Parameter identification for a stochastic SEIRS epidemic model: case study influenza

Journal of Mathematical Biology - A recent parameter identification technique, the local lagged adapted generalized method of moments, is used to identify the time-dependent disease transmission...     

The use of neural networks to aid in microorganism identification: a case study ofHaemophilus species identification

The adipamidase of a mutant strainBrevibacterium sp. R312 involved in the degradation of adiponitrile to adipic acid was purified. Its N-terminal amino acid sequence was shown to be identical toBrevibacterium sp. R312 enantio-selective amidase andRhodococcus sp. N-774 amidase.     

Molecular resolution of marine turtle stock composition in fishery bycatch: a case study in the Mediterranean

Based on an extensive sampling regime from both nesting populations and bycatch, frequency analyses of mitochondrial (mt) DNA control region haplotypes in the Mediterranean were used to assess the genetic structure and stock composition of the loggerhead sea turtle, Caretta caretta, in different marine fisheries. The analyses show the following. (i) In drifting longline fisheries working in Mediterranean pelagic habitats 53–55% of turtles caught originated from the Mediterranean stock; (ii) In bottom-trawl fisheries all turtle bycatch is derived from this regional stock; (iii) This regional stock contribution to fishery bycatch suggests that the population size of the Mediterranean loggerhead nesting population is significantly larger than previously thought. This is consistent with a recent holistic estimate based on the discovery of a large rookery in Libya. (iv) Present impact of fishery-related mortality on the Mediterranean nesting population is probably incompatible with its long-term conservation. Sea turtle conservation regulations are urgently needed for the Mediterranean fisheries. (v) The significant divergence of mtDNA haplotype frequencies of the Turkish loggerhead colonies define this nesting population as a particularly important management unit. Large immature and adult stages from this management unit seem to be harvested predominantly by Egyptian fisheries. (vi) Combined with other data, our findings suggest that all the nesting populations in the Mediterranean should be considered as management units sharing immature pelagic habitats throughout the Mediterranean (and possibly the eastern Atlantic), with distinct and more localized benthic feeding habitats in the eastern basin used by large immatures and adults. (vii) Between the strict oceanic pelagic and the benthic stages, immature turtles appear to live through an intermediate neritic stage, in which they switch between pelagic and benthic foods.     

Computational identification of three-way junctions in folded RNAs: a case study in Arabidopsis

Three-way junctions in folded RNAs have been investigated both experimentally and computationally. The interest in their analysis stems from the fact that they have significantly been found to possess a functional role. In recent work, three-way junctions have been categorized into families depending on the relative lengths of the segments linking the three helices. Here, based on ideas originating from computational geometry, an algorithm is proposed for detecting three-way junctions in data sets of genes that are related to a metabolic pathway of interest. In its current implementation, the algorithm relies on a moving window that performs energy minimization folding predictions, and is demonstrated on a set of genes that are involved in purine metabolism in plants. The pattern matching algorithm can be extended to other organisms and other metabolic cycles of interest in which three-way junctions have been or will be discovered to play an important role. In the test case presented here with, the computational prediction of a three-way junction in Arabidopsis that was speculated to have an interesting functional role is verified experimentally.     

Stable isotope analyses in otoliths of silver carp: a pilot study in identification of natal sources and stock differences

Silver carp, Hypophthalmichthys molitrix, is one of the four major fishes in China for fishing and aquaculture. The Yangtze River and associated waterbodies are important home to silver carp. In this study, we collected 135 otoliths of juvenile silver carp from the two rivers and the Poyang Lake, and analyzed for stable oxygen and carbon isotope ratios (δ¹⁸O and δ¹³C). The isotopic data and correlation of δ¹⁸O versus δ¹³C showed a clear separation and significant differences (p?<?0.001 for both δ¹³C and δ¹⁸O) between otoliths from the Ganjiang River and the Yangtze River at δ¹⁸O values around ?10‰. The Poyang Lake samples were overlapped with those of the Ganjiang River, but distinctly different from the Yangtze River samples. These isotopic signatures agree well with the previous genetic investigation results that there are marked distinctions between one population in the Ganjiang River and the other in the Yangtze River, and the Poyang Lake population belongs to the Ganjiang River rather than to the Yangtze River. Thus we concluded that stable isotope analyses of otoliths can be effectively used to study natal sources and stock differences of silver carp.     

Parameter identification of a dynamic model of CHO cell cultures: an experimental case study

In this paper, we address the problem of parameter identification in dynamic models of animal cultures, and we propose a step-by-step procedure, which gradually considers more detailed models. This procedure allows subsets of parameters to be estimated at each step, which can be used in the initialization of the next identification step. Finally, the full parameter set can be re-estimated starting from the results of the last step. The efficiency of the procedure is illustrated with a simulation case study and with the identification of a dynamic model from experimental data collected in CHO cell culture.     

Microsatellites and single nucleotide polymorphisms in avian hybrid identification: a comparative case study

The correct identification of hybrids is essential in avian hybridisation studies, but selection of the appropriate set of genetic markers for this purpose is at times complicated. Microsatellites and single nucleotide polymorphisms (SNPs) are currently the most commonly used markers in this field. We compare the efficiency of these two marker types, and their combination, in the identification of the threatened avian species, the greater spotted eagle and the lesser spotted eagle, as well as hybrids between the two species. We developed novel SNP markers from genome-wide distributed 122 candidate introns using only sympatric samples, and tested these markers successfully in 60 sympatric and allopatric spotted eagles using Bayesian model-based approaches. Comparatively, only one out of twelve previously described avian nuclear intron markers showed significant species-specific allele frequency difference, thus stressing the importance of selecting the proper markers. Twenty microsatellites outperformed selected nine SNPs in species identification, but were poorer in hybrid detection, whereas the resolution power of ten microsatellites remained too low for correct assignment. A combination of SNPs and microsatellites resulted in the most efficient and accurate identification of all individuals. Our study shows that the use of various sets of markers could lead to strikingly different assignment results, hybridisation studies may have been affected by too low a resolution power of used markers, and that an appropriate set of markers is essential for successful hybrid identification.     

Standing stock of microzooplankton on coral reefs: a preliminary study

The standing stock of microzooplankton on mid-shelf coral reefsin the central Great Barrier Reef was investigated based onsamples collected with a Niskin bottle in February and October1989 The observed net decrease in standing stock of microzooplanktonacross the reef flat suggests that a lack of information ontheir standing stock on coral reefs has led to an underestimateof the allochthonous energy input to coral reef systems.     

Cyanogenic glycosides: a case study for evolution and application of cytochromes P450

Cyanogenic glycosides are ancient biomolecules found in more than 2,650 higher plant species as well as in a few arthropod species. Cyanogenic glycosides are amino acid-derived β-glycosides of α-hydroxynitriles. In analogy to cyanogenic plants, cyanogenic arthropods may use cyanogenic glycosides as defence compounds. Many of these arthropod species have been shown to de novo synthesize cyanogenic glycosides by biochemical pathways that involve identical intermediates to those known from plants, while the ability to sequester cyanogenic glycosides appears to be restricted to Lepidopteran species. In plants, two atypical multifunctional cytochromes P450 and a soluble family 1 glycosyltransferase form a metabolon to facilitate channelling of the otherwise toxic and reactive intermediates to the end product in the pathway, the cyanogenic glycoside. The glucosinolate pathway present in Brassicales and the pathway for cyanoalk(en)yl glucoside synthesis such as rhodiocyanosides A and D in Lotus japonicus exemplify how cytochromes P450 in the course of evolution may be recruited for novel pathways. The use of metabolic engineering using cytochromes P450 involved in biosynthesis of cyanogenic glycosides allows for the generation of acyanogenic cassava plants or cyanogenic Arabidopsis thaliana plants as well as L. japonicus and A. thaliana plants with altered cyanogenic, cyanoalkenyl or glucosinolate profiles.     

Identifying the last supper: utility of the DNA barcode library for bloodmeal identification in ticks

Ticks are among the most important vectors of disease in the Northern Hemisphere, and a better understanding of their feeding behaviour and life cycle is critical to the management and control of tick-borne zoonoses. DNA-based tools for the identification of residual bloodmeals in hematophagous arthropods have proven useful in the investigation of patterns of host use in nature. Using a blind test approach, we challenged the utility of the DNA barcode library for the identification of vertebrate bloodmeals in engorged, field-collected Ixodes scapularis. Universal vertebrate primers for the COI barcode region successfully amplified DNA from the host bloodmeal and only rarely amplified tick DNA. Of the 61 field-collected ticks, conclusive genus- and species-level identification was possible for 72% of the specimens. In all but two cases, barcode-based identification of the bloodmeal was consistent with the morphological identification of the vertebrate host the ticks were collected from. Possible explanations for mismatches or ambiguities are presented. This study validates the utility of the DNA barcode library as a valuable and reliable resource for the identification of unknown bloodmeals in arthropod vectors of disease. Future directions aimed at the refinement of these techniques to gain additional information and to improve the amplification success of digested vertebrate DNA in tick bloodmeals are discussed.     

In sickness and in health: the widespread application of creatine supplementation

There is an extensive and still growing body of the literature supporting the efficacy of creatine (Cr) supplementation. In sports, creatine has been recognized as the most effective nutritional supplement in enhancing exercise tolerance, muscle strength and lean body mass. From a clinical perspective, the application of Cr supplementation is indeed exciting. Evidences of benefits from this supplement have been reported in a broad range of diseases, including myopathies, neurodegenerative disorders, cancer, rheumatic diseases, and type 2 diabetes. In addition, after hundreds of published studies and millions of exposures creatine supplementation maintains an excellent safety profile. Thus, we contend that the widespread application of this supplement may benefit athletes, elderly people and various patient populations. In this narrative review, we aimed to summarize both the ergogenic and therapeutic effects of Cr supplementation. Furthermore, we reviewed the impact of Cr supplementation on kidney function.     

Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo,Mexico

DNA barcoding constitutes a fundamental tool for species identification, especially for highly diverse geographic regions. Here, we characterize and evaluate the plant core barcoding regions matK and rbcL to identify the 25 conifer species from the state of Hidalgo, Mexico, including 10 species in various threat categories. Sequence quality, linguistic complexity, and the presence of the barcode gap were estimated. Two methods were compared for successful species identification: BRONX (Barcode Recognition Obtained with Nucleotide eXposés) and the least inclusive clade. We generated 77 sequences for matK and 88 for rbcL. The matK region had higher haplotype diversity and nucleotide diversity (Π), including six indels. The analysis of 77 specimens with complete sequences (matK + rbcL) resulted in 21 nonspecies-specific unique haplotypes for the 25 conifer species. Higher sequence quality and linguistic complexity were observed in rbcL than in matK. Every diagnosable species had a barcode gap. Ninety-seven specimens were assigned unambiguously to family and genus, regardless of the marker or method employed. The analysis of matK with BRONX produced the highest species level identification success (44%). Despite the low specimen identification success at the specific level, it will be possible to establish local management, conservation, and monitoring projects for at least half of the threatened species even when specimens do not exhibit diagnostic morphological characters. The low divergence between closely related species may result from the slow rate of molecular evolution of the core barcoding markers or from hybridization or incomplete lineage sorting. Similar identification success is expected for groups with comparable life history traits under similar conditions as this study. A reduction in the geographic area will not necessarily translate into higher identification success, especially for high-diversity regions and centres of diversification.