Crystal structure of the TAO2 kinase domain: activation and specificity of a Ste20p MAP3K

TAO2 is a mitogen-activated protein kinase kinase kinase (MAP3K) that doubly phosphorylates and activates the MAP kinase kinases (MAP2Ks) MEK3 and MEK6. The structure of the kinase domain of TAO2 (1-320) has been solved in its phosphorylated active conformation. The structure, together with structure-based mutagenic analysis, reveals that positively charged residues in the substrate binding groove mediate the first step in the dual phosphorylation of MEK6, on the threonine residue in the motif DS*VAKT*I (*denotes phosphorylation site) of MEK6. TAO2 is a Ste20p homolog, and the structure of active TAO2, in comparison with that of low-activity p21-activated protein kinase (PAK1), a Ste20p-related MAP4K, reveals how this group of kinases is activated by phosphorylation. Finally, active TAO2 displays unusual interactions with ATP, involving, in part, a subgroup-specific C-terminal extension of TAO2. The observed interactions may be useful in making specific inhibitors of TAO kinases.     

Pollution effects in Visakhapatnam harbour,India: An overview of 23 years of investigations and monitoring

Visakhapatnam Harbour, a semi-enclosed water body on the east coast of India, is subject to a high degree of pollution caused by industrial and urban wastes. Studies carried out during the last twenty years or so at 6 selected stations in the harbour revealed appreciable hydrographic and biotic changes. Over the years, the concentration of nitrites (max. 5 mg/l) and phosphates (9.6 mg/l) has increased. Dissolved oxygen registered all-time-high values (max. 21.6 mg/l) caused by periodic outbursts of phytoplankton, notably,Skeletonema costatum and other species. Benthic conditions have also changed and only certain pollution-tolerant species (e.g.Capitella capitata) inhabited the bottom sediments that contained a heavy load (2.5%) of organic matter. In the harbour, increased pollution led to the disappearence of stenoecious species and their replacement with other forms known for their tolerance to pollution. The paper describes the major changes which have occurred in water quality and organisms in the harbour as a result of pollution increase during the last two decades.     

In vitro and in silico characterization of angiogenic inhibitors from <Emphasis Type="Italic">Sophora interrupta</Emphasis>

Sophora interrupta Bedd, (Fabaceae) is used in Indian folk medicine to treat cancer. Angiogenesis is one of the crucial characteristics of cancer metastasis and is regulated by vascular endothelial growth factor (VEGF). In this study, we examined the antiangiogenic properties of the root ethyl acetate extract of Sophora interrupta by various methods. In vitro antioxidant activity (100–600 μg/ml) of S. interrupta ethyl acetate (SEA) extract was evaluated by DPPH and ABTS, anti-inflammatory activity (50, 100 and 150 μg/ml) by estimating nitric oxide (NO) levels, anti-angiogenic activity (200 and 500 μg/ml) was validated by chorio allantoic membrane (CAM) assay and in silico molecular dynamic (MD) simulations analyses (25 ns) were performed to identify the anti-angiogenic compounds extracted from root extract. The antioxidative activity of SEA extract at IC₅₀ (200?±?0.6 μg/mL) is equal to that of ascorbic acid at IC₅₀ (50?±?0.6 μg/mL), and the anti-inflammatory activity of SEA extract at IC₅₀ (150?±?0.2 μg/mL) was inhibited significantly by nitric oxide (NO) production. The SEA extract significantly reduced the sprouting of new blood vessels at ID₅₀ 500?±?0.13 μg/mL in the CAM assay. Gas chromatography–mass spectrometry analysis of the SEA extract detected 34 secondary metabolites, of which 6a,12a-dihydro-6H-(1,3)dioxolo(5,6)benzofuro(3,2-c)chromen-3-ol (maackiain) and funiculosin formed strong hydrogen bond interactions with Lys 920, Thr 916 and Cys 919 (2H), as well as Glu 917 of VEGFR2, and these interactions were similar to those of the anti-angiogenic compound axitinib. Significant findings in all the assays performed indicate that SEA extract has potential anti-angiogenic compounds that may interfere with VEGF-induced cancer malignancy.     

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions

Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.The emerging problems of increased food demand, declining water tables, and increasingly unpredictable growing environments due to climate change require increasingly adaptable varieties in order to maintain high rice (Oryza sativa) yields under variable conditions. Although genotype × environment variation has typically been viewed as a challenge to plant breeding efforts (Basford and Cooper, 1998; Cooper et al., 1999), the variation across environments known as adaptive phenotypic plasticity is likely to be an important trait for future crop plants, as it increases plant fitness and survival (Nicotra and Davidson, 2010). In some future growing seasons, rice may face edaphic stresses such as drought stress (due to low rainfall or reduced availability of irrigation) and lower nutrient availability (due to decreased fertilizer or water availability), whereas in other seasons, the growing conditions may remain optimal. Specialized root architectures, although effective for a specific stress-prone environment, can be functionally maladaptive in different conditions (Ho et al., 2005; Poot and Lambers, 2008). Therefore, increased plasticity in root traits in terms of allocational, morphological, anatomical, or developmental plasticity (Sultan, 2000) could improve crop performance across future growing seasons (Aspinwall et al., 2015).A number of previous studies have reported that plasticity in certain root traits conferred improved plant performance under stress or variable growth conditions to which the crop may be exposed. Under different types of drought stress, plasticity in root length density or total root length (Kano-Nakata et al., 2011; Tran et al., 2015) and lateral root length and/or branching (Suralta et al., 2010; Kano et al., 2011; Kano-Nakata et al., 2013) has been observed to improve shoot biomass, water uptake, and photosynthesis under drought in rice. Plasticity in the level of root aerenchyma development (measured as root porosity) was reported to result in higher shoot dry matter (Niones et al., 2013) and grain yield (Niones et al., 2012) under transient drought stress in rice, and plasticity in other anatomical traits has been hypothesized as a major reason for wheat (Triticum aestivum) being more drought tolerant than rice (Kadam et al., 2015). In a set of 42 native and crop species, plasticity in root depth was a better predictor of shoot response to drought than absolute root depth (Reader et al., 1993). Under low nitrogen, plasticity in specific root area, specific root length, and root tissue density conferred the least reduction in relative growth rate in 10 perennial herbaceous species (Useche and Shipley, 2010), and plasticity in maize (Zea mays) root growth angle improved yield (Trachsel et al., 2013). These examples provide strong evidence that root phenotypic plasticity can result in improved plant performance across variable conditions that include edaphic stress and would be an effective target for crop improvement efforts.Deciphering the genetic and molecular mechanisms controlling root phenotypic plasticity will be necessary for effective selection and crop breeding efforts. Despite the likely genetic complexity behind the regulation of trait expression according to environmental conditions, phenotypic plasticity is heritable and selectable (for review, see Nicotra and Davidson, 2010). Genetic regions identified to be related to root phenotypic plasticity traits in crops include quantitative trait loci (QTLs) for root hair length plasticity in maize under low phosphorus (Zhu et al., 2005a), lateral root number plasticity in maize under low phosphorus (Zhu et al., 2005b), plasticity in aerenchyma development in response to drought stress in rice (Niones et al., 2013), and plasticity in lateral root growth in response to drought stress in rice (Niones et al., 2015). In wheat translocation lines, a plastic response of increased root biomass to drought was located to chromosome 1BS (Ehdaie et al., 2011). These identified genetic regions can be used in selection for the development of stress-tolerant crops.Future rice crops will likely experience a range of soil conditions including prolonged aerobic periods, drought stress (progressive or intermittent), low soil fertility, and flooding. Rice may be established by either transplanting or direct seeding depending upon the amount and duration of initial rainfall. Therefore, the identification of root phenotypic plasticity traits suitable for adaptability to the particular range of conditions faced by rice crops, as well as the genetic regions responsible for those plasticity traits, may facilitate selection for wide adaptation of rice genotypes to variable conditions to confer stable yield. To address these needs, this study was conducted to identify the rice root phenotypic plasticity traits conferring adaptability across variable growth conditions by comparing contrasting genotypes from crosses between traditional and modern varieties. Our aim was to effectively quantify root architectural plasticity in order to identify which root traits may play the most important roles in rice adaptability. We hypothesized that the most plastic genotypes may show the most stable yields across environments.     

Genome‐wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola

Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola‐meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome‐wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome‐wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes.     

Adverse Events in Robotic Surgery: A Retrospective Study of 14 Years of FDA Data

BackgroundUse of robotic systems for minimally invasive surgery has rapidly increased during the last decade. Understanding the causes of adverse events and their impact on patients in robot-assisted surgery will help improve systems and operational practices to avoid incidents in the future.MethodsBy developing an automated natural language processing tool, we performed a comprehensive analysis of the adverse events reported to the publicly available MAUDE database (maintained by the U.S. Food and Drug Administration) from 2000 to 2013. We determined the number of events reported per procedure and per surgical specialty, the most common types of device malfunctions and their impact on patients, and the potential causes for catastrophic events such as patient injuries and deaths.ResultsDuring the study period, 144 deaths (1.4% of the 10,624 reports), 1,391 patient injuries (13.1%), and 8,061 device malfunctions (75.9%) were reported. The numbers of injury and death events per procedure have stayed relatively constant (mean = 83.4, 95% confidence interval (CI), 74.2–92.7 per 100,000 procedures) over the years. Surgical specialties for which robots are extensively used, such as gynecology and urology, had lower numbers of injuries, deaths, and conversions per procedure than more complex surgeries, such as cardiothoracic and head and neck (106.3 vs. 232.9 per 100,000 procedures, Risk Ratio = 2.2, 95% CI, 1.9–2.6). Device and instrument malfunctions, such as falling of burnt/broken pieces of instruments into the patient (14.7%), electrical arcing of instruments (10.5%), unintended operation of instruments (8.6%), system errors (5%), and video/imaging problems (2.6%), constituted a major part of the reports. Device malfunctions impacted patients in terms of injuries or procedure interruptions. In 1,104 (10.4%) of all the events, the procedure was interrupted to restart the system (3.1%), to convert the procedure to non-robotic techniques (7.3%), or to reschedule it (2.5%).ConclusionsDespite widespread adoption of robotic systems for minimally invasive surgery in the U.S., a non-negligible number of technical difficulties and complications are still being experienced during procedures. Adoption of advanced techniques in design and operation of robotic surgical systems and enhanced mechanisms for adverse event reporting may reduce these preventable incidents in the future.     

Characterization of SNP and Structural Variations in the Mitochondrial Genomes of Tilletia indica and Its Closely Related Species Formed Basis for a Simple Diagnostic Assay

Tilletia indica causes the disease Karnal bunt in wheat. The disease is under international quarantine regulations. Comparative mitochondrial (mt) genome analysis of T. indica ({"type":"entrez-nucleotide","attrs":{"text":"KX394364","term_id":"1128620031","term_text":"KX394364"}}KX394364 and {"type":"entrez-nucleotide","attrs":{"text":"DQ993184","term_id":"115361453","term_text":"DQ993184"}}DQ993184) and T. walkeri ({"type":"entrez-nucleotide","attrs":{"text":"EF536375","term_id":"144925993","term_text":"EF536375"}}EF536375) has found 325 to 328 SNPs, 57 to 60 short InDels (from 1 to 13 nt), two InDels (30 and 61 nt) and five (>200 nt) presence/absence variations (PAVs) between the two species. The mt genomes of both species have identical gene order. The numbers of SNPs and InDels between the mt genomes of the two species are approximately nine times of the corresponding numbers between the two T. indica isolates. There are eight SNPs between T. indica and T. walkeri that resulted in amino acid substitutions in the mt genes of cob, nad2 and nad5. In contrast, there is no amino acid substitution in the mt genes of the T. indica isolates from the SNPs found. The five PAVs present in T. indica ({"type":"entrez-nucleotide","attrs":{"text":"DQ993184","term_id":"115361453","term_text":"DQ993184"}}DQ993184) are absent in T. walkeri. Four PAVs are more than 1 kb and are not present in every T. indica isolate. Analysis of their presence and absence separates a collection of T. indica isolates into 11 subgroups. Two PAVs have ORFs for the LAGLIDAG endonuclease and two have ORFs for the GIY-YIG endonuclease family, which are representatives of homing endonuclease genes (HEGs). These intron- encoded HEGs confer intron mobility and account for their fluid distribution in T. indica isolates. The small PAV of 221 bp, present in every T. indica isolate and unique to the species, was used as the genetic fingerprint for the successful development of a rapid, highly sensitive and specific loop mediated isothermal amplification (LAMP) assay. The simple procedure of the LAMP assay and the easy detection formats will enable the assay to be automated for high throughput diagnosis.     

Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses

Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.     

Dispersal by generalist frugivores affects management of an invasive plant

In the past century, our understanding of the processes driving plant invasion and its consequences for natural and anthropogenic systems has increased considerably. However, the management of invasive plants remains a challenge despite ever more resources being allocated to their removal. Often invasive plants targeted for ‘eradication’ are well‐established, have multiple modes of reproduction, long‐term seed banks, and strong associations with native and non‐native mutualists that ensure dispersal and facilitate spread. The pantropical weed, Lantana camara (Lantana), is one of the most invasive woody plants globally. We illustrate that, for Lantana, eradication is an unrealistic management goal given the short‐term removal approaches, irrespective of the effectiveness of removal methods. We assessed the role of dispersal by avian frugivores in the recolonization of managed areas by Lantana in the seasonally dry, tropical forests of northern and southern India. We estimated the distribution of Lantana, its dispersal potential and the proximity between managed areas and source populations. We found that Lantana was dispersed by many generalist frugivorous birds and that most managed areas were well within the median dispersal distance from source plants facilitating rapid recolonization of managed areas. We conclude that given the difficulty of eradicating long‐established invasive plants, management practices should entail long‐term monitoring and control in priority areas for as long as Lantana occurs in the landscape.     

Discovery of Mycobacterium tuberculosis α-1,4-Glucan Branching Enzyme (GlgB) Inhibitors by Structure- and Ligand-based Virtual Screening

GlgB (α-1,4-glucan branching enzyme) is the key enzyme involved in the biosynthesis of α-glucan, which plays a significant role in the virulence and pathogenesis of Mycobacterium tuberculosis. Because α-glucans are implicated in the survival of both replicating and non-replicating bacteria, there exists an exigent need for the identification and development of novel inhibitors for targeting enzymes, such as GlgB, involved in this pathway. We have used the existing structural information of M. tuberculosis GlgB for high throughput virtual screening and molecular docking. A diverse database of 330,000 molecules was used for identifying novel and efficacious therapeutic agents for targeting GlgB. We also used three-dimensional shape as well as two-dimensional similarity matrix methods to identify diverse molecular scaffolds that inhibit M. tuberculosis GlgB activity. Virtual hits were generated after structure and ligand-based screening followed by filters based on interaction with human GlgB and in silico pharmacokinetic parameters. These hits were experimentally evaluated and resulted in the discovery of a number of structurally diverse chemical scaffolds that target M. tuberculosis GlgB. Although a number of inhibitors demonstrated in vitro enzyme inhibition, two compounds in particular showed excellent inhibition of in vivo M. tuberculosis survival and its ability to get phagocytosed. This work shows that in silico docking and three-dimensional chemical similarity could be an important therapeutic approach for developing inhibitors to specifically target the M. tuberculosis GlgB enzyme.