Unity and diversity in human language

Human language is both highly diverse-different languages have different ways of achieving the same functional goals-and easily learnable. Any language allows its users to express virtually any thought they can conceptualize. These traits render human language unique in the biological world. Understanding the biological basis of language is thus both extremely challenging and fundamentally interesting. I review the literature on linguistic diversity and language universals, suggesting that an adequate notion of 'formal universals' provides a promising way to understand the facts of language acquisition, offering order in the face of the diversity of human languages. Formal universals are cross-linguistic generalizations, often of an abstract or implicational nature. They derive from cognitive capacities to perceive and process particular types of structures and biological constraints upon integration of the multiple systems involved in language. Such formal universals can be understood on the model of a general solution to a set of differential equations; each language is one particular solution. An explicit formal conception of human language that embraces both considerable diversity and underlying biological unity is possible, and fully compatible with modern evolutionary theory.     

Simple and fast alignment of metabolic pathways by exploiting local diversity

MOTIVATION: An important tool for analyzing biological networks is the ability to perform homology searches, i.e. given a pattern network one would like to be able to search for occurrences of similar (sub)networks within a set of host networks. In the context of metabolic pathways, Pinter et al. [Bioinformatics, 2005] proposed to solve this computationally hard problem by restricting it to the case where both the pattern and host networks are trees. This restriction, however, severely limits the applicability of their algorithm. RESULTS: We propose a very fast and simple algorithm for the alignment of metabolic pathways that does not restrict the topology of the host or pattern network in any way; instead, our algorithm exploits a natural property of metabolic networks that we call 'local diversity property'. Experiments on a test bed of metabolic pathways from the BioCyc database indicate that our algorithm is much faster than the restricted algorithm of Pinter et al.-the metabolic pathways of two organisms can be aligned in mere seconds-and yet has a wider range of applicability and yields new biological insights. Our ideas can likely be extended to work for the alignment of various types of biological networks other than metabolic pathways. AVAILABILITY: Our algorithm has been implemented in C++ as a user-friendly metabolic pathway alignment tool called METAPAT. The tool runs under Linux or Windows and can be downloaded at http://theinf1.informatik.uni-jena.de/metapat/     

Future of adenoviruses in the gene therapy of arthritis

Recombinant adenoviruses are straightforward to produce at high titres, have a promiscuous host-range, and, because of their ability to infect nondividing cells, lend themselves to in vivo gene delivery. Such advantages have led to their widespread and successful use in preclinical studies of arthritis gene therapy. While adenoviral vectors are well suited to 'proof of principle' experiments in laboratory animals, there are several barriers to their use in human studies at this time. Transient transgene expression limits their application to strategies, such as synovial ablation, which do not require extended periods of gene expression. Moreover, there are strong immunological barriers to repeat dosing. In addition, safety concerns predicate local, rather than systemic, delivery of the virus. Continued engineering of the adenoviral genome is producing vectors with improved properties, which may eventually overcome these issues. Promising avenues include the development of 'gutted' vectors encoding no endogenous viral genes and of adenovirus–AAV chimeras. Whether these will offer advantages over existing vectors, which may already provide safe, long-term gene expression following in vivo delivery, remains to be seen.     

Virus chimeras for gene therapy, vaccination, and oncolysis: adenoviruses and beyond

Several challenges need to be addressed when developing viruses for clinical applications in gene therapy, vaccination, or viral oncolysis, including specific and efficient target cell transduction, virus delivery via the blood stream, and evasion of pre-existing immunity. With rising frequency, these goals are tackled by generating chimeric viruses containing nucleic acid fragments or proteins from two or more different viruses, thus combining different beneficial features of the parental viruses. These chimeras have boosted the development of virus-based treatment regimens for major inherited and acquired diseases, including cancer. Using adenoviruses as the paradigm and prominent examples from other virus families, we review the technological and functional advances in therapeutic virus chimera development and recent successful applications that can pave the way for future therapies.     

Unity and diversity in biochemistry.

A consideration of A Biochemical Phylogeny of the Protists, by M.A. Ragan and D.J. Chapman (Academic Press, 1978) and Biochemical Adaptation to Environmental Change, ed. by R.M.S. Smellie and J.F. Pennock (the Biochemical Society, 1976), within some thoughts on biochemical evolution.     

Unity in diversity: Lessons from macaque societies

The macaque radiation is as old as the hominin radiation, approximately 7 million years. After Homo, Macaca has the widest geographical range among primates, and both of these genera are present in tropical and temperate regions as well. Whereas the single extant representative of the genus Homo diverged through processes of cultural diversification, extant species of macaques emerged through processes of evolutionary diversification. Macaque societies are characterized by profound unity and great diversity, and can best be described as variations on the same theme. To understand macaque variation and adaptation, we must take into account the processes that insure the persistence of their societies across generations and environments.     

Two pathways for store-mediated calcium entry differentially dependent on the actin cytoskeleton in human platelets

A major pathway for stimulated Ca(2+) entry in non-excitable cells is activated following depletion of intracellular Ca(2+) stores. Secretion-like coupling between elements in the plasma membrane (PM) and Ca(2+) stores has been proposed as the most likely mechanism to activate this store-mediated Ca(2+) entry (SMCE) in several cell types. Here we identify two mechanisms for SMCE in human platelets activated by depletion of two independent Ca(2+) pools, which are differentially modulated by the actin cytoskeleton. Ca(2+) entry induced by depletion of a 2,5-di-(tert-butyl)-1,4-hydroquinone (TBHQ)-sensitive pool is increased by disassembly of the actin cytoskeleton and that induced by a TBHQ-insensitive pool is reduced. Stabilization of the actin cytoskeleton prevented Ca(2+) entry by both mechanisms. We propose that the membrane-associated actin network prevents constitutive Ca(2+) entry via both pathways. Reorganization of the actin cytoskeleton permits the activation of Ca(2+) entry via both mechanisms, but only SMCE activated by the TBHQ-insensitive pool requires new actin polymerization, which may support membrane trafficking toward the PM.     

Unity and diversity in the insect photoperiodic mechanism*

This review examines some of the models to account for time measurement in insect photoperiodism. It considers the supporting evidence for these models and the attempts to discriminate among them. Although hourglass timers may exist, it is suggested that most photoperiodic mechanisms, including many hourglass‐like timers, are circadian‐based, making Bünning's original hypothesis, that the circadian system somehow provides the essential “clockwork” for photoperiodic timing, the most persuasive unifying principle. The apparent diversity among modern species in their modes of time measurement is probably the result of differences between the underlying circadian systems that were adopted for seasonal night length measurement as the insects, or groups of insects, moved northwards into areas with a pronounced winter season. Photoperiodic time measurement, therefore, exhibits both unity (in their common circadian basis) and diversity in detail. Attention to this diversity may provide invaluable insights into the problem of photoperiodic time measurement at comparative, and molecular, levels.     

Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity

The neurexins are neuronal proteins that function as cell adhesion molecules during synaptogenesis and in intercellular signaling. Although mammalian genomes contain only three neurexin genes, thousands of neurexin isoforms may be expressed through the use of two alternative promoters and alternative splicing at up to five different positions in the pre-mRNA. To begin understanding how the expression of the neurexin genes is regulated, we have determined the complete nucleotide sequence of all three human neurexin genes: NRXN1, NRXN2, and NRXN3. Unexpectedly, two of these, NRXN1 ( approximately 1.1 Mb) and NRXN3 ( approximately 1.7 Mb), are among the largest known human genes. In addition, we have identified several conserved intronic sequence elements that may participate in the regulation of alternative splicing. The sequences of these genes provide insight into the mechanisms used to generate the diversity of neurexin protein isoforms and raise several interesting questions regarding the expression mechanism of large genes.     

Oncolytic adenoviruses in anticancer therapy: Current status and prospects

Lytic virus infection results in production of a virus progeny and lysis of the infected cell. Tumor cells are usually more sensitive to virus infection. Studies indicate that viral oncolysis provides a promising alternative approach to cancer therapy. The ability of viruses to selectively kill cancer cells is long known, but construction of virus variants with an improved therapeutic potential was impossible until recent advances in virus and cell molecular biology and the development of modern methods for directed modification of viruses. Adenoviruses are one of the best studied models of oncolytic viruses. These DNA viruses are convenient for genetic manipulation and show minimal pathogenicity. The review summarizes the data on the directions and approaches to generation of highly efficient variants of oncolytic adenoviruses. The approaches include introduction of directed genetic modifications into the virus genome, accelerated selection of oncolytic virus variants following treatment with mutagens, the use of adenoviruses as vectors to introduce therapeutic gene products, optimization of viral delivery systems, minimization of the negative effects from the host immune system, etc. The dynamic development of studies in the field holds promise that many variants of oncolytic adenoviruses will find clinical application in the nearest future.     

Overreliance on the hexon gene, leading to misclassification of human adenoviruses

The genome of human adenovirus (HAdV) D30 was sequenced in depth. Sequence assembly and analysis revealed two distinct viral sequences with identical hexon genes, which were the same as the one previously reported for HAdV-D30. However, one of the two viruses was found to be a recombinant of HAdV-D29. Exclusive reliance on serum neutralization can lead to mischaracterization of adenoviruses and miss coinfections. Whole-genome sequencing remains the gold standard for proper classification of HAdVs.     

Cytochromes P450: exploiting diversity and enabling application as biocatalysts

The remarkable chemical reactivity and substrate range displayed by cytochromes P450 (P450s) renders them attractive as potential catalysts for a host of challenging chemical reactions in industry. The opportunities afforded by these biocatalysts are increased by the availability of greater diversity provided by the genomic resource and the variant libraries of well-known P450s produced by rational and random engineering techniques. The exploitation of this enormous diversity will require novel tools in screening, to identify enzyme reactions of interest, and also in the enabling of these valuable activities through protein engineering and bioprocess optimisation.     

Yaba-like disease virus: an alternative replicating poxvirus vector for cancer gene therapy

Vaccinia virus is being investigated as a replicating vector for tumor-directed gene therapy. However, the majority of cancer patients have preformed immunologic reactivity against vaccinia virus, as a result of smallpox vaccination, which may limit its use as a vector. The Yaba-like disease (YLD) virus was investigated here as an alternative, replicating poxvirus for cancer gene therapy. We have demonstrated that the YLD virus does not cross-react with vaccinia virus antibodies, and it replicates efficiently in human tumor cells. YLD virus can be expanded and purified to high titer in CV-1 cells under conditions utilized for vaccinia virus. The YLD virus RNA polymerase was able to express genes regulated by a synthetic promoter designed for use in orthopoxviruses. We sequenced the YLD virus TK gene and created a shuttle plasmid, which allowed the recombination of the green fluorescent protein (GFP) gene into the YLD virus. In a murine model of ovarian cancer, up to 38% of cells in the tumor expressed the GFP transgene 12 days after intraperitoneal virus delivery. YLD virus has favorable characteristics as a vector for cancer gene therapy, and this potential should be explored further.     

Retroviral vectors containing putative internal ribosome entry sites: development of a polycistronic gene transfer system and applications to human gene therapy.

Recombinant retroviral vectors producing multicistronic mRNAs were constructed. Picornavirus putative internal ribosome entry sites (IRES) were used to confer cap-independent translation of an internal cistron. Internal cistrons were engineered by ligation of various lengths of the IRES of encephalomyocarditis (EMC) virus or polio virus to the E. coli chloramphenicol acetyltransferase (CAT) gene. The IRES/CAT fusions were introduced into retroviral vectors 3' to the translation stop codon of the neomycin phosphotransferase (NEO) gene, and the molecular constructs transfected into retroviral vector packaging lines. Retroviral vector producer cells efficiently express the internal CAT gene product only when the full length IRES is used. Both the EMC/CAT and polio/CAT retroviral vectors produced high titer vector supernatant capable of productive transduction of target cells. To test the generality of this gene transfer system, a retroviral vector containing an IRES fusion to the human adenosine deaminase (ADA) gene was constructed. Producer cell supernatant was used to transduce NIH/3T3 cells, and transduced cells were shown to express NEO, and ADA. Novel three-gene-containing retroviral vectors were constructed by introducing the EMC/ADA fusion into either an existing internal-promoter-containing vector, or a polio/CAT bicistronic vector. Producer cell clones of the three-gene vectors synthesize all three gene products, were of high titer, and could productively transduce NIH/3T3 cells. By utilizing cap-independent translation units, IRES vectors can produce polycistronic mRNAs which enhance the ability of retroviral-mediated gene transfer to engineer cells to produce multiple foreign proteins.