3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information‐rich hydropathic interaction environments described by maps

Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low‐resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (π–π stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone‐dependent (?, ψ) bins, a map similarity metric based on the correlation coefficient was applied to each map‐map pair to build matrices suitable for clustering with k‐means. The first bin (?200° ≤ ? < –155°; ?205° ≤ ψ < –160°), representing 631 tyrosines, reduced to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single χ₁/χ₂ rotamer. The last environment has weak or no interactions with the tyrosine ring and its χ₁/χ₂ rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. Proteins 2015; 83:1118–1136. © 2015 Wiley Periodicals, Inc.     

Nuclear targeted silver nanospheres perturb the cancer cell cycle differently than those of nanogold

Plasmonic nanoparticle research has become increasingly active due to potential uses in biomedical applications. However, little is known about the intracellular effects these nanoparticles have on mammalian cells. The aim of this work is to investigate whether silver nanoparticles (AgNPs) conjugated with nuclear and cytoplasmic targeting peptides exhibit the same intracellular effects on cancer cells as peptide-conjugated gold nanoparticles (AuNPs). Nuclear and cytoplasmic targeting spherical AgNPs with a diameter of 35 nm were incubated in a cancer (HSC-3) and healthy (HaCat) cell line. By utilizing flow cytometry, confocal microscopy, and real-time dark field imaging, we were able to analyze how targeting AgNPs affect the cell cycle and cell division. These experiments demonstrated that nuclear-targeting AgNPs cause DNA double-strand breaks and a subsequent increase in the sub G1 (apoptotic) population in our cancer cell model at much lower concentrations than previously reported for nuclear targeting AuNPs. Unlike the M phase accumulation seen in cancer cells treated with AuNPs, an accumulation in the G2 phase of the cell cycle was observed in both cell models when treated with AgNPs. Additionally, real-time dark field imaging showed that cancer cells treated with nuclear targeting AgNPs did not undergo cell division and ultimately underwent programmed cell death. A possible explanation of the observed results is discussed in terms of the chemical properties of the nanoparticles.     

Hormonal, follicular and endometrial dynamics in letrozole-treated versus natural cycles in patients undergoing controlled ovarian stimulation

Background

To investigate the effect of pelvic floor Neuromuscular Electrical Stimulation (NMES) Therapy in improving endometrial thickness in women with thin endometrium.

Methods

41 patients undergoing assisted reproduction with a thin endometrium (less than or equal to7 mm) were recruited and advised to go for a pelvic floor NMES in frozen-thawed embryo transfer cycle. PHENIX Neuromuscular Electrical Stimulation Therapy System was used according to the manufacturer's recommended protocol for 20 to 30 minutes of intermittent vaginal electrical stimulation on the treatment days.

Results

A total of 20 and 21 were included in the NMES and non-NMES groups respectively. 12 out of 20 (60%) patients developed endometrial thickness equal to or more than 8 mm after the NMES therapy, which was the primary outcome. The mean thickness of endometrium before and after was respectively 5.60 mm (0.82 mm) and 7.93 mm (1.42 mm) in the therapy group versus 5.50 mm (1.00) and 6.78 mm (0.47) in the control group; the difference was statistically significant (P = 0.002). There was higher pregnancy rate in the NMES group (42% versus 35%) but the difference was not statistically significant.

Conclusion

Neuromuscular Electrical stimulation therapy may be effective for the patients with a thin endometrium. Further studies are needed to investigate its effectiveness.     

Lead phytotoxicity on wheat (Triticum aestivum L.) seed germination and seedlings growth

Lead (Pb) is an environmental pollutant extremely toxic to plants and other living organisms including humans. To assess Pb phytotoxicity, experiments focusing on germination of wheat seeds were germinated in a solution containing Pb (NO(3))(2) (0.05; 0.1; 0.5; 1g/L) during 6 days. Lead accumulation in seedlings was positively correlated with the external concentrations, and negatively correlated with morphological parameters of plant growth. Lead increased lipid peroxidation, enhanced soluble protein concentrations and induced a significant accumulation of proline in roots. Esterase activity was enhanced in the presence of lead, whereas α-amylase activity was significantly inhibited. Antioxidant enzymes activities, such as, ascorbate peroxidase, peroxidase, superoxide dismutase, catalase and glutathione S-transferase were generally significantly increased in the presence of lead in a dose-dependent manner. The present results thus provide a model system to screen for natural compounds able to counteract the deleterious effects of lead.     

Accuracy and reproducibility of voxel based superimposition of cone beam computed tomography models on the anterior cranial base and the zygomatic arches

Superimposition of serial Cone Beam Computed Tomography (CBCT) scans has become a valuable tool for three dimensional (3D) assessment of treatment effects and stability. Voxel based image registration is a newly developed semi-automated technique for superimposition and comparison of two CBCT scans. The accuracy and reproducibility of CBCT superimposition on the anterior cranial base or the zygomatic arches using voxel based image registration was tested in this study. 16 pairs of 3D CBCT models were constructed from pre and post treatment CBCT scans of 16 adult dysgnathic patients. Each pair was registered on the anterior cranial base three times and on the left zygomatic arch twice. Following each superimposition, the mean absolute distances between the 2 models were calculated at 4 regions: anterior cranial base, forehead, left and right zygomatic arches. The mean distances between the models ranged from 0.2 to 0.37 mm (SD 0.08-0.16) for the anterior cranial base registration and from 0.2 to 0.45 mm (SD 0.09-0.27) for the zygomatic arch registration. The mean differences between the two registration zones ranged between 0.12 to 0.19 mm at the 4 regions. Voxel based image registration on both zones could be considered as an accurate and a reproducible method for CBCT superimposition. The left zygomatic arch could be used as a stable structure for the superimposition of smaller field of view CBCT scans where the anterior cranial base is not visible.     

Fungal populations and mycotoxins in silage in Assiut and Sohag governorates in Egypt,with a special reference to characteristic Aspergilli toxins

Forty silage samples were collected from Assiut and Sohag governorates in Egypt to measure the presence of fungal population in silage. Forty-three species and 2 species varieties belonging to 17 genera were isolated using glucose Czapeks and Sabourauds dextrose agar media at 28 ^°C. The most prevalent genera were Aspergillus (57.5 and 100 of the samples), Penicillium (100 and 55%) on the two mentioned media, respectively. Also, Fusarium oxysporum and Gibberella fujikurori were recovered in moderate incidences. Mycotoxin profiles were also determined in these samples: Aflatoxins showed the highest incidence rates of occurrence, it occurred in 22.5% of all samples analyzed. Other mycotoxins were detected from all samples (T₂ toxins and sterigmatocystin at incidence of 7.5 and 5%, respectively). The screening of the characteristics mycotoxins of different isolates of Aspergillus isolated from silage samples was tested. The results clarified that some mycotoxins (aflatoxins – aspergillic acid – beta nitro propionic acid – cyclopiazonic acid– kojic acid and sterigmatocystin) were produced by some isolates of A. flavus. Some isolates of A.fumigatus could produce gliotoxin and verrucologen. All of A. niger isolates tested were able to produce kojic acid. One isolate of A. ochraceous formed ochratoxin A and other isolate produced penicillic acid. Concerning A. terreus isolates, the results showed that 5 isolates were able to produce citrinin and 4 isolates had ability to produce patulin. A. versicolor isolates showed the ability to produce ochratoxin A.     

Glutathione S-transferase M1, T1 and P1 polymorphisms and bladder cancer risk in Egyptians

Previous studies suggest that bladder cancer risk may vary with GST genotype but these results are inconsistent. The aim of this study was to explore whether GSTM1, GSTT1 and GSTP polymorphisms were associated with increased bladder cancer risk in an Egyptian population. GSTM1, GSTT1 and GSTP1 genotype frequencies were determined in bladder cancer cases (n=72) and healthy controls with no history of malignancies (n=82) using PCR-based techniques. The GSTT1*2 genotype was particularly associated with increased risk (OR 2.71, 95%CI 1.27-5.73) and the GSTM1*2 genotype to a lesser extent (OR 1.63, 95%CI 0.85-3.10). 18.1% of cases but only 7.3% of controls were GSTP1*B*B homozygotes (OR 2.38, 95%CI 0.83-6.87). The presence of two or more a priori at-risk genotypes was associated with increased bladder cancer risk (OR 2.42; 95%CI 1.47-3.97). These results suggest that polymorphisms in the GST genes are associated with increased risk of bladder cancer among Egyptians.     

Diversity of the microeukaryotic community in sulfide-rich Zodletone Spring (Oklahoma)

The microeukaryotic community in Zodletone Spring, a predominantly anaerobic sulfide and sulfur-rich spring, was examined using an 18S rRNA gene cloning and sequencing approach. The majority of the 288 clones sequenced from three different locations at Zodletone Spring belonged to the Stramenopiles, Alveolata, and Fungi, with members of the phylum Cercozoa, order Diplomonadida, and family Jakobidae representing a minor fraction of the clone library. No sequences suggesting the presence of novel kingdom level diversity were detected in any of the three libraries. A large fraction of stramenopile clones encountered were monophyletic with either members of the genus Cafeteria (order Bicosoecida) or members of the order Labyrinthulida (slime nets), both of which have so far been encountered mainly in marine habitats. The majority of the observed fungal clone sequences belonged to the ascomycetous yeasts (order Saccharomycetales), were closely related to yeast genera within the Hymenobasidiomycetes (phylum Basidiomycetes), or formed a novel fungal lineage with several previously published or database-deposited clones. To determine whether the unexpected abundance of fungal sequences in Zodletone Spring clone libraries represents a general pattern in anaerobic habitats, we generated three clone libraries from three different anaerobic settings (anaerobic sewage digester, pond sediment, and hydrocarbon-exposed aquifer sediments) and partially sequenced 210 of these clones. Phylogenetic analysis indicated that clone sequences belonging to the kingdom Fungi represent a significant fraction of all three clone libraries, an observation confirmed by phospholipid fatty acid and ergosterol analysis. Overall, this work reveals an unexpected abundance of Fungi in anaerobic habitats, describes a novel, yet-uncultured group of Fungi that appears to be widespread in anaerobic habitats, and indicates that several of the previously considered marine protists could also occur in nonmarine habitats.