PRODUCTION OF NARINGINASE FROM A NEW SOIL ISOLATE,Bacillus methylotrophicus: ISOLATION,OPTIMIZATION AND SCALE-UP STUDIES

Five strains of naringin-degrading bacteria were isolated and found to be positive for extracellular naringinase activity. The one that showed highest activity in the selective medium was identified by 16S rRNA analysis as Bacillus methylotrophicus. The best combination of carbon–nitrogen source was determined by employing two-level full factorial analyses, comprising 24 experiments in shake flasks. Sucrose–yeast extract showed significant increase in naringinase activity (7.46 U/L) compared to the basal medium. Naringinase production was found to be inducible and naringin was found to be the best inducer among naringin, naringenin, hesperidin, and L-rhamnose. Inoculum size of 2% (v/v) and age of 48 hr favored naringinase and biomass production. Highest naringinase activity of 8 U/L was observed at the initial medium pH of 6. Response surface modeling was applied based on central composite design to determine the effects of three independent variables (sucrose, yeast extract, and naringin) and their mutual interactions. In total, 20 experiments were conducted and a statistical model was developed, which predicted naringinase production of 10.61 U/L. Subsequently, verification experiments were conducted and validity of the model was verified. Bioreactor studies conducted with the optimized medium showed an enzyme production of 12.05 U/L within 34 hr of fermentation.     

Cilia born out of shock and stress

EMBO J (2013) 32 23, 3029–3040 10.1038/emboj.2013.223; published online October112013Primary cilia are cell surface sensory organelles, whose dysfunction underlies various human genetic diseases collectively termed ciliopathies. A new study in The EMBO Journal by Villumsen et al now reveals how stress–response pathways converge to stimulate ciliogenesis by modulating protein composition of centriolar satellites. Better understanding of these mechanisms should bring us closer to identifying the cellular defects that underlie ciliopathies caused by mutations in centriolar satellite proteins.Centrioles are barrel-shaped structures with two distinct identities. In proliferating cells centrioles provide structural support for the centrosome, a key microtubule-organizing centre, whereas in quiescent cells centrioles are converted into basal bodies and promote the assembly of primary cilia. In centrosomes, centrioles are embedded in pericentriolar material (PCM), a dynamic structure responsible for microtubule nucleation. PCM proteins exhibit cell cycle-dependent localisation, achieved at least in part by the regulation of their transport. Centriolar satellites, dense fibrous granules frequently clustered around the interphase centrosome, have been implicated in microtubule-dependent protein transport to centrosomes (Kubo et al, 1999). In particular, PCM-1, the core constituent of centriolar satellites, is required for centrosomal accumulation of several PCM components (Dammermann and Merdes, 2002). Although the proteomic composition of satellites is still elusive, the growing list of satellite proteins includes CEP131/AZI1 (Staples et al, 2012), CEP290 (Stowe et al, 2012), Bardet-Biedl syndrome protein 4 (BBS4) and Oral facial digital syndrome protein (OFD1; Lopes et al, 2011). Mutations in OFD1, CEP290 and BBS4 cause ciliopathies (Kim et al, 2008), underscoring a functional link between satellites and ciliogenesis. So far, two roles have been proposed for satellites in cilia formation: First, in cycling cells they may serve to sequester essential ciliary proteins (Stowe et al, 2012). Second, upon initiation of the ciliogenesis programme, centriolar satellite components seem to promote the recruitment of specific ciliary proteins to basal bodies (Ferrante et al, 2006; Lopes et al, 2011; Stowe et al, 2012).In a new study in The EMBO Journal, Villumsen et al (2013) now describe how stress–response pathways conspire to control ciliogenesis. The authors observed that specific environmental stresses, such as ultraviolet light radiation (UV) or heat shock, but not ionizing radiation (IR), trigger rapid displacement of PCM-1, AZI1 and CEP290 from centriolar satellites. However, OFD1 remained associated with satellites, indicating that centriolar satellites persist despite UV-induced removal of PCM-1. This might come as some surprise, since PCM-1 depletion by RNA interference (RNAi) is thought to disrupt satellite integrity (Kim et al, 2008; Lopes et al, 2011); however, satellite loss upon PCM-1 RNAi may be a consequence of prolonged depletion of PCM-1, while acute PCM-1 displacement by stress might only ‘remodel'' centriolar satellites. It is also possible that not all satellites are created equal, and they do vary in protein composition (Kim et al, 2008; Staples et al, 2012). If so, UV-induced PCM-1 removal may disrupt some, but not all satellites.A good candidate regulator of centriolar satellite remodelling was the stress-activated MAP kinase p38, and indeed, Villumsen et al (2013) found p38 MAPK activity to be stimulated by both UV and heat shock but not IR in U2OS cells, mirroring those very stress pathways that also cause displacement of AZI1 and PCM-1 from satellites. Furthermore, p38 MAPK was essential for UV-induced dispersal of PCM-1 and AZI1. The authors then tested the hypothesis that stress-induced centriolar satellite remodelling could involve changes in the interactome of AZI1, and—consistent with an earlier proteomics study (Akimov et al, 2011)—identified PCM-1, CEP290 and the mindbomb E3 ubiquitin protein ligase 1 (MIB1) as the main AZI1 binding partners. GFP-MIB1 localized to centriolar satellites and mono-ubiquitylated AZI1, PCM-1 and CEP290 in cycling cells. In response to UV, both ubiquitylation of these proteins and MIB1 activity were reduced; notably, UV-induced MIB1 inactivation was independent of p38 MAPK activity, indicating that these two enzymes may act via distinct pathways (Figure 1A).Open in a separate windowFigure 1(A) Regulation of centriolar satellite remodelling. (B) Schematic summary of how centriolar satellite remodelling might facilitate ciliogenesis. See text for details.What could be the purpose of MIB1-dependent ubiquitylation of these satellite proteins? It certainly does not seem to regulate subcellular targeting, as in MIB1-depleted cells, AZI1 and PCM-1 both localised normally to centriolar satellites and could still be displaced by UV. Instead, ubiquitylation seems to suppress the interaction between AZI1 and PCM-1, consistent with the observation that UV, a condition that also reduces their ubiquitylation, enhances the binding of AZI1 to PCM-1.PCM-1, CEP290 and AZI1 all participate in ciliogenesis (Kim et al, 2008; Wilkinson et al, 2009; Stowe et al, 2012), raising the possibility that MIB1 might also affect this process. Indeed, serum starvation, which is known to promote cilia formation, attenuated MIB1 activity. Furthermore, MIB1 overexpression reduced the ciliogenesis observed in serum-starved cells, while MIB1 depletion in proliferating cells triggered a marked increase in the proportion of cells that formed cilia; this seems to reflect a direct effect of MIB1 on ciliogenesis, since neither MIB1 depletion nor overexpression altered cell cycle progression. Taken together, downregulation of MIB1 enzymatic activity appears to be a pre-requisite for efficient ciliogenesis, regardless of whether it is triggered by physiological ciliogenesis-promoting signals or by environmental stresses, making MIB1 a novel negative regulator of cilia formation.The recent discovery of ciliopathy-associated mutations in constituents of the DNA damage response signalling pathway pointed to a connection between DNA damage and ciliogenesis (Chaki et al, 2012). With the new link between UV and centriolar satellites, the authors next asked if UV radiation might affect ciliogenesis. Remarkably, UV and heat shock both triggered cilia assembly in RPE-1 cells in a p38 MAPK-dependent manner. MIB1 depletion further enhanced ciliogenesis after UV radiation, again implying an additive effect of p38 MAPK signalling and MIB1 suppression (Figure 1A).While finer details on the precise role of centriolar satellite components in cilia formation are still lacking, a more coherent picture is finally starting to emerge. In cycling cells, ubiquitination by MIB1 could serve to limit the interaction between AZI1 and PCM-1 on centriolar satellites (Figure 1B). Under these conditions PCM-1 may bind and sequester CEP290, an essential ciliogenic protein, thereby precluding untimely cilia formation (Stowe et al, 2012). Both during normal and stress-induced ciliogenesis programs, remodelling of centriolar satellites creates a permissive environment for cilia formation, and a key step in this process is downregulation of MIB1 activity. While it remains to be established how the latter is achieved, it is clear that MIB1 inactivation causes loss of ubiquitylation and increased binding between AZI1 and PCM-1. Preferential interaction of PCM-1 with AZI1 could in turn facilitate release of CEP290 from centriolar satellites and its subsequent accumulation at the centrosome. Once CEP290 reaches the optimum concentration at the centriole/basal body, it could serve to tether AZI1–PCM-1 complexes. PCM-1 could then concentrate Rab8 GTPase near centrosomes, allowing CEP290 to recruit Rab8 into the cilium, where it acts to extend the ciliary membrane (Kim et al, 2008).Collectively, the findings reported here provide strong experimental support to the notion that centriolar satellites are negative regulators of ciliogenesis in proliferating cells. Their role is central to limit untimely formation of cilia in cells. Environmental strains elicit stress–response pathways that converge to relieve the ciliogenesis block imposed by satellites. It is tempting to speculate that stress-induced cilia might serve as signalling platforms and contribute to checkpoint activation or perhaps initiation of repair mechanisms, but more work is needed to establish the true purpose of ciliogenesis in this context. It is of considerable interest that a recent study reports that autophagy, another stress-induced pathway, selectively removes OFD1 from satellites to promote ciliogenesis (Tang et al, 2013). Therefore stress-mediated centriolar satellite remodelling seems to be an evolving theme in the control of ciliogenesis.     

Role of protein kinase N2 (PKN2) in cigarette smoke-mediated oncogenic transformation of oral cells

Smoking is the leading cause of preventable death worldwide. Though cigarette smoke is an established cause of head and neck cancer (including oral cancer), molecular alterations associated with chronic cigarette smoke exposure are poorly studied. To understand the signaling alterations induced by chronic exposure to cigarette smoke, we developed a cell line model by exposing normal oral keratinocytes to cigarette smoke for a period of 12 months. Chronic exposure to cigarette smoke resulted in increased cellular proliferation and invasive ability of oral keratinocytes. Proteomic and phosphoproteomic analyses showed dysregulation of several proteins involved in cellular movement and cytoskeletal reorganization in smoke exposed cells. We observed overexpression and hyperphosphorylation of protein kinase N2 (PKN2) in smoke exposed cells as well as in a panel of head and neck cancer cell lines established from smokers. Silencing of PKN2 resulted in decreased colony formation, invasion and migration in both smoke exposed cells and head and neck cancer cell lines. Our results indicate that PKN2 plays an important role in oncogenic transformation of oral keratinocytes in response to cigarette smoke. The current study provides evidence that PKN2 can act as a potential therapeutic target in head and neck squamous cell carcinoma, especially in patients with a history of smoking.     

Physiological and biochemical characterization of NERICA‐L‐44: a novel source of heat tolerance at the vegetative and reproductive stages in rice

The predicted increase in the frequency and magnitude of extreme heat spikes under future climate can reduce rice yields significantly. Rice sensitivity to high temperatures during the reproductive stage is well documented while the same during the vegetative stage is more speculative. Hence, to identify and characterize novel heat‐tolerant donors for both the vegetative and reproductive stages, 71 rice accessions, including approximately 75% New Rice for Africa (NERICAs), were phenotyped across field experiments during summer seasons in Delhi, India, and in a controlled environment study at International Rice Research Institute , Philippines. NERICA‐L‐44 (NL‐44) recorded high seedling survival (52%) and superior growth and greater reproductive success exposed to 42.2°C (sd ± 2.3) under field conditions. NL‐44 and the heat‐tolerant check N22 consistently displayed lower membrane damage and higher antioxidant enzymes activity across leaves and spikelets. NL‐44 recorded 50–60% spikelet fertility, while N22 recorded 67–79% under controlled environment temperature of 38°C (sd ±1.17), although both had about 87% fertility under extremely hot field conditions. N22 and NL‐44, exposed to heat stress (38°C), had similar pollen germination percent and number of pollen tubes reaching the ovary. NL‐44 maintained low hydrogen peroxide production and non‐photochemical quenching (NPQ) with high photosynthesis while N22 avoided photosystem II damage through high NPQ under high‐temperature stress. NL‐44 with its reproductive stage resilience to extreme heat stress, better antioxidant scavenging ability in both vegetative tissue and spikelets and superior yield and grain quality is identified as a novel donor for increasing heat tolerance at both the vegetative and reproductive stages in rice.     

Focus on Chromatin/Epigenetics: Histone H2B Monoubiquitination Mediated by HISTONE MONOUBIQUITINATION1 and HISTONE MONOUBIQUITINATION2 Is Involved in Anther Development by Regulating Tapetum Degradation-Related Genes in Rice

Water scarcity and the increasing severity of water deficit stress are major challenges to sustaining irrigated rice (Oryza sativa) production. Despite the technologies developed to reduce the water requirement, rice growth is seriously constrained under water deficit stress compared with other dryland cereals such as wheat (Triticum aestivum). We exposed rice cultivars with contrasting responses to water deficit stress and wheat cultivars well adapted to water-limited conditions to the same moisture stress during vegetative growth to unravel the whole-plant (shoot and root morphology) and organ/tissue (root anatomy) responses. Wheat cultivars followed a water-conserving strategy by reducing specific leaf area and developing thicker roots and moderate tillering. In contrast, rice ‘IR64’ and ‘Apo’ adopted a rapid water acquisition strategy through thinner roots under water deficit stress. Root diameter, stele and xylem diameter, and xylem number were more responsive and varied with different positions along the nodal root under water deficit stress in wheat, whereas they were relatively conserved in rice cultivars. Increased metaxylem diameter and lower metaxylem number near the root tips and exactly the opposite phenomena at the root-shoot junction facilitated the efficient use of available soil moisture in wheat. Tolerant rice ‘Nagina 22’ had an advantage in root morphological and anatomical attributes over cultivars IR64 and Apo but lacked plasticity, unlike wheat cultivars exposed to water deficit stress. The key traits determining the adaptation of wheat to dryland conditions have been summarized and discussed.Among cereals, rice (Oryza sativa) and wheat (Triticum aestivum) are the most important staple food crops, and they belong to the family Poaceae. These two cereals share a common ancestor and diverged about 65 million years ago (Sorrells et al., 2003). Rice eventually developed strong adaptation potential for fully flooded conditions across tropical to temperate environments, while wheat became well adapted to aerobic conditions mostly restricted to temperate environments. Rice, with a semiaquatic behavior, consumes about 30% of the total fresh water available for agricultural crops worldwide, which equates to a 2- to 3-fold higher consumption than other cereals such as wheat and maize (Zea mays; Peng et al., 2006). Despite a significantly lower water requirement, the potential yield of wheat in a favorable environment (9 tons ha⁻¹) is comparable with the yield of fully flooded rice (9 tons ha⁻¹) in the dry season at the International Rice Research Institute (IRRI; Fischer and Edmeades, 2010). Hence, rice records very low water productivity compared with wheat and other dryland cereals. Because of growing concerns about water scarcity and the increased frequency and magnitude of water deficit stress events under current and future climates, increasing or even sustaining rice yield under fully flooded conditions is highly challenging. To minimize the total water requirement for cultivating rice, several water-saving technologies have been developed, such as direct-seeded aerobic rice cultivation (Bindraban et al., 2006). These water-saving technologies increased water productivity substantially compared with flooded conditions but were invariably associated with a yield penalty. A major challenge that water-saving technologies including aerobic rice currently face is the lack of mechanistic understanding for further genetic improvement.By virtue of its wider adaptation to a range of edaphic conditions, rice is considered to possess the diversity to adapt to upland or aerobic scenarios extending into water deficit conditions (Khush, 1997). Genetic differences in rice root biomass and rooting depth and variation in root morphology with water deficit stress exposure are well documented (Kato et al., 2006, 2007; Henry et al., 2011; Kano et al., 2011). But the underlying mechanisms differing across diverse germplasm that influence water uptake under water deficit stress are not fully understood (Gowda et al., 2011). A recent report has documented water deficit-tolerant genotypes recording a lower bleeding rate and narrow xylem diameter under stress (Henry et al., 2012). Contrastingly, a higher root hydraulic conductivity helped to maintain a higher photosynthetic rate (Adachi et al., 2010), with tolerant cultivars maintaining greater root hydraulic conductivity than susceptible cultivars (Matsuo et al., 2009). Furthermore, upland rice cultivars with deeper roots outperformed lowland cultivars possessing a shallow root system when encountered with water deficit stress (Uga et al., 2013). Additionally, major-effect grain yield metaquantitative trait loci under water deficit stress identified in rice were found to colocalize on the genomes of other dryland cereals such as wheat, maize, and pearl millet (Pennisetum glaucum; Swamy et al., 2011), indicating a possible common evolutionary pathway for water deficit adaptation across cereals. Despite these achievements and the relatedness among cereals, rice does not respond in a way similar to other dryland cereals to water deficit stress conditions. To bring in a revolutionary change in future breeding strategies for upland/aerobic rice and for water deficit tolerance in rice, there is a need for a fundamental understanding and identification of the key traits that determine the water deficit stress response in well-adapted dryland cereals. Hence, comparing whole-plant responses (shoot and root) of rice with those of other dryland cereals such as wheat is essential.A comparative study between two C₃ cereals (rice and wheat) will help identify the core adaptive mechanisms and/or a suite of traits that render wheat to grow with less water and more tolerance of water deficit stress. Such comparative analysis should target key morphological, physiological, anatomical, and agronomic traits throughout the crop growth cycle, as water deficit stress occurs at both early (vegetative stage) and late (reproductive stage) seasons in rice (Pandey et al., 2007). Extensive research efforts are currently ongoing to reduce the impact of water deficit stress during the reproductive stage in rice (Venuprasad et al., 2008; Verulkar et al., 2010; Vikram et al., 2011; Kumar et al., 2014) and in wheat (Olivares-Villegas et al., 2007; Lopes and Reynolds, 2010; Pinto et al., 2010). Therefore, our study focused on stress during the vegetative stage to identify key checkpoints that determine whole-plant responses of representative rice cultivars adapted to lowland, upland/aerobic, or water deficit conditions and of wheat cultivars with moderate to high water deficit tolerance. Cultivars from both species were exposed to moisture levels that resemble aerobic conditions and water deficit stress during the vegetative stage. Our study follows a previous report that has successfully demonstrated the approach to expose rice and wheat to the same moisture stress conditions (Praba et al., 2009) and is designed to address the following specific objectives: (1) to quantify the adaptive plasticity in shoot and root morphology and biomass partitioning among different plant parts (leaves, stem, and root); (2) to estimate the key supportive physiological mechanisms such as whole-plant water use efficiency (WUE) and leaf-level carbon isotope discrimination (Δ13C); and (3) to dissect root anatomical plasticity across different key zones in both rice and wheat roots exposed to water deficit stress. Finally, novel traits that benefit dryland adaptation in wheat compared with high water-requiring rice cultivars are highlighted.     

Genetic Diversity of Mycobacterium tuberculosis Isolates from Assam,India: Dominance of Beijing Family and Discovery of Two New Clades Related to CAS1_Delhi and EAI Family Based on Spoligotyping and MIRU-VNTR Typing

Tuberculosis (TB) is one of the major public health concerns in Assam, a remote state located in the northeastern (NE) region of India. The present study was undertaken to explore the circulating genotypes of Mycobacterium tuberculosis complex (MTBC) in this region. A total of 189 MTBC strains were collected from smear positive pulmonary tuberculosis cases from different designated microscopy centres (DMC) from various localities of Assam. All MTBC isolates were cultured on Lowenstein-Jensen (LJ) media and subsequently genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Spoligotyping of MTBC isolates revealed 89 distinct spoligo patterns. The most dominant MTBC strain belonged to Beijing lineage and was represented by 35.45% (n = 67) of total isolates, followed by MTBC strains belonging to Central Asian-Delhi (CAS/Delhi) lineage and East African Indian (EAI5) lineage. In addition, in the present study 43 unknown spoligo patterns were detected. The discriminatory power of spoligotyping was found to be 0.8637 based on Hunter Gaston Discriminatory Index (HGDI). On the other hand, 24-loci MIRU-VNTR typing revealed that out of total 189 MTBC isolates from Assam 185 (97.9%) isolates had unique MIRU-VNTR profiles and 4 isolates grouped into 2 clusters. Phylogenetic analysis of 67 Beijing isolates based on 24-loci MIRU-VNTR typing revealed that Beijing isolates from Assam represent two major groups, each comprising of several subgroups. Neighbour-Joining (NJ) phylogenetic tree analysis based on combined spoligotyping and 24-loci MIRU-VNTR data of 78 Non-Beijing isolates was carried out for strain lineage identification as implemented by MIRU-VNTRplus database. The important lineages of MTBC identified were CAS/CAS1_Delhi (41.02%, n = 78) and East-African-Indian (EAI, 33.33%). Interestingly, phylogenetic analysis of orphan (23.28%) MTBC spoligotypes revealed that majority of these orphan isolates from Assam represent two new sub-clades Assam/EAI and Assam/CAS. The prevalence of multidrug resistance (MDR) in Beijing and Non-Beijing strains was found to be 10.44% and 9.01% respectively. In conclusion, the present study has shown the predominance of Beijing isolates in Assam which is a matter of great concern because Beijing strains are considered to be ecologically more fit enabling wider dissemination of M. tuberculosis. Other interesting finding of the present study is the discovery of two new clades of MTBC isolates circulating in Assam. More elaborate longitudinal studies are required to be undertaken in this region to understand the transmission dynamics of MTBC.     

Complement-Fixation Test for Detection of Herpes-like Viruses in Cell Cultures of Burkitt''s Lymphoma

Although biopsies of Burkitt's tumors contained no detectable complement-fixing (CF) antigen or antigens, tumor cell lines contained CF antigen or antigens related to the presence of a herpes-like virus particle.     

Lipid content of brain, brain membrane lipid domains, and neurons from acid sphingomyelinase deficient mice

The cholesterol, sphingolipid, and glycerophospholipid content of total brain, of detergent-resistant membranes prepared from the total brain, and of cerebellar granule cells differentiated in culture from wild type (WT) and acid sphingomyelinase knockout (ASMKO) were studied. Brains derived from 7-month-old ASMKO animals showed a fivefold higher level of sphingomyelin and a significant increase in ganglioside content, mainly because of monosialogangliosides GM3 and GM2 accumulation, while the cholesterol and glycerophospholipid content was unchanged with respect to WT animals. An increase in sphingomyelin, but not in gangliosides, was also detected in cultured cerebellar granule neurons from ASMKO mice, indicating that ganglioside accumulation is not a direct consequence of the enzyme defect. When a detergent-resistant membrane fraction was prepared from ASMKO brains, we observed that a higher detergent-to-protein ratio was needed than in WT animals. This likely reflects a reduced fluidity in restricted membrane areas because of a higher enrichment in sphingolipids in the case of ASMKO brain.