Asymmetric boundary shifts of tropical montane Lepidoptera over four decades of climate warming

Aim To estimate whether species have shifted at equal rates at their leading edges (cool boundaries) and trailing edges (warm boundaries) in response to climate change. We provide the first such evidence for tropical insects, here examining elevation shifts for the upper and lower boundaries shifts of montane moths. Threats to species on tropical mountains are considered. Location Mount Kinabalu, Sabah, Malaysia. Methods We surveyed Lepidoptera (Geometridae) on Mount Kinabalu in 2007, 42 years after the previous surveys in 1965. Changes in species upper and lower boundaries, elevational extents and range areas were assessed. We randomly subsampled the data to ensure comparable datasets between years. Estimated shifts were compared for endemic versus more widespread species, and for species that reached their range limits at different elevations. Results Species that reached their upper limits at 2500–2700 m (n= 28 species, 20% of those considered) retreated at both their lower and upper boundaries, and hence showed substantial average range contractions (?300 m in elevational extent and ?45 km² in estimated range area). These declines may be associated with changes in cloud cover and the presence of ecological barriers (geological and vegetation transitions) which impede uphill movement. Other than this group, most species (n= 109, 80% of the species considered) expanded their upper boundaries upwards (by an average of 152 m) more than they retreated at their lower boundaries (77 m). Main conclusions Without constraints, leading margins shifted uphill faster than trailing margins retreated, such that many species increased their elevational extents. However, this did not result in increases in range area because the area of land available declines with increasing elevation. Species close to a major ecological/geological transition zone on the mountain flank declined in their range areas. Extinction risk may increase long before species reach the summit, even when undisturbed habitats are available.     

Distance‐driven species turnover in Bornean rainforests: homogeneity and heterogeneity in primary and post‐logging forests

Selective logging is practiced extensively within tropical rainforests of south‐east Asia, and its impact on local biodiversity is well documented. Little is known, however, about the impact of selective logging on patterns of spatial heterogeneity of species. We set out to test the hypothesis that selective logging will lead to a homogenization of the associated faunal assemblages, using moths (Lepidoptera) as our subject taxa. Large‐scale transects were established within primary and post‐logging lowland mixed dipterocarp rainforests around the Danum Valley Conservation Area and surroundings, Sabah, Malaysia (4°50′N–5°00′N and 117°35′E–117°45′E). Five study sites were located within each habitat with geometrically increasing inter‐site distances. Macro‐moths plus Pyraloidea were sampled by light trapping in 2007 and 2008. Vegetation state was also measured at each site. A clear distance–decay relationship (decreasing assemblage similarity with increasing geographic distances) was observed in primary forest but was absent in the post‐logging forest. Large, comparable numbers of macro‐moth species were found in both primary and post‐logging forests. There were no significant differences in moth assemblage composition between primary and post‐logging forests. There are important structural differences between primary and post‐logging forests reflected in the moth assemblages. A two‐stage hypothesis combining both neutral and niche concepts is probably the most parsimonious explanation of these results. First, the composition of the moth assemblage is almost certainly determined locally by the variety of plant–hosts available to larvae, with the plants representing important niche dimensions for the moth species. Second the turnover (or lack of same) in the underlying plant assemblage probably reflects clumping and, in turn, dispersal capacity of the commoner plants in each forest type. Although the impact of selective logging may be subtle, this study suggests that selective logging results in the spatial homogenization of macro‐moth assemblages.     

Trajectory log file sensitivity: A critical analysis using DVH and EPID

Aim

The aim of this study was to investigate the sensitivity of the trajectory log file based quality assurance to detect potential errors such as MLC positioning and gantry positioning by comparing it with EPID measurement using the most commonly used criteria of 3%/3?mm.

High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution

Olfactory receptors (ORs), which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected by the relatively small repertoire size and the high fraction ( approximately 55%) of human pseudogenes. Since several recent low-resolution surveys suggested that OR genomic loci are frequently affected by copy-number variants (CNVs), we hypothesized that CNVs may play an important role in the evolution of the human olfactory repertoire. We used high-resolution oligonucleotide tiling microarrays to detect CNVs across 851 OR gene and pseudogene loci. Examining genomic DNA from 25 individuals with ancestry from three populations, we identified 93 OR gene loci and 151 pseudogene loci affected by CNVs, generating a mosaic of OR dosages across persons. Our data suggest that approximately 50% of the CNVs involve more than one OR, with the largest CNV spanning 11 loci. In contrast to earlier reports, we observe that CNVs are more frequent among OR pseudogenes than among intact genes, presumably due to both selective constraints and CNV formation biases. Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee. Interestingly, among the latter we observed an enrichment in CNV losses over gains, a finding potentially related to the known diminution of the human OR repertoire. Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs. Importantly, these experiments allowed us to uncover nine common deletion alleles that affect 15 OR genes and five pseudogenes. Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content. Furthermore, these deletion alleles may be used in future genetic association studies of olfactory inter-individual differences.     

Dose-dependent differential upregulation of CCN1/Cyr61 and CCN3/NOV by the gap junction protein Connexin43 in glioma cells

Gap junctions form channels that allow exchange of materials between cells and are composed of transmembrane protein subunits called connexins. While connexins are believed to mediate cellular signaling by permitting intercellular communication to occur, there is also increasing evidence that suggest connexins may mediate growth control via a junction-independent mechanism. Connexin43 (Cx43) is the most abundant gap junction protein found in astrocytes, and gliomas exhibit reduced Cx43 expression. We have previously observed that restoration of Cx43 levels in glioma cells led to increased expression of CCN3 (NOV) proteins. We now report that overexpression of Cx43 in C6-glioma cells (C6-Cx43) also upregulates the expression of CCN1 (Cyr61). Both CCN1 and CCN3 belong to the Cyr61/Connective tissue growth factor/Nephroblastoma-overexpressed (CCN) family of secretory proteins. The CCN proteins are tightly associated with the extracellular matrix and have important roles in cell proliferation and migration. CCN1 promotes growth in glioma cells, as shown by the increased proliferation rate of CCN1-overexpressing C6 cells. In addition to its effect on cell growth, CCN1 also increased the motility of glioma cells in the presence of extracellular substrates such as fibronectin. Gliomas expressing high levels of Cx43 preferentially upregulated CCN3 which resulted in reduced growth rate. CCN3 could also be observed in Cx43 gap junction plaques in confluent C6-Cx43H culture at the stationary phase of their growth. Our results suggest that the dissimilar growth characteristics between high and low Cx43 expressors may be due to differential regulation of CCN3 by varying levels of Cx43.     

DEFOG: a practical scheme for deciphering families of genes

We developed a novel efficient scheme, DEFOG (for "deciphering families of genes"), for determining sequences of numerous genes from a family of interest. The scheme provides a powerful means to obtain a gene family composition in species for which high-throughput genomic sequencing data are not available. DEFOG uses two key procedures. The first is a novel algorithm for designing highly degenerate primers based on a set of known genes from the family of interest. These primers are used in PCR reactions to amplify the members of the gene family. The second combines oligofingerprinting of the cloned PCR products with clustering of the clones based on their fingerprints. By selecting members from each cluster, a low-redundancy clone subset is chosen for sequencing. We applied the scheme to the human olfactory receptor (OR) genes. OR genes constitute the largest gene superfamily in the human genome, as well as in the genomes of other vertebrate species. DEFOG almost tripled the size of the initial repertoire of human ORs in a single experiment, and only 7% of the PCR clones had to be sequenced. Extremely high degeneracies, reaching over a billion combinations of distinct PCR primer pairs, proved to be very effective and yielded only 0.4% nonspecific products.