Colonisation patterns and vertical movements of stream invertebrates in the interstitial zone: a case study in the Apennines, NW Italy

We examined vertical migration and colonisation patterns of stream macroinvertebrates within the substratum of an Apennine creek in NW Italy. Macrobenthos was sampled at three depths in the streambed (0–5, 5–10, 10–15 cm) by means of artificial baskets filled with natural substratum. We placed 42 traps (5×5×15 cm), i.e. 21 top-opened (T-traps) and 21 bottom-opened (B-traps), each composed of three overlapping baskets (high-H, medium-M and low-L), to evaluate differences in the vertical movements. We also collected Surber samples to compare interstitial assemblages with streambed communities. The multilevel traps yielded 42 taxa, compared with 60 taxa in the natural riverbed. Interstitial traps were rapidly colonised; both taxa richness and organism number increased during the 42-day study period. We found active migration in both vertical directions, but there were more invertebrates in the top-opened traps than in the bottom-opened traps. In the T-traps the most colonised baskets were those placed at the H level, while in the B-traps the L level baskets were more rapidly colonised. The interstitial assemblages differed markedly from the streambed communities in both composition and functional organisation, with more collector-gatherers and predators in the interstitial zone and more filterers and scrapers in the natural riverbed. In Apennine lotic systems, the interstitial zone is an important habitat for stream macrobenthos, although it may not be used by all species.     

Structural studies on the acidic exopolysaccharide from Haloferax denitrificans ATCC 35960.

The structure of a linear, acidic exopolysaccharide isolated from the Archaeon Haloferax denitrificans ATCC 35960 has been determined using NMR spectroscopy. The sugar residues in the repeating unit of the polysaccharide were identified as Gal and GlcA2,3NAc after the assignment of the 1H and 13C resonances using COSY, HOHAHA, HMQC and HMQC-TOCSY experiments. The sequence of the residues in the polysaccharide was established from the inter-residue connectivities observed in the HMQC-NOESY plot. The only sugar released on acid hydrolysis was shown to be D-Gal by GLC analysis, while the absolute configuration of the acidic sugars was shown to be D by comparison of the carbon chemical shifts with those of model compounds. Partial acid hydrolysis yielded a tetrasaccharide, terminated by D-Gal at the reducing end, whose structure confirmed that of the repeating unit of the polysaccharide as-->4)-beta-D-GlcpA2,3NAc-(1-->4)-beta-D-GlcpA2, 3NAc-(1-->4)-alpha-D-GlcpA2,3NAc-(1-->3)-alpha-D-Galp- (1-->, where D-GlcpA2,3NAc is 2,3-diacetamido-2,3-dideoxy-D-glucopyranosiduronic acid.     

Factors influencing limit values for pine needle litter decomposition: a synthesis for boreal and temperate pine forest systems

We synthesized available data for decomposition of pine (Pinus) needle litter in pine forests to determine the litter chemical characteristics and climate factors that explained variation in the limit value, i.e. the level of accumulated mass loss at which the decomposition process either continues at a very low rate or possibly stops. Our data base included 56 separate studies on decomposition of pine needle litter, spanning Scots pine, lodgepole pine, Aleppo pine, stone pine and white pine, mainly incubated at the site of collection. Studies had 5 to 19 samplings, on average 10, and the decomposition was followed to a mass loss ranging from 47 to 83%, on average 67%. The periods from 3.0 to 5.4 years, on average 3.9 years, were of sufficient duration to allow estimates of limit values of decomposition. We used a linear mixed model with regression effects to relate limit values to potential explanatory variables, namely the sites’ long-term mean annual temperature (MAT) and mean annual precipitation (MAP) and to substrate-chemistry factors. Regarding the latter, we explored two models; one that included initial concentrations of water solubles, lignin, N, P, K, Ca, Mg, and Mn and one that included only lignin, N, Ca, and Mn to focus on those nutrients known to influence lignin degradation. Using backward elimination significant explanatory variables were determined. For litter decomposed in its site of origin we found the limit value to depend mainly on the initial concentration of Mn, with higher Mn concentrations resulting in higher accumulated mass loss. Thus, litter with higher Mn reached a higher limit value and left a smaller stable fraction. This is likely due to the fact that Mn is an essential component of ligninolytic enzymes important for degrading litter in the later stages of decomposition. Manganese has received little attention in decomposition studies to date. Given its significance in this synthesis, the role of Mn in influencing variation in the late stages of decomposition among ecosystems and among litters of other genera besides Pinus deserves further attention.     

Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages

Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.     

The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins

The New York Consortium on Membrane Protein Structure (NYCOMPS) was formed to accelerate the acquisition of structural information on membrane proteins by applying a structural genomics approach. NYCOMPS comprises a bioinformatics group, a centralized facility operating a high-throughput cloning and screening pipeline, a set of associated wet labs that perform high-level protein production and structure determination by x-ray crystallography and NMR, and a set of investigators focused on methods development. In the first three years of operation, the NYCOMPS pipeline has so far produced and screened 7,250 expression constructs for 8,045 target proteins. Approximately 600 of these verified targets were scaled up to levels required for structural studies, so far yielding 24 membrane protein crystals. Here we describe the overall structure of NYCOMPS and provide details on the high-throughput pipeline.     

Protein degradation sets the fraction of active ribosomes at vanishing growth

Growing cells adopt common basic strategies to achieve optimal resource allocation under limited resource availability. Our current understanding of such “growth laws” neglects degradation, assuming that it occurs slowly compared to the cell cycle duration. Here we argue that this assumption cannot hold at slow growth, leading to important consequences. We propose a simple framework showing that at slow growth protein degradation is balanced by a fraction of “maintenance” ribosomes. Consequently, active ribosomes do not drop to zero at vanishing growth, but as growth rate diminishes, an increasing fraction of active ribosomes performs maintenance. Through a detailed analysis of compiled data, we show that the predictions of this model agree with data from E. coli and S. cerevisiae. Intriguingly, we also find that protein degradation increases at slow growth, which we interpret as a consequence of active waste management and/or recycling. Our results highlight protein turnover as an underrated factor for our understanding of growth laws across kingdoms.     

Biosensors and molecular imaging

The increase in the understanding of the physical and functional properties of the biological material, from the cellular level down to single molecules, owes its success to the development of suitable high-sensitivity platforms to image the biomaterial and analyze its response to specific stimuli. Imaging has indeed reached molecular capabilities, thanks to optical or magnetic markers [1], to the atomic force microscopy (AFM) in surface reconstruction [2], and is nearing success in three-dimensional (3-D) reconstruction thanks to X-ray holography [3].