Revising the British Red Data List for birds: the biological basis of U.K. conservation priorities

The list of British Red Data birds (Batten et al. 1990) includes 117 species, 109 of which qualified on one or more quantitative criteria referring to rarity, localized distribution, population decline and international importance. A wealth of data on bird population levels and trends in the United Kingdom and Europe has recently become available, allowing refinement and improvement of the criteria for qualification. Here we propose that in assigning priorities for conservation action in the U.K. (Britain and Northern Ireland), three biological axes need to be considered: national threat (measured as rarity, localized distribution and population decline in the U.K.), international importance (the proportion of the European population in the U.K.) and international threat (European/global conservation status). Only the first two of these axes were considered by Batten et al. (1990). Each of these axes has been sub-divided into high, medium and low categories using quantitative thresholds, and from this we produce a national 'conservation cube' (three axes, each with three categories and thus 27 cells). Data permitting, every species in the U.K. can be allocated to one of these cells. We suggest that species high on either (or both) of the national or international threat axes be considered as species of high conservation priority (the red list) and that among the remainder those that rank at least medium on one of the axes be considered as of medium conservation priority (the amber list). All other species are of low conservation priority (the green list). We suggest that this three-axis model could be applicable to other taxa and countries.     

Structure and regulation of the anthranilate synthase genes in Pseudomonas aeruginosa: II. Cloning and expression in Escherichia coli

The genes for the large and small subunits of anthranilate synthase (trpE and trpG, respectively) have been cloned from Pseudomonas aeruginosa PAC174 into E. coli by R-prime formation with the broad-host- range plasmid R68.44. Sequential subcloning into plasmid vectors reduced the active Pseudomonas DNA fragment to a length of 3.1 kb. We obtained evidence that this region contains the promoter for its own expression and retains a vestigial regulatory response to tryptophan scarcity or excess.      

Mycosin-1, a subtilisin-like serine protease of Mycobacterium tuberculosis, is cell wall-associated and expressed during infection of macrophages

Background  

Exported proteases are commonly associated with virulence in bacterial pathogens, yet there is a paucity of information regarding their role in Mycobacterium tuberculosis. There are five genes (mycP1-5) present within the genome of Mycobacterium tuberculosis H37Rv that encode a family of secreted, subtilisin-like serine proteases (the mycosins). The gene mycP1 (encoding mycosin-1) was found to be situated 3700 bp (four ORF's) from the RD1 deletion region in the genome of the attenuated vaccine strain M. bovis BCG (bacille de Calmette et Guérin) and was selected for further analyses due to the absence of expression in this organism.     

Epigenetic reprogramming in the mammalian embryo: struggle of the clones

During preimplantation development in mammals, distinct epigenetic marks on oocyte and sperm DNA are remodeled to an embryonic pattern. A recent study examining global methylation of repetitive elements in various mammals showed that the reprogramming that occurs during normal preimplantation development is aberrant in cloned embryos.     

Evolution by leaps: gene duplication in bacteria

Background  

Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities.     

Macromolecular changes caused by formalin fixation and antigen retrieval

Although the mechanics of formalin fixation and antigen retrieval have been studied extensively and reviewed periodically, little attention has been directed toward conformational changes in target molecules. Formaldehyde changes the shape of tissue molecules by appending small hydroxymethyl groups to them. These adducts, in turn, can react with other tissue molecules to form crosslinks, or they can participate in a variety of reactions during tissue processing, including formation of imines, ethoxymethyl adducts, and further crosslinks. Under the influence of alcohol dehydration, fixed DNA may fragment and form a variety of depurination products. The situation becomes even more complex with short fixation times because under these conditions, the dehydrating agent used for tissue processing denatures macromolecules in other ways, most notably through rearrangement of molecular shape to move hydrophobic realms outward and hydrophilic areas inward (hydrophobic inversions). How tissue molecules are modified affects the outcome of immunohistochemical staining and prospects for restoration of antigenicity. Immunoreacitivity may be compromised because epitopes are either sterically hidden, but otherwise unaffected, or they have been altered more directly. Enzyme-based retrieval methods are best suited for the former because they literally snip the molecule apart to reveal the portions of interest. Heat-induced retrieval with buffers can demodify affected epitopes by removing adducts and breaking crosslinks. The choice of temperature and pH is usually critical for optimal retrieval. Effective temperatures are directly related to the strength of bonds-higher temperatures are needed to break stronger bonds. The pH of the retrieval solution determines the charge on the tissue molecule; the goal is to create a charge that causes the demodified molecule to assume a near natural conformation. Rational use of these concepts should lead to better control of immunohistochemical reactions.     

Poleward shifts in breeding bird distributions in New York State

Like other regions of the northern hemisphere, the northeastern United States has experienced a general increase in regional temperatures over the past 20 years. Quantifying the ecological implications of these changing temperatures has been severely constrained by a lack of multispecies distributional data by which to compare long-term changes. We used the New York State Breeding Bird Atlas, a statewide survey of 5332 25 km² blocks surveyed in 1980–1985 and 2000–2005, to test several predictions that the birds of New York State are responding to climate change. Our objective was to use an information-theoretic approach to analyze changes in three geographic range characteristics, the center of occurrence, range boundaries, and states of occurrence to address several predictions that the birds of New York State are moving polewards and up in elevation. As expected, we found all bird species ( n =129) included in this analysis showed an average northward range shift in their mean latitude of 3.58 km [ Prob ( H _a|data)=0.87)]. Past studies have found that northern range boundaries are more likely to be influenced by climatic factors than southern range boundaries. Consequently, we predicted that northward shifts would be more evident in northern as opposed to southern range boundaries. We found, however, that the southern range boundaries of northerly birds moved northward by 11.4 km [ n =43, Prob ( H _a|data)=0.92], but this pattern was less evident in northern range boundaries of southerly birds. In addition, we found that bird species demonstrated a general shift downhill in their mean elevation, but demonstrated little change in their elevational boundaries. The repeated pattern of a predicted northward shift in bird ranges in various geographic regions of the world provides compelling evidence that climate change is driving range shifts.