Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert.

The Atacama Desert, the driest, with the highest radiation, and one of the most ancient deserts in the world, is a hostile environment for life. We have a collection of 74 unique bacterial isolates after cultivation and confirmation by 16S rRNA gene sequencing. Pigmentation, biofilm formation, antimicrobial production against MG1655 and HG003, and antibiotic resistance were assessed on these isolates.

Change in Biotypic Diversity of Russian Wheat Aphid (Hemiptera: Aphididae) Populations in the United States.

A key component of Russian wheat aphid, Diuraphis noxia (Kurdjumov), management has been through planting resistant wheat cultivars. A new biotype, RWA2, appeared in 2003 which caused widespread damage to wheat cultivars containing the Dn4 gene. Biotypic diversity in Russian wheat aphid populations has not been addressed since 2005 when RWA2 dominated the biotype complex.

Clinical and biochemical studies support smokeless tobacco's carcinogenic potential in the human oral cavity.

In 2007, the International Agency for Research on Cancer presented compelling evidence that linked smokeless tobacco use to the development of human oral cancer. Although these findings imply vigorous local carcinogen metabolism, little is known about levels and distribution of phase I, II, and III (drug egress) enzymes in human oral mucosa. In this study here, we integrated clinical data, and imaging and histopathologic analyses of an oral squamous cell carcinoma that arose at the site of smokeless tobacco quid placement in a patient.

Computational methods for protein sequence analysis.

This unit is presented as a guide to addressing the issue of what to do with a protein sequence once it is obtained. A theoretical background for protein sequence analysis is provided first, followed by a discussion of matrix methods for sequence comparison (Matrix Methods for Sequence Comparison: Dot Plots). Sequence similarity searching is then presented, including the BLAST and FASTA databases.

Comparing the benefits of diet and exercise in the treatment of dyslipidemia.

Background: Lifestyle changes are advocated as a first line of treatment for dyslipidemia. However, few studies have directly compared various combinations of diets and exercise.

Methods: In a randomized controlled pilot study, we compared the standard lifestyle recommendations (NCEP step I diet with regular exercise) and more intense interventions including the NCEP step I diet with a supervised aerobic exercise program and the step II diet with and without a supervised aerobic exercise program.

Sensitivity of biological models to errors in parameter estimates.

Since A. M. Turing's paper proposing a mathematical basis for pattern formation in developing organisms many mathematical approaches have been proposed to model biological phenomenon.

The identification of markers segregating with resistance to Schistosoma mansoni infection in the snail Biomphalaria glabrata.

Both snail and parasite genes determine the susceptibility of the snail Biomphalaria glabrata to infection with the trematode Schistosoma mansoni. To identify molecular markers associated with resistance to the parasite in the snail host, we performed genetic crosses between parasite-resistant and -susceptible isogenic snails. Because resistance to infection in adult snails is controlled by a single locus, DNA samples from individual F2 and F1 backcross progeny, segregating for either the resistant or susceptible phenotypes, were pooled (bulked segregant).

Cluster analysis and data visualization of large-scale gene expression data.

The discovery of any new gene requires an analysis of the expression context for that gene. Now that the cDNA and genomic sequencing projects are progressing at such a rapid rate, high throughput gene expression screening approaches are beginning to appear to take advantage of that data. We present a strategy for the analysis for large-scale quantitative gene expression measurement data from time course experiments.

Large-scale temporal gene expression mapping of central nervous system development.

We used reverse transcription-coupled PCR to produce a high-resolution temporal map of fluctuations in mRNA expression of 112 genes during rat central nervous system development, focusing on the cervical spinal cord. The data provide a temporal gene expression "fingerprint" of spinal cord development based on major families of inter- and intracellular signaling genes. By using distance matrices for the pair-wise comparison of these 112 temporal gene expression patterns as the basis for a cluster analysis, we found five basic "waves" of expression that characterize distinct phases of development.

Effect of prosthetic superstructure accuracy on the osteointegrated implant bone interface.

Objective: This study evaluated the biologic result of forces induced by a misfitting prosthetic superstructure on implants placed in a New Zealand white rabbit tibia model.

Study Design: Nine rabbits had two dental implants placed in both right and left proximal tibias. After 6 weeks, one animal was sacrificed for baseline integration data, and the remaining animals had fitting or misfitting prosthetic superstructures attached to the implants for 12 weeks.

Intraphagosomal oxygen in stimulated macrophages.

A new electron paramagnetic resonance (EPR)-based method was developed to obtain selective information on pO2 in a specific intracellular compartment (phagosomes). This method did not require the use of a broadening agent thereby eliminating one of the potential sources of experimental error with EPR oximetry. An oxygen-sensitive probe (4-(Trimethylammonium) 2,2,6,6-tetramethylpiperidine-d17-1-oxyl iodide (d-Cat1)) which has a net positive charge, was incorporated selectively into the phagosomes of macrophages stimulated with zymosan.

Nucleic acid sequences coding for internal antisense peptides: are there implications for protein folding and evolution?

We have asked whether coding segments of nucleic acids generate amino acid sequences which have an antisense relationship to other amino acid sequences in the same chain (i.e. 'Internal Antisense'), and if so, could the internal antisense content be related to the structure of the encoded protein? Computer searches were conducted with the coding sequences for 132 proteins.

Comparison of the resistance of miniplates and microplates to various in vitro forces.

A comparison of the Luhr Mini System (Howmedica, Inc, Rutherford, NJ) and the Luhr Micro System (Howmedica, Inc) was undertaken to determine resistance to various forces using a biomechanical model. Miniplates and microplates were first tested to determine their resistance to forces of displacement on flat bend, edge bend, tension, and compression generated by a materials testing system machine. Then, miniplates and microplates were attached to fresh porcine ribs, fixed to a custom-made jig, and subjected to the same forces of displacement.

Reliability of a facebow transfer procedure.

The three-dimensional orientation of a maxillary cast mounting from a simulated-kinematic facebow transfer was evaluated in multiple trials among three operators on a single subject. The anterior and posterior anatomic facial reference points were marked on the subject. Each operator performed a separate series of trials to reset the anterior facebow component, the two posterior facebow components, and a control series with no resetting of any facebow components relative to the subject.

Inhibition of SV40 gene expression by microinjected small antisense RNA and DNA molecules.

We tested the impact of antisense RNA and DNA molecules on SV40 gene expression by microinjection into TC7 cells. Short antisense stretches, complementary to either hairpin or loop structures on the T antigen mRNA, inhibited T antigen synthesis. In contrast, full-length antisense RNA and DNA molecules did not effect T antigen synthesis.

Mechanism of mRNA binding to bovine mitochondrial ribosomes.

The binding of mRNA to bovine mitochondrial ribosomes was investigated using triplet codons, homopolymers and heteropolymers of various lengths, and human mitochondrial mRNAs. In the absence of initiation factors and initiator tRNA, mitochondrial ribosomes do not bind triplet codons (AUG and UUU) or homopolymers (oligo(U] shorter than about 10 nucleotides. The RNA binding domain on the 28 S mitoribosomal subunit spans approximately 80 nucleotides of the mRNA, judging from the size of the fragments of poly(U,G) and natural mRNAs protected from RNase T1 digestion by this subunit, but the major binding interaction with the ribosome appears to occur over a 30-nucleotide stretch.

Accumulation and decay of DG42 gene products follow a gradient pattern during Xenopus embryogenesis.

The DG42 gene is expressed during a short window during embryogenesis of Xenopus laevis. The mRNA for this gene can be first detected just after midblastula, peaks at late gastrula, and decays by the end of neurulation. The sequence of the DG42 cDNA and genomic DNA predicts a 70,000-Da protein that is not related to any other known protein.

Cloning, nucleotide sequence and expression of the pyrBI operon of Salmonella typhimurium LT2.

The pyrB-pyrI region of the Salmonella typhimurium LT2 chromosome has been cloned and sequenced. The two genes were found to constitute an operon, with pyrI being the distal gene and separated from pyrB by a 15-bp intercistronic region. Sequence analysis revealed the presence of two potential promoters; transcription initiated from the promoter proximal to pyrB would produce a transcript which could direct the synthesis of a 33-amino-acid leader peptide.

20 years cogeneration at a hospital.

Virtually all of the recoverable heat energy from the engine generator sets--jacket cooling, flue gas, and oil cooler--can be used to meet space cooling, space heating, and process loads at a 300 bed hospital.