Modelling of underwater light in freshwater lakes using survival and failure time analysis

1. This study presents a new approach to modelling subsurface irradiance using concepts from survival and failure time analysis. The model applies a modified Weibull distribution function to predict downwelling irradiance. Data sets from forty-seven Norwegian sites show extremely high coefficients of determination, up to 99.99%, when analysed by the Weibull model.
2. The uncritical use of a single k _d value to model underwater light conditions is likely to result in poor estimates of received irradiance. This error may amount to several hundred per cent. The practice of force-fitting linear least-squares regressions to log-transformed irradiance data inevitably leads to highly biased estimates of the true fraction of incident irradiance entering the water.
3. Wave effects causing fluctuations of subsurface irradiance are modelled with synthetic data and compared with field observations. Fluctuations of surface elevation by waves produce skewed frequency distributions of the underwater light field. The result of these effects, which are to reduce the accuracy of estimated model parameters, can be largely eliminated by carefully designing field procedures used for the acquisition of subsurface light data.     

Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface

Background

A large number of studies have been carried out to obtain amino acid propensities for ??-helices and ??-sheets. The obtained propensities for ??-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the ??-sheet propensities obtained by several studies differed significantly, indicating that the context significantly affects ??-sheet propensity.

Results

We calculated amino acid propensities for ??-helices and ??-sheets for 39 and 24 protein folds, respectively, and addressed whether they correlate with the fold. The propensities were also calculated for exposed and buried sites, respectively. Results showed that ??-helix propensities do not differ significantly by fold, but ??-sheet propensities are diverse and depend on the fold. The propensities calculated for exposed sites and buried sites are similar for ??-helix, but such is not the case for the ??-sheet propensities. We also found some fold dependence on amino acid frequency in ??-strands. Folds with a high Ser, Thr and Asn content at exposed sites in ??-strands tend to have a low Leu, Ile, Glu, Lys and Arg content (correlation coefficient = ?0.90) and to have flat ??-sheets. At buried sites in ??-strands, the content of Tyr, Trp, Gln and Ser correlates negatively with the content of Val, Ile and Leu (correlation coefficient = ?0.93). "All-??" proteins tend to have a higher content of Tyr, Trp, Gln and Ser, whereas "??/??" proteins tend to have a higher content of Val, Ile and Leu.

Conclusions

The ??-helix propensities are similar for all folds and for exposed and buried residues. However, ??-sheet propensities calculated for exposed residues differ from those for buried residues, indicating that the exposed-residue fraction is one of the major factors governing amino acid composition in ??-strands. Furthermore, the correlations we detected suggest that amino acid composition is related to folding properties such as the twist of a ??-strand or association between two ?? sheets.     

The Simulium vernum group (Diptera: Simuliidae) in Europe: multiple character sets for assessing species status

The value of using characters from multiple sources – chromosomes, ecology, gene sequences, and morphology – to evaluate the species status of closely related black flies is demonstrated for three European members of the Simulium vernum group: Simulium crenobium (Knoz, 1961), Simulium juxtacrenobium Bass & Brockhouse, 1990, and Simulium vernum s.s. Macquart, 1826. Simulium juxtacrenobium is a chromosomally, molecularly, and morphologically distinct species that diverged from S. crenobium and S. vernum s.s. about 2 Mya. It is specialized for intermittent streams, is univoltine, and is recorded for the first time from northern Europe, based on collections from Finland and Sweden, representing a range extension of about 1800 km. In contrast, S. crenobium, although confirmed as a distinct species, differs from S. vernum s.s. by only a few larval and chromosomal characters, and by a breeding habitat restricted to mountain spring brooks. Whereas all four character sets independently support the specific distinctness of S. juxtacrenobium and S. vernum s.s., multiple character sets are required to establish the specific validity of S. crenobium.     

The rarity concept and the commonness of rarity in freshwater zooplankton

1. Regional distribution, frequency of occurrence and relative abundance were scored in 2467 Norwegian lakes for all the recorded 130 species of crustacean zooplankton. The majority of species were rare in the sense that 65% of species were recorded in fewer than 10% of localities. Only six species were recorded in more than 50% of localities, and the median number of species in a given locality was 14 (i.e. 10% of the total species pool). 2. Abundances of all species were scored according to the fraction of lakes in which they were recorded, their geographical range of distribution, and their numerical abundance. Typically the most rare species were rare by all three criteria, and vice versa for the common species, pointing to rarity as an inherent property of some species. For some species this rarity reflects being on the edge of their distributional range, while for others rarity seems to be a consequence of their life cycle strategies. 3. Some of the truly rare species have high dispersal rates and high colonization abilities, but are rapidly replaced by other species. Others are confined to specific habitats, often highly eutrophic, pointing to highly specialized niche adaptations. 4. A major cause for the few truly common species seems to be the limited number of species that are able to coexist within a given locality, reflecting ‘the ghost of competition past’ and predation pressure. 5. While species composition and species richness may reflect colonization abilities and stochastic events, the presence or absence of species is not only a random lottery but also a consequence of species‐specific attributes.     

Patterns of inbreeding depression in a population of Brassica cretica (Brassicaceae): evidence from family-level analyses

In this investigation, we have collected family-structured data from a partly self-compatible, outcrossing population of Brassica cretica to estimate and compare the effects of one-generation selfing on different types of characters. Inbreeding not only depressed characters that should be positively correlated with fitness irrespective of habitat, e.g. germinability, leaf number and inflorescence size, but also resulted in later flowering, smaller and more asymmetric flowers, and an increased production of basal branches. Population-level estimates of inbreeding depression were similar in magnitude to estimates reported in other wild plant species. There was a tendency for direct components of fitness to exhibit a stronger response to inbreeding than other characters, but only when the differences between selfed and outbred offspring were measured in standard deviation units. Family-level estimates of inbreeding depression were weakly correlated across characters. Given these and other observations, we hypothesize that the genetic basis of inbreeding depression varies across the life cycle and that changes in local inbreeding will lead to shifts in the mean phenotypes of B. cretica populations. However, judging from data on current levels of population divergence, quite large changes in inbreeding will be required to influence large-scale patterns of variation in this species.  © 2002 The Linnean Society of London. Biological Journal of the Linnean Society , 2002, 76 , 317–325.     

Morphology and morphogenesis of ensiform leaves, syndesmy of shoots and an understanding of the thalloid plant body in species of Apinagia, Mourera and Marathrum (Podostemaceae)

The flattened, irregularly shaped and lobed or dissected leaves of Apinagia riedelii , A. latifolia , A. goejei , Mourera aspera and Marathrum utile (subfamily Podostemoideae) are ensiform in structure. After the typical bifacial inception, further growth of leaves proceeds in the midrib area, i.e. in the median plane of the leaf. The lower leaf zone is characterized by a sheath that orientates 'at the side of the blade', i.e. at the adaxial edge of the sword-like leaf. The ensiform blades are lobed, incised or pinnately dissected with the tips terminated in elongated threads or thin filaments. Leaves of Apinagia riedelii resemble pinnately dissected compound leaves. The dissected structure represents a secondary superimposition of the ensiform shape and a parallel development to compound leaves. It is interpreted as an adaptation to the rapid current, established in the floating shoots of these aquatic plants. The basal portions of main shoots and successive branches are fused due to a retarded separation. Fusion of this kind has been termed a syndesmy. The fused region of shoots is superseded by the fusion of the lower leaf zones of (distichously positioned) adjacent leaves, occurring at their margins. The fused leaf bases form a cavity for the terminal flower bud of each shoot and cover it in the form of a hood. The flower buds are hidden from external view. The meristematic growing zones are thus protected and enclosed within the syndesmic plant body which, in this way, attains the 'thalloid' appearance especially developed in Apinagia goejei and A. latifolia but also present in the other species. The results of this study enable an understanding of the particular appearance of these Podostemoideae as modifications of the typical structures according to the 'principle of variable proportions'.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 47–71.     

Terrestrial Activity in Pitheciins (Cacajao,Chiropotes, and Pithecia)

Neotropical monkeys of the genera Cacajao, Chiropotes, and Pithecia (Pitheciidae) are considered to be highly arboreal, spending most of their time feeding and traveling in the upper canopy. Until now, the use of terrestrial substrates has not been analyzed in detail in this group. Here, we review the frequency of terrestrial use among pitheciin taxa to determine the ecological and social conditions that might lead to such behavior. We collated published and unpublished data from 14 taxa in the three genera. Data were gleaned from 53 published studies (including five on multiple pitheciin genera) and personal communications of unpublished data distributed across 31 localities. Terrestrial activity was reported in 61% of Pithecia field studies (11 of 18), in 34% of Chiropotes studies (10 of 29), and 36% of Cacajao studies (4 of 11). Within Pithecia, terrestrial behavior was more frequently reported in smaller species (e.g. P. pithecia) that are vertical clingers and leapers and make extensive use of the understory than in in the larger bodied canopy dwellers of the western Amazon (e.g. P. irrorata). Terrestrial behavior in Pithecia also occurred more frequently and lasted longer than in Cacajao or Chiropotes. An apparent association was found between flooded habitats and terrestrial activity and there is evidence of the development of a “local pattern” of terrestrial use in some populations. Seasonal fruit availability also may stimulate terrestrial behavior. Individuals also descended to the ground when visiting mineral licks, escaping predators, and responding to accidents such as a dropped infant. Overall, the results of this review emphasize that terrestrial use is rare among the pitheciins in general and is usually associated with the exploitation of specific resources or habitat types. Am. J. Primatol. 74:1106‐1127, 2012. © 2012 Wiley Periodicals, Inc.     

Modelling of underwater light in freshwater lakes using survival and failure time analysis

1. This study presents a new approach to modelling subsurface irradiance using concepts from survival and failure time analysis. The model applies a modified Weibull distribution function to predict downwelling irradiance. Data sets from forty-seven Norwegian sites show extremely high coefficients of determination, up to 99.99%, when analysed by the Weibull model.
2. The uncritical use of a single k _d value to model underwater light conditions is likely to result in poor estimates of received irradiance. This error may amount to several hundred per cent. The practice of force-fitting linear least-squares regressions to log-transformed irradiance data inevitably leads to highly biased estimates of the true fraction of incident irradiance entering the water.
3. Wave effects causing fluctuations of subsurface irradiance are modelled with synthetic data and compared with field observations. Fluctuations of surface elevation by waves produce skewed frequency distributions of the underwater light field. The result of these effects, which are to reduce the accuracy of estimated model parameters, can be largely eliminated by carefully designing field procedures used for the acquisition of subsurface light data.     

The faunal drugstore: Animal-based remedies used in traditional medicines in Latin America

Zootherapy is the treatment of human ailments with remedies made from animals and their products. Despite its prevalence in traditional medical practices worldwide, research on this phenomenon has often been neglected in comparison to medicinal plant research. This review discusses some related aspects of the use of animal-based remedies in Latin America, identifies those species used as folk remedies, and discusses the implications of zootherapy for public health and biological conservation. The review of literature revealed that at least 584 animal species, distributed in 13 taxonomic categories, have been used in traditional medicine in region. The number of medicinal species catalogued was quite expansive and demonstrates the importance of zootherapy as an alternative mode of therapy in Latin America. Nevertheless, this number is certainly underestimated since the number of studies on the theme are very limited. Animals provide the raw materials for remedies prescribed clinically and are also used in the form of amulets and charms in magic-religious rituals and ceremonies. Zootherapeutic resources were used to treat different diseases. The medicinal fauna is largely based on wild animals, including some endangered species. Besides being influenced by cultural aspects, the relations between humans and biodiversity in the form of zootherapeutic practices are conditioned by the social and economic relations between humans themselves. Further ethnopharmacological studies are necessary to increase our understanding of the links between traditional uses of faunistic resources and conservation biology, public health policies, sustainable management of natural resources and bio-prospecting.