Inter-Vertebral Flexibility of the Ostrich Neck: Implications for Estimating Sauropod Neck Flexibility

The flexibility and posture of the neck in sauropod dinosaurs has long been contentious. Improved constraints on sauropod neck function will have major implications for what we know of their foraging strategies, ecology and overall biology. Several hypotheses have been proposed, based primarily on osteological data, suggesting different degrees of neck flexibility. This study attempts to assess the effects of reconstructed soft tissues on sauropod neck flexibility through systematic removal of muscle groups and measures of flexibility of the neck in a living analogue, the ostrich (Struthio camelus). The possible effect of cartilage on flexibility is also examined, as this was previously overlooked in osteological estimates of sauropod neck function. These comparisons show that soft tissues are likely to have limited the flexibility of the neck beyond the limits suggested by osteology alone. In addition, the inferred presence of cartilage, and varying the inter-vertebral spacing within the synovial capsule, also affect neck flexibility. One hypothesis proposed that flexibility is constrained by requiring a minimum overlap between successive zygapophyses equivalent to 50% of zygapophyseal articular surface length (ONP50). This assumption is tested by comparing the maximum flexibility of the articulated cervical column in ONP50 and the flexibility of the complete neck with all tissues intact. It is found that this model does not adequately convey the pattern of flexibility in the ostrich neck, suggesting that the ONP50 model may not be useful in determining neck function if considered in isolation from myological and other soft tissue data.     

Linear mixed models with flexible distributions of random effects for longitudinal data

Normality of random effects is a routine assumption for the linear mixed model, but it may be unrealistic, obscuring important features of among-individual variation. We relax this assumption by approximating the random effects density by the seminonparameteric (SNP) representation of Gallant and Nychka (1987, Econometrics 55, 363-390), which includes normality as a special case and provides flexibility in capturing a broad range of nonnormal behavior, controlled by a user-chosen tuning parameter. An advantage is that the marginal likelihood may be expressed in closed form, so inference may be carried out using standard optimization techniques. We demonstrate that standard information criteria may be used to choose the tuning parameter and detect departures from normality, and we illustrate the approach via simulation and using longitudinal data from the Framingham study.     

The blood/vascular system in a phylogenetic perspective

The genetically and experimentally accessible organs of Drosophila, such as the heart or blood-forming tissues, have become a fertile ground for systematic projects of gene discovery and for functional studies of gene networks and signaling pathways. One argument justifying this approach is the often-tacit assumption that clear-cut homologies can be established between the Drosophila organs and their vertebrate counterparts. Here we investigate this assumption by surveying pertinent aspects of vascular structure and development in different invertebrate phyla, in the hope that this information will help to reveal the ancestral condition of the vascular system. Evolutionary scenarios that derive the structure of the cardiovascular system of extant animal taxa from the ancestral condition will be used to qualify hypotheses regarding homologies that are based on molecular similarities.     

豆科根瘤内气体交换和气体扩散模型研究

近年来的研究表明根瘤皮层内存在着可调节的气体扩散屏障,它是由根瘤皮层内的一层细胞及填充在胞间隙的水层构成的,而根瘤是通过改变填充该层胞间隙的水层厚度来调节对气体扩散的阻力。本文概述了关于模拟豆科根瘤内气体交换和气体扩散的数学模型研究,阐明调节根瘤内含类菌体细胞维持低氧分压的有关问题。模型研究使我们获得了对共生固氮根瘤内极为复杂的微生态环境的初步认识,有待于通过改进试验和借助其他理论进一步探索根瘤气体交换和气体扩散的本质。     

Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation

Adaptability to a variety of environmental conditions is a prominent feature of Homo sapiens. We hypothesize that this feature can be explained by evolutionary changes in gene promoters active in the brain prefrontal cortex leading to a more flexible gene regulation network. The genotype-dependent range of gene expression can be broader in humans than in other higher primates. Thus, we searched for specific signatures of evolutionary changes in promoter architectures of multiple hominid genes, including the genes active in human cortical neurons that may indicate an increase of variability of gene expression rather than just changes in the level of expression, such as downregulation or upregulation of the genes. We performed a whole-genome search for genetic-based alterations that may impact gene regulation “flexibility” in a process of hominids evolution, such as (i) CpG dinucleotide content, (ii) predicted nucleosome-DNA dissociation constant, and (iii) predicted affinities for TATA-binding protein (TBP) in gene promoters. We tested all putative promoter regions across the human genome and especially gene promoters in active chromatin state in neurons of prefrontal cortex, the brain region critical for abstract thinking and social and behavioral adaptation. Our data imply that the origin of modern man has been associated with an increase of flexibility of promoter-driven gene regulation in brain. In contrast, after splitting from the ancestral lineages of H. sapiens, the evolution of ape species is characterized by reduced flexibility of gene promoter functioning, underlying reduced variability of the gene expression.     

Sedimentation velocity of intrinsically disordered proteins: what information can we actually obtain?

Intrinsically disordered proteins are a challenge to characterise structurally because of their innate flexibility. Hydrodynamic methods such as sedimentation velocity analytical ultracentrifugation have been proposed as methods for their characterisation. By examining in detail this assumption we show that although velocity measurements do yield information on gross conformation, the information is restricted to only the weight averaged sedimentation and diffusion coefficients of the conformational ensemble.     

微阵列数据揭示基因在癌样本中广泛表达

癌的发生与发展过程涉及大量基因的异常表达。在目前基因表达谱分析中采用的标准化方法通常假设在疾病中差异表达的基因的比例很小并且差异上、下调的比例大致相等。这个被研究者所广泛采用的标准化的前提假设尚未被充分地论证过。通过分析胰腺癌的两套表达谱数据,我们发现在胰腺癌样本中基因表达的中值显著高于正常样本,提示传统的标准化假设并不适用于胰腺癌表达谱数据。采用标准化数据会导致错误地判断大量的差异下调的基因并失查许多差异上调的基因。采用原始数据分析发现在胰腺癌中的基因表达有广泛上调的特征,为深入研究胰腺癌的发生和发展机制提供了新线索。     

Correlation between gene expression and GO semantic similarity

This research analyzes some aspects of the relationship between gene expression, gene function, and gene annotation. Many recent studies are implicitly based on the assumption that gene products that are biologically and functionally related would maintain this similarity both in their expression profiles as well as in their gene ontology (GO) annotation. We analyze how accurate this assumption proves to be using real publicly available data. We also aim to validate a measure of semantic similarity for GO annotation. We use the Pearson correlation coefficient and its absolute value as a measure of similarity between expression profiles of gene products. We explore a number of semantic similarity measures (Resnik, Jiang, and Lin) and compute the similarity between gene products annotated using the GO. Finally, we compute correlation coefficients to compare gene expression similarity against GO semantic similarity. Our results suggest that the Resnik similarity measure outperforms the others and seems better suited for use in gene ontology. We also deduce that there seems to be correlation between semantic similarity in the GO annotation and gene expression for the three GO ontologies. We show that this correlation is negligible up to a certain semantic similarity value; then, for higher similarity values, the relationship trend becomes almost linear. These results can be used to augment the knowledge provided by clustering algorithms and in the development of bioinformatic tools for finding and characterizing gene products.     

Phenotypic flexibility in basal metabolic rate and the changing view of avian physiological diversity: a review

Comparative analyses of avian energetics often involve the implicit assumption that basal metabolic rate (BMR) is a fixed, taxon-specific trait. However, in most species that have been investigated, BMR exhibits phenotypic flexibility and can be reversibly adjusted over short time scales. Many non-migrants adjust BMR seasonally, with the winter BMR usually higher than the summer BMR. The data that are currently available do not, however, support the idea that the magnitude and direction of these adjustments varies consistently with body mass. Long-distance migrants often exhibit large intra-annual changes in BMR, reflecting the physiological adjustments associated with different stages of their migratory cycles. Phenotypic flexibility in BMR also represents an important component of short-term thermal acclimation under laboratory conditions, with captive birds increasing BMR when acclimated to low air temperatures and vice versa. The emerging view of avian BMR is of a highly flexible physiological trait that is continually adjusted in response to environmental factors such as temperature. The within-individual variation observed in avian BMR demands a critical re-examination of approaches used for comparisons across taxa. Several key questions concerning the shapes and other properties of avian BMR reaction norms urgently need to be addressed, and hypotheses concerning metabolic adaptation should explicitly account for phenotypic flexibility.     

Chromatin looping and the probability of transcription

Recent studies of several multigene clusters have shown that gene activation by a remote enhancer is associated with chromatin loop formation. It is not fully understood how a chromatin loop forms in a nucleus or how it is involved in gene regulation. In this article, we propose that the major feature that determines loop formation is the flexibility of chromatin, and that this flexibility is modulated by histone acetylation (and other modifications). Thus, histone modifications will modulate distribution of the preferential looping site in chromatin, which, in turn, determines the probability of interaction between a remote enhancer and the cognate genes. This model can explain gene expression changes in the Hoxd gene cluster and the beta-globin locus.     

Microarray analysis of relative gene expression stability for selection of internal reference genes in the rhesus macaque brain

Background  

Normalization of gene expression data refers to the comparison of expression values using reference standards that are consistent across all conditions of an experiment. In PCR studies, genes designated as "housekeeping genes" have been used as internal reference genes under the assumption that their expression is stable and independent of experimental conditions. However, verification of this assumption is rarely performed. Here we assess the use of gene microarray analysis to facilitate selection of internal reference sequences with higher expression stability across experimental conditions than can be expected using traditional selection methods.     

Potential influence of the first PCR cycles in real-time comparative gene quantifications

There is an underlying assumption in real-time PCR that the amplification efficiency is equal from the first cycles until a signal can be detected. In this study, we evaluated this assumption by analyzing genes with known gene copy number using real-time PCR comparative gene quantifications. Listeria monocytogenes has six 23S rRNA gene copies and one copy of the hlyA gene. We determined 23S rRNA gene copy numbers between 0.9 and 1.6 relative to hlyA when applying the comparative gene quantification approach. This paper focuses on the first cycles of PCR to explain the difference between known and determined gene copy numbers. Both theoretical and experimental evaluations were done. There are three different products (types 1-3) dominating in the first cycles. Type 1 is the original target, type 2 are undefined long products, while type 3 are products that accumulate during PCR. We evaluated the effects of type 1 and 2 products during the first cycles by cutting the target DNA with a restriction enzyme that cuts outside the boundaries of the PCR products. The digestion resulted in a presumed increased amplification efficiency for type 1 and 2 products. Differences in the amplification efficiencies between type 1, 2, and 3 products may explain part of the error in the gene copy number determinations using real-time PCR comparative gene quantifications. Future applications of real-time PCR quantifications should account for the effect of the first few PCR cycles on the conclusions drawn.     

Identification of regions of potential flexibility in protein structures: folding units and correlations with intron positions

An algorithm has been developed to estimate flexibility for potential hinge motion at specified residues, that is, the mutual movement of two domains by rotation around a set of main-chain dihedral angles with torsion angles of neighboring side chains as variables. Such conformational changes must occur without severe atomic collisions. Flexible hinges have been found that satisfy such criteria. Sequence flexibility charts were obtained by plotting the flexibility of each residue against the residue number. Such charts were calculated for 10 proteins (ovomucoid third domain, cytochrome c, lysozyme, hemoglobin β-chain, α-chymotrypsin, elastase, carboxypeptidase A, dihydrofolate reductase, triosephosphate isomerase, and alcohol dehydrogenase) taken from the Protein Data Bank. The first step of unfolding is likely to occur at the hinge point with the largest flexibility. Following this idea, the polypeptide chain can be dissected into several folding units according to the sequence flexibility chart. When two domains are separated by conformational changes at such a hinge, the sequence flexibility chart for each domain changes, and it is recalculated and used to indicate subsequent unfolding steps. In this process of iterative estimation of flexibile hinges, some well-isolated hinges, or the border line between flexible and inflexible regions, were found to be directly at or close to the positions of splice junctions in the eukaryotic genes. Of a total of 45 splice junctions in the 10 proteins examined in this paper, 38 junctions can be identified as flexible hinges between folding units. We suggest that the iterative estimation of flexible hinges may define an array of possible folding/unfolding paths, and that the exon–intron arrangement in the gene may be closely correlated with the folding process of the protein.     

Individual consistency and flexibility in human social information use

Copying others appears to be a cost-effective way of obtaining adaptive information, particularly when flexibly employed. However, adult humans differ considerably in their propensity to use information from others, even when this ‘social information’ is beneficial, raising the possibility that stable individual differences constrain flexibility in social information use. We used two dissimilar decision-making computer games to investigate whether individuals flexibly adjusted their use of social information to current conditions or whether they valued social information similarly in both games. Participants also completed established personality questionnaires. We found that participants demonstrated considerable flexibility, adjusting social information use to current conditions. In particular, individuals employed a ‘copy-when-uncertain’ social learning strategy, supporting a core, but untested, assumption of influential theoretical models of cultural transmission. Moreover, participants adjusted the amount invested in their decision based on the perceived reliability of personally gathered information combined with the available social information. However, despite this strategic flexibility, participants also exhibited consistent individual differences in their propensities to use and value social information. Moreover, individuals who favoured social information self-reported as more collectivist than others. We discuss the implications of our results for social information use and cultural transmission.     

Somatic association of homoeologous chromosomes in Triticum aestivum

The distributions of distances between members of homoeologous pairs was studied in common wheat in root-tip cells and meiocytes. In the majority of the pairs the mean distances were found to be significantly shorter than that calculated for two randomly distributed chromosomes. It could be concluded that homoeologues are loosely associated in somatic cells and more markedly so in meiocytes. However, this association is less intimate than that established previously for homologues. The tests were made in material which carries the association suppressor gene in two doses and the present findings support the assumption that in this dosage the suppressor gene has a smaller effect on homologues than on homoeologues.     

Gene "volatility" is most unlikely to reveal adaptation

It has recently been claimed that adaptive molecular evolution can be detected within single genome sequences by use of gene "volatility" scores. However, the approach used was entirely based on the assumption that synonymous codon usage is normally shaped by selection for low volatility; this is most unlikely to be true. Furthermore, even if that assumption could be justified, the method would clearly lack power, detecting only genes where a very large number of nonsynonymous substitutions had occurred. Volatility scores are susceptible to other influences. The unusually high volatilities of the Mycobacterium tuberculosis and Plasmodium falciparum genes that were identified as putatively having undergone adaptive changes were largely the result of internally repetitive structures, in which unusual codon usage was caused by the mechanisms that generated this repetition rather than by adaptive changes.