Bioenergy from permanent grassland – A review: 2. Combustion

The aim of this review is to summarize current knowledge on suitability and sustainability of grassland biomass for combustion. In the first section grassland management for solid biofuel as well as information on harvest, postharvest and firing technology are described. An extensive grassland management system with one late cut and low level of fertilization is favored for grass as a solid biofuel. The grass harvest usually involves drying in the field and clearing with conventional farm machinery. Pelleting or briquetting improves the biofuel quality. Grass combustion is possible as stand-alone biomass-firing or co-firing with other fuels. Firing herbaceous biomass requires various specific adaptations of the different combustion technologies. In the second section economic and environmental aspects are discussed. Costs for biomass supply mainly depend on yields and harvesting technologies, while combustion costs are influenced by the size and technical design of the plant. Market prices for grass and possible subsidies for land use are crucial for profitability. Regarding biogeochemical cycles a specific feature of combustion is the fact that none of the biomass carbon and nitrogen removed at harvest is available for return to the grassland. These exports can be compensated for by fixation from the air given legumes in the vegetation and sufficient biomass production. Greenhouse gas emissions can be considerably reduced by grass combustion. Solid biofuel production has a potential for predominantly positive impacts on biodiversity due to the extensive grassland management.     

HIV-1 Populations in Semen Arise through Multiple Mechanisms

HIV-1 is present in anatomical compartments and bodily fluids. Most transmissions occur through sexual acts, making virus in semen the proximal source in male donors. We find three distinct relationships in comparing viral RNA populations between blood and semen in men with chronic HIV-1 infection, and we propose that the viral populations in semen arise by multiple mechanisms including: direct import of virus, oligoclonal amplification within the seminal tract, or compartmentalization. In addition, we find significant enrichment of six out of nineteen cytokines and chemokines in semen of both HIV-infected and uninfected men, and another seven further enriched in infected individuals. The enrichment of cytokines involved in innate immunity in the seminal tract, complemented with chemokines in infected men, creates an environment conducive to T cell activation and viral replication. These studies define different relationships between virus in blood and semen that can significantly alter the composition of the viral population at the source that is most proximal to the transmitted virus.     

The modular adaptor protein ARH is required for low density lipoprotein (LDL) binding and internalization but not for LDL receptor clustering in coated pits

ARH is an adaptor protein required for efficient endocytosis of low density lipoprotein (LDL) receptors (LDLRs) in selected tissues. Individuals lacking ARH (ARH-/-) have severe hypercholesterolemia due to impaired hepatic clearance of LDL. Immortalized lymphocytes, but not fibroblasts, from ARH-deficient subjects fail to internalize LDL. To further define the role of ARH in LDLR function, we compared the subcellular distribution of the LDLR in lymphocytes from normal and ARH-/- subjects. In normal lymphocytes LDLRs were predominantly located in intracellular compartments, whereas in ARH-/- cells the receptors were almost exclusively on the plasma membrane. Biochemical assays and quantification of LDLR by electron microscopy indicated that ARH-/- lymphocytes had >20-fold more LDLR on the cell surface and a approximately 27-fold excess of LDLR outside of coated pits. The accumulation of LDLR on the cell surface was not due to failure of receptors to localize in coated pits since the number of LDLRs in coated pits was similar in ARH-/- and normal cells. Despite the dramatic increase in cell surface receptors, LDL binding was only 2-fold higher in the ARH-/- lymphocytes. These findings indicate that ARH is required not only for internalization of the LDL.LDLR complex but also for efficient binding of LDL to the receptor and suggest that ARH stabilizes the associations of the receptor with LDL and with the invaginating portion of the budding pit, thereby increasing the efficiency of LDL internalization.     

Micro-homology intermediates: RecA’s transient sampling revealed at the single molecule level

Recombinase A (RecA) is central to homologous recombination. However, despite significant advances, the mechanism with which RecA is able to orchestrate a search for homology remains elusive. DNA nanostructure-augmented high-speed AFM offers the spatial and temporal resolutions required to study the RecA recombination mechanism directly and at the single molecule level. We present the direct in situ observation of RecA-orchestrated alignment of homologous DNA strands to form a stable recombination product within a supporting DNA nanostructure. We show the existence of subtle and short-lived states in the interaction landscape, which suggests that RecA transiently samples micro-homology at the single RecA monomer-level throughout the search for sequence alignment. These transient interactions form the early steps in the search for sequence homology, prior to the formation of stable pairings at >8 nucleotide seeds. The removal of sequence micro-homology results in the loss of the associated transient sampling at that location.     

Macroalgae exhibit diverse responses to human disturbances on coral reefs

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships between specific macroalgae taxa and local human-driven disturbance. Using genus-level monitoring data from 1205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationships between the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responses to human disturbances impedes the ability to diagnose and respond appropriately to these threats.     

A Cluster Operating System Supporting Parallel Computing

The single factor limiting the harnessing of the enormous computing power of clusters for parallel computing is the lack of appropriate software. Present cluster operating systems are not built to support parallel computing – they do not provide services to manage parallelism. The cluster operating environments that are used to assist the execution of parallel applications do not provide support for both Message Passing (MP) or Distributed Shared Memory (DSM) paradigms. They are only offered as separate components implemented at the user level as library and independent servers. Due to poor operating systems users must deal with computers of a cluster rather than to see this cluster as a single powerful computer. A Single System Image of the cluster is not offered to users. There is a need for an operating system for clusters. We claim and demonstrate that it is possible to develop a cluster operating system that is able to efficiently manage parallelism, support Message Passing and DSM and offer the Single System Image. In order to substantiate the claim the first version of a cluster operating system, called GENESIS, that manages parallelism and offers the Single System Image has been developed.     

CAF-1 and Rtt101p function within the replication-coupled chromatin assembly network to promote H4 K16ac,preventing ectopic silencing

Replication-coupled chromatin assembly is achieved by a network of alternate pathways containing different chromatin assembly factors and histone-modifying enzymes that coordinate deposition of nucleosomes at the replication fork. Here we describe the organization of a CAF-1-dependent pathway in Saccharomyces cerevisiae that regulates acetylation of histone H4 K16. We demonstrate factors that function in this CAF-1-dependent pathway are important for preventing establishment of silenced states at inappropriate genomic sites using a crippled HMR locus as a model, while factors specific to other assembly pathways do not. This CAF-1-dependent pathway required the cullin Rtt101p, but was functionally distinct from an alternate pathway involving Rtt101p-dependent ubiquitination of histone H3 and the chromatin assembly factor Rtt106p. A major implication from this work is that cells have the inherent ability to create different chromatin modification patterns during DNA replication via differential processing and deposition of histones by distinct chromatin assembly pathways within the network.