scholarly journals PatchPerPixMatch for Automated 3d Search of Neuronal Morphologies in Light Microscopy

2021 ◽  
Author(s):  
Lisa Mais ◽  
Peter Hirsch ◽  
Claire Managan ◽  
Kaiyu Wang ◽  
Konrad Rokicki ◽  
...  
Keyword(s):  
Visual Inspection ◽  
Expression Patterns ◽  
Computationally Efficient ◽  
Neuron Morphology ◽  
Automated Method ◽  
Target Neuron ◽  
Transgenic Lines ◽  
Gal4 Expression ◽  
Projection Images ◽  
Instance Segmentation

Studies of individual neurons in the Drosophila nervous system are facilitated by transgenic lines that sparsely and repeatably label respective neurons of interest. Sparsity can be enhanced by means of intersectional approaches like the split-GAL4 system, which labels the positive intersection of the expression patterns of two (denser) GAL4 lines. To this end, two GAL4 lines have to be identified as labelling a neuron of interest. Current approaches to tackling this task include visual inspection, as well as automated search in 2d projection images, of single cell multi-color flip-out (MCFO) acquisitions of GAL4 expression patterns. There is to date no automated method available that performs full 3d search in MCFO imagery of GAL4 lines, nor one that leverages automated reconstructions of the labelled neuron morphologies. To close this gap, we propose PatchPerPixMatch, a fully automated approach for finding a given neuron morphology in MCFO acquisitions of Gen1 GAL4 lines. PatchPerPixMatch performs automated instance segmentation of MCFO acquisitions, and subsequently searches for a target neuron morphology by minimizing an objective that aims at covering the target with a set of well-fitting segmentation fragments. PatchPerPixMatch is computationally efficient albeit being full 3d, while also highly robust to inaccuracies in the automated neuron instance segmentation. We are releasing PatchPerPixMatch search results for ~30,000 neuron morphologies from the Drosophila hemibrain in ~20,000 MCFO acquisitions of ~3,500 Gen1 GAL4 lines.

scholarly journals High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns

Plant Methods ◽  
2010 ◽  
Vol 6 (1) ◽  
pp. 18 ◽  
Author(s):  
Yong-Li Xiao ◽  
Julia C Redman ◽  
Erin L Monaghan ◽  
Jun Zhuang ◽  
Beverly A Underwood ◽  
...  
Keyword(s):  
High Throughput ◽  
Expression Patterns ◽  
Transgenic Lines

scholarly journals High-resolution in situ analysis of Cas9 germline transcript distributions in gene-drive Anopheles mosquitoes

2021 ◽  
Author(s):  
Gerard Terradas ◽  
Anita Hermann ◽  
Anthony A James ◽  
William McGinnis ◽  
Ethan Bier
Keyword(s):  
Expression Patterns ◽  
Resistant Mutant ◽  
Gene Drive ◽  
Anopheles Mosquitoes ◽  
Transgenic Lines ◽  
Endogenous Genes ◽  
Pathogen Control ◽  
Beneficial Traits ◽  
Germline Transcript ◽  
Female Germline

Abstract Gene drives are programmable genetic elements that can spread beneficial traits into wild populations to aid in vector-borne pathogen control. Two different drives have been developed for population modification of mosquito vectors. The Reckh drive (vasa-Cas9) in Anopheles stephensi displays efficient allelic conversion through males but generates frequent drive-resistant mutant alleles when passed through females. In contrast, the AgNos-Cd1 drive (nos-Cas9) in An. gambiae achieves almost complete allelic conversion through both genders. Here, we examined the subcellular localization of RNA transcripts in the mosquito germline. In both transgenic lines, Cas9 is strictly co-expressed with endogenous genes in stem and pre-meiotic cells of the testes, where both drives display highly efficient conversion. However, we observed distinct co-localization patterns for the two drives in female reproductive tissues. These studies suggest potential determinants underlying efficient drive through the female germline. We also evaluated expression patterns of alternative germline genes for future gene-drive designs.

scholarly journals Overexpression of a Banana Aquaporin Gene MaPIP1;1 Enhances Tolerance to Multiple Abiotic Stresses in Transgenic Banana and Analysis of Its Interacting Transcription Factors

2021 ◽  
Vol 12 ◽  
Author(s):  
Yi Xu ◽  
Juhua Liu ◽  
Caihong Jia ◽  
Wei Hu ◽  
Shun Song ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Promoter Region ◽  
Expression Patterns ◽  
Soluble Sugar ◽  
Ion Leakage ◽  
Aquaporin Gene ◽  
Gene Response ◽  
Transcription Factor Genes ◽  
Transgenic Lines ◽  
Response To Stress

Aquaporins can improve the ability of plants to resist abiotic stresses, but the mechanism is still not completely clear. In this research, overexpression of MaPIP1;1 in banana improved tolerance to multiple stresses. The transgenic plants resulted in lower ion leakage and malondialdehyde content, while the proline, chlorophyll, soluble sugar, and abscisic acid (ABA) contents were higher. In addition, under high salt and recovery conditions, the content of Na+ and K+ is higher, also under recovery conditions, the ratio of K+/Na+ is higher. Finally, under stress conditions, the expression levels of ABA biosynthesis and response genes in the transgenic lines are higher than those of the wild type. In previous studies, we proved that the MaMADS3 could bind to the promoter region of MaPIP1;1, thereby regulating the expression of MaPIP1;1 and affecting the drought tolerance of banana plants. However, the mechanism of MaPIP1;1 gene response to stress under different adversity conditions might be regulated differently. In this study, we proved that some transcription factor genes, including MaERF14, MaDREB1G, MaMYB1R1, MaERF1/39, MabZIP53, and MaMYB22, showed similar expression patterns with MaPIP1;1 under salt or cold stresses, and their encoded proteins could bind to the promoter region of MaPIP1;1. Here we proposed a novel MaPIP1;1-mediated mechanism that enhanced salt and cold tolerance in bananas. The results of this study have enriched the stress-resistant regulatory network of aquaporins genes and are of great significance for the development of molecular breeding strategies for stress-resistant fruit crops.

scholarly journals Pre-analytical quality control in hemostasis laboratories: visual evaluation of hemolysis index alone may cause unnecessary sample rejection

2019 ◽  
Vol 43 (2) ◽  
pp. 67-76
Author(s):  
Simona Storti ◽  
Elena Battipaglia ◽  
Maria Serena Parri ◽  
Andrea Ripoli ◽  
Stefania Lombardi ◽  
...  
Keyword(s):  
Regression Analysis ◽  
Linear Regression ◽  
Visual Inspection ◽  
Clinical Chemistry ◽  
Linear Regression Analysis ◽  
Reference Method ◽  
Analytical Performance ◽  
Visual Evaluation ◽  
Automated Method ◽  
Visual Index

Abstract Background Visual inspection is the most widespread method for evaluating sample hemolysis in hemostasis laboratories. The hemolysis index (HI) was determined visually (visual index, VI) and measured on an ACL TOP 750 (IL Werfen) system with a hemolysis-icterus-lipemia index (HIL) module. These values were compared with those measured on clinical chemistry systems Unicel DXC600 and AU680 and with quantitation of free-hemoglobin (Hb) performed by a spectrophotometric measurement method (SMM). Methods The HI was measured in 356 sodium citrate plasma samples, 306 of which were visibly hemolyzed to varying degrees and 50 were not hemolyzed. The analytical performance of each method was evaluated. Results Linear regression analysis, calculated between SMM and the other systems in the study, returned coefficients of determination r2 = 0.853 (AU680), r2 = 0.893 (DXC600) and r2 = 0.917 (ACL TOP 750). An r2 = 0.648 was obtained for linear regression analysis between VI and ACL TOP 750. In addition, ACL TOP 750 showed an excellent correlation in multivariate analysis (r2 = 0.958), showing good sensitivity (0.939) and specificity (0.934) and a diagnostic accuracy of 94%. By comparison, DXC600 and AU680 showed coefficients of determination of 0.945 and 0.923, respectively. A cut-off was set at 0.15 g/L free-Hb, as determined by the automated method, such that any hemostasis samples measuring above this threshold should not be analyzed. Based on this criterion, samples were classified as accepted or rejected, and the number of samples discarded during VI or ACL TOP 750 measurements was compared. Conclusions This study confirmed that hemostasis laboratories should consider introducing an objective, automated and standardized method to check samples for hemolysis. By relying solely on visual inspection, up to 50% of samples could be unnecessarily rejected. The ACL TOP 750 system demonstrated a satisfactory analytical performance, giving results comparable to those of the reference method.

scholarly journals Time Series Expression Analyses Using RNA-seq: A Statistical Approach

2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Sunghee Oh ◽  
Seongho Song ◽  
Gregory Grabowski ◽  
Hongyu Zhao ◽  
James P. Noonan
Keyword(s):  
Time Series ◽  
Statistical Approach ◽  
Expression Patterns ◽  
Temporal Analysis ◽  
Rna Seq ◽  
Computationally Efficient ◽  
Evolutionary Trajectory ◽  
Dynamic Methods ◽  
Series Expression ◽  
Time Lagged

RNA-seq is becoming thede factostandard approach for transcriptome analysis with ever-reducing cost. It has considerable advantages over conventional technologies (microarrays) because it allows for direct identification and quantification of transcripts. Many time series RNA-seq datasets have been collected to study the dynamic regulations of transcripts. However, statistically rigorous and computationally efficient methods are needed to explore the time-dependent changes of gene expression in biological systems. These methods should explicitly account for the dependencies of expression patterns across time points. Here, we discuss several methods that can be applied to model timecourse RNA-seq data, including statistical evolutionary trajectory index (SETI), autoregressive time-lagged regression (AR(1)), and hidden Markov model (HMM) approaches. We use three real datasets and simulation studies to demonstrate the utility of these dynamic methods in temporal analysis.

scholarly journals Analysis of Gal4 Expression Patterns in Adult Drosophila Females

2020 ◽  
Vol 10 (11) ◽  
pp. 4147-4158
Author(s):  
Lesley N. Weaver ◽  
Tianlu Ma ◽  
Daniela Drummond-Barbosa
Keyword(s):  
Genetic Manipulation ◽  
Expression Patterns ◽  
Cell Types ◽  
Tissue Expression ◽  
Whole Body ◽  
Specific Gene ◽  
Specific Cell ◽  
Gene Pathway ◽  
Gal4 Expression ◽  
Adult Drosophila

Precise genetic manipulation of specific cell types or tissues to pinpoint gene function requirement is a critical step in studies aimed at unraveling the intricacies of organismal physiology. Drosophila researchers heavily rely on the UAS/Gal4/Gal80 system for tissue-specific manipulations; however, it is often unclear whether the reported Gal4 expression patterns are indeed specific to the tissue of interest such that experimental results are not confounded by secondary sites of Gal4 expression. Here, we surveyed the expression patterns of commonly used Gal4 drivers in adult Drosophila female tissues under optimal conditions and found that multiple drivers have unreported secondary sites of expression beyond their published cell type/tissue expression pattern. These results underscore the importance of thoroughly characterizing Gal4 tools as part of a rigorous experimental design that avoids potential misinterpretation of results as we strive for understanding how the function of a specific gene/pathway in one tissue contributes to whole-body physiology.

scholarly journals Transcription of Drosophila Troponin I Gene Is Regulated by Two Conserved, Functionally Identical, Synergistic Elements

2004 ◽  
Vol 15 (3) ◽  
pp. 1185-1196 ◽  
Author(s):  
María-Cruz Marín ◽  
José-Rodrigo Rodríguez ◽  
Alberto Ferrús
Keyword(s):  
Transcription Initiation ◽  
Troponin I ◽  
Regulatory Element ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Initiation Site ◽  
Transcription Initiation Site ◽  
Upstream Regulatory Element ◽  
Transgenic Lines

The Drosophila wings-up A gene encodes Troponin I. Two regions, located upstream of the transcription initiation site (upstream regulatory element) and in the first intron (intron regulatory element), regulate gene expression in specific developmental and muscle type domains. Based on LacZ reporter expression in transgenic lines, upstream regulatory element and intron regulatory element yield identical expression patterns. Both elements are required for full expression levels in vivo as indicated by quantitative reverse transcription-polymerase chain reaction assays. Three myocyte enhancer factor-2 binding sites have been functionally characterized in each regulatory element. Using exon specific probes, we show that transvection is based on transcriptional changes in the homologous chromosome and that Zeste and Suppressor of Zeste 3 gene products act as repressors for wings-up A. Critical regions for transvection and for Zeste effects are defined near the transcription initiation site. After in silico analysis in insects (Anopheles and Drosophila pseudoobscura) and vertebrates (Ratus and Coturnix), the regulatory organization of Drosophila seems to be conserved. Troponin I (TnI) is expressed before muscle progenitors begin to fuse, and sarcomere morphogenesis is affected by TnI depletion as Z discs fail to form, revealing a novel developmental role for the protein or its transcripts. Also, abnormal stoichiometry among TnI isoforms, rather than their absolute levels, seems to cause the functional muscle defects.

Automated Grain Mapping Using Wide Angle Convergent Beam Electron Diffraction in Transmission Electron Microscope for Nanomaterials

2011 ◽  
Vol 17 (6) ◽  
pp. 859-865 ◽  
Author(s):  
Vineet Kumar
Keyword(s):  
Grain Size ◽  
Electron Microscope ◽  
Transmission Electron Microscope ◽  
Visual Inspection ◽  
Mapping Method ◽  
Wide Angle ◽  
Inspection Method ◽  
Automated Method ◽  
Transmission Electron ◽  
Convergent Beam

AbstractThe grain size statistics, commonly derived from the grain map of a material sample, are important microstructure characteristics that greatly influence its properties. The grain map for nanomaterials is usually obtained manually by visual inspection of the transmission electron microscope (TEM) micrographs because automated methods do not perform satisfactorily. While the visual inspection method provides reliable results, it is a labor intensive process and is often prone to human errors. In this article, an automated grain mapping method is developed using TEM diffraction patterns. The presented method uses wide angle convergent beam diffraction in the TEM. The automated technique was applied on a platinum thin film sample to obtain the grain map and subsequently derive grain size statistics from it. The grain size statistics obtained with the automated method were found in good agreement with the visual inspection method.

scholarly journals A scalable method for automatically measuring pharyngeal pumping in C. elegans

2016 ◽  
Author(s):  
Monika Scholz ◽  
Dylan J. Lynch ◽  
Kyung Suk Lee ◽  
Erel Levine ◽  
David Biron
Keyword(s):  
Caenorhabditis Elegans ◽  
Food Availability ◽  
High Throughput ◽  
Visual Inspection ◽  
Automated Analysis ◽  
C Elegans ◽  
Automated Method ◽  
Controlled Environments ◽  
Pharyngeal Pumping ◽  
Feeding Environments

We describe a scalable automated method for measuring the pharyngeal pumping of Caenorhabditis elegans in controlled environments. Our approach enables unbiased measurements for prolonged periods, a high throughput, and measurements in controlled yet dynamically changing feeding environments. The automated analysis compares well with scoring pumping by visual inspection, a common practice in the field. In addition, we observed overall low rates of pharyngeal pumping and long correlation times when food availability was oscillated.

scholarly journals Identification and characterization of a novel multi-stress responsive gene in Arabidopsis

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244030
Author(s):  
Faiza Tawab ◽  
Iqbal Munir ◽  
Zeeshan Nasim ◽  
Mohammad Sayyar Khan ◽  
Saleha Tawab ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Survival Rates ◽  
Crop Productivity ◽  
Cell Wall Protein ◽  
Transcriptome Data ◽  
Gus Assay ◽  
Transgenic Lines ◽  
Responsive Gene ◽  
Identification And Characterization

Abiotic stresses especially salinity, drought and high temperature result in considerable reduction of crop productivity. In this study, we identified AT4G18280 annotated as a glycine-rich cell wall protein-like (hereafter refer to as GRPL1) protein as a potential multistress-responsive gene. Analysis of public transcriptome data and GUS assay of pGRPL1::GUS showed a strong induction of GRPL1 under drought, salinity and heat stresses. Transgenic plants overexpressing GRPL1-3HA showed significantly higher germination, root elongation and survival rate under salt stress. Moreover, the 35S::GRPL1-3HA transgenic lines also showed higher survival rates under drought and heat stresses. GRPL1 showed similar expression patterns with Abscisic acid (ABA)-pathway genes under different growth and stress conditions, suggesting a possibility that GRPL1 might act in the ABA pathway that is further supported by the inability of ABA-deficient mutant (aba2-1) to induce GRPL1 under drought stress. Taken together, our data presents GRPL1 as a potential multi-stress responsive gene working downstream of ABA.

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