The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent "tuning knobs" in the genome adaptive landscapes of given species.

The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality.

BACKGROUND: Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. RESULTS: This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar 'Tommy Atkins'. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins', supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between 'Tommy Atkins' x 'Kensington Pride' was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the 'Tommy Atkins' x 'Kensington Pride' mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. CONCLUSIONS: The availability of the complete 'Tommy Atkins' mango genome will aid global initiatives to study mango genetics.

Hemodynamic Changes in an Actively Rupturing Abdominal Aortic Aneurysm.

Computational fluid dynamics were used to assess hemodynamic changes in an actively rupturing abdominal aortic aneurysm (AAA) over a 9-day period. Active migration of contrast from the lumen into the thickest region of intraluminal thrombus (ILT) was demonstrated until it ultimately breached the adventitial layer. Four days after symptom onset, there was a discrete disruption of adventitial calcium with bleb formation at the site of future rupture. Rupture occurred in a region of low wall shear stress and was associated with a marked increase in AAA diameter from 6.6 to 8.4 cm. The cross-sectional area of the flow lumen increased across all time points from 6.28 to 12.08 cm2. The increase in luminal area preceded the increase in AAA diameter and was characterized by an overall deceleration in recirculation flow velocity with a coinciding increase in flow velocity penetrating the ILT. We show that there are significant hemodynamic and structural changes in the AAA flow lumen in advance of any appreciable increase in aortic diameter or rupture. The significant increase in AAA diameter with rupture suggests that AAA may actually rupture at smaller sizes than those measured on day of rupture. These findings have implications for algorithms the predict AAA rupture risk.

Genetic diversity of avocado (Persea americana Mill.) germplasm using pooled sequencing.

BACKGROUND: Discovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a costly process, due to loss of loci that are proven to be non-informative when genotyping the germplasm. RESULTS: Our study on a collection of 100 accessions comprised the three race types, Guatemalan, Mexican, and West Indian. To increase the chances of discovering polymorphic loci, three pools of genomic DNA, one from each race, were sequenced and the reads were aligned to a reference transcriptome. In total, 507,917 polymorphic loci were identified in the entire collection. Of these, 345,617 were observed in all three pools, 117,692 in two pools, 44,552 in one of the pools, and only 56 (0.0001%) were homozygous in the three pools but for different alleles. The polymorphic loci were validated using 192 randomly selected SNPs by genotyping the accessions within each pool. The sensitivity of polymorphic locus prediction ranged from 0.77 to 0.94. The correlation between the allele frequency estimated from the pooled sequences and actual allele frequency from genotype calling of individual accessions was r = 0.8. A subset of 109 SNPs were then used to evaluate the genetic relationships among avocado accessions and the genetic diversity of the collection. The three races were distinctly clustered by projecting the genetic variation on a PCA plot. As expected, by estimating the kinship coefficient for all the accessions, many of the cultivars from the California breeding program were closely related to each other, especially, the Hass-like ones. The green-skin avocados, e.g., 'Bacon', 'Zutano', 'Ettinger' and 'Fuerte' were also closely related to each other. CONCLUSIONS: A framework for SNP discovery and genetically characterizing of a breeder's accessions was described. Sequencing pools of gDNA is a cost-effective approach to create a genome-wide stock of polymorphic loci for a breeding program. Reassessing the botanical and the genetic knowledge about the germplasm accessions is valuable for future breeding. Kinship analysis may be used as a first step in finding a parental candidates in a parentage analyses.

Modulation of innate immunity in Nile tilapia (Oreochromis niloticus) by dietary supplementation of Bacillus subtilis endospores.

Dietary supplementation of probiotics is growing as a scientifically valid alternative to antibiotics for enhancement of overall animal health and productivity in aquaculture. Strains of Bacillus subtilis are regarded as attractive probiotic candidates to the fish farming industry; however, there is a limited number of studies focused on the use of specific strains probiotics in tilapia, and therefore complicating replication. The objective of this study was to examine the effect of the strains NZ86 (NRRL B-50136) and O14VRQ (NRRL B-67221) of B. subtilis on various parameters of the innate immunity in Nile tilapia (Oreochromis niloticus) in a 51-day feeding trial. Supplementation of tilapia with either strain resulted in significant increases (p < 0.05) in plasma lysozyme concentration of varying degrees throughout the trial. Meanwhile, alternative complement activity was significantly elevated (p < 0.05) only after feeding of the NZ86 strain after 14 and 51 days. Conversely, supplementation with O14VRQ resulted in a significant increase (p < 0.05) in the percent of neutrophils in the peripheral blood of tilapia by day 28. At the end of the trial, there was a trend towards increased phagocytic and respiratory burst activities observed in immune organ derived leukocytes. Feeding with either probiotic appeared to have an up-regulation on the gene expression of both pro-inflammatory cytokines in the intestine, yet only O14VRQ was significantly different than the control. Moreover, the occurrence of these results could be associated with supplementation of the probiotic strains, given that Bacillus bacteria were observed to populate the intestines of the dietary treatment groups. These results suggest the potential roles of these B. subtilis probiotic candidates to stimulate immune responses both locally and systemically in tilapia.

Cyclopropane fatty acid biosynthesis in plants: phylogenetic and biochemical analysis of Litchi Kennedy pathway and acyl editing cycle genes.

KEY MESSAGE: This report describes the most extensive known gene discovery study from an oilseed that produces cyclopropane fatty acids, a novel industrial feedstock. Nature contains hundreds of examples of plant species that accumulate unusual fatty acids in seed triacylglycerols (TAG). Although lipid metabolic genes have been cloned from several exotic plant species, the underlying mechanisms that control the production of novel TAG species are still poorly understood. One such class of unusual fatty acids contain in-chain cyclopropane or cyclopropene functionalities that confer chemical and physical properties useful in the synthesis of lubricants, cosmetics, dyes, coatings, and other types of valuable industrial feedstocks. These cyclopropyl fatty acids, or CPFAs, are only produced by a small number of plants, primarily in the order Malvidae. Litchi chinensis is one member of this group; its seed oil contains at least 40 mol% CPFAs. Several genes, representing early, middle, and late steps in the Litchi fatty acid and TAG biosynthetic pathways have been cloned and characterized here. The tissue-specific and developmental transcript expression profiles and biochemical characteristics observed indicate which enzymes might play a larger role in Litchi seed TAG biosynthesis and accumulation. These data, therefore, provide insights into which genes likely represent the best targets for either silencing or overexpression, in future metabolic engineering strategies aimed at altering CPFA content.

Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction.

UNLABELLED: Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait prediction is usually represented as linear regression models. In many cases, for the same set of samples and markers, multiple traits are observed. Some of these traits might be correlated with each other. Therefore, modeling all the multiple traits together may improve the prediction accuracy. In this work, we view the multitrait prediction problem from a machine learning angle: as either a multitask learning problem or a multiple output regression problem, depending on whether different traits share the same genotype matrix or not. We then adapted multitask learning algorithms and multiple output regression algorithms to solve the multitrait prediction problem. We proposed a few strategies to improve the least square error of the prediction from these algorithms. Our experiments show that modeling multiple traits together could improve the prediction accuracy for correlated traits. AVAILABILITY AND IMPLEMENTATION: The programs we used are either public or directly from the referred authors, such as MALSAR (http://www.public.asu.edu/~jye02/Software/MALSAR/) package. The Avocado data set has not been published yet and is available upon request. CONTACT: dhe@us.ibm.com.

Low wall shear stress predominates at sites of abdominal aortic aneurysm rupture.

OBJECTIVE: Aortic diameter as the primary criterion in the decision to repair abdominal aortic aneurysms (AAAs) has drawbacks as some rupture below size thresholds, whereas others reach extreme size without rupture. Predictions of static aortic wall stress have also failed to reliably predict rupture potential. The objective of this study was to computationally assess blood flow characteristics at the site of infrarenal AAA rupture. On the basis of the finite element literature correlating rupture location with high static local wall stress, we hypothesized that a computational fluid dynamics approach would also demonstrate rupture at regions of high pressure and wall shear stress (WSS). METHODS: Three-dimensional AAA geometry was generated from computed tomography angiography images of seven ruptured AAAs. Aortic blood flow velocity, pressure, and WSS were computationally determined. Flow characteristics at the site of rupture were determined and compared across all cases. RESULTS: AAA size at the time of rupture was 8.3 ± 0.9 cm. Only three of the seven AAAs ruptured at the site of maximal diameter. Blood flow velocity in the aneurysmal aorta showed dominant flow channels with zones of recirculation, where low WSS predominated. Regardless of aneurysm size or configuration, rupture occurred in or near these flow recirculation zones in all cases. WSS was significantly lower and thrombus deposition was more abundant at the site of rupture. CONCLUSIONS: This computational study was the first to assess blood flow characteristics at the site of infrarenal AAA rupture in realistic aortic geometries. In contradiction to our initial hypothesis, rupture occurred not at sites of high pressure and WSS but rather at regions of predicted flow recirculation, where low WSS and thrombus deposition predominated. These findings raise the possibility that this flow pattern may lead to thrombus deposition, which may elaborate adventitial degeneration and eventual AAA rupture.

Relevant parameters for laser surgery of soft tissue.

In recent years, the laser has become an important tool in hospitals. Laser surgery in particular has many advantages. However, there is still a lack of the understanding of the influence of the relevant parameters for laser surgery. In order to fill this gap, the parameters pulse frequency, use of an exhaustion system, air cooling, laser power, laser scan speed, laser line energy and waiting time between cuts were analysed by ANOVA using inter-animal variation as a benchmark. The quality of the cuts was quantized by a previously published scoring system. A total of 1710 cuts were performed with a [Formula: see text] laser. Of the parameters investigated, laser power and scan speed have the strongest influence. Only the right combination of these two parameters allows good results. Other effects, such as the use of pulsed or continuous wave (CW) laser operation, or air cooling, show a small or negligible influence. By modulating only the laser power and scan speed, an almost perfect cut can be achieved with a [Formula: see text] laser, regardless of the external cooling used or the laser pulse duration or repetition rate from CW to nanosecond pulses.

iXora: exact haplotype inferencing and trait association.

BACKGROUND: We address the task of extracting accurate haplotypes from genotype data of individuals of large F1 populations for mapping studies. While methods for inferring parental haplotype assignments on large F1 populations exist in theory, these approaches do not work in practice at high levels of accuracy. RESULTS: We have designed iXora (Identifying crossovers and recombining alleles), a robust method for extracting reliable haplotypes of a mapping population, as well as parental haplotypes, that runs in linear time. Each allele in the progeny is assigned not just to a parent, but more precisely to a haplotype inherited from the parent. iXora shows an improvement of at least 15% in accuracy over similar systems in literature. Furthermore, iXora provides an easy-to-use, comprehensive environment for association studies and hypothesis checking in populations of related individuals. CONCLUSIONS: iXora provides detailed resolution in parental inheritance, along with the capability of handling very large populations, which allows for accurate haplotype extraction and trait association. iXora is available for non-commercial use from http://researcher.ibm.com/project/3430.

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica).

Shellfish, such as the Eastern oyster (Crassostrea virginica), are an important agricultural commodity. Previous research has demonstrated the importance of the native microbiome of oysters against exogenous challenges by non-native pathogens. However, the taxonomic makeup of the oyster microbiome and the impact of environmental factors on it are understudied. Research was conducted quarterly over a calendar year (February 2020 through February 2021) to analyze the taxonomic diversity of bacteria present within the microbiome of consumer-ready-to-eat live Eastern oysters. It was hypothesized that a core group of bacterial species would be present in the microbiome regardless of external factors such as the water temperature at the time of harvest or post-harvesting processing. At each time point, 18 Chesapeake Bay (eastern United States) watershed aquacultured oysters were acquired from a local grocery store, genomic DNA was extracted from the homogenized whole oyster tissues, and the bacterial 16S rRNA gene hypervariable V4 region was PCR-amplified using barcoded primers prior to sequencing via Illumina MiSeq and bioinformatic analysis of the data. A core group of bacteria were identified to be consistently associated with the Eastern oyster, including members of the phyla Firmicutes and Spirochaetota, represented by the families Mycoplasmataceae and Spirochaetaceae, respectively. The phyla Cyanobacterota and Campliobacterota became more predominant in relation to warmer or colder water column temperature, respectively, at the time of oyster harvest.

Promoter insertion leads to polyembryony in mango - a case of convergent evolution with citrus.

Sexual reproduction in plants is the main pathway for creating new genetic combinations in modern agriculture. In heterozygous plants, after the identification of a plant with desired traits, vegetative propagation (cloning) is the primary path to create genetically uniform plants. Another natural plant mechanism that creates genetically uniform plants (clones) is apomixis. In fruit crops like citrus and mango, sporophytic apomixis results in polyembryony, where seeds contain multiple embryos, one of which is sexually originated and the others are vegetative clones of the parent mother tree. Utilizing the mango genome and genetic analysis of a diverse germplasm collection, we identified MiRWP as the gene that causes polyembryony in mango. There is a strong correlation between a specific insertion in the gene's promoter region and altered expression in flowers and developing fruitlets, inducing multiple embryos. The MiRWP gene is an ortholog of CitRWP that causes polyembryony in citrus. Based on the data, we speculate that promoter insertion events, which occurred independently in citrus and mango, induced nucellar embryogenesis. The results suggest convergent evolution of polyembryony in the two species. Further work is required to demonstrate the utility of these genes (mango and citrus) in other biological systems as a tool for the clonal production of other crops.

Interrelationships of petiolar air canal architecture, water depth, and convective air flow in Nymphaea odorata (Nymphaeaceae).

PREMISE OF THE STUDY: Nymphaea odorata grows in water up to 2 m deep, producing fewer larger leaves in deeper water. This species has a convective flow system that moves gases from younger leaves through submerged parts to older leaves, aerating submerged parts. Petiolar air canals are the convective flow pathways. This study describes the structure of these canals, how this structure varies with water depth, and models how convective flow varies with depth. • METHODS: Nymphaea odorata plants were grown at water depths from 30 to 90 cm. Lamina area, petiolar cross-sectional area, and number and area of air canals were measured. Field-collected leaves and leaves from juvenile plants were analyzed similarly. Using these data and data from the literature, we modeled how convective flow changes with water depth. • KEY RESULTS: Petioles of N. odorata produce two central pairs of air canals; additional pairs are added peripherally, and succeeding pairs are smaller. The first three pairs account for 96% of air canal area. Air canals form 24% of petiolar cross-sectional area. Petiolar and air canal cross-sectional areas increase with water depth. Petiolar area scales with lamina area, but the slope of this relationship is lower in 90 cm water than at shallower depths. In our model, the rate of convective flow varied with depth and with the balance of influx to efflux leaves. • CONCLUSIONS: Air canals in N. odorata petioles increase in size and number in deeper water but at a decreasing amount in relation to lamina area. Convective flow also depends on the number of influx to efflux laminae.

Development of a Controlled Laboratory-scale Inoculation System to Study Vibrio parahaemolyticus-oyster Interactions.

Prevalence of seafood-borne gastroenteritis caused by the human pathogen Vibrio parahaemolyticus is increasing globally despite current preventative measures. The United States Centers for Disease Control have designated V. parahaemolyticus as a reportable emerging human pathogen. The Eastern oyster (Crassostrea virginica) is a natural reservoir of the bacterium in marine environments, but little is actually known regarding interactions between oysters and V. parahaemolyticus. Therefore, a laboratory-scale Biosafety Level-2 (BSL2) inoculation system was developed wherein Chesapeake Bay region oysters harvested during summer or winter months, were exposed to the clinical RIMD2210633 strain carrying a chloramphenicol-selective marker (VP RIMDmC). Homogenized whole oyster tissues were spread on selective and differential agar medium to measure viable VP RIMDmC levels. Endogenous Vibrio spp. cell numbers were significantly reduced followed chloramphenicol treatment and this likely contributed to higher VP RIMDmC oyster-associated levels, especially using winter-harvested animals. Summer-harvested oysters had significantly higher existing Vibrio levels and a lower level of artificial oyster-associated VP RIMDmC. Thus, the pre-existing microbiome appears to afford some protection from an external V. parahaemolyticus challenge. Overall, this system successfully enabled controlled manipulation of parameters influencing V. parahaemolyticus-oyster interactions and will be useful in safely testing additional pertinent environmental variables and potential mitigation strategies.

Development and evaluation of a scoring system for assessing incisions in laser surgery.

The idea of laser surgery is nearly as old as the laser itself. From the first trials to modern laser surgery systems, it was and is the aim to selectively cut the tissue in the focus spot without causing harm to surrounding structures. This is only possible when the correct parameters for the surgical laser are chosen. Usually, this is done by parameter studies. However, the concrete evaluation scheme often differs between groups and more precise approaches require staining and microscopic evaluation. To overcome these issues, a macroscopic scoring system is presented and evaluated. It can be shown that the scoring system works well and, thus, a laser cut can be evaluated within a few seconds. At the same time, the whole cutting front is taken into account. The presented scoring system is evaluated by the intra class correlation (ICC). The final agreement between different raters is more than 0.7. Therefore, the scoring system can be used to optimize and evaluate the cutting process and it should be suitable for comparing the results between different groups. Definitely, it can be applied for scoring within a group to enable e.g., a profound statistical analysis for a parameter study.

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6.

BACKGROUND: The fermented dried seeds of Theobroma cacao (cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected. RESULTS: Here, we describe the construction of a BAC-based integrated genetic-physical map of the T. cacao cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size of T. cacao is 374.6 Mbp. A comparative analysis with A. thaliana, V. vinifera, and P. trichocarpa suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the two T. cacao cultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed. CONCLUSIONS: The results presented in this study are a stand-alone resource for functional exploitation and enhancement of Theobroma cacao but are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of the T. cacao genome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.

BACKGROUND: BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. RESULTS: This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. CONCLUSIONS: Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

Increased matrix metalloproteinase 9 activity correlates with flow-mediated intraluminal thrombus deposition and wall degeneration in human abdominal aortic aneurysm.

OBJECTIVE: We have previously demonstrated that human abdominal aortic aneurysm (AAA) rupture occurs in zones of low wall shear stress where flow recirculation and intraluminal thrombus (ILT) deposition are increased. Matrix metalloproteinase-9 (MMP-9) is involved in the pathogenesis of AAA via its lytic effect on collagen and elastin. We hypothesize that flow-mediated ILT deposition promotes increased local inflammatory and MMP-9 activity that leads to AAA wall degeneration. The purpose of this study was to examine the correlation between predicted pulsatile flow dynamics and regional differences in MMP-9, elastin, collagen, and ILT deposition in human AAA. METHODS: Full-thickness aortic tissue samples were collected from 24 patients undergoing open AAA repair. Control infrarenal aortic tissue was obtained from 6 patients undergoing aortobifemoral bypass. Full-thickness aortic tissue and ILT were assessed for MMP-9 levels using a cytokine array assay. Histologic and immunohistochemical assessment of inflammation, collagen and elastin content, and MMP-9 levels were also measured. Three-dimensional AAA geometry was generated from computed tomography angiogram (CTA) images using Mimics software and computational fluid dynamics was used to predict pulsatile aortic blood flow. RESULTS: The majority of AAA showed eccentric ILT deposition which was correlated with predicted recirculation blood flow (R2 = -0.17; P < .05). The regions of high ILT were associated with significant increases in inflammation and loss of elastin and collagen compared with regions of low ILT, or with control tissue. MMP-9 was significantly higher in areas of high ILT deposition compared with areas devoid of ILT. Tissue MMP-9 was correlated with the thickness of ILT deposition (R2 = 0.46; P < .05), and was also present in high levels in thick compared with thin ILT. CONCLUSIONS: We have shown a correlation between flow-mediated ILT deposition with increased tissue levels of MMP-9 activity, increased inflammatory infiltrate, and decreased elastin and collagen content in stereotactically sampled human AAA, suggesting that ILT deposition is associated with local increases in proteolytic activity that may preferentially weaken and promote rupture at selected regions.

A Highly Sensitive Method to Detect Avocado Sunblotch Viroid for the Maintenance of Infection-Free Avocado Germplasm Collections.

The United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Subtropical Horticulture Research Station (SHRS) in Miami, FL holds a large germplasm collection of avocado (Persea americana). The recent threat of infection by laurel wilt has encouraged the creation of a backup collection at a disease-free site. Creating the backup collection is complicated by infection of some trees in the germplasm collection with avocado sunblotch viroid (ASBVd). Infected trees are frequently asymptomatic, necessitating the use of a molecular diagnostic assay. Although a reverse-transcription based assay already exists and has been used to assay all germplasm at the station, some trees showed inconsistent results. We have developed a more sensitive and specific assay involving pre-amplification of the entire viroid cDNA followed by detection using real-time PCR and a TaqMan assay. A second screening of all germplasm identified additional ASBVd -infected trees and allowed us to confidently remove these trees from the station. This method enables avocado germplasm curators to proceed with the creation of a viroid-free backup collection.

Loss of cultural song diversity and the convergence of songs in a declining Hawaiian forest bird community.

The effects of population decline on culturally transmitted behaviours in animals have rarely been described, but may have major implications to population viability. Learned vocal signals in birds are of critical importance to behaviours associated with reproduction, intrasexual interactions and group cohesion, and the complexity of vocal signals such as song can serve as an honest signal of an individual's quality as well as the viability of a population. In this study, we examined how rapid population declines recently experienced by Hawaiian honeycreepers on the island of Kaua'i (USA) may have influenced the diversity, complexity and similarity of learned honeycreeper songs. We analysed the acoustic characteristics of songs recorded during three time periods over a 40-year time frame for three species of declining Kaua'i honeycreepers. We detected a loss of song complexity and diversity over the 40-year time period that paralleled dramatic population declines. Concurrent with the loss of complexity, we also found that the acoustic characteristics of the three honeycreepers' songs became more similar to one another. To our knowledge, this is the first documentation of convergence of acoustic characteristics among rapidly declining species. The reduction in song complexity and diversity and convergence of songs not only signals a loss of culturally transmitted behaviours in these endemic Hawaiian honeycreepers, but also potential challenges to the recovery of these rapidly declining species. Moreover, the present study highlights that there is a 'hidden' cost to declining populations beyond just the loss of individuals that is not often considered, the loss of culturally transmitted social behaviours.