The motility symbiont of the termite gut flagellate Caduceia versatilis is a member of the "Synergistes" group

The flagellate Caduceia versatilis in the gut of the termite Cryptotermes cavifrons reportedly propels itself not by its own flagella but solely by the flagella of ectosymbiotic bacteria. Previous microscopic observations have revealed that the motility symbionts are flagellated rods partially embedded in the host cell surface and that, together with a fusiform type of ectosymbiotic bacteria without flagella, they cover almost the entire surface. To identify these ectosymbionts, we conducted 16S rRNA clone analyses of bacteria physically associated with the Caduceia cells. Two phylotypes were found to predominate in the clone library and were phylogenetically affiliated with the "Synergistes" phylum and the order Bacteroidales in the Bacteroidetes phylum. Probes specifically targeting 16S rRNAs of the respective phylotypes were designed, and fluorescence in situ hybridization (FISH) was performed. As a result, the "Synergistes" phylotype was identified as the motility symbiont; the Bacteroidales phylotype was the fusiform ectobiont. The "Synergistes" phylotype was a member of a cluster comprising exclusively uncultured clones from the guts of various termite species. Interestingly, four other phylotypes in this cluster, including the one sharing 95% sequence identity with the motility symbiont, were identified as nonectosymbiotic, or free-living, gut bacteria by FISH. We thus suggest that the motility ectosymbiont has evolved from a free-living gut bacterium within this termite-specific cluster. Based on these molecular and previous morphological data, we here propose a novel genus and species, "Candidatus Tammella caduceiae," for this unique motility ectosymbiont of Caducaia versatilis.     

In Sickness and in Health: The Role of TRAPP and Associated Proteins in Disease

Transport protein particle (TRAPP) represents a series of related protein complexes that function in specific stages of inter‐organelle traffic. They share a core of subunits that can activate the GTPase Rab1 through a guanine nucleotide exchange factor (GEF) activity and are distinguished by ‘accessory’ subunits giving each complex its distinct function. The subunits are ubiquitously expressed and, thus, mutations in TRAPP subunits would be expected to be embryonic lethal. However, since its discovery, a number of subunits have been found to be mutated in several diverse human disorders suggesting that some of these subunits may have cell‐ or tissue‐specific functions. Here we review the current state of knowledge with respect to TRAPP subunit mutations in human disease. We suggest ideas to explain their tissue‐specific phenotypes and present avenues for future investigation.      

Cytomorphometric differences among individual "moderate dysplasia" cells derived from cervical intraepithelial neoplasia

Individual abnormal cervical epithelial cells can be categorized either by the lesion from which they are derived or by their unique cytologic characteristics. In building a data base for image analysis of cervical epithelial cells, categories of cells were defined according to distinct cytomorphologic characteristics, without knowledge of the lesion of origin. The three individual scorers, two cytopathologists and one senior cytotechnologist, most frequently agreed upon the cells classified as "moderate dysplasia." The measurements of digitized cells in this category had the smallest confidence intervals of any of the abnormal cell categories. For these two reasons, as well as the ubiquitous nature of "moderate dysplasia" cells in smears obtained from all patients with cervical epithelial neoplasia, cells in this category were studied in greater detail. Significant differences were noted in cell measurements among cells in this class when the cells came from patients with different grades of cervical neoplasia. The findings indicate that visually similar "moderate dysplasia" cells can be separated by digitized measurements into clusters dependent upon the parent lesion. The biologic implications are not yet clear, but such findings suggest that each disease is perhaps a committed lesion from inception. Therefore, predictability of ultimate outcome could be based on image analysis of cells derived from early cervical lesions, which would allow therapy to be performed on a more logical basis.     

Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes

Background

Model organisms have contributed substantially to our understanding of the etiology of human disease as well as having assisted with the development of new treatment modalities. The availability of the human, mouse and, most recently, the rat genome sequences now permit the comprehensive investigation of the rodent orthologs of genes associated with human disease. Here, we investigate whether human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change.

Results

Human disease genes are unevenly distributed among human chromosomes and are highly represented (99.5%) among human-rodent ortholog sets. Differences are revealed in evolutionary conservation and selection between different categories of human disease genes. Although selection appears not to have greatly discriminated between disease and non-disease genes, synonymous substitution rates are significantly higher for disease genes. In neurological and malformation syndrome disease systems, associated genes have evolved slowly whereas genes of the immune, hematological and pulmonary disease systems have changed more rapidly. Amino-acid substitutions associated with human inherited disease occur at sites that are more highly conserved than the average; nevertheless, 15 substituting amino acids associated with human disease were identified as wild-type amino acids in the rat. Rodent orthologs of human trinucleotide repeat-expansion disease genes were found to contain substantially fewer of such repeats. Six human genes that share the same characteristics as triplet repeat-expansion disease-associated genes were identified; although four of these genes are expressed in the brain, none is currently known to be associated with disease.

Conclusions

Most human disease genes have been retained in rodent genomes. Synonymous nucleotide substitutions occur at a higher rate in disease genes, a finding that may reflect increased mutation rates in the chromosomal regions in which disease genes are found. Rodent orthologs associated with neurological function exhibit the greatest evolutionary conservation; this suggests that rodent models of human neurological disease are likely to most faithfully represent human disease processes. However, with regard to neurological triplet repeat expansion-associated human disease genes, the contraction, relative to human, of rodent trinucleotide repeats suggests that rodent loci may not achieve a 'critical repeat threshold' necessary to undergo spontaneous pathological repeat expansions. The identification of six genes in this study that have multiple characteristics associated with repeat expansion-disease genes raises the possibility that not all human loci capable of facilitating neurological disease by repeat expansion have as yet been identified.     

Heart position in snakes: response to "phylogeny, ecology, and heart position in snakes"

Here we comment on a recent article (Gartner et al. 2010 ) that addresses previous adaptive interpretations of heart position in the context of gravity effects on blood circulation of snakes. The authors used phylogenetically based statistical methods and concluded that both habitat and phylogeny influence heart position, which they contend is relatively more posterior in arboreal compared to terrestrial species. Their result is based on measurements of heart position relative to snout-vent length, rather than total body length as in previous studies. However, gravity acts on the total length of the arterial-venous vasculature, and caudal segments of continuous blood columns cannot be ignored. Arboreal snakes have relatively long tails; therefore anterior hearts appear to be more "posterior" when the position is described relative to a shorter trunk. There is no physiologically valid explanation for the alleged posterior heart position in arboreal snakes, and multiple lines of published evidence to the contrary are ignored. The authors secondarily evaluated their data set with estimates for total body length based on measurements from other taxa. They found no statistical difference between heart position in arboreal versus terrestrial species, yet their article implied otherwise. Gartner et al. ( 2010 ) contrasted "aquatic" and terrestrial species throughout their paper, and they claimed there is no correlation between heart position and habitat among "aquatic and terrestrial species." But they did not include any aquatic species in their data set. Therefore, the article confuses rather than promotes understanding of cardiovascular adaptation to gravity.     

基于椭圆脐点突变模型的大熊猫生存状态研究

得益于有力的保护,大熊猫受威胁等级由"濒危"降为"易危"。根据全国大熊猫调查数据,近年来,大熊猫野生种群与栖息地面积总体上均处于持续增加态势;同时,大熊猫栖息地破碎化与局域种群隔离也呈加剧的趋势。两相对比,形成悖论现象,难以正确认知当前大熊猫的生存状态。大熊猫作为高度特化的K对策大型动物,其生存高度依赖于栖息地生态系统,极易受栖息地丧失与破碎化的影响。对大熊猫生存状态的研究,不应局限于栖息地或种群等单项指标的变化,而应基于系统科学的整体视角。结合全国第三、四次大熊猫调查数据,对大熊猫野生种群数量与栖息地及潜在栖息地的面积进行复相关分析,发现大熊猫野生种群数量与栖息地、潜在栖息地的面积之间存在着高度显著正相关,表明三者之间存在着稳定而密切的耦合关系,进而建立了大熊猫种群与栖息地、潜在栖息地之间的耦合函数。突变理论作为一种成熟的系统科学理论,提供了较完备的数学方法,利用系统中少量的关键指标便可实现对系统行为的刻画。基于突变理论,以大熊猫分布区生态系统为研究对象,选取了大熊猫种群数量、栖息地与潜在栖息地的面积为系统关键指标,利用种群与栖息地、潜在栖息地之间的耦合函数,构建了"大熊猫—栖息地"系统椭圆脐点突变模型,对生态系统的稳定性进行研究。发现虽然野生种群数量、栖息地与潜在栖息地的面积均持续增长,但严峻的局域种群生存危机与栖息地的高度破碎化,从总体上削弱了系统的稳定性,大熊猫分布区生态系统的稳定性处于持续下降态势,且濒临系统临界状态,生态系统具有较大的退化压力,大熊猫的生存危机依然严峻。     

Clinical and Treatment Aspects of Brown–Black Fungi

Brown–black (or dematiaceous) fungi are responsible for a wide variety of infectious syndromes in both immunocompetent and immunocompromised patients, including local infections, allergic disease, pneumonia, brain abscess, and disseminated infection. They are distinct from the more common hyaline molds, Aspergillus and Fusarium, that cause human disease. They are often found in soil and generally distributed worldwide. In recent years, these fungi have been increasingly recognized as important pathogens. Dematiaceous fungi may have unique pathogenic mechanisms owing to the presence of melanin in their cell walls, which imparts the characteristic dark color to their spores and hyphae. Diagnosis rests on careful microscopic and pathologic examination, as there are no specific laboratory tests to reliably identify these fungi. Therapy depends upon the clinical syndrome, although disseminated infection often has high mortality. Triazoles such as voriconazole, posaconazole, and itraconazole are the most active antifungal agents available. Further studies are needed to better understand the pathogenesis and optimal treatment of these uncommon infections.     

Water availability drives habitat quality for the butterfly <Emphasis Type="Italic">Plebejus argus</Emphasis> in a Mediterranean sand dune landscape

For terrestrial species, habitat is frequently defined as physical patches of a certain land cover type in a matrix of non-habitat. However, the appropriate definition of habitat quality requires more detailed information on the resources and conditions that are necessary for the maintenance of the species (‘resource-based habitat approach’). In arthropods, their life cycle comprises several clearly differentiated stages that may depend on different resources and conditions for successful development; in turn, males and females may have different habitat requirements due to their different behaviours. Here we examine the habitat quality for males, females and eggs of the butterfly Plebejus argus in a continuous sand dune landscape in southern Spain. For both sexes, abundance was related to host plant density (negatively) and distance to heathland vegetation (a surrogate for higher water availability; negatively for males and hump-shaped for females); and, for males only, positively with flower presence. Egg abundance was positively related to mutualistic ant frequency and flower presence, and negatively to distance to heathland. Hence, female and male adults and eggs of P. argus partly differed in their dependence on resources and conditions, although distance to wetter areas of heathland was the common variable for all models. This suggests that soil humidity is the key variable for P. argus habitat quality, probably through both direct effects on individuals and indirect effects on interacting species (mutualistic ants and nectar sources). As a result, we found a high spatial congruence in habitat quality between males and females, and a moderate congruence between adults and eggs.     

Geographical distribution and habitat occurrence of the Water Shrew (Neomys fodiens) in the Weald of South-East England

A survey of 96 sites in a range of riparian habitats in the catchments of five rivers during June–August 1998 used the bait tube method to investigate the geographical distribution and habitat occurrence of Water Shrews (Neomys fodiens) in the Weald of South‐East England. Water Shrews were found at 42% of sites, and were widely distributed in all river catchments except the Mole. They occurred in many riparian habitats, including rivers, streams, canals and ditches, with a range of physical and biotic characteristics. There were no signs of habitat avoidance in response to human disturbance but Water Shrews were absent from the river catchment with lowest water quality. Logistic regression analysis was used to model the effect of habitat variables on the presence of Water Shrews, with current speed, water depth, bank incline and bank‐side vegetation identified as important variables. Fast‐flowing shallow waters had a significant positive effect on their presence, whereas scarce herbaceous vegetation and a bank of low incline had a significant negative effect. These habitat variables appear to be reliable indicators of the probability of finding Water Shrews at a particular site, and have implications for habitat management and conservation.     

Pathogenic archaea: do they exist?

Archaea are microorganisms that are distinct from bacteria and eukaryotes. They are prevalent in extreme environments, and yet found in most ecosystems. They are a natural component of the microbiota of most, if not all, humans and other animals. Despite their ubiquity and close association with humans, animals and plants, no pathogenic archaea have been identified. Because no archaeal pathogens have yet been identified, there is a general assumption that archaeal pathogens do not exist. This review examines whether this is a good assumption by investigating the potential for archaea to be or become pathogens. This is achieved by addressing: the diversity of archaea versus known pathogens, opportunities for archaea to demonstrate pathogenicity and be detected as pathogens, reports linking archaea with disease, and immune responses to archaea. In addition, molecular and genomic data are examined for the presence of systems utilised in pathogenesis. The view of this report is that, although archaea can presently be described as non-pathogenic, they have the potential to be (discovered as) pathogens. The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future.     

The interactions between humans and mammals in Africa in relation to conservation: a review

Most human-mammal interactions are detrimental to wild mammals. In Africa, mammalian population numbers and the geographical distribution of many species have been reduced due to hunting, pastoralism, habitat modification and disease control. The importance of each of these factors depends on the species, its location and habitat, and density of the human population. In contrast, some small- and medium-sized species have benefited from human activities, and there has been an increase in the population numbers of some species in well-managed and well-protected conservation areas. There appears to be a strong negative correlation (at least for some well-studied species) between density of humans and density of mammals. Recently, several African countries, notably in southern Africa, have developed the principle of integrated rural development in which local people are involved in the planning and administration of their traditional lands. Managed conservation areas are an integral part of good land-use policies. Surveys indicate that most Africans living close to conservation areas, especially those with a higher level of education, understand and support the ideals of conservation; nevertheless it is important that the benefits of conservation and integrated development (such as money, jobs, and food) directly benefit the local people. Conservation of mammals (and all other species) in Africa in the future will only succeed if there is participation at the grass roots level, better food production in designated agricultural areas, reduction in the rate of increase of human populations, stabilization of human densities, and active programmes of conservation education.     

Water and Solute Balance in the Transition to Land

Terrestrial crabs are physiologically rather similar to theiraquatic relatives, despite their markedly different access towater and ions. They have high evaporation rates and void vitalsalts in isosmotic urine. Some of them manage to have fairlymiserly water and ion budgets, but others succeed despite profligacy.There is no single solution to the challenges of terrestriallife; each pairing of animal and environment must be seen asa system in which a unique suite of behaviors compensates forlimited physiological prowess. By exploiting temporal and spatialvariability of available microhabitats, each species assemblesa "composite habitat" in which it can balance the "debit" sidesof its water and ion budgets with the requisite "credits."     

The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders.

Mitochondria possess their own translational machinery, which is composed of components distinct from their cytoplasmic counterparts. To investigate the possible involvement of mitochondrial ribosomal defects in human disease, we mapped nuclear genes that encode mitochondrial ribosomal proteins (MRPs). We generated sequence-tagged sites (STSs) of individual MRP genes that were able to be detected by PCR. They were placed on an STS content map of the human genome by typing of radiation hybrid panels. We located 54 MRP genes on the STS-content map and assigned these genes to cytogenetic bands of the human chromosomes. Although mitochondria are thought to have originated from bacteria, in which the genes encoding ribosomal proteins are clustered into operons, the mapped MRP genes are widely dispersed throughout the genome, suggesting that transfer of each MRP gene to the nuclear genome occurred individually. We compared the assigned positions with candidate regions for mendelian disorders and found certain genes that might be involved in particular diseases. This map provides a basis for studying possible roles of MRP defects in mitochondrial disorders.     

Naturally occurring murine leukemia viruses in wild mice: characterization of a new "amphotropic" class.

A new class of murine leukemia viruses, isolated from wild Mus musculus trapped in California, is described. These viruses, designated "amphotropic," replicate in mouse, rabbit, mink, human, guinea pig, and rat cells, but not in hamster, quail, or duck cells. They show N-tropism for mouse cells, and do not trigger the XC cell response. They are distinct by interference and virus neutralization testing from the previously recognized mouse-tropic and xenotropic MuLV classes. Mouse-tropic viruses occuring along with three of the four amphotropic isolates were found to be distinguishable by virus neutralization from other mouse-tropic murine leukemia virus strains of laboratory mouse origin.     

Staying cool or staying safe in a human-dominated landscape: which is more relevant for brown bears?

Pigeon et al. (2016) Staying cool in a changing landscape: the influence of maximum daily ambient temperature on grizzly bear habitat selection. Oecologia 181:1101. doi: 10.1007/s00442-016-3630-5 analyzed the effect of ambient temperature on the habitat selection of grizzly bears (Ursus arctos) in Alberta, Canada. They concluded that temperature played a significant role in bear habitat selection and that it was unlikely that human activity introduced biases to the habitat selection of bears. However, Pigeon et al. did not consider variables related to human activities in their analyses. They also misinterpreted previous research that has accounted for temperature in the habitat selection of brown bears. There is much literature published on the negative effects of human disturbance on wildlife in general and on bears in particular. Downplaying the role of human disturbance could have important negative consequences if, in fact, human disturbance were a more important factor than thermoregulation. Indeed, dismissing the importance of human influence, in the face of contradictory evidence, could tempt managers to disregard an important factor that is difficult and often unpopular to deal with in their conservation plans.     

Pyramidal neurons: dendritic structure and synaptic integration

Pyramidal neurons are characterized by their distinct apical and basal dendritic trees and the pyramidal shape of their soma. They are found in several regions of the CNS and, although the reasons for their abundance remain unclear, functional studies--especially of CA1 hippocampal and layer V neocortical pyramidal neurons--have offered insights into the functions of their unique cellular architecture. Pyramidal neurons are not all identical, but some shared functional principles can be identified. In particular, the existence of dendritic domains with distinct synaptic inputs, excitability, modulation and plasticity appears to be a common feature that allows synapses throughout the dendritic tree to contribute to action-potential generation. These properties support a variety of coincidence-detection mechanisms, which are likely to be crucial for synaptic integration and plasticity.     

Differential Habitat Use and Niche Partitioning by <Emphasis Type="Italic">Pseudomonas</Emphasis> Species in Human Homes

Many species of Pseudomonas have the ability to use a variety of resources and habitats, and as a result Pseudomonas are often characterized as having broad fundamental niches. We questioned whether actual habitat use by Pseudomonas species is equally broad. To do this, we sampled extensively to describe the biogeography of Pseudomonas within the human home, which presents a wide variety of habitats for microbes that live in close proximity to humans but are not part of the human flora, and for microbes that are opportunistic pathogens, such as Pseudomonas aeruginosa. From 960 samples taken in 20 homes, we obtained 163 Pseudomonas isolates. The most prevalent based on identification using the SepsiTest BLAST analysis of 16S rRNA () were Pseudomonas monteilii (42 isolates), Pseudomonas plecoglossicida, Pseudomonas fulva, and P. aeruginosa (approximately 25 each). Of these, all but P. fulva differed in recovery rates among evaluated habitat types (drains, soils, water, internal vertebrate sites, vertebrate skin, inanimate surfaces, and garbage/compost) and all four species also differed in recovery rates among subcategories of habitat types (e.g., types of soils or drains). We also found that at both levels of habitat resolution, each of these six most common species (the four above plus Pseudomonas putida and Pseudomonas oryzihabitans) were over- or under-represented in some habitats relative to their contributions to the total Pseudomonas collected across all habitats. This pattern is consistent with niche partitioning. These results suggest that, whereas Pseudomonas are often characterized as generalists with broad fundamental niches, these species in fact have more restricted realized niches. Furthermore, niche partitioning driven by competition among Pseudomonas species may be contributing to the observed variability in habitat use by Pseudomonas in this system.     

Intraspecific morphological and genetic differentiation in <Emphasis Type="Italic">Scrophularia grayana</Emphasis> (Scrophulariaceae)

Scrophularia grayana, which is distributed throughout northern Japan and Sakhalin, and its locally endemic variety var. grayanoides, have been examined morphometrically and genetically. Principal-component analysis using a total of 26 morphological characteristics revealed that these taxa are morphologically differentiated, but that the difference is not distinct. These two taxa have the same number of chromosomes in the somatic cells, 2n = 94, suggesting that ploidal level difference is not relevant to their divergence. The distributions of the taxa are adjoining in the north of Japanese mainland Honshu. Nevertheless, principal-coordinate analysis using putative 112 ISSR loci indicated they are genetically very distinct. Many taxon-specific alleles were found, and many of the alleles were fixed in each taxon. This genetic information suggests that a relatively long time has passed since the taxa became differentiated and that gene flow has rarely occurred between them, although morphological similarity has been maintained, probably because of natural selective forces. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

Ecomorphological relationships of a guild of ground-foraging birds in northern California,USA

Summary We studied habitat and morphological relationships of nine species of birds comprising a groundforaging guild within four distinct locations in northern California. Although the nine species overlapped extensively in habitat use, we observed subtle differences among species in specific characteristics of the habitats they used. About 40% of all cases were classified to the correct species based on a discriminant analysis (DA) of habitats across all study areas. Classification success from DAs on habitats within study areas ranged from 42 to 66%. Morphologies of species differed to varying degrees as 91% of all cases were classified to correct species by a DA of morphological variables. This morphological separation suggested that each species used different modes of obtaining resources. We found only weak relationships between habitat use and morphology. Morphology predicted from 13.6 to 19.0% of the variation in habitat use within each study area and only 13.9% of the habitat variation across all study areas. Habitat predicted from 6.2 to 14.6% of the morphological variation within each study area and 6.9% across all study areas. We suggest that complimentary relationships of habitat and morphology enabled species within this guild to use unique sets of resources.