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Article ; Online: Not teaching evolution is an injustice.

Shashidhara, L S / Joshi, Amitabh

2023 Volume 380, Issue 6652, Page(s) 1303

Abstract: Since April, India has been roiled by controversy around the excision of several topics, including evolution and the periodic table, from school textbooks (up to grade 10) by the National Council for Educational Research and Training (NCERT). This was ... ...

Abstract	Since April, India has been roiled by controversy around the excision of several topics, including evolution and the periodic table, from school textbooks (up to grade 10) by the National Council for Educational Research and Training (NCERT). This was projected as an exercise in "rationalization" of content aimed at reducing the study load on students. The move was opposed by large numbers of academics and worried citizens. As the exclusion of specific topics in history and contemporary politics appeared to be in line with the ideology of the ruling party, many critics assumed that the removal of science topics was also ideologically motivated. In turn, this spurred supporters of NCERT and the government to dismiss all criticism as being entirely political, rather than academic. Both sides in this debate have traded exaggerated accusations of mala fide intent, leading to crucial broader issues being obscured.
Language	English
Publishing date	2023-06-29
Publishing country	United States
Document type	Editorial
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adj3557
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Article ; Online: Haltere development in D. melanogaster: implications for the evolution of appendage size, shape and function.

Khan, Soumen / Dilsha, C / Shashidhara, L S

The International journal of developmental biology

2020 Volume 64, Issue 1-2-3, Page(s) 159–165

Abstract: Differential specification of dorsal flight appendages, wing and haltere, in Drosophila provides an excellent model system to address a number of important questions in developmental biology at the levels of molecules, pathways, tissues, organs, ... ...

Abstract	Differential specification of dorsal flight appendages, wing and haltere, in Drosophila provides an excellent model system to address a number of important questions in developmental biology at the levels of molecules, pathways, tissues, organs, organisms and evolution. Here we discuss the mechanism by which the Hox protein Ubx recognizes and regulates its downstream targets, implications of the same in growth control at cellular and organ level and finally the evolution of haltere from ancestral hindwings in other holometabolous insects.
MeSH term(s)	Animals ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/embryology ; Drosophila melanogaster/physiology ; Gene Expression Regulation, Developmental ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Organogenesis ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Wings, Animal/anatomy & histology ; Wings, Animal/embryology ; Wings, Animal/physiology
Chemical Substances	Drosophila Proteins ; Homeodomain Proteins ; Transcription Factors ; Ubx protein, Drosophila
Language	English
Publishing date	2020-07-06
Publishing country	Spain
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1036070-0
ISSN	1696-3547 ; 0214-6282
ISSN (online)	1696-3547
ISSN	0214-6282
DOI	10.1387/ijdb.190133LS
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Article ; Online: A Micro-evolutionary Change in Target Binding Sites as a Key Determinant of Ultrabithorax Function in Drosophila.

Khan, Soumen / Pradhan, Saurabh J / Giraud, Guillaume / Bleicher, Françoise / Paul, Rachel / Merabet, Samir / Shashidhara, L S

Journal of molecular evolution

2023 Volume 91, Issue 5, Page(s) 616–627

Abstract: Hox genes encode Homeodomain-containing transcription factors, which specify segmental identities along the anterior-posterior axis. Functional changes in Hox genes have been directly implicated in the evolution of body plans across the metazoan lineage. ...

Abstract	Hox genes encode Homeodomain-containing transcription factors, which specify segmental identities along the anterior-posterior axis. Functional changes in Hox genes have been directly implicated in the evolution of body plans across the metazoan lineage. The Hox protein Ultrabithorax (Ubx) is expressed and required in developing third thoracic (T3) segments in holometabolous insects studied so far, particularly, of the order Coleoptera, Lepidoptera and Diptera. Ubx function is key to specify differential development of the second (T2) and T3 thoracic segments in these insects. While Ubx is expressed in the third thoracic segment in developing larvae of Hymenopteran Apis mellifera, the morphological differences between T2 and T3 are subtle. To identify evolutionary changes that are behind the differential function of Ubx in Drosophila and Apis, which are diverged for more than 350 million years, we performed comparative analyses of genome wide Ubx-binding sites between these two insects. Our studies reveal that a motif with a TAAAT core is a preferred binding site for Ubx in Drosophila, but not in Apis. Biochemical and transgenic assays suggest that in Drosophila, the TAAAT core sequence in the Ubx binding sites is required for Ubx-mediated regulation of two of its target genes studied here; CG13222, a gene that is normally upregulated by Ubx and vestigial (vg), whose expression is repressed by Ubx in T3. Interestingly, changing the TAAT site to a TAAAT site was sufficient to bring an otherwise unresponsive enhancer of the vg gene from Apis under the control of Ubx in a Drosophila transgenic assay. Taken together, our results suggest an evolutionary mechanism by which critical wing patterning genes might have come under the regulation of Ubx in the Dipteran lineage.
Language	English
Publishing date	2023-06-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	120148-7
ISSN	1432-1432 ; 0022-2844
ISSN (online)	1432-1432
ISSN	0022-2844
DOI	10.1007/s00239-023-10123-2
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Article: Developmental Robustness: The Haltere Case in

Giraud, Guillaume / Paul, Rachel / Duffraisse, Marilyne / Khan, Soumen / Shashidhara, L S / Merabet, Samir

Frontiers in cell and developmental biology

2021 Volume 9, Page(s) 713282

Abstract: Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, ... ...

Abstract	Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, we present a "self-sufficient" molecular model to explain the development of a particular flight organ that is under the control of the Hox gene
Language	English
Publishing date	2021-07-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2021.713282
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Article ; Online: Promoter Proximal Pausing Limits Tumorous Growth Induced by the Yki Transcription Factor in

Nagarkar, Sanket / Wasnik, Ruchi / Govada, Pravallika / Cohen, Stephen / Shashidhara, L S

Genetics

2020 Volume 216, Issue 1, Page(s) 67–77

Abstract: Promoter proximal pausing (PPP) of RNA polymerase II has emerged as a crucial rate-limiting step in the regulation of gene expression. Regulation of PPP is brought about by complexes 7SK snRNP, P-TEFb (Cdk9/cycT), and the negative elongation factor (NELF) ...

Abstract	Promoter proximal pausing (PPP) of RNA polymerase II has emerged as a crucial rate-limiting step in the regulation of gene expression. Regulation of PPP is brought about by complexes 7SK snRNP, P-TEFb (Cdk9/cycT), and the negative elongation factor (NELF), which are highly conserved from
MeSH term(s)	Animals ; Carcinogenesis/genetics ; Cyclin-Dependent Kinase 9/genetics ; Cyclin-Dependent Kinase 9/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster ; Gene Expression Regulation, Neoplastic ; Imaginal Discs/growth & development ; Imaginal Discs/metabolism ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Promoter Regions, Genetic ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Trans-Activators/genetics ; Trans-Activators/metabolism ; Wings, Animal/growth & development ; Wings, Animal/metabolism ; YAP-Signaling Proteins
Chemical Substances	Drosophila Proteins ; HEXIM protein, Drosophila ; Nuclear Proteins ; RNA-Binding Proteins ; Trans-Activators ; YAP-Signaling Proteins ; Yki protein, Drosophila ; bicoid-interacting protein 3, Drosophila (EC 2.1.1.) ; Methyltransferases (EC 2.1.1.-) ; Cyclin-Dependent Kinase 9 (EC 2.7.11.22)
Language	English
Publishing date	2020-07-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.120.303419
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Article ; Online: ChIP for Hox proteins from Drosophila imaginal discs.

Agrawal, Pavan / Shashidhara, L S

Methods in molecular biology (Clifton, N.J.)

2014 Volume 1196, Page(s) 241–253

Abstract: Chromatin immunoprecipitation (ChIP) is a technique that reveals in vivo location of a protein bound to DNA. ChIP coupled with DNA microarrays (ChIP-chip) or next-generation sequencing (ChIP-seq) allows for identification of binding sites of ... ...

Abstract	Chromatin immunoprecipitation (ChIP) is a technique that reveals in vivo location of a protein bound to DNA. ChIP coupled with DNA microarrays (ChIP-chip) or next-generation sequencing (ChIP-seq) allows for identification of binding sites of transcription factors on a global scale. Here we describe a protocol for ChIP to identify binding of the Ultrabithorax (Ubx) Hox transcription factors from imaginal discs of Drosophila larvae. The protocol can be extended to other model organisms and transcription factors.
MeSH term(s)	Animals ; Chromatin/genetics ; Chromatin/metabolism ; Chromatin Immunoprecipitation/methods ; Drosophila/metabolism ; High-Throughput Nucleotide Sequencing ; Homeodomain Proteins/metabolism ; Imaginal Discs/metabolism
Chemical Substances	Chromatin ; Homeodomain Proteins
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-1242-1_15
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Article ; Online: Proceedings of the 3rd Indian Cancer Genome Atlas Conference 2022: Biobanking to Omics: Collecting the Global Experience.

Joshi, Sneha / Mishra, Rupa / Kulkarni, Madhura / Kelkar, Devaki A / Harikrishnan, Keerthi / Vaid, Pooja / V, Gomathi / John, Jisha / Tamhane, Siddhi / Deshpande, Anand / Badve, Sunil / Chintamani / Mehrotra, Ravi / Shashidhara, L S / Kothari, Ashutosh / Koppiker, Chaitanyanand

JCO global oncology

2023 Volume 9, Page(s) e2200176

Abstract: On January 13th and 14th 2022, the Center for Translational Cancer Research organized the virtual third Indian Cancer Genome Atlas (ICGA) Conference 2022 "Biobanking to Omics - Collecting the Global Experience." This conference was planned as the ... ...

Abstract	On January 13th and 14th 2022, the Center for Translational Cancer Research organized the virtual third Indian Cancer Genome Atlas (ICGA) Conference 2022 "Biobanking to Omics - Collecting the Global Experience." This conference was planned as the steppingstone to help ICGA understand the road ahead and the probable roadblocks in its preparatory phase as ICGA begins to streamline the tumor tissue biobanking and multi-omics efforts in the Indian subcontinent. The first day of the conference was dedicated to updates on the current status of ICGA, the future prospect, and the global understanding of multi-omics efforts. The key highlights included two keynote speeches by Dr Wui Jin Koh, Senior Vice President and Chief Medical Office, National Comprehensive Cancer Network, and by Dr Christina Curtis, Associate Professor, Stanford University School of Medicine. The first day ended with an intriguing panel discussion on "ICGA updates and Future Steps." The second day focused on biobanking practices across the globe and several aspects of biobank setup such as infrastructure, maintenance, quality control, patient consent, and lessons learned from established biobanking setups. The talk by Rosita Kammler, Head, Translational Research Coordination, International Breast Cancer Study Group, Switzerland, and Ruhul Amin, Director, Bangladesh Medical Research Council were the key highlights. The second day also ended with an engaging panel discussion on "Tumor tissue biobanking - national and international perspectives." Overall, the conference was well received and had good attendance from national and international students, researchers, and faculty from academia as well as industry.
MeSH term(s)	Humans ; Biological Specimen Banks ; Neoplasms/genetics ; Neoplasms/therapy ; Bangladesh
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2687-8941
ISSN (online)	2687-8941
DOI	10.1200/GO.22.00176
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Article ; Online: Ataxin 2-binding protein 1 is a context-specific positive regulator of Notch signaling during neurogenesis in

Shukla, Jay Prakash / Deshpande, Girish / Shashidhara, L S

Development (Cambridge, England)

2017 Volume 144, Issue 5, Page(s) 905–915

Abstract: The role of the Notch pathway during the lateral inhibition that underlies binary cell fate choice is extensively studied, but the context specificity that generates diverse outcomes is less well understood. In the peripheral nervous system ... ...

Abstract	The role of the Notch pathway during the lateral inhibition that underlies binary cell fate choice is extensively studied, but the context specificity that generates diverse outcomes is less well understood. In the peripheral nervous system of
MeSH term(s)	Animals ; Crosses, Genetic ; Drosophila Proteins/metabolism ; Drosophila melanogaster/metabolism ; Gene Expression Regulation, Developmental ; Membrane Proteins/metabolism ; Neurogenesis ; Phenotype ; RNA-Binding Proteins/metabolism ; Receptors, Notch/metabolism ; Repressor Proteins/metabolism ; Sense Organs ; Signal Transduction ; Transcription Factors/metabolism
Chemical Substances	Drosophila Proteins ; Membrane Proteins ; RNA-Binding Proteins ; Rbfox1 protein, Drosophila ; Receptors, Notch ; Repressor Proteins ; Su(H) protein, Drosophila ; Transcription Factors
Language	English
Publishing date	2017-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.140657
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Article ; Online: Burden of COVID-19 and case fatality rate in Pune, India: an analysis of the first and second wave of the pandemic.

Bogam, Prasad / Joshi, Aparna / Nagarkar, Sanket / Jain, Divyashri / Gupte, Nikhil / Shashidhara, L S / Monteiro, Joy Merwin / Mave, Vidya

IJID Regions (Online)

2021 Volume 2, Page(s) 74–81

Abstract: Objective: To assess trends in case incidence and fatality rate between the first and second waves, we analyzed programmatic COVID-19 data from Pune city, an epicenter of COVID-19 cases in India.: Method: The trends of cases incidence, time-to-death ... ...

Abstract	Objective: To assess trends in case incidence and fatality rate between the first and second waves, we analyzed programmatic COVID-19 data from Pune city, an epicenter of COVID-19 cases in India. Method: The trends of cases incidence, time-to-death and case fatality rate (CFR) were analyzed. Poisson regression models adjusted for age and gender were used to determine the independent effect of pandemic waves on mortality. Results: Of 465 192 COVID-19 cases, 162 182 (35%) were reported in the first wave and 4146 (2.5%) deaths, and 275 493 (59%) in the second wave and 3184 (1.1%) deaths ( Conclusion: The burden of COVID-19 cases and deaths was more significant in the second wave; however, the CFR declined as the pandemic progressed. Nevertheless, investigating new therapies and implementing mass vaccination against COVID-19 are urgently needed.
Language	English
Publishing date	2021-12-18
Publishing country	England
Document type	Journal Article
ISSN	2772-7076
ISSN (online)	2772-7076
DOI	10.1016/j.ijregi.2021.12.006
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Article ; Online: Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India.

Environmental science and pollution research international

2023 Volume 30, Issue 56, Page(s) 118976–118988

Abstract: The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis ... ...

Abstract	The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens within a population before clinical cases emerge. In the present study, we aimed to assess the trend and dynamics of SARS-CoV-2 variants using a longitudinal approach. Our objective included early detection and monitoring of these variants to enhance our understanding of their prevalence and potential impact. To achieve our goals, we conducted real-time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing on 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) in Pune city, India, spanning from November 2021 to April 2022. Our comprehensive analysis identified 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2. Notably, fragments of Omicron variant were detected in WW samples prior to its first clinical detection in Botswana. Furthermore, we observed highly contagious sub-lineages of the Omicron variant, including BA.1 (~28%), BA.1.X (1.0-72%), BA.2 (1.0-18%), BA.2.X (1.0-97.4%) BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-21.83%), with varying prevalence rates. Overall, the present study demonstrated the practicality of WBE in the early detection of SARS-CoV-2 variants, which could help track future outbreaks of SARS-CoV-2. Such approaches could be implicated in monitoring infectious agents before they appear in clinical cases.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Pandemics ; COVID-19/epidemiology ; India ; Genomics ; Wastewater
Chemical Substances	Wastewater
Language	English
Publishing date	2023-11-03
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-023-30709-z
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