A novel tool for individual haplotype inference using mixed data

Background

In many studies, researchers may recruit samples consisting of independent trios and unrelated individuals. However, most of the currently available haplotype inference methods do not cope well with these kinds of mixed data sets.

Methods

We propose a general and simple methodology using a mixture of weighted multinomial (MIXMUL) approach that combines separate haplotype information from unrelated individuals and independent trios for haplotype inference to the individual level.

Results

The new MIXMUL procedure improves over existing methods in that it can accurately estimate haplotype frequencies from mixed data sets and output probable haplotype pairs in optimized reconstruction outcomes for all subjects that have contributed to estimation. Simulation results showed that this new MIXMUL procedure competes well with the EM-based method, i.e. FAMHAP, under a few assumed scenarios.

Conclusion

The results showed that MIXMUL can provide accurate estimates similar to those haplotype frequencies obtained from FAMHAP and output the probable haplotype pairs in the most optimal reconstruction outcome for all subjects that have contributed to estimation. If available data consist of combinations of unrelated individuals and independent trios, the MIXMUL procedure can be used to estimate the haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.     

Non-volatile components of the essential oil secretory cavities of Eucalyptus leaves: Discovery of two glucose monoterpene esters, cuniloside B and froggattiside A

The essential oils extracted from the embedded foliar secretory cavities of many Eucalyptus species are of economic value as pharmaceuticals and fragrance additives. Recent studies have indicated that Eucalyptus secretory cavities may not be exclusively involved in the biosynthesis and storage of essential oils. Therefore, we selected three species upon which to perform an examination of the contents of foliar secretory cavities: Eucalyptus froggattii, E. polybractea and E. globulus. This paper describes the isolation and structural characterization of two non-volatile glucose monoterpene esters, which we have named cuniloside B and froggattiside A, from within the secretory cavities of these species, and shows the presence of these compounds in solvent extracts of the leaves from two other species of Eucalyptus. Both compounds were found in high proportions relative to the essential oils extracted from the leaves. We propose that many other carbohydrate monoterpene esters previously isolated from bulk leaf extracts of various Eucalyptus species may also be localized within the non-volatile fraction of foliar secretory cavities.     

Babesia bovis: successful vaccination against homologous challenge in splenectomised calves using a fraction of haemagglutinating antigen

A soluble extract from lysed bovine erythrocytes infected with Babesia bovis, was separated by preparative agarose electrophoresis. A fraction with a mobility of plasma β globulins was shown to contain babesial antigen confined mainly to the infected erythrocyte and was used to vaccinate a group of four calves. Following challenge with homologous B. bovis all four calves vaccinated with the antigen survived the infection whereas all the calves in a control group of four died from infection.     

Immunopathophysiology of Babesia bovis and Plasmodium falciparum infections

Babesia bovis and Plasmodium falciparum are both vector-borne parasites primarily infecting the erythrocytes of their respective hosts. They have obvious differences, yet the diseases caused by these parasites share many common features. Both have generated a considerable body of research but, perhaps because of the classical distinction between veterinary and medical parasitology, many of the similarities between the two have been neglected. As this review shows however, many of the pathophysiological changes in B. bovis infections are poorly described for P. falciparum - and vice versa. Examples are the roles of lipid peroxidation, neutrophil adhesion and production of tumour necrosis factor (TNF) in malaria, which have been largely unstudied in babesiosis, or conversely the roles of fibronectin, immune complexes, cryofibrinogen and the complement cascade in babesiosis, which have been little studied (partly for ethical reasons) in human malaria. To clarify such questions, it may be that each of these diseases may serve as a partial model for the other.     

Selective inhibition of prostaglandin biosynthesis by gold salts and phenylbutazone

Gold salts and phenylbutazone selectively inhibit the synthesis of PGF_2α and PGE₂ respectively. Lowered production of one prostaglandin species is accompanied by an increased production of the other. Selective inhibition by these drugs was observed in the presence of adrenaline, reduced glutathione and copper sulphate under conditions when most anti-inflammatory compounds inhibited PGE₂ and PGF_2α syntheses equally. It is postulated that selective inhibitors may have a different mode of action in vivo and beneficial effects may be related to the endogenous ratio of PGE to PGF required for normal function.     

Babesia bovis (argentina): analysis of fibrinogen-like proteins during infection

Fibrinogen and fibrinogen-like proteins (FLP) were isolated from plasma and serum of cattle acutely infected with Babesia bovis. The sizes and chain structures of these proteins were examined and clotting assays performed. The results indicated that the blood was in a hypercoagulable state due mainly to enhanced production of hydrogen bonded fibrin and offset partly by slight inhibition of chain cross-linking. The latter appeared due to a Factor XIII inhibitor. Reduction of A alpha chains of plasma FLP was not evident, nor could lower molecular weight remnants be regularly detected strongly suggesting that fibrin(ogen) lysis rarely occurred. Similarly the size and chain structure of the majority of noncoagulable FLP of serum was consistent with their being the product of coagulation and not fibrinolysis. Only in heavily infected splenectomized cattle were products from lysed cross-linked fibrin detected and these constituted only about 3% of total serum FLP.     

Formation of temporary flagellar structures during insect organogenesis

Cilia and flagella are rare in nongerminal tissues of anthropods, and are generally thought to be restricted to sperm and sensory cells in insects (2). Whitten (5) has reported the presence of kinetosomes at the base of mitotrichia in the dipteran fly Sarcophaga bullata, but reports no evidence of the organization of fibrous elements characteristic of cilia and or flagella. During an ultrastructural analysis of morphogenesis of the colleterial gland of the silk moth Hyalophora cecropia, we found the first example of paired flagella associated with an insect secretory cell. These structures are also unusual in that they serve a temporary role in morphogenesis and subsequently disappear at the terminal stages of differentiation.     

Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals

Differential rates of nucleotide substitution among different gene segments and between distinct evolutionary lineages is well documented among mitochondrial genes and is likely a consequence of locus-specific selective constraints that delimit mutational divergence over evolutionary time. We compared sequence variation of 18 homologous loci (15 coding genes and 3 parts of the control region) among 10 mammalian mitochondrial DNA genomes which allowed us to describe different mitochondrial evolutionary patterns and to produce an estimation of the relative order of gene divergence. The relative rates of divergence of mitochondrial DNA genes in the family Felidae were estimated by comparing their divergence from homologous counterpart genes included in nuclear mitochondrial DNA (Numt, pronounced "new might"), a genomic fossil that represents an ancient transfer of 7.9 kb of mitochondrial DNA to the nuclear genome of an ancestral species of the domestic cat (Felis catus). Phylogenetic analyses of mitochondrial (mtDNA) sequences with multiple outgroup species were conducted to date the ancestral node common to the Numt and the cytoplasmic (Cymt) mtDNA genes and to calibrate the rate of sequence divergence of mitochondrial genes relative to nuclear homologous counterparts. By setting the fastest substitution rate as strictly mutational, an empirical "selective retardation index" is computed to quantify the sum of all constraints, selective and otherwise, that limit sequence divergence of mitochondrial gene sequences over time.