An Empirical Potential Study of the Interaction of L—;Lysine—;L—;Alanine—;L—;Alanine Tripeptide with Four models of B—;DNA with different Compositions

Abstract

The empirical potential including the intra- and intermolecular energy terms was used to study the interaction of L-Lysine-L-Alanine-L-Alanine Tripeptide with four models of B-DNA with different compositions. On the basis of a detailed search of the respective potential energy surface, it was found that the peptide is preferentially bounded to the AT-rich sequences. Analysis of the different energy contributions indicated that the electrostatic term is responsible for this preference. The results agree with the experimental data on the selectivity of some DNA—binding proteins and polypeptides to AT—;rich DNA.     

Anaerobic microbial dehalogenation of organohalides — state of the art and remediation strategies

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Mechanisms of mechanosensing — mechanosensitive channels,function and re-engineering

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Structure peculiarities of cell walls of <Emphasis Type="Italic">Acremonium chrysogenum</Emphasis>—an autotroph of cephalosporin C

Alterations of cell walls of Acremonium chrysogenum occurring at intensive synthesis of cephalosporin C has been studied. It is shown, using electron microscopy, that the cell wall of the cells of ATCC 11550 strain (“wild” type) became looser and thicker during growth. The cell wall of the cells of strain 26/8 (hyperautotroph of cephalosporin C) considerably degraded by the end of the stationary phase. Biochemical analysis has shown that these alterations entailed decrease of the proteins’ content covalently or noncovalently linked with the polysaccharides of cell walls of both strains. An increase of sensitivity of cell walls of the strain-hyperautotroph to an activity of lytic enzymes of chitinase, laminarinase, proteinase K, and lyticase preparation has been observed during the growth, but this increase has not been found in the case of “wild” type strain. The obtained results evidence to the structure failure of the cell wall of A. chrysogenum entailing the intensive creation of antibiotic.     

Anesthetic effects of a three-drugs mixture —comparison of administrative routes and antagonistic effects of atipamezole in mice—

The anesthetic mixture of medetomidine (MED), midazolam (MID) and butorphanol (BUT) produced anesthetic duration of around 40 minutes (min) in ICR mice. We reported that this anesthetic mixture produced almost the same anesthetic effects in both male and female BALB/c and C57BL/6J strains. Intraperitoneal (IP) administration of drugs has been widely used in mice. However, various injectable routes of the anesthetic mixture may cause different anesthetic effects. First, we examined effects of the anesthetic mixture by subcutaneous (SC) and intravenous (IV) injection compared to IP injection. After injection of the anesthetic mixture, administration of atipamezole (ATI) induced mice recovery from anesthesia. Secondly, we examined how different dosage and optimum injection timing of ATI affected mice recovery from anesthesia. We used an anesthetic score to measure anesthetic duration and a pulse oximeter to monitor vital signs under anesthesia. Usually, drugs from SC injection work more weakly than IP or IV injection. However, we found no significant differences of anesthetic duration among the three different injection routes. Antagonistic effects of ATI (0.3 mg/kg and 1.5 mg/kg) worked equally when administered at 30 min after injection of the anesthetic mixture. Antagonistic effects of ATI (1.5 mg/kg) were stronger than ATI (0.3 mg/kg) at 10 min after injection of the anesthetic mixture. The anesthetic mixture is a useful drug to induce nearly the same anesthetic effects by different injection routes and has an antagonist of ATI which helps mice quickly recover from anesthesia. These results may contribute to the welfare of laboratory animals.     

Effects of <Superscript>60</Superscript>Co gamma radiation dose on initial structural biomechanical properties of ovine bone—patellar tendon—bone allografts

Gamma radiation is established as a procedure for inactivating bacteria, fungal spores and viruses. Sterilization of soft tissue allografts with high dose ⁶⁰Co gamma radiation has been shown to have adverse effects on allograft biomechanical properties. In the current study, bone-patellar tendon-bone (BPTB) allografts from 32 mature sheep were divided into two treatment groups: low-dose radiation at 15 kGy (n = 16) and high-dose radiation at 25 kGy (n = 16) with the contralateral limb serving as a 0 kGy (n = 32) non-irradiated control. Half of the tendons from all treatment groups were biomechanically tested to determine bulk BPTB mechanical properties, cancellous bone compressive properties, and interference screw pull-out strength. The remaining tissues were prepared, implanted, and mechanically tested in an acute in vitro anterior crucial ligament (ACL) reconstruction. Low-dose radiation did not adversely affect mechanical properties of the tendon allograft, bone, or ACL reconstruction compared to internal non-irradiated control. However, high-dose radiation compromised bulk tendon load at failure and ultimate strength by 26.9 and 28.9%, respectively (P < 0.05), but demonstrated no negative effect on the cancellous bone compressive properties or interference screw pull-out strength. Our findings suggest that low dose radiation (15 kGy) does not compromise the mechanical integrity of the allograft tissue, yet high dose radiation (25 kGy) significantly alters the biomechanical integrity of the soft tissue constituent.     

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background

Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.

Methodology/Principal Findings

The T. rangeli haploid genome is ∼24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heat-shock proteins.

Conclusions/Significance

Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets.     

Localisation of <Emphasis Type="Italic">Arabidopsis</Emphasis> NDPK2—revisited

Phytochromes are light responsive photoreceptors in plants that influence development and differentiation during the entire plant life cycle. Plant nucleoside diphosphate kinase 2 (NDPK2) has been reported to be a component of the light-mediated signalling cascade and to interact physically with phytochrome A in the cytosol. By using diverse methods as in vitro imports, in vivo localisation of GFP-fusion proteins and immuno blotting of plant cell fractions we clearly localise NDPK2 only to chloroplasts but not to the cytosol, demonstrating that although high affinity protein–protein interactions can occur in vitro, their physiological relevance can be artificial if the proteins are localised to different cell compartments in vivo.     

Presence of Ornithine in the Urate-binding α<Subscript>1</Subscript>—<Subscript>2</Subscript>Globulin

THE urate-binding α₁–α₂ globulin has been isolated from human plasma in a highly purified state¹. The protein was purified by DEAE-‘Sephadex’, ammonium sulphate precipitation and semi-preparative Polyacrylamide gel electrophoresis. The urate-binding α₁–α₂ globulin is a rod-shaped glycoprotein, containing 12.1% carbohydrate, with an isoelectric point of 4.6 and a molecular weight of 67,000 ± 4,000. Amino-acid analysis indicated an unknown basic compound which appeared as an extra peak just in front of lysine¹. To identify this compound, high voltage paper electrophoresis has been carried out on a plate electrophoresis apparatus in pyridine-acetate buffer pH 3.5. A spot separated out corresponding to ornithine. Amino-acid analysis on a BC-200 automatic analyser (Bio-Cal Instruments Co., West Germany), with a 54 cm column at 55° C and with 0.35 M sodium citrate buffer, pH 5.28, as elution buffer at a flow-rate of 150 ml./h, showed that ornithine was present. The presence of ornithine in the protein hydrolysate was also verified by gas chromatography/mass spectrometry².     

Towards metagenome-scale models for industrial applications — the case of Lactic Acid Bacteria

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Highlights► Genome-scale metabolic modelling is being increasingly applied in LAB research. ► Novel techniques that broaden applicability of models remain to be applied to LAB. ► Additional constraints allow better predictions of genome-scale metabolic models. ► Novel approaches to move from modelling monocultures to mixed cultures are being developed. ► The feasibility of metagenome-based modelling approaches is being appreciated.     

Dynamic metabolic flux analysis — tools for probing transient states of metabolic networks

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Somewhat in control — the role of transcription in regulating microbial metabolic fluxes

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Micropropagation of <Emphasis Type="Italic">Leptadenia reticulata</Emphasis>—A medicinal plant

Summary Leptadenia reticulata (Retz.) Wight. & Arn., an important herbal medicinal plant, belongs to the family Asclepiadaceae. This plant has been known for its medicinal uses since 4500 BC. Presently this is an endangered species. There is a need for applying non-conventional methods of propagation for conservation and sustainable utilization of biodiversity of Leptadenia reticulata. We developed a micropropagation method for mass multiplication of L. reticulata. Explants harvested from greenhouse-maintained and field-grown plants were used to establish cultures of L. reticulata. The nodal shoot segments were surface-sterilized and cultured on Murashige and Skoog (MS) medium along with additives (25 mg l⁻¹ each of adenine sulfate, arginine, and citric acid, and 50 mg l⁻¹ ascorbic acid) containing 0.6 μM indole-3-acetic acid (IAA) and 9 μM N⁶-benzyladenine (BA). Three to four shoots differentiated from each node within 25–30 d at 26±2°C and 36 μmol m⁻² s⁻¹ spectral flux photon (SFP) for 12 hd⁻¹. Shoots were further multiplied by (1) repeated transfer of mother explant on fresh medium containing 0.6 μM IAA and 2.2 μM BA, and (2) subculture of in vitro-differentiated shoots on MS medium with 6.6 μM BA and 0.6 μM IAA. After three or four subcultures, the basal clump with shoot bases was divided into three or four subclumps and multiplied on the fresh medium. From each clump 15–20 shoots regenerated within 25 d. Ninety percent of the in vitro-produced shoots rooted ex vitro if these were pulse-treated with 123 μM each of indole-3-butyric acid and β-naphthoxyacefic acid. The plantlets were transferred to bottles containing sterile ‘soilrite’ (soilless compost and soil conditioner) moistened with half-strength MS macrosalts. Ninety-five percent of the plantlets were hardened in the bottles within 15 d. The hardened plants were then transferred to black polybags in the nursery. Field transferred plants are growing normally and have flowered. The protocol developed is reproducible. From a single nodal segment about 1700 hardened plants could be regenerated within 174 d.     

<Emphasis Type="Italic">Candida</Emphasis> — Agent of the diaper dermatitis?

Occurrence of Candida spp. was determined in a population of 60 infants, 1-15-month-old, with diaper dermatitis, admitted to a neonatal intensive care unit in Hospital Saca (Kosice, Slovakia). Specimens were obtained from the perianal, pubic, inguinal, or gluteal areas that showed signs of secondary infection as manifested by erythema, oozing, vesiculopustular lesions, and pus formation. The most frequently isolated species was C. albicans (41), followed by C. parapsilosis (8), C. tropicalis (4), C. pulcherrima (4), C. guilliermondii (2), and C. zeylanoides (1). Other organisms present in the mixed culture from the diaper area were Staphylococcus aureus (6), Escherichia coli (3), and 2 strains of each group B and D streptococci, and Proteus mirabilis. Infants diapered exclusively in disposable diapers showed less rash than those diapered exclusively or sometimes in cloth diapers.     

CO<Subscript>2</Subscript> Sensitivity of Voltage Gating and Gating Polarity of GapJunction Channels—Connexin40 and its COOH-Terminus-Truncated Mutant

The CO₂ sensitivity of transjunctional voltage (V _j) gating was studied by dual voltage clamp in oocytes expressing mouse Cx40 or its COOH terminus (CT)-truncated mutant (Cx40-TR). V _j sensitivity, determined by a standard V _j protocol (20 mV V _j steps, 120 mV maximal), decreased significantly with exposure to 30% CO₂. The Boltzmann values of control versus CO₂-treated oocytes were: V ₀ = 36.3 and 48.7 mV, n = 5.4 and 3.7, and G _{j min} = 0.21 and 0.31, respectively. CO₂ also affected the kinetics of V _j-dependent inactivation of junctional current (I _j); the time constants of two-term exponential I _j decay, measured at V _j = 60 mV, increased significantly with CO₂ application. Similar results were obtained with Cx40-TR, suggesting that CT does not play a role in this phenomenon. The sensitivity of Cx40 channels to 100% CO₂ was also unaffected by CT truncation. There is evidence that CO₂ decreases the V _j sensitivity of Cx26, Cx50 and Cx37 as well, whereas it increases that of Cx45 and Cx32 channels. Since Cx40, Cx26, Cx50 and Cx37 gate at the positive side of V _j, whereas Cx45 and Cx32 gate at negative V _j, it is likely that V _j behavior with respect to CO₂-induced acidification varies depending on gating polarity, possibly involving the function of the postulated V _j sensor (NH₂-terminus).This revised version was published online in June 2005 with a corrected cover date.     

Who's In and Who's Out—Compositional Control of Biomolecular Condensates

Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid–liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.     

Effect of culture conditions on growth of green alga — <Emphasis Type="Italic">Haematococcus pluvialis</Emphasis> and astaxanthin production

Influence of culture conditions such as light, temperature and C/N ratio was studied on growth of Haematococcus pluvialis and astaxanthin production. Light had significant effect on astaxanthin production and it varied with its intensity and direction of illumination and effective culture ratio (ECR, volume of culture medium/volume of flask). A 6-fold increase in astaxanthin production (37 mg/L) was achieved with 5.1468·10⁷ erg·m⁻²·s⁻¹ light intensity (high light, HL) at effective culture ratio of 0.13 compared to that at 0.52 ECR, while the difference in the astaxanthin production was less than 2 — fold between the effective culture ratios at 1.6175·10⁷ erg·m⁻²·s⁻¹ light intensity (low light, LL). Multidirectional (three-directional) light illumination considerably enhanced the astaxanthin production (4-fold) compared to unidirectional illumination. Cell count was high at low temperature (25 °C) while astaxanthin content was high at 35 °C in both autotrophic and heterotrophic media. In a heterotrophic medium at low C/N ratio H. pluvialis growth was higher with prolonged vegetative phase, while high C/N ratio favoured early encystment and higher astaxanthin formation.