Dynamics of finite populations

Summary A time-homogeneous stochastic process was used to derive exact expressions for the ultimate probability of fixation or loss and the expected time to fixation or loss of an allele in a haploid population whose size is a Poisson random variable. The treatment included selection and multiple alleles.Contribution no. 165 Department of Statistics, Kansas Agricultural Experiment Station, Manhattan, Kansas 66502.     

NMR-assisted protein structure prediction with MELDxMD

We describe the performance of MELD-accelerated molecular dynamics (MELDxMD) in determining protein structures in the NMR-data-assisted category in CASP13. Seeded from web server predictions, MELDxMD was found best in the NMR category, over 17 targets, outperforming the next-best groups by a factor of ~4 in z-score. MELDxMD gives ensembles, not single structures; succeeds on a 326-mer, near the current upper limit for NMR structures; and predicts structures that match experimental residual dipolar couplings even though the only NMR-derived data used in the simulations was NOE-based ambiguous atom–atom contacts and backbone dihedrals. MELD can use noisy and ambiguous experimental information to reduce the MD search space. We believe MELDxMD is a promising method for determining protein structures from NMR data.     

Luxol Fast Blue Combined With the Periodic Acid-Schiff Procedure for Cytological Staining of Kidney

Rat kidneys fixed in Regaud's fluid were stained by luxol fast blue (LFB), by the periodic acid-Schiff (PAS) method, and by LFB combined with PAS. When used separately the PAS stains the brush border, hyaline droplets and basement membranes reddish, the LFB stains the mitochondria, hyaline bodies and basement membranes greenish-blue. The combined LFB-PAS method stains the brush border reddish and the mitochondria dark blue, while the hyaline bodies and basement membranes are purplish colored. The LFB-PAS method provides color contrasts which show cytological features that are particularly significant in the kidney.     

Luminescence properties of neodymium,samarium, and europium niobate and tantalate thin films

Thin films of lanthanide orthoniobate LnNbO₄ (LnNO) and orthotantalate LnTaO₄ (LnTO), (Ln = Nd, Sm, Eu) were fabricated using the sol–gel method with subsequent spin-coating on the PbZrO₃/Al₂O₃ substrate and annealing at 1000°C. X-ray diffraction patterns showed monoclinic M-LnNbO₄ or M´-LnTaO₄, which coexists with the orthorhombic or tetragonal phase. X-ray photoelectron spectroscopy demonstrated the presence of Nd³⁺, Sm³⁺/Sm²⁺ and Eu³⁺/Eu²⁺ ions. The luminescence properties of polymorphic films were investigated. Excitation spectra of PbZrO₃ interlayer represented broad bands at 410 and 550 nm that were assigned to charge transfer bands (CTB). In all films, the CTB broad band at ~275 nm related to charge transfer transition of Ln³⁺→O²⁻ and NbO₄³⁻ or TaO₄³⁻ groups. In excitation spectra, ⁴I_9/2→⁴G_5/2 (Nd³⁺), ⁶H_5/2→⁶P_3/2 (Sm³⁺) and ⁷F₀→⁵L₆ (Eu³⁺) transitions (at 585, 402 and 395 nm), respectively were found to be more intense than any other Ln³⁺ transition. The emission spectra showed narrow and intense bands at 1065, 600, and 614 nm that were ascribed to Nd³⁺, Sm³⁺, and Eu³⁺ 4f–f intraconfigurational transitions ⁴F_3/2→⁴I_11/2, ⁴G_5/2→⁶H_7/2, and ⁵D₀→⁷F₂, respectively. The excellent luminescence properties of films make them new potential groups for visible and/or near-infrared applications such as sensors and imaging equipment.     

responses of fungi to tropane alkaloids produced by a medicinal plant <Emphasis Type="Italic">Hyoscyamus muticus</Emphasis> (Egyptian Henbane)

Antifungal activity of hyoscyamine (Hcy) and scopolamine (Sco) were determined by TLC-bioautography against fungi associated with H. muticus grown in Egypt, and those isolated from other plants grown in Japan. All 40 fungal strains were tolerant to Sco and sensitive to Hcy, exhibiting a growth inhibition zone around the Hcy spot on the bioautography plate. The strains were grouped into three types based on the appearance of the inhibition zone: (i) 17 strains exhibiting a clear inhibition zone, which remained clear at 8 d after incubation (type I); (ii) 22 strains exhibiting the inhibition zone with a brown circle surrounding the zone and regrowth within the inhibition zone (type II); (iii) 1 strain exhibiting the inhibition zone with no brown circle and regrowth within the inhibition zone (type III). In the type II and III strains, Hcy disappeared, and other alkaloids were found in the inhibition zones in its place. Hcy feeding experiments using Penicillium purpurogenum (type II) and Cunninghamella elegans (type III) revealed that these fungi may convert Hcy to a new alkaloid compound.     

Plant growth promotion and biological control of Pythium aphanidermatum, a pathogen of cucumber, by endophytic actinomycetes

Aims:  To evaluate the potential of Actinoplanes campanulatus , Micromonospora chalcea and Streptomyces spiralis endophytic in cucumber roots, to promote plant growth and to protect seedlings and mature plants of cucumber from diseases caused by Pythium aphanidermatum , under greenhouse conditions.
Methods and Results:  Three endophytic isolates, out of 29, were selected through tests aimed at understanding their mechanisms of action as biocontrol agents and plant growth promoters. When applied individually or in combination, they significantly promoted plant growth and reduced damping-off and crown and root rot of cucumber. The combination of the three isolates resulted in significantly better suppression of diseases and plant growth promotion, than where the plants were exposed to individual strains.
Conclusions:  The three selected actinomycete isolates colonized cucumber roots endophytically for 8 weeks, promoted plant growth and suppressed pathogenic activities of P. aphanidermatum on seedling and mature cucumber plants.
Significance and Impact of the Study:  The results clearly show that the endophytic, glucanase-producing actinomycetes used, especially as a combined treatment, could replace metalaxyl, which is the currently recommended fungicide for Pythium diseases in the United Arab Emirates. These endophytic isolates also have the potential to perform as plant growth promoters, which is a useful attribute for crop production in nutrient impoverished soils.     

Structure of a transient intermediate for GTP hydrolysis by ras

The flexibility of the conserved 57DTAGQ61 motif is essential for Ras proper cycling in response to growth factors. Here, we increase the flexibility of the 57DTAGQ61 motif by mutating Gln61 to Gly. The crystal structure of the RasQ61G mutant reveals a new conformation of switch 2 that bears remarkable structural homology to an intermediate for GTP hydrolysis revealed by targeted molecular dynamics simulations. The mutation increased retention of GTP and inhibited Ras binding to the catalytic site, but not to the distal site of Sos. Most importantly, the thermodynamics of RafRBD binding to Ras are altered even though the structure of switch 1 is not affected by the mutation. Our results suggest that interplay and transmission of structural information between the switch regions are important factors for Ras function. They propose that initiation of GTP hydrolysis sets off the separation of the Ras/effector complex even before the GDP conformation is reached.     

The Cutting Balloon--a new technology?

The Cutting Balloon consists of a standard balloon dilatation catheter with four microtome-sharp blades that incise the plaque and minimize arterial wall trauma. It was used in 31 patients; nine had calcified arteries, ten had non-compliant lesions, three had in-stent restenosis and nine had aorto-ostial lesions. Seventeen lesions were predilated, 28 were post-dilated and 18 required stent implantation. The procedure was very effective in aorto-ostial lesions, non-compliant lesions that were not responsive to high-pressure balloon dilatation, and was partially successful in calcified arteries. It has a very specific niche in selected lesions.