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Abstract Background The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease. Results Relative Synonymous Codon Usage (RSCU) values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA). The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through in toto transfer of an avian influenza virus. Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes. Conclusions Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses.

Nothronychus was a large, derived therizinosaur from the Upper Cretaceous of Utah and New Mexico. The genus is known from elements that have been referred to single individuals. Therizinosaurs were unusual maniraptoran theropods close to the origin of birds. The axial skeleton is extensively pneumatized, but CT scans reveal an apneumatic synsacrum. Inferred air sacs invade the basicranium, the presacral vertebrae, and the proximal caudal vertebrae, but bypassed the sacrum resulting in a caudosacral hiatus similar to some sauropods and reflecting the development of multiple diverticula from the abdominal air sac. The vertebral pneumatic chambers are described here and compared with those observed in the theropod Allosaurus and the recent avian Dinornis. The vertebrae of Nothronychus are intermediate between those two theropods. It is inferred to have possessed avian‐like abdominal air sacs. This theropod would have had unidirectional lungs, as in birds, but this character cannot be related to endothermy. CT‐scans of the vertebra of Nothronychus graffami reveal an intermediate structure between more basal theropods and birds. Uni‐directional airflow as in birds is supported, but this trait does not necessarily imply endothermy. [ABSTRACT FROM AUTHOR]

Abstract Background The pluripotency and self-renewal capabilities, which define the "stemness" state, of mouse embryonic stem (ES) cells, are usually investigated by functional assays or quantitative measurements of the expression levels of known ES cell markers. Strong correlations between these expression levels and functional assays, particularly at the early stage of cell differentiation, have usually not been observed. An effective molecular diagnostic to properly identify the differentiation state of mouse ES cells, prior to further experimentation, is needed. Results A novel molecular pattern recognition procedure has been developed to diagnose the differentiation state of ES cells. This is based on mRNA transcript levels of genes differentially expressed between ES cells and their differentiating progeny. Large publicly available ES cell data sets from various platforms were used to develop and test the diagnostic model. Signature patterns consisting of five gene expression levels achieved high accuracy at determining the cell state (sensitivity and specificity > 97%). Conclusion The effective ES cell state diagnostic scheme described here can be implemented easily to assist researchers in identifying the differentiation state of their cultures. It also provides a step towards standardization of experiments relying on cells being in the stem cell or differentiating state.

Abstract Background Diseases of cartilage, such as arthritis and degenerative disc disease, affect the majority of the general population, particularly with ageing. Discovery and understanding of the genes and pathways involved in cartilage biology will greatly assist research on the development, degeneration and disorders of cartilage. Description We have established the Integrated Cartilage Gene Database (iCartiGD) of genes that are known, based on results from high throughput experiments, to be expressed in cartilage. Information about these genes is extracted automatically from public databases and presented as a single page report via a web-browser. A variety of flexible search options are provided and the chromosomal distribution of cartilage associated genes can be presented. Conclusion iCartiGD provides a comprehensive source of information on genes known to be expressed in cartilage. It will remain current due to its automatic update capability and provide researchers with an easily accessible resource for studies involving cartilage. Genetic studies of the development and disorders of cartilage will benefit from this database.

Abstract Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454.

A hybrid gel has been developed by combining two supramolecular gelators. Each gelator endows the hybrid gel with its own characteristics. One gelator enables pH-mediated controlled release of the active pharmaceutical ingredient naproxen, while the other new gelator enhances mechanical stability. Self-assembly thus gives multi-functional gels with potential applications. [ABSTRACT FROM AUTHOR]

Byline: Liping Du, Shuanhu Wu, Alan Wee-Chung Liew, David K. Smith, Hong Yan We propose a new strategy to analyse the periodicity of gene expression profiles using Singular Spectrum Analysis (SSA) and Autoregressive (AR) model based spectral estimation. By combining the advantages of SSA and AR modelling, more periodic genes are extracted in the Plasmodium falciparum data set, compared with the classical Fourier analysis technique. We are able to identify more gene targets for new drug discovery, and by checking against the seven well-known malaria vaccine candidates, we have found five additional genes that warrant further biological verification.

The studies have highlighted the key role of solubility in affecting gelation and have shown that many facets of the gel-forming process have depended on this major parameter. The key parameters developed from considering gelator solubility, [T.sub.calc] and critical concentration ([C.sub.crit]) and their subtle impact on thermal stability ([T.sub.gel]) and minimum gelation concentration (MGC) are used in the field of self-assembling gel-phase materials.

The one- and two-component gelation systems that are direct structural analogues are compared and the molecular recognition pathways that underpin fibrillar self-assembly are observed. The self-assembly of these dendrimers in toluene is elucidated using thermal measurements, scanning electron microscopy, and small-angle X-ray scattering.

A study is conducted to illustrate that using two components enhances the tunability of gel-phase materials and highlights three simple ways in which the macroscopic properties and microstructural features of these gels can be conducted. The ability of both the molecular structures of the two components and the concentration of the sample employed to control the Tgel endows the materials with considerable additional tunability.

The hindlimb musculature of the basal therizinosaur Falcarius utahensis is reconstructed using observable muscle scars, information from extant birds and crocodylians, and current models of Tyrannosaurus rex. Its ancestral phylogenetic position within Therizinosauria based on recent analyses is accepted here. Falcarius is characterized by a propubic pelvis, whereas the more derived therizinosaur Nothronychus had an incipiently opisthopubic pelvis with a highly modified ilium. Therefore, the femur of Falcarius was modelled with a plesiomorphic vertical orientation at rest. The M. caudofemoralis longus was well-developed, indicating a hip-propelled gait, with a sinuous stride. These results strongly suggest that the opisthopubic pelvis, associated muscular changes, avian stance and mode of walking evolved more than once: once within the therizinosaur lineage and once beneath the paravian node. The center of mass would have been located roughly under the acetabulum. Falcarius would have been characterized by a narrow abdomen and a non-waddling gait, in contrast to the more derived Nothronychus , with an inferred knee-based retraction system. • A muscle reconstruction is provided for the hindlimb of the basal therizinosaur Falcarius utahensis is provided. • Anatomical associated with the development of the opisthopubic pelvis within the therizinosaur lineage are discussed. • The evolution of the opisthopubic pelvis must have occurred at least twice within maniraptorans. [ABSTRACT FROM AUTHOR]