Recently integrated human Alu repeats: finding needles in the haystack

Alu elements undergo amplification through retroposition and integration into new locations throughout primate genomes. Over 500,000 Alu elements reside in the human genome, making the identification of newly inserted Alu repeats the genomic equivalent of finding needles in the haystack. Here, we present two complementary methods for rapid detection of newly integrated Alu elements. In the first approach we employ computational biology to mine the human genomic DNA sequence databases in order to identify recently integrated Alu elements. The second method is based on an anchor-PCR technique which we term Allele-Specific Alu PCR (ASAP). In this approach, Alu elements are selectively amplified from anchored DNA generating a display or 'fingerprint' of recently integrated Alu elements. Alu insertion polymorphisms are then detected by comparison of the DNA fingerprints generated from different samples. Here, we explore the utility of these methods by applying them to the identification of members of the smallest previously identified subfamily of Alu repeats in the human genome termed Ya8. This subfamily of Alu repeats is composed of about 50 elements within the human genome. Approximately 50% of the Ya8 Alu family members have inserted in the human genome so recently that they are polymorphic, making them useful markers for the study of human evolution. This revised version was published online in July 2006 with corrections to the Cover Date.     

Simple additive effects are rare: a quantitative review of plant biomass and soil process responses to combined manipulations of CO2 and temperature

In recent years, increased awareness of the potential interactions between rising atmospheric CO₂ concentrations ([ CO₂ ]) and temperature has illustrated the importance of multifactorial ecosystem manipulation experiments for validating Earth System models. To address the urgent need for increased understanding of responses in multifactorial experiments, this article synthesizes how ecosystem productivity and soil processes respond to combined warming and [ CO₂ ] manipulation, and compares it with those obtained in single factor [ CO₂ ] and temperature manipulation experiments. Across all combined elevated [ CO₂ ] and warming experiments, biomass production and soil respiration were typically enhanced. Responses to the combined treatment were more similar to those in the [ CO₂ ]‐only treatment than to those in the warming‐only treatment. In contrast to warming‐only experiments, both the combined and the [ CO₂ ]‐only treatments elicited larger stimulation of fine root biomass than of aboveground biomass, consistently stimulated soil respiration, and decreased foliar nitrogen (N) concentration. Nonetheless, mineral N availability declined less in the combined treatment than in the [ CO₂ ]‐only treatment, possibly due to the warming‐induced acceleration of decomposition, implying that progressive nitrogen limitation (PNL) may not occur as commonly as anticipated from single factor [ CO₂ ] treatment studies. Responses of total plant biomass, especially of aboveground biomass, revealed antagonistic interactions between elevated [ CO₂ ] and warming, i.e. the response to the combined treatment was usually less‐than‐additive. This implies that productivity projections might be overestimated when models are parameterized based on single factor responses. Our results highlight the need for more (and especially more long‐term) multifactor manipulation experiments. Because single factor CO₂ responses often dominated over warming responses in the combined treatments, our results also suggest that projected responses to future global warming in Earth System models should not be parameterized using single factor warming experiments.     

Description of a Nanobody-based Competitive Immunoassay to Detect Tsetse Fly Exposure

Background

Tsetse flies are the main vectors of human and animal African trypanosomes. The Tsal proteins in tsetse fly saliva were previously identified as suitable biomarkers of bite exposure. A new competitive assay was conceived based on nanobody (Nb) technology to ameliorate the detection of anti-Tsal antibodies in mammalian hosts.

Methodology/Principal Findings

A camelid-derived Nb library was generated against the Glossina morsitans morsitans sialome and exploited to select Tsal specific Nbs. One of the three identified Nb families (family III, TsalNb-05 and TsalNb-11) was found suitable for anti-Tsal antibody detection in a competitive ELISA format. The competitive ELISA was able to detect exposure to a broad range of tsetse species (G. morsitans morsitans, G. pallidipes, G. palpalis gambiensis and G. fuscipes) and did not cross-react with the other hematophagous insects (Stomoxys calcitrans and Tabanus yao). Using a collection of plasmas from tsetse-exposed pigs, the new test characteristics were compared with those of the previously described G. m. moristans and rTsal1 indirect ELISAs, revealing equally good specificities (> 95%) and positive predictive values (> 98%) but higher negative predictive values and hence increased sensitivity (> 95%) and accuracy (> 95%).

Conclusion/Significance

We have developed a highly accurate Nb-based competitive immunoassay to detect specific anti-Tsal antibodies induced by various tsetse fly species in a range of hosts. We propose that this competitive assay provides a simple serological indicator of tsetse fly presence without the requirement of test adaptation to the vertebrate host species. In addition, the use of monoclonal Nbs for antibody detection is innovative and could be applied to other tsetse fly salivary biomarkers in order to achieve a multi-target immunoprofiling of hosts. In addition, this approach could be broadened to other pathogenic organisms for which accurate serological diagnosis remains a bottleneck.     

Integrating phenotypic and expression profiles to map arsenic-response networks

Background  

Arsenic is a nonmutagenic carcinogen affecting millions of people. The cellular impact of this metalloid in Saccharomyces cerevisiae was determined by profiling global gene expression and sensitivity phenotypes. These data were then mapped to a metabolic network composed of all known biochemical reactions in yeast, as well as the yeast network of 20,985 protein-protein/protein-DNA interactions.     

Dispersal of the alien raccoon dog Nyctereutes procyonoides in Southern Brandenburg, Germany

The raccoon dog Nyctereutes procyonoides, an East Asian canid species, was introduced into the European part of the former USSR since 1928. Within 50 years (1935–1984), it colonised a territory of 1.4 million km² in Europe. A telemetry study took place in Southern Brandenburg in a 60 km² sized study area with a typical mosaic structured East German agricultural landscape. For catching raccoon dogs, 20 trap boxes were set there in an area of 46 km², and between February 2001 and July 2004, 15 (5 males, 10 females) adult and 46 (25 males, 21 females) juvenile raccoon dogs were eartagged and adults additionally fitted with radio collars (Biotrack, 150–151 MHz). Data on dispersal behaviour was collected by the relocation points of 11 juveniles (6 males, 5 females). Four juvenile males dispersed even more than 40 km from their trapping places. Additionally, dispersal of two adult males could be documented. This behaviour probably indicates that the German raccoon dog population still is in a process of colonising. This canid’s ability for colonising spacious and distant areas during comparative short periods of time and its preference for habitats with richness of water possibly make this species to be an important vector of fox tapeworm Echinococcus multilocularis—a very dangerous zoonosis.     

Dynamics of the peptide hormone motilin studied by time resolved fluorescence spectroscopy

Time resolved fluorescence was used to study the dynamics on the nanosecond and subnanosecond time scale of the peptide hormone motilin. The peptide is composed of 22 amino acid residues and has one tyrosine residue in position 7, which was used as an intrinsic fluorescence probe. The measurements show that two rotational correlation times, decreasing with increasing temperature, are needed to account for the fluorescence polarization anisotropy decay data. Viscosity measurements combined with the fluorescence measurements show that the rotational correlation times vary approximately as viscosity with temperature. The shorter rotational correlation time (0.08 ns in an aqueous solution with 30% hexafluoropropanol, HFP at 20°C) should be related to internal movement of the tyrosine side chain in the peptide while the longer rotational correlation time (2.2 ns in 30% HFP at 20°C) describes the motion of the whole peptide. In addition, the interaction of motilin or the derivative motilin (Y7F) –23W (with tyrosine substituted by phenylalanine and with a tryptophan fluorophore added to the C-terminal) with negatively charged phospholipid vesicles (DOPG) was studied. The results show the development of a long anisotropy decay time which reflects partial immobilization of the peptide by interaction with the vesicles.Correspondence to: A. Gräslund     

The magnitude of the antibody and memory B cell responses during priming with a protein-polysaccharide conjugate vaccine in human infants is associated with the persistence of antibody and the intensity of booster response

Rapid waning of anti-polysaccharide bactericidal Ab and vaccine effectiveness is observed following infant immunization with the serogroup C meningococcal (MenC) glycoconjugate vaccine. This is despite the demonstrable presence of immunological memory. Persistence of functional Ab, therefore, appears to be the key determinant of MenC conjugate vaccine effectiveness. Ab persistence is thought to depend in the short term on the survival of plasma cells generated during priming and in the longer term on the production of new Ab secreting cells from memory B cells. In this study, we found a strong association between the level of MenC-specific Ab and the frequency of memory B cells measured at 5 mo of age (1 mo after 3-dose primary immunization with MenC conjugate vaccine), and the persistence of functional Ab at one year of age. These findings suggest that these two parameters are good markers of B cell responses to priming and can be used as predictors of long term humoral immunity induced by glycoconjugate vaccines received in early infancy.