Lae,Lee, Hong Kyu,Chan, Juliana American Diabetes Association 2008 Diabetes Vol.57 No.8
<P><B>OBJECTIVE—</B> Recent genome-wide association studies have identified six novel genes for type 2 diabetes and obesity and confirmed <I>TCF7L2</I> as the major type 2 diabetes gene to date in Europeans. However, the implications of these genes in Asians are unclear.</P><P><B>RESEARCH DESIGN AND METHODS—</B> We studied 13 associated single nucleotide polymorphisms from these genes in 3,041 patients with type 2 diabetes and 3,678 control subjects of Asian ancestry from Hong Kong and Korea.</P><P><B>RESULTS—</B> We confirmed the associations of <I>TCF7L2</I>, <I>SLC30A8</I>, <I>HHEX</I>, <I>CDKAL1</I>, <I>CDKN2A</I>/<I>CDKN2B</I>, <I>IGF2BP2</I>, and <I>FTO</I> with risk for type 2 diabetes, with odds ratios ranging from 1.13 to 1.35 (1.3 × 10<SUP>−12</SUP> < <I>P</I><SUB>unadjusted</SUB> < 0.016). In addition, the A allele of rs8050136 at <I>FTO</I> was associated with increased BMI in the control subjects (<I>P</I><SUB>unadjusted</SUB> = 0.008). However, we did not observe significant association of any genetic variants with surrogate measures of insulin secretion or insulin sensitivity indexes in a subset of 2,662 control subjects. Compared with subjects carrying zero, one, or two risk alleles, each additional risk allele was associated with 17% increased risk, and there was an up to 3.3-fold increased risk for type 2 diabetes in those carrying eight or more risk alleles. Despite most of the effect sizes being similar between Asians and Europeans in the meta-analyses, the ethnic differences in risk allele frequencies in most of these genes lead to variable attributable risks in these two populations.</P><P><B>CONCLUSIONS—</B> Our findings support the important but differential contribution of these genetic variants to type 2 diabetes and obesity in Asians compared with Europeans.</P>
Yamauchi, Toshimasa,Hara, Kazuo,Maeda, Shiro,Yasuda, Kazuki,Takahashi, Atsushi,Horikoshi, Momoko,Nakamura, Masahiro,Fujita, Hayato,Grarup, Niels,Cauchi, Stephane,Ng, Daniel P K,Ma, Ronald C W,Tsunoda, Nature Publishing Group, a division of Macmillan P 2010 Nature genetics Vol.42 No.10
We conducted a genome-wide association study of type 2 diabetes (T2D) using 459,359 SNPs in a Japanese population with a three-stage study design (stage 1, 4,470 cases and 3,071 controls; stage 2, 2,886 cases and 3,087 controls; stage 3, 3,622 cases and 2,356 controls). We identified new associations in UBE2E2 on chromosome 3 and in C2CD4A-C2CD4B on chromosome 15 at genome-wide significant levels (rs7612463 in UBE2E2, combined P = 2.27 ? 10<SUP>??9</SUP>; rs7172432 in C2CD4A-C2CD4B, combined P = 3.66 ? 10<SUP>??9</SUP>). The association of these two loci with T2D was replicated in other east Asian populations. In the European populations, the C2CD4A-C2CD4B locus was significantly associated with T2D, and a combined analysis of all populations gave P = 8.78 ? 10<SUP>??14</SUP>, whereas the UBE2E2 locus did not show association to T2D. In conclusion, we identified two new loci at UBE2E2 and C2CD4A-C2CD4B associated with susceptibility to T2D.
( Yun Yu ),( Xiao Jun Ouyang ),( Qing-lin Lou ),( Liu Bao Gu ),( Yong Zhen Mo ),( Gary T. Ko ),( Chun Chung Chow ),( Wing Yee So ),( Ronald Ma ),( Alice Kong ),( Nicola Brown ),( Jennifer Nan ),( Juli 대한내과학회 2012 The Korean Journal of Internal Medicine Vol.27 No.1
Background/Aims: The application of glycated hemoglobin (HbA1c) for the diagnosis of diabetes is currently under extensive discussion. In this study, we explored the validity of using HbA1c as a screening and diagnostic test in Chinese subjects recruited in Nanjing, China. Methods: In total, 497 subjects (361 men and 136 women) with fasting plasma glucose (PG) ≥ 5.6 mmol/L were recruited to undergo the oral glucose tolerance test (OGTT) and HbA1c test. Plasma lipid, uric acid, and blood pressure were also measured. Results: Using a receiver operating characteristic curve, the optimal cutoff point of HbA1c related to diabetes diagnosed by the OGTT was 6.3%, with a sensitivity and specificity of 79.6% and 82.2%, respectively, and the area under the curve was 0.87 (95% confidence interval, 0.83 to 0.92). A HbA1c level of 6.5% had a sensitivity and specificity of 62.7% and 93.5%, respectively. When comparing the HbA1c ≥ 6.5% or OGTT methods for diagnosing diabetes, the former group had significantly higher HbA1c levels and lower levels of fasting and 2-hour PG than the latter group. No significant difference was observed in the other metabolism indexes between the two groups. Conclusions: Our results suggest that HbA1c ≥ 6.5% has reasonably good specificity for diagnosing diabetes in Chinese subjects, which is in concordance with the American Diabetes Association recommendations.
Cho, Yoon Shin,Chen, Chien-Hsiun,Hu, Cheng,Long, Jirong,Hee Ong, Rick Twee,Sim, Xueling,Takeuchi, Fumihiko,Wu, Ying,Go, Min Jin,Yamauchi, Toshimasa,Chang, Yi-Cheng,Kwak, Soo Heon,Ma, Ronald C W,Yamamo Nature Publishing Group, a division of Macmillan P 2012 Nature genetics Vol.44 No.1
We conducted a three-stage genetic study to identify susceptibility loci for type 2 diabetes (T2D) in east Asian populations. We followed our stage 1 meta-analysis of eight T2D genome-wide association studies (6,952 cases with T2D and 11,865 controls) with a stage 2 in silico replication analysis (5,843 cases and 4,574 controls) and a stage 3 de novo replication analysis (12,284 cases and 13,172 controls). The combined analysis identified eight new T2D loci reaching genome-wide significance, which mapped in or near GLIS3, PEPD, FITM2-R3HDML-HNF4A, KCNK16, MAEA, GCC1-PAX4, PSMD6 and ZFAND3. GLIS3, which is involved in pancreatic beta cell development and insulin gene expression, is known for its association with fasting glucose levels. The evidence of an association with T2D for PEPD and HNF4A has been shown in previous studies. KCNK16 may regulate glucose-dependent insulin secretion in the pancreas. These findings, derived from an east Asian population, provide new perspectives on the etiology of T2D.