Fusarium Disease of Maize and Its Management through Sustainable Approach

Fusarium causing disease in maize is probably the one of the most serious diseases among the crop plants all over the world. It not only damages the maize plant, reduces its potential yield and its nutritional values but imposes threatening to the human life through the induction of mycotoxin development. F. graminearum and F. moniliforme syn. Fusarium verticillioides are two important maize pathogens that cause substantial damage to its ear, stalk and foliage, causing contamination of grains with mycotoxins. Since conventional methods of controlling the diseases including the chemical methods proved not enough for total control of the disease with creating situation even worse for our surroundings, the application of PGPR and PGPF can play significant role to control the damage caused by Fusarium

DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.

The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces cerevisiae), mtDNA is a ∼80 kbp linear molecule and Abf2p, a double HMG-box protein, packages and maintains it. The protein binds DNA in a non-sequence-specific manner, but displays a distinct 'phased-binding' at specific DNA sequences containing poly-adenine tracts (A-tracts). We present here two crystal structures of Abf2p in complex with mtDNA-derived fragments bearing A-tracts. Each HMG-box of Abf2p induces a 90° bend in the contacted DNA, causing an overall U-turn. Together with previous data, this suggests that U-turn formation is the universal mechanism underlying mtDNA compaction induced by HMG-box proteins. Combining this structural information with mutational, biophysical and computational analyses, we reveal a unique DNA binding mechanism for Abf2p where a characteristic N-terminal flag and helix are crucial for mtDNA maintenance. Additionally, we provide the molecular basis for A-tract mediated exclusion of Abf2p binding. Due to high prevalence of A-tracts in yeast mtDNA, this has critical relevance for nucleoid architecture. Therefore, an unprecedented A-tract mediated protein positioning mechanism regulates DNA packaging proteins in the mitochondria, and in combination with DNA-bending and U-turn formation, governs mtDNA compaction

Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects

Antibiotics have been used to cure bacterial infections for more than 70 years, and these low-molecular-weight bioactive agents have also been used for a variety of other medicinal applications. In the battle against microbes, antibiotics have certainly been a blessing to human civilization by saving millions of lives. Globally, infections caused by multidrug-resistant (MDR) bacteria are on the rise. Antibiotics are being used to combat diversified bacterial infections. Synthetic biology techniques, in combination with molecular, functional genomic, and metagenomic studies of bacteria, plants, and even marine invertebrates are aimed at unlocking the world’s natural products faster than previous methods of antibiotic discovery. There are currently only few viable remedies, potential preventive techniques, and a limited number of antibiotics, thereby necessitating the discovery of innovative medicinal approaches and antimicrobial therapies. MDR is also facilitated by biofilms, which makes infection control more complex. In this review, we have spotlighted comprehensively various aspects of antibiotics viz. overview of antibiotics era, mode of actions of antibiotics, development and mechanisms of antibiotic resistance in bacteria, and future strategies to fight the emerging antimicrobial resistant threat

Search for post-merger gravitational waves from the remnant of the binary neutron star merger GW170817

In Advanced LIGO, detection and astrophysical source parameter estimation of the binary black hole merger GW150914 requires a calibrated estimate of the gravitational-wave strain sensed by the detectors. Producing an estimate from each detector's differential arm length control loop readout signals requires applying time domain filters, which are designed from a frequency domain model of the detector's gravitational-wave response. The gravitational-wave response model is determined by the detector's opto-mechanical response and the properties of its feedback control system. The measurements used to validate the model and characterize its uncertainty are derived primarily from a dedicated photon radiation pressure actuator, with cross-checks provided by optical and radio frequency references. We describe how the gravitational-wave readout signal is calibrated into equivalent gravitational-wave-induced strain and how the statistical uncertainties and systematic errors are assessed. Detector data collected over 38 calendar days, from September 12 to October 20, 2015, contain the event GW150914 and approximately 16 of coincident data used to estimate the event false alarm probability. The calibration uncertainty is less than 10% in magnitude and 10 degrees in phase across the relevant frequency band 20 Hz to 1 kHz

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

In Advanced LIGO, detection and astrophysical source parameter estimation of the binary black hole merger GW150914 requires a calibrated estimate of the gravitational-wave strain sensed by the detectors. Producing an estimate from each detector's differential arm length control loop readout signals requires applying time domain filters, which are designed from a frequency domain model of the detector's gravitational-wave response. The gravitational-wave response model is determined by the detector's opto-mechanical response and the properties of its feedback control system. The measurements used to validate the model and characterize its uncertainty are derived primarily from a dedicated photon radiation pressure actuator, with cross-checks provided by optical and radio frequency references. We describe how the gravitational-wave readout signal is calibrated into equivalent gravitational-wave-induced strain and how the statistical uncertainties and systematic errors are assessed. Detector data collected over 38 calendar days, from September 12 to October 20, 2015, contain the event GW150914 and approximately 16 of coincident data used to estimate the event false alarm probability. The calibration uncertainty is less than 10% in magnitude and 10 degrees in phase across the relevant frequency band 20 Hz to 1 kHz

Exploring structure-function relationship of the mitochondrial DNA packaging protein Abf2p and its dialogue with the DNA

[eng] Mitochondria are intracellular double-membrane bound organelles in eukaryotic cells that act as the major suppliers of adenosine triphosphate (ATP). They possess their own DNA (mtDNA) that codes for components of the oxidative phosphorylation (OXPHOS) pathway. mtDNA is assembled into nucleo-protein structures called nucleoids and maintained differently compared to histone mediated packaging of nuclear DNA. The molecular basis of mtDNA packaging and maintenance remains poorly understood. In Saccharomyces cerevisiae (budding yeast), mtDNA is a ~80kb linear molecule, packaged by Abf2p, a double-HMG-box DNA binding protein. Abf2p interacts with DNA in a non-sequence- specific manner, but displays a distinct and yet unexplained ‘phased-binding’ at specific AT-rich DNA stretches containing poly-adenine tracts (A-tracts). Molecular details of DNA binding and maintenance by this protein as well as the mechanism behind its ‘phased binding’ behavior remain to be elucidated. In this doctoral thesis, crystal structures of Abf2p in complex with mtDNA derived fragments bearing A-tracts are presented. The structures reveal that Abf2p binds and induces 180ᵒ U-turn bends in the DNA. Additionally, it avoids binding to A-tracts, giving rise to a unique ‘dual binding’ phenomenon where a single protein molecule binds two DNAs simultaneously. To probe the functional roles played by the different protein structural parts, in vitro and in vivo assays were carried out with different truncation constructs of the protein. These revealed that a 12-residue N-terminal helix, unique to this protein, is crucial for its DNA binding activity. The N-helix+HMG-box1 module possesses a considerably higher DNA binding efficiency compared to HMG-box2, the latter binding little or no DNA on its own. This establishes the predominant role played by the N-helix+HMG-box1 module in the DNA binding event and indicates a hierarchy between the two boxes in the same context. The dynamics of the protein and protein-DNA complex were probed via in-solution (Small Angle X-ray Scattering or SAXS) and simulation (Molecular dynamics or MD) techniques that revealed key mechanisms pertaining to the DNA binding event where the N-helix acts like a pin lock to consolidate DNA binding. Combined with the in vitro and in vivo assays, this provides for a model for DNA binding where the N-helix+HMG-box1 module initiates the DNA binding event, the N-helix locks in and concomitantly or subsequently, HMG-box2 is coaxed into a conformation amenable to DNA binding. Thus, key insights into Abf2p DNA binding mechanism were obtained. The SAXS and MD studies additionally showed that Abf2p is an intrinsically highly flexible protein with considerable relative conformational freedom between the two HMG-boxes that forms a compact species on DNA binding. Additional computational analysis of Abf2p binding on A-tract containing DNA revealed a DNA-structure mediated protein positioning mechanism where the narrow minor groove and intrinsic stiffness of the A-tracts prevent Abf2p binding and thus indirectly guide it to neighboring hospitable sites. The said mechanism would play a key role in orchestrating global nucleoid architecture, given that S. cerevisiae mtDNA has a high percentage of A-tracts. Additionally, the crystal structures disclose an inherent capability of the protein to bind separate DNA strands, that would facilitate DNA packaging by this protein and form an essential mechanistic feature of the process. Analysis of thermodynamics of Abf2p/DNA interactions via isothermal titration calorimetry (ITC) showed a two-phase exothermic-endothermic profile in presence of A-tracts, distinct from that in presence of DNA without A-tracts. The findings reported here thus advance our understanding of mtDNA packaging in the yeast mitochondria from a structural and mechanistic point of view.[cat] Els mitocondris posseeixen un ADN (ADNmt) que codifica components de la via de la fosforilació oxidativa. L’ADNmt es compacta en unes estructures nucleo-proteiques, els nucleoides, que s’estructuren de manera diferent a l'ADN nuclear. La base molecular de l’empaquetament de l’ADNmt és desconegut. A Saccharomyces cerevisiae l’ADNmt és una molècula lineal d’uns 80kb empaquetada per la proteïna Abf2p, que conté dos dominis HMG-box d’unió a ADN. Abf2p contacta l'ADN de forma no específica, però també mostra una unió en fase en regions riques en poli-adenina (regions poly-A). Els detalls moleculars d’aquests dos tipus d’unió encara no s'han dilucidat. En aquesta tesi doctoral es presenten les estructures cristal·logràfiques de l’Abf2p en complex amb fragments d'ADNmt derivats de l’ADN de llevat, que demostren que Abf2p uneix i indueix una curvatura de 180ᵒ a l'ADN. A més a més, en els cristalls, l’Abf2p evita la unió a una regió poly-A induïnt un fenomen únic de d’unió d’una molècula de proteïna a dues molècules d’ADN. Per investigar la funció dels diferents dominis d’Abf2p en la unió ADN hem dut a terme assajos in vitro i in vivo amb fragments i amb la proteïna sencera que mostren que una hèlix de 12 residus N-terminal, única per aquesta proteïna, és crucial per a la unió. A més a més hem estudiat la dinàmica del complex proteïna-ADN en solució per mètodes biofísics (SAXS i ITC) que demostren la flexibilitat de la proteïna i que corroboren el condicionament de la regió poly-A en la unió. Finalment, per dinàmica molecular (MD) hem descobert que l'ADN utilitzat per cristal·litzar té unes propietats estructurals en les regions poly-A, amb un solc menor molt estret, que condicionen el posicionament d’Abf2p. Aquest fenomen és clau en l'organització de l'arquitectura global del nucleoide, atès que en S. cerevisiae l’ADNmt té fins al 30% de regions poly-A, atípic en altres genomes. A més, les estructures cristal·lines mostren la capacitat inherent de la proteïna per unir molècules d'ADN independents, que podrien facilitar el seu empaquetament. Els resultats aquí presentats són un avenç en la nostra comprensió de l’empaquetament de l’ADNmt en el llevat

Exploring structure-function relationship of the mitochondrial DNA packaging protein Abf2p and its dialogue with the DNA

Peer Reviewe

The evening Gnome: a collection of poems(Saubhik De Sarkar)

by Dolonchampa Chakraborty and Arka Chattopadhya

Microgreens: Food for the Future

44-46Microgreens are projected as ‘super food’ because of their high nutritional profiles