Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.     

The rise of the rhizosolenid diatoms

The 18S ribosomal DNA molecular phylogeny and lipid composition of over 120 marine diatoms showed that the capability to biosynthesize highly branched isoprenoid (HBI) alkenes is restricted to two specific phylogenetic clusters, which independently evolved in centric and pennate diatoms. The molecular record of C25 HBI chemical fossils in a large suite of well-dated marine sediments and petroleum revealed that the older cluster, composed of rhizosolenid diatoms, evolved 91.5 +/- 1.5 million years ago (Upper Turonian), enabling an accurate dating of the pace of diatom evolution that is unprecedented. The rapid rise of the rhizosolenid diatoms probably resulted from a major reorganization of the nutrient budget in the mid-Cretaceous oceans, triggered by plate tectonics.     

The Consumption of <Emphasis Type="Italic">Hibiscus sabdariffa</Emphasis> Dried Calyx Ethanolic Extract Reduced Lipid Profile in Rats

The scientific basis for the statement that plants and their active constituents play an important role in the prevention of chronic and degenerative diseases is continously advancing. The object of the present study was to evaluate the effect of Hibiscus sabdariffa L. dried calyx ethanolic extract on the serum lipid profile of Sprague-Dawley rats. The rats were fed during 4 weeks with either a basal diet, containing high cholesterol (1%), cholic acid (0.25%), lard oil (10%), or a supplemental diet with H. sabdariffa extract at 5%, 10%, and 15% levels (SD₅, SD₁₀, SD₁₅). Weight gain and faeces dry weight were both very significantly less (p ≤ 0.01) in SD₁₀ and SD₁₅ groups as compared to the control group, as was food efficiency in SD₁₅. In the case of SD₁₀, food efficiency was only significantly lower (p ≤ 0.05). Faeces dry weight in SD₅ however, was the only one found to be significantly higher (p ≤ 0.05). Triacylglycerols and LDL levels were both significantly less (p ≤ 0.05) in all groups (SD₅, SD₁₀, and SD₁₅) as compared to the control. For total lipids, SD₁₀ and SD₁₅ showed significantly lower levels (p ≤ 0.05), whereas very significant differences (p ≤ 0.01) were observed in the case of SD₅. All groups had lower cholesterol levels compared to controls; however, only the SD₅ group was statistically significant (p ≤ 0.05). No significant results were found in any group in the cases of either phospholipid or HDL levels. A hypothesis of hibiscus acid racemization, (+)-HCA to (−)-HCA, mediated by intestinal flora enzymes possibly explains the significant triacylglycerol decrease in all experimental groups. VLDL, the precursor of LDL, is composed predominantly of triacylglycerols, suggesting that the significant decrease in LDL is related to observed triacylglycerol synthesis inhibition. Five percent H. sabdariffa extract addition showed the best results in the reduction of serum lipids under study conditions.     

Use of intracytoplasmic sperm injection (ICSI) to generate transgenic animals

Even though intracytoplasmic sperm injection (ICSI) has been widely used for the production of offspring in human infertility clinics and in reproductive research laboratories using mice, many researchers engaged in animal transgenesis still consider it somewhat cumbersome. The greatest advantage of ICSI-mediated transgenesis is that it allows introduction of very large DNA transgenes (e.g., yeast artificial chromosomes), with relatively high efficiency into the genomes of hosts, as compared to pronuclear injection. Recently, we have developed an active form of intracytoplasmic sperm injection-mediated transgenesis (ICSI-Tr) with fresh sperm utilizing transposons. The transgenic efficiencies rival all transgenic techniques except that of lentiviral methods.     

Application of Exogenous Esterified Hyaluronan to Equine Distal Limb Wounds

The objective of this study was to evaluate the efficacy of topical application of a hyaluronan (HA) derivative in wound healing with respect to the rate of epithelialization, fibroplasia, angiogenesis and contraction, magnitude of the local inflammatory response, local expression of transforming growth factor-β 1 and 3 (TGF-β 1 and 3), tumor necrosis factor-α (TNF-α), and collagen type III deposition. In six healthy adult horses, six full-thickness skin wounds were created on the dorsal aspect of both metacarpi using a sterile template. Sites were sampled at 0, 1, 2, 5, 14, 21, and 35 days following wounding. Wounds on one limb were dressed with commercially available esterified HA fleece under a nonadherent dressing. The opposite limb was covered with the nonadherent dressing alone (control). Images of the most proximal wounds were used to determine the area of total healing and the relative contributions of epithelialization and contraction to healing. At each sample time, a control and treatment biopsy were taken for histological evaluation and special stains. All samples were evaluated for degree of inflammation, fibroplasia and angiogenesis; in situ hybridization for type III collagen, TGFβ1 and 3, and immunohistochemistry for TNF-α. Mean percentages of total wound healing, epithelialization, and wound contraction were not significantly different between control and treatment groups. In treated horses, initial wound expansion was significantly decreased during the first 2 weeks. Mononuclear cell numbers, counted in the granulation tissue, increased in both control and treated limbs over the entire course of the study. However at day 35 the macrophage numbers counted in the treated horses were significantly increased compared with the control limbs (P < .05). Although not statistically significant, relative staining for type III collagen in the treated wounds was less than that of control wounds. Results of the present study do not support a benefit of an exogenous HA-derivative in the healing of distal limb wounds in horses. The shortcomings of the study design are discussed.     

Molecular analysis of the sex chromosomes of the platyfish Xiphophorus maculatus: Towards the identification of a new type of master sexual regulator in vertebrates

In contrast to mammals and birds, fish display an amazing diversity of genetic sex determination systems, with frequent changes during evolution possibly associated with the emergence of new sex chromosomes and sex‐determining genes. To better understand the molecular and evolutionary mechanisms driving this diversity, several fish models are studied in parallel. Besides the medaka (Oryzias latipes Temminck and Schlegel, 1846) for which the master sex‐determination gene has been identified, one of the most advanced models for studying sex determination is the Southern platyfish (Xiphophorus maculatus, Günther 1966). Xiphophorus maculatus belongs to the Poeciliids, a family of live‐bearing freshwater fish, including platyfish, swordtails and guppies that perfectly illustrates the diversity of genetic sex‐determination mechanisms observed in teleosts. For X. maculatus, bacterial artificial chromosome contigs covering the sex‐determination region of the X and Y sex chromosomes have been constructed. Initial molecular analysis demonstrated that the sex‐determination region is very unstable and frequently undergoes duplications, deletions, inversions and other rearrangements. Eleven gene candidates linked to the master sex‐determining gene have been identified, some of them corresponding to pseudogenes. All putative genes are present on both the X and the Y chromosomes, suggesting a poor degree of differentiation and a young evolutionary age for platyfish sex chromosomes. When compared with other fish and tetrapod genomes, syntenies were detected only with autosomes. This observation supports an independent origin of sex chromosomes, not only in different vertebrate lineages but also between different fish species.     

Quantification of a broad spectrum of lignans in cereals, oilseeds, and nuts

Twenty-four plant lignans were analyzed by high-performance liquid chromatography-tandem mass spectrometry in bran extracts of 16 cereal species, in four nut species, and in two oilseed species (sesame seeds and linseeds). Eighteen of these were lignans previously unidentified in these species, and of these, 16 were identified in the analyzed samples. Four different extraction methods were applied as follows: alkaline extraction, mild acid extraction, a combination of alkaline and mild acid extraction, or accelerated solvent extraction. The extraction method was of great importance for the lignan yield. 7-Hydroxymatairesinol, which has not previously been detected in cereals because of destructive extraction methods, was the dominant lignan in wheat, triticale, oat, barley, millet, corn bran, and amaranth whole grain. Syringaresinol was the other dominant cereal lignan. Wheat and rye bran had the highest lignan content of all cereals; however, linseeds and sesame seeds were by far the most lignan-rich of the studied species.     

Identification of allyl esters in garlic cheese

This study describes the identification of six allyl esters in a garlic cheese preparation and in a commercial cream cheese. The extracts were prepared by liquid/liquid extraction and concentrated by the SAFE process. The identification of the allyl esters of acetic, butyric, hexanoic, heptanoic, octanoic, and decanoic acids is based on the correlation of their mass spectrometric data and chromatographic retention time data obtained from the extracts with those of authentic standards. In addition to the gas chromatography (GC)/mass spectrometry analysis, the flavor ingredients were characterized by GC sniffing by a trained flavorist. Some of the esters were isolated by preparative GC.     

Occurrence of two forms of Y chromosome in rainbow trout (Oncorhynchus mykiss) males from Rutki strain

Morphologically differentiated sex chromosomes are found in only few salmonid species. Some populations of rainbow trout, Oncorhynchus mykiss, exhibit chromosomal polymorphism related to sex. We found sex-related chromosomal polymorphism in fish from the synthetic Rutki strain, Poland, in approximately 85% (n = 22) of examined males (XY-like) whereas the remaining males (n = 4) possessed chromosomes similar to these observed in females (XX-like). To investigate whether males possessing XX-like chromosomes were genotypic males or genotypic females with altered phenotypic sex, androgenetic progeny of four males (representing both XY-like and XX-like forms, n = 2 + 2) was examined. Androgenetic progeny (F₁) of all four fathers consisted of both phenotypic females and males. F₁ male progeny of two fathers showed XX-like chromosomes whereas F₁ male progeny of the other two fathers possessed YY-like (supermale) chromosomes. F₁ were reared further until they were sexually mature. Two males from each of four F₁ families were used to produce F₂ androgenetic and control F₂ generation. All F₂ individuals, androgenetics and control, were phenotypic males at sexual maturation. The results indicate that males possessing XX-like chromosomes are genetic males and they are not sex-reversed females. Thus, the Y chromosome can exist in different morphological forms in farmed rainbow trout. The Y^S chromosome (shorter form, unlike the X chromosome) has a shorter or absent p-arm and lacks the pericentromeric cluster of AT-rich chromatin and the 5S rDNA sequences that are found in the Y^L chromosome (longer form, like the X chromosome).     

Opportunities and challenges for analysis of wildlife trade using CITES data – seahorses as a case study

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