Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection.

Like other complex multicellular organisms, plants are composed of different cell types with specialized shapes and functions. For example, most laminar leaves consist of multiple photosynthetic cell types. These cell types include the palisade mesophyll, which typically forms one or more cell layers on the adaxial side of the leaf. Despite their importance for photosynthesis, we know little about how palisade cells differ at the molecular level from other photosynthetic cell types. To this end, we have used a combination of cell-specific profiling using fluorescence-activated cell sorting and single-cell RNA-sequencing methods to generate a transcriptional blueprint of the palisade mesophyll in Arabidopsis thaliana leaves. We find that despite their unique morphology, palisade cells are otherwise transcriptionally similar to other photosynthetic cell types. Nevertheless, we show that some genes in the phenylpropanoid biosynthesis pathway have both palisade-enriched expression and are light-regulated. Phenylpropanoid gene activity in the palisade was required for production of the ultraviolet (UV)-B protectant sinapoylmalate, which may protect the palisade and/or other leaf cells against damaging UV light. These findings improve our understanding of how different photosynthetic cell types in the leaf can function uniquely to optimize leaf performance, despite their transcriptional similarities.

Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress.

Gene regulation is a dynamic process involving changes ranging from the remodeling of chromatin to preferential translation. To understand integrated nuclear and cytoplasmic gene regulatory dynamics, we performed a survey spanning the epigenome to translatome of Arabidopsis (Arabidopsis thaliana) seedlings in response to hypoxia and reoxygenation. This included chromatin assays (examining histones, accessibility, RNA polymerase II [RNAPII], and transcription factor binding) and three RNA assays (nuclear, polyadenylated, and ribosome-associated). Dynamic patterns of nuclear regulation distinguished stress-induced and growth-associated mRNAs. The rapid upregulation of hypoxia-responsive gene transcripts and their preferential translation were generally accompanied by increased chromatin accessibility, RNAPII engagement, and reduced Histone 2A.Z association. Hypoxia promoted a progressive upregulation of heat stress transcripts, as evidenced by RNAPII binding and increased nuclear RNA, with polyadenylated RNA levels only elevated after prolonged stress or reoxygenation. Promoters of rapidly versus progressively upregulated genes were enriched for cis-elements of ethylene-responsive and heat shock factor transcription factors, respectively. Genes associated with growth, including many encoding cytosolic ribosomal proteins, underwent distinct histone modifications, yet retained RNAPII engagement and accumulated nuclear transcripts during the stress. Upon reaeration, progressively upregulated and growth-associated gene transcripts were rapidly mobilized to ribosomes. Thus, multilevel nuclear regulation of nucleosomes, transcript synthesis, accumulation, and translation tailor transient stress responses.plantcell;31/11/2573/FX1F1fx1.

Conserved and nuanced hierarchy of gene regulatory response to hypoxia.

A dynamic assembly of nuclear and cytoplasmic processes regulate gene activity. Hypoxic stress and the associated energy crisis activate a plurality of regulatory mechanisms including modulation of chromatin structure, transcriptional activation and post-transcriptional processes. Temporal control of genes is associated with specific chromatin modifications and transcription factors. Genome-scale technologies that resolve transcript subpopulations in the nucleus and cytoplasm indicate post-transcriptional processes enable cells to conserve energy, prepare for prolonged stress and accelerate recovery. Moreover, the harboring of gene transcripts associated with growth in the nucleus and macromolecular RNA-protein complexes contributes to the preferential translation of stress-responsive gene transcripts during hypoxia. We discuss evidence of evolutionary variation in integration of nuclear and cytoplasmic processes that may contribute to variations in flooding resilience.

Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis.

The response of Arabidopsis thaliana to low-oxygen stress (hypoxia), such as during shoot submergence or root waterlogging, includes increasing the levels of ∼50 hypoxia-responsive gene transcripts, many of which encode enzymes associated with anaerobic metabolism. Upregulation of over half of these mRNAs involves stabilization of five group VII ethylene response factor (ERF-VII) transcription factors, which are routinely degraded via the N-end rule pathway of proteolysis in an oxygen- and nitric oxide-dependent manner. Despite their importance, neither the quantitative contribution of individual ERF-VIIs nor the cis-regulatory elements they govern are well understood. Here, using single- and double-null mutants, the constitutively synthesized ERF-VIIs RELATED TO APETALA2.2 (RAP2.2) and RAP2.12 are shown to act redundantly as principle activators of hypoxia-responsive genes; constitutively expressed RAP2.3 contributes to this redundancy, whereas the hypoxia-induced HYPOXIA RESPONSIVE ERF1 (HRE1) and HRE2 play minor roles. An evolutionarily conserved 12-bp cis-regulatory motif that binds to and is sufficient for activation by RAP2.2 and RAP2.12 is identified through a comparative phylogenetic motif search, promoter dissection, yeast one-hybrid assays, and chromatin immunopurification. This motif, designated the hypoxia-responsive promoter element, is enriched in promoters of hypoxia-responsive genes in multiple species.

Lighting the shadows: methods that expose nuclear and cytoplasmic gene regulatory control.

Within cells, myriad interconnected processes orchestrate the progression of gene expression from chromatin, to mRNA, and to protein. Assessment of DNA methylation, histone modification, transcript isoform abundance, and the proteome are frequently performed to examine this progression, but do not resolve many intermediary steps in the coordinated regulation of gene expression. Here, we consider single and multiplexed technologies that yield genome-wide assessment of gene and mRNA activity, from transcription factor access to DNA to de novo synthesis of protein. An emphasis is placed on methods that can resolve gene regulatory processes in cells of defined identity within multicellular organs at spatial and temporal scales, leading to more effective design of gene regulatory cassettes for biotechnology.

Analysis of HIV type 1 gp41 sequences in diverse HIV type 1 strains.

The HIV fusion inhibitor enfuvirtide (ENF/Fuzeon) targets the env gp41 transmembrane domain. Mutations in gp41 are associated with ENF resistance. We developed a prototype assay to genotype a 676-bp region spanning the heptad repeat domains (HR1 and HR2) of HIV-1 gp41. Plasma samples were collected from 126 HIV-1-infected blood donors in Cameroon, Brazil, Uganda, South Africa, Thailand, and Argentina. Based on analysis of gag p24, pol integrase, and env gp41 genes, the panel was composed of subtypes A/A2 (18), B (11), C (14), D (10), F/F2 (9), G (7), CRF01_AE (9), CRF02_AG (33), and recombinant strains (15). Genotyping was successful for 119 of the 126 samples (94.4%). Although numerous amino acid polymorphisms were detected in some samples, none had primary mutations associated with ENF resistance. The gp41 HIV-1 research reagents developed by Celera are useful tools for genotyping analysis of the gp41 region in diverse HIV-1 strains.

Rheumatoid arthritis: current pharmacologic treatment and anesthetic considerations.

A diagnosis of rheumatoid arthritis carries with it a lifelong progressive disease; however twenty percent of patients enjoy periods of partial to total remission. After remission, the disease will frequently plague previously unaffected joints. Life expectancy is reduced by an average of three to seven years. Complications of RA include vasculitis and amyloidosis affecting any vessel, including the aorta. Additionally, complications of therapy such as chronic NSAID use leading to GI bleeding and infections associated with long term steroid use, can add to the difficulties of the disease. The recent discovery and use of anticytokines and DMARDs has lead to greatly reduced symptomology associated with RA and greater patient comfort. Side effects of drugs should be well understood including the risk of bleeding from NSAIDs. Management and surgical intervention of problems that arise from this disease vary dramatically. The anesthesiologist must be aware of airway pathologies, pain management techniques, and available pharmacology parameters.

Transition to quorum sensing in an Agrobacterium population: A stochastic model.

Understanding of the intracellular molecular machinery that is responsible for the complex collective behavior of multicellular populations is an exigent problem of modern biology. Quorum sensing, which allows bacteria to activate genetic programs cooperatively, provides an instructive and tractable example illuminating the causal relationships between the molecular organization of gene networks and the complex phenotypes they control. In this work we--to our knowledge for the first time--present a detailed model of the population-wide transition to quorum sensing using the example of Agrobacterium tumefaciens. We construct a model describing the Ti plasmid quorum-sensing gene network and demonstrate that it behaves as an "on-off" gene expression switch that is robust to molecular noise and that activates the plasmid conjugation program in response to the increase in autoinducer concentration. This intracellular model is then incorporated into an agent-based stochastic population model that also describes bacterial motion, cell division, and chemical communication. Simulating the transition to quorum sensing in a liquid medium and biofilm, we explain the experimentally observed gradual manifestation of the quorum-sensing phenotype by showing that the transition of individual model cells into the "on" state is spread stochastically over a broad range of autoinducer concentrations. At the same time, the population-averaged values of critical autoinducer concentration and the threshold population density are shown to be robust to variability between individual cells, predictable and specific to particular growth conditions. Our modeling approach connects intracellular and population scales of the quorum-sensing phenomenon and provides plausible answers to the long-standing questions regarding the ecological and evolutionary significance of the phenomenon. Thus, we demonstrate that the transition to quorum sensing requires a much higher threshold cell density in liquid medium than in biofilm, and on this basis we hypothesize that in Agrobacterium quorum sensing serves as the detector of biofilm formation.

Study of Bone Marrow and Embryonic Stem Cell-Derived Human Mesenchymal Stem Cells for Treatment of Escherichia coli Endotoxin-Induced Acute Lung Injury in Mice.

UNLABELLED: : Mesenchymal stem cells (MSCs) can be derived from multiple tissue sources. However, the optimal source of MSCs for cell-based therapy for acute lung injury (ALI) is unclear. In the present experiments, we studied bone marrow (BM)-derived and embryonic stem cell-derived human MSC (ES-MSCs) as a therapeutic agent in Escherichia coli endotoxin-induced ALI in mice. We hypothesized that ES-MSCs would be more potent than BM-MSCs owing to its more primitive source of origin. ALI was induced by the intratracheal instillation of endotoxin at 4 mg/kg into 10-12-week-old C57BL/6 mice with or without BM-MSCs, ES-MSCs, or normal human lung fibroblasts as a cellular control. Compared with the endotoxin-injured mice at 48 hours, the administration of ES-MSCs provided results similar to those of BM-MSCs, significantly reducing the influx of white blood cells and neutrophils and decreasing the secretion of the inflammatory cytokines, macrophage inflammatory protein-2 and tumor necrosis factor-α, in the injured alveolus. BM-MSCs also reduced extravascular lung water, a measure of pulmonary edema, by 60% and the total protein levels, a measure of lung permeability, by 66%. However, surprisingly, ES-MSCs did not have these protective effects, which was partially explained by the increased secretion of matrix metallopeptidase 9 by ES-MSCs, an enzyme known to increase lung protein permeability. In conclusion, both BM-MSCs and ES-MSCs markedly decreased endotoxin-induced inflammation. However, ES-MSCs did not show any beneficial effect on reducing pulmonary edema and lung protein permeability compared with BM-MSCs, suggesting that not all MSCs behave in a similar fashion. Our results highlight the need perhaps for a disease-specific potency assay for MSCs. SIGNIFICANCE: To determine the optimal source of mesenchymal stem cells (MSCs) for cell-based therapy for acute lung injury, bone marrow (BM)- and embryonic stem cell-derived human MSC (ES-MSCs) were compared as therapeutic agents for Escherichia coli endotoxin-induced lung injury in mice. ES-MSCs behaved similarly to BM-MSCs by markedly decreasing the inflammatory response induced by endotoxin. However, unlike BM-MSCs, ES-MSCs provided no protective effects against increasing lung water and protein permeability, in part because of an increase in expression of matrix metallopeptidase 9 by ES-MSCs. In patients with acute respiratory distress syndrome, impaired alveolar fluid clearance (i.e., no resolution of pulmonary edema fluid) has been associated with higher mortality rates. Although ES-MSCs might ultimately be found to have properties superior to those of BM-MSCs, such as for immunomodulation, these results highlight the need for a disease-specific potency assay for stem cell-based therapy.

Stromal protein degradation is incomplete in Arabidopsis thaliana autophagy mutants undergoing natural senescence.

BACKGROUND: Degradation of highly abundant stromal proteins plays an important role in the nitrogen economy of the plant during senescence. Lines of evidence supporting proteolysis within the chloroplast and outside the chloroplast have been reported. Two extra-plastidic degradation pathways, chlorophagy and Rubisco Containing Bodies, rely on cytoplasmic autophagy. RESULTS: In this work, levels of three stromal proteins (Rubisco large subunit, chloroplast glutamine synthetase and Rubisco activase) and one thylakoid protein (the major light harvesting complex protein of photosystem II) were measured during natural senescence in WT and in two autophagy T-DNA insertion mutants (atg5 and atg7). Thylakoid-localized protein decreased similarly in all genotypes, but stromal protein degradation was incomplete in the two atg mutants. In addition, degradation of two stromal proteins was observed in chloroplasts isolated from mid-senescence leaves. CONCLUSIONS: These data suggest that autophagy does contribute to the complete proteolysis of stromal proteins, but does not play a major degenerative role. In addition, support for in organello degradation is provided.

Rheonix CARD(®) Technology: An Innovative and Fully Automated Molecular Diagnostic Device.

A versatile microfluidic platform for the evolving molecular diagnostics industry is described. It incorporates low cost Rheonix CARD(®) (Chemistry and Reagent Device) technology to analyze a variety of clinical specimens. A patented lamination process incorporates all pumps, valves, microchannels and reaction compartments into an inexpensive disposable plastic device. Once an untreated clinical specimen is introduced, all assay steps, including cell lysis, nucleic acid purification, multiplex PCR, and end-point analysis, are automatically performed. Three distinct CARD assays are described which utilize either a low density microarray for multiplex detection of amplicons or an integrated primer extension assay to detect single nucleotide polymorphisms of interest. The STI (Sexually Transmitted Infections) CARD(®) is able to simultaneously detect four sexually transmitted infectious agents (N. gonorrhoeae, C.trachomatis, T. pallidum and T. vaginalis). Human C33A cervical epithelial cells were spiked with different levels of genomic DNA from the four species of interest, singly or in combination, and applied to the CARD device. Using multiplex PCR amplification of the targets followed by microarray detection, the CARD device was able to correctly detect a minimum of 10 copies of each of the four pathogens. The HPV (Human Papillomavirus) CARD(®) was able to detect and distinguish 20 different clinically relevant HPV types using cloned HPV DNA. In addition, the HPV CARD could identify HPV types in vaginal specimens previously demonstrated to contain high or low risk HPV using a currently commercially available testing method. Finally, the detection of specific single nucleotide polymorphisms (SNP) associated with warfarin dosing sensitivity was achieved on the Warfarin Genotyping CARD(®) by analyzing human buccal swabs. Once multiplex PCR was completed, the SNPs were detected using a primer extension assay.