Influence of morphology and material properties on the range of motion of the costovertebral joint – a probabilistic finite element analysis

Abstract

The motion of the costovertebral joint (CVJ) is governed by the material properties and its morphology. The goal of this numerical study was to identify the material and morphology parameters with the greatest influence on the motion of the CVJ. A fully parametric finite element model of the anatomy and material properties of the CVJ was developed. The impact of five morphology and thirteen material parameters was investigated and compared to in vitro data. The motion was influenced in particular by the rotational stiffness of the articulatio capitis costae and the lateral position of the fovea costalis transveralis.     

Molecular genetic analysis of the suprageneric system of casebearer moths,with a description of a new genus from the tribe Carpochenini Cǎpuşe, 1973 (Lepidoptera,Coleophoridae)

Based on a complex approach including morphological and molecular genetic methods, the taxonomic position of two casebearer moth species Coleophora tsherkesi Falkovitsh, 1970 and C. isabellina Falkovitsh, 1970 (Lepidoptera, Coleophoridae) is discussed. On the phylogenetic tree based on the cytochrome oxidase subunit I gene (COI), two species form a common cluster with species of the genera Ionescumia, Carpochena, and Goniodoma. Data on the molecular phylogeny and morphology justify the placement of Coleophora tsherkesi and C. isabellina in a separate genus Falkmisa Anikin et Dyomin, gen. n. Thus, the tribe Carpochenini includes three genera: Ionescumia, Carpochena, and Falkmisa.     

Phylogeny of the Alismatales (Monocotyledons) and the relationship of Acorus (Acorales?)

A phylogenetic analysis of the early branching lineages of the monocotyledons is performed using data from two plastid genes (rbcL and matK), five mitochondrial genes (atp1, ccmB, cob, mttB and nad5) and morphology. The complete matrix includes 93 terminals representing Acorus, the 14 families currently recognized within Alismatales, and numerous lineages of monocotyledons and other angiosperms. Total evidence analysis results in an almost completely resolved strict consensus tree, but all data partitions, genomic as well as morphological, are incongruent. The effects of RNA editing and potentially processed paralogous sequences are explored and discussed. Despite a decrease in incongruence length differences after exclusion of edited sites, the major data partitions remain significantly incongruent. The 14 families of Alismatales are all found to be monophyletic, but Acorus is found to be included in Alismatales rather than being the sister group to all other monocotyledons. The placement is strongly supported by the mitochondrial data, atp1 in particular, but it cannot be explained as an artifact caused by patterns of editing or by sampling of processed paralogues.     

SNA – a toolbox for the stoichiometric analysis of metabolic networks

Background  

Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem.     

Phylogeny and spatio‐temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum (Rosaceae) in the Malesian region

The goals of this study were to reconstruct the phylogeny of Prunus subgenus Laurocerasus section Mesopygeum and to provide a preliminary assessment of its spatio‐temporal diversification in the Malesian region. We inferred the phylogeny using nuclear ITS and ETS and plastid psbA‐trnH, rps16, rpl16, and trnC‐petN sequences. Our analyses support the monophyly of sect. Mesopygeum. Within sect. Mesopygeum, we identified four main subclades: (i) Prunus lancilimba from continental Asia; (ii) Prunus ruthii from Malay Peninsula; (iii) a subclade comprising species from areas centered on the Sunda shelf and also a few species from continental Asia and Wallacea; and (iv) a subclade composed of species from areas of the Sahul shelf, with a small number of taxa also from areas of the Sunda shelf, continental Asia, and the Philippines. We estimated that sect. Mesopygeum originated in continental Asia at c. 44.71 Mya (95% HPD: 31.66–46.90). Nine dispersals between major geographic areas were inferred. From continental Asia, three and two dispersals were inferred to the Sunda shelf and the Sahul shelf in the mid‐Oligocene, respectively. Two dispersals were inferred from the Sahul shelf region to the Sunda shelf in late Oligecene and early Miocene, respectively. There were also two dispersals inferred from the Sunda shelf region, one to the Philippines and one to Wallacea, in the middle and late Miocene, respectively. The diversification in sect. Mesopygeum was likely driven by active geologic events and orogenies in the Neogene in the Malesian region.     

Computational analysis of the interactions of a novel cephalosporin derivative with β-lactamases

Background

One of the main concerns of the modern medicine is the frightening spread of antimicrobial resistance caused mainly by the misuse of antibiotics. The researchers worldwide are actively involved in the search for new classes of antibiotics, and for the modification of known molecules in order to face this threatening problem. We have applied a computational approach to predict the interactions between a new cephalosporin derivative containing an additional β-lactam ring with different substituents, and several serine β-lactamases representative of the different classes of this family of enzymes.

Results

The results of the simulations, performed by using a covalent docking approach, has shown that this compound, although able to bind the selected β-lactamases, has a different predicted binding score for the two β-lactam rings, suggesting that one of them could be more resistant to the attack of these enzymes and stay available to perform its bactericidal activity.

Conclusions

The detailed analysis of the complexes obtained by these simulations suggests possible hints to modulate the affinity of this compound towards these enzymes, in order to develop new derivatives with improved features to escape to degradation.

     

Vibrational sensitivity of the wing of the pigeon (Columba livia) — a study using heart rate conditioning

Summary The vibrational sensitivity of awake pigeons was tested with the heart rate conditioning method. This method proved to be a very sensitive instrument for the behavioural measurement of the pigeon's sensitivity to mechanical stimuli.Sine wave vibrational stimuli between 50 and 2000 Hz were applied to the 1st, 7th and 16th primary feathers of the wing. The resulting threshold curves were U- or V-shaped with 3 characteristics: (i) The frequency of best response was either 800 or 900 Hz. (ii) Within the broad frequency range of vibrational sensitivity (50 to 2000 Hz) the sensitivity was extremely high at the best frequency: threshold amplitudes lay between 0.5 and 0.09 m. (iii) The threshold curves showed very sharp tuning at best frequency with bandwidths between 0.3 and 0.7 octaves (measured at best frequency 10fold above threshold). The functional meaning of the characteristic vibrational sensitivity of the wing for flight control is discussed; it is interpreted as an adaptation to special situations occurring during flight.Abbreviations CR conditioned response - CS conditioned stimulus - ECG electrocardiogram - HC(s) Herbst corpuscle(s) - UCS unconditioned stimulus All experiments were carried out at the Ruhr-Universität Bochum, Lehrstuhl für Allgemeine Zoologie     

Theoretical description of halogen bonding – an insight based on the natural orbitals for chemical valence combined with the extended-transition-state method (ETS-NOCV)

In the present study we have characterized the halogen bonding in selected molecules H₃N–ICF₃ (1-NH ₃ ), (PH₃)₂C–ICF₃ (1-CPH ₃ ), C₃H₇Br–(IN₂H₂C₃)₂C₆H₄ (2-Br), H₂–(IN₂H₂C₃)₂C₆H₄ (2-H ₂ ) and Cl–(IC₆F₅)₂C₇H₁₀N₂O₅ (3-Cl), containing from one halogen bond (1-NH ₃ , 1-CPH ₃ ) up to four connections in 3-Cl (the two Cl–HN and two Cl–I), based on recently proposed ETS-NOCV analysis. It was found based on the NOCV-deformation density components that the halogen bonding C–X ^… B (X-halogen atom, B-Lewis base), contains a large degree of covalent contribution (the charge transfer to X ^… B inter-atomic region) supported further by the electron donation from base atom B to the empty σ*(C–X) orbital. Such charge transfers can be of similar importance compared to the electrostatic stabilization. Further, the covalent part of halogen bonding is due to the presence of σ-hole at outer part of halogen atom (X). ETS-NOCV approach allowed to visualize formation of the σ-hole at iodine atom of CF₃I molecule. It has also been demonstrated that strongly electrophilic halogen bond donor, [C₆H₄(C₃H₂N₂I)₂][OTf]₂, can activate chemically inert isopropyl bromide (2-Br) moiety via formation of Br–I bonding and bind the hydrogen molecule (2-H ₂ ). Finally, ETS-NOCV analysis performed for 3-Cl leads to the conclusion that, in terms of the orbital-interaction component, the strength of halogen (Cl–I) bond is roughly three times more important than the hydrogen bonding (Cl–HN).

Amplification of the COL2A1 3′ variable region used for segregation analysis in a family with the Stickler syndrome

Summary Amplification of a variable region 3 to the human type II collagen gene (COL2A1) has permitted segregation analysis in a three generation Stickler syndrome pedigree. This family had previously proved uninformative for the known restriction fragment length dimorphisms. Amplification of the variable region revealed five distinguishable alleles, of which three were segregating in this family. The lod score in favour of linkage was 2.86 at zero recombination.     

Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer

Genome-wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 10q11.2, harboring the microseminoprotein-β (MSMB) gene. Both the gene product of MSMB, the prostate secretory protein 94 (PSP94) and its binding protein (PSPBP), have been previously investigated as serum biomarkers for prostate cancer progression. Recent functional work has shown that different alleles of the significantly associated SNP in the promoter of MSMB found to be associated with prostate cancer risk, rs10993994, can influence its expression in tumors and in vitro studies. Since it is plausible that additional variants in this region contribute to the risk of prostate cancer, we have used next-generation sequencing technology to resequence a ~97-kb region that includes the area surrounding MSMB (chr10: 51,168,025–51,265,101) in 36 prostate cancer cases, 26 controls of European origin, and 8 unrelated CEPH individuals in order to identify additional variants to investigate in functional studies. We identified 241 novel polymorphisms within this region, including 142 in the 51-kb block of linkage disequilibrium (LD) that contains rs10993994 and the proximal promoter of MSMB. No sites were observed to be polymorphic within the exons of MSMB.     

Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(α)I

5-Hydroxymethylcytosine (5-hmC) is a newly discovered DNA base in mammalian cells that is believed to be another important epigenetic modification. Here we report the use of a methylation-insensitive restriction enzyme Taq^αI coupled with selective chemical labeling of 5-hmC in a combined glycosylation restriction analysis (CGRA) to detect 5-hmC in TCGA sequences. This method, differentiates fully versus hemi-hydroxymethylated cytosine in the CpG dinucleotide, adds a new tool to facilitate biological studies of 5-hmC.     

Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects

Hexapoda includes 33 commonly recognized orders, most of them insects. Ongoing controversy concerns the grouping of Protura and Collembola as a taxon Ellipura, the monophyly of Diplura, a single or multiple origins of entognathy, and the monophyly or paraphyly of the silverfish (Lepidotrichidae and Zygentoma s.s.) with respect to other dicondylous insects. Here we analyze relationships among basal hexapod orders via a cladistic analysis of sequence data for five molecular markers and 189 morphological characters in a simultaneous analysis framework using myriapod and crustacean outgroups. Using a sensitivity analysis approach and testing for stability, the most congruent parameters resolve Tricholepidion as sister group to the remaining Dicondylia, whereas most suboptimal parameter sets group Tricholepidion with Zygentoma. Stable hypotheses include the monophyly of Diplura, and a sister group relationship between Diplura and Protura, contradicting the Ellipura hypothesis. Hexapod monophyly is contradicted by an alliance between Collembola, Crustacea and Ectognatha (i.e., exclusive of Diplura and Protura) in molecular and combined analyses.     

Functional analysis of the C-terminal region of γ-glutamyl kinase of Saccharomyces cerevisiae

γ-Glutamyl kinase (GK) is the rate-limiting enzyme in proline synthesis in microorganisms. Most microbial GKs contain an N-terminal kinase domain and a C-terminal pseudouridine synthase and archaeosine transglycosylase (PUA) domain. In contrast, higher eukaryotes possess a bifunctional Δ(1)-pyrroline-5-carboxylate synthetase, which consists of a PUA-free GK domain and a γ-glutamyl phosphate reductase (GPR) domain. Here, to examine the role of the C-terminal region, including the PUA domain of Saccharomyces cerevisiae GK, we constructed a variety of truncated yeast GK and GK/GPR fusion proteins from which the C-terminal region was deleted. A complementation test in Escherichia coli and S. cerevisiae and enzymatic analysis of recombinant proteins revealed that a 67-residue linker sequence between a 255-residue kinase domain and a 106-residue PUA domain is essential for GK activity. It also appeared that 67 or more residues of the C-terminal region, not the PUA domain itself, are required for the full display of GK activity. Further, the GK/GPR fusion protein was functional in E. coli, but decreased stability and Mg-binding ability as compared to wild-type GK. These results suggest that the C-terminal region of S. cerevisiae GK is involved in the folding and/or the stability of the kinase domain.     

The combined impact of mechanical factors on the wall stress of the human ascending aorta – a finite elements study

Background

Biomechanical factors influence stress in the aortic wall. The aim of this study was to assess how the diameter and shape of the vessel, blood pressure and longitudinal systolic aortic stretching (SAS) caused by the contraction of the myocardium influence stress in the aortic wall.

Methods

Three computational models of the non-dilated aorta and aneurysms of the ascending aorta and aortic root were created. Then, finite elements analyses were carried out. The models were subjected to blood pressure (120 mmHg and 160 mmHg) and longitudinal systolic aortic stretching (0 mm, 5 mm, 10 mm and 15 mm). The influence of wall elasticity was examined too.

Results

Blood pressure had a smaller impact on the stress than the SAS. An increase in blood pressure from 120 mmHg to 160 mmHg increased the peak wall stress (PWS) on average by 0.1 MPa in all models. A 5 mm SAS caused a 0.1–0.2 MPa increase in PWS in all the models. The increase in PWS caused by a 10 mm and 15 mm SAS was 0.2 MPa and 0.4 MPa in the non-dilated aorta, 0.2–0.3 MPa and 0.3–0.5 MPa in the aneurysm of the ascending aorta, and 0.1–0.2 MPa and 0.2–0.3 MPa in the aortic root aneurysm model, respectively. The loss of elasticity of the aneurysmal wall resulted in an increase of PWS by 0.1–0.2 MPa.

Conclusions

Aortic geometry, wall stiffness, blood pressure and SAS have an impact on PWS. However, SAS had the biggest impact on wall stress. The results of this study may be useful in future patient-specific computational models used to assess the risk of aortic complications.

     

Cryptohelops menaticus – a new genus and species of the tribe Helopini (Coleoptera: Tenebrionidae) from the Palaeocene of Menat (France)

A new genus and species, Cryptohelops menaticus gen. et sp. n., are described from the Palaeocene of Menat (France). The new genus belongs to the subtribe Helopina of the tribe Helopini (subfamily Tenebrioninae of Tenebrionidae) based on the coarse and dense punctation of the hypomera, shape of the prosternum and metepisterna, a similar appearance to the native genera Helops and Stenohelops and the structure of the epipleura. The new genus also resembles Raiboscelis and Entomogonus by having the protibiae excised along the base of the inner side. The new genus is the oldest representative of the tribe Helopini. Four species of Helops sensu lato previously described from the Oligocene (H. wetteravicus K. Heyden et L. Heyden, 1865) and Miocene (H. atticus Redtenbacher in Ungern, 1867; H. meissneri Heer, 1847 and H. molassicus Heer, 1883) lack important diagnostic characters and should be regarded as members of the tribe Helopini with uncertain generic attribution.     

Phylogeny of ladybirds (Coleoptera: Coccinellidae): Are the subfamilies monophyletic?

The Coccinellidae (ladybirds) is a highly speciose family of the Coleoptera. Ladybirds are well known because of their use as biocontrol agents, and are the subject of many ecological studies. However, little is known about phylogenetic relationships of the Coccinellidae, and a precise evolutionary framework is needed for the family. This paper provides the first phylogenetic reconstruction of the relationships within the Coccinellidae based on analysis of five genes: the 18S and 28S rRNA nuclear genes and the mitochondrial 12S, 16S rRNA and cytochrome oxidase subunit I (COI) genes. The phylogenetic relationships of 67 terminal taxa, representative of all the subfamilies of the Coccinellidae (61 species, 37 genera), and relevant outgroups, were reconstructed using multiple approaches, including Bayesian inference with partitioning strategies. The recovered phylogenies are congruent and show that the Coccinellinae is monophyletic but the Coccidulinae, Epilachninae, Scymninae and Chilocorinae are paraphyletic. The tribe Chilocorini is identified as the sister-group of the Coccinellinae for the first time.     

Role of the N-terminal region of the a chain in β1-bungarotoxin from the venom ofBungarus multicinctus (Taiwan-banded krait)

The N-terminal α-amino groups of β₁-bungarotoxin (β₁-Bgt) fromBungarus multicinctus venom were modified with trinitrobenzene sulfonic acid and the modified derivative was separated by high performance liquid chromatography. The trinitrophenylated (TNP) derivative contained two TNP groups at the α-amino groups of A chain and B chain and showed a marked decrease in enzymatic activity. Methionine residues at positions 6 and 8 of the A chain were oxidized with chloramine T or cleaved with cyanogen bromide to remove the N-terminal octapeptide. Oxidation of methionine residues and removal of the N-terminal octapeptide caused a precipitous decrease in enzymatic activity, whereas antigenicity remained unchanged. The presence of dihexanoyllecithin influenced the interaction between β₁-Bgt and 8-antilinonaphthalene sulfonate (ANS) and revealed that β₁-Bgt consists of two types of ANS-binding sites, one at the substrate binding site of the A chain and the other might be at the B chain. The modified derivatives still retained their affinity for Ca²⁺ and ANS, indicating that the N-terminal region is not involved in Ca²⁺ and substrate binding. A fluorescence study revealed that the α-amino group of the A chain was in the vicinity of substrate binding site and that the TNP α-amino groups were in proximity to Trp-19 of the A chain. In addition, the study showed that the N-terminal region is important for stabilizing the architectural environment of Trp-19. The results, together with the proposal that Trp-19 of the A chain is involved in substrate binding, suggest that the N-terminal region of the A chain plays a crucial role in maintaining a functional active site for β₁-Bgt.     

Near-bottom performance of the Acoustic Doppler Velocimeter (ADV) – a comparative study

In a laboratory flume, a comparative study on the near-bottom performance of the Acoustic Doppler Velocimeter (ADV) was conducted. Two different ADV systems were tested for different configurations and two flow velocities (9 cm s⁻¹, 18 cm s⁻¹). The results were compared with synchronous measurements with a Laser Doppler Anemometer (LDA). Near-bottom velocity measurements with the ADV have to be interpreted carefully as the ADV technique underestimates flow velocities in a zone close to the sediment. The height of this zone above the sediment varies with different ADV systems and configurations. The values for nominal sampling volume height (SVH) given by the software often underestimate the true, effective sampling volume heights. Smaller nominal SVH improve the ADV near-bottom performance, but the vertical extent of the zone in which the ADV underestimates flow by more than 20% may be larger than true SVH/2 by a factor of 2 (=true SVH). When the measurement volume approaches the bottom, ADV data quality parameters (signal-to-noise-ratio (SNR) and signal amplitude) exceeding the average ‘open water’ level, are clear indicators that the ADV has begun to underestimate the flow velocity. Unfortunately, this is not a safe indicator for the range of reliable measurements as the ADV may begin to underestimate velocities even with unchanged ‘open water’ data quality parameters. Thus, one can only recommend avoiding measurements below a distance from the bottom that was defined empirically comparing the ADV and the LDA velocity profiles. This distance is 2.5 times nominal sampling volume height for the tested ADV systems and experimental settings.