The influence of ventilation systems on water depth penetration of emergent macrophytes

1. Roots of emergent macrophytes depend on oxygen transported from aerial parts by diffusion and, in some species, by pressurised ventilation. The aim of this study was to determine if species with pressurised ventilation grow in deeper water in situ than species lacking this ability.
2. Species with pressurised ventilation grew significantly deeper than species lacking pressurised ventilation, and this was true in substrates with low as well as high redox potential.
3. Two species with low or non-detectable flow rates ( Schoenoplectus lacustris and Equisetum fluviatile , respectively) were found in unexpectedly deep water. Thus, pressurised ventilation is not a prerequisite for growth in deep water. It is, however, suggested that species with pressurised ventilation have a competitive advantage in deep water resulting in long-term competitive exclusion of species lacking pressurised ventilation.     

Potential short-term earthquake forecasting by farm animal monitoring

Whether changes in animal behavior allow for short-term earthquake predictions has been debated for a long time. Before, during and after the 2016/2017 earthquake sequence in Italy, we deployed bio-logging tags to continuously observe the activity of farm animals (cows, dogs, and sheep) close to the epicenter of the devastating magnitude M6.6 Norcia earthquake (Oct–Nov 2016) and over a subsequent longer observation period (Jan–Apr 2017). Relating 5,304 (in 2016) and 12,948 (in 2017) earthquakes with a wide magnitude range (0.4 ≤ M ≤ 6.6) to continuously measured animal activity, we detected how the animals collectively reacted to earthquakes. We also found consistent anticipatory activity prior to earthquakes during times when the animals were in a building (stable), but not during their time on a pasture. We detected these anticipatory patterns not only in periods with high, but also in periods of low seismic activity. Earthquake anticipation times (1–20 hr) are negatively correlated with the distance between the farm and earthquake hypocenters. Our study suggests that continuous bio-logging of animal collectives has the potential to provide statistically reliable patterns of pre-seismic activity that could yield valuable insights for short-term earthquake forecasting. Based on a priori model parameters, we provide empirical threshold values for pre-seismic animal activities to be used in real-time observation stations.     

Biology in a gray box: targeting the emergent properties of protein complexes: 2011 Yale Chemical Biology Symposium

At the 2011 Yale Chemical Biology Symposium, Jason Gestwicki presented a novel yet intuitive approach to drug screening. This method, which he termed "gray box" screening, targets protein complexes that have been reconstituted in vitro. Therefore, the gray box screen can achieve greater phenotypic complexity than biochemical assays but avoids the need for target identification that follows cell-based assays. Dr. Gestwicki's research group was able to use the gray box screen to identify myricetin as an inhibitor of the DnaK-DnaJ chaperone complex. This review will discuss Dr. Gestwicki's approach to identifying DnaK-DnaJ inhibitors as well as where the gray box screen fits among traditional techniques in drug discovery.     

Hallmarks of mycolic acid biosynthesis: a comparative genomics study

Mycolic acids, which render unique qualities to mycobacteria, are known to be important for mycobacterial growth, survival, and pathogenicity. It is of interest to understand the evolutionary origins of the mycolic acid pathway (MAP), as well as the common minimum principles critical for generating the capability of mycolic acid biosynthesis. The recent curation of a comprehensive model of the MAP in Mycobacterium tuberculosis and the availability of a large number of genome sequences make it feasible to carry out detailed sequence and phylogenetic analyses, to address these questions. A comprehensive phylogenetic pathway profile analysis was carried out for 318 fully sequenced bacterial genomes, for each of the proteins present in the MAP. The organisms were clustered on the basis of co-occurrence of the MAP proteins in their proteome, while the proteins were clustered on the basis of their phylogenetic profiles. The MAP proteins were also searched against the nonredundant sequence database, to identify similar proteins from other phyla. The pathway profiles indicate that four proteins and certain protein domains stand out as more characteristic to mycolate producing organisms. Further analysis leads to the identification of the desaturases DesA1 and DesA2 and certain domains of Fas and Pks13 as hallmarks of the pathway. The roles of these proteins in some other organisms, as well as the distribution of these proteins across all known genome sequences are also briefly discussed. The clustering of organisms, carried out to group organisms with similar profiles, provides a means of obtaining finer classification as compared to the standard taxonomic method. The results indicate that the MAP and hence the capacity of mycolic acid production in mycobacteria is an example of an emergent property that has come about by recruiting enzymes from unrelated pathways in plants, presumably through lateral gene transfer. The understanding of the hallmarks of mycolic acid biosynthesis will also find application in evaluating drug targets.     

Shifts in reciprocal river‐riparian arthropod fluxes along an urban‐rural landscape gradient

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云南高原湖滨带3种挺水植物对水体N的净化能力及响应

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Rhythms and alternating patterns in plants as emergent properties of a model of interaction between development and functioning

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Dynamical systems for predictive control of autonomous robots

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