'Escentric' molecules

Can a fragrance be revolutionary? In this commentary, the creation of two unusual, extravagant fine fragrances, ‘escentr?c01’ and ‘molecule01’, is described. In response to the fantasy components found in release notes of many recent perfume launches, both center around a single real fragrance raw material, the transparent woody aroma chemical ‘Iso E Super’ ( 1 + 2 ). The perfume ‘escentr?c01’ contains 65% of it, accompanied by Trisamber ( 3 ), red pepper, lime oil, incense and musks, while ‘molecule01’ consists exclusively of ‘Iso E Super’ ( 1 + 2 ). The elegant woody note lives here its own eccentric life – the revolution starts.     

Morphological effects of transcardially perfused SDS on the rat brain

Background information. For explanation of the formation of ‘dark’ neurons, an enigmatic phenomenon in neuropathology, we hypothesized recently that all spaces between the ultrastructural elements visible in the traditional transmission electron microscope are filled with a gel structure that stores free energy in the form of non‐covalent interactions, is continuous in the whole soma—dendrite domains of neurons, and is capable of whole‐cell phase transition. This hypothesis was deduced from the fact that ‘dark’ neurons can be formed, even under conditions extremely unfavourable for enzyme‐mediated biochemical processes, if initiated by a physical damage. In order to gain further information on this gel structure, we perfused transcardially rats for 5 min with physiological saline containing 1 mM SDS before the perfusion of a fixative for electron microscopy. Results. Dramatic compaction of visibly intact ultrastructural elements was caused in the whole soma—dendrite domains of thinly scattered neurons (‘dark’ neurons), whereas substantial cytoplasmic swelling and patchy ultrastructural disintegration occurred in numerous other neurons (‘light’ neurons). Similar morphological changes were observed in scattered astrocytes, oligodendrocytes, pericytes and endothelial cells. Conclusions. These observations: (i) support the existence of the above intracellular gel structure in neurons; (ii) allow the conclusion that this gel structure is present in the form of an ubiquitous trabecular network surrounded by a confluent system of fluid cytoplasm; (iii) draw attention to the possibility that the previous two statements also apply to other cell types of the brain tissue; and (iv) suggest that pressure‐induced direct channels exist between neurons and astrocytes.     

Applications of novel affinity cassette methods: use of peptide fusion handles for the purification of recombinant proteins.

In this article, recent progress related to the use of different types of polypeptide fusion handles or 'tags' for the purification of recombinant proteins are critically discussed. In addition, novel aspects of the molecular cassette concept are elaborated, together with areas of potential application of these fundamental principles in molecular recognition. As evident from this review, the use of these concepts provides a powerful strategy for the high throughput isolation and purification of recombinant proteins and their derived domains, generated from functional genomic or zeomic studies, as part of the bioprocess technology leading to their commercial development, and in the study of molecular recognition phenomena per se. In addition, similar concepts can be exploited for high sensitivity analysis and detection, for the characterisation of protein bait/prey interactions at the molecular level, and for the immobilisation and directed orientation of proteins for use as biocatalysts/biosensors.     

Vertebral column and associated elements in dipnoans and comparison with other fishes: development and homology.

A vertebral column consisting of a persistent notochord and ossified arcocentra is the primitive condition for Gnathostomata; it still persists in primitive actinopterygians and sarcopterygians. Advanced actinopterygians and sarcopterygians develop numerous types of centra that include, among others, the presence of holocentrum, chordacentrum, and autocentrum. The chordacentrum, a mineralization or calcification of the fibrous sheath of the notochord, is only found in actinopterygians, whereas an autocentrum is a synapomorphy of teleosts above Leptolepis coryphaenoides. The chordacentrum, formed by migration of cartilaginous cells from the arches into the fibrous sheath of the notochord and usually covered by a thin calcification, is a unique feature of chondrichthyans. The actinopterygian chordacentrum and the chondrichthyan chordacentrum are not homologous. The postcaudal cartilaginous centrum is only known in postcaudal vertebrae of living dipnoans. The holocentrum is present in certain fossil dipnoans and actinopterygians, where it has been independently acquired. It is formed by proliferation of cartilage cells around the elastica externa of the notochord. These cells later ossify, forming a compact centrum. A vertebral column formed by a persistent notochord without vertebral centra is the primitive pattern for all vertebrates. The formation of centra, which is not homologous among vertebrate groups, is acquired independently in some lineages of placoderms, most advanced actinopterygians, and some dipnoans and rhipidistians. Several series of structures are associated with the vertebral column such as the supraneurals, interhaemals, radials, and ribs. In living dipnoans median neural spine, "supraneural," and dorsal radial result from growth and distal differentiation of one median cartilage into two or three median bones during ontogeny. The median neural spine articulates with the neural arch and fuses with it in the caudal vertebrae early in ontogeny. Two bones differentiate in the anterior abdominal vertebrae, i.e., the proximal neural spine and the distal "supraneural." Three bones differentiate in front of the dorsal fin, i.e., the proximal neural spine, the middle "supraneural", and the distal radial; the same pattern is observed in front of the anal fin (the proximal haemal spine, the middle interhaemal, and the distal radial). Considering that the three dorsal (and also the three ventral) bones originate from growth of only one cartilage, they cannot be serial homologs of the neural spines, or "supraneural." They are linear homologs of the median neural cartilage in living dipnoans. The development of these elements differs within osteichthyans from sarcopterygians to actinopterygians, in which the neural spine originates as a continuation of the basidorsal arcualia and in which the supraneural and radial originate from independent cartilages that appear at different times during early ontogeny. The ribs of living dipnoans are unique in that they are not articulated with parapophyses, like in primitive fossil dipnoans, but a remnant of the ventral arcuale surrounded by a small arcocentrum remains at its base. A true caudal fin is absent in living dipnoans. The postcaudal cartilages extend to the caudal tip of the body separating dorsal and ventral rays (or the camptotrichia). Actinotrichia are present in young dipnoans. They are also known in extant actinistians and actinopterygians. They probably represent the primitive state for teleostomes. In contrast, the camptotrichia are unique for extant dipnoans (and probably Carboniferous and younger dipnoans). Lepidotrichia apparently developed many times among osteichthyans.     

Molecular identification of Ehrlichia species and 'Candidatus Neoehrlichia mikurensis' from ticks and wild rodents in Shizuoka and Nagano Prefectures, Japan

A total of 293 ticks and 111 wild rodents that were collected in Shizuoka and Nagano Prefectures, Japan, were examined for infection of Ehrlichia species and 'Candidatus Neoehrlichia mikurensis.' The 16S rDNA or the omp-1 gene of these bacterial DNAs were detected from the spleens of tick-inoculated mice (5 positive/total 29 mice) or from the spleens of wild rodents (25 positive/total 111 rodents) by PCR amplifi-cation. Sequencing of the 16S rDNA revealed Ehrlichia spp. from the 5 tick-inoculated mice and 8 wild rodents, and 'Candidatus N. mikurensis' from 17 wild rodents. The data suggest the presence of additional genetic variants, and potential vectors and/or reservoirs for these bacteria in central Japan.     

'P' solubilization potential of plant growth promoting Pseudomonas mutants at low temperature

Pseudomonas fluorescens strain GRS₁, PRS₉ and their cold tolerant mutants were examined for their tricalcium phosphate (TCP) solubilizing activity in NBRIP (broth) media at 10°C and 25°C. Invariably, all the cold tolerant mutants of GRS₁ and PRS₉ were found more efficient than their respective wild type counterparts for ‘P’ solubilization activity at 10°C as compared to 25°C. ‘P’ solubilization potential of CRM was found maximum among all the strains followed by CRPF₆ and CRPF₄. To the best of out knowledge, this is the first report regarding low temperature ‘P’ solubilization activity.     

Recent Results in the Search for New Molecules with Ambergris Odor

The synthesis of new odorant molecules is still a challenging task for the fragrance chemist, because now as ever it is difficult to predict the odor properties of small organic molecules. Therefore, certain tools, such as, e.g., lead‐structure optimization of existing odorants, are helpful techniques. In this article, we describe the synthesis and the odor properties of a new molecule derived by the so‐called ‘seco’ lead‐structure optimization of the ambergris compound Ambroxide^®. Based on these results, more representatives with similar structures have been synthesized and evaluated for their olfactory properties.     

Antimicrobial activity of ethylenediaminedisuccinate metal complexes

It is shown that metal complexes of the biodegradable ligand ethylenediaminedisuccinic acid (edds) present antimicrobial activity towards fungi and bacteria. [Cd(edds)], in particular, is more toxic than free Cd2+ to Aspergillus niger, behaving as a 'Trojan Horse' in the facilitated delivery of the toxic metal into the fungus.     

Can heterochrony help explain the high morphological diversity within the genus Niphargus (Crustacea: Amphipoda)?

Postembryonic development of nine species of Niphargus (Crustacea: Amphipoda) was studied, with spine development and shifts in allometric growth being combined in developmental sequences that were compared across species. The developmental sequences show high diversity with respect to the position of individual events in the sequence, as well as a high frequency of events being inapplicable in some species. Within Niphargus, the highest degree of independence between events occurs mainly in early mid-aged instars, where the shifts in position are both the largest in magnitude and also the most frequent in occurrence. Constructive troglomorphic features of subterranean species were inferred to develop more because of accelerated growth rather than a delayed offset of growth. Shifts in both relative timing and growth rate appeared to have played a role in the evolution of sexually dimorphic elongated appendages. Growth patterns differed greatly between species for individual sexually dimorphic and troglomorphic traits, hinting at their possible independent origin. The independence between developmental events that was generally apparent might indicate the existence of an important genetic basis for the extreme intrageneric morphological variation arising from numerous highly variable body parts being combined in a ‘mosaic’ manner. Moreover, we suggest that the overall diversity of the genus might actually be underestimated in light of possible convergent features accompanied by ‘cryptic’ speciation. We conclude that both sequential and growth heterochrony appear to have played a key role in the evolution of Niphargus, the most diverse genus of freshwater amphipods. A preliminary list of heterochronic characters is provided.     

Opsin gene sequence variation across phylogenetic and population histories in Mysis (Crustacea: Mysida) does not match current light environments or visual-pigment absorbance spectra

The hypothesis that selection on the opsin gene is efficient in tuning vision to the ambient light environment of an organism was assessed in 49 populations of 12 Mysis crustacean species, inhabiting arctic marine waters, coastal littoral habitats, freshwater lakes ('glacial relicts') and the deep Caspian Sea. Extensive sequence variation was found within and among taxa, but its patterns did not match expectations based on light environments, spectral sensitivity of the visual pigment measured by microspectrophotometry or the history of species and populations. The main split in the opsin gene tree was between lineages I and II, differing in six amino acids. Lineage I was present in marine and Caspian Sea species and in the North American freshwater Mysis diluviana, whereas lineage II was found in the European and circumarctic fresh- and brackish-water Mysis relicta, Mysis salemaai and Mysis segerstralei. Both lineages were present in some populations of M. salemaai and M. segerstralei. Absorbance spectra of the visual pigment in nine populations of the latter three species showed a dichotomy between lake (λ(max) =554-562 nm) and brackish-water (Baltic Sea) populations (λ(max) = 521-535 nm). Judged by the shape of spectra, this difference was not because of different chromophores (A2 vs. A1), but neither did it coincide with the split in the opsin tree (lineages I/II), species identity or current light environments. In all, adaptive evolution of the opsin gene in Mysis could not be demonstrated, but its sequence variation did not conform to a neutral expectation either, suggesting evolutionary constraints and/or unidentified mechanisms of spectral tuning.     

Synthesis and biological evaluation of 4beta-[(4-substituted)-1,2,3-triazol-1-yl]podophyllotoxins as potential anticancer agents

A series of novel 4beta-[(4-substituted)-1,2,3-triazol-1-yl]podophyllotoxin derivatives were synthesized by employing Cu(I)-catalyzed click chemistry and evaluated for their anticancer activity against a panel of seven human cancer cell lines (HT-29, HCT-15, 502713, HOP-62, A-549, MCF-7, and SF-295). The compounds 9b, 9c, 9e, 9f, and 9h showed significant cytotoxic activities especially against HT-29, HCT-15, 502713 cell lines.     

Three novel, structurally unique spirocyclic alkaloids from the halotolerant B-17 fungal strain of Aspergillus variecolor

During our search for novel antitumor lead compounds from microorganisms living under extreme conditions, three novel alkaloids, variecolortides A-C (1-3), were isolated from the mycelia of the halotolerant fungal strain Aspergillus variecolor B-17. The new compounds were found to share an unprecedented 'spiro-anthronopyranoid diketopiperazine' structure, with a stable hemiaminal function, as corroborated by in-depth NMR-spectroscopic and mass-spectrometric analyses, as well as by a single-crystal X-ray analysis of 1. All compounds were shown to exhibit weak cytotoxic and antioxidant activities.     

Exploring the temporal consequences of chasing the elements in Rosen's relational diagrams

In the work 'Life Itself', Rosen showed that a formal mechanism cannot be 'closed to efficient cause'. Additionally, he claimed that organisms are 'closed to efficient cause' and that, by logical extension, organisms cannot be mechanisms. This paper shows that it is possible for mechanisms to be 'nearly closed to efficient cause', with the requirement that some unentailed efficient-cause agents are placed inside the system. Populations of these 'nearly closed to efficient cause' systems can be defined based on the ability to isolate each component in its own 'reaction chamber'. Diagrams from these populations are drawn from a couple of different perspectives, and comments are made on how these diagrams can be related to the more conventional language of chemistry.     

Environmental and genetic influences on body mass and resting metabolic rates (RMR) in a natural population of weasel Mustela nivalis

Body mass (BM) and resting metabolic rates (RMR) are two inexorably linked traits strongly related to mammalian life histories. Yet, there have been no studies attempting to estimate heritable variation and covariation of BM and RMR in natural populations. We used a marker‐based approach to construct a pedigree and then the ‘animal model’ to estimate narrow sense heritability (h²) of these traits in a free‐living population of weasels Mustela nivalis—a small carnivore characterised by a wide range of BM and extremely high RMR. The most important factors affecting BM of weasels were sex and habitat type, whereas RMR was significantly affected only by seasonal variation of this trait. All environmental factors had only small effect on estimates of additive genetic variance of both BM and RMR. The amount of additive genetic variance associated with BM and estimates of heritability were high and significant in males (h² = 0.61), but low and not significant in females (h² = 0.32), probably due to small sample size for the latter sex. The results from the two‐trait model revealed significant phenotypic (r_P = 0.62) and genetic correlation (r_A = 0.89) between BM and whole body RMR. The estimate of heritability of whole body RMR (0.54) and BM corrected RMR (0.45) were lower than estimates of heritability for BM. Both phenotypic and genetic correlations between BM corrected RMR and BM had negative signals (r_P = ?0.42 and r_A = ?0.58). Our results indicate that total energy expenditures of individuals can quickly evolve through concerted changes in BM and RMR.     

‘Petite’ mutagenesis and mitotic crossing-over in yeast by DNA-targeted alkylating agents

Although the biological properties (cytotoxicity, mutagenicity and carcinogenicity) of alkylating agents result from their bonding interactions with DNA, such compounds generally do not show any special binding affinity for DNA. A series of acridine-linked aniline mustards of widely-varying alkylator reactivity have been designed as DNA-directed alkylating agents. We have considered whether such DNA targeting has an effect on mutagenic properties by evaluating this series of drugs in comparison with their untargeted counterparts for toxic, recombinogenic and mutagenic properties in Saccharomyces cerevisae strain D5. The simple untargeted aniline mustards are effective inducers of mitotic crossing-over in this strain, but resemble other reported alkylators in being rather inefficient inducers of the “petite” or mitochondrial mutation in yeast. However, the majority of the DNA-targeted mustards were very efficient petite, mutagens, while showing little evidence of mitotic crossing-over or other nuclear events. The 100% conversion of cells into petites and the lack of a differential between growing and non-growing cells are similar to the effects of the well characterised mitochondrial mutagen ethidium bromide. These data suggest very different modes of action between the DNA-targeted alkylators and their non-targeted counterparts.     

‘Bite-and-Switch’ approach using computationally designed molecularly imprinted polymers for sensing of creatinine

A method for the selective detection of creatinine is reported, which is based on the reaction between polymerised hemithioacetal, formed by allyl mercaptan, o-phthalic aldehyde, and primary amine leading to the formation of fluorescent isoindole complex. This method has been demonstrated previously for the detection of creatine using creatine-imprinted molecularly imprinted polymers (MIPs) Since MIPs created using traditional methods were unable to differentiate between creatine and creatinine, a new approach to the rational design of a molecularly imprinted polymer (MIP) selective for creatinine was developed using computer simulation. A virtual library of functional monomers was assigned and screened against the target molecule, creatinine, using molecular modelling software. The monomers giving the highest binding score were further tested using simulated annealing in order to mimic the complexation of the functional monomers with template in the monomer mixture. The result of this simulation gave an optimised MIP composition. The computationally designed polymer demonstrated superior selectivity in comparison to the polymer prepared using traditional approach, a detection limit of 25 μM and good stability. The ‘Bite-and-Switch’ approach combined with molecular imprinting can be used for the design of assays and sensors, selective for amino containing substances.     

Fruit misshapen in strawberry cultivars (Fragaria×ananassa) is related to achenes functionality

Fruit deformation is a phenomenon commonly observed in commercial strawberry cultivars (Fragaria×ananassa) with a negative impact on the economic benefit of crop production. To better understand this physiopathy, we evaluated fruit size and the relative amount of ‘small’ (<0.4 mm) and ‘big’ achenes (>0.6 mm) in misshapen (MF) and well‐formed (WF) fruits from ‘Camarosa’, ‘Ventana’ and ‘Medina’ strawberry cultivars growing in the field. In ‘Camarosa’, size‐dependent achenes functionality was assessed by analysing achenes germinability and differences in time to ripening between MF and WF. We found that the occurrence of fruit deformation was not only strongly dependent on the cultivar (i.e. genetic factor) but also was promoted by low temperatures (i.e. environmental factor). Regardless of the cultivar, MF showed higher percentage of ‘small’ non‐functional achenes than WF, indicating a failure in achene development, which could be related to the functional integrity of reproductive structures. To test this hypothesis, we performed an experiment by pollinating strawberry flowers with pollen developed under low and mild temperatures. Low temperatures reduced pollen viability, and flowers pollinated with low quality pollen led to a higher amount of MF. However, fruit deformation was not completely explained by differences in pollen quality, neither by differences in pistil maturity and receptivity nor ovule viability, suggesting that non‐functional achenes might result from a disruption in postfertilisation processes such as embryo abortion as a consequence of low temperatures.     

A new method for rapid identification of ansamycin compounds by inactivating KLM gene clusters in potential ansamycin-producing actinomyces

Aims: In this study, we explored the possibility of construction of a ‘universal targeting vector’ by Red/ET recombination to inactivate L gene encoding 3‐amino‐5‐hydroxybenzoic acid (AHBA)‐oxidoreductase in AHBA biosynthetic gene cluster to facilitate the detection of ansamycins production in actinomycetes. Methods and Results: Based on the conserved regions of linked AHBA synthase (K), oxidoreductase (L) and phosphatase (M) gene clusters, degenerate primers were designed and PCR was performed to detect KLM gene clusters within 33 AHBA synthase gene‐positive actinomycetes strains. Among them, 22 KLM gene cluster‐positive strains were identified. A ‘universal targeting vector’ was further constructed using the 50‐nt homologous sequences chosen from four strains internal L gene in KLM gene clusters through Red/ET recombination. The L gene from nine of the KLM gene cluster‐positive actinomycetes strains was inactivated by insertion of a kanamycin (Km) resistance marker into its internal region from the ‘universal targeting vector’. By comparison of the metabolites produced in parent strains with those in L gene‐inactivated mutants, we demonstrated the possible ansamycins production produced by these strains. One strain (4089) was proved to be a geldanamycin producer. Three strains (3‐20, 7‐32 and 8‐32) were identified as potential triene‐ansamycins producers. Another strain (3‐27) was possible to be a streptovaricin C producer. Strains 24‐100 and 4‐124 might be served as ansamitocin‐like producers. Conclusions: The results confirmed the feasibility that a ‘universal targeting vector’ could be constructed through Red/ET recombination using the conserved regions of KLM gene clusters to detect ansamycins production in actinomycetes. Significance and Impact of the Study: The ‘universal targeting vector’ provides a rapid approach in certain degree to detect the potential ansamycin producers from the 22 KLM gene cluster‐positive actinomycetes strains.     

Sero-prevalence of paratuberculosis in young kids using ‘Bison type’, Mycobacterium avium subsp. paratuberculosis antigen in plate ELISA

Two Mycobacterium avium subsp. paratuberculosis (MAP) antigens (native—S 5, ‘Bison type’ and commercial antigens ‘Bovine’), were compared for screening of kids against paratuberculosis infection. Using MAP (S 5) antigen (‘Bison type’) in plate ELISA, 47 serum samples driven from farmer's herds of Jakhrana, Sirohi, and Marwari breeds in their home tract in Rajasthan state were screened. Of the 47 kids randomly sampled, 8.5% were found sero-positive by plate ELISA test. Breed-wise sero-prevalence was 10.5%, 7.6%, and nil in the Jakhrana, Sirohi, and Marwari male kids, respectively. Whereas, none of the serum sample was found positive using commercial MAP ‘Bovine’ antigen. Sero-prevalence of paratuberculosis has been found to be low in young kids (2 months old) belonging to the farmer's herds of Jakhrana and Marwari in their home tracts.     

Out-of-Africa origin and dispersal-mediated diversification of the butterfly genus Junonia (Nymphalidae: Nymphalinae)

The relative importance of dispersal and vicariance in the diversification of taxa has been much debated. Within butterflies, a few studies published so far have demonstrated vicariant patterns at the global level. We studied the historical biogeography of the genus Junonia (Nymphalidae: Nymphalinae) at the intercontinental level based on a molecular phylogeny. The genus is distributed over all major biogeographical regions of the world except the Palaearctic. We found dispersal to be the dominant process in the diversification of the genus. The genus originated and started diversifying in Africa about 20 Ma and soon after dispersed into Asia possibly through the Arabian Peninsula. From Asia, there were dispersals into Africa and Australasia, all around 5 Ma. The origin of the New World species is ambiguous; the ancestral may have dispersed from Asia via the Beringian Strait or from Africa over the Atlantic, about 3 Ma. We found no evidence for vicariance at the intercontinental scale. We argue that dispersal is as important as vicariance, if not more, in the global diversification of butterflies.