Relationships between forest age and soil macroinvertebrate biodiversity.

General EcologySuccession is a process describing directional, continuous and non-seasonal changes in the species richness and abundance of ecological communities. Fire disturbance in six burn plots spanning a 102-year period has spurred secondary succession in tree communities and macroinvertebrate communities, providing a burn chronosequence along which links between these communities can be characterized. In this study, we aimed to address the following questions: 1. Does soil macroinvertebrate diversity change with forest age? 2. Is there a relationship between macroinvertebrate community diversity and tree community diversity? 3. Are there correlations between tree species and soil macroinvertebrate orders, and how do these potential relationships change over time?. Soil macroinvertebrates were sampled four times from four pitfall traps in each of the six burn plots (years: 1911, 1936, 1948,1954, 1980, and 1998), along with concurrent measurements of overstory and understory plant species abundance.. Soil macroinvertebrates diversity did not increase with forest age. Tree species succession in the burn plots conformed to the Intermediate Disturbance Hypothesis (diversity was lowest immediately following fire disturbance [1911 – 1948], increase to a climax at its midpoint [1954], and decreased thereafter). Macroinvertebrate diversity did not follow this pattern. Chi-Square analysis revealed significant short-term and long-term changes in soil macroinvertebrate communities. We found significant positive correlations between larvae and bigtooth aspen, millipedes and red oak, spiders and red oak, beetles and white pine, and a negative correlation between beetles and bigtooth aspen. Further research needs to be conducted to explore underlying factors affecting soil macroinvertebrate community change after disturbance events.http://deepblue.lib.umich.edu/bitstream/2027.42/101128/1/Bernstein_Gingerich_Schafer_Tait_2013.pd

Llama-Derived Single Domain Antibodies Specific for Abrus Agglutinin

Llama derived single domain antibodies (sdAb), the recombinantly expressed variable heavy domains from the unique heavy-chain only antibodies of camelids, were isolated from a library derived from llamas immunized with a commercial abrin toxoid preparation. Abrin is a potent toxin similar to ricin in structure, sequence and mechanism of action. The selected sdAb were evaluated for their ability to bind to commercial abrin as well as abrax (a recombinant abrin A-chain), purified abrin fractions, Abrus agglutinin (a protein related to abrin but with lower toxicity), ricin, and unrelated proteins. Isolated sdAb were also evaluated for their ability to refold after heat denaturation and ability to be used in sandwich assays as both capture and reporter elements. The best binders were specific for the Abrus agglutinin, showing minimal binding to purified abrin fractions or unrelated proteins. These binders had sub nM affinities and regained most of their secondary structure after heating to 95 °C. They functioned well in sandwich assays. Through gel analysis and the behavior of anti-abrin monoclonal antibodies, we determined that the commercial toxoid preparation used for the original immunizations contained a high percentage of Abrus agglutinin, explaining the selection of Abrus agglutinin binders. Used in conjunction with anti-abrin monoclonal and polyclonal antibodies, these reagents can fill a role to discriminate between the highly toxic abrin and the related, but much less toxic, Abrus agglutinin and distinguish between different crude preparations

Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.

Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be 'BRCA1-like' or 'non-BRCA1-like', which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively. Approximately one third of the BRCA1-like breast cancers have a BRCA1 mutation, one third has hypermethylation of the BRCA1 promoter and one third has an unknown reason for being BRCA1-like. This classification is indicative of patients' response to high dose alkylating and platinum containing chemotherapy regimens, which targets the inability of BRCA1 deficient cells to repair DNA double strand breaks. We investigated whether this classification can be reliably obtained with next generation sequencing and copy number platforms other than the bacterial artificial chromosome (BAC) array Comparative Genomic Hybridization (aCGH) on which it was originally developed. We investigated samples from 230 breast cancer patients for which a CN profile had been generated on two to five platforms, comprising low coverage CN sequencing, CN extraction from targeted sequencing panels (CopywriteR), Affymetrix SNP6.0, 135K/720K oligonucleotide aCGH, Affymetrix Oncoscan FFPE (MIP) technology, 3K BAC and 32K BAC aCGH. Pairwise comparison of genomic position-mapped profiles from the original aCGH platform and other platforms revealed concordance. For most cases, biological differences between samples exceeded the differences between platforms within one sample. We observed the same classification across different platforms in over 80% of the patients and kappa values of at least 0.36. Differential classification could be attributed to CN profiles that were not strongly associated to one class. In conclusion, we have shown that the genomic regions that define our BRCA1-like classifier are robustly measured by different CN profiling technologies, providing the possibility to retro- and prospectively investigate BRCA1-like classification across a wide range of CN platforms

Targeting cells with single vectors using multiple-feature Boolean logic

Precisely defining the roles of specific cell types is an intriguing frontier in the study of intact biological systems and has stimulated the rapid development of genetically encoded tools for observation and control. However, targeting these tools with adequate specificity remains challenging: most cell types are best defined by the intersection of two or more features such as active promoter elements, location and connectivity. Here we have combined engineered introns with specific recombinases to achieve expression of genetically encoded tools that is conditional upon multiple cell-type features, using Boolean logical operations all governed by a single versatile vector. We used this approach to target intersectionally specified populations of inhibitory interneurons in mammalian hippocampus and neurons of the ventral tegmental area defined by both genetic and wiring properties. This flexible and modular approach may expand the application of genetically encoded interventional and observational tools for intact-systems biology

Structural brain correlates of childhood inhibited temperament: an ENIGMA-Anxiety Mega-analysis

NWORubicon 019.201SG.022Pathways through Adolescenc

THE CHARACTERIZATION OF TRAITS ASSOCIATED WITH FREEZING TOLERANCE IN PERENNIAL RYEGRASS

Plants are constantly subjected to adverse environmental conditions that alter their growth and productivity, with an estimation that approximately 50% of annual average crop yields are reduced due to abiotic stresses. Freezing stress causes desiccation and ice damage in plants and is becoming more important as temperatures and unpredictable weather patterns increase. Normally, plants acclimate to cold temperatures as winter approaches and deacclimate as temperatures warm in the spring. Cold acclimation in fall is required for plants to build up their cellular defenses against desiccation and intracellular ice formation, while deacclimation is the process in which plants metabolize protective compounds for regrowth during spring. Recent trends in weather conditions, including increased frequency of winter temperature extremes, suggest an increase in issues associated with lower cold acclimation capacity and higher rates of premature deacclimation. Although cool-season temperate crops are usually tolerant to low temperatures, some species are sensitive to winter temperature extremes. Therefore, research into mechanisms associated with overwintering is crucial to better understand how to maximize plant overwintering survival. Freezing tolerance has been difficult to characterize due to its complexity, myriad stresses associated with it, and the balance between cold acclimation and deacclimation. The objectives of this dissertation research were to study the different physiological and molecular mechanisms associated with cold acclimation and deacclimation resistance in perennial ryegrass (Lolium perenne) differing in freezing tolerance capacities. We screened plants to investigate the genetic variability in freezing tolerance and deacclimation resistance, which resulted in us identifying two genotypes that had the greatest differences in their responses to cold acclimation and deacclimation. We further found that the genotype sensitive to deacclimation had a higher crown moisture content and photosynthetic activity during cold acclimation and deacclimation, which could predispose the genotype to rehydration and regrowth during warming events. Lastly, we examined global transcriptome responses to deacclimation, and identified biological processes and pathways that could account for differences seen in deacclimation resistance, which include growth, photosynthesis, and flower development. These results provide information on physiological and transcriptomic responses for overwintering in perennial ryegrass, which can improve management practices and breeding programs for cultivar selection