On Use of Distinct Respondents in Randomized Response Surveys

It is well known for direct response surveys (DR), where the responses are obtained from the respondents directly, that the sample mean, based on distinct units of a simple random sample selected with replacement (SRSWR) method, is more efficient than the sample mean based on all the units including repetition. In this paper, it is shown that a linear unbiased estimator based on distinct units is inadmissible for estimating a finite population mean when the sample is selected by an arbitrary with replacement (WR) sampling scheme and the responses are obtained independently by some RR technique. Efficiencies for a few linear unbiased estimators are compared under SRSWR sampling.     

On the Estimation of Population Mean in Stratified Sampling

When stratified random sampling is used for the estimation of population mean, use of ‘Combined ratio estimator’ is well known. Some improved estimators for population mean are proposed which are better than ‘Combined ratio estimator’ and some other well known existing ones, from the point of view of bias and mean square error. An empirical illustration is given.     

On the Use of Two-stage Cluster Samples in Epidemiological Population Studies

This paper discusses the need to account for the sampling scheme in an analysis of epidemiological population data which were collected by a two-stage cluster sample. An example is presented where for validity reasons one should generally account for the sampling scheme, though a rule-of-thumb is given to estimate the effect of not doing so. The example concerns one of the centers (Augsburg, F. R. G.) participating in the WHO MONICA Project, which was designed to study the relationship between changes in risk factor levels, as measured by several surveys in each center, and changes in cardiovascular incidence rates, as measured by a registry system for each center. Variance estimation methods which either account for or ignore the sampling scheme are compared for a particular sampling scheme. Easily computable upper bounds on the effect on variances of ignoring the sampling scheme are presented, both over all possible variables, and for a particular variable.     

Sampling strategy,occurrence and diversity of free‐living protozoa in domestic refrigerators

Aims: Evaluation of a sampling method to recover free‐living protozoa (FLP) from plastic surfaces. Application of the method on different areas inside domestic refrigerators. Methods and Results: Plastic coupons seeded with representatives of FLP were swabbed with cotton wools. The recovery efficiency was the highest for Chilomonas paramecium, followed by Tetrahymena pyriformis and the lowest for Acanthamoeba polyphaga. From 43 refrigerators, 19 and 26 were considered FLP positive when sample cultures were incubated at 7°C and 20°C, respectively. The number of FLP‐positive cultures was the highest in samples taken from vegetable trays followed by discharge gutters, whereas interior walls were rarely FLP positive. Higher numbers of taxa were observed in enrichment cultures incubated at 20°C instead of 7°C. The combination of microscopy and denaturing gradient gel electrophoresis revealed that discharge gutters occasionally were contaminated with a persistent protozoan population of flagellates (Cercozoa) and amoebae (Tubulinea). The FLP‐positive status of refrigerator surfaces was correlated with a high aerobic plate count. Conclusions: The cotton wool sampling method is useful to sample FLP from plastic surfaces. FLP are part of the microbial communities in domestic refrigerators. Significance and Impact of the Study: Knowledge on the occurrence of FLP in food‐related indoor environments is scarce. For the first time, a high protozoan diversity in domestic refrigerators is described.     

On the heritability of blue‐green eggshell coloration

Abstract Avian blue‐green eggshell coloration has been proposed as a female signal of genetic or phenotypic quality to males. However, little is known about the relative importance of additive genetic and environmental effects as sources of eggshell colour variation in natural populations. Using 5 years of data and animal models, we explored these effects in a free‐living population of pied flycatchers. Permanent environmental and year effects were negligible, although year environmental variance (V_Year) was significant for all but one of the traits. However, we found high–moderate narrow‐sense heritabilities for some colour parameters. Within‐clutch colour variability showed the highest coefficient of additive genetic variation (i.e. evolvability). Previous evidence suggests that eggshell colour is sexually selected in this species, males enhancing parental effort in clutches with higher colour variability and peak values. Eggshell colour could be driven by good‐genes selection in pied flycatchers although further genetic studies should confirm this possibility.     

On the Probability of a Negative Estimator of Heteroscedasticity in the Random Coefficient Model

In the estimation of a linear regression model with random coefficients, sometimes negative estimates of variances of random coefficients are obtained–an undesirable feature. In this paper we have obtained the asymptotic bounds of the probability of obtaining negative estimators. A simple illustration is also provided for the purpose.     

On the Use of the Negative Binomial in Epidemiology

The use of the negative binomial, or the method of inverse sampling (e.g. (1), (2)), is suggested for prospective studies. This method usually has the advantage of fostering an early decision on the statistical significance of some etiological factor in examining successive patient records. Several limiting situations for the distribution are discussed regarding the prevalence of a disease. An example illustrates the method.     

Use of the Maximum Likelihood Method in the Analysis of Phenotypic Stability

The stability variance is an important estimator of phenotypic stability of genotypes. It may be estimated by method of moments and by maximum likelihood. We demonstrate by Monte Carlo simulation that, given a sufficient number of environments, maximum likelihood estimates (MLE's) are slightly better if ranking of genotypes is the experimenter's major aim. A likelihood ratio test is available for different hypotheses.     

The use of marker‐based relationship information to estimate the heritability of body weight in a natural population: a cautionary tale

A number of procedures have been developed that allow the genetic parameters of natural populations to be estimated using relationship information inferred from marker data rather than known pedigrees. Three published approaches are available; the regression, pair‐wise likelihood and Markov Chain Monte Carlo (MCMC) sib‐ship reconstruction methods. These were applied to body weight and molecular data collected from the Soay sheep population of St. Kilda, which has a previously determined pedigree. The regression and pair‐wise likelihood approaches do not specify an exact pedigree and yielded unreliable heritability estimates, that were sensitive to alteration of the fixed effects. The MCMC method, which specifies a pedigree prior to heritability estimation, yielded results closer to those determined using the known pedigree. In populations of low average relationship, such as the Soay sheep population, determination of a reliable pedigree is more useful than indirect approaches that do not specify a pedigree.     

Lake Kainji,Nigeria; A summary of the changes within the fish population since the impoundment of the Niger in 1968

The relative composition of the major fish families in Lake Kainji between 1974 and 1975 is analysed and compared with pre- and post-impoundment data collected by previous workers. Trends in the fishery are assessed, and it is concluded that the cichlids, particularly Sarotherodon (= Tilapia) galilaeus Artedi, are becoming the dominant commercially valuable fish. No evidence was found of a significant recovery in the formerly abundant citharinids.The value of the sampling technique is discussed and criticised in relation to under-assessment of certain species, notably S. galilaeus. The Schilbeidae were found to be one of the most numerous families in the lake but are commercially under-exploited.Department of Zoology, University of Reading     

Characterization of a group of pyrroloquinoline quinone‐dependent dehydrogenases that are involved in the conversion of L‐sorbose to 2‐Keto‐L‐gulonic acid in Ketogulonicigenium vulgare WSH‐001

Ketogulonicigenium vulgare WSH‐001 is an industrial strain used for vitamin C production. Based on genome sequencing and pathway analysis of the bacterium, some of its potential pyrroloquinoline quinone (PQQ)‐dependent dehydrogenases were predicted, including KVU_pmdA_0245, KVU_2142, KVU_2159, KVU_1366, KVU_0203, KVU_0095, and KVU_pmdB_0115. BLAST and function domain searches showed that enzymes encoded by these genes may act as putative PQQ‐dependent L ‐sorbose dehydrogenases (SDH) or L ‐sorbosone dehydrogenases (SNDH). To validate whether these dehydrogenases are PQQ‐dependent or not, these seven putative dehyrogenases were overexpressed in Escherichia coli BL21 (DE3) and purified for characterization. Biochemical and kinetic characterization of the purified proteins have led to the identification of seven enzymes that possess the ability to oxidize L ‐sorbose or L ‐sorbosone to varying degrees. In addition, the dehydrogenation of sorbose in K. vulgare is validated to be PQQ dependent, identification of these PQQ‐dependent dehydrogenases expanded the PQQ‐dependent dehydrogenase family. Besides, the optimal combination of enzymes that could more efficiently catalyze the conversion of sorbose to gulonic acid was proposed. These are important in supporting the development of metabolic engineering strategies and engineering of efficient strains for one‐step production of vitamin C in the future. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1398–1404, 2013     

Comparison of a Molecular and an Immobilized Gadolinium(III)‐tris[(1R,4S)‐3‐heptafluorobutanoyl‐camphor] as Catalyst in the Asymmetric Danishefsky‐Hetero‐Diels‐Alder‐Reaction

On‐column reaction gas chromatography combines the power of separation and rapid analysis of reactants and reaction products with screening of reactions in a single step. Not only conversions but the reaction rates at various temperatures can be obtained from single measurements, making this approach superior to the time‐consuming measurements typically performed in reaction progress analysis. However, this approach has only been used in the investigation of interconversion processes, rearrangement reactions, and only a few examples of higher‐order reactions are known. Here we present the screening of immobilized gadolinium(III)‐tris[(1R,4S)‐3‐heptafluorobutanoyl‐camphor] in the Danishefsky‐hetero‐Diels‐Alder‐reaction by enantioselective on‐column reaction gas chromatography utilizing cryogenic focusing to achieve catalytic conversions in this higher‐order reaction and subsequent separation of the enantiomeric product mixture to determine the enantiomeric ratio. The results obtained by this approach could be transferred to the conventional batch reaction at a larger scale, demonstrating that on‐column reaction chromatography provides reliable results in the screening of enantioselective reactions. Chirality 26:243–248, 2014. © 2014 Wiley Periodicals, Inc.     

Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate

Aims

The aim of the study was to develop an approach to enrich ionic liquid tolerant micro‐organisms that efficiently decompose lignocellulose in a thermophilic and high‐solids environment.

Methods and Results

High‐solids incubations were conducted, using compost as an inoculum source, to enrich for thermophilic communities that decompose switchgrass in the presence of the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate ([C2mim][OAc]). Ionic liquid levels were increased from 0 to 6% on a total weight basis incrementally. Successful enrichment of a community that decomposed lignocellulose at 55°C in the presence of 6% [C2mim][OAc] was achieved, when the [C2mim][OAc] level was increased stepwise from 2% to 4% to 5% to 6%. Pyrosequencing results revealed a shift in the community and a sharp decrease in richness, when thermophilic conditions were applied.

Conclusions

A community tolerant to a thermophilic, high‐solids environment containing 6% [C2mim][OAc] was enriched from compost. Gradually increasing [C2mim][OAc] concentrations allowed the community to adapt to [C2mim][OAc].

Significance and Impact of the Study

A successful approach to enrich communities that decompose lignocellulose under thermophilic high‐solids conditions in the presence of elevated levels of [C2mim][OAc] has been developed. Communities yielded from this approach will provide resources for the discovery of enzymes and metabolic pathways relevant to biomass pretreatment and fuel production.     

Genetic alteration of UDP‐rhamnose metabolism in Botrytis cinerea leads to the accumulation of UDP‐KDG that adversely affects development and pathogenicity

Botrytis cinerea is a model plant‐pathogenic fungus that causes grey mould and rot diseases in a wide range of agriculturally important crops. A previous study has identified two enzymes and corresponding genes (bcdh, bcer) that are involved in the biochemical transformation of uridine diphosphate (UDP)‐glucose, the major fungal wall nucleotide sugar precursor, to UDP‐rhamnose. We report here that deletion of bcdh, the first biosynthetic gene in the metabolic pathway, or of bcer, the second gene in the pathway, abolishes the production of rhamnose‐containing glycans in these mutant strains. Deletion of bcdh or double deletion of both bcdh and bcer has no apparent effect on fungal development or pathogenicity. Interestingly, deletion of the bcer gene alone adversely affects fungal development, giving rise to altered hyphal growth and morphology, as well as reduced sporulation, sclerotia production and virulence. Treatments with wall stressors suggest the alteration of cell wall integrity. Analysis of nucleotide sugars reveals the accumulation of the UDP‐rhamnose pathway intermediate UDP‐4‐keto‐6‐deoxy‐glucose (UDP‐KDG) in hyphae of the Δbcer strain. UDP‐KDG could not be detected in hyphae of the wild‐type strain, indicating fast conversion to UDP‐rhamnose by the BcEr enzyme. The correlation between high UDP‐KDG and modified cell wall and developmental defects raises the possibility that high levels of UDP‐KDG result in deleterious effects on cell wall composition, and hence on virulence. This is the first report demonstrating that the accumulation of a minor nucleotide sugar intermediate has such a profound and adverse effect on a fungus. The ability to identify molecules that inhibit Er (also known as NRS/ER) enzymes or mimic UDP‐KDG may lead to the development of new antifungal drugs.     

Role of the non‐hypervariable FR3 D‐E loop in single‐domain antibody recognition of haptens and carbohydrates

Single‐domain antibodies (sdAbs), the variable domains of camelid heavy chain‐only antibodies, are generally thought to poorly recognize nonproteinaceous small molecules and carbohydrates in comparison with conventional antibodies. However, the structures of anti‐methotrexate, anti‐triclocarban and anti‐cortisol sdAbs revealed unexpected contributions of the non‐hypervariable “CDR4” loop, formed between β‐strands D and E of framework region 3, in binding. Here, we investigated the potential role of CDR4 in sdAb binding to a hapten, 15‐acetyl‐deoxynivalenol (15‐AcDON), and to carbohydrates. We constructed and panned a phage‐displayed library in which CDR4 of the 15‐AcDON‐specific sdAb, NAT‐267, was extended and randomized. From this library, we identified one sdAb, MA‐232, bearing a 14‐residue insertion in CDR4 and showing improved binding to 15‐AcDON by ELISA and surface plasmon resonance. On the basis of these results, we constructed a second set of phage‐displayed libraries in which the CDR4 and other regions of three hapten‐ or carbohydrate‐binding sdAbs were diversified. With the goal of identifying sdAbs with novel glycan‐binding specificities, we panned the library against four tumor‐associated carbohydrate antigens but were unable to enrich binding phages. Thus, we conclude that while CDR4 may play a role in binding of some rare hapten‐specific sdAbs, diversifying this region through molecular engineering is probably not a general solution to sdAb carbohydrate recognition in the absence of a paired V_L domain.