A pilot randomized controlled trial of group-based indoor gardening and art activities demonstrates therapeutic benefits to healthy women.

BACKGROUND: There is mounting anecdotal and empirical evidence that gardening and art-making afford therapeutic benefits. OBJECTIVES: This randomly controlled pilot study tested the hypothesis that participation in group-based indoor gardening or art-making activities for one hour twice a week for four weeks would provide quantifiably different therapeutic benefits to a population of healthy women ages 26-49. METHODS: A population of 42 volunteers was randomly assigned to parallel gardening or art-making treatment groups. A total of 36 participants initiated the treatment protocol and 32 (Gardening n = 15 and Art n = 17) received the interventions and completed all assessments. Treatments included eight one-hour group-based gardening or art intervention sessions. Self-report psychometric assessments were conducted for anxiety, depression symptomatology, mood disturbance, stress, satisfaction with discretionary social activities, and quality of life measures. Cardiac physiological data were also collected. Outcomes were measured at baseline, during, and post-intervention. RESULTS: Engaging in both gardening and art-making activities resulted in apparent therapeutic improvements for self-reported total mood disturbance, depression symptomatology, and perceived stress with different effect sizes following eight one-hour treatment sessions. Gardening also resulted in improvements for indications of trait anxiety. Based on time-course evidence, dosage responses were observed for total mood disturbance, perceived stress, and depression symptomatology for both gardening and art-making. However, gardening or art-making did not have an apparent influence on heart rate or blood pressure or result in marked improvement for satisfaction with discretionary leisure activities. CONCLUSION: The data did not support the hypothesis of differential therapeutic benefits of gardening and art-making for healthy women. When taken together, group-based gardening or art-making can provide quantitatively measurable improvements in healthy women's psychosocial health status that imply potentially important public health benefits. TRIAL REGISTRATION: ClinicalTrials.gov NCT03266120.

CD33M inhibits microglial phagocytosis, migration and proliferation, but the Alzheimer's disease-protective variant CD33m stimulates phagocytosis and proliferation, and inhibits adhesion.

CD33 is a Siglec (sialic acid-binding immunoglobulin-type lectin) receptor on microglia. Human CD33 can be alternatively spliced into two isoforms: the long isoform (CD33M) and a shorter isoform (CD33m) that lacks the sialic acid-binding site. CD33m appears to protect against Alzheimer's disease; however, it remains unclear how. To investigate potential mechanisms by which CD33m may confer protection, we expressed the CD33m and CD33M isoforms of human CD33 in mouse BV-2 and human CHME3 microglial cells and assessed microglia functions. In the BV-2 cells, CD33M inhibited microglial phagocytosis of beads, synapses, debris and dead cells, while CD33m increased phagocytosis of beads, debris and cells. RNAi knockdown of the endogenous mouse CD33 increased phagocytosis and prevented CD33m's (but not CD33M's) effect on phagocytosis. CD33M increased cell attachment but inhibited cell proliferation, while CD33m did the opposite. We also found that CD33M inhibited cell migration. In human CHME3 cells, CD33M increased cell attachment, but inhibited phagocytosis, proliferation and migration, whereas CD33m did the opposite. We conclude that CD33M inhibits microglial phagocytosis, inhibits migration and increases adhesion, while CD33m increases phagocytosis, proliferation and inhibits adhesion. Thus, CD33m might protect against Alzheimer's disease by increasing microglial proliferation, movement and phagocytosis of debris and dead cells.

Lipopolysaccharide activates microglia via neuraminidase 1 desialylation of Toll-like Receptor 4.

Most cell surface receptors are sialylated, i.e. have sialic acid as the terminal residue of their sugar chains, but can be desialylated by sialidases, such as neuraminidase 1 (Neu1). Desialylation by Neu1 can activate immune cells, such as neutrophils, macrophages and monocytes. We investigated the role of Neu1 in activation of microglia using BV-2 cells (a murine microglial cell line) by cytokine ELISAs, enzyme activity assays, antibody/lectin binding and proximity labelling. We found that lipopolysaccharide (LPS) activation caused an increase in Neu1 protein on the cell surface, and an increase in surface sialidase activity that was prevented by Neu1 knockdown. Moreover, LPS induced interleukin 6 (IL-6) and MCP-1 release, which was reduced by Neu1 knockdown and increased by Neu1 over-expression. Neu1 knockdown also prevented the maintenance of IL-6 release by microglia after LPS was removed. Sialidase treatment of the cells was sufficient to induce IL-6 release, prevented by inhibiting toll-like receptor 4 (TLR4). Neu1 was found in close proximity to TLR4 on the surface of cells, and LPS induced desialylation of TLR4 on the cell surface, prevented by Neu1 knockdown. Sialic acid-binding immunoglobulin-like lectin E was found to bind to TLR4 via sialic acid residues and inhibit IL-6 release by BV-2 cells. We conclude that LPS causes Neu1 to translocate to the cell surface, where it desialylates TLR4, releasing inhibitory sialic acid-binding immunoglobulin-like lectin E, enhancing and maintaining inflammatory activation of the microglia. Thus, sialylation is a potent regulator of microglial activation, and Neu1 may be a target to reduce activation of microglia.

TET2 Regulates the Neuroinflammatory Response in Microglia.

Epigenomic mechanisms regulate distinct aspects of the inflammatory response in immune cells. Despite the central role for microglia in neuroinflammation and neurodegeneration, little is known about their epigenomic regulation of the inflammatory response. Here, we show that Ten-eleven translocation 2 (TET2) methylcytosine dioxygenase expression is increased in microglia upon stimulation with various inflammogens through a NF-κB-dependent pathway. We found that TET2 regulates early gene transcriptional changes, leading to early metabolic alterations, as well as a later inflammatory response independently of its enzymatic activity. We further show that TET2 regulates the proinflammatory response in microglia of mice intraperitoneally injected with LPS. We observed that microglia associated with amyloid ß plaques expressed TET2 in brain tissue from individuals with Alzheimer's disease (AD) and in 5xFAD mice. Collectively, our findings show that TET2 plays an important role in the microglial inflammatory response and suggest TET2 as a potential target to combat neurodegenerative brain disorders.

Effective Knockdown of Gene Expression in Primary Microglia With siRNA and Magnetic Nanoparticles Without Cell Death or Inflammation.

Microglia, the resident immune cells of the brain, have multiple functions in physiological and pathological conditions, including Alzheimer's disease (AD). The use of primary microglial cell cultures has proved to be a valuable tool to study microglial biology under various conditions. However, more advanced transfection methodologies for primary cultured microglia are still needed, as current methodologies provide low transfection efficiency and induce cell death and/or inflammatory activation of the microglia. Here, we describe an easy, and effective method based on the Glial-Mag method (OZ Biosciences) using magnetic nanoparticles and a magnet to successfully transfect primary microglia cells with different small interfering RNAs (siRNAs). This method does not require specialist facilities or specific training and does not induce cell toxicity or inflammatory activation. We demonstrate that this protocol successfully decreases the expression of two key genes associated with AD, the triggering receptor expressed in myeloid cells 2 (TREM2) and CD33, in primary microglia cell cultures.

Galectin-3 released in response to traumatic brain injury acts as an alarmin orchestrating brain immune response and promoting neurodegeneration.

Traumatic brain injury (TBI) is currently a major cause of morbidity and poor quality of life in Western society, with an estimate of 2.5 million people affected per year in Europe, indicating the need for advances in TBI treatment. Within the first 24 h after TBI, several inflammatory response factors become upregulated, including the lectin galectin-3. In this study, using a controlled cortical impact (CCI) model of head injury, we show a large increase in the expression of galectin-3 in microglia and also an increase in the released form of galectin-3 in the cerebrospinal fluid (CSF) 24 h after head injury. We report that galectin-3 can bind to TLR-4, and that administration of a neutralizing antibody against galectin-3 decreases the expression of IL-1ß, IL-6, TNFα and NOS2 and promotes neuroprotection in the cortical and hippocampal cell populations after head injury. Long-term analysis demonstrated a significant neuroprotection in the cortical region in the galectin-3 knockout animals in response to TBI. These results suggest that following head trauma, released galectin-3 may act as an alarmin, binding, among other proteins, to TLR-4 and promoting inflammation and neuronal loss. Taking all together, galectin-3 emerges as a clinically relevant target for TBI therapy.

Use of Dehydrated Agar to Estimate Microbial Water Quality for Horticulture Irrigation.

Petrifilms are dehydrated agar culture plates that have been used to quantify colony forming units (CFU) mL of either aerobic bacteria (Petrifilm-AC) or fungus (Petrifilm-YM), depending on substrate composition. Microbes in irrigation systems can indicate biofilm risk and potential clogging of irrigation emitters. The research objective was to compare counts on Petrifilms versus traditional, hydrated-agar plates using samples collected from recirculated irrigation waters and cultures of isolated known species. The estimated count (in CFU mL) from a recirculated irrigation sample after 7 d of incubation on Petrifilm-YM was only 5.5% of the count quantified using sabouraud dextrose agar (SDA) with chloramphenicol after 14 d. In a separate experiment with a known species, Petrifilm-YM did not successfully culture zoospores of . Isolates of viable zoospores were cultured successfully on potato-dextrose agar (PDA), with comparable counts with a vegetable juice medium supplemented with the antibiotics pimaricin, ampicillin, rifamycin, pentochloronitrobenzene and hymexazol (PARP-H). The quantification of pv. Begoniaceae on Petrifilm-AC was not significantly different ( < 0.05) than on PDA, but was lower than on Reasoner and Goldrich agar (R2A) or with a hemocytometer. The current formulation of Petrifilm-YM is unlikely to be a useful monitoring method for plant pathogens in irrigation water because of the inability to successfully culture oomycetes. However, Petrifilm-AC was an effective method to quantify bacteria and can provide an easy-to-use on-farm tool to monitor biofilm risk and microbial density.

Novel phytase from Pteris vittata resistant to arsenate, high temperature, and soil deactivation.

Arsenate interferes with enzymatic processes and inhibits inorganic phosphorus (Pi) uptake in many plants. This study examined the role of phytase and phosphatase in arsenate tolerance and phosphorus (P) acquisition in the arsenic hyperaccumulator Pteris vittata . Enzyme-mediated hydrolysis of phytate in P. vittata extracts was not inhibited by arsenate at 5 mM or by heating at 100 °C for 10 min. Root exudates of P. vittata exhibited the highest phytase activity (18 nmol Pi mg(-1) protein min(-1)) when available P was low, allowing its growth on media amended with phytate as the sole source of P. Phosphorus concentration in P. vittata gametophyte tissue grown on phytate was equivalent to plants grown with inorganic phosphate at 2208 mg kg(-1), and arsenic was increased from 1777 to 2630 mg kg(-1). After 2 h of mixing with three soils, P. vittata phytase retained more activity, decreasing from ∼ 26 to ∼ 25 nmol Pi mg(-1) protein min(-1), whereas those from Pteris ensiformis and wheat decreased from ∼ 18 to ∼ 1 nmol Pi mg(-1) protein min(-1). These results suggest P. vittata has a uniquely stable phytase enabling its P acquisition in P-limiting soil environments. Furthermore, the P. vittata phytase has potential use as a soil amendment, a transgenic tool, or as a feed additive supplement, reducing the need for nonrenewable, polluting P fertilizers.

Transcriptional and metabolic insights into the differential physiological responses of arabidopsis to optimal and supraoptimal atmospheric CO2.

BACKGROUND: In tightly closed human habitats such as space stations, locations near volcano vents and closed culture vessels, atmospheric CO(2) concentration may be 10 to 20 times greater than Earth's current ambient levels. It is known that super-elevated (SE) CO(2) (>1,200 µmol mol(-1)) induces physiological responses different from that of moderately elevated CO(2) (up to 1,200 µmol mol(-1)), but little is known about the molecular responses of plants to supra-optimal [CO(2)]. METHODOLOGY/PRINCIPAL FINDINGS: To understand the underlying molecular causes for differential physiological responses, metabolite and transcript profiles were analyzed in aerial tissue of Arabidopsis plants, which were grown under ambient atmospheric CO(2) (400 µmol mol(-1)), elevated CO(2) (1,200 µmol mol(-1)) and SE CO(2) (4,000 µmol mol(-1)), at two developmental stages early and late vegetative stage. Transcript and metabolite profiling revealed very different responses to elevated versus SE [CO(2)]. The transcript profiles of SE CO(2) treated plants were closer to that of the control. Development stage had a clear effect on plant molecular response to elevated and SE [CO(2)]. Photosynthetic acclimation in terms of down-regulation of photosynthetic gene expression was observed in response to elevated [CO(2)], but not that of SE [CO(2)] providing the first molecular evidence that there appears to be a fundamental disparity in the way plants respond to elevated and SE [CO(2)]. Although starch accumulation was induced by both elevated and SE [CO(2)], the increase was less at the late vegetative stage and accompanied by higher soluble sugar content suggesting an increased starch breakdown to meet sink strength resulting from the rapid growth demand. Furthermore, many of the elevated and SE CO(2)-responsive genes found in the present study are also regulated by plant hormone and stress. CONCLUSIONS/SIGNIFICANCE: This study provides new insights into plant acclimation to elevated and SE [CO(2)] during development and how this relates to stress, sugar and hormone signaling.

Growth performance and root transcriptome remodeling of Arabidopsis in response to Mars-like levels of magnesium sulfate.

BACKGROUND: Martian regolith (unconsolidated surface material) is a potential medium for plant growth in bioregenerative life support systems during manned missions on Mars. However, hydrated magnesium sulfate mineral levels in the regolith of Mars can reach as high as 10 wt%, and would be expected to be highly inhibitory to plant growth. METHODOLOGY AND PRINCIPAL FINDINGS: Disabling ion transporters AtMRS2-10 and AtSULTR1;2, which are plasma membrane localized in peripheral root cells, is not an effective way to confer tolerance to magnesium sulfate soils. Arabidopsis mrs2-10 and sel1-10 knockout lines do not mitigate the growth inhibiting impacts of high MgSO(4).7H(2)O concentrations observed with wildtype plants. A global approach was used to identify novel genes with potential to enhance tolerance to high MgSO(4).7H(2)O (magnesium sulfate) stress. The early Arabidopsis root transcriptome response to elevated concentrations of magnesium sulfate was characterized in Col-0, and also between Col-0 and the mutant line cax1-1, which was confirmed to be relatively tolerant of high levels of MgSO(4).7H(2)O in soil solution. Differentially expressed genes in Col-0 treated for 45 min. encode enzymes primarily involved in hormone metabolism, transcription factors, calcium-binding proteins, kinases, cell wall related proteins and membrane-based transporters. Over 200 genes encoding transporters were differentially expressed in Col-0 up to 180 min. of exposure, and one of the first down-regulated genes was CAX1. The importance of this early response in wildtype Arabidopsis is exemplified in the fact that only four transcripts were differentially expressed between Col-0 and cax1-1 at 180 min. after initiation of treatment. CONCLUSIONS/SIGNIFICANCE: The results provide a solid basis for the understanding of the metabolic response of plants to elevated magnesium sulfate soils; it is the first transcriptome analysis of plants in this environment. The results foster the development of Mars soil-compatible plants by showing that cax1 mutants exhibit partial tolerance to magnesium sulfate, and by elucidating a small subset (500 vs. >10,000) of candidate genes for mutation or metabolic engineering that will enhance tolerance to magnesium sulfate soils.

Surgical treatment of nasal obstruction in rhinoplasty.

Often, rhinoplasty patients present not just for aesthetic correction, but for improvement of their nasal breathing due to functional abnormalities or problems. Because the aesthetic and functional problems must be addressed together, an understanding of both the internal and external anatomy is essential. In this article, the authors review the differential diagnosis of nasal obstruction and the important components of a thorough examination. In this article, medical treatment options are not discussed, but just as an exacting aesthetic analysis leads to an appropriate cosmetic rhinoplasty plan, a thorough functional analysis will dictate the appropriate medical or surgical treatment.

Overexpression of the CBF2 transcriptional activator in Arabidopsis delays leaf senescence and extends plant longevity.

Leaf senescence is a programmed developmental process governed by various endogenous and exogenous factors, such as the plant developmental stage, leaf age, phytohormone levels, darkness, and exposure to stresses. It was found that, in addition to its well-documented role in the enhancement of plant frost tolerance, overexpression of the C-repeat/dehydration responsive element binding factor 2 (CBF2) gene in Arabidopsis delayed the onset of leaf senescence and extended the life span of the plants by approximately 2 weeks. This phenomenon was exhibited both during developmental leaf senescence and during senescence of detached leaves artificially induced by either darkness or phytohormones. Transcriptome analysis using the Affymetrix ATH1 genome array revealed that overexpression of CBF2 significantly influenced the expression of 286 genes in mature leaf tissue. In addition to 30 stress-related genes, overexpression of CBF2 also affected the expression of 24 transcription factor (TF) genes, and 20 genes involved in protein metabolism, degradation, and post-translational modification. These results indicate that overexpression of CBF2 not only increases frost tolerance, but also affects other developmental processes, most likely through interactions with additional TFs and protein modification genes. The present findings shed new light on the crucial relationship between plant stress tolerance and longevity, as reported for other eukaryotic organisms.

Metabolomics of temperature stress.

Plants possess inducible tolerance mechanisms that extend the temperature range for survival during acute temperature stress. The inducible mechanisms of cold acclimation and acquired thermotolerance involve highly complex processes. These include perception and signal transduction of non-optimal temperatures or their physical consequences on cellular components that program extensive modification of the transcriptome, proteome, metabolome and composition and physical structure of the cytoplasm, membranes and cell walls. Therefore, a systems biology approach will be necessary to advance the understanding of plant stress responses and tolerance mechanisms. One promise of systems biology is that it will greatly enhance our understanding of individual and collective functions and thereby provide a more holistic view of plant stress responses. Past studies have found that several metabolites that could functionally contribute to induced stress tolerance have been associated with stress responses. Recent metabolite-profiling studies have refocused attention on these and other potentially important components found in the 'temperature-stress metabolome'. These metabolomic studies have demonstrated that active reconfiguration of the metabolome is regulated in part by changes in gene expression initiated by temperature-stress-activated signaling and stress-related transcription factors. One aspect of metabolism that is consistent across all of the temperature-stress metabolomic studies to date is the prominent role of central carbohydrate metabolism, which seems to be a major feature of the reprogramming of the metabolome during temperature stress. Future metabolomic studies of plant temperature-stress responses should reveal additional metabolic pathways that have important functions in temperature-stress tolerance mechanisms.

Transcriptome profiling of grapefruit flavedo following exposure to low temperature and conditioning treatments uncovers principal molecular components involved in chilling tolerance and susceptibility.

A pre-storage conditioning (CD) treatment of 16 degrees C for 7 d enhanced chilling tolerance of grapefruit and reduced the development of chilling injuries during storage at 5 degrees C. To gain a better understanding of the molecular mechanisms involved in the responses of citrus fruit to low temperatures, we performed genome-wide transcriptional profiling analysis of RNA isolated from grapefruit flavedo using the newly developed Affymetrix Citrus GeneChip microarray. Utilizing very restrictive cut-off criteria, including pair-wise anova comparisons significantly different at P < or = 0.05 and induction or repression of transcript levels by at least fourfold, we found that out of 30 171 probe sets on the microarray, 1345 probe sets were significantly affected by chilling in both control and CD-treated fruits, 509 probe sets were affected by chilling specifically in the CD-treated fruits, and 417 probe sets were specifically expressed in chilling-sensitive control fruits. Overall, exposure to chilling led to expression arrest of general cellular metabolic activity, including concretive down-regulation of cell wall, pathogen defence, photosynthesis, respiration, and protein, nucleic acid and secondary metabolism. On the other hand, chilling enhanced adaptation processes that involve changes in the expression of transcripts related to membranes, lipid, sterol and carbohydrate metabolism, stress stimuli, hormone biosynthesis, and modifications in DNA binding and transcription factors.

Glucan, water dikinase activity stimulates breakdown of starch granules by plastidial beta-amylases.

Glucan phosphorylating enzymes are required for normal mobilization of starch in leaves of Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum), but mechanisms underlying this dependency are unknown. Using two different activity assays, we aimed to identify starch degrading enzymes from Arabidopsis, whose activity is affected by glucan phosphorylation. Breakdown of granular starch by a protein fraction purified from leaf extracts increased approximately 2-fold if the granules were simultaneously phosphorylated by recombinant potato glucan, water dikinase (GWD). Using matrix-assisted laser-desorption ionization mass spectrometry several putative starch-related enzymes were identified in this fraction, among them beta-AMYLASE1 (BAM1; At3g23920) and ISOAMYLASE3 (ISA3; At4g09020). Experiments using purified recombinant enzymes showed that BAM1 activity with granules similarly increased under conditions of simultaneous starch phosphorylation. Purified recombinant potato ISA3 (StISA3) did not attack the granular starch significantly with or without glucan phosphorylation. However, starch breakdown by a mixture of BAM1 and StISA3 was 2 times higher than that by BAM1 alone and was further enhanced in the presence of GWD and ATP. Similar to BAM1, maltose release from granular starch by purified recombinant BAM3 (At4g17090), another plastid-localized beta-amylase isoform, increased 2- to 3-fold if the granules were simultaneously phosphorylated by GWD. BAM activity in turn strongly stimulated the GWD-catalyzed phosphorylation. The interdependence between the activities of GWD and BAMs offers an explanation for the severe starch excess phenotype of GWD-deficient mutants.

Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content.

Exposure of Arabidopsis to low temperatures results in cold acclimation where freezing tolerance is enhanced. To achieve a wider view of the role of transcriptome to biochemical changes that occur during cold acclimation, analyses of concurrent transcript and metabolite changes during cold acclimation was performed revealing the dynamics of selected gene-metabolite relationships. Exposure to low temperature resulted in broad transcriptional and metabolite responses. Principal component analysis revealed sequentially progressive, global changes in both gene expression and metabolite profiles during cold acclimation. Changes in transcript abundance for many metabolic processes, including protein amino acid biosynthetic pathways and soluble carbohydrates, during cold acclimation were observed. For some metabolic processes, changes in transcript abundance temporally correlated with changes in metabolite levels. For other metabolic processes, changes in transcript levels were not correlated with changes in metabolite levels. The present findings demonstrate that regulatory processes independent of transcript abundance represent a key part of the metabolic adjustments that occur during cold acclimation.

Postharvest heat and conditioning treatments activate different molecular responses and reduce chilling injuries in grapefruit.

A combination of hot water (a rinse at 62 degrees C for 20 s) and conditioning (pre-storage at 16 degrees C for 7 d) treatments synergistically reduced chilling injury development in grapefruit (Citrus paradisi, cv. "Star Ruby") during cold storage at 2 degrees C, suggesting that the treatments may activate different chilling tolerance responses. To study the molecular mechanisms involved, chilling- and conditioning-responsive genes were isolated by polymerase chain reaction (PCR) cDNA subtraction, cDNA libraries were constructed from hot water- and conditioning-treated fruit, and cDNA sequencing was used to identify putative stress-responsive and chilling tolerance genes. PCR cDNA subtraction revealed the identification of 17 chilling-responsive and heat- and conditioning-induced genes, and the expression patterns of 11 additional stress-related genes, antioxidant defensive genes, and genes encoding enzymes involved in membrane lipid modifications were characterized. It was found that hot water and conditioning treatments had little effect on gene expression by themselves, but rather had a priming effect, and enabled the fruit to activate their defence responses after subsequent exposure to chilling. RNA gel blot hybridizations revealed that the expression patterns of eight genes, including HSP19-I, HSP19-II, dehydrin, universal stress protein (USP), EIN2, 1,3;4-beta-D-glucanase, and superoxide dismutase (SOD), were specifically regulated by the heat treatment, and four genes, including fatty acid desaturase2 (FAD2) and lipid transfer protein (LTP), were specifically regulated by the conditioning treatment. Furthermore, four more genes were identified, including a translation initiation factor (SUI1), a chaperonin, and alcohol dehydrogenase (ADH), that were commonly regulated by both heat and conditioning treatments. According to these data, it is suggested that pre-storage heat and conditioning treatments may enhance fruit chilling tolerance by activating different molecular mechanisms. The hot water treatment activates mainly the expression of various stress-related genes, whereas the conditioning treatment activates mainly the expression of lipid membrane modification enzymes.

RNA interference of Arabidopsis beta-amylase8 prevents maltose accumulation upon cold shock and increases sensitivity of PSII photochemical efficiency to freezing stress.

It has been suggested that beta-amylase (BMY) induction during temperature stress in Arabidopsis could lead to starch-dependent maltose accumulation, and that maltose may contribute to protection of the electron transport chain and proteins in the chloroplast stroma during acute stress. A time-course transcript profiling analysis for cold shock at 4 degrees C revealed that BMY8 (At4g17090) was induced specifically in response to cold shock, while major induction was not observed for any of the other eight beta-amylases. A parallel metabolite-profiling analysis revealed a robust transient maltose accumulation during cold shock. BMY8 RNAi lines with lower BMY8 expression exhibited a starch-excess phenotype, and a dramatic decrease in maltose accumulation during a 6-h cold shock at 4 degrees C. The decreased maltose content was also accompanied by decreased glucose, fructose and sucrose content in the BMY8 RNAi plants, consistent with the roles of beta-amylase and maltose in transitory starch metabolism. BMY8 RNAi lines with reduced soluble sugar content exhibited diminished chlorophyll fluorescence as F(v)/F(m) ratio compared with wild type, suggesting that PSII photochemical efficiency was more sensitive to freezing stress. Together, carbohydrate analysis and freezing stress results of BMY8 RNAi lines indicate that increased maltose content, by itself or together through a maltose-dependent increase in other soluble sugars, contributes to the protection of the photosynthetic electron transport chain during freezing stress.

Non-linear PCA: a missing data approach.

MOTIVATION: Visualizing and analysing the potential non-linear structure of a dataset is becoming an important task in molecular biology. This is even more challenging when the data have missing values. RESULTS: Here, we propose an inverse model that performs non-linear principal component analysis (NLPCA) from incomplete datasets. Missing values are ignored while optimizing the model, but can be estimated afterwards. Results are shown for both artificial and experimental datasets. In contrast to linear methods, non-linear methods were able to give better missing value estimations for non-linear structured data. APPLICATION: We applied this technique to a time course of metabolite data from a cold stress experiment on the model plant Arabidopsis thaliana, and could approximate the mapping function from any time point to the metabolite responses. Thus, the inverse NLPCA provides greatly improved information for better understanding the complex response to cold stress. CONTACT: scholz@mpimp-golm.mpg.de.