We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage lambda Red recombinase, which is synthesized under the control of an inducible promoter on an easily curable, low copy number plasmid. To demonstrate the utility of this approach, we generated PCR products by using primers with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites. By using the respective PCR products, we made 13 different disruptions of chromosomal genes. Mutants of the arcB, cyaA, lacZYA, ompR-envZ, phnR, pstB, pstCA, pstS, pstSCAB-phoU, recA, and torSTRCAD genes or operons were isolated as antibiotic-resistant colonies after the introduction into bacteria carrying a Red expression plasmid of synthetic (PCR-generated) DNA. The resistance genes were then eliminated by using a helper plasmid encoding the FLP recombinase which is also easily curable. This procedure should be widely useful, especially in genome analysis of E. coli and other bacteria because the procedure can be done in wild-type cells.

/pdf/one-step-inactivation-of-chromosomal-genes-in-escherichia-25avsrekpc.pdf

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Freshwater biodiversity is the over-riding conservation priority during the International Decade for Action - 'Water for Life' - 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8% of the Earth's surface, yet this tiny fraction of global water supports at least 100000 species out of approximately 1.8 million - almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the 'Water for Life' decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as 'receivers' of land-use effluents, and the problems posed by endemism and thus non-substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and - in the case of migrating aquatic fauna - downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade-offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long-term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management - one that has been appropriately termed 'reconciliation ecology'.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/96AA265E3D88C95FB802E7A73CCB4332/S1464793105006950a.pdf/div-class-title-freshwater-biodiversity-importance-threats-status-and-conservation-challenges-div.pdf

Freshwater biodiversity: importance, threats, status and conservation challenges

Superimposition methods for comparing configurations of landmarks in two or more specimens are reviewed. These methods show differences in shape among specimens as residuals after rotation, translation, and scaling them so that they align as well as possible. A new method is presented that generalizes Siegel and Benson's (1982) resistant-fit theta-rho analysis so that more than two objects can be compared at the same time. Both least-squares and resistant-fit approaches are generalized to allow for affine transformations (uniform shape change). The methods are compared, using artificial data and data on 18 landmarks on the wings of 127 species of North American mosquitoes. Graphical techniques .are also presented to help sum- marize the patterns of differences in shape among the objects being compared. (Morphometrics; resistant-fit; least-squares; theta-rho analysis; rotational fit; affine transformations.) An important problem in morphomet- is now easy to display a transformation grid rics is that of comparing configurations of that maps the configuration of landmarks landmarks in two or more specimens. of one organism exactly into those of Thompson (1917) suggested an elegant ap- another. proach, using "transformation grids," that An alternative approach to fitting a mod- depicts the overall form of one organism el that completely describes the differences as a distortion in the shape of a reference between two organisms is to fit a very sim- organism. The basic idea was to place a ple model that only takes into consider- Cartesian coordinate grid over the refer- ation global parameters such as differences ence organism and then distort the image in rotation, translation, and scale. Geo- of the organism (including the grid) in var- metrically, this corresponds to superim- ious ways until the form of the second or- posing one organism on top of another so ganism was achieved. The differences in that its landmarks align as well as possible shapes of the two organisms are shown by (in some sense) with the positions of the the deviations of the fitted grid (usually corresponding landmarks on the second. bent and stretched in various ways) from Differences in shape are then shown by the original simple square grid. Thompson differences in positions of corresponding (1917) sketched the grids subjectively landmarks. Shape differences between two without an explicit specification of which organisms are found by studying these re- landmarks were used. Not all landmarks siduals. These methods are the subject of shown in pairs of drawings are located ex- the present paper. actly where the superimposed grids would Sneath (1967) investigated the problem imply they should be. This means that the of finding the optimal translation, rota- grids should be more complex than those tion, and size change of one object in order shown in Thompson (1917) in order to ac- for it to be superimposed on another. The curately show the differences between two two objects were represented as sets of x,y- organisms. Bookstein (1978) developed the coordinates of landmarks. A least-squares method of biorthogonal grid analysis criterion was used to measure the goodness which quantifies Thompson's approach and of fit of one object to another. Gower (1971) makes it objective. But it is complex and further developed Sneath's (1967) method has not been applied very often. A recent and expressed the operations in terms of b~ak-through (Bookstein, 1989) is the use matrix algebra. Siegel and Benson (1982) of methods based on thin-plate splines. It made the important observation that a

https://www.jstor.org/stable/pdfplus/2992207.pdf

Extensions of the Procrustes Method for the Optimal Superimposition of Landmarks

ilbstract. Autocorrelation is a very general statistical property of ecological variables observed across geographic space; its most common forms are patches and gradients. Spatial autocorrelation. which comes either from the physical forcing of environmental variables or from community processes, presents a problem for statistical testing because autocorrelated data violate the assumption of independence of most standard statistical procedures. The paper discusses first how autocorrelation in ecological variables can be described and measured. with emphasis on mapping techniques. Then. proper statistical testing in the presence of autocorrelation is briefly discussed. Finally. ways are presented of explicitly introducing spatial structures into ecological models. Two approaches are proposed: in the raw-data approach, the spatial structure takes the form of a polynomial of the x and .v geographic coordinates of the sampling stations; in the matrix approach. the spatial structure is introduced in the form of a geographic distance matrix among locations. These two approaches are compared in the concluding section. A table provides a list of computer programs available for spatial analysis.

https://www.jstor.org/stable/pdfplus/1939924.pdf

Spatial Autocorrelation: Trouble or New Paradigm?

Morphometrics in Evolutionary Biology.

Humphries, J. M., F. L. Bookstein, B. Chernoff, G. R. Smith, R. L. Elder, and S. G. Poss (Museum of Zoology, Centerfor Human Growth and Development, Museum of Paleontology, and Division of Biological Sciences, The University of Michigan, Ann Arbor, Michigan 48109) 1981. Multivariate discrimination by shape in relation to size. Syst. Zool., 30:291-308.-The diverse methods for analyzing size-free shape differences tend to be guided by computational expediency rather than geometric principles. We question the use of ratios and ad hoc combinations of spatially unrelated measures. Neither are linear discriminant functions or series of independent regressions helpful to the visualization of shape differences. A bridge is needed between traditional quantitative methods and the geometrical analysis of shape. In principle any measured transects between landmarks of a form can serve as characters in a morphometric analysis. Systematic studies use a highly non-random sample of these, particularly biased regarding geometrical information. We suggest defining size and shape in terms of factors-estimates of information common to a universe of measured distances. The model presented here calculates a linear combination of variables that quantifies shape differences among populations, independent of size. In analyses in which the first two principal components confound size and shape, size is removed from one axis with shear coefficients derived from regression of general size on principal components centered by group. The general size factor is estimated by the principal axis of the within-group covariance matrix of the log-transformed data. Residuals from the regression of general size on the transformed axes approximate a shape-discriminating factor that is uncorrelated with size within group and displays the interpopulation shape differences borne by the first two principal components. The results bear a direct and interpretable correspondence to biorthogonal analysis of shape difference. [Multivariate analysis; principal components; discriminant functions; morphometrics; size-free shape; allometry; fishes.] Systematists need procedures that allow them to discriminate among groups of organisms that vary in size. The groups included in a study can be chosen a priori (e.g., several species or geographic populations within a species) or a posteriori (as a conclusion resulting from some method of analysis). However the groups are chosen, it has long been considered desirable to discriminate among them on the basis of size-free shape derived from distance measures. The terms shape and size have been used in various and sometimes conflicting ways (Huxley, 1932; Thompson, 1942; Simpson, Roe and Lewontin, 1960; Gould, 1966; Mosimann, 1970; Sprent, 1972; Bookstein, 1978). We construe size and shape not as measured variables, but as general factors, linear combinations most parsimoniously accounting for the associations among the distance measures. Size, in particular, is not a single variable such as biomass or a standard length, but a factor which, when called upon to predict all the distance measures within a population, leaves the smallest mean squared residual. We prefer a factor whose algebraic form acknowledges the allometric relationship (Jolicoeur, 1963). Our shape discriminators need to be independent of size (Flessa and Bray, 1977; Mosimann and James, 1979) in order to partition out the effects of growth (e.g., individuals of differing age and size). In general, shape can be defined as the geometry of the organism after "information about position, scale, and orientation" has been removed (Bookstein, 1978:8). There is then an endless variety of shape information remaining. While the quantification of size as a general factor de-

Multivariate discrimination by shape in relation to size

A tubenose goby (Proterorhinus marmoratus), a European endangered species native to the Black and Caspian seas, was recovered on 11 April 1990 from the travelling screens of the Belle River Power P...

Gerald R. Smith

Papers

Morphometrics in Evolutionary Biology.

Multivariate discrimination by shape in relation to size

Establishment of gobiidae in the great lakes basin

Homologous recombination in procaryotes.

So Many Fishes, So Little Time: An Overview of Recent Ichthyological Discovery in Continental Waters