Development and validation of a novel SNP panel for the genetic characterization of Italian chicken breeds by next-generation sequencing discovery and array genotyping

The aim of this study was to compare the intra and inter genetic variability and population structure of 7 indigenous chicken breeds of the Veneto region, through a novel panel of 64 SNP, each located in an exonic region and mostly on different chromosomes. A total of 753 blood samples from 7 local chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo, Polverara, Pepòi, Robusta Lionata, Robusta Maculata, and Padovana) was collected and analyzed. Two strains of Polverara (Nera and Bianca) and Padovana (Dorata and Camosciata) were included in the study. The observed heterozygosity ranged from 0.124 (Pèpoi) to 0.244 (Ermellinata di Rovigo), and the expected heterozygosity varied from 0.132 (Millefiori di Lonigo) to 0.300 (Ermellinata di Rovigo). Global FIS results (0.114) indicated a low-medium inbreeding effect, with values ranging from 0.008 (Millefiori di Lonigo) to 0.223 (Ermellinata di Rovigo). Pairwise FST values (0.167) for all populations ranged from 0.020 (Polverara Nera and Polverara Bianca) to 0.193 (Robusta Lionata and Polverara Nera), indicating that the studied breeds were genetically highly differentiated. The software STRUCTURE was used to detect the presence of population substructures, and the most probable number of clusters (K) of the 10 chicken populations was at K = 8. The affiliation was successful in all Veneto chicken breeds. The present SNP marker results, compared with previous data obtained using microsatellites, provided a reliable estimate of genetic diversity within and between the studied breeds, and demonstrated the utility of the proposed panel as a rapid, efficient, and cost-effective tool for periodical monitoring of the genetic variability among poultry populations. In addition, the present SNP panel could represent a resource for a systematic approach with relevant impact on breeding program decisions and could turn out to be a reliable tool for genetic traceability of indigenous chicken meat. Adoption of a periodical monitoring system of genetic diversity is a fundamental tool in conservation actions and should increase the value of typical and niche products.

The microbiological conditions of carcasses from large game animals in Italy

This study investigates the microbiological conditions of large game animal carcasses following evisceration. Carcasses of animals (N=291) hunted in the Upper Susa Valley (Italian Alps) were analysed for pH, Aerobic Viable Count (AVC), Enterobacteriaceae, Yersinia spp., Listeria monocytogenes and Salmonella spp. After shooting, evisceration occurred within 60 min in 90.7% of animals and sampling within 90 min in 88.3% of animals. Mean pH values (5.97: ruminants; 5.77: wild boar) were similar to those of regularly slaughtered domestic species. AVC values were highest in animals shot in the abdomen. Within species, AVC and Enterobacteriaceae values did not differ across different shooting-evisceration/sampling times. However, these counts exceeded 5 and 2.5 log, respectively, in 18% of wild boar and 39% of ruminants; the highest values were detected in wild boar. No pathogens were detected in any species. These results reveal inadequate hygiene in game meat handling/harvesting, implicating the need for improved practices.

Development of a multiplex PCR assay for the identification of pathogenic genes of Escherichia coli in milk and milk products

A multiplex PCR for the simultaneous detection of some pathogenic genes of enteropathogenic, enterotoxigenic and verocytotoxin-producing Escherichia coli was developed. In this study primers found in literature as well as primers to the purpose designed were used. In this way, it was possible to generate specific fragments of 96, 170, 229, 285, 348, 414 and 510 bp for Hlya, St, EaeA, Lt, Vt1, UidA and Vt2 genes, respectively. When applied to bacterial strains experimentally inoculated in milk and milk products, the proposed PCR showed a detection limit of 5 x 10(4)CFU/ml for Hyla, St, Eaea, Vt1 primers, while for Lt and Vt2 primers the limit resulted of 10(6)CFU/ml.

A multiplex PCR assay for the identification of animal species in feedstuffs

A multiplex Polymerase Chain Reaction (PCR) assay was applied to feedstuff analysis for the identification of the most used species in rendering plants (ruminant, poultry, fish and pork materials). Primers were designed in different regions of mitochondrial DNA (12S rRNA, tRNA Val and 16S rRNA) after alignment of the available sequences in the GenBank database. The primers generated specific fragments of 104-106, 183, 220-230 and 290 bp length for ruminants, poultry, fish and pork, respectively. The detection limit was 0.004% for fish primers and 0.002% for ruminants, poultry and pork primers. The multiplex PCR proposed in this study can be considered a valid alternative to the microscopic method for the detection of animal derived materials banned by a European Union Regulation as a preventive measure against the spread of Bovine Spongiform Encephalopathy.

Virulence and molecular diversity of parthenogenetic root-knot nematodes, Meloidogyne spp

Root-knot nematodes (RKN) are sedentary endoparasites causing severe damage to a wide variety of crops, including tomato. Among them, the parthenogenetic species Meloidogyne arenaria, M. incognita and M. javanica are of particular economic importance. The genetic diversity and relationships of 17 populations belonging to these three major species, either avirulent or virulent against the tomato Mi resistance gene, were investigated in order to determine whether (a)virulence of the nematodes could be related to their molecular fingerprints. Genomic polymorphisms between populations were assessed by using amplified fragment length polymorphism (AFLP) markers, and data were treated by means of a multiple correspondence analysis. A total of 1550 polymorphic amplified DNA fragments were identified and used to compute the relationships between the populations. As expected, the three RKN species were clearly distributed into distinct groups, but combination of data for virulence phenotypes and DNA markers showed that clustering of populations was not associated with their (a)virulence against the tomato Mi resistance gene. Such a lack of correlation indicates that most of the observed DNA polymorphism is independent of virulence, which is presumably under host selection. This result demonstrates that virulent populations do not share a common origin, and strongly suggests that they might have appeared late after the establishment of these clonal lineages, as the result of independent mutational events.

Spectrum of resistance to root-knot nematodes and inheritance of heat-stable resistance in in pepper (Capsicum annuum L.)

Capsicum annuum L. has resistance to root-knot nematodes (RKN) (Meloidogyne spp.), severe polyphagous pests that occur world-wide. Several single dominant genes confer this resistance. Some are highly specific, whereas others are effective against a wide range of species. The spectrum of resistance to eight clonal RKN populations of the major Meloidogyne species, M. arenaria (2 populations), M. incognita (2 populations), M. javanica (1 population), and M. hapla (3 populations) was studied using eight lines of Capsicum annuum. Host susceptibility was determined by counting the egg masses (EM) on the roots. Plants were classified into resistant (R; EM ≤ 5) or susceptible (H; EM >5) classes. The french cultivar Doux Long des Landes was susceptible to all nematodes tested. The other seven pepper lines were highly resistant to M. arenaria, M. javanica and one population of M. hapla. Variability in resistance was observed for the other two populations of M. hapla. Only lines PM687, PM217, Criollo de Morelos 334 and Yolo NR were resistant to M. incognita. To investigate the genetic basis of resistance in the highly resistant line PM687, the resistance of two progenies was tested with the two populations of M. incognita: 118 doubled-haploid (DH) lines obtained by androgenesis from F(1) hybrids of the cross between PM687 and the susceptible cultivar Yolo Wonder, and 163 F(2) progenies. For both nematodes populations, the segregation patterns 69 R / 49 S for DH lines and 163 R / 45 S for F(2) progenies were obtained at 22°C and at high temperatures (32°C and 42°C). The presence of a single dominant gene that totally prevented multiplication of M. incognita was thus confirmed and its stability at high temperature was demonstrated. This study confirmed the value of C. annuum as a source of complete spectrum resistance to the major RKN.

RPE, a plant gene involved in early developmental steps of nematode feeding cells

Sedentary plant-parasitic nematodes are able to induce the redifferentiation of root cells into multinucleate nematode feeding sites (NFSs). We have isolated by promoter trapping an Arabidopsis thaliana gene that is essential for the early steps of NFS formation induced by the root-knot nematode Meloidogyne incognita. Its pattern of expression is similar to that of key regulators of the cell cycle, but it is not observed with the cyst nematode. Later in NFS development, this gene is induced by both root-knot and cyst nematodes. It encodes a protein similar to the D-ribulose-5-phosphate 3-epimerase (RPE) (EC 5.1.3.1), a key enzyme in the reductive Calvin cycle and the oxidative pentose phosphate pathway (OPPP). Quantitative RT-PCR showed the accumulation of RPE transcripts in potato, as in Arabidopsis NFS. Homozygous rpe plants have a germination mutant phenotype that can be rescued in dwarf plants on sucrose-supplemented medium. During root development, this gene is expressed in the meristems and initiation sites of lateral roots. These results suggest that the genetic control of NFSs and the first stages of meristem formation share common steps and confirms the previous cytological observations which indicate that root cells undergo metabolic reprogramming when they turn into NFSs.

High-resolution DNA fingerprinting of parthenogenetic root-knot nematodes using AFLP analysis

Amplified fragment length polymorphism (AFLP) analysis has been used to characterize 15 root-knot nematode populations belonging to the three parthenogenetic species Meloidogyne arenaria, M. incognita and M. javanica. Sixteen primer combinations were used to generate AFLP patterns, with a total number of amplified fragments ranging from 872 to 1087, depending on the population tested. Two kinds of polymorphic DNA fragments could be distinguished: bands amplified in a single genotype, and bands polymorphic between genotypes (i.e. amplified in not all but at least two genotypes). Based on presence/absence of amplified bands and pairwise similarity values, all the populations tested were clustered according to their specific status. Significant intraspecific variation was revealed by AFLP, with DNA fragments polymorphic among populations within each of the three species tested. M. arenaria appeared as the most variable species, while M. javanica was the least polymorphic. Within each specific cluster, no general correlation could be found between genomic similarity and geographical origin of the populations. The results reported here showed the ability of the AFLP procedure to generate markers useful for genetic analysis in root-knot nematodes.

Reproduction of Virulent Isolates of Meloidogyne incognita on Susceptible and Mi-resistant Tomato

The reproductive potential of natural and laboratory-selected Meloidogyne incognita isolates virulent against the tomato Mi resistance gene, all derived from a single egg-mass, were compared when the nematodes were inoculated on susceptible and resistant tomato. Fewer second-stage juveniles (P = 0.01) of the two virulent populations selected under laboratory conditions matured to females on the resistant tomato compared to the susceptible cultivar. In contrast, no differences were found between the number of egg masses produced on the resistant versus the susceptible tomato by the two natural virulent isolates. No clear general trends concerning the fecundity of the females could be inferred from the comparative analysis of the numbers of eggs per egg mass x tomato cultivar combination. These observations suggested that the genetic changes induced under environmentally controlled nematode growth might be different from those occurring in natural Mi-resistance breaking biotypes grown without environmental control.

Genetic variation inMeloidogyne incognita virulence against the tomatoMi resistance gene: evidence from isofemale line selection studies

Resistance to the parthenogenetic root-knot nematodeMeloidogyne incognita is controlled in tomato by the single dominant geneMi, against which virulent pathotypes are able to develop. Isofemale lines (i.e., families) were established from a natural avirulent isolate ofM. incognita in order to study the genetic variability and inheritance of the nematode virulence. From the progeny of individual females, the production of egg masses on the root system of theMi-resistant tomato 'Piersol' was analyzed in artificial selection experiments. A family analysis revealed, after two successive generations, a strongly significant variation between the 63 isofemale lines tested, and the results obtained for the mothers and their daughters were also significantly correlated. These results together clearly demonstrate the existence of a genetic variability and inheritance for this character. In a second experiment, a four-generation selection was performed on 31 other isofemale lines. The results revealed a significant response to selection apparently limited only to the two families able to produce, in first generation, a significant minimal egg-mass number on the resistant cultivar.

Cloning and characterization of two satellite DNAs in the low-C-value genome of the nematode Meloidogyne spp

Two highly reiterated StyI satellite DNAs have been cloned from two nematode species: one from Meloidogyne hapla and another from M. incognita. The monomeric units of these two satellites have a repeat length of 169 and 295 bp, respectively. These StyI repeated element families constitute 5% of the M. hapla and 2.5% of the M. incognita haploid genomes. The A + T content is elevated in both families (i.e., 68% and 77%, respectively). Nucleotide methylation and transcriptional activity are negative. No similarity was found between the two satellites, nor to other known highly repetitive elements. These StyI satellite DNAs are quite homogenous in sequence, showing on average 3% and 3.5% divergence from their respective calculated consensus sequence. An internal subrepeating unit of about 11 bp is observed in the StyI satellite monomer sequences of M. hapla, suggesting that it could have evolved from a shorter sequence. Because of the small size of the Meloidogyne genome (51 Mb) and the abundance of repeated sequences, this genus approaches a limit in terms of coding fraction.

Expression and biochemical characterization of the DNA binding activity of TcA, the putative transposase of Caenorhabditis elegans transposable element Tc1

The TcA protein is one of the proteins essential for Tc1 transposition. In order to study the biochemical parameters of Tc1 transposition mechanism, we used TcA protein overproduced in baculovirus system for DNA binding experiments. We show that, despite its relatively strong non specific affinity for DNA, TcA exhibits a better affinity for its Tc1 specific binding sites. The K0.5 is 3.8 nM for the Tc1 whereas in the same type of experiment the K0.5 is 24 nM for calf thymus DNA. The ratio value between specific and non specific DNA binding activity of the TcA protein was also exhibited by other transposases such as those of the bacteriophage Mu, Tn 10 and the Drosophila P element. This nonspecific DNA binding activity may be involved in determining sites of transposable element insertion.

Sequences homologous to Tc(s) transposable elements of Caenorhabditis elegans are widely distributed in the phylum nematoda

To have a better understanding of the evolutionary history of mobile elements within the nematodes, we examined the distribution and the conservation of homologues to transposable elements from Caenorhabditis elegans (Tc1, Tc2, Tc3, Tc4, Tc5, and FB1) in 19 nematode species belonging to the class Secernentea. Our results show that Tc1 elements display a distribution restricted to the family Rhabditidae with poor conservation. The Tc2 and FB1 homologous elements have the same patchy distribution within the Rhabditidae. They were only found in Caenorhabditis and in Teratorhabditis. The Tc3 element is widely distributed among nematode species. Tc3 homologous elements are present in the majority of the Rhabditidae but also in two genera within the family Panagrolaimidae, and in Bursaphelenchus, which belongs to the order Aphelenchida. Tc4 and Tc5 homologues show the most limited distribution of all tested elements, being strictly limited to C. elegans. These data indicate that in some cases, the distribution of transposable elements in the nematode cannot be explained by strict vertical transmission. The distribution of Tc3, Tc4, and Tc5 suggests that horizontal transmission may have occurred between reproductively isolated species during their evolutionary history.

Isolation of a Repeated DNA Probe Showing Polymorphism among Meloidogyne incognita Populations

Several Meloidogyne incognita geographic populations were characterized by analysis of the restriction fragment length polymorphisms (RFLP) obtained after digestion of their total DNA and hybridization with a [(3)(2)P]-labeled probe. The probe consisted of a 1.7-kb-repeated DNA sequence, isolated from a M. incognita genomic library, that hybridized to multiple BamH I fragments in the genome of each isolate. The patterns showed sufficient polymorphism to enable the accurate differentiation of all the populations tested.

Resistance in Lycopersicon peruvianum to Isolates of Mi Gene-Compatible Meloidogyne Populations

Root-knot nematode resistance of F progeny of an intraspecific hybrid (Lycopersicon peruvianum var. glandulosum Acc. No. 126443 x L. peruvianum Acc. No. 270435), L. esculentum cv. Piersol (possessing resistance gene Mi), and L. esculentum cv. St. Pierre (susceptible) was compared. Resistance to 1) isolates of two Meloidogyne incognita populations artificially selected for parasitism on tomato plants possessing the Mi gene, 2) the wild type parent populations, 3) four naturally occurring resistance (Mi gene)-breaking populations of M. incognita, M. arenaria, and two undesignated Meloidogyne spp., and 4) a population of M. hapla was indexed by numbers of egg masses produced on root systems in a greenhouse experiment. Artificially selected M. incognita isolates reproduced abundantly on Piersol, but not (P = 0.01) on resistant F hybrids. Thus, the gene(s) for resistance in the F hybrid differs from the Mi gene in Piersol. Four naturally occurring resistance-breaking populations reproduced extensively on Piersol and on the F hybrid, demonstrating ability to circumvent both types of resistance. Meloidogyne hapla reproduced on F hybrid plants, but at significantly (P = 0.01) lower levels than on Piersol.

Enterococcal sepsis and lung microvascular injury in sheep

In a common bile duct contamination model, we studied the effect of Streptococcus faecalis compared with Escherichia coli in sheep with chronic lymph fistulas to investigate the role of enterococcus in acute lung injury and acute sepsis. Early pulmonary hypertension in the E coli group was not expressed in the S faecalis group, probably due to a failure of S faecalis to illicit a thromboxane A2 response. In the late period, E coli was associated with significantly greater lung microvascular damage compared with S faecalis. The lack of difference between groups with respect to complement activation suggests the action of chemotactic factors, in addition to complement, mediating granulocyte aggregation, and neutropenia. In this model, S faecalis demonstrated limited pathogenicity as expressed in lung microvascular injury compared with E coli.

Allo-anti-Chido in a Ch-positive patient

Allo-anti-Chido (Ch) was detected in a patient whose red cells typed as Ch+. The C4 allotype of the patient was A4,B2 which associates strongly with the Ch phenotype Ch:1,-2,3,4,-5,6. Anti-Ch2 + Ch5 were the Ch specificities identified. Absence of only Ch2 and Ch5 determinants on the C4B protein allowed this unique immune response to blood transfusion.

Plasma separation using a hollow fiber membrane device

A disposable hollow fiber device was evaluated by collecting approximately 550 ml of normal donor plasma (n = 43) and by performing sham (n = 10) and therapeutic (n = 12) plasma exchanges. Blood was processed at 70 ml per min, and plasma flux averaged 23 (collection) and 25 (exchange) ml per min (mean separation efficiencies of 52 and 60%, respectively). The procedures were tolerated well by all donors and patients. The plasma hemoglobin concentration in separated plasma averaged 1 mg per dl, and cell contamination was negligible (mean of 1, 3, and 6 RBCs, platelets and WBCs/microliter, respectively). There was no evidence of in vivo classical or alternative pathway complement activation as assessed by total hemolytic complement generation (CH50), alternative pathway hemolytic activity (AP50), C3 conversion, or C5 activation, nor were unexpected changes seen in the results of laboratory tests performed after the procedure. Sieving coefficients during sham plasma exchange averaged as follows: albumin, 1.03; IgM, 1.0, IgG, 1.0; IgA, 0.98; factor V, 1.07; factor VII, 0.89; factor VIII, 1.05; and factor IX, 1.19. The device appears to be useful for separation of cell-free plasma from blood during therapeutic plasma exchange procedures.

Molecular polymorphism and phylogenetic relationship in some Meloidogyne spp.: application to the taxonomy of Meloidogyne

Proteins and various isozymes were investigated by direct analysis of single specimens in order to check molecular genetic variability, which is not rare in Meloidogyne species in spite of parthenogenetic reproduction. Variability was found in esterases, ocglycerophosphate, malate dehydrogenases, and some other proteins. Other loci appear monomorphic in the genus (for example, catalase), Distinct pools of genes are in a relative accordance with the common described species. Characteristic electrophoretograms are given for M. arenaria, M. javanica, M. incognita, M. hapla, and M. naasi, and it appears that nonspecific esterases are a useful tool supplementing morphology for specific characterization. Because the biochemical evidence is less subjective than the morphological, we believe it is more reliable.

Carbono acumulado en la biomasa vegetal de la reserva de Villavicencio (Mendoza-Argentina)

Las reservas naturales en las zonas áridas cumplen un papel destacado en el almacenamiento de carbono. La vegetación de la Reserva de Villavicencio acumula en total 98798 Mg (2,1 Mg/ha) de carbono; considerando la vegetación de la Puna y del Monte no quemado el 91,2% del carbono se encuentra en la parte aérea (hojas y tallo) y el 8,8 % restante en el sistema radical. La vegetación del Monte, caracterizada por el matorral de Larrea cuneifolia, acumula 77905 Mg (3,9 Mg/ha), 78,8% del carbono total del área. En el matorral no quemado las nanofanerófitas acumulan el 28,8%, en el área incendiada en el 2000 el 50,4% y en la quemada en el 2005 las caméfitas el 95,5%. En la vegetación del piso de la Puna, con 20893 Mg de carbono (0,78 Mg/ha) Almacenado, domina el pastizal de Jarava vaginata que acumula el 88% del carbono; la parte aérea (follaje de gramíneas y hojas y tallos de caméfitas) almacena el 90% del carbono. En general, y considerando ambos pisos de vegetación, 19,8% del carbono presente en toda la Reserva lo acumulan las nanofanerófitas, las hemicriptófitas el 32,8%, las caméfitas el 28,8% y las suculentas (cactáceas) el 18,4%. La evaluación del carbono acumulado, considerando las diversas unidades de vegetación, es necesaria para el manejo del área protegida y para una mejor comprensión del papel de estos ambientes en la mitigación del carbono atmosférico