Development and application of genomic tools to the restoration of green abalone in southern California

Due to severe declines in abundance throughout southern California, the green abalone (Haliotis fulgens Philippi 1845) became protected under a state-sponsored fishery moratorium in 1997 and was declared a NOAA NMFS Species of Concern in 2004. Recently, H. fulgens was chosen for possible stock restoration via translocation of wild adults to depleted habitat and supplementation through releasing cultured individuals. Before a management plan could be developed, however, an understanding of the species’ natural population genetic structure was needed. We used a genomic technique called restriction site associated DNA sequencing (RADSeq) to address the issue. RADSeq enabled discovery of 1,209 single nucleotide polymorphisms theoretically spread genome-wide in H. fulgens. Analyses suggested the species may be panmictic throughout our sampled range, with an effective population size (N_e) of 1,100–3,600. Hence, limitations to management, such as requiring local broodstock and restricting translocation potential, might be unnecessary. Sites with larger populations may be suitable sources for restoration of depleted sites (e.g. the Palos Verdes Peninsula), although the extent of local adaptation remains unknown. Despite this potential for restoration, results gathered on a sample of cultured H. fulgens illustrated how quickly genetic diversity can be lost through captive breeding. To help mitigate a drop in N_e due to hatchery supplementation, we recommend collection and replacement of ≥100 wild abalone per generation for broodstock and close management of the proportion of cultured individuals in the wild. Successful implementation will depend on operational capacity and the resilience of the source populations to broodstock collection.     

Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

Despite over three decades of progress, extraction of high molecular weight (HMW) DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N₂ grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1–V3 region) pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered.     

Assessing Sleep Disturbance in Low Back Pain: The Validity of Portable Instruments

Although portable instruments have been used in the assessment of sleep disturbance for patients with low back pain (LBP), the accuracy of the instruments in detecting sleep/wake episodes for this population is unknown. This study investigated the criterion validity of two portable instruments (Armband and Actiwatch) for assessing sleep disturbance in patients with LBP. 50 patients with LBP performed simultaneous overnight sleep recordings in a university sleep laboratory. All 50 participants were assessed by Polysomnography (PSG) and the Armband and a subgroup of 33 participants wore an Actiwatch. Criterion validity was determined by calculating epoch-by-epoch agreement, sensitivity, specificity and prevalence and bias- adjusted kappa (PABAK) for sleep versus wake between each instrument and PSG. The relationship between PSG and the two instruments was assessed using intraclass correlation coefficients (ICC 2, 1). The study participants showed symptoms of sub-threshold insomnia (mean ISI = 13.2, 95% CI = 6.36) and poor sleep quality (mean PSQI = 9.20, 95% CI = 4.27). Observed agreement with PSG was 85% and 88% for the Armband and Actiwatch. Sensitivity was 0.90 for both instruments and specificity was 0.54 and 0.67 and PABAK of 0.69 and 0.77 for the Armband and Actiwatch respectively. The ICC (95%CI) was 0.76 (0.61 to 0.86) and 0.80 (0.46 to 0.92) for total sleep time, 0.52 (0.29 to 0.70) and 0.55 (0.14 to 0.77) for sleep efficiency, 0.64 (0.45 to 0.78) and 0.52 (0.23 to 0.73) for wake after sleep onset and 0.13 (−0.15 to 0.39) and 0.33 (−0.05 to 0.63) for sleep onset latency, for the Armband and Actiwatch, respectively. The findings showed that both instruments have varied criterion validity across the sleep parameters from excellent validity for measures of total sleep time, good validity for measures of sleep efficiency and wake after onset to poor validity for sleep onset latency.     

Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments

The production of macromolecular crystals suitable for structural analysis is one of the most important and limiting steps in the structure determination process. Often, preliminary crystallization trials are performed using hundreds of empirically selected conditions. Carboxylic acids and/or their salts are one of the most popular components of these empirically derived crystallization conditions. Our findings indicate that almost 40 % of entries deposited to the Protein Data Bank (PDB) reporting crystallization conditions contain at least one carboxylic acid. In order to analyze the role of carboxylic acids in macromolecular crystallization, a large-scale analysis of the successful crystallization experiments reported to the PDB was performed. The PDB is currently the largest source of crystallization data, however it is not easily searchable. These complications are due to a combination of a free text format, which is used to capture information on the crystallization experiments, and the inconsistent naming of chemicals used in crystallization experiments. Despite these difficulties, our approach allows for the extraction of over 47,000 crystallization conditions from the PDB. Initially, the selected conditions were investigated to determine which carboxylic acids or their salts are most often present in crystallization solutions. From this group, selected sets of crystallization conditions were analyzed in detail, assessing parameters such as concentration, pH, and precipitant used. Our findings will lead to the design of new crystallization screens focused around carboxylic acids.     

Mutualism fails when climate response differs between interacting species

Successful species interactions require that both partners share a similar cue. For many species, spring warming acts as a shared signal to synchronize mutualist behaviors. Spring flowering plants and the ants that disperse their seeds respond to warming temperatures so that ants forage when plants drop seeds. However, where warm‐adapted ants replace cold‐adapted ants, changes in this timing might leave early seeds stranded without a disperser. We investigate plant seed dispersal south and north of a distinct boundary between warm‐ and cold‐adapted ants to determine if changes in the ant species influence local plant dispersal. The warm‐adapted ants forage much later than the cold‐adapted ants, and so we first assess natural populations of early and late blooming plants. We then transplant these plants south and north of the ant boundary to test whether distinct ant climate requirements disrupt the ant–plant mutualism. Whereas the early blooming plant's inability to synchronize with the warm‐adapted ant leaves its populations clumped and patchy and its seedlings clustered around the parents in natural populations, when transplanted into the range of the cold‐adapted ant, effective seed dispersal recovers. In contrast, the mutualism persists for the later blooming plant regardless of location because it sets seed later in spring when both warm‐ and cold‐adapted ant species forage, resulting in effective seed dispersal. These results indicate that the climate response of species interactions, not just the species themselves, is integral in understanding ecological responses to a changing climate. Data linking phenological synchrony and dispersal are rare, and these results suggest a viable mechanism by which a species' range is limited more by biotic than abiotic interactions – despite the general assumption that biotic influences are buried within larger climate drivers. These results show that biotic partner can be as fundamental a niche requirement as abiotic resources.     

Active synovial matrix metalloproteinase-2 is associated with radiographic erosions in patients with early synovitis

Serum and synovial tissue expression of the matrix metalloproteinase (MMP)-2 and -9 and their molecular regulators, MMP-14 and TIMP-2 was examined in 28 patients with inflammatory early synovitis and 4 healthy volunteers and correlated with the presence of erosions in the patients. Immunohistological staining of MMP-2, MMP-14 and TIMP-2 localized to corresponding areas in the synovial lining layer and was almost absent in normal synovium. Patients with radiographic erosions had significantly higher levels of active MMP-2 than patients with no erosions, suggesting that activated MMP-2 levels in synovial tissue may be a marker for a more aggressive synovial lesion.     

Selective Removal of Nitrogen from Quinoline and Petroleum by Pseudomonas ayucida IGTN9m

Enrichment culture experiments employing soil and water samples obtained from petroleum-contaminated environments succeeded in the isolation of a pure culture possessing the ability to utilize quinoline as a sole nitrogen source but did not utilize quinoline as a carbon source. This culture was identified as Pseudomonas ayucida based on a partial 16S rRNA gene sequence, and the strain was given the designation IGTN9m. Examination of metabolites using thin-layer chromatography and gas chromatography-mass spectrometry suggests that P. ayucida IGTN9m converts quinoline to 2-quinolinone and subsequently to 8-hydroxycoumarin. Resting cells of P. ayucida IGTN9m were shown to be capable of selectively removing about 68% of quinoline from shale oil in a 16-h treatment time. These results suggest that P. ayucida IGTN9m may be useful in petroleum biorefining for the selective removal of organically bound nitrogen from petroleum.     

MOLECULAR ANALYSES OF LINEAR CHLOROPLAST PLASMIDS FROM ERNODESMIS VERTICILLATA

Ernodesmis verticillata contains novel, linear plasmid-like DNA molecules in its chloroplasts, whose function remains unclear. Their molecular architecture is putatively a "hairpin," wherein every molecule consists of a long inverted repeat folded back on itself. Thus, each molecule is composed of a terminal (telomeric) domain, a central inverted repeat, and a "loop" domain. Cloning strategies have been devised for characterizing the terminal and loop regions, since they might contain landmark features like replication origins. Polymerase chain reaction (PCR) was used to amplify loop domains of native molecules, and ligation of the PCR products with commercial cloning vectors initially yielded 11 clones. So far, no recognizable sequences have turned up in the loop domains of the molecules. Unlike what has been reported for most linear plasmids, we have been unable to verify that any proteins are associated with either the 5'- or 3'-ends of the Ernodesmis plasmids. In fact, the 5'-end of each molecule contains a terminal phosphate that is accessible to alkaline phosphatase and subsequently to T4 polynucleotide kinase in vitro. It is also possible to modify the 3'-end with terminal deoxynucleotidyl transferase (TdT) for homopolymeric tailing. Poly-(C) tailing of native molecules promotes their annealing to poly-(G) tailed vectors, for cloning of the terminal domains. An initial library of 14 TdT clones (10 unique) indicates that short (11–28 bp) direct repeats occur near the termini of the plasmids. Shorter (4–6 bp) inverted repeats at the very ends may lead to terminal foldbacks that might serve to protect the termini.     

Conidial germination and germ tube elongation of Phomopsis amaranthicola and Microsphaeropsis amaranthi on leaf surfaces of seven Amaranthus species: Implications for biological control

Microsphaeropsis amaranthi and Phomopsis amaranthicola are potential biological control agents for several Amaranthus species. In an effort to understand the initial infection processes with these pathogens, a study was conducted of the conidial germination and germ tube length (μm) on the weed leaf surfaces at 21 °C and 28 °C. Weeds included Amaranthus rudis, A. palmeri, A. powellii, A. retroflexus, A. spinosus, A. hybridus, and A. albus. For P. amaranthicola, conidial germination and germ tube length varied among the seven weed species at both temperatures, while for M. amaranthi the differences in germ tube lengths were significant among weed species only at 21 °C. While the conidia of M. amaranthi and P. amaranthicola germinated on the leaf surfaces of all seven weed species, temperature appeared to impact the number and length of germ tubes on the leaf surfaces. The percentage of germinated conidia and the length of germ tubes at both temperatures were often greater for M. amaranthi than for P. amaranthicola. In order for the fungal pathogen to successfully infect and kill a weedy host, conidia must germinate and form a germ tube, two processes that vary with host species and temperature for M. amaranthi and P. amaranthicola. The extent to which successive infection processes, e.g., penetration, invasion and colonization, contribute to host specificity warrants study.