New evidence from embryology in angiosperm classification

New embryological evidence in angiosperm classification is presented from two different lines of research. One deals with a new field in embryological research, the other keeps within the classical framework. The new approach encouraged by the author refers to the exploration of the chemical composition of the pollen tube as a taxonomic tool. The presence of callose in several pollen tubes and the lack of this compound in others has been correlated with other embryological and taxonomical features within the Tubiflorae, showing a great deal of correspondence. In order to exemplify the classical approach, two families have been selected: Loranthaceae and Hydnoraceae. The Loranthaceae have a special structure called the mamelon, usually interpreted as a placenta. Recent research based on the position of the ar–chesporial tissue shows that not all mamelons should be regarded as homologous structures. Based on this finding, a new scheme of evolutionary lines is proposed. In connection with the holoparasitic family Hydnoraceae, the author discusses its relationships with Mitrastemonaceae and Annonaceae on grounds of embryology and floral morphology.     

Flavonoid chemistry and angiosperm evolution

A consideration of the distribution of flavonoid compounds in angiosperms indicates that exceptions exist to current thought on the presence of particular structural types occurring in primitive versus advanced flowering plants. As additional thorough survey work is done, the exceptions become increasingly common and the generalizations are weakened. A methodological problem in flavonoid surveys concerns documenting the “absence” of particular compounds and the question of quantitative versus qualitative variation of certain constituents. Consideration of flavonoid biosynthesis suggests that simple genetic differences likely control the classes of compounds present and this in turn indicates that caution be used in placing phylogenetic significance on such differences. Features of floral morphology used in studying angiosperm phylogeny have a complex genetic-developmental basis as compared to the genetic factors governing the presence of various flavonoid classes. This ostensibly is an important factor in explaining why reversals in certain trends of floral morphology are rarely noted and why these features are usually constant at higher taxonomic levels. By contrast, variation of flavonoid classes (by virtue of the small genetic differences controlling the presence of different classes) occurs at lower taxonomic levels. Genetic and enzymological studies of flavonoid biosynthesis also indicate that a single compound may be synthesized via different pathways, and this has significant implications for the use of flavonoid distribution in a phylogenetic sense. Given similar selection pressures, the same compounds may arise independently in distantly related plants. Clearly, this has occurred with floral anthocyanidins, where the distribution of particular compounds is related to pollinators. Flavonoid compounds will continue to be useful systematically at the generic level or lower, and possibly at the familial level in some instances. However, studies of the genetics and enzymology of flavonoid compounds in different groups of plants are needed if flavonoids are to be employed in a phylogenetic or evolutionary sense at higher taxonomic levels in the angiosperms. Much additional work in the difficult area of flavonoid functions is to be desired. Many more investigations of comparative flavonoid chemistry of fossil and extant members of what are considered the same genus must be carried out if any appreciation of flavonoid change through evolutionary time is to be achieved.     

Electricity-free, sequential nucleic acid and protein isolation

Traditional and emerging pathogens such as Enterohemorrhagic Escherichia coli (EHEC), Yersinia pestis, or prion-based diseases are of significant concern for governments, industries and medical professionals worldwide. For example, EHECs, combined with Shigella, are responsible for the deaths of approximately 325,000 children each year and are particularly prevalent in the developing world where laboratory-based identification, common in the United States, is unavailable (1). The development and distribution of low cost, field-based, point-of-care tools to aid in the rapid identification and/or diagnosis of pathogens or disease markers could dramatically alter disease progression and patient prognosis. We have developed a tool to isolate nucleic acids and proteins from a sample by solid-phase extraction (SPE) without electricity or associated laboratory equipment (2). The isolated macromolecules can be used for diagnosis either in a forward lab or using field-based point-of-care platforms. Importantly, this method provides for the direct comparison of nucleic acid and protein data from an un-split sample, offering a confidence through corroboration of genomic and proteomic analysis. Our isolation tool utilizes the industry standard for solid-phase nucleic acid isolation, the BOOM technology, which isolates nucleic acids from a chaotropic salt solution, usually guanidine isothiocyanate, through binding to silica-based particles or filters (3). CUBRC's proprietary solid-phase extraction chemistry is used to purify protein from chaotropic salt solutions, in this case, from the waste or flow-thru following nucleic acid isolation(4). By packaging well-characterized chemistries into a small, inexpensive and simple platform, we have generated a portable system for nucleic acid and protein extraction that can be performed under a variety of conditions. The isolated nucleic acids are stable and can be transported to a position where power is available for PCR amplification while the protein content can immediately be analyzed by hand held or other immunological-based assays. The rapid identification of disease markers in the field could significantly alter the patient's outcome by directing the proper course of treatment at an earlier stage of disease progression. The tool and method described are suitable for use with virtually any infectious agent and offer the user the redundancy of multi-macromolecule type analyses while simultaneously reducing their logistical burden.     

New evidence from the ultrastructural and micromorphological fields in angiosperm classification

Based on TEM investigations of some 1850 species and SEM examinations of about 6000 species of the Angiospermae, this is a survey of ultrastructural and micromorphological data (excluding pollen wall characters) which contribute valuable information for the classification of angiosperms. TEM characters predominately relate to phloem features, such as sieve–element plastids and crystalline P–protein, and to those equally present in other tissues, e.g. nuclear protein crystals and dilated ER–cisternae (DC). Of these, the sieve–element plastids with their types and subtypes (S, PI–PVI) and their over 20 forms represent the most thoroughly investigated TEM character. SEM characters mainly relate to epidermal surface features and can be grouped into four categories: (1) Cellular arrangement or cellular pattern; (2) Shape of cells (the “primary sculpture” of a surface); (3) Relief of outer cell walls (“the secondary sculpture” superimposed on the primary sculpture), caused mainly by cuticular striations and superficially visible wall inclusions and wall thickenings; (4) Epicuticular secretions (the “tertiary sculpture” superimposed on the secondary sculpture), i.e. mainly waxes and related substances. Ultrastructural evidence from sieve–element plastids for the classification of Mag–noliiflorae, Caryophylliflorae, Fabiflorae and the unity of the Monocotyledoneae is discussed, while further plastid data are listed for single families (e.g. Buxaceae, Cyrillaceae, Erythroxylaceae, Eucryphiaceae, Gunneraceae, Rhizophoraceae, Vitaceae). Crystalline P–protein dominates in Malviflorae, Violiflorae and Fabiflorae. Nuclear protein crystals are a specific feature of sieve elements of Boraginaceae. DC characterize Capparales s.lat. Micromorphological evidence derived from specific trichomes is presented as an aid to the characterization of Urticales and Loasales, while a detailed analysis of the micromorphology of the seed coat of Cactaceae and Orchidaceae provided new information for the classification of these families at the tribal and generic levels. As a completely new systematic feature for the classification of the Monocotyledoneae first results of micromorphological differences in wax crystalloids and their orientation patterns are presented: The Liliiflorae s. str. are clearly separated against the Zingiberiflorae–Commeliniflorae (incl. Velloziales, Bromeliales, Typhales) and Areciflorae, both characterized by two mutually exclusive and very specific wax types and delimited against taxa with unspecific waxes in the rest of the monocotyledons and all dicotyledons.     

Universal labeling chemistry for nucleic acid detection on DNA-arrays

We show here a new and efficient aqueous chemistry for labeling of any class of nucleic acids for their detection on DNA chip. The labels contain a diazo function as reactive moiety and biotin as detectable unit. The highly selective reaction of diazo group on the phosphate does not disrupt base pairing recognition and hybridization specificity.     

Periodate oxidation in chemistry of nucleic acid. Dialdehyde derivatives of nucleosides, nucleotides, and oligonucleotides

The employment of periodate oxidation in the chemistry of nucleic acids and their components is reviewed. The reaction mechanism, structural requirements to substrates, and synthesis of dialdehyde derivatives of nucleosides, nucleotides, and oligonucleotides are discussed in the first part. The second part involves chemical, physicochemical, and biological properties of the dialdehyde derivatives, as well as their use for the affinity modifications of proteins.     

MouseV k gene classification by nucleic acid sequence similarity

Analyses of immunoglobulin (Ig) variable (V) region gene usage in the immune response, estimates ofV gene germline complexity, and other nucleic acid hybridization-based studies depend on the extent to which such genes are related (i. e., sequence similarity) and their organization in gene families. While mouseIgh heavy chainV region (V _H ) gene families are relatively well-established, a corresponding systematic classification ofIgk light chainV region (V _k ) genes has not been reported. The present analysis, in the course of which we reviewed the known extent of theV _k germline gene repertoire andV _k gene usage in a variety of responses to foreign and self antigens, provides a classification of mouseV _k genes in gene families composed of members with >80% overall nucleic acid sequence similarity. This classification differed in several aspects from that ofV _H genes: only someV _k gene families were as clearly separated (by >25% sequence dissimilarity) as typicalV _H gene families; mostV _k gene families were closely related and, in several instances, members from different families were very similar (>80%) over large sequence portions; frequently, classification by nucleic acid sequence similarity diverged from existing classifications based on amino-terminal protein sequence similarity. Our data have implications forV _k gene analyses by nucleic acid hybridization and describe potentially important differences in sequence organization betweenV _H andV _k genes.     

Amino acid sequence of UP1, an hnRNP-derived single-stranded nucleic acid binding protein from calf thymus

The UP1 single-stranded nucleic acid binding protein from calf thymus (Herrick, G. & Alberts, B.M. (1976) J. Biol. Chem. 251, 2124-2132) has recently been shown to be a proteolytic fragment derived from the A1 heterogeneous nuclear ribonucleoprotein (hnRNP) (Pandolfo et al. (1985) Nucleic Acids Res. 13, 6577-6590). The NH2-terminus of the 22,162 dalton UP1 protein appears to be blocked, which suggests that UP1 represents the NH2-terminal two thirds of this 32,000 dalton hnRNP protein. The complete amino acid sequence for UP1 was derived from automated sequencing of peptides that were purified by HPLC from digests with trypsin, chymotrypsin, Staphylococcus aureus protease, endoproteinase Lys-C, and cyanogen bromide. Trichloroacetic acid precipitation followed by enzymatic digestion in 2 M urea proved to be the best approach for generating UP1 peptides. By carboxymethylating after, rather than before, digestion it was possible to avoid problems associated with the insolubility of the carboxymethylated UP1. All of the resulting peptides in amounts varying from 2 to 15 nmol were coupled to aminopolystyrene prior to solid-phase sequencing. Using these methods, no difficulties were encountered in assigning glutamic acid residues or in completely sequencing peptides that contained up to 25-30 residues. The relative ease with which the UP1 protein was sequenced, requiring only about a year to complete, and the comparatively modest amount of protein required, less than 5 mg, attests to the usefulness of water soluble carbodiimide coupling and solid-phase sequencing for determining the primary structures of proteins. In addition to serving as a basis for determining structural relationships among various mammalian single-stranded nucleic acid binding proteins, the amino acid sequence of UP1 reveals that the A1 hnRNP protein contains a region of internal sequence homology that apparently corresponds to two independent nucleic acid binding sites.     

Efficient prediction of nucleic acid binding function from low-resolution protein structures

Structural genomics projects as well as ab initio protein structure prediction methods provide structures of proteins with no sequence or fold similarity to proteins with known functions. These are often low-resolution structures that may only include the positions of C alpha atoms. We present a fast and efficient method to predict DNA-binding proteins from just the amino acid sequences and low-resolution, C alpha-only protein models. The method uses the relative proportions of certain amino acids in the protein sequence, the asymmetry of the spatial distribution of certain other amino acids as well as the dipole moment of the molecule. These quantities are used in a linear formula, with coefficients derived from logistic regression performed on a training set, and DNA-binding is predicted based on whether the result is above a certain threshold. We show that the method is insensitive to errors in the atomic coordinates and provides correct predictions even on inaccurate protein models. We demonstrate that the method is capable of predicting proteins with novel binding site motifs and structures solved in an unbound state. The accuracy of our method is close to another, published method that uses all-atom structures, time-consuming calculations and information on conserved residues.     

Compression of nucleic acid and protein sequence data

This paper describes the application of text compression methodsto machine-readable files of nucleic acid and protein sequencedata. Two main methods are used to reduce the storage requirementsof such files, these being n-gram coding and run-length coding.A Pascal program combining both of these techniques resultedin a compression figure of 74.6% for the GenBank database anda program that used only n-gram coding gave a compression figureof 42.8% for the Protein Identification Resource database. Received on November 29, 1985; accepted on February 24, 1986     

New,sensitive, radioactive-free bioluminescence-enhanced detection system in protein blotting and nucleic acid hybridization

A relatively simple, very sensitive bioluminescence-enhanced detection system for protein blotting and nucleic acid hybridization is described. The method utilizes antibodies conjugated with alkaline phosphatase or nucleotide probes complexed with alkaline phosphatase. Then the alkaline phosphatase takes part in a reaction by releasing D -luciferin (Photinus pyralis) from D -luciferin-O-phosphate. Liberated D -luciferin reacts with luciferase, ATP and oxygen under light emission. Light is measured using the Argus-100 a photon counting camera system or photographic films. Bound alkaline phosphatase conjugated antibodies or hybridized nucleotide probes can be visualized. The limit of detection is at present 5 to 50 fg of protein (IgG), corresponding, for example to 30 to 300 × 10^?21 mol. This means a much higher sensitivity of the detection system in comparison to systems used at present. Experiments concerning nucleic acid hybridization and visualization of the emitted light by a photon counting camera (Argus-100) are under investigation.