Influence of HLA-A, B, and -DRB1 genes and panel-reactive antibodies on the waitlist time for kidney transplantation in the state of Sao Paulo-Brazil.

BACKGROUND: Brazil ranks second in the absolute number of transplants. However, the supply remains insufficient to meet the demands, resulting in a lengthy waitlist. This study aimed to analyze whether the frequency of human leukocyte antigen (HLA) and the value of calculated panel reactive antibody (cPRA) would influence the waiting time for kidney transplantation. METHODS: The HLA-A, B, and -DRB1 frequencies and the cPRA value were analyzed in 11,186 kidney transplant candidates included in the waitlist from 2006 to 2016. RESULTS: The most frequent alleles were HLA-A*02, HLA-B*35, and HLA-DRB1*13. The overall mean length of stay on the list was 986 ± 1001 days. The mean waiting time for the three most frequent alleles of the HLA-A and B loci showed no significant difference when compared with the least frequent alleles; however, for the HLA-DRB1 locus, the most frequent alleles showed a shorter waiting time. In the association between HLA and PRA, the average length of stay on the list increased according to the candidate's degree of sensitization, regardless of the analyzed HLA frequency. CONCLUSION: The length of stay on the waitlist is influenced by the frequency of the HLA alleles of the DRB1 locus and the degree of sensitization.

Phenotypic and molecular basis for genetic variation in jelly palms (Butia sp.): where are we now and where are we headed to?

We compiled studies that addressed morphological and physicochemical traits, as well as population genetic studies involving jelly palms, genus Butia (Arecaceae). First, we conducted a bibliometric study with selected articles, by revising the fundamental contributions to unraveling phenotypic traits that have been used for describing the phenotypic variation within and among populations. Moreover, we sought to comprehend the patterns of genetic diversity and structure that have been presented so far, based on molecular markers. Finally, we conducted a review of the gene sequences registered to NCBI for Butia. Overall, morphological descriptors have been proposed to depict population-level variability, but the most significant results are available from chemical properties and characterization of metabolites, revealing important traits to being explored. Yet, limited information is available to describe population variation and their genetic components. On the molecular level, almost all studies so far provided results with classical molecular markers. The literature of SNP markers for Butia species is virtually non-existent. Given the current endangered state of Butia species, it is urgent that researchers pursue updated genomic technologies to invest in in-depth characterizations of the genetic diversity and structure of jelly palms. The current state of population fragmentation urges effective measures toward their conservation.

Genetic Structure and Biodiversity in Wild Centropomus parallelus and in Wild and Recently Domesticated Centropomus undecimallis Populations.

Centropomus undecimalis (common snook) and Centropomus parallelus (fat snook) have a wide distribution from southern Florida to southern Brazil. Due to their value as a food source, these species have been heavily exploited through predatory fishing, posing a conservation challenge. To assess their genetic diversity and population structure, we used microsatellite markers. Our findings revealed genetic differences among populations of the same species, highlighting the need for targeted conservation efforts. The microsatellite markers proved effective in assessing genetic variability, providing valuable insights for management and conservation. The parameters Ho (observed heterozygosity) and He (expected heterozygosity) were reliable indicators of genetic diversity, and specific loci showed varying allele numbers across populations. Our study contributes to understanding population genetics in these snook species and supports their conservation. Despite not being classified as endangered, genetic differences among populations emphasize the importance of considering population-level characteristics in conservation strategies. This research lays the foundation for future studies and actions aimed at preserving these valuable fish species. In summary, our study demonstrates the significance of microsatellite markers in assessing genetic variability and population structure in common snook and fat snook, informing conservation efforts for these species.

Genetic and chemodiversity in native populations of Schinus terebinthifolia Raddi along the Brazilian Atlantic forest.

Schinus terebinthifolia is a species native to different ecoregions in the Brazilian Atlantic Forest. The plant is listed on the National Relation of Medicinal Plants and recommended as phytomedicine, however while extractive exploitation prevails as the main route of raw material a significant variation of compounds will be detected. To assure the expansion of productive chain it is important to start by studying population diversity and chemical variations. We used SSR markers for studies of genetic structure among populations from dense ombrophilous forest (ES); the deciduous seasonal forest (SM); the savanna (DOU) and the sandbanks (ITA and MSP), and compared the results to their chemical profiles of essential oil. Genetic structure revealed differences among populations and significant fixation rates. Pairwise studies and Bayesian analysis showed similarities between ITA and SM and between DOU and MSP, proving that the patterns of distribution for the species do not follow the isolation by distance or similarity by environmental conditions. The comparison between PCA of genotypes and chemodiversity reinforces the unique profile for each population despite the environmental similarity observed and genetic analysis. The most divergent genotype and chemical group was found at the ombrophilous forest, strong evidence that we should undertake conservation efforts to prevent losses of biodiversity in that area.

Assessing Diversity, Plasmodium Infection and Blood Meal Sources in Mosquitoes (Diptera: Culicidae) from a Brazilian Zoological Park with Avian Malaria Transmission.

Avian malaria parasites are widespread parasites transmitted by Culicidae insects belonging to different genera. Even though several studies have been conducted recently, there is still a lack of information about potential vectors of Plasmodium parasites, especially in Neotropical regions. Former studies with free-living and captive animals in São Paulo Zoo showed the presence of several Plasmodium and Haemoproteus species. In 2015, a pilot study was conducted at the zoo to collect mosquitoes in order to find out (i) which species of Culicidae are present in the study area, (ii) what are their blood meal sources, and (iii) to which Plasmodium species might they be potential vectors. Mosquitoes were morphologically and molecularly identified. Blood meal source and haemosporidian DNA were identified using molecular protocols. A total of 25 Culicidae species were identified, and 6 of them were positive for Plasmodium/Haemoproteus DNA. Ten mosquito species had their source of blood meal identified, which were mainly birds, including some species that were positive for haemosporidian parasites in the former study mentioned. This study allowed us to expand the list of potential vectors of avian malaria parasites and to improve our knowledge of the evolutionary and ecological relationships between the highly diverse communities of birds, parasites, and vectors present at São Paulo Zoo.

Development and characterization of microsatellite markers in Campomanesia adamantium, a native plant of the Cerrado ecoregions of South America.

PREMISE: A novel set of nuclear microsatellite markers was developed and characterized for Campomanesia adamantium (Myrtaceae) and tested for cross-amplification in the related species C. sessiliflora. METHODS AND RESULTS: Forty-one primer pairs were designed for simple sequence repeat loci, of which 36 successfully amplified and were polymorphic. The number of alleles ranged from two to 14, with an average of 8.14 alleles per locus. Additionally, cross-amplification was tested in C. sessiliflora; more than 55.5% of the microsatellite loci amplified, confirming the use of these microsatellite markers in a related species. CONCLUSIONS: We developed a set of microsatellite markers that will be useful for future studies of genetic diversity and population structure of C. adamantium and a closely related species, which will aid in future conservation efforts.

Genetic ancestry effects on the distribution of toll-like receptors (TLRs) gene polymorphisms in a population of the Atlantic Forest, São Paulo, Brazil.

The innate immune system governed by toll-like receptors (TLRs) provides the first line of defense against pathogens. Surface-localized TLR1 and TLR6 are known to detect parasite components. TLR encoding genes were shown to display signatures of recent positive selection in Europeans and might be involved in local adaptation at immune-related genes. To verify the influence of Brazilian population admixture on the distribution of polymorphisms in TLRs, we analyzed the genotype frequencies of 24 polymorphisms distributed across five TLR genes in a Southeastern Brazilian population where autochthonous cases of malaria occur in small foci of transmission. The estimation of ancestry showed mainly European ancestry (63%) followed by African ancestry (22%). Mean proportions of European ancestry differed significantly between the genotypes of the TLR1 (I602S) gene and in the TLR6 (P249S) gene. The chance of having the G allele in TLR1 gene increases as European ancestry increases as well as the chance of having the T allele in the TLR6 gene. The 602S allele is related to a ''hypo-responsiveness'' possibly explaining the high prevalence of asymptomatic malaria cases in areas of Southeastern Brazil. Our results underline the necessity to include informative ancestry markers in genetic association studies in order to avoid biased results.

Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

HLA-A, -B, and -DRB1 allele and haplotype diversity in a cohort of Brazilian renal transplant candidates.

The distribution of organs for renal transplant depends on HLA matching between donor and recipient. This study aimed to characterize the allele and haplotype frequencies of HLA-A, -B, and -DRB1 in a cohort of renal transplant candidates populations in the region of Sao José do Rio Preto (State of São Paulo), to compare the allele frequencies between Caucasian and Black in that region, as well as to compare these frequencies with different Brazilian populations reported. The HLA-A, -B, and -DRB1 allele and haplotypes frequencies were analyzed in a sample of 2.624 individuals and classified according to the ethnic group (2.347 Caucasians and 277 Blacks). The HLA class I (A, B) and class II (DRB1) specificities were determined by complement-dependent microlymphocytotoxic (CDC) and Polymerase Chain Reaction/Sequence Specific Priming (PCR-SSP) methods, respectively. Twenty-one HLA-A, 34 HLA-B and 13 HLA-DRB1 allelic groups were identified. The most frequent alleles for each locus were HLA-A(∗)02, HLA-B(∗)35, and HLA-DRB1(∗)11. The most frequent haplotypes found were A(∗)01 B(∗)08 DRB1(∗)03 among Caucasians and A(∗)29 B(∗)15 DRB1(∗)04 among Blacks. The most common alleles for each locus among RTx were HLA-A(∗)02, HLA-B(∗)35 and HLA-DRB1(∗)11. The haplotypes A(∗)01 B(∗)08 DRB1(∗)03 and A(∗)29 B(∗)44 DRB1(∗)07 prevailed among Caucasians and Blacks, respectively. This study provides the first data on the HLA-A, HLA-B and HLA-DRB1 allele and haplotype frequencies of renal transplant candidates populations in the region of Sao José do Rio Preto.

Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil.

Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80-216 m) and an upland site (1010-1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.

Development of microsatellite markers for Qualea grandiflora (Vochysiaceae), a typical species of the Brazilian cerrado.

PREMISE OF THE STUDY: Microsatellite primers were developed to investigate genetic diversity and population structure of Qualea grandiflora, a typical species of the Brazilian cerrado. METHODS AND RESULTS: Eight microsatellite loci were isolated using an enrichment cloning protocol. These loci were tested on a population of 110 individuals of Q. grandiflora collected from a cerrado fragment in São Paulo State, Brazil. The loci polymorphism ranges from seven to 19 alleles and the average heterozygosity value is 0.568, while the average polymorphic information content is 0.799. CONCLUSIONS: The developed markers were found to be highly polymorphic, indicating their applicability to studies of population genetic diversity in Q. grandiflora.

Development and characterization of microsatellite markers for Hebanthe eriantha (Amaranthaceae).

PREMISE OF THE STUDY: Hebanthe eriantha (Amaranthaceae) is extensively collected and used in folk medicine. Microsatellite markers were developed and characterized to investigate the genetic structure and diversity of germplasm collections of this species. METHODS AND RESULTS: Eleven highly polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from two to eight. The observed and expected heterozygosities ranged from 0.000 to 0.808 and 0.455 to 0.851, respectively. CONCLUSIONS: These results show the utility of microsatellite loci for studies of population genetics in H. eriantha, which are important for the future conservation and cultivation of this medicinal species.

Development of a novel set of microsatellite markers for castor bean, Ricinus communis (Euphorbiaceae).

PREMISE OF STUDY: Microsatellite primers were developed for castor bean (Ricinus communis L.) to investigate genetic diversity and population structure, and to provide support to germplasm management. METHODS AND RESULTS: Eleven microsatellite loci were isolated using an enrichment cloning protocol and used to characterize castor bean germplasm from the collection at the Instituto Agronômico de Campinas (IAC). In a survey of 76 castor bean accessions, the investigated loci displayed polymorphism ranging from two to five alleles. CONCLUSIONS: The information derived from microsatellite markers led to significant gains in conserved allelic richness and provides support to the implementation of several molecular breeding strategies for castor bean.

Genetic diversity among Brazilian soybean cultivars based on SSR loci and pedigree data

In this study, simple sequence repeats (SSR) loci and pedigree data were used to investigate the genetic relationship in a group of 168 Brazilian soybean cultivars. Eighteen SSR loci produced an average of 5.06 alleles and a mean gene diversity of 0.58 for the cultivars studied. Genetic distance (GD) was determined using the modified Roger's Wright distance, and a final dendrogram was in agreement with the cultivar pedigree. A distance matrix based on the coefficient of parentage scores was also generated for the cultivars, which ranged from 0 to 1, with a mean of 0.18, whereas SSR-based genetic similarity (1- GD) ranged from 0.01 to 0.90, with a mean of 0.25. Mantel's Z test showed that the similarity matrices generated from both the data sets were low, but significantly correlated (r = 0.31, p<0.001). The results showed that SSR data and pedigree analyses could help to quantify more accurately the degree of relationship among the soybean cultivars.

Locos microssatélites e dados de genealogia foram utilizados para avaliar a diversidade genética de um grupo de 168 cultivares brasileiras de soja. Os dezoito locos utilizados apresentaram em média 5,06 alelos por loco e coeficiente de diversidade genética médio de 0,58. O dendrograma final resultante da matriz de distância genética de Roger modificado por Wright, apresentou boa concordância com a ancestralidade dos grupos formados. Também foi estimado os coeficientes de parentesco entre as cultivares, sendo observada variação de 0 a 1 com média de 0,18, enquanto que as similaridades para os locos microssatélites (1- GD) variou de 0,01 a 0,90 com média de 0,25. A correlação entre as duas matrizes obtidas determinada pelo teste Z de Mantel apresentou valor baixo, 0,31, mas significativo (p<0,001). Os resultados obtidos sugerem que os locos microssatélites aliados às informações de genealogia proporcionam melhor análise da diversidade genética de cultivares de soja.