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Quantitative estimates of the genetic effects of ionizing radiation on human beings have been carried out by a number of investigators [1-3]. Estimates of this kind involve extrapolating from induced mutation rates in such organisms as Drosophila and mice. Quantitative estimates of the somatic, or "direct," effects of radiation must also be attempted if the biological hazards of ionizing radiation are to be fully assessed. In the case of direct effects, it is particularly difficult to extrapolate from results with lower organisms, and it becomes important to have data on man himself. [ABSTRACT FROM AUTHOR]

The homeobox-complex (HOX-C) programs much of the basic body plan and forms, in most metazoans, one continuous cluster with the order of genes paralleling their order of expression along the body axis. Here we compare the HOX-C organization of several Drosophila species and of Anopheles gambiae, a representative of lower Dipterans. We develop a model to account for the evolution of the HOX-C in the Diptera. [ABSTRACT FROM AUTHOR]

The bithorax complex (BX-C) of Drosophila, one of two complexes that act as master regulators of the body plan of the fly, has now been entirely sequenced and comprises ≈315,000 bp, only 1.4% of which codes for protein. Analysis of this sequence reveals significantly overrepresented DNA motifs of unknown, as well as known, functions in the non-protein-coding portion of the sequence. The following types of motifs in that portion are analyzed: (i) concatamers of mono-, di-, and trinucleotides; (ii) tightly clustered hexanucleotides (spaced ≤5 bases apart); (iii) direct and reverse repeats longer than 20 bp; and (iv) a number of motifs known from biochemical studies to play a role in the regulation of the BX-C. The hexanucleotide AGATAC is remarkably overrepresented and is surmised to play a role in chromosome pairing. The positions of sites of highly overrepresented motifs are plotted for those that occur at more than five sites in the sequence, when <0.5 case is expected. Expected values are based on a third-order Markov chain, which is the optimal order for representing the BXCALL sequence. [ABSTRACT FROM AUTHOR]

Transabdominal (Tab) is a dominant gain-of-function mutation that results in islands of sexually dimorphic abdominal cuticle in the dorsal thorax of the adult fly. This phenotype has complete penetrance and constant expressivity, and we show that it results from ectopic expression of ABD-BII, one of two proteins derived from the Abdominal B (Abd-B) domain of the bithorax complex (BX-C) and one that is normally expressed only in terminal portions of the abdomen. In Tab/+ animals ABD-BII is ectopically expressed in the relevant imaginal "wing" disc as three islands of cells whose location on the fate map corresponds to the three islands of transformed cuticle in each half of the adult thorax. Tab is associated with an inseparable inversion bringing sequences in 90E next to sequences in the transcription unit encoding ABD-BII in 89E. That 90E sequences drive ectopic expression of ABD-BII is indicated by our finding that such sequences in a P-element transformant express the reporter gene's product (β-galactosidase) in the same three islands of wing disc cells. On morphological grounds, the transformed islands in the adult thorax correspond to subsets of muscle attachment cells. Ectopic expression of a homeodomain protein thus creates a unique and invariant pattern of sexual dimorphism. [ABSTRACT FROM AUTHOR]

Transabdominal (Tab), a dominant mutation in the Bithorax Complex (BX-C) of Drosophila, creates a sexually dimorphic pattern of segmental transformation that has complete penetrance and expressivity. Specific regions within the notum of the second thoracic segment (T2) are transformed into abdominal-like cuticle; thus, the Tab/+ notum has sets of short stripes that are black in males and only bordered with black in females. Also, Tab/+ abdominal tergites, A1-A6, inclusive, have small patches of A7-like tergite cuticle. Tab is inseparable from an 89E/90D inversion, whose DNA breakpoint in 89E is at +188 kb in the infra-abdominal-8 (iab-8) region of the BX-C. When probed with a pupal cDNA from the iab-7 region, labeling above background was not detected in wild-type wing discs but was detected in, and confined to, the notal region of Tab/+ wing discs. The Tab/+ phenotype is assumed to result from cis-overexpression of iab-7 in localized regions of segments T2-A6, inclusive. [ABSTRACT FROM AUTHOR]

The homeotic mutations in the right half of the bithorax complex of Drosophila cause segmental transformations in the second through the eighth segments of the fly. A chromosomal walk in the bithorax complex has now been extended 215 kb through the right half of the complex, and lesions for over 40 mutations have been located on the DNA map. The mutations can be grouped in a series of phenotypic classes, one for each abdominal segment, although each mutation typically affects more than one segment. The mutant lesions of each class are clustered, and they are aligned on the chromosome in the order of the body segments that they affect. Complementation tests suggest interactions between widely spaced DNA regions; indeed, the right half cannot be split anywhere without some loss of function. [ABSTRACT FROM AUTHOR]

The bithorax complex in Drosophila melanogaster is a cluster of homeotic genes that specify developmental pathways for many of the body segments of the fly. The DNA of the bithorax complex has been isolated, and a region of 195,000 base pairs that covers the left half of the complex is described here. The lesions associated with many of the bithorax complex mutants have been identified, and most are due to DNA rearrangements. Most of the spontaneous mutants have insertions of a particular mobile element named "gypsy.ȝ This element affects the functions of sequences removed from the site of insertion. Mutant lesions for a given phenotypic class are distributed over large DNA distances of up to 73,000 base pairs. [ABSTRACT FROM AUTHOR]

The bithorax complex (BX-C) is a set of master control genes that regulates other genes outside the complex to program much of the development of the thorax and abdomen of the fly. The emphasis in this paper will be on how the genes of the complex are themselves regulated, rather than on how they regulate other genes. [ABSTRACT FROM AUTHOR]

The bithorax complex (BX-C) in Drosophila is a giant cluster of closely linked genes that plays a major role in determining the segmentation pattern of the organism. From developmental and cytogenetic studies of this complex it now appears that orderly derepression of BX-C genes controls the orderly differentiation of body segments commencing with the thorax and proceeding posteriorly. The available evidence also suggests that the level of development which a given one of these segments achieves is a function of the particular subset of BX-C genes that is active in that segment. This paper summarizes the current status of our knowledge of what the BX-C genes do during development and how they are regulated. [ABSTRACT FROM AUTHOR]

Drosophila, like many other higher organisms, begins development as a tandem array of more or less identical body segments. During later development, these gradually diverge in morphology until the extensive differentiation of body segments seen in the adult is achieved. The genetic control of this divergence is, by now, moderately well understood. The differentiation of the third thoracic and of all abdominal segments appears to be under the control of a cluster of genes known as the bithorax complex (BX-C) (Lewis, 1978). As reviewed below, the genes of this complex appear to be differentially regulated along the body axis so that each body segment is characterized by a unique subset of active BX-C genes. The activities of these genes are thought to directly determine segmental identity. Recently, it has been proposed that more anteriorly located segments, including those in the head as well as the first and second thoracic segments, are under the control of another gene cluster that has been named the Antennapedia complex (ANT-C) by Kaufman et al. (1980). These authors suggest that the ANT-C genes may function in a manner analogous to that of the BX-C genes. [ABSTRACT FROM AUTHOR]

The bithorax gene complex in Drosophila contains a minimum of eight genes that seem to code for substances controlling levels of thoracic and abdominal development. The state of repression of at least four of these genes is controlled by cis-regulatory elements and a separate locus (Polycomb) seems to code for a repressor of the complex. The wild-type and mutant segmentation patterns are consistent with an antero—posterior gradient in repressor concentration along the embryo and a proximo-distal gradient along the chromosome in the affinities for repressor of each gene's cis-regulatory element. [ABSTRACT FROM AUTHOR]

The classical example of multiple allelism is the series of eye-color mutants at the white (w) locus in Drosophila melanogaster. The alternative interpretation of this series, namely, that it is made up of "pseudoalleles," or closely linked genes with similar effects, has usually been considered ruled out by two kinds of evidence. In the first place early attempts to resolve the series by crossing over failed in spite of numerous tests involving most of the mutants available at the time. Secondly, a heterozygote for two different mutant genes of the series does not have the phenotype expected for nonallelic genes, namely, wild type (or red) eye color, but instead has a mutant eye color which is usually intermediate between the colors of the two respective homozygotes. In recent years, however, several cases have been found in which nonallelic genes give a positive phenotypic test for allelism by virtue of a position effect. [ABSTRACT FROM AUTHOR]

In Drosophila melanogaster it has been established that the action of at least some genes is affected by their position in the chromosomes. Critical evidence for this phenomenon of position effect has been given by Sturtevant (1925), Dubinin and Sidorow (1935), and Panshin (1935). Position effects have been detected only in cases in which the relative position of a gene with respect to its neighbors has been altered by a chromosomal rearrangement. It is conceivable that the effective position of a gene may also be changed as a result of a substitution in an adjacent gene of one allele by another. Such a possibility was put to experimental test by Sturtevant (1928) for the dominant mutants, Delta (Dl) and Hairless (H), three units apart in the third chromosome; however, no difference could be demonstrated between Dl H/++ and Dl+/+H. [ABSTRACT FROM AUTHOR]

Females homozygous for the sex-linked dominant, Bar, occasionally give rise to wild-type reversions and to forms with more extreme eye reduction than Bar. This behavior was shown by Sturtevant to result from unequal crossing over. The Bar-reverted type was considered to be a deficiency for the Bar gene; while the extreme form, called Ultra-Bar or Double-Bar, was interpreted as a duplication for that gene. Later, Wright suggested that Bar itself had something additional present which when lost by unequal crossing over would give back a normal chromosome (Bar-reverted). [ABSTRACT FROM AUTHOR]

In a genetics experiment conducted in November 1937 with Drosophila melanogaster and involving the dominant mutant Star (S, in chromosome 2- at locus 1.3; causing an irregularity in the arrangement of eye facets and facet hairs, the homozygote being lethal), a number of flies appeared with small narrow eyes. When these were mated inter se, all of the F1 had abnormal eyes, but these varied in size from that of S/+ (see Table 4) to a narrow slit of red pigment on which only a few facets were scattered. A clue to the manner of inheritance of the type with narrow eyes was found by mating a narrow-eye male to a wild-type female, with the result shown in Table 1. [ABSTRACT FROM AUTHOR]

In its endeavor to merge together the biosciences and biopolicy, the group of researchers at the KWI-A did the legwork for the National Socialist regime knowingly and willingly. The institute's scientists provided the genetic health and race policy of the "New Germany" with a fixed basis of legitimation, defended it with the weight of their scientific authority at international congresses, and in this manner helped to reduce foreign political pressure on the National Socialist state. Their popular science writings and lectures for the German public were propaganda for the biopolicy of the Nazi rulers. In a multiplicity of courses and training sessions they made a vital contribution to the instruction and further education of professionals — above all health officers and judges — who played an important role in implementing biopolicy. Through scientific consulting as members of advisory boards and expert staffs, the institute's scientists collaborated directly in laying the foundation for this policy and keeping it up to date. As experts, they played a key role in the registration and selection of Jews, Sinti, and Roma, "Rhineland bastards," "foreign nationals," "the genetically ill," and people with physical or mental disabilities. [ABSTRACT FROM AUTHOR]

On March 8, 1940, Eugen Fischer wrote a long, confidential letter to Otmar von Verschuer, director of the Institute for Genetic Biology and Race Hygiene at the University of Frankfurt at that time. In this letter Fischer expressed critique — and certainly also self-critique — about the scientific development of his institute since the mid-1930s. [ABSTRACT FROM AUTHOR]

After a short phase of upheaval characterized by provocation and friction in the years 1933/34, a modus vivendi settled in between the Kaiser Wilhelm Institute for Anthropology, Human Genetics and Eugenics and the National Socialist "health leadership," which could best be described as the reciprocal instrumentalization of science and politics. To pick up on an interpretive figure drafted by Mitchell Ash and recently further developed by Sheila F. Weiss, politics and science represented "resources for each other," and this was the case for the KWI-A as well.1 This was true not only for the period after 1933. As described above at length, from the very beginning the KWI-A had attempted to extend its sphere of influence into the realm of political activity, demanding public funding in return — the very prototype of a state-dominated Kaiser Wilhelm Institute. In the "Third Reich," too, it was willing to put its specialized knowledge into the service of the new regime, which for its part — to a higher degree than the governments of the Weimar Republic — was willing to ground its political decision-making processes on scientific expertise and legitimation. Important political actors soon recognized the potential value of the KWI-A as a resource for "knowledge, apparatus, personnel, institutional structure or rhetoric,"2 which they exploited to realize their political objectives. Conversely, the interest of influential men in power in a scientific foundation for population, health, and social policy constituted a resource for the KWI-A, primarily in terms of financing. However, it is important to distinguish carefully between the two levels of means and ends: On the level of means — jockeying for power and influence, positions, and money — politicians and scientists contracted a strategic alliance, which was renegotiated over and again to strike a balance between both parties' interests. On the level of ends — in the biopolitical Utopia of a scientifically guided dictatorship of development, which aspired to control birth and death, sexuality and reproduction, body and germ line, variability and evolution — there was vast convergence and congruence: politicians and scientists worked together out of conviction. This is where the actual basis of the alliance between science and politics lies. [ABSTRACT FROM AUTHOR]

The development of the Kaiser Wilhelm Institute for Anthropology, Human Genetics, and Eugenics in the years from 1927 to 1933 was linked closely with the glory and misery of the Weimar welfare state. While the founding of the institute took place in the last, narrow window of relative stabilization, in the period when the expansion of the social state reached its tentative zenith and end point with the introduction of unemployment insurance, the phase during which the institute was actually set up was characterized by the existential crises of the social state in the context of the economic depression in the late Weimar Republic. This was indeed fertile soil for the institute, whose raison d'être from the outset was, after all, to raise the social state to a new level on the basis of a comprehensive, scientifically guided biopolicy, and this task was all the more urgent in the period of crisis. Social, political, and economic events shifted the institute in Dahlem to the focal point of the biopolicy debates. At the close of the Weimar Republic it had become firmly established at the interface between science, the public, and politics. [ABSTRACT FROM AUTHOR]

The linkage of race hygiene, science, and politics in the early Weimar Republic was the context in which the initiative to found an extra-university research institution for the fields of anthropology, human genetics, and eugenics took shape. This triangle was the result of converging interests: race hygiene conceived of itself as an applied science, aspiring to a scientific foundation for its practical agenda, and hoping to establish itself as a new discipline between biology, genetics, medicine, psychiatry, hygiene, anthropology, demographics, national economy, and sociology, and to influence state and society through scientific policy consulting. The modern interventionist state, in turn, demanded expertise from the human sciences to the extent that it laid claim to the control over birth and death, sexuality and reproduction, body and germline, variability and evolution, as part of a comprehensive biopolicy.1 After all, the human sciences ultimately offered the modern interventionist state their expertise in exchange for funding. In this process race hygiene functioned as a kind of relay switched between scientific knowledge and biopolicy interest. [ABSTRACT FROM AUTHOR]

From its founding in 1927 until its dissolution in 1945, the Kaiser Wilhelm Institute for Anthropology, Human Genetics, and Eugenics (KWI-A) in Berlin-Dahlem transgressed many a boundary; indeed, the transgression of boundaries was in a sense its raison d'être from the outset. Initially this applied to the boundaries within the disciplinary canon of the human sciences. Even from its basic conception, the institute, centered around the person of its founding director Eugen Fischer (1874-1967), was to unify anthropology, genetics, and eugenics under one roof. In keeping with the understanding predominant in Germany between the wars, anthropology went beyond the scope of the framework of the ascendant "race theory" to cover not only physical anthropology, including paleoanthropology, but also elements of what we today would call cultural and social anthropology. Thus, this anthropology extended far into the fields of archeology, paleontology, prehistory and early history, history and sociology, and especially into ethnology and folklore. Human genetics, in turn, was more than the attempt to apply to humans the genetics developed by Thomas Hunt Morgan (1866-1945) and his school in the USA on the model of drosophila. In Germany, Morgan's genetics, which concentrated on investigating the dissemination of genetic traits on the chromosomes and their morphological structure, was received with skepticism for two reasons. The first criticism was that this special orientation of the genetics neglected the problem of how genetic traits are manifested, so that the labyrinthine path from the genotype to the phenotype and the forces involved other than genes remained in the dark. Second, German geneticists — probably a consequence of the holistic style of thinking in the sciences predominant in Germany — found it unsatisfying that Morgan's genetics studied, so to speak, development without evolution. German genetics, in contrast, attempted to link together genetics and evolutionary biology. Eugenics, finally, was located from its very establishment in the boundary area between many human sciences: biology, genetics, medicine, psychiatry, hygiene, anthropology, demography, political economy, and sociology. What was undertaken in Dahlem was thus nothing less than the attempt to develop a new, transdisciplinary key science of humans. [ABSTRACT FROM AUTHOR]

Most blueberry breeding activity is focused on northern highbush, southern highbush and rabbiteye types. The major objectives of blueberry breeders center on high plant vigor, improved disease resistance, flavor, longer storing fruit and expanded harvest dates. Cranberry breeders have concentrated on early maturing fruit, uniform large size, intense color, keeping quality, high productivity, disease resistance and plant vigor. Considerable variability exists in blueberry and cranberry for most of the horticulturally important traits, and while only a limited number of genetic studies have been performed, most inheritance patterns fit quantitative models. Several genes have been identified through molecular, genetic and genomic approaches that are associated with cold hardiness. Wide hybridization is commonly employed in blueberry breeding and southern highbush types were derived primarily by incorporating genes from the diploid species Vaccinium darrowii into the highbush background via unreduced gametes. A wide array of molecular markers has been used in blueberry for fingerprinting and linkage mapping, and a major QTL regulating the chilling requirement in diploids has been identified. Transgenic blueberries have been produced with herbicide resistance and the Bt gene (Bacillus thuringiensis) has been incorporated into cranberry. A large EST library of highbush blueberry has been produced. [ABSTRACT FROM AUTHOR]

Few crops are as genetically diverse as blackberry, with several Rubus species in its background. This diversity is being used by plant breeders to fill a myriad of marketing opportunities. Several strategies are being employed to broaden the climatic zone of blackberries including the development of primocane fruiting plants, mixing eastern and western germplasm and reducing chilling requirements. Efforts are also being made to improve harvest efficiency through appropriate architecture and thornlessness to keep hand and machine picking costs as low as possible. New knowledge about basic fruit chemistry and the volatiles associated with flavor is giving breeders opportunities they have never had in the past to improve fruit quality. While blackberries are more disease tolerant than raspberries, breeders are still working to develop resistance to major fungal diseases, and most recently, several virus diseases. Molecular tools have been developed to understand taxonomy and to explore the potential of marker assisted selection, although traditional plant breeding approaches are still the primary methods being used to develop new cultivars. [ABSTRACT FROM AUTHOR]

Several dozen publicly-sponsored breeding programs around the world are developing new fresh market and processing apricot cultivars. Apricots have a more limited environmental range than other tree fruits, and therefore, many breeders are interested in broadening adaptations for specific growing regions. Plum Pox Virus resistance is a widely pursued objective and there are ongoing efforts to identify molecular markers that are closely linked to disease resistance. Fruit sugars, acids, pigments and volatile aromatic compounds are being quantified in newly bred and historically important cultivars. Researchers have identified and characterized several stylar ribonucleases associated with self-unfruitfulness. Molecular phylogenetic studies are examining the dispersion routes of apricot germplasm from its centers of origin to those cultivars currently in production. Although several linkage maps have been developed using diverse parents and a wide variety of molecular markers from apricot and other Prunus crops, the scarcity of documented monogenic characters in apricot limits the effectiveness of marker assisted selection for economically important traits. [ABSTRACT FROM AUTHOR]

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The major cultivated strawberry species, Fragaria x ananassa, is a hybrid of two native species, F. chiloensis and F. virginiana. Strawberry breeders are focused on improving local adaptations, fruit quality, productivity and disease resistance, and many are interested in developing new day-neutral cultivars. Some of the major pathogens worldwide are Botrytis cinerea, Colletotrichum spp., Phytophthora cactorum, Phytophthora fragariaeandVerticillium albo-atrum. The genetics of many of the horticulturally important traits have been investigated in strawberry and a number of genes have been characterized and cloned that are highly expressed during fruit ripening and maturation. Marker systems have been developed in strawberry for genetic linkage mapping and QTL have been identified for the day neutrality trait and several other fruit characteristics. Transgenic strawberries have been produced with herbicide and pest resistance and an effective marker-free transformation process has been developed. Two major EST libraries have been generated as genomic resources. [ABSTRACT FROM AUTHOR]

All raspberry breeders are interested in improving fruit quality and\break increasing the efficiency of fruit production. The development of primocane fruiting cultivars with excellent shipping quality has allowed major raspberry industries to emerge in non-traditional areas such as California. An increased interest in fruit chemistry, particularly anthocyanins, has led to many studies determining the inheritance of these compounds. Progress towards resistance to major diseases such as Phytophthora root rot has been made through greater understanding of the inheritance of these traits, and the use of novel and traditional germplasm resources. Black raspberry breeding efforts have been greatly increased in the early 21st Century in response to increased disease pressure and raised consumer awareness of the high levels of antioxidants in their fruit. A genetic linkage map of red raspberry (‘Glen Moy' × ‘Latham') has been constructed and used to search for QTL associated with cane spininess, root sucker density and root sucker spread. Transformation was used to develop a red raspberry cultivar with resistance to Raspberry bushy dwarf virus, although it was not commercialized. [ABSTRACT FROM AUTHOR]

Most of the plums grown commercially are either the hexaploid, Prunus domestica (European) or the diploid, P. salicina (Asian or Japanese). Common goals of European plum breeders are cold hardiness, modest tree size, self fertility and productivity. Some of the key abiotic problems confronting Japanese plum production are susceptibility to spring frosts, insufficient winter hardiness and limited soil adaptations. Fruit quality and disease resistance are important goals in all plum breeding projects. The genetics of only a few traits have been investigated in plum; however, significant progress has been made in identifying horticulturally useful germplasm. A Myrobalan plum clone was crossed with an almond-peach hybrid to generate a microsatellite genetic linkage map and a resistance gene to the root knot nematode (Ma) was identified. A transgenic European plum clone was produced that carries the plum pox virus coat protein gene (PPV-CP) and has strong resistance to all four major serotypes of PPV. [ABSTRACT FROM AUTHOR]

Kiwifruit are still a relatively minor crop making up perhaps 0.2% of total world annual production of fruit. The kiwifruit of commerce are large-fruited selections of two closely related species Actinidia chinensis and A deliciosa. Most current kiwifruit cultivars are selections from the wild or from seedling populations and only a few result from planned hybridizations. The main emphasis in the breeding programs underway is on fruit novelty, flavor, size, time of harvest, flesh color, length of storage life, environmental adaptation and vine productivity. Until recently, nearly all the kiwifruit grown commercially outside China were of one green-fruited cultivar of A.deliciosa; now yellow-fleshed, sweeter flavored kiwifruit are becoming important in international trade. To take advantage of the considerable diversity within the genus requires good germplasm resources and a better knowledge of the reproductive biology of kiwifruit. The main constraints to breeding include dioecy, the long generation time and the complexity of some key traits as well as the need for support structures, the exuberant vegetative growth and the need to control growth to ensure fruiting. Many of the traits associated with fruit quality are quantitatively inherited. Use of molecular biological and biotechnological techniques should facilitate improvement programs. [ABSTRACT FROM AUTHOR]

Grape is a major crop worldwide in which production is primarily driven by the ability to grow high-quality fruit. Breeding objectives vary by region and market class of grape, but many programs seek to combine high quality fruit with improved disease resistance and environmental adaptation, or to continue advances in quality attributes. Grapevines are predominantly a grafted crop, making grape rootstocks, and rootstock breeding, vitally important in the growth of the global viticulture industry. There are vast germplasm resources available within the genus Vitis, but worldwide production is dominated by cultivars of one species, V. vinifera. Species other than V. vinifera are of significant interest as useful sources of desirable traits in many modern breeding programs. Little is known concerning the genetic control of most traits in grape beyond the fact that many are quantitatively controlled. Substantial international effort has occurred in the development of molecular genetic and genomic resources for grape. Many tools are now in place to identify the causal genes underlying important traits and to better understand the allelic diversity that exists in important genes. [ABSTRACT FROM AUTHOR]

The cultivation of Ribes fruits (black- and redcurrants and gooseberries) is aimed at both fresh and processing markets, with the blackcurrant R. nigrum particularly important in the latter. Breeding is increasingly focused on national and regional requirements, and for blackcurrant the specific quality requirements of the processing industry are key objectives in many programmes, alongside agronomic traits such as yield and pest resistance. Durable resistance to foliar pathogens and damaging pests such as gall mite remains a high priority, partly due to increasing interest in integrated crop management systems. Many Ribes species, especially the darker-fruited blackcurrant types, contain high concentrations of polyphenolic compounds, notably anthocyanins and flavonols, and these components are of growing importance due to their link to human health, together with high levels of ascorbic acid (vitamin C). The development of marker-assisted breeding strategies in Ribes is in progress, to improve breeding efficiency and time to cultivar, and QTLs affecting several important phenological, agronomic and fruit quality traits have been located on the recently-developed linkage map for blackcurrant. Additionally, markers linked to key traits such as gall mite resistance are under development. [ABSTRACT FROM AUTHOR]

looseness-1Two major cherry species are grown for their fruit, the diploid sweet cherry and the tetraploid sour cherry. For both these species, new cultivars are needed that possess improved fruit quality and disease resistance. Genetic variation exists for most of the desired traits; however, little is known about their inheritance. The one exception is self-compatibility, where the molecular genetic basis has been elucidated in both sweet and sour cherry and molecular markers are available to identify self-compatible individuals in segregating progeny populations. Complete genetic linkage maps in cherry are just now being generated and as a result QTL analyses in cherry lag behind those in other Prunus species, most notably peach. Successful regeneration and transformation of cherry has been reported; however, utilizing this technology for gene function analysis and cultivar generation is still in its infancy. [ABSTRACT FROM AUTHOR]

The vast majority of PCR protocols have been developed to amplify soluble DNA or RNA, which has been extracted from its in situ environment, i.e. from clinical or environmental samples. However, the process of removing target nucleic acid from its in situ environment necessarily means that questions such as: is the nucleic acid specific for a particular diseased tissue type; is the nucleic acid derived from extracellular or internalised bacteria or parasites; is viral DNA integrated into the host chromosome or present in episomal form? etc, cannot easily be answered. In situ hybridisation (ISH) and in situ amplification (ISA) techniques help provide the answers to these questions, as the nucleic acid is not extracted during testing. In addition, in situ protocols are the assays of choice when investigating the local expression of particular genes. Many pathology laboratories maintain extensive historical collections of well-preserved, most frequently paraffin embedded, tissue specimens. In addition, collections of native, deep-frozen samples are usually available as well. These archives have most probably previously been investigated using pathological staining techniques and/or ISH tests. However, non-PCR-based ISH protocols tend to exhibit a limited sensitivity, even though several non-nucleic acidbased immunohistochemical signal amplification methodologies have been developed (e.g. use of tyramine derivatives [Speel et al., 1999]). This is why the development of in situ amplification (in situ PCR) techniques has been so important. These methods allow for the investigation of both tissue sections and cell suspensions, such that nucleic acid targets may be detected in an exquisitely specific manner in their native, tissue- or cell-embedded environment. However, this technology itself also faces a range of technical obstacles, including (1) the fact that DNA targets must be made accessible to PCR enzymes and reagents, (2) PCR inhibitors should be removed or diluted without extensive tissue damage, (3) PCR amplimers must remain at the site of their synthesis, (4) non-specific amplification must be prevented, (5) target DNA degradation may be a problem even before PCR thermocycling begins, and (6) the PCR thermocycling conditions should not destroy the physical status of the sample tissue or its intracellular compartmentalization. Perhaps most important is the initial processing and preparation of (tissue) samples even before PCR thermocycling begins, steps being necessary to control any (pre-) autolytic processes that may occur during post-mortem tissue processing. In this respect, the extent of fixative penetration, duration of fixation, type of fixative used, nuclease and protease inhibition in the specimens, the presence of DNA degrading metal ions, acidification of the fixative, extensive cross-linking of proteins and nucleic acids etc, should all be optimised prior to PCR processing [Golenberg et al., 1996]. In addition, immersion in paraffin, the use of aggressive detergents, the presence of picric acid or mercury containing fixatives, hypo-osmosis, electrostatics, and heat treatment can all frustrate the application of ISA. These considerations are especially important with respect to the preservation of RNAs, and mRNAs in particular, and it is always necessary to control for both false positive and false negative results in ISA protocols. It should also be remembered that the effect of fixation is not always beneficial, as the use of fresh specimens is advisable in certain situations [Jackson et al., 1990]. This chapter aims to summarise the most important considerations for the implementation of ISA (in situ PCR) protocols in the clinical laboratory. Advances in both tissue processing and ISA protocols have helped to establish a technology that generates reliable results, provided that tissue sections are handled correctly, before, during and after ISA processing. [ABSTRACT FROM AUTHOR]

The commercial availability of thermostable DNA dependent DNA polymerase enzymes has been the major factor in facilitating the success of PCR amplification. Initially, the Klenow fragment of DNA-dependent DNA polymerase I (involved in replication and repair in the bacterium Escherichia coli), was employed in PCR amplification [Saiki et al., 1985; Mullis et al., 1992; Saiki et al., 1986]. The Klenow fragment is actually a hydrolytic product of the native E. coli DNA-dependent DNA polymerase enzyme which lacks a 5′-3′ exonuclease activity (Fig. 2.3). The Klenow fragment polymerase was used in the first PCR protocols developed, but has the huge disadvantage of exhibiting an optimum reaction temperature at 37°C and being heat labile at the temperatures used in PCR thermocycling reactions. This lability meant that originally, fresh enzyme had to be added after each and every PCR cycle, making the PCR procedure time consuming, labour intensive and highly prone to contamination. Further, it was impossible to generate PCR fragments longer than 400 bp and further processing (using for example Southern blotting or dot spot hybridization), was usually required to identify the presence/absence of specific amplification products from the mixture of amplimers produced. A breakthrough was achieved however in 1976, when Chien et al. [1976] described a 94kD thermostable DNA-dependant DNA polymerase derived from a eubacterium called Thermus aquaticus, whose natural habitat is hot thermal springs (with ambient temperatures of 70-75°C). This thermostable DNA polymerase or "Taq" enzyme was found to possess similar properties to E. coli DNA dependant DNA polymerase I, with strong homology being found at the amino acid level so: the 3′-OH nucleotide addition site, the dNTP/DNA binding sites, and the 5′-3′ exonuclease sites of the two enzymes (Fig. 7.1). Unfortunately however, though this new Taq polymerase did exhibit some endogenous reverse transcriptase activity, it was found that the 3′-5′ proofreading domain (whereby misincorporated nucleotides are removed from double stranded DNA and replaced by the correct complementary nucleotide) was missing. Moreover, despite the obvious thermoresistant qualities of Taq polymerase, it took a further 2 years for the enzyme to be included in a published PCR protocol [Saiki et al., 1986], after which, there was an explosive increase in interest in PCR mediated amplification protocols. To date, many different types of thermostable DNA dependent DNA polymerases have been discovered in many different thermophilic organisms (Section 7.5), with the majority of these enzymes having their own particular characteristics and being available from commercial suppliers. However, Taq thermostable DNA polymerase (along with its variants) still remains the most widely used polymerase in PCR reactions performed today. [ABSTRACT FROM AUTHOR]

When quality issues are discussed in any manufacturing or result-orientated process, then two key terms are often quoted, namely "quality control" and "quality assurance". These two terms are often used interchangeably, but in fact refer to two different procedures. Quality control refers to a system of routine and consistent controls, which help ensure data integrity, data correctness and data completeness. Moreover, quality control helps identify and correct any errors or omissions that have occurred during processing, as well as recording and archiving processing results and quality control data. On the other hand, quality assurance involves a planned system of review procedures, preferably performed by an independent "third party" laboratory, which monitors quality control procedures and verifies that quality objectives have been (and are being) met. Over the past few years, PCR applications and protocols have been developed, optimized, and implemented, for use within a wide range of clinical disciplines. As with the development of any "in house" assay whose results influence clinical decision making, quality criteria for these new PCR protocols have had to be developed in order to comply with both good laboratory practice (GLP) and (inter)national guidelines. Quality criteria for "classical" diagnostic tests such as culture-based assays and ELISAs have already been defined and parallel guidelines for quality controlling, as well as quality assuring, novel PCR-based assays are under continuous development and refinement. Efficiency, sensitivity, specificity, accuracy and reproducibility are all extremely important factors with regard to the official acceptance of novel PCR assays within the clinical diagnostic laboratory, especially now that PCR-based techniques are increasingly being used as diagnostic tools and affecting patient treatment regimens. It should be noted however, that not all PCR assays have to comply with strict clinically oriented quality guidelines, a fact often true in relation to PCR assays used within "research-only" environments. This means that the decision over which PCR assays should be strictly quality controlled depends on the use to be made of the results, which ultimately lies in the hands of the laboratory scientists using that particular PCR assay. Some common concepts and terms used in assessing the quality criteria of newly developed or newly implemented PCR assays within the clinical diagnostic laboratory are presented below. For a more detailed discussion, the reader is referred to two particular reviews [Niesters, 2002; Neumaier et al., 1998]. [ABSTRACT FROM AUTHOR]

Three distinct levels of quality control should be considered when setting up PCR applications for use in the clinical laboratory. The primary level of quality control involves the organization of the laboratory and relevant logistical aspects, which are areas of major importance with respect to the avoidance of PCR contamination and the prevention of false positive clinical results. The secondary level of quality control involves PCR design, optimization and assay quality control per se. Finally, there may be individual quality considerations that are specifically related to individual types of PCR methodologies (especially reverse transcription PCR methodologies). [ABSTRACT FROM AUTHOR]

Deoxynucleotide triphosphates (dNTPs) are the essential building blocks of nucleic acid molecules, and as such are necessary components of PCR mixes as no new (amplified) DNA could be generated without them. The four individual deoxynucleotides which make up a DNA sequence (i.e. deoxyadenosine triphosphate, dATP; deoxythymidine triphosphate, dTTP; deoxycytosine triphosphate, dCTP; and deoxyguanosine triphosphate, dGTP) are usually added to PCR and RT-PCR mixes in equimolar amounts, though if the target DNA sequence to be PCR amplified comprises mainly dATP/dTTP (AT ratio) or mainly dGTP/dCTP (GC ratio), then the molar ratio of dNTPs added to the PCR mix may be altered in order to take into account this imbalance. dNTPs are usually purchased either individually or as an (equimolar) mix from commercial suppliers (e.g. Roche, Promega, etc.), and are chemically stable when stored in slightly alkaline aqueous solutions at -20°C. However, it should be noted that dNTPs are naturally acidic in solution; hence working and stock solutions may have to be neutralized with alkaline compounds prior to long-term storage. Neutralized dNTP solutions are normally adjusted to 10 mM stock solutions by spectrophotometry, or by adding the correct volume of sterile water to the lyophilized product directly after its chemical synthesis. Some PCRs may profit from the use of highly purified "PCR-grade" dNTPs (Roche) which contain less than 0.9% deoxynucleotide diphosphates (dNDP), are >99% pure, and free from contaminants such as modified nucleotides and tetrapyrophosphate. These (more expensive) high-purity dNTPs may be helpful in successfully amplifying PCR DNA from preparations containing very low copy numbers of target DNA. In some PCR applications and protocols, one of the four dNTPs may be replaced by an analogous, dNTP, e.g. inosine,7-deaza-2′ -deoxyguanosine, or a modified dNTP, e.g. a biotin-, fluorophore- or radioactively-labeled dNTP. Such modifications allow further downstream post-PCR processing applications to be performed. [ABSTRACT FROM AUTHOR]

The most important phase of the PCR protocol is the amplification phase, comprising a pre-determined number of amplification cycles (or thermocycles). In the vast majority of cases, a typical thermocycle comprises three distinct but sequential steps. In sequential order, these steps include: (1) a template nucleic acid/amplified PCR DNA melting step, required to dissociate double stranded DNA ready for primer hybridisation (usually 90-95°C for 30-60 seconds), (2) a primer annealing step performed at a temperature that has been calculated to be optimal for the PCR primer pair being used (usually 40-70°C for 30-60 seconds), and (3) a final DNA chain extension step at an optimum temperature for the enzyme of choice to promote the full extension and amplification of the DNA sequence (usually around 70-75°C for 60-120 seconds). It should be noted that both annealing and elongation steps of each thermocycle are performed at "stringent" temperatures, facilitating a reduction in the likelihood of non-specific hybridization between primers and regions of DNA which contain similar but not identical DNA sequences. Exceptions to this rule do exist for certain PCR protocols, e.g. PCR using "degenerate" primers. Finally, some PCR thermocycle protocols utilise only two (instead of 3) steps, by combining the annealing and DNA chain extension steps into a single step using a single annealing and chain extension temperature. [ABSTRACT FROM AUTHOR]

The standard qualitative PCR protocol (as initially developed) involves the exponential amplification of a specific DNA sequence which is achieved by subjecting an optimized PCR mix to a predetermined number of thermocycles (cyclical heating and cooling steps). Each thermocycle within this standard PCR protocol actually comprises three distinct steps, namely: (i) a nucleic acid denaturation step (to disassociate the double-stranded DNA helix into single strands), followed by (ii) a primer annealing step (to allow the specific hybridization of a 15-25 base pair oligonucleotide primer), followed by (iii) a DNA extension/amplification step (to -number of thermocycles are complete, and exponential DNA amplification has been performed, the presence or absence of specific target DNA sequences in the final PCR mix (and hence the presence or absence of specific target DNA sequences in the original sample) is established. Over the last few decades, many useful adaptations/ variations of this standard qualitative PCR protocol have been developed. Some of the most important of these variants/adaptations are outlined below. [ABSTRACT FROM AUTHOR]

The analysis of PCR amplification products (amplimers) is an essential step in determining the quality (i.e. the presence or absence of non-specific amplimers) and quantity (relative values or exact values) of the DNA target that has been amplified. In general, the techniques used to analyze PCR products may be divided into two distinct groups: (1) the ex-vitro techniques where analysis is performed outside of the PCR reaction vessel (for example analysis using gel electrophoresis, DNA hybridisation, etc.), and (2) the more recently developed in-vitro techniques, where analysis is performed inside the PCR reaction vessel and during PCR thermocycling per se. Both the ex-vitro and in-vitro techniques require that the PCR products be first visualized in some way prior to analysis, with some of the methodologies used for PCR product visualization being shared by both groups. Ultimately however, the "gold-standard" in PCR amplimer analysis is direct sequencing of the amplimer to determine its actual nucleotide composition. [ABSTRACT FROM AUTHOR]

In order to decrease the likelihood of non-specific primer binding occurring during the initial (i.e. pre-first cycle) stage of the PCR thermocycling program (when the temperature is low enough to allow partial binding of the primer), one of the reaction components (usually the DNA polymerase or magnesium salt) may be omitted from the reaction mix and added once the initial target DNA melting temperature of 90-95°C is reached (PCR amplification will not proceed in the absence of magnesium ions). Unfortunately however, the simple act of opening and closing a PCR reaction tube greatly increases the chance of contamination of that tube. One elegant alternative to this problem is to physically separate the reaction components into two separate compartments, e.g. via a thin layer of wax. Magnesium chloride solution may then be added to the upper surface of the wax bead. The wax bead then melts at a temperature that is too high for non-specific binding of the PCR primers to the DNA template to occur. Some suppliers provide wax beads already impregnated with magnesium salt. Other elegant alternatives devised to decrease the likelihood of non-specific primer binding during the initial stage of the PCR thermocycling program, include heat-activatable thermostable DNA polymerases, which require approximately 10 minutes of heat activation at around 90°C before becoming activate. Other methods utilise polymerases coated with antibodies, which inhibit the action of the polymerase until the temperature is high enough to denature and remove the antibodies. All of these approaches are collectively named "hot-start" procedures (Chapter 7). When performing multiple PCRs in a single "batch" (i.e. at the same time), it is advisable to prepare a "master mix" of reaction ingredients (comprising a multiple number of individual reaction mixes prepared in a single tube), and then pipette out the individual volumes into individual reaction tubes, rather than pipetting each separate component into every individual reaction tube one after the other. This process significantly reduces the number of pipetting actions that need to be performed and as such greatly contributes to the reproducibility and reliability of the PCR test protocol. The volume of a particular reagent required in a master mix is dependent on the number of PCRs to be performed, and may be calculated by multiplying the volume of the ingredient required for a single reaction, by the number of tests to be performed, including duplicates and positive and negative control samples. Additionally, for every master mix reaction prepared, an extra aliquot of each ingredient should be added (in order to account for volume errors inherent in any repeat pipetting action). Preferably, once prepared, the master mix should be immediately dispensed or stored on ice for short periods of time. Mastermixes and/ or individual PCR reaction mix aliquots may be stored frozen for a prolonged period of time and immediately thawed prior to use. In this case, it is preferable to prepare master mixes without thermostable DNA polymerase and then add the required volume of enzyme after thawing (immediately prior to PCR thermocycling). The time period during which frozen mastermix aliquots may be stored without loss of PCR amplification sensitivity should ideally be determined for each particular mix to be prepared and be routinely quality controlled [Kofler and Klausegger, 1999]. From the authors' own experience, PCR master mix aliquots without thermostable DNA polymerase may be stored for 2-3 months at -20°C without loss of PCR sensitivity. [ABSTRACT FROM AUTHOR]

The amount of nucleic acid present within a particular cell differs greatly between the various classes of organisms and between tissue types, with microorganisms harbouring smaller genomes than the more complex nucleated cells of eukaryotes. This is partially due to the presence of various families of repeat DNA sequences present in eukaryotic DNA that are essentially absent in prokaryotes. These sequences do not seem to participate in gene coding and their precise function is still largely unknown. Viruses, which are dependent on host cell replication machinery, generally have the smallest recorded genomes, with certain plant viruses containing a genome not larger than a few kilobasepairs (kbp), for example the tobacco necrosis virus genome is only 3.8 kbp in length. However, viruses are not self-replicating and the smallest genome for a self-replicating organism belongs to the bacterium Mycoplasma genitalium at 5.8 × 105 bp [Fraser et al., 1995]. That said, the symbiotic mini-bacterium Carsonella rudii lives within the cells of the hackberry petiole gall psyllid Pachypsylla venustai (an insect) and has a genome of only 159,662 basepairs, or less than 300 genes. This mini-bacterium is dependant on its host for nutrients [Nakabachi et al., 2006]. In contrast, amphibians and flowering plants possess the largest genomes (4 × 108 to 1 × 1011 bp), with human cells possessing approximately 3 × 109 bp on 2 × 23 linear chromosomes. The overall number of nucleotides in human DNA is in the order of one billion, of which 3.5% are predicted to encode proteins approximating to 30,000 genes (if we assume an average gene length of 1,000 nucleotides). An optimised PCR amplification protocol is able to selectively amplify one individual gene (or fragment) from within all of these other genes, exons and accompanying nucleic acids, e.g. extrachromosomal plasmids, episomal viruses, ribosomal RNA, messenger RNA, etc. [ABSTRACT FROM AUTHOR]

Chemically synthesised nucleotide primer molecules (also called oligonucleotides or oligos) are essential components to the success of PCR amplification. After (specific) hybridisation to a complementary region of the target DNA, the primers provide the 3′hydroxyl ends by which DNA polymerase mediated DNA synthesis proceeds (Fig. 1.1). The position of the primers along the single stranded DNA strands defines the total length of the PCR amplification product generated. Primers designed to yield relatively short PCR amplification products (100-200 nucleotides), generate product (amplimers) more efficiently than primers designed to yield relatively long PCR amplification products (3,000-5,000 bp). This is especially true for DNA template molecules where significant secondary structure is present. Hence, PCR primers are usually designed to amplify a region of maximum 3,000-5,000 bp in length. However, using specifically adapted "long and accurate" PCR protocols, the amplification of fragments up to 40 kbp in length is feasible. PCR primers are the main determinants of PCR specificity. In order to amplify a specific DNA sequence, the sequence of the primer annealing sites on the target DNA must be known. Further, in order to limit the chance of non-specific primer binding (where one or more bases are not complementary to the target sequence), or the chance of the primers binding to a similar sequence elsewhere on the target DNA, primers are usually designed to be in the order of 18-22 nucleotides in length (Section 5.1). A limited group of generally short primers has the capacity to hybridise to multiple sites on target nucleic acid, these include oligo-dT-based primers and random hexamer/decamer primers. Another category of PCR primers that have the potential to anneal to multiple sites are those that target genomic repeat sequences, which may be used to amplify genomically polymorphic repeat regions (i.e. regions varying in repeat sequence length between individual isolates) and generate "DNA fingerprints" for individual isolates [Van Belkum et al., 1998]. Also, primers designed to be complementary to conserved DNA sequences present in ribosomal genes are able to amplify specific ribosomal gene sequence fragments from all organisms, whether eukaryote or prokaryote. [ABSTRACT FROM AUTHOR]

In principle, PCR generates large quantities of DNA from a minute amount of nucleic acid starting material using a methodology similar to (but much simpler than) that seen in living cells. For living cells, in vivo DNA synthesis is dependent upon a well defined but complex set of enzymes and co-factors, which have evolved to act in a concerted fashion during the synthetic phase (S-phase) of the cell cycle. In comparison, PCR facilitates in vitro DNA synthesis in a much simpler fashion, making use of a smaller set of defined ingredients and reaction conditions involving relatively high temperatures. The range of factors contributing to successful PCR amplification is reviewed below. [ABSTRACT FROM AUTHOR]

The polymerase chain reaction (PCR) allows the specific and exponential synthesis of a predetermined DNA region via the use of two small, specifically designed fragments of DNA (primers or oligonucleotides), which form the two termini of the nucleic acid molecule to be amplified. PCR amplification reactions in general are highly specific, specificity being determined by the correct hybridisation of primer specific sequences to complementary sequences present on the target DNA molecule to be amplified. PCR primers comprise specific nucleotide sequences which are designed to hybridise to either the parallel or anti-parallel strand of the target DNA molecule, and as such since primers need to be precisely complementary to their target sequences, some sequence data from the terminal ends of the DNA is required for primer design (Fig. 1.1). Once hybridised to the target DNA, the primers provide the double stranded 3′-hydroxyl terminus required by thermostable DNA dependent DNA polymerases to begin the synthesis of a new DNA strand (complementary to the strand to which the primer has hybridised). Moreover, because PCR uses two primers (one designed for each strand of the DNA molecule to be amplified), repeated cycles of primer hybridisation (annealing) and disassociation allows DNA amplification in the 5′ to 3′ direction on both strands to occur, with the primers effectively acting as Okazaki fragments [Marinus, 1976]. PCR amplification is in fact a cyclical process where the sample DNA is initially denatured in order to unwind and separate the DNA double helix into single strands. This is usually achieved by heating the DNA sample in an aqueous environment, usually at a temperature of 94°C for 30 seconds to 5 minutes. Hybridisation of the specific oligonucleotide primers to each strand is then achieved by lowering the temperature of the reaction mix to the annealing temperature (Tm) which is usually set between 40°C and 65°C (dependent on the design of the oligonucleotide sequences used as primers). After the primer hybridisation step, the temperature is raised to approximately 72°C, (an optimal temperature for thermostable DNA polymerase mediated DNA strand replication), and the whole cycle is then repeated a pre-determined number of times. After each cycle of replication, each newly synthesised double stranded DNA molecule (known as an amplimer or amplicon) contains terminal sequences, which are complementary to the primer sequences used (Fig. 1.2). This process allows each amplimer to serve as a template for replication in subsequent rounds of PCR cycling, resulting in a theoretical doubling (exponential amplification) of the number of target molecules during each cycle. Some of the fundamental principles introduced above are detailed in a large body of international scientific literature (e.g. [Jain, 2002; Lubeck and Hoorfar, 2003; Klein, 2002; Wolk et al., 2001; Foy and Parkes, 2001; Erlich, 1999; Kiechle, 1999; Lisby, 1999]). [ABSTRACT FROM AUTHOR]

In the first part of this paper we overview protein structures, their spontaneous formation ("folding") and thermodynamic and kinetic aspects of this phenomenon. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the "two-state" ("denatured state" ↔ "native state") transition proceeds without accumulation of metastable intermediates, and only the transition state, i.e., the most unstable state in the folding pathway, is outlined by its essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of protein's folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. And, at last, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of transition state) in a reasonable concordance with experimental data. [ABSTRACT FROM AUTHOR]

A model for three competing bacterial strains that incorporates mutation and/or phenotypic switching is studied. We consider three different strains: wild, mutated and phenotypic bacteria generated by an inhibitor introduced in the environment. Our model considers that all new phenotypic bacteria are sensitive to the inhibitor and there is no phenotypic replication. Two steady state regimes are identified, finding that the strain surviving is the one arising from mutation of the wild strain. The model may also show three steady state regimes with the persistence of the three bacteria in the system. [ABSTRACT FROM AUTHOR]

There is now a paradigm in the study of an efficient modelling of biomolecular structure. The foundations of the physics and the elucidation of biological function of living organisms will be asserted on a clear geometrical language according the best ideas of D'arcy Thompson [1], Rashevsky [2], Schrödinger [3] and Anfmsen [4]. The present work aims to give a possible mathematical description of one of Nature's services of noticeable importance in the organization of life and its maintenance: the specific geometric form of macromolecular structure as provided by the mathematical problem of organization of Steiner Minimal Trees. The energy minimization process which lead to the formation of a biomacromolecule can be understood and modelled by the search process of organization of Steiner trees as the representatives of the possible molecular configurations corresponding to local minima of the free energy. Life maintenance and the survival of the living organism is guaranteed by the competence of staying away from the Global minimum structure and its associated Steiner Minimal Tree. [ABSTRACT FROM AUTHOR]

A central focus of ecological research is to understand the distribution and abundance of species (DAS) across a range of spatial and temporal scales. Such knowledge is critical to our ability to design sustainable ecological reserves, to predict extinction rates under habitat loss or climate change, to estimate species diversity from incomplete census data, and to decipher the fundamental forces shaping ecosystems [16, 25, 44]. Moreover, it is increasingly becoming evident that the spatial structure of populations influences the potential for coexistence of species and the likelihood that cooperative phenomena will emerge in the face of selfish or competitive behaviors [33, 36]. [ABSTRACT FROM AUTHOR]

Let matrix A represent a data set of m features and n samples. Each element of the matrix, aij, corresponds to the expression of the i-th feature in the j-th sample. Biclustering is a classification of the samples as well as features into k classes. In other words, we need to classify columns and rows of the matrix A. Doing so, let S1, S2,..., Sk and F1, F2,..., Fk denote the classes of the samples (columns) and features (rows), respectively. Formally biclustering can be defined as follows. [ABSTRACT FROM AUTHOR]