Global Analysis of the HrpL Regulon in the Plant Pathogen Pseudomonas syringae pv. tomato DC3000 Reveals New Regulon Members with Diverse Functions

The type III secretion system (T3SS) is required for virulence in the gram-negative plant pathogen Pseudomonas syringae pv. tomato DC3000. The alternative sigma factor HrpL directly regulates expression of T3SS genes via a promoter sequence, often designated as the “hrp promoter.” Although the HrpL regulon has been extensively investigated in DC3000, it is not known whether additional regulon members remain to be found. To systematically search for HrpL-regulated genes, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) and bulk mRNA sequencing (RNA-Seq) to identify HrpL-binding sites and likely hrp promoters. The analysis recovered 73 sites of interest, including 20 sites that represent new hrp promoters. The new promoters lie upstream of a diverse set of genes encoding potential regulators, enzymes and hypothetical proteins. PSPTO_5633 is the only new HrpL regulon member that is potentially an effector and is now designated HopBM1. Deletions in several other new regulon members, including PSPTO_5633, PSPTO_0371, PSPTO_2130, PSPTO_2691, PSPTO_2696, PSPTO_3331, and PSPTO_5240, in either DC3000 or ΔhopQ1-1 backgrounds, do not affect the hypersensitive response or in planta growth of the resulting strains. Many new HrpL regulon members appear to be unrelated to the T3SS, and orthologs for some of these can be identified in numerous non-pathogenic bacteria. With the identification of 20 new hrp promoters, the list of HrpL regulon members is approaching saturation and most likely includes all DC3000 effectors.     

Analyzing Spatial Heterogeneity in DCE- and DW-MRI Parametric Maps to Optimize Prediction of Pathologic Response to Neoadjuvant Chemotherapy in Breast Cancer

The purpose of this study is to investigate the ability of multivariate analysis of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion-weighted MRI (DW-MRI) parametric maps, obtained early in the course of therapy, to predict which patients will achieve pathologic complete response (pCR) at the time of surgery. Thirty-three patients underwent DCE-MRI (to estimate K^trans, v_e, k_ep, and v_p) and DW-MRI [to estimate the apparent diffusion coefficient (ADC)] at baseline (t₁) and after the first cycle of neoadjuvant chemotherapy (t₂). Four analyses were performed and evaluated using receiver-operating characteristic (ROC) analysis to test their ability to predict pCR. First, a region of interest (ROI) level analysis input the mean K^trans, v_e, k_ep, v_p, and ADC into the logistic model. Second, a voxel-based analysis was performed in which a longitudinal registration algorithm aligned serial parameters to a common space for each patient. The voxels with an increase in k_ep, K^trans, and v_p or a decrease in ADC or v_e were then detected and input into the regression model. In the third analysis, both the ROI and voxel level data were included in the regression model. In the fourth analysis, the ROI and voxel level data were combined with selected clinical data in the regression model. The overfitting-corrected area under the ROC curve (AUC) with 95% confidence intervals (CIs) was then calculated to evaluate the performance of the four analyses. The combination of k_ep, ADC ROI, and voxel level data achieved the best AUC (95% CI) of 0.87 (0.77–0.98).     

Prevalence and risk factors for vitamin C deficiency in north and south India: a two centre population based study in people aged 60 years and over

Background

Studies from the UK and North America have reported vitamin C deficiency in around 1 in 5 men and 1 in 9 women in low income groups. There are few data on vitamin C deficiency in resource poor countries.

Objectives

To investigate the prevalence of vitamin C deficiency in India.

Design

We carried out a population-based cross-sectional survey in two areas of north and south India. Randomly sampled clusters were enumerated to identify people aged 60 and over. Participants (75% response rate) were interviewed for tobacco, alcohol, cooking fuel use, 24 hour diet recall and underwent anthropometry and blood collection. Vitamin C was measured using an enzyme-based assay in plasma stabilized with metaphosphoric acid. We categorised vitamin C status as deficient (<11 µmol/L), sub-optimal (11–28 µmol/L) and adequate (>28 µmol/L). We investigated factors associated with vitamin C deficiency using multivariable Poisson regression.

Results

The age, sex and season standardized prevalence of vitamin C deficiency was 73.9% (95% confidence Interval, CI 70.4,77.5) in 2668 people in north India and 45.7% (95% CI 42.5,48.9) in 2970 from south India. Only 10.8% in the north and 25.9% in the south met the criteria for adequate levels. Vitamin C deficiency varied by season, and was more prevalent in men, with increasing age, users of tobacco and biomass fuels, in those with anthropometric indicators of poor nutrition and with lower intakes of dietary vitamin C.

Conclusions

In poor communities, such as in our study, consideration needs to be given to measures to improve the consumption of vitamin C rich foods and to discourage the use of tobacco.     

A Computational Model of Neuro-Glio-Vascular Loop Interactions

We present a computational, biophysical model of neuron-astrocyte-vessel interaction. Unlike other cells, neurons convey “hunger” signals to the vascular network via an intervening layer of glial cells (astrocytes); vessels dilate and release glucose which fuels neuronal firing. Existing computational models focus on only parts of this loop (neuron→astrocyte→vessel→neuron), whereas the proposed model describes the entire loop. Neuronal firing causes release of a neurotransmitter like glutamate which triggers release of vasodilator by astrocytes via a cascade of biochemical events. Vasodilators released from astrocytic endfeet cause blood vessels to dilate and release glucose into the interstitium, part of which is taken up by the astrocyticendfeet. Glucose is converted into lactate in the astrocyte and transported into the neuron. Glucose from the interstitium and lactate (produced from glucose) influx from astrocyte are converted into ATP in the neuron. Neuronal ATP is used to drive the Na⁺/K⁺ATPase pumps, which maintain ionic gradients necessary for neuronal firing. When placed in the metabolic loop, the neuron exhibits sustained firing only when the stimulation current is more than a minimum threshold. For various combinations of initial neuronal [ATP] and external current, the neuron exhibits a variety of firing patterns including sustained firing, firing after an initial pause, burst firing etc. Neurovascular interactions under conditions of constricted vessels are also studied. Most models of cerebral circulation describe neurovascular interactions exclusively in the “forward” neuron→vessel direction. The proposed model indicates possibility of “reverse” influence also, with vasomotion rhythms influencing neural firing patterns. Another idea that emerges out of the proposed work is that brain''s computations may be more comprehensively understood in terms of neuro-glial-vascular dynamics and not in terms of neural firing alone.     

The p75 neurotrophin receptor is localized to primary cilia in adult murine hippocampal dentate gyrus granule cells

The densely ciliated granule cell layer of the adult murine hippocampal dentate gyrus is one of two sites of adult neurogenesis. The granule cells have already been proven to localize their SSTR3 (somatostatin receptor 3) receptors to their so-called primary cilia. Here we show for the first time that 70-90% of these cells in 7-18 months-old wild-type and 3×Tg-AD (Alzheimer disease transgenic) mice also load p75^NTR receptors into the structures containing SSTR3, i.e., their primary cilia. On the other hand, p75^NTR’s TrkA co-receptors were not localized to cilia but conventionally distributed throughout the cell surface. Significantly fewer cells (20-40%) in the hippocampal CA1 and CA3 regions and cerebral cortex have p75^NTR containing cilia. While we don’t know what the impact of the cilial localization of p75^NTR on dentate gyral adult neurogenesis and memory encoding might be, the cilia’s amyloid β-activatable p75^NTR receptors could be damaging or lethal to the hippocampal functioning of amyloid β-accumulating Alzheimer brain.     

Do Basal Ganglia Amplify Willed Action by Stochastic Resonance? A Model

Basal ganglia are usually attributed a role in facilitating willed action, which is found to be impaired in Parkinson''s disease, a pathology of basal ganglia. We hypothesize that basal ganglia possess the machinery to amplify will signals, presumably weak, by stochastic resonance. Recently we proposed a computational model of Parkinsonian reaching, in which the contributions from basal ganglia aid the motor cortex in learning to reach. The model was cast in reinforcement learning framework. We now show that the above basal ganglia computational model has all the ingredients of stochastic resonance process. In the proposed computational model, we consider the problem of moving an arm from a rest position to a target position: the two positions correspond to two extrema of the value function. A single kick (a half-wave of sinusoid, of sufficiently low amplitude) given to the system in resting position, succeeds in taking the system to the target position, with high probability, only at a critical noise level. But for suboptimal noise levels, the model arm''s movements resemble Parkinsonian movement symptoms like akinetic rigidity (low noise) and dyskinesias (high noise).     

Parathyroid hormone stimulates protein kinase C but not adenylate cyclase in mouse epidermal keratinocytes.

Intact human parathyroid hormone, hPTH [1-84], and the hPTH [1-34] fragment stimulated membrane-associated protein kinase C (PKC) activity in immortalized (but still differentiation-competent) murine BALB/MK-2 skin keratinocytes. Unexpectedly, the hormone and its fragment did not stimulate adenylate cyclase. The failure of PTH to stimulate adenylate cyclase activity was not due to the lack of a functioning receptor-cyclase coupling mechanism because the cells were stimulated to synthesize cyclic adenosine monophosphate (cyclic AMP) by the beta-adrenergic drug isoproterenol. Thus, skin keratinocytes seem to have an unconventional PTH receptor that is coupled to a PKC-activating mechanism but not to adenylate cyclase. These observations suggest that normal and neoplastic skin keratinocytes respond to the PTH-related peptide that they make and secrete.     

Waging war on physical inactivity: using modern molecular ammunition against an ancient enemy.

A hypothesis is presented based on a coalescence of anthropological estimations of Homo sapiens' phenotypes in the Late Paleolithic era 10,000 years ago, with Darwinian natural selection synergized with Neel's idea of the so-called thrifty gene. It is proposed that humans inherited genes that were evolved to support a physically active lifestyle. It is further postulated that physical inactivity in sedentary societies directly contributes to multiple chronic health disorders. Therefore, it is imperative to identify the underlying genetic and cellular/biochemical bases of why sedentary living produces chronic health conditions. This will allow society to improve its ability to effect beneficial lifestyle changes and hence improve the overall quality of living. To win the war against physical inactivity and the myriad of chronic health conditions produced because of physical inactivity, a multifactorial approach is needed, which includes successful preventive medicine, drug development, optimal target selection, and efficacious clinical therapy. All of these approaches require a thorough understanding of fundamental biology and how the dysregulated molecular circuitry caused by physical inactivity produces clinically overt disease. The purpose of this review is to summarize the vast armamentarium at our disposal in the form of the extensive scientific basis underlying how physical inactivity affects at least 20 of the most deadly chronic disorders. We hope that this information will provide readers with a starting point for developing additional strategies of their own in the ongoing war against inactivity-induced chronic health conditions.     

Spearmint R2R3‐MYB transcription factor MsMYB negatively regulates monoterpene production and suppresses the expression of geranyl diphosphate synthase large subunit (MsGPPS.LSU)

Many aromatic plants, such as spearmint, produce valuable essential oils in specialized structures called peltate glandular trichomes (PGTs). Understanding the regulatory mechanisms behind the production of these important secondary metabolites will help design new approaches to engineer them. Here, we identified a PGT‐specific R2R3‐MYB gene, MsMYB, from comparative RNA‐Seq data of spearmint and functionally characterized it. Analysis of MsMYB‐RNAi transgenic lines showed increased levels of monoterpenes, and MsMYB‐overexpressing lines exhibited decreased levels of monoterpenes. These results suggest that MsMYB is a novel negative regulator of monoterpene biosynthesis. Ectopic expression of MsMYB, in sweet basil and tobacco, perturbed sesquiterpene‐ and diterpene‐derived metabolite production. In addition, we found that MsMYB binds to cis‐elements of MsGPPS.LSU and suppresses its expression. Phylogenetic analysis placed MsMYB in subgroup 7 of R2R3‐MYBs whose members govern phenylpropanoid pathway and are regulated by miR858. Analysis of transgenic lines showed that MsMYB is more specific to terpene biosynthesis as it did not affect metabolites derived from phenylpropanoid pathway. Further, our results indicate that MsMYB is probably not regulated by miR858, like other members of subgroup 7.     

Does Neighborhood Floral Display Matter? Fruit Set in Carpenter Bee‐pollinated Heterophragma quadriloculare and Beetle‐pollinated Lasiosiphon eriocephalus

Fruit set is pollen‐limited in the self‐incompatible tree Heterophragma quadriloculare (Bignoniaceae), pollinated by long‐distance flying carpenter bees, and in the self‐compatible shrub Lasiosiphon eriocephalus (Thymdeaceae), pollinated by weak‐flying, sedentary beetles. We studied a single H. quadriloculare population over high and low flowering years and found no difference in bee visitation rates between these years. For H. quadriloculare, neighborhood floral display did not make a significant contribution to reproductive success. We investigated dense and sparse L. eriocephalus populations in the same year. In the low density L. eriocephalus population, individual floral displays were higher than in the dense population, yet reproductive success was low, indicating that plant isolation was a major factor influencing fruit set. This result was due to the extremely low number of beetles per plant and per flower in this population. In the dense L. eriocephalus population, although the displays of individual neighbors were smaller and plants were closer, neighborhood floral display did not contribute significantly to reproductive success, whereas the effect of individual floral display was ambiguous. Species with self‐incompatible rather than self‐compatible breeding systems are expected to experience neighborhood effects on reproductive success; however, at the spatial scale and floral display levels of plants in this study, only individual floral display affected fruit set in H. quadriloculare, whereas neither individual nor neighborhood display influenced fruit set in L. eriocephalus. Therefore, pollinator type, pollinator behavior, and plant and population isolation, rather than breeding system alone, will determine if neighborhood floral display affects fruit set.