Lineage-specific gene duplication and loss in human and great ape evolution

Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.     

Forensic pollen geolocation techniques used to identify the origin of boll weevil re-infestation

The boll weevil, Anthonomus grandis, entered the United States of America in the early twentieth century and became a major pest in cotton, Gossypium spp. Shortly after the passage of Tropical Storm Erin on 16 August 2007 through the South Texas/Winter Garden boll weevil eradication zone, over 150 boll weevils were captured in the Southern Rolling Plains (SRP) eradication zone that was essentially weevil-free since 2003. Pollen analyses were made of the SRP weevils and weevils collected in two suspected source zones, Cameron (Southern Blacklands eradication zone) and Uvalde (Winter Garden eradication zone). An additional examination of the palynological evidence and examination of additional pollen residue shed new light on this event and strengthens the conclusion that the Uvalde area was the source of the SRP weevils. A total of 192 pollen grains from 39 taxa were found in the SRP weevils: 1904 pollen grains from ten taxa from the Cameron weevils and 148 grains from 28 taxa in the Uvalde weevils. The SRP weevils shared 16 taxa, including Phermeranthus sp. (flameflower) with the Uvalde weevils and only five taxa with the Cameron weevils. Common taxa between SRP and Uvalde weevils and the lack of the dominant ‘low spine’ Asteraceae that occurred in all Cameron samples confirm that the SRP weevils originated from the South Texas/Winter Garden zone. Problems associated with this type of research are similar to those in forensic palynology. These problems include the unknown origin of the weevils, pollen contamination and care and storage of the samples.     

The use of ETOH for the dilution of honey

Since the beginning of honey production, certain honey types are preferred because they taste better, are better for cooking, or do not rapidly crystallize. Pollen found in honey is used to determine the honey's type. Techniques used to extract pollen from honey vary in the amount of honey examined, the amount of water used to dilute the honey, and the time and speed of centrifugation. These variations address the disparity in pollen recovery that is due to the specific gravity and sinking rates of the different pollen types. Ethyl alcohol (ETOH) was used as a dilution liquid for honey and compared to two water-dilution techniques, one with a short centrifugation time (1?minute) and the other using a long centrifugation time (10?minutes). The ETOH samples were centrifuged for 3?minutes. All samples were centrifuged at 4000 r.p.m. Significantly higher pollen concentration values were found in the ETOH-diluted samples. Pollen concentration values of the ETOH-diluted samples were 5.26 times greater than water-diluted, short centrifugation samples, and 3.26 times greater than water-diluted, long centrifugation samples. ETOH-diluted samples produced 16% more taxa than the water-diluted short centrifugation technique, and 10% more taxa than the water-diluted long centrifugation technique. The pollen spectra were not consistent across the three techniques. Additional research is needed to determine the efficiency of other ETOH concentrations in recovering pollen from honey. We recommend that the ETOH-dilution technique become the standard technique for the extraction of pollen from honey for pollen analyses because of the improved pollen recovery.     

Feeding dynamics of the copepod Diacyclops thomasi before, during and following filamentous cyanobacteria blooms in a large, shallow temperate lake

Cyanobacteria blooms are an increasing problem in temperate freshwater lakes, leading to reduced water quality and in some cases harmful effects from toxic cyanobacteria species. To better understand the role of zooplankton in modulating cyanobacteria blooms, from 2008 to 2010 we measured water quality and plankton abundance, and measured feeding rates and prey selectivity of the copepod Diacyclops thomasi before, during and following summertime cyanobacteria blooms in a shallow, eutrophic lake (Vancouver Lake, Washington, USA). We used a combined field and experimental approach to specifically test the hypothesis that copepod grazing was a significant factor in establishing the timing of cyanobacteria bloom initiation and eventual decline in Vancouver Lake. There was a consistent annual succession of zooplankton taxa, with cyclopoid copepods (D. thomasi) dominant in spring, followed by small cladocerans (Eubosmina sp.). Before each cyanobacteria bloom, large cladocerans (Daphnia retrocurva, Daphnia laevis) peaked in abundance but quickly disappeared, followed by brief increases in rotifers. During the cyanobacteria blooms, D. thomasi was again dominant, with small cladocerans abundant in autumn. Before the cyanobacteria blooms, D. thomasi substantially consumed ciliates and dinoflagellates (up to 100% of prey biomass per day), which likely allowed diatoms to flourish. A shift in copepod grazing toward diatoms before the blooms may have then helped to facilitate the rapid increase in cyanobacteria. Copepod grazing impact was the highest during the cyanobacteria blooms both years, but focused on non-cyanobacteria prey; copepod grazing was minimal as the cyanobacteria blooms waned. We conclude that cyclopoid copepods may have an indirect role (via trophic cascades) in modulating cyanobacteria bloom initiation, but do not directly contribute to cyanobacteria bloom decline.     

Ecological function of constructed perennial stream channels on reclaimed surface coal mines

Mountaintop removal–valley fill mining results in the conversion of steep, forested headwater catchments to low gradient and open canopy channels. We compared the ecological functions of five reference stream channels to five constructed channels (age ranging from 3 to 20 years) on reclaimed mines in southern West Virginia. Variables included stream flow, habitat, water chemistry, riparian vegetation, organic matter (OM) processing, and invertebrate and amphibian communities. Although dissolved metal concentrations remained low, constructed channels produced significantly higher levels of conductivity and total dissolved solids as compared to reference streams. Macroinvertebrate and amphibian richness were comparable between constructed and reference channels; however, there was a distinct shift from sensitive lotic taxa in reference channels to tolerant lentic taxa in constructed channels. Constructed channels also had reduced OM decomposition rates. Nevertheless, constructed channels had significantly higher OM retention than reference channels, and consequently exhibited significantly higher overall OM processing and higher dissolved carbon concentrations. As the time since reclamation increased, we observed slight declines in conductivity and significant increases in total invertebrate richness. Our results provide measures of functional equivalencies between reference and constructed streams, which can serve as a basis for informed permitting and mitigation decisions in mined watersheds.     

5-HT2 Receptors Facilitate JC Polyomavirus Entry

The human JC polyomavirus (JCPyV) causes the rapidly progressing demyelinating disease progressive multifocal leukoencephalopathy (PML). The disease occurs most often in individuals with AIDS but also occurs in individuals receiving immunomodulatory therapies for immune-related diseases such as multiple sclerosis. JCPyV infection of host cells requires the pentasaccharide lactoseries tetrasaccharide c (LSTc) and the serotonin receptor 5-hydroxytryptamine (5-HT) receptor 5-HT_2AR. While LSTc is involved in the initial attachment of virus to cells via interactions with VP1, the mechanism by which 5-HT_2AR contributes to infection is not clear. To further define the roles of serotonin receptors in infection, HEK293A cells, which are poorly permissive to JCPyV, were transfected with 14 different isoforms of serotonin receptor. Only 5-HT₂ receptors were found to support infection by JCPyV. None of the other 11 isoforms of serotonin receptor supported JCPyV infection. Expression of 5-HT₂ receptors did not increase binding of JCPyV to cells, but this was not unexpected, given that the cells uniformly expressed the major attachment receptor, LSTc. Infection of these cells remained sensitive to inhibition with soluble LSTc, confirming that LSTc recognition is required for JCPyV infection. Virus internalization into HEK293A cells was significantly and specifically enhanced when 5HT₂ receptors were expressed. Taken together, these data confirm that the carbohydrate LSTc is the attachment receptor for JCPyV and that the type 2 serotonin receptors contribute to JCPyV infection by facilitating entry.     

United States Forest Disturbance Trends Observed Using Landsat Time Series

Disturbance events strongly affect the composition, structure, and function of forest ecosystems; however, existing US land management inventories were not designed to monitor disturbance. To begin addressing this gap, the North American Forest Dynamics (NAFD) project has examined a geographic sample of 50 Landsat satellite image time series to assess trends in forest disturbance across the conterminous United States for 1985–2005. The geographic sample design used a probability-based scheme to encompass major forest types and maximize geographic dispersion. For each sample location disturbance was identified in the Landsat series using the Vegetation Change Tracker (VCT) algorithm. The NAFD analysis indicates that, on average, 2.77 Mha y^?1 of forests were disturbed annually, representing 1.09% y^?1 of US forestland. These satellite-based national disturbance rates estimates tend to be lower than those derived from land management inventories, reflecting both methodological and definitional differences. In particular, the VCT approach used with a biennial time step has limited sensitivity to low-intensity disturbances. Unlike prior satellite studies, our biennial forest disturbance rates vary by nearly a factor of two between high and low years. High western US disturbance rates were associated with active fire years and insect activity, whereas variability in the east is more strongly related to harvest rates in managed forests. We note that generating a geographic sample based on representing forest type and variability may be problematic because the spatial pattern of disturbance does not necessarily correlate with forest type. We also find that the prevalence of diffuse, non-stand-clearing disturbance in US forests makes the application of a biennial geographic sample problematic. Future satellite-based studies of disturbance at regional and national scales should focus on wall-to-wall analyses with annual time step for improved accuracy.     

Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes

The ribosome is an evolutionarily conserved organelle essential for cellular function. Ribosome construction requires assembly of approximately 80 different ribosomal proteins (RPs) and four different species of rRNA. As RPs co-assemble into one multi-subunit complex, mutation of the genes that encode RPs might be expected to give rise to phenocopies, in which the same phenotype is associated with loss-of-function of each individual gene. However, a more complex picture is emerging in which, in addition to a group of shared phenotypes, diverse RP gene-specific phenotypes are observed. Here we report the first two mouse mutations (Rps7^Mtu and Rps7^Zma) of ribosomal protein S7 (Rps7), a gene that has been implicated in Diamond-Blackfan anemia. Rps7 disruption results in decreased body size, abnormal skeletal morphology, mid-ventral white spotting, and eye malformations. These phenotypes are reported in other murine RP mutants and, as demonstrated for some other RP mutations, are ameliorated by Trp53 deficiency. Interestingly, Rps7 mutants have additional overt malformations of the developing central nervous system and deficits in working memory, phenotypes that are not reported in murine or human RP gene mutants. Conversely, Rps7 mouse mutants show no anemia or hyperpigmentation, phenotypes associated with mutation of human RPS7 and other murine RPs, respectively. We provide two novel RP mouse models and expand the repertoire of potential phenotypes that should be examined in RP mutants to further explore the concept of RP gene-specific phenotypes.