Spatial variation in the ongoing and widespread decline of a keystone plant species

Extensive dieback in dominant plant species in response to climate change is increasingly common. Climatic conditions and related variables, such as evapotranspiration, vary in response to topographical complexity. This complexity plays an important role in the provision of climate refugia. In 2008/2009, an island‐wide dieback event of the keystone cushion plant Azorella macquariensis Orchard (Apiaceae) occurred on sub‐Antarctic Macquarie Island. This signalled the start of a potential regime shift, suggested to be driven by increasing vapour pressure deficit. Eight years later, we quantified cover and dieback across the range of putative microclimates to which the species is exposed, with the aim of explaining dieback patterns. We test for the influence of evapotranspiration using a suite of topographic proxies and other variables as proposed drivers of change. We found higher cover and lower dieback towards the south of the island. The high spatial variation in A. macquariensis populations was best explained by latitude, likely a proxy for macroscale climate gradients and geology. Dieback was best explained by A. macquariensis cover and latitude, increasing with cover and towards the north of the island. The effect sizes of terrain variables that influence evapotranspiration rates were small. Island‐wide dieback remains conspicuous. Comparison between a subset of sites and historical data revealed a reduction of cover in the north and central regions of the island, and a shift south in the most active areas of dieback. Dieback remained comparatively low in the south. The presence of seedlings was independent of dieback. This study provides an empirical baseline for spatial variation in the cover and condition of A. macquariensis, both key variables for monitoring condition and ‘cover‐debt’ in this critically endangered endemic plant species. These findings have broader implications for understanding the responses of fellfield ecosystems and other Azorella species across the sub‐Antarctic under future climates.     

Red panda fine‐scale habitat selection along a Central Himalayan longitudinal gradient

Red panda Ailurus fulgens, an endangered habitat specialist, inhabits a narrow distribution range in bamboo abundance forests along mountain slopes in the Himalaya and Hengduan Mountains. However, their habitat use may be different in places with different longitudinal environmental gradients, climatic regimes, and microclimate. This study aimed to determine the habitat variables affecting red panda distribution across different longitudinal gradients through a multivariate analysis. We studied habitat selection patterns along the longitudinal gradient in Nepal's Himalaya which is grouped into the eastern, central, and western complexes. We collected data on red panda presence and habitat variables (e.g., tree richness, canopy cover, bamboo abundance, water availability, tree diameter, tree height) by surveys along transects throughout the species’ potential range. We used a multimodal inference approach with a generalized linear model to test the relative importance of environmental variables. Although the study showed that bamboo abundance had a major influence, habitat selection was different across longitudinal zones. Both canopy cover and species richness were unimportant in eastern Nepal, but their influence increased progressively toward the west. Conversely, tree height showed a decreasing influence on habitat selection from Eastern to Western Nepal. Red panda's habitat selection revealed in this study corresponds to the uneven distribution of vegetation assemblages and the dry climatic gradient along the eastern‐western Himalayas which could be related to a need to conserve energy and thermoregulate. This study has further highlighted the need of importance of bamboo conservation and site‐specific conservation planning to ensure long‐term red panda conservation.     

Leishmania (Viannia) braziliensis: epidemiology of canine cutaneous leishmaniasis in the State of Paraná (Brazil)

The present study examines the role that dogs play in the maintenance of the Leishmania cycle in the State of Paraná, Southern Brazil. Dogs were examined in three regions where cutaneous leishmaniasis is endemic or epidemic (R1-Vale da Ribeira; R2-Central region of Paraná State and R3-Northern region). To determine serum prevalence rates ELISA was used. In regions endemic for Trypanosoma cruzi (R1 and R3), serum from dogs seroreactive towards Leishmania antigen was subjected to T. cruzi adsorption in order to eliminate cross-reaction with common antigen epitopes. Concomitantly, dogs with cutaneous lesions were biopsied to isolate and identify parasites using RAPD. Leishmania were classified by the phenetic method using the Jaccard coefficient of similarity, and grouped by Unweighted Pair-Group Method using an Arithmetic Average (UPGMA). A total of 410 dogs were studied. In R1 (Vale da Ribeira) 159 dogs were evaluated of which 10 had anti-Leishmania antibody. In R2 (Central Paraná), 39 animals were examined of which 8 were seropositive. In R3 (the North) 212 dogs were evaluated of which 39 animals were seropositive. Thirteen dogs had cutaneous lesions and the parasites were isolated from a dog with mucocutaneous lesion in R1, two animals with simple skin lesions in R2 and 10 dogs with multiple lesions in R3. The identification of the parasite by molecular methods showed it to be L. (Viannia) braziliensis. Based on this information, the role of domestic dogs in Leishmania infection of cutaneous leishmaniasis in Paraná is discussed.     

Method for generation of human hyperdiversified antibody fragment library

The selection of antibody fragments from libraries using in vitro screening technologies has proven to be a very good alternative to the classical hybridoma technology, and has overcome the laborious process of antibody humanization. However, the complexity of the library is critical in the probability of being able to directly isolate a high affinity antibody specific to a target. We report a method to make hyperdiversified antibody fragment libraries, based on human immunoglobulin variable genes mimicking the somatic hypermutation process. This mutagenesis technology, MutaGen, was used for the first time on the entire variable domain (frameworks and CDRs) of large repertoires of human variable antibody domains. Our MutaGen process uses low-fidelity human polymerases, known as mutases, suggested to be involved in the somatic hypermutation process of immunoglobulin genes. Depending on the mutases used, we generated complementary mutation patterns with randomly distributed mutations. The libraries were generated with an average of 1.8 mutations per 100 amino acids. The hyperdiversified antibody fragment libraries constructed with our process should enable the selection of antibody fragments specific to virtually any target.     

Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain

Directed evolution represents a versatile tool to tailor enzyme properties to needs in industrial applications and to understand structure-function relationships. Genetic diversity is commonly generated using error-prone PCR. Exploration of sequence space by random mutagenesis strongly favors transitions when enzyme-based mutagenesis methods are employed (Wong, T. S., Zhurina, D., Schwaneberg, U., Comb. Chem. High Throughput Screen. 2006, 9, 271-288). The genetic code has been organized in a manner that limits chemical diversity when a single transition mutation occurs in a codon (Wong, T. S., Roccatano, D., Schwaneberg, U., Biocatal. Biotransformation 2006, in press). Are transitions more beneficial than transversions for adapting biocatalysts to non-natural process conditions? In a statistical analysis performed with the Mutagenesis Assistant Program (MAP), we compared the consequences of transition and transversion bias on amino acid substitution patterns of the P450 BM-3 heme domain. For the analysis, we used a recently introduced benchmarking system consisting of a protein structure indicator, an amino acid diversity indicator with a codon diversity coefficient, and a chemical diversity indicator. A detailed analysis for the P450 BM-3 heme domain showed that an ideal transversion bias generates more diverse amino acid substitution patterns with a significantly different chemical composition than an ideal transition bias. Emphasis is given on the theoretical analysis with a brief discussion on potential implication of transition and transversion bias in directed evolution experiments.     

Mendelian randomization analysis of the causal impact of body mass index and waist-hip ratio on rates of hospital admission

We analyze how measures of adiposity – body mass index (BMI) and waist hip ratio (WHR) – causally influence rates of hospital admission. Conventional analyses of this relationship are susceptible to omitted variable bias from variables that jointly influence both hospital admission and adipose status. We implement a novel quasi-Poisson instrumental variable model in a Mendelian randomization framework, identifying causal effects from random perturbations to germline genetic variation. We estimate the individual and joint effects of BMI, WHR, and WHR adjusted for BMI. We also implement multivariable instrumental variable methods in which the causal effect of one exposure is estimated conditionally on the causal effect of another exposure. Data on 310,471 participants and over 550,000 inpatient admissions in the UK Biobank were used to perform one-sample and two-sample Mendelian randomization analyses. The results supported a causal role of adiposity on hospital admissions, with consistency across all estimates and sensitivity analyses. Point estimates were generally larger than estimates from comparable observational specifications. We observed an attenuation of the BMI effect when adjusting for WHR in the multivariable Mendelian randomization analyses, suggesting that an adverse fat distribution, rather than a higher BMI itself, may drive the relationship between adiposity and risk of hospital admission.     

Forecasting the potential distribution of Spodoptera exigua and S. littoralis (Lepidoptera,Noctuidae) in Iran

The beet armyworm, Spodoptera exigua (Hübner, 1808) and the Egyptian cotton leafworm, S. littoralis (Boisduval, 1833), are amongst the most notorious agricultural pest species in Iran. Spodoptera exigua is considered a serious pest of different crops, whereas S. littoralis is known as an important pest of cotton.In this paper, the potential distribution areas of these species in Iran and the important climatic factors affecting their distribution were predicted using the MaxEnt model and the ArcGIS. The results indicate that the main environmental variables contributing to S. exigua’s distribution were precipitation of the coldest quarter (bio19), average wind speed in April (wind4), and annual precipitation (bio12). Also, minimum temperature of the coldest month (bio6), mean temperature of coldest quarter (bio11), altitude and average wind speed in May (wind5) were dominant climatic factors that affected the potential distribution of S. littoralis. These species overlapped in most parts of coastal areas in the southern and northern parts of Iran, with an average overlapping range of 33.2%. Considering their preferred host plants in Iran, it is necessary to strengthen biosurveillance programes and management of these two species in their suitable areas to prevent further invasion, which endangers agricultural security.     

三峡库区水体中固氮微生物多样性及其影响因素

【目的】研究分析不同时空条件下三峡库区水体固氮微生物多样性,并探讨其与地球化学参数的相关性。【方法】采集三峡库区不同时间(三月份和六月份)和空间(干流与支流)的水体样品,对其进行地球化学参数分析,并通过构建克隆文库分析样品中固氮功能基因(nifH)的多样性进而探讨其与水体地化参数的相关关系。【结果】统计分析显示三峡库区水体固氮微生物α-多样性和群落组成具有时空差异。支流水体样品的固氮微生物α-多样性高于干流水体样品;六月水体样品的固氮微生物α-多样性高于三月水体样品。三峡库区三月水体样品中的固氮微生物群落以Proteobacteria (50.3%)和Firmicutes (40.0%)为主;六月水体样品的固氮微生物群落以Proteobacteria(48.4%)、Firmicutes(25.4%)和Cyanobacteria(19.0%)为主。Mantel检验结果显示:固氮微生物群落结构的差异与温度、pH和DIC等地球化学参数具有显著(P0.05)相关性,其中温度和pH的相关性系数最大。【结论】三峡库区固氮微生物的种群结构和多样性具有时空差异,影响三峡水库水体中固氮微生物群落结构与多样性的主要环境因素为温度和pH,同时浊度、DIC、氨氮也对库区水体固氮微生物群落结构和多样性有一定的影响。     

Binary Responses and the Three-period Cross-over

Problems with carry-over effects in the simple two-period cross-over have lead to interest in more complex cross-over designs. A method for analysing the optimum two-treatment three-period design with binary response variables is given by making a simple extension to Gart's logistic model. The method gives independent tests for, and estimates of the difference in treatment and first-order carry-over effects. An example of the analysis is given, using the loglinear models facility in GLIM.