Detection of subclinical hemorrhage using electrical impedance: a porcine study.

Objective.Analyze the performance of electrical impedance tomography (EIT) in an innovative porcine model of subclinical hemorrhage and investigate associations between EIT and hemodynamic trends.Approach. Twenty-five swine were bled at slow rates to create an extended period of subclinical hemorrhage during which the animal's heart rate (HR) and blood pressure (BP) remained stable from before hemodynamic deterioration, where stable was defined as <15% decrease in BP and <20% increase in HR-i.e.hemorrhages were hidden from standard vital signs of HR and BP. Continuous vital signs, photo-plethysmography, and continuous non-invasive EIT data were recorded and analyzed with the objective of developing an improved means of detecting subclinical hemorrhage-ideally as early as possible.Main results. Best area-under-the-curve (AUC) values from comparing bleed to no-bleed epochs were 0.96 at a 80 ml bleed (∼15.4 min) using an EIT-data-based metric and 0.79 at a 120 ml bleed (∼23.1 min) from invasively measured BP-i.e.the EIT-data-based metric achieved higher AUCs at earlier points compared to standard clinical metrics without requiring image reconstructions.Significance.In this clinically relevant porcine model of subclinical hemorrhage, EIT appears to be superior to standard clinical metrics in early detection of hemorrhage.

Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress-adapted Arabidopsis halleri.

Heavy metal-rich toxic soils and ordinary soils are both natural habitats of Arabidopsis halleri, a diploid perennial and obligate outcrosser in the sister clade of the genetic model plant Arabidopsis thaliana. The molecular divergence underlying survival in sharply contrasting environments is unknown. Here we comparatively address metal physiology and transcriptomes of A. halleri originating from the most highly heavy metal-contaminated soil in Europe, Ponte Nossa, Italy (Noss), and from non-metalliferous (NM) soils. Plants from Noss exhibit enhanced hypertolerance and attenuated accumulation of cadmium (Cd), and their transcriptomic Cd responsiveness is decreased, compared to plants of NM soil origin. Among the condition-independent transcriptome characteristics of Noss, the most highly overrepresented functional class of 'meiotic cell cycle' comprises 21 transcripts with elevated abundance in vegetative tissues, in particular Argonaute 9 (AGO9) and the synaptonemal complex transverse filament protein-encoding ZYP1a/b. Increased AGO9 transcript levels in Noss are accompanied by decreased long terminal repeat retrotransposon expression. Similar to Noss, plants from other highly metalliferous sites in Poland and Germany share elevated somatic AGO9 transcript levels in comparison to plants originating from NM soils in their respective geographic regions. Transcript levels of Iron-Regulated Transporter 1 (IRT1) are very low and transcript levels of Heavy Metal ATPase 2 (HMA2) are strongly elevated in Noss, which can account for its altered Cd handling. We conclude that in plants adapted to the most extreme abiotic stress, broadly enhanced functions comprise genes with likely roles in somatic genome integrity maintenance, accompanied by few alterations in stress-specific functional networks.

Dissecting the Genetic Basis of Local Adaptation in Soybean.

Soybean (Glycine max) is the most widely grown oilseed in the world and is an important source of protein for both humans and livestock. Soybean is widely adapted to both temperate and tropical regions, but a changing climate demands a better understanding of adaptation to specific environmental conditions. Here, we explore genetic variation in a collection of 3,012 georeferenced, locally adapted landraces from a broad geographical range to help elucidate the genetic basis of local adaptation. We used geographic origin, environmental data and dense genome-wide SNP data to perform an environmental association analysis and discover loci displaying steep gradients in allele frequency across geographical distance and between landrace and modern cultivars. Our combined application of methods in environmental association mapping and detection of selection targets provide a better understanding of how geography and selection may have shaped genetic variation among soybean landraces. Moreover, we identified several important candidate genes related to drought and heat stress, and revealed important genomic regions possibly involved in the geographic divergence of soybean.

Vitamin Variation in Capsicum Spp. Provides Opportunities to Improve Nutritional Value of Human Diets.

Chile peppers, native to the Americas, have spread around the world and have been integrated into the diets of many cultures. Much like their heat content, nutritional content can vary dramatically between different pepper types. In this study, a diverse set of chile pepper types were examined for nutrient content. Some pepper types were found to have high levels of vitamin A, vitamin C, or folate. Correlations between nutrient content, species, cultivation status, or geographic region were limited. Varietal selection or plant breeding offer tools to augment nutrient content in peppers. Integration of nutrient rich pepper types into diets that already include peppers could help combat nutrient deficiencies by providing a significant portion of recommended daily nutrients.

Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants.

BACKGROUND: The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS: On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS: Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans.

Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.

Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean.

Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.

A roadmap for functional structural variants in the soybean genome.

Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.

Targeted mutagenesis for functional analysis of gene duplication in legumes.

Assessment of gene function oftentimes requires mutant populations that can be screened by forward or reverse genetic analysis. The situation becomes more complicated in polyploidy or paleopolyploid genomes that have two or more copies for most genes. Here we describe a method for engineering zinc-finger nucleases (ZFNs) for the purpose of creating targeted mutations in the paleopolyploid soybean genome. ZFNs are recombinant proteins composed of an engineered zinc-finger array fused to a nonspecific cleavage domain. When engineered to recognize a specific nucleotide sequence, the cleavage domain will generate highly mutagenic DNA double-strand breaks frequently resulting in insertions and deletions at the target locus. Depending on the number of target sites present within the genome, this method has the capacity to target either single- or multi-copy gene families. In this chapter, we describe an inexpensive, rapid, and user-friendly approach for ZFN assembly and application in soybean based on the previously described context-dependent assembly method.

Structural variants in the soybean genome localize to clusters of biotic stress-response genes.

Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural and gene content variations were assessed among four soybean (Glycine max) genotypes using array hybridization and targeted resequencing. Many chromosomes exhibited relatively low rates of structural variation (SV) among genotypes. However, several regions exhibited both copy number and presence-absence variation, the most prominent found on chromosomes 3, 6, 7, 16, and 18. Interestingly, the regions most enriched for SV were specifically localized to gene-rich regions that harbor clustered multigene families. The most abundant classes of gene families associated with these regions were the nucleotide-binding and receptor-like protein classes, both of which are important for plant biotic defense. The colocalization of SV with plant defense response signal transduction pathways provides insight into the mechanisms of soybean resistance gene evolution and may inform the development of new approaches to resistance gene cloning.

Early opacification and subsequent in vivo clearing of a silicone intraocular lens.

OBJECTIVE: To report a case of early opacification and spontaneous in vivo clearing of a silicone intraocular lens (IOL). METHODS: A 79-year-old women underwent uncomplicated cataract extraction and subsequent implantation of a +21.5 D AMO Z9002 (Abbott Medical Optics, Santa Ana, CA) silicone lens. RESULTS: On postoperative day 1, the patient presented with a translucent, milky white appearing, diffuse IOL opacification. On postoperative day 8, the IOL periphery had cleared, but a full thickness haze persisted in the central portion of the optic. By postoperative day 14, the IOL had cleared. To date, the lens has remained clear. CONCLUSION: One possible mechanism might be exposure to industrial chemicals; however, the manufacturer reports no other similar lens opacities from this manufacturing batch of IOLs. We recommend that surgeons who implant or have implanted an AMO Z9002 silicone IOL and observe similar findings follow the patient closely for resolution of the haze.

Serious complications of cosmetic NewColorIris implantation.

PURPOSE: This case report describes serious postoperative complications and markedly elevated intraocular pressure (IOP) associated with the NewColorIris cosmetic implant. METHODS: We report an interventional case series of two patients who suffered multiple complications after NewColorIris implantation carried out in Panama. Assessment included visual acuity, photography, endothelial cell count and anterior segment optical coherence tomography (OCT) when possible. RESULTS: Both patients presented with endothelial cell loss, uveitis, pigment dispersion and elevated IOP. Anterior segment OCT demonstrated irregularities in the position and configuration of the implants within the anterior chamber with resultant areas of implant-iris and implant-endothelial contact. One patient had acute postoperative hyphaema that resolved with anterior chamber tissue plasminogen activator injection. Both patients required explantation OU, one eye has required trabeculectomy, and one eye with bullous keratopathy is being evaluated for Descemet's stripping endothelial keratoplasty. CONCLUSIONS: Implantation of the NewColorIris cosmetic implant can lead to serious complications including hyphaema, uncontrolled IOP, severe endothelial cell loss, bullous keratopathy and anterior uveitis. Explantation may lead to improvement, but permanent damage to the trabecular meshwork and corneal endothelium persists.

In situ nuclear disassembly: efficient phacoemulsification without nuclear rotation using lateral sweep sculpting and in situ cracking techniques.

We describe an in situ nuclear disassembly technique using a simplified form of sculpting and cracking, enhanced by phacoemulsification technology with a Kelman-style tip. The technique does not require mobilization or rotation of the nucleus within the capsular bag, and hydrodissection is optional. The technique requires a Kelman-style curved tip and Kuglen hook and takes advantage of the versatility of the curved phacoemulsification needle for sculpting and cracking. Since in situ nuclear disassembly requires no rotation of the nucleus for extraction, it is useful in cases in which zonules are compromised or the surgeon suspects posterior lenticonus and the potential for loss of integrity of the posterior capsule.

Opaque contact lens treatment for older children with amblyopia.

PURPOSE: To investigate the usefulness of daily-wear opaque contact lens treatment for older children with amblyopia. METHODS: A retrospective chart review of all children undergoing opaque contact lens therapy for amblyopia between 2000 and 2003 was performed. All patients were included except for those younger than 5 years of age, those undergoing maintenance treatment only, those lost to follow-up, or those unable to cooperate with Snellen visual acuity testing. RESULTS: Thirteen children were identified, and seven met the inclusion criteria. The seven patients had a mean age of 7.5 years (range, 5.7-8.7 years). The causes of amblyopia were anisometropia (five patients), cataract (one patient), and strabismus (one patient). For all seven patients, the mean logMAR improvement in visual acuity was 0.52 (range, 0.26-1.22). The average duration of opaque contact lens use was 9.3 months (range, 2-21 months). Compliance problems were encountered in three patients. No major complications occurred, but one patient had an episode of mild superficial punctate keratitis. CONCLUSIONS: Daily-wear opaque contact lens treatment is a useful occlusion method for amblyopia treatment in older children with various practical and social impediments to skin patching. Meaningful improvement in visual acuity can be obtained, even in children older than 8 years of age.

Comparison of Colvard pupillometer and infrared digital photography for measurement of the dark-adapted pupil diameter.

PURPOSE: To investigate the accuracy of pupil diameter measurement using the Colvard pupillometer and to determine the learning curve for inexperienced examiners. SETTING: Texas Tech University Health Sciences Center, Lubbock, Texas, USA. METHODS: In this population study, subjects with normal pupillary behavior were tested by 1 of 2 investigators (examiner A, examiner B). After 5 minutes of dark adaptation at 1 lux, digital infrared pupil photography of the right eye was performed, followed by measurement of the horizontal pupil diameter and vertical pupil diameter with the Colvard pupillometer. The photographs were digitally analyzed to determine the horizontal and vertical pupil diameters. During phase I of the study, examiners were masked to the results of infrared pupil photography; during phase II, they reviewed the infrared pupil photography results after each testing session. Bland-Altman plots were created to detect measurement bias; results were graphed by subject test sequence to assess learning. A test difference of less than +/-0.5 mm was considered clinically acceptable. RESULTS: Fifty-nine subjects were tested in phase I, of whom 39 had adequate infrared pupil photography for analysis; 40 were tested in phase II, of whom 34 were included. The mean age of the analyzed subjects was 27 years (range 18 to 44 years). For all subjects, the infrared pupil photography median horizontal pupil diameter was 7.09 mm +/- 0.75 (SD) (range 5.44 to 8.79 mm); the median vertical pupil diameter was 7.22 +/- 0.79 mm (range 5.45 to 9.10 mm). Examiner A initially had a negative bias (Colvard pupillometer value less than infrared pupil photography value) for both horizontal and vertical pupil diameter measurements, which resolved during phase I after 23 subjects were tested; 18 of the final 19 subjects tested (11 phase I, 8 phase II) showed a test difference of less than 0.5 mm for all readings. The pupil diameter did not affect the bias. Examiner B had a strong positive bias that persisted throughout the study. Testing 26 subjects in 5 sessions during phase II did not improve the accuracy. During the final testing session, 3 of 8 subjects had a test difference of 0.5 mm or more in at least 1 dimension. The pupil diameter did not affect the bias. CONCLUSION: The Colvard pupillometer is susceptible to user errors causing unidirectional bias and seems to have a steep and variable learning curve.