Properties and incompatibility behavior of miniplasmids derived from the bireplicon plasmid pCG86

Summary Many plasmids belonging to the F incompatibility groups contain more than one basic replicon. The chimeric plasmid pCG86 is an example of such a multireplicon plasmid. The two basic replicons of pCG86, RepFIIA/FIC and RepFIB have been cloned and re-ligated, the copy numbers of the clones have been determined, and the incompatibility behavior of plasmids containing the ligated replicons and the individual replicons has been studied. The bireplicon plasmids are not expected to be incompatible as recipients with monoreplicon RepFIB or RepFIIA/RepFIC plasmids, since when one replicon is challenged by an incoming replicon, the other should be able to handle the plasmid's replication. In our studies, we found that challenge with either monoreplicon plasmid resulted in incompatibility. This incompatibility was increased in bireplicon plasmids in which RepFIB was duplicated. We conclude that in the bireplicon plasmids, challenging the replication control of one replicon by an incompatible plasmid can interfere with the replication originating from the second replicon.     

Distribution of different cell types within the rat thymus in the neonatal period of life

Summary This study attempted to define reciprocal positions of cell types within the thymus. Random or non-random contacts between specific cell types were analyzed by means of graph theory. For analysis, thymus blocks were sectioned serially and, then, thymus cells were categorized into types, based on morphological criteria. The distribution of individual cell types within the cortex, cortico-medullary zone and medulla was presented in form of a map. In the analysis, three types of epithelial cell, characteristic of each thymus zone, macrophages, Langerhans-like cells and lymphocytes were found in non-random relations to one another. Moreover, characteristic groups of cells associated with one another were also demonstrated.This study was supported by the Polish Academy of Sciences     

Effects of biological traits on capture-induced parturition in a freshwater stingray and perspectives for species management

Elasmobranchs are particularly vulnerable to overexploitation and population depletion, especially due to their life-history traits, such as low reproductive output and slow growth. Given that capture-induced parturition (abortion or premature birth) is a common consequence of fisheries in elasmobranchs, but still little studied, we investigated how the abortion/premature birth process varies in response to reproductive traits in a freshwater stingray, Potamotrygon amandae. Our results revealed that capture-induced parturition was affected by reproductive traits, such as litter size (one to seven) and gestation stage. The event occurred faster in pregnant females with high litter size during late pregnancy. Also, as found in other elasmobranchs, litter size was positively correlated with maternal size. These findings indicate that larger pregnant females in late pregnancy are more vulnerable to capture-induced parturition. This study improves our understanding of the capture-induced parturition process in stingrays, and provides useful information for management strategies and future recommendations for elasmobranch conservation.     

Mangroves buffer marine protected area from impacts of Bovoni Landfill,St. Thomas,United States Virgin Islands

One of the many ecosystem services that mangrove systems provide is their ability to act as buffers between the land and sea, protecting human development from storm surges while also trapping terrestrial pollutants. In St. Thomas, United States Virgin Islands, an ecologically-important mangrove system sits between Bovoni Landfill and a marine protected area, the St. Thomas East End Reserves. To characterize the physical processes driving this mangrove system, groundwater hydraulic head, sediment cores, sediment surface temperatures, and water and sediment chemistry were analyzed. Hydraulic head data from January to November 2014 were used to determine vertical and horizontal groundwater flow directions. Water and sediment samples were tested for heavy metals potentially originating from Bovoni Landfill. Stratigraphic context was provided by the sediment cores and used to infer past environmental conditions. Subsamples were taken from these cores and analyzed for dry bulk density, organic matter content (through loss on ignition), and heavy metals using electron microscopy. Vertical groundwater velocity and sediment porosity were determined by calibrating a one-dimensional finite difference heat transport model to near surface temperature data from depths of 0, 7, 14, and 21 cm. Groundwater was found to flow from the terrestrial upland, through the mangroves, and toward the ocean for the majority of the study. Flow reversal was seen after long periods of little precipitation. In the surface and shallow groundwater samples, trace metal concentrations were measured from 23 to 105 μg/L for Cr, Ni, Sn, and Zn. Sediment samples collected near the landfill contained Bi, Cr, Sn, Ti, and Zn. Very slow flushing of sediment pore water was indicated by the vertical groundwater velocities produced from the heat transport model, which ranged from ±10^–7 to ±10^–9 m/s. This study revealed that the mangrove system is an important buffer system protecting the outer lagoon of the marine protected area from terrestrial contaminants via sediment trapping and slowing of water fluxes from the upland area into the lagoon. The results presented here can be used as a baseline for future studies and are relevant to local managers and to landfill closure plans.     

Protein rotation and chromophore orientation in reconstituted bacteriorhodopsin vesicles

Bacteriorhodopsin has been reconstituted into lipid vesicles with dipalmitoyl and dimyristoyls phosphatidylcholine. Circular dichroism (CD) measurements show that the proteins are in a monomeric state above the main lipid phase transition temperature (T_c), 41 and 23°C for dipalmitoyl and dimyristoyl phosphatidylcholine, respectively. Below T_c, the CD spectrum is the same as that found for the purple membrane. The latter result implies that the orientation of the chromophore at these temperatures is most likely the same as in the purple membrane ($\text{70° ± 5°}$ from the normal to the membrane plane).Transient dichroism measurements show that below T_c the proteins are immobile, while above this temperature protein rotation around an axis normal to the plane of the membrane is occurring. In addition, from the data the angle of the chromophore for the rotating proteins with respect to the rotational diffusion axis can be calculated. This angle is found to be $\text{30° ± 3°}$ and $\text{29° ± 4°}$ in dimyristoyl phosphatidylcholine and dipalmitoyl phosphatidylcholine, respectively. This is considerably smaller than the value of $\text{70° ± 5°}$ for the natural biomembrane. A reversible reorientation of the chromophore above and below the respective main T_c transition temperature could explain the change of angle observed provided that all the molecules rotate above T_c.     

The Temporal and Spatial Invasion Genetics of the Western Corn Rootworm (Coleoptera: Chrysomelidae) in Southern Europe

This study describes the genetics of the western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte in southern Europe during the introduction (1996–2001) and establishment/spread (2002–2011) phases of its invasion. The Diabrotica microsatellite core-set was used to perform traditional population genetics analyses. Our results indicated that during the introduction phase genetic diversity and population genetic structure were lower overall as compared to the establishment/spread phase. Unusually high genetic differentiation was found between the Italy and southern Europe comparisons, including high differentiation between Italian populations separated by a short distance during the establishment/spread phase. STRUCTURE analysis revealed two genetic clusters during the introduction phase and two genetic clusters during the establishment/spread phase. However, bottlenecked populations were only detected during the invasion phase. A small but significant isolation by distance effect was noted in both phases. Serbia was the geographic source of WCR to Croatia and Hungary in the introduction phase, while the United States of America was the possible source of WCR to Italy in 2001. These introductory populations were the subsequent source of individuals sampled during the establishment/spread phase. Repeated introductions and admixture events in southern Europe may have resulted in genetically diverse WCR populations that have attained 83% of all known alleles worldwide.     

A realistic assessment of methods for extracting gene/protein interactions from free text

Background  

The automated extraction of gene and/or protein interactions from the literature is one of the most important targets of biomedical text mining research. In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users. Hence we have specifically avoided methods that are complex to install or require reimplementation, and we coupled our chosen extraction methods with a state-of-the-art biomedical named entity tagger.