CLASI-FISH: Principles of combinatorial labeling and spectral imaging

Although the number of phylotypes present in a microbial community may number in the hundreds or more, until recently, fluorescence in situ hybridization has been used to label, at most, only a handful of different phylotypes in a single sample. We recently developed a technique, CLASI-FISH for combinatorial labeling and spectral imaging – fluorescence in situ hybridization, to greatly expand the number of distinguishable taxa in a single FISH experiment. The CLASI technique involves labeling microbes of interest with combinations of probes coupled with spectral imaging to allow the use of fluorophores with highly overlapping excitation and emission spectra. Here, we present the basic principles and theory of CLASI-FISH along with some guidelines for performing CLASI-FISH experiments. We further include a protocol for creating fluorescence spectral reference standards, a vital component of successful CLASI-FISH.     

Heteroaryl urea inhibitors of fatty acid amide hydrolase: Structure–mutagenicity relationships for arylamine metabolites

The structure–activity relationships for a series of heteroaryl urea inhibitors of fatty acid amide hydrolase (FAAH) are described. Members of this class of inhibitors have been shown to inactivate FAAH by covalent modification of an active site serine with subsequent release of an aromatic amine from the urea electrophile. Systematic Ames II testing guided the optimization of urea substituents by defining the structure–mutagenicity relationships for the released aromatic amine metabolites. Potent FAAH inhibitors were identified having heteroaryl amine leaving groups that were non-mutagenic in the Ames II assay.     

Diet and Food Choice in Peruvian Red Uakaris (<Emphasis Type="Italic">Cacajao calvus ucayalii</Emphasis>): Selective or Opportunistic Seed Predation?

Even primates considered dietary specialists tend to eat a combination of fruit pulp, seeds, other plant parts, or animals. Specialist seed predators could either feed on seeds preferentially, or to avoid competition when ripe pulps are scarce. Pitheciin monkeys have specialized dentition that allows them to feed on seeds protected by hard shells, and the upper limit on the hardness of these is likely to be a function of jaw size. We recorded the diet of Peruvian red uakaris (Cacajao calvus ucayalii) on the Yavari River, Peru, to test the prediction that this seed predator would feed on the seeds of hard-shelled fruits preferentially over softer ones in relation to their availability in the forest. We also tested predictions that adult male, adult female, and juvenile diets would differ, with larger individuals eating more hard fruits. Uakaris ate 55.4% seeds, 38.9% pulps and arils, and 5.6% other items, but proportions varied through the year. More pulps, especially from the palm Mauritia flexuosa, were eaten when fruit availability was low, and more hard fruits were positively selected for than softer ones. Juveniles did not open the hardest fruit species opened by adults, and adult males ate harder fruits than females. These results provide evidence that seed eating in some primates has evolved beyond a means of avoiding competition for the ripe pulps typically preferred by many primates. Specialist seeding-eating primates therefore occupy divergent niches that require separate consideration from those of similar-sized primates.     

Playing with bone and fat

The relationship between bone and fat formation within the bone marrow microenvironment is complex and remains an area of active investigation. Classical in vitro and in vivo studies strongly support an inverse relationship between the commitment of bone marrow-derived mesenchymal stem cells or stromal cells to the adipocyte and osteoblast lineage pathways. In this review, we focus on the recent literature exploring the mechanisms underlying these differentiation events and discuss their implications relevant to osteoporosis and regenerative medicine.     

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.     

Integrating multiple analytical approaches to spatially delineate and characterize genetic population structure: an application to boreal caribou (<Emphasis Type="Italic">Rangifer tarandus caribou</Emphasis>) in central Canada

Individual-based clustering (IBC) methods have become increasingly popular for the characterization and delineation of genetic population units for numerous species. These methods delineate populations based on the genetic assumptions of a breeding unit which may provide a better representation of the behaviour of the species. The increasing use of IBC has resulted in the development of several analytical models all of which vary in their theoretical assumptions to infer genetic population structure. In this paper, we report a comparative strategy utilizing three IBC methods to characterize the spatial genetic structure of the boreal population of woodland caribou (Rangifer tarandus caribou) in central Canada. In addition, we implement both tests for isolation-by-distance (IBD) and frequency-based assignment tests to validate the consensus genetic clusters as defined by IBC. We also compare indirect metrics of genetic diversity and gene flow using both a priori defined herds and the IBC defined populations. Although our results show some concordance between both pre-defined herds and IBC derived genetic clusters, the IBC analyses identified a cluster that was cryptic to observation-based caribou herds and found no difference between several adjacent herds. By comparing multiple IBC methods and integrating both IBD and indirect genetic diversity metrics a posteriori, our strategy provides an effective means to delineate wildlife population structure and accurately assess genetic diversity and connectivity.     

Effects of ultraviolet-B radiation on plants during mild water stress. III. Effects on photosynthetic recovery and growth in soybean

Soybean { Glycine max (L.) Merr. ev. Essex} was grown from seed in a greenhouse under ultraviolet-B (UV-B, 280–320 nm) radiation supplied by filtered FS-40 sunlamps. On a weighted, total daily dose basis these plants received either 0 (control) or 2875 effective J m⁻² day⁻¹ UV-B_BE. When weighted with the generalized plant action spectrum (Caldwell 1971), this simulated the solar ultraviolet-B irradiance expected to occur at College Park, Maryland, USA (39°N) in the event the global stratospheric ozone column is reduced by 23%. The effects of ultraviolet radiation on the photosynthetic recovery from water stress were measured with an infrared gas analyzer. These effects were examined in plants which were either well-watered or previously preconditioned to water stress, during two distinct phenological stages of development. During the early stages of soybean growth, enhanced levels of UV-B reduced net photosynthesis by 25%, and water stress also reduced photosynthesis to nearly the same extent (by 20%). The combination of these two stresses resulted in smaller biomass than that produced by plants exposed to either stress independently. Photosynthesis in older, larger plants was much more sensitive to water stress and was reduced by as much as 50–60% in non-preconditioned plants. Although non-irradiated, non-preconditioned (control) plants recovered to only within 60% of their prestressed value, preconditioned plants recovered to within 70–80% during the 3 day recovery period. Both water stress and UV-B radiation affected non-stomatal conductance, while stomatal conductance was primarily affected by water stress.     

Testosterone Affects Neural Gene Expression Differently in Male and Female Juncos: A Role for Hormones in Mediating Sexual Dimorphism and Conflict

Despite sharing much of their genomes, males and females are often highly dimorphic, reflecting at least in part the resolution of sexual conflict in response to sexually antagonistic selection. Sexual dimorphism arises owing to sex differences in gene expression, and steroid hormones are often invoked as a proximate cause of sexual dimorphism. Experimental elevation of androgens can modify behavior, physiology, and gene expression, but knowledge of the role of hormones remains incomplete, including how the sexes differ in gene expression in response to hormones. We addressed these questions in a bird species with a long history of behavioral endocrinological and ecological study, the dark-eyed junco (Junco hyemalis), using a custom microarray. Focusing on two brain regions involved in sexually dimorphic behavior and regulation of hormone secretion, we identified 651 genes that differed in expression by sex in medial amygdala and 611 in hypothalamus. Additionally, we treated individuals of each sex with testosterone implants and identified many genes that may be related to previously identified phenotypic effects of testosterone treatment. Some of these genes relate to previously identified effects of testosterone-treatment and suggest that the multiple effects of testosterone may be mediated by modifying the expression of a small number of genes. Notably, testosterone-treatment tended to alter expression of different genes in each sex: only 4 of the 527 genes identified as significant in one sex or the other were significantly differentially expressed in both sexes. Hormonally regulated gene expression is a key mechanism underlying sexual dimorphism, and our study identifies specific genes that may mediate some of these processes.     

An Ion-channel Modulator from the Saliva of the Brown Ear Tick has a Highly Modified Kunitz/BPTI Structure

Ra-KLP, a 75 amino acid protein secreted by the salivary gland of the brown ear tick Rhipicephalus appendiculatus has a sequence resembling those of Kunitz/BPTI proteins. We report the detection, purification and characterization of the function of Ra-KLP. In addition, determination of the three-dimensional crystal structure of Ra-KLP at 1.6 Å resolution using sulphur single-wavelength anomalous dispersion reveals that much of the loop structure of classical Kunitz domains, including the protruding protease-binding loop, has been replaced by β-strands. Even more unusually, the N-terminal portion of the polypeptide chain is pinned to the ”Kunitz head” by two disulphide bridges not found in classical Kunitz/BPTI proteins. The disulphide bond pattern has been further altered by the loss of the bridge that normally stabilizes the protease-binding loop. Consistent with the conversion of this loop into a β-strand, Ra-KLP shows no significant anti-protease activity; however, it activates maxiK channels in an in vitro system, suggesting a potential mechanism for regulating host blood supply during feeding.