Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.

Correlation Between Sagittal Balance and Mechanical Distal Junctional Failure in Degenerative Pathology of the Spine: A Retrospective Analysis

STUDY DESIGN

Retrospective cohort study.

OBJECTIVES

This study aimed to investigate the failure of the caudal end of lumbar posterior fixation in terms of pre-operative and post-operative spinopelvic parameters, correction performed, demographic and clinical data.

METHODS

The lumbar, thoraco-lumbar and lumbo-sacral posterior fixations performed with pedicle screws and rods in 2017-2019 were retrospectively analyzed. As 81% failures occurred within 4 years, an observational period of 4 years was chosen. The revision surgeries due to the failure in the caudal end were collected in the junctional group. Fixations which have not failed were gathered in the control group. The main spinopelvic parameters were measured for each patient on standing lateral radiographs with the software Surgimap. Demographic and clinical data were extracted for both groups.

RESULTS

Among the 457 patients who met the inclusion criteria, the junctional group included 101 patients, who required a revision surgery. The control group collected 356 primary fixations. The two most common causes of revision surgeries were screws pullout (57 cases) and rod breakage (53 cases). SVA, PT, LL, PI-LL and TPA differed significantly between the two groups (P = .021 for LL, P < .0001 for all the others). The interaction between the two groups and the pre-operative and post-operative conditions was significant for PT, SS, LL, TK, PI-LL and TPA (P < .005). Sex and BMI did not affect the failure onset.

CONCLUSIONS

Mechanical failure is more likely to occur in patients older than 40 years with a thoraco-lumbar fixation where PT, PI-LL and TPA were not properly restored.

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

Vaccinium as a comparative system for understanding of complex flavonoid accumulation profiles and regulation in fruit

The genus Vaccinium L. (Ericaceae) contains premium berryfruit crops including blueberry, cranberry, bilberry and lingonberry. Consumption of Vaccinium berries is strongly associated with various potential health and many of these benefits are attributed to the relatively high concentrations of flavonoids, including the anthocyanins that provide the attractive red and blue berry colours. Since these phytochemicals are increasingly appealing to consumers, they have become a crop breeding target. There has been substantial recent progress in Vaccinium genomics and genetics together with new functional data on the transcriptional regulation of flavonoids. This is helping to unravel the developmental control of flavonoids and to identify genetic regions and genes that can be selected for, to further improve Vaccinium crops, and advance our understanding of flavonoid regulation and biosynthesis across a broader range of fruit crops. In this update we consider the recent progress in understanding flavonoid regulation in fruit crops, using Vaccinium as an example, and highlighting the significant gains in both genomic tools and functional analysis.

The origins of the camper's chiasm asymmetry: a cadaveric study and clinical implications for flexor tendons surgery

The Camper's chiasm (CC) originates from the decussation of tendon fibers of the flexor digitorum superficialis at the level of the proximal phalanx. Previous studies described several conformations of the CC, but none has studied the asymmetry pattern for each finger. We lack studies about the relationship between the vincula tendinum and the morphology of the CC. We aimed to study the precise pattern of asymmetry and the aforementioned relationship in a cadaveric study. We studied the fingers of 9 fresh frozen human hands (thumb excluded). We observed the distribution of the fibers and categorized each CC according to the Gonzalez classification. Finally, we recorded the inset point of the vincula longa superficiales (VLS) according to Schmidt. We found 7 symmetrical CCs, while the remaining 29 showed an asymmetrical pattern that matched with the site of insertion of the VLS. For the index and long fingers, we detected a dominance of the ulnar slip. For the ring and little finger, we found a higher radial dominance. The inset point of the VLS always coincided with the side of slip dominance, whereas in symmetrical CCs, the VLS was symmetrical as well. Since the vascular role of the vincula tendinum, we speculate that the asymmetry of the CC may be of vascular origin.

Biomechanical consequences of cement discoplasty: An in vitro study on thoraco-lumbar human spines

With the ageing of the population, there is an increasing need for minimally invasive spine surgeries to relieve pain and improve quality of life. Percutaneous Cement Discoplasty is a minimally invasive technique to treat advanced disc degeneration, including vacuum phenomenon. The present study aimed to develop an in vitro model of percutaneous cement discoplasty to investigate its consequences on the spine biomechanics in comparison with the degenerated condition. Human spinal segments (n = 27) were tested at 50% body weight in flexion and extension. Posterior disc height, range of motion, segment stiffness, and strains were measured using Digital Image Correlation. The cement distribution was also studied on CT scans. As main result, percutaneous cement discoplasty restored the posterior disc height by 41% for flexion and 35% for extension. Range of motion was significantly reduced only in flexion by 27%, and stiffness increased accordingly. The injected cement volume was 4.56 ± 1.78 ml (mean ± SD). Some specimens (n = 7) exhibited cement perforation of one endplate. The thickness of the cement mass moderately correlated with the posterior disc height and range of motion with different trends for flexions vs. extension. Finally, extreme strains on the discs were reduced by percutaneous cement discoplasty, with modified patterns of the distribution. To conclude, this study supported clinical observations in term of recovered disc height close to the foramen, while percutaneous cement discoplasty helped stabilize the spine in flexion and did not increase the risk of tissue damage in the annulus.

High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content

Highbush blueberry (Vaccinium corymbosum, 2n = 4x = 48) is the most cultivated type of blueberry, both in New Zealand and overseas. Its perceived nutritional value is conferred by phytonutrients, particularly anthocyanins. Identifying the genetic mechanisms that control the biosynthesis of these metabolites would enable faster development of cultivars with improved fruit qualities. Here, we used recently released tools for genetic mapping in autotetraploids to build a high-density linkage map in highbush blueberry and to detect quantitative trait loci (QTLs) for fruit anthocyanin content. Genotyping was performed by target sequencing, with ∼18,000 single nucleotide polymorphism (SNP) markers being mapped into 12 phased linkage groups (LGs). Fruits were harvested when ripe for two seasons and analyzed with high-performance liquid chromatography-mass spectrometry (HPLC-MS): 25 different anthocyanin compounds were identified and quantified. Two major QTLs that were stable across years were discovered, one on LG2 and one on LG4, and the underlying candidate genes were identified. Interestingly, the presence of anthocyanins containing acylated sugars appeared to be under strong genetic control. Information gained in this study will enable the design of molecular markers for marker-assisted selection and will help build a better understanding of the genetic control of anthocyanin biosynthesis in this crop.

Post-traumatic entrapment of the median nerve in the ulno-humeral joint: Diagnosis, treatment and literature review

BACKGROUND

The incidence of median nerve injuries in pediatric elbow dislocations is approximately 3% and avulsion of the open medial epicondylar epiphysis in the pediatric population is one predisposing factor that may explain this age predilection. These lesions can be difficult to diagnose in the acute phase because symptoms tend to be mild or delayed, consequently their management can be challenging and functional outcome poorer.

METHODS

We present the case of an unrecognized median nerve entrapment in a 16-year-old boy with posterior dislocation of the elbow and a medial epicondyle fracture, treated initially with close reduction and open stabilization with a cannulated screw. Assessment is supported by a review of similar reported cases available in literature.

RESULTS

We discuss the diagnostic approach and the surgical options that can be used for this type of injury.

CONCLUSIONS

High clinical suspicion of entrapment is imperative in presence of signs of damage to the median nerve in the pediatric patient immediately after the reduction of an elbow dislocation. If diagnosis of entrapment is made the therapeutic choice between neurolysis and nerve graft depends on the lesion severity. In the presence of a Fourrier's type 4 lesion, neurolysis should be avoided, while nerve resection and grafting are recommended.

Preservation of terminal branches of the palmar cutaneous branch of the median nerve in open carpal tunnel release

PURPOSE

Post-operative pain in the palm and scar area is the most common complication after carpal tunnel release and injury to the terminal branches of the palmar cutaneous nerve is generally considered one of the causes for this complication. The Authors performed an intraoperative study preserving the terminal branches of the palmar cutaneous branch of the median nerve and verifying the frequency, location and direction of the branches that cross an interthenar incision.

METHOD AND MATERIAL

Eighty-five consecutive patients (57 F - 28 M, mean age 66 y) underwent carpal tunnel release between February and June 2021. The cutaneous branches crossing the incision were identified and preserved by careful dissection. Subsequently they were counted and classified by their direction and distance from the proximal border of the transverse carpal ligament.

RESULTS

Sensory branches were found in 40 % of cases (34/85) and their origin was observed at an average of 1.05 cm (0-1.8 cm) distal from the proximal border of the carpal tunnel. A total of 44 branches were observed of which 23 branches crossed the incision with a transverse course and 21 with an oblique, generally proximal-distal radio-ulnar course. The subcutaneous layer overlying the distal third of the transverse carpal ligament was found to be devoid of sensory branches, therefore it can be considered a relatively safe area.

CONCLUSION

Isolation and protection of palmar sensory branches is important for improving carpal tunnel release results. This goal can be more easily achieved by locating the skin incision on the distal third of the transverse carpal ligament, where the sensory branches have a lower frequency, possibly associated with a second proximal incision (biportal technique) to better visualize the proximal portion of the ligament and antebrachial fascia.

Unraveling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus)

Growth directly influences production rate and therefore is one of the most important and well-studied traits in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus mapping and genome-wide association studies for 10 growth traits that were observed over 2 years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism markers, and discovered 8 quantitative trait loci for height, length, and weight on linkage groups 3, 14, and 18. Using genome-wide association studies, we further identified 113 single nucleotide polymorphism-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the genome-wide association studies colocated with the quantitative trait loci previously mentioned, demonstrating that combining quantitative trait locus mapping and genome-wide association studies represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping quantitative trait loci, genomic selection, and further detailed functional analysis of the genes underlying growth in trevally.

Combined Methodologies for Determining In Vitro Bioavailability of Drugs and Prediction of In Vivo Bioequivalence From Pharmaceutical Oral Formulations

With the aim of developing an in vitro model for the bioavailability (BA) prediction of drugs, we focused on the study of levonorgestrel (LVN) released by 1.5 mg generic and brand-name tablets. The developed method consisted in combining a standard dissolution test with an optimized parallel artificial membrane permeability assay (PAMPA) to gain insights into both drug release and gastrointestinal absorption. Interestingly, the obtained results revealed that the tablet standard dissolution test, combined with an optimized PAMPA, highlighted a significant decrease in the release (15 ± 0.01 μg min⁻¹ vs 30 ± 0.01 μg min⁻¹) and absorption (19 ± 7 × 10^–6 ± 7 cm/s Pe vs 41 ± 15 × 10^–6 cm/s Pe) profiles of a generic LVN tablet when compared to the brand-name formulation, explaining unbalanced in vivo bioequivalence (BE). By using this new approach, we could determine the actual LVN drug concentration dissolved in the medium, which theoretically can permeate the gastrointestinal (GI) barrier. In fact, insoluble LVN/excipient aggregates were found in the dissolution media giving rise to non-superimposable dissolution profiles between generic and brand-name LVN tablets. Hence, the results obtained by combining the dissolution test and PAMPA method provided important insights confirming that the combined methods can be useful in revealing crucial issues in the prediction of in vivo BE of drugs.

Palmar fracture-dislocation of the trapezoid with median nerve contusion. Case report and literature review

Complete dislocations of the trapezoid are very uncommon injuries. The authors present a case of open palmar trapezoid fracture-dislocation with significant displacement of the fracture, acute carpal tunnel syndrome and other concomitant carpometacarpal injuries. A review of the literature search for palmar trapezoid dislocations and treatments was performed.

Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus

Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300-1400 year old specimens (n = 2) of the extinct "horned" crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

Development of an UHPLC-diode arrays detector (DAD) method for the analysis of polydatin in human plasma

A new chromatographic method by Ultra High Performance Liquid Chromatographic (UHPLC) technology, has been developed and validated for the determination of polydatin and resveratrol, as potential metabolite, in human plasma. After the optimization of the chromatographic conditions, the method has been validated on spiked human plasma samples. The optimized extraction allowed to obtain analytes recovery up to 98.48 ± 4.03 %. Then, the isocratic elution in reversed phase mode, provides the separation of polydatin and resveratrol in less than 10.0 min. Chromatographic analysis was performed on a C18, 10 cm x 3.0 mm, 2.7 μm stationary phase, by using triethanolamine phosphate solution (0.1 M, pH = 3.7) and ACN 85:15 (v/v) as mobile phase at a flow rate of 0.5 mL/min. The UV detector was set at 306 nm for the analysis of both polydatin and resveratrol. The limit of detection (LoD) and the limit of quantification (LoQ) for polydatin in plasma samples were found to be 7.82 ± 0.38 nM and 26.06 ± 1.28 nM respectively. The method was found to be accurate and precise with a coefficient for intra- and inter-day variation below 5 %. All the reported data demonstrate how the developed method is rapid and sensitive. Moreover, results of the analysis of plasma samples, obtained from orally treated volunteers with nutritional supplements containing polydatin, have shown the method to be suitable for the pharmacokinetic characterization of polydatin and resveratrol, as metabolite, in humans.

Retrospective study in clinical governance and financing system impacts of the COVID-19 pandemic in the hand surgery and microsurgery HUB center

Introduction

The authors presented a retrospective study in the surgical activity of the HUB center for Hand Surgery and Microsurgery in Emilia-Romagna comparing the data between March and April 2020, in the peak of Covid pandemic, with the same period in 2019.

Materials and methods

During the two months period of March–April 2020 versus 2019 the authors analyzed the surgical procedures performed in elective and emergency surgery with hospitalization and Day or Outpatient surgery regime. Surgical treatments with no hospitalization were planned in the Day-Surgery Service. The financing system impacts were analyzed according to the Diagnosis Related Groups (DRG), the costs accounting method mostly used in European countries.

Results

An overall reduction of 68.5% was recorded in surgical procedures, with a more relevant reduction of 92.3% in elective surgery and a significantly less relevant reduction of 37.2% in urgent one. Replantation did not present a reduction in number of cases, while cutting lesions of tendons at the hand and fingers increased such as the bone and ligament injuries during domestic accidents. The negative impact in the financial system recorded a reduction of 32.5%.

Discussion

The epidemiology of hand trauma looks not only at the artisanal and industrial injuries, but also mostly at the accidents in daily life activities. The data of the study evidenced the significantly increase in the injuries occurring in the domestic environment. Elective surgery was canceled. The 86% of surgical procedures performed were urgent ones and the 72.8% of these were possible in Day and Outpatient surgery with significantly reduction in hospitalization. All procedures followed a rigid process for patient and healthcare workers with regard for personal protection and safety. Telemedicine was arranged in emergencies, and economic damage was analyzed also in the following rebound effect during summer period.

Conclusions

The significantly less reduction recorded in urgent surgery vs the more relevant reduction in elective one showed how the hand injuries remained a major issue also during the lockdown. The data highlighted the relevant role of the organizational aspects of the surgical procedures and planning in hand trauma. Despite the financial impact of the elective surgery, the presence of a functional and skill Emergency Service and Day-Surgery Service resulted fundamental in the efficacy and efficiency of the patient management and in containment of economic damage. The telemedicine was significantly limited by liability and risk management issues.

Dissecting Genetic Resistance to Fire Blight in Three Pear Populations

Fire blight, caused by the bacterial pathogen Erwinia amylovora, is a persistent problem for pear (Pyrus spp.) growers in the United States. Growing resistant cultivars is one of the best options for managing fire blight. The cultivars Potomac and Old Home and the selection NJA2R59T69 display resistance to fire blight. As such, three mapping populations (El Dorado × Potomac, Old Home × Bartlett, and NJA2R59T69 × Bartlett) were developed to identify genomic regions associated with resistance to fire blight. Progeny were phenotyped during 2017 and 2018 by inoculating multiple actively growing shoots of field-grown seedling trees with E. amylovora isolate E153n via the cut-leaf method. Genotyping was conducted using the recently developed Axiom Pear 70 K Genotyping Array and chromosomal linkage groups were created for each population. An integrated two-way pseudo-testcross approach was used to map quantitative trait loci (QTLs). Resistance QTLs were identified on chromosome 2 for each population. The QTLs identified in the El Dorado × Potomac and Old Home × Bartlett populations are in the same region as QTLs that were previously identified in Harrow Sweet and Moonglow. The QTL in NJA2R59T69 mapped proximally to the previously identified QTLs and originated from an unknown Asian or occidental source. Future research will focus on further characterizing the resistance regions and developing tools for DNA-informed breeding.

Quantitative phenotyping of shell suture strength in walnut (Juglans regia L.) enhances precision for detection of QTL and genome-wide association mapping

Walnut shell suture strength directly impacts the ability to maintain shell integrity during harvest and processing, susceptibility to insect damage and other contamination, and the proportion of kernel halves recovered during cracking. Suture strength is therefore an important breeding objective. Here, two methods of phenotyping this trait were investigated: 1) traditional, qualitative and rather subjective scoring on an interval scale by human observers, and; 2) quantitative and continuous measurements captured by a texturometer. The aim of this work was to increase the accuracy of suture strength phenotyping and to then apply two mapping approaches, quantitative trait loci (QTL) mapping and genome wide association (GWAS) models, in order to dissect the genetic basis of the walnut suture trait. Using data collected on trees within the UC Davis Walnut Improvement Program (n = 464), the genetic correlation between the texturometer method and qualitatively scored method was high (0.826). Narrow sense heritability calculated using quantitative measurements was 0.82. A major QTL for suture strength was detected on LG05, explaining 34% of the phenotypic variation; additionally, two minor QTLs were identified on LG01 and LG11. All three QTLs were confirmed with GWAS on corresponding chromosomes. The findings reported in this study are relevant for application towards a molecular breeding program in walnut.

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)

BACKGROUND

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis.

FINDINGS

A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

CONCLUSIONS

We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

Background

Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies.

Results

By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping.

Conclusions

The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.

Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics

Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants. Our review of the published data suggests that, although many gene families are conserved among herbaceous and tree species, some gene families, such as those involved in resistance to biotic and abiotic stresses and in the synthesis and transport of sugars, are often expanded in tree genomes. As the genomes of more tree species are sequenced, comparative genomics will further elucidate the complexity of tree genomes and how this relates to traits unique to trees.

Environmental nanoparticles are significantly over-expressed in acute myeloid leukemia

The increase in the incidence of acute myeloid leukemia (AML) may suggest a possible environmental etiology. PM2.5 was declared by IARC a Class I carcinogen. No report has focused on particulate environmental pollution together with AML. The study investigated the presence and composition of particulate matter in blood with a Scanning Electron Microscope coupled with an Energy Dispersive Spectroscope, a sensor capable of identifying the composition of foreign bodies. 38 peripheral blood samples, 19 AML cases and 19 healthy controls, were analyzed. A significant overload of particulate matter-derived nanoparticles linked or aggregated to blood components was found in AML patients, while almost absent in matched healthy controls. Two-tailed Student's t-test, MANOVA and Principal Component Analysis indicated that the total numbers of aggregates and particles were statistically different between cases and controls (MANOVA, P<0.001 and P=0.009 respectively). The particles detected showed to contain highly-reactive, non-biocompatible and non-biodegradable metals; in particular, micro- and nano-sized particles grouped in organic/inorganic clusters, with statistically higher frequency of a subgroup of elements in AML samples. The demonstration, for the first time, of an overload of nanoparticles linked to blood components in AML patients could be the basis for a possible, novel pathogenetic mechanism for AML development.

Genome mapping of postzygotic hybrid necrosis in an interspecific pear population

Deleterious epistatic interactions in plant inter- and intraspecific hybrids can cause a phenomenon known as hybrid necrosis, characterized by a typical seedling phenotype whose main distinguishing features are dwarfism, tissue necrosis and in some cases lethality. Identification of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding purposes. Development of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these genes. Although hybrid necrosis has been reported in several plant taxa, including Rosaceae species, this phenomenon has not been described previously in pear. In the interspecific pear population resulting from a cross between PEAR3 (Pyrus bretschneideri × Pyrus communis) and 'Moonglow' (P. communis), we observed two types of hybrid necrosis, expressed at different stages of plant development. Using a combination of previously mapped and newly developed genetic markers, we identified three chromosome regions associated with these two types of lethality, which were genetically independent. One type resulted from a negative epistatic interaction between a locus on linkage group 5 (LG5) of PEAR3 and a locus on LG1 of 'Moonglow', while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from 'Moonglow'.

The draft genome sequence of European pear (Pyrus communis L. 'Bartlett')

We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids

We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.

Natural diversity in the model legume Medicago truncatula allows identifying distinct genetic mechanisms conferring partial resistance to Verticillium wilt

Verticillium wilt is a major threat to alfalfa (Medicago sativa) and many other crops. The model legume Medicago truncatula was used as a host for studying resistance and susceptibility to Verticillium albo-atrum. In addition to presenting well-established genetic resources, this wild plant species enables to investigate biodiversity of the response to the pathogen and putative crosstalk between disease and symbiosis. Symptom scoring after root inoculation and modelling of disease curves allowed assessing susceptibility levels in recombinant lines of three crosses between susceptible and resistant lines, in a core collection of 32 lines, and in mutants affected in symbiosis with rhizobia. A GFP-expressing V. albo-atrum strain was used to study colonization of susceptible plants. Symptoms and colonization pattern in infected M. truncatula plants were typical of Verticillium wilt. Three distinct major quantitative trait loci were identified using a multicross, multisite design, suggesting that simple genetic mechanisms appear to control Verticillium wilt resistance in M. truncatula lines A17 and DZA45.5. The disease functional parameters varied largely in lines of the core collection. This biodiversity with regard to disease response encourages the development of association genetics and ecological approaches. Several mutants of the resistant line, impaired in different steps of rhizobial symbiosis, were affected in their response to V. albo-atrum, which suggests that mechanisms involved in the establishment of symbiosis or disease might have some common regulatory control points.

Antibiotic pressure compensates the biological cost associated with Pseudomonas aeruginosa hypermutable phenotypes in vitro and in a murine model of chronic airways infection

OBJECTIVES

Hypermutable strains of Pseudomonas aeruginosa frequently emerge during chronic airways infection in cystic fibrosis (CF) patients. While the increased accumulation of mutations by hypermutable strains determines a biological cost for the colonization of secondary environments, the mutator phenotypes might confer a selective advantage under antibiotic treatment in a CF airways environment.

METHODS

To test this hypothesis, the reference strain PAO1 and clonal pairs of CF clinical hypermutable and wild-type P. aeruginosa strains belonging to different genotypes were subjected to competition experiments in vitro and in a mouse model of chronic infection.

RESULTS

Both in vitro and in vivo, under antibiotic selection pressure, clinical hypermutable P. aeruginosa strains and the reference PAO1ΔmutS outcompeted their wild-type strains, promoting P. aeruginosa hypermutable strains in the airways colonization. This advantage for the hypermutable strain did not occur in the absence of antibiotic treatments. Severe histopathological lesions were detected during chronic murine airways infection after antibiotic pressure, indicating that the advantage of the hypermutable population in the lungs may contribute to disease progression.

CONCLUSIONS

Overall, these results showed that P. aeruginosa hypermutability, previously associated with a biological cost, increases colonization potential under selection pressure in a context of CF chronic airways infection and can contribute to lung damage during long-term persistence.

Concentration and surface of absorption: concepts and applications to gastrointestinal patches delivery

Gastrointestinal patches represent a novel multiparticulate drug delivery system able to increase the intestinal absorption of drugs with poor bioavailability. The number of patches to administer is a critical issue since it is related to the surface and drug concentration at the absorption site. The objective of this article is to evaluate the effect of the number of administered patches on the final absorption of leuprolide, a peptide chosen as model drug, assuming complete adhesion of all the devices to the intestinal membrane. The same dose of leuprolide was encapsulated into 2, 4 and 6 patches; the resulting intestinal absorption profiles were measured with the Ussing chamber ex vivo experimental setup and compared between them. The results showed that varying the number of patches, the final absorption does not present statistically significant changes, indicating that changes in concentration are balanced by change in absorption surface. These experimental findings can also be explained considering the equation that links the drug flow to surface and concentration at the absorption site, showing that the drug flow is related only to the geometry of each individual patch.

Pseudomonas aeruginosa microevolution during cystic fibrosis lung infection establishes clones with adapted virulence

RATIONALE

During long-term lung infection in patients with cystic fibrosis (CF), Pseudomonas aeruginosa strains develop mutations leading to clonal expansion. This microevolution is believed to be correlated with a reduced virulence.

OBJECTIVES

We tested this hypothesis in models of lung infection, using mice with different genetic backgrounds.

METHODS

From infected airways of six patients with CF, 25 P. aeruginosa clones were isolated during a period of up to 16.3 years and genotypically and phenotypically characterized. Virulence of the 8 early, 6 intermediate, and 11 late CF isolates and 5 environmental strains was assessed by monitoring acute mortality versus survival and P. aeruginosa chronic persistence versus lung clearance in mice of different genetic backgrounds, including CF mice.

MEASUREMENTS AND MAIN RESULTS

Different patients harbored clonally unrelated strains, but early, intermediate, and late P. aeruginosa isolates from single patients were clonally related, allowing comparative in vivo analysis. Although late isolates were attenuated in causing acute mortality in the mouse models, compared with early and intermediate clonal isolates and environmental strains, they did not differ from early and intermediate clonal isolates in their capacity to establish chronic infection and cause extensive inflammation in the murine respiratory tract.

CONCLUSIONS

Our findings indicate that clonal expansion of P. aeruginosa strains during microevolution within CF lungs leads to populations with altered but not reduced virulence. These P. aeruginosa clones with adapted virulence play a critical role in the pathogenesis of chronic infections and may serve to define virulence determinants as targets for novel therapies.

Biological cost of hypermutation in Pseudomonas aeruginosa strains from patients with cystic fibrosis

The high prevalence of hypermutable (mismatch repair-deficient) Pseudomonas aeruginosa strains in patients with cystic fibrosis (CF) is thought to be driven by their co-selection with adaptive mutations required for long-term persistence. Whether the increased mutation rate of naturally hypermutable strains is associated with a biological benefit or cost for the colonization of secondary environments is not known. Thirty-nine P. aeruginosa strains were collected from ten patients with CF during their course of chronic lung infections and screened for hypermutability. Seven hypermutable P. aeruginosa strains (18 %) isolated from six patients with CF (60 %) were identified and assigned to five different genotypes. Complementation and sequence analysis in the mutS, mutL and uvrD genes of these hypermutable P. aeruginosa strains revealed novel mutations. To understand the consequences of hypermutation for the fitness of the organisms, five pairs of clinical wild-type/hypermutable, clonally related P. aeruginosa strains and the laboratory strains PAO1/PAO1DeltamutS were subjected to competition in vitro and in the agar-beads mouse model of chronic airway infection. When tested in competition assay in vitro, the wild-type outcompeted four clinical hypermutable strains and the PAO1DeltamutS strain. In vivo, all of the hypermutable strains were less efficient at establishing lung infection than their wild-type clones. These results suggest that P. aeruginosa hypermutation is associated with a biological cost, reducing the potential for colonization of new environments and therefore strain transmissibility.

Retrieval analysis of clinical explanted vena cava filters

Vena cava filters are the most commonly used mechanical devices to prevent pulmonary embolism. A retrievable permanent filter has been available since 1999. That has allowed the direct study of thrombi captured in humans and the punctual interaction of blood and device at long and short term. Through traditional histologic methods, captured thrombi and the tissues formed around the filter were observed. An innovative environmental scanning electron microscopy technique allowed detection of micro- and nanosized foreign bodies inside thrombi and tissues, and chemical analysis could be carried out by means of energy dispersive spectroscopy. All specimens contained different quantities of foreign debris ranging from few tens of microns to 50 nanometers; their chemistry was not homogeneous when patients were compared, and also differed considerably within the same filter. The constant presence of debris deeply embedded in all thrombi observed may mean that they are the cause that triggered the formation of those thrombi as a result of the interaction between foreign bodies and blood components.

Raman scattering study of GaN nanostructures obtained by bottom-up and top-down approaches

GaN nanocolumnar structures were grown by plasma-assisted molecular beam epitaxy (PAMBE) and also fabricated by electron cyclotron resonance reactive ion etching (ECR-RIE) of a compact GaN film parallel to the [111] direction of the Si(111) substrates. Scanning electron microscopy shows that the nanocolumns fabricated by PAMBE have a length of about 300-500 nm with diameters ranging from 20 to 150 nm while nanowhiskers formed by RIE have diameters of 40-80 nm and a height between 1.4 and 1.7 µm. A comparative study of the vibrational spectrum (including optical and interface phonons) of the nanostructures using conventional macro-Raman and micro-Raman scattering as well as surface-enhanced Raman scattering is presented.

In-vivo short- and long-term evaluation of the interaction material-blood

Through an innovative electron microscopy technique, thrombi and fibrotic tissue taken from 14 explanted vena cava filters were observed. Twelve cases showed the presence of micro-and nano-sized inorganic, non biodegradable nor biocompatible particles which did not belong to the metal the device was made of and which could be the sole cause or, more likely, a pre-existing cause for thrombosis. In two cases, those debris activated immunological reactions typical of a foreign body. The presence of inorganic particles in the blood was never detected before and their effects on human health are hardly known. Their thrombogenicity should be added to the Virchow's Triad as a fourth factor and could be the explanation to many of the cases of pulmonary embolism where no thrombotic focus could be demonstrated.

Detection of micro- and nano-sized biocompatible particles in the blood

The research deals with new scanning electron microscopic evaluations of the interface between blood and explanted temporary vena cava filters from patients affected by blood disorders. The biological tissues adherent to the filter and the small thrombi formed in vivo were detached from the metallic structure of the device, fixed, dehydrated and prepared for the histological and the electron microscopy. The analyses showed that both samples (thrombus and newly formed tissue) contained foreign, in some cases nano-sized, bodies. The chemistry of these particles was different and varied, and unusual compounds containing non-biocompatible elements like bismuth, lead, wolfram, tungsten were also detected. The interaction between these debris travelling in the blood stream and the blood itself leads to suspect that the formation of the thrombus can originate from these inorganic and inert foreign bodies that act as triggering agent of the blood coagulation.

Synthesis and dopaminergic activity of heterocyclic analogues of 5,6-dihydroxy-2-aminotetralins

The heterocyclic analogues of 5,6-dihydroxy-2-aminotetralins (6) were synthesized and their in vitro dopaminergic activity was compared to that of (-)-DP-5,6-ADTN and the novel potent agonist Z12571. The results show that changing the cathecol ring for a heterocycle decreases the D1-like activity of the target molecules 6. However, the D2-like activity of tetrahydroquinoline (6j) was comparable to that of (-)-DP-5,6-ADTN.