Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia.

BACKGROUND: Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. METHODS: This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7-13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software. RESULTS: The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023). CONCLUSION: The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care.

Sea trout (Salmo trutta) straying rate decreases as distance from river mouth increases.

For both conservation and management purposes, it is important to identify the natal origin of migratory individuals entering a river, particularly in genetically spatially structured species like brown trout (Salmo trutta) where the migrant ecotype (called sea trout) can originate from different populations. Nonetheless, little attention has been paid to the spatial distribution of non-local fish at the level of an entire river catchment. The objective of the study was to quantify the proportion of non-local sea trout entering a river catchment (i.e., straying rate) and estimate the spatial extent of their upstream migration. Here, the authors considered dispersal in three distinct rivers, taking advantage of 10 sampling sites. Sea trout, either trapped or rod-caught, were genotyped and genetically assigned to their source populations using appropriate baselines. Based on 1437 sea trout fish classified as local or non-local, the authors empirically demonstrate that straying rate declines in each river as distance from the coast increases in a non-linear fashion. Straying rate exceeds 50% near the mouth, and then decreases gradually to reach <10% 40-50 km inland. A similar spatial pattern is found in the three rivers investigated suggesting an underlying common behaviour of non-local sea trout. The data and results presented here suggest that straying in is far more constrained spatially than first expected. The majority of non-local sea trout were found within the first 25 km of the estuary in the three rivers investigated.

Combination Immunotherapy With LIGHT and Interleukin-2 Increases CD8 Central Memory T-Cells In Vivo.

BACKGROUND: The generation of long-term durable tumor immunity and prolonged disease-free survival depends on the ability to generate and support CD8+ central memory T-cells. Microsatellite-stable colon cancer is resistant to currently available immunotherapies; thus, development of novel mechanisms to increase both lymphocyte infiltration and central memory formation are needed to improve outcomes in these patients. We have previously demonstrated that both interleukin-2 (IL-2) and LIGHT (TNFSF14) independently enhance antitumor immune responses and hypothesize that combination immunotherapy may increase the CD8+ central memory T-cell response. METHODS: Murine colorectal cancer tumors were established in syngeneic mice. Tumors were treated with control, soluble, or liposomal IL-2 at established intervals. A subset of animal tumors overexpressed tumor necrosis superfamily factor LIGHT (TNFSF14). Peripheral blood, splenic, and tumor-infiltrating lymphocytes were isolated for phenotypic studies and flow cytometry. RESULTS: Tumors exposed to a combination of LIGHT and IL-2 experienced a decrease in tumor size compared with IL-2 alone that was not demonstrated in wild-type tumors or between other treatment groups. Combination exposure also increased splenic central memory CD8+ cells compared with IL-2 administration alone, while not increasing tumor-infiltrating lymphocytes. In the periphery, the combination enhanced levels of circulating CD8 T-cells and central memory T-cells, while also increasing circulating T-regulatory cells. CONCLUSIONS: Combination of IL-2, whether soluble or liposomal, with exposure to LIGHT results in increased CD8+ central memory cells in the spleen and periphery. New combination immunotherapy strategies that support both effector and memory T-cell functions are critical to enhancing durable antitumor responses and warrant further investigation.

Development and characterization of 49 novel microsatellite markers in the African catfish, Clarias gariepinus (Burchell, 1822).

The African catfish or sharp tooth catfish (Clarias gariepinus) is one of the important species (due to its high environmental tolerance and easily controllable breeding habits) that can significantly contribute to reducing hunger in many countries. It is farmed in numerous African, Asian, and European countries. Moreover, during the last decades its production has grown significantly worldwide. Currently, following the carp, this species is produced in the second largest volume in Hungary. Despite its economic importance, the stocks have been maintained without genetic control or guided breeding. Molecular genetic data on bred populations or strains are very limited. In order to investigate the genetic structure of the stocks, 49 new microsatellite markers were characterized and tested on 32 individuals from a Hungarian farmed stock. All these markers were polymorph. The number of alleles per locus ranged from 2 to 11. The observed and expected overall heterozygosities were between 0.519 and 0.544 respectively and the overall inbreeding coefficient (Fis: 0.063) does not reveal the presence of inbreeding. However, 63% of the markers showed significant deviations from HWE. The results suggest that the maintenance of genetic variation within the stock require high attention in closed bred populations. These new markers provide a useful tool for population and conservation genetics of natural and bred African catfish populations.

Novel microsatellite markers discovery in Patagonian toothfish (Dissostichus eleginoides) using high-throughput sequencing.

Patagonian toohfish (Dissostichus eleginoides), is a sub Antartic notothenioid fish key in the marine ecosystem that sustains fishery of higher commercial value in the world. However, there are a scarce knowledge or information about its population genetic background, product of the almost null information of molecular markers available for this species. Here, we use high-throughput sequencing technology (Illumina platform) to develop 1071 microsatellite loci, of which 22 loci were selected to evaluation. Polymorphism and genetic diversity of each locus was assessed in two locations distant by 2370 km. Considering both locations, a mean PIC value of 0.748 was estimated. Selected microsatellite loci showed among two to seventeen alleles by locus in the first location and two to twelve in the second. The observed heterozygosity varied from 0.18 to 0.91 and from 0.12 to 0.87 for the first and second location, respectively. While, the expected heterozygosity ranged from 0.15 to 0.92 and from 0.11 to 0.90. Three loci were monomorphic in only one location. Microsatellite markers developed here will be useful in future studies on conservation, fishery and population genetics of this species.

Genetic mixed-stock analysis of lake-run brown trout Salmo trutta fishery catches in the Inari Basin, northern Finland: implications for conservation and management.

Genetic mixed-stock analysis (MSA) of wild lake-run brown trout Salmo trutta fishery catches (n = 665) from the Inari Basin (northern Finland) between 2006 and 2008 was carried out using a previously characterized baseline with 30 populations (n = 813) and 13 microsatellite loci. Altogether, 12 populations contributed significantly to mixed-stock fisheries, with the Ivalojoki system being the major contributor (70%) to the total catch. When catches were analysed regionally, geographically nearby populations were the main contributors to the local catches, indicating that a large proportion of S. trutta occupy lacustrine areas near the natal river mouth rather than dispersing throughout the lake. Similarly, far upstream populations contributed insignificantly to catches. These findings have important implications for the conservation and sustainable fishery management of the Inari system.

Assessment of genetic diversity and population structure of Neocaridina denticulata sinensis in the Baiyangdian drainage area, China, using microsatellite markers and mitochondrial cox1 gene sequences.

Neocaridina denticulata sinensis is a crustacean of major economic significance in the Baiyangdian drainage area. In this study, the first assessment of N. denticulata sinensis genetic diversity and population structure was performed based on sequence analysis of nine polymorphic microsatellite loci and the mitochondrial cytochrome oxidase subunit I (cox1) gene. Samples (n = 192) were collected from four different regions in the Baiyangdian drainage area i.e., Baiyangdian Lake, Jumahe River, Xidayang Reservoir, and Fuhe River. Microsatellite loci analysis identified high levels of genetic diversity represented by observed heterozygosity (Ho) of 0.6865 âˆ¼ 0.9583, expected heterozygosity (He) of 0.7151 âˆ¼ 0.8723, and polymorphism information content (PIC) of 0.6676 âˆ¼ 0.8585. Based on the analysis of cox1 sequences, haplotype diversity (Hd) ranged from 0.568 to 0.853 while nucleotide diversity (π) ranged from 0.0029 to 0.2236. Furthermore, there was no evidence of expansion events in the N. denticulata sinensis populations. Pairwise FST revealed pronounced genetic differentiation, and clustering analyses showed defined genetic structures within the N. denticulata sinensis population. Three groups were identified from four sampled stocks, with Xidayang Reservoir, and Fuhe River populations clustered in the same group. This work identified novel molecular markers and provided an important reference to guide management strategies to assist conservation of N. denticulata sinensis resources.

Forensic DNA typing from teeth using demineralized root tips.

Teeth are widely used samples in forensic human genetic identification due to their persistence and practical sampling and processing. Their processing, however, has changed very little in the last 20 years, usually including powdering or pulverization of the tooth. The objective of this study was to present demineralized root tips as DNA sources while, at the same time, not involving powdering the samples or expensive equipment for teeth processing. One to five teeth from each of 20 unidentified human bodies recovered from midwest Brazil were analyzed. Whole teeth were demineralized in EDTA solution with daily solution change. After a maximum of approximately seven days, the final millimeters of the root tip was excised. This portion of the sample was used for DNA extraction through a conventional organic protocol. DNA quantification and STR amplification were performed using commercial kits followed by capillary electrophoresis on 3130 or 3500 genetic analyzers. For 60% of the unidentified bodies (12 of 20), a full genetic profile was obtained from the extraction of the first root tip. By the end of the analyses, full genetic profiles were obtained for 85% of the individuals studied, of which 80% were positively identified. This alternative low-tech approach for postmortem teeth processing is capable of extracting DNA in sufficient quantity and quality for forensic casework, showing that root tips are viable nuclear DNA sources even after demineralization.

Assessment of genetic diversity of an endangered tooth-carp, Aphanius farsicus (Teleostei: Cyprinodontiformes: Cyprinodontidae) using microsatellite markers.

Genetic structure of an endemic tooth-carp fish, Aphanius farsicus from four different water bodies in the Maharlu Lake basin was investigated by applying five microsatellite markers. All of the five examined microsatellite loci showed polymor-phism pattern. A total of four alleles were detected at five microsatellite loci, with an average of 2.8 to 3.5 alleles per locus. Average values of observed and expected heterozygosity were 0.95±0.09 and 0.64±0.02 respectively. None of the tests of linkage disequilibrium were significant between each pair of loci and no deviation from Hardy-Weinberg equilibrium were detected to test for heterozygote deficiency within populations. The Nei's genetic distance values ranged between 0.03 - 0.13. Analysis of pairwise genetic differentiation between each pair of the populations revealed that fixation index (FST) values ranged from 0.013 to 0.039 and RST ranged from 0.005 to 0.065. High genetic diversity observed within the populations (99%) and low diversity (1%) among them indicating probably high level of gene flow among the studied populations of Fars tooth-carp at the present time or in the past. Regarding low genetic differentiation among the studied populations and results of population assignment test, two hypotheses are suggested and supporting evidence for each hypothesis are provided.

Using heterozygosity-fitness correlations to study inbreeding depression in an isolated population of white-tailed deer founded by few individuals.

A heterozygosity-fitness correlations (HFCs) may reflect inbreeding depression, but the extent to which they do so is debated. HFCs are particularly likely to occur after demographic disturbances such as population bottleneck or admixture. We here study HFC in an introduced and isolated ungulate population of white-tailed deer Odocoileus virginianus in Finland founded in 1934 by four individuals. A total of 422 ≥ 1-year-old white-tailed deer were collected in the 2012 hunting season in southern Finland and genotyped for 14 microsatellite loci. We find significant identity disequilibrium as estimated by g 2. Heterozygosity was positively associated with size- and age-corrected body mass, but not with jaw size or (in males) antler score. Because of the relatively high identity disequilibrium, heterozygosity of the marker panel explained 51% of variation in inbreeding. Inbreeding explained approximately 4% of the variation in body mass and is thus a minor, although significant source of variation in body mass in this population. The study of HFC is attractive for game- and conservation-oriented wildlife management because it presents an affordable and readily used approach for genetic monitoring that allowing identification of fitness costs associated with genetic substructuring in what may seem like a homogeneous population.

Evidence of multiple paternity and cooperative parental care in the so called monogamous silver arowana Osteoglossum bicirrhosum (Osteoglossiformes: Osteoglossidae)

Monogamy is rare in fishes and is usually associated with elaborate parental care. When parental care is present in fishes, it is usually the male that is responsible, and it is believed that there is a relationship between the high energetic investment and the certainty of paternity (except in the case of sneaker males). Osteoglossum bicirrhosum is considered a monogamous fish, and has particular behavioral traits that permit the study of mating systems and parental care, such as male mouthbrooding. We investigated the genetic relationships of males with the broods found in their oral cavities in Osteoglossum samples collected in a natural environment in the lower Purus river basin, Amazonas, Brazil. Fourteen broods were analyzed for parentage (268 young and 14 adult males) using eight microsatellite loci. The results indicate that eleven broods show a monogamous system. In one brood, however, approximately 50% of the young were genetically compatible with being offspring of another male, and in another two broods, none of the subsampled young were compatible with the genotypes of the brooding male. The result of this first brood may be explained by the extra-parental contribution of a sneaker male, whereas cooperative parental care may explain the result in the other two broods. Monogamia é rara em peixes e está geralmente associada a cuidado parental elaborado. Quando cuidado parental está presente em peixes, usualmente o macho é responsável, e acredita-se que exista uma relação entre investimento energético elevado e a certeza da paternidade (exceto no caso de machos oportunistas). Osteoglossum bicirrhosum é considerado monogâmico e possui determinadas características comportamentais que permitem o estudo de sistemas de acasalamento e cuidado parental, como incubação bucal dos ovos e filhotes pelos machos. Quatorze ninhadas (268 filhotes e 14 machos adultos) foram coletadas em ambiente natural na bacia do baixo rio Purus, Amazonas, Brasil e analisadas para parentesco utilizando oito loci de microssatélites. Os resultados sugeriram, para onze ninhadas, um sistema de acasalamento monogâmico. Em uma ninhada, no entanto, cerca de 50% dos jovens eram geneticamente compatíveis como sendo descendentes de outro macho, e em outras duas ninhadas nenhum dos filhotes amostrados eram filhos dos machos que estavam realizando o cuidado. O resultado da primeira ninhada pode ser explicado pela contribuição extra-par de um macho oportunista, enquanto que o cuidado parental cooperativo pode explicar os resultados nas outras duas ninhadas.