A collocation approach to the numerical calculation of simple gradients in reaction-diffusion systems

Reaction diffusion equations are frequently used to model pattern formation problems in biology, but numerical experiments in two or three space dimensions can be expensive in computing time. We show that the spectral method with collocation is a particularly efficient method for the numerical study of the evolution of simple patterns in such models. In many cases of interest, the scheme is sufficiently simple and efficient for calculations to be carried out on a micro-computer.     

Structural homogeneity of mitochondrial DNA in the mitochondrial nucleoid of Physarum polycephalum

Mitochondrial DNA (mtDNA) of Physarum polycephalum was isolated gently by CsCl centrifugation. The mtDNA was linear with molecular weights ranging from 25·10⁶ to 45·10⁶ and heterogeneous in size. Nevertheless, thermal transition profiles of the mtDNA suggested that this DNA fraction was more homogeneous than nuclear DNA. Exhaustive digestions of this DNA with restriction endonucleases yielded unique fragments, and then the total of their molecular weights of each digest was around 45·10⁶. This value is equivalent to the maximum molecular weight estimated using electron microscopy and electrophoresis. Moreover, EcoRI digests of the mtDNA fractionated by the sucrose gradient showed unequimolar quantities of large fragments and a high background between bands. These results suggest that the mtDNA of Physarum has a homogeneous base sequence, and that the size heterogeneity of the mtDNA is attributable to degradation of the DNA under isolation procedures. The mtDNA was cleaved by EcoRI and XhoI to yield 16 and 7 fragments, respectively. A physical map of these fragments was constructed using the routine mapping procedures. The physical map showed that the mitochondrial genome of Physarum was linear with a molecular weight of 45·10⁶. We concluded therefore that the mitochondrial nucleoid is a structure in which the homogeneous mtDNA is highly amplified.     

The asymptotic behavior of solutions of the buffered bistable system

In this paper, we study a model for calcium buffering with bistable nonlinearity. We present some results on the stability of equilibrium states and show that there exists a threshold phenomenon in our model. In comparing with the model without buffers, we see that stationary buffers cannot destroy the asymptotic stability of the associated equilibrium states and the threshold phenomenon. Moreover, we also investigate the propagation property of solutions with initial data being a disturbance of one of the stable states which is confined to a half-line. We show that the more stable state will eventually dominate the whole dynamics and that the speed of this propagation (or invading process) is positive.     

Two domains of the epidermal growth factor receptor are involved in cytoskeletal interactions

Epidermal growth factor receptor can interact directly with F-actin through an actin-binding domain. In the present study, a mutant EGFR, lacking a previously identified actin-binding domain (ABD 1), was still able to bind elements of the cytoskeleton. A second EGFR actin-binding domain (ABD 2) was identified in the region of the receptor that includes Tyr-1148 by a yeast two-hybrid assay. GST fusion proteins comprising ABD 1 or ABD 2 bound actin in vitro and competed for actin-binding with the full-length EGFR. EGFR binding to actin was also studied in intact cells using fluorescence resonance energy transfer (FRET). The localization of the EGFR/actin-binding complex changed after EGF stimulation. Fusion proteins containing mutations in ABD1 or ABD2 did not display a FRET signal. The results lead to the conclusion that the interaction between ABD1 and ABD2 and actin during EGF-induced signal transduction, and thus between EGFR and actin, are important in cell activation.     

The yeast O-acyltransferase Gup1p interferes in lipid metabolism with direct consequences on the sphingolipid-sterol-ordered domains integrity/assembly

Saccharomyces cerevisiae Gup1p is a membrane-bound O-acyltransferase. Previous works involved GUP1 in a wide range of crucial processes for cell preservation and functioning. These include cytoskeleton polarization and secretory/endocytic pathway, GPI-anchor remodelling, wall composition and integrity, and membrane lipids, with a reduction in phospholipids and an increase in acylglycerols. DRM fractions were found in considerably lower amounts in gup1Δ than in wt strain. Additionally, the proteins presumably associated with lipid micro domains, Gas1p and Pma1p, were present in much smaller amounts in the mutant DRMs. Pma1p is also found in minor quantities in the whole cells extracts of the gup1Δ mutant. Accordingly, H⁺-ATPase activity was reduced in about 40%. Deletion of GUP1 resulted in higher sensibility to specific sphingolipid biosynthesis inhibitors and a notorious resistance to ergosterol biosynthesis inhibitors. Furthermore, the majority of mutant cells displayed an even (less punctuated) sterol distribution. The present work presents improvements to DRMs extraction methodology and filipin-sterol staining, provides evidence supporting that Gup1p is involved in lipid metabolism and shows the direct consequences of its absence on the plasma membrane sphingolipid-sterol-ordered domains integrity/assembly.     

Characterization of the functional domains of Escherichia coli RNase II

RNase II is a single-stranded-specific 3'-exoribonuclease that degrades RNA generating 5'-mononucleotides. This enzyme is the prototype of an ubiquitous family of enzymes that are crucial in RNA metabolism and share a similar domain organization. By sequence prediction, three different domains have been assigned to the Escherichia coli RNase II: two RNA-binding domains at each end of the protein (CSD and S1), and a central RNB catalytic domain. In this work we have performed a functional characterization of these domains in order to address their role in the activity of RNase II. We have constructed a large set of RNase II truncated proteins and compared them to the wild-type regarding their exoribonucleolytic activity and RNA-binding ability. The dissociation constants were determined using different single- or double-stranded substrates. The results obtained revealed that S1 is the most important domain in the establishment of stable RNA-protein complexes, and its elimination results in a drastic reduction on RNA-binding ability. In addition, we also demonstrate that the N-terminal CSD plays a very specific role in RNase II, preventing a tight binding of the enzyme to single-stranded poly(A) chains. Moreover, the biochemical results obtained with RNB mutant that lacks both putative RNA-binding domains, revealed the presence of an additional region involved in RNA binding. Such region, was identified by sequence analysis and secondary structure prediction as a third putative RNA-binding domain located at the N-terminal part of RNB catalytic domain.     

The use of suicide gene systems in vascular cells in vitro

To investigate the efficiency of suicide gene systems on vascular cells,HSV-tk/GCV and EC-CD/5-FC systems were established on vascular endothelial cells in vitro by retroviral transduction.Both modified cell lines were highly sensitive to prodrugs,the IC50 for GCV was less than 0.4 μM,and IC50 for 5-FC was less than 75μM,while the parental endothelial cells were insensitive even at the highest concentrations of prodrugs in this experiment.Mixed cellular assay showed that significant bystander effect was exhibited in modifed endothelial cells,when only 10% or 30% of the mixed cells were tk positive and exposed to 20μM GCV for 6 days.more than 60% or 90% of the wholoe polulation was killed.Similar result was also found in CD positve cells.These results indicated that both HSV-tk/GCV and EC-CD/5-FC systems could efficiently suppress endothelial cell growth in vitro.     

The location and the significance of a cross-link between the sarcin/ricin domain of ribosomal RNA and the elongation factor-G

During translocation peptidyl-tRNA moves from the A-site to the P-site and mRNA is displaced by three nucleotides in the 3' direction. This reaction is catalyzed by elongation factor-G (EF-G) and is associated with ribosome-dependent hydrolysis of GTP. The molecular basis of translocation is the most important unsolved problem with respect to ribosome function. A critical question, one that might provide a clue to the mechanism of translocation, is the precise identity of the contacts between EF-G and ribosome components. To make the identification, a covalent bond was formed, by ultraviolet irradiation, between EF-G and a sarcin/ricin domain (SRD) oligoribonucleotide containing 5-iodouridine. The cross-link was established, by mass spectroscopy and by Edman degradation, to be between a tryptophan at position 127 in the G domain in EF-G and either one of two 5-iodouridine nucleotides in the sequence UAG2655U in the SRD. G2655 is a critical identity element for the recognition of the factor's ribosomal binding site. The site of the cross-link provides the first direct evidence that the SRD is in close proximity to the EF-G catalytic center. The proximity suggests that the SRD RNA has a role in the activation of GTP hydrolysis that leads to a transition in the conformation of the factor and to its release from the ribosome.     

Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2

Several autoinflammatory diseases with distinct clinical manifestations have been associated with sequence variations in the gene products PYPAF1/CIAS1 and NOD2/CARD15. Both proteins belong to the PYD/CARD-containing family of apoptosis regulators and activators of pro-inflammatory caspases. To gain insight into the dysfunctional role of sequence alterations, we assembled a structure-based multiple sequence alignment of family members and related proteins. This allowed us to analyze the putative effect of the alterations on the function of nucleotide-binding (NACHT) and leucine-rich repeat (LRR) domains shared by the family members. In support of this analysis, we carefully selected template structures for the NACHT and LRR domains and mapped the genetic variations onto 3D domain models. Additionally, we propose a model of the NACHT and LRR domain complex. Our study revealed that many of the disease-associated sequence variants are located close to highly conserved sequence regions of functional relevance and are spatially adjacent in the predicted 3D structure. The implications on the domain functions such as NTP-hydrolysis or oligomerization are discussed.     

NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region

Group II chaperonins close their cavity with the help of conserved, helical extensions, the so-called protrusions, which emanate from the apical or substrate-binding domains. A comparison of previously solved crystal structures of the apical domains of the thermosome from Thermoplasma acidophilum showed structural plasticity in the protrusion parts induced by extensive packing interactions. In order to assess the influence of the crystal contacts we investigated both the alpha and beta-apical domains (alpha-ADT and beta-ADT) in solution by NMR spectroscopy. Secondary structure assignments and 15N backbone relaxation measurements showed mostly rigid structural elements in the globular parts of the domains, but revealed intrinsic structural disorder and partial helix fraying in the protrusion regions. On the other hand, a beta-turn-motif conserved in archaeal group II chaperonins might facilitate substrate recognition. Our results help us to specify the idea of the open, substrate-accepting state of the thermosome and may provide an additional jigsaw piece in understanding the mode of substrate binding of group II chaperonins.     

Different domains of C. elegans PAR-3 are required at different times in development

Polarity is a fundamental cellular feature that is critical for generating cell diversity and maintaining organ functions during development. In C. elegans, the one-cell embryo is polarized via asymmetric localization of the PAR proteins, which in turn are required to establish the future anterior-posterior axis of the embryo. PAR-3, a conserved PDZ domain-containing protein, acts with PAR-6 and PKC-3 (atypical protein kinase; aPKC) to regulate cell polarity and junction formation in a variety of cell types. To understand how PAR-3 localizes and functions during C. elegans development, we produced targeted mutations and deletions of conserved domains of PAR-3 and examined the localization and function of the GFP-tagged proteins in C. elegans embryos and larvae. We find that CR1, the PAR-3 self-oligomerization domain, is required for PAR-3 cortical distribution and function only during early embryogenesis and that PDZ2 is required for PAR-3 to accumulate stably at the cell periphery in early embryos and at the apical surface in pharyngeal and intestinal epithelial cells. We also show that phosphorylation at S863 by PKC-3 is not essential in early embryogenesis, but is important in later development. Surprisingly neither PDZ1 nor PDZ3 are essential for localization or function. Our results indicate that the different domains and phosphorylated forms of PAR-3 can have different roles during C. elegans development.     

Mechanistic similarities in docking of the FYVE and PX domains to phosphatidylinositol 3-phosphate containing membranes

Phosphatidylinositol 3-phosphate [PtdIns(3)P], a phospholipid produced by PI 3-kinases in early endosomes and multivesicular bodies, often serves as a marker of endosomal membranes. PtdIns(3)P recruits and activates effector proteins containing the FYVE or PX domain and therefore regulates a variety of biological processes including endo- and exocytosis, membrane trafficking, protein sorting, signal transduction and cytoskeletal rearrangement. Structures and PtdIns(3)P binding modes of several FYVE and PX domains have recently been characterized, unveiling the molecular basis underlying multiple cellular functions of these proteins. Here, structural and functional aspects and current mechanisms of the multivalent membrane anchoring by the FYVE and PX domains are reviewed and compared.     

Identification of Plasmodium berghei Oocyst Rupture Protein 2 (ORP2) domains involved in sporozoite egress from the oocyst

Sporozoites are the infective form of malaria parasites which are transmitted from the mosquito salivary glands to a new host in a mosquito blood meal. The sporozoites develop inside the sporogonic oocyst and it is crucial for the continuation of the life cycle that the oocyst ruptures to release sporozoites. We recently described two Plasmodium Oocyst Rupture Proteins (ORP1 and ORP2), localized at the oocyst capsule, that are each essential for rupture of the oocysts. Both ORPs contain a histone fold domain implicated in the mechanism of oocyst rupture, possibly through the formation of a heterodimer between the two histone fold domains. To gain an understanding of the function of the different regions of the ORP2 protein, we generated deletion mutants. We monitored oocyst formation and rupture as well as sporozoites in the salivary gland. Our results show that different regions of ORP2 play independent roles in sporozoite egress. Deleting the N-terminal histone fold domain of ORP2 blocked sporozoite egress from the oocyst. Progressive deletions from the C-terminal resulted in no or significantly impaired sporozoite egress.     

The role of individual amino acids in the dimerization of CR4 and ACR4 transmembrane domains

CRINKLY4 is a growth factor-like plant receptor kinase designated as CR4 in Zea mays and ACR4 in Arabidopsis. Using the TOXCAT system, a genetic assay that measures helix interactions in a natural membrane environment, we have previously demonstrated that the dimerization potential of the ACR4 transmembrane (TM) domain is significantly weaker than that of CR4 TM domain, even though 13 of the 24 residues are identical. Neither of the TM domains contain the GxxxG motif that has been shown to be important for the dimerization of the TM segments of several receptors. To further investigate the relationship between protein sequence and dimerization potential, we (a) mutated each of the 11 differing residues in the CR4 TM domain to the corresponding residue of ACR4 (b) made reciprocal mutations in ACR4 and (c) made hybrids consisting of half CR4 and half ACR4 TM domains. Our results suggest that most mutations in ACR4 or CR4 TM domains have low to moderate effects on the dimerization potential and that residues in the N-terminal half of the CR4 TM domain are important for dimerization.     

Modeling the Role of Diffusion Coefficients on Turing Instability in a Reaction-diffusion Prey-predator System

The paper is concerned with the effect of variable dispersal rates on Turing instability of a non-Lotka-Volterra reaction-diffusion system. In ecological applications, the dispersal rates of different species tends to oscillate in time. This oscillation is modeled by temporal variation in the diffusion coefficient with large as well as small periodicity. The case of large periodicity is analyzed using the theory of Floquet multipliers and that of the small periodicity by using Hill's equation. The effect of such variation on the resulting Turing space is studied. A comparative analysis of the Turing spaces with constant diffusivity and variable diffusivities is performed. Numerical simulations are carried out to support analytical findings.     

Ultrastructural investigations on the muscular systems in the barnacle, Tetraclita squamosa japonica

Four muscular systems of the Tetraclita squamosa barnacle were observed by means of an electron microscope and it was revealed that these systems each bore different types of muscle cells. The four systems were the adductor (A), the lateral scutal depressor (LSD), the ventral scutal depressor (VSD), and the tergal depressor (TD). The A-system included cross stiated muscle cells which showed long sarcomeres (about 10 μm) and rather disordered arrays of myofilaments. The LSD-system included cross striated muscles which had medium length sarcomeres (about 6.7 μm) and rather ordered myofilamental arrays. The VSD-system was constructed of cross striated muscle cells which bore shorter sarcomeres (4.6 μm) than the previous three systems and ordered myofilamental arrays. This last type of cell also bore well-developed sarcoplasmic reticular systems. The TD-system included smooth muscle cells which showed rather ordered arrays of myofilaments and dense-bodies. Each muscular system, as described above, included to its advantage one type of cross striated or smooth muscle cell for its characteristic contraction. The relations between ultrastructures and functions of each muscular system will now be discussed.     

The effects of circumferential pressure on the soleus muscle F-wave in healthy subjects

Circumferential pressure (CP) was shown to decrease muscle activity in subjects without neuromuscular disorders and in individuals with spinal cord injury and cerebrovascular accidents. The mechanism for this decrease is unknown although it is hypothesized to be spinal in origin. The purpose of this study was to investigate the effect CP has on the soleus F-wave. Results will help determine the mechanism CP uses to effect motoneuron reflex excitability. Thirty-seven healthy volunteers participated. A 16 cm air-splint was placed around the calf and during the pressure phase of the experiment it was inflated to 40–45 mm Hg. F-waves were evoked by supra maximally stimulating (20% > Mmax) the tibial nerve with a 0.1 ms pulse at 0.2 Hz using a bipolar surface electrode on the skin of the popliteal fossa. Fifty F-waves were recorded before (baseline), during, and 3) after CP was applied. F-waves were then identified and mean latency, persistence, and mean F/Mmax amplitude ratios were measured and calculated. Friedman Repeated Measures on Ranks tests were conducted on each of the three parameters (p ? 0.05). No statistically significant difference was found for any of the F-wave parameters evaluated. These results were contrary to previous CP studies that observed a significant decrease in muscle activity. Possible reasons for this discrepancy are discussed.     

马铃薯S病毒外壳蛋白基因的克隆与原核表达

依据马铃薯S病毒 (PotatovirusS ,PVS)外壳蛋白 (CP)基因序列 (885bp)设计合成了两对引物 ,通过RT PCR扩增得到长 0 .8kb的目的片段 ,将目的片段转入大肠杆菌 ,酶切鉴定证明得到了含有目的片段的重组子 ,测定序列结果与其他PVS分离物CP基因的序列比较 ,发现其核苷酸同源性达 95 %左右 ;构建了含PVSCP基因的融合蛋白原核表达载体 ,并在大肠杆菌中得到表达 ,SDS PAGE测定融合蛋白的分子量为 5 8kD。