Arif Ashraf

Arif Ashraf
University of Massachusetts Amherst | UMass Amherst · Department of Biology

Plant Biologist | Science Writer

About

51
Publications
18,524
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
182
Citations
Introduction
I worked with hidden half of plant—root—during PhD. Now, as a postdoc, work with the exposed half of the plant—leaf—where we find stomata. Question is how these things are connected? It's a POLARIZED answer! For the root development, I looked at auxin transporters—PIN—polarized proteins. Now, for the stomatal development, I look at LRR RLK—PAN—polarized proteins. Don't you see—it's a POLARIZED journey!
Featured research
Article
Full-text available
Intricate and reproducible patterning of root tissues is critical for root function and plant survival. In particular, patterning of the ground tissue (endodermis and cortex) is vital to regulating material exchange and storage. Interestingly, ground tissue patterns are variable in different plant species. For example, the model plant Arabidopsis thaliana, where the canonical genetic circuit for ground tissue patterning was defined, contains only one layer of endodermis and one layer of cortex. In contrast, maize has eight layers of cortex, but the formation mechanism of multiple cortex layers is not well understood.
Article
Full-text available
Radiocesium, accumulated in the soil by nuclear accidents is a major environmental concern. The transport process of cesium (Cs⁺) is tightly linked to the indispensable plant nutrient potassium (K⁺) as they both belong to the group I alkali metal with similar chemical properties. Most of the transporters that had been characterized to date as Cs⁺ transporters are directly or indirectly linked to K⁺. Using a combinatorial approach of physiology, genetics, cell biology and root uptake assay, here we identified two ATP-Binding Cassette (ABC) proteins, ABCG37 and ABCG33 as facilitators of Cs⁺ influx. The gain-of-function mutant of ABCG37 (abcg37-1) showed increased sensitivity to Cs⁺-induced root growth inhibition, while the double knock out mutant of ABCG33 and ABCG37 (abcg33-1abcg37-2) showed resistance. Single loss-of-function mutant of ABCG33 and ABCG37 did not show any alteration in Cs⁺ response. In planta short term radioactive Cs⁺ uptake assay along with the growth and uptake assays in heterologous system confirmed ABCG33 and ABCG37 as Cs⁺ uptake carriers. Potassium response and content were unaffected in the double mutant background and the yeast cells lacking potassium uptake carriers transformed with ABCG33 and ABCG37 failed to grow in absence of K⁺, confirming that Cs⁺ uptake by ABCG33 and ABCG37 is independent of K⁺. Collectively, this work identified two ABC proteins as new Cs⁺ influx carriers, which act redundantly and independent of K⁺ uptake pathway.
Article
Full-text available
Arsenic contamination is a major environmental issue as it may lead to serious health hazard. Reduced trivalent form of inorganic arsenic, arsenite, is in general more toxic to plants compared with the fully oxidized pentavalent arsenate. The uptake of arsenite in plants has been shown to be mediated through a large subfamily of plant aquaglyceroporins, nodulin 26-like intrinsic proteins (NIPs). However, the efflux mechanisms, as well as the mechanism of arsenite-induced root growth inhibition, remain poorly understood. Using molecular physiology, synchrotron imaging, and root transport assay approaches, we show that the cellular transport of trivalent arsenicals in Arabidopsis thaliana is strongly modulated by PIN FORMED 2 (PIN2) auxin efflux transporter. Root transport assay using radioactive arsenite, X-ray fluorescence imaging (XFI) coupled with X-ray absorption spectroscopy (XAS), and ICP-MS analysis revealed that pin2 plants accumulate higher concentrations of arsenite in roots compared to wild-type. At the cellular level, arsenite specifically targets intracellular sorting of PIN2 and thereby alters the cellular auxin homeostasis. Consistently, loss of PIN2 results in aresenite hypersensitivity in roots. XFI coupled with XAS further revealed that loss of PIN2 results in specific accumulation of arsenical species, but not the other metals like iron, zinc or calcium in the root tip. Collectively, these results demonstrate that PIN2 functions in the distribution of arsenical species in planta.
Article
Full-text available
Endosomal trafficking plays an important role in regulating plant growth and development both at optimal and stressed conditions. Cold stress response in Arabidopsis root is directly linked to inhibition of the endosomal trafficking of auxin efflux carriers. However, the cellular components that link cold stress and the endosomal trafficking remain elusive. By screening available endosomal trafficking mutants against root growth recovery response under cold stress, we identified GNOM, a SEC7 containing ARF‐GEF, as a major modulator of cold response. Contrasting response of partial loss of function mutant gnom B4049/emb30‐1 and the engineered Brefeldin A (BFA) resistant GNOM line, both of which contain mutations within SEC7 domain, to cold stress at whole plant level highlights the importance of this domain in modulating plants cold response pathway. Cold stress selectively and transiently inhibits GNOM expression. The engineered point mutation at 696 amino acid position (Methionine to Leucine) that makes GNOM resistant to BFA, in fact results in overexpression of GNOM both at transcriptional and translational levels, and also alters its subcellular localization. Overexpression and altered cellular localization of GNOM were found to be directly linked to conferring striking cold resistant phenotype in Arabidopsis. Collectively, these results provide a mechanistic link between GNOM, BFA sensitive GNOM regulated trafficking and cold stress. This article is protected by copyright. All rights reserved.
Article
Arabidopsis stomatal development requires asymmetric cell division, where the nucleus moves to the division site based on cellular polarity cues. A new study reveals the role of distinct cytoskeletal networks, both guided by the polarity factor BASL, for nuclear movement before and after division.
Additional affiliations
July 2019 - present
University of Massachusetts Amherst
Position
  • PostDoc Position
April 2019 - June 2019
Michigan State University
Position
  • PostDoc Position
October 2017 - March 2019
The University of Tokyo
Position
  • Student

Publications

Publications (46)
Article
Full-text available
Endosomal trafficking plays an important role in regulating plant growth and development both at optimal and stressed conditions. Cold stress response in Arabidopsis root is directly linked to inhibition of the endosomal trafficking of auxin efflux carriers. However, the cellular components that link cold stress and the endosomal trafficking remain...
Article
Full-text available
Arsenic contamination is a major environmental issue as it may lead to serious health hazard. Reduced trivalent form of inorganic arsenic, arsenite, is in general more toxic to plants compared with the fully oxidized pentavalent arsenate. The uptake of arsenite in plants has been shown to be mediated through a large subfamily of plant aquaglyceropo...
Article
Arabidopsis stomatal development requires asymmetric cell division, where the nucleus moves to the division site based on cellular polarity cues. A new study reveals the role of distinct cytoskeletal networks, both guided by the polarity factor BASL, for nuclear movement before and after division.
Article
Full-text available
Radiocesium, accumulated in the soil by nuclear accidents is a major environmental concern. The transport process of cesium (Cs⁺) is tightly linked to the indispensable plant nutrient potassium (K⁺) as they both belong to the group I alkali metal with similar chemical properties. Most of the transporters that had been characterized to date as Cs⁺ t...
Article
Full-text available
Intricate and reproducible patterning of root tissues is critical for root function and plant survival. In particular, patterning of the ground tissue (endodermis and cortex) is vital to regulating material exchange and storage. Interestingly, ground tissue patterns are variable in different plant species. For example, the model plant Arabidopsis t...
Article
Full-text available
The root has been considered the hidden half of the plant, but it has many forms, shapes, and functions. Some are not hidden, such as shoot-borne roots (adventitious roots, crown, and brace roots) (Figure 1). These shoot-borne roots form either as a part of the regular developmental process or due to external influences like wounding and flooding.
Article
Full-text available
Unlike animals, plants are unable to escape unfavorable conditions, such as extremities of temperature. Among abiotic variables, the temperature is notableas it affects plants from the molecular to the organismal level. Because of global warming, understanding temperature effects on plants is salient today and should be focused not only on rising t...
Article
Full-text available
Cold stress has always been a significant limitation for plant development and causes substantial decreases in crop yield. Some temperate plants, such as Arabidopsis, have the ability to carry out internal adjustment, which maintains and checks the metabolic machinery during cold temperatures. This cold acclimation process requires prior exposure t...
Conference Paper
Full-text available
Both plants and animals rely on asymmetric cell division to generate new cell types, which is a core characteristic of multicellular organisms. Prior to asymmetric cell division, cell polarity is established. Cell polarity establishment and asymmetric cell division are universally important, although proteins important for polarity differ in plants...
Article
Full-text available
The success story of plant-based medicine has been overlooked during the advent of the modern pharmaceutical industry. Despite the negligence of the multibillion-dollar drug industry, people entirely rely on medicinal plants in some parts of the world. In this study, we have emphasized going back to those traditional medicinal practices to figure o...
Article
Full-text available
Mechanosensing is one of the fundamental cellular processes that helps cells respond to universal stimuli such as light, touch, gravity, and stresses. PIEZOs are the most well-characterized mechanosensors in mammals and can be activated by applying pressure from either a patch-clamp recording pipette or a blunt glass pipette, as the Greek word piez...
Article
Full-text available
The cis-regulatory elements facilitate the binding of sequence-specific transcription factors for activating or repressing the expression of target genes. The expression level of each gene may vary in different cell types due to differential regulatory elements within the accessible chromatin regions (ACRs), which can dictate cell-fate decisions an...
Article
Full-text available
Objective: MPDB 2.0 is built to be the continuation of MPDB 1.0, to serve as a more comprehensive data repertoire for Bangladeshi medicinal plants, and to provide a user-friendly interface for researchers, health practitioners, drug developers, and students who wish to study the various medicinal & nutritive plants scattered around Bangladesh and...
Conference Paper
Full-text available
Both plants and animals rely on asymmetric cell division to generate new cell types, which is a core characteristic of multicellular organisms. Prior to asymmetric cell division, cell polarity is established. Cell polarity establishment and asymmetric cell division are universally important, although proteins important for polarity differ in plants...
Article
Full-text available
The plant hormone cytokinin, an N6-substituted adenine derivative, was first discovered by Carlos Miller and Folke Skoog nearly 70 years ago as being able to promote cell division. Since then, there have been great advances in our understanding of cytokinin biosynthesis, perception and signaling, and expanded roles across plant growth and developme...
Conference Paper
Full-text available
Both plants and animals rely on asymmetric cell division to generate new cell types, which is a core characteristic of multicellular organisms. Prior to asymmetric cell division, cell polarity is established. Cell polarity establishment and asymmetric cell division are universally important, although proteins important for polarity differ in plants...
Preprint
Full-text available
Medicinal plants are generally defined as rare herbals with potent medicinal activities that can be used as an alternative treatment for diseases. Recent studies exploring novel medicine developments, originating from folk-medicinal practices challenges this notion and suggests that both the circumference of the term medicinal plant and their poten...
Article
Full-text available
Legume plants, such as the model systems, Medicago truncatula and Lotus japonica, and crop plants like soybean (Glycine max) and common bean (Phaseolus vulgaris), are able to utilize atmospheric nitrogen due to their symbiosis with nitrogen-fixing soil bacteria, rhizobia (Roy et al., 2020). Interestingly, this symbiosis is limited to only a few pla...
Article
Full-text available
Multicellular organisms maintain their growth and development in a dynamic and coordinated fashion. Cell polarity plays a key role in regulating cellular differentiation and proliferation. In plants, several developmental processes such as embryogenesis, leaf venation, stomatal patterning and phyllotaxy depend on cellular polarity establishment. On...
Article
Full-text available
The plant hormone cytokinin regulates diverse biological processes, including embryogenesis, cell division and differentiation, root and shoot architecture, vascular development, and formation of shoot and root lateral organs. The endoplasmic reticulum (ER) is considered as the primary cytokinin perception site based on the known subcellular locali...
Article
Full-text available
Plant cells are totipotent in nature during their life cycle and have the capacity to regenerate a whole plant from somatic cells through somatic embryogenesis (Ikeuchi et al., 2016). An appropriate chemical or mechanical induction is sufficient to induce this process. Compared with the discovery of induced pluripotent stem cells (iPSCs) from fibro...
Article
Full-text available
Medicinal plants have been used from the beginning of human civilization, which is mostly evident from the ancient script and traditional herbal medicine recipe. Despite the historically enriched demonstration about the use of plant as therapeutics, the pharmaceutical industries lack interest on phytochemical research compared with synthetic drug....
Preprint
Success story of plant-based medicine had been overlooked during the advent of modern pharmaceutical industry. Despite the negligence of the multimillion-dollar drug industry, people entirely rely on medicinal plants in some part of the world. In this study, we have emphasized on going back to those traditional medicinal practices to figure out the...
Preprint
Full-text available
Radiocesium, accumulated in the soil by nuclear accidents is a major environmental concern. The transport process of cesium (Cs+) is tightly linked to the indispensable plant nutrient potassium (K+) as they both belong to the group I alkali metal with similar chemical properties. Most of the transporters that had been characterized to date as Cs+ t...
Preprint
Full-text available
Arsenic contamination is a major environmental issue as it may lead to serious health hazard. Reduced trivalent form of inorganic arsenic, arsenite, is in general more toxic to plants compared with the fully oxidized pentavalent arsenate. The uptake of arsenite in plants has been shown to be mediated through a large subfamily of plant aquaglyceropo...
Chapter
Full-text available
A brief article about the experience and journey of 2019 Ambassador of the Year of American Society of Plant Biologists, Arif Ashraf.
Thesis
Full-text available
The growth and development of plants are constantly challenged due to the change in the environment or stressful conditions. These unfavorable environmental conditions include biotic stress, such as invasion of virus, parasites, and insects, and abiotic stress, such as drought, heat, cold, salinity, nutrient deficiency, and excess of toxic compound...
Chapter
Full-text available
Eric Schaller is professor at the department of Biological sciences in Dartmouth College and principle investigator of Phytohormone Signaling Laboratory (https://www.dartmouth.edu/~psl/). He received his B.S. in Biochemistry from Michigan State University. He did his Ph.D. in Molecular Biology from the University of Wisconsin-Madison and worked wit...
Conference Paper
Full-text available
GNOM is the most characterized membrane-associated guanine nucleotide exchange factor of small GTPase ADP-ribosylation factor (ARF GEF) in Arabidopsis thaliana. It plays an important role in intracellular endosomal trafficking. As a component of recycling endosomal pathway, GNOM localizes predominantly in the cytosol and plasma membrane and, partia...
Chapter
Phytohormones play an important role in every aspect of plant growth and development. Studies of hormonal biosynthesis, signaling, and transportation pathway facilitate our understanding for the basic developmental mechanisms. As a sessile organism, inability of plants to escape the adverse conditions is manifested through the alteration of growth...
Conference Paper
Full-text available
In last few decades, discovery and extensive use of three molecular tools; restriction enzymes, plasmid, and ligase had a significant impact on genetic engineering. It allowed us to cut the genetic material from one source and introduce it to another organism to get the desired traits or results. However, genome editing in precise position was stil...
Chapter
Full-text available
Membership corner interview for American Society of Plant Biologists
Article
Full-text available
Arsenic and cadmium toxicity has demonstrated to be a crucial problem and there are many health issues interconnected with each other. The toxicity of these metals has no biological role even though remain present in some or the other form, hazardous for the human health and its proper functioning. As a result, from the very beginning, the research...
Conference Paper
Full-text available
Endosomal trafficking plays important role in regulating plants cold stress response as cold stress inhibits intracellular trafficking of a specific set of proteins, including PIN FORMED (PIN) proteins. However, mechanistic explanation based on specific pathway, such as early, late, and recycling endosomal pathway is still elusive. To elucidate the...
Conference Paper
AIM: Identification of cesium specific transporters and decipher the molecular mechanism in the model plant Arabidopsis thaliana for using phytoremediation purpose. METHODS: Arabidopsis thaliana mutants were screened based on root growth response for cesium chloride. Root growth was rigorously analyzed based on kinematic analysis, meristematic cel...
Chapter
Full-text available
Philip N. Benfey is currently Paul Kramer Professor and Director of Duke Center for Systems Biology; and Howard Hughes Medical Institute (HHMI) Investigator. He graduated from the University of Paris and received his PhD in Cell and Developmental Biology from Harvard University under the guidance of Dr. Philip Leder. He did post-doctoral research a...
Conference Paper
Full-text available
Root system is one of the most important components for plant growth and development. Development of roots consists of cell division and elongation. Phytohormones, such as auxin, ethylene and cytokinin, play vital role for root development. We took a genetic approach to understand the role of auxin and ethylene in root mersitem development. Our res...
Article
Full-text available
This study aims to design epitope-based peptides for the utility of vaccine development by targeting outer membrane protein F (Omp F), because two available licensed vaccines, live oral Ty21a and injectable polysaccharide, are 50% to 80% protective with a higher rate of side effects. Conventional vaccines take longer time for development and have l...
Article
Full-text available
Unlabelled: The term of medicinal plants include a various types of plants used in herbalism with medicinal activities. These plants are considered as rich resources of ingredients which can be used as complementary and alternative medicines and, also in drug developments and synthesis. In addition, some plants regarded as valuable origin of nutri...
Article
Full-text available
The characterization of promoter is important for developing stress tolerant crops as well as understanding the role of promoters in regulating gene expression. The current study was initiated with an aim to characterize the Adh promoter under salinity and submergence stress in rice calli. The upstream regions (~1kb) of the Adh gene was amplified f...
Thesis
Full-text available
Controlled expression of transgenes is a prerequisite for achieving abiotic stress tolerant crops. Tissue or signal responsive promoters are therefore in high demand in practical plant biotechnology. The characterization of promoter is important for developing salt tolerant crops as well as understanding the role of promoters in regulating gene exp...
Thesis
Full-text available
Study of the regulation of gene expression based on transcriptional reprogramming under abiotic stress through experimentally validated DNA transcription factor binding motifs has become essential for understanding stress-inducible gene expression. The goal is to make classifier for differentiating between constitutive and stress inducible cis-regu...
Article
Full-text available
To obtain better therapeutic efficacy, nanotechnology based drug delivery system has been showing its endless possibilities and eventually bringing transformation in the perspective of upcoming medication system. Precision in developing biomaterial maintaining proper physicochemical properties and target specificity can unveil desired therapeutic o...
Article
Full-text available
Higher plants like rice, barley and maize have unique silicon accumulation characteristic. Silicon is taken up in the form of silicic acid by silicon transporter protein in root. The uniqueness of silicon accumulation in different plants is caused by both the physiologic and molecular diversity in the species even in different parts of a single pla...
Article
Full-text available
Rice and other higher plants like wheat, maize, sorghum etc. are highly silicon accumulating species and show differences in silicon accumulation. This difference is due to both physiologic and molecular distinction between intra and interspecies capacity to uptake silicon by silicon transporter in the form of silicic acid. To understand the comple...
Conference Paper
Full-text available
Foot and Mouth Disease Virus (FMDV) is an extremely contagious and rapidly evolving picornavirus infecting cloven-hoofed cattle, which was first recorded in Europe in 1544. FMDV endemic in Bangladesh causes annual loss approximately US$125 million declining meat and milk productivity of cattle. FMDV has 7 distinct serotypes (A, O, C, Asia-1, SAT-1,...

Questions

Questions (7)
Question
I’ve been having following issues while building my reference genome in snpEff.
1. It is suggested to change the configuration file. No matter, where I’m putting the information about my reference genome in the configuration file, while running the java executable file, it can’t read.
2. In addition to the previous issue, the reference genome file provided in .fa format to build. But, it looks like while running the .jar file, it’s showing that “reference genome.fa.genome” is not found.
Does anyone build the reference genome using snpEff latest version or have idea about configuring file or reference file format issue?
I’ve looked at the instruction of snpEff and other related stuffs as well.
Question
I've been using Zea_mays.B73_RefGen_v4.dna.toplevel as reference genome for my analysis. At the same time, I need to use maize HapMap file? Does anyone used B74 RefGenv4 and HapMap3? I'm having trouble to connect CyberDuck to acquire data from Cyverse iPlant platform. What is the easier or alternative way to acquire HapMap data in the local machine?
Question
I've been aiming to do BSA-Seq analysis and was trying to upload 4 SRA files through accession-based approach, according to Galaxy it's fasted compared to use FTP or directly load the data from local machine, to Galaxy for downstream analysis. I've found that even after one day with a very decent institutional internet connection, I couldn't make it.
Does anyone has experience to circumvent such large data file uploading challenges?
Question
I'm isolating maize protoplast from etiolated leaf and transforming with the combination of plasmids to check the TF activation, for instance, construct with TF, construct with reporter. Most of the cases, it contains Luc and GFP (fusing in both the N-and C-terminal). I'm using total plasmid concentration ranging from 5 ug to 55 ug and amount of protoplast is 1/2X10^5 cells.
I'm observing the busrting of protoplast occasionally.
> How to avoid the brusting of protoplast?
> Anyone was experiencing the same issue and tricks to overcome the problem?

Network

Cited By

Projects

Projects (6)
Project
This project aims to generate the database of traditionally used medicinal plants and their active compounds. Identified active compounds will help to find the drug targets by leveraging large scale RNA-seq data. Eventually, potential active compounds will be tested for the drug development.
Project
Most of my projects directed towards the root development, abiotic stress, and hormonal crosstalk. In this project, I focused on the plant hormones and the role of their biosynthesis, signaling, transport, and crosstalk in the low-temperature stress response.