Detection of novel allelic variations in soybean mutant population using Tilling by Sequencing

One of the most important tools in genetic improvement is mutagenesis, which is a useful tool to induce genetic and phenotypic variation for trait improvement and discovery of novel genes. JTN-5203 (MG V) mutant population was generated using an induced ethyl methane sulfonate (EMS) mutagenesis and was used for detection of induced mutations in FAD2-1A and FAD2-1B genes using reverse genetics approach. Optimum concentration of EMS was used to treat 15,000 bulk JTN-5203 seeds producing 1,820 M2 population. DNA was extracted, normalized, and pooled from these individuals. Specific primers were designed from FAD2-1A and FAD2-1B genes that are involved in the fatty acid biosynthesis pathway for further analysis using next-generation sequencing. High throughput mutation discovery through TILLING-by-Sequencing approach was used to detect novel allelic variations in this population. Several mutations and allelic variations with high impacts were detected for FAD2-1A and FAD2-1B. This includes GC to AT transition mutations in FAD2-1A (20%) and FAD2-1B (69%). Mutation density for this population is estimated to be about 1/136kb. Through mutagenesis and high-throughput sequencing technologies, novel alleles underlying the mutations observed in mutants with reduced polyunsaturated fatty acids will be identified, and these mutants can be further used in breeding soybean lines with improved fatty acid profile, thereby developing heart-healthy-soybeans

Development and Phenotypic Screening of an Ethyl Methane Sulfonate Mutant Population in Soybean

Soybean is an important oil-producing crop in the Fabaceae family and there are increasing demands for soybean oil and other soybean products. Genetic improvement of soybean is needed to increase its production. In order to provide genetic diversity and resources for identifying important genes, a new ethyl methane sulfonate (EMS) mutagenized soybean population was generated using the newly released germplasm, JTN-5203 (maturity group V). Treatment of soybean seeds with 60 mM EMS concentration was found to be suitable for inducing mutation. A total of 1,820 M1 individuals were produced from 15,000 treated seeds. The resulting M2 population was planted in the field for phenotyping. After harvest, seed traits including total oil, protein, starch, moisture content, fatty acid and amino acid compositions were measured by NIR. Phenotypic variations observed in this population include changes in leaf morphology, plant architecture, seed compositions, and yield. Of most interest, we identified plants with increased amounts of total protein (50% vs. 41% for control) and plants with higher amounts of total oil (25% vs. 21.2% control). Similarly, we identified plants with increases in oleic acid content and decreases in linoleic acid and linolenic acid. This EMS mutant population will be used for further studies including screening for various traits such as amino acid pathways, allergens, phytic acids, and other important soybean agronomic traits. In addition, these mutant individuals will be evaluated in the next generation to assess the heritability. Beneficial traits from these mutants can be exploited for future soybean breeding programs. This germplasm can also be used for discovering novel mutant alleles and for functional gene expression analysis using reverse genetics tools such as TILLING

Application of Nanotrap technology for high sensitivity measurement of urinary outer surface protein A carboxyl-terminus domain in early stage Lyme borreliosis

Objectives: Prompt antibiotic treatment of early stage Lyme borreliosis (LB) prevents progression to severe multisystem disease. There is a clinical need to improve the diagnostic specificity of early stage Lyme assays in the period prior to the mounting of a robust serology response. Using a novel analyte harvesting nanotechnology, Nanotrap particles, we evaluated urinary Borrelia Outer surface protein A (OspA) C-terminus peptide in early stage LB before and after treatment, and in patients suspected of late stage disseminated LB. Method: We employed Nanotrap particles to concentrate urinary OspA and used a highly specific anti-OspA monoclonal antibody (mAb) as a detector of the C-terminus peptides. We mapped the mAb epitope to a narrow specific OspA C-terminal domain OspA236-239 conserved across infectious Borrelia species but with no homology to human proteins and no cross-reactivity with relevant viral and non-Borrelia bacterial proteins. 268 urine samples from patients being evaluated for all categories of LB were collected in a LB endemic area. The urinary OspA assay, blinded to outcome, utilized Nanotrap particle pre-processing, western blotting to evaluate the OspA molecular size, and OspA peptide competition for confirmation. Results: OspA test characteristics: sensitivity 1.7 pg/mL (lowest limit of detection), % coefficient of variation (CV) = 8 %, dynamic range 1.7-30 pg/mL. Pre-treatment, 24/24 newly diagnosed patients with an erythema migrans (EM) rash were positive for urinary OspA while false positives for asymptomatic patients were 0/117 (Chi squared p < 10-6). For 10 patients who exhibited persistence of the EM rash during the course of antibiotic therapy, 10/10 were positive for urinary OspA. Urinary OspA of 8/8 patients switched from detectable to undetectable following symptom resolution post-treatment. Specificity of the urinary OspA test for the clinical symptoms was 40/40. Specificity of the urinary OspA antigen test for later serology outcome was 87.5 % (21 urinary OspA positive/24 serology positive, Chi squared p = 4.072e-15). 41 of 100 patients under surveillance for persistent LB in an endemic area were positive for urinary OspA protein. Conclusions: OspA urinary shedding was strongly linked to concurrent active symptoms (e.g. EM rash and arthritis), while resolution of these symptoms after therapy correlated with urinary conversion to OspA negative

Optical neuroimaging and neurostimulation in surgical training and assessment: A state-of-the-art review

IntroductionFunctional near-infrared spectroscopy (fNIRS) is a non-invasive optical neuroimaging technique used to assess surgeons' brain function. The aim of this narrative review is to outline the effect of expertise, stress, surgical technology, and neurostimulation on surgeons' neural activation patterns, and highlight key progress areas required in surgical neuroergonomics to modulate training and performance.MethodsA literature search of PubMed and Embase was conducted to identify neuroimaging studies using fNIRS and neurostimulation in surgeons performing simulated tasks.ResultsNovice surgeons exhibit greater haemodynamic responses across the pre-frontal cortex than experts during simple surgical tasks, whilst expert surgical performance is characterized by relative prefrontal attenuation and upregulation of activation foci across other regions such as the supplementary motor area. The association between PFC activation and mental workload follows an inverted-U shaped curve, activation increasing then attenuating past a critical inflection point at which demands outstrip cognitive capacity Neuroimages are sensitive to the impact of laparoscopic and robotic tools on cognitive workload, helping inform the development of training programs which target neural learning curves. FNIRS differs in comparison to current tools to assess proficiency by depicting a cognitive state during surgery, enabling the development of cognitive benchmarks of expertise. Finally, neurostimulation using transcranial direct-current-stimulation may accelerate skill acquisition and enhance technical performance.ConclusionFNIRS can inform the development of surgical training programs which modulate stress responses, cognitive learning curves, and motor skill performance. Improved data processing with machine learning offers the possibility of live feedback regarding surgeons' cognitive states during operative procedures

Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues

The Gaia mission

Gaia is a cornerstone mission in the science programme of the EuropeanSpace Agency (ESA). The spacecraft construction was approved in 2006, following a study in which the original interferometric concept was changed to a direct-imaging approach. Both the spacecraft and the payload were built by European industry. The involvement of the scientific community focusses on data processing for which the international Gaia Data Processing and Analysis Consortium (DPAC) was selected in 2007. Gaia was launched on 19 December 2013 and arrived at its operating point, the second Lagrange point of the Sun-Earth-Moon system, a few weeks later. The commissioning of the spacecraft and payload was completed on 19 July 2014. The nominal five-year mission started with four weeks of special, ecliptic-pole scanning and subsequently transferred into full-sky scanning mode. We recall the scientific goals of Gaia and give a description of the as-built spacecraft that is currently (mid-2016) being operated to achieve these goals. We pay special attention to the payload module, the performance of which is closely related to the scientific performance of the mission. We provide a summary of the commissioning activities and findings, followed by a description of the routine operational mode. We summarise scientific performance estimates on the basis of in-orbit operations. Several intermediate Gaia data releases are planned and the data can be retrieved from the Gaia Archive, which is available through the Gaia home page. http://www.cosmos.esa.int/gai

Development of improved soybean (Glycine max, L. Merill) germplasm through induced and targeted mutagenesis

Soybean (Glycine max L. Merill) is an important oil-producing crop under Fabaceae family and is utilized in various industries. With increasing demands for soybean oil and other soybean products, its production must be increased. Genetic improvement of the crop is important to meet the increasing demands for soybean. A new soybean mutant population was generated through induced Ethyl methanesulfonate (EMS) mutagenesis using the newly released germplasm, JTN-5203 (maturity group V)—a variety that can be cultivated in Tennessee was developed. Initially, EMS concentration was optimized to get the suitable concentration. Seeds were treated with different concentrations of EMS varying from 0 to 150 mM. The optimum concentration obtained was 60 mM and was used to treat bulk JTN-5203 seeds. A total of 1,820 M2 population was produced from 15,000 treated seeds. The M2 population were planted in the field and DNA were extracted from 6,400 individual plants. Extracted DNA were quantified, standardized, and pooled to create a mutant library for high throughput TILLING. Phenotypic variations were recorded in the M2 generation including changes in leaf morphology, plant architecture, and chlorophyll contents. Also, a different mutant germplasm generated through fast neutron (FN) were mass screened for resistance to two different herbicides: glyphosate and metribuzin, which conferred by EPSPS and psbA genes, respectively. With a total of 16,000 FN mutants screened for these herbicides, no herbicide resistant mutant was found. Aside from EMS and FN mutagenesis, site specific mutagenesis using CRISPR/Cas9 system was used in targeting psbA and PDS genes. Guide RNAs specific to the target genes were designed and cloned to a binary vector that contains the Cas9 gene. Soybean cotyledons were transformed with the Cas9 vector through Agrobacterium-mediated transformation. Initial observations showed some putative transformants on shoot induction media. The EMS mutant population will be used for further studies including screening for various traits such as herbicide tolerance, fatty acid profile and other important soybean agronomic traits. Beneficial traits from these mutants can be exploited for future soybean breeding programs. This germplasm can also be used for discovering novel mutant alleles and for functional gene expression analysis using reverse genetics tools such as TILLING

Optical neuroimaging and neurostimulation in surgical training and assessment:A state-of-the-art review

Introduction: Functional near-infrared spectroscopy (fNIRS) is a non-invasive optical neuroimaging technique used to assess surgeons' brain function. The aim of this narrative review is to outline the effect of expertise, stress, surgical technology, and neurostimulation on surgeons' neural activation patterns, and highlight key progress areas required in surgical neuroergonomics to modulate training and performance. Methods: A literature search of PubMed and Embase was conducted to identify neuroimaging studies using fNIRS and neurostimulation in surgeons performing simulated tasks. Results: Novice surgeons exhibit greater haemodynamic responses across the pre-frontal cortex than experts during simple surgical tasks, whilst expert surgical performance is characterized by relative prefrontal attenuation and upregulation of activation foci across other regions such as the supplementary motor area. The association between PFC activation and mental workload follows an inverted-U shaped curve, activation increasing then attenuating past a critical inflection point at which demands outstrip cognitive capacity Neuroimages are sensitive to the impact of laparoscopic and robotic tools on cognitive workload, helping inform the development of training programs which target neural learning curves. FNIRS differs in comparison to current tools to assess proficiency by depicting a cognitive state during surgery, enabling the development of cognitive benchmarks of expertise. Finally, neurostimulation using transcranial direct-current-stimulation may accelerate skill acquisition and enhance technical performance. Conclusion: FNIRS can inform the development of surgical training programs which modulate stress responses, cognitive learning curves, and motor skill performance. Improved data processing with machine learning offers the possibility of live feedback regarding surgeons' cognitive states during operative procedures.</p

Optical neuroimaging and neurostimulation in surgical training and assessment:A state-of-the-art review

Introduction: Functional near-infrared spectroscopy (fNIRS) is a non-invasive optical neuroimaging technique used to assess surgeons' brain function. The aim of this narrative review is to outline the effect of expertise, stress, surgical technology, and neurostimulation on surgeons' neural activation patterns, and highlight key progress areas required in surgical neuroergonomics to modulate training and performance. Methods: A literature search of PubMed and Embase was conducted to identify neuroimaging studies using fNIRS and neurostimulation in surgeons performing simulated tasks. Results: Novice surgeons exhibit greater haemodynamic responses across the pre-frontal cortex than experts during simple surgical tasks, whilst expert surgical performance is characterized by relative prefrontal attenuation and upregulation of activation foci across other regions such as the supplementary motor area. The association between PFC activation and mental workload follows an inverted-U shaped curve, activation increasing then attenuating past a critical inflection point at which demands outstrip cognitive capacity Neuroimages are sensitive to the impact of laparoscopic and robotic tools on cognitive workload, helping inform the development of training programs which target neural learning curves. FNIRS differs in comparison to current tools to assess proficiency by depicting a cognitive state during surgery, enabling the development of cognitive benchmarks of expertise. Finally, neurostimulation using transcranial direct-current-stimulation may accelerate skill acquisition and enhance technical performance. Conclusion: FNIRS can inform the development of surgical training programs which modulate stress responses, cognitive learning curves, and motor skill performance. Improved data processing with machine learning offers the possibility of live feedback regarding surgeons' cognitive states during operative procedures.</p