An Undergraduate Cell Biology Lab: Western Blotting to Detect Proteins from Drosophila Eye

We have developed an undergraduate laboratory to allow detection and localization of proteins in the compound eye of Drosophila melanogaster, a.k.a fruit fly. This lab was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of Western Blotting technique to study protein localization in the adult eye of Drosophila. Western blotting, a two-day laboratory exercise, can be used to detect the presence of proteins of interests from total protein isolated from a tissue. The first day involves isolation of proteins from the tissue and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide) gel electrophoresis to separate the denatured proteins in accordance to their molecular weight/s. The separated proteins are then transferred to the Nitrocellulose or Polyvinylidene difluoride (PVDF) membrane in an overnight transfer. The second day lab involves detection of proteins (transferred to the membrane) using Ponceau-S stain, followed by immunochemistry to detect the protein of interest along the total protein transferred to the membrane. The presence of our protein of interest is carried out by using a primary antibody against the protein, followed by binding of secondary antibody which is tagged to an enzyme. The protein band can be detected by using the kit, which provides substrate to the enzyme. The protein levels can be quantified, compared, and analyzed by calculating the respective band intensities. Here, we have used fly eyes to detect the difference in level of expression of Tubulin (Tub) and Wingless (Wg) proteins in the adult eye of Drosophila in our class. The idea of this laboratory exercise is to: (a) familiarize students with the underlying principles of protein chemistry and its application to diverse areas of research, (b) to enable students to get a hands-on-experience of this biochemical technique

Multimapper: Data Density Sensitive Topological Visualization

Mapper is an algorithm that summarizes the topological information contained in a dataset and provides an insightful visualization. It takes as input a point cloud which is possibly high-dimensional, a filter function on it and an open cover on the range of the function. It returns the nerve simplicial complex of the pullback of the cover. Mapper can be considered a discrete approximation of the topological construct called Reeb space, as analysed in the $1$-dimensional case by [Carriere et al.,2018]. Despite its success in obtaining insights in various fields such as in [Kamruzzaman et al., 2016], Mapper is an ad hoc technique requiring lots of parameter tuning. There is also no measure to quantify goodness of the resulting visualization, which often deviates from the Reeb space in practice. In this paper, we introduce a new cover selection scheme for data that reduces the obscuration of topological information at both the computation and visualisation steps. To achieve this, we replace global scale selection of cover with a scale selection scheme sensitive to local density of data points. We also propose a method to detect some deviations in Mapper from Reeb space via computation of persistence features on the Mapper graph.Comment: Accepted at ICDM

Approximation Algorithms for Continuous Clustering and Facility Location Problems

We consider the approximability of center-based clustering problems where the points to be clustered lie in a metric space, and no candidate centers are specified. We call such problems "continuous", to distinguish from "discrete" clustering where candidate centers are specified. For many objectives, one can reduce the continuous case to the discrete case, and use an $\alpha$-approximation algorithm for the discrete case to get a $\beta\alpha$-approximation for the continuous case, where $\beta$ depends on the objective: e.g. for $k$-median, $\beta = 2$, and for $k$-means, $\beta = 4$. Our motivating question is whether this gap of $\beta$ is inherent, or are there better algorithms for continuous clustering than simply reducing to the discrete case? In a recent SODA 2021 paper, Cohen-Addad, Karthik, and Lee prove a factor-$2$ and a factor-$4$ hardness, respectively, for continuous $k$-median and $k$-means, even when the number of centers $k$ is a constant. The discrete case for a constant $k$ is exactly solvable in polytime, so the $\beta$ loss seems unavoidable in some regimes. In this paper, we approach continuous clustering via the round-or-cut framework. For four continuous clustering problems, we outperform the reduction to the discrete case. Notably, for the problem $\lambda$-UFL, where $\beta = 2$ and the discrete case has a hardness of $1.27$, we obtain an approximation ratio of $2.32 < 2 \times 1.27$ for the continuous case. Also, for continuous $k$-means, where the best known approximation ratio for the discrete case is $9$, we obtain an approximation ratio of $32 < 4 \times 9$. The key challenge is that most algorithms for discrete clustering, including the state of the art, depend on linear programs that become infinite-sized in the continuous case. To overcome this, we design new linear programs for the continuous case which are amenable to the round-or-cut framework.Comment: 24 pages, 0 figures. Full version of ESA 2022 paper https://drops.dagstuhl.de/opus/volltexte/2022/16971 . This version adds a link to the conference version and fixes minor formatting issue

48770 (GMR17E04)

dpp enhancer - 48770 Id - GMR17E04 Location 2L: 2428913..2432834 Base pairs – 3921 b

48784 (GMR17G08)

dpp enhancer - 48784 Id - GMR 17G08 Location 2L:2450278,2451074 Base pairs – 796 b

Clinico-radiological and pathological correlation of interstitial lung diseases: a prospective single centre study

Background: Current investigation was done to study the role of HRCT chest in the diagnosis and characterization of interstitial lung diseases, yield of transbronchial lung biopsy and role of multidisciplinary approach of diagnosis.Methods: We prospectively analyzed clinical features and radiological findings in 38 patients of ILD. Radiological diagnosis on HRCT was made in every case depending on type of predominant abnormality and pattern of involvement. Following this, TBLB was done in every case.Results: ILD was diagnosed in all cases on HRCT. Most common ILD type was UIP (31.5%) followed by sarcoidosis (21%) and NSIP (15.7%). Other ILD subtypes encountered were, RB-ILD, AIP and acute silicosis. In 68.4% cases, there was definitive diagnosis on TBLB. Out of which in 15.7% cases, HRCT and TBLB diagnosis were different. In 15.3% cases, TBLB gave diagnosis of only non- specific ILD.Conclusions: HRCT can detect ILD in 100% cases & can characterize ILD into various patterns. But, HRCT alone without clinical correlation and pathology can cause diagnostic confusion in many cases. However, multidisciplinary approach by engaging clinician, radiologist and pathologist can lead to accurate diagnosis in many cases of ILD. TBLB is a safe, minimally invasive procedure which can establish correct diagnosis in many cases especially in broncho-centric diseases

Popular Matchings in the Hospital-Residents Problem with Two-Sided Lower Quotas

We consider the hospital-residents problem where both hospitals and residents can have lower quotas. The input is a bipartite graph G = (???,E), each vertex in ??? has a strict preference ordering over its neighbors. The sets ? and ? denote the sets of residents and hospitals respectively. Each hospital has an upper and a lower quota denoting the maximum and minimum number of residents that can be assigned to it. Residents have upper quota equal to one, however, there may be a requirement that some residents must not be left unassigned in the output matching. We call this as the residents\u27 lower quota. We show that whenever the set of matchings satisfying all the lower and upper quotas is non-empty, there always exists a matching that is popular among the matchings in this set. We give a polynomial-time algorithm to compute such a matching

Alzheimer\u27s Disease: The Silver Tsunami of the 21st Century

Alzheimer\u27s disease (AD), a fatal progressive neurodegenerative disorder, has no cure to date. One of the causes of AD is the accumulation of amyloid-beta 42 (Aß42) plaques, which result in the onset of neurodegeneration. It is not known how these plaques trigger the onset of neurodegeneration. There are several animal models developed to (i) study etiology of disease, (ii) look for genetic modifiers, and (iii) identify chemical inhibitors that can block neurodegeneration and help to find cure for this disease. An insect model of Drosophila melanogaster has also provided new insights into the disease. Here we will discuss the utility of the Drosophila eye model to study Alzheimer\u27s disease

Cullin-4 Regulates Wingless and JNK Signaling-Mediated Cell Death in the Drosophila Eye.

In all multicellular organisms, the fundamental processes of cell proliferation and cell death are crucial for growth regulation during organogenesis. Strict regulation of cell death is important to maintain tissue homeostasis by affecting processes like regulation of cell number, and elimination of unwanted/unfit cells. The developing Drosophila eye is a versatile model to study patterning and growth, where complex signaling pathways regulate growth and cell survival. However, the molecular mechanisms underlying regulation of these processes is not fully understood. In a gain-of-function screen, we found that misexpression of cullin-4 (cul-4), an ubiquitin ligase, can rescue reduced eye mutant phenotypes. Previously, cul-4 has been shown to regulate chromatin remodeling, cell cycle and cell division. Genetic characterization of cul-4 in the developing eye revealed that loss-of-function of cul-4 exhibits a reduced eye phenotype. Analysis of twin-spots showed that in comparison with their wild-type counterparts, the cul-4 loss-of-function clones fail to survive. Here we show that cul-4 clones are eliminated by induction of cell death due to activation of caspases. Aberrant activation of signaling pathways is known to trigger cell death in the developing eye. We found that Wingless (Wg) and c-Jun-amino-terminal-(NH2)-Kinase (JNK) signaling are ectopically induced in cul-4 mutant clones, and these signals co-localize with the dying cells. Modulating levels of Wg and JNK signaling by using agonists and antagonists of these pathways demonstrated that activation of Wg and JNK signaling enhances cul-4 mutant phenotype, whereas downregulation of Wg and JNK signaling rescues the cul-4 mutant phenotypes of reduced eye. Here we present evidences to demonstrate that cul-4 is involved in restricting Wg signaling and downregulation of JNK signaling-mediated cell death during early eye development. Overall, our studies provide insights into a novel role of cul-4 in promoting cell survival in the developing Drosophila eye