Microsatellite markers for the Indian golden silkmoth, Antheraea assama (Saturniidae: Lepidoptera)

Antheraea assama, an economically important and scientifically unexplored Indian wild silkmoth, is unique among saturniid moths. For this species, a total of 87 microsatellite markers was derived from 35 000 expressed sequence tags and a microsatellite-enriched sub-genomic library. Forty individuals collected from Tura and West Garo Hills region of Northeast India were screened for each of these loci. Ten loci from expressed sequence tags and one from genomic library were found to be polymorphic. These microsatellite markers will be useful resources for population genetic studies of A. assama and other closely related species of saturniids. This is the first report on development of microsatellite markers for any saturniid species

LFM based Wideband DOA Estimation using Deep Neural Network at Low SNR

This work focuses on deep learning-based wideband direction-of-arrival (DoA) estimation for a wideband in particular LFM in case of extreme noise. We propose a convolutional neural network (CNN) that utilizes the correlation matrix to estimate and trained using multi-channel data in low SNR conditions. By using a systematic approach and treating the problem as a way to identify multiple possible DoAs, the CNN is trained to predict DoAs under different SNR conditions. This allows the CNN to accurately estimate the directions from which signals are coming, regardless of the level of noise in the environment. The architecture proposed exhibits robustness to noise, works effectively with a small number of snapshots, and achieves high resolution in angle estimation. Experimental findings demonstrate notable enhancements in performance under low SNR conditions when compared to existing methods, without the need for parameter tuning for correlated and uncorrelated sources. The enhanced robustness of our solution has broad applications in various fields, including wireless array sensors, acoustic microphones, and sonars

A GATA-binding protein expressed predominantly in the pupal ovary of the silkworm, Bombyx mori

Preferential localization of Bkm (Banded krait minor-satellite) DNA sequences on Y/W chromosomes of higher eukaryotes, which remain highly condensed in somatic cells but undergo extensive decondensation in the germ cells during early stages of development, led to the postulation for the existence of a sex- and tissue-specific Bkm-binding protein (BBP). Accordingly, we purified and characterized a BmBBP expressed predominantly in pupal ovary of the silkworm (Bombyx mori). 2D-PAGE revealed BmBBP as moderately basic (pI 7.8-8, in the range expected for DNA-binding proteins) and Matrix Assisted Laser Desorption/Ionization Time of Flight exhibited a value of 37.5-kDa. BmBBP neither contains nor requires divalent metal ions for its DNA-binding activity, suggesting that it does not belong to the well-studied GATA-family of transcription factors. BmBBP is unusually strong in its DNA-binding characteristics to Bkm (GATA-repeats), which suggests its probable role in bringing about coordinated chromatin conformational changes to activate genes present in associated chromosomal domains. Fluorescence immuno-localization studies employing specific anti-BmBBP antibodies revealed its presence in the follicle cells and in the ooplasm, as well as the nucleus of different developmental stages of oocytes

Glass is a viable substrate for precision force microscopy of membrane proteins

Scientific Reports ; 5:12550 ; DOI: 10.1038/srep12550.Chada, N. et al. Glass is a Viable Substrate for Precision Force Microscopy of Membrane Proteins. Sci. Rep. 5, 12550; doi: 10.1038/srep12550 (2015).8 pages.Received: 01 April 2015 ; Accepted: 02 July 2015 ; Published: 31 July 2015.Though ubiquitous in optical microscopy, glass has long been overlooked as a specimen supporting surface for high resolution atomic force microscopy (AFM) investigations due to its roughness. Using bacteriorhodopsin from Halobacterium salinarum and the translocon SecYEG from Escherichia coli, we demonstrate that faithful images of 2D crystalline and non-crystalline membrane proteins in lipid bilayers can be obtained on microscope cover glass following a straight-forward cleaning procedure. Direct comparison between AFM data obtained on glass and on mica substrates show no major differences in image fidelity. Repeated association of the ATPase SecA with the cytoplasmic protrusion of SecYEG demonstrates that the translocon remains competent for binding after tens of minutes of continuous AFM imaging. This opens the door for precision long-timescale investigations of the active translocase in near-native conditions and, more generally, for integration of high resolution biological AFM with many powerful optical techniques that require non-birefringent substrates.Includes bibliographical references

Glass is a viable substrate for atomic force microscopy of membrane proteins : [abstract]

Abstract only."2314-Pos Board B6.""Page 458a, Tuesday, February 18, 2014."--At top of page.Abstract in program book: Since its invention in the mid-1980s, the atomic force microscope (AFM) has become an invaluable complementary tool for studying membrane proteins in near-native environments. Historically, mica is the most common substrate utilized for biological AFM. Glass being amorphous, transparent, and optically homogeneous has its own set of advantages over mica and has the potential to broaden the use the AFM into fields that require high quality non-birefringent optical access. The use of silanized glass as AFM substrates has been reported as a means to fine tune surface chemistry. However, such coatings usually require hours of additional preparation time and can lead to increased surface roughness. In this work, we present a simple technique for preparing borosilicate glass as a substrate for two membrane systems: non-crystalline translocons (SecYEG) of the general secretary system from E. coli, and bacteriorhodopsin (BR) from H. salinarum. For both these membrane proteins, quantitative comparisons of the measured protein structures on glass versus mica substrates show agreement. An additional advantage of glass is that lipid coverage is rapid (< 10 minutes) and complete (occupying the entire surface). A goal is to study the bacterial export system using recently developed precision measurement techniques such as ultra-stable AFM

Glass is a viable substrate for atomic force microscopy of membrane proteins : [abstract]

Abstract only."2314-Pos Board B6.""Page 458a, Tuesday, February 18, 2014."--At top of page.Abstract in program book: Since its invention in the mid-1980s, the atomic force microscope (AFM) has become an invaluable complementary tool for studying membrane proteins in near-native environments. Historically, mica is the most common substrate utilized for biological AFM. Glass being amorphous, transparent, and optically homogeneous has its own set of advantages over mica and has the potential to broaden the use the AFM into fields that require high quality non-birefringent optical access. The use of silanized glass as AFM substrates has been reported as a means to fine tune surface chemistry. However, such coatings usually require hours of additional preparation time and can lead to increased surface roughness. In this work, we present a simple technique for preparing borosilicate glass as a substrate for two membrane systems: non-crystalline translocons (SecYEG) of the general secretary system from E. coli, and bacteriorhodopsin (BR) from H. salinarum. For both these membrane proteins, quantitative comparisons of the measured protein structures on glass versus mica substrates show agreement. An additional advantage of glass is that lipid coverage is rapid (< 10 minutes) and complete (occupying the entire surface). A goal is to study the bacterial export system using recently developed precision measurement techniques such as ultra-stable AFM

Ensemble Classification of Alzheimer's Disease and Mild Cognitive Impairment Based on Complex Graph Measures from Diffusion Tensor Images

The human brain is a complex network of interacting regions. The gray matter regions of brain are interconnected by white matter tracts, together forming one integrative complex network. In this article, we report our investigation about the potential of applying brain connectivity patterns as an aid in diagnosing Alzheimer's disease and Mild Cognitive Impairment (MCI). We performed pattern analysis of graph theoretical measures derived from Diffusion Tensor Imaging (DTI) data representing structural brain networks of 45 subjects, consisting of 15 patients of Alzheimer's disease (AD), 15 patients of MCI, and 15 healthy subjects (CT). We considered pair-wise class combinations of subjects, defining three separate classification tasks, i.e., AD-CT, AD-MCI, and CT-MCI, and used an ensemble classification module to perform the classification tasks. Our ensemble framework with feature selection shows a promising performance with classification accuracy of 83.3% for AD vs. MCI, 80% for AD vs. CT, and 70% for MCI vs. CT. Moreover, our findings suggest that AD can be related to graph measures abnormalities at Brodmann areas in the sensorimotor cortex and piriform cortex. In this way, node redundancy coefficient and load centrality in the primary motor cortex were recognized as good indicators of AD in contrast to MCI. In general, load centrality, betweenness centrality, and closeness centrality were found to be the most relevant network measures, as they were the top identified features at different nodes. The present study can be regarded as a “proof of concept” about a procedure for the classification of MRI markers between AD dementia, MCI, and normal old individuals, due to the small and not well-defined groups of AD and MCI patients. Future studies with larger samples of subjects and more sophisticated patient exclusion criteria are necessary toward the development of a more precise technique for clinical diagnosis

Glass : a multi-platform specimen supporting substrate for precision single molecule studies of membrane proteins : [abstract]

Abstract only."852-Pos Board B632.""Page 170a, Sunday, February 8, 2015."--At top of page.Abstract in program book: High resolution (~ 1 nm lateral resolution) biological AFM imaging has been carried out almost exclusively using freshly cleaved mica as a specimen supporting surface, but mica suffers from a fundamental limitation that has hindered AFM’s broader integration with many modern optical methods. Mica exhibits biaxial birefringence; indeed, this naturally occurring material is used commercially for constructing optical wave plates. In general, propagation through birefringent material alters the polarization state and bifurcates the propagation direction of light in a manner which varies with thickness. This makes it challenging to incorporate freshly cleaved mica substrates with modern optical methods, many of which employ highly focused and polarized laser beams passing through then specimen plane. Using bacteriorhodopsin from Halobacterium salinarum and the translocon SecYEG from Escherichia coli, we demonstrate that faithful images of 2D crystalline and non-crystalline membrane proteins in lipid bilayers can be obtained on common microscope cover glass following a straight-forward cleaning procedure. Direct comparison between data obtained on glass and on mica show no significant differences in AFM image fidelity. This work opens the door for combining high resolution biological AFM with powerful optical methods that require optically isotropic substrates such as ultra-stable1 and direct 3D AFM2. In turn, this capability should enable long timescale conformational dynamics measurements of membrane proteins in near-native conditions

Conditional over-expression of PITX1 causes skeletal muscle dystrophy in mice

Paired-like homeodomain transcription factor 1 (PITX1) was specifically up-regulated in patients with facioscapulohumeral muscular dystrophy (FSHD) by comparing the genome-wide mRNA expression profiles of 12 neuromuscular disorders. In addition, it is the only known direct transcriptional target of the double homeobox protein 4 (DUX4) of which aberrant expression has been shown to be the cause of FSHD. To test the hypothesis that up-regulation of PITX1 contributes to the skeletal muscle atrophy seen in patients with FSHD, we generated a tet-repressible muscle-specific Pitx1 transgenic mouse model in which expression of PITX1 in skeletal muscle can be controlled by oral administration of doxycycline. After PITX1 was over-expressed in the skeletal muscle for 5 weeks, the mice exhibited significant loss of body weight and muscle mass, decreased muscle strength, and reduction of muscle fiber diameters. Among the muscles examined, the tibialis anterior, gastrocnemius, quadricep, bicep, tricep and deltoid showed significant reduction of muscle mass, while the soleus, masseter and diaphragm muscles were not affected. The most prominent pathological change was the development of atrophic muscle fibers with mild necrosis and inflammatory infiltration. The affected myofibers stained heavily with NADH-TR with the strongest staining in angular-shaped atrophic fibers. Some of the atrophic fibers were also positive for embryonic myosin heavy chain using immunohistochemistry. Immunoblotting showed that the p53 was up-regulated in the muscles over-expressing PITX1. The results suggest that the up-regulation of PITX1 followed by activation of p53-dependent pathways may play a major role in the muscle atrophy developed in the mouse model

"Of Mice and Measures": A Project to Improve How We Advance Duchenne Muscular Dystrophy Therapies to the Clinic

A new line of dystrophic mdx mice on the DBA/2J (D2) background has emerged as a candidate to study the efficacy of therapeutic approaches for Duchenne muscular dystrophy (DMD). These mice harbor genetic polymorphisms that appear to increase the severity of the dystropathology, with disease modifiers that also occur in DMD patients, making them attractive for efficacy studies and drug development. This workshop aimed at collecting and consolidating available data on the pathological features and the natural history of these new D2/mdx mice, for comparison with classic mdx mice and controls, and to identify gaps in information and their potential value. The overall aim is to establish guidance on how to best use the D2/mdx mouse model in preclinical studies