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      Volume 39, Issue 4

      September 2014,   pages  543-738

    • Editorial: Remembering Obaid - One Year Later

      Shahid Jameel Utpal Banerjee K VijayRaghavan

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    • Commentary: Recalling Obaid

      Maurice S Fox

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    • Remembering Obaid Siddiqi, a pioneer in the study of temperature-sensitive paralytic mutants in Drosophila

      Barry Ganetzky Chun-Fang Wu

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      Although Obaid Siddiqi’s major research focus in neurogenetics was on chemosensation and olfaction in Drosophila, he made seminal contributions to the study of temperature-sensitive paralytic mutants that paved the way for research that we and many other investigators have continued to pursue. Here we recount Siddiqi’s investigation and the impact it had on our own studies especially at a formative stage of our careers. We acknowledge our debt to Obaid Siddiqi and remember him fondly as an inspired and inspiring scientist, mentor, role model and human being.

    • Molecular determinants of odorant receptor function in insects

      Anandasankar Ray Wynand Van Der Goes Van Naters John R Carlson

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      The olfactory system of Drosophila melanogaster provides a powerful model to study molecular and cellular mechanisms underlying function of a sensory system. In the 1970s Siddiqi and colleagues pioneered the application of genetics to olfactory research and isolated several mutant Drosophila with odorant-specific defects in olfactory behaviour, suggesting that odorants are detected differentially by the olfactory system. Since then basic principles of olfactory system function and development have emerged using Drosophila as a model. Nearly four decades later we can add computational methods to further our understanding of how specific odorants are detected by receptors. Using a comparative approach we identify two categories of short amino acid sequence motifs: ones that are conserved family-wide predominantly in the C-terminal half of most receptors, and ones that are present in receptors that detect a specific odorant, 4-methylphenol, found predominantly in the N-terminal half. The odorant-specific sequence motifs are predictors of phenol detection in Anopheles gambiae and other insects, suggesting they are likely to participate in odorant binding. Conversely, the family-wide motifs are expected to participate in shared functions across all receptors and a mutation in the most conserved motif leads to a reduction in odor response. These findings lay a foundation for investigating functional domains within odorant receptors that can lead to a molecular understanding of odor detection.

    • A map of taste neuron projections in the Drosophila CNS

      Jae Young Kwon Anupama Dahanukar Linnea A Weiss John R Carlson

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      We provide a map of the projections of taste neurons in the CNS of Drosophila. Using a collection of 67 GAL4 drivers representing the entire repertoire of Gr taste receptors, we systematically map the projections of neurons expressing these drivers in the thoracico-abdominal ganglion and the suboesophageal ganglion (SOG). We define 9 categories of projections in the thoracico-abdominal ganglia and 10 categories in the SOG. The projection patterns are modular, and can be interpreted as combinations of discrete pattern elements. The elements can be interpreted in terms of the taste organ from which the projections originate, the structures from which they originate, and the quality of taste information that they represent. The extensive diversity in projection patterns provides an anatomical basis for functional diversity in responses elicited by different taste stimuli.

    • Serotonergic neurons of the Drosophila air-puff-stimulated flight circuit

      Sufia Sadaf Gaiti Hasan

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      Monoaminergic modulation of insect flight is well documented. Recently, we demonstrated that synaptic activity is required in serotonergic neurons for Drosophila flight. This requirement is during early pupal development, when the flight circuit is formed, as well as in adults. Using a Ca2+-activity-based GFP reporter, here we show that serotonergic neurons in both prothoracic and mesothoracic segments are activated upon air-puff-stimulated flight. Moreover ectopic activation of the entire serotonergic system by TrpA1, a heat activated cation channel, induces flight, even in the absence of an air-puff stimulus.

    • Ultradian rhythm unmasked in the Pdf clock mutant of Drosophila

      Yuuichi Seki Teiichi Tanimura

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      A diverse range of organisms shows physiological and behavioural rhythms with various periods. Extensive studies have been performed to elucidate the molecular mechanisms of circadian rhythms with an approximately 24 h period in both Drosophila and mammals, while less attention has been paid to ultradian rhythms with shorter periods. We used a video-tracking method to monitor the movement of single flies, and clear ultradian rhythms were detected in the locomotor behaviour of wild type and clock mutant flies kept under constant dark conditions. In particular, the Pigment-dispersing factor mutant (Pdf01) demonstrated a precise and robust ultradian rhythmicity, which was not temperature compensated. Our results suggest that Drosophila has an endogenous ultradian oscillator that is masked by circadian rhythmic behaviours.

    • Insights into brain development and disease from neurogenetic analyses in Drosophila melanogaster

      Heinrich Reichert

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      Groundbreaking work by Obaid Siddiqi has contributed to the powerful genetic toolkit that is now available for studying the nervous system of Drosophila. Studies carried out in this powerful neurogenetic model system during the last decade now provide insight into the molecular mechanisms that operate in neural stem cells during normal brain development and during abnormal brain tumorigenesis. These studies also provide strong support for the notion that conserved molecular genetic programs act in brain development and disease in insects and mammals including humans.

    • Clipboard: Continuous evolution of laboratory strains of bacteria and yeast

      Savita Chib

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    • Gender based disruptive selection maintains body size polymorphism in Drosophila melanogaster

      Jaya Handa K T Chandrashekara Khushboo Kashyap Geetanjali Sageena Mallikarjun N Shakarad

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      Darwinian fitness in holometabolous insects like the fruit fly Drosophila melanogaster is reported to be positively correlated with body size. If large individuals in a population have higher fitness, then one would expect directional selection to operate leading to uniformly large individuals. However, size polymorphism persists in nature and needs further probing. We assessed the effect of body size on some of the fitness and fitness-related traits in replicate populations of genotypically large, genotypically small and phenotypically small D. melanogaster flies. In this study, the time taken to attain reproductive maturity and copulation duration were independent of fly size. Fecundity and longevity of large females were significantly higher when they partnered genotypically small males than when they were with genotypically larger or phenotypically small males. The increased female longevity when in association with genotypically small males was not due to selective early death of males that would release the female partner from presumed cost of persistent courtship. On the contrary, the genotypically as well as phenotypically small males had significantly higher longevity than large males. The virility of the genotypically small males was not significantly different from that of genotypically large males. Our results clearly show that selection on body size operates in the opposite direction (disruptive selection) for the two genders, thus explaining the persistence of size polymorphisms in the holometabolous insect, Drosophila melanogaster.

    • 2ʹ-O-methyl nucleotide modified DNA substrates influence the cleavage efficiencies of BamHI and BglII

      Zhaoxue Tong Bin Zhao Guojie Zhao Hong Shang Yifu Guan

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      Induction of endonucleolytic DNA cleavage is an essential event that links the initiating stimuli to the final effects of cells. The cleavage efficiency and thus the final yield could be affected by many factors, including structures of DNA substrates, composite structures of enzymes–substrates or enzymes–nucleic analogs and so on. However, it is not clear whether a nucleotide derivative-substituted in DNA substrates can influence the efficiency of enzymatic cleavage. To investigate the effect of sugar pucker conformation on DNA–protein interactions, we used 2′-𝑂-methyl modified nucleotides (OMeN) to modify DNA substrates of isocaudemers BamHI and BglII in this study, and used FRET assay as an efficient method for analysis of enzyme cleavage. Experimental results demonstrated that OMeN-substituted recognition sequences influenced the cleavage rates significantly in a position-dependent manner. OMeN substitutions can reduce the cleavage as expected. Surprisingly, OMeN substitutions can also enhance the cleavage rates. The kinetics parameters of 𝑉max and 𝐾m have been obtained by fitting the Michaelis-Menten kinetic equation. These 2′-OMe nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property could enrich our understanding about the endonuclease cleavage mechanism and enhance our ability to regulate the enzymatic cleavage efficiency for applications in synthetic biology.

    • Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

      Arnab Roy Umesh Varshney Debnath Pal

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      Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

    • Limnology and cyanobacterial diversity of high altitude lakes of Lahaul-Spiti in Himachal Pradesh, India

      Y Singh J I S Khattar D P Singh P Rahi A Gulati

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      Limnological data of four high altitude lakes from the cold desert region of Himachal Pradesh, India, has been correlated with cyanobacterial diversity. Physico-chemical characteristics and nutrient contents of the studied lakes revealed that Sissu Lake is mesotrophic while Chandra Tal, Suraj Tal and Deepak Tal are ultra-oligotrophic. Based on morphology and 16S rRNA gene sequence, a total of 20 cyanobacterial species belonging to 11 genera were identified. Canonical correspondence analysis distinguished three groups of species with respect to their occurrence and nutrient/physical environment demand. The first group, which included Nostoc linckia, N. punctiforme, Nodularia sphaerocarpa, Geitlerinema acutissimum, Limnothrix redekii, Planktothrix agardhii and Plank. clathrata, was characteristic of water with high nutrient content and high temperature. The second group, including Gloeocapsopsis pleurocapsoides, Leptolyngbya antarctica, L. frigida, Pseudanabaena frigida and N. spongiaeforme, occurred in oligotrophic water with high pH and low temperature. The distribution of third group of Cyanobium parvum, Synechocystis pevalekii, L. benthonica, L. foveolarum, L. lurida, L. valderiana, Phormidium autumnale and P. chalybeum could not be associated with a particular environmental condition because of their presence in all sampling sites.

    • Conserved C-terminal nascent peptide binding domain of HYPK facilitates its chaperone-like activity

      Swasti Raychaudhuri Rachana Banerjee Subhasish Mukhopadhyay Nitai P Bhattacharyya

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      Human HYPK (Huntingtin Yeast-two-hybrid Protein K) is an intrinsically unstructured chaperone-like protein with no sequence homology to known chaperones. HYPK is also known to be a part of ribosome-associated protein complex and present in polysomes. The objective of the present study was to investigate the evolutionary influence on HYPK primary structure and its impact on the protein’s function. Amino acid sequence analysis revealed 105 orthologs of human HYPK from plants, lower invertebrates to mammals. C-terminal part of HYPK was found to be particularly conserved and to contain nascent polypeptide-associated alpha subunit (NPAA) domain. This region experiences highest selection pressure, signifying its importance in the structural and functional evolution. NPAA domain of human HYPK has unique amino acid composition preferring glutamic acid and happens to be more stable from a conformational point of view having higher content of 𝛼-helices than the rest. Cell biology studies indicate that overexpressed C-terminal human HYPK can interact with nascent proteins, co-localizes with huntingtin, increases cell viability and decreases caspase activities in Huntington’s disease (HD) cell culture model. This domain is found to be required for the chaperone-like activity of HYPK in vivo. Our study suggested that by virtue of its flexibility and nascent peptide binding activity, HYPK may play an important role in assisting protein (re)folding.

    • Skin anti-photoaging properties of ginsenoside Rh2 epimers in UV-B-irradiated human keratinocyte cells

      Sun-Joo Oh Sihyeong Lee Woo-Yong Choi Chang-Jin Lim

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      Ginseng, one of the most widely used herbal medicines, has a wide range of therapeutic and pharmacological applications. Ginsenosides are the major bioactive ingredients of ginseng, which are responsible for various pharmacological activities of ginseng. Ginsenoside Rh2, known as an antitumour ginsenoside, exists as two different stereoisomeric forms, 20(𝑆)-ginsenoside Rh2 [20(𝑆)-Rh2] and 20(𝑅)-ginsenoside Rh2 [20(𝑅)-Rh2]. This work aimed to assess and compare skin anti-photoaging activities of 20(𝑆)-Rh2 and 20(𝑅)-Rh2 in UV-B-irradiated HaCat cells. 20(𝑆)-Rh2, but not 20(𝑅)-Rh2, was able to suppress UV-B-induced ROS production in HaCat cells. Both stereoisomeric forms could not modulate cellular survival and NO level in UV-B-irradiated HaCat cells. Both 20(𝑆)-Rh2 and 20(𝑅)-Rh2 exhibited suppressive effects on UV-B-induced MMP-2 activity and expression in HaCat cells. In brief, the two stereoisomers of ginsenoside Rh2, 20(𝑆)-Rh2 and 20(𝑅)-Rh2, possess skin anti-photoaging effects but possibly in different fashions.

    • Herpes simplex virus types 1 and 2 modulate autophagy in SIRC corneal cells

      Goran Petrovski Kata Pásztor László Orosz Réka Albert Edina Mencel Morten C Moe Kai Kaarniranta Andrea Facskó Klára Megyeri

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      Autophagy and apoptosis function as important early cellular defense mechanisms in infections and other diseases. The outcome of an infection is determined by a complex interplay between the pathogenic microorganism and these intracellular pathways. To better understand the cytopathogenicity of Herpes simplex virus types 1 and 2 (HSV-1 and - 2), we studied the effect of these viruses on the autophagic and apoptotic processes in the SIRC corneal cell line. Infection with the KOS strain of HSV-1 and a wild-type strain of HSV-2 enhanced autophagosome formation, triggered cytoplasmic acidification, increased LC3B lipidation and elevated the ratio of apoptotic cells. The autophagy inhibitor bafilomycin A1 triggered a significant increase in the apoptotic responses of HSV-1- and HSV-2-infected cells. Thus, both HSV types affect autophagy and apoptosis in a coordinated fashion, and autophagy plays cytoprotective role in HSV-infected cells via antagonizing apoptosis. Together these data implicate autophagy in the pathogenic mechanism of herpetic keratitis.

    • Platelet-derived growth factor mediates interleukin-13-induced collagen I production in mouse airway fibroblasts

      Jiamei Lu Yanting Zhu Wei Feng Yilin Pan Shaojun Li Dong Han Lu Liu Xinming Xie Guizuo Wang Manxiang Li

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      Interleukin-13 (IL-13) is associated with the production of collagen in airway remodelling of asthma. Yet, the molecular mechanisms underlying IL-13 induction of collagen remain unclear; the aim of this study is to address this issue. IL-13 dose- and time-dependently-induced collagen I production in primary cultured airway fibroblasts; this was accompanied with the STAT6 phosphorylation, and pre-treatment of cells with JAK inhibitor suppressed IL-13-induced collagen I production. Further study indicated that IL-13 stimulated JAK/STAT6-dependent PDGF production and subsequent ERK1/2 MAPK activation in airway fibroblasts, and the presence of either PDGF receptor blocker or MEK inhibitor partially suppressed IL-13-induced collagen I production. Taken together, our study suggests that activation of JAK/STAT6 signal pathway and subsequent PDGF generation and resultant ERK1/2 MAPK activation mediated IL-13-induced collagen I production in airway fibroblasts.

    • Determining sensitive stages for learning to detect predators in larval bronzed frogs: Importance of alarm cues in learning

      Anuradha Batabyal Sachin M Gosavi Narahari P Gramapurohit

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      Successful survival and reproduction of prey organisms depend on their ability to detect their potential predators accurately and respond effectively with suitable defences. Predator detection can be innate or can be acquired through learning.We studied prey–predator interactions in the larval bronzed frogs (Sylvirana temporalis), which have the innate ability to detect certain predators. We conducted a series of experiments to determine if the larval S. temporalis rely solely on innate predator detection mechanisms or can also learn to use more specific cues such as conspecific alarm cues for the purpose. The results of our study clearly indicate that larval S. temporalis use both innate and learned mechanisms for predator detection. Predator-naïve tadpoles could detect kairomones alone as a potential threat and responded by reducing activity, suggesting an innate predator detection mechanism. Surprisingly, predator-naïve tadpoles failed to detect conspecific alarm cues as a potential threat, but learned to do so through experience. After acquiring the ability to detect conspecific alarm cues, they could associate novel predator cues with conspecific alarm cues. Further, post feeding stages of larval S. temporalis are sensitive for learning to detect conspecific alarm cues to label novel predators.

    • DNA barcoding of a new record of epi-endophytic green algae Ulvella leptochaete (Ulvellaceae, Chlorophyta) in India

      Felix Bast Satej Bhushan Aijaz Ahmad John

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      Epi-endophytic green algae comprise one of the most diverse and phylogenetically primitive groups of green algae and are considered to be ubiquitous in the world’s oceans; however, no reports of these algae exist from India. Here we report the serendipitous discovery of Ulvella growing on intertidal green algae Cladophora glomerata and benthic red algae Laurencia obtusa collected from India. DNA barcodes at nuclear ribosomal DNA Internal Transcriber Spacer (nrDNA ITS) 1 and 2 regions for Indian isolates from the west and east coasts have been generated for the first time. Based on morphology and DNA barcoding, isolates were identified as Ulvella leptochaete. Phylogenetic reconstruction of concatenated dataset using Maximum Likelihood method differentiated Indian isolates from other accessions of this alga available in Genbank, albeit with low bootstrap support. Monophyly of Ulvella leptochaete was obvious in both of our phylogenetic analyses. With this first report of epi-endophytic algae from Indian territorial waters, the dire need to catalogue its cryptic diversity is highlighted and avenues of future research are discussed.

    • Lantana camara L. (Verbenaceae) invasion along streams in a heterogeneous landscape

      Geetha Ramaswami Raman Sukumar

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      Streams are periodically disturbed due to flooding, act as edges between habitats and also facilitate the dispersal of propagules, thus being potentially more vulnerable to invasions than adjoining regions. We used a landscape-wide transect-based sampling strategy and a mixed effects modelling approach to understand the effects of distance from stream, a rainfall gradient, light availability and fire history on the distribution of the invasive shrub Lantana camara L.(lantana) in the tropical dry forests of Mudumalai in southern India. The area occupied by lantana thickets and lantana stem abundance were both found to be highest closest to streams across this landscape with a rainfall gradient. There was no advantage in terms of increased abundance or area occupied by lantana when it grew closer to streams in drier areas as compared to moister areas. On an average, the area covered by lantana increased with increasing annual rainfall. Areas that experienced greater number of fires during 1989–2010 had lower lantana stem abundance irrespective of distance from streams. In this landscape, total light availability did not affect lantana abundance. Understanding the spatially variable environmental factors in a heterogeneous landscape influencing the distribution of lantana would aid in making informed management decisions at this scale.

    • Does malaria epidemiology project Cameroon as `Africa in miniature'?

      Huguette Gaelle Ngassa Mbenda Gauri Awasthi Poonam K Singh Inocent Gouado Aparup Das

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      Cameroon, a west-central African country with a ∼20 million population, is commonly regarded as ‘Africa in miniature’ due to the extensive biological and cultural diversities of whole Africa being present in a single-country setting. This country is inhabited by ancestral human lineages in unique eco-climatic conditions and diverse topography. Over 90% Cameroonians are at risk of malaria infection, and ∼41% have at least one episode of malaria each year. Historically, the rate of malaria infection in Cameroon has fluctuated over the years; the number of cases was about 2 million in 2010 and 2011. The Cameroonian malaria control programme faces an uphill task due to high prevalence of multidrug-resistant parasites and insecticide-resistant malaria vectors. Above all, continued human migration from the rural to urban areas as well as population exchange with adjoining countries, high rate of ecological instabilities caused by deforestation, poor housing, lack of proper sanitation and drainage system might have resulted in the recent increase in incidences of malaria and other vector-borne diseases in Cameroon. The available data on eco-environmental variability and intricate malaria epidemiology in Cameroon reflect the situation in the whole of Africa, and warrant the need for in-depth study by using modern surveillance tools for meaningful basic understanding of the malaria triangle (host-parasite-vector-environment).

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