Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach

The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue substitutions from amino acid sequences is also important because the rate matrix can be used to develop scoring matrices for sequence alignment. Here we use a continuous time Markov process to model the substitution rates of residues and develop a Bayesian Markov chain Monte Carlo method for rate estimation. We validate our method using simulated artificial protein sequences. Because different local regions such as binding surfaces and the protein interior core experience different selection pressures due to functional or stability constraints, we use our method to estimate the substitution rates of local regions. Our results show that the substitution rates are very different for residues in the buried core and residues on the solvent-exposed surfaces. In addition, the rest of the proteins on the binding surfaces also have very different substitution rates from residues. Based on these findings, we further develop a method for protein function prediction by surface matching using scoring matrices derived from estimated substitution rates for residues located on the binding surfaces. We show with examples that our method is effective in identifying functionally related proteins that have overall low sequence identity, a task known to be very challenging.     

Are residues in a protein folding nucleus evolutionarily conserved?

Protein is the working molecule of the cell, and evolution is the hallmark of life. It is important to understand how protein folding and evolution influence each other. Several studies correlating experimental measurement of residue participation in folding nucleus and sequence conservation have reached different conclusions. These studies are based on assessment of sequence conservation at folding nucleus sites using entropy or relative entropy measurement derived from multiple sequence alignment. Here we report analysis of conservation of folding nucleus using an evolutionary model alternative to entropy-based approaches. We employ a continuous time Markov model of codon substitution to distinguish mutation fixed by evolution and mutation fixed by chance. This model takes into account bias in codon frequency, bias-favoring transition over transversion, as well as explicit phylogenetic information. We measure selection pressure using the ratio omega of synonymous versus non-synonymous substitution at individual residue site. The omega-values are estimated using the PAML method, a maximum-likelihood estimator. Our results show that there is little correlation between the extent of kinetic participation in protein folding nucleus as measured by experimental phi-value and selection pressure as measured by omega-value. In addition, two randomization tests failed to show that folding nucleus residues are significantly more conserved than the whole protein, or the median omega value of all residues in the protein. These results suggest that at the level of codon substitution, there is no indication that folding nucleus residues are significantly more conserved than other residues. We further reconstruct candidate ancestral residues of the folding nucleus and suggest possible test tube mutation studies for testing folding behavior of ancient folding nucleus.     

Trace elements in hair of blackfoot disease

Blackfoot disease is a peripheral vascular disease resulting in gangrene of the lower extremities. Though extensive epidemiological study has implicated that high arsenic content in artesian well water of the endemic area, bears some important connection with the disease, the etiology of the disease is still unknown. In this study, attention is paid to multielement determination in order to find out whether the trace elements in hair of Blackfoot disease patients are different from those of the controls. Experimental results indicate that the concentrations of As and Se in hair of patients are significantly higher than those of the controls, but Ca and Zn are significantly lower than those of the controls. The possible connection of these elements with the etiology of the disease is discussed.     

A compact computational model for cell construct development in perfusion culture

A problem nowadays tissue engineers encounter in developing sizable tissue implants is the nonuniform spread of cells and/or extracellular matrices. Research shows such a nutrients transport restriction may be improved by employing hydrodynamic culture systems. We propose a compact model for the simulation of cell growth in a porous construct under direct perfusion. Unlike the previous model proposed in the literature, which composes a cellular scaffold sandwiched between two culture media layers, the current model includes only the scaffold layer to simplify the mathematical and computational complex. Results show the present single-layer model can predict cell spreads and the nutrient and metabolic waste distribution as accurately as does the three-layer model. Only if the hydrodynamic aspects such as the pressure and viscous stress are prominent to know, should the more sophisticated analyses with the three-layer model be employed. The compact model provides comparable investigations for the tissue-engineering construct developments.     

Analysis of Malassezia microbiota in healthy superficial human skin and in psoriatic lesions by multiplex real-time PCR

Yeasts from the genus Malassezia are members of the normal biota of human skin, and may play a role in dermatopathology. Our previous study of the fungal microbiota from healthy subjects and from patients with psoriasis using clone library analysis revealed the presence of five Malassezia species and four uncharacterized phylotypes. We now compared the Malassezia microbiota from six healthy body locations and two psoriatic lesions, and evaluated its stability over time using multiplex real-time PCR. Samples from each body location were obtained monthly, for 4 months. Dual-labeled probes were designed to recognize four Malassezia sp. and two uncharacterized groups, and a genus-specific probe was also developed. A good correspondence was obtained between real-time PCR data and clone library analyses. Malassezia restricta was the most abundant species in the majority of samples, and high amounts of Malassezia globosa were also detected. The uncharacterized phylotype 1 was usually detected in lower proportions, nevertheless it was present in most samples. The microbiota was host-specific and relatively stable over time. In accordance with our previous observations, no significant dichotomy between samples from healthy skin and from psoriatic lesions was found; the samples clustered according to the subject, rather than health status.     

T cell-dendritic cell immunological synapses contain TCR-dependent CD28-CD80 clusters that recruit protein kinase C theta

Short-lived TCR microclusters and a longer-lived protein kinase Ctheta-focusing central supramolecular activation cluster (cSMAC) have been defined in model immunological synapses (IS). In different model systems, CD28-mediated costimulatory interactions have been detected in microclusters, the cSMAC, or segregated from the TCR forming multiple distinct foci. The relationship between TCR and costimulatory molecules in the physiological IS of T cell-dendritic cell (DC) is obscure. To study the dynamic relationship of CD28-CD80 and TCR interactions in the T cell-DC IS during Ag-specific T cell activation, we generated CD80-eCFP mice using bacterial artificial chromosome transgenic technology. In splenic DCs, endogenous CD80 and CD80-eCFP localized to plasma membrane and Golgi apparatus, and CD80-eCFP was functional in vivo. In the OT-II T cell-DC IS, multiple segregated TCR, CD80, and LFA-1 clusters were detected. In the T cell-DC synapse CD80 clusters were colocalized with CD28 and PKCtheta, a characteristic of the cSMAC. Acute blockade of TCR signaling with anti-MHC Ab resulted in a rapid reduction in Ca(2+) signaling and the number and size of the CD80 clusters, a characteristic of TCR microclusters. Thus, the T cell-DC interface contains dynamic costimulatory foci that share characteristics of microclusters and cSMACs.     

Fire ant-detecting canines: a complementary method in detecting red imported fire ants

In this investigation, detection dogs are trained and used in identifying red imported fire ants, Solenopsis invicta Buren, and their nests. The methodology could assist in reducing the frequency and scope of chemical treatments for red imported fire ant management and thus reduce labor costs and chemical use as well as improve control and quarantine efficiency. Three dogs previously trained for customs quarantine were retrained to detect the scents of red imported fire ants. After passing tests involving different numbers of live red imported fire ants and three other ant species--Crematogaster rogenhoferi Mayr, Paratrechina longicornis Latreille, and Pheidole megacephala F.--placed in containers, ajoint field survey for red imported fire ant nests by detection dogs and bait traps was conducted to demonstrate their use as a supplement to conventional detection methods. The most significant findings in this report are (1) with 10 or more red imported fire ants in scent containers, the dogs had >98% chance in tracing the red imported fire ant. Upon the introduction of other ant species, the dogs still achieved on average, a 93% correct red imported fire ant indication rate. Moreover, the dogs demonstrated great competence in pinpointing emerging and smaller red imported fire ant nests in red imported fire ant-infested areas that had been previously confirmed by bait trap stations. (2) Along with the bait trap method, we also discovered that approximately 90% of red imported fire ants foraged within a distance of 14 m away from their nests. The results prove detection dogs to be most effective for red imported fire ant control in areas that have been previously treated with pesticides and therefore containing a low density of remaining red imported fire ant nests. Furthermore, as a complement to other red imported fire ant monitoring methods, this strategy will significantly increase the efficacy of red imported fire ant control in cases of individual mount treatment.