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PubMed2002

Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences.

The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near full-length proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.

Argentina↗
PubMed1996

Pathogenicity and phylogenetic evaluation of the variant Newcastle disease viruses termed "pigeon PMV-1 viruses" based on the nucleotide sequence of the fusion protein gene.

The nucleotide sequences of the entire F genes of two isolates of the pigeon PMV-1 (PPMV-1) variant of Newcastle disease virus (NDV) were determined using RTPCR. The deduced amino acid sequences of the F0 protein showed four differences between isolate 760/83 which had been passaged 4 times in chickens and gave an intravenous pathogenicity index in chickens (IVPI) of 2.01 and isolate 1168/84 which had received six passages in chickens and had an IVPI of 0.00. The F genes of virus from two passage levels of isolate 1447/84, 0 with IVPI value 0.00 and six with IVPI value 0.58, were partially sequenced to cover the areas of variation between 760/83 and 1168/84. The two passage levels of 1447/84 showed identical sequences in these areas which in turn were identical of those of 760/83. It was concluded that the recorded differences in intravenous pathogenicity were unlikely to be associated with differences in the primary structure of the F0 protein. Phylogenetic comparisons of the F gene sequences of the two PPMV-1 viruses with those published for other NDV strains and isolates showed that the PPMV-1 viruses formed a new fourth lineage but were closely related to strain Warwick with which they presumably shared a common origin.

Amino Acid Sequence↗
PubMed2003

Phylogeny of ruminants secretory ribonuclease gene sequences of pronghorn (Antilocapra americana).

Phylogenetic analyses based on primary structures of mammalian ribonucleases, indicated that three homologous enzymes (pancreatic, seminal and brain ribonucleases) present in the bovine species are the results of gene duplication events, which occurred in the ancestor of the ruminants after divergence from other artiodactyls. In this paper sequences are presented of genes encoding pancreatic and brain-type ribonuclease genes of pronghorn (Antilocapra americana). The seminal-type ribonuclease gene could not be detected in this species, neither by PCR amplification nor by Southern blot analyses, indicating that it may be deleted completely in this species. Previously we demonstrated of a study of amino acid sequences of pancreatic ribonucleases of a large number of ruminants the monophyly of bovids and cervids, and that pronghorn groups with giraffe. Here we present phylogenetic analyses of nucleotide sequences of ribonucleases and other molecules from ruminant species and compare these with published data. Chevrotain (Tragulus) always groups with the other ruminants as separate taxon from the pecora or true ruminants. Within the pecora the relationships between Bovidae, Cervidae, Giraffidae, and pronghorn (Antilocapra) cannot be decided with certainty, although in the majority of analyses Antilocapra diverges first, separately or joined with giraffe. Broad taxon sampling and investigation of specific sequence features may be as important for reliable conclusions in phylogeny as the lengths of analyzed sequences.

Amino Acid Sequence↗
PubMed1978

Phylogenetic implications of the microbody-lipid globule complex in zoosporic fungi.

Chytridiomycetous fungal zoospores contain a unique and intricate association of organelles, the 'microbody-lipid globule complex' (MLC). The spatial arrangement of organelles in the MLC appears important in the utilization of lipid globules for energy, but in addition, the structural association of organelles in the MLC reveals phylogenetic trends within this diverse group of organisms. Variations in the structure of the MLC correlate well with current phylogenetic concepts of aquatic fungi, yet suggest new relationships among these posteriorly uniflagellate zoospores. Based upon the organization of organelles in the MLC, 4 basic patterns of MLCs can be recognized, and these correspond to the 4 orders of Chytridiomycetes. The MLC in its simplest form consists of a microbody appressed to the edge of a lipid globule. In more highly organized MLCs, mitochondria subtend the microbody and a cisterna surmounts one side of the lipid globule. The organization and structure is still more complex in other MLCs where ER is elaborated into a tubular network of membranes or where small microbodies or mitochondria fuse into 'giant' organelles. The structural organization of the MLC provides an additional criterion by which the phylogeny of awuatic fungi can be evaluated.

Fungi↗
PubMed2004

Aligned 18S and insect phylogeny.

The nuclear small subunit rRNA (18S) has played a dominant role in the estimation of relationships among insect orders from molecular data. In previous studies, 18S sequences have been aligned by unadjusted automated approaches (computer alignments that are not manually readjusted), most recently with direct optimization (simultaneous alignment and tree building using a program called "POY"). Parsimony has been the principal optimality criterion. Given the problems associated with the alignment of rRNA, and the recent availability of the doublet model for the analysis of covarying sites using Bayesian MCMC analysis, a different approach is called for in the analysis of these data. In this paper, nucleotide sequence data from the 18S small subunit rRNA gene of insects are aligned manually with reference to secondary structure, and analyzed under Bayesian phylogenetic methods with both GTR+I+G and doublet models in MrBayes. A credible phylogeny of Insecta is recovered that is independent of the morphological data and (unlike many other analyses of 18S in insects) not contradictory to traditional ideas of insect ordinal relationships based on morphology. Hexapoda, including Collembola, are monophyletic. Paraneoptera are the sister taxon to a monophyletic Holometabola but weakly supported. Ephemeroptera are supported as the sister taxon of Neoptera, and this result is interpreted with respect to the evolution of direct sperm transfer and the evolution of flight. Many other relationships are well-supported but several taxa remain problematic, e.g., there is virtually no support for relationships among orthopteroid orders. A website is made available that provides aligned 18S data in formats that include structural symbols and Nexus formats.

Animals↗
PubMed2001

NAD+-dependent DNA ligase encoded by a eukaryotic virus.

We report the production, purification, and characterization of an NAD(+)-dependent DNA ligase encoded by the Amsacta moorei entomopoxvirus (AmEPV), the first example of an NAD(+) ligase from a source other than eubacteria. AmEPV ligase lacks the zinc-binding tetracysteine domain and the BRCT domain that are present in all eubacterial NAD(+) ligases. Nonetheless, the monomeric 532-amino acid AmEPV ligase catalyzed strand joining on a singly nicked DNA in the presence of a divalent cation and NAD(+). Neither ATP, dATP, nor any other nucleoside triphosphate could substitute for NAD(+). Structure probing by limited proteolysis showed that AmEPV ligase is punctuated by a surface-accessible loop between the nucleotidyltransferase domain, which is common to all ligases, and the N-terminal domain Ia, which is unique to the NAD(+) ligases. Deletion of domain Ia of AmEPV ligase abolished the sealing of 3'-OH/5'-PO(4) nicks and the reaction with NAD(+) to form ligase-adenylate, but had no effect on phosphodiester formation at a pre-adenylated nick. Alanine substitutions at residues within domain Ia either reduced (Tyr(39), Tyr(40), Asp(48), and Asp(52)) or abolished (Tyr(51)) sealing of a 5'-PO(4) nick and adenylyl transfer from NAD(+) without affecting ligation of DNA-adenylate. We conclude that: (i) NAD(+)-dependent ligases exist in the eukaryotic domain of the phylogenetic tree; and (ii) ligase structural domain Ia is a determinant of cofactor specificity and is likely to interact directly with the nicotinamide mononucleotide moiety of NAD(+).

Alanine↗
PubMed2002

Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.

Diplomonads, such as Giardia, and their close relatives retortamonads have been proposed as early-branching eukaryotes that diverged before the acquisition-retention of mitochondria, and they have become key organisms in attempts to understand the evolution of eukaryotic cells. In this phylogenetic study we focus on a series of eukaryotes suggested to be relatives of diplomonads on morphological grounds, the "excavate taxa". Phylogenies of small subunit ribosomal RNA (SSU rRNA) genes, alpha-tubulin, beta-tubulin, and combined alpha- + beta-tubulin all scatter the various excavate taxa across the diversity of eukaryotes. But all phylogenies place the excavate taxon Carpediemonas as the closest relative of diplomonads (and, where data are available, retortamonads). This novel relationship is recovered across phylogenetic methods and across various taxon-deletion experiments. Statistical support is strongest under maximum-likelihood (ML) (when among-site rate variation is modeled) and when the most divergent diplomonad sequences are excluded, suggesting a true relationship rather than an artifact of long-branch attraction. When all diplomonads are excluded, our ML SSU rRNA tree actually places retortamonads and Carpediemonas away from the base of the eukaryotes. The branches separating excavate taxa are mostly not well supported (especially in analyses of SSU rRNA data). Statistical tests of the SSU rRNA data, including an "expected likelihood weights" approach, do not reject trees where excavate taxa are constrained to be a clade (with or without parabasalids and Euglenozoa). Although diplomonads and retortamonads lack any mitochondria-like organelle, Carpediemonas contains double membrane-bounded structures physically resembling hydrogenosomes. The phylogenetic position of Carpediemonas suggests that it will be valuable in interpreting the evolutionary significance of many molecular and cellular peculiarities of diplomonads.

Animals↗
PubMed1989

Isolation and sequence of four small nuclear U RNA genes of Trypanosoma brucei subsp. brucei: identification of the U2, U4, and U6 RNA analogs.

Trypanosomes use trans splicing to place a common 39-nucleotide spliced-leader sequence on the 5' ends of all of their mRNAs. To identify likely participants in this reaction, we used antiserum directed against the characteristic U RNA 2,2,7-trimethylguanosine (TMG) cap to immunoprecipitate six candidate U RNAs from total trypanosome RNA. Genomic Southern analysis using oligonucleotide probes constructed from partial RNA sequence indicated that the four largest RNAs (A through D) are encoded by single-copy genes that are not closely linked to one another. We have cloned and sequenced these genes, mapped the 5' ends of the encoded RNAs, and identified three of the RNAs as the trypanosome U2, U4, and U6 analogs by virtue of their sequences and structural homologies with the corresponding metazoan U RNAs. The fourth RNA, RNA B (144 nucleotides), was not sufficiently similar to known U RNAs to allow us to propose an identify. Surprisingly, none of these U RNAs contained the consensus Sm antigen-binding site, a feature totally conserved among several classes of U RNAs, including U2 and U4. Similarly, the sequence of the U2 RNA region shown to be involved in pre-mRNA branchpoint recognition in yeast, and exactly conserved in metazoan U2 RNAs, was totally divergent in trypanosomes. Like all other U6 RNAs, trypanosome U6 did not contain a TMG cap and was immunoprecipitated from deproteinized RNA by anti-TMG antibody because of its association with the TMG-capped U4 RNA. These two RNAs contained extensive regions of sequence complementarity which phylogenetically support the secondary-structure model proposed by D. A. Brow and C. Guthrie (Nature [London] 334:213-218, 1988) for the organization of the analogous yeast U4-U6 complex.

Animals↗
PubMed1997

Analysis of the haemagglutinin gene of current wild-type canine distemper virus isolates from Germany.

The haemagglutinin (H) gene sequences from three wild-type canine distemper viruses (CDV) isolated during 1994-1995 were sequenced to determine whether contemporary strains had undergone significant genetic changes relative to the currently used vaccine strains. The new isolates were closely related to each other (> 99%) and displayed about 90-91% sequence homology to the Onderstepoort and Convac vaccine strains. There were one to four additional potential glycosylation sites compared to the vaccine strains which were also present in a German dog CDV isolate dating from 1990. However, only a very slight reduction in neutralizing titre against the new isolates was found when compared with the Onderstepoort and Rockborn vaccine strains. Cysteine and proline residues were well conserved indicating a conserved three dimensional structure for the protein. By phylogenetic analysis the recent isolates showed a narrow clustering close to the previous canine isolates indicating a linear pattern of evolutionary changes. A comparison with published CDV H gene sequences suggested the presence of different lineages of CDV on a global scale and possible cocirculation of more than one genotype of CDV.

Amino Acid Sequence↗
PubMed2004

Collagens and collagen-related matrix components in the human and mouse eye.

The three-dimensional structure of the eye plays an important role in providing a correct optical environment for vision. Much of this function is dependent on the unique structural features of ocular connective tissue, especially of the collagen types and their supramolecular structures. For example, the organization of collagen fibrils is largely responsible for transparency and refraction of cornea, lens and vitreous body, and collagens present in the sclera are largely responsible for the structural strength of the eye. Phylogenetically, most of the collagens are highly conserved between different species, which suggests that collagens also share similar functions in mice and men. Despite considerable differences between the mouse and the human eye, particularly in the proportion of the different tissue components, the difficulty of performing systematic histologic and molecular studies on the human eye has made mouse an appealing alternative to studies addressing the role of individual genes and their mutations in ocular diseases. From a genetic standpoint, the mouse has major advantages over other experimental animals as its genome is better known than that of other species and it can be manipulated by the modern techniques of genetic engineering. Furthermore, it is easy, quick and relatively cheap to produce large quantities of mice for systematic studies. Thus, transgenic techniques have made it possible to study consequences of specific mutations in genes coding for structural components of ocular connective tissues in mice. As these changes in mice have been shown to resemble those in human diseases, mouse models are likely to provide efficient tools for pathogenetic studies on human disorders affecting the extracellular matrix. This review is aimed to clarify the role of collagenous components in the mouse and human eye with a closer look at the new findings of the collagens in the cartilage and the eye, the so-called "cartilage collagens".

Animals↗
PubMed1982

On the ultrastructure of the ventricular endocardium and bulbar endothelium in 3 teleostean species.

The endocardium in the ventricle and the endothelium in the bulbus arteriosus are described in 3 phylogenetically distant teleostean species, Betta splendens, Pistella riddlei, and Xiphophorus maculatus. The ventricular endocardial cells are attenuated and contain a number of bristle-coated vesicles (BCV). In the former 2 species these cells contain numerous ribosomes, a low number of moderately electron dense bodies (MDB) and a poorly developed agranular endoplasmic reticulum (AER). In the latter species, however, these cells are poor in ribosomes, but very rich in MDB and AER. In the species studied the bulbar endothelial cells contain high numbers of ribosomes, whereas BCV and AER are poorla developed. In P. riddlei these cells have a height of 3-7 microns and are closely packed by MBD, whereas in B. splendens and X. maculatus they appear to be flat and contain a very low number of MDB. The results of the present work are compared with those scare findings previously reported for the teleostean ventricular endocardium. The structural differences described may reflect phylogenetical distances.

Animals↗
PubMed2006

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package.

BACKGROUND: Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. RESULTS: Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. CONCLUSION: Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via http://www.arb-home.de.

Algorithms↗
PubMed2003

Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system.

Communication structures vary greatly in size and can be structurally and behaviorally integrated with other systems. In structurally integrated systems, dramatic changes in size may impose trade-offs with the size of neighboring structures. In spiny lobsters (Palinuridae), there is a fivefold difference in size of the antennular plate, on which sound producing apparatus is located, such that the antennular plate reaches 38% carapace length in some sound producers (Stridentes) compared to only 4% carapace length in non-sound producing spiny lobsters (Silentes). We examined whether this major variation in antennular plate size imposes trade-offs with the adjoining antennae, specifically in the context that the signal producing structures and antennae are both used in predator defense. We recorded and analyzed lobster sounds in order to test whether size increases in the acoustic morphology were correlated with production of particular signal features. Antennal and antennular plate structures were measured across the family, including both Stridentes and Silentes. Phylogenetic comparative methods were used to test for correlated evolutionary change among the structures and signal features. We analyzed the phylogenetic relationships of the Palinuridae based on morphological characters and ribosomal DNA evidence (16S, 18S and 28S nuclear and mitochondrial ribosomal RNA gene regions). We found that the number of sound pulses was positively correlated with length of the sound producing apparatus. Opposite to the predicted trade-offs, we found that the size of the antennular plate was positively correlated with size of the surrounding antennae within Stridentes. Nevertheless, when Stridentes were compared to Silentes, the latter had relatively larger antennae for a given antennular plate size than did the sound producing taxa. These results suggest that body size does not limit size increases in acoustic structures within Stridentes, however the presence and associated constructional costs of a sound producing apparatus may impose a trade-off when taxa with and without the apparatus are compared. Alternatively, since both systems are used in predator defense, this pattern may indicate greater selection for antennal force production in Silentes, which lack the additional acoustic mode of predator defense.

Animal Communication↗
PubMed2006

Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.

BACKGROUND: Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking. RESULTS: We propose a novel method to compare the protein structures in an accurate and efficient manner. Such a method can be used to not only reveal divergent evolution, but also identify circular permutations and further detect active-sites. Specifically, we define the structure alignment as a multi-objective optimization problem, i.e., maximizing the number of aligned atoms and minimizing their root mean square distance. By controlling a single distance-related parameter, theoretically we can obtain a variety of optimal alignments corresponding to different optimal matching patterns, i.e., from a large matching portion to a small matching portion. The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. In addition to solid theoretical background, numerical experiments demonstrated significant improvement of our approach over the existing methods in terms of quality and efficiency. In particular, we show that divergent evolution, circular permutations and active-sites (or structural motifs) can be identified by our method. The software SAMO is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/samo/ and http://intelligent.eic.osaka-sandai.ac.jp/chenen/samo.htm. CONCLUSION: A novel formulation is proposed to accurately align protein structures in the framework of multi-objective optimization, based on a sequence order-independent strategy. A fast and accurate algorithm based on the bipartite matching algorithm is developed by exploiting the special features. Convergence of computation is shown in experiments and is also theoretically proven.

Algorithms↗
PubMed1991

A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences.

We describe a new computer program that identifies conserved secondary structures in aligned nucleotide sequences of related single-stranded RNAs. The program employs a series of hash tables to identify and sort common base paired helices that are located in identical positions in more than one sequence. The program gives information on the total number of base paired helices that are conserved between related sequences and provides detailed information about common helices that have a minimum of one or more compensating base changes. The program is useful in the analysis of large biological sequences. We have used it to examine the number and type of complementary segments (potential base paired helices) that can be found in common among related random sequences similar in base composition to 16S rRNA from Escherichia coli. Two types of random sequences were analyzed. One set consisted of sequences that were independent but they had the same mononucleotide composition as the 16S rRNA. The second set contained sequences that were 80% similar to one another. Different results were obtained in the analysis of these two types of random sequences. When 5 sequences that were 80% similar to one another were analyzed, significant numbers of potential helices with two or more independent base changes were observed. When 5 independent sequences were analyzed, no potential helices were found in common. The results of the analyses with random sequences were compared with the number and type of helices found in the phylogenetic model of the secondary structure of 16S ribosomal RNA. Many more helices are conserved among the ribosomal sequences than are found in common among similar random sequences. In addition, conserved helices in the 16S rRNAs are, on the average, longer than the complementary segments that are found in comparable random sequences. The significance of these results and their application in the analysis of long non-ribosomal nucleotide sequences is discussed.

Base Composition↗
PubMed2000

Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae).

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.

Asteraceae↗
PubMed2001

Mammalian reovirus L2 gene and lambda2 core spike protein sequences and whole-genome comparisons of reoviruses type 1 Lang, type 2 Jones, and type 3 Dearing.

The reovirus L2 genome segment encodes the core spike protein lambda2, which mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. Complete nucleotide-sequence determinations were made for the L2 genome segments of eight mammalian reoviruses, including the prototype isolates of serotypes 1 and 2: Lang (T1L) and Jones (T2J), respectively. Each L2 segment was found to be 3912 or 3915 bases in length. Partial nucleotide-sequence determinations were also made for the 3916-base L2 segment of reovirus type 3 Dearing (T3D), the prototype isolate of serotype 3. The whole-genome sequence of reovirus T3D was reported previously. The T1L L2 analysis represents completion of the whole-genome sequence of that isolate as well. The T2J L2 analysis leaves only the sequence of the M1 segment yet to be reported from the genome of that isolate. The T2J M1 sequence made available from analysis in another lab was used for initiating whole-genome comparisons of reoviruses T1L, T2J, and T3D in this report. The nine L2 gene sequences and deduced lambda2 protein sequences were used to gain further insights into the biological variability, structure, and functions of lambda2 through comparisons of the sequences and reference to the crystal structure of core-bound lambda2. Phylogenetic comparisons suggest the presence of three evolutionary lines of divergent L2 alleles among the nine isolates. Localized regions of conserved amino acids in the lambda2 crystal structure include active-site clefts of the RNA capping enzyme domains, sites of interactions between lambda2 domains within the pentameric spike structure, and sites of interaction between lambda2 subunits and other proteins in viral particles.

Amino Acid Sequence↗
PubMed2004

Correlation between pollen morphology and pollination mechanisms in the Hydrocharitaceae.

The pollen morphology of 11 genera and 11 species of the Hydrocharitaceae and one species of the Najadaceae was studied using scanning and transmission electron microscopies, and the exine structures and sculptures are discussed in relation to pollination mechanisms and the molecular phylogeny. The pollen grains of the Hydrocharitaceae are spherical, inaperturate, and form monads or tetrads, while those of the Najadaceae are elliptical, inaperturate, and form monads. The entomophilous genera Egeria, Blyxa, Ottelia, Stratiotes, and Hydrocharis share pollen grains that have projections like spines or bacula. The anemophilous genus Limnobium has reticulate pollen grains. The hypohydrophilous genera Thalassia and Najas are characterized by pollen grains with reduced exine structures. The pollen-epihydrophilous genera Elodea and Hydrilla have tightly arranged small spinous pollen grains, and the male flower-epihydrophilous genera Enhalus and Vallisneria have reduced reticulate or gemmate exines. Character state reconstruction of the exine structures and sculptures using a molecular phylogenetic tree suggests that variation in the exine is generally correlated with the pollination mechanism; the selective pressures acting on the pollination mechanisms have reduced the exine structure in hypohydrophilous plants and resulted in various exine sculptures that are adapted to the different pollination mechanisms in entomophilous, anemophilous, and pollen-epihydrophilous plants.

Biological Evolution↗