Reassessment of the Devonian problematicum Protonympha as another post‐Ediacaran vendobiont

Protonympha is an enigmatic fossil represented by two species from the Middle Devonian (Protonympha transversa) and Late Devonian (Protonympha salicifolia) of New York. Although interpreted in the past as a polychaete worm or starfish arm, Protonympha is not found with marine fossils, but with fossil plants. This fossil plant community was a swamp woodland of Lepidosigillaria whitei, with ground cover of Haskinsia colophylla, fringing brackish to freshwater coastal lagoons of the Catskill Delta. Protonympha shares with Ediacaran Vendobionta a quilted body of unskeletonized biopolymer that is unusually resistant to burial compaction. In overall form, Protonympha is most like the Ediacaran genus Spriggina. Protonympha has branching and tapering tubular structures radiating from the bottom. These rhizine‐like structures, thallus stratification and internal chambers revealed by petrographic thin sections suggest affinities with lichenized fungi. As for Cambrian Swartpuntia and Ordovician–Silurian Rutgersella, Protonympha may have been a post‐Ediacaran vendobiont.     

Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci

The sequences of the capsular biosynthetic (cps) loci of 90 serotypes of Streptococcus pneumoniae have recently been determined. Bioinformatic procedures were used to predict the general functions of 1,973 of the 1,999 gene products and to identify proteins within the same homology group, Pfam family, and CAZy glycosyltransferase family. Correlating cps gene content with the 54 known capsular polysaccharide (CPS) structures provided tentative assignments of the specific functions of the different homology groups of each functional class (regulatory proteins, enzymes for synthesis of CPS constituents, polymerases, flippases, initial sugar transferases, glycosyltransferases [GTs], phosphotransferases, acetyltransferases, and pyruvyltransferases). Assignment of the glycosidic linkages catalyzed by the 342 GTs (92 homology groups) is problematic, but tentative assignments could be made by using this large set of cps loci and CPS structures to correlate the presence of particular GTs with specific glycosidic linkages, by correlating inverting or retaining linkages in CPS repeat units with the inverting or retaining mechanisms of the GTs predicted from their CAZy family membership, and by comparing the CPS structures of serotypes that have very similar cps gene contents. These large-scale comparisons between structure and gene content assigned the linkages catalyzed by 72% of the GTs, and all linkages were assigned in 32 of the serotypes with known repeat unit structures. Clear examples where very similar initial sugar transferases or glycosyltransferases catalyze different linkages in different serotypes were also identified. These assignments should provide a stimulus for biochemical studies to evaluate the reactions that are proposed.     

The problematic Hadimopanella, Kaimenella, Milaculum and Utahphospha identified as sclerites of Palaeoscolecida

Hinz, I., Kraft, P., Mergl, M. & Müller, K. J. 1990 04 15: The problematic Hadimopanella, Kaimenella, Milaculum and Utahphospha identified as sclerites of Palaeoscolecida. Lefhaia , Vol. 23 , pp. 217–221. Oslo. ISSN 024–1164.
Hadimopanella Gedik, 1 977 , Kaimenella Marss, 1988 and Milaculum Müller, 1973 have been established on the basis of isolated elements of unknown origin. Recently, the latter genus has been tentatively related to the Agnatha (van den Boogaard 1988). By contrast, Bendix-Almgreen & Peel (1988) assigned Hadimopanella to the chordate stock but definitely excluded it from vertebrates. Well-preserved worm-like organisms of Palaeoscolecida Conway Morris & Robison. 1986 are known from the Lower Cambrian to the Lower Ordovician. They have their outer surface covered with a pattern of sequin-like sclerites which evidence the systematic affiliation with the isolated sclerites mentioned above. Based on similar structures on the outer surface, Utahphospha Miiller & Miller, 1976 is considered to belong to the same group. * Early Palaeozoic fossils, Palaeoscolecida, isolated sclerites, phosphatization .     

Structure-dependent sequence alignment for remotely related proteins

MOTIVATION: The quality of a model structure derived from a comparative modeling procedure is dictated by the accuracy of the predicted sequence-template alignment. As the sequence-template pairs are increasingly remote in sequence relationship, the prediction of the sequence-template alignments becomes increasingly problematic with sequence alignment methods. Structural information of the template, used in connection with the sequence relationship of the sequence-template pair, could significantly improve the accuracy of the sequence-template alignment. In this paper, we describe a sequence-template alignment method that integrates sequence and structural information to enhance the accuracy of sequence-template alignments for distantly related protein pairs. RESULTS: The structure-dependent sequence alignment (SDSA) procedure was optimized for coverage and accuracy on a training set of 412 protein pairs; the structures for each of the training pairs are similar (RMSD< approximately 4A) but the sequence relationship is undetectable (average pair-wise sequence identity = 8%). The optimized SDSA procedure was then applied to extend PSI-BLAST local alignments by calculating the global alignments under the constraint of the residue pairs in the local alignments. This composite alignment procedure was assessed with a testing set of 1421 protein pairs, of which the pair-wise structures are similar (RMSD< approximately 4A) but the sequences are marginally related at best in each pair (average pair-wise sequence identity = 13%). The assessment showed that the composite alignment procedure predicted more aligned residues pairs with an average of 27% increase in correctly aligned residues over the standard PSI-BLAST alignments for the protein pairs in the testing set.     

Crystal structures of fusion proteins with large-affinity tags

The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest.     

Carboxylic ester hydrolases: Classification and database derived from their primary,secondary, and tertiary structures

We classified the carboxylic ester hydrolases (CEHs) into families and clans by use of multiple sequence alignments, secondary structure analysis, and tertiary structure superpositions. Our work for the first time has fully established their systematic structural classification. Family members have similar primary, secondary, and tertiary structures, and their active sites and reaction mechanisms are conserved. Families may be gathered into clans by their having similar secondary and tertiary structures, even though primary structures of members of different families are not similar. CEHs were gathered from public databases by use of Basic Local Alignment Search Tool (BLAST) and divided into 91 families, with 36 families being grouped into five clans. Members of one clan have standard α/β‐hydrolase folds, while those of other two clans have similar folds but with different sequences of their β‐strands. The other two clans have members with six‐bladed β‐propeller and three‐α‐helix bundle tertiary structures. Those families not in clans have a large variety of structures or have no members with known structures. At the time of writing, the 91 families contained 321,830 primary structures and 1378 tertiary structures. From these data, we constructed an accessible database: CASTLE (CArboxylic eSTer hydroLasEs, http://www.castle.cbe.iastate.edu ).     

Making a clean break: addiction and Ulysses contracts

I examine current models of self-destructive addictive behaviour, and argue that there is an important place for Ulysses contracts in coping with addictive behaviour that stems from certain problematic preference structures. Given the relevant preference structures, interference based on a Ulysses contract need not involve questionably favouring an agent's past preferences over her current preferences, but can actually be justified in terms of the agent's current concerns and commitments.     

LATE DEVONIAN (FAMENNIAN) LUNGFISHES FROM THE CATSKILL FORMATION OF PENNSYLVANIA, USA

Abstract:  Occurrences of fossil lungfishes (Dipnoi: Sarcopterygii) in the Famennian Catskill Formation of Pennsylvania are reviewed. A nearly complete dermal skull roof is assigned to a new genus and species, Apatorhynchus opistheretmus . Other recently discovered lungfish specimens include an incomplete postcranium similar to that of the Frasnian genus Fleurantia , a small parasphenoid of uncertain affinities, and isolated toothplates. Previously described dipnoan remains from the Catskill Formation include a partial skull roof of Soederberghia groenlandica , toothplates assigned to several species of Dipterus , a putative rostral or symphysial region placed in the problematic form taxon Ganorhynchus , and sedimentary structures interpreted as burrows. The toothplates attributed to Dipterus are indeterminate and are placed in open nomenclature, while the specimen identified as Ganorhynchus is not convincingly dipnoan. The status of the burrows remains uncertain pending the discovery of lungfish remains within these or similar structures in Catskill deposits. The distinct ichthyofaunas within the Catskill Formation and their lungfish components are briefly reviewed. Lungfishes are found in the Holoptychius - and Bothriolepis -dominated faunas common in the Catskill succession, as well as in the compositionally distinctive Red Hill assemblage. Many of the Devonian continental faunas that contain tetrapods also include long-snouted, denticle-bearing lungfishes ('rhynchodipterids', fleurantiids, or both). The composition of Late Devonian ichthyofaunas may have predictive qualities that will allow researchers to identify localities likely to produce the remains of early tetrapods.     

Investigation of a physical basis for conformational similarity in proteins

Amino acid residues in a globular protein fold against one another into a compact structure. We have sought common physical factors within similarly folded backbone structures in such proteins which might influence the folding and which could be used in predicting the backbone structure. The physical factors examined are the 10 orthogonal ones identified by Kideraet al. (1985a). Comparison of the smoothed physical factor profiles between sequences, which have similar backbone structures, shows that there is good agreement among the profiles of helical stretches, but not for other backbone structures that have been examined. This is ascribed to the fact that helical structures involve local interactions, which then require similar physical profiles to form, but that other structures are not so strongly locally determined in the native structure.On leave from University of the Witwatersrand, Wits 2050, South Africa.     

Conformational analysis of d(C3G3), a B-family duplex in solution

NMR and circular dichroism studies of the duplex formed by the self-complementary DNA hexanucleotide d(C3G3) indicate that it is a B-type structure but differs from standard B-form. An analysis of NMR coupling constants within the deoxyribose moieties yields a 70% or greater contribution from pseudorotation phase angles corresponding to the C3'-exo conformation, a conformation similar to the C2'-endo conformation associated with B-form DNA. Intranucleotide interproton distances are consistent with a B-form structure, but some internucleotide distances are intermediate between A- and B-form structures. Circular dichroism spectra have B-form characteristics but also include an unusual negative band at 282 nm. The solution spectroscopic results are in contrast with X-ray crystallographic studies which find A-form structures for similar sequences.     

STUDIES OF CARBONIFEROUS FUNGI. II. THE STRUCTURE AND ORGANIZATION OF MYCOCARPON,SPOROCARPON, DUBIOCARPON,AND COLEOCARPON (ASCOMYCOTINA)

The problematic organism, Sporocarpon, was among the first fossil fungi to be described. The genus was actually a heterogeneous assemblage of fungal forms, and was eventually divided into several taxa including Sporocarpon, Dubiocarpon, and Mycocarpon. In the present paper these organisms, as well as a similar, previously undescribed genus, Coleocarpon; are described from Lower, Middle, and Upper Pennsylvanian strata in North America, and from Upper Carboniferous sediments in England. Although initially considered to be radiolarian-like protozoa, these structures show far more similarity to ascomycetous cleistothecia. All forms are ornamented, spherical bodies with a complex wall which encloses scattered asci and ascospores. Taxa are distinguished primarily by differences in the organization of the cleistothecial wall. Structurally similar organisms are found today among the Eurotiales.     

A comparative study of the structure of egg-white riboflavin binding protein from the domestic fowl and Japanese quail.

1. The riboflavin binding proteins from domestic fowl and Japanese quail have been isolated and their structures compared by circular dichroism, fluorescence and peptide mapping. 2. The two proteins have similar secondary structures, but differ in their tertiary structures as reflected in the environments of aromatic amino acid side chains. 3. Differences in amino acid sequence between the proteins are indicated by the digestion patterns obtained with thermolysin, chymotrypsin and V8 proteinase from Staphylococcus aureus. Both proteins are resistant to digestion by trypsin.     

A new ATP-binding fold in actin, hexokinase and Hsc70

One of a cell biologist's favourite occupations is to discover the proteins that perform newly described functions in the cell. Very often lately, this has resulted in the identification of protein families whose related amino acid sequences reflect similar functions, but can proteins with totally unrelated sequences have similar structures and functions? In this review, Ken Holmes, Chris Sander and Alfonso Valencia describe the structural similarities between three well-known proteins that have no readily detectable primary sequence similarities but for which X-ray crystallography has revealed very similar structures. A comparison of their structures provides insights into their common mechanisms of action and into protein evolution, and has been used to detect related proteins in sequence data bases.     

多毛纲环节动物软背鳞虫的电镜观察与描述及其与Wiwaxia骨片微结构的比较

通过对现生环节动物门（Annelida）多毛纲（Polychaeta）叶须虫目（Phyllodocidae）鳞沙蚕亚目动物（Aphroditiformia）软背鳞虫（Lepidonotus helotypus Grube,1877）的鳞片、刚毛等疣足附属物的超微结构观察及其与Wiwaxia骨片的比较研究,探讨Wiwaxia的系统分类位置。研究结果表明,软背鳞虫的刚毛与Wiwaxia骨片具有以下相似性：1）两者表面均具有浅纵纹;2）均向身体背中线方向倾斜或弯曲;3）着生方式均以刚毛囊或类似根状基的结构插入软组织。此外,文中首次对鳞片上的锥形突起与Wiwaxia骨片的相似性进行比较和探讨。结果显示,Wiwaxia骨片与鳞沙蚕刚毛具有一定相似性,但在形态上仍存在显著差异（如二者的排列方式不同,Wiwaxia骨片上不存在鳞沙蚕刚毛的覆瓦状结构等）。     

Overwintering ecology of two social halictine bees,Lasioglossum duplex andL. problematicum

Overwintering of two social halictine bees, Lasioglossum duplex (Dalla Torre ) and L. problematicum (Blüthgen ), was studied. In L. duplex many females stay near the old nests, each female preparing a hibernaculum separated from the natal nest. In L. problematicum most females overwinter communally within the natal nest. This difference in overwintering habits relates to the social structure in the next spring. L. duplex is nearly always solitary in spring although later becoming eusocial, whereas many nests of L. problematicum are polygynous, beginning in early spring. L. duplex overwinters much deeper () in the soil than does L. problematicum (), but both species are safe from drops in soil temperature, which is above 0°C even in midwinter, and the bees' supercooling points are lower than −6°C. This cold resistance and the storage of sufficient food in the crop are reflected in the winter survival, which is much higher (79%) than the rate of successful nests in the spring active phase (25%).     

Similarity of domain organization of proteins in phylogenetically distant organisms as a basis of meiosis conservatism

The cytological mechanism of meiosis is very conservative in all eukaryotes. Some meiosis-specific structural proteins of yeasts, nematode Caenorhabditis elegans, Drosophila, and mammals, which play identical roles in cells during meiosis, do not have homology of the primary structure, but their domain organization and conformation are similar. The enzymes of meiotic recombination in yeasts and plants have similar epitopes. These facts suggest that the similarity of the higher level of organization of the meiosis-specific proteins allows these proteins to form similar subcellular structures and produce similar cytological picture of meiosis and similar functions of these subcellular structures. Finally, this leads to a conservative scheme of meiosis in evolutionally distant eukaryotes.     

Atypical Chordoid Structures in the Aristotle's Lantern of Regular Echinoids

Regular sea–urchins, as a rule, prepare and process their food as pellets in their buccal cavity before ingesting them. This is obtained through the synergistic interaction of the five teeth with five fleshy protuberances (paradental tongues) which extend into the oral cavity and work like tongues. Each of these structures consists of two anatomically distinct parts: the outer component is a deep pouch of the terminal tract of the pharynx and shows a histological organization similar to that usually shown by the pharyngeal wall itself. The deeper component (paradental axis) is represented by a supporting rod and shows a peculiar histological structure, which consists of glycogen containing vesiculate cells mixed to slim muscle fibres and held together by a thin fibrillar stroma. The paradental axes are very problematic structures in terms of comparative anatomy and phylogenetic aspects. Their microscopic and submicroscopic organization is unusual for an echinoderm and recalls that of different types of chordoid organs commonly found in other invertebrates (Protostomata and Deuterostomata).     

Examining protein surface structure in highly conserved sequence variants with mass spectrometry

A simple mass spectrometry-based method capable of examining protein structure called SNAPP (selective noncovalent adduct protein probing) is used to evaluate the structural consequences of point mutations in naturally occurring sequence variants from different species. SNAPP monitors changes in the attachment of noncovalent adducts to proteins as a function of structural state. Mutations that lead to perturbations to the electrostatic surface structure of a protein affect noncovalent attachment and are easily observed with SNAPP. Mutations that do not alter the tertiary structure or electrostatic surface structure yield similar results by SNAPP. For example, bovine, porcine, and human insulin all have very similar backbone structures and no basic or acidic residue mutations, and the SNAPP distributions for all three proteins are very similar. In contrast, four variants of cytochrome c (cytc) have varying degrees of sequence homology, which are reflected in the observed SNAPP distributions. Bovine and pigeon cytc have several basic or acidic residue substitutions relative to horse cytc, but the SNAPP distributions for all three proteins are similar. This suggests that these mutations do not significantly influence the protein surface structure. On the other hand, yeast cytc has the least sequence homology and exhibits a unique, though related, SNAPP distribution. Even greater differences are observed for lysozyme. Hen and human lysozyme have identical tertiary structures but significant variations in the locations of numerous basic and acidic residues. The SNAPP distributions are quite distinct for the two forms of lysozyme, suggesting significant differences in the surface structures. In summary, SNAPP experiments are relatively easy to perform, require minimal sample consumption, and provide a facile route for comparison of protein surface structure between highly homologous proteins.     

The origin of tetraradial symmetry in cnidarians

Serially arranged sets of eight septa‐like structures occur in the basal part of phosphatic tubes of Sphenothallus from the early Ordovician (early Floian) Fenxiang Formation in Hubei Province of China. They are similar in shape, location and number, to cusps in chitinous tubes of extant coronate scyphozoan polyps, which supports the widely accepted cnidarian affinity of this problematic fossil. However, unlike the recent Medusozoa, the tubes of Sphenothallus are flattened at later stages of development, showing biradial symmetry. Moreover, the septa (cusps) in Sphenothallus are obliquely arranged, which introduces a bilateral component to the tube symmetry. This makes Sphenothallus similar to the Early Cambrian Paiutitubulites, having similar septa but with even more apparent bilateral disposition. Biradial symmetry also characterizes the Early Cambrian tubular fossil Hexaconularia, showing a similarity to the conulariids. However, instead of being strictly tetraradial like conulariids, Hexaconularia shows hexaradial symmetry superimposed on the biradial one. A conulariid with a smooth test showing signs of the ‘origami’ plicated closure of the aperture found in the Fenxiang Formation supports the idea that tetraradial symmetry of conulariids resulted from geometrical constrains connected with this kind of closure. Its minute basal attachment surface makes it likely that the holdfasts characterizing Sphenothallus and advanced conulariids are secondary features. This concurs with the lack of any such holdfast in the earliest Cambrian Torellella, as well as in the possibly related Olivooides and Quadrapyrgites. Bilaterally arranged internal structures in polyps representing probably the oldest medusozoans support the suggestions based on developmental evidence that the ancestor of cnidarians also was a bilaterally symmetrical animal. This is one more example of fossil data that strictly fit the molecular phylogenetic evidence but not necessarily morphology‐based zoological interpretations.     

Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

Restrained molecular dynamics simulations are a robust, though perhaps underused, tool for the end-stage refinement of biomolecular structures. We demonstrate their utility-using modern simulation protocols, optimized force fields, and inclusion of explicit solvent and mobile counterions-by re-investigating the solution structures of two RNA hairpins that had previously been refined using conventional techniques. The structures, both domain 5 group II intron ribozymes from yeast ai5γ and Pylaiella littoralis, share a nearly identical primary sequence yet the published 3D structures appear quite different. Relatively long restrained MD simulations using the original NMR restraint data identified the presence of a small set of violated distance restraints in one structure and a possibly incorrect trapped bulge nucleotide conformation in the other structure. The removal of problematic distance restraints and the addition of a heating step yielded representative ensembles with very similar 3D structures and much lower pairwise RMSD values. Analysis of ion density during the restrained simulations helped to explain chemical shift perturbation data published previously. These results suggest that restrained MD simulations, with proper caution, can be used to "update" older structures or aid in the refinement of new structures that lack sufficient experimental data to produce a high quality result. Notable cautions include the need for sufficient sampling, awareness of potential force field bias (such as small angle deviations with the current AMBER force fields), and a proper balance between the various restraint weights.