Image processing and machine learning in the morphological analysis of blood cells

INTRODUCTION

This review focuses on how image processing and machine learning can be useful for the morphological characterization and automatic recognition of cell images captured from peripheral blood smears.

METHODS

The basics of the 3 core elements (segmentation, quantitative features, and classification) are outlined, and recent literature is discussed. Although red blood cells are a significant part of this context, this study focuses on malignant lymphoid cells and blast cells.

RESULTS

There is no doubt that these technologies may help the cytologist to perform efficient, objective, and fast morphological analysis of blood cells. They may also help in the interpretation of some morphological features and may serve as learning and survey tools.

CONCLUSION

Although research is still needed, it is important to define screening strategies to exploit the potential of image-based automatic recognition systems integrated in the daily routine of laboratories along with other analysis methodologies.

Characterization of the animal by-product meal industry in Costa Rica: Manufacturing practices through the production chain and food safety

Animal by-product rendering establishments are still relevant industries worldwide. Animal by-product meal safety is paramount to protect feed, animals, and the rest of the food chain from unwanted contamination. As microbiological contamination may arise from inadequate processing of slaughterhouse waste and deficiencies in good manufacturing practices within the rendering facilities, we conducted an overall establishment's inspection, including the product in several parts of the process.An evaluation of the Good Manufacturing Practices (GMP) was carried out, which included the location and access (i.e., admission) to the facilities, integrated pest management programs, physical condition of the facilities (e.g., infrastructure), equipments, vehicles and transportation, as well as critical control points (i.e., particle size and temperature set at 50 mm, 133°C at atmospheric pressure for 20 min, respectively) recommended by the OIE and the European Commission. The most sensitive points according to the evaluation are physical structure of the facilities (avg 42.2%), access to the facilities (avg 48.6%), and cleaning procedures (avg 51.4%).Also, indicator microorganisms (Salmonella spp., Clostridium spp., total coliforms, E. coli, E. coli O157:H7) were used to evaluate the safety in different parts of the animal meal production process. There was a prevalence of Salmonella spp. of 12.9, 14.3, and 33.3% in Meat and Bone Meal (MBM), poultry by-products, and fish meal, respectively. However, there were no significant differences (P = 0.73) in the prevalence between the different animal meals, according to the data collected.It was also observed that renderings associated with the poultry industry (i.e., 92.0%) obtained the best ratings overall, which reflects a satisfactory development of this sector and the integration of its production system as a whole.

Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns

The analysis of runs of homozygosity (ROH), using high throughput genomic data, has become a valuable and frequently used methodology to characterize the genomic and inbreeding variation of livestock and wildlife animal populations. However, this methodology has been scarcely used in highly inbred domestic animals. Here, we analyzed and characterized the occurrence of ROH fragments in highly inbred (HI; average pedigree-based inbreeding coefficient F_PED = 0.164; 0.103 to 0.306) and outbred Retinta bulls (LI; average F_PED = 0.008; 0 to 0.025). We studied the length of the fragments, their abundance, and genome distribution using high-density microarray data. The number of ROH was significantly higher in the HI group, especially for long fragments (>8Mb). In the LI group, the number of ROH continuously decreased with fragment length. Genome-wide distribution of ROH was highly variable between samples. Some chromosomes presented a larger number of fragments (BTA1, BTA19, BTA29), others had longer fragments (BTA4, BTA12, BTA17), while other ones showed an increased ROH accumulation over specific loci (BTA2, BTA7, BTA23, BTA29). Similar differences were observed in the analysis of 12 individuals produced by a similar inbred event (F_PED3 = 0.125). The correlation between the fraction of the genome covered by ROH (F_ROH) and F_PED was high (0.79), suggesting that ROH-based estimations are indicative of inbreeding levels. On the other hand, the correlation between F_PED and the microsatellite-based inbreeding coefficient (F_MIC) was only moderate (r = 0.44), suggesting that STR-based inbreeding estimations should be avoided. Similarly, we found a very low correlation (r = -0.0132) between recombination rate and ROH abundance across the genome. Finally, we performed functional annotation analyses of genome regions with significantly enriched ROH abundance. Results revealed gene clusters related to pregnancy-associated proteins and immune reaction. The same analysis performed for regions enriched with recently formed ROH (> 8 Mb) showed gene clusters related to flagellum assembly. In both cases, the processes were related to male and female reproductive functions, which may partially explain the reduced fertility associated with inbred populations.

Gastric Plication and Sleeve Gastrectomy in an Experimental Model of Obesity: New Insights into Weight Loss, Intake and Metabolic Results

AIM

Laparoscopic gastric plication (LGP) is a bariatric surgical technique based on the anatomical principles of laparoscopic sleeve gastrectomy (LSG), but its effects on the metabolic profile are still uncertain. The aim of our study is to compare the changes in weight, metabolic parameters and gastric histology following intervention by gastric plication (GP) and sleeve gastrectomy (SG) in an experimental model of obesity.

METHODS

To conduct the study, 32 8-week-old male Sprague-Dawley rats (Charles River®) were fattened by means of a cafeteria diet and randomly assigned to the following experimental groups: group 1: GP (n = 12); group 2: SG (n = 12) and group 3: sham (n = 8).

RESULTS

Unlike the SG group, the GP group attained the weight of the sham group at the end of the experiment (week 16). The GP group continued to eat more cafeteria diet than the SG group. In addition, the SG group achieved better glycaemic control than the GP group. Significantly higher plasma ghrelin levels were observed at week 16 in the GP group than in the SG group (2.29 ± 0.5 vs 1.07 ± 0.4, p < 0.05), which also occurred for the glucagon plasmatic levels (62.71 ± 36.2 vs 24.63 ± 9.3, p < 0.05).

CONCLUSIONS

GP is not as effective as SG and cannot be considered a metabolic surgery due to observed hormonal variations. The animals subjected to a GP continued to have a high appetite for the cafeteria diet unlike the animals submitted to an SG. Hormonal mechanisms possibly related to glucagon and ghrelin may be involved in this metabolic response.

Hair extensions need to be considered during preoperative assessment

Hair extensions are an increasingly common hairstyling practice. Others have demonstrated these devices can lead to hair and scalp injuries. We describe a recent case where such an injury was narrowly avoided in a patient undergoing a long surgical procedure. We suggest that preoperative assessment procedures need to be aware of such devices and provide advice to patients accordingly.

Analysis of Gastric Physiology After Laparoscopic Sleeve Gastrectomy (LSG) With or Without Antral Preservation in Relation to Metabolic Response: a Randomised Study

INTRODUCTION

Laparoscopic sleeve gastrectomy is one of the most common techniques in bariatric surgery, but there is no consensus on the optimal distance from the pylorus to start the gastric transection. The aim of this study is to determine the differences in gastric emptying, gastric distension and metabolic response between two starting distances.

MATERIAL AND METHODS

This is a prospective randomised study of 60 patients (30 patients with the section at 3 cm and 30 patients at 8 cm from the pylorus). We calculate at 6 and 12 months from surgery gastric emptying by scintigraphy (T1/2 min), gastric volume by CT scan (cc) and metabolic response by blood sample analysis (glucose, HbA1c, insulin, HOMA-IR, GLP-1, GIP and C-peptide).

RESULTS

Gastric emptying increases the speed significantly in both groups but is greater in the 3-cm group (p < 0.05). Dividing groups into type 2 diabetic patients and non-diabetic patients, the speed in non-diabetic patients is significantly higher for the 3-cm group. Residual volume increases significantly in both groups, and there are no differences between them. One year after surgery, there are significant improvements in the hyperinsulinaemia in the patients of the 3-cm group with respect to the 8-cm group, but only in diabetic patients. No differences between groups are found regarding changes in GLP-1 or GIP.

CONCLUSIONS

Gastric emptying is faster in patients with antrum resection. The distance does not influence the gastric emptying of diabetic patients. Other mechanisms may explain metabolic response besides GLP-1 and its association with improvements in diabetes via gastric emptying.

YODA MAP3K kinase regulates plant immune responses conferring broad-spectrum disease resistance

Mitogen-activated protein kinases (MAPKs) cascades play essential roles in plants by transducing developmental cues and environmental signals into cellular responses. Among the latter are microbe-associated molecular patterns perceived by pattern recognition receptors (PRRs), which trigger immunity. We found that YODA (YDA) - a MAPK kinase kinase regulating several Arabidopsis developmental processes, like stomatal patterning - also modulates immune responses. Resistance to pathogens is compromised in yda alleles, whereas plants expressing the constitutively active YDA (CA-YDA) protein show broad-spectrum resistance to fungi, bacteria, and oomycetes with different colonization modes. YDA functions in the same pathway as ERECTA (ER) Receptor-Like Kinase, regulating both immunity and stomatal patterning. ER-YDA-mediated immune responses act in parallel to canonical disease resistance pathways regulated by phytohormones and PRRs. CA-YDA plants exhibit altered cell-wall integrity and constitutively express defense-associated genes, including some encoding putative small secreted peptides and PRRs whose impairment resulted in enhanced susceptibility phenotypes. CA-YDA plants show strong reprogramming of their phosphoproteome, which contains protein targets distinct from described MAPKs substrates. Our results suggest that, in addition to stomata development, the ER-YDA pathway regulates an immune surveillance system conferring broad-spectrum disease resistance that is distinct from the canonical pathways mediated by described PRRs and defense hormones.

Prevalence of twin foaling and blood chimaerism in purebred Spanish horses

Twin foaling is associated with chimaerism in several domestic species and is recognised in horses. In this study, 21,097 purebred Spanish (Pura Raza Español) horse births from the 2015 to 2016 breeding season were investigated for chimaerism. Twin foaled and chimaeric individuals were assessed on the basis of foaling records, short-tandem repeat (STR) parentage test results and a sex-linked STR-based technique. Fourteen twin pregnancies with 23 twin foals born alive were identified (0.066% twin foaling prevalence), including five blood chimaeric cases (21.7%; overall prevalence 0.011%), suggesting that this genetic condition is extremely low in horses. Furthermore, no true chimaeras were detected. This is the first large scale study analysing the occurrence of chimaerism in a horse population and the first assessment of twin foaling in purebred Spanish horses.

Thaw depth spatial and temporal variability at the Limnopolar Lake CALM-S site, Byers Peninsula, Livingston Island, Antarctica

A new Circumpolar Active Layer Monitoring (CALM) site was established in 2009 at the Limnopolar Lake watershed in Byers Peninsula, Livingston Island, Antarctica, to provide a node in the western Antarctic Peninsula, one of the regions that recorded the highest air temperature increase in the planet during the last decades. The first detailed analysis of the temporal and spatial evolution of the thaw depth at the Limnopolar Lake CALM-S site is presented here, after eight years of monitoring. The average values range between 48 and 29cm, decreasing at a ratio of 16cm/decade. The annual thaw depth observations in the 100×100 m CALM grid are variable (Variability Index of 34 to 51%), although both the Variance Coefficient and the Climate Matrix Analysis Residual point to the internal consistency of the data. Those differences could be explained then by the terrain complexity and node-specific variability due to the ground properties. The interannual variability was about 60% during 2009-2012, increasing to 124% due to the presence of snow in 2013, 2015 and 2016. The snow has been proposed here as one of the most important factors controlling the spatial variability of ground thaw depth, since its values correlate with the snow thickness but also with the ground surface temperature and unconfined compression resistance, as measured in 2010. The topography explains the thaw depth spatial distribution pattern, being related to snowmelt water and its accumulation in low-elevation areas (downslope-flow). Patterned grounds and other surface features correlate well with high thaw depth patterns as well. The edaphic factor (E=0.05842m²/°C·day; R²=0.63) is in agreement with other permafrost environments, since frozen index (F>0.67) and MAAT (<-2°C) denote a continuous permafrost existence in the area. All these characteristics provided the basis for further comparative analyses between others nearby CALM sites.

Plant cell wall-mediated immunity: cell wall changes trigger disease resistance responses

Plants have evolved a repertoire of monitoring systems to sense plant morphogenesis and to face environmental changes and threats caused by different attackers. These systems integrate different signals into overreaching triggering pathways which coordinate developmental and defence-associated responses. The plant cell wall, a dynamic and complex structure surrounding every plant cell, has emerged recently as an essential component of plant monitoring systems, thus expanding its function as a passive defensive barrier. Plants have a dedicated mechanism for maintaining cell wall integrity (CWI) which comprises a diverse set of plasma membrane-resident sensors and pattern recognition receptors (PRRs). The PRRs perceive plant-derived ligands, such as peptides or wall glycans, known as damage-associated molecular patterns (DAMPs). These DAMPs function as 'danger' alert signals activating DAMP-triggered immunity (DTI), which shares signalling components and responses with the immune pathways triggered by non-self microbe-associated molecular patterns that mediate disease resistance. Alteration of CWI by impairment of the expression or activity of proteins involved in cell wall biosynthesis and/or remodelling, as occurs in some plant cell wall mutants, or by wall damage due to colonization by pathogens/pests, activates specific defensive and growth responses. Our current understanding of how these alterations of CWI are perceived by the wall monitoring systems is scarce and few plant sensors/PRRs and DAMPs have been characterized. The identification of these CWI sensors and PRR-DAMP pairs will help us to understand the immune functions of the wall monitoring system, and might allow the breeding of crop varieties and the design of agricultural strategies that would enhance crop disease resistance.

Plasticity effect of rider-horse interaction on genetic evaluations for Show Jumping discipline in sport horses

To obtain a sport horse that excels in the highest levels of competition, breeders must take into account certain genetic and environmental factors that could influence the sport horse's performance, such as the rider-horse interaction (RHI). The main aim of this study was to describe this interaction in a genetic model by modelling it in relation to the horse's age. A total of 31,129 sport results from Spanish Sport Horses were used from a total of 1,101 animals evaluated, and these were grouped in three age levels and had been ridden by 606 different riders. Only riders who had ridden more than one horse (and vice-versa) were considered for the analyses. Five linear models with different random effects were analysed according to the covariates, the homogeneity/heterogeneity of the RHI and the relevant residual random effects. The model of best fit was then selected for the genetic evaluation of the animal. In general, models including the RHI effect (M2, M4 and M5) fitted better than the other models, and the best fit was obtained for M4 (with heterogeneous residual variance). The genetic variance increased constantly with age, whereas heritability showed a response on three intervals. This study revealed the varied evolution of the RHI with age, showing the different "plastic abilities" of this relationship.

Non-branched β-1,3-glucan oligosaccharides trigger immune responses in Arabidopsis

Fungal cell walls, which are essential for environmental adaptation and host colonization by the fungus, have been evolutionarily selected by plants and animals as a source of microbe-associated molecular patterns (MAMPs) that, upon recognition by host pattern recognition receptors (PRRs), trigger immune responses conferring disease resistance. Chito-oligosaccharides [β-1,4-N-acetylglucosamine oligomers, (GlcNAc)_n ] are the only glycosidic structures from fungal walls that have been well-demonstrated to function as MAMPs in plants. Perception of (GlcNAc)_4-8 by Arabidopsis involves CERK1, LYK4 and LYK5, three of the eight members of the LysM PRR family. We found that a glucan-enriched wall fraction from the pathogenic fungus Plectosphaerella cucumerina which was devoid of GlcNAc activated immune responses in Arabidopsis wild-type plants but not in the cerk1 mutant. Using this differential response, we identified the non-branched 1,3-β-d-(Glc) hexasaccharide as a major fungal MAMP. Recognition of 1,3-β-d-(Glc)₆ was impaired in cerk1 but not in mutants defective in either each of the LysM PRR family members or in the PRR-co-receptor BAK1. Transcriptomic analyses of Arabidopsis plants treated with 1,3-β-d-(Glc)₆ further demonstrated that this fungal MAMP triggers the expression of immunity-associated genes. In silico docking analyses with molecular mechanics and solvation energy calculations corroborated that CERK1 can bind 1,3-β-d-(Glc)₆ at effective concentrations similar to those of (GlcNAc)₄ . These data support that plants, like animals, have selected as MAMPs the linear 1,3-β-d-glucans present in the walls of fungi and oomycetes. Our data also suggest that CERK1 functions as an immune co-receptor for linear 1,3-β-d-glucans in a similar way to its proposed function in the recognition of fungal chito-oligosaccharides and bacterial peptidoglycan MAMPs.

Glutathione Transferase U13 Functions in Pathogen-Triggered Glucosinolate Metabolism

Glutathione (GSH) and indole glucosinolates (IGs) exert key functions in the immune system of the model plant Arabidopsis (Arabidopsis thaliana). Appropriate GSH levels are important for execution of both pre- and postinvasive disease resistance mechanisms to invasive pathogens, whereas an intact PENETRATION2 (PEN2)-pathway for IG metabolism is essential for preinvasive resistance in this species. Earlier indirect evidence suggested that the latter pathway involves conjugation of GSH with unstable products of IG metabolism and further processing of the resulting adducts to biologically active molecules. Here we describe the identification of Glutathione-S-Transferase class-tau member 13 (GSTU13) as an indispensable component of the PEN2 immune pathway for IG metabolism. gstu13 mutant plants are defective in the pathogen-triggered biosynthesis of end products of the PEN2 pathway, including 4-O-β-d-glucosyl-indol-3-yl formamide, indole-3-ylmethyl amine, and raphanusamic acid. In line with this metabolic defect, lack of functional GSTU13 results in enhanced disease susceptibility toward several fungal pathogens including Erysiphe pisi, Colletotrichum gloeosporioides, and Plectosphaerella cucumerina Seedlings of gstu13 plants fail also to deposit the (1,3)-β-glucan cell wall polymer, callose, after recognition of the bacterial flg22 epitope. We show that GSTU13 mediates specifically the role of GSH in IG metabolism without noticeable impact on other immune functions of this tripeptide. We postulate that GSTU13 connects GSH with the pathogen-triggered PEN2 pathway for IG metabolism to deliver metabolites that may have numerous functions in the innate immune system of Arabidopsis.

150 Runs of Homozygosity Analysis and their Possible Influence on Sperm Motility in Highly Consanguineous Bulls

Inbreeding depression is associated with emergence of deleterious effects and loss of genetic variability. Widespread use of genotyping technologies and new approaches for identification of runs-of-homozygosity (ROH) provide valuable tools to better understand the effects of inbreeding depression. We have previously demonstrated that inbreeding affects sperm motility patterns in cattle (Dorado et al. 2016 Reprod. Fertil. Dev. 29, 712-720; 10.1071/RD15324), with an increase in individuals presenting a hyperactivated-like motility. In this study, we characterised ROH patterns and performed gene ontology analysis of a large, highly consanguineous cattle population. Thirty-three Retinta bulls [average inbreeding percentage FPED = 16.57% (10.25 to 30.62%)] were genotyped using the Axiom® BOS 1 High-Density SNP Array (Thermo Fisher Scientific, Waltham, MA, USA). The ROH were estimated using CGATOH package and classified upon their length into 5 categories: 1-2, 2-4, 4-8, 8-16, and >16 Mb, which are inversely related to inbreeding events occurring 50 to 3 generations before, respectively. The ROH showed an average length of 3.73 Mb (1.48 to 6.71 Mb). Total FROH was partially explained by the increase in ROH fragments longer than 8 Mb, which is consistent with recent inbreeding events that occurred in this population in the last 6 generations. Additionally, the distribution of ROH varied notably between chromosomes. For instance, >16 Mb runs (very recent inbreeding event) were absent in BTA26 and BTA29, whereas certain loci on BTA7, BTA13, and BTA24 showed >16 Mb runs in 9 animals. To identify candidate biological functions affected by inbreeding, we performed functional analysis of the genome areas covered by ROH >8 Mb (our pedigree data covered 5.87 equivalent complete generations) using the Functional Annotation Clustering tool implemented in DAVID. Candidate regions were defined by occurring in ROH >8 in more than 6 animals and by a distance <1 Mb between adjacent single nucleotide polymorphisms. Eight significant gene clusters (enrichment score >1.30; P < 0.05) were identified, with 2 of these clusters related to sperm motility. One of these clusters (score 1.72) contained 23 genes coding microtubule-related proteins, which are associated with cellular movement structures such as flagella. The other cluster (score 1.42), included 4 genes related to dynein and motile cilium assembly ATPase complexes, associated with movement of eukaryotic flagella. We observed an additional cluster representing an ATP-binding feature, which included 77 genes (score 1.43). These results indicate that inbreeding could affect sperm motility by altering microtubule structure and motility. However, the fact that ROH were unevenly distributed across the genome, even in a highly inbred cattle population, also suggests that different metabolic pathways could be affected in individuals with similar inbreeding values. Therefore, the use of inbreeding coefficients as predictors for sperm quality should be approached carefully.

Alteration of cell wall xylan acetylation triggers defense responses that counterbalance the immune deficiencies of plants impaired in the β-subunit of the heterotrimeric G-protein

Arabidopsis heterotrimeric G-protein complex modulates pathogen-associated molecular pattern-triggered immunity (PTI) and disease resistance responses to different types of pathogens. It also plays a role in plant cell wall integrity as mutants impaired in the Gβ- (agb1-2) or Gγ-subunits have an altered wall composition compared with wild-type plants. Here we performed a mutant screen to identify suppressors of agb1-2 (sgb) that restore susceptibility to pathogens to wild-type levels. Out of the four sgb mutants (sgb10-sgb13) identified, sgb11 is a new mutant allele of ESKIMO1 (ESK1), which encodes a plant-specific polysaccharide O-acetyltransferase involved in xylan acetylation. Null alleles (sgb11/esk1-7) of ESK1 restore to wild-type levels the enhanced susceptibility of agb1-2 to the necrotrophic fungus Plectosphaerella cucumerina BMM (PcBMM), but not to the bacterium Pseudomonas syringae pv. tomato DC3000 or to the oomycete Hyaloperonospora arabidopsidis. The enhanced resistance to PcBMM of the agb1-2 esk1-7 double mutant was not the result of the re-activation of deficient PTI responses in agb1-2. Alteration of cell wall xylan acetylation caused by ESK1 impairment was accompanied by an enhanced accumulation of abscisic acid, the constitutive expression of genes encoding antibiotic peptides and enzymes involved in the biosynthesis of tryptophan-derived metabolites, and the accumulation of disease resistance-related secondary metabolites and different osmolites. These esk1-mediated responses counterbalance the defective PTI and PcBMM susceptibility of agb1-2 plants, and explain the enhanced drought resistance of esk1 plants. These results suggest that a deficient PTI-mediated resistance is partially compensated by the activation of specific cell-wall-triggered immune responses.

BREEDING AND GENETICS SYMPOSIUM: Breeding for resilience to heat stress effects in dairy ruminants. A comprehensive review

Selection for heat tolerant (HT) animals in dairy production has been so far linked to estimation of declines in production using milk recording and meteorological information on the day of control using reaction norms. Results from these models show that there is a reasonable amount of genetic variability in the individual response to high heat loads, which makes feasible selection of HT animals at low costs. However, the antagonistic relationship between level of production and response to heat stress (HS) implies that selection for HT animals under this approach must be done with caution so that productivity is not damaged. Decomposition of the genetic variability in principal components (PC) can provide selection criteria independent of milk production level although biological interpretation of PC is difficult. Moreover, given that response to heat stress for each animal is estimated with very sparse information collected under different physiological and management circumstances, biased (normally underestimation) and lack of accuracy may be expected. Alternative phenotypic characterization of HT can come from the use of physiological traits, which have also shown moderate heritability. However, costs of a large scale implementation based on physiological characteristics has precluded its use. Another alternative is the use of biomarkers that define heat tolerance. A review of biomarkers of HS from more recent studies is provided. Of particular interest are milk biomarkers, which together with infrared spectra prediction equations can provide useful tools for genetic selection. In the 'omics' era, genomics, transcriptomics, proteomics and metabolomics have been already used to detect genes affecting HT. A review of findings in these areas is also provided. Except for the slick hair gene, there are no other genes for which variants have been clearly associated with HT. However, integration of omics information could help in pointing at knots of the HS control network and, in the end, to a panel of markers to be used in the selection of HT animals. Overall, HT is a complex phenomenon that requires integration of fine phenotypes and omics information to provide accurate tools for selection without damaging productivity. Technological developments to make on-farm implementation feasible and with greater insight into the key biomarkers and genes involved in HT are needed.

A computational approach for inferring the cell wall properties that govern guard cell dynamics

Guard cells dynamically adjust their shape in order to regulate photosynthetic gas exchange, respiration rates and defend against pathogen entry. Cell shape changes are determined by the interplay of cell wall material properties and turgor pressure. To investigate this relationship between turgor pressure, cell wall properties and cell shape, we focused on kidney-shaped stomata and developed a biomechanical model of a guard cell pair. Treating the cell wall as a composite of the pectin-rich cell wall matrix embedded with cellulose microfibrils, we show that strong, circumferentially oriented fibres are critical for opening. We find that the opening dynamics are dictated by the mechanical stress response of the cell wall matrix, and as the turgor rises, the pectinaceous matrix stiffens. We validate these predictions with stomatal opening experiments in selected Arabidopsis cell wall mutants. Thus, using a computational framework that combines a 3D biomechanical model with parameter optimization, we demonstrate how to exploit subtle shape changes to infer cell wall material properties. Our findings reveal that proper stomatal dynamics are built on two key properties of the cell wall, namely anisotropy in the form of hoop reinforcement and strain stiffening.

Late complications of percutaneous tracheostomy using the balloon dilation technique

OBJECTIVE

The purpose of this study was to determine the late complications in critically ill patients requiring percutaneous tracheostomy (PT) using the balloon dilation technique.

DESIGN

A prospective, observational cohort study was carried out.

SCOPE

Two medical-surgical intensive care units (ICU).

PATIENTS

All mechanically ventilated adult patients consecutively admitted to the ICU with an indication of tracheostomy.

INTERVENTIONS

All patients underwent PT according to the Ciaglia Blue Dolphin^® method, with endoscopic guidance. Survivors were interviewed and evaluated by fiberoptic laryngotracheoscopy and tracheal computed tomography at least 6 months after decannulation.

VARIABLES

Intraoperative, postoperative and long-term complications and mortality (in-ICU, in-hospital) were recorded.

RESULTS

A total of 114 patients were included. The most frequent perioperative complication was minor bleeding (n=20) and difficult cannula insertion (n=19). Two patients had severe perioperative complications (1.7%) (major bleeding and inability to complete de procedure in one case and false passage and desaturation in the other). All survivors (n=52) were evaluated 211±28 days after decannulation. None of the patients had symptoms. Fiberoptic laryngotracheoscopy and computed tomography showed severe tracheal stenosis (>50%) in 2patients (3.7%), both with a cannulation period of over 100 days.

CONCLUSIONS

Percutaneous tracheostomy using the Ciaglia Blue Dolphin^® technique with an endoscopic guide is a safe procedure. Severe tracheal stenosis is a late complication which although infrequent, must be taken into account due to its lack of clinical expressiveness. Evaluation should be considered in those tracheostomized critical patients who have been cannulated for a long time.

Linkage disequilibrium, persistence of phase, and effective population size in Spanish local beef cattle breeds assessed through a high-density single nucleotide polymorphism chip

Linkage disequilibrium (LD) and persistence of phase are fundamental approaches for exploring the genetic basis of economically important traits in cattle, including the identification of QTL for genomic selection and the estimation of effective population size () to determine the size of the training populations. In this study, we have used the Illumina BovineHD chip in 168 trios of 7 Spanish beef cattle breeds to obtain an overview of the magnitude of LD and the persistence of LD phase through the physical distance between markers. Also, we estimated the time of divergence based on the persistence of the LD phase and calculated past from LD estimates using different alternatives to define the recombination rate. Estimates of average (as a measure of LD) for adjacent markers were close to 0.52 in the 7 breeds and decreased with the distance between markers, although in long distances, some LD still remained (0.07 and 0.05 for markers 200 kb and 1 Mb apart, respectively). A panel with a lower boundary of 38,000 SNP would be necessary to launch a successful within-breed genomic selection program. Persistence of phase, measured as the pairwise correlations between estimates of in 2 breeds at short distances (10 kb), was in the 0.89 to 0.94 range and decreased from 0.33 to 0.52 to a range of 0.01 to 0.08 when marker distance increased from 200 kb to 1 Mb, respectively. The magnitude of the persistence of phase between the Spanish beef breeds was similar to those found in dairy breeds. For across-breed genomic selection, the size of the SNP panels must be in the range of 50,000 to 83,000 SNP. Estimates of past showed values ranging from 26 to 31 for 1 generation ago in all breeds. The divergence among breeds occurred between 129 and 207 generations ago. The results of this study are relevant for the future implementation of within- and across-breed genomic selection programs in the Spanish beef cattle populations. Our results suggest that a reduced subset of the SNP panel would be enough to achieve an adequate precision of the genomic predictions.

PCA3 as a second-line biomarker in a prospective controlled randomized opportunistic prostate cancer screening programme

OBJECTIVES

PCA3 performance as a single second line biomarker is compared to the European Randomised Study of Screening for Prostate Cancer risk calculator model 3 (ERSPC RC-3) in an opportunistic screening in prostate cancer (PCa).

MATERIAL AND METHODS

5,199 men, aged 40-75y, underwent prostate-specific antigen (PSA) screening and digital rectal examination (DRE). Men with a normal DRE and PSA ≥3ng/ml had a PCA3 test done. All men with PCA3 ≥35 underwent an initial biopsy (IBx) -12 cores-. Men with PCA3 <35 were randomized 1:1 to either IBx or observation. We compared them to those obtained with ERSPC RC-3.

RESULTS

PCA3 test was performed on 838 men (16.1%). In PCA3(+) and PCA3(-) groups, global PCa detection rates were 40.9% and 14.7% with a median follow-up (FU) of 21.7 months (P<.001). In the PCA3(+) arm (n=301, 35.9%), PCa was identified in 115 men at IBx (38.2%). In the randomized arm, 256 underwent IBx and PCa was found in 46 (18.0%) (P<.001). The biopsy-sparing potential would have been 64.1% as opposed to 76.6% if we had used ERSPC RC-3. However, the estimated false negative cases for HGPCa would have been reduced by 37.1% (89 to 56 patients). Moreover, if we had applied PCA3-35 to avoid IBx, 14.7% PCa and 9.1% of clinical significant PCa patients would not have been diagnosed during this FU.

CONCLUSIONS

When PCA3-35 is used as a second-line biomarker when PSA ≥3ng/ml and DRE is normal, IBx could be avoided in 12.5% less than if ERSPC RC-3 is used and would reduce the false negative cases by 36.2%. At a FU of 21.7 months, this dual protocol would miss 9.1% of clinically significant PCa, so strict FU is mandatory with established biopsy criteria based on PSA and DRE in cases with PCA3 <35.

Polμ deficiency induces moderate shortening of P53-/- mouse lifespan and modifies tumor spectrum

Non-homologous end joining (NHEJ) is the main mechanism for double strand break (DSB) DNA repair. The error-prone DNA polymerase mu (Polμ) is involved in immunoglobulin variable region rearrangement and in general, NHEJ in non-lymphoid cells. Deletion of NHEJ factors in P53^-/- mice, which are highly prone to development of T cell lymphoma, generally increases cancer incidence and shifts the tumor spectrum towards aggressive pro-B lymphoma. In contrast, Polμ deletion increased sarcoma incidence, proportionally reducing pro-B lymphoma development on the P53-deficient background. Array comparative genomic hybridization (aCGH) analyses showed DNA copy number alterations in both P53^-/- and Polμ^-/-P53^-/- lymphomas. Our results also indicate that the increase in sarcoma incidence in Polμ^-/-P53^-/- mice could be associated with Cdk4 and Kub3 amplification and overexpression. These results identify a role for Polμ in the prevention of sarcomagenesis on a murine P53-deficient background, in contrast to most other NHEJ factors.

Identification of a new Y chromosome haplogroup in Spanish native cattle

The aim of this work was to perform a thorough analysis of the diversity of Y-haplotypes in Spanish cattle. A total of 207 Bos taurus males were sampled across 25 European breeds, with a special focus on rare, local Spanish populations. Animals were genotyped with five Y-specific microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1), two indels (ZFY10 and USP9Y) and one SNP (UTY19). A new haplogroup, distinct from those described by Götherström et al. (2005), was identified and named Y1.2. Samples representing the three B. taurus Y-haplogroups were genotyped for four additional Y chromosome SNPs (rs121919254, rs121919281, rs121919323 and rs137049553). Among these SNPs, only rs121919281 was informative in B. taurus and helped to confirm the new Y1.2 haplogroup. Analysis of a larger dataset of standardized haplotypes for 1507 individuals from 57 populations from Spain, other European countries and Africa showed the new Y1.2 haplogroup to be found exclusively in Spanish breeds. This finding reinforces the importance of local Spanish cattle as reservoirs of genetic diversity as well as the importance of the Iberian Peninsula in the history of cattle.

Detección de regiones genómicas con elevado desequilibrio de ligamiento en poblaciones de vacuno de carne españolas con análisis de BovineHD BeadChip

El objetivo de este trabajo fue evaluar el patrón de desequilibrio de ligamiento a lo largo del genoma en siete poblaciones españolas autóctonas de vacuno de carne (Asturiana de los Valles, Avileña Negra-Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta y Rubia Gallega). Para ello, se utilizó el BovineHD BeadChip con el que se genotiparon 171 tríos formados por individuo/padre/madre. Después del filtrado, se dispuso de 573.134 SNP. A partir de esta información se definió un parámetro que mide el desequilibrio medio del genoma por regiones de 1Mb en cada una de las poblaciones. Los resultados mostraron que el desequilibrio de ligamiento es muy heterogéneo a lo largo del genoma y que, además, esta heterogeneidad es consistente entre poblaciones. Las causas de esta heterogeneidad pueden ser, o bien estructurales y atribuibles a una menor tasa de mutación y/o recombinación, o bien consecuencia de procesos de selección estabilizadora.

Characterization of Plant Cell Wall Damage-Associated Molecular Patterns Regulating Immune Responses

The plant cell wall is one of the first defensive barriers that pathogens need to overcome to successfully colonize plant tissues. Plant cell wall is considered a dynamic structure that regulates both constitutive and inducible defense mechanisms. The wall is a potential source of a diverse set of Damage-Associated Molecular Patterns (DAMPs), which are signalling molecules that trigger immune responses. However, just a few active wall ligands, such as oligogalacturonic acids (OGs), have been characterized so far. To identify additional wall-derived DAMPs, we obtained different plant wall fractions and tested their capacity to trigger immune responses using a calcium read-out system. To characterize the active DAMPs structures present in these fractions, we applied Glycome Profiling, a technology that uses a large and diverse set of specific monoclonal antibodies against wall carbohydrate ligands. The methods describe here can be used in combination with other biochemical approaches to identify and purify new plant cell wall DAMPs.

Effect of inbreeding depression on bull sperm quality and field fertility

The present study investigated the effect of inbreeding depression on sperm quality using automated and objective methods and subsequent effects on beef bull field fertility. Individual inbreeding coefficient (F) values and field fertility data were determined using a dataset of AI bulls belonging to the Spanish Retinta Breeders Association (Asociación Nacional de Criadores de Ganado Vacuno Selecto de Raza Retinta (ANCRE)). Animals were clustered in two groups according to the F values as follows: (1) a high inbreeding group (HI; F ≥ 13.5%, mean 16.3); and (2) a non-inbreeding group (NI; F = 0%). In total, 17 different assessments were performed in both experimental groups, including evaluation of sperm morphology, acrosomal and DNA status, sperm plasma membrane integrity and function (hypo-osmotic swelling test), 10 kinetic parameters and the structure of sperm subpopulations. Sperm morphology, acrosomal and DNA status and osmotic tolerance were similar in both groups. Three velocity parameters (curvilinear velocity, straight line velocity and average path velocity) and the amplitude of lateral head displacement were higher in HI (P < 0.05). Cluster analysis of kinematic parameters revealed three different sperm subpopulations (sP1, sP2 and sP3), with the proportion of the sP1 population (highly active but non-progressive spermatozoa) being significantly (P < 0.05) higher in the HI group. Field fertility was assessed using two calving record datasets. In a smaller database including only bulls evaluated in the present study, there was a significant increase in the calving interval of cows sired with HI bulls. Conversely, in an extended genetic analysis of the ANCRE database, inbreeding only explained a small part of the variation in calving interval, and the results of regression analysis were not significant among bulls. The findings of the present study suggest that high inbreeding levels have a moderate effect on bull semen quality, with an increased percentage of highly active but non-progressive spermatozoa, but only when F values reached a certain threshold. This motility pattern could explain, in part, the higher calving interval produced by inbred bulls under field conditions.

On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations

Background

Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. The aim of this study was to compare the performance of a subset of these procedures by using a dataset on seven Spanish autochthonous beef cattle populations.

Results

Analysis of the correlations between the logarithms of the statistics that were obtained by 11 tests for detecting signatures of selection at each single nucleotide polymorphism confirmed that they can be clustered into the three main groups mentioned above. A factor analysis summarized the results of the 11 tests into three canonical axes that were each associated with one of the three groups. Moreover, the signatures of selection identified with the first and second groups of tests were shared across populations, whereas those with the third group were more breed-specific. Nevertheless, an enrichment analysis identified the metabolic pathways that were associated with each group; they coincided with canonical axes and were related to immune response, muscle development, protein biosynthesis, skin and pigmentation, glucose metabolism, fat metabolism, embryogenesis and morphology, heart and uterine metabolism, regulation of the hypothalamic–pituitary–thyroid axis, hormonal, cellular cycle, cell signaling and extracellular receptors.

Conclusions

We show that the results of the procedures used to identify signals of selection differed substantially between the three groups of tests. However, they can be classified using a factor analysis. Moreover, each canonical factor that coincided with a group of tests identified different signals of selection, which could be attributed to processes of selection that occurred at different evolutionary times. Nevertheless, the metabolic pathways that were associated with each group of tests were similar, which suggests that the selection events that occurred during the evolutionary history of the populations probably affected the same group of traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0258-1) contains supplementary material, which is available to authorized users.

Association analysis of g.68G → A SNP in CAPN1 gene with carcass and meat quality traits in goose raised in organic <i>dehesa</i>

Abstract. Meat quality is an important concern for the poultry industry. Domestic geese products obtained from free-range systems usually have rather tough meat, and it is necessary to select them to improve meat tenderness. The relation of the calpain 1 (CAPN1) gene with the post-mortem tenderness process of meat has been demonstrated in several species. Thus, the objective of the present study was to identify polymorphisms in this gene and to perform an association analysis between these polymorphisms and related economic traits in goose raised in the dehesa ecosystem. For the analysis, 50 geese of 3 different subpopulations (20 Embden Anser anser; 20 Toulouse Anser anser; 10 F1 cross) were studied. The experimental protocols were followed complying with principles of animal welfare. A novel SNP was found in the CAPN1 gene, g.68G → A. This polymorphism was statistically associated with different carcass and meat quality traits such as thigh muscle width (P = 0.020) and the b* 10-day meat colour parameter (P = 0.024) for the global goose population. The association of this gene with meat tenderness (Warner–Bratzler shear force) was confirmed in the case of female individuals of the Toulouse breed (P = 0.043). The results suggest the possibility of using molecular markers in CAPN1 gene as a potential tool for improving carcass and meat quality traits in goose breeding programmes.