A Proposal for a Consolidated Structural Model of the CagY Protein of .

CagY is the largest and most complex protein from (Hp) type IV secretion system (T4SS), playing a critical role in the modulation of gastric inflammation and risk for gastric cancer. CagY spans from the inner to the outer membrane, forming a channel through which Hp molecules are injected into human gastric cells. Yet, a tridimensional structure has been reported for only short segments of the protein.

Micronutrients of the one-carbon metabolism cycle are altered in mothers and neonates by gestational diabetes and are associated with weight, height and head circumference at birth.

While several studies have previously described the levels of one-carbon metabolism-related micronutrients in women with gestational diabetes mellitus (GDM) and their neonates, the results in these literature reports have been contradictory. We hypothesized that the concentrations of micronutrients involved in the one-carbon cycle are altered in pregnant women and their neonates by GDM, and that these changes could further modify the neonatal anthropometry. Micronutrient levels were measured in 123 pregnant women with normal glucose levels (M-ND) and their neonates (N-ND), as well as in 54 pregnant women with gestational diabetes (M-GDM) and their neonates (M-GDM).

In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization.

In this study we evaluate the capacity of Virtual Hybridization to identify between highly related bacterial strains. Eight genomic fingerprints were obtained by virtual hybridization for the Bacillus anthracis genome set, and a set of 15,264 13-nucleotide short probes designed to produce genomic fingerprints unique for each organism. The data obtained from each genomic fingerprint were used to obtain hybridization patterns simulating a DNA microarray.

Design of a set of probes with high potential for influenza virus epidemiological surveillance.

An Influenza Probe Set (IPS) consisting in 1,249 9-mer probes for genomic fingerprinting of closely and distantly related Influenza Virus strains was designed and tested in silico. The IPS was derived from alignments of Influenza genomes. The RNA segments of 5,133 influenza strains having diverse degree of relatedness were concatenated and aligned.

Universal fingerprinting chip server.

Unlabelled: The Virtual Hybridization approach predicts the most probable hybridization sites across a target nucleic acid of known sequence, including both perfect and mismatched pairings. Potential hybridization sites, having a user-defined minimum number of bases that are paired with the oligonucleotide probe, are first identified. Then free energy values are evaluated for each potential hybridization site, and if it has a calculated free energy of equal or higher negative value than a user-defined free energy cut-off value, it is considered as a site of high probability of hybridization.

LifePrint: a novel k-tuple distance method for construction of phylogenetic trees.

Purpose: Here we describe LifePrint, a sequence alignment-independent k-tuple distance method to estimate relatedness between complete genomes.

Methods: We designed a representative sample of all possible DNA tuples of length 9 (9-tuples). The final sample comprises 1878 tuples (called the LifePrint set of 9-tuples; LPS9) that are distinct from each other by at least two internal and noncontiguous nucleotide differences.

Bacterial classification using genomic fingerprints obtained by virtual hybridization.

In silico genomic fingerprints were produced by virtual hybridization of 191 fully sequenced bacterial genomes using a set of 15,264 13-mer probes specially designed to produce universal whole genome fingerprints. A novel approach for constructing phylogenetic trees, based on comparative analysis of genomic fingerprints, was developed. The resultant bacterial phylogenetic tree had strong similarities to those produced from the alignment of conserved sequences.

Single oligoarray-based detection of specific M918T mutation in RET oncogene in multiple endocrine neoplasia type 2B.

The most important mutation associated with Multiple Endocrine Neoplasia type 2B (MEN 2B) is the change of thymine to cytosine in codon 918 of exon 16 in the RET oncogene (ATG → ACG). The aim of this work was to develop a single oligoarray by using tandem hybridization to detect the T918C/RET mutation for MEN 2B patients. Two genetically non-related families were studied; each family had a member affected by MEN2B.

Geographical variation in human papillomavirus prevalence in Mexican women with normal cytology.

Objective: To determine the prevalence of human papillomavirus (HPV) infection and genotype distribution in Mexican women with similar lifestyles from two geographical regions who receive medical care from the Mexican Navy Health System, and to identify the associated sociodemographic and reproductive characteristics.

Methods: Cervical swabs from 671 women, beneficiaries of the Mexican Navy Health System, from two distinct southern coast regions of Mexico, were analyzed. Data were obtained regarding sociodemographic variables and sexual and reproductive history.

[Microarray design using virtual hybridization to study variations in REP-CMT1A sites].

Background: Gene PMP22 is duplicated in patients with CMT1A. Duplication is due to an unequal chromatid interchange during meiosis that takes place between two 24 Kb regions named REP-CMT1A proximal and distal sites. Homology is approximately 98%.

Capillary electrophoresis for the detection of PMP22 gene duplication: study in Mexican patients.

Charcot-Marie-Tooth (CMT) disease is the most common inherited disorder of the human peripheral nerve, with an estimated overall prevalence of 17-40/10 000 [1]. The typical phenotype presents peroneal muscular atrophy and pes cavus [2]. CMT is usually divided into two large types, about two-thirds of the patients have CMT type 1 (CMT1), that affects the layer of myelin (demyelination).

[Strategies for clinical and molecular diagnosis of Charcot-Marie-Tooth 1A among Mexican patients].

Background: Charcot-Marie-Tooth (CMT) is the most common inherited disorder of the human peripheral nerve. The mos tfrequent subtype, CMT1A, is associated with duplication of approximately 1.5 Mb fragment in 17p11-p12, that includes the PMP22 gene.

In silico evaluation of a novel DNA chip based fingerprinting technology for viral identification.

The identification of microorganisms by whole genome DNA fingerprinting was tested "in silico". 94 HPV genome sequences were submitted to virtual hybridization analysis on a DNA chip with 342 probes. This Universal Fingerprinting Chip (UFC) constitutes a representative set of probes of all the possible 8-mer sequences having at least two internal and non contiguous sequence differences between all them.

Rat DNA polymerase beta substitutes the repairing activity of DNA polymerase I in the lethal effect of UV light.

The aim of this work was to search if the rat DNA polymerase beta can substitute the capability of DNA polymerase I to repair damage caused by the UV light in Escherichia coli. The oriC origin of replication from p beta 5 was replaced by the rep origin from pSC101 and named p beta 6. The presence of pol beta in the new construct was verified by PCR.

Low density DNA microarray for detection of most frequent TP53 missense point mutations.

Background: We have developed an oligonucleotide microarray (genosensor) utilizing a double tandem hybridization technique to search for 9 point mutations located in the most frequently altered codons of the TP53 gene. Isolated and multiplexed PCR products, 108 and 92 bp long, from exons 7 and 8, respectively, were obtained from 24 different samples. Single-stranded target DNA was then prepared from isolated or multiplexed PCR products, through cyclic DNA synthesis.

Effects of lindane on the photosynthetic apparatus of the cyanobacterium Anabaena: fluorescence induction studies and immunolocalization of ferredoxin-NADP+ reductase.

Intention, Goal, Scope, Background: Cyanobacteria have the natural ability to degrade moderate amounts of organic pollutants. However, when pollutant concentration exceeds the level of tolerance, bleaching of the cells and death occur within 24 hours. Under stress conditions, cyanobacterial response includes the short-term adaptation of the photosynthetic apparatus to light quality, named state transitions.

Detection of mutations in RET proto-oncogene codon 634 through double tandem hybridization.

We developed a procedure to detect the 7 point mutations at Cys634 of the proto-oncogene RET, which is responsible for medullary thyroid carcinoma (MTC). Genomic DNA was prepared from blood samples obtained from normal and MTC-affected individuals belonging to a family with a history of the disease. The RET genotype for each individual was first established by performing restriction and sequencing analyses.

Display and release of the Plasmodium falciparum circumsporozoite protein using the autotransporter MisL of Salmonella enterica.

The Salmonella enterica MisL (protein of membrane insertion and secretion) is an autotransporter with high homology to AIDA-I (adhesin involved in diffuse adherence) of enteropathogenic Escherichia coli. Considering that it has been reported that the MisL beta translocator domain is able to display heterologous passenger peptides to the bacterial surface, we developed a system to display proteins and release them to the external environment by means of proteolytic cleavage. Plasmids were constructed encoding 8 or 53 repeats of the NANP (Asp-Ala-Asp-Pro) tetrapeptide, which is the main B cell epitope of the Plasmodium falciparum circumsporozoitic protein (CSP), fused to the the MisL beta-domain and including the recognition cleavage sequence from the E.

Development of two multiplex polymerase chain reactions for the detection of enterotoxigenic strains of Staphylococcus aureus isolated from foods.

Two multiplex polymerase chain reactions were developed for the detection of enterotoxigenic strains of Staphylococcus aureus: one multiplex reaction for the simultaneous detection of enterotoxigenic strains type A (entA), type B (entB), and type E (entE) and another for the simultaneous detection of enterotoxigenic strains type C (entC) and type D (entD). Both reactions were standardized with the use of the reference enterotoxigenic strains of S. aureus: FRI 722, producer of staphylococcal enterotoxin (SE) type A (SEA); FRI 1007, producer of SEB; FRI 137, producer of SEC1; FRI 472, producer of SED; and FRI 326, producer of SEE.

Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization.

An oligonucleotide microarray hybridization system to differentiate microbial species was designed and tested. Seven microbial species were studied, including one Bacillus and six Pseudomonas strains. DNA sequences near the 5' end of 16S rRNA genes were aligned and two contiguous regions of high variability, flanked by highly conserved sequences, were found.

Differential activities of the SoxR protein of Escherichia coli: SoxS is not required for gene activation under iron deprivation.

When Escherichia coli cells are under superoxide stress, proteins SoxR and SoxS, acting sequentially, control the expression of a set of repair and defense genes. One of these genes, fumC, encoding fumarase C, was reported to be also activated by iron deprivation in a soxRS-dependent manner. However, the same condition failed to induce the expression of a soxS'::lacZ fusion.

Mutation detection by stacking hybridization on genosensor arrays.

A new strategy for analysis of point mutations using oligonucleotide array (genosensor) hybridization was investigated. In the new approach, a single-stranded target strand is preannealed with a labeled "stacking oligonucleotide," and then the partially duplex labeled target molecule is hybridized to an array of glass-tethered oligonucleotide probes, targeted to the region on the target immediately adjacent to the stacking oligomer. In this configuration, the base-stacking interactions between the "capture probe" and the contiguously stacking oligomer stabilize the binding of the target molecule to its complementary probe on the genosensor array.