Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments

Cyanobacteria are important primary producers in many marine ecosystems and their abundances and growth rates depend on their ability to assimilate various nitrogen sources. To examine the diversity of nitrate-utilizing marine cyanobacteria, we developed PCR primers specific for cyanobacterial assimilatory nitrate reductase (narB) genes. We obtained amplification products from diverse strains of cultivated cyanobacteria and from several marine environments. Phylogenetic trees constructed with the narB gene are congruent with those based on ribosomal RNA genes and RNA polymerase genes. Analysis of sequence library data from coastal and oligotrophic marine environments shows distinct groups of Synechococcus sp. in each environment; some of which are represented by sequences from cultivated organisms and others that are unrelated to known sequences and likely represent novel phylogenetic groups. We observed spatial differences in the distribution of sequences between two sites in Monterey Bay and differences in the vertical distribution of sequence types at the Hawai'i Ocean Time-series Station ALOHA, suggesting that nitrogen assimilation in Synechococcus living in different ecological niches can be followed with the nitrate reductase gene.     

Landscape movements of migratory birds and bats reveal an expanded scale of stopover

Many species of birds and bats undertake seasonal migrations between breeding and over-wintering sites. En-route, migrants alternate periods of flight with time spent at stopover--the time and space where individuals rest and refuel for subsequent flights. We assessed the spatial scale of movements made by migrants during stopover by using an array of automated telemetry receivers with multiple antennae to track the daily location of individuals over a geographic area ~20 × 40 km. We tracked the movements of 322 individuals of seven migratory vertebrate species (5 passerines, 1 owl and 1 bat) during spring and fall migratory stopover on and adjacent to a large lake peninsula. Our results show that many individuals leaving their capture site relocate within the same landscape at some point during stopover, moving as much as 30 km distant from their site of initial capture. We show that many apparent nocturnal departures from stopover sites are not a resumption of migration in the strictest sense, but are instead relocations that represent continued stopover at a broader spatial scale.     

Relationships between expanding pinyon–juniper cover and topography in the central Great Basin, Nevada

Aim Increasing geographical range and density of conifers is a major form of land‐cover change in the western United States, affecting fire frequency, biogeochemistry and possibly biodiversity. However, the extent and magnitude of the change are uncertain. This study aimed to quantify the relationship between changing conifer cover and topography. Location The central Great Basin in the state of Nevada, USA. Methods We used a series of Landsat Thematic Mapper satellite images from 1986, 1995 and 2005 to map change in pinyon–juniper woodlands (Pinus monophylla, Juniperus spp.) in the montane central Great Basin of Nevada. We derived fractional greenness for each year using spectral mixture analysis and identified all areas with an above average increase in greenness from 1986 to 1995 and 1995 to 2005. Results Areas with high fractional greenness in 2005 were most likely to occur at elevations between 2200 and 2600 m a.s.l. Increases in fractional greenness between 1986 and 2005 were most likely to occur at elevations below 2000 m a.s.l. and on south‐facing slopes. However, relationships between elevation and increasing greenness for individual mountain ranges varied considerably from the average trend. Fractional greenness values measured by Landsat suggest that the majority of pinyon–juniper woodlands have not reached their maximum potential tree cover. Main conclusions Expansion of pinyon–juniper at low elevations and on south‐facing slopes probably reflects increasing precipitation in the 20th century, higher water use efficiency caused by increasing atmospheric CO₂ in the late 20th century and livestock grazing at the interface between shrubland and woodland. Identification of the spatial relationships between changing fractional greenness of pinyon–juniper woodland and topography can inform regional land management and improve projections of long‐term ecosystem change.     

Oral curcumin supplementation improves fine motor function in the middle-aged rhesus monkey

Aged individuals experience decreased fine motor function of the hand and digits, which could result, in part, from the chronic, systemic state of inflammation that occurs with aging. Recent research for treating age-related inflammation has focused on the effects of nutraceuticals that have anti-inflammatory properties. One particular dietary polyphenol, curcumin, the principal curcuminoid of the spice turmeric, has been shown to have significant anti-inflammatory effects and there is mounting evidence that curcumin may serve to reduce systemic inflammation. Therefore, it could be useful for alleviating age-related impairments in fine motor function. To test this hypothesis we assessed the efficacy of a dietary intervention with a commercially available optimized curcumin to ameliorate or delay the effects of aging on fine motor function of the hand of rhesus monkeys. We administered oral daily doses of curcumin or a control vehicle to 11 monkeys over a 14- to 18-month period in which they completed two rounds of fine motor function testing. The monkeys receiving curcumin were significantly faster at retrieving a food reward by round 2 of testing than monkeys receiving a control vehicle. Further, the monkeys receiving curcumin demonstrated a greater degree of improvement in performance on our fine motor task by round 2 of testing than monkeys receiving a control vehicle. These findings reveal that fine motor function of the hand and digits is improved in middle-aged monkeys receiving chronic daily administration of curcumin.     

PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.     

A method for assessing recovery of fine motor function of the hand in a rhesus monkey model of cortical injury: an adaptation of the Fugl–Meyer Scale and Eshkol–Wachman Movement Notation

Motor dysfunction of the upper extremity can result from stroke, cortical injury and neurological diseases and causes significant disruption of activities of daily living. While some spontaneous recovery in terms of compensatory movements does occur after injury to cortical motor areas, full recovery is rare. The distinction between complete recovery and compensatory recovery is important as the development of compensatory movements in the upper extremity may not translate into full functional use in human patients. However, current animal models of stroke do not distinguish full recovery from compensatory recovery. We have developed a Non-Human Primate Grasp Assessment Scale (GRAS) to quantify the precise recovery of composite movement, individual digit action, and finger-thumb pinch in our rhesus monkey model of cortical injury. To date, we have applied this GRAS scale to assess the recovery of fine motor function of the hand in young control and cell-therapy treated monkeys with cortical injury confined to the hand representation in the dominant primary motor cortex. We have demonstrated that with this scale we can detect and quantify significant impairments in fine motor function of the hand, the development of compensatory function during recovery and finally a return to full fine motor function of the hand in monkeys treated with a cell therapy.