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Article ; Online: Does conserved domain SOD1 mutation has any role in ALS severity and therapeutic outcome?

Pal, Surinder / Tiwari, Abha / Sharma, Kaushal / Sharma, Suresh Kumar

BMC neuroscience

2020 Volume 21, Issue 1, Page(s) 42

Abstract: Background: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative fatal disease that can affect the neurons of brain and spinal cord. ALS genetics has identified various genes to be associated with disease pathology. Oxidative stress ... ...

Abstract	Background: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative fatal disease that can affect the neurons of brain and spinal cord. ALS genetics has identified various genes to be associated with disease pathology. Oxidative stress induced bunina and lewy bodies formation can be regulated through the action of SOD1 protein. Hence, in the present study we aim to analyse the structural and functional annotation of various reported SOD1 variants throughout and their putative correlation with the location of mutation and degree of ALS severity by inferring the structural and functional alterations in different SOD1 variants. Methods: We have retrieved around 69 SNPs of SOD1 gene from Genecards. Structural annotation of SOD1 variants were performed using SWISS Model, I-Mutant 2.0, Dynamut, ConSurf. Similarly, the functional annotation of same variants were done using SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB. Ramachandran plot was also obtained for six synonymous SNPs to compare the amino acid distribution of wild-type SOD1 (WT SOD1) protein. Frequency analysis, Chi square analysis, ANOVA and multiple regression analysis were performed to compare the structural and functional components among various groups. Results and conclusion: Results showed the mutations in conserved domain of SOD1 protein are more deleterious and significantly distort the tertiary structure of protein by altering Gibb's free energy and entropy. Moreover, significant changes in SIFT, PHP-SNP, PolyPhen2, PROVEAN and RegulomeDB scores were also observed in mutations located in conserved domain of SOD1 protein. Multiple regression results were also suggesting the significant alterations in free energy and entropy for conserved domain mutations which were concordant with structural changes of SOD1 protein. Results of the study are suggesting the biological importance of location of mutation(s) which may derive the different disease phenotypes and must be dealt accordingly to provide precise therapy for ALS patients.
MeSH term(s)	Amino Acids/metabolism ; Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/pathology ; Amyotrophic Lateral Sclerosis/therapy ; Conserved Sequence ; Entropy ; Gene Frequency ; Genetic Variation ; Humans ; Polymorphism, Single Nucleotide/genetics ; Superoxide Dismutase-1/genetics ; Treatment Outcome
Chemical Substances	Amino Acids ; SOD1 protein, human ; Superoxide Dismutase-1 (EC 1.15.1.1)
Language	English
Publishing date	2020-10-09
Publishing country	England
Document type	Journal Article
ISSN	1471-2202
ISSN (online)	1471-2202
DOI	10.1186/s12868-020-00591-3
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Article: Association of Plasma Biomarkers for Angiogenesis and Proteinopathy in Indian Amyotrophic Lateral Sclerosis Patients.

Modgil, Shweta / Khosla, Radhika / Tiwari, Abha / Sharma, Kaushal / Anand, Akshay

Journal of neurosciences in rural practice

2020 Volume 11, Issue 4, Page(s) 573–580

Abstract: ... ...

Abstract	Background
Language	English
Publishing date	2020-08-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2601242-X
ISSN	0976-3155 ; 0976-3147
ISSN (online)	0976-3155
ISSN	0976-3147
DOI	10.1055/s-0040-1714314
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Article: Angiogenesis-Centered Molecular Cross-Talk in Amyotrophic Lateral Sclerosis Survival: Mechanistic Insights.

Thakur, Keshav / Tiwari, Abha / Sharma, Kaushal / Modgil, Shweta / Khosla, Radhika / Anand, Akshay

Critical reviews in eukaryotic gene expression

2020 Volume 30, Issue 2, Page(s) 137–151

Abstract: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that is characterized with progressive muscle atrophy. We have attempted to establish the link between angiogenesis and cellular survival in the pathogenesis of ALS by compiling evidence ... ...

Abstract	Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that is characterized with progressive muscle atrophy. We have attempted to establish the link between angiogenesis and cellular survival in the pathogenesis of ALS by compiling evidence described in various scientific reports. The phenotypes of human ALS have earlier been captured in the mutant SOD1 mice as well as by targeted deletion of the hypoxia response element (HRE) from the promoter of the mouse gene for vascular endothelial growth factor (VEGF). Indirect evidence shows that angiogenesis can help prevent oxidative stress, and hence, enhance cell survival. VEGF and angiogenin chiefly regulate the process of angiogenesis. Transactive response DNA-binding protein 43 (TDP-43) is usually found inside the nucleus, but in large number of cases of ALS, it accumulates in the cytoplasm (TDP-43 proteinopathy). Interestingly, TDP-43 proteinopathy is found to be aggravated in the presence of the OPTN mutation, which is the genetic factor that is responsible for such accumulation. Interaction of TDP-43 with progranulin can further affect the angiogenesis in ALS patients by regulating activity of VEGF receptors, but conclusive evidence is needed to establish its role in pathogenesis of ALS. Certain mutations in UBQLN2 and UBQLN4 indicate that ubiquitination has a role in ALS pathobiology, but its link to angiogenesis has not been adequately studied. Recent studies have shown that several mutations in RNA-binding proteins (RBPs) can also cause ALS. Conclusively, in this review, we have attempted to argue the role of angiogenesis in enhanced ALS survival rate is probably regulated with the activation of NF-κβ. Additionally, interaction between OPTN and TDP-43 can also impact the transcription of various angiogenic molecules. Whether targeting angiogenic substances or TDP-43 can provide clues about extending ALS survival rate, in combination with current treatments, can only be evaluated after additional studies.
Language	English
Publishing date	2020-06-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	1071345-1
ISSN	1045-4403
ISSN	1045-4403
DOI	10.1615/CritRevEukaryotGeneExpr.2020031020
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Article: Association of Plasma Biomarkers for Angiogenesis and Proteinopathy in Indian Amyotrophic Lateral Sclerosis Patients

Modgil, Shweta / Khosla, Radhika / Tiwari, Abha / Sharma, Kaushal / Anand, Akshay

Journal of Neurosciences in Rural Practice

2020 Volume 11, Issue 04, Page(s) 573–580

Abstract: Background: Amyotrophic lateral sclerosis (ALS) is a rare motor neuron disease with progressive degeneration of motor neurons. Various molecules have been explored to provide the early diagnostic/prognostic tool for ALS without getting much success in ... ...

Abstract	Background: Amyotrophic lateral sclerosis (ALS) is a rare motor neuron disease with progressive degeneration of motor neurons. Various molecules have been explored to provide the early diagnostic/prognostic tool for ALS without getting much success in the field and miscellaneous reports studied in various population. Objective: The study was aimed to see the differential expression of proteins involved in angiogenesis (angiogenin [ANG], vascular endothelial growth factor [VEGF], vascular endothelial growth factor receptor 2 [VEGFR2], etc), proteinopathy (transactive response DNA binding protein-43 [TDP-43] and optineurin [OPTN]), and neuroinflammation (monocyte chemoattractant protein-1[MCP-1]) based on the characteristics of ALS pathology. Though, suitable panel based on protein expression profile can be designed to robust the ALS identification by enhancing the prognostic and diagnostic efficacy for ALS. Methods: A total of 89 ALS patients and 98 nonneurological controls were analyzed for the protein expression. Expression of angiogenic (VEGF, VEGFR2, and ANG), neuroinflammation (MCP-1), and proteinopathy (TDP-43 and OPTN) markers were estimated in plasma of the participants. Proteins were normalized with respective value of total protein before employing statistical analysis. Results: Analysis has exhibited significantly reduced expression of angiogenic, proteinopathy, and neuroinflammation biomarkers in ALS patients in comparison to controls. Spearman’s correlation analysis has showed the positive correlation to each protein. Conclusion: Altered expression of these proteins is indicating the prominent function in ALS pathology which may be interdependent and may have a synergistic role. Hence, a panel of expression can be proposed to diagnose ALS patient which may also suggest the modulation of therapeutic strategy according to expression profile of patient.
Keywords	amyotrophic lateral sclerosis ; angiogenic markers (VEGF, VEGFR2, angiogenin) ; TDP-43 ; optineurin ; MCP-1/ CCL-2
Language	English
Publishing date	2020-08-20
Publisher	Thieme Medical and Scientific Publishers Pvt. Ltd.
Publishing place	Stuttgart ; New York
Document type	Article
ZDB-ID	2601242-X
ISSN	0976-3155 ; 0976-3147 ; 0976-3155
ISSN (online)	0976-3155
ISSN	0976-3147 ; 0976-3155
DOI	10.1055/s-0040-1714314
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Article ; Online: The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies.

Bohra, Abhishek / Tiwari, Abha / Kaur, Parwinder / Ganie, Showkat Ahmad / Raza, Ali / Roorkiwal, Manish / Mir, Reyazul Rouf / Fernie, Alisdair R / Smýkal, Petr / Varshney, Rajeev K

Plant & cell physiology

2022 Volume 63, Issue 11, Page(s) 1554–1572

Abstract: Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some ...

Abstract	Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
MeSH term(s)	Humans ; Domestication ; Edible Grain/genetics ; Fabaceae/genetics ; Plant Breeding ; Crops, Agricultural/genetics
Language	English
Publishing date	2022-06-15
Publishing country	Japan
Document type	Review ; Journal Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcac086
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Article: Breeding More Crops in Less Time: A Perspective on Speed Breeding.

Samantara, Kajal / Bohra, Abhishek / Mohapatra, Sourav Ranjan / Prihatini, Riry / Asibe, Flora / Singh, Lokendra / Reyes, Vincent P / Tiwari, Abha / Maurya, Alok Kumar / Croser, Janine S / Wani, Shabir Hussain / Siddique, Kadambot H M / Varshney, Rajeev K

Biology

2022 Volume 11, Issue 2

Abstract: Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and ... ...

Abstract	Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and breeding. In this context, speed breeding (SB), relying mainly on photoperiod extension, temperature control, and early seed harvest, has the potential to accelerate the rate of plant improvement. Well demonstrated in the case of long-day plants, the SB protocols are being extended to short-day plants to reduce the generation interval time. Flexibility in SB protocols allows them to align and integrate with diverse research purposes including population development, genomic selection, phenotyping, and genomic editing. In this review, we discuss the different SB methodologies and their application to hasten future plant improvement. Though SB has been extensively used in plant phenotyping and the pyramiding of multiple traits for the development of new crop varieties, certain challenges and limitations hamper its widespread application across diverse crops. However, the existing constraints can be resolved by further optimization of the SB protocols for critical food crops and their efficient integration in plant breeding pipelines.
Language	English
Publishing date	2022-02-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology11020275
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Article: Breeding More Crops in Less Time: A Perspective on Speed Breeding

Samantara, Kajal / Bohra, Abhishek / Mohapatra, Sourav Ranjan / Prihatini, Riry / Asibe, Flora / Singh, Lokendra / Reyes, Vincent P. / Tiwari, Abha / Maurya, Alok Kumar / Croser, Janine S. / Wani, Shabir Hussain / Siddique, Kadambot H. M. / Varshney, Rajeev K.

Biology. 2022 Feb. 10, v. 11, no. 2

2022

Abstract	Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and breeding. In this context, speed breeding (SB), relying mainly on photoperiod extension, temperature control, and early seed harvest, has the potential to accelerate the rate of plant improvement. Well demonstrated in the case of long-day plants, the SB protocols are being extended to short-day plants to reduce the generation interval time. Flexibility in SB protocols allows them to align and integrate with diverse research purposes including population development, genomic selection, phenotyping, and genomic editing. In this review, we discuss the different SB methodologies and their application to hasten future plant improvement. Though SB has been extensively used in plant phenotyping and the pyramiding of multiple traits for the development of new crop varieties, certain challenges and limitations hamper its widespread application across diverse crops. However, the existing constraints can be resolved by further optimization of the SB protocols for critical food crops and their efficient integration in plant breeding pipelines.
Keywords	crossing ; genomics ; marker-assisted selection ; phenotype ; plant improvement ; temperature
Language	English
Dates of publication	2022-0210
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology11020275
Database	NAL-Catalogue (AGRICOLA)

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Article: Global gene expression analysis of pigeonpea with male sterility conditioned by A2 cytoplasm

Bohra, Abhishek / Prasad, Gandam / Rathore, Abhishek / Saxena, Rachit K / Naik SJ, Satheesh / Pareek, Shalini / Jha, Rintu / Pazhamala, Lekha / Datta, Dibendu / Pandey, Gaurav / Tiwari, Abha / Maurya, Alok Kumar / Soren, Khela Ram / Akram, Mohd / Varshney, Rajeev K / Singh, Narendra P

The plant genome. 2021 Nov., v. 14, no. 3

2021

Abstract: Cytoplasmic male sterility(CMS), a maternally inherited trait, provides a promising means to harness yield gains associated with hybrid vigor. In pigeonpea [Cajanus cajan (L.) Huth], nine types of sterility‐inducing cytoplasm have been reported, of which ...

Abstract	Cytoplasmic male sterility(CMS), a maternally inherited trait, provides a promising means to harness yield gains associated with hybrid vigor. In pigeonpea [Cajanus cajan (L.) Huth], nine types of sterility‐inducing cytoplasm have been reported, of which A₂ and A₄ have been successfully deployed in hybrid breeding. Unfortunately, molecular mechanism of the CMS trait is poorly understood because of limited research invested. More recently, an association between a mitochondrial gene (nad7) and A₄‐CMS has been demonstrated in pigeonpea; however, the mechanism underlying A₂‐CMS still remains obscure. The current investigation aimed to analyze the differences in A₂‐CMS line (ICPL 88039A) and its isogenic maintainer line (ICPL 88039B) at transcriptome level using next‐generation sequencing. Gene expression profiling uncovered a set of 505 genes that showed altered expression in response to CMS, of which, 412 genes were upregulated while 93 were downregulated in the fertile maintainer line vs. the CMS line. Further, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses revealed association of CMS in pigeonpea with four major pathways: glucose and lipid metabolism, ATP production, pollen development and pollen tube growth, and reactive oxygen species (ROS) scavenging. Patterns of digital gene expression were confirmed by quantitative real‐time polymerase chain reaction (qRT‐PCR) of six candidate genes. This study elucidates candidate genes and metabolic pathways having potential associations with pollen development and male sterility in pigeonpea A₂‐CMS. New insights on molecular mechanism of CMS trait in pigeonpea will be helpful to accelerate heterosis utilization for enhancing productivity gains in pigeonpea.
Keywords	Cajanus cajan ; cytoplasm ; cytoplasmic male sterility ; gene expression ; gene ontology ; glucose ; heterosis ; hybrids ; lipid metabolism ; mitochondrial genes ; pigeon peas ; pollen ; pollen tubes ; protein-protein interactions ; quantitative polymerase chain reaction ; reactive oxygen species ; transcriptome
Language	English
Dates of publication	2021-11
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2375444-8
ISSN	1940-3372 ; 0011-183X
ISSN (online)	1940-3372
ISSN	0011-183X
DOI	10.1002/tpg2.20132
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Effectiveness of Yoga as the Public Health Intervention Module in the Management of Diabetes and Diabetes Associated Dementia in South East Asia: A Narrative Review.

Bali, Parul / Kaur, Navneet / Tiwari, Abha / Bammidi, Sridhar / Podder, Vivek / Devi, Chandra / Kumar, Saurabh / Sivapuram, Madhava Sai / Ghani, Abdul / Modgil, Shweta / Malik, Neeru / Anand, Akshay

Neuroepidemiology

2020 Volume 54, Issue 4, Page(s) 287–303

Abstract: Background: Diabetes mellitus (DM) is widely spread in South Asian (ASEAN) and Indian sub-continent. The increasing healthcare costs of DM can be prevented in the developing world by improved public healthcare interventions. Modifiable risk factors of ... ...

Abstract	Background: Diabetes mellitus (DM) is widely spread in South Asian (ASEAN) and Indian sub-continent. The increasing healthcare costs of DM can be prevented in the developing world by improved public healthcare interventions. Modifiable risk factors of DM like sedentary lifestyle, obesity, and stressful conditions are associated with its progression; however, the epidemiological data collected by Public Institutions are limited. Summary: A review of published literature describing geographic distribution of DM and associated dementia in South Asian region, particularly India, was conducted with the purpose of assessing the feasibility and challenges associated with the Yoga-based risk reduction. PubMed and Google Scholar databases were searched for DM and dementia-related articles by using a combination of keywords: Diabetes, Diabetes related Dementia Southeast Asia, Pre-diabetes, Yoga, lifestyle modification, Dementia and Exercise. The epidemiological data generated from these diseases have not prompted to any major public health policies. Yoga can be a cost-effective intervention for the prevention of Type 2 DM (T2DM) and its associated cognitive decline when detected early. If nationwide intervention of Yoga is brought about by the state, its integration in health care will become more meaningful and acceptable. Key Message: Studies suggest that Yoga and change in lifestyle can modify the health risks associated with T2DM and associated dementia if it is mainstreamed with the public health initiative of Ayushman Bharat scheme.
MeSH term(s)	Asia, Southeastern/epidemiology ; Cognitive Dysfunction/epidemiology ; Cognitive Dysfunction/etiology ; Cognitive Dysfunction/prevention & control ; Dementia/epidemiology ; Dementia/etiology ; Dementia/prevention & control ; Diabetes Complications/epidemiology ; Diabetes Complications/etiology ; Diabetes Complications/prevention & control ; Diabetes Mellitus, Type 2/complications ; Diabetes Mellitus, Type 2/epidemiology ; Diabetes Mellitus, Type 2/rehabilitation ; Humans ; India/epidemiology ; Public Health ; Yoga
Language	English
Publishing date	2020-02-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	603189-4
ISSN	1423-0208 ; 0251-5350
ISSN (online)	1423-0208
ISSN	0251-5350
DOI	10.1159/000505816
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Article: Mapping QTL for important seed traits in an interspecific F2 population of pigeonpea.

Bohra, Abhishek / Jha, Rintu / Lamichaney, Amrit / Singh, Deepak / Jha, Uday C / Naik, S J Satheesh / Datta, Dibendu / Maurya, Alok K / Tiwari, Abha / Yadav, Vivekanand / Singh, Farindra / Singh, Indra P / Singh, Narendra P

3 Biotech

2020 Volume 10, Issue 10, Page(s) 434

Abstract: Seed traits present important breeding targets for enhancing grain yield and quality in various grain legume crops including pigeonpea. The present study reports significant genetic variation for six seed traits including seed length (SL), seed width (SW) ...

Abstract	Seed traits present important breeding targets for enhancing grain yield and quality in various grain legume crops including pigeonpea. The present study reports significant genetic variation for six seed traits including seed length (SL), seed width (SW), seed thickness (ST), seed weight (SWT), electrical conductivity (EC) and water uptake (WU) among
Language	English
Publishing date	2020-09-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-020-02423-x
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