Phytoremediation and Nanoremediation : Emerging Techniques for Treatment of Acid Mine Drainage Water

Drainage from mining sites containing sulfur bearing rocks is known as acid mine drainage (AMD). Acid mine drainage water is a serious environmental pollutant that has its effects on plants, animals and microflora of a region. Mine water drainage mainly occurs due to anthropogenic activities like mining that leave the sulfur bearing rocks exposed. This drainage water poses as a potent soil, water and ground water pollutant. Although a lot of remediation measures have been implemented in the past but, none of them have been able to solve the problem completely. This review intends to focus on new emerging and better techniques in the form of phytoremediation and nanoremediation for treatment of acid mine drainage water. Besides, the review also gives more importance to the phytoremediation technique over nanoremediation because of the cost effectiveness and eco-friendly nature of the first and the nascent status of the latter. A hypothetical model discussing the use of hyperaccumulator plants in remediation of acid mine water has been proposed. The model also proposes natural induction of the phytoremedial ability of the plants involved in the remediation process. The proposed model assisted by inputs from further research, may be helpful in proper treatment of acid mine drainage water in the near future

Alfaviiruse nsP2 valk biokeemilisest vaatekohast: lugu mitmedomäänse valgu ensümaatilisest analüüsist

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Chikungunya viirus (CHIKV) on suure meditsiinilise tähtsusega viirus mis kuulub alfaviiruste perekonda sugukonnas Togaviridae. Pregusel ajal ei ole CHIKV vastast vaktsiini ega spetsiifilist ravi. CHIKV paljunemine nakatatud rakkudes sõltub tema RNA genoomilt sünteesitavatest replikaasi valkudest. NsP2 on nelja replikaasi valgu seas suurim ja tal on palju teadaolevaid või eeldatavaid aktiivsuseid. Käesolevas töös näidati eksperimentaalselt, et CHIKV nsP2 omab kaheahelalist RNAd lahtiharutavat aktiivsust ning võib läbi viia ka vastupidist protsessi – soodustada kaheahelalise RNA moodustamist. Mõlemad need funktsioonid on olemas ainult täispikal nsP2 valgul. Peale selle näidati, et nsP2 omab ka NTPaset ja proteaaset aktiivsust. Kuna ka need aktiivsused on kõige tugevamad täispikal valgul siis saab saadud tulemustest järeldada, et CHIKV nsP2 toimib kui üks tervik: valgu erinevad osad seonduvad omavahel ja mõjutavad vastastikku üksteise aktiivsusi. Lisaks sellele leiti, et nsP2 aktiivsuseid mõjutavad ka mutatsioonid, mis on seotud mitte-tsütotoksilise fenotüübiga st. viiruse võimetusega maha suruda raku biosünteese ja põhjustada raku surma. Siiski ei saa kogutud andmeist teha järeldust milline või millised defektid nsP2 funktsioonides seda fenotüüpi põhjustavad. Lisaks nsP2 funktsionaalsele analüüsile viidi läbi ka muude CHIKV replikaasi valkude ekspresserimine ja puhastamine. Saadud kõrge kvaliteediga valke kasutati efektiivsete polüklonaalsete antiseerumite saamiseks. Nüüdseks on need töövahedid kasutusel paljudes laborites üle maailma ja on võimaldanud välja selgitada palju uusi fakte CHIKV (ja alfaviiruste üldse) molekulaarbioloogia kohta.Chikungunya virus (CHIKV, genus Alphavirus, family Togaviridae) has a positive sense RNA genome with length approximately 12 kb. It codes for four nonstructural (ns) proteins designated as nsP1, nsP2, nsP3 and nsP4 and for five or six structural proteins. Ns-proteins are involved in replication of virus RNA, in addition they also have functions unrelated to RNA replication. Out of all the nsPs, nsP2 plays a pivotal role towards regulation of CHIKV RNA replication. The protein was known to have NTPase, RTPase and protease activity and its N-terminal region was presumed to have helicase activity. Out of the enzymatic activities of nsP2 the helicase related functionalities were most insufficiently studied. Further, it was not known why two different and seemingly disconnected functional entities such as protease and helicase are present on a single polypeptide and what could be the importance of N terminal most part of nsP2 on the helicase activity. The bioinformatical, biochemical and biophysical approaches were employed to characterize the helicase related activities and to reveal the apparent minimal requirements for these activities. The bioinformatics platform suggests that the 3D-structure of the first 470 aa of nsP2 resembles the fold pattern of ToMV helicase which is a superfamily 1 of helicase. In particular, this fragment was predicted to consist from three domains. From these the extreme N terminal domain appears to be disordered while the other two domains possess RecA-like fold which is commonly found in NTPases. The biochemical analysis, carried out with purified full length and manipulated versions of nsP2, revealed that the C-terminal part of nsP2, which was known to have protease activity, is also essential for RNA helicase activity. Thus, the presence of protease region in nsP2 is clearly not accidental and these different functional domains are co-evolved to accomplish more significant tasks. The use of biophysical method (CD spectroscopy) confirmed that secondary structures of wt and manipulated versions of nsP2 are comparable; this indicates that functional defects detected in various enzymatic activities did not result from misfolding of mutant proteins. This also applies to forms of nsP2 which were engineered to contain mutations associated with noncytotoxic (NCT) phenotype of CHIKV replicons. It was found, all analyzed nsP2 enzymatic activities (protease, NTPase and helicase activities) were invariably affected by the NCT related mutations. In general, however, there was no significant correlation observed between extent of enzymatic defect(s) of nsP2 and phenotype of corresponding replicon. Thus, the development of NCT phenotype is apparently more complicated and could involve a number of underneath viral replication related functionalities. Finally, a number of ns-proteins from different alphaviruses were expressed, purified to raise polyclonal sera. These represent tools for detection of viral proteins using different immunological, such as western blot and immunofluorescence, methods. Similarly, the standardized enzymatic assays of nsP2 represent platform for screening and analysis of potential inhibitors of CHIKV infection. Taken together, these works elevated general understanding of nsP2 from a biochemical perspective and provided useful tools for studies aiming to understand molecular biology of alphaviruses

Evaluation of haematological and behavioural changes in Channa punctatus (Bloch) on short-term exposure to a commercial-grade synthetic pyrethroid pesticide

This study aims to assess the acute toxicity of commercial-grade Cypermethrin (10% EC) and evaluate the hematological and behavioral alterations in a freshwater fish Channa punctatus upon short-term exposure to Cypermethrin. A four-day static acute toxicity test was performed to estimate the median lethal concentration (LC50) value of Cypermethrin. During the acute toxicity test, the behavior of the control and cypermethrin exposed fish was critically observed and recorded. After completing the acute toxicity test, the hematological effects of Cypermethrin in C. punctatus were evaluated using two sublethal dosages (0.08 mg/L and 0.12 mg/L). Results of the study revealed that this pesticide induced significant mortality in C. punctatus with a 96-h L50 value of 0.263 mg/L. Cypermethrin exposed fish showed hyperactivity, irritability, erratic swimming, frequent surface visit, etc. Exposure to sublethal concentrations of Cypermethrin for a short period resulted in a significant decline (P<0.05) in total erythrocytes count (TEC), packed cell volume (PCV), mean corpuscular volume (MCV), and hemoglobin (Hb) concentration as compared to control groups. In contrast, pesticide-exposed groups had a significant increase (P<0.05) in mean corpuscular hemoglobin concentration (MCHC) and total leucocyte count (TLC). It is apparent from the results of the study that this commercial formulation is toxic to the studied fish. This study also revealed hematological and behavioral alterations in C. Punctatus which could be used as biomarkers for incipient Cypermethrin intoxication

Human-Scale Computing: A Case for Progressive Narrow Waist for Internet Applications

In the era where personal devices and applications are pervasive, individuals are continuously generating and interacting with a vast amount of data. Despite this, access to and control over such data remains challenging due to its scattering across various app providers and formats. This paper presents Human-Scale Computing, a vision and an approach where every individual has straightforward, unified access to their data across all devices, apps, and services. Key to this solution is the Human Scale Portal, a progressively designed intermediary that integrates different applications and service providers. This design adopts a transitional development and deployment strategy, involving an initial bootstrapping phase to engage application providers, an acceleration phase to enhance the convenience of access, and an eventual solution. We believe that this progressive "narrow waist" design can bridge the gap between the current state of data access and our envisioned future of human-scale access.Comment: 6 pages, 1 figur

MODER2: First-order Markov Modeling and Discovery of Monomeric and Dimeric Binding Motifs

Motivation: Position-specific probability matrices (PPMs, also called position-specific weight matrices) have been the dominating model for transcription factor (TF)-binding motifs in DNA. There is, however, increasing recent evidence of better performance of higher order models such as Markov models of order one, also called adjacent dinucleotide matrices (ADMs). ADMs can model dependencies between adjacent nucleotides, unlike PPMs. A modeling technique and software tool that would estimate such models simultaneously both for monomers and their dimers have been missing. Results: We present an ADM-based mixture model for monomeric and dimeric TF-binding motifs and an expectation maximization algorithm MODER2 for learning such models from training data and seeds. The model is a mixture that includes monomers and dimers, built from the monomers, with a description of the dimeric structure (spacing, orientation). The technique is modular, meaning that the co-operative effect of dimerization is made explicit by evaluating the difference between expected and observed models. The model is validated using HT-SELEX and generated datasets, and by comparing to some earlier PPM and ADM techniques. The ADM models explain data slightly better than PPM models for 314 tested TFs (or their DNA-binding domains) from four families (bHLH, bZIP, ETS and Homeodomain), the ADM mixture models by MODER2 being the best on average.Peer reviewe

Arribazón de medusa azul Porpita porpita en las playas de Visakhapatnam, India (Bahía occidental de Bengala)

Porpita porpita occurs in the tropical and sub-tropical waters of the Pacific, Atlantic, and Indian Oceans, and the mass numbers of stranded colonies seem to be increasing. Although its presence in Indian waters is minimal, this is the first record ever made of P. porpita in Visakhapatnam coastal waters. The present study provided a detailed description of the species and its global distribution. Further, the perceived increase in gelatinous zooplankton blooms in the observed area indicates that jellyfish can negatively affect fisheries because they compete with zooplanktivorous fish, prey upon fish eggs and larvae, and indirectly compete with higher trophic levels by reducing the plankton available to planktivores. Conversely, jellyfishes also play a vital role in regulating global marine plankton food webs, spatio-temporal dynamics, and biomass, which is a role that has been generally neglected so far.Porpita porpita se encuentra en las aguas tropicales y subtropicales de los océanos Pacífico, Atlántico e Índico, y el número masivo de colonias varadas parece estar aumentando. Aunque su presencia en las aguas de la India es mínima, este es el primer registro de P. porpita en las aguas costeras de Visakhapatnam. El presente estudio proporcionó una descripción detallada de la especie y su distribución global. Además, el aumento percibido en las floraciones de zooplancton gelatinoso en el área observada, indica que las medusas pueden afectar negativamente a las pesquerías porque compiten con los peces zooplanctívoros, se alimentan de huevos y larvas de peces, e indirectamente compiten con niveles tróficos más altos al reducir el plancton disponible para los planctívoros. Por el contrario, las medusas también juegan un papel vital en la regulación de las redes alimentarias del plancton marino global, la dinámica espacio-temporal y la biomasa, un papel que generalmente se ha descuidado hasta ahora.  

Evaluation of the Effect of Tagetes erecta Leaves Hydroalcoholic Extract on Blood Clotting Time

People were afflicted with a variety of illnesses prior to the revolution, and there was no access to medications sufficiently, at that time herbal agents fulfilled the demand for medications. In these modern days due to the huge side effects as well as drug resistance of marketed drugs, the demand for herbal medicines is increasing. We are all busy in our lives these days, we are traveling here and there to maintain our social duties. Due to this, the number of accidents is increasing around us. When a blood vessel is injured, blood clotting, or coagulation, is a crucial process that reduces excessive bleeding. So, the drugs that are able to reduce clotting time are essential for us. In this research we evaluated the blood clotting effect of two different doses (250mg/kg and 500mg/kg) of Tagetes erecta leaves hydroalcoholic extract on the albino wistar rat, and compared the effect with a marketed standard drug Tranexamic Acid (Pause 500 mg)

The Scikit HEP Project -- overview and prospects

Scikit-HEP is a community-driven and community-oriented project with the goal of providing an ecosystem for particle physics data analysis in Python. Scikit-HEP is a toolset of approximately twenty packages and a few "affiliated" packages. It expands the typical Python data analysis tools for particle physicists. Each package focuses on a particular topic, and interacts with other packages in the toolset, where appropriate. Most of the packages are easy to install in many environments; much work has been done this year to provide binary "wheels" on PyPI and conda-forge packages. The Scikit-HEP project has been gaining interest and momentum, by building a user and developer community engaging collaboration across experiments. Some of the packages are being used by other communities, including the astroparticle physics community. An overview of the overall project and toolset will be presented, as well as a vision for development and sustainability.Comment: 6 pages, 3 figures, Proceedings of the 24th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2019), Adelaide, Australia, 4-8 November 201

Chikungunya virus infectivity, RNA replication and non-structural polyprotein processing depend on the nsP2 protease's active site cysteine residue

Chikungunya virus (CHIKV), genus Alphavirus, family Togaviridae, has a positive-stand RNA genome approximately 12 kb in length. In infected cells, the genome is translated into non-structural polyprotein P1234, an inactive precursor of the viral replicase, which is activated by cleavages carried out by the non-structural protease, nsP2. We have characterized CHIKV nsP2 using both cell-free and cell-based assays. First, we show that Cys478 residue in the active site of CHIKV nsP2 is indispensable for P1234 processing. Second, the substrate requirements of CHIKV nsP2 are quite similar to those of nsP2 of related Semliki Forest virus (SFV). Third, substitution of Ser482 residue, recently reported to contribute to the protease activity of nsP2, with Ala has almost no negative effect on the protease activity of CHIKV nsP2. Fourth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 completely abolished RNA replication in CHIKV and SFV trans-replication systems. In contrast, trans-replicases with Ser482 to Ala mutation were similar to wild type counterparts. Fifth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 abolished the rescue of infectious virus from CHIKV RNA transcripts while Ser482 to Ala mutation had no effect. Thus, CHIKV nsP2 is a cysteine protease.Peer reviewe

Design and Validation of Novel Chikungunya Virus Protease Inhibitors

Chikungunya virus (CHIKV; genus Alphavirus) is the causative agent of chikungunya fever. CHIKV replication can be inhibited by some broad-spectrum antiviral compounds; in contrast, there is very little information about compounds specifically inhibiting the enzymatic activities of CHIKV replication proteins. These proteins are translated in the form of a nonstructural (ns) P1234 polyprotein precursor from the CHIKV positive-strand RNA genome. Active forms of replicase enzymes are generated using the autoproteolytic activity of nsP2. The available three-dimensional (3D) structure of nsP2 protease has made it a target for in silico drug design; however, there is thus far little evidence that the designed compounds indeed inhibit the protease activity of nsP2 and/or suppress CHIKV replication. In this study, a set of 12 compounds, predicted to interact with the active center of nsP2 protease, was designed using target-based modeling. The majority of these compounds were shown to inhibit the ability of nsP2 to process recombinant protein and synthetic peptide substrates. Furthermore, all compounds found to be active in these cell-free assays also suppressed CHIKV replication in cell culture, the 50% effective concentration (EC50) of the most potent inhibitor being similar to 1.5 mu M. Analysis of stereoisomers of one compound revealed that inhibition of both the nsP2 protease activity and CHIKV replication depended on the conformation of the inhibitor. Combining the data obtained from different assays also indicates that some of the analyzed compounds may suppress CHIKV replication using more than one mechanism.Peer reviewe