Assignment of human ferritin genes to chromosomes 11 and 19q13.3→19qter

Summary Extracts of hamster-human and mouse-human hybrids, some with translocations involving chromosome 19, have been assayed for both human spleen ferritin (rich in L subunits) and human heart ferritin (rich in H subunits). Hybrid lines retaining part of the long arm of chromosome 19 including the region 19q13.319qter produced human L type ferritin. This confirms the previous assignment of the ferritin gene to chromosome 19 (Caskey et al. 1983). However, lines retaining chromosome 11 were found to contain human H type ferritin suggesting that the gene for the H subunit is on this chromosome. The presence of chromosome 6 was not necessary for the expression of either H or L type human ferritin. It thus seems unlikely that the gene for idiopathic haemochromatosis is a ferritin gene.     

Utilization of wild relatives in the genetic improvement of Arachis hypogaea L.

Summary Synthetic amphidiploids were established in 32 combinations involving 8 diploid wild species representing both A and B genomes of section Arachis. Bivalent and multivalent associations in the amphidiploids of 7 A genome species confirm that these species have identical genomes. Contrastingly, high bivalent frequencies in amphidiploids involving the A and B genome species suggest that A. batizocoi has a distinct B genome that is partially homologous to the other genome A represented in the rest of the species. Crossability, chromosome pairing and pollen and pod fertility in hybrids between A. hypogaea and amphidiploids have revealed that these amphidiploids can be used as a genetic bridge for the transfer of genes from the wild species into the cultivated groundnut.Submitted as Journal Article No. 530 by International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)     

Presence and abundance of CENP-B box sequences in great ape subsets of primate-specific α-satellite DNA

CENP-B, a highly conserved centromere-associated protein, binds to -satellite DNA, the centromeric satellite of primate chromosomes, at a 17-bp sequence, the CENP-B box. By fluorescence in situ hybridization (FISH) with an oligomer specific for the CENP-B box sequence, we have demonstrated the abundance of CENP-B boxes on all chromosomes (except the Y) of humans, chimpanzee, pygmy chimpanzee, gorilla, and orangutan. This sequence motif was not detected in the genomes of other primates, including gibbons, Old and New World monkeys, and prosimians. Our results indicate that the CENP-B box containing subtype of -satellite DNA may have emerged recently in the evolution of the large-bodied hominoids, after divergence of the phylogenetic lines leading to gibbons and apes; the box is thus on the order of 15–25 million years of age. The rapid process of dispersal and fixation of the CENP-B box sequence throughout the human and great ape genomes is thought to be a consequence of concerted evolution of -satellite subsets on both homologous and nonhomologous chromosomes.Correspondence to: T. Haaf     

Prehension synergies during nonvertical grasping,II: Modeling and optimization

This study examines various optimization criteria as potential sources of constraints that eliminate (or at least reduce the degree of) mechanical redundancy in prehension. A model of nonvertical grasping mimicking the experimental conditions of Pataky et al. (current issue) was developed and numerically optimized. Several cost functions compared well with experimental data including energylike functions, entropylike functions, and a motor command function. A tissue deformation function failed to predict finger forces. In the prehension literature, the safety margin (SM) measure has been used to describe grasp quality. We demonstrate here that the SM is an inappropriate measure for nonvertical grasps. We introduce a new measure, the generalized safety margin (GSM), which reduces to the SM for vertical and two-digit grasps. It was found that a close-to-constant GSM accounts for many of the finger force patterns that are observed when grasping an object oriented arbitrarily with respect to the gravity field. It was hypothesized that, when determining finger forces, the CNS assumes that a grasped object is more slippery than it actually is. An operative friction coefficient of approximately 30\% of the actual coefficient accounted for the offset between experimental and optimized data. The data suggest that the CNS utilizes an optimization strategy when coordinating finger forces during grasping.     

Contributions of plant molecular systematics to studies of molecular evolution

Dobzhansky stated that nothing in biology makes sense except in the light of evolution. A close corollary, and the central theme of this paper, is that everything makes a lot more sense in the light of phylogeny. Systematics is in the midst of a renaissance, heralded by the widespread application of new analytical approaches and the introduction of molecular techniques. Molecular phylogenetic analyses are now commonplace, and they have provided unparalleled insights into relationships at all levels of plant phylogeny. At deep levels, molecular studies have revealed that charophyte green algae are the closest relatives of the land plants and suggested that liverworts are sister to all other extant land plants. Other studies have suggested that lycopods are sister to all other vascular plants and clarified relationships among the ferns. The impact of molecular phylogenetics on the angiosperms has been particularly dramatic – some of the largest phylogenetic analyses yet conducted have involved the angiosperms. Inferences from three genes (rbcL, atpB, 18S rDNA) agree in the major features of angiosperm phylogeny and have resulted in a reclassification of the angiosperms. This ordinal-level reclassification is perhaps the most dramatic and important change in higher-level angiosperm taxonomy in the past 200 years. At lower taxonomic levels, phylogenetic analyses have revealed the closest relatives of many crops and model organisms for studies of molecular genetics, concomitantly pointing to possible relatives for use in comparative studies and plant breeding. Furthermore, phylogenetic information has contributed to new perspectives on the evolution of polyploid genomes. The phylogenetic trees now available at all levels of the taxonomic hierarchy for angiosperms and other green plants should play a pivotal role in comparative studies in diverse fields from ecology to molecular evolution and comparative genetics.     

Highly repetitive component α and related alphoid DNAs in man and monkeys

The genomes of Old-World, New-World, and prosimian primates contain members of a large class of highly repetitive DNAs that are related to one another and to component DNA of the African green monkey by their sequence homologies and restriction site periodicities. The members, of this class of highly repetitive DNAs are termed the alphoid DNAs, after the prototypical member, component of the African green monkey which was the first such DNA to be identified (Maio, 1971) and sequenced (Rosenberg et al., 1978). The alphoid DNAs appear to be uniquely primate sequences. — From the restriction enzyme cleavage patterns and Southern blot hybridizations under different stringency conditions, the alphoid DNAs comprise multiple sequence families exhibiting varying degrees of homology to component DNA. They also share common elements in their restriction site periodicities (172 · n base-pairs), in the long-range organization of their repeating units, and in their banding behavior in CsCl and Cs₂SO₄ buoyant density gradients, in which they band within the bulk DNA as cryptic repetitive components. — In the three species from the Family Cercopithecidae examined, the alphoid DNAs represent the most abundant, tandemly repetitive sequence components, comprising about 24% of the African green monkey genome and 8 to 10% of the Rhesus monkey and baboon genomes. In restriction digests, the bulk of the alphoid DNAs among the Cercopithecidae appeared quantitatively reduced to a simple series of arithmetic segments based on a 172 base-pair (bp) repeat. In contrast with these simple restriction patterns, complex patterns were observed when human alphoid DNAs were cleaved with restriction enzymes. Detailed analysis revealed that the human genome contains multiple alphoid sequence families which differ from one another both in their repeat sequence organization and in their degree of homology to the African green monkey component DNA. — The finding of alphoid sequences in other Old-World primate families, in a New-World monkey, and in a prosimian primate attests to the antiquity of these sequences in primate evolution and to the sequence conservatism of a large class of mammalian highly repetitive DNA. In addition, the relative conservatism exhibited by these sequences may distinguish the alphoid DNAs from more recently evolved highly repetitive components and satellite DNAs which have a more restricted taxonomical distribution.     

Polyploidy, evolutionary opportunity, and crop adaptation

The finding that even the smallest of plant genomes has incurred multiple genome-wide chromatin duplication events, some of which may predate the origins of the angiosperms and therefore shape all of flowering plant biology, adds new importance to the molecular analysis of polyploidization/diploidization cycles and their phenotypic consequences. Early clues as to the possible phenotypic consequences of polyploidy derive from recent QTL mapping efforts in a number of diverse crop plants of recent and well-defined polyploid origins. A small sampling examples of the role(s) of polyploidy in conferring crop adaptation from human needs include examples of (1) dosage effects of multiple alleles in autopolyploids, and (2) intergenomic heterosis conferring novel traits or transgressive levels of existing traits, associated with merging divergent genomes in a common allopolyploid nucleus. A particularly interesting manifestation of #2 is the evolution of complementary alleles at corresponding (homoeologous) loci in divergent polyploid taxa derived from a common ancestor. Burgeoning genomic data for both botanical models and major crops offer new avenues for investigation of the molecular and phenotypic consequences of polyploidy, promising new insights into the role of this important process in the evolution of botanical diversity.     

Transformation of lithocholic acid to a new bile acid, 3α, 15β-dihydroxy-5β-cholanic acid by Cunninghamella blakesleeana ST-22

Summary A fungus identified as Cunninghamella blakesleeana (Lendner) can carry out 15-hydroxylation of lithocholic acid to a new bile acid (3,15-dihydroxy-5-cholanic acid). By optimizing the fermentation conditions, the amount of the product increased from 0.17 g/l to 1.2 g/l. Hydrophilicity measurements and in vitro cholesterol solubilization tests showed that 3, 15-dihydroxy-5-cholanic acid was as effective as ursodeoxycholic acid in cholesterol solubilization.Abbreviations LCA lithocholic acid (3-hydroxy-5-cholanic acid) - 3, 15-DHC (3, 15-dihydroxy-5-cholanic acid) - DMSO dimethyl sulfoxide - CHES 2-[N-cyclohexylamino]ethanesulfonic acid     

Immunological and biochemical analysis of a null mutant of α-glycerolphosphate dehydrogenase from Drosophila melanogaster

Summary A Drosophila null mutant(BO-1-4) of -glycerolphosphate dehydrogenase induced by ethylmethane sulfonate(EMS) was analyzed by double immunodiffusion, enzyme immuno-inactivation, immunoelectrophoresis and two-dimensional electrophoresis. Based on all the immunological evidence, this mutant appears to express no protein that can cross-react with the antiserum specific to -glycerolphosphate dehydrogenase. A protein spot corresponding to -glycerolphosphate dehydrogenase was identified on two-dimensional gels of the soluble fly homogenates. The absence of this protein spot on two-dimensional gels of this null mutant further supported the immunological data. The activities of seven other enzymes in the related metabolic pathways were determined for the mutant and the control Drosophila. The null mutant does not show significant alterations in activities of these enzymes. The relationship between the deficiency of this enzyme and the inability for the sustained flight of the null mutant was discussed in terms of cellular metabolic regulations.Abbreviations used -GPD -glycerolphosphate dehydrogenase (EC 1.1.1.8) - EMS ethylmethane sulfonate - TEMED N,N,N,N-tetramethylene diamine - pI isolectric point - CRM immunological cross-reacting material     

DNA polymorphisms associated with a new α1-antitrypsin PI Q0 variant (PI Q0riedenburg)

Summary A new PI Q0 variant (PI Q0_riedenburg) is described; it is caused by a complete deletion of the ₁-antitrypsin (₁AT) gene. The deletion gives rise to four new restriction fragment length polymorphisms (RFLPs) detected with a genomic probe of the 5 region of the gene. Analysis of the RFLPs indicates that the deletion starts immediately upstream of exon Ic. The deletion extends into the 3 flanking region of the gene but does not include the ₁AT-related gene (the PIL gene), which is located 12 kb downstream of the ₁AT gene.     

Molecular evolution of the nicotinic acetylcholine receptor: An example of multigene family in excitable cells

An extensive phylogenetic analysis of the nicotinic-acetylcholine-receptor subunit gene family has been performed by cladistic and phenetic methods. The conserved parts of amino acid sequences have been analyzed by CLUSTAL V and PHYLIP software. The structure of the genes was also taken in consideration. The results show that a first gene duplication may have occurred before the appearance of Bilateria. Three subfamilies then appeared: I-the neuronal -bungarotoxin binding-site subunits (7, 8); III-the neuronal nicotinic subunits (2–6, 2–4), which also contain the muscle acetylcholine-binding subunit (1); and IV—the muscle non- subunits (1, , ). The Insecta subunits (subfamily II) could be orthologous to family III and IV. Several tissular switches of expression from neuron to muscle and the converse can be inferred from the extant expression of subunits and the reconstructed trees. The diversification of the neuronal nicotinic subfamily begins in the stem lineage of chordates, the last duplications occurring shortly before the onset of the mammalian lineage. Such evolution parallels the increase in complexity of the cholinergic systems.Abbreviations -Bgt -bungarotoxin - ACh acetylcholine - MP maximum of parsimony - MYA million years ago - NJ neighbor-joining - nAChR nicotinic acetylcholine receptor Correspondence to: N. Le Novère     

A new scenario of plastid evolution: plastid primary endosymbiosis before the divergence of the “Plantae,” emended

A recent hypothesis on the origin of eukaryotic phototrophs proposes that red algae, green plants (land plants plus green algae), and glaucophytes constitute the primary photosynthetic eukaryotes, whose plastids may have originated directly from a cyanobacterium-like prokaryote via primary endosymbiosis, whereas the plastids of other lineages of eukaryotic phototrophs appear to be the result of secondary endosymbiotic events involving a phototrophic eukaryote and a host cell. However, the phylogenetic relationships among the three lineages of primary photosynthetic eukaryotes remained unresolved because previous nuclear multigene phylogenies used incomplete red algal gene sequences derived mainly from Porphyra (Rhodophyceae, one of the two lineages of the Rhodophyta), and lacked sequences from the Cyanidiophyceae (the other red algal lineage). Recently, the complete nuclear genome sequences from the red alga Cyanidioschyzon merolae 10D of the Cyanidiophyceae were determined. Using this genomic information, nuclear multigene phylogenetic analyses of various lineages of mitochondrion-containing eukaryotes were conducted. Since bacterial and amitochondrial eukaryotic genes present serious problems to eukaryotic phylogenies, basal eukaryotes were deduced based on the paralogous comparison of the concatenated - and -tubulin. The comparison demonstrated that cellular slime molds (Amoebozoa) represent the most basal position within the mitochondrion-containing organisms. With the cellular slime molds as the outgroup, phylogenetic analyses based on a 1,525-amino acid sequence of four concatenated nuclear genes [actin, elongation factor-1( EF-1), -tubulin, and -tubulin] resolved the presence of two large, robust monophyletic groups and the basal eukaryotic lineages (Amoebozoa). One of the two groups corresponded to the Opisthokonta (Metazoa and Fungi), whereas the other included various lineages containing primary and secondary plastids (red algae, green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, dinoflagellates, and Heterolobosea, for which the red algae represented the most basal lineage. Therefore, the plastid primary endosymbiosis likely occurred once in the common ancestor of the latter group, and the primary plastids were subsequently lost in the ancestor(s) of organisms within the group that now lacks primary plastids. A new concept of Plantae was proposed for phototrophic and nonphototrophic organisms belonging to this group on the basis of their common history of plastid primary endosymbiosis. This new scenario of plastid evolution is discussed here, and is compared with recent genome information and findings on the secondary endosymbiosis of the Euglena plastid.     

Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench

The thermophilic strains HTA426 and HTA462 isolated from the Mariana Trench were identified as Geobacillus kaustophilus and G. stearothermophilus, respectively, based on physiologic and phylogenetic analyses using 16S rDNA sequences and DNA–DNA relatedness. The genome size of HTA426 and HTA462 was estimated at 3.23–3.49 Mb and 3.7–4.49 Mb, respectively. The nucleotide sequences of three independent -phage inserts of G. stearothermophilus HTA462 have been determined. The organization of protein coding sequences (CDSs) in the two -phage inserts was found to differ from that in the contigs corresponding to each insert assembled by the shotgun clones of the G. kaustophilus HTA426 genome, although the CDS organization in another insert is identical to that in the HTA426 genome.     

Isolation of a halobacterial phage with a fully cytosine-methylated genome

Summary A new bacteriophage from Halobacterium halobium has been isolated and partially characterized. It is not homologous to the phage H (Schnabel, et al. 1982) which infects the same bacterium, though it appeared spontaneously in a culture of H adapted to H. halobium NRL/JW. The size and morphology of N are comparable to that of other known halophages. The genome of N consists of linear double-stranded DNA, 56 kb in size, whose dCMP is totally replaced by 5-methyl-dCMP. This is the second case of a fully cytosine-methylated genome, the bacteriophage XP12 from Xanthomonas oryzae, being so far the only one reported. Like H, the N, genome seems to have terminal redundancy and circular permutation. N is the first halobacterial phage which survives prolonged exposure to low ionic strength environments. After 48 h incubation in distilled water a loss in infectivity of less than 50% is observed.     

The effect of spectral light deprivation on the spectral sensitivity of the honey bee

Summary The spectral sensitivity of spontaneous phototactic behavior was tested in short wavelength deprived bees and in control bees kept outdoors. Tests were performed with a y-maze with one branch illuminated, the other dark. The relative sensitivities for the control group were: green to blue to UV = 10.272.14. Short wavelength deprived bees show a distinct decrease in their sensitivity to short wavelengths. The relation green to blue to UV here was 10.220.27. Forager bees from outdooors, short wavelength deprived for 10 days, showed a relation of green to blue to UV of 10.261.04. Electrophysiological investigation of the compound eye using electroretinogram recordings showed no difference between deprived and control animals.     

Natural genetic engineering of plant cells: the molecular biology of crown gall and hairy root disease

During the past decade, the molecular mechanisms of crown gall and hairy root development have been elucidated in considerable detail. It now appears that the genetic colonization of plant cells by Agrobacterium evolved by continual adaptation of groups of genes that existed long before the evolution of this plant-microbe association. This is most evident for the signal transduction system leading to vir gene induction, and for the early steps of T-DNA transfer to plant cells which have probably evolved from the bacterial conjugation and protein export machinery. However, the later steps, i.e. nuclear targeting of the T-DNA-protein complex, and integration into the host genome by illegitimate recombination are reminiscent of viral infection, where the T-complex resembles a viral particle. The present article reviews the current knowledge of the molecular basis of crown gall and hairy root tumorigenesis, with some emphasis on the mechanisms of signal exchange between plants and bacteria, as well as of T-DNA excision, transfer, integration and expression.The authors are with Plant Molecular Biology, Department of Biology, Biozentrum, Marie-Curie-Str. 9, University of Frankfurt am Main, D-60439 Frankfurt, Germany     

Feast and famine in plant genomes

Plant genomes vary over several orders of magnitude in size, even among closely related species, yet the origin, genesis and significance of this variation are not clear. Because DNA content varies over a sevenfold range among diploid species in the cotton genus (Gossypium) and its allies, this group offers opportunities for exploring patterns and mechanisms of genome size evolution. For example, the question has been raised whether plant genomes have a one-way ticket to genomic obesity, as a consequence of retroelement accumulation. Few empirical studies directly address this possibility, although it is consistent with recent insights gleaned from evolutionary genomic investigations. We used a phylogenetic approach to evaluate the directionality of genome size evolution among Gossypium species and their relatives in the cotton tribe (Gossypieae, Malvaceae). Our results suggest that both DNA content increase and decrease have occurred repeatedly during evolution. In contrast to a model of unidirectional genome size change, the frequency of inferred genome size contraction exceeded that of expansion. In conjunction with other evidence, this finding highlights the dynamic nature of plant genome size evolution, and suggests that poorly understood genomic contraction mechanisms operate on a more extensive scale that previously recognized. Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents.     

Mitochondrial DNA rearrangements in somatic hybrids of Solanum tuberosum and Solanum brevidens

Summary Thirty somatic hybrids between Solanum tuberosum and Solanum brevidens were analysed for mitochondrial and chloroplast genome rearrangements. In all cases, the chloroplast genomes were inherited from one of the parental protoplast populations. No chloroplast DNA alterations were evident but a range of mitochondrial DNA alterations, from zero to extensive intra- and inter-molecular recombinations, were found. Such recombinations involved specific recombination hot spots in the mitochondrial genome. Not all hybrids regenerated from a common callus possessed identical mitochondrial genomes, suggesting that sorting out of mitochondrial populations in the callus may have been incomplete at the plant regeneration stage. Sorting out of organelles in planta was not observed.     

The vicissitudes of evolutionary theory

Conclusion I have referrred to the data-generating capacity of the alternative research program, that it should stimulate fruitful hypotheses. Conversely, static theory (i.e., analysis dependent on mathematical logic to impose regularities on non-linear processes) is vulnerable to serendipitous data which violates its deductive structure. In that spirit, Jerison cautions: Where hints are found in brain structure, for example, of asymmetries in the brain, we can exploit them as a basis for good hypothesis, but we should also recognize that hypotheses created in this way are likely to be weak.Brain asymmetry data, surely among the least linear evidence available — topological irregularities of convoluted space — have been integrated in Holloway's program as but one phenotypic window on the evolution of complex cognitive functioning. There are no a priori methodological nor theoretical exclusions of this kind of data, for they complement an open-ended research program.Furthermore, asymmetry evidence may yet satisfy a test for phyletic evolution (gradualism) demanded by the punctuational model — the provision of data for gradual character change, especially if the character is complex, appears to have functional significance and can be shown to be associated with palaeoenvironmental change. Finally, these new considerations have stimulated additional questions for students of brain evolution. Among the more interesting of these is whether the growing evidence of asymmetry, its sexual dimorphism and other kinds of population distribution, and its functional lateralization in general, suggest ongoing foci for selection pressures in our continuing evolution.Evolutionary study, in its reliance on positivistic technique and conformance to standards of scientific proof, is being assimilated within the general tendency of all science, toward more and more mathematical modeling. Mathematical simulations are not more isomorphic with evolutionary processes than are other kinds of syntheses. In fact, models incorporating extremely limited fossil data mislead us with their inferential chains of necessity. Projected into an inevitable future, they are ironic equations of social processes born in evolutionary times.A science which seeks to manipulate nature nevertheless cannot undo what happened in evolution. The errors and indeterminateness of human evolution are constraints on the species no longer embedded in nature. Their scientific status is not the issue. They can be interpreted, however. We can rationalize an ideological mastery of generalized biological processes which debases our own history. Or we can achieve an authentic understanding of its originality as part of our own making. That would be a beginning, for evolution has not ended, in realizing the creative possibilities of human consciousness. But, then again, over all of these natural constraints and cultural possibilities lies the shadow of genetic engineering. The clash between Western science and universal humanity will be fought on that ground, should we survive the nuclear age.Bernard Belasco is an Associate Professor at Baruch College of the City University of New York.     

The Origin of Eukaryotes Is Suggested as the Symbiosis of Pyrococcus into γ-Proteobacteria by Phylogenetic Tree Based on Gene Content

Attempts were made to define the relationship among the three domains (eukaryotes, archaea, and eubacteria) using phylogenetic tree analyses of 16S rRNA sequences as well as of other protein sequences. Since the results are inconsistent, it is implied that the eukaryotic genome has a chimeric structure. In our previous studies, the origin of eukaryotes to be the symbiosis of archaea into eubacteria using the whole open reading frames (ORF) of many genomes was suggested. In these studies, the species participating in the symbiosis were not clarified, and the effect of gene duplication after speciation (in-paralog) was not addressed. To avoid the influence of the in-paralog, we developed a new method to calculate orthologous ORFs. Furthermore, we separated eukaryotic in-paralogs into three groups by sequence similarity to archaea, eubacteria (other than -proteobacteria), and -proteobacteria and treated them as individual organisms. The relationship between the three ORF groups and the functional classification was clarified by this analysis. The introduction of this new method into the phylogenetic tree analysis of 66 organisms (4 eukaryotes, 13 archaea, and 49 eubacteria) based on gene content suggests the symbiosis of pyrococcus into -proteobacteria as the origin of eukaryotes.