CMS physics technical design report : Addendum on high density QCD with heavy ions

Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Biotic and Abiotic Drivers of Sap Flux in Mature Green Ash Trees (Fraxinus pennsylvanica) Experiencing Varying Levels of Emerald Ash Borer (Agrilus planipennis) Infestation

While the relationship between abiotic drivers of sap flux are well established, the role of biotic disturbances on sap flux remain understudied. The invasion of the emerald ash borer (Agrilus planipennis Fairmaire, EAB) into North America in the 1990s represents a significant threat to ash trees (Fraxinus spp.), which are a substantial component of temperate forests. Serpentine feeding galleries excavated by EAB larvae in the cambial and phloem tissue are linked to rapid tree mortality. To assess how varying levels of EAB infestation impact the plant water status and stress levels of mature green ash (Fraxinus pennsylvanica Marshall) trees, we combined tree-level sap flux measurements with leaf-level gas exchange, isotopes, morphology and labile carbohydrate measurements. Results show sap flux and whole tree water use are reduced by as much as 80% as EAB damage increases. Heavily EAB impacted trees exhibited reduced leaf area and leaf mass, but maintained constant levels of specific leaf area relative to lightly EAB-impacted trees. Altered foliar gas exchange (reduced light saturated assimilation, internal CO2 concentrations) paired with depleted foliar δ13C values of heavily EAB impacted trees point to chronic water stress at the canopy level, indicative of xylem damage. Reduced photosynthetic rates in trees more impacted by EAB likely contributed to the lack of nonstructural carbohydrate (soluble sugars and starch) accumulation in leaf tissue, further supporting the notion that EAB damages not only phloem, but xylem tissue as well, resulting in reduced water availability. These findings can be incorporated into modeling efforts to untangle post disturbance shifts in ecosystem hydrology

Impacts of the Invasive Emerald Ash Borer on Ash Tree Physiology and Forest Ecology

Invasive species are widely recognized as altering species and community dynamics, but their impacts on biogeochemical cycling and ecosystem processes are less understood. I investigated the impacts of the emerald ash borer (Agrilus planipennis Fairmaire, EAB), a phloem feeding beetle that was inadvertently introduced to the US in the 1990’s, on ash tree physiology and forest ecosystem dynamics

Evidence of Ash Tree (Fraxinus spp.) Specific Associations with Soil Bacterial Community Structure and Functional Capacity

The spread of the invasive emerald ash borer (EAB) across North America has had enormous impacts on temperate forest ecosystems. The selective removal of ash trees (Fraxinus spp.) has resulted in abnormally large inputs of coarse woody debris and altered forest tree community composition, ultimately affecting a variety of ecosystem processes. The goal of this study was to determine if the presence of ash trees influences soil bacterial communities and/or functions to better understand the impacts of EAB on forest successional dynamics and biogeochemical cycling. Using 16S rRNA amplicon sequencing of soil DNA collected from ash and non-ash plots in central Ohio during the early stages of EAB infestation, we found that bacterial communities in plots with ash differed from those without ash. These differences were largely driven by Acidobacteria, which had a greater relative abundance in non-ash plots. Functional genes required for sulfur cycling, phosphorus cycling, and carbohydrate metabolism (specifically those which breakdown complex sugars to glucose) were estimated to be more abundant in non-ash plots, while nitrogen cycling gene abundance did not differ. This ash-soil microbiome association implies that EAB-induced ash decline may promote belowground successional shifts, altering carbon and nutrient cycling and changing soil properties beyond the effects of litter additions caused by ash mortality

Distribution and symptoms of epiphyte infection in major carrageenophyte-producing farms

High density commercial farming of carrageenophyte Kappaphycus alvarezii is often plagued with “ice-ice” disease and epiphyte infection, which eventually leads to reduced production and in some cases collapse of crop. Epiphyte outbreak has been occurring regularly in major carrageenophyte farms in the Philippines, Indonesia, Malaysia and Tanzania. Infected materials from these countries were studied to establish baseline information on the epiphyte’s identity, density, symptoms and secondary infection on the host seaweed. The causative organism was identified as Neosiphonia apiculata (Hollenberg) Masuda et Kogame, based on its morphological features. Epiphyte density on host seaweed materials decreased in the following order: the Philippines (88.5 epi cm-2), Tanzania (69.0 epi cm-2), Indonesia (56.5 epi cm-2) and Malaysia (42.0 epi cm-2). Initial symptoms were the presence of tiny black spots, indicating the embedded tetrasporeling in seaweed cortex layer. Vegetative form emerged after 2 weeks measuring less than 0.5 mm in length with a density of less than 25.0 epi cm-2. Upon maturation, infected seaweed takes on a “hairy” appearance with “goose-bumps” like cortical swellings. The epiphyte appears as a solitary plant with multiple secondary rhizoids or as multiple epiphytes appearing from a single cortical opening. At the end of infection, the epiphytes left dark pits on the cortical swelling, and the carrageenophytes are infected by opportunistic bacteria. Bacterial enumeration of healthy and infected seaweed materials showed an increase of more than 300% in total bacterial count on infected materials dominated by Alteromonas sp., Flavobacterium sp. and Vibrio sp