A physical map for an Asian malaria mosquito, Anopheles stephensi

Physical mapping is a useful approach for studying genome organization and evolution as well as for genome sequence assembly. The availability of polytene chromosomes in malaria mosquitoes provides a unique opportunity to develop high-resolution physical maps. We report a 0.6-Mb-resolution physical map consisting of 422 DNA markers hybridized to 379 chromosomal sites of the Anopheles stephensi polytene chromosomes. This makes An. stephensi second only to Anopheles gambiae in density of a physical map among malaria mosquitoes. Three hundred sixty-three (363) probes hybridized to single chromosomal sites, whereas 59 clones yielded multiple signals. This physical map provided a suitable basis for comparative genomics, which was used for determining inversion breakpoints, duplications, and origin of novel genes across species.

Reconstructing ancestral autosomal arrangements in the Anopheles gambiae complex

Members of the Anopheles gambiae complex have remarkably distinct ecological adaptations, behaviors, and degrees of vectorial capacity. Inferring phylogenetic relationships in the complex is crucial for identifying the genomic changes associated with the origin and loss of epidemiologically important traits. However, the high level of sequence similarity, genetic introgression, and shared molecular ancestral polymorphisms makes reconstruction of the A. gambiae complex phylogeny difficult. Phylogenetic relationships among the members of species complexes can be inferred from the distribution of fixed chromosomal inversions if outgroup arrangements are known. The aim of this work is to test a possibility of determining ancestral autosomal arrangements in the A. gambiae complex using outgroup chromosomes and a combination of bioinformatic and cytogenetic approaches. The minimum number of inversions between members of the A. gambiae complex and the outgroup species A. funestus and A. stephensi was calculated using the Multiple Genome Rearrangements (MGR) and Sorting Permutation by Reversals and block-INterchanGes (SPRING) programs. The physical mapping of A. merus chromosomes identified molecular coordinates of the proximal 2Ro+ inversion breakpoint in A. gambiae. DNA probes from 2La+ and 2Ro+ inversion breakpoints of the A. gambiae were mapped to the A. stephensi chromosomes. Assuming monophyletic origin of the inversions, this study concludes that physical mapping of ingroup and outgroup species can be used for identifying inversion breakpoints and ancestral autosomal arrangements within species complexes. Molecular characterization of the breakpoints in both ingroup and outgroup species will provide a solid basis for reconstructing the inversion history in the A. gambiae complex.

A major genetic locus controlling natural Plasmodium falciparum infection is shared by East and West African Anopheles gambiae

Background

Genetic linkage mapping identified a region of chromosome 2L in the Anopheles gambiae genome that exerts major control over natural infection by Plasmodium falciparum. This 2L Plasmodium-resistance interval was mapped in mosquitoes from a natural population in Mali, West Africa, and controls the numbers of P. falciparum oocysts that develop on the vector midgut. An important question is whether genetic variation with respect to Plasmodium-resistance exists across Africa, and if so whether the same or multiple geographically distinct resistance mechanisms are responsible for the trait.

Methods

To identify P falciparum resistance loci in pedigrees generated and infected in Kenya, East Africa, 28 microsatellite loci were typed across the mosquito genome. Genetic linkage mapping was used to detect significant linkage between genotype and numbers of midgut oocysts surviving to 7–8 days post-infection.

Results

A major malaria-control locus was identified on chromosome 2L in East African mosquitoes, in the same apparent position originally identified from the West African population. Presence of this resistance locus explains 75% of parasite free mosquitoes. The Kenyan resistance locus is named EA_Pfin1 (East Africa_ Plasmodium falciparum Infection Intensity).

Conclusion

Detection of a malaria-control locus at the same chromosomal location in both East and West African mosquitoes indicates that, to the level of genetic resolution of the analysis, the same mechanism of Plasmodium-resistance, or a mechanism controlled by the same genomic region, is found across Africa, and thus probably operates in A. gambiae throughout its entire range.

A standard cytogenetic photomap for the mosquito Anopheles stephensi (Diptera: Culicidae): application for physical mapping

To facilitate physical genome mapping, we have developed a new cytogenetic photomap for Anopheles stephensi (Liston) (Diptera: Culicidae), an important malaria vector in Asia. The high-resolution images of the ovarian polytene chromosomes have been straightened and divided by numbered divisions and lettered subdivisions. The exact chromosomal locations of eight DNA probes have been determined by fluorescent in situ hybridization. Using the DNA sequences, we have established correspondence between chromosomal arms among An. stephensi, Anopheles gambiae (Patton), and Anopheles funestus (Giles). The results support previous cytogenetic observations of arm translocations taking place during diversification of the species. To make the cytogenetic map useful for population genetics studies, we have indicated the chromosomal positions for the breakpoints of 19 polymorphic inversions.

Two fluoradene derivatives: pseudosymmetry, eccentric ellipsoids and a phase transition

Structures of two derivatives of the curved fluoradene ring system (C(19)H(12)) have been determined. Both have phases that are highly pseudosymmetric. At room temperature crystals of 7b-triisopropylsilylfluoradene (C(28)H(32)Si) have a P1 cell that contains two independent molecules (Z' = 2) and that is almost centered. Crystals of 7b-(2,4-dinitrophenyl)fluoradene (C(25)H(14)N(2)O(4)) have both a P2(1)/c cell with Z' = 1 and a P2(1)/c cell with Z' = 2. The molecular volumes in these two P2(1)/c structures differ by 0.7%, but the structures are otherwise virtually the same; the two independent molecules in the larger cell are related by a pseudotranslation. Some of the atomic ellipsoids in the P2(1)/c, Z' = 1 structure are very large and eccentric, and there are some hints in the diffraction pattern of an incipient phase transition, but the Z' = 1 and Z' = 2 phases are clearly different. The P2(1)/c, Z' = 2 crystal at 295 K probably contains some volume fraction of the Z' = 1 phase; when the temperature is lowered to 273 K this fraction is decreased markedly. The pronounced pseudosymmetry in the P1 and P2(1)/c structures that have Z' = 2 has been investigated by analysing the atomic coordinates, by performing refinements in the smaller pseudocells and by making separate Wilson plots for the classes of reflections which are systematically strong and systematically weak. All three approaches are informative, but they reveal different information. Least-squares fits of coordinates of corresponding atoms measure the similarity of the molecular conformations. The Wilson plots allow a quantitative comparison of the intensities of the strong and weak reflections and thus an assessment of the deviations of the true structure from the smaller pseudocell structure. Comparison of the atomic displacements obtained in the full and pseudocell refinements shows where the structural distortions are largest and provides an indication of their directions.

[Two-photon fluorescence from recombinant green fluorescent protein]

The photoconversion process of recombinant green fluorescent protein (rGFP) was investigated by two-photon excitation. The results indicated that the rGFP had very strong two-photon excitation fluorescence. The changes of two-photon-induced fluorescence polarization suggest that there is a proton transfer process between two different proton states of rGFP chromophores. The conformation of rGFP chromophores could be changed upon illumination, which partly block the energy transfer processes from amino acid residues to chromophores in rGFP, and result in the decrease of two-photon-induced fluorescence intensity. The fluorescence from amino acid residues in rGFP was also observed by three-photon excitation, which resulted from the blocked amino acid residues in rGFP. These results suggested that it is necessary to optimize rGFP excitation and detection for quantitative fluorescence microscopy.

Platinum(II) hydrazido complexes

Reaction of 1,2-dimethylhydrazine with the platinum hydroxo complex [(dppp)Pt(mu-OH)](2)(BF(4))(2) gives the bridging 1,2-dimethylhydrazido(-2) product [(dppp)(2)Pt(2)(mu-eta(2):eta(2)-MeNNMe)](BF(4))(2) 1. Crystals of 1.CH(2)Cl(2) from CH(2)Cl(2)/Et(2)O are monoclinic (C/2) with a = 19.690(1), b = 18.886(1), c = 17.170 (1) A, and beta = 92.111(1) degrees. Treatment of [(dppp)Pt(mu-OH)](2)(OTf)(2) with 1,1-dimethylhydrazine gives [(dppp)(2)Pt(2)(mu-OH)(mu-NHNMe(2))](OTf)(2) 2. Crystals of 2.CH(2)Cl(2) from CH(2)Cl(2)/Et(2)O are triclinic (P-1) with a = 12.910 (3), b = 13.927(3), c = 17.5872 (3) A, alpha = 87.121(3), beta = 89.997(4), and gamma = 84.728(3) degrees. Reaction of [(dppp)Pt(mu-OH)](2)(OTf)(2) with 1 equiv of phenylhydrazine in CH(2)Cl(2) gives [(dppp)(2)Pt(2)(mu-OH)(mu-NHNHPh)](OTf)(2) 3. Two equivalents of phenylhydrazine with [(dppp)Pt(mu-OH)](2)(X)(2) gives [(dppp)Pt(mu-NHNHPh)](2)(X)(2) 4 (X = BF(4), OTf). Crystals of 3.ClCH(2)CH(2)Cl from ClCH(2)CH(2)Cl/(i)()Pr(2)O are monoclinic (P2(1)/n) with a = 20.990(2), b = 13.098(1), c = 25.773 (2) A, and beta = 112.944(2) degrees. Crystals of 4(X = BF(4)).ClCH(2)CH(2)Cl(.)()2((t)()BuOMe) from ClCH(2)CH(2)Cl/(t)()BuOMe are monoclinic (C2/m) with a = 30.508(1), b = 15.203(1), c = 19.049 (1) A, and beta = 118.505(2) degrees.

Expression of connexin 30 in the developing mouse cochlea

Mutations in the GJB6 gene encoding connexin 30 (Cx30) can cause dominant forms of nonsyndromic deafness. By studying immunohistochemical localization of Cx30 in the mouse cochlea at different ages from 0 to 30 days after birth, we found that the expression of Cx30 is nearly the same as that of Cx26. These findings suggest that as well as Cx26, Cx30 may also contribute to the generation and maturation of endocochlear potential.

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Expression of connexin 26 and Na,K-ATPase in the developing mouse cochlear lateral wall: functional implications

The immunohistochemical localization of connexin 26 (a gap junction protein) and Na,K-ATPase in the mouse cochlear lateral wall was studied at different ages between 0 and 30 days after birth (DAB). Connexin 26-like immunoreactivity was sparsely distributed among the connective tissue cells just lateral to the future marginal cells of the stria vascularis on 0 DAB. In the mice of 3-6 DAB, connexin 26 was observed in the strial basal cell area, and was increased in its distribution density on 10 DAB. Connexin 26 was sparsely distributed among the fibrocytes in the spiral ligament and the suprastrial zone on 10 DAB, and its distribution density increased rapidly in the mouse on 12 DAB. The immunohistochemical distribution reached the adult pattern in the cochlear lateral wall on 15 DAB. Weak Na, K-ATPase-like immunoreactivity was observed in the epithelial cells, corresponding to the future strial marginal cells, on 0 DAB. Its staining intensity was enhanced with the increase of age, and reached the adult pattern on 10 DAB. In contrast, Na,K-ATPase-like immunoreactivity in the type II fibrocytes and suprastrial fibrocytes was first detected on 12 DAB, and reached the mature level on 15 DAB. It is well known that the endolymphatic potential (EP) reaches the adult level 2 weeks after birth. The expression patterns of connexin 26 and Na,K-ATPase in the fibrocytes of the spiral ligament and the suprastrial zone coincided with the rapid growth and maturation of EP. These findings may suggest a role for the gap junctional communications and Na,K-ATPase activity of the fibrocytes within the cochlear lateral wall in the generation and maturation of EP.

Trends in anemia treatment with erythropoietin usage and patient outcomes

Recombinant erythropoietin, first approved for Medicare reimbursement in June 1989, was prescribed at initial doses for dialysis patients of 2,500 to 2,700 U per administration independent of hematocrit level. By 1997, however, patients with hematocrits less than 30% were administered 6,000 U/dose, compared with 4,500 U administered to patients with hematocrits of 33% to 36%. Since 1990, the percentage of patients with hematocrits less than 30% decreased from 60% to 22% in 1997, whereas the percentage of patients with hematocrits of 33% to 36% increased from 10% to 30%. In 1997, Medicare initiated the Hematocrit Measurement Audit (HMA) policy, which was directed at reducing the percentage of claims for hematocrits greater than 36% and increasing the stability of the hematocrit levels. The policy change achieved the initial effect but resulted in a reduction of the mean hematocrit as well. The policy was changed in 1998 in response to patient and provider concerns. Mortality studies show that hematocrits less than 30% (or hemoglobin levels < 110 g/L) are associated with an 18% to 40% increased associated risk for death. Higher hematocrits of 33% to 36% appear to be associated with a 7% reduced risk for death. The risk for hospitalization parallels that of mortality. Patients with sustained hematocrits of 33% to 36% over 1 year appear to have the best outcome compared with patients with hematocrits that decrease. The latter are at greater risk than those patients in whom the hematocrits increase. In conclusion, dramatic improvements in hemodialysis patient hematocrits have occurred since 1989. Mortality and hospitalization studies support the National Kidney Foundation Dialysis Outcomes Quality Initiative (NKF DOQI) target hematocrit range of 33% to 36% as providing the best associated outcomes.