incubated with 20 ml Sepharose-immobilized monoclonal anti-HA antibodies (Covance). Beads were washed with buffer T without BSA before elution. DSP-induced crosslinks in eluted proteins were thiol-cleaved before separation by 8-16% SDS-PAGE and detection by Sypro Ruby (Bio-Rad). Quinone analysesLipid extractions and quinone detection were performed as described 19 . Hydrogenosomes (5.5 mg protein) were extracted and resuspended in 150 ml 9:1 methanol/ethanol, of which 50 ml was injected onto an HPLC system linked to an ECD. Sequence analysesAccession numbers for sequences used to reconstruct NuoF and NuoE phylogenies are listed in Supplementary Tables 2 and 3. NuoF sequences were aligned with CLUSTALX. NuoE sequences were aligned with Wisconsin Package Version 10.2 programs (Genetics Computer Group). A profile hidden Markov model (HMM) was built from Escherichia coli, Neurospora crassa, Bos taurus, Paracoccus denitrificans and Thermus thermophilus sequences with HMMBUILD. Additional sequences were aligned to the profile with HMMALIGN. Both alignments were edited to remove C-and N-terminal extensions. Analyses of NuoF and NuoE evolution were performed with MRBAYES 30 with the JTT amino-acid substitution model and with two Markov chains Monte Carlo. Chains were run for 100,000 generations, with sampling every 50 generations. The first 5,000 generations were discarded as burn-in. Consensus trees satisfying the more than 50 majority rule were drawn with Treeview, and probabilities of branch partitions were calculated.

Phytohormone overproduction in crown gall tumors is due to the expression of several T-DNA genes. The Infection of a wound site by Agrobacterium tumefaciens strains containing Ti (tumor-inducing) plasmids results in the neoplastic plant disease known as crown gall (1-5). In the plant genome, the integrated region (T-DNA) of the Ti plasmid expresses two phenotypic traits characteristic of transformed cells: phytohormone autonomy and opine synthesis. The T-DNA in tumors incited by octopine-type Ti plasmids encodes eight transcripts (6). Five of these map within three loci (tmr, tms, tml), which affect tumor morphology (7-11). Transposon inactivation of the tms locus (transcripts 1 and 2) or the tmr locus (transcript 4) results in tumors that proliferate shoots or roots, respectively. Inactivation of the tml locus (transcripts 6a and 6b) results in larger tumors on certain plant species. The region of T-DNA containing these loci is shown to be highly conserved in octopine and nopaline plasmids (12)(13)(14). The nucleotide sequences of the tmr (15,16) and tms (15,(17)(18)(19) genes have been recently determined and have been shown to be highly conserved. The synthesis of several proteins from the T-DNA region has been demonstrated in Escherichia coli minicells and in coupled transcription/translation systems of E. coli and A. tumefaciens (20). Three of these proteins had molecular weights identical to the predicted sizes of the tmr and tms gene products, as determined from the nucleotide sequence.Previous studies have also shown that the tms and tmr loci are involved in auxin and cytokinin metabolism, respectively (9-11, 21, 22). Tumors incited by tms mutants have decreased endogenous auxin levels (21) and are auxin dependent in culture (23,24

A cross-sectional case-control study (ratio ‫ס‬ 3:1) was conducted over a 15-month period to determine the prevalence and consequences of cryptosporidiosis in hospitalized diarrheic children (0−5 years old) at Mulago Hospital in Kampala, Uganda. Cryptosporidium parvum was detected and genotyped among 2,446 children of whom 1,779 (72.7%) had diarrhea, and 667 (27.3%) were age-and sex-matched controls. Of the 1,779 children with diarrhea, 532 (29.9%) had persistent (> 14 days) diarrhea and 1,247 (70.1%) had acute diarrhea. Overall, 444 (25.0%) of the 1,779 children with diarrhea had C. parvum, compared with only 57 (8.5%) of the 667 children without diarrhea (2 ‫ס‬ 80.2, P Յ 0.0001). Within this group of infected children, 72.8% were infected with genotype 1, 18.4% with genotype 2, and 4.1% with a mixture of both genotypes, and 4.1% isolates were either unclassified or C. meleagridis. The prevalence was highest during the rainy months of April to June. Of the 532 children with persistent diarrhea, 166 (31.2%) had C. parvum compared with 278 (22.3%) of the 1,247 children with acute diarrhea (2 ‫ס‬ 15.8, P Յ 0.0001). There was a significant association between C. parvum and malnutrition including stunting, being underweight, and wasting. Unfavorable outcome (death or failure to resolve within 14 days) occurred in 139 (72.8%) of the 191 children with C. parvum, and in only 65.1% of the 545 without (odds ratio ‫ס‬ 1.117, 95% confidence interval ‫ס‬ 1.005−1.243, P ‫ס‬ 0.05), Of the 191 children with C. parvum, 24 (12.6%) died, compared with 34 (6.2%) of the 545 without C. parvum (P ‫ס‬ 0.005). Mortality rates were higher among children with severe dehydration and persistent diarrhea, and in stunted or underweight children infected with C. parvum. Among Ugandan children, cryptosporidiosis, which remains untreatable, is frequently associated with diarrhea and other serious and unfavorable consequences.

Cryptosporidium hominis causes diarrhea in humans and has been associated with community outbreaks. This study describes the infectivity, illness, and serologic response after experimental challenge of 21 healthy adult volunteers with 10-500 C. hominis (TU502) oocysts. Sixteen subjects (76.2%) had evidence of infection; the 50% infectious dose (ID(50)) was estimated to be 10-83 oocysts using clinical and microbiologic definitions of infection, respectively. Diarrhea occurred in 40% of subjects receiving 10 oocysts with a stepwise increase to 75% in those receiving 500 oocysts. A serum IgG response was seen in those receiving more than 30 oocysts. Greatest responses were seen in volunteers with diarrhea and oocyst shedding. Volunteers with no evidence of infection had indeterminant or negative IgG responses. Cryptosporidium hominis 10 oocysts) and is clinically is infectious for healthy adults (ID(50) = similar to C. parvum-induced illness. In contrast to C. parvum, C. hominis elicted a serum IgG response in most infected persons.

Enterocytozoon bieneusi is the most common microsporidian associated with human disease, particularly in the immunocompromised population. In the setting of HIV infection, it is associated with diarrhea and wasting syndrome. Like all microsporidia, E. bieneusi is an obligate, intracellular parasite, but unlike others, it is in direct contact with the host cell cytoplasm. Studies of E. bieneusi have been greatly limited due to the absence of genomic data and lack of a robust cultivation system. Here, we present the first large-scale genomic dataset for E. bieneusi. Approximately 3.86 Mb of unique sequence was generated by paired end Sanger sequencing, representing about 64% of the estimated 6 Mb genome. A total of 3,804 genes were identified in E. bieneusi, of which 1,702 encode proteins with assigned functions. Of these, 653 are homologs of Encephalitozoon cuniculi proteins. Only one E. bieneusi protein with assigned function had no E. cuniculi homolog. The shared proteins were, in general, evenly distributed among the functional categories, with the exception of a dearth of genes encoding proteins associated with pathways for fatty acid and core carbon metabolism. Short intergenic regions, high gene density, and shortened protein-coding sequences were observed in the E. bieneusi genome, all traits consistent with genomic compaction. Our findings suggest that E. bieneusi is a likely model for extreme genome reduction and host dependence.