JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom.

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Plants and global warming: challenges and strategies for a warming world.

KEY MESSAGE: In this review, we made an attempt to create a holistic picture of plant response to a rising temperature environment and its impact by covering all aspects from temperature perception to thermotolerance. This comprehensive account describing the molecular mechanisms orchestrating these responses and potential mitigation strategies will be helpful for understanding the impact of global warming on plant life. Organisms need to constantly recalibrate development and physiology in response to changes in their environment. Climate change-associated global warming is amplifying the intensity and periodicity of these changes. Being sessile, plants are particularly vulnerable to variations happening around them. These changes can cause structural, metabolomic, and physiological perturbations, leading to alterations in the growth program and in extreme cases, plant death. In general, plants have a remarkable ability to respond to these challenges, supported by an elaborate mechanism to sense and respond to external changes. Once perceived, plants integrate these signals into the growth program so that their development and physiology can be modulated befittingly. This multifaceted signaling network, which helps plants to establish acclimation and survival responses enabled their extensive geographical distribution. Temperature is one of the key environmental variables that affect all aspects of plant life. Over the years, our knowledge of how plants perceive temperature and how they respond to heat stress has improved significantly. However, a comprehensive mechanistic understanding of the process still largely elusive. This review explores how an increase in the global surface temperature detrimentally affects plant survival and productivity and discusses current understanding of plant responses to high temperature (HT) and underlying mechanisms. We also highlighted potential resilience attributes that can be utilized to mitigate the impact of global warming.

SHORTROOT-Mediated Intercellular Signals Coordinate Phloem Development in Arabidopsis Roots.

Asymmetric cell division (ACD) and positional signals play critical roles in the tissue patterning process. In the Arabidopsis (Arabidopsis thaliana) root meristem, two major phloem cell types arise via ACDs of distinct origins: one for companion cells (CCs) and the other for proto- and metaphloem sieve elements (SEs). The molecular mechanisms underlying each of these processes have been reported; however, how these are coordinated has remained elusive. Here, we report a new phloem development process coordinated via the SHORTROOT (SHR) transcription factor in Arabidopsis. The movement of SHR into the endodermis regulates the ACD for CC formation by activating microRNA165/6, while SHR moving into the phloem regulates the ACD generating the two phloem SEs. In the phloem, SHR sequentially activates NAC-REGULATED SEED MORPHOLOGY 1 (NARS1) and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN 2 (SND2), and these three together form a positive feedforward loop. Under this regulatory scheme, NARS1, generated in the CCs of the root differentiation zone, establishes a top-down signal that drives the ACD for phloem SEs in the meristem. SND2 appears to function downstream to amplify NARS1 via positive feedback. This new regulatory mechanism expands our understanding of the sophisticated vascular tissue patterning processes occurring during postembryonic root development.plantcell;32/5/1519/FX1F1fx1.

Advantage of zinc oxide nanoparticles over silver nanoparticles for the management of Aeromonas veronii infection in Xiphophorus hellerii.

Bacterial pathogens cause significant challenge to the ornamental fish industry. Eventhough antibiotic administration has been recommended to manage fish diseases, there is alarming concern with emergence of antibiotic resistance. This indicates the need for the development of alternative methods with multi-targeted action to manage fish diseases. In the study, silver (AgNPs) and zinc oxide (ZnONPs) nanoparticles have been evaluated for its activity against Aeromonas veronii. Both the AgNPs and ZnONPs were found to have bactericidal activity against A. veronii. In vivo experiments with A. veronii was found to cause severe mortality in Xiphophorus hellerii with a LD50 of 1.4 × 108 CFU/mL. However, treatment with AgNPs and ZnONPs each at a concentration of 1 mg/L was found to enhance the survival rate of X. hellerii to 83.3% and 100% respectively. Further histopathological analysis showed alterations in gill, intestine and liver of X. hellerii due to A. veronii in the infection control. In the case of AgNPs treated group, symptoms of moderate tissue damage could be observed. However, the ZnONPs treated X. hellerii showed normal histological features with minimum tissue damage. The bath dip method further confirmed the protective ability of the zinc oxide nanoparticles (1 mg/L) on X. hellerii.

A potential antifungal and growth-promoting bacterium Bacillus sp. KTMA4 from tomato rhizosphere.

Plant growth-promoting rhizobacteria are indigenous beneficial bacteria that will enhance plant growth as well as suppress phytopathogens. In the present study, the isolate KTMA4 showed the highest inhibition against major phytopathogens of tomato; Fusarium oxysporum (66%) and Alternaria solani (54%) after seven days of incubation. Analysis of the 16S rRNA gene sequence revealed that the isolate KTMA4 is Bacillus cereus (MG547975). The isolate produced in vitro plants growth-promoting factors such as Indole-3-acetic acid, ammonia, catalase, siderophore and 1-aminocyclopropane-1-carboxylate deaminase and it has nitrogen fixation ability. The bacterial strain has also produced lytic enzymes such as amylase, cellulase, xylanase, lipase, and protease. Moreover, the bacterium Bacillus cereus KTMA4 effectively produced biofilm, biosurfactants and salt-tolerant (5% NaCl). The bacterium exhibited intrinsic antibiotic resistance. The in vivo studies using tomato plants grown from seeds treated with the bacterial strain KTMA4 demonstrated an enhancement in seed germination percentage (86.66 ± 2.88) and vigour index (637.5 ± 21.65) over the uninoculated control (germination percentage- 28.33 ± 2.88 and vigour index- 42.5 ± 4.33). 60 days of greenhouse study revealed that the bacterial isolate enhanced the plant growth significantly (P ≤ 0.05) compared to the uninoculated control and the treated plants. Therefore the study suggests that the newly isolated rhizosphere bacterial strain can be used as a potential biocontrol agent against a multitude of fungal pathogens as well as a biofertilizer inoculant for tomato cultivation.

Surface functionalization of central venous catheter with mycofabricated silver nanoparticles and its antibiofilm activity on multidrug resistant Acinetobacter baumannii.

The mycofabrication of silver nanoparticles (AgNPs) through green chemistry protocol is an advanced methodological progress in medical nanotechnology. Mycofabricated AgNPs are less toxic due to an aura of biomolecules around the nanoparticles. Hence the mycofabricated AgNPs can be used for clinical applications. The present study explores the antibiofilm activity of mycogenerated AgNPs, which were synthesized by the enzymatic reduction of silver nitrate using the marine algicolous endophytic fungus Penicillium polonicum ARA10. The mycogenerated AgNPs showed very specific and potent bactericidal activity against Acinetobacter baumannii. Anti-A.baumannii activities of mycogenerated AgNPs on planktonic as well as biofilm embedded cells were explored. The physical impact of synthesized AgNPs on A.baumannii was investigated by scanning electron microscopy and fluorescence microscopy. A bionanocomposite coating for the central venous catheter (CVC) was formulated using the mycogenerated AgNPs and polydopamine. The bionanocomposite surface was characterized by field emission scanning electron microscopy, water contact angle measurement, and Raman spectroscopy. The results showed that the mycogenerated AgNPs have potent antibiofilm activity on biofilms of A.baumannii. The scanning electron microscopy (SEM) and fluorescence microscopy images showed noticeable aberrations on the ultrastructure of A.baumannii. The SEM and FE-SEM images of biofilms on the surface of CVC samples proved that the AgNPs at minimum bactericidal concentration could destroy the structure of biofilms and lyses the bacterial cell. Thus, the present study establishes a new way to the development of 'antibacterial surfaces' based on mycogenerated AgNPs.

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria.

Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development.

Grasses suppress shoot-borne roots to conserve water during drought.

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.

Green synthesized silver nanoparticles by marine endophytic fungus Penicillium polonicum and its antibacterial efficacy against biofilm forming, multidrug-resistant Acinetobacter baumanii.

Acinetobacter baumanii, a gram-negative, non-motile, encapsulated coccobacillus which causes infections worldwide. The objective of this study was to find a fungal strain that could be utilized to biosynthesize antibacterial silver nanoparticles (AgNPs) against Acinetobacter baumanii. The present investigation explains rapid and extracellular biosynthesis of silver nanoparticles by the algicolous endophytic fungus, Penicillium polonicum, isolated from the marine green alga Chetomorpha antennina. The obtained silver nanoparticles were characterized by UV-Vis spectroscopy, Raman spectroscopy, Fourier transformation infrared (FTIR), and Transmission electron microscopy (TEM). The SNPs showed a characteristic UV- visible peak at 430 nm with an average size of 10-15 nm. As evident from the FTIR and Raman spectra, possibly the protein components of fungal extract have caused the reduction of silver nitrate. Parametric optimization, including the concentration of AgNO3, ratio of cell filtrate and AgNO3, fungal biomass, reaction time, pH, and presence of light, was done for rapid AgNPs production. The antibacterial efficacy of AgNPs against multi-drug-resistant, biofilm-forming Acinetobacter baumanii, was evaluated by well diffusion assay. The Minimum inhibitory concentration (MIC) of AgNP was 15.62 µgml-1 and the minimum bactericidal concentration (MBC) was 31.24 µgml-1. Killing kinetic assay revealed complete killing of the bacterial cells within 6 h. Log reduction and percent survival of bacterial cells were analyzed from killing kinetic study. Bactericidal nature of synthesized nanoparticles was confirmed by fluorescent microscopical analysis. The effect of AgNPs on the ultrastructure of bacterial pathogen was evaluated by Transmission electron microscopy.

Community-Based Accompaniment with Supervised Antiretrovirals for HIV-Positive Adults in Peru: A Cluster-Randomized Trial.

We conducted a cluster-randomized trial to estimate effects of directly observed combination antiretroviral therapy (DOT-cART) on retention with viral suppression among HIV-positive adults in Peru. We randomly allocated facilities to receive the 12-month intervention plus the standard of care, including adherence support provided through accompaniment. In the intervention arm, health workers supervised doses, twice daily, and accompanied patients to appointments. Among 356 patients, intention-to-treat analyses showed no statistically significant benefit of DOT, relative to no-DOT, at 12 or 24 months (adjusted probability of primary outcome: 0.81 vs. 0.73 and 0.76 vs. 0.68, respectively). A statistically significant benefit of DOT was found in per-protocol and as-treated analyses at 12 months (0.83 for DOT vs. 0.73 for no DOT, p value: 0.02 per-protocol, 0.01 as-treated), but not 24 months. Rates of retention with viral suppression were high in both arms. Among adults receiving robust adherence support, the added effect of time-limited DOT, if any, is small-to-moderate.

Studies on biofilm formation and virulence factors associated with uropathogenic Escherichia coli isolated from patient with acute pyelonephritis.

The current study aims to the detection of pathogenic potential and virulence factor identification of uropathogenic Escherichia coli BRL-17 isolated from patients urine. The organism was isolated from the patient with chronic pyelonephritis. The identification of organism was done by analyzing gram staining, biochemical, 16S rDNA analysis, Raman microscopy and SEM analysis. The pathogenic potential was identified by multiplex PCR analysis of virulence factor genes like sfa, hly D, pap C. The biofilm forming ability was tested by congo red agar assay and tissue culture plate assay. The result of gram staining and biochemical analysis shows the characteristics of E-coli. The 16S rDNA analysis of the clinically isolated uropathogen showed 100% similarity with uropathogenic Escherichia coli strain. Raman microscopy and SEM confirms the organism as E-coli. The Multiplex PCR study identifies virulence genes like sfa, hly D, pap C in isolated E-coli. The presence of P fimbriae coded pap C gene, S fimbriae coded sfa gene and hemolysin-D coded hly D gene discloses its potential to cause urinary tract infection. Biofilm assay result enhances the organism's role as strong biofilm former. This biofilm forming ability of Escherichia coli strain BRL-17 made the organism to escape from host immune system and helps to colonize in bladder and kidney. This also helps to enhance the resistance to antibiotics. Our study confirms the organism as multidrug resistant, highly virulent, strong biofilm forming E-coli. The strain may be used for the development of animal models of pyelonephritis for the purpose of drug discovery.

PHABULOSA controls the quiescent center-independent root meristem activities in Arabidopsis thaliana.

Plant growth depends on stem cell niches in meristems. In the root apical meristem, the quiescent center (QC) cells form a niche together with the surrounding stem cells. Stem cells produce daughter cells that are displaced into a transit-amplifying (TA) domain of the root meristem. TA cells divide several times to provide cells for growth. SHORTROOT (SHR) and SCARECROW (SCR) are key regulators of the stem cell niche. Cytokinin controls TA cell activities in a dose-dependent manner. Although the regulatory programs in each compartment of the root meristem have been identified, it is still unclear how they coordinate one another. Here, we investigate how PHABULOSA (PHB), under the posttranscriptional control of SHR and SCR, regulates TA cell activities. The root meristem and growth defects in shr or scr mutants were significantly recovered in the shr phb or scr phb double mutant, respectively. This rescue in root growth occurs in the absence of a QC. Conversely, when the modified PHB, which is highly resistant to microRNA, was expressed throughout the stele of the wild-type root meristem, root growth became very similar to that observed in the shr; however, the identity of the QC was unaffected. Interestingly, a moderate increase in PHB resulted in a root meristem phenotype similar to that observed following the application of high levels of cytokinin. Our protoplast assay and transgenic approach using ARR10 suggest that the depletion of TA cells by high PHB in the stele occurs via the repression of B-ARR activities. This regulatory mechanism seems to help to maintain the cytokinin homeostasis in the meristem. Taken together, our study suggests that PHB can dynamically regulate TA cell activities in a QC-independent manner, and that the SHR-PHB pathway enables a robust root growth system by coordinating the stem cell niche and TA domain.

Visual Information Fusion through Bayesian Inference for Adaptive Probability-Oriented Feature Matching.

This work presents a visual information fusion approach for robust probability-oriented feature matching. It is sustained by omnidirectional imaging, and it is tested in a visual localization framework, in mobile robotics. General visual localization methods have been extensively studied and optimized in terms of performance. However, one of the main threats that jeopardizes the final estimation is the presence of outliers. In this paper, we present several contributions to deal with that issue. First, 3D information data, associated with SURF (Speeded-Up Robust Feature) points detected on the images, is inferred under the Bayesian framework established by Gaussian processes (GPs). Such information represents a probability distribution for the feature points’ existence, which is successively fused and updated throughout the robot’s poses. Secondly, this distribution can be properly sampled and projected onto the next 2D image frame in t+1, by means of a filter-motion prediction. This strategy permits obtaining relevant areas in the image reference system, from which probable matches could be detected, in terms of the accumulated probability of feature existence. This approach entails an adaptive probability-oriented matching search, which accounts for significant areas of the image, but it also considers unseen parts of the scene, thanks to an internal modulation of the probability distribution domain, computed in terms of the current uncertainty of the system. The main outcomes confirm a robust feature matching, which permits producing consistent localization estimates, aided by the odometer’s prior to estimate the scale factor. Publicly available datasets have been used to validate the design and operation of the approach. Moreover, the proposal has been compared, firstly with a standard feature matching and secondly with a localization method, based on an inverse depth parametrization. The results confirm the validity of the approach in terms of feature matching, localization accuracy, and time consumption.

Stem cell function during plant vascular development.

The plant vascular system, composed of xylem and phloem, evolved to connect plant organs and transport various molecules between them. During the post-embryonic growth, these conductive tissues constitutively form from cells that are derived from a lateral meristem, commonly called procambium and cambium. Procambium/cambium contains pluripotent stem cells and provides a microenvironment that maintains the stem cell population. Because vascular plants continue to form new tissues and organs throughout their life cycle, the formation and maintenance of stem cells are crucial for plant growth and development. In this decade, there has been considerable progress in understanding the molecular control of the organization and maintenance of stem cells in vascular plants. Noticeable advance has been made in elucidating the role of transcription factors and major plant hormones in stem cell maintenance and vascular tissue differentiation. These studies suggest the shared regulatory mechanisms among various types of plant stem cell pools. In this review, we focus on two aspects of stem cell function in the vascular cambium, cell proliferation and cell differentiation.

HAWAIIAN SKIRT regulates the quiescent center-independent meristem activity in Arabidopsis roots.

Root apical meristem (RAM) drives post-embryonic root growth by constantly supplying cells through mitosis. It is composed of stem cells and their derivatives, the transit-amplifying (TA) cells. Stem cell organization and its maintenance in the RAM are well characterized, however, their relationships with TA cells remain unclear. SHORTROOT (SHR) is critical for root development. It patterns cell types and promotes the post-embryonic root growth. Defective root growth in the shr has been ascribed to the lack of quiescent center (QC), which maintains the surrounding stem cells. However, our recent investigation indicated that SHR maintains TA cells independently of QC by modulating PHABULOSA (PHB) through miRNA165/6. PHB controls TA cell activity by modulating cytokinin levels and type B Arabidopsis Response Regulator activity, in a dosage-dependent manner. To further understand TA cell regulation, we conducted a shr suppressor screen. With an extensive mutagenesis screen followed by genome sequencing of a pooled F2 population, we discovered two suppressor alleles with mutations in HAWAIIAN SKIRT (HWS). HWS, encoding an F-box protein with kelch domain, is expressed, partly depending on SHR, in the root cap and in the pericycle of the differentiation zone. Interestingly, root growth in the shr hws was more active than the wild-type roots for the first 7 days after germination, without recovering QC. Contrary to shr phb, shr hws did not show a recovery of cytokinin signaling. These indicate that HWS affects QC-independent TA cell activities through a pathway distinctive from PHB.

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.

A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.

An inexpensive method for kinematic calibration of a parallel robot by using one hand-held camera as main sensor.

This paper presents a novel method for the calibration of a parallel robot, which allows a more accurate configuration instead of a configuration based on nominal parameters. It is used, as the main sensor with one camera installed in the robot hand that determines the relative position of the robot with respect to a spherical object fixed in the working area of the robot. The positions of the end effector are related to the incremental positions of resolvers of the robot motors. A kinematic model of the robot is used to find a new group of parameters, which minimizes errors in the kinematic equations. Additionally, properties of the spherical object and intrinsic camera parameters are utilized to model the projection of the object in the image and thereby improve spatial measurements. Finally, several working tests, static and tracking tests are executed in order to verify how the robotic system behaviour improves by using calibrated parameters against nominal parameters. In order to emphasize that, this proposed new method uses neither external nor expensive sensor. That is why new robots are useful in teaching and research activities.

[Fat-forming solitary fibrous tumor with NAB2/ STAT6 gene fusion. Case report of genial location and literature review]. / Tumor fibroso solitario variedad lipomatosa con fusión génica NAB2/STAT6. Estudio de un caso de localización geniana y revisión de la literatura.

The lipomatous variety solitary fibrous tumor is a soft tissue neoplasm composed of mature adipose tissue and hemangiopericytoma areas. A 53-year-old man consulted for facial asymmetry and maxillofacial magnetic resonance imaging showed a cystic lesion, 3 x 2 cm in size, in front of the anterior wall of the maxillary sinus. Histologically, there were dense spindle cells expressing CD34, CD99, Bcl-2, and STAT6, myxoid zones, hemangiopericytomatous blood vessels, and S100 positive adipocytes. NAB2/STAT6 gene fusion was revealed by RT-PCR. The main differential diagnosis was raised with the spindle cell lipoma and malignant variant of the lipomatous solitary fibrous tumor. STAT6 overexpression and NAB2/STAT6 gene fusion are specific for lipomatous solitary fibrous tumor and the presence of lipoblasts and atypical lipomatous tumor areas suggests malignancy. These tumors located in the head and neck region have a benign biological behavior.

Rotula aquatica Lour. mitigates oxidative stress and inflammation in acute pyelonephritic rats.

The current study evaluates the efficacy of methanolic extract of Rotula aquatica Lour. (MERA) against inflammatory changes associated with acute pyelonephritis. The antioxidant enzymes such as SOD, CAT, GPx, GR and oxidative stress markers like GSH content, malondialdehyde (MDA) level, nitrate level, reactive oxygen species (ROS) level and renal toxicity markers were evaluated in this study. The mRNA level expression of Toll-like receptor 4 (TLR-4), nuclear transcription factor kappa B (NF-κB), tumour necrosis factor-alpha (TNF-α), interleukin-6 (IL-6) and Tamm Horsfall protein (THP) were studied by RT-PCR analysis. The oral administration of MERA increases the antioxidant enzyme status in pyelonephritis rat. The elevated levels of oxidative stress markers in pyelonephritic rats were ameliorated by the administration of MERA at 100 mg/kg and 200 mg/kg bwt of the rat. The mRNA level expression of major genes were restored to normal level by MERA.