Whole-genome sequence and mass spectrometry study of the snow blight fungus Phacidium infestans (Karsten) DSM 5139 growing at freezing temperatures

Phacidium infestans (synonym Gremmenia infestans) is a significant pathogen that impacts Pinus species across the northern regions of Europe and Asia. This study introduces the genome sequence of P. infestans Karsten DSM 5139 (Phain), obtained through Pacbio technology. The assembly resulted in 44 contigs, with a total genome size of 36,805,277 bp and a Guanine-Cytosine content of 46.4%. Genome-mining revealed numerous putative biosynthetic gene clusters that code for virulence factors and fungal toxins. The presence of the enzyme pisatin demethylase was indicative of the potential of Phain to detoxify its environment from the terpenoid phytoalexins produced by its host as a defense mechanism. Proteomic analysis revealed the potential survival strategies of Phain under the snow, which included the production of antifreeze proteins, trehalose synthesis enzymes, desaturases, proteins related to elongation of very long-chain fatty acids, and stress protein responses. Study of protein GH11 endoxylanase expressed in Escherichia coli showed an acidic optimum pH (pH 5.0) and a low optimum temperature (45 °C), which is reflective of the living conditions of the fungus. Mass spectrometry analysis of the methanol extract of Phain, incubated at - 3 °C and 22 °C, revealed differences in the produced metabolites. Both genomic and mass spectrometry analyses showed the ability of Phain to adapt its metabolic processes and secretome to freezing temperatures through the production of osmoprotectant and cryoprotectant metabolites. This comprehensive exploration of Phain's genome sequence, proteome, and secretome not only advances our understanding of its unique adaptive mechanisms but also expands the possibilities of biotechnological applications.

Progress and prospects of C4 trait engineering in plants

Incorporating C₄ photosynthetic traits into C₃ crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C₃ , C₄ , and C₃ -C₄ intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C₄ photosynthetic traits in C₃ crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C₃ crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C₃ crops for sustaining food, fibre and fuel production around the globe.

Relative contribution of different members of OsDREB gene family to osmotic stress tolerance in indica and japonica ecotypes of rice

Drought/osmotic stress is the single largest production constraint in rain-fed rice cultivation. Different members of the DREB gene family are known to contribute to osmotic stress tolerance. In this study, an attempt was made to understand their relative contribution towards osmotic stress tolerance in indica and japonica ecotypes of rice. Two genotypes (one tolerant and one susceptible) from each ecotype were grown hydroponically, and 21-day-old seedlings were subjected to polyethylene glycol-induced osmotic stress (15% PEG-6000, equivalent to -3.0 bars osmotic potential). The tolerant genotypes CR143 and Moroberekan were found to have superior root traits (total root length, surface area and volume), better plant water status and increased total dry biomass as compared to their susceptible counterparts after 10 days of osmotic stress. Different members of the DREB gene family were differentially induced in response to osmotic shock (1 h after stress) and osmotic stress (24 h after stress), which also differed between the two rice ecotypes. From the gene expression profiles of 10 DREB genes (both DREB1 and DREB2 families), in indica two DREB genes, DREB1B and DREB1G, were significantly correlated with stress tolerance indices, whereas in japonica significant correlations with five DREB genes (DREB1A, DREB1B, DREB1D, DREB1E and DREB2B) were observed. We found that only one member, i.e. DREB1B, showed a significant correlation with drought tolerance indices in both indica and japonica ecotypes. This study provides an overview of the relative contribution of different members of the DREB gene family and their association with drought/osmotic stress tolerance in rice.

A lysosome-targeted DNA nanodevice selectively targets macrophages to attenuate tumours

Activating CD8+ T cells by antigen cross-presentation is remarkably effective at eliminating tumours. Although this function is traditionally attributed to dendritic cells, tumour-associated macrophages (TAMs) can also cross-present antigens. TAMs are the most abundant tumour-infiltrating leukocyte. Yet, TAMs have not been leveraged to activate CD8+ T cells because mechanisms that modulate their ability to cross-present antigens are incompletely understood. Here we show that TAMs harbour hyperactive cysteine protease activity in their lysosomes, which impedes antigen cross-presentation, thereby preventing CD8+ T cell activation. We developed a DNA nanodevice (E64-DNA) that targets the lysosomes of TAMs in mice. E64-DNA inhibits the population of cysteine proteases that is present specifically inside the lysosomes of TAMs, improves their ability to cross-present antigens and attenuates tumour growth via CD8+ T cells. When combined with cyclophosphamide, E64-DNA showed sustained tumour regression in a triple-negative-breast-cancer model. Our studies demonstrate that DNA nanodevices can be targeted with organelle-level precision to reprogram macrophages and achieve immunomodulation in vivo.

Tissue-specific targeting of DNA nanodevices in a multicellular living organism

Nucleic acid nanodevices present great potential as agents for logic-based therapeutic intervention as well as in basic biology. Often, however, the disease targets that need corrective action are localized in specific organs, and thus realizing the full potential of DNA nanodevices also requires ways to target them to specific cell types in vivo. Here, we show that by exploiting either endogenous or synthetic receptor-ligand interactions and leveraging the biological barriers presented by the organism, we can target extraneously introduced DNA nanodevices to specific cell types in Caenorhabditis elegans, with subcellular precision. The amenability of DNA nanostructures to tissue-specific targeting in vivo significantly expands their utility in biomedical applications and discovery biology.

Combined application of ascorbic acid and endophytic N-fixing Azotobacter chroococcum Avi2 modulates photosynthetic efficacy, antioxidants and growth-promotion in rice under moisture deficit stress

This group has previously reported the role of ascorbic acid (AA) as an antioxidant for survivability and ability to enhancing diazotrophic efficacy in Azotobacter chroococcum Avi2 under hydrogen peroxide (H₂O₂) stress. However, the present study showed the combined application of AA and Avi2 in drought-susceptible (IR64 and Naveen) and drought-tolerant (Ankit and Satyabhama) rice cultivars to determine their photosynthetic efficacy (chlorophyll fluorescence-imaging), antioxidants, and plant growth-promotion (PGP) under moisture deficit stress (MS, -60 kPa). The results indicated that combined application of AA and Avi2 significantly (p < 0.05) increased the total chlorophyll, relative water content, electrolytic leakage, super oxide dismutase, and catalase activities in all rice cultivars as compared to other MS treatments, whereas stress indicators like proline and H₂O₂ contents were proportionally increased under MS and their concentration were normalized under combined application of AA and Avi2. Photochemical quenching, non-photochemical quenching, photosynthetic electron transport rate, and the effective quantum efficiency were found to be increased significantly (p < 0.05) in Avi2 + AA as compared to other MS treatments. Moreover, rice roots harbored significantly (p < 0.05) higher copy number of nifH gene in Avi2 + AA treatment followed by Avi2 compared to flooded control and other MS treatments. Combined application of AA and Avi2 also increased the grain yield significantly (p < 0.05) by 7.09 % and 3.92 % in drought-tolerant (Ankit and Satyabhama, respectively) and 31.70 % and 34.19 % in drought-susceptible (IR64 and Naveen, respectively) rice cultivars compared to MS treatment. Overall, the present study indicated that AA along with Avi2 could be an effective formulation to alleviate MS vis à vis enhances PGP traits in rice.

Neutrophil elastase selectively kills cancer cells and attenuates tumorigenesis

Cancer cell genetic variability and similarity to host cells have stymied development of broad anti-cancer therapeutics. Our innate immune system evolved to clear genetically diverse pathogens and limit host toxicity; however, whether/how innate immunity can produce similar effects in cancer is unknown. Here, we show that human, but not murine, neutrophils release catalytically active neutrophil elastase (ELANE) to kill many cancer cell types while sparing non-cancer cells. ELANE proteolytically liberates the CD95 death domain, which interacts with histone H1 isoforms to selectively eradicate cancer cells. ELANE attenuates primary tumor growth and produces a CD8+T cell-mediated abscopal effect to attack distant metastases. Porcine pancreatic elastase (ELANE homolog) resists tumor-derived protease inhibitors and exhibits markedly improved therapeutic efficacy. Altogether, our studies suggest that ELANE kills genetically diverse cancer cells with minimal toxicity to non-cancer cells, raising the possibility of developing it as a broad anti-cancer therapy.

Macrocyclic polyketides with siderophore mode of action from marine heterotrophic Shewanella algae: Prospective anti-infective leads attenuate drug-resistant pathogens

AIMS

Biotechnological and chemical characterization of previously undescribed homologous siderophore-type macrocyclic polyketides from heterotrophic Shewanella algae Microbial Type Culture Collection (MTCC) 12715 affiliated with Rhodophycean macroalga Hypnea valentiae of marine origin, with significant anti-infective potential against drug-resistant pathogens.

METHODS AND RESULTS

The heterotrophic bacterial strain in symbiotic association with intertidal macroalga H. valentiae was isolated to homogeneity in a culture-dependent method and screened for bioactivities by spot-over-lawn assay. The bacterial organic extract was purified and characterized by extensive chromatographic and spectroscopic methods, respectively, and was assessed for antibacterial activities with disc diffusion and microtube dilution methods. The macrocyclic polyketide compounds exhibited wide-spectrum of anti-infective potential against clinically significant vancomycin-resistant Enterococcus faecalis (VREfs), methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa and Klebsiella pneumonia with minimum inhibitory concentration of about 1-3 µg ml^-1 , insomuch as the antibiotics chloramphenicol and ampicillin were active at ≥6·25 µg ml^-1 . The studied compounds unveiled Fe³⁺ chelating activity, which designated that their prospective anti-infective activities against the pathogens could be due to their siderophore mechanism of action. In support of that, the bacterium exhibited siderophore production on bioassay involving the cast upon culture agar plate, and the presence of siderophore biosynthetic gene (≈1000 bp) (MF 981936) further corroborated the inference. In silico molecular modelling with penicillin-binding protein (PBP2a) coded by mecA genes of MRSA (docking score -11·68 to -12·69 kcal mol^-1 ) verified their in vitro antibacterial activities. Putative biosynthetic pathway of macrocyclic polyketides through stepwise decarboxylative condensation initiated by malonate-acyl carrier protein further validated their structural and molecular attributes.

CONCLUSIONS

The studied siderophore-type macrocyclic polyketides from S. algae MTCC 12715 with significant anti-infective potential could be considered as promising candidates for pharmaceutical and biotechnological applications, especially against emerging multidrug-resistant pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study exhibited the heterotrophic bacteria in association with intertidal macroalga as propitious biological resources to biosynthesize novel antibacterial agents.

What biologists want from their chloride reporters – a conversation between chemists and biologists

Impaired chloride transport affects diverse processes ranging from neuron excitability to water secretion, which underlie epilepsy and cystic fibrosis, respectively. The ability to image chloride fluxes with fluorescent probes has been essential for the investigation of the roles of chloride channels and transporters in health and disease. Therefore, developing effective fluorescent chloride reporters is critical to characterizing chloride transporters and discovering new ones. However, each chloride channel or transporter has a unique functional context that demands a suite of chloride probes with appropriate sensing characteristics. This Review seeks to juxtapose the biology of chloride transport with the chemistries underlying chloride sensors by exploring the various biological roles of chloride and highlighting the insights delivered by studies using chloride reporters. We then delineate the evolution of small-molecule sensors and genetically encoded chloride reporters. Finally, we analyze discussions with chloride biologists to identify the advantages and limitations of sensors in each biological context, as well as to recognize the key design challenges that must be overcome for developing the next generation of chloride sensors.

DNA nanodevices map enzymatic activity in organelles

Cellular reporters of enzyme activity are based on either fluorescent proteins or small molecules. Such reporters provide information corresponding to wherever inside cells the enzyme is maximally active and preclude minor populations present in subcellular compartments. Here we describe a chemical imaging strategy to selectively interrogate minor, subcellular pools of enzymatic activity. This new technology confines the detection chemistry to a designated organelle, enabling imaging of enzymatic cleavage exclusively within the organelle. We have thus quantitatively mapped disulfide reduction exclusively in endosomes in Caenorhabditis elegans and identified that exchange is mediated by minor populations of the enzymes PDI-3 and TRX-1 resident in endosomes. Impeding intra-endosomal disulfide reduction by knocking down TRX-1 protects nematodes from infection by Corynebacterium diphtheriae, revealing the importance of this minor pool of endosomal TRX-1. TRX-1 also mediates endosomal disulfide reduction in human cells. A range of enzymatic cleavage reactions in organelles are amenable to analysis by this new reporter strategy.

A DNA nanomachine chemically resolves lysosomes in live cells

Lysosomes are multifunctional, subcellular organelles with roles in plasma membrane repair, autophagy, pathogen degradation and nutrient sensing. Dysfunctional lysosomes underlie Alzheimer's disease, Parkinson's disease and rare lysosomal storage diseases, but their contributions to these pathophysiologies are unclear. Live imaging has revealed lysosome subpopulations with different physical characteristics including dynamics, morphology or cellular localization. Here, we chemically resolve lysosome subpopulations using a DNA-based combination reporter that quantitatively images pH and chloride simultaneously in the same lysosome while retaining single-lysosome information in live cells. We call this technology two-ion measurement or 2-IM. 2-IM of lysosomes in primary skin fibroblasts derived from healthy individuals shows two main lysosome populations, one of which is absent in primary cells derived from patients with Niemann-Pick disease. When patient cells are treated with relevant therapeutics, the second population re-emerges. Chemically resolving lysosomes by 2-IM could enable decoding the mechanistic underpinnings of lysosomal diseases, monitoring disease progression or evaluating therapeutic efficacy.

A pH-correctable, DNA-based fluorescent reporter for organellar calcium

It is extremely challenging to quantitate lumenal Ca²⁺ in acidic Ca²⁺ stores of the cell because all Ca²⁺ indicators are pH sensitive, and Ca²⁺ transport is coupled to pH in acidic organelles. We have developed a fluorescent DNA-based reporter, CalipHluor, that is targetable to specific organelles. By ratiometrically reporting lumenal pH and Ca²⁺ simultaneously, CalipHluor functions as a pH-correctable Ca²⁺ reporter. By targeting CalipHluor to the endolysosomal pathway, we mapped lumenal Ca²⁺ changes during endosomal maturation and found a surge in lumenal Ca²⁺ specifically in lysosomes. Using lysosomal proteomics and genetic analysis, we found that catp-6, a Caenorhabditis elegans homolog of ATP13A2, was responsible for lysosomal Ca²⁺ accumulation-an example of a lysosome-specific Ca²⁺ importer in animals. By enabling the facile quantification of compartmentalized Ca²⁺, CalipHluor can expand the understanding of subcellular Ca²⁺ importers.

FAST implementation in Bangladesh: high frequency of unsuspected tuberculosis justifies challenges of scale-up

SETTING

National Institute of Diseases of the Chest and Hospital, Dhaka; Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, Dhaka; and Chittagong Chest Disease Hospital, Chittagong, Bangladesh.

OBJECTIVE

To present operational data and discuss the challenges of implementing FAST (Find cases Actively, Separate safely and Treat effectively) as a tuberculosis (TB) transmission control strategy.

DESIGN

FAST was implemented sequentially at three hospitals.

RESULTS

Using Xpert® MTB/RIF, 733/6028 (12.2%, 95%CI 11.4-13.0) patients were diagnosed with unsuspected TB. Patients with a history of TB who were admitted with other lung diseases had more than twice the odds of being diagnosed with unsuspected TB as those with no history of TB (OR 2.6, 95%CI 2.2-3.0, P < 0.001). Unsuspected multidrug-resistant TB (MDR-TB) was diagnosed in 89/1415 patients (6.3%, 95%CI 5.1-7.7). Patients with unsuspected TB had nearly five times the odds of being diagnosed with MDR-TB than those admitted with a known TB diagnosis (OR 4.9, 95%CI 3.1-7.6, P < 0.001). Implementation challenges include staff shortages, diagnostic failure, supply-chain issues and reliance on external funding.

CONCLUSION

FAST implementation revealed a high frequency of unsuspected TB in hospitalized patients in Bangladesh. Patients with a previous history of TB have an increased risk of being diagnosed with unsuspected TB. Ensuring financial resources, stakeholder engagement and laboratory capacity are important for sustainability and scalability.

Subcellular Nanorheology Reveals Lysosomal Viscosity as a Reporter for Lysosomal Storage Diseases

We describe a new method to measure viscosity within subcellular organelles of a living cell using nanorheology. We demonstrate proof of concept by measuring viscosity in lysosomes in multiple cell types and disease models. The lysosome is an organelle responsible for the breakdown of complex biomolecules. When different lysosomal proteins are defective, they are unable to break down specific biological substrates, which get stored within the lysosome, causing about 70 fatal diseases called lysosomal storage disorders (LSDs). Although the buildup of storage material is critical to the pathology of these diseases, methods to monitor cargo accumulation in the lysosome are lacking for most LSDs. Using passive particle tracking nanorheology and fluorescence recovery after photobleaching, we report that viscosity in the lysosome increases significantly during cargo accumulation in several LSD models. In a mammalian cell culture model of Niemann Pick C, lysosomal viscosity directly correlates with the levels of accumulated cholesterol. We also observed increased viscosity in diverse LSD models in Caenorhabditis elegans, revealing that lysosomal viscosity is a powerful reporter with which to monitor substrate accumulation in LSDs for new diagnostics or to assay therapeutic efficacy.

Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules

Achieving triggered release of small molecules with spatial and temporal precision at designated cells within an organism remains a challenge. By combining a cell-targetable, icosahedral DNA-nanocapsule loaded with photoresponsive polymers, we show cytosolic delivery of small molecules with the spatial resolution of single endosomes in specific cells in Caenorhabditis elegans. Our technology can report on the extent of small molecules released after photoactivation as well as pinpoint the location at which uncaging of the molecules occurred. We apply this technology to release dehydroepiandrosterone (DHEA), a neurosteroid that promotes neurogenesis and neuron survival, and determined the timescale of neuronal activation by DHEA, using light-induced release of DHEA from targeted DNA nanocapsules. Importantly, sequestration inside the DNA capsule prevents photocaged DHEA from activating neurons prematurely. Our methodology can in principle be generalized to diverse neurostimulatory molecules.

High lumenal chloride in the lysosome is critical for lysosome function

Lysosomes are organelles responsible for the breakdown and recycling of cellular machinery. Dysfunctional lysosomes give rise to lysosomal storage disorders as well as common neurodegenerative diseases. Here, we use a DNA-based, fluorescent chloride reporter to measure lysosomal chloride in Caenorhabditis elegans as well as murine and human cell culture models of lysosomal diseases. We find that the lysosome is highly enriched in chloride, and that chloride reduction correlates directly with a loss in the degradative function of the lysosome. In nematodes and mammalian cell culture models of diverse lysosomal disorders, where previously only lysosomal pH dysregulation has been described, massive reduction of lumenal chloride is observed that is ~10³ fold greater than the accompanying pH change. Reducing chloride within the lysosome impacts Ca²⁺ release from the lysosome and impedes the activity of specific lysosomal enzymes indicating a broader role for chloride in lysosomal function.

DOI:http://dx.doi.org/10.7554/eLife.28862.001

In cells, worn out proteins and other unnecessary materials are sent to small compartments called lysosomes to be broken down and recycled. Lysosomes contain many different proteins including some that break down waste material into recyclable fragments and others that transport the fragments out of the lysosome. If any of these proteins do not work, waste products build up and cause disease. There are around 70 such lysosomal storage diseases, each arising from a different lysosomal protein not working correctly.

A recently developed “nanodevice” called Clensor can measure the levels of chloride ions inside cells. Clensor is constructed from DNA, and its fluorescence changes when it detects chloride ions. Although chloride ions have many biological roles, chloride ion levels had not been measured inside a living organism. Now, Chakraborty et al. – including some of the researchers who developed Clensor – have used this nanodevice to examine chloride ion levels in the lysosomes of the roundworm Caenorhabditis elegans. This revealed that the lysosomes contain high levels of chloride ions. Furthermore, reducing the amount of chloride in the lysosomes made them worse at breaking down waste.

Do lysosomes affected by lysosome storage diseases also contain low levels of chloride ions? To find out, Chakraborty et al. used Clensor to study C. elegans worms and mouse and human cells whose lysosomes accumulate waste products. In all these cases, the levels of chloride in the diseased lysosomes were much lower than normal. This had a number of effects on how the lysosomes worked, such as reducing the activity of key lysosomal proteins.

Chakraborty et al. also found that Clensor can be used to distinguish between different lysosomal storage diseases. This means that in the future, Clensor (or similar methods that directly measure chloride ion levels in lysosomes) may be useful not just for research purposes. They may also be valuable for diagnosing lysosomal storage diseases early in infancy that, if left undiagnosed, are fatal.

DOI:http://dx.doi.org/10.7554/eLife.28862.002

Nucleic Acid-Based Nanodevices in Biological Imaging

The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

Abstract P1-08-10: Introduction of H1047R oncogenic mutation of PI3K p110alpha subunit in HER2-overexpressing mammary epithelial cells confers a "stem-like" phenotype and acute sensitivity to HSP90 inhibition

The Human Epidermal Growth Factor Receptor 2 (HER2) oncogene is amplified in one-fifth of breast cancers (BC). However, development of resistance against standard anti-HER2 therapies poses a major clinical challenge. Anti-tumor efficacy of HER2-targeting agents depends on inhibition of the downstream phosphatidylinositol-3 kinase (PI3K) signaling cascade. Gain-of-function somatic mutations in the gene encoding the PI3K catalytic subunit p110alpha (PIK3CA), co-expressed in about 40% of HER2+ BC, have been implicated in conferring resistance to HER2 monoclonal antibody herceptin. The single amino acid alteration H1047R within the kinase domain of PIK3CA is one of three hot spot mutations prevalent in BC.

Previously, we demonstrated that introduction of H1047R mutation in HER2-overexpressing MCF10A mammary epithelial cells enhances cellular transformation and decreases herceptin sensitivity by inducing secretion of endogenous ErbB ligand heregulin. However, genetic ablation of HER3, the major co-receptor for HER2 and the solitary receptor for heregulin, was insufficient for complete inhibition of cell growth, indicating the existence of additional mechanism/s responsible for the heightened aggressiveness and decreased drug sensitivity of HER2/H1047RPI3K cells. In the current study, we looked further into the molecular changes within these cells that might be responsible for these phenomena.

When compared with the HER2/WTPI3K cells, the HER2/H1047RPI3K cells revealed a significant increase in CD44high/CD24low/negative populations, common markers of BC stem cells, as well as molecular and phenotypic changes associated with epithelial-to-mesenchymal transition. These observations are in agreement with previously published report on mouse model of HER2/H1047RPI3K BC. Further analyses demonstrated additional stem cell-associated characteristics in HER2/H1047RPI3K cells, such as expression of angiogenic and inflammatory cytokines, ability to induce chemotaxis and invasion, activation of TGFb and NFKb signaling pathways. Connectivity map (CMap) analysis of the gene expression signatures from HER2/H1047RPI3K cells revealed a negative association with those from BC cells treated with 17AAG, an inhibitor of the heat shock protein 90 (HSP90). In line with this, HER2/H1047RPI3K-expressing cells are found to be more sensitive to HSP90 inhibition compared to the pan-ErbB inhibitor lapatinib.

Cancer stem cells are implicated in drug resistance and tumor recurrence. Enrichment of cell population expressing high levels of stem cell markers and stem cell-related features could be one of major mechanisms by which BC cells co-expressing HER2 and H1047RPI3K adapt to anti-HER2 therapeutic agents. Acute dependence on molecular chaperone HSP90 provides a unique, yet practical opportunity to effectively inhibit tumors harboring both molecular alterations, since HSP90 inhibitors have already shown encouraging clinical activity in herceptin-resistant setting.

Citation Format: Surendran S, Bhola N, Arteaga CL, Chakraborty K, Chakrabarty A. Introduction of H1047R oncogenic mutation of PI3K p110alpha subunit in HER2-overexpressing mammary epithelial cells confers a "stem-like" phenotype and acute sensitivity to HSP90 inhibition [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-08-10.

Antimicrobial properties of cultivable bacteria associated with seaweeds in the Gulf of Mannar on the southeast coast of India

In this study, 234 bacterial strains were isolated from 7 seaweed species in the Gulf of Mannar on the southeast coast of India. The strains having consistent antimicrobial activity were chosen for further studies, and this constituted about 9.8% of the active strains isolated. Phylogenetic analysis using 16S rDNA sequencing with the help of classical biochemical identification indicated the existence of 2 major phyla, Firmicutes and Proteobacteria. Antimicrobial activity analysis combined with the results of amplifying genes encoding for polyketide synthetase and nonribosomal peptide synthetase showed that seaweed-associated bacteria had broad-spectrum antimicrobial activity. These epibionts might be beneficial to seaweeds by limiting or preventing the development of competing or fouling bacteria. Phylogenetic analysis of ketosynthase (KS) regions with respect to the diverse range of KS domains showed that the KS domains from the candidate isolates were of Type I. The bacterial cultures retained their antimicrobial activities after plasmid curing, which further suggested that the antimicrobial activity of these isolates was not encoded by plasmid, and the genes encoding the antimicrobial product might be present within the genome. Seaweed-associated bacteria with potential antimicrobial activity suggested that the seaweed species are an ideal ecological niche harboring specific bacterial diversity representing a largely underexplored source of antimicrobial secondary metabolites.

Rational design of a quantitative, pH-insensitive, nucleic acid based fluorescent chloride reporter

Chloride plays a major role in cellular homeostasis by regulating the lumenal pH of intracellular organelles. We have described a pH-independent, fluorescent chloride reporter called Clensor that has successfully measured resting chloride in organelles of living cells. Here, we describe the rational design of Clensor. Clensor integrates a chloride sensitive fluorophore called 10,10'-bis[3-carboxypropyl]-9,9'-biacridinium dinitrate (BAC) with the programmability, modularity and targetability available to nucleic acid scaffolds. We show that simple conjugation of BAC to a DNA backbone fails to yield a viable chloride-sensitive reporter. Fluorescence intensity and lifetime investigations on a series of BAC-functionalized structural variants yielded molecular insights that guided the rational design and successful realization of the chloride sensitive fluorescent reporter, Clensor. This study provides some general design principles that would aid the realization of diverse ion-sensitive nucleic acid reporters based on the sensing strategy of Clensor.

A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells

The concentration of chloride ions in the cytoplasm and subcellular organelles of living cells spans a wide range (5-130 mM), and is tightly regulated by intracellular chloride channels or transporters. Chloride-sensitive protein reporters have been used to study the role of these chloride regulators, but they are limited to a small range of chloride concentrations and are pH-sensitive. Here, we show that a DNA nanodevice can precisely measure the activity and location of subcellular chloride channels and transporters in living cells in a pH-independent manner. The DNA nanodevice, called Clensor, is composed of sensing, normalizing and targeting modules, and is designed to localize within organelles along the endolysosomal pathway. It allows fluorescent, ratiometric sensing of chloride ions across the entire physiological regime. We used Clensor to quantitate the resting chloride concentration in the lumen of acidic organelles in Drosophila melanogaster. We showed that lumenal lysosomal chloride, which is implicated in various lysosomal storage diseases, is regulated by the intracellular chloride transporter DmClC-b.

Successful treatment of nilotinib-induced pleural effusion with prednisone

Chronic myeloid leukemia is characterized by a unique reciprocal translocation between chromosomes 9 and 22 resulting in deregulated tyrosine kinase activity. Tyrosine kinase inhibitors, such as imatinib, dasatinib, and nilotinib have revolutionized treatment of Chronic myeloid leukemia. However, tyrosine kinase inhibitors' use has presented new challenges in managing both acute and chronic toxicities, particularly 'off-target' toxicities like pleural effusion. Pleural effusions are seen less often with imatinib and very rarely with nilotinib. A 66-year-old male presented to emergency department with complaints of mild chest pain and dyspnea of 3 days duration with progressive worsening, including dyspnea at rest. Patient was currently taking nilotinib after failing imatinib for chronic myeloid leukemia. Nilotinib was put on hold. After exclusion of cardiac and pulmonary etiologies patient was treated for community acquired pneumonia with minimal improvement. Despite the very low incidence of pleural effusion with nilotinib (<1%), he was started on 20 mg of prednisone PO for 3 days. Patient had a dramatic improvement within 48 h after beginning prednisone. This treatment approach suggests that pleural effusions associated with nilotinib can be successfully treated in the same way as pleural effusions associated with dasatinib.

Differential expression of salt overly sensitive pathway genes determines salinity stress tolerance in Brassica genotypes

The objective of the present study was to examine the role of SOS pathway in salinity stress tolerance in Brassica spp. An experiment was conducted in pot culture with 4 Brassica genotypes, i.e., CS 52 and CS 54, Varuna and T 9 subjected to two levels of salinity treatments along with a control, viz., 1.65 (S(0)), 4.50 (S(1)) and 6.76 (S(2)) dS m(-1). Salinity treatment significantly decreased relative water content (RWC), membrane stability index (MSI) and chlorophyll (Chl) content in leaves and potassium (K) content in leaf, stem and root of all the genotypes. The decline in RWC, MSI, Chl and K content was significantly less in CS 52 and CS 54 as compared to Varuna and T 9. In contrast, the sodium (Na) content increased under salinity stress in all the plant parts in all the genotypes, however, the increase was less in CS 52 and CS 54, which also showed higher K/Na ratio, and thus more favourable cellular environment. Gene expression studies revealed the existence of a more efficient salt overly sensitive pathway composed of SOS1, SOS2, SOS3 and vacuolar Na(+)/H(+) antiporter in CS 52 and CS 54 compared to Varuna and T 9. Sequence analyses of partial cDNAs showed the conserved nature of these genes, and their intra and intergenic relatedness. It is thus concluded that existence of an efficient SOS pathway, resulting in higher K/Na ratio, could be one of the major factor determining salinity stress tolerance of Brassica juncea genotypes CS 52 and CS 54.

Tunable, colorimetric DNA-based pH sensors mediated by A-motif formation

A colorimetric pH sensor has been developed based on GNP aggregation mediated by A-motif formation under acidic conditions. The pH response of the sensor can be tuned in the range of pH 2-5.5 by changing the length and the sequence of the A-motif forming poly dA tracts.

Morphometry of seminiferous tubules of human testes in different age groups in Bangladeshi cadavers

This cross sectional descriptive study was done to observe the mean diameter of seminiferous tubules and to determine its differences between different age groups in Bangladeshi male. Thirty human testes of different age groups were collected by purposive sampling technique. Among them 22 specimens were collected from cadavers during routine postmortem examination and 8 specimens were from dead fetuses from Gynaecology & Obstetrics Department. The specimens were grouped into three categories Group A (28 to 42 weeks of gestational age), Group B (Up to 14 years) and Group C (15 to 70 years). The mean diameter of seminiferous tubules was measured and significant differences of the dimensions between different age groups were determined. The mean±SD diameter was 85.37±15.51 μm in Group A, 144.04±63.34 μm in Group B and 227.92±22.47 μm in Group C. Statistically, differences between age groups were calculated by using Unpaired Students 't' test. The present study revealed that the diameter increased with age and mean differences were statistically significant between Groups A&C, B&C and A&B.

Internet addiction: consensus, controversies, and the way ahead

OBJECTIVES

To review the fast-growing literature on Internet addiction.

METHODS

Descriptive review, using electronic databases as well as hand-search of relevant publications or cross-references from 1970 to 2010.

RESULTS

There are no universally accepted definitions for the captioned condition, but investigators seem to agree that it involves problematic computer usage that is time-consuming and causes distress or impairs functioning in important life domains. Several aetiological models have been proposed, from the diverse perspectives of learning theory, cognitive behavioural theory, social learning, reward deficiency, culture, genetics and neurobiology. Controversies abound, ranging from conceptual (whether behavioural addictions are true addictions), technical (which component of Internet use is a person 'addicted' to), and practical (how should Internet addiction be diagnosed, if it exists at all). However, using various instruments and populations, Internet addiction has been suggested as having a prevalence of 0.3 to 38%, with a young male preponderance. Several screening, diagnostic, and severity assessment instruments are now available, but few have been subjected to rigorous psychometric testing. Psychiatric co-morbidity is common. Treatment modalities lack a firm evidence base, but antidepressants, mood stabilisers, and cognitive behavioural therapy and other psychotherapies have been used.

CONCLUSIONS

Recently, the American Psychiatric Association recommended including Internet addiction in its forthcoming 5th edition of the Diagnostic and Statistical Manual of Mental Disorders, but only as an appendix and not in the main body of the addictive disorders. This appears to be a fairly balanced and cautious approach, which can hopefully give rise to more meaningful research in this important but controversial area.

Mediastinal teratoma mimicking massive pleural effusion

Immature mediastinal teratoma is very rare, found in only 1% of all mediastinal teratomas. Raised serum alpha feto-protein acts as important surrogate marker for both diagnosis and follow up in such cases. Surgery and adjuvant chemotherapy are keys in the management, especially in patients older than 15 years of age. We present a 14-year-boy presenting clinico-radiologically as left sided massive pleural effusion. Raised serum marker as well as excision biopsy of the mediastinal mass following thoracotomy were indicative of a diagnosis of immature teratoma.

Characterization of chemical modification of tryptophan by matrix-assisted laser desorption/ionization mass spectrometry

Tert- butylation of tryptophan (2', 5', 7'- tri tertiary butyl tryptophan), formed during acidolytic cleavage of synthetic peptides Ac-KLVYWAE-CONH(2) (A-YW) and Ac-KLVWWAE-CONH(2) (A-WW), that are analogs of the fragment of Alzheimer's beta-amyloid peptide Ac-KLVFFAE-CONH(2), during solid-phase peptide synthesis, was characterized by matrix-assisted laser desorption/ionization time of flight/time of flight (MALDI TOF/TOF) mass spectrometry. Crude peptide was fractionated by high performance liquid chromatography. Peptide fractions were sequenced and modified tryptophan was determined with the help of MALDI TOF/TOF mass spectra. Thus, it is possible to pinpoint the particular tryptophan residue that undergoes modification during synthesis of peptides containing multiple tryptophan residues.

Restoration by aspirin of impaired plasma maspin level in human breast cancer

Maspin, an anti breast cancer protein, is produced in the normal mammary cells but not in malignant cells in breast cancer. We investigated the effect of aspirin induced increase of plasma nitric oxide (NO) on plasma maspin production in breast cancer patients. Fifteen breast cancer patients (35-65 years), who had not yet undergone any cancer therapy, and an equal number of age matched normal female volunteers participated in the study. They were asked not to take any medication for two weeks. All participants then ingested 150 mg of aspirin. Plasma NO and maspin levels were determined before and at 60 min after the ingestion of aspirin. It was found that the maspin level in plasma increased to 4.63+/-0.02 nM from the basal 0.95+/-0.012 nM (p<0.001) with increase of plasma NO from 0.60+/-0.03 microM to 2.08+/-0.030 microM (p<0.001) in breast cancer patients. In normal volunteers the basal maspin increased from 4.76+/-0.041 to 9.36+/-0.036 nM (p<0.001) with increase of NO from 2.15+/-0.08 to 3.36+/-0.04 microM (p<0.001) at the same period. These results indicated that the ingestion of aspirin might be beneficial for breast cancer through increased maspin production.

Purification and characterization of a thermostable alpha-amylase from Bacillus stearothermophilus

A soil isolate of Bacillus stearothermophilus was found to synthesize thermostable alpha-amylase. The enzyme was purified to homogeneity by ammonium sulfate fractionation and IECC on DEAE-cellulose column. The purified enzyme was considered to be a monomeric protein with a molar mass of 64 kDa, as determined by SDS-PAGE. The enzyme showed a wide range of pH tolerance and maximum activity at pH 7.0. The temperature tolerance was up to 100 degrees C with more than 90% catalytic activity; the maximum activity was observed at 50 degrees C. Divalent metal ions exhibited inhibitory effect on the enzyme activity. However, proteinase inhibitor did not react positively.

Cervical mass lesion presenting as reflex sympathetic dystrophy of the hand

A case with multiple small joint swelling and skin dystrophic changes in the right hand was initially treated as seronegative non-specific arthritis. Later, a triple phase bone scan indicated reflex sympathetic dystrophy (RSD) and the primary lesion was shown on MRI scan to be a cervical cord mass with associated sub-acute haematoma. The case underscores the need to consider RSD in the differential diagnosis of such conditions and the importance of a detailed neurological examination in RSD with no local causative factor.