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1.  Expression of the mevalonate pathway enzymes in the Lutzomyia longipalpis (Diptera: Psychodidae) sex pheromone gland demonstrated by an integrated proteomic approach 
Journal of proteomics  2013;96:117-132.
In Latin America, Lutzomyia longipalpis is the main vector of the protozoan parasite Leishmania infantum, which is the causal agent of American Visceral Leishmaniasis. This insect uses male-produced pheromones for mate recognition. Elucidation of pheromone biogenesis or its regulation may enable molecular strategies for mating disruption and, consequently, the vector's population management. Motivated by our recent results of the transcriptomic characterization of the L. longipalpis pheromone gland, we performed a proteomic analysis of this tissue combining SDS-PAGE, and mass spectrometry followed by an integrative data analysis. Considering that annotated genome sequences of this sand fly are not available, we designed an alternative workflow searching MS/MS data against two customized databases using three search engines: Mascot, OMSSA and ProLuCID. A total of 542 proteins were confidently characterized, 445 of them using a Uniref100-insect protein database, and 97 using a transcript translated database. In addition, use of PEAKS for de novo peptide sequencing of MS/MS data confirmed ∼90% identifications made with the combination of the three search engines. Our results include the identification of six of the seven enzymes of the mevalonate-pathway, plus the enzymes involved in sesquiterpenoid biosynthesis, all of which are proposed to be involved in pheromone production in L. longipalpis.
Biological significance
L. longipalpis is the main vector of the protozoan parasite L. infantum, which is the causal agent of American Visceral Leishmaniasis. One of the control measures of such disease is focused on vector population control. As this insect uses male-produced pheromones for mate recognition, the elucidation of pheromone biogenesis or its regulating process may enable molecular strategies for mating disruption and, consequently, this vector's population management. On this regard, in this manuscript we report expression evidence, at the protein level, of several molecules potentially involved in the pheromone production of L. longipalpis. Our results include the identification of the mevalonate-pathway enzymes, plus the enzymes involved in sesquiterpenoid biosynthesis, all of which are proposed to be involved in pheromone production in L. longipalpis. In addition, considering that the annotated genome sequences of this sand fly are not yet available, we designed an alternative workflow searching MS/MS data against proteomic and transcript translated customized databases, using three search engines: Mascot, OMSSA, and ProLuCID. In addition, a de novo peptide sequencing software (PEAKS) was used to further analyze the MS/MS data. This approach made it possible to identify and annotate 542 proteins for the pheromone gland of L. longipalpis. Importantly, all annotated protein sequences and raw data are available for the research community in protein repositories that provide free access to the data.
doi:10.1016/j.jprot.2013.10.028
PMCID: PMC3917562  PMID: 24185139
Lutzomyia longipalpis; Male pheromone gland; Proteomics; Proteome; Mevalonate pathway
2.  1,1′:4′,1′′-Terphenyl-2′,5′-dicarb­oxy­lic acid dimethyl sulfoxide-d 6 disolvate 
The asymmetric unit of the title solvate, C20H14O4·2C2D6OS, contains half of the substituted terephthalic acid mol­ecule and one solvent mol­ecule. The centroid of the central benzene ring in the acid mol­ecule is coincident with a crystallographic inversion center. Neither the carboxyl nor the phenyl substituents are coplanar with the central aromatic ring, showing dihedral angles of 53.18 (11) and 47.83 (11)°, respectively. The dimethyl sulfoxide solvent mol­ecules are hydrogen bonded to the carb­oxy­lic acid groups.
doi:10.1107/S1600536812012056
PMCID: PMC3344129  PMID: 22606132
3.  Phenyl 3,5-di-tert-butyl-2-hy­droxy­benzoate 
The title mol­ecule, C21H26O3, has a six-membered planar carbon ring as the central core, substituted at position 1 with phen­oxy­carbonyl, at position 2 with hy­droxy and at positions 3 and 5 with tert-butyl groups. The structure shows two independent but very similar mol­ecules within the asymmetric unit. For both independent mol­ecules, the ester carboxyl­ate group is coplanar with the central core, as reflected by the small C—C—O—C torsion angles [179.95 (17) and 173.70 (17)°]. In contrast, the phenyl substituent is almost perpendicular to the carboxyl­ate –CO2 fragment, as reflected by C—O—C—C torsion angles, ranging from 74 to 80°. The coplanarity between the central aromatic ring and the ester carboxyl­ate –CO2– group allows the formation of an intra­molecular hydrogen bond, with O⋯O distances of 2.563 (2) and 2.604 (2) Å.
doi:10.1107/S1600536810044028
PMCID: PMC3011503  PMID: 21589569
4.  Detecting single-nucleotide polymorphism by single-nucleotide polymorphism interactions in rheumatoid arthritis using a two-step approach with machine learning and a Bayesian threshold least absolute shrinkage and selection operator (LASSO) model 
BMC Proceedings  2009;3(Suppl 7):S63.
The objective of this study was to detect interactions between relevant single-nucleotide polymorphisms (SNPs) associated with rheumatoid arthritis (RA). Data from Problem 1 of the Genetic Analysis Workshop 16 were used. These data consisted of 868 cases and 1,194 controls genotyped with the 500 k Illumina chip. First, machine learning methods were applied for preselecting SNPs. One hundred SNPs outside the HLA region and 1,500 SNPs in the HLA region were preselected using information-gain theory. The software weka was used to reduce colinearity and redundancy in the HLA region, resulting in a subset of 6 SNPs out of 1,500. In a second step, a parametric approach to account for interactions between SNPs in the HLA region, as well as HLA-nonHLA interactions was conducted using a Bayesian threshold least absolute shrinkage and selection operator (LASSO) model incorporating 2,560 covariates. This approach detected some main and interaction effects for SNPs in genes that have previously been associated with RA (e.g., rs2395175, rs660895, rs10484560, and rs2476601). Further, some other SNPs detected in this study may be considered in candidate gene studies.
PMCID: PMC2795964  PMID: 20018057
5.  8,8-Diethyl-1,4,5,8-tetra­hydro­naphthalene-1,4,5-trione 
The title mol­ecule, C14H14O3, contains two fused six-membered carbon rings with keto groups at positions 1, 4 and 5 and a gem-diethyl group at position 8. The mol­ecule is close to planar (maximum deviation = 0.044 Å), with one ethyl group at each side of the mol­ecular plane, with exception of the keto group at position 1 which is slightly deviated from the plane and disordered over two positions one on each side of it (occupancies 0.80/0.20). The packing of the mol­ecule shows weak bonded chains along a through C—H⋯O contacts and two intramolecular C—H⋯O interactions are also present.
doi:10.1107/S1600536809001755
PMCID: PMC2968259  PMID: 21581946
6.  4-Acetyl-3,3-diethyl-5-hydr­oxy-2-morpholino-2,3-dihydro-1-benzofuran 
In the title compound, C18H25NO4, the benzofuran ring is almost planar and the morpholino ring displays a chair conformation. The packing of compound has a one-dimensional structure constructed through inter­molecular O—H⋯O hydrogen bonds. The conformation is stabilized by intra­molecular C—H⋯N and C—H⋯O inter­actions.
doi:10.1107/S1600536808034065
PMCID: PMC2959820  PMID: 21581304
7.  (E)-3-(2,3-Dimethoxyphenyl)-1-(2-hydroxy-4-methoxyphenyl)prop-2-en-1-one 
The mol­ecular conformation of the title compound, C18H18O5, is stabilized by a strong intra­molecular hydrogen bond between the hydroxyl and carbonyl groups. The C=C double bond displays an E configuration while the carbonyl group shows an S-cis configuration relative to the double bond. The dihedral angle between the two rings is 15.0 (1)°.
doi:10.1107/S1600536808026949
PMCID: PMC2960490  PMID: 21201807
8.  9,10-Dihydr­oxy-4,4-dimethyl-5,8-dihydro­anthracen-1(4H)-one 
In the title mol­ecule, C16H16O3, the ring system is planar and an intramolecular hydrogen bond is present. The mol­ecular packing is dominated by an inter­molecular hydrogen bond and by π-stacking inter­actions [inter­planar separation 3.8012 Å].
doi:10.1107/S1600536808010891
PMCID: PMC2961891  PMID: 21202942
9.  2-(2-Pyridylamino)pyridinium tetra­chlorido­zincate(II) 
The structure of the title compound, (C10H10N3)2[ZnCl4], is composed of C10H9N3H+ (DPAH+) cations and [ZnCl4]2− anions. The two pyridyl rings of DPAH+ are approximately coplanar, with a dihedral angle of 7.2 (2)° between their corresponding least-squares planes. The proton is disordered in a one-to-one ratio over the two chemically equivalent pyridyl N atoms. An intra­molecular hydrogen bond is formed between the pyridinium H atom and the pyridyl N atom of the other pyridyl ring. The Zn atom lies on a twofold rotation axis. There are also some weak N—H⋯Cl hydrogen bonds. These inter­actions lead to the formation of an alternating zigzag chain in the solid state. The results clearly show that reducing agents normally used in hydro­thermal syntheses, such as metallic zinc employed here, are also active in terms of coordination chemistry.
doi:10.1107/S1600536808007745
PMCID: PMC2961562  PMID: 21202468

Results 1-9 (9)