Search

Your search keyword '"Kalpana P"' showing total 26 results
Start Over Author "Kalpana P" Journal nature communications
26 results on '"Kalpana P"'

1. Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

Author

Marjan M. Naeini, Felicity Newell, Lauren G. Aoude, Vanessa F. Bonazzi, Kalpana Patel, Guy Lampe, Lambros T. Koufariotis, Vanessa Lakis, Venkateswar Addala, Olga Kondrashova, Rebecca L. Johnston, Sowmya Sharma, Sandra Brosda, Oliver Holmes, Conrad Leonard, Scott Wood, Qinying Xu, Janine Thomas, Euan Walpole, G. Tao Mai, Stephen P. Ackland, Jarad Martin, Matthew Burge, Robert Finch, Christos S. Karapetis, Jenny Shannon, Louise Nott, Robert Bohmer, Kate Wilson, Elizabeth Barnes, John R. Zalcberg, B. Mark Smithers, John Simes, Timothy Price, Val Gebski, Katia Nones, David I. Watson, John V. Pearson, Andrew P. Barbour, and Nicola Waddell

Subjects
Science
Abstract

Abstract Oesophageal adenocarcinoma is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigate whole genome, transcriptomic and methylation data from 115 oesophageal adenocarcinoma patients mostly from the DOCTOR phase II clinical trial (Australian New Zealand Clinical Trials Registry-ACTRN12609000665235), with exploratory analysis pre-specified in the study protocol of the trial. We report genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also show that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorises patients into four immune clusters correlated with survival. The immune suppressed cluster is associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster is associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.

Published
2023
Full Text
View/download PDF

2. Towards a unified open access dataset of molecular interactions

Author

Pablo Porras, Elisabet Barrera, Alan Bridge, Noemi del-Toro, Gianni Cesareni, Margaret Duesbury, Henning Hermjakob, Marta Iannuccelli, Igor Jurisica, Max Kotlyar, Luana Licata, Ruth C. Lovering, David J. Lynn, Birgit Meldal, Bindu Nanduri, Kalpana Paneerselvam, Simona Panni, Chiara Pastrello, Matteo Pellegrini, Livia Perfetto, Negin Rahimzadeh, Prashansa Ratan, Sylvie Ricard-Blum, Lukasz Salwinski, Gautam Shirodkar, Anjalia Shrivastava, and Sandra Orchard

Subjects
Science
Abstract

The IMEx consortium provides one of the largest resources of curated, experimentally verified molecular interaction data. Here, the authors review how IMEx evolved into a fundamental resource for life scientists and describe how IMEx data can support biomedical research.

Published
2020
Full Text
View/download PDF

3. Dimerization deficiency of enigmatic retinitis pigmentosa-linked rhodopsin mutants

Author

Birgit Ploier, Lydia N. Caro, Takefumi Morizumi, Kalpana Pandey, Jillian N. Pearring, Michael A. Goren, Silvia C. Finnemann, Johannes Graumann, Vadim Y. Arshavsky, Jeremy S. Dittman, Oliver P. Ernst, and Anant K. Menon

Subjects
Science
Abstract

Retinitis pigmentosa is often caused by mutations that affect the activity or transport of rhodopsin, but some mutations cause disease even though an apparently functional protein is produced. Here the authors show that three such enigmatic mutants retain scramblase activity but are unable to dimerize.

Published
2016
Full Text
View/download PDF

4. Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

Author

M. Naeini, Marjan, Newell, Felicity, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lampe, Guy, Koufariotis, Lambros T., Lakis, Vanessa, Addala, Venkateswar, Kondrashova, Olga, Johnston, Rebecca L., Sharma, Sowmya, Brosda, Sandra, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Qinying, Thomas, Janine, Walpole, Euan, Tao Mai, G., Ackland, Stephen P., Martin, Jarad, Burge, Matthew, Finch, Robert, Karapetis, Christos S., Shannon, Jenny, Nott, Louise, Bohmer, Robert, Wilson, Kate, Barnes, Elizabeth, Zalcberg, John R., Mark Smithers, B., Simes, John, Price, Timothy, Gebski, Val, Nones, Katia, Watson, David I., Pearson, John V., Barbour, Andrew P., and Waddell, Nicola

Published
2023
Full Text
View/download PDF

9. Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling

Author

Guo, Long, Iida, Aritoshi, Bhavani, Gandham SriLakshmi, Gowrishankar, Kalpana, Wang, Zheng, Xue, Jing-yi, Wang, Juan, Miyake, Noriko, Matsumoto, Naomichi, Hasegawa, Takanori, Iizuka, Yusuke, Matsuda, Masashi, Nakashima, Tomoki, Takechi, Masaki, Iseki, Sachiko, Yambe, Shinsei, Nishimura, Gen, Koseki, Haruhiko, Shukunami, Chisa, Girisha, Katta M., and Ikegawa, Shiro

Published
2021
Full Text
View/download PDF

11. Towards a unified open access dataset of molecular interactions

Author

Porras, Pablo, Barrera, Elisabet, Bridge, Alan, del-Toro, Noemi, Cesareni, Gianni, Duesbury, Margaret, Hermjakob, Henning, Iannuccelli, Marta, Jurisica, Igor, Kotlyar, Max, Licata, Luana, Lovering, Ruth C., Lynn, David J., Meldal, Birgit, Nanduri, Bindu, Paneerselvam, Kalpana, Panni, Simona, Pastrello, Chiara, Pellegrini, Matteo, Perfetto, Livia, Rahimzadeh, Negin, Ratan, Prashansa, Ricard-Blum, Sylvie, Salwinski, Lukasz, Shirodkar, Gautam, Shrivastava, Anjalia, and Orchard, Sandra

Published
2020
Full Text
View/download PDF

15. Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients

Author

Patrick, Matthew T., Stuart, Philip E., Raja, Kalpana, Gudjonsson, Johann E., Tejasvi, Trilokraj, Yang, Jingjing, Chandran, Vinod, Das, Sayantan, Callis-Duffin, Kristina, Ellinghaus, Eva, Enerbäck, Charlotta, Esko, Tõnu, Franke, Andre, Kang, Hyun M., Krueger, Gerald G., Lim, Henry W., Rahman, Proton, Rosen, Cheryl F., Weidinger, Stephan, Weichenthal, Michael, Wen, Xiaoquan, Voorhees, John J., Abecasis, Gonçalo R., Gladman, Dafna D., Nair, Rajan P., Elder, James T., and Tsoi, Lam C.

Published
2018
Full Text
View/download PDF

16. Excessive reactive oxygen species induce transcription-dependent replication stress

Author

Martin Andrs, Henriette Stoy, Barbora Boleslavska, Nagaraja Chappidi, Radhakrishnan Kanagaraj, Zuzana Nascakova, Shruti Menon, Satyajeet Rao, Anna Oravetzova, Jana Dobrovolna, Kalpana Surendranath, Massimo Lopes, and Pavel Janscak

Subjects
Science
Abstract

Excessive oxidative stress is widely perceived as a key factor in cancer progression. Here, the authors reveal that oxidative stress induces transcription-dependent replication fork stalling that appears to be a major source of chromosomal rearrangements found in human cancers.

Published
2023
Full Text
View/download PDF

17. The Atr-Chek1 pathway inhibits axon regeneration in response to Piezo-dependent mechanosensation

Author

Feng Li, Tsz Y. Lo, Leann Miles, Qin Wang, Harun N. Noristani, Dan Li, Jingwen Niu, Shannon Trombley, Jessica I. Goldshteyn, Chuxi Wang, Shuchao Wang, Jingyun Qiu, Katarzyna Pogoda, Kalpana Mandal, Megan Brewster, Panteleimon Rompolas, Ye He, Paul A. Janmey, Gareth M. Thomas, Shuxin Li, and Yuanquan Song

Subjects
Science
Abstract

The Atr-Check1 pathway is involved in cell cycle and the DNA damage response. Here, the authors show that the Atr-Check1 pathway can inhibit axon regeneration in response to Piezo-mediated mechanosensation, affecting functional recovery.

Published
2021
Full Text
View/download PDF

18. Size, microhabitat, and loss of larval feeding drive cranial diversification in frogs

Author

Carla Bardua, Anne-Claire Fabre, Julien Clavel, Margot Bon, Kalpana Das, Edward L. Stanley, David C. Blackburn, and Anjali Goswami

Subjects
Science
Abstract

The evolution of metamorphic species may be constrained by different ecologies of the larval and adult stages. Here, Bardua et al. show that in frogs, adult ecology is more important than larval ecology for skull evolution, but species that don’t feed as tadpoles evolve faster than those that do.

Published
2021
Full Text
View/download PDF

19. INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication

Author

Updesh Dixit, Savita Bhutoria, Xuhong Wu, Liming Qiu, Menachem Spira, Sheeba Mathew, Richard Harris, Lucas J. Adams, Sean Cahill, Rajiv Pathak, P. Rajesh Kumar, Minh Nguyen, Seetharama A. Acharya, Michael Brenowitz, Steven C. Almo, Xiaoqin Zou, Alasdair C. Steven, David Cowburn, Mark Girvin, and Ganjam V. Kalpana

Subjects
Science
Abstract

HIV-1 integrase (IN) binds the host factor INI1/SMARCB1, which is required at multiple stages of HIV-1 replication. Here, the authors show that the same IN residues are involved in INI1 and RNA binding and in influencing particle morphogenesis and suggest that the IN-binding INI1 domain is structurally similar to HIV TAR RNA.

Published
2021
Full Text
View/download PDF

20. Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling

Author

Long Guo, Aritoshi Iida, Gandham SriLakshmi Bhavani, Kalpana Gowrishankar, Zheng Wang, Jing-yi Xue, Juan Wang, Noriko Miyake, Naomichi Matsumoto, Takanori Hasegawa, Yusuke Iizuka, Masashi Matsuda, Tomoki Nakashima, Masaki Takechi, Sachiko Iseki, Shinsei Yambe, Gen Nishimura, Haruhiko Koseki, Chisa Shukunami, Katta M. Girisha, and Shiro Ikegawa

Subjects
Science
Abstract

Sclerosing bone disorder (SBD) includes a broad spectrum of monogenic diseases characterised by increased bone density. Here, the authors describe a previously unknown SBD in four families caused by mutations in TMEM53 and demonstrate the role this protein plays in BMP signalling during bone formation.

Published
2021
Full Text
View/download PDF

21. Broadly neutralizing plasma antibodies effective against autologous circulating viruses in infants with multivariant HIV-1 infection

Author

Nitesh Mishra, Shaifali Sharma, Ayushman Dobhal, Sanjeev Kumar, Himanshi Chawla, Ravinder Singh, Muzamil Ashraf Makhdoomi, Bimal Kumar Das, Rakesh Lodha, Sushil Kumar Kabra, and Kalpana Luthra

Subjects
Science
Abstract

Some infants develop broadly neutralizing antibodies (bnAbs) to HIV in a shorter time frame than adults, but the reasons aren’t well understood. Here, the authors study a cohort of 51 HIV-1 clade C perinatally infected infants of Indian origin and find that multivariant infection is associated with bnAbs in elite neutralizers.

Published
2020
Full Text
View/download PDF

22. Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation

Author

Ravi Kiran Koripella, Manjuli R. Sharma, Kalpana Bhargava, Partha P. Datta, Prem S. Kaushal, Pooja Keshavan, Linda L. Spremulli, Nilesh K. Banavali, and Rajendra K. Agrawal

Subjects
Science
Abstract

Translation within mitochondria is carried out by specialized mitoribosomes and translational factors. Here the authors describe cryo-EM structures of the human mitochondrial translation elongation factor G1 in complex with human mitoribosomes, revealing distinct mechanism that include conformational changes at the polypeptide exit tunnel.

Published
2020
Full Text
View/download PDF

23. LRRK2 kinase activity regulates lysosomal glucocerebrosidase in neurons derived from Parkinson’s disease patients

Author

Daniel Ysselstein, Maria Nguyen, Tiffany J. Young, Alex Severino, Michael Schwake, Kalpana Merchant, and Dimitri Krainc

Subjects
Science
Abstract

Mutations in LRRK2 and GBA1, which encodes glucocerebrosidase (GCase), are associated with Parkinson’s disease. Here the authors show that LRRK2 is a negative regulator of lysosomal GCase activity, using dopaminergic neurons derived from iPSCs from PD patients with LRRK2 mutations.

Published
2019
Full Text
View/download PDF

24. Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients

Author

Matthew T. Patrick, Philip E. Stuart, Kalpana Raja, Johann E. Gudjonsson, Trilokraj Tejasvi, Jingjing Yang, Vinod Chandran, Sayantan Das, Kristina Callis-Duffin, Eva Ellinghaus, Charlotta Enerbäck, Tõnu Esko, Andre Franke, Hyun M. Kang, Gerald G. Krueger, Henry W. Lim, Proton Rahman, Cheryl F. Rosen, Stephan Weidinger, Michael Weichenthal, Xiaoquan Wen, John J. Voorhees, Gonçalo R. Abecasis, Dafna D. Gladman, Rajan P. Nair, James T. Elder, and Lam C. Tsoi

Subjects
Science
Abstract

Approximately 30% of psoriasis patients develop psoriatic arthritis (PsA) and early diagnosis is crucial for the management of PsA. Here, Patrick et al. develop a computational pipeline involving statistical and machine-learning methods that can assess the risk of progression to PsA based on genetic markers.

Published
2018
Full Text
View/download PDF

25. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons

Author

Kalpana Makhijani, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire Herboso, Katelyn Kukar, Itrat Batool, Stephanie Wachner, Katrina S. Gold, Corinna Wong, Michael B. O’Connor, and Katja Brückner

Subjects
Science
Abstract

Hematopoietic sites in theDrosophilalarva require the local peripheral nervous system for blood cells (hemocytes) to survive and proliferate, but how this is mediated is unclear. Here, the authors identify Activin-β from sensory neurons as signalling to hemocytes, affecting proliferation and adhesion.

Published
2017
Full Text
View/download PDF

26. Repression of GSK3 restores NK cell cytotoxicity in AML patients

Author

Reshmi Parameswaran, Parameswaran Ramakrishnan, Stephen A. Moreton, Zhiqiang Xia, Yongchun Hou, Dean A. Lee, Kalpana Gupta, Marcos deLima, Rose C. Beck, and David N. Wald

Subjects
Science
Abstract

Natural killer cells of acute myeloid leukaemia patients lack cytotoxic activity. Here the authors show that these cells have elevated GSK3β, and that its inhibition prolongs survival of mice transplanted with human AML and stimulates NK cytotoxicity via increased adhesion of NK cells to their targets.

Published
2016
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results