Contribution of Pseudogenes to Sequence Diversity

Pseudogenes are very common in the genomes of a wide range of organisms and, although they were originally considered as genetic junk, now several functions have been attributed to them. One important function of pseudogenes, as discussed in this chapter, is to provide material for genetic diversity. This is most prominent in the case of immunological recognition molecules such as immunoglobulins and B- and T-cell receptors, as well as in the case of antigenic variation in intracellular pathogens. Other examples discussed are olfactory receptors, ribosomal proteins, cytochrome P450s, and pseudokinases

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable

The importance of understanding annual and shorter-term temperature patterns and variation in the surface levels of polar soils for terrestrial biota

Ground temperatures in the top few centimetres of the soil profile are key in many biological processes yet remain very poorly documented, especially in the polar regions or over longer timescales. They can vary greatly seasonally and at various spatial scales across the often highly complex and heterogeneous polar landscapes. It is challenging and often impossible to extrapolate soil profile temperatures from meteorological air temperature records. Furthermore, despite the justifiably considerable profile given to contemporary large-scale climate change trends, with the exception of some sites on Greenland, few biological microclimate datasets exist that are of sufficient duration to allow robust linkage and comparison with these large-scale trends. However, it is also clear that the responses of the soil-associated biota of the polar regions to projected climate change cannot be adequately understood without improved knowledge of how landscape heterogeneity affects ground and sub-surface biological microclimates, and of descriptions of these microclimates and their patterns and trends at biologically relevant physical and temporal scales. To stimulate research and discussion in this field, we provide an overview of multi-annual temperature records from 20 High Arctic (Svalbard) and maritime Antarctic (Antarctic Peninsula and Scotia Arc) sites. We highlight important features in the datasets that are likely to have influence on biology in polar terrestrial ecosystems, including (a) summer ground and sub-surface temperatures vary much more than air temperatures; (b) winter ground temperatures are generally uncoupled from air temperatures; (c) the ground thawing period may be considerably shorter than that of positive air temperatures; (d) ground and air freeze–thaw patterns differ seasonally between Arctic and Antarctic; (e) rates of ground temperature change are generally low; (f) accumulated thermal sum in the ground usually greatly exceeds air cumulative degree days. The primary purpose of this article is to highlight the utility and biological relevance of such data, and to this end the full datasets are provided here to enable further analyses by the research community, and incorporation in future wider comparative studies

Living on Cold Substrata: New Insights and Approaches in the Study of Microphytobenthos Ecophysiology and Ecology in Kongsfjorden

Organisms in shallow waters at high latitudes are under pressure due to climate change. These areas are typically inhabited by microphytobenthos (MPB) communities, composed mainly of diatoms. Only sparse information is available on the ecophysiology and acclimation processes within MPBs from Arctic regions. The physico-chemical environment and the ecology and ecophysiology of benthic diatoms in Kongsfjorden (Svalbard, Norway) are addressed in this review. MPB biofilms cover extensive areas of sediment. They show high rates of primary production, stabilise sediment surfaces against erosion under hydrodynamic forces,and affect the exchange of oxygen and nutrients across the sediment-water interface. Additionally, this phototrophic community represents a key component in the functioning of the Kongsfjorden trophic web, particularly as a major food source for benthic suspension- or deposit-feeders. MPB in Kongsfjorden is confronted with pronounced seasonal variations in solar radiation, low temperatures, and hyposaline (meltwater) conditions in summer, as well as long periods of ice and snow cover in winter. From the few data available, it seems that these organisms can easily cope with these environmental extremes. The underlying physiological mechanisms that allow growth and photosynthesis to continue under widely varying abiotic parameters, along with vertical migration and heterotrophy, and biochemical features such as a pronounced fatty-acid metabolism and silicate incorporation are discussed. Existing gaps in our knowledge of benthic diatoms in Kongsfjorden, such as the chemical ecology of biotic interactions, need to be filled. In addition, since many of the underlying molecular acclimation mechanisms are poorly understood, modern approaches based on transcriptomics, proteomics, and/or metabolomics, in conjunction with cell biological and biochemical techniques, are urgently needed. Climate change models for the Arctic predict other multifactorial stressors, such as an increase in precipitation and permafrost thawing, with consequences for the shallow-water regions. Both precipitation and permafrost thawing are likely to increase nutrient-enriched, turbid freshwater runoff and may locally counteract the expected increase in coastal radiation availability. So far, complex interactions among factors, as well as the full genetic diversity and physiological plasticity of Arctic benthic diatoms, have only rarely been considered. The limited existing information is described and discussed in this review

Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry

YesBackground. The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. Methodology/Principal Findings. To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. Conclusions. This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.This work was supported by the grants from the Flanders Research Foundation, SOFI-B Grant to CRK, http://www.fwo.be/, a Public Health Service Grant from the National Institutes of Health to CEC, (grant # AI-051334), https://www.nih.gov/ and a grant from the Grant Agency of the Czech Republic to DS and MS (P302/12/0574, GP14-29596P), https:// gacr.cz/

Malignant Tumors of the Central Nervous System

Malignant tumors of the central nervous system in adults comprise a heterogeneous group of malignancies, the largest subgroups comprising astrocytomas, ependymomas, and oligodendrogliomas. Glioblastomas are the most common tumor type, and they have dismal prognosis. Due to differences in cell type of origin, as well as pathogenesis, it is plausible that their etiology also differs between tumor types. The etiology of malignant CNS tumors is largely unknown and no occupational risk factors have been definitively identified. High doses of ionizing radiation increase the risk, but in occupational settings the dose levels appear too small to result in discernible excesses. Several studies have assessed possible effect of extremely low frequency and radiofrequency electromagnetic fields, but the results are inconsistent. Increased brain tumor risk has been reported in agricultural workers, but no specific exposure has been linked to them. Pesticides have been analyzed in several studies without showing a clear increase in risk.acceptedVersionPeer reviewe