Cloning and characterization of the UBC gene from lotus (Nelumbo nucifera).

Protein ubiquitination is extensively involved in the regulation of a considerable number of physiological processes in plant cells. E2 (ubiquitin-conjugating enzyme, UBC), one of the essential enzymes of eukaryotic ubiquitination, catalyzes protein ubiquitination together with E1 and E3. In this study, we cloned four full-length cDNA NnUBCs of Nelumbo nucifera. With the same coding sequence length of 459 bp and coding 153 amino acids, these four genes are highly homologous with the AtUBC1 and AtUBC2 of Arabidopsis thaliana. Quantitative fluorescence polymerase chain reaction showed that these four genes exhibited different expression patterns in different tissues of N. nucifera. Overall, the expression of NnUBC3 was the highest in all plant tissues. Tests of different stress treatments showed that NnUBC3 plays an important role in response to heat, salt, and drought stresses in N. nucifera. Moreover, transgenic Arabidopsis plants (Atubc1-1Atubc2-1 mutant) expressing NnUBC3 presented a wild-type phenotype, indicating that NnUBC3 performs the same function as AtUBC1 and AtUBC2.

Mutation analysis of four Chinese families with pure hereditary spastic paraplegia: pseudo- X-linked dominant inheritance and male lethality due to a novel ATL1 mutation.

We studied four Chinese families with pure hereditary spastic paraplegia (HSP) to investigate the clinical features and associated genetic mutations. Linkage analysis was performed for all families to map the disease locus onto autosomal chromosomes, and related loci involved in HSP on the X chromosome were also examined. Polymerase chain reaction (PCR) sequencing was used to detect gene mutations. To confirm the influence of a splice-site mutation on mRNA, we used reverse transcription-PCR and direct sequencing. Linkage analysis and ATL1 gene sequencing of amniocytes were performed for prenatal genetic diagnosis. One missense variant (c.1517T>A) and a splice-site mutation (c.1245+1G>A) in SPAST, and two missense variants (c.715C>T, c.1204T>G) in ATL1 were identified. The c.1245+1G>A mutation caused a deletion of exon 9 in the SPAST gene. Prenatal genetic diagnosis showed that fetus did not carry the ALT1 c.1204T>G mutation. Follow-up was maintained for 5 years, and the negative result was confirmed by evidence of a healthy growing boy. We identified two novel mutations and two previously reported mutations in SPAST and ATL1, respectively. The family with the ATL1 c.1204T>G mutation exhibited male-lethality, female infancy-onset, and pseudo- X-linked dominant transmission, which had never been previously reported for HSP. Characteristic facial features were also noticed. The boy on whom prenatal gene diagnosis was performed is healthy and without unusual facies, suggesting that the c.1204T>G mutation might be related to these features. The results extend the genetic spectrum of HSP and suggest that linkage analysis remains a powerful tool in gene discovery studies.

Development and characterization of genic-SSR markers from different Asia lotus (Nelumbo nucifera) types by RNA-seq.

Nelumbo nucifera is an important economic vegetable and traditional medicine, but available genetic resources remain limited. Next generation sequencing has proven to be a rapid and effective means of identifying genic simple sequence repeat (genic-SSR) markers. This study developed genic-SSRs for N. nucifera using Illumina sequencing technology to assess diversity across cultivated and wild lotus. A total of 105,834 uni-contigs were produced with an average read length of 722 bp. Exactly 11,178 genic-SSR loci were identified in 9523 uni-contigs. Di-nucleotide (64.5%) was the most abundant SSR, followed by tri-nucleotide (23%), tetra-nucleotide (8.9%), penta-nucleotide (2.5%), and hexa-nucleotide (1%) repeat types. The most common di- and tri-nucleotide repeat motifs were AG/CT (51%) and AAG/CTT (8%), respectively. Based on these SSRs sequences, 6568 primer pairs were designed, of which 72 primers were randomly selected for synthesis and validation, and 38 in-silico polymorphic primers were obtained using in-house perl scripts. A total of 110 primers were screened in the lotus samples and the results showed that 101 primers yielded amplification products, of which 80 were polymorphs. The number of alleles ranged from 2 to 17 and the PIC (polymorphism information content) ranged from 0.19 to 0.87 with a mean value of 0.55. An Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram based on Jaccard's similarity coefficients showed that the correlation between geographical source and genotype was low. This study describes the distribution of genic-SSRs in the expressed portion of the lotus genome. These genic-SSRs have an important role to play in molecular mapping, diversity analysis, and marker-assisted selection strategies in Nelumbo.

Evaluation of the function status of the ulnar nerve in carpal tunnel syndrome.

Many carpal tunnel syndrome (CTS) patients have symptoms in both the median and ulnar digits more frequently than in the median digits alone. This is possibly because of close anatomical contiguity of the carpal tunnel and Guyon's canal, and the high pressure may also affect the latter, causing indirect compression of ulnar nerve fibers. Thus, we evaluated the functional status of the ulnar nerve in patients with CTS in order to investigate the relationship between ulnar nerve impairment and sensory symptoms of the ulnar territory. Electrophysiological studies were conducted in CTS patients and healthy controls. CTS patients were divided into the mild/moderate group and severe group; they were further divided into the symptomatic and asymptomatic subgroups according to the sensory symptom of the fifth digit region. The findings suggest that CTS patients could have coexisting ulnar nerve wrist entrapments that might exacerbate the severity of CTS. Sensory impairment in the ulnar territory was observed more frequently in the mild/moderate stage of CTS, which is associated with ulnar nerve involvement. These findings also suggest that damage to the ulnar nerve fibers caused by compression forces in Guyon's canal may underlie the ulnar spread of symptoms in CTS.

T174M polymorphism in the angiotensinogen gene and risk of myocardial infarction: a meta-analysis.

Numerous studies have evaluated the association between the T174M polymorphism in the angiotensinogen (AGT) gene and myocardial infarction (MI) risk. However, the specific association remains controversial because of small sample sizes and varied study designs among different studies. We performed a meta-analysis to assess this correlation. A comprehensive search was conducted to identify all published articles regarding the association between the AGT gene T174M polymorphism and MI risk from different databases. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated, and heterogeneity and publication bias were assessed. A total of 1032 patients with lung cancer and 1286 controls from 6 comparative studies were included in this meta-analysis. The results revealed a significant association between the AGT gene T174M polymorphism and MI risk (MM vs TT: OR = 2.87, 95%CI = 1.71-4.83; dominant model: OR = 1.57, 95%CI = 1.10-2.25; recessive model: OR = 0.41, 95%CI = 0.25-0.66). In subgroup analysis by nationality, we observed a significant association between the AGT gene T174M polymorphism and susceptibility to MI in both Caucasian and Asian populations. In conclusion, the T174M polymorphism in the AGT gene may be related to an increased risk of MI. Further larger studies are needed to confirm these conclusions.

Differences in frequencies of UGT1A9, 1A7, and 1A1 genetic polymorphisms in Chinese Tibetan versus Han Chinese populations.

As part of a series of pharmacogenomics studies of the Chinese population, we investigated genetic polymorphisms of some UGT1A regions. The three genes that were analyzed were UGT1A9, 1A7, and 1A1; we sequenced their exons, together with promoters, surrounding introns and 3'-untranslated regions (3'UTR) in 100 unrelated-healthy Chinese Tibetan individuals. We compared the data with information on Han Chinese of the same region, which we downloaded from the HapMap database. We identified 40 polymorphisms; 16 of them were shared by the two populations. We then analyzed their linkage disequilibrium map. The UGT1As cluster can be divided into two linkage blocks in the Tibetan population: Block 1 (UGT1A9, UGT1A7), Block 2 (3'-UTR). Furthermore, we identified haplotypes and selected their tagSNPs. In exon 1 of UGT1A7 gene, 393G>A (Arg131Gln, rs17868324) was found at a frequency of 44.4% in the Tibetan population, compared to only 0.7% in the Han population. The linkage blocks in the Han Chinese sample differed from that of the Chinese Tibetan group; the former had Block 1 (UGT1A9, UGT1A7), Block 2 (UGT1A7), and Block 3 (3'-UTR). These findings provide fundamental information for future molecular genetic studies of the UGT1A gene cluster as well as for personalized medicine in Chinese.

A novel mutation of the MFN2 gene in a Chinese family with Charcot-Marie-Tooth disease.

Charcot-Marie-Tooth (CMT) is a group of clinically and genetically heterogeneous inherited neuromuscular disorders. At present, more than 30 loci have been reported to be associated with CMT disease; point mutations in the mitofusin 2 (MFN2) gene is one of the most common causes. We studied a Chinese family with CMT disease in which the phenotype of affected individuals varied, and the weakness condition of the distal legs in males, except the proband, was less severe than in females in this family. Linkage analysis and PCR sequencing revealed a missense mutation (NM_014874.3:c.1066 A>G) in the MFN2 gene, resulting in an animo acid substitution of threonine to alanine in condon 356 (Thr356Ala). This is a novel phenotype and mutation for CMT family.