Use of Mineral Licks by White-Bellied Spider Monkeys (<Emphasis Type="BoldItalic">Ateles belzebuth</Emphasis>) and Red Howler Monkeys (<Emphasis Type="BoldItalic">Alouatta seniculus</Emphasis>) in Eastern Ecuador

Geophagy occurs in all primate groups and is particularly common in species that consume greater quantities of plant material, i.e., leaves, fruit. The function of geophagy is not fully understood and likely varies over space and time, perhaps in connection with changes in diet. Central to a better understanding of geophagy in primate ecology is knowledge of the occurrence of such behavior among different species and seasons. We used camera traps triggered by heat and motion to document the use of mineral licks by primates over a 3-yr period at a lowland forest site in eastern Ecuador (Tiputini Biodiversity Station). Such mineral licks can be important sources of minerals, nutrients, and other compounds for a wide range of species in Amazonian forests. Although 10 species of primates are known from the study site, we obtained photographs of only 2 species, Ateles belzebuth (white-bellied spider monkey) and Alouatta seniculus (red howler) at 2 of 4 saladeros surveyed. From late December 2004 through early January 2008, we recorded 192 photographs with a total of 318 Ateles belzebuth representing ≥66 separate visits. Comparable numbers for Alouatta seniculus were 80, 121, and 37. We recorded both species visiting a mineral lick at the same time on ≥7 occasions. Use of mineral licks varied across months; we recorded more visits from November through February, the drier period at Tiputini. Visits also varied by hour, with no visits before 0830 or after 1630; Ateles belzebuth showed a stronger mid-day peak in visits. Average visit length (calculated as the time between the first and last photographs of a given visit) was similar between the 2 species but median visit length was more than twice as long for Ateles belzebuth (15 min) as for Alouatta seniculus (6 min). Results indicate that mineral licks are important in the ecology of these species, but further studies are needed to determine the precise benefit(s) obtained and how benefits may vary with diet and other factors.     

A method for determining zygosity of transgenic zebrafish by TaqMan real-time PCR

When producing a genetically modified organism, intended genes are often integrated into a target genome by random insertions. Subsequently, it is often desirable to know the gene copy number of the transgenic organism and the zygosity of its offspring. Because of the random insertions, the estimation can be made only by quantitative measurement of the genes. Even though TaqMan real-time PCR has been used in gene expression analysis, it is routinely used to quantify differences larger than twofold or more than one PCR cycle. In this study, we employed TaqMan quantitative PCR to determine zygosity of transgenic fluorescent zebrafish in which a homozygote and a hemizygote differ by only twofold. We measured relative quantities of the transgene by taking the threshold cycle (Ct) of both the transgene and an internal control zebrafish genomic DNA. Using scatterplots and statistical inference, we demonstrated that homozygotes and hemizygotes could be differentiated unambiguously when multiple measurements were taken. We discuss the relationship between the repetitive measurements and TaqMan precision with a statistical model. The result illustrates that the method can be extended to some areas that require even higher precision such as determining the polyploidy of an organism.     

GrainGenes 2.0. an improved resource for the small-grains community

GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.     

Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy

Lignin composition in relation to its basic phenylpropanoid units, particularly the syringyl to guaiacyl (S/G) ratio, is an important property for biomass characterization and varies greatly as a function of species, genotype and environment. A rapid screening method is highly desirable to assess lignin composition in a large number of samples. We have developed a nondestructive and label-free Fourier transform Raman (FT-Raman) spectroscopic method that is capable of rapidly and reliably measuring the S/G ratio with minimal sample preparation. A variety of feedstocks, including hardwood (Eucalyptus globulus), softwood (Pinus radiata), herbaceous plants (Zea mays, Panicum virgatum, and Sorghum bicolor), and a model dicot (Arabidopsis thaliana) were measured using this technique and the corresponding S/G ratio was calculated after spectral deconvolution based on the S and G bands identified using a known library of model compounds. The results obtained using this technique were successfully validated by pyrolysis-gas chromatography/mass spectrometry (pyro-GC/MS). This technique holds significant promise in the rapid screening of engineered feedstocks as part of a comprehensive screening methodology that is correlated with biomass recalcitrance.     

Rapid detection of protein tyrosine kinase activity in recombinant yeast expressing a universal substrate

Yeast two-hybrid systems are powerful proteomics tools for the discovery of protein-protein interactions. However, these systems are typically unable to detect interactions dependent on post-translational modifications such as tyrosine phosphorylation. We report a novel yeast tribrid system that expresses a potentially universal protein tyrosine kinase (PTK) substrate to detect diverse PTKs. Validation with the oncogenic kinases v-Abl and v-Src, which exhibit divergent substrate specificities, demonstrated significant potential for cloning PTKs en masse from cDNA libraries.     

Mechanisms of stable serum resistance of Neisseria gonorrhoeae

Neisseria gonorrhoeae that resist complement-dependent killing by normal human serum (NHS) are sometimes killed by immune convalescent sera from patients recovering from disseminated gonococcal infection (DGI). In these studies, killing by immune serum was prevented or blocked by immunoglobulin G (IgG) or F(ab)₂ isolated from NHS. Purified human IgG antibodies directed against gonococcal protein III, contained most of the blocking activity in IgG. In addition, immune convalescent DGI serum, which did not exhibit bactericidal activity, was restored to killing by selective immunodepletion of protein III antibodies. Blocking IgG or F(ab)₂ prepared from IgG, partially inhibited binding of bactericidal antibody to N. gonorrhoeae. Also, binding of a monoclonal antibody recognizing N. gonorrhoeae outer membrane protein PIII was almost completely inhibited by blocking F(ab)₂.Presensitization of N. gonorrhoeae with increasing concentrations of blocking IgG or F(ab)₂ before incubation with bactericidal antibody and an antibody free source of complement, increased consumption and deposition of the third component of human complement (C3) and the ninth component of complement (C9) but inhibited killing in dose-related fashion.     

Recording information on protein complexes in an information management system

The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein-protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described.     

Enzymes of aerobic respiration on iron

Abstract: Bacteria capable of aerobic respiration on ferrous ions are spread throughout eubacterial and archaebacterial phyla. Comparative spectroscopic analyses revealed that phylogenetically distinct organisms expressed copious quantities of spectrally distinct redox-active biomolecules during autotrophic growth on soluble iron. Thiobaeillus ferrooxidans, Leptospirillum ferrooxidans, Sulfobacillus thermosulfidooxidans , and Metallosphaera sedula possessed iron respiratory chains dominated by a blue copper protein, a novel red cytochrome, a novel yellow protein, and a novel yellow cytochrome, respectively. Further investigation of each type of respiratory chain will be necessary to deduce the advantages and disadvantages of each.