Beta 1 isoform-specific regulation of a triiodothyronine-induced gene during cerebellar development.

Although tissue-specific expression of the alpha 1 and beta 1 thyroid hormone receptors (TR-alpha 1 and TR-beta 1) suggests isoform-specific function, transfection studies to date have failed to show consistent differences in their ability to regulate gene expression. We here provide evidence that TR-beta 1 but not TR-alpha 1 regulates the expression of the gene coding for PCP-2 in cerebellar Purkinje cells during neonatal rat development and that such regulation appears to be both T3 dependent and T3 independent. Examination of neonatal rats revealed that the levels of three mRNAs expressed in cerebellar Purkinje cells (myoinositol-1,4,5-triphosphate receptor, calbindin, and PCP-2) rise from neonatal day 1 to day 15. This rise is preceded by the previously documented surge in brain T3 and TR-beta 1. Methimazole-induced hypothyroidism sharply reduces, but does not abolish, the rise in these mRNAs. Concomitant T3 administration normalizes the process. In order to establish more directly the role of TR-beta 1 and T3, cotransfection experiments were performed in CHO cells with PCP-2-lacZ construct and TR isoforms. These studies showed that TR-beta 1, even in the absence of T3, regulated the expression of the transfected PCP-2 construct. T3 augments the response to TR-beta 1 alone by 40% (P < .01). TR-alpha 1 had no effect on PCP-2-lacZ expression either in the presence or absence of T3.(ABSTRACT TRUNCATED AT 250 WORDS)     

The Shannon information entropy of protein sequences.

A comprehensive data base is analyzed to determine the Shannon information content of a protein sequence. This information entropy is estimated by three methods: a k-tuplet analysis, a generalized Zipf analysis, and a "Chou-Fasman gambler." The k-tuplet analysis is a "letter" analysis, based on conditional sequence probabilities. The generalized Zipf analysis demonstrates the statistical linguistic qualities of protein sequences and uses the "word" frequency to determine the Shannon entropy. The Zipf analysis and k-tuplet analysis give Shannon entropies of approximately 2.5 bits/amino acid. This entropy is much smaller than the value of 4.18 bits/amino acid obtained from the nonuniform composition of amino acids in proteins. The "Chou-Fasman" gambler is an algorithm based on the Chou-Fasman rules for protein structure. It uses both sequence and secondary structure information to guess at the number of possible amino acids that could appropriately substitute into a sequence. As in the case for the English language, the gambler algorithm gives significantly lower entropies than the k-tuplet analysis. Using these entropies, the number of most probable protein sequences can be calculated. The number of most probable protein sequences is much less than the number of possible sequences but is still much larger than the number of sequences thought to have existed throughout evolution. Implications of these results for mutagenesis experiments are discussed.     

Biodeterioration of Mayan buildings at uxmal and tulum,Mexico

Uxmal and Tulum are two important Mayan sites in the Yucatan peninsula. The buildings are mainly composed of limestone and grey/black discoloration is seen on exposed walls and copious greenish biofilms on inner walls. The principal microorganisms detected on interior walls at both Uxmal and Tulum were cyanobacteria; heterotrophic bacteria and filamentous fungi were also present. A dark‐pigmented mitosporic fungus and Bacillus cereus, both isolated from Uxmal, were shown to be acidogenic in laboratory cultures. Cyanobacteria belonging to rock‐degrading genera Synechocystis and Gloeocapsa were identified at both sites. Surface analysis previously showed that calcium ions were present in the biofilms on buildings at Uxmal and Tulum, suggesting the deposition of biosolubilized stone. Apart from their potential to degrade the substrate, the coccoid cyanobacteria supply organic nutrients for bacteria and fungi, which can produce organic acids, further increasing stone degradation.     

Integration, phylogeny, and the hominid cranial base

Basicranial features were examined in catarrhine primates and early hominids in order to demonstrate how information about morphological integration can be incorporated into phylogenetic analysis. Hypotheses purporting to explain the functional and structural relationships of basicranial characters were tested using factor analysis. Characters found to be functionally or structurally related to each other were then further examined in order to determine whether there was evidence that they were phylogenetically independent. If phylogenetic independence could not be demonstrated, then the characters were presumed to be integrated and were grouped into a complex. That complex was then treated as if it were a single character for the purposes of cladistic analysis. Factor analysis revealed that five basicranial features may be structurally related to relative brain size in hominoids. Depending on how one defines phylogenetic independence, as few as two, or as many as all of those characters might be morphologically integrated. A cladistic analysis of early hominids based on basicranial features revealed that the use of integrated complexes had a substantial effect on the phylogenetic position of Australopithecus africanus, a species whose relationships are poorly resolved. Moreover, the use of complexes also had an effect on reanalyses of certain published cladistic data sets, implying that those studies might have been biased by patterns of basicranial integration. These results demonstrate that patterns of morphological integration need to be considered carefully in all morphology-based cladistic analyses, regardless of taxon or anatomical focus. However, an important caveat is that the functional and structural hypotheses tested here predicted much higher degrees of integration than were observed. This result warns strongly that hypotheses of integration must be tested before they can be adequately employed in phylogenetic analysis. The uncritical acceptance of an untested hypothesis of integration is likely to be as disruptive to a cladistic analysis as when integration is ignored.     

Functional implications of squamosal suture size in paranthropus boisei

It has been hypothesized that the extensively overlapping temporal and parietal bones of the squamosal sutures in Paranthropus boisei are adaptations for withstanding loads associated with feeding. Finite element analysis (FEA) was used to investigate the biomechanical effects of suture size (i.e., the area of overlap between the temporal and parietal bones) on stress, strain energy, and strain ratio in the squamosal sutures of Pan troglodytes and P. boisei (specimen OH 5) during biting. Finite element models (FEMs) of OH 5 and a P. troglodytes cranium were constructed from CT scans. These models contain sutures that approximate the actual suture sizes preserved in both crania. The FEM of Pan was then modified to create two additional FEMs with squamosal sutures that are 50% smaller and 25% larger than those in the original model. Comparisons among the models test the effect of suture size on the structural integrity of the squamosal suture as the temporal squama and parietal bone move relative to each other during simulated premolar biting. Results indicate that with increasing suture size there is a decreased risk of suture failure, and that maximum stress values in the OH 5 suture were favorable compared to values in the Pan model with the normal suture size. Strain ratios suggest that shear is an important strain regime in the squamosal suture. This study is consistent with the hypothesis that larger sutures help reduce the likelihood of suture failure under high biting loads. Am J Phys Anthropol 153:260–268, 2014. © 2013 Wiley Periodicals, Inc.     

Masticatory biomechanics and its relevance to early hominid phylogeny: an examination of palatal thickness using finite-element analysis

It has been proposed that morphological characters functionally related to mastication may be unreliable indicators of early hominid phylogeny. One hypothesis states that masticatory characters are highly prone to homoplasy. A second hypothesis states that such characters are likely to be morphologically integrated and thus violate the assumption of character independence implicit in all phylogenetic analyses. Evaluation of these hypotheses requires that masticatory features be accurately identified, but, to date, there have been relatively few attempts to test precisely which early hominid features are functionally related to chewing. This paper uses finite-element analysis to evaluate the functional relationships of a character--palatal thickness--that is one of several Paranthropus synapomorphies putatively related to mastication. A finite-element model of 145,680 elements was created from sixty-one 2-mm-thick CT scans of a Macaca fascicularis skull. The model was assigned the elastic properties of facial bone and loaded with muscle forces corresponding to the moment of centric occlusion during mastication. The model was constrained so as to produce a reaction force (corresponding to the bite force) at M(1). With a few exceptions, the strain patterns in the finite-element model compare well with those gathered from published and unpublished bone-strain experiments. The model was then modified to have a thick palate. The model was reloaded using an identical loading regime, and the strain patterns of the original and thick-palate models were compared. Although a thickened palate acts to reduce palatal strain, strains are elevated in other facial regions. This suggests that a thick palate would not have evolved in isolation as an adaptation to withstand masticatory stress. Rather, a thick palate may have evolved in concert with a suite of other facial features that share a stress-resistance function. This appears to be consistent with hypotheses positing that at least some facial features related to chewing evolved in an integrated fashion. More functional studies of other facial features are needed, as are formal studies of morphological integration.     

Musical experience and the aging auditory system: implications for cognitive abilities and hearing speech in noise

Much of our daily communication occurs in the presence of background noise, compromising our ability to hear. While understanding speech in noise is a challenge for everyone, it becomes increasingly difficult as we age. Although aging is generally accompanied by hearing loss, this perceptual decline cannot fully account for the difficulties experienced by older adults for hearing in noise. Decreased cognitive skills concurrent with reduced perceptual acuity are thought to contribute to the difficulty older adults experience understanding speech in noise. Given that musical experience positively impacts speech perception in noise in young adults (ages 18-30), we asked whether musical experience benefits an older cohort of musicians (ages 45-65), potentially offsetting the age-related decline in speech-in-noise perceptual abilities and associated cognitive function (i.e., working memory). Consistent with performance in young adults, older musicians demonstrated enhanced speech-in-noise perception relative to nonmusicians along with greater auditory, but not visual, working memory capacity. By demonstrating that speech-in-noise perception and related cognitive function are enhanced in older musicians, our results imply that musical training may reduce the impact of age-related auditory decline.     

Fusion patterns of craniofacial sutures in rhesus monkey skulls of known age and sex from Cayo Santiago

Bones of the face and cranial vault meet at sutural boundaries. These sutures are of great importance for craniofacial growth. Although the effects that the sutures have on modulating craniofacial strains have been investigated, how sutural fusion influences primate craniofacial biomechanics and adaptation are less considered. Confounding this problem is the lack of any systematic data on patterns of craniofacial sutural fusion from animals of known age and sex. This study examined the status of 28 sutures in Macaca mulatta skulls from a collection of animals of known age and sex from Cayo Santiago, Puerto Rico. Survival analysis showed that most animals died before all sutures fused. There was high variation in the age at which individual sutures or sutural sections were fused in M. mulatta, and significant differences in the amount of sutural fusion among regions and between males and females. Intensive fusion of sutures took place between ages 5 and 15. Sutures in the facial area tended to be less fused than in the cranial vault. Between adolescence and adulthood, males tended to have more sutural fusion than females, especially in the facial area. These differences might be biomechanical adaptations during ontogeny to craniofacial sexual dimorphism. These findings enrich our understanding of variation in sutural morphology in rhesus monkeys. Comparative information across primate species is essential for understanding the biomechanics of craniofacial form throughout primate evolution.