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in the Escherichia coli and Saccharomyces cerevisiae responses to oxidative stress. Annu Rev Microbiol 2000, 54:439–461.PubMedCrossRef 15. Jenkins DE, Schultz JE, Matin A: Starvation-induced cross protection against heat or H2O2 challenge in Escherichia coli. J Bacteriol 1988,170(9):3910–3914.PubMed 16. Moreau PL: Diversion of the metabolic flux from pyruvate dehydrogenase to pyruvate oxidase decreases oxidative stress during glucose metabolism in nongrowing Escherichia coli cells incubated under aerobic, phosphate starvation conditions. J Bacteriol 2004, Selleck PD173074 186:7364–7368.PubMedCrossRef 17. Saby S, Leroy P, Block JC: Escherichia coli resistance to chlorine and glutathione synthesis in Dorsomorphin nmr response to oxygenation and starvation. Appl Environ

Microbiol 1999,65(12):5600–5603.PubMed 18. Snyder JA, Haugen BJ, Buckles EL, Lockatell CV, Johnson DE, Donnenberg MS, Welch RA, Mobley HL: Transcriptome of uropathogenic Escherichia coli during urinary tract infection. Infect Immun 2004,72(11):6373–6381.PubMedCrossRef 19. Gordon DM, Riley MA: A theoretical and experimental analysis of bacterial growth in the bladder. Mol Microbiol 1992,6(4):555–562.PubMedCrossRef 20. Hull RA, Hull SI: Nutritional requirements for growth of uropathogenic Escherichia coli in human urine. Infect Immun 1997,65(5):1960–1961.PubMed 21. Russo TA, Carlino UB, Mong A, Jodush ST: Identification of genes in an extraintestinal isolate of Escherichia coli with increased expression LXH254 cell line after exposure to human urine. Infect Immun 1999,67(10):5306–5314.PubMed 22. Mobley HL, Green DM, Trifillis AL, Johnson DE, Chippendale GR, Lockatell CV, Jones BD, Warren JW: Pyelonephritogenic Escherichia coli and killing of cultured human renal proximal tubular epithelial cells: role of hemolysin in some strains. Infect Immun 1990,58(5):1281–1289.PubMed

23. Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P, et al.: Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Aurora Kinase Acad Sci USA 2006,103(15):5977–5982.PubMedCrossRef 24. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, et al.: Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009,5(1):e1000344.PubMedCrossRef 25. Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, Tenaillon O: Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol 2007,24(11):2373–2384.PubMedCrossRef 26. Andersson P, Engberg I, Lidin-Janson G, Lincoln K, Hull R, Hull S, Svanborg C: Persistence of Escherichia coli bacteriuria is not determined by bacterial adherence. Infect Immun 1991,59(9):2915–2921.PubMed 27.

Custom-synthesized oligonucleotides for the PCR were purchased from GeneDesign (Osaka, Japan). DNA sequencing and

informatic analysis To sequence the DNA BI 2536 concentration fragments amplified by PCR, the fragments were purified with the PCR Gel Extraction Kit (QIAGEN, Valencia, CA) according to the manufacturer’s protocol. DNA sequencing was performed with the ABI PRISM 3130 (Applied Biosystems, Foster City, CA) and the BigDye v3.1 cycle sequencing kit (Applied Biosystems). The Genetyx sequence analysis program (Software Development, Tokyo, Japan) was used for computer analysis of DNA sequences. Homology searches against deposited sequences were performed with the aid of data from the National Center for Biotechnology Information TSA HDAC supplier (NCBI) using the BLAST network service http://​www.​ncbi.​nlm.​nih.​gov and the BLAST service at the Genome Information Research Center http://​genome.​naist.​jp/​bacteria/​vpara/​. Sequence information was obtained from the NCBI. The computer program CLUSTAL W was used for the nucleotide sequence alignment and phylogenetic analysis. Construction of vscN2 deletion GS-4997 supplier mutant strains of V. mimicus A four-primer PCR technique was used to engineer an in-frame deletion mutation as described previously [14]. Briefly, the upstream and downstream sequences of vscN2 of T3SS2α or T3SS2β were amplified using the pairs listed

in Additional file 1. The two fragments, amplified with primers 1 and 3, and 2 and 4, respectively, were used as templates for a second PCR using primers 1 and 4, which generated a PCR product containing the desired deletion. The amplified fragments were then sequenced and subcloned into an R6K-ori suicide vector pYAK1 and transformed into E. Interleukin-2 receptor coli SM10λpir. Cytotoxicity assays For cytotoxicity assays, eukaryotic cells were seeded at

3 × 104 cells well-1 in 96-well plates and cultured for 48 h to confluency. The cells were co-cultured with PBS-washed bacteria at a multiplicity of infection (moi) of 10 for 2- 6 h. The release of lactate dehydrogenase (LDH) into the medium was quantified by using a CytoTox96 non-radioactive cytotoxicity kit (Promega) according to the manufacturer’s instructions. The LDH release (per cent cytotoxicity) was calculated with the following equation: [optical density at 492 nm (OD492) of experimental release - OD492 of spontaneous release]/(OD492 of maximum release – OD492 of spontaneous release) × 100. Spontaneous release is defined as the amount of LDH released from the cytoplasm of uninfected cells, and maximum release as the total amount of LDH released after the complete lysis of uninfected cells. Statistical analysis Statistical significance was determined with the t test. A P value of < 0.05 was considered statistically significant.

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A. (2007). On a Hypothetical Generational Relationship between HCN and Constituents of the Reductive Citric Acid Cycle. Chem. Biodiversity 4:554–573. Haldane, J. B. S. 1929. The Origin of Life. The Rationalist Annual. Reproduced in: Bernal, J.D., The Origin of Life The Weidenfeld and Nicolson Natural History, R. Carrington, editor, London: Readers Union, 1967, pp. 242–249. Lazcano, A., Miller, S. L. (1996). The Origin and Early Volasertib Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time. Cell 85:793–798. Oparin, A. I. (1924). The Origin of Life. Proiskhodenie Zhini. English translation in: Bernal, J.D., The Origin of Life The Weidenfeld and Nicolson Natural History, R. Carrington, editor, London: Readers Union, 1967, pp. 199–234. Pascal, R., Boiteau, L., Commeyras, A. (2005). From the Prebiotic Synthesis of a-Amino Acids Towards a Primitive Translation Apparatus for the Synthesis of Peptides. Topics in Current Chemistry, 259:69–122. Pross, A. (2005). Stability in chemistry and biology: Life as a kinetic state of matter. Pure Appl. Chem. 77, 1905–1921. Shapiro, R. (2006). Small molecule interactions were central to the origin of life. Q. Rev. Biol. 81, 106–125. Wells, T. N. C., Ho, C. K.,

Fersht, A. R. (1986). Free Energy of Hydrolysis of Tyrosyl Adenylate and Its Binding to Wild-Type and Engineered Mutant Tyrosyl-tRNA Synthetases. Biochemistry 25, 6603–6608. E-mail: robert.​pascal@univ-montp2.​fr C646 in vivo Molecular Evolution of Clouds Having Fer-1 research buy Varying Initial Composition Eduardo Monfardini Penteado, Hlio Jaques Rocha-Pinto Observatrio do Valongo/UFRJ Many

molecules important for life are produced and destroyed in interstellar clouds. The collapse of such clouds may originate stars hosting planetary systems. During GBA3 formation of such systems, molecules of the molecular cloud, aggregated in grains, will be incorporated to the protoplanets, influencing the chemical evolution of the enviroment, maybe favoring the evolution of life at rocky planets located at the stellar habitable zones. Moreover, small bodies, like comets, that hits the formation planet, can carry molecules originated from the molecular cloud. Using astrochemistry equations (Herbst and Klemperer, 1973), we try to describe the evolution of the abundance of that molecules that are important for life from several initial interstellar compositions. These varying initial chemical compositions consider the change of the elemental abundances expected by the Chemical Evolution of the Galaxy (Tinsley, 1980). A system of first order differential equations that describes the varable abundances of each molecule at the gas fase is solved numerically, making possible the knoledge of how the abundance of such molecules change with time and initial chemical composition. We describe preliminary results for how the abundance of many molecules change with time, such as H2O, HCO, HCN, NH4, OH and CN. Herbst, E. And Klemperer, W., 1973.

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of race and sex differences. Am J Dis Child 1989, 143:1346–1349.PubMed 31. Bell NH, Shary J, Stevens J, Garza M, Gordon L, Edwards J: Demonstration that bone mass is greater in black than in white children. J Bone Atezolizumab purchase Miner Res 1991, 6:719–723.PubMedCrossRef 32. Theobald TM, Cauley JA, Gluer CC, Bunker CH, Ukoli FA, Genant HK: Black-white differences in hip geometry. Study of osteoporotic fractures research group. Osteoporos Int 1998, 8:61–67.PubMedCrossRef 33. Cosman F, Morgan DC, Nieves JW, Shen V, Luckey MM, Dempster DW, Lindsay R, Parisien M: Resistance to bone resorbing effects of PTH in black women. J Bone Miner Res 1997, 12:958–966.PubMedCrossRef 34. Dawson-Hughes B, Heaney RP, Holick MF, Lips P, Meunier PJ, Vieth R: Estimates of optimal vitamin D status. Osteoporos Int 2005, 16:713–716.PubMedCrossRef 35.

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M, Lewiecki EM, Bolognese MA, Weinstein RL, Ding B, San Martin J, McClung MR (2011) Effect of denosumab on bone mineral density and biochemical markers of bone turnover: six-year results of a phase 2 clinical trial. J check details Clin Endocrinol Metab 96:394–402PubMedCrossRef 14. Cummings SR, San Martin J, McClung MR, Siris ES, Eastell R, Reid IR, Delmas P, Zoog HB, Austin M, Wang A, Kutilek S, Adami S, Zanchetta J, Libanati C, Siddhanti S, Christiansen C (2009) Denosumab for prevention of fractures in postmenopausal women with osteoporosis. N Engl J Med 361:756–765PubMedCrossRef 15. Bone HG, Hosking D, Devogelaer JP, Tucci JR, Emkey MLN8237 in vivo RD, Tonino RP, Rodriguez-Portales JA, Downs RW, Gupta J, Santora

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aeruginosa PAOU than in PAO1 during stationary phase (from 16 h of growth, a typical growth curve is shown on Figure 2B). To ascertain that the results were not biased by the reporter selleckchem gene and/or vector, we

assayed rhlG mRNA levels by quantitative reverse transcription-PCR (qRT-PCR) in plasmid-free PAOU and PAO1 strains at 20 h of growth. The rhlG mRNAs were 3-fold less abundant in PAOU than in the wildtype strain PAO1 (Additional file 1: Figure S1, Expression levels of rhlG gene). These results confirmed the involvement of AlgU in rhlG transcription, in agreement with the sequence of the novel LY3023414 chemical structure promoter identified by our 5′-RACE PCR experiment. Figure 2 Transcriptional activity of prrhlG . Promoter activity was followed by measuring the luminescence from P. aeruginosa PAO1 wildtype (squares) and mutant strains, harbouring pAB134, which contains the prrhlG::luxCDABE transcriptional fusion.

Activity was compared between the wildtype PAO1 strain and PAOU (algU mutant, triangles) (A); PAO1 and PAO6358 (rpoN mutant, diamonds) (B), and PAO1 and PDO100 (rhlI mutant) strain complemented with C4-HSL (open circles) or not (blacks circles) (C). Activity is expressed in Relative Units of Luminescence per 0.5 second Gemcitabine in function of time growth. Gain for luminescence detection was automatically set for each experiment. Results are representative of 2 complete experiments and of several additional experiments with fewer time points, standard deviations were < 6% for all values. Curve without symbol in panel B: growth curve of PAO1. We did not identify

the transcription start site at position −65 (Figure 1) resulting from a σ54-dependent promoter [4]. To rule out the involvement of σ54 in our strain and conditions, we used the prrhlG::luxCDABE fusion in P. aeruginosa PAO6358, which was constructed from PAO1 by deleting a large part of the rpoN gene encoding σ54 [24]. The luminescence was 1.7 to 7 fold lower in P. aeruginosa PAO6358 than in PAO1 from 8 to 30 h of growth (Figure 2B), indicating that σ54 plays indeed an important role in rhlG transcription. This was furthermore confirmed by qRT-PCR, which showed that rhlG mRNAs were 5-fold less abundant in PAO6358 than in PAO1 at 20 h of growth in PPGAS (Additional file 1: Figure S1). Altogether, three promoters, each dependent Methisazone on a distinct sigma factor (σ70, AlgU and σ54), are thus involved in rhlG transcription. The quorum sensing signal molecule C4-HSL inhibits rhlGtranscription Since the putative “lux box” found in the rhlG promoter region (Figure 1) was proposed to be the binding site of the quorum sensing regulator RhlR [9], we examined the prrhlG activity in P. aeruginosa PDO100 strain in which the rhlI gene is inactivated [25]. This gene encodes the RhlI enzyme responsible for the synthesis of C4-HSL which activates RhlR. The prrhlG::luxCDABE fusion led to luminescence values about 1.6-fold higher in P.

0 Ovary 5 17.9 Pancreas 3 10.7

Colon 2 7.1 Prostate 2 7.1 Glioblastoma multiforme 1 3.6 Ro 61-8048 ic50 selleckchem Hepatocellular carcinoma 1 3.6 Mesothelioma 1 3.6 Neuroendocrine 1 3.6 NSCLC 1 3.6 Oligodendroglioma 1 3.6 SCLC 1 3.6 Sarcoma 1 3.6 Thyroid 1 3.6 Prior systemic therapy     Yes 22 78.6 No 6 21.4 Once disease progression was observed, most patients elected to resume or initiate chemotherapy and/or targeted therapy. Seven (25%) patients requested to continue experimental treatment in combination with chemotherapy. Continuation of experimental treatment was allowed if desired by the patient and approved by the patient’s oncologist. Discovery of tumor-specific frequencies The exact duration of each examination was not recorded but lasted on average three hours. Each patient was examined an average of 3.3 ± 3.4 times (range 1 – 26). Frequency discovery was performed in patients with disease progression, stable disease or partial response. In general, we found more frequencies in patients with evidence Tideglusib of disease progression and large tumor bulk than in patients with stable disease, small tumor bulk or evidence of response. When we restrict the analysis of patients examined in 2006 and 2007, i.e. at a time when we had gathered more than 80% of the common tumor frequencies, we found that patients with evidence of disease progression had positive biofeedback responses to 70% or more of the frequencies previously discovered

in patients with the same disease. Conversely, patients with evidence of response to their current therapy had biofeedback responses to 20% or less

of the frequencies previously discovered in patients with the same disease. We also observed that patients examined on Org 27569 repeated occasions developed biofeedback responses to an increasing number of tumor-specific frequencies over time whenever there was evidence of disease progression. Whenever feasible, all frequencies were individually retested at each frequency detection session. These findings suggest that a larger number of frequencies are identified at the time of disease progression. A total of 1524 frequencies ranging from 0.1 to 114 kHz were identified during a total of 467 frequency detection sessions (Table 1). The number of frequencies identified in each tumor type ranges from two for thymoma to 278 for ovarian cancer. Overall, 1183 (77.6%) of these frequencies were tumor-specific, i.e. they were only identified in patients with the same tumor type. The proportion of tumor-specific frequencies ranged from 56.7% for neuroendocrine tumors to 91.7% for renal cell cancer. A total of 341 (22.4%) frequencies were common to at least two different tumor types. The number of frequencies identified was not proportional to either the total number of patients studied or the number of frequency detection sessions (Table 1). Treatment with tumor-specific amplitude-modulated electromagnetic fields Twenty eight patients received a total of 278.4 months of experimental treatment.

This MLST study similarly evidenced (Figure 3) three clusters of L. interrogans (corresponding to isolates grouped in L. interrogans clusters 1, 4 and 5). The clustering of isolates was in agreement with the lfb1-derived phylogeny. This result suggests that in the New Pifithrin-�� price Caledonian context, these lfb1-derived L. interrogans clusters are monophyletic

and probably each correspond to a single serovar. Again, L. interrogans cluster 5 did not contain any sequence of a known reference isolate, suggesting that it might correspond to a serovar not yet described, or at least not included in public sequence databases. Though the MLST phylogeny suggests that strains from this latter cluster could be related to the serovar Australis, seroconversions observed in New Caledonian patients infected with this strain merely point to Pyrogenes, a serogroup regarded as serologically related to Australis (data not shown). Whether ATPase inhibitor this cluster corresponds to a serovar not yet described or to a serovar described but which corresponding gene sequences have not been published GDC-0449 nmr remains to be studied. To further identify L. interrogans clusters 2 and 3 and to evaluate the feasibility of direct MLST from clinical specimen DNA extracts, we then tried to evaluate

the sequence polymorphism of the MLST targets using these clinical samples. Unfortunately, though both glmU and pntA could successfully be amplified and sequenced from extracts of patients containing ca. 200 leptospires per serum ml or more, none of the patients identified in these 2 clusters had leptospiraemia higher than 50 leptospires per ml. Interestingly, none of the isolate of our collection had lfb1 sequences identical to any of these two clusters. Because our isolate collection contains only strains collected until the year 2000, it cannot be known whether strains from these clusters were present in New Caledonia before 2001. They most probably already represented a limited part of the human cases

during this earlier period, as suggested by their low incidence over more than 2 years from 2008-february 2010 (see Table 4). It can also be hypothesized that strains from these clusters are of limited virulence to humans, therefore only associated with low leptospiraemia and would therefore seldom Liothyronine Sodium be evidenced, either by cultures (before 2001) or PCR (after 2001). Within L. borgpetersenii isolates, only two of the seven genes used in the MLST study of L. interrogans could be amplified. Actually, the set of primers used here was described by Thaipadungpanit et al [20] for use in L. interrogans isolates and was not supposed to amplify these genes in isolates from other species. Other MLST schemes have been used over a wider range of Leptospira species [18, 19]. These could have allowed a better typing of New Caledonian L. borgpetersenii isolates or clinical specimens. An ongoing program aimed at sequencing the complete genomes of a very large number of pathogenic Leptospira isolates (Vinetz J., com. pers.

References 1. Bosher JM, Labouesse M: RNA interference: genetic wand and genetic watchdog. Nature Cell Biol 2000, 2:31–36.CrossRef 2. Keene KM, Foy BD, Sanchez-Vargas I, Beaty BJ, Blair CD, Olson KE: RNA interference acts as a natural antiviral response to O’nyong-nyong virus (Alphavirus; Togaviridae) infection of Anopheles

gambiae . P Natl Acad Sci USA 2004, 101:17240–17245.CrossRef 3. Campbell CL, Keene KM, Brackney DE, Olson KE, Blair CD, Wilusz J, Foy BD: Aedes aegypti uses RNA interference in defense against Sindbis virus infection. BMC Microbiol 2008, 8:47.PubMedCrossRef 4. Cirimotich CM, Scott JC, Phillips AT, Geiss BJ, Olson KE: Suppression of RNA interference increases alphavirus replication and virus-associated mortality in Aedes aegypti mosquitoes. BMC Microbiol 2009, 9:49.PubMedCrossRef 5. Myles KM, Wiley MR, Morazzani selleck chemicals llc buy Ganetespib EM, Adelman ZN: Alphavirus-derived small RNAs

modulate pathogenesis in disease vector mosquitoes. P Natl Acad Sci USA 2008, 105:19938–19943.CrossRef 6. Sanchez-Vargas I, Scott JC, Poole-Smith BK, Franz AWE, Barbosa-Solomieu V, Wilusz J, Olson KE, Blair CD: Dengue virus type 2 infections of Aedes aegypti are modulated by the mosquito’s RNA interference pathway. PLOS Pathog 2009, 5:e1000299.PubMedCrossRef 7. Uchil PD, Satchidanandam V: Architecture of the flavivirus replication complex. Protease, nuclease, and detergents reveal encasement within double-layered membrane compartments. J Biol Chem 2003, 278:24388–24398.PubMedCrossRef 8. Medlock JM, Snow KR,

Leach S: Possible ecology and epidemiology of medically important mosquito-borne arboviruses in Great Britain. Epidemiol and Infect 2006, 135:466–482.CrossRef 9. Myles KM, Pierro DJ, Olson KE: Comparison of the transmission potential of two genetically distinct Sindbis viruses after oral infection of Aedes aegypti (Diptera: Culicidae). J Med Entomol 2004, 41:95–106.PubMedCrossRef 10. Taylor RM, Hurlbut HS, Work TH, Kingston JR, Frothingham TE: Sindbis virus: A newly recognized arthropod-transmitted virus. Am J Trop Med Hyg 1955, 4:844–862.PubMed 11. McKnight KL, Carbohydrate Simpson DA, Lin S, Knott TA, Polo JM, Pence DF, Johannsen DB, Heidner HW, Davis NL, Johnston RE: Deduced consensus sequence of Sindbis virus strain AR339: Mutations contained in laboratory strains which affect cell culture and in vivo phenotypes. J Virol 1996, 70:1981–1989.PubMed 12. Klimstra WB, Ryman KD, Johnston RE: Adaptation of Sindbis virus to BHK cells selects for use of heparin sulfate as an attachment receptor. J Virol 1998, 72:7357–7366.PubMed 13. Pierro DJ, Powers EL, Olson KE: Genetic find more determinants of Sindbis virus strain TR339 affecting midgut infection in the mosquito Aedes aegypti . J Gen Virol 2007, 88:1545–1554.PubMedCrossRef 14. Hardy JL, Houk EJ, Kramer LD, Reeves WC: Intrinsic factors affecting vector competence of mosquitoes for arboviruses. Annu Rev Entomol 1983, 28:229–262.PubMedCrossRef 15.

​tcdb.​org). To establish homology (common ancestry), either between two proteins or between two internal segments in a set of homologous proteins, the SSearch, IC and GAP programs were initially used [13, 14, 21, 35]. To establish homology among putative full-length homologues or repeat sequences of greater than 60 amino acyl residues, a value of 10 standard deviations (S.D.) was considered sufficient [4, 18]. According to Dayhoff et al.[36], this

value corresponds to a probability of 10-24 that this degree of similarity arose by chance [36]. We have found that a single iteration with a cut-off value of e-4 for the initial BLAST search, and a cut-off value of e-5 for the selleck kinase inhibitor second iteration, reliably retrieves homologues with few false positives. Nevertheless, all proteins giving BLAST e-values of e-7 or larger were tested for homology using the GAP program with default settings, requiring a comparison score of at least 10 S.D. in order to conclude that these proteins share a common origin. All hits that satisfied these criteria were put through a modified CD-Hit program with a 90% cut-off value [13, 24] to eliminate redundancies, fragmentary sequences and sequences with greater that 90% identity with a kept protein. gi-Extract IKK inhibitor from TCDB was used to extract the gi numbers of homologues, which were then searched through

NCBI to obtain the FASTA sequences. A multiple alignment

was generated with the ClustalW2 program, and homology of all aligned sequences throughout the relevant transmembrane domains was established using the SSearch and GAP programs [13, 21, 35]. Internal regions were examined for repeats whose dissimilar segments were compared with potentially homologous regions of the same proteins using the PRKACG SSearch and GAP programs with default settings. The ATP hydrolyzing (ABC) domains of these systems were excluded, and only the transmembrane domains or proteins were used in the analyses. Topological analyses Average hydropathy, amphipathicity and similarity plots for multiply aligned sets of homologues were generated with the AveHAS program [37], while web-based hydropathy, amphipathicity and MLN4924 in vivo predicted topology for an individual protein were estimated using the WHAT program [25] as well as the TMHMM 2.0 [38], HMMTOP [29], and TOPCONS [topcons.cbr.su.se/] programs. Some of these programs were updated as described by Yen et al.[13, 21]. Sequences were spliced for statistical analyses as described by Zhou et al.[15]. The global alignment program with displayed TMSs (GAP-DT), in combination with the SSearch and GAP programs, was used to determine where an extra transmembrane domain might have been inserted into or added to a transporter of a smaller number of TMSs to give rise to a transporter with a larger number of TMSs.