Identification for surrogate drought tolerance in maize inbred lines utilizing high-throughput phenomics approach.

Screening for drought tolerance requires precise techniques like phonemics, which is an emerging science aimed at non-destructive methods allowing large-scale screening of genotypes. Large-scale screening complements genomic efforts to identify genes relevant for crop improvement. Thirty maize inbred lines from various sources (exotic and indigenous) maintained at Dryland Agriculture Research Station were used in the current study. In the automated plant transport and imaging systems (LemnaTec Scanalyzer system for large plants), top and side view images were taken of the VIS (visible) and NIR (near infrared) range of the light spectrum to capture phenes. All images were obtained with a thermal imager. All sensors were used to collect images one day after shifting the pots from the greenhouse for 11 days. Image processing was done using pre-processing, segmentation and flowered by features' extraction. Different surrogate traits such as pixel area, plant aspect ratio, convex hull ratio and calliper length were estimated. A strong association was found between canopy temperature and above ground biomass under stress conditions. Promising lines in different surrogates will be utilized in breeding programmes to develop mapping populations for traits of interest related to drought resilience, in terms of improved tissue water status and mapping of genes/QTLs for drought traits.

Micronutrient productivity: a comprehensive parameter for biofortification in rice (Oryza sativa L.) grain.

BACKGROUND: Enhancing the micronutrient content of staple crops such as rice will improve human nutrition and address the problem of hidden hunger globally. Rice grains consumed after polishing lack adequate amounts of micronutrients. The present study aims to reveal the effects of polishing on micronutrient content and to identify superior genotype(s) to improve yield and micronutrient content after polishing. RESULTS: AM65 exhibited the highest zinc content, and AM180 had the highest iron content, even after polishing. There was little or no difference between the genotypes for zinc content in bran, indicating a possible threshold for micronutrient accumulation in the aleurone layer. A comprehensive selection criterion called 'micronutrient productivity' was used to select for both yield and micronutrient parameters. AM65 and ARB6 showed high zinc and iron productivity indices. OsZIP4b and OsZIP6c markers showed an association with iron content on an agarose gel. Sequencing of markers revealed that OsYSL15 and OsZIP6c were associated with grain zinc content and OsZIP3b, OsMTP1a, and OsYSL4b with grain iron content. These markers can be used for selecting superior accessions. CONCLUSION: AM65 was loaded with micronutrients and manifested a positive correlation with the grain yield, and it is undoubtedly 'super elite'. Bran does not drain the grain but rather acts as gateway for micronutrient transportation to the endosperm. Micronutrient productivity is a comprehensive parameter for the biofortification of grain. © 2018 Society of Chemical Industry.

New Dark Area Sensitive Tone Mapping for Deep Learning Based Traffic Sign Recognition.

In this paper, we propose a new Intelligent Traffic Sign Recognition (ITSR) system with illumination preprocessing capability. Our proposed Dark Area Sensitive Tone Mapping (DASTM) technique can enhance the illumination of only dark regions of an image with little impact on bright regions. We used this technique as a pre-processing module for our new traffic sign recognition system. We combined DASTM with a TS detector, an optimized version of YOLOv3 for the detection of three classes of traffic signs. We trained ITSR on a dataset of Korean traffic signs with prohibitory, mandatory, and danger classes. We achieved Mean Average Precision (MAP) value of 90.07% (previous best result was 86.61%) on challenging Korean Traffic Sign Detection (KTSD) dataset and 100% on German Traffic Sign Detection Benchmark (GTSDB). Result comparisons of ITSR with latest D-Patches, TS detector, and YOLOv3 show that our new ITSR significantly outperforms in recognition performance.

Large scale changes in the transcriptome of Eisenia fetida during regeneration.

Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum Annelida, in which the genomes of the marine oligochaete Capitella telata and the freshwater leech Helobdella robusta have been sequenced and studied. Herein, we report the transcriptomic changes in Eisenia fetida (Indian isolate) during regeneration. Following injury, E. fetida regenerates the posterior segments in a time spanning several weeks. We analyzed gene expression changes both in the newly regenerating cells and in the adjacent tissue, at early (15days post amputation), intermediate (20days post amputation) and late (30 days post amputation) by RNAseq based de novo assembly and comparison of transcriptomes. We also generated a draft genome sequence of this terrestrial red worm using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm showed that many miRNA gene families have undergone extensive duplications. Sox4, a master regulator of TGF-beta mediated epithelial-mesenchymal transition was induced in the newly regenerated tissue. Genes for several proteins such as sialidases and neurotrophins were identified amongst the differentially expressed transcripts. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. We identified 315 novel differentially expressed transcripts in the transcriptome, that have no homolog in any other species. Surprisingly, 82% of these novel differentially expressed transcripts showed poor potential for coding proteins, suggesting that novel ncRNAs may play a critical role in regeneration of earthworm.

G-protein-coupled receptor signaling and polarized actin dynamics drive cell-in-cell invasion.

Homotypic or entotic cell-in-cell invasion is an integrin-independent process observed in carcinoma cells exposed during conditions of low adhesion such as in exudates of malignant disease. Although active cell-in-cell invasion depends on RhoA and actin, the precise mechanism as well as the underlying actin structures and assembly factors driving the process are unknown. Furthermore, whether specific cell surface receptors trigger entotic invasion in a signal-dependent fashion has not been investigated. In this study, we identify the G-protein-coupled LPA receptor 2 (LPAR2) as a signal transducer specifically required for the actively invading cell during entosis. We find that G12/13 and PDZ-RhoGEF are required for entotic invasion, which is driven by blebbing and a uropod-like actin structure at the rear of the invading cell. Finally, we provide evidence for an involvement of the RhoA-regulated formin Dia1 for entosis downstream of LPAR2. Thus, we delineate a signaling process that regulates actin dynamics during cell-in-cell invasion.

Inhibiting the growth of pancreatic adenocarcinoma in vitro and in vivo through targeted treatment with designer gold nanotherapeutics.

BACKGROUND: Pancreatic cancer is one of the deadliest of all human malignancies with limited options for therapy. Here, we report the development of an optimized targeted drug delivery system to inhibit advanced stage pancreatic tumor growth in an orthotopic mouse model. METHODPRINCIPAL FINDINGS: Targeting specificity in vitro was confirmed by preincubation of the pancreatic cancer cells with C225 as well as Nitrobenzylthioinosine (NBMPR - nucleoside transporter (NT) inhibitor). Upon nanoconjugation functional activity of gemcitabine was retained as tested using a thymidine incorporation assay. Significant stability of the nanoconjugates was maintained, with only 12% release of gemcitabine over a 24-hour period in mouse plasma. Finally, an in vivo study demonstrated the inhibition of tumor growth through targeted delivery of a low dose of gemcitabine in an orthotopic model of pancreatic cancer, mimicking an advanced stage of the disease. CONCLUSION: We demonstrated in this study that the gold nanoparticle-based therapeutic containing gemcitabine inhibited tumor growth in an advanced stage of the disease in an orthotopic model of pancreatic cancer. Future work would focus on understanding the pharmacokinetics and combining active targeting with passive targeting to further improve the therapeutic efficacy and increase survival.

Designing nanoconjugates to effectively target pancreatic cancer cells in vitro and in vivo.

BACKGROUND: Pancreatic cancer is the fourth leading cause of cancer related deaths in America. Monoclonal antibodies are a viable treatment option for inhibiting cancer growth. Tumor specific drug delivery could be achieved utilizing these monoclonal antibodies as targeting agents. This type of designer therapeutic is evolving and with the use of gold nanoparticles it is a promising approach to selectively deliver chemotherapeutics to malignant cells. Gold nanoparticles (GNPs) are showing extreme promise in current medicinal research. GNPs have been shown to non-invasively kill tumor cells by hyperthermia using radiofrequency. They have also been implemented as early detection agents due to their unique X-ray contrast properties; success was revealed with clear delineation of blood capillaries in a preclinical model by CT (computer tomography). The fundamental parameters for intelligent design of nanoconjugates are on the forefront. The goal of this study is to define the necessary design parameters to successfully target pancreatic cancer cells. METHODOLOGY/PRINCIPAL FINDINGS: The nanoconjugates described in this study were characterized with various physico-chemical techniques. We demonstrate that the number of cetuximab molecules (targeting agent) on a GNP, the hydrodynamic size of the nanoconjugates, available reactive surface area and the ability of the nanoconjugates to sequester EGFR (epidermal growth factor receptor), all play critical roles in effectively targeting tumor cells in vitro and in vivo in an orthotopic model of pancreatic cancer. CONCLUSION: Our results suggest the specific targeting of tumor cells depends on a number of crucial components 1) targeting agent to nanoparticle ratio 2) availability of reactive surface area on the nanoparticle 3) ability of the nanoconjugate to bind the target and 4) hydrodynamic diameter of the nanoconjugate. We believe this study will help define the design parameters for formulating better strategies for specifically targeting tumors with nanoparticle conjugates.

Magnetite (Fe3O4) nanocrystals affect the expression of genes involved in the TGF-beta signalling pathway.

An understanding of interaction of nanomaterials with living systems is fundamental to address nanosafety issues, which, in turn will dictate the future prospects of nanomedicine. Herein, we examine the molecular effects of uptake of Magnetite (Fe(3)O(4)) Nanocrystals (MNC) using a transcriptomics approach. The uptake of MNC was studied by electron microscopy. This was followed by transcriptional profiling using whole genome microarrays, functional analysis of microarray data, real time PCR and biochemical assay for CASP9. Transcriptional profiling revealed 69 genes to be differentially expressed upon MNC treatment. Many of these genes are associated with TGF-beta signaling and include ID1, ID2, ID3, CASP9, SMAD6 and SMAD7, which are important negative regulators of signaling pathways involved in development and tumorigenesis. Moreover, upon treatment with MNC, expression of CASP9 was also found to decrease in a dose dependent manner. This approach could help us to identify specific effects of MNC upon cells and give us simultaneous clues about their biocompatibility and therapeutic potential. The MNC can specifically interfere with TGF-beta signaling by inhibiting the expression of ID and SMAD genes. As TGF-beta signaling invokes different responses in undifferentiated cells and adult tissues in a cell-type specific manner, our findings have far reaching implications in cellular development, differentiation and cancer.

Thermoregulation and aggregation in neonatal bearded dragons (Pogona vitticeps).

Ectothermic vertebrates, such as reptiles, thermoregulate behaviorally by choosing from available temperatures in their environment. As neonates, bearded dragons (Pogona vitticeps) are often observed to aggregate in vertical strata. A proximate mechanism for this behavior is the thermal advantage of heat storage (i.e., grouped lizards benefit through a decreased surface area to volume ratio), although competition for limited thermal resources, or aggregation for social reasons are alternative explanations. This study was designed to gain an understanding of how aggregation and thermoregulation interact. We observed that both isolated and grouped individuals achieved a similar level of thermoregulation (mean T(b) over trial) within a thermal gradient, but that individuals within a group had lower thermoregulatory precision. An experimental design in which light and ambient temperature (T(a)) (20 versus 30 degrees C) were altered established that a light bulb (source of heat) was a limited and valuable resource to both isolated and grouped neonatal lizards. Lizards aggregated more when the light was on at both temperatures, suggesting that individuals were equally attracted to or repelled from the heat source, depending on the ambient temperature. These data suggest aggregation occurs in neonatal bearded dragons through mutual attraction to a common resource. Further, increased variability in thermal preference occurs in groups, demonstrating the potential for agonistic behaviors to compromise optimal thermoregulation in competitive situations, potentially leading to segregation, rather than aggregation.

Phenylalanine-rich peptides potently bind ESAT6, a virulence determinant of Mycobacterium tuberculosis, and concurrently affect the pathogen's growth.

BACKGROUND: The secretory proteins of Mycobacterium tuberculosis (M. tuberculosis) have been known to be involved in the virulence, pathogenesis as well as proliferation of the pathogen. Among this set, many proteins have been hypothesized to play a critical role at the genesis of the onset of infection, the primary site of which is invariably the human lung. METHODOLOGY/PRINCIPAL FINDINGS: During our efforts to isolate potential binding partners of key secretory proteins of M. tuberculosis from a human lung protein library, we isolated peptides that strongly bound the virulence determinant protein Esat6. All peptides were less than fifty amino acids in length and the binding was confirmed by in vivo as well as in vitro studies. Curiously, we found all three binders to be unusually rich in phenylalanine, with one of the three peptides a short fragment of the human cytochrome c oxidase-3 (Cox-3). The most accessible of the three binders, named Hcl1, was shown also to bind to the Mycobacterium smegmatis (M. smegmatis) Esat6 homologue. Expression of hcl1 in M. tuberculosis H37Rv led to considerable reduction in growth. Microarray analysis showed that Hcl1 affects a host of key cellular pathways in M. tuberculosis. In a macrophage infection model, the sets expressing hcl1 were shown to clear off M. tuberculosis in much greater numbers than those infected macrophages wherein the M. tuberculosis was not expressing the peptide. Transmission electron microscopy studies of hcl1 expressing M. tuberculosis showed prominent expulsion of cellular material into the matrix, hinting at cell wall damage. CONCLUSIONS/SIGNIFICANCE: While the debilitating effects of Hcl1 on M. tuberculosis are unrelated and not because of the peptide's binding to Esat6-as the latter is not an essential protein of M. tuberculosis-nonetheless, further studies with this peptide, as well as a closer inspection of the microarray data may shed important light on the suitability of such small phenylalanine-rich peptides as potential drug-like molecules against this pathogen.

Water soluble nanoparticles from PEG-based cationic hyperbranched polymer and RNA that protect RNA from enzymatic degradation.

Recent advances in understanding biological systems have proven that RNA is not merely the carrier of genetic information, but also a key molecule in regulation of gene expression and other crucial metabolic processes. Therefore, it is being considered as an ideal therapeutic candidate both for metabolic and genetic disorders. However, research involving RNA molecules faces a practical limitation since RNA is highly labile. We have developed a novel method to protect RNA from cleavage by complexing it with a hyperbranched cationic polymer. It was found that total cellular RNA isolated from yeast spontaneously interacts with the positively charged polymer to form a spherical nanoparticle morphology. This interaction protects the RNA against enzymatic degradation. This methodology can be easily adapted for long-term storage of RNA, long distance transfer of RNA, and genetic engineering using RNA as a building block.

The effects of oxidative stress on the liver sieve.

BACKGROUND/AIMS: Oxidative stress is implicated in the pathogenesis of age-related and disease-associated changes in the hepatic sinusoid. We studied the effects of oxidative stress on the morphology of the liver, focusing specifically on the hepatic sinusoidal endothelium (the 'liver sieve'). METHODS: The effects of tert-butyl hydroperoxide on the intact liver and isolated sinusoidal endothelial cells were assessed by electron microscopy, immunohistochemistry and biochemical analysis. RESULTS: Immunohistochemistry revealed a dose-dependent increase in peri-sinusoidal 3-nitrotyrosine staining, particularly in the regions adjacent to the portal triads. Electron microscopy showed dose-dependent formation of large intracellular gaps in the sinusoidal endothelium with reduction in the diameter of the remaining endothelial fenestrations. Activated Kupffer cells extending processes through the fenestrations to contact hepatocytes were noted. Biochemical analysis of total liver tissue showed no significant changes in malondialdehyde content but a decrease in the ratio of GSH to GSSG. tert-Butyl hydroperoxide administered directly onto isolated liver sinusoidal endothelial cells was associated with similar gap formation, indicating a direct effect on the endothelial cells by tert-butyl hydroperoxide. CONCLUSIONS: Oxidative stress selectively damages hepatic sinusoidal endothelial cells. This has implications for those processes associated with changes in the sinusoidal endothelium such as ageing, cirrhosis and exposure to hepatotoxins.