Individual carboxypeptidase D domains have both redundant and unique functions in Drosophila development and behavior

Metallocarboxypeptidase D (CPD) functions in protein and peptide processing. The Drosophila CPD svr gene undergoes alternative splicing, producing forms containing 1–3 active or inactive CP domains. To investigate the function of the various CP domains, we created transgenic flies expressing specific forms of CPD in the embryonic-lethal svr ^PG33 mutant. All constructs containing an active CP domain rescued the lethality with varying degrees, and full viability required inactive CP domain-3. Transgenic flies overexpressing active CP domain-1 or -2 were similar to each other and to the viable svr mutants, with pointed wing shape, enhanced ethanol sensitivity, and decreased cold sensitivity. The transgenes fully compensated for a long-term memory deficit observed in the viable svr mutants. Overexpression of CP domain-1 or -2 reduced the levels of Lys/Arg-extended adipokinetic hormone intermediates. These findings suggest that CPD domains-1 and -2 have largely redundant functions in the processing of growth factors, hormones, and neuropeptides.     

Recent patterns and mechanisms of carbon exchange by terrestrial ecosystems.

Knowledge of carbon exchange between the atmosphere, land and the oceans is important, given that the terrestrial and marine environments are currently absorbing about half of the carbon dioxide that is emitted by fossil-fuel combustion. This carbon uptake is therefore limiting the extent of atmospheric and climatic change, but its long-term nature remains uncertain. Here we provide an overview of the current state of knowledge of global and regional patterns of carbon exchange by terrestrial ecosystems. Atmospheric carbon dioxide and oxygen data confirm that the terrestrial biosphere was largely neutral with respect to net carbon exchange during the 1980s, but became a net carbon sink in the 1990s. This recent sink can be largely attributed to northern extratropical areas, and is roughly split between North America and Eurasia. Tropical land areas, however, were approximately in balance with respect to carbon exchange, implying a carbon sink that offset emissions due to tropical deforestation. The evolution of the terrestrial carbon sink is largely the result of changes in land use over time, such as regrowth on abandoned agricultural land and fire prevention, in addition to responses to environmental changes, such as longer growing seasons, and fertilization by carbon dioxide and nitrogen. Nevertheless, there remain considerable uncertainties as to the magnitude of the sink in different regions and the contribution of different processes.     

A preliminary classification of the natural vegetation of Colorado

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Rodent populations, biomass, and community relationships in Artemisia tridentata, Rush Valley, Utah

Three desert Artemisia tridentata communities in Rush Valley, Utah, were trapped for small rodents during the summer of 1970, and population densities were estimated for each population category using Lincoln's index. Animals were weighed and rodent biomass calculated by species throughout the summer. Population, biomass, and other data were then analyzed to gain an understanding of the community relationships of the three study areas to each other as well as to the A. tridentata community types of the Great Basin. Peromyscus maniculatus, Eutamias minimus, and Reithrodontomys megalotis were common to area 1, whereas P. maniculatus, E. minimus, and Perognathus parvus were common to areas 2 and 3. The peak estimated standing crops were 182.8 (74.0). 143.1 (57.9), and 129.7 g/acre (52.5 g/ha) for areas 2, 1, and 3 respectively. The population and biomass of area 2 peaked in midsummer, area 1 early summer, and area 3 late summer.     

Natural variability of vegetation, soils, and physiography in the bristlecone pine forest of the Rocky Mountains

Pinus aristata Engelm. forest vegetation in Colorado was studied to determine vegetation composition and the relationship between vegetation and environment. Species percent cover, tree size class, and environmental variables were recorded for 49 plots. Previously collected data for 4 plots form New Mexico were included. Environmental variables included latitude, longitude, elevation, slope, aspect, topographic position, parent material, percent rock cover, mean rock size, litter depth, estimated plot age class, and evidence of anthropogenic disturbance. Soils were analyzed for texture, depth, and percent carbon and nitrogen. Pinus aristata foliage was analyzed for percent nitrogen and phosphorus. Direct and indirect gradient analyses (CANOCO) were used to determine environmental factors associated with community composition. Vegetation in P. aristata forests is influenced primarily by elevation and soil pH. Substrate, soil texture, topographic position, and geographic location are secondary factors. Six plant associations were identified using cluster analysis (listed in an elevational sequence from low to high): Pinus aristata/ Festuca arizonica Vasey, Pinus aristata / Festuca thurberi Vasey, Pinus aristata / Juniperus communis L., Pinus aristata / Vaccinium myrtilus L., Pinus aristata / Ribes montigenum McClatchie, and Pinus aristata / Trifolium dasyphyllum Torr. & Gray.     

Circularity,indispensability, and mathematical explanation in science

In this paper I consider the objection that the Enhanced Indispensability Argument (EIA) is circular and hence fails to support mathematical platonism. The objection is that the explanandum in any mathematical explanation of a physical phenomenon is itself identified using mathematical concepts. Hence the explanandum is only genuine if the truth of some mathematical theory is already presupposed. I argue that this objection deserves to be taken seriously, that it does sometimes undermine support for EIA, but that there is no reason to think that circularity is an unavoidable feature of mathematical explanation in science.     

Pili in Gram-negative and Gram-positive bacteria — structure, assembly and their role in disease

Many bacterial species possess long filamentous structures known as pili or fimbriae extending from their surfaces. Despite the diversity in pilus structure and biogenesis, pili in Gram-negative bacteria are typically formed by non-covalent homopolymerization of major pilus subunit proteins (pilins), which generates the pilus shaft. Additional pilins may be added to the fiber and often function as host cell adhesins. Some pili are also involved in biofilm formation, phage transduction, DNA uptake and a special form of bacterial cell movement, known as ‘twitching motility’ In contrast, the more recently discovered pili in Gram-positive bacteria are formed by covalent polymerization of pilin subunits in a process that requires a dedicated sortase enzyme. Minor pilins are added to the fiber and play a major role in host cell colonization. This review gives an overview of the structure, assembly and function of the best-characterized pili of both Gram-negative and Gram-positive bacteria. Received 08 August 2008; received after revision 24 September 2008; accepted 01 October 2008     

A copy number variation morbidity map of developmental delay

To understand the genetic heterogeneity underlying developmental delay, we compared copy number variants (CNVs) in 15,767 children with intellectual disability and various congenital defects (cases) to CNVs in 8,329 unaffected adult controls. We estimate that ～14.2% of disease in these children is caused by CNVs >400 kb. We observed a greater enrichment of CNVs in individuals with craniofacial anomalies and cardiovascular defects compared to those with epilepsy or autism. We identified 59 pathogenic CNVs, including 14 new or previously weakly supported candidates, refined the critical interval for several genomic disorders, such as the 17q21.31 microdeletion syndrome, and identified 940 candidate dosage-sensitive genes. We also developed methods to opportunistically discover small, disruptive CNVs within the large and growing diagnostic array datasets. This evolving CNV morbidity map, combined with exome and genome sequencing, will be critical for deciphering the genetic basis of developmental delay, intellectual disability and autism spectrum disorders.