Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories

The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). In both genera, heterodichogamy is controlled by a single dominant allele. We fine-map the locus in each genus, and find two ancient (>50 Mya) structural variants involving different genes that both segregate as genus-wide trans-species polymorphisms. The Juglans locus maps to a ca. 20 kb structural variant adjacent to a probable trehalose phosphate phosphatase (TPPD-1), homologs of which regulate floral development in model systems. TPPD-1 is differentially expressed between morphs in developing male flowers, with increased allele-specific expression of the dominant haplotype copy. Across species, the dominant haplotype contains a tandem array of duplicated sequence motifs, part of which is an inverted copy of the TPPD-1 3' UTR. These repeats generate various distinct small RNAs matching sequences within the 3' UTR and further downstream. In contrast to the single-gene Juglans locus, the Carya heterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in developing flowers. The dominant haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows markedly reduced genetic diversity and is over twice as long as its recessive counterpart due to accumulation of various types of transposable elements. We did not detect either genetic system in other heterodichogamous genera within Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.

SNPs in a Large Genomic Scaffold Are Strongly Associated with Cr1R, Major Gene for Resistance to White Pine Blister Rust in Range-Wide Samples of Sugar Pine (Pinus lambertiana)

Sugar pine, Pinus lambertiana Douglas, is a keystone species of montane forests from Baja California to southern Oregon. Like other North American white pines, populations of sugar pine have been greatly reduced by the disease white pine blister rust (WPBR) caused by a fungal pathogen, Cronartium ribicola, that was introduced into North America early in the twentieth century. Major gene resistance to WPBR segregating in natural populations has been documented in sugar pine. Indeed, the dominant resistance gene in this species, Cr1, was genetically mapped, although not precisely. Genomic single nucleotide polymorphisms (SNPs) placed in a large scaffold were reported to be associated with the allele for this major gene resistance (Cr1^R). Forest restoration efforts often include sugar pine seed derived from the rare resistant individuals (typically Cr1^R/Cr1^r) identified through an expensive 2-year phenotypic testing program. To validate and geographically characterize the variation in this association and investigate its potential to expedite genetic improvement in forest restoration, we developed a simple PCR-based, diploid genotyping of DNA from needle tissue. By applying this to range-wide samples of susceptible and resistant (Cr1^R) trees, we show that the SNPs exhibit a strong, though not complete, association with Cr1^R. Paralleling earlier studies of the geographic distribution of Cr1^R and the inferred demographic history of sugar pine, the resistance-associated SNPs are marginally more common in southern populations, as is the frequency of Cr1^R. Although the strength of the association of the SNPs with Cr1^R and thus, their predictive value, also varies with geography, the potential value of this new tool in quickly and efficiently identifying candidate WPBR-resistant seed trees is clear.

Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays

Viruses are considered of major importance in strawberry (Fragaria × ananassa Duchesne) production given their negative impact on plant vigor and growth. Strawberry accessions from the National Clonal Germplasm Repository were screened for viruses using high throughput sequencing (HTS). Analyses of sequence information from 45 plants identified multiple variants of 14 known viruses, comprising strawberry mottle virus (SMoV), beet pseudo yellows virus (BPYV), strawberry pallidosis-associated virus (SPaV), tomato ringspot virus (ToRSV), strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry crinkle virus (SCV), strawberry polerovirus 1 (SPV-1), apple mosaic virus (ApMV), strawberry chlorotic fleck virus (SCFaV), strawberry crinivirus 4 (SCrV-4), strawberry crinivirus 3 (SCrV-3), Fragaria chiloensis latent virus (FClLV) and Fragaria chiloensis cryptic virus (FCCV). Genetic diversity of sequenced virus isolates was investigated via sequence homology analysis, and partial-genome sequences were deposited into GenBank. To confirm the HTS results and expand the detection of strawberry viruses, new reverse transcription quantitative PCR (RT-qPCR) assays were designed for the above-listed viruses. Further in silico and in vitro validation of the new diagnostic assays indicated high efficiency and reliability. Thus, the occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, additionally, this study describes the design and validation of multiple RT-qPCR assays for strawberry viruses, which represent important detection tools for clean plant programs.

Comparative genomics of six Juglans species reveals disease-associated gene family contractions

Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high-quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance-related wall-associated kinase (WAK), Catharanthus roseus receptor-like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole-genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array

Over the last 20 years, global production of Persian walnut (Juglans regia L.) has grown enormously, likely reflecting increased consumption due to its numerous benefits to human health. However, advances in genome-wide association (GWA) studies and genomic selection (GS) for agronomically important traits in walnut remain limited due to the lack of powerful genomic tools. Here, we present the development and validation of a high-density 700K single nucleotide polymorphism (SNP) array in Persian walnut. Over 609K high-quality SNPs have been thoroughly selected from a set of 9.6 m genome-wide variants, previously identified from the high-depth re-sequencing of 27 founders of the Walnut Improvement Program (WIP) of University of California, Davis. To validate the effectiveness of the array, we genotyped a collection of 1284 walnut trees, including 1167 progeny of 48 WIP families and 26 walnut cultivars. More than half of the SNPs (55.7%) fell in the highest quality class of 'Poly High Resolution' (PHR) polymorphisms, which were used to assess the WIP pedigree integrity. We identified 151 new parent-offspring relationships, all confirmed with the Mendelian inheritance test. In addition, we explored the genetic variability among cultivars of different origin, revealing how the varieties from Europe and California were differentiated from Asian accessions. Both the reconstruction of the WIP pedigree and population structure analysis confirmed the effectiveness of the Applied Biosystems™ Axiom™ J. regia 700K SNP array, which initiates a novel genomic and advanced phase in walnut genetics and breeding.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing

The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing

The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly.

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

Background

The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.

Results

We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.

Conclusions

In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences

Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution.

Comparison of indirect and direct blood pressure monitoring in normotensive swine

The gold standard for blood pressure measurement in pigs is direct monitoring of arterial pressure, but this is an invasive technique adding complexity to surgical procedures. We sought to compare direct measurements obtained via catheterization to more easily-obtained indirect measurements using a sphygmomanometer with an automated cuff. Simultaneous measurements via an arterial pressure transducer and a child-size cuff were performed in pigs undergoing abdominal surgical procedures under normotensive conditions. Correlation between direct and indirect measurements was good (r=0.881). Systolic blood pressures for the cuff were higher than those for arterial measurements, while diastolic pressures were lower for the cuff than arterial. A Bland-Altman analysis confirmed this bias at the extremes of the normotensive range. For highly accurate readings, especially under stressed conditions, direct arterial catheterization remains the preferred method of measuring blood pressure. When monitoring surgical procedures, the more convenient blood pressure cuff can provide reliable measurements.

Validating the Injury Severity Score (ISS) in different populations: ISS predicts mortality better among Hispanics and females

INTRODUCTION

The Injury Severity Score (ISS) is the most commonly used measure of injury severity. The score has been shown to have excellent predictive capability for trauma mortality and has been validated in multiple data sets. However, the score has never been tested to see if its discriminatory ability is affected by differences in race and gender.

OBJECTIVE

This study is aimed at validating the ISS in men and women and in three different race/ethnic groups using a nationwide database.

METHODS

Retrospective analysis of patients age 18-64 y in the National Trauma Data Bank 7.0 with blunt trauma was performed. ISS was categorized as mild (<9,) moderate (9-15), severe (16-25), and profound (>25). Logistic regression was done to measure the relative odds of mortality associated with a change in ISS categories. The discriminatory ability was compared using the receiver operating characteristics curves (ROC). A P value testing the equality of the ROC curves was calculated. Age stratified analyses were also conducted.

RESULTS

A total of 872,102 patients had complete data for the analysis on ethnicity, while 763,549 patients were included in the gender analysis. The overall mortality rate was 3.7%. ROC in Whites was 0.8617, in Blacks 0.8586, and in Hispanics 0.8869. Hispanics have a statistically significant higher ROC (P value < 0.001). Similar results were observed within each age category. ROC curves were also significantly higher in females than in males.

CONCLUSION

The ISS possesses excellent discriminatory ability in all populations as indicated by the high ROCs.

Direct detection of bacterial pathogens in representative dairy products using a combined bacterial concentration-PCR approach

AIMS

To develop a simple, rapid method to concentrate and purify bacteria and their nucleic acids from complex dairy food matrices in preparation for direct pathogen detection using polymerase chain reaction (PCR).

METHODS AND RESULTS

Plain non-fat yogurt and cheddar cheese were each seeded with Listeria monocytogenes or Salmonella enterica serovar. Enteritidis in the range of 10(1)-10(6) CFU per 11-g sample. Samples were then processed for bacterial concentration using high-speed centrifugation (9700 g) followed by DNA extraction, PCR amplification, and amplicon confirmation by hybridization. Bacterial recoveries after centrifugation ranged from 53 to >100% and 71 to >100% for serovar. Enteritidis and L. monocytogenes, respectively, in the non-fat yogurt samples; and from 77 to >100% and 69 to >100% for serovar. Enteritidis and L. monocytogenes, respectively, in the cheddar cheese samples. There were no significant differences in recovery efficiency at different inocula levels, and losses to discarded supernatants were always <5%, regardless of dairy product or pathogen.

CONCLUSIONS

When followed by pathogen detection using PCR and confirmation by amplicon hybridization, detection limits of 10(3) and 10(1) CFU per 11-g sample were achieved for L. monocytogenes and serovar. Enteritidis, respectively, in both product types and without prior cultural enrichment.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study represents progress toward the rapid and efficient direct detection of pathogens from complex food matrices at detection limits approaching those that might be anticipated in naturally contaminated products.

Variations on the Hermann grid: an extinction illusion

When the white disks in a scintillating grid are reduced in size, and outlined in black, they tend to disappear. One sees only a few of them at a time, in clusters which move erratically on the page. Where they are not seen, the grey alleys seem to be continuous, generating grey crossings that are not actually present. Some black sparkling can be seen at those crossings where no disk is seen. The illusion also works in reverse contrast.

Current status of the AbioCor implantable replacement heart

BACKGROUND

The AbioCor implantable replacement heart (IRH) has been developed as an alternative to transplant (ie, destination therapy). We report our experience with the AbioCor IRH in a bovine model at the University of Louisville.

METHODS

Male Holstein cows were used (85 to 115 kg). The internal controller, battery, and secondary transcutaneous energy transfer coil were implanted in the right flank. After cardiopulmonary bypass, the thoracic unit was implanted orthotopically. After removal of air and weaning from cardiopulmonary bypass, the AbioCor was connected to internal components and energy transfer through transcutaneous energy transfer coils was achieved.

RESULTS

Nineteen animals underwent implantation of the AbioCor IRH for a proposed 30-day duration. There were 6 deaths, none related to device malfunction. All animals demonstrated normal hemodynamics with normal pressures in the aorta, pulmonary artery, left atrium, and right atrium. There was no significant hemolysis and all animals demonstrated normal end organ function. The internal battery allowed for brief periods of untethered mobility.

CONCLUSIONS

The AbioCor IRH has resulted in normal hemodynamics and normal end organ function without evidence of hemolysis in a bovine model.

Risedronate pharmacokinetics and intra- and inter-subject variability upon single-dose intravenous and oral administration

PURPOSE

To determine the pharmacokinetics and absolute bioavailability of risedronate after single-dose oral administration of 30 mg risedronate as a tablet and an aqueous solution, and 0.3 mg risedronate as an intravenous infusion.

METHODS

This study was a randomized, three-treatment, four-period, partial replicate crossover study involving 33 healthy volunteers. Treatments were administered 7 weeks apart, and the third treatment was repeated during the fourth period. Serum and urine were collected over 72 hours and 672 hours, respectively.

RESULTS

Following intravenous administration, renal clearance accounted for 87% of total clearance, with 65% of the dose excreted within 24 hours and 85% of the dose excreted within four weeks. The absolute bioavailability was approximately 0.62% after both oral formulations, and the relative bioavailability of the tablet compared with the oral solution was 104%. The rate and extent of absorption from the two formulations were bioequivalent based on the range proposed for highly variable drugs. Intrasubject variability following oral administration was 50-80%, and was primarily associated with absorption.

CONCLUSION

The majority of the total clearance after intravenous administration of risedronate was renal clearance, indicating that only a small percentage of a systemic dose is potentially incorporated, or "cleared," into bone. The absolute bioavailability of orally administered risedronate is approximately 0.6%, and is independent of formulation. Variability in the pharmacokinetics following oral administration is primarily associated with intrasubject variability in absorption.

Neck posture and feeding habits of two jurassic sauropod dinosaurs

Articulated digital reconstructions of two diplodocid sauropods revealed cervical poses and feeding envelopes. The necks of Diplodocus and Apatosaurus were nearly straight but gently declined such that the heads, which were themselves angled downward relative to the neck, were close to ground level in their neutral, undeflected posture. Both necks were less flexible than conventionally depicted, and Diplodocus was less capable of lateral and dorsal curvature than Apatosaurus. The results suggest that these sauropods were adapted to ground feeding or low browsing, contrary to the view that diplodocid sauropods were high browsers.

Design and implementation of a patient classification system for rehabilitation nursing

Development of a prototype patient classification (PCS) instrument designed specifically for rehabilitation patients is the focus of this article. The process of instrument development is discussed, as well as strategies used in implementing the PCS. These strategies include: staff education, management support, data collection, data analysis--including the development of supporting information systems, and ongoing use of the rehabilitation PCS. Changes engendered by implementation of the PCS also are discussed.

Mice deficient for the amyloid precursor protein gene

To understand the in vivo function of the amyloid precursor protein (APP) we generated an APP null mutation in mice by homologous recombination in embryonic stem (ES) cells. We show here that homozygous APP deficient mice were produced at expected frequencies. Neither APP mRNA nor protein could be detected in these animals. Yet the homozygous APP mutant mice are fertile and do not show overt abnormalities at up to 12 weeks of age. Neuroanatomical studies of the brain did not reveal significant differences in the knockout mice as compared to the wild-type controls. These results argue against an essential function of APP in mouse embryonic and early neuronal development.

beta-Amyloid precursor protein-deficient mice show reactive gliosis and decreased locomotor activity

In several pedigrees of early onset familial Alzheimer's disease (FAD), point mutations in the beta-amyloid precursor protein (APP) gene are genetically linked to the disease. This finding implicates APP in the pathogenesis of Alzheimer's disease in these individuals. To understand the in vivo function of APP and its processing, we have generated an APP-null mutation in mice. Homozygous APP-deficient mice were viable and fertile. However, the mutant animals weighed 15%-20% less than age-matched wild-type controls. Neurological evaluation showed that the APP-deficient mice exhibited a decreased locomotor activity and forelimb grip strength, indicating a compromised neuronal or muscular function. In addition, four out of six homozygous mice showed reactive gliosis at 14 weeks of age, suggesting an impaired neuronal function as a result of the APP-null mutation.

Integration by association: combining three-dimensional cues to extrinsic surface shape

Surface shape is visually derived from multiple sources of three-dimensional (3-D) information. The apparent unity of the percept creates an assumption that there are perceptual processes that resolve and combine the different channels of information within some common 3-D representation. However, integration by the explicit conversion of the information from different sources into a common representation is computationally difficult and unnecessary. An alternative, integration by association, is discussed and related to a variety of experimental results on 3-D-cue conflict.

Induction of increased levels of proteoglycan fragments in synovial fluid (SF) and increased levels of stromelysin in cartilage, synovium and SF by intraarticular injection of canine monocyte conditioned medium into dogs

OBJECTIVE

To study the effects of the intraarticular injection of canine monocyte conditioned medium (cMCM) into dogs on proteoglycan fragment and stromelysin levels in the joint.

METHODS

cMCM was injected intraarticularly into dogs, and the levels of proteoglycan fragments in synovial fluid (SF) as well as stromelysin levels in cartilage, synovium, and SF were assessed after 12 h.

RESULTS

There was a 4-fold increase of proteoglycan fragment levels and a 6-fold increase in stromelysin levels in SF, and a 4.4-fold increase in stromelysin levels in cartilage extracts. Elevated mRNA levels were detected in both synovium and cartilage. By immunofluorescence staining, stromelysin was localized in chondrocytes throughout the cartilage and in synovial cells.

CONCLUSION

Intraarticular injection of cMCM stimulated the expression of stromelysin mRNA and protein in cartilage and synovium and caused marked increases in stromelysin protein and proteoglycan fragment levels in SF.

The formation and maintenance of the definitive endoderm lineage in the mouse: involvement of HNF3/forkhead proteins

Little is known about genes that govern the development of the definitive endoderm in mammals; this germ layer gives rise to the intestinal epithelium and various other cell types, such as hepatocytes, derived from the gut. The discovery that the rat hepatocyte transcription factor HNF3 is similar to the Drosophila forkhead gene, which plays a critical role in gut development in the fly, led us to isolate genes containing the HNF3/forkhead (HFH) domain that are expressed in mouse endoderm development. We recovered mouse HNF3 beta from an embryo cDNA library and found that the gene is first expressed in the anterior portion of the primitive streak at the onset of gastrulation, in a region where definitive endoderm first arises. Its expression persists in axial structures derived from the mouse equivalent of Hensen's node, namely definitive endoderm and notochord, and in the ventral region of the developing neural tube. Expression of the highly related gene, HNF3 alpha, appears to initiate later than HNF3 beta and is first seen in midline endoderm cells. Expression subsequently appears in notochord, ventral neural tube, and gut endoderm in patterns similar to HNF3 beta. Microscale DNA binding assays show that HNF3 proteins are detectable in the midgut at 9.5 days p.c. At later stages HNF3 mRNAs and protein are expressed strongly in endoderm-derived tissues such as the liver. HNF3 is also the only known hepatocyte-enriched transcription factor present in a highly de-differentiated liver cell line that retains the capacity to redifferentiate to the hepatic phenotype. Taken together, these studies suggest that HNF3 alpha and HNF3 beta are involved in both the initiation and maintenance of the endodermal lineage. We also discovered a novel HFH-containing gene, HFH-E5.1, that is expressed transiently in posterior ectoderm and mesoderm at the primitive streak stage, and later predominantly in the neural tube. HFH-E5.1 is highly similar in structure and expression profile to the Drosophila HFH gene FD4, suggesting that HFH family members have different, evolutionarily conserved roles in development.

Choosing a Career: Why Not Nursing for More High School Seniors?

Using a descriptive design, 641 college-bound high school seniors (CBHSS) in the Washington, DC, metropolitan area were surveyed to determine why nursing is not selected more frequently as a career. The findings indicated that the decision to choose or not choose nursing was significantly influenced by demographic characteristics (age, ethnicity, and race), past experiences with nurses/illness, and characteristics preferred in a future career. Those respondents who selected nursing cited wanting to help people, to do important work, and to work with a variety of people as important reasons for their choice. Those not choosing nursing indicated dislike of dying people and the salary as the main reasons for choosing another career.

Low density lipoprotein is protected from oxidation and the progression of atherosclerosis is slowed in cholesterol-fed rabbits by the antioxidant N,N'-diphenyl-phenylenediamine

The oxidative modification of low density lipoprotein (LDL) may play an important role in atherosclerosis. We found that the antioxidant N,N'-diphenyl-1,4-phenylenediamine (DPPD) inhibits in vitro LDL oxidation at concentrations much lower than other reported antioxidants. To test whether DPPD could prevent atherosclerosis, New Zealand White rabbits were fed either a diet containing 0.5% cholesterol and 10% corn oil (control group) or the same diet also containing 1% DPPD (DPPD-fed group) for 10 wk. Plasma total cholesterol levels were not different between the two groups, but DPPD feeding increased the levels of triglyceride (73%, P = 0.007) and HDL cholesterol (26%, P = 0.045). Lipoproteins from DPPD-fed rabbits contained DPPD and were much more resistant to oxidation than control lipoproteins. After 10 wk, the DPPD-fed animals had less severe atherosclerosis than did the control animals: thoracic aorta lesion area was decreased by 71% (P = 0.0007), and aortic cholesterol content was decreased by 51% (P = 0.007). Although DPPD cannot be given to humans because it is a mutagen, our results indicate that orally active antioxidants can have antiatherosclerotic activity. This strongly supports the theory that oxidized LDL plays an important role in the pathogenesis of atherosclerosis.

Antimicrobial action of nisin against Salmonella typhimurium lipopolysaccharide mutants

The antimicrobial activity of nisin against outer membrane lipopolysaccharide mutants of Salmonella typhimurium LT2 was investigated. Nisin sensitivity was associated with the extent of saccharide deletions from the outer membrane core oligosaccharide. The results indicated that the core oligosaccharide in lipopolysaccharide plays a role in nisin sensitivity.

Nisin treatment for inactivation of Salmonella species and other gram-negative bacteria

Nisin, produced by Lactococcus lactis subsp. lactis, has a broad spectrum of activity against gram-positive bacteria and is generally recognized as safe in the United States for use in selected pasteurized cheese spreads to control the outgrowth and toxin production of Clostridium botulinum. This study evaluated the inhibitory activity of nisin in combination with a chelating agent, disodium EDTA, against several Salmonella species and other selected gram-negative bacteria. After a 1-h exposure to 50 micrograms of nisin per ml and 20 mM disodium EDTA at 37 degrees C, a 3.2- to 6.9-log-cycle reduction in population was observed with the species tested. Treatment with disodium EDTA or nisin alone produced no significant inhibition (less than 1-log-cycle reduction) of the Salmonella and other gram-negative species tested. These results demonstrated that nisin is bactericidal to Salmonella species and that the observed inactivation can be demonstrated in other gram-negative bacteria. Applications involving the simultaneous treatment with nisin and chelating agents that alter the outer membrane may be of value in controlling food-borne salmonellae and other gram-negative bacteria.

Combining binocular and monocular curvature features

A study is reported of the perception of visual surfaces in wire-frame stimuli generated by combinations of monocular surface contours and binocular disparity that provide differing information about 3-D relief. Observers vary considerably in the relative contribution made by the binocular and monocular cues to the perception of overall 3-D form. Without training, many observers may entirely fail to perceive surface curvature from the binocular disparity patterns, interpreting the form of the surface only according to the monocular information. For other observers, both cues contribute to the end percept, with the monocular interpretation dominating where the disparity information indicates planarity and with disparity dominating where disparity information suggests curvature and the monocular interpretation suggests planarity. Where stereo and monocular interpretations indicate inconsistent surface curvature features at a common location, more complex resolution strategies are suggested.

Selection and analysis of galactose metabolic pathway variants of a mouse liver cell line

To study the genetic expression and regulation of galactose-metabolizing enzymes, we mutagenized the mouse liver H2.35 cell line and selected for cell clones resistant to the toxic galactose analog, 2-deoxy-D-galactose (2-DOG). One cloned line, designated H12.10, was stably resistant to high levels of 2-DOG and was completely deficient in galactokinase activity. Galactokinase activity and growth sensitivity to 2-DOG could be restored by transfecting H12.10 cells with a plasmid containing the Escherichia coli galactokinase (galK) gene fused to a eucaryotic promoter; thus, the 2-DOG selection could be directed against transfected recombinant constructs in a liver cell line. We also found that H2.35 cells could not utilize galactose as a primary carbon source because of a deficiency in galactose-1-phosphate uridyltransferase; a variant line of H2.35 cells selected in galactose medium expressed higher levels of uridyltransferase activity. Finally, we found that in all mammalian cell lines tested, galactokinase expression was the same whether the medium contained glucose, galactose, or both sugars. These studies demonstrate differences between mammalian cells and yeast cells in the regulation of gal enzymes, and they define different schemes for obtaining altered expression of genes in the galactose metabolic pathway. The isogenic liver cell lines described here can also serve as model systems for studying galactosemias, which are inherited disorders of galactose metabolism in humans.

Communicating with Asian patients

Images

The analogy between stereo depth and brightness

Apparent depth in stereograms exhibits various simultaneous-contrast and induction effects analogous to those reported in the luminance domain. This behavior suggests that stereo depth, like brightness, is reconstructed, ie recovered from higher-order spatial derivatives or differences of the original signal. The extent to which depth is analogous to brightness is examined. There are similarities in terms of contrast effects but dissimilarities in terms of the lateral inhibition effects traditionally attributed to underlying spatial-differentiation operators.

Binocular depth from surfaces versus volumes

Subjects were asked to compare the relative depths of two binocular targets embedded in different random dot stereogram backgrounds. The disparities of the background points were either randomized, corresponding to a scattering of points within a volume, or arranged according to a sawtooth (triangle-wave) disparity profile (i.e., a set of slanted planar surfaces separated by sharp depth discontinuities). When the targets were embedded in the random volume, their depths were perceived in accordance with their relative disparities. But when the target points were embedded in the sawtooth surfaces their depths were systematically misperceived in a manner predicted by the incorrect depth interpretation of the background points. Rather than seeing a sawtooth pattern, the background points resembled a staircase in depth, and the targets, which appeared embedded in different steps, were misjudged in depth accordingly. The effect suggests a distinction between the depth processing of isolated binocular features and those associated with continuous surfaces.

Binocular depth from surfaces versus volumes

Subjects were asked to compare the relative depths of two binocular targets embedded in different random dot stereogram backgrounds. The disparities of the background points were either randomized, corresponding to a scattering of points within a volume, or arranged according to a sawtooth (triangle-wave) disparity profile (i.e., a set of slanted planar surfaces separated by sharp depth discontinuities). When the targets were embedded in the random volume, their depths were perceived in accordance with their relative disparities. But when the target points were embedded in the sawtooth surfaces their depths were systematically misperceived in a manner predicted by the incorrect depth interpretation of the background points. Rather than seeing a sawtooth pattern, the background points resembled a staircase in depth, and the targets, which appeared embedded in different steps, were misjudged in depth accordingly. The effect suggests a distinction between the depth processing of isolated binocular features and those associated with continuous surfaces.

Nursing diagnoses in wellness childbearing settings

Although most nurses recognize the benefits of nursing diagnoses, difficulties surrounding clinical application of the NANDA system have often occurred. Many nurses feel that the NANDA system focuses mainly on illness or problem diagnoses, which makes application to healthy processes and areas such as childbearing more difficult. Examples of the flexibility of the NANDA system for stating diagnoses involving healthy processes as well as illness/problem diagnoses for postpartum clients are cited to illustrate that with simple modifications and in combination with a conceptual framework, this system can be used to formulate individualized diagnoses in childbearing settings.

The concave cusp as a determiner of figure-ground

The tendency to interpret as figure, relative to background, those regions that are lighter, smaller, and, especially, more convex is well known. Wherever convex opaque objects abut or partially occlude one another in an image, the points of contact between the silhouettes form concave cusps, each indicating the local assignment of figure versus ground across the contour segments. It is proposed that this local geometric feature is a preattentive determiner of figure-ground perception and that it contributes to the previously observed tendency for convexity preference. Evidence is presented that figure-ground assignment can be determined solely on the basis of the concave cusp feature, and that the salience of the cusp derives from local geometry and not from adjacent contour convexity.

Integrating stereopsis with monocular interpretations of planar surfaces

Experiments are reported that involved spatial judgments of planar surfaces that had contradictory stereo and monocular information. Tasks included comparing the relative depths of two points on the depicted surface and judging the surface's apparent spatial orientation. It was found that for planar surfaces the 3D perception was dominated by the monocular interpretation, despite the strongly contradictory stereo information. We propose that stereo information is effectively integrated only where the surface exhibits curvature features or edge discontinuities, i.e. where the second spatial derivatives of disparity are nonzero. Planar surfaces induce constant gradients of disparity and are thus effectively featureless to stereopsis. Further observations are reported regarding nonplanar surfaces, where contradictory monocular information can still be effectively rivalrous with that suggested stereoscopically.

On gradients and texture "gradients"

Texture gradients, systematic variations in image texture due to perspective projection of surface texture, provide information about the shape and disposition of surfaces relative to a viewer. Although this three-dimensional information is usually described in terms of mathematical relationships involving gradients of image properties (Cutting & Millard, 1984), the perceptual processes that derive this information need not necessarily measure or register these gradients explicitly (Stevens, 1981). It is difficult to conclude, therefore, that the perception of, say, flatness or curvature derives from processes that capitalize on these gradient relationships, per se. The difficulty becomes most apparent when attempting to formalize the perceptual computations and the spatial information that is made explicit.

Multiple endocrine neoplasia, type I. Association with marfanoid habitus, optic atrophy, and other abnormalities

A patient had a parathyroid adenoma and prolactin-secreting pituitary tumor, suggestive of the multiple endocrine neoplasia (MEN) I syndrome. The presence of a marfanoid habitus--found more typically in MEN III syndrome--as well as mitral valve prolapse, mental retardation, and bilateral optic atrophy suggests a new variant of the MEN syndrome, possibly representing widespread dysplasia of endocrine and other tissues.

Evidence relating subjective contours and interpretations involving interposition

Subjective contours, according to one theory, outline surfaces that are apparently interposed between the viewer and background (because of the disruption of background figures, sudden termination of lines, and other interposition 'cues') but are not explicitly outlined by intensity discontinuities. This theory predicts that if the cues are not interpreted as evidence of interposition, no intervening surface need be postulated, hence no subjective contours would be seen. This prediction, however, is difficult to test because observers normally interpret the cues as interposition evidence and normally see the subjective contours. Tests are reported on a patient with visual agnosia who is unable to make the usual interposition interpretations and unable to see subjective contours, but has normal ability to interpret standard visual illusions, stereograms, and in particular, stereogram versions of the standard subjective contour figures, which elicit to him strong subjective edges in depth (corresponding to the subjective contours viewed in the monocular versions of the figures.

Slant-tilt: the visual encoding of surface orientation

A specific form for the internal representation of local surface orientation is proposed, which is similar to Gibson's (1950) "amount and direction of slant". Slant amount is usually quantified by the angle sigma between the surface normal and the line of sight (0 degrees less than or equal to sigma less than or equal to 90 degrees). Slant direction corresponds to the direction of the gradient of distance from the viewer to the surface, and may be defined by the image direction tau to which the surface normal would project (0 degrees less than or equal to tau less than or equal to 360 degrees). Since the direction of slant is specified by the tilt of the projected surface normal, it is referred to as surface tilt (Stevens, 1979; Marr, 1982). The two degrees of freedom of orientation are therefore quantified by slant, an angle measured perpendicular to the image plane, and tilt, an angle measured in the image plane. The slant-tilt form provides several computational advantages relative to some other proposals and is consistent with various psychological phenomena. Slant might be encoded by various means, e.g. by the cosine of the angle, by the tangent, or linearly by the angle itself. Experimental results are reported that suggest that slant is encoded by an internal parameter that varies linearly with slant angle, with resolution of roughly one part in 100. Thus we propose that surface orientation is encoded in human vision by two quantities, one varying linearly with slant angle, the other varying linearly with tilt angle.

The information content of texture gradients

Texture gradients are systematic variations in projected surface texture. It is expected that image variables such as texture density or size carry information about the surface orientation and distance. This article reexamines the information content of texture gradients and reviews the relevant psychophysics. Slant is shown to be difficult to infer from a texture gradient, but tilt (the direction of slant) is easily and reliably determined. Regarding distance, a new texture measure is introduced that has a simple geometric definition, and from which distance can be readily computed. Variables affecting the precision and the accuracy of the distance computation are discussed.