Antibody diversity: Can more than one gene encode each variable region?

The germ line and somatic mutation theories of antibody diversity inadequately explain some recent structural and genetic data. The episomal insertion theory or some modification of it, seems more consistent with contemporary observations that suggest that immunoglobulin variable regions contain information encoded in separate portions of the genome. The model proposes that at least three groups of genes control the synthesis of a single polypeptide chain. Thegroup one genes code for the relatively invariant portions of the variable region and are few in number (perhaps one per subgroup). A larger number ofgroup two genes encode the hypervariable regions, while a small number ofgroup three genes encode the constant regions. A copy choice mechanism is favored for the gene interaction necessary for the synthesis of a single polypeptide chain.     

Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?

Selenocysteine (Sec) is co-translationally inserted into selenoproteins in response to codon UGA with the help of the selenocysteine insertion sequence (SECIS) element. The number of selenoproteins in animals varies, with humans having 25 and mice having 24 selenoproteins. To date, however, only one selenoprotein, thioredoxin reductase, has been detected in Caenorhabditis elegans, and this enzyme contains only one Sec. Here, we characterize the selenoproteomes of C.elegans and Caenorhabditis briggsae with three independent algorithms, one searching for pairs of homologous nematode SECIS elements, another searching for Cys- or Sec-containing homologs of potential nematode selenoprotein genes and the third identifying Sec-containing homologs of annotated nematode proteins. These methods suggest that thioredoxin reductase is the only Sec-containing protein in the C.elegans and C.briggsae genomes. In contrast, we identified additional selenoproteins in other nematodes. Assuming that Sec insertion mechanisms are conserved between nematodes and other eukaryotes, the data suggest that nematode selenoproteomes were reduced during evolution, and that in an extreme reduction case Sec insertion systems probably decode only a single UGA codon in C.elegans and C.briggsae genomes. In addition, all detected genes had a rare form of SECIS element containing a guanosine in place of a conserved adenosine present in most other SECIS structures, suggesting that in organisms with small selenoproteomes SECIS elements may change rapidly.     

Detritivores in Kenyan highland streams: more evidence for the paucity of shredders in the tropics?

1. The relationship between coarse particulate organic matter (CPOM) standing stock and benthic macroinvertebrate assemblages in Kenyan highland streams was determined by sampling seven sites on three rivers (2000–2700 m a.s.l.). Taxa recorded were allocated to functional feeding groups using published literature, mouthpart analysis and examination of gut contents. Patterns were compared with five structurally similar streams in three areas of Europe (south-west France, south-east England, north-east England).
2. Number of individuals and proportion of detritivores in Kenyan streams were equivalent to, or greater than, those in European sites. Shredders were, however, almost completely absent from Kenyan sites, despite high standing stocks of CPOM. Shredders were abundant in all European sites.
3. The phenomenon of low shredder abundance has been observed in other tropical streams in south-east Asia and Central and South America but, in contrast to these regions, the African rivers studied were devoid of shrimps or fish which may occupy the shredding niche elsewhere.
4. These preliminary data suggest that shredder-mediated detritus processing, which is a key functional component of streams in the North Temperate Zone, does not operate in East African streams. There are three possible reasons for this. The first is that tropical African rivers are functionally different to those in temperate regions. This could be because of enhanced microbial activity replacing shredder activity at high temperatures. Alternatively, it could be a result of low palatability of detrital inputs from dominant riparian trees in the region. The second and third are methodological: that our allocation to functional feeding groups is incorrect, and that our sampling methods missed a potentially key shredding taxon – the freshwater crab Potamonautes sp.     

Photoinactivation of photosystem II: is there more than one way to skin a cat?

We briefly review the main mechanisms proposed for photodamage to photosystem II (PSII), at the donor and acceptor sides, and then discuss the mechanism whereby filamentous cyanobacteria inhabiting biological sand crusts such as Microcoleus sp. are able to avoid serious damage to their photosynthetic machinery. We show that the decline in fluorescence following exposure to excess light does not reflect a reduction in PSII activity but rather the activation of a non-radiative charge recombination in PSII. Furthermore, we show that the difference in the thermoluminescent peak temperature intensities in these organisms, in the presence and absence of inhibitors such as dichlorophenyl-dimethylurea (DCMU), is smaller than observed in model organisms suggesting that the redox gap between Q(A)? and P???+ is smaller. On the basis of these data, we propose that this could enable an alternative, pheophytin-independent recombination, thereby minimizing the damaging 1O? production associated with radiative recombination.     

Wnt signal transduction: more than one wat to skin a (beta-)cat?

Genetic and biochemical studies have suggested that signal transduction by the Wnt pathway is very different to the familiar protein-kinase cascade of the Ras pathway. Among the more intriguing findings is that beta-catenin, a component of intercellular adhesive junctions, is a central component in the Wnt signalling pathway. Recent studies suggest ways in which beta-catenin might serve as a focal point for regulation of adhesion, gene expression and cell proliferation.     

The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods?

The complete sequence of the mitochondrial genome of the giant tiger prawn, Penaeus monodon (Arthropoda, Crustacea, Malacostraca), is presented. The gene content and gene order are identical to those observed in Drosophila yakuba. The overall AT composition is lower than that observed in the known insect mitochondrial genomes, but higher than that observed in the other two crustaceans for which complete mitochondrial sequence is available. Analysis of the effect of nucleotide bias on codon composition across the Arthropoda reveals a trend with the crustaceans represented showing the lowest proportion of AT-rich codons in mitochondrial protein genes. Phylogenetic analysis among arthropods using concatenated protein-coding sequences provides further support for the possibility that Crustacea are paraphyletic. Furthermore, in contrast to data from the nuclear gene EF1alpha, the first complete sequence of a malacostracan mitochondrial genome supports the possibility that Malacostraca are more closely related to Insecta than to Branchiopoda.     

Why is it important to simultaneously use more than one chiroptical spectroscopic method for determining the structures of chiral molecules?

In recent years, four different chiroptical spectroscopic methods, namely vibrational circular dichroism, vibrational Raman optical activity, electronic circular dichroism, and optical rotatory dispersion, have become popular for establishing the absolute configuration and predominant conformations of chiral molecules in solution state. Many individual laboratories normally utilize only one of these methods to derive the molecular structural information. Although that approach may be satisfactory for most of the molecules studied, it is to be noted that in some instances a single method can give ambiguous conclusions or may not give complete structural information. This article summarizes the situations where simultaneous use of more than one chiroptical spectroscopic method is required to obtain molecular structural information and recommends the routine application of more than one chiroptical spectroscopic method for any given molecule.     

Time, telomeres and tumours: is cellular senescence more than an anticancer mechanism?

Normal diploid cells, by definition, have a limited life span: they senesce after a set number of divisions both in vivo and in culture. It has been hypothesized that the molecular mechanism that measures the life span of a cell probably involves the shortening of telomeres that occurs with each round of DNA replication. This loss of telomeres is thought to induce antiproliferative signals that result in the induction of cellular senescence. In this article, Woodring Wright and Jerry Shay present a hypothesis for the mechanisms by which telomere shortening regulates cellular physiology and argue that cellular senescence is not only an anticancer mechanism but is also the cause of many of the degenerative changes of aging.     

Gene-based modelling for rice: an opportunity to enhance the simulation of rice growth and development?

Process-based crop simulation models require employment of new knowledge for continuous improvement. To simulate growth and development of different genotypes of a given crop, most models use empirical relationships or parameters defined as genetic coefficients to represent the various cultivar characteristics. Such a loose introduction of different cultivar characteristics can result in bias within a simulation, which could potentially integrate to a high simulation error at the end of the growing season when final yield at maturity is predicted. Recent advances in genetics and biomolecular analysis provide important opportunities for incorporating genetic information into process-based models to improve the accuracy of the simulation of growth and development and ultimately the final yield. This improvement is especially important for complex applications of models. For instance, the effect of the climate change on the crop growth processes in the context of natural climatic and soil variability and a large range of crop management options (e.g., N management) make it difficult to predict the potential impact of the climate change on the crop production. Quantification of the interaction of the environmental variables with the management factors requires fine tuning of the crop models to consider differences among different genotypes. In this paper we present this concept by reviewing the available knowledge of major genes and quantitative trait loci (QTLs) for important traits of rice for improvement of rice growth modelling and further requirements. It is our aim to review the assumption of the adequacy of the available knowledge of rice genes and QTL information to be introduced into the models. Although the rice genome sequence has been completed, the development of gene-based rice models still requires additional information than is currently unavailable. We conclude that a multidiscipline research project would be able to introduce this concept for practical applications.     

Regenerative medicine for the treatment of spinal cord injury: more than just promises?

Spinal cord injury triggers a complex set of events that lead to tissue healing without the restoration of normal function due to the poor regenerative capacity of the spinal cord. Nevertheless, current knowledge about the intrinsic regenerative ability of central nervous system axons, when in a supportive environment, has made the prospect of treating spinal cord injury a reality. Among the range of strategies under investigation, cell‐based therapies offer the most promising results, due to the multifactorial roles that these cells can fulfil. However, the best cell source is still a matter of debate, as are clinical issues that include the optimal cell dose as well as the timing and route of administration. In this context, the role of biomaterials is gaining importance. These can not only act as vehicles for the administered cells but also, in the case of chronic lesions, can be used to fill the permanent cyst, thus creating a more favourable and conducive environment for axonal regeneration in addition to serving as local delivery systems of therapeutic agents to improve the regenerative milieu. Some of the candidate molecules for the future are discussed in view of the knowledge derived from studying the mechanisms that facilitate the intrinsic regenerative capacity of central nervous system neurons. The future challenge for the multidisciplinary teams working in the field is to translate the knowledge acquired in basic research into effective combinatorial therapies to be applied in the clinic.     

Tissue engineering skin flaps: which vascular carrier, arteriovenous shunt loop or arteriovenous bundle, has more potential for angiogenesis and tissue generation?

This study was designed to clarify which vascular carrier, the arteriovenous shunt loop or the arteriovenous bundle, has more potential as a vascular carrier for an artificial skin flap in rats. An arteriovenous shunt loop was constructed between the femoral artery and vein using an interpositional artery (group I) or vein (group II) graft. For arteriovenous bundle groups, the femoral artery and vein were used and subdivided into two groups: distal ligation type (group III) and flow-through type (group IV). The vascular pedicle was wrapped with an artificial dermis and implanted beneath the inguinal skin for 4 weeks. For the control group, a folded sheet of artificial dermis without any vascular carrier was embedded. In experiment 1, the volumes of generated tissue within the artificial dermis were measured in the experimental and control groups (n = 5 in each group). In experiment 2, the origin of new blood vessels sprouting from the arteriovenous shunt loop and arteriovenous bundle were evaluated histologically. The volume of generated tissue in the shunt groups was significantly greater than that in the bundle groups (p < 0.01). However, the bundle groups also showed a great potential for producing new tissue. Serial histological studies showed that new capillaries were derived not only from the vasa vasorum of the femoral vessels but directly from the femoral vein in both the shunt and the bundle groups. This "sprouting" was extensively exhibited in the group III. Although the arteriovenous shunt loop showed a greater potential for producing new tissue and capillaries, the distal ligation type of bundle was thought to be an effective and practical vascular carrier for producing a tissue-engineered skin flap.     

Insensitivity to road salt: an advantage for the American bullfrog?

The health of freshwater ecosystems is negatively affected by a multitude of pollutants. In northern latitudes, road deicing agents enter nearby ponds and waterways elevating chloride concentrations in winter and spring. Few studies have examined how amphibians respond to road salt contamination and no study has focused on the response of an invasive amphibian. We examined the effects of NaCl, the most commonly used deicing agent, on the embryos and tadpoles of the American bullfrog, Lithobates catesbeianus, a species that is invasive in many regions around the world. In the first experiment, we exposed L. catesbeianus embryos to ecologically relevant levels of chloride for 60 days. The second experiment examined the indirect consequences of chloride contamination by exposing L. catesbeianus tadpoles to dragonfly larvae. Lithobates catesbeianus did not experience reduced survival, growth, or ability to evade predation in elevated chloride concentrations compared to controls. The lack of a response by L. catesbeianus suggests that its population growth will not be negatively impacted by road salt contamination. This result may be good news for L. catesbeianus, but raises concern for sympatric amphibians that have to contend with negative impacts of both chloride contamination and non-native L. catesbeianus.     

Genomic rearrangements in trypanosomatids: an alternative to the "one gene" evolutionary hypotheses?

Most molecular trees of trypanosomatids are based on point mutations within DNA sequences. In contrast, there are very few evolutionary studies considering DNA (re) arrangement as genetic characters. Waiting for the completion of the various parasite genome projects, first information may already be obtained from chromosome size-polymorphism, using the appropriate algorithms for data processing. Three illustrative models are presented here. First, the case of Leishmania (Viannia) braziliensis/L. (V.) peruviana is described. Thanks to a fast evolution rate (due essentially to amplification/deletion of tandemly repeated genes), molecular karyotyping seems particularly appropriate for studying recent evolutionary divergence, including eco-geographical diversification. Secondly, karyotype evolution is considered at the level of whole genus Leishmania. Despite the fast chromosome evolution rate, there is qualitative congruence with MLEE- and RAPD-based evolutionary hypotheses. Significant differences may be observed between major lineages, likely corresponding to major and less frequent rearrangements (fusion/fission, translocation). Thirdly, comparison is made with Trypanosoma cruzi. Again congruence is observed with other hypotheses and major lineages are delineated by significant chromosome rearrangements. The level of karyotype polymorphism within that "species" is similar to the one observed in "genus" Leishmania. The relativity of the species concept among these two groups of parasites is discussed.     

The sinus venosus myocardium contributes to the atrioventricular canal: potential role during atrioventricular node development?

The presence of distinct electrophysiological pathways within the atrioventricular node (AVN) is a prerequisite for atrioventricular nodal reentrant tachycardia to occur. In this study, the different cell contributions that may account for the anatomical and functional heterogeneity of the AVN were investigated. To study the temporal development of the AVN, the expression pattern of ISL1, expressed in cardiac progenitor cells, was studied in sequential stages performing co‐staining with myocardial markers (TNNI2 and NKX2‐5) and HCN4 (cardiac conduction system marker). An ISL1+/TNNI2+/HCN4+ continuity between the myocardium of the sinus venosus and atrioventricular canal was identified in the region of the putative AVN, which showed a pacemaker‐like phenotype based on single cell patch‐clamp experiments. Furthermore, qPCR analysis showed that even during early development, different cell populations can be identified in the region of the putative AVN. Fate mapping was performed by in ovo vital dye microinjection. Embryos were harvested and analysed 24 and 48 hrs post‐injection. These experiments showed incorporation of sinus venosus myocardium in the posterior region of the atrioventricular canal. The myocardium of the sinus venosus contributes to the atrioventricular canal. It is postulated that the myocardium of the sinus venosus contributes to nodal extensions or transitional cells of the AVN since these cells are located in the posterior region of the AVN. This finding may help to understand the origin of atrioventricular nodal reentrant tachycardia.