Characterization of the inhibition mechanism of a tissuefactor inhibiting single-chain variable fragment: a combined computational approach

Journal of Molecular Modeling - In order to predict the impact sensitivity of high explosives, we designed and evaluated several models based on the trigger linkage hypothesis and the Arrhenius...     

Evolutionary stasis of a deep subsurface microbial lineage

Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found in geographically widespread deep subsurface locations. In order to constrain models for subsurface microbial evolution, we compared CDA genomes from Africa, North America and Eurasia using single cell genomics. Unexpectedly, 126 partial single amplified genomes from the three continents, a complete genome from of an isolate from Eurasia, and metagenome-assembled genomes from Africa and Eurasia shared >99.2% average nucleotide identity, low frequency of SNP’s, and near-perfectly conserved prophages and CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, and unusually strong purifying selection as likely explanations for these unexpected results. We therefore conclude that the analyzed CDA populations underwent only minimal evolution since their physical separation, potentially as far back as the breakup of Pangea between 165 and 55 Ma ago. High-fidelity DNA replication and repair mechanisms are the most plausible explanation for the highly conserved genome of CDA. CDA presents a stark contrast to the current model organisms in microbial evolutionary studies, which often develop adaptive traits over far shorter periods of time.Subject terms: Environmental microbiology, Molecular evolution, Bacterial genetics     

Response of the grapevine rootstock Richter 110 to inoculation with native and selected arbuscular mycorrhizal fungi and growth performance in a replant vineyard

Two indigenous arbuscular mycorrhizal (AM) fungi from the Mediterranean wine growing area in the Northeast of Spain were isolated and classified as Glomus intraradices Schenck & Smith. Both native fungi were found to increase the growth of the vine rootstock 110 Richter under greenhouse conditions compared with G. intraradices (BEG 72) and a phosphorus (P) fertilization treatment. The effectivity of field inoculation of Cabernet Sauvignon plants grafted on Richter 110 with the former native fungi and with G. intraradices BEG 72 in a replant vineyard severely infested by the root-rot fungus Armillaria mellea (Vahl ex Fr.) Kummer was assessed. The native fungi were not effective at enhancing plant development, and only G. intraradices BEG 72, resulted in a positive response. Field inoculation with this selected fungus increased plant shoot dry weight at the end of the first growing season.     

Hexavalent chromium bioreduction and chemical precipitation of sulphate as a treatment of site-specific fly ash leachates

Most of the power generation globally is by coal-fired power plants resulting in large stockpiles of fly ash. The trace elements associated with the ash particles are subjected to the leaching effects of precipitation which may lead to the subsequent contamination of surface and groundwater systems. In this study, we successfully demonstrate an efficient and sustainable dual treatment remediation strategy for the removal of high levels of Cr⁶⁺ and SO₄ ^2? introduced by fly ash leachate generated by a power station situation in Mpumalanga, South Africa. The treatment consisted of a primary fixed-bed bioreactor kept at a reduction potential for Cr⁶⁺ reduction. Metagenome sequencing clearly indicated a diverse bacterial community containing various bacteria, predominantly of the phylum Proteobacteria which includes numerous species known for their ability to detoxify metals such as Cr⁶⁺. This was followed by a secondary BaCO₃/dispersed alkaline substrate column for SO₄ ^2? removal. The combination of these two systems resulted in the removal of 99% Cr⁶⁺ and 90% SO₄ ^2?. This is the first effective demonstration of an integrated system combining a biological and chemical strategy for the remediation of multi-contaminants present in fly ash leachate in South Africa.     

Novel synthetic Bacillus thuringiensiscry1B gene and the cry1B-cry1Ab translational fusion confer resistance to southwestern corn borer, sugarcane borer and fall armyworm in transgenic tropical maize

In order to develop a resistance management strategy to control tropical pests based on the co-expression of different toxins, a fully modified Bacillus thuringiensis cry1B gene and the translational fusion cry1B-cry1Ab gene have been developed. Both constructs were cloned under the control of a maize ubiquitin-1 or a rice actin-1 promoter and linked to the bar gene driven by the CaMV 35S promoter. Immature embryos from the tropical lines CML72, CML216, and their hybrids, were used as the target for transformation by microprojectile bombardment. Twenty five percent of the transformed maize plants with cry1B expressed a protein that is active against southwestern corn borer and sugarcane borer. Ten percent of the transgenic maize expressed single fusion proteins from the translational fusion gene cry1B-1Ab and showed resistance to these two pests as well as to the fall armyworm. Transgenic maize plants that carried the cry1B gene in T1 to T3 progenies transmitted trangenes with expected Mendelian segregation and conferred resistance to the two target insects. Molecular analyses confirmed the cry genes integration, the copy number, the size of protein(s) expressed in maize plants, the transmission, and the inheritance of the introduced cry gene. These new transgenic products will provide another recourse for reducing the build-up of resistance in pest populations. Received: 25 September 2000 / Accepted: 15 December 2000     

Agronomical and physiological characterization of salinity tolerance in a commercial tomato hybrid

The salt tolerance of the commercial F1 tomato hybrid (Lycopersicon esculentum Mill) Radja (GC-793) has been agronomically and physiologically evaluated under greenhouse conditions, using a control (nutrient solution), a moderate (70 mM NaCl added to the nutrient solution) and a high salt level (140 mM NaCl), applied for 130 days. The results show that Radja is a Na⁺-excluder genotype, tolerant to moderate salinity. Fruit yield was reduced by 16% and 60% and the shoot biomass by 30% and more than 75% under moderate and high salinities, respectively. At 90 days of salt treatment (DST), the mature leaves feeding the 4th truss at fruiting accumulated little Na⁺ (178 mmol kg^-1 DW). At this time, the sucrose concentration in these leaves even increased with moderate salinity and the amino acid proline was not accumulated under salt conditions as compared to control. At 130 DST, Na⁺ was accumulated mainly by the roots in proportion to the salt level applied, while in leaves appreciable amounts were found only at high salinity (452 mmol kg^-1 DW). In the leaves, Cl^- was always accumulated in proportion to the salt level and in a very much greater amounts than Na⁺ (until 1640 mmol kg^-1 DW). The sucrose content was reduced in all plants by salinity, and was distributed preferentially toward the distal stem and peduncle of a truss at fruiting under moderate salinity, and toward the basal stem and root at high salinity. Moreover, proline was accumulated in different organs of the plant only at high salinity, coinciding with Na⁺ accumulation in leaves. Attempts are made to find a clear relationship between physiological behaviour triggered by stress and the agronomical behaviour, in order to assess the validity of physiological traits used for salt-tolerance selection and breeding in tomato.     

Effect of aromatic plant species on vesicular-arbuscular mycorrhizal establishment in Pistacia terebinthus

The inoculation of Pistacia terebinthus with vesicular-arbuscular mycorrhizal (VAM) fungi and the spread of the infection were studied using a mixed cropping system, under glasshouse conditions, with Salvia officinalis, Lavandula officinalis and Thymus vulgaris colonized by Glomus mosseae as an inoculation method. This method was compared with soil inoculum placed under the seed or distributed evenly in the soil. Indirect inoculation with all the aromatic plants tested significantly increased VAM root colonization of P. terebinthus compared with the use of soil inoculum, although the effect on plant growth was different for each one of the aromatic species used as inoculum source. Inoculation with L. officinalis and T. vulgaris were the best treatments resulting in high VAM colonization and growth enhancement of P. terebinthus.     

Constitutive monocyte-restricted activity of NF-M, a nuclear factor that binds to a C/EBP motif.

In a search for monocyte-specific nuclear factors, we analyzed in human cells the promoter of the chicken myelomonocytic growth factor, a gene that, in the chicken, is expressed in myeloid and myelomonocytic cells. Reporter gene constructs were active in monocytic Mono Mac 6 cells and in monoblastic THP-1 cells but not in the hematopoietic stem cell line K562. When a region with homology to the sequence recognized by CAAT enhancer-binding proteins (C/EBP) was inactivated by site-directed mutagenesis, the reporter activity was reduced by a factor of 10. Multimers of this region, termed F, in front of a heterologous promoter were active in Mono Mac 6 and THP-1 cells but not in K562 cells, WIL2 B cells, BT20 mammary carcinoma cells, MelJuso melanoma cells, or SK-Hep-1 hepatoma cells. Gel shift analysis with the F oligonucleotide identified DNA-binding activity in monocytic Mono Mac 6, monoblastic THP-1, and myelomonocytic HL60 cells. No binding was detected in myelomonocytic RC2A cells, in myeloid KG-1 cells, or in the hematopoietic stem cell line K562. Furthermore, a panel of solid tumor cell lines, representing various tissues, were also negative. Stimulation by PMA could not induce this binding factor in any of the negative cell lines. Analysis of primary cells (granulocytes, T cells, monocytes, and alveolar macrophages) revealed binding activity only in monocytes and macrophages. This DNA-binding factor, termed NF-M, was found to consist of two molecules, of 50 and 72 kDa, as determined by affinity cross-linking. Binding of NF-M was competed by the region F oligonucleotide and by the C/EBP motif from the albumin enhancer but not by an AP-2 motif. These data suggest that NF-M is a member of the C/EBP family of nuclear factors. The monocyte-restricted activity of NF-M suggests that this nuclear factor may be involved in regulation of monocyte-specific genes.     

Molecular cloning of the chicken myelomonocytic growth factor (cMGF) reveals relationship to interleukin 6 and granulocyte colony stimulating factor.

Normal as well as retrovirally transformed avian myeloid precursor cells require the colony stimulating factor cMGF for their survival, proliferation and colony formation in vitro. cMGF has been shown to be a glycoprotein which is active in the picomolar concentration range. Co-expression of kinase type oncogenes in v-myb or v-myc transformed myeloid cells induces cMGF expression and confers factor independence via an autocrine mechanism. Here we describe the molecular cloning of cMGF from a myeloblast cDNA library and show that it is a 201 amino acid residue secretory protein which is modified by signal peptide cleavage and glycosylation during translocation into the lumen of membrane vesicles. A bacterially expressed trpE-cMGF fusion protein induces proliferation of E26 transformed myeloblasts in a cMGF bioassay suggesting that glycosylation is not absolutely necessary for biological activity. Sequence comparison reveals that cMGF is distantly related to G-CSF and IL-6.     

Loss of Breathing Modulation of Heart Rate Variability in Patients with Recent and Long Standing Diabetes Mellitus Type II

Healthy subjects under rhythmic breathing have heart interbeat intervals with a respiratory band in the frequency domain that can be an index of vagal activity. Diabetes Mellitus Type II (DM) affects the autonomic nervous system of patients, thus it can be expected changes on the vagal activity. Here, the influence of DM on the breathing modulation of the heart rate is evaluated by analyzing in the frequency domain heart interbeat interval (IBI) records obtained from 30 recently diagnosed, 15 long standing DM patients, and 30 control subjects during standardized clinical tests of controlled breathing at 0.1 Hz, supine rest and standing upright. Fourier spectral analysis of IBI records quantifies heart rate variability in different regions: low-frequencies (LF, 0.04–0.15 Hz), high-frequencies (HF, 0.15–0.4 Hz), and a controlled breathing peak (RP, centered around 0.1 Hz). Two new parameters are introduced: the frequency radius r_f (square root of the sum of LF and HF squared) and β (power of RP divided by the sum of LF and HF). As diabetes evolves, the controlled breathing peak loses power and shifts to smaller frequencies, indicating that heart rate modulation is slower in diabetic patients than in controls. In contrast to the traditional parameters LF, HF and LF/HF, which do not show significant differences between the three populations in neither of the clinical tests, the new parameters r_f and β, distinguish between control and diabetic subjects in the case of controlled breathing. Sympathetic activity that is driven by the baroreceptor reflex associated with the 0.1 Hz breathing modulations is affected in DM patients. Diabetes produces not only a rigid heartbeat with less autonomic induced variability (r_f diminishes), but also alters the coupling between breathing and heart rate (reduced β), due to a progressive decline of vagal and sympathetic activity.