Relative Diversity and Community Structure of Ciliates in Stream Biofilms According to Molecular and Microscopy Methods

Ciliates are an important component of aquatic ecosystems, acting as predators of bacteria and protozoa and providing nutrition for organisms at higher trophic levels. Understanding of the diversity and ecological role of ciliates in stream biofilms is limited, however. Ciliate diversity in biofilm samples from four streams subject to different impacts by human activity was assessed using microscopy and terminal restriction fragment length polymorphism (T-RFLP) analysis of 18S rRNA sequences. Analysis of 3′ and 5′ terminal fragments yielded very similar estimates of ciliate diversity. The diversity detected using microscopy was consistently lower than that suggested by T-RFLP analysis, indicating the existence of genetic diversity not apparent by morphological examination. Microscopy and T-RFLP analyses revealed similar relative trends in diversity between different streams, with the lowest level of biofilm-associated ciliate diversity found in samples from the least-impacted stream and the highest diversity in samples from moderately to highly impacted streams. Multivariate analysis provided evidence of significantly different ciliate communities in biofilm samples from different streams and seasons, particularly between a highly degraded urban stream and less impacted streams. Microscopy and T-RFLP data both suggested the existence of widely distributed, resilient biofilm-associated ciliates as well as ciliate taxa restricted to sites with particular environmental conditions, with cosmopolitan taxa being more abundant than those with restricted distributions. Differences between ciliate assemblages were associated with water quality characteristics typical of urban stream degradation and may be related to factors such as nutrient availability and macroinvertebrate communities. Microscopic and molecular techniques were considered to be useful complementary approaches for investigation of biofilm ciliate communities.Heterotrophic microeukaryotes such as ciliates are thought to be of considerable importance in aquatic ecosystems, as they are major predators of bacteria and constitute a nutritional resource for other protozoa, invertebrates, and probably fish larvae (9, 22, 36, 52, 62, 63, 71). In addition, protozoan bacterivory contributes to enhanced decomposition of leaf detritus—a vital nutrient resource in streams—by increasing turnover of bacterial populations through predation (57). It is not well understood, however, how ciliate diversity and community structure in streams are affected by changing environmental conditions, or how ciliate communities affect other stream biota and processes. The effects of various physical, chemical, and biological factors on freshwater protozoan communities have been considered by a number of studies, but most of these have focused upon planktonic organisms in lentic habitats (for example, see references 2, 11, and 44). However, the complex microbial communities in biofilms have been recognized as important contributors to critical ecological processes, such as auxotrophic primary production, nitrogen fixation, and nutrient cycling, and may underpin the function of stream food webs (31, 45, 61). The few studies which have investigated benthic habitats in lotic systems have found evidence of the existence of diverse communities of abundant ciliates (3, 20, 56) and shifts in community structure in response to ecophysiological parameters (30, 42, 43). With one exception, however, these investigations were based on aquatic sediments, and the organisms within epilithic biofilms have continued to receive little attention.Most studies of ciliate diversity and ecology have utilized microscopy-based methods of identification (for example, see references 3 and 56), as ciliate cells are relatively large and morphologically diverse. Such methods demand a high level of taxonomic expertise, however, and are difficult and time-consuming—for example, many ciliates are fragile and fast moving, and they often require difficult fixing and staining protocols for reliable identification. Molecular biological tools offer the possibility of more accurate and efficient methods for protozoan study and may provide a useful complement to traditional approaches (12, 18, 28, 65), yet we know of only a few molecular studies of environmental ciliate diversity (18, 20, 37). A series of recent investigations used culture-independent analysis of 18S rRNA gene sequences to reveal the existence of diverse microeukaryote communities in assorted marine, anoxic, and extreme environments (40, 48, 66, 69, 70, 72). Furthermore, a growing body of evidence suggests the existence of significant genetic diversity among various ciliate taxa which has escaped detection by microscopy (14, 18, 23, 34, 60, 64, 78), pointing to the potential for molecular techniques to generate new insights into ciliate diversity and ecology, and suggesting a need for comparison of the effectiveness of these different techniques in environmental samples.Terminal restriction fragment length polymorphism (T-RFLP) analysis provides an efficient, inexpensive, and semiquantitative means for comparing microbial molecular diversity between different samples and has been widely used to investigate bacterial communities, although only a few studies have applied T-RFLP methods to the analysis of microeukaryote diversity (6, 16, 17). In this study, ciliate diversity and community structure were investigated in biofilm samples from streams representing a range of levels of anthropogenic degradation, with the objective of testing the null hypothesis that human impacts have no effect upon this important heterotrophic component of stream ecosystems. To achieve this, ciliate-targeted PCR primers were used in conjunction with T-RFLP and multivariate statistical analyses. Additionally, ciliate diversity measures obtained using molecular techniques were compared with those derived from microscopy-based methods in order to assess the relative effectiveness of these approaches.     

Virion Incorporation of the Herpes Simplex Virus Type 1 Tegument Protein VP22 Occurs via Glycoprotein E-Specific Recruitment to the Late Secretory Pathway

The mechanism by which herpesviruses acquire their tegument is not yet clear. One model is that outer tegument proteins are recruited by the cytoplasmic tails of viral glycoproteins. In the case of herpes simplex virus tegument protein VP22, interactions with the glycoproteins gE and gD have been shown. We have previously shown that the C-terminal half of VP22 contains the necessary signal for assembly into the virus. Here, we show that during infection VP22 interacts with gE and gM, as well as its tegument partner VP16. However, by using a range of techniques we were unable to demonstrate VP22 binding to gD. By using pulldown assays, we show that while the cytoplasmic tails of both gE and gM interact with VP22, only gE interacts efficiently with the C-terminal packaging domain of VP22. Furthermore, gE but not gM can recruit VP22 to the Golgi/trans-Golgi network region of the cell in the absence of other virus proteins. To examine the role of the gE-VP22 interaction in infection, we constructed a recombinant virus expressing a mutant VP22 protein with a 14-residue deletion that is unable to bind gE (ΔgEbind). Coimmunoprecipitation assays confirmed that this variant of VP22 was unable to complex with gE. Moreover, VP22 was no longer recruited to its characteristic cytoplasmic trafficking complexes but exhibited a diffuse localization. Importantly, packaging of this variant into virions was abrogated. The mutant virus exhibited poor growth in epithelial cells, similar to the defect we have observed for a VP22 knockout virus. These results suggest that deletion of just 14 residues from the VP22 protein is sufficient to inhibit binding to gE and hence recruitment to the viral envelope and assembly into the virus, resulting in a growth phenotype equivalent to that produced by deleting the entire reading frame.The herpesvirus tegument is the virion compartment located between the DNA-containing capsid and the virus envelope (6). Although it is well defined that the viral capsid assembles in the nucleus (37, 38) and the viral envelope is acquired from cellular membranes (3, 24), the mechanism of tegument protein acquisition is still to be established. At least 20 virus-encoded components are recruited into the herpes simplex virus type 1 (HSV-1) tegument (32), and there is increasing evidence to suggest that subsets of these proteins may be added as assembly progresses along the maturation pathway (28). To ensure efficient incorporation, it is likely that individual tegument proteins are specifically targeted to their cellular site of recruitment. Such targeting could involve interaction with a viral partner, a cellular partner, or both. A clearer understanding of how individual tegument proteins are acquired by newly assembling virions will help to define the herpesvirus assembly pathway.A number of protein-protein interactions between individual tegument proteins (13, 40, 42), and between tegument proteins and glycoproteins (19, 20, 22, 32), have been described that may provide useful insight into the assembly process. In particular, the interaction of tegument proteins with the cytoplasmic tails of virus glycoproteins provides an attractive mechanism for the virion recruitment of at least the outer components of the tegument. In the case of VP22, the homologues from pseudorabies virus (PRV) and HSV-1 have been shown to interact with the cytoplasmic tail of gE (19, 20, 32). However, the role of this interaction in virus infection has not yet been clearly defined and the fact that additional glycoprotein interactions have been described, with gM in the case of PRV and gD in the case of HSV-1, may point to potential redundancy in the mechanism of VP22 packaging (4, 19, 20). In addition, we and others have previously shown that HSV-1 VP22 interacts directly with a second tegument protein, namely, VP16 (13, 33), an interaction that could provide an alternative route for VP22 to enter the virion. In a previous study, we concluded that the region of VP22 containing its VP16 interaction domain was required but not sufficient for optimal VP22 packaging into the assembling virion, with an additional C-terminal determinant also involved (23). We also demonstrated that the same region of VP22 that was required for virion packaging was essential to target the protein to its characteristic cytoplasmic trafficking complexes, suggesting that these specific sites may be the location in the cell for VP22 assembly into the virion (23). Since that study, O''Regan and coworkers have reported that the C-terminal half of HSV-1 VP22 also contains the binding site for gE (32), providing a possible candidate for an additional VP22 binding partner. Furthermore, as HSV-1 VP22 has been shown to bind to gD and PRV VP22 interacts with gM, it is possible that the C terminus of VP22 contains a gD and/or a gM binding site (4, 20).In the present study, we aimed to clarify the molecular mechanism by which VP22 is recruited into the virus particle. We show that HSV-1 VP22 binds efficiently to VP16, gE, and gM in the infected cell, but we cannot detect an interaction with gD. We show that the packaging domain of VP22 binds to the cytoplasmic tail of gE but not gM and that the same region of VP22 is recruited to the secretory pathway by gE in the absence of other virus proteins. Finally, we show that a mutant VP22 protein lacking a 14-residue peptide from its packaging domain is unable to interact with gE during infection, exhibits a different subcellular localization, and fails to assemble into the virus particle. This is the first characterization of a single protein-protein interaction essential for the packaging of an HSV-1 tegument protein.     

An Assessment of Air As a Source of DNA Contamination Encountered When Performing PCR

Sensitive molecular methods, such as the PCR, can detect low-level contamination, and careful technique is required to reduce the impact of contaminants. Yet, some assays that are designed to detect high copy-number target sequences appear to be impossible to perform without contamination, and frequently, personnel or laboratory environment are held responsible as the source. This complicates diagnostic and research analysis when using molecular methods. To investigate the air specifically as a source of contamination, which might occur during PCR setup, we exposed tubes of water to the air of a laboratory and clean hood for up to 24 h. To increase the chances of contamination, we also investigated a busy open-plan office in the same way. All of the experiments showed the presence of human and rodent DNA contamination. However, there was no accumulation of the contamination in any of the environments investigated, suggesting that the air was not the source of contamination. Even the air from a busy open-plan office was a poor source of contamination for all of the DNA sequences investigated (human, bacterial, fungal, and rodent). This demonstrates that the personnel and immediate laboratory environment are not necessarily to blame for the observed contamination.     

Isolation and identification of mucinolytic actinomycetes

Biochemical and physiological tests, and 16S rRNA gene sequences, were used to classify nine Actinomycete strains isolated from soil and sand samples in Thailand. These strains were isolated based on their ability to readily degrade mucin glycoproteins. A turbidometric based mucinolytic assay was developed to confirm this. In addition all strains showed significant production of proteases. Phylogenetic analysis of the strains revealed that from the nine isolated Actinomycete strains eight were closely related to Streptomyces species and one was identified as belonging to the genus Kitasatospora. The biochemical and physiological tests performed identified two strain pairs that were similar (with only 3.9% difference observed) and this was in accordance with the phylogenetic results obtained. The remaining strains were distinct from each other, with the soil-isolated strains forming a separate clade to the sand-isolated strains in the inferred phylogenetic trees. The isolated mucinolytic Actinomycete strains will be the subject of further investigations into their proteolytic and glycosidic activity. Mucin degrading enzymes such as these are studied for their potential to be used for the development of a drug delivery system.     

Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

Background  

Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes, found in fungi and bacteria, which biosynthesize peptides without the aid of ribosomes. Although their metabolite products have been the subject of intense investigation due to their life-saving roles as medicinals and injurious roles as mycotoxins and virulence factors, little is known of the phylogenetic relationships of the corresponding NRPSs or whether they can be ranked into subgroups of common function. We identified genes (NPS) encoding NRPS and NRPS-like proteins in 38 fungal genomes and undertook phylogenomic analyses in order to identify fungal NRPS subfamilies, assess taxonomic distribution, evaluate levels of conservation across subfamilies, and address mechanisms of evolution of multimodular NRPSs. We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including α-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi.     

Genetic dissimilarity,genetic diversity,and mate preferences in humans

It is clear that genes at the major histocompatibility complex (MHC) are involved in mate preferences in a range of species, including humans. However, many questions remain regarding the MHC's exact influence on mate preference in humans. Some research suggests that genetic dissimilarity and individual genetic diversity (heterozygosity) at the MHC influence mate preferences, but the evidence is often inconsistent across studies. In addition, it is not known whether apparent preferences for MHC dissimilarity are specific to the MHC or reflect a more general preference for genome-wide dissimilarity, and whether MHC-related preferences are dependent on the context of mate choice (e.g., when choosing a short-term and long-term partner). Here, we investigated whether preferences for genetic dissimilarity are specific to the MHC and also whether preferences for genetic dissimilarity and diversity are context dependent. Genetic dissimilarity (number of alleles shared) influenced male, but not female, partner preferences, with males showing a preference for the faces of MHC-dissimilar females in both mating contexts. Genetic diversity [heterozygosity (H) and standardized mean (d²)] influenced both male and female preferences, regardless of mating context. Females preferred males with greater diversity at MHC loci (H) and males preferred females with greater diversity at non-MHC loci (d²) in both contexts. Importantly, these findings provide further support for a special role of the MHC in human sexual selection and suggest that male and female mate preferences may work together to potentially enhance both male and female reproductive success by increasing genetic diversity in offspring.     

Mixed-mode pattern in Doublefoot mutant mouse limb--Turing reaction-diffusion model on a growing domain during limb development

It has been suggested that the Turing reaction-diffusion model on a growing domain is applicable during limb development, but experimental evidence for this hypothesis has been lacking. In the present study, we found that in Doublefoot mutant mice, which have supernumerary digits due to overexpansion of the limb bud, thin digits exist in the proximal part of the hand or foot, which sometimes become normal abruptly at the distal part. We found that exactly the same behaviour can be reproduced by numerical simulation of the simplest possible Turing reaction-diffusion model on a growing domain. We analytically showed that this pattern is related to the saturation of activator kinetics in the model. Furthermore, we showed that a number of experimentally observed phenomena in this system can be explained within the context of a Turing reaction-diffusion model. Finally, we make some experimentally testable predictions.