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1.  Variation in the Degree of Pectin Methylesterification during the Development of Baccharis dracunculifolia Kidney-Shaped Gall 
PLoS ONE  2014;9(4):e94588.
Insect galls may be study models to test the distribution of pectins and arabinogalactan-proteins (AGPs) and their related functions during plant cell cycles. These molecules are herein histochemically and immunocitochemically investigated in the kidney-shaped gall induced by Baccharopelma dracunculifoliae (Psyllidae) on leaves of Baccharis dracunculifolia DC. (Asteraceae) on developmental basis. The homogalacturonans (HGAs) (labeled by JIM5) and the arabinans (labeled by LM6) were detected either in non-galled leaves or in young galls, and indicated stiffening of epidermal cell walls, which is an important step for cell redifferentiation. The labeling of HGAs by JIM7 changed from young to senescent stage, with an increase in the rigidity of cell walls, which is important for the acquaintance of the final gall shape and for the mechanical opening of the gall. The variation on the degree of HGAs during gall development indicated differential PMEs activity during gall development. The epitopes recognized by LM2 (AGP glycan) and LM5 (1–4-β-D-galactans) had poor alterations from non-galled leaves towards gall maturation and senescence. Moreover, the dynamics of pectin and AGPs on two comparable mature kidney-shaped galls on B. dracunculifolia and on B. reticularia revealed specific peculiarities. Our results indicate that similar gall morphotypes in cogeneric host species may present distinct cell responses in the subcelular level, and also corroborate the functions proposed in literature for HGAs.
PMCID: PMC3991646  PMID: 24747777
2.  Healthcare associated infections caused by coagulase-negative Staphylococci in a neonatal intensive care unit 
This study sought to evaluate infections related to health care caused by coagulase-negative Staphylococci in a neonatal intensive care unit by assessing antimicrobial susceptibility profiles and potentially effective antibiotic regimens.
This was a retrospective descriptive study performed on a case series of healthcare-associated infections, and the antimicrobial susceptibility profiles were evaluated. Newborns from other hospitals who were admitted to a neonatal intensive care unit in Rio de Janeiro between January 1, 2010, and June 30, 2012, were studied.
In total, 765 patients were admitted, totaling 3,051 patient-days, and the incidence density of general infection was 18.9 per 1,000 patient-days. The rate of central venous catheter use was 71.6%, and the positive culture rate for all sites and all infections related to health care were 68.4%. Coagulase-negative Staphylococci were identified in 11 (19.2%) of 57 health care-related infections, and infections with extended-spectrum beta-lactamase producing Klebsiella pneumoniae and Candida sp. constituted 5 cases each. Of the 11 cases of coagulase-negative Staphylococci, 10 (90.9%) were primary bloodstream infections. The sensitivity of the coagulase-negative Staphylococci isolates to vancomycin, clindamycin, ciprofloxacin, oxacillin and gentamycin was 100%, 81.8%, 72.7%, 27.2% and 22.2%, respectively. There were no deaths directly attributed to coagulase-negative Staphylococci infection.
Coagulase-negative Staphylococci was the main agent identified in healthcare-associated infections, with low rates of infections related to central venous catheter. In hospitals with a high oxacillin resistance profile, similar to those included in this study, vancomycin may be used as an initial therapy, although clindamycin represents a viable alternative.
PMCID: PMC4031843  PMID: 24213088
Cross-infection; Intensive care, neonatal; Staphylococcus
3.  Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development 
BMC Genomics  2013;14:78.
Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores.
The study generated 846,762 high quality sequence reads, with an average length of 334 bp and totalling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases.
Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapped to exon regions in the reference M. acuminata DH Pahang whole genome sequence. A total of 4068 genic-SSR loci were identified in Calcutta 4 and 4095 in Cavendish Grande Naine. A subset of 95 potential defense-related gene-derived simple sequence repeat (SSR) loci were validated for specific amplification and polymorphism across M. acuminata accessions. Fourteen loci were polymorphic, with alleles per polymorphic locus ranging from 3 to 8 and polymorphism information content ranging from 0.34 to 0.82.
A large set of unigenes were characterized in this study for both M. acuminata Calcutta 4 and Cavendish Grande Naine, increasing the number of public domain Musa ESTs. This transcriptome is an invaluable resource for furthering our understanding of biological processes elicited during biotic stresses in Musa. Gene-based markers will facilitate molecular breeding strategies, forming the basis of genetic linkage mapping and analysis of quantitative trait loci.
PMCID: PMC3635893  PMID: 23379821
Musa acuminata; Mycosphaerella musicola; Biotic stress; Transcriptome; 454 pyrosequencing; SSR
4.  Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata 
AoB Plants  2012;2012:pls030.
Many varieties of banana (Musa acuminata) lack resistance to biotic stresses. An EST collection was developed, including transcripts expressed in banana-Mycosphaerella fijiensis interactions. Developed polymorphic gene-derived SSR markers are applicable for genetic mapping, diversity characterization and marker assisted breeding.
Background and aims
Banana (Musa acuminata) is a crop contributing to global food security. Many varieties lack resistance to biotic stresses, due to sterility and narrow genetic background. The objective of this study was to develop an expressed sequence tag (EST) database of transcripts expressed during compatible and incompatible banana–Mycosphaerella fijiensis (Mf) interactions. Black leaf streak disease (BLSD), caused by Mf, is a destructive disease of banana. Microsatellite markers were developed as a resource for crop improvement.
cDNA libraries were constructed from in vitro-infected leaves from BLSD-resistant M. acuminata ssp. burmaniccoides Calcutta 4 (MAC4) and susceptible M. acuminata cv. Cavendish Grande Naine (MACV). Clones were 5′-end Sanger sequenced, ESTs assembled with TGICL and unigenes annotated using BLAST, Blast2GO and InterProScan. Mreps was used to screen for simple sequence repeats (SSRs), with markers evaluated for polymorphism using 20 diploid (AA) M. acuminata accessions contrasting in resistance to Mycosphaerella leaf spot diseases.
Principal results
A total of 9333 high-quality ESTs were obtained for MAC4 and 3964 for MACV, which assembled into 3995 unigenes. Of these, 2592 displayed homology to genes encoding proteins with known or putative function, and 266 to genes encoding proteins with unknown function. Gene ontology (GO) classification identified 543 GO terms, 2300 unigenes were assigned to EuKaryotic orthologous group categories and 312 mapped to Kyoto Encyclopedia of Genes and Genomes pathways. A total of 624 SSR loci were identified, with trinucleotide repeat motifs the most abundant in MAC4 (54.1 %) and MACV (57.6 %). Polymorphism across M. acuminata accessions was observed with 75 markers. Alleles per polymorphic locus ranged from 2 to 8, totalling 289. The polymorphism information content ranged from 0.08 to 0.81.
This EST collection offers a resource for studying functional genes, including transcripts expressed in banana–Mf interactions. Markers are applicable for genetic mapping, diversity characterization and marker-assisted breeding.
PMCID: PMC3521319  PMID: 23240072
5.  A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome 
BMC Plant Biology  2009;9:40.
Arachis hypogaea (peanut) is an important crop worldwide, being mostly used for edible oil production, direct consumption and animal feed. Cultivated peanut is an allotetraploid species with two different genome components, A and B. Genetic linkage maps can greatly assist molecular breeding and genomic studies. However, the development of linkage maps for A. hypogaea is difficult because it has very low levels of polymorphism. This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability.
In this work, we constructed a B-genome linkage map, which will complement the previously published map for the A-genome of Arachis, and produced an entire framework for the tetraploid genome. This map is based on an F2 population of 93 individuals obtained from the cross between the diploid A. ipaënsis (K30076) and the closely related A. magna (K30097), the former species being the most probable B genome donor to cultivated peanut. In spite of being classified as different species, the parents showed high crossability and relatively low polymorphism (22.3%), compared to other interspecific crosses. The map has 10 linkage groups, with 149 loci spanning a total map distance of 1,294 cM. The microsatellite markers utilized, developed for other Arachis species, showed high transferability (81.7%). Segregation distortion was 21.5%. This B-genome map was compared to the A-genome map using 51 common markers, revealing a high degree of synteny between both genomes.
The development of genetic maps for Arachis diploid wild species with A- and B-genomes effectively provides a genetic map for the tetraploid cultivated peanut in two separate diploid components and is a significant advance towards the construction of a transferable reference map for Arachis. Additionally, we were able to identify affinities of some Arachis linkage groups with Medicago truncatula, which will allow the transfer of information from the nearly-complete genome sequences of this model legume to the peanut crop.
PMCID: PMC2674605  PMID: 19351409

Results 1-5 (5)