A New Stem-splitting Symptom in Safflower Caused by Macrophomina phaseolina

Safflower is known to be attacked by several seed‐borne fungi, of which Macrophomina phaseolina is one of the most important pathogens causing serious yield losses. During routine experiments, a new stem‐split symptom was observed in M. phaseolina‐infected plants resulting in poor growth and reduced size of inflorescences. Stem‐split was observed in 30‐day‐old plants as minute cracks approximately 2–3 cm above the soil surface, which over time extended to both upward and downward directions, resulting in the formation of a wider split. The split portion was hollow and brown with a white to grey mycelial mat of the fungus on the inner surface. Such plants became lodged, ultimately resulting in poor seed yield compared with healthy plants. The stem‐split plants showed delayed flowering by 1 week over healthy plants. One of the three M. phaseolina isolates used for inoculation of seeds and plants was more aggressive but all isolates were able to reproduce the stem‐split symptoms found on naturally infected safflower plants in the field.     

A comprehensive review on pharmacological properties and biotechnological aspects of Genus <Emphasis Type="Italic">Chlorophytum</Emphasis>

Genus Chlorophytum Ker Gawl secures its position chiefly as commercial plants with a wide range of applications, right from pharmaceutical to ornamental, and with a promising economical return also. Few species of this genus are now enlisted under “threatened plant category” due to rash harvesting from its wild habitat, as it is utilized extensively in various industries. Great challenges are associated with its conventional propagation approach. The accomplishment and rapidity in the propagation of few species of Chlorophytum have constantly been a key concern for farmers and researchers. In this regard, in vitro propagation is an efficient technique to triumph over regeneration-associated problems. Available literature was surveyed rigorously to extract the information on pharmacological utilities and recent advancements in in vitro regeneration of genus Chlorophytum. Since 1990s to till now, a number of efforts were made in different aspects of Chlorophytum under both in vitro and ex vitro conditions. Current review intends to provide a comprehensive overview of important properties and biotechnological aspects, viz. bioactive constituents and inherent properties of such as aphrodisiac potential, anti-diabetic, anti-microbial, anti-tumor and anti-oxidant, and in vitro production of genus Chlorophytum. Conclusively, proposed article is an attempt to provide overall update of various studies conducted with members of Chlorophytum genus that will possibly be helpful in proper, fullest and sustainable utilization of this important group.     

Essentiality Assessment of Cysteinyl and Lysyl-tRNA Synthetases of Mycobacterium smegmatis

Discovery of mupirocin, an antibiotic that targets isoleucyl-tRNA synthetase, established aminoacyl-tRNA synthetase as an attractive target for the discovery of novel antibacterial agents. Despite a high degree of similarity between the bacterial and human aminoacyl-tRNA synthetases, the selectivity observed with mupirocin triggered the possibility of targeting other aminoacyl-tRNA synthetases as potential drug targets. These enzymes catalyse the condensation of a specific amino acid to its cognate tRNA in an energy-dependent reaction. Therefore, each organism is expected to encode at least twenty aminoacyl-tRNA synthetases, one for each amino acid. However, a bioinformatics search for genes encoding aminoacyl-tRNA synthetases from Mycobacterium smegmatis returned multiple genes for glutamyl (GluRS), cysteinyl (CysRS), prolyl (ProRS) and lysyl (LysRS) tRNA synthetases. The pathogenic mycobacteria, namely, Mycobacterium tuberculosis and Mycobacterium leprae, were also found to possess two genes each for CysRS and LysRS. A similar search indicated the presence of additional genes for LysRS in gram negative bacteria as well. Herein, we describe sequence and structural analysis of the additional aminoacyl-tRNA synthetase genes found in M. smegmatis. Characterization of conditional expression strains of Cysteinyl and Lysyl-tRNA synthetases generated in M. smegmatis revealed that the canonical aminoacyl-tRNA synthetase are essential, while the additional ones are not essential for the growth of M. smegmatis.     

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.     

Stochastic simulation GUI for biochemical networks

MOTIVATION: This article describes the development of a useful graphical user interface for stochastic simulation of biochemical networks which allows model builders to run stochastic simulations of their models and perform statistical analysis on the results. These include the construction of correlations, power-spectral densities and transfer functions between selected inputs and outputs. AVAILABILITY: The software is licensed under the BSD open source license and is available at http://sourceforge.net/projects/jdesigner. In addition, a more detailed account of the algorithms employed in the tool can be found at the Wiki at http://www.sys-bio.org/sbwWiki. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Identifying directed links in large scale functional networks: application to brain fMRI

Background

Biological experiments increasingly yield data representing large ensembles of interacting variables, making the application of advanced analytical tools a forbidding task. We present a method to extract networks of correlated activity, specifically from functional MRI data, such that: (a) network nodes represent voxels, and (b) the network links can be directed or undirected, representing temporal relationships between the nodes. The method provides a snapshot of the ongoing dynamics of the brain without sacrificing resolution, as the analysis is tractable even for very large numbers of voxels.

Results

We find that, based on topological properties of the networks, the method provides enough information about the dynamics to discriminate between subtly different brain states. Moreover, the statistical regularities previously reported are qualitatively preserved, i.e. the resulting networks display scale-free and small-world topologies.

Conclusion

Our method expands previous approaches to render large scale functional networks, and creates the basis for an extensive and -due to the presence of mixtures of directed and undirected links- richer motif analysis of functional relationships.

     

High performance computing environment for multidimensional image analysis

Background

The processing of images acquired through microscopy is a challenging task due to the large size of datasets (several gigabytes) and the fast turnaround time required. If the throughput of the image processing stage is significantly increased, it can have a major impact in microscopy applications.

Results

We present a high performance computing (HPC) solution to this problem. This involves decomposing the spatial 3D image into segments that are assigned to unique processors, and matched to the 3D torus architecture of the IBM Blue Gene/L machine. Communication between segments is restricted to the nearest neighbors. When running on a 2 Ghz Intel CPU, the task of 3D median filtering on a typical 256 megabyte dataset takes two and a half hours, whereas by using 1024 nodes of Blue Gene, this task can be performed in 18.8 seconds, a 478× speedup.

Conclusion

Our parallel solution dramatically improves the performance of image processing, feature extraction and 3D reconstruction tasks. This increased throughput permits biologists to conduct unprecedented large scale experiments with massive datasets.

     

<Emphasis Type="Italic">BRCA1</Emphasis> and <Emphasis Type="Italic">BRCA2</Emphasis> germline mutation analysis among Indian women from south India: identification of four novel mutations and high-frequency occurrence of 185delAG mutation

Mutations in the BRCA1 and BRCA2 genes profoundly increase the risk of developing breast and/or ovarian cancer among women. To explore the contribution of BRCA1 and BRCA2 mutations in the development of hereditary breast cancer among Indian women, we carried out mutation analysis of the BRCA1 and BRCA2 genes in 61 breast or ovarian cancer patients from south India with a positive family history of breast and/or ovarian cancer. Mutation analysis was carried out using conformation-sensitive gel electrophoresis (CSGE) followed by sequencing. Mutations were identified in 17 patients (28.0%); 15 (24.6%) had BRCA1 mutations and two (3.28%) had BRCA2 mutations. While no specific association between BRCA1 or BRCA2 mutations with cancer type was seen, mutations were more often seen in families with ovarian cancer. While 40% (4/10) and 30.8% (4/12) of families with ovarian or breast and ovarian cancer had mutations, only 23.1% (9/39) of families with breast cancer carried mutations in the BRCA1 and BRCA2 genes. In addition, while BRCA1 mutations were found in all age groups, BRCA2 mutations were found only in the age group of ≤40 years. Of the BRCA1 mutations, there were three novel mutations (295delCA; 4213T→A; 5267T→G) and three mutations that have been reported earlier. Interestingly, 185delAG, a BRCA1 mutation which occurs at a very high frequency in Ashkenazi Jews, was found at a frequency of 16.4% (10/61). There was one novel mutation (4866insT) and one reported mutation in BRCA2. Thus, our study emphasizes the importance of mutation screening in familial breast and/or ovarian cancers, and the potential implications of these findings in genetic counselling and preventive therapy.     

ISSR marker based analysis of micropropagated plantlets of Nothapodytes foetida

A DNA-based, inter simple sequence repeat (ISSR) markers were used to monitor genetic stability in micropropagated plantlets of Nothapodytes foetida. A total of 146 clear and distinct bands were produced using 26 primers resulting in 3 212 fragments. Out of 146, 135 bands (92.4 %) were monomorphic and 11 bands (7.53 %) were polymorphic which ranged from 200 to 21 226 bp in size. The number of bands per each primer varied from 1 to 11 with an average of 5.6 bands per primer. The banding pattern for each primer was uniform and comparable to mother plant from which the cultures had been established. The dendrogram based on the unweighted pair-group method with arithmetic averaging (UPGMA) depicted about 97 % homology between the mother plant and micropropagated plants. An attempt was made to reintroduce the micropropagated plants in the natural habitat and over 500 plants were successfully established.     

Developments in coffee biotechnology—in vitro plant propagation and crop improvement

Coffee is an important plantation crop grown in about 80 countries across the globe. In recent years, coffee attained lot of attention in the biotechnology research area. Since last three decades, there has been a steady flow of information on coffee biotechnology and now it is entering into the genomic era. Major milestones in coffee biotech research are successful in vitro manipulation and multiplication of coffee, development of gene transfer protocols and generation of transgenic coffee plants with specific traits. The isolation of genes involved in caffeine biosynthetic pathway has opened up new avenues for generating caffeine free transgenic coffee. With the initiation of international coffee genomics initiatives, the genomic research in coffee is expected to reach new dimensions. The IPR issues may play crucial role in sharing of benefits during international collaborations in near future. This review focuses on the basic and applied aspects of coffee biotechnology for newer potentials.