Rich inflection and the production of finite verbs in child language

Children acquiring languages with rich inflection produce verbal morphology earlier in development than those learning languages with more impoverished inflection. In this paper, I present data from bilingual children acquiring Basque and Spanish, two null-subject languages with rich morphology which show a lead-lag pattern in the acquisition of inflection. Verbal inflection appears earlier in Spanish than in Basque, and although children produce few root infinitives in either language, they produce fewer in Spanish than in Basque. This is surprising, given that Basque has even “richer” verbal inflection than Spanish insofar as Basque has more obligatory morphological distinctions than Spanish does. These results lead me to propose that a combination of factors facilitate the early emergence of inflection in languages such as Spanish, including nominative/accusative case marking as well as morphological complexity, rather than solely the richness of the verbal paradigm.     

语码转换在微生物学双语教学中的应用

改革传统的双语教学,探索高校新型的双语教学方式已经成为教育教学改革的必然趋势.语码转换是指在一个语段或语篇中使用两种或两种以上语言的现象.为了保证双语教学效果,提高教学质量,在微生物学授课过程中应用语码转换的方式进行渗透式双语授课,适时适量地向学生渗透专业英语语汇、语句、语段或语篇,激发了学生的学习热情,增强了学生英语表达的自信心.     

Microsatellite analysis of genetic variation in black bear populations

Measuring levels of genetic variation is an important aspect of conservation genetics The informativeness of such measurements is related to the variability of the genetic markers used; a particular concern in species, such as bears, which are characterized by low levels of genetic variation resulting from low population densities and small effective population sizes We describe the development of microsatellite analysis in bears and its use in assessing interpopulation differences in genetic variation in black bears from three Canadian National Parks These markers are highly variable and allowed identification of dramatic differences in both distribution and amount of variation between populations Low levels of variation were observed in a population from the Island of Newfoundland The significance of interpopulation differences in variability was tested using a likelihood ratio test of estimates of θ= 4 N_eu.     

Spatial distribution as a measure of conservation needs: an example with Asiatic black bears in south-western China

Aim To create a fine‐scale map of the distribution of Asiatic black bears, identify landscape variables affecting the spatial range of this species and assess population trends using presence–absence data and opinions of local villagers. Location Sichuan Province, south‐western China. Methods We divided the province into 15 × 15 km cells, stratified them by forest cover, elevation and road density and randomly selected 494 cells (21% of province) for surveys. In each cell, we interviewed villagers and ground‐verified their reports of bear presence. We ground‐truthed reports of bear absence by conducting transects for bear sign in the best available habitat. We used logistic regression to identify key variables affecting presence of bears and predict their occurrence in unsampled cells. Results We detected bears in 360 cells (73%). Models correctly predicted bear occurrence in 90.3% of cells where we detected bears and 84.5% of sampled cells where bears were absent. Models predicted 42.7% of Sichuan to be occupied by bears. Bear occurrence was strongly related to forest cover throughout the province. Roads had a negative effect in western region of province. Agricultural lands had a negative effect only when they were distant from forests. Villagers were accurate in their knowledge of bear presence or absence. Interviewed villagers (n = 1816) thought that bears were increasing in 32%, stable in 10%, and decreasing in 58% of cells with bears. Where bear populations were perceived to be declining, villagers identified poaching as the most common cause. Main conclusions Our fine‐scale distribution map can be used for future monitoring and the key landscape factors related to occupancy by bears can be used in management plans for this species. Interviewing local villagers is an efficient and reliable means of assessing distribution, and changes therein, for animals such as bears that often interact with people and leave obvious signs.     

Speaker Input Variability Does Not Explain Why Larger Populations Have Simpler Languages

A learner’s linguistic input is more variable if it comes from a greater number of speakers. Higher speaker input variability has been shown to facilitate the acquisition of phonemic boundaries, since data drawn from multiple speakers provides more information about the distribution of phonemes in a speech community. It has also been proposed that speaker input variability may have a systematic influence on individual-level learning of morphology, which can in turn influence the group-level characteristics of a language. Languages spoken by larger groups of people have less complex morphology than those spoken in smaller communities. While a mechanism by which the number of speakers could have such an effect is yet to be convincingly identified, differences in speaker input variability, which is thought to be larger in larger groups, may provide an explanation. By hindering the acquisition, and hence faithful cross-generational transfer, of complex morphology, higher speaker input variability may result in structural simplification. We assess this claim in two experiments which investigate the effect of such variability on language learning, considering its influence on a learner’s ability to segment a continuous speech stream and acquire a morphologically complex miniature language. We ultimately find no evidence to support the proposal that speaker input variability influences language learning and so cannot support the hypothesis that it explains how population size determines the structural properties of language.     

A wavelet‐based approach to evaluate the roles of structural and functional landscape heterogeneity in animal space use at multiple scales

The functional relationship between habitat utilization and landscape spatial heterogeneity is fundamental to understanding the spatial nature of animal distribution across scales. Although structural and functional properties of landscape spatial heterogeneity can have different consequences for animal species, few studies have explicitly considered both forms of heterogeneity, partly due to the lack of general methods for direct assessment of scale‐specific associations between variables. We present a wavelet‐based approach to evaluate the roles of structural and functional landscape spatial heterogeneity in animal space use at multiple spatial scales. As a case study, we examined scale‐specific space use patterns of American black bears Ursus americanus in response to structural and functional spatial heterogeneity as well as spatial patterns of vegetation age‐classes in a Canadian boreal forest. We found strong differences in the effects of structural and functional spatial heterogeneity and the scales at which they are associated with the patterns of habitat use by black bears. Functional heterogeneity alone affected space use at 800 and 1600‐m scales, but had significant effects when interacting with structural heterogeneity at 400, 800, and 1600‐m scales. Compared with male bears, female black bears were most sensitive to patterns of forage abundance at intermediate scales, or more specifically, in young and regenerating forests that provide abundant soft mast in boreal forests. Our study highlights the importance of accounting for scale‐dependent properties of (structural and functional) spatial heterogeneity in assessing the ecological effects of landscape components and the effectiveness of the wavelet transform technique in identifying such scale‐specific relationships.     

Genomic selection: prediction of accuracy and maximisation of long term response

Genomic selection refers to the use of dense markers covering the whole genome to estimate the breeding value of selection candidates for a quantitative trait. This paper considers prediction of breeding value based on a linear combination of the markers. In this case the best estimate of each marker’s effect is the expectation of the effect conditional on the data. To calculate this requires a prior distribution of marker effects. If the marker effects are normally distributed with constant variance, BLUP can be used to calculate the estimated effects of the markers and hence the estimated breeding value (EBV). In this case the model is equivalent to a conventional animal model in which the relationship matrix among the animals is estimated from the markers instead of the pedigree. The accuracy of the EBV can approach 1.0 but a very large amount of data is required. An alternative model was investigated in which only some markers have non-zero effects and these effects follow a reflected exponential distribution. In this case the expected effect of a marker is a non-linear function of the data such that apparently small effects are regressed back almost to zero and consequently these markers can be deleted from the model. The accuracy in this case is considerably higher than when marker effects are normally distributed. If genomic selection is practiced for several generations the response declines in a manner that can be predicted from the marker allele frequencies. Genomic selection is likely to lead to a more rapid decline in the selection response than phenotypic selection unless new markers are continually added to the prediction of breeding value. A method to find the optimum index to maximise long term selection response is derived. This index varies the weight given to a marker according to its frequency such that markers where the favourable allele has low frequency receive more weight in the index.     

Black bear spatial responses to the Wallow Wildfire in Arizona

The Wallow Fire, the largest wildfire in Arizona history, encompassed 2,170 km² and provided a rare opportunity to examine habitat selection and home ranges of American black bears (Ursus americanus) before and after a wildfire. We had fitted global positioning system (GPS) collars on 47 bears from 2005 to April 2011, and 10 of these were still collared when the fire started in May 2011. We captured and collared an additional 7 black bears within the fire perimeter post-fire (Jul–Sep 2011 and Jun 2012). To evaluate how black bears were affected by the fire, we fit a step selection function using a conditional mixed effects Poisson regression model to estimate the relative strength of black bear habitat selection in response to burn severity. Additionally, we estimated home range sizes using an autocorrelated kernel density estimator by means of a continuous-time movement model. We then used a generalized linear model with a negative binomial error distribution and mixed effects to estimate the effect of the burn severity on black bear home range size, while controlling for sex and drought. In spring and summer in years prior to the fire, bears selected areas that later burned in the fire. After the fire, bears used all burn severities, but their selection for high-severity burns decreased significantly in summer 2011 and fall 2012. Home range sizes were 3.06 times larger pre-fire than post-fire. Our study demonstrates that black bears continued to use all burn severities after a major wildfire, and that post-fire conditions did not result in expanded black bear home ranges.     

Nek1 shares structural and functional similarities with NIMA kinase

The Aspergillus NIMA serine/threonine kinase plays a pivotal role in controlling entrance into mitosis. A major function attributed to NIMA is the induction of chromatin condensation. We show here that the founder murine NIMA-related kinase, Nek1, is larger than previously reported, and that the full-length protein conserves the structural hallmarks of NIMA. Even though Nek1 bears two classical nuclear localization signals (NLS), the endogenous protein localizes to the cytoplasm. Ectopic overexpression of various Nek1 constructs suggests that the C-terminus of Nek1 bears cytoplasmic localization signal(s). Overexpression of nuclear constructs of Nek1 resulted in abnormal chromatin condensation, with the DNA mainly confined to the periphery of the nucleus. Advanced condensation phenotype was associated with nuclear pore complex dispersal. The condensation was not accompanied by up-regulation of mitotic or apoptotic markers. A similar phenotype has been described following NIMA overexpression, strengthening the notion that the mammalian Nek1 kinase has functional similarity to NIMA.     

Mepimbat tedul proujek: Indigenous knowledge of culturally significant freshwater turtles addresses species knowledge gaps in Northern Australia

Indigenous biocultural knowledge offers valuable insights for species conservation; however, like biological diversity, associated cultural knowledge is also often threatened. This paper demonstrates how Indigenous biocultural knowledge of species can contribute to addressing gaps in species occurrence data and conservation knowledge using a case study from the South East Arnhem Land Indigenous Protected Area (SEAL IPA), northern Australia. Using a series of mapping workshops and interviews this collaborative project recorded Indigenous biocultural knowledge of the distribution, ecology, cultural significance and threats to freshwater turtles (freshwoda teduls in the local Indigenous language, Roper River Kriol). Based on past freshwoda tedul hunting experiences, 74 Indigenous knowledge holders identified 753 past freshwoda tedul occurrences, significantly adding to the 12 occurrences previously listed for the SEAL IPA in Australia's online species database, the Atlas of Living Australia. Importantly, these were the first ‘memory’ records of past species sightings by Indigenous people to be recognized and added to Australia's national species database. In addition, a blog summarizing this research was promoted through the Atlas of Living Australia, raising awareness of the Indigenous biocultural knowledge associated with these species. The Mepimbat tedul proujek revealed the cultural significance of freshwoda teduls and reported declines in abundance since the turn of the century, implicating invasive hard-hooved ungulates (buffalo, pig) and reduced rainfall. The addition of non-sacred Indigenous knowledge to free online species databases may offer innovative solutions for storage, interaction and sharing of indigenous knowledge, with opportunities for intergenerational and cross-cultural learning and broader application in conservation management and decision-making.     

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences,structures and functions

The eightfold (betaalpha) barrel structure, first observed in triose-phosphate isomerase, occurs ubiquitously in nature. It is nearly always an enzyme and most often involved in molecular or energy metabolism within the cell. In this review we bring together data on the sequence, structure and function of the proteins known to adopt this fold. We highlight the sequence and functional diversity in the 21 homologous superfamilies, which include 76 different sequence families. In many structures, the barrels are "mixed and matched" with other domains generating additional variety. Global and local structure-based alignments are used to explore the distribution of the associated functional residues on this common structural scaffold. Many of the substrates/co-factors include a phosphate moiety, which is usually but not always bound towards the C-terminal end of the sequence. Some, but not all, of these structures, exhibit a structurally conserved "phosphate binding motif". In contrast metal-ligating residues and catalytic residues are distributed along the sequence. However, we also found striking structural superposition of some of these residues. Lastly we consider the possible evolutionary relationships between these proteins, whose sequences are so diverse that even the most powerful approaches find few relationships, yet whose active sites all cluster at one end of the barrel. This extreme example of the "one fold-many functions" paradigm illustrates the difficulty of assigning function through a structural genomics approach for some folds.     

A computational framework to empower probabilistic protein design

MOTIVATION: The task of engineering a protein to perform a target biological function is known as protein design. A commonly used paradigm casts this functional design problem as a structural one, assuming a fixed backbone. In probabilistic protein design, positional amino acid probabilities are used to create a random library of sequences to be simultaneously screened for biological activity. Clearly, certain choices of probability distributions will be more successful in yielding functional sequences. However, since the number of sequences is exponential in protein length, computational optimization of the distribution is difficult. RESULTS: In this paper, we develop a computational framework for probabilistic protein design following the structural paradigm. We formulate the distribution of sequences for a structure using the Boltzmann distribution over their free energies. The corresponding probabilistic graphical model is constructed, and we apply belief propagation (BP) to calculate marginal amino acid probabilities. We test this method on a large structural dataset and demonstrate the superiority of BP over previous methods. Nevertheless, since the results obtained by BP are far from optimal, we thoroughly assess the paradigm using high-quality experimental data. We demonstrate that, for small scale sub-problems, BP attains identical results to those produced by exact inference on the paradigmatic model. However, quantitative analysis shows that the distributions predicted significantly differ from the experimental data. These findings, along with the excellent performance we observed using BP on the smaller problems, suggest potential shortcomings of the paradigm. We conclude with a discussion of how it may be improved in the future.     

Transfer of genetic information within a colony of Haemophilus influenzae.

Different Haemophilus cultures were mixed and then spotted onto an agar plate. These mixed colonies were incubated at 37 degrees C and then scored for the presence of recombinants. It was found that conjugative plasmids transferred very efficiently and quickly under these conditions, but only between cells of the same species. Four small plasmids did not transfer at all, nor were they mobilized by the two conjugative plasmids studied. Chromosomal markers transferred very inefficiently. The evidence favored transfer by genetic transformation rather than by conjugation. When mixed cultures were inoculated into broth and then incubated, the transfer of conjugative plasmids was not observed. Transfer of chromosomal markers occurred only when the media used contained Eugonbroth in addition to brain heart infusion, and even then it was very inefficient. The addition of DNase completely eliminated such transfers. This and other evidence indicate that in cell suspensions, chromosomal marker transfer also occurs through transformation. A corrected map of several genetic markers is presented.     

The morphome in constructive and abstractive models of morphology

Although the definition and usage of the term ‘morphome’ differs in the academic literature, the original definition of a morphome by Aronoff (1994) is that it is a function which determines the distribution of form within the inflectional paradigm and beyond. More importantly, however, morphomes suppose the existence of what Aronoff terms ‘a morphomic level’ which embodies an empirical claim about the structure of language: ‘the mapping from morphosyntax to phonological realization is not direct but passes through an intermediate level’ (Aronoff in Morphology by itself, MIT Press, Cambridge, 1994:25). This is a strong claim concerning all types of morphological exponence. In this article, after an analysis of Aronoff’s model of morphology, I draw upon the distinction which Blevins (J. Linguist. 42:531–573, 2006) makes between constructive and abstractive models of morphology. I note that the introduction of a morphomic level merely constitutes an incorporation of a partial paradigmatic dimension into a constructive model of morphology. With reference to a semantically and phonologically unmotivated distribution of allomorphy in Romance I argue that although the introduction of the morphomic level is beneficial, since it can formalise systematic and ‘psychologically real’ homonymies in synchronic grammars in a way which is not merely coincidental, a constructive morphomic theory of morphology does not present significant advantages over abstractive theories as regards the formalisation of the synchronic facts and presents disadvantages as regards the motivation of diachronic tendencies which this particular distribution of allomorphy shows cross-linguistically. I argue that these historical tendencies support a more paradigmatic theory of morphology inherent in abstractive models, which consider the word as the basic unit of analysis and word formation a matter of analogical deduction based on the predictable capacity of stored exemplar paradigms and principal parts.     

Molecular Structure of Human-Liver Glycogen

Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.     

Dendritic cells derived from peripheral monocytes express endothelial markers and in the presence of angiogenic growth factors differentiate into endothelial-like cells

CD14-positive monocytes obtained from human peripheral blood were cultured with GM-CSF and IL-4. During the early culture phase immature dendritic cells (DCs) developed which not only expressed CD1a, HLA-DR and CD86, but also expressed the endothelial cell markers von Willebrand factor (vWF), VE-cadherin and VEGF receptors Flt-1 and Flt-4. Further maturation of DCs was achieved by prolonged cultivation with TNFalpha. These cells showed typical DC morphology and like professional antigen-presenting cells (APCs) expressed CD83 and high levels of HLA-DR and CD86. However, if immature DCs were grown with VEGF, bFGF and IGF-1 on fibronectin/vitronectin-coated culture dishes, a marked change in morphology into caudated or oval cells occurred. In the presence of these angiogenic growth factors the cultured cells developed into endothelial-like cells (ELCs), characterized by increased expression of vWF, KDR and Flt-4 and a disappearance of CD1a and CD83. Addition of IL-4 and Oncostatin M also increased VE-cadherin expression, and the loosely adherent cells formed clusters, cobblestones and network-like structures. vWF- expressing ELCs mainly originated from CD1a-positive cells, and VEGF was responsible for the decrease in the expression of the DC markers CD1a and CD83. In mixed leukocyte cultures, mature DCs were more potent APCs than ELCs. Moreover, Ac-LDL uptake, and the formation of tubular structures on a plasma matrix was restricted to ELCs. These results suggest that in the presence of specific cytokines immature DCs have the potential to differentiate along different lineages, i.e. into a cell type resembling ELCs.     

Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues

Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.     

Type II restriction endonucleases: structural, functional and evolutionary relationships.

Type II restriction endonucleases are a paradigm for site-specific cleavage of DNA. Recent structural analyses, in particular in the presence of various divalent metals, have shed new insight into the mechanisms of catalysis. In addition, during this past year the crystal structure determinations of MutH, lambda-exonuclease and FokI have revealed that these proteins are also members of the same family.     

From a molecules’ perspective – contributions of ancient DNA research to understanding cave bear biology

Abstract

Few members of the Pleistocene megafauna have been as extensively studied as cave bears. Multidisciplinary research into cave bears has provided insights into their morphology, ecology, and evolution. Genetic studies have profited from the availability of large numbers of well-preserved remains. As a result, ‘ancient DNA (aDNA)’ from cave bears has provided significant insights into cave bear ecology, phylogeography and even potential causes of their extinction. Here I review the contributions that genetic research has made to our understanding of cave bear biology and evaluate the potential that new, genomic tools provide to shed further light onto how these iconic representatives of the Pleistocene megafauna lived and died.