MTV sings jubilation for telomere biology in Drosophila

Telomere protects the ends of linear chromosomes. Telomere dysfunction fuels genome instability that can lead to diseases such as cancer. For over 30 years, Drosophila has fascinated the field as the only major model organism that does not rely on the conserved telomerase enzyme for end protection. Instead of short DNA repeats at chromosome ends, Drosophila has domesticated retrotransposons. In addition, telomere protection can be entirely sequence-independent under normal laboratory conditions, again dissimilar to what has been established for telomerase-maintained systems. Despite these major differences, recent studies from us and others have revealed remarkable similarities between the 2 systems. In particular, with the identification of the MTV complex as an ssDNA binding complex essential for telomere integrity in Drosophila (Zhang et al. 2016 Plos Genetics), we have now established several universal principles that are intrinsic to chromosome extremities but independent of the underlying DNA sequences or the telomerase enzyme. Telomere studies in Drosophila will continue to yield fundamental insights that are instrumental to the understanding of the evolution of telomere and telomeric functions.     

Macroinvertebrate‐based bioassessment of rivers in Addis Ababa,Ethiopia

Chemical‐based studies have shown pollution of rivers in Addis Ababa, Ethiopia. However, as bioassessment is not a component of the river assessment and monitoring programmes, information on the ecological status of the rivers is limited. The study assessed the ecological status of the Little and Greater Akaki Rivers using macroinvertebrates. Macroinvertebrates were collected from twelve sites twice in the dry and wet seasons. There was abundance of few tolerant, collector‐gatherer taxa with a loss of most sensitive taxa that used to be part of the river systems. Macroinvertebrate communities from upper and lower reaches showed complete differentiation on the nonmetric multidimensional scaling (NMS) ordination graph with upstream reaches composed of relatively sensitive taxa while the lower reaches dominated by tolerant taxa. Multiresponse permutation procedure (MRPP) showed significant difference between the two reaches. Macroinvertebrate communities from the dry and wet seasons did not show differentiation on the NMS ordination graph and MRPP did not show significant difference. Both rivers scored low in the South African Scoring System (SASS 5) and ETHbios, indicating ecological degradation. The results suggest that several decades of environmental degradation might have led to impoverished regional species pool, consisting mainly tolerant and generalist taxa constant throughout the year.     

Ice age legacies in the geographical distribution of tree species richness in Europe

Aim This study uses a high‐resolution simulation of the Last Glacial Maximum (LGM) climate to assess: (1) whether LGM climate still affects the geographical species richness patterns in the European tree flora and (2) the relative importance of modern and LGM climate as controls of tree species richness in Europe. Location The parts of Europe that were unglaciated during the LGM. Methods Atlas data on the distributions of 55 tree species were linked with data on modern and LGM climate and climatic heterogeneity in a geographical information system with a 60‐km grid. Four measures of species richness were computed: total richness, and richness of the 18 most restricted species, 19 species of medium incidence (intermediate species) and 18 most widespread species. We used ordinary least‐squares regression and spatial autoregressive modelling to test and estimate the richness–climate relationships. Results LGM climate constituted the best single set of explanatory variables for richness of restricted species, while modern climate and climatic heterogeneity was best for total and widespread species richness and richness of intermediate species, respectively. The autoregressive model with all climatic predictors was supported for all richness measures using an information‐theoretic approach, albeit only weakly so for total species richness. Among the strongest relationships were increases in total and intermediate richness with climatic heterogeneity and in restricted richness with LGM growing‐degree‐days. Partial regression showed that climatic heterogeneity accounted for the largest unique variation fraction for intermediate richness, while LGM climate was particularly important for restricted richness. Main conclusions LGM climate appears to still affect geographical patterns of tree species richness in Europe, albeit the relative importance of modern and LGM climate depends on range size. Notably, LGM climate is a strong richness control for species with a restricted range, which appear to still be associated with their glacial refugia.     

A comparison of direct and indirect 15N isotope techniques for estimating crop N uptake from organic residues

Experiments were carried out to compare the direct approach for estimating crop N uptake from ¹⁵N labelled organic inputs, to two indirect approaches, ¹⁵N isotope dilution and A value. In the first experiment soils received 25, 50, 75, or 100 mg N kg soil⁻¹ in the form of Casuarina equisitifolia residues in addition to ammonium sulphate fertiliser, to give a total of 100 mg N kg soil⁻¹ added. This was a cross labelling design, thus two matching sets of treatments, were set up, identical in all but the position of the ¹⁵N label. Maize (Zea mays L.) plants were grown in the soils amended with residues for 11 weeks and N derived from residues (Ndfr) estimated using the A-value or the direct approach. The A-value approach appeared to significantly overestimate %Ndfr compared to the direct method. In the second experiment contrasting residues were added to soil, fababean (Vicia faba L. var. minor), alfalfa (Medicago sativa L.), soyabean fixing, (Glycine max (L.) Merrill), soyabean non-fixing, barley (Hordeum vulgare L.) and maize. This was also cross-labelling design, labelled and unlabelled residues were used. Maize plants were grown in these soils for 11 weeks and %Ndfr in the maize plants estimated using ¹⁵ N isotope dilution and the direct approach. The ¹⁵ N isotope dilution approach also overestimated %Ndfr compared to the direct method in this experiment. Pool substitution appeared to be responsible for the discrepancy between the direct and indirect techniques. It was concluded that ¹⁵N isotope dilution and A-value approaches as used in these experiments (i.e where residues and ¹⁵N label are added simultaneously) were not appropriate techniques for estimating N derived from organic residues in soils. This revised version was published online in June 2006 with corrections to the Cover Date.     

Structure-function correlation during the etioplast-chloroplast transition in cucumber cotyledonary leaves

We studied the development of chloroplasts from etioplasts in the cotyledonary leaves of 4-d-old dark-grown cucumber (Cucumis sativus) seedlings after irradiation (20 μmol m^-2 s^-1). Upon irradiation, the triggering of chlorophyll (Chl) synthesis and accumulation showed a relatively short lag phase. The irradiation of etiolated seedlings initiated the synthesis of apoproteins of pigment-protein complexes. While Chl-protein 2 (CP2) was detected at 6 h after irradiation, CP1 only after 29 h. The appearance and accumulation of some of the apoproteins were monitored by Western-blotting. LHC2 apoprotein was detected after a 6 h-irradiation. The amounts of D1 protein of photosystem (PS) 2 and PsaA/B protein of PS1 were quantitated by ELISA. Further, the thylakoid membrane function during this time period in terms of PS1- and PS2-mediated electron transfer activity and intersystem electron pool size were analyzed. While PS1 activity was detected after 4 h, PS2-mediated O₂ evolution was detected only after a 17 h-irradiation. F_v/F_m value of Chl a fluorescence measurements indicated that the photochemical efficiency of these leaves reached its maximum after 29 h of irradiation. The intersystem pool size of cotyledonary leaves was equivalent to that of the control cotyledonary leaves grown for 25 h under continuous irradiation. Thus etioplasts develop into fully functional chloroplasts after approximately 25 h when 4 d-dark grown cucumber seedlings are continuously moderately irradiated. The development of photosynthetic electron transport chain seems to be limited in time at the level of PS2, possibly at the donor side. This revised version was published online in September 2006 with corrections to the Cover Date.     

Colour-coded sampling: the pan trap colour preferences of oligolectic and nonoligolectic bees associated with a vernal pool plant

1. Pan traps or water traps have been used widely to sample agricultural insect pests, but no formal studies have assessed the utility of these traps as sampling devices for bees. 2. Coloured pan traps, used as flower models, can efficiently and selectively sample an oligolectic bee, Andrena (Hesperandrena) limnanthis, and other bees associated with white-flowered Limnanthes douglasii rosea. 3. Females and males of A. limnanthis unexpectedly exhibit different colour preferences. Females are strongly attracted to white and blue traps, but discriminate against yellow traps. Males prefer white traps over blue and yellow traps. Consequently, blue traps are selective for females only, while white traps are selective for both sexes. 4. Non-A. limnanthis bees were caught in significantly greater numbers in yellow than in blue or white traps. These bees included generalists, as well as specialists that are oligolectic on mostly yellow-flowered species. 5. Colour of traps had a significant effect on the numbers of A. limnanthis females and males, and non-A. limnanthis bees caught in traps. These results indicate that quantitative sampling of bees by pan trap methods can be highly sensitive to trap colour.     

Detection of mutations in PCR products from clinical samples by surface plasmon resonance

Two different strategies for scanning and screening of mutations in polymerase chain reaction (PCR) products by hybridization analysis are described, employing real-time biospecific interaction analysis (BIA) for detection. Real-time BIA was used to detect differences in hybridization responses between PCR products and different 17-mer oligonucleotide probes. For the analysis using a biosensor instrument, two different experimental formats were investigated based on immobilization of either biotinylated PCR products or oligonucleotide probes onto a sensor chip. Applied on the human tumour suppressor p53 gene, differences in hybridization levels for full-match and mismatch situations employing both formats allowed the detection of point mutations in exon 6 PCR products, derived from a breast tumour biopsy sample. In addition, a mutant sample sequence could be detected in a 50/50 background of wild type exon 6 sequence. The suitability of the different formats for obtaining a regenerable system and a high throughput of samples is discussed. © 1997 John Wiley & Sons, Ltd.     

Predicting species establishment using absent species and functional neighborhoods

Species establishment within a community depends on their interactions with the local environment and resident community. Such environmental and biotic filtering is frequently inferred from functional trait and phylogenetic patterns within communities; these patterns may also predict which additional species can establish. However, differentiating between environmental and biotic filtering can be challenging, which may complicate establishment predictions. Creating a habitat‐specific species pool by identifying which absent species within the region can establish in the focal habitat allows us to isolate biotic filtering by modeling dissimilarity between the observed and biotically excluded species able to pass environmental filters. Similarly, modeling the dissimilarity between the habitat‐specific species pool and the environmentally excluded species within the region can isolate local environmental filters. Combined, these models identify potentially successful phenotypes and why certain phenotypes were unsuccessful. Here, we present a framework that uses the functional dissimilarity among these groups in logistic models to predict establishment of additional species. This approach can use multivariate trait distances and phylogenetic information, but is most powerful when using individual traits and their interactions. It also requires an appropriate distance‐based dissimilarity measure, yet the two most commonly used indices, nearest neighbor (one species) and mean pairwise (all species) distances, may inaccurately predict establishment. By iteratively increasing the number of species used to measure dissimilarity, a functional neighborhood can be chosen that maximizes the detection of underlying trait patterns. We tested this framework using two seed addition experiments in calcareous grasslands. Although the functional neighborhood size that best fits the community's trait structure depended on the type of filtering considered, selecting these functional neighborhood sizes allowed our framework to predict up to 50% of the variation in actual establishment from seed. These results indicate that the proposed framework may be a powerful tool for studying and predicting species establishment.