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Good manufacturing practice (GMP) compliance in the biologics sector: plasma fractionation.

The U.S. blood supply is the safest it has ever been. Due to blood safety and the introduction of viral inactivation/clearance technologies, protein therapies derived from human blood have also in recent years had a history of product safety. Nevertheless, since 1995, the plasma-fractionation industry has experienced increased compliance-related actions by the Food and Drug Administration (FDA), as shown by a substantive increase in the number of FDA 483 inspectional observations, FDA warning letters and other FDA regulatory action. An evaluation of these trends shows that they reflect the implementation by the FDA of increased inspectional interest in the plasma-fractionation industry and an evolution of inspectional practices and standards of current good manufacturing practice (cGMP). Plasma fractionators have responded to FDA actions by carefully evaluating and addressing each inspectional observation, assessing impact to product and taking appropriate actions, including corrective actions to prevent future occurrence. They have made major investments in facilities, quality systems, personnel and training to meet the evolving standards of cGMP and in an effort to implement these standards systemically. Through industry associations, manufacturers have further enhanced product safety by adopting additional voluntary standards for plasma to prevent the entry of potentially unsuitable plasma into the production process. The industry remains committed to application of cGMP and to working with the FDA in further evolution of these standards while striving to assure a continued supply of safe, pure and effective plasma-derived therapies.

Biotechnology↗

Musca domestica, a window on the evolution of sex-determining mechanisms in insects.

The genetic cascades regulating sex determination of the housefly, Musca domestica, and the fruitfly, Drosophila melanogaster, appear strikingly different. The bifunctional switch gene doublesex, however, is present at the bottom of the regulatory cascades of both species, and so is transformer-2, one of the genetic elements required for the sex-specific regulation of doublesex. The upstream regulators are different: Drosophila utilizes Sex-lethal to coordinate the control of sex determination and dosage compensation, i.e., the process that equilibrates the difference of two X chromosomes in females versus one X chromosome in males. In the housefly, Sex-lethal is not involved in sex determination, and dosage compensation, if existent at all, is not coupled with sexual differentiation. This allows for more adaptive plasticity in the housefly system. Accordingly, natural housefly populations can vary greatly in their mechanism of sex determination, and new types can be generated in the laboratory.

Animals↗

[Role of oxygen in the vital activity of aerobic organisms].

New experimental data that underlie construction of an adaptive-metabolic conception as to curative effect of hyperbaric oxygenation are systematized in the aspect of evolution. Oxygen under high pressure (300 kPa, 60 min) exerts a specific effect on functions of redox and antiredox systems and nonspecific effect determining adaptation mechanisms of functional (regulatory, effector), metabolic (bioenergy, detoxication, biosynthetic) and morphogenetic (cellular and intracellular regeneration) types at different (hyper-, normo- and hypobiotic) levels of vital activity as dependent on the metabolic activity of the functional structures under pathology conditions.

Adaptation, Physiological↗

Zinc finger proteins in early Xenopus development.

The C2H2-type zinc finger motif defines a large super family of specific DNA and specific RNA binding proteins. Individual members of this protein family have been demonstrated to carry important regulatory functions in embryogenesis. We have isolated a large collection of C2H2-type zinc finger proteins from Xenopus laevis. Some of these proteins are highly conserved in evolution and found to be differentially expressed during embryonic development of the central nervous system. We also summarize our recent findings on the biochemical characterization of RNA and DNA binding activities in vitro for other Xenopus zinc finger proteins, which fall into structurally defined, distinct subfamilies.

Amino Acid Sequence↗

Data-based model and parameter evaluation in dynamic transcriptional regulatory networks.

Finding the causality and strength of connectivity in transcriptional regulatory networks from time-series data will provide a powerful tool for the analysis of cellular states. Presented here is the design of tools for the evaluation of the network's model structure and parameters. The most effective tools are found to be based on evolution strategies. We evaluate models of increasing complexity, from lumped, algebraic phenomenological models to Hill functions and thermodynamically derived functions. These last functions provide the free energies of binding of transcription factors to their operators, as well as cooperativity energies. Optimization results based on published experimental data from a synthetic network in Escherichia coli are presented. The free energies of binding and cooperativity found by our tools are in the same physiological ranges as those experimentally derived in the bacteriophage lambda system. We also use time-series data from high-density oligonucleotide microarrays of yeast meiotic expression patterns. The algorithm appropriately finds the parameters of pairs of regulated regulatory yeast genes, showing that for related genes an overall reasonable computation effort is sufficient to find the strength and causality of the connectivity of large numbers of them.

Algorithms↗

MicroRNAs in plants.

MicroRNAs (miRNAs) are an extensive class of ~22-nucleotide noncoding RNAs thought to regulate gene expression in metazoans. We find that miRNAs are also present in plants, indicating that this class of noncoding RNA arose early in eukaryotic evolution. In this paper 16 Arabidopsis miRNAs are described, many of which have differential expression patterns in development. Eight are absolutely conserved in the rice genome. The plant miRNA loci potentially encode stem-loop precursors similar to those processed by Dicer (a ribonuclease III) in animals. Mutation of an Arabidopsis Dicer homolog, CARPEL FACTORY, prevents the accumulation of miRNAs, showing that similar mechanisms direct miRNA processing in plants and animals. The previously described roles of CARPEL FACTORY in the development of Arabidopsis embryos, leaves, and floral meristems suggest that the miRNAs could play regulatory roles in the development of plants as well as animals.

Base Sequence↗

The immune system: a weapon of mass destruction invented by evolution to even the odds during the war of the DNAs.

Living systems operate under interactive selective pressures. Populations have the ability to anticipate the future by generating a repertoire of elements that cope with new selective pressures. If the repertoire of such elements were transcendental, natural selection could not operate because any one of them would be too rare. This is the problem that vertebrates faced in order to deal with a vast number of pathogens. The solution was to invent an immune system that underwent somatic evolution. This required a random repertoire that was generated somatically and divided the antigenic universe into combinatorials of determinants. As a result, it became virtually impossible for pathogens to escape recognition but the functioning of such a repertoire required two new regulatory mechanisms: 1) a somatic discriminator between Not-To-Be-Ridded ('Self') and To-Be-Ridded ('Non-self') antigens, and 2) a way to optimize the magnitude and choice of the class of the effector response. The principles governing this dual regulation are analyzed in the light of natural selection.

Animals↗

Molecular evolution of the primate developmental genes MSX1 and PAX9.

In primates, the craniofacial skeleton and the dentition are marked by high levels of interspecific variation. Despite this, there are few comparative species studies conducted at the molecular level to investigate this functional diversity. We have determined nucleotide sequences of MSX1 and PAX9, two developmental genes, in a sample of 27 diverse primate species in order to identify coding or regulatory variation that may be associated with phenotypic diversity. Our analyses have identified four highly conserved noncoding sequences, including one that is conserved across primates and with dogs but not with mice. Although we find that substitution rates vary significantly across MSX1 exons, comparisons of nonsynonymous and synonymous substitution rates (dN/dS) suggest that, as a whole, MSX1 and PAX9 amino acid sequences have been under functional constraint throughout primate evolution. Compared to all other primates in our sample, our analysis of exon 1 in MSX1 finds an unusual pattern of amino acid substitution for Tarsius syrichta, a member of a lineage (tarsiers) that has many unique features among primates. For example, tarsiers are the only extant primates without deciduous incisors, and MSX1 is expressed exclusively in the incisor regions during the earliest stages of dental development. Our overall results provide insight into the utility of comparative species analyses of highly conserved developmental genes and their roles in the evolution of complex phenotypes.

Amino Acid Sequence↗

Evidence of undiscovered cell regulatory mechanisms: phosphoproteins and protein kinases in mitochondria.

The finding that mitochondria contain substrates for protein kinases lead to the discovery that protein kinases are located in the mitochondria of certain tissues and species. These include pyruvate dyhydrogenase kinase, branched-chain alpha-ketoacid dehydrogenase kinase, protein kinase A, protein kinase Cdelta, stress-activated kinase and A-Raf as well as unidentified kinases. Recent evidence suggests that mitochondrial protein kinases may be involved in physiological processes such as apoptosis and steroidogenesis. Additionally, the novel finding of low-molecular-weight GTP-binding proteins in mitochondria suggests the possibility that these may interact with mitochondrial protein kinases to regulate the activity of mitochondrial effector proteins. The fact that there are components of cellular regulatory systems in mitochondria indicates the exciting possibility of undiscovered systems regulating mitochondrial physiology.

Animals↗

The control of body size in insects.

Control mechanisms that regulate body size and tissue size have been sought at both the cellular and organismal level. Cell-level studies have revealed much about the control of cell growth and cell division, and how these processes are regulated by nutrition. Insulin signaling is the key mediator between nutrition and the growth of internal organs, such as imaginal disks, and is required for the normal proportional growth of the body and its various parts. The insulin-related peptides of insects do not appear to control growth by themselves, but act in conjunction with other hormones and signaling molecules, such as ecdysone and IDGFs. Size regulation cannot be understood solely on the basis of the mechanisms that control cell size and cell number. Size regulation requires mechanisms that gather information on a scale appropriate to the tissue or organ being regulated. A new model mechanism, using autocrine signaling, is outlined by which tissue and organ size regulation can be achieved. Body size regulation likewise requires a mechanism that integrates information at an appropriate scale. In insects, this mechanism operates by controlling the secretion of ecdysone, which is the signal that terminates the growth phase of development. The mechanisms for size assessment and the pathways by which they trigger ecdysone secretion are diverse and can be complex. The ways in which these higher-level regulatory mechanisms interact with cell- and molecular- level mechanisms are beginning to be elucidated.

Animals↗

Complete nucleotide sequence of a cDNA derived from calf lens gamma-crystallin mRNA: presence of Alu I-like DNA sequences.

The nucleotide sequence of a cloned cDNA derived from gamma-crystallin mRNA of calf lens was determined. The cloned cDNA contains the entire coding region 522 bp long, 30 nucleotides of the 5' noncoding region, and 67 residues in the 3' noncoding region followed by a poly(A) tail of 25 nucleotides. The deduced amino acid sequence directly demonstrates for the first time that the calf gamma-crystallin contains 174 residues. The nucleotide sequence contains a number of interesting features including a 32-bp sequence in the 3' region with 70% complementarity to the 3' end of the first monomer unit of the consensus Alu I DNA. Within this region, a 32-bp sequence shows about 80% homology with a segment of hamster 4.5S RNA. The possible evolutionary and regulatory significance of these sequences is discussed.

Amino Acid Sequence↗

Sequence analysis of active mariner elements in natural populations of Drosophila simulans.

Active and inactive mariner elements from natural and laboratory populations of Drosophila simulans were isolated and sequenced in order to assess their nucleotide variability and to compare them with previously isolated mariner elements from the sibling species Drosophila mauritiana and Drosophila sechellia. The active elements of D. simulans are very similar among themselves (average 99.7% nucleotide identity), suggesting that the level of mariner expression in different natural populations is largely determined by position effects, dosage effects and perhaps other factors. Furthermore, the D. simulans elements exhibit nucleotide identities of 98% or greater when compared with mariner elements from the sibling species. Parsimony analysis of mariner elements places active elements from the three species into separate groups and suggests that D. simulans is the species from which mariner elements in D. mauritiana and D. sechellia are most likely derived. This result strongly suggests that the ancestral form of mariner among these species was an active element. The two inactive mariner elements sequenced from D. simulans are very similar to the inactive peach element from D. mauritiana. The similarity may result from introgression between D. simulans and D. mauritiana or from selective constraints imposed by regulatory effects of inactive elements.

Animals↗

Back on the ground: genome analysis of convergent flight loss in rails.

Similar phenotypic traits can evolve independently in response to comparable environmental challenges. A striking example of this process is the repeated and irreversible loss of flight in birds, particularly on islands. The rail family (Rallidae) provides an exceptional model for studying this phenomenon, as nearly a quarter of the 130 extant species have independently become flightless. Here, we present the first genome-wide comparative analysis of multiple independent flightless rail lineages to identify the molecular basis of flight loss. We compared coding regions from 7 rail species (4 flightless and 3 volant) using more than 11,000 alignments and multiple phylogeny-based tests, including branch-site models of selection, relative evolutionary rate analyses, and assessments of function-altering amino acid substitutions. Across all analyses, 116 genes showed significant associations with flightlessness, of which 37 were linked to biological functions related to flight capacity-such as muscle, bone, limb, and heart development-or to traits reflecting ecological consequences of flight loss, including immune response, renal function, lipid metabolism, cognition, and sensory perception. Many genes under selection in flightless species were also involved in gene regulation and post-translational modification. These findings suggest that convergent loss of flight in rails arises not from major mutations in a few key loci but from numerous small, repeated genetic changes affecting both developmental pathways and regulatory mechanisms.

Animals↗

Major morphological effects of a regulatory gene: Pgm1-t in rainbow trout.

We have investigated the morphological effects of a genetic locus, Pgm1-t, that affects the expression of a phosphoglucomutase locus (Pgm1) in liver of rainbow trout (Salmo gairdneri). We have previously shown that embryos with liver Pgm1 expression hatch earlier than those without liver Pgm1 expression. We predicted that this difference in developmental rate should cause a reduction in meristic counts in the more rapidly developing fish with liver Pgm1 expression. Eight meristic (countable) characters in nine full-sib groups segregating for the presence or absence of liver Pgm1 expression are in agreement with this prediction. In eight of the nine families, there is a significant difference in the multivariate distribution of the eight meristic counts between full sibs with and without liver Pgm1 expression. This separation in multivariate space is based on a tendency for lower meristic counts in fish with liver Pgm1 expression. The magnitude of these morphological differences is similar to that between two subspecies of cutthroat trout (Salmo clarki) that show substantial genetic divergence at structural loci encoding enzymes (Nei's D = 0.34). These data support the view that small changes in the developmental process caused by genetic differences at regulatory genes can have large effects on morphology.

Animals↗

Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes.

The progress in genome characterizations has opened new routes for studying enzyme families. The availability of the human genome enabled us to delineate the large family of short-chain dehydrogenase/reductase (SDR) members. Although the human genome releases are not yet final, we have already found 63 members. We have also compared these SDR forms with those of three model organisms: Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. We detect eight SDR ortholog clusters in a cross-genome comparison. Four of these clusters represent extended SDR forms, a subgroup found in all life forms. The other four are classical SDRs with activities involved in cellular differentiation and signalling. We also find 18 SDR genes that are present only in the human genome of the four genomes studied, reflecting enzyme forms specific to mammals. Close to half of these gene products represent steroid dehydrogenases, emphasizing the regulatory importance of these enzymes.

Animals↗

Gene structure of chum salmon somatolactin, a presumed pituitary hormone of the growth hormone/prolactin family.

From a chum salmon genomic DNA library, clones coding for somatolactin (SL), a presumed pituitary hormone belonging to the GH/PRL family, were isolated and analyzed. The salmon SL gene was 16 kilobases (kb) in length, this being the largest among mammalian GH (approximately 2 kb) and PRL (approximately 10 kb) and fish GH (approximately 4 kb) genes. As in the case of mammalian GH/PRL genes, the salmon SL gene was comprised of five exons in contrast to rainbow trout and Atlantic salmon GH genes, which each have six exons. Upstream from the transcriptional initiation site were found one TATA box identical to those of mammalian PRL genes and four consensus sequences corresponding to the Pit-1/GHF-1 binding element which is essential to the expression of mammalian GH and/or PRL genes. The similarity in amino acid sequences and organization of the SL gene with mammalian GH/PRL genes indicates that the SL gene is quite likely produced from an ancestral gene common to GH/PRL genes by gene duplication. Based on these considerations, an evolutionary model for the GH/PRL/SL gene family was made and shows the common ancestral gene to originate not from duplication of a primordial gene but from shuffling of independent exons and a regulatory sequence.

Amino Acid Sequence↗

Lens differentiation and crystallin regulation: a chick model.

The vertebrate lens is a transparent polarized tissue that acts as the gateway for vision. The chick lens is an excellent model for studying tissue organogenesis, since it is both accessible and easily manipulated during embryonic stages. The chick lens consists of two morphologically discrete compartments, the epithelium and the fiber-cell mass. Evidence indicates that the early phases of lens development involve several sequential events, including tissue interactions, cell proliferation and differentiation. The morphological change during lens development is associated with the concurrent and distinct functions of numerous transcription factors. Diffusible molecules from the complementary neural tissue play vital roles during the entire process of lens development. Lens tissue is characterized by the ample production of crystallins, lens specific proteins which provide structural integrity and functional properties to the lens. Thus, the study of crystallin regulation should provide insight into the development of a functional lens during embryogenesis. This process has been shown to involve a complex and evolutionary conserved pathway supported by different regulatory proteins.

Animals↗

Mechanisms of T-cell homing to skin.

Although many individual components of the lymphocyte's migratory machinery have been identified and analyzed for function in vitro, interesting questions remain regarding the in vivo integration of these components. How does the lymphocyte "choose" a direction for migration in the complex cytokine/chemokine environment of inflamed dermis when multiple chemokines secreted by multiple cell types are present? Can differences in chemokine expression explain the clinical and histologic differences seen in different inflammatory skin disease? What are the roles of proteins such as VAP-1? Our present understanding of lymphocyte migration has already led to the use of monoclonal antibodies to integrins such as LFA-1 that can potentially be of therapeutic use in skin diseases such as psoriasis. Small molecule inhibitors of T lymphocyte-specific receptors such as CCR4 or CXCR3 are promising agents for controlling T cell-mediated inflammation but have yet to be developed. These receptors may have greater selective expression on skin-homing T cells and thus may decrease the risk of iatrogenic immunosuppression. Close cooperation between the pharmaceutical industry and basic scientists will hopefully lead to the evolution of such compounds and toward more effective treatment of inflammatory skin diseases.

Antibodies, Monoclonal↗