Total Chemical Synthesis, Assembly of Human Torque Teno Virus Genome

Torque teno virus(TTV) is a nonenveloped virus containing a single-stranded,circular DNA genome of approximately 3.8kb.We completely synthesized the 3 808 nucleotides of the TTV(SANBAN isolate) genome,which contains a hairpin structure and a GC-rich region.More than 100 overlapping oligonucleotides were chemically synthesized and assembled by polymerase chain assembly reaction(PCA),and the synthesis was completed with splicing by overlap extension(SOEing).This study establishes the methodological basis of the chemical synthesis of a viral genome for use as a live attenuated vaccine or gene therapy vector.

Novel splicing variant of the human orphan nuclear receptor Nurr1 gene

Background Nurr1 is a member of the nuclear receptor superfamily of transcription factors. The objective of the present study was to identify novel splicing variants of the gene in neuronal and non-neuronal tissues and determine their functions. Methods Reverse transcription-polymerase chain reaction (RT-PCR) analysis was used to screen for Nurr1 splice variants in the adult human central nervous system (CNS) and in other tissues such as lymphocytes,and liver,muscle,and kidney cells. Functional assays of the variants were performed by measuring Nurr1 response element (NuRE) transcriptional activity in vitro . Results In this study,the authors identified a novel splicing variant of Nurr1 within exon 5,found in multiple adult human tissues,including lymphocytes,and liver,muscle,and kidney cells,but not in the brain or spinal cord. Sequencing analysis showed the variant has a 75 bp deletion between nucleotides 1402 and 1476. A functional assay of the Nurr1-c splicing variant,performed by measuring NuRE transcriptional activity in vitro,detected a 39% lower level of luciferase (LUC) activity ( P <0.05).Conclusion A novel splicing variant of Nurr1 exists in human non-neuronal tissues and functional assays suggest that the variant may act as an alternate transcription regulator.

Expression of two alternative splicing isoforms of fragile X gene in human placenta

Fragile X (Fra (X)) syndrome is the most frequent cause of inherited mentalretardation, and it is associated with the fragile site at Xq27.3. In 1991, the FMR1(fragile X mental retardation 1) gene was cloned in the vicinity of this site. The muationand abnormal expression of FMR1 are the direct causes of Fra(X) syndrome. The

Exploring Codon Usage Patterns of Alternatively Spliced Genes in Human Chromosome 1

In this study, 414 whole protein-coding sequences (238 004 codons) of alternatively spliced genes of human chromosome 1 have been employed to explore the patterns of codon usage bias among genes. Overall codon usage data analysis indicates that G- and C-ending codons are predominant in the genes. The base usage in all three codon positions suggests a selection-mutation balance. Multivariate statistical analysis reveals that the codon usage variation has a strong positive correlation with the expressivities of the genes (r=0.5790, P<0.0001). All 27 codons identified as optimal are G- and C-ending codons. Correlation analysis shows a strong negative correlation between the gene length and codon adaptation index value (r=0.2252, P<0.0001), and a significantly positive correlation between the gene length and Nc values (r=0.1876, P<0.0001). These results suggest that the comparatively shorter genes in the genes have higher codon usage bias to maximize translational efficiency, and selection may also contribute to the reduction of highly expressed proteins.

Subcutaneous and intramuscular fat transcriptomes show large differences in network organization and associations with adipose traits in pigs

Subcutaneous fat(SCF)and intramuscular fat(IMF)deposition is relevant to health in humans,as well as meat production and quality in pigs.In this study,we generated RNA sequence data for 122 SCF,120 IMF,and 87 longissimus dorsi muscle(LDM)samples using 155 F6 pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds.The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F6 pigs.We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity,and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF,containing genes that were associated with the immune process and DNA double-strand repair,respectively.We identified 215 SCF genes related to kinase inhibitor activity,mitochondrial fission,and angiogenesis,and 90 IMF genes related to lipolysis and fat cell differentiation,displayed a tissue-specific association with back fat thickness and IMF content,respectively.We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissuedependent predictability for the two adipose traits.Alternative splicing of genes was also found to be associated with SCF or IMF deposition,but the association was much less extensive than that based on expression levels.This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition.These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.

Emerging targets in cancer drug resistance

Drug resistance is a complex phenomenon that frequently develops as a failure to chemotherapy during cancer treatment.Malignant cells increasingly generate resistance to various chemotherapeutic drugs through distinct mechanisms and pathways.Understanding the molecular mechanisms involved in drug resistance remains an important area of research for identification of precise targets and drug discovery to improve therapeutic outcomes.This review highlights the role of some recent emerging targets and pathways which play critical role in driving drug resistance.