Ajoene, a Major Organosulfide Found in Crushed Garlic, Induces NAD(P)H:quinone Oxidoreductase Expression Through Nuclear Factor E2-related Factor-2 Activation in Human Breast Epithelial Cells

BACKGROUND: NAD(P)H:quinone oxidoreductase-1 (NQO1) is a widely-distributed flavin adenine dinucleotide-dependent flavoprotein that promotes obligatory 2-electron reductions of quinones, quinoneimines, nitroaromatics, and azo dyes. This reduces quinone levels and thereby minimizes generation of excess reactive oxygen species (ROS) formed by redox cycling, and concurrent depletion of intracellular thiol pools. Ajoene is derived from crushed garlic. It is formed by a reaction involving two allicin molecules, and is composed of allyl sulfide and vinyl disulfide. Ajoene is present in two isomers, E- and Z-form. METHODS: Expression of antioxidant enzymes and nuclear factor E2-related factor-2 (Nrf2) was measured by Western blot analysis. NQO1 promoter activity was assessed by the luciferase reporter gene assay. ROS accumulation was monitored by using the fluorescence-generating probe 2′,7′-dichlorofluorescein diacetate. The intracellular glutathione levels were measured by using a commercially available kit. RESULTS: Z-ajoene significantly up-regulated the expression of representative antioxidant enzyme NQO1 in non-tumorigenic breast epithelial MCF-10A cells at non-toxic concentrations. Z-ajoene enhanced up-regulation and nuclear translocation of Nrf2, which plays a pivotal role in the induction of many genes encoding antioxidant enzymes and other cytoprotective proteins. Z-ajoene treatment also increased the activity of nqo1-promoter harboring antioxidant response element consensus sequences in MCF-10A cells. Silencing of Nrf2 by small interfering RNA abrogated ajoene-induced expression of NQO1. Z-ajoene activated extracellular signal-regulated kinase (ERK). Inhibition of ERK activation by U0126 abrogated ability of Z-ajoene to activate Nrf2 and to induce NQO1 expression. Intracellular ROS accumulation was observed after treatment with Z-ajoene, whereas the E-isoform was not effective. The inhibition of ROS by treatment with N-acetylcysteine, a radical scavenger, abrogated Z-ajoene-induced expression of NQO1 as well as activation of ERK and Nrf2, suggesting that Z-ajoene augments the Nrf2-dependent antioxidant defense via ROS generation and ERK activation. CONCLUSIONS: Z-ajoene induces NQO1 expression in MCF-10A cells through ROS-mediated activation of Nrf2.

The Different Expression Patterns of HSP22, a Late Embryogenesis Abundant-like Protein, in Hypertrophic H9C2 Cells Induced by NaCl and Angiotensin II

BACKGROUND: High-NaCl diet is a contributing factor for cardiac hypertrophy. The role of HSP22 as a protective protein during cardiac hypertrophy due to hypernatremia is unclear. Accordingly, this study aimed to establish a cellular hypernatremic H9C2 model and to compare the expression of HSP22 in Ca2+ homeostasis between a high-NaCl and angiotensin II-induced hypertrophic cellular H9C2 model. METHODS: Real-time PCR was performed to compare the mRNA expression. Flow cytometry and confocal microscopy were used to analyze the cells. RESULTS: The addition of 30 mM NaCl for 48 h was the most effective condition for the induction of hypertrophic H9C2 cells (termed the in vitro hypernatremic model). Cardiac cellular hypertrophy was induced with 30 mM NaCl and 1 µM angiotensin II for 48 h, without causing abnormal morphological changes or cytotoxicity of the culture conditions. HSP22 contains a similar domain to that found in the consensus sequences of the late embryogenesis abundant protein group 3 from Artemia. The expression of HSP22 gradually decreased in the in vitro hypernatremic model. In contrast to the in vitro hypernatremic model, HSP22 increased after exposure to angiotensin II for 48 h. Intracellular Ca2+ decreased in the angiotensin II model and further decreased in the in vitro hypernatremic model. Impaired intracellular Ca2+ homeostasis was more evident in the in vitro hypernatremic model. CONCLUSION: The results showed that NaCl significantly decreased HSP22. Decreased HSP22, due to the hypernatremic condition, affected the Ca2+ homeostasis in the H9C2 cells. Therefore, hypernatremia induces cellular hypertrophy via impaired Ca2+ homeostasis. The additional mechanisms of HSP22 need to be explored further.

N-glycoproteomic analysis of human follicular fluid during natural and stimulated cycles in patients undergoing in vitro fertilization / 대한생식의학회지

OBJECTIVE: Hyperstimulation methods are broadly used for in vitro fertilization (IVF) in patients with infertility; however, the side effects associated with these therapies, such as ovarian hyperstimulation syndrome (OHSS), have not been well studied. N-glycoproteomes are subproteomes used for the remote sensing of ovarian stimulation in follicular growth. Glycoproteomic variation in human follicular fluid (hFF) has not been evaluated. In this study, we aimed to identify and quantify the glycoproteomes and N-glycoproteins (N-GPs) in natural and stimulated hFF using label-free nano-liquid chromatography/electrospray ionization-quad time-of-flight mass spectrometry. METHODS: For profiling of the total proteome and glycoproteome, pooled protein samples from natural and stimulated hFF samples were selectively isolated using hydrazide chemistry to obtain the total proteomes and glycoproteomes. N-GPs were validated by the consensus sequence N-X-S/T (92.2% specificity for the N-glycomotif at p<0.05). All data were compared between natural versus hyperstimulated hFF samples. RESULTS: We detected 41 and 44 N-GPs in the natural and stimulated hFF samples, respectively. Importantly, we identified 11 N-GPs with greater than two-fold upregulation in stimulated hFF samples compared to natural hFF samples. We also validated the novel N-GPs thyroxine-binding globulin, vitamin D-binding protein, and complement proteins C3 and C9. CONCLUSION: We identified and classified N-GPs in hFF to improve our understanding of follicular physiology in patients requiring assisted reproduction. Our results provided important insights into the prevention of hyperstimulation side effects, such as OHSS.

Molecular identification of Saint Louis encephalitis virus genotype IV in Colombia

Saint Louis encephalitis virus (SLEV) is a member of the Japanese-encephalitis virus serocomplex of the genus Flavivirus. SLEV is broadly distributed in the Americas and the Caribbean Islands, where it is usually transmitted by mosquitoes of the genus Culex and primarily to birds and mammalian-hosts. Humans are occasionally infected by the virus and are dead-end hosts. SLEV causes encephalitis in temperate regions, while in tropical regions of the Americas, several human cases and a wide biological diversity of SLEV-strains have been reported. The phylogenetic analysis of the envelope (E) protein genes indicated eight-genotypes of SLEV with geographic overlap. The present paper describes the genotyping of two SLEV viruses detected in mosquito-pools collected in northern Colombia (department of Cordoba). We used reverse transcription-polymerase chain reaction to amplify a fragment of theE-gene to confirm the virus identity and completeE-gene sequencing for phylogenetic analysis and genotyping of the two-SLEV viruses found circulating in Córdoba. This is the first report of SLEV genotype IV in Colombia (Córdoba) in mosquitoes from a region of human inhabitation, implicating the risk of human disease due to SLEV infection. Physicians should consider SLEV as a possible aetiology for undiagnosed febrile and neurologic syndromes among their patients who report exposure to mosquito-bites.

In silico genome-wide screening for TnrA-regulated genes of Bacillus clausii

Bacillus clausii TnrA transcription factor is required for global nitrogen regulation. In order to obtain an overview of gene regulation by TnrA in B. clausii KSM-K16, the entire genome of B. clausii was screened for the consensus sequence, 5'-TGTNAN7TNACA-3' known as the TnrA box, and 13 transcription units were found containing a putative TnrA box. The TnrA targets identified in this study were tnrA, glnA, nrgA, nasFDEB, puc genes, licT, the two operons of the oligopeptide ABC transporter, lytR, transcriptional regulator of the Lrp/AsnC family, sodium-dependent transporter of SNF family, hyu genes and a biochemically uncharacterized protein

An examination of the OMIM database for associating mutation to a consensus reference sequence

Gene mutation (e.g. substitution, insertion and deletion) and related phenotype information are important biomedical knowledge. Many biomedical databases (e.g. OMIM) incorporate such data. However, few studies have examined the quality of this data. In the current study, we examined the quality of protein single-point mutations in the OMIM and identified whether the corresponding reference sequences align with the mutation positions. Our results show that close to 20% of mutation data cannot be mapped to a single reference sequence. The failed mappings are caused by position conflict, site shifting (peptide, N-terminal methionine) and other types of data error. We propose a preliminary model to resolve such inconsistency in the OMIM database.

Molecular characterizations of phosphoprotein of rabies virus circulating in Korea / 대한수의학회지

Rabies is a major zoonotic disease that causes approximately 55,000 human deaths worldwide on an annual basis. The nucleocapsid protein and glycoprotein genes of the Korean rabies virus (RABV) have been subjected to molecular and phylogenetic analyses. Although the phosphoprotein (P) has several important functions in viral infection and pathogenicity, the genetic characterizations of the P of Korean RABV isolates have not yet been established. In the present study, we conducted genetic analyses of P genes of 24 RABV isolates circulating in the Republic of Korea (hereafter, Korea) from 2008 to 2011. This study revealed that the P genes of Korean RABVs are genetically similar to those of RABV strains of lyssavirus genotype I including V739 (dogs, Korea), NNV-RAB-H (humans, India), NeiMeng925 (raccoon dogs, China), and RU9.RD (raccoon dogs, Russia). Among Korean isolates, the RABV P genes showed low variability in the variable domains among Korean isolates; they had specific consensus sequences and amino acid substitutions capable of identifying geographic characteristics and retained specific sequences thought to be important for viral function. These results provide important genetic characteristics and epidemiological information pertaining to the P gene of the Korean RABV.

Comparative analysis of three methods for HPV DNA detection in cervical samples / Análisis comparativo de tres métodos para la detección del ADN de VPH en muestras de cuello uterino

High risk HPV infection is considered to play a central role in cervical carcinogenesis. HPV DNA testing has shown to be a very useful tool for screening and following cervical infections. The aim of this study was to compare three methods for HPV DNA detection, along with cytology and colposcopy analysis. Cervical samples were collected from 100 sexually active women in Mérida, western Venezuela. HPV infection was screened using Hybrid-Capture 2 (HC2), L1-Nested-PCR and E6/E7-PCR assays. 40% of the samples (40/100) were HPV positive by at least one of the DNA detection methods. HC2 detected HPV in 12% specimens. L1- and E6/E7-PCRs showed 50% sensitivity and 77% specificity.The agreement rate between HC2 and both PCR assays was 65%. Kappa value showed moderate concordance between HC2 and both PCR methods (κ=0.55; CI 95%). Also moderate concordance was seen when L1- and E6/E7-PCRs were compared (κ=0.48; CI 95%). There was a significant association between the Schiller test and E6/E7-PCR (p=0.006) for HPV infection. An acceptable agreement between all three assays for HPV detection was observed. Nevertheless, different PCR formats need to be further analyzed in order to make the right choice of method for HPV testing.

La infección con VPH de alto riesgo es el principal factor etiológico asociado al desarrollo de carcinogénesis cervical y las pruebas de detección de ADN-VPH han mostrado ser una herramienta esencial para la pesquisa y seguimiento de estas infecciones. El objetivo del estudio ha sido comparar tres métodos para la detección del ADN viral, en combinación con los análisis colposcópico y citológico. Se obtuvieron muestras cervicales de 100 mujeres sexualmente activas, en Mérida, Venezuela. La detección de infecciones por VPH se realizó por Captura Híbrida 2 (CH2) y los ensayos de PCR “L1-Nested-PCR” y “E6/E7-PCR”. 40% de las muestras (40/100) fueron positivas para VPH por al menos uno de los métodos aplicados. 12% de las muestras analizadas fueron positivas para VPH por CH2. Las dos PCR utilizadas mostraron un 50% de sensibilidad y 77% de especificidad. La coincidencia observada entre CH2 y las dos PCR fue del 65%. La determinación del valor Kappa mostró una concordancia moderada entre CH2 y ambos métodos de PCR (κ=0,55; CI 95%). También existió concordancia moderada al comparar las PCR de las regiones L1 y E6/E7 de VPH (κ=0,48; CI 95%). Hubo una asociación significativa entre el resultado del test de Schiller y la PCR E6/E7 (p=0,006) para la infección por VPH. Se determinó una concordancia aceptable entre los tres métodos aplicados para la detección de VPH; sin embargo, las PCR deben ser analizadas en trabajos futuros con el fin de establecer las pruebas más adecuadas para la detección viral.

Structural shifts of gut flora in rat acute alcoholic liver injury and jianpi huoxue decoction's effect displayed by ERIC-PCR fingerprint / 中国结合医学杂志

<p><b>OBJECTIVE</b>To study the structural shifts of gut flora in rats with acute alcoholic liver injury (AALI), and the effect of jianpi huoxue decoction (JPHXD) on the gut flora.</p><p><b>METHODS</b>Thirty-six Sprague-Dawley rats were randomly allocated to the control, AALI and JPHXD groups equally. The rats in the control group were given water and those in AALI and JPHXD groups were given ethanol by intragastric gavage for 5 days, while rats in the JPHXD group were administered JPHXD simultaneously. The blood and liver tissue were collected at the end of the experiment. The activities of serum alkaline aminotransferase (ALT), aspartate aminotransferase (AST), hepatic γ-glutamyltranspetidase (γ-GT) and hepatic triglyceride (TG) levels were determined. Plasma endotoxin level in the portal vein was measured. Pathological changes of liver tissues were determined by hematoxylin and eosin (HE) staining and oil red O staining. The total DNA of gut flora were extracted from fecal samples by Bead-beating method and determined by ERIC-PCR fingerprint method. The similarity cluster analysis and principal component analysis were performed to analyze the ERIC-PCR fingerprint respectively.</p><p><b>RESULTS</b>In the AALI group, the ratio of liver/body weight, activities of ALT, AST and hepatic γ-GT, amount of hepatic TG were elevated significantly compared with those in the control group (all P<0.01). JPHXD decreased the ratio, activities of ALT, AST, γ-GT and TG significantly compared with those in the AALI group (P<0.05 or P<0.01). HE and oil red O staining showed that fat deposited markedly in liver tissue, while JPHXD alleviated pathological changes markedly. Plasma LPS level in rat portal vein in the AALI group increased significantly (P<0.01), but it was decreased significantly in the JPHXD group (P<0.01). The cluster analysis and principal component analysis of ERIC-PCR fingerprint showed that gut flora in the AALI group changed markedly, and JPHXD could recover gut flora to some extent.</p><p><b>CONCLUSIONS</b>The structure of gut flora shifted markedly during acute alcoholic liver injury, JPHXD had prevention effect through the modification of gut flora.</p>

hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA

Human NUDT16 (hNUDT16) is a decapping enzyme initially identified as the human homolog to the Xenopus laevis X29. As a metalloenzyme, hNUDT16 relies on divalent cations for its cap-hydrolysis activity to remove m⁷GDP and m²²⁷GDP from RNAs. Metal also determines substrate specificity of the enzyme. So far, only U8 small nucleolar RNA (snoRNA) has been identified as the substrate of hNUDT16 in the presence of Mg²(+). Here we demonstrate that besides U8, hNUDT16 can also actively cleave the m⁷GDP cap from mRNAs in the presence of Mg²(+) or Mn²(+). We further show that hNUDT16 does not preferentially recognize U8 or mRNA substrates by our cross-inhibition and quantitative decapping assays. In addition, our mutagenesis analysis identifies several key residues involved in hydrolysis and confirms the key role of the REXXEE motif in catalysis. Finally an investigation into the subcellular localization of hNUDT16 revealed its abundance in both cytoplasm and nucleus. These findings extend the substrate spectrum of hNUDT16 beyond snoRNAs to also include mRNA, demonstrating the pleiotropic decapping activity of hNUDT16.

Genome-wide identification of exported proteins of the novel bacterium Phenylobacterium zucineum HLK1(T) using a consensus computational strategy / 浙江大学学报·医学版

<p><b>OBJECTIVE</b>To predict the exported proteins of the novel bacterium Phenylobacterium zucineum HLK1(T) using genome-wide computational identification by searching the export signals including N-terminal signal peptides and alpha-transmembrane helices.</p><p><b>METHODS</b>The computational identification of signal sequences was based on a consensus between multiple predictive tools, including SignalP V3.0, LipoP V1.0, Phobius and TMHMM 2.0. Type IV signal peptides and proteins exported via TAT machinery were searched manually based on the conservative motifs. All the predicted proteins were classified according to the Cluster of Orthologous Group (COG) standard.</p><p><b>RESULT</b>In the total 3861 proteins encoded by P. zucineum HLK1(T) 1 378 (35.7%) were predicted to be exported proteins, most of which (totally 735, 19.0% of the proteome and 53.3% of all the exported proteins) were uncleavable transmembrane helices. In addition, 499 type I signal peptides (12.9%, 36.2%), 101 lipoproteins (2.6%, 7.3%) were also identified. Four Type IV signal peptides and 12 TAT proteins were detected as well. According to the COG classification standard, most of these exported proteins were P proteins related to inorganic ion transport and metabolism and S proteins whose functions were unknown.</p><p><b>CONCLUSION</b>The genome of HLK1(T) coded various types of exported proteins which may play an important role in the interaction between P. zucineum and the host cell, and facilitate the strain to invade into the cell.</p>

Congestive heart failure due to an iatrogenic arteriovenous fistula in a patient with neurofibromatosis-1 / 대한내과학회지

A 39-year-old woman, who 3 months prior had undergone sono-guided biopsy for pelvic masses, was admitted to our hospital with dyspnea. After the procedure, a large arteriovenous (AV) fistula was detected. The patient developed dyspnea with pain and swelling of the right leg and subsequently visited our hospital. Multiple cafe-au-lait spots and subcutaneous nodules were noted and a continuous bruit was heard in the right pelvic area. Transthoracic echocardiography revealed marked dilatation of the right atrium, right ventricle, and inferior vena cava. An angiogram showed multiple AV fistulas between the right iliac arteries and veins. The patient underwent aortoiliofemoral bypass surgery. Follow-up echocardiography after surgery showed dramatic improvement in heart function. Molecular analysis revealed a novel variation (c.4270-1G>a) at the 24th intron-exon splicing consensus sequence of the neurofibromin 1 (NF1) gene. This is a rare case of AV fistula that developed after biopsy and caused right-sided heart failure in a patient with neurofibromatosis.

Experience on Sequencing of Mitochondrial DNA from 1200 Year Old Bone Using Cloning / 대한법의학회지

Ancient bones have undergone natural decomposition and have been exposed to external environment for long period. Ancient DNA from old bone is usually fragmented. In addition, various kinds of inhibitors are co-extracted. All these may inhibit proper sequencing reaction. Cloning is regarded as the standard method when sequencing aDNA. When cloning, each clone from the same sample may not be of same sequence, and to exact consensus sequence may be difficult. Here we present our experience on 1200 year old bone from Russia, Primorsky Kray area. We have tried to sequence for HV I, II region of mtDNA using modified mini-primer set, which consisted of 7 set to cover the HV I, II. We cloned the PCR product and sequenced all the clones. Amplification efficiency and subsequent success rates were different for each mini primer set. Loci of variation that differ from consensus sequences were rather frequent, and the pattern were variable depending on sample. Except major polymorphic sites that are important when haplogroup designation, 16129 was the most frequent site that was discarded when extracting haplogroup designation.

Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences

The production of nucleic acid sequences by automatic DNA sequencer machines is always associated with some base-calling errors. In order to produce a high-quality DNA sequence from a molecule of interest, researchers normally sequence the same sample many times. Considering base-calling errors as rare events, re-sequencing the same molecule and assembling the reads produced are frequently thought to be a good way to generate reliable sequences. However, a relevant question on this issue is: how many times the sample needs to be re-sequenced to minimize costs and achieve a high-fidelity sequence? We examined how both the number of re-sequenced reads and PHRED trimming parameters affect the accuracy and size of final consensus sequences. Hundreds of single-pool reaction pUC18 reads were generated and assembled into consensus sequences with CAP3 software. Using local alignment against the published pUC18 cloning vector sequence, the position and number of errors in the consensus were identified and stored in MySQL databases. Stringent PHRED trimming parameters proved to be efficient for the reduction of errors; however, this procedure also decreased consensus size. Moreover, re-sequencing did not have a clear effect on the removal of consensus errors, although it was able to slightly increase consensus.

Model-based comparative prediction of transcription-factor binding motifs in anabolic responses in bone / 基因组蛋白质组与生物信息学报·英文版

Understanding the regulatory mechanism that controls the alteration of global gene expression patterns continues to be a challenging task in computational biology. We previously developed an ant algorithm, a biologically-inspired computational technique for microarray data, and predicted putative transcription-factor binding motifs (TFBMs) through mimicking interactive behaviors of natural ants. Here we extended the algorithm into a set of web-based software, Ant Modeler, and applied it to investigate the transcriptional mechanism underlying bone formation. Mechanical loading and administration of bone morphogenic proteins (BMPs) are two known treatments to strengthen bone. We addressed a question: Is there any TFBM that stimulates both "anabolic responses of mechanical loading" and "BMP-mediated osteogenic signaling"? Although there is no significant overlap among genes in the two responses, a comparative model-based analysis suggests that the two independent osteogenic processes employ common TFBMs, such as a stress responsive element and a motif for peroxisome proliferator-activated receptor (PPAR). The post-modeling in vitro analysis using mouse osteoblast cells supported involvements of the predicted TFBMs such as PPAR, Ikaros 3, and LMO2 in response to mechanical loading. Taken together, the results would be useful to derive a set of testable hypotheses and examine the role of specific regulators in complex transcriptional control of bone formation.

Conservation of cis-Regulatory Element Controlling Timely Translation in the 3'-UTR of Selected Mammalian Maternal Transcripts

The earliest stages of mammalian embryogenesis are governed by the activity of maternally inherited transcripts and proteins. Cytoplasmic polyadenylation of selected maternal mRNA has been reported to be a major control mechanism of delayed translation during preimplantation embryogenesis in mice. The presence of cis-elements required for cytoplasmic polyadenylation (e.g., CPE) can serve as a useful tag in the screening of maternal genes partaking in key functions in the transcriptionally dormant egg and early embryo. However, due to its relative simplicity, UA-rich sequences satisfying the canonical rule of known CPE consensus sequences are often found in the 3'-UTR of maternal transcripts that do not actually undergo cytoplasmic polyadenylation. In this study, we developed a method to confirm the validity of candidate CPE sequences in a given gene by a multiplex comparison of 3'-UTR sequences between mammalian homologs. We found that genes undergoing cytoplasmic polyadenylation tend to create a conserved block around the CPE, while CPE-like sequences in the 3'-UTR of genes lacking cytoplasmic polyadenylation do not exhibit such conservation between species. Through this cross-species comparison, we also identified an alternative CPE in the 3'-UTR of tissue-type plasminogen activator (tPA), which is more likely to serve as a functional element. We suggest that verification of CPEs based on sequence conservation can provide a convenient tool for mass screening of factors governing the earliest processes of mammalian embryogenesis.

Identification of novel substrates for human checkpoint kinase Chk1 and Chk2 through genome-wide screening using a consensus Chk phosphorylation motif

Checkpoint kinase 1 (Chk1) and Chk2 are effector kinases in the cellular DNA damage response and impairment of their function is closely related to tumorigenesis. Previous studies revealed several substrate proteins of Chk1 and Chk2, but identification of additional targets is still important in order to understand their tumor suppressor functions. In this study, we screened novel substrates for Chk1 and Chk2 using substrate target motifs determined previously by an oriented peptide library approach. The potential candidates were selected by genome-wide peptide database searches and were examined by in vitro kinase assays. ST5, HDAC5, PGC-1alpha, PP2A PR130, FANCG, GATA3, cyclin G, Rad51D and MAD1alpha were newly identified as in vitro substrates for Chk1 and/or Chk2. Among these, HDAC5 and PGC-1alpha were further analyzed to substantiate the screening results. Immunoprecipitation kinase assay of full-length proteins and site-directed mutagenesis analysis of the target motifs demonstrated that HDAC5 and PGC-1alpha were specific targets for Chk1 and/or Chk2 at least in vitro.

Studies on the Development of Viral Detection Markers for the Quality Control of Blood

According to the serological screening methods of antigen-antibody reaction such as ELISA, it has been known that the complete detection of viral infections of HBV, HCV, and HIV-1 viruses in the blood and blood related-products is not much reliable. Therefore, nucleic acid amplification testing methods (NAT) adopted to detect the small quantitative viral nucleic acids could support the basis of using and supplying the blood and its related products safely. This research work is basically designed to describe the simultaneous blood screening system by multiplex or duplex tests for detection of HBV, HCV, and HIV-1 viruses in the blood at one time with low price and labor. It is aimed at easy detection by using the conventional agarose gel electrophoresis. Thus, we tried to detect and identify the viral components in the blood sample according to their different size of PCR products. We decided a set of consensus sequences to recognize each viral DNA fragments after running the multiplex PCR in one tube. This was done by nested RT-PCR using two different RNA viral genomic templates followed by multiplex PCR with addition of viral DNA and their primers after purifying the viral genomic nucleic acids. Those specific primers could be used without any interference to amplify each viral genome in the blood samples. The sensitivities with different viral loads were evaluated on the agarose gel electrophoresis. Three different viral agents in the blood samples could be tested by this multiplex (RT)-PCR with three different primers.

A fully resolved consensus between fully resolved phylogenetic trees

Nowadays, there are many phylogeny reconstruction methods, each with advantages and disadvantages. We explored the advantages of each method, putting together the common parts of trees constructed by several methods, by means of a consensus computation. A number of phylogenetic consensus methods are already known. Unfortunately, there is also a taboo concerning consensus methods, because most biologists see them mainly as comparators and not as phylogenetic tree constructors. We challenged this taboo by defining a consensus method that builds a fully resolved phylogenetic tree based on the most common parts of fully resolved trees in a given collection. We also generated results showing that this consensus is in a way a kind of [quot ]median[quot ] of the input trees; as such it can be closer to the correct tree in many situations.