Ligase-based multiple DNA analysis by using an electrochemical sensor array

We herein report an electrochemical biosensor for the sequence-specific detection of DNA with high discrimination ability for single-nucleotide polymorphisms (SNPs). This DNA sensor was constructed by a pair of flanking probes that "sandwiched" the target. A 16-electrode electrochemical sensor array was employed, each having one individual DNA capture probe immobilized at gold electrodes via gold-thiol chemistry. By coupling with a biotin-tagged detection probe, we were able to detect multiple DNA targets with a single array. In order to realize SNP detection, a ligase-based approach was employed. In this method, both the capture probe and the detection probe were in tandem upon being hybridized with the target. Importantly, we employed a ligase that specifically could ligate tandem sequences only in the absence of mismatches. As a result, when both probes were complementary to the target, they were ligated in the presence of the ligase, thus being retained at the surface during the subsequent stringent washing steps. In contrast, if there existed 1-base mismatch, which could be efficiently recognized by the ligase, the detection probe was not ligated and subsequently washed away. A conjugate of avidin-horseradish peroxidase was then attached to the biotin label at the end of the detection probe via the biotin-avidin bridge. We then electrochemically interrogated the electrical current for the peroxidase-catalyzed reduction of hydrogen peroxide. We demonstrated that the electrochemical signal for the wild-type DNA was significantly larger than that for the sequence harboring the SNP.     

Health-promoting effects of bovine colostrum in Type 2 diabetic patients can reduce blood glucose, cholesterol, triglyceride and ketones

Bovine colostrum (BC) has been reported to enhance immune function, reduce fat accumulation and facilitate the movement of glucose to the muscle. However, very few attempts have been made to examine its anti-diabetic effects in diabetes patients. The aim of this study was to evaluate whether BC decreases blood glucose, as well as cholesterol, triglyceride (TG) and ketones levels, which can be elevated by obesity and stress in Type 2 diabetic patients. Sixteen patients (men=8, women=8) with Type 2 diabetes were randomized into the study. Each ingested 5 g of BC on an empty stomach every morning and night for 4 weeks. Blood glucose, ketones (beta-hydroxybutyric acid), total cholesterol and TGs were measured every week. In both the men and women, blood glucose levels at 2 and 8 h postprandial decreased continually during the experimental period. The rate of decrease in blood glucose at 8 h postprandial was not different between the men and women, but was higher in the women (14.25+/-2.66) than in the men (10.96+/-1.82%) at 2 h postprandial. Total cholesterol and TG levels decreased significantly in both the men and women after 4 weeks. Also, beta-hydroxybutyric acid level decreased with BC ingestion, but this was not significant. These results suggest that BC can decrease levels of blood glucose and ketones, as well as reduce cholesterol and TGs, all of which may cause complications in Type 2 diabetic patients.     

Elucidation of the stability and functional regions of the human coronavirus OC43 nucleocapsid protein

Human coronavirus OC43 (HCoV‐OC43) is one of the causes of the “common cold” in human during seasons of cold weather. The primary function of the HCoV‐OC43 nucleocapsid protein (N protein) is to recognize viral genomic RNA, which leads to ribonucleocapsid formation. Here, we characterized the stability and identified the functional regions of the recombinant HCoV‐OC43 N protein. Circular dichroism and fluorescence measurements revealed that the HCoV‐OC43 N protein is more highly ordered and stabler than the SARS‐CoV N protein previously studied. Surface plasmon resonance (SPR) experiments showed that the affinity of HCoV‐OC43 N protein for RNA was approximately fivefold higher than that of N protein for DNA. Moreover, we found that the HCoV‐OC43 N protein contains three RNA‐binding regions in its N‐terminal region (residues 1–173) and central‐linker region (residues 174–232 and 233–300). The binding affinities of the truncated N proteins and RNA follow the order: residues 1–173–residues 233–300 > residues 174–232. SPR experiments demonstrated that the C‐terminal region (residues 301–448) of HCoV‐OC43 N protein lacks RNA‐binding activity, while crosslinking and gel filtration analyses revealed that the C‐terminal region is mainly involved in the oligomerization of the HCoV‐OC43 N protein. This study may benefit the understanding of the mechanism of HCoV‐OC43 nucleocapsid formation.     

Ethylene and nitric oxide are involved in maintaining ion homeostasis in <Emphasis Type="Italic">Arabidopsis</Emphasis> callus under salt stress

In the present study, the role of ethylene in nitric oxide (NO)-mediated protection by modulating ion homeostasis in Arabidopsis callus under salt stress was investigated. Results showed that the ethylene-insensitive mutant etr1-3 was more sensitive to salt stress than the wild type (WT). Under 100 mM NaCl, etr1-3 callus displayed a greater electrolyte leakage and Na⁺/K⁺ ratio but a lower plasma membrane (PM) H⁺-ATPase activity compared to WT callus. Application of exogenous 1-aminocyclopropane-1-carboxylic acid (ACC, an ethylene precursor) or sodium nitroprusside (SNP, a NO donor) alleviated NaCl-induced injury by maintaining a lower Na⁺/K⁺ ratio and an increased PM H⁺-ATPase activity in WT callus but not in etr1-3 callus. The SNP actions in NaCl stress were attenuated by a specific NO scavenger or an ethylene biosynthesis inhibitor in WT callus. Under 100 mM NaCl, the NO accumulation and ethylene emission appeared at early time, and NO production greatly stimulated ethylene emission in WT callus. In addition, ethylene induced the expression of PM H⁺-ATPase genes under salt stress. The recovery experiment showed that NaCl-induced injury was reversible, as signaled by the similar recovery of Na⁺/K⁺ ratio and PM H⁺-ATPase activity in WT callus. Taken together, the results indicate that ethylene and NO cooperate in stimulating PM H⁺-ATPase activity to modulate ion homeostasis for salt tolerance, and ethylene may be a part of the downstream signal molecular in NO action.     

Design of an Insulin Analog with Enhanced Receptor Binding Selectivity: RATIONALE, STRUCTURE, AND THERAPEUTIC IMPLICATIONS*

Insulin binds with high affinity to the insulin receptor (IR) and with low affinity to the type 1 insulin-like growth factor (IGF) receptor (IGFR). Such cross-binding, which reflects homologies within the insulin-IGF signaling system, is of clinical interest in relation to the association between hyperinsulinemia and colorectal cancer. Here, we employ nonstandard mutagenesis to design an insulin analog with enhanced affinity for the IR but reduced affinity for the IGFR. Unnatural amino acids were introduced by chemical synthesis at the N- and C-capping positions of a recognition α-helix (residues A1 and A8). These sites adjoin the hormone-receptor interface as indicated by photocross-linking studies. Specificity is enhanced more than 3-fold on the following: (i) substitution of Gly^A1 by d-Ala or d-Leu, and (ii) substitution of Thr^A8 by diaminobutyric acid (Dab). The crystal structure of [d-Ala^A1,Dab^A8]insulin, as determined within a T₆ zinc hexamer to a resolution of 1.35 Å, is essentially identical to that of human insulin. The nonstandard side chains project into solvent at the edge of a conserved receptor-binding surface shared by insulin and IGF-I. Our results demonstrate that modifications at this edge discriminate between IR and IGFR. Because hyperinsulinemia is typically characterized by a 3-fold increase in integrated postprandial insulin concentrations, we envisage that such insulin analogs may facilitate studies of the initiation and progression of cancer in animal models. Future development of clinical analogs lacking significant IGFR cross-binding may enhance the safety of insulin replacement therapy in patients with type 2 diabetes mellitus at increased risk of colorectal cancer.     

OB Fold-containing Protein 1 (OBFC1), a Human Homolog of Yeast Stn1, Associates with TPP1 and Is Implicated in Telomere Length Regulation

The telosome/shelterin, a six-protein complex formed by TRF1, TRF2, RAP1, TIN2, POT1, and TPP1, functions as the core of the telomere interactome, acting as the molecular platform for the assembly of higher order complexes and coordinating cross-talks between various protein subcomplexes. Within the telosome, there are two oligonucleotide- or oligosaccharide-binding (OB) fold-containing proteins, TPP1 and POT1. They can form heterodimers that bind to the telomeric single-stranded DNA, an activity that is central for telomere end capping and telomerase recruitment. Through proteomic analyses, we found that in addition to POT1, TPP1 can associate with another OB fold-containing protein, OBFC1/AAF44. The yeast homolog of OBFC1 is Stn1, which plays a critical role in telomere regulation. We show here that OBFC1/AAF44 can localize to telomeres in human cells and bind to telomeric single-stranded DNA in vitro. Furthermore, overexpression of an OBFC1 mutant resulted in elongated telomeres in human cells, implicating OBFC1/AAF4 in telomere length regulation. Taken together, our studies suggest that OBFC1/AAF44 represents a new player in the telomere interactome for telomere maintenance.Telomeres are specialized linear chromosome end structures, which are regulated and protected by networks of protein complexes (1–4). Telomere length, structure, and integrity are critical for the cells and the organism as a whole. Telomere dysregulation can lead to DNA damage response, cell cycle checkpoint, genome instability, and predisposition to cancer (5–9). Mammalian telomeres are composed of double-stranded (TTAGGG)_n repeats followed by 3′-single-stranded overhangs (10). In addition to the telomerase that directly mediates the addition of telomere repeats to the end of chromosomes (11, 12), a multitude of telomere-specific proteins have been identified that form the telosome/shelterin complex and participate in telomere maintenance (9, 13). The telosome in turn acts as the platform onto which higher order telomere regulatory complexes may be assembled into the telomere interactome (14). The telomere interactome has been proposed to integrate the complex and labyrinthine network of protein signaling pathways involved in DNA damage response, cell cycle checkpoint, and chromosomal end maintenance and protection for telomere homeostasis and genome stability.Of the six telomeric proteins (TRF1, TRF2, RAP1, TIN2, POT1, and TPP1) that make up the telosome, TRF1 and TRF2 have been shown to bind telomeric double-stranded DNA (15, 16), whereas the OB³ fold-containing protein POT1 exhibits high affinities for telomeric ssDNA in vitro (17, 18). Although the OB fold of TPP1 does not show appreciable ssDNA binding activity, heterodimerization of TPP1 and POT1 enhances the POT1 ssDNA binding (17, 18). More importantly, POT1 depends on TPP1 for telomere recruitment, and the POT1-TPP1 heterodimer functions in telomere end protection and telomerase recruitment. Notably, the OB fold of TPP1 is critical for the recruitment of the telomerase (18). Disruption of POT1-TPP1 interaction by dominant negative inhibition, RNA interference, or gene targeting could lead to dysregulation of telomere length as well DNA damage responses at the telomeres (18–21).In budding yeast, the homolog of mammalian POT1, Cdc13, has been shown to interact with two other OB fold-containing proteins, Stn1 and Ten1, to form a Cdc13-Stn1-Ten1 (CST) complex (22, 23). The CST complex participates in both telomere length control and telomere end capping (22, 23). The presence of multiple OB fold-containing proteins from yeast to human suggests a common theme for telomere ssDNA protection (4). Indeed, it has been proposed that the CST complex is structurally analogous to the replication factor A complex and may in fact function as a telomere-specific replication factor A complex (23). Notably, homologs of the CST complex have been found in other species such as Arabidopsis (24), further supporting the notion that multiple OB fold proteins may be involved in evolutionarily conserved mechanisms for telomere end protection and length regulation. It remains to be determined whether the CST complex exists in mammals.Although the circuitry of interactions among telosome components has been well documented and studied, how core telosome subunits such as TPP1 help to coordinate the cross-talks between telomere-specific signaling pathways and other cellular networks remains unclear. To this end, we carried out large scale immunoprecipitations and mass spectrometry analysis of the TPP1 protein complexes in mammalian cells. Through these studies, we identified OB fold-containing protein 1 (OBFC1) as a new TPP1-associated protein. OBFC1 is also known as α-accessory factor AAF44 (36). Sequence alignment analysis indicates that OBFC1 is a homolog of the yeast Stn1 protein (25). Further biochemical and cellular studies demonstrate the association of OBFC1 with TPP1 in live cells. Moreover, we showed that OBFC1 bound to telomeric ssDNA and localized to telomeres in mammalian cells. Dominant expression of an OBFC1 mutant led to telomere length dysregulation, indicating that OBFC1 is a novel telomere-associated OB fold protein functioning in telomere length regulation.     

The Class II Phosphatidylinositol 3 kinase C2β Is Required for the Activation of the K+ Channel KCa3.1 and CD4 T-Cells

The Ca²⁺-activated K⁺ channel KCa3.1 is required for Ca²⁺ influx and the subsequent activation of T-cells. We previously showed that nucleoside diphosphate kinase beta (NDPK-B), a mammalian histidine kinase, directly phosphorylates and activates KCa3.1 and is required for the activation of human CD4 T lymphocytes. We now show that the class II phosphatidylinositol 3 kinase C2β (PI3K-C2β) is activated by the T-cell receptor (TCR) and functions upstream of NDPK-B to activate KCa3.1 channel activity. Decreased expression of PI3K-C2β by siRNA in human CD4 T-cells resulted in inhibition of KCa3.1 channel activity. The inhibition was due to decreased phosphatidylinositol 3-phosphate [PI(3)P] because dialyzing PI3K-C2β siRNA-treated T-cells with PI(3)P rescued KCa3.1 channel activity. Moreover, overexpression of PI3K-C2β in KCa3.1-transfected Jurkat T-cells led to increased TCR-stimulated activation of KCa3.1 and Ca²⁺ influx, whereas silencing of PI3K-C2β inhibited both responses. Using total internal reflection fluorescence microscopy and planar lipid bilayers, we found that PI3K-C2β colocalized with Zap70 and the TCR in peripheral microclusters in the immunological synapse. This is the first demonstration that a class II PI3K plays a critical role in T-cell activation.     

Cdh1 Regulates Cell Cycle through Modulating the Claspin/Chk1 and the Rb/E2F1 Pathways

APC/Cdh1 is a major cell cycle regulator and its function has been implicated in DNA damage repair; however, its exact role remains unclear. Using affinity purification coupled with mass spectrometry, we identified Claspin as a novel Cdh1-interacting protein and further demonstrated that Claspin is a novel Cdh1 ubiquitin substrate. As a result, inactivation of Cdh1 leads to activation of the Claspin/Chk1 pathway. Previously, we demonstrated that Rb interacts with Cdh1 to influence its ability to degrade Skp2. Here, we report that Cdh1 reciprocally regulates the Rb pathway through competing with E2F1 to bind the hypophosphorylated form of Rb. Although inactivation of Cdh1 in HeLa cells, with defective p53/Rb pathways, led to premature S phase entry, acute depletion of Cdh1 in primary human fibroblasts resulted in premature senescence. Acute loss of many other major tumor suppressors, including PTEN and VHL, also induces premature senescence in a p53- or Rb-dependent manner. Similarly, we showed that inactivation of the p53/Rb pathways by overexpression of SV40 LT-antigen partially reversed Cdh1 depletion–induced growth arrest. Therefore, loss of Cdh1 is only beneficial to cells with abnormal p53 and Rb pathways, which helps explain why Cdh1 loss is not frequently found in many tumors.     

Effect of monoclonal antibody on expression of lipid metabolism related genes in porcine adipocytes

In order to study the mechanism of monoclonal antibody (McAb) against a porcine 40-kDa adipocyte-specific plasma membrane protein in reducing fat deposition, porcine primary adipocytes were treated with the McAb during the process of adipocyte differentiation; its effect on expression of lipid metabolism related genes was investigated. Adipocytes were treated with 1-methyl-3-isobutylmethylxanthine (IDX) plus 10 μg/mL of the McAb or without McAb. The mRNA levels of adipocyte differentiation related genes (PPARγ and C/EBPα), lipid metabolism related genes (FAS, HSL, CPT-1B, DGAT and A-FABP) and adiponectin gene (AdipoQ) were determined using real-time quantitative PCR. The results showed that the differentiated adipocyte number and triglyceride (TG) content in adipocytes treated with the McAb were lower than that in cells without McAb during the whole process of adipocyte differentiation. The McAb significantly reduced mRNA expression of PPARγ, C/EBPα, FAS, DGAT, A-FABP and adiponectin genes, but increased mRNA expression of HSL and CPT-1B genes during the medium and latter stage of adipocyte differentiation. This suggested that the McAb decreased triglycerol accumulation in adipocyte by both inhibiting adipocyte differentiation and regulating lipid metabolism, especially at the medium and latter stage of porcine adipocyte differentiation.     

The Structural Adaptation of Aerial Parts of Invasive <Emphasis Type="Italic">Alternanthera philoxeroides</Emphasis> to Water Regime

Alternanthera philoxeroides has successfully invaded diverse habitats with considerably various water availability, threatening biological diversity in many parts of the world. Because its genetic variation is very low, phenotypic plasticity is believed to be the primary strategy for adapting to the diverse habitats. In the present paper, we investigated the plastic changes of anatomical traits of the aerial parts of A. philoxeroides from flooding to wet then to drought habitat; the results are as follows: A. philoxeroides could change anatomical structures sensitively to adapt to water regime. As a whole, effects of water regime on structures in stem were greater than those in leaf. Except for principal vein diameter and stoma density on leaf surfaces, all other structural traits were significantly affected by water regime. Among which, cuticular wax layer, collenchyma cell wall, phloem fiber cell wall, and hair density on both leaf surfaces thickened significantly with decrease of water availability, whereas, pith cavity and vessel lumen in stem lessened significantly; wet habitat is vital for the spread of A. philoxeroides from flooding to drought habitat and vice versa, because in this habitat, it had the greatest structural variations; when switching from flooding to wet then to drought habitat, the variations of cuticular wax layer, collenchyma cell wall, phloem fiber cell wall, pith cavity area ratio, diameter of vessel lumen, and hair density on both leaf surfaces, played the most important role. These responsive variables contribute most to the adaptation of A. philoxeroides to diverse habitats with considerably various water availability.