Next generation crop models: A modular approach to model early vegetative and reproductive development of the common bean (Phaseolus vulgaris L).

The next generation of gene-based crop models offers the potential of predicting crop vegetative and reproductive development based on genotype and weather data as inputs. Here, we illustrate an approach for developing a dynamic modular gene-based model to simulate changes in main stem node numbers, time to first anthesis, and final node number on the main stem of common bean (Phaseolus vulgaris L.). In the modules, these crop characteristics are functions of relevant genes (quantitative trait loci (QTL)), the environment (E), and QTL × E interactions. The model was based on data from 187 recombinant inbred (RI) genotypes and the two parents grown at five sites (Citra, FL; Palmira, Colombia; Popayan, Colombia; Isabela Puerto Rico; and Prosper, North Dakota). The model consists of three dynamic QTL effect models for node addition rate (NAR, No. d- 1), daily rate of progress from emergence toward flowering (RF), and daily maximum main stem node number (MSNODmax), that were integrated to simulate main stem node number vs. time, and date of first flower using daily time steps. Model evaluation with genotypes not used in model development showed reliable predictions across all sites for time to first anthesis (R2 = 0.75) and main stem node numbers during the linear phase of node addition (R2 = 0.93), while prediction of the final main stem node number was less reliable (R2 = 0.27). The use of mixed-effects models to analyze multi-environment data from a wide range of genotypes holds considerable promise for assisting development of dynamic QTL effect models capable of simulating vegetative and reproductive development.

Chromosomal microarray provides enhanced targetable gene aberration detection when paired with next generation sequencing panel in profiling lung and colorectal tumors.

The development of targeted therapies based on specific genomic alterations has altered the treatment and management of lung and colorectal cancers. Chromosomal microarray (CMA) has allowed identification of copy number variations (CNVs) in lung and colorectal cancers in great detail, and next-generation sequencing (NGS) is used extensively to analyze the genome of cancers for molecular subtyping and use of molecularly guided therapies. The main objective of this study was to evaluate the utility of combining CMA and NGS for a comprehensive genomic assessment of lung and colorectal adenocarcinomas, especially for detecting drug targets. We compared the results from NGS and CMA data from 60 lung and 51 colorectal tumors. From CMA analysis, 33% were amplified, 89% showed gains, 75% showed losses and 41% demonstrated loss of heterozygosity; pathogenic variants were identified in 81% of colon and 67% lung specimens through NGS. KRAS mutations commonly occurred with loss in TP53 and there was significant loss of BRCA1 and NF1 among male patients with lung cancer. For clinically actionable targets, 23% had targetable CNVs when no pathogenic variants were detected by NGS. The data thus indicate that combining the two approaches provides significant benefit in a routine clinical setting not available by NGS alone.

Lyme neuroborreliosis: a treatable cause of acute ocular motor disturbances in children.

BACKGROUND: Lyme neuroborreliosis (LNB) designates central nervous system involvement caused by the tick-borne spirochaete Borrelia burgdorferi (Bb). The present study describes a spectrum of acquired ocular motor disorders in children with LNB. METHODS: Six paediatric patients (age 3-15 years) with ocular motor symptoms as first manifestations of LNB evaluated by a paediatrician and ophthalmologist are presented. Diagnosis was based on new onset ocular motor disturbances and detection of cerebrospinal fluid (CSF) pleocytosis and intrathecal synthesis of Bb IgM and/or IgG antibodies by lumbar puncture. The children were evaluated before and after antibiotic treatment with a follow-up time of 1-7 months. Videos were obtained both pre and post treatment in four patients. RESULTS: Two children presented with acquired nystagmus, one with combined nystagmus and partial sixth nerve palsy, one with partial sixth nerve palsy, one with ptosis and one with Adie's pupil. Five of the patients presented with severe fatigue, malaise, nausea, headache and fever. Four had recognised a tick bite recently, and two developed erythema migrans. Intrathecal synthesis of IgM and/or IgG antibodies specific for Bb was positive in all children, and five showed CSF pleocytosis. Cerebral MRI or CT of the brain were normal. Treatment with intravenous or oral antibiotics produced rapid clinical improvement in five of the six children. CONCLUSIONS: LNB can present as acute ocular motor disorders in conjunction with fatigue and other clinical manifestations. In endemic areas, children with unexplained, acquired ocular motor abnormalities should be evaluated for LNB, a treatable medical condition.

Brain and testicular tumors in mice with progenitor cells lacking BAX and BAK.

The proapoptotic BCL-2 family proteins BAX and BAK serve as essential gatekeepers of the intrinsic apoptotic pathway and, when activated, transform into pore-forming homo-oligomers that permeabilize the mitochondrial outer membrane. Deletion of Bax and Bak causes marked resistance to death stimuli in a variety of cell types. Bax(-/-)Bak(-/-) mice are predominantly non-viable and survivors exhibit multiple developmental abnormalities characterized by cellular excess, including accumulation of neural progenitor cells in the periventricular, hippocampal, cerebellar and olfactory bulb regions of the brain. To explore the long-term pathophysiological consequences of BAX/BAK deficiency in a stem cell niche, we generated Bak(-/-) mice with conditional deletion of Bax in Nestin-positive cells. Aged Nestin(Cre)Bax(fl/fl)Bak(-/-) mice manifest progressive brain enlargement with a profound accumulation of NeuN- and Sox2-positive neural progenitor cells within the subventricular zone (SVZ). One-third of the mice develop frank masses comprised of neural progenitors, and in 20% of these cases, more aggressive, hypercellular tumors emerged. Unexpectedly, 60% of Nestin(Cre)Bax(fl/fl)Bak(-/-) mice harbored high-grade tumors within the testis, a peripheral site of Nestin expression. This in vivo model of severe apoptotic blockade highlights the constitutive role of BAX/BAK in long-term regulation of Nestin-positive progenitor cell pools, with loss of function predisposing to adult-onset tumorigenesis.

Abnormal metabolic brain networks in Tourette syndrome.

OBJECTIVES: To identify metabolic brain networks that are associated with Tourette syndrome (TS) and comorbid obsessive-compulsive disorder (OCD). METHODS: We utilized [(18)F]-fluorodeoxyglucose and PET imaging to examine brain metabolism in 12 unmedicated patients with TS and 12 age-matched controls. We utilized a spatial covariance analysis to identify 2 disease-related metabolic brain networks, one associated with TS in general (distinguishing TS subjects from controls), and another correlating with OCD severity (within the TS group alone). RESULTS: Analysis of the combined group of patients with TS and healthy subjects revealed an abnormal spatial covariance pattern that completely separated patients from controls (p < 0.0001). This TS-related pattern (TSRP) was characterized by reduced resting metabolic activity of the striatum and orbitofrontal cortex associated with relative increases in premotor cortex and cerebellum. Analysis of the TS cohort alone revealed the presence of a second metabolic pattern that correlated with OCD in these patients. This OCD-related pattern (OCDRP) was characterized by reduced activity of the anterior cingulate and dorsolateral prefrontal cortical regions associated with relative increases in primary motor cortex and precuneus. Subject expression of OCDRP correlated with the severity of this symptom (r = 0.79, p < 0.005). CONCLUSION: These findings suggest that the different clinical manifestations of TS are associated with the expression of 2 distinct abnormal metabolic brain networks. These, and potentially other disease-related spatial covariance patterns, may prove useful as biomarkers for assessing responses to new therapies for TS and related comorbidities.

Omega-3 fatty acid effect on alveolar bone loss in rats.

Gingival inflammation and alveolar bone resorption are hallmarks of adult periodontitis, elicited in response to oral micro-organisms such as Porphyromonas gingivalis. We hypothesized that omega (omega)-3 fatty acids (FA) dietary supplementation would modulate inflammatory reactions leading to periodontal disease in infected rats. Rats were fed fish oil (omega-3 FA) or corn oil (n-6 FA) diets for 22 weeks and were infected with P. gingivalis. Rats on the omega-3 FA diet exhibited elevated serum levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), documenting diet-induced changes. PCR analyses demonstrated that rats were orally colonized by P. gingivalis; increased IgG antibody levels substantiated this infection. P. gingivalis-infected rats treated with omega-3 FA had significantly less alveolar bone resorption. These results demonstrated the effectiveness of an omega-3 FA-supplemented diet in modulating alveolar bone resorption following P. gingivalis infection, and supported that omega-3 FA may be a useful adjunct in the treatment of periodontal disease.

One-step acclimatization of plantlets using a mist reactor.

A mist reactor was used to grow and acclimatize carnation plants in vitro without using ex vitro acclimatization techniques. The acclimatization protocol in the reactor consisted of altering the mist-on period during the course of the culture period and a stepwise reduction in the relative humidity surrounding the plants from 98% to 70% relative humidity (RH) during the final week of in vitro growth. After transfer and further growth in a greenhouse for 5 weeks, survival was 91% for plants grown in reactors, 81% from vented boxes, and 50% from unvented boxes. Ex vitro survival directly correlated with increased in vitro rooting and decreased hyperhydration. In vitro rooting also correlated with high-quality plants, but did not significantly correlate with low hyperhydration, as normal plants often lacked roots. After 5 weeks in the greenhouse, the quantity of mid- and high-quality plants obtained from reactors and ventilated boxes was similar. Conditions in the mist reactor can be manipulated to produce plants that are readily acclimatized and are equal or better in quality and yield than plants produced using conventional methods.

Regulation and localization of tyrosine216 phosphorylation of glycogen synthase kinase-3beta in cellular and animal models of neuronal degeneration.

Inactivation of glycogen synthase kinase-3beta (GSK3beta) by S(9) phosphorylation is implicated in mechanisms of neuronal survival. Phosphorylation of a distinct site, Y(216), on GSK3beta is necessary for its activity; however, whether this site can be regulated in cells is unknown. Therefore we examined the regulation of Y(216) phosphorylation on GSK3beta in models of neurodegeneration. Nerve growth factor withdrawal from differentiated PC12 cells and staurosporine treatment of SH-SY5Y cells led to increased phosphorylation at Y(216), GSK3beta activity, and cell death. Lithium and insulin, agents that lead to inhibition of GSK3beta and adenoviral-mediated transduction of dominant negative GSK3beta constructs, prevented cell death by the proapoptotic stimuli. Inhibitors induced S(9) phosphorylation and inactivation of GSK3beta but did not affect Y(216) phosphorylation, suggesting that S(9) phosphorylation is sufficient to override GSK3beta activation by Y(216) phosphorylation. Under the conditions examined, increased Y(216) phosphorylation on GSK3beta was not an autophosphorylation response. In resting cells, Y(216) phosphorylation was restricted to GSK3beta present at focal adhesion sites. However, after staurosporine, a dramatic alteration in the immunolocalization pattern was observed, and Y(216)-phosphorylated GSK3beta selectively increased within the nucleus. In rats, Y(216) phosphorylation was increased in degenerating cortical neurons induced by ischemia. Taken together, these results suggest that Y(216) phosphorylation of GSK3beta represents an important mechanism by which cellular insults can lead to neuronal death.

Controlling hyperhydration of carnations (Dianthus caryophyllus L.) grown in a mist reactor.

Carnations (Dianthus caryophyllus L.) grown in vitro often develop physiological abnormalities such as hyperhydration. The amount of hyperhydration and growth was compared between carnations grown in mist reactors and conventional semisolid micropropagation systems (vented or unvented GA7 culture boxes). Plants grown in the mist reactor with long misting times (10 min h(-1)) produced more dry mass than those grown with <10 min h(-1); however, more misting also produced more hyperhydrated plants (70% hyperhydration). Control of hyperhydration in the mist reactor involved either reducing the overall nutrient mist supply or altering the mist supply throughout the culturing period. Stepped decreases in the mist supply throughout the 3-week period or an overall decrease in the duration of misting reduced hyperhydration to 13% and 5%, respectively. However, for both misting regimes, the biomass of normal (healthy) plants (fresh and dry weights) was limited. Further analysis suggested that, although normal plant biomass increased with longer mist exposure, hyperhydration levels also increased while the water content, based on percent dry weight, approached that of hyperhydrated plants. Sufficient normal plant development (fresh weight, leaf and shoot numbers, height, and rooting) with < 50% hyperhydration was obtained by weekly, stepped increases in the nutrient mist supply.

A head immobilization system for radiation simulation, CT, MRI, and PET imaging.

An aquaplast mask/marker immobilization system for the routine radiation therapy treatment of head and neck disease is described. The system utilizes a commercially available thermoplastic mesh indexed and mounted to a rigid frame attached to the therapy couch. The apparatus is designed to permit CT, MRI, and PET diagnostic scans of the patient to be performed in the simulation and treatment position utilizing the same mask, thereby facilitating image correlation. Studies employing weekly simulation indicate that patient treatment position movement can be restricted to 3 mm over the course of treatment. This easily constructed system permits rapid mask formation to be performed on the treatment simulator, resulting in an immobilization device comparable to masks produced with vacuum-forming techniques. Details of construction, verification, and central axis CT, MRI, PET markers are offered.

Three-dimensional motion analysis of an improved head immobilization system for simulation, CT, MRI, and PET imaging.

A mask/marker immobilization system for the routine radiation therapy treatment of head and neck disease is described, utilizing a commercially available thermoplastic mesh, indexed and mounted to a rigid frame attached to the therapy couch. Designed to permit CT, MRI, and PET diagnostic scans of the patient to be performed in the simulation and treatment position employing the same mask, the system has been tested in order to demonstrate the reproducibility of immobilization throughout a radical course of irradiation. Three-dimensional analysis of patient position over an 8-week course of daily radiation treatment has been performed for nine patients from digitization of anatomic points identified on orthogonal radiographs. Studies employing weekly simulation indicate that patient treatment position movement can be restricted to 2 mm over the course of treatment. This easily constructed system permits rapid mask formation to be performed on the treatment simulator, resulting in an immobilization device comparable to masks produced with vacuum-forming techniques. Details of motion analysis and central axis CT, MRI, and PET markers are offered.