Potential-Dependent Adhesion Forces between dsDNA and Electroactive Surfaces.

A promising approach to regulating the interactions between polyelectrolytes and materials is the use of electroactive surfaces that can change their charge state. However, common electroactive groups are too unstable to be practical for this purpose. Here we have performed a single molecule force spectroscopy study of the interactions between dsDNA and an 1,1'-biferrocenylene (BFD = bis(fulvalene)diiron)-terminated self-assembled monolayer surface that allows us to reversibly change the charge state. We found that the interaction force between DNA and the surface is correlated to the oxidation state of the BFD groups, which is conveniently controlled by the electrochemical potentials. We discovered that the electroactive SAM produces much stronger interaction forces than its nonelectroactive counterpart. A model based on the Grahame equation was able to quantitatively reproduce the experimentally observed relation between the applied potentials and adhesion forces. Our electroactive surface provides a model system for quantitative studies of the interactions between polyelectrolyte and charged surfaces in liquid. These insights may enable new opportunities for actively manipulating the binding, orientations, and conformations of polyelectrolytes for biosensing, nanomotors, and other applications.

[Characterization of the novel HLA-A*24:191 allele and analysis of its MHC molecular modeling structure].

OBJECTIVE: To characterize a novel HLA allele, A*24:191, its DNA sequence, MHC modeling structure, and the possible influence of the amino-acid residue variations on the molecule. METHODS: The HLA sequence was determined by Luminex PCR-SSO and PCR-SBT. Its MHC molecular structure and the possible effects of the amino-acid residue variations were modeled and analyzed with Phyre2, RCSB PDB and HistoCheck software. RESULTS: The PCR-SBT revealed the novel A*24:191 differs from A*24:02 in exon 2 at position 256, 265, 270 with G>C, G>C, A>T. The MHC molecular structure prediction showed that, compared with A*24:02, the 62nd residue of A*24:191 changed from the acidic E to a neutral Q, both with the side chain extending outside the α helix pointing forward the groove, (Risler's score, R=2), the 65th changed from the smaller neutral G extending inside the helix to a basic R with a long-chain extending upward outside the helix (R=52), and the 66th changed from the basic K to a neutral N both with a long side chain extending inside the groove (R=31). The above residues are located on the α helix of the α 1 domain which constituting the side wall of the peptide-binding groove. The DSS Score=3.85. From the surface image of the molecule, it can be clearly seen that the variations of the properties, sizes and configurations of the residues caused significant changes in the shape of the surface structure of the α helix. CONCLUSION: It suggested that the residue variations are likely to change the peptide binding properties as well as the TCR and antibody binding characteristics of the molecule.

[Identification of a rare platelet-specific antigen HPA-10bw allele among ethnic Han Chinese population in Shandong].

OBJECTIVE: To study the polymorphism of human platelet antigen (HPA) system 10 among ethnic Han Chinese from Shandong, China so as to supplement the data of platelet donor bank in the region. METHODS: Peripheral blood samples of platelet donors from the region were genotyped for HPA-10 alleles by PCR-sequence specific primer (PCR-SSP) and direct sequencing. RESULTS: Among 1401 donors, a rare heterozygote carrier of HPA-10w (a+b+) was identified, which gave an allelic frequency of approximately 0.035%. CONCLUSION: The detection of rare HPA-10bw antigen allele among ethnic Han Chinese from Shandong is useful for the diagnosis and prevention of neonatal alloimmune thrombocytopenia and post-transfusion purpura in the region.

[Congenital Fibrinogen Deficiency Caused by Novel FGG Gene Mutation].

OBJECTIVE: To detect and analyze coagulation related indexes and genotypes of a patient with congenital fibrinogen deficiency and his family members, and to investigate the possible molecular pathogenesis. METHODS: Four peripheral blood samples (proband and 3 family members) were collected and the prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT), fibrinogen (Fg), D-Dimer and eight coagulation factor indicators were detected. All exons and flanking sequences of the FGA, FGB, and FGG genes encoding the three peptide chains of fibrinogen were sequenced and analyzed by bioinformatics. RESULTS: Among the eight coagulation factors of the proband and the elder sister, F Ⅴ and F Ⅷ were slightly higher, TT was significantly prolonged, and Fg was significantly reduced. Sequencing results showed that c.901C>T heterozygous mutation existed in the FGG gene. Bioinformatics analysis showed that the mutation changed the original protein structure and reduced the number of hydrogen bonds. CONCLUSION: The fibrinogen gamma chain c.901C>T heterozygous mutation is the main cause of congenital fibrinogen deficiency in this family. This mutation is reported for the first time at home and abroad.

An investigation of the prevalence of Giardia agilis in anuran amphibians from fourteen areas in China.

Giardia agilis is a Giardia species which is morphological distinguishable for its very narrow and elongated trophozoite. Although there were a few studies about its morphology since its first report in 1882, none investigations about its prevalence have ever been reported to date. We investigated the prevalence of G. agilis in 25 anuran amphibian species from five provinces of China using both morphological and molecular methods. Of the 463 tested samples, 195 (42.1%) were positive. The 195 positive samples were from nine species, which are scatteredly distributed in four anuran amphibian families. The statistical prevalence among adults of different frog species showed no significant difference, and so did among tadpoles. Thus, G. agilis is probably able to infect all anuran amphibians without species-bias. More interestingly, the prevalence in the tadpoles is significantly higher than in their adults. The prevalence in Kaloula verrucosa tadpoles from the same area showed no significant differences between none-legged stage and two-legged stage, but the prevalence in these two developmental stages is significantly higher than in the four-legged stage. And the prevalence in four-legged stage is still much higher than in adults. A turning point of prevalence appeared in the period of tadpole tail degeneration. Moreover, all the positive samples were from the areas with relatively high altitude (more than 870 m). The fact that G. agilis tends to easily infect the frogs living in high altitude areas indicated it has evolved the ability to adapted the dramatic temperature change in poikilothermal animals. Therefore, G. agilis has evolved some special successful parasitism strategies for parasitizing the poikilothermal hosts with metamorphosis such as anuran amphibians.

A new species of Giardia Künstler, 1882 (Sarcomastigophora: Hexamitidae) in hamsters.

BACKGROUND: Giardia spp. are flagellated protozoan parasites that infect humans and many other vertebrates worldwide. Currently seven species of Giardia are considered valid. RESULTS: Here, we report a new species, Giardia cricetidarum n. sp. in hamsters. Trophozoites of G. cricetidarum n. sp. are pear-shaped with four pairs of flagella and measure on average 14 µm (range 12-18 µm) in length and 10 µm (range 8-12 µm) in width. The trophozoites of the new species are generally larger and stouter than those of most of the other Giardia spp. and exhibit the lowest length/width ratio (c.1.40) of all recognized Giardia species. Cysts of G. cricetidarum n. sp. are ovoid and measure on average 11 µm (range 9-12 µm) in length and 10 µm (range 8-10 µm) in width and are indistinguishable from the cysts of other Giardia species. Molecular phylogenetic analyses based on beta-giardin, small subunit rRNA, and elongation factor-1 alpha loci all demonstrated that G. cricetidarum n. sp. is genetically distinct from all currently accepted Giardia spp. Investigation of the host range indicated that the new species was only found in hamsters (including Phodopus sungorus, P. campbelli and Mesocricetus auratus), while all the other described mammal-parasitizing species (G. muris, G. microti and G. intestinalis) each infect multiple hosts. Cross-transmission studies further demonstrated the apparent host specificity of G. cricetidarum n. sp. as it only infected hamsters. Trophozoites were found in high numbers in hamster intestines (5 × 105 - 5 × 106) and was rarely detected co-infecting with other Giardia spp. in the common hamster, suggesting it has some advantages in parasitizing hamsters. CONCLUSIONS: This study has identified a new species of Giardia, which appears to be specific to hamsters, and together with the three other mammal-parasitizing Giardia species with different host ranges, may be able to be used as a model system for the study of evolutionary divergence of host parasitism strategies in Giardia.

Sense-antisense gene overlap is probably a cause for retaining the few introns in Giardia genome and the implications.

BACKGROUND: It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive. Actually the reverse question -- how the few introns can be retained under the evolutionary selection pressure of intron loss -- is equally significant but was rarely studied, except that it was conjectured that the essential functions of some introns prevent their loss. The situation that extremely few (eight) spliceosome-mediated cis-spliced introns present in the relatively simple genome of Giardia lamblia provides an excellent opportunity to explore this question. RESULTS: Our investigation found three types of distribution patterns of the few introns in the intron-containing genes: ancient intron in ancient gene, later-evolved intron in ancient gene, and later-evolved intron in later-evolved gene, which can reflect to some extent the dynamic evolution of introns in Giardia. Without finding any special features or functional importance of these introns responsible for their retention, we noticed and experimentally verified that some intron-containing genes form sense-antisense gene pairs with transcribable genes on their complementary strands, and that the introns just reside in the overlapping regions. CONCLUSIONS: In Giardia's evolution, despite constant evolutionary selection pressure of intron loss, intron gain can still occur in both ancient and later-evolved genes, but only a few introns are retained; at least the evolutionary retention of some of the introns might not be due to the functional constraint of the introns themselves but the causes outside of introns, such as the constraints imposed by other genomic functional elements overlapping with the introns. These findings can not only provide some clues to find new genomic functional elements -- in the areas overlapping with introns, but suggest that "functional constraint" of introns may not be necessarily directly associated with intron loss and gain, and that the real functions are probably still outside of our current knowledge. REVIEWERS: This article was reviewed by Mikhail Gelfand, Michael Gray, and Igor Rogozin.

Giardia's primitive GPL biosynthesis pathways with parasitic adaptation 'patches': implications for Giardia's evolutionary history and for finding targets against Giardiasis.

Giardia is a worldwide spread protozoan parasite colonizing in small intestines of vertebrates, causing Giardiasis. The controversy about whether it is an extremely primitive eukaryote or just a highly evolved parasite has become a fetter to its uses as a model for both evolutionary and parasitological studies for years. Glycerophospholipid (GPL) synthesis is a conserved essential cellular process, and thus may retain some original features reflecting its evolutionary position, and this process should also have undergone parasitic adaptation to suit Giardia's dietary lipid-rich environment. Thus, GPL synthesis pathways may be a perfect object to examine the controversy over Giardia. Here, we first clarified Giardia's previously confusing GPL synthesis by re-identifying a reliable set of GPL synthesis genes/enzymes. Then using phylogenetic and comparative genomic analyses, we revealed that these pathways turn out to be evolutionarily primitive ones, but with many secondary parasitic adaptation 'patches' including gene loss, rapid evolution, product relocation, and horizontal gene transfer. Therefore, modern Giardia should be a mosaic of 'primary primitivity' and 'secondary parasitic adaptability', and to make a distinction between the two categories of features would restart the studies of eukaryotic evolution and parasitic adaptation using Giardia as a model system.

DAT1 methylation is associated with methylphenidate response on oppositional and hyperactive-impulsive symptoms in children and adolescents with ADHD.

OBJECTIVES: To examine the association of the DNA methylation of DAT1 and DRD4 gene with methylphenidate (MPH) response in attention deficit hyperactivity disorder (ADHD). METHODS: One hundred and eleven DSM-IV defined ADHD Chinese Han children were recruited. Inattention, hyperactivity-impulsivity and oppositional symptoms were evaluated by the Swanson, Nolan and Pelham-IV-parent rating scale (SNAP-IV-P) at baseline and 6 weeks after MPH treatment. DNA methylation of CpG sites in the promoter sequences of DAT1 and DRD4 was examined for association with treatment response. RESULTS: Greater improvement on the SNAP-IV-P total score and percentage change from baseline score were both significantly correlated with DAT1 methylation (rho =-0.222, P = .019 and rho = -0.203, P = .032, respectively). A secondary analysis demonstrated that the effect of DAT1 methylation on symptom response was primarily related to the percentage change in oppositional symptoms (rho = -0.242; P = .012), with a smaller significant effect on hyperactivity-impulsivity (rho = -0.192; P = .045). No significant correlation was found between the treatment effect on inattention and DAT1 methylation (rho = -0.101; P = .292). No significant correlation was observed between mean DRD4 methylation and measures of treatment outcome or baseline symptoms. CONCLUSIONS: Our findings provide initial evidence for the involvement of the epigenetic alterations of DAT1 in modulating the response to MPH treatment in ADHD, primarily on oppositional and hyperactive-impulsive symptoms.

Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals.

Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.

Risk miRNA screening of ovarian cancer based on miRNA functional synergistic network.

BACKGROUND: miRNAs are proved to have causal roles in tumorgenesis involving various types of human cancers, but the mechanism is not clear. We aimed to explore the effect of miRNAs on the development of ovarian cancer and the underlying mechanism. METHODS: The miRNA expression profile GSE31801 was downloaded from GEO (Gene Expression Omnibus) database. Firstly, the differentially expressed miRNAs were screened. Target genes of the miRNAs were collected from TargetScan, PicTar, miRanda, and DIANA-microT database, then the miRNA-miRNA co-regulating network was constructed using miRNA pairs with common regulated target genes. Next, the functional modules in the network were studied, the miRNA pairs regulated at least one modules were enriched to form the miRNA functional synergistic network (MFSN). RESULTS: Risk miRNA were selected in MFSN according to the topological structure. Transcript factors (TFs) in MFSN were identified, followed by the miRNA-transcript factor networks construction. Totally, 42 up- and 61 down-regulated differentially expressed miRNAs were identified, of which 68 formed 2292 miRNA pairs in the miRNA-miRNA co-regulating network. GO: 0007268 (synaptic transmission) and GO: 0019226 (transmission of nerve impulse) were the two common functions of miRNAs in MFSN, and hsa-miR-579 (36), hsa-miR-942 (31), hsa-miR-105 (31), hsa-miR-150 (34), and hsa-miR-27a* (32) were selected as the hub nodes in MFSN. CONCLUSIONS: In all, 17 TFs, including CREM, ERG, and CREB1 were screened as the cancer related TFs in MFSN. Other TFs, such as BIN1, FOXN3, FOXK1, FOXP2, and ESRRG with high degrees may be inhibited in ovarian cancer. MFSN gave us a new shed light on the mechanism studies in ovarian cancer.

Gene-gene interaction network analysis of ovarian cancer using TCGA data.

BACKGROUND: The Cancer Genome Atlas (TCGA) Data portal provides a platform for researchers to search, download, and analysis data generated by TCGA. The objective of this study was to explore the molecular mechanism of ovarian cancer pathogenesis. METHODS: Microarray data of ovarian cancer were downloaded from TCGA database, and Limma package in R language was used to identify the differentially expressed genes (DEGs) between ovarian cancer and normal samples, followed by the function and pathway annotations of the DEGs. Next, NetBox software was used to for the gene-gene interaction (GGI) network construction and the corresponding modules identification, and functions of genes in the modules were screened using DAVID. RESULTS: Our studies identified 332 DEGs, including 146 up-regulated genes which mainly involved in the cell cycle related functions and cell cycle pathway, and 186 down-regulated genes which were enriched in extracellular region par function, and Ether lipid metabolism pathway. GGI network was constructed by 127 DEGs and their significantly interacted 209 genes (LINKERs). In the top 10 nodes ranked by degrees in the network, 5 were LINKERs. Totally, 7 functional modules in the network were selected, and they were enriched in different functions and pathways, such as mitosis process, DNA replication and DNA double-strand synthesis, lipid synthesis processes and metabolic pathways. AR, BRCA1, TFDP1, FOXM1, CDK2, and DBF4 were identified as the transcript factors of the 7 modules. CONCLUSION: our data provides a comprehensive bioinformatics analysis of genes, functions, and pathways which may be involved in the pathogenesis of ovarian cancer.

Electrochemical etching of gold within nanoshaved self-assembled monolayers.

Wet etching of metal substrates with patterned self-assembled monolayers (SAMs) is an inexpensive and convenient method to produce metal nanostructures. For this method to be relevant to the fabrication of high precision plasmonic structures, the kinetics of nanoscale etching process, particularly in the lateral direction, must be elucidated and controlled. We herein describe an in situ atomic force microscopy (AFM) study to characterize the etching process within patterned SAMs with nanometer resolution and in real time. The in situ study was enabled by several unique elements, including single crystalline substrates to minimize the variability of facet-dependent etch rate, high-resolution nanoshaved SAM patterns, electrochemical-potential-controlled etching, and AFM kymographs to improve temporal resolution. Our approach has successfully quantified the extent of both lateral etching and vertical etching at different potentials. Our study reveals the presence of an induction period prior to the onset of significant lateral etching, which would be difficult to observe with the limited time resolution and sample-to-sample variation of ex situ studies. By increasing the vertical etch rate during this induction period with higher potentials, gold was etched up to 40 nm in the vertical direction with minimal lateral etching. High-resolution etching was also demonstrated on single crystal gold microplates, which are high quality gold thin films suitable for plasmonics studies.

Nanografting sodium dodecyl sulfate under potential control: new insights into tip-directed molecular assembly.

We have demonstrated that under potential control, sodium dodecyl sulfate can form ordered and stable patterns within nanoscale regions of a pre-existing SAM where thiol molecules have been mechanically removed. The results offer novel insights into the mechanism of nanografting and new routes to fabricating diverse chemical structures on surfaces.

High-density gold nanowire arrays by lithographically patterned nanowire electrodeposition.

Here we describe a new method for preparing multiple arrays of parallel gold nanowires with dimensions and separation down to 50 nm. This method uses photolithography to prepare an electrode consisting of a patterned nickel film on glass, onto which a gold and nickel nanowire array is sequentially electrodeposited. After the electrodeposition, the nickel is stripped away, leaving behind a gold nanowire array, with dimensions governed by the gold electrodeposition parameters, spacing determined by the nickel electrodeposition parameters, and overall placement and shape dictated by the photolithography.

Polymorphisms in PPARD, PPARG and APM1 associated with four types of traditional Chinese medicine constitutions.

Based on the theory of constitution of Traditional Chinese Medicine (TCM), the human population is divided into nine constitutions including one balanced constitution (Normality) and eight unbalanced constitutions (Yang-deficiency, Yin-deficiency, Phlegm-wetness, Qi-deficiency, Wetness-heat, Blood stasis, Depressed constitution, and Inherited special constitution). Different constitutions have specific metabolic features and different susceptibility to certain diseases. However, whether a genetic basis accounts for such constitution classification is yet to be determined. Here we performed a genetic study to assess the association between genetic variations of metabolic genes including PPARD, PPARG and APM1 and the constitutions. A total of 233 individuals of the Han population in China were classified into four groups, Normality, Yang-deficiency, Yin-deficiency and Phlegm-wetness with whom 23 single nucleotide polymorphisms (SNPs) in the three genes were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Biased distribution of PPARD rs2267669 and rs2076167, APM1 rs7627128 and rs1063539 in Yang-deficiency, PPARG Pro12Ala in Yin-deficiency and PPARD rs2076167, APM1 rs266729 and rs7627128 in Phlegm-wetness were observed. The frequencies of Haplotype13 (Hap13) of PPARG in Yin-deficiency, Hap25 of APM1 in Yang-deficiency and Hap2 of PPARD and Hap14 of PPARG in Phlegm-wetness, were significantly different from those in Normality, suggesting those might be group-associated haplotypes. These results suggested that single SNP and haplotypes of PPARD, PPARG and APM1 may underlie the genetic basis of the constitutions classified in TCM.

Lack of association of TLR4 gene Asp299Gly and Thr399Ile polymorphisms with rheumatoid arthritis in Chinese Han population of Yunnan Province.

Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of synovium and subsequent joint destruction. Recently, genetic polymorphisms within the toll-like receptor 4 (TLR4) genes have been reported to be associated with RA. To analyze the association between the genetic polymorphisms within TLR4 gene and the susceptibility to RA in Chinese people, two functional variants, Asp299Gly and Thr399Ile, in the TLR4 gene were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing techniques from 213 RA patients and 247 ethnically matched controls. None polymorphisms of Asp299Gly and Thr399Ile were detected in all RA cases and controls, which indicates that there is no relevance between these two SNPs and RA in the Chinese Han population. Further studies with extended single nucleotide polymorphisms (SNP) should be performed.