Article
Biology
Kate A. Rawlinson, Adam J. Reid, Zhigang Lu, Patrick Driguez, Anna Wawer, Avril Coghlan, Geetha Sankaranarayanan, Sarah K. Buddenborg, Carmen Diaz Soria, Catherine McCarthy, Nancy Holroyd, Mandy Sanders, Karl F. Hoffmann, David Wilcockson, Gabriel Rinaldi, Matthew Berriman
Summary: The study revealed daily rhythms in the transcriptomes of adult Schistosoma mansoni, providing insights into internal processes and host interactions relevant to within-host survival and between-host transmission. If these daily rhythms are driven by an intrinsic circadian clock, the oscillatory mechanism must be distinct from that in other animals. This information will benefit the development and delivery of treatments against schistosomiasis.
Article
Cell Biology
Deepak Sharma, Caitlin R. Wessel, Mahboobeh Mahdavinia, Fabian Preuss, Faraz Bishehsar
Summary: The circadian control of pancreatic function may be influenced by aging. This study shows that the pancreatic transcriptome undergoes reorganization during aging, with the aged pancreas exhibiting gain of rhythms in extrinsic cellular pathways and potential involvement of fibroblast-associated mechanisms.
Article
Plant Sciences
Yanli Xiang, Thomas Sapir, Pauline Rouillard, Marina Ferrand, Jose M. Jimenez-Gomez
Summary: This study reveals the significant impact of phase changes on photoperiod perception in tomato during domestication, while changes in period have minimal effect.
Article
Neurosciences
Ashley A. Farre, Chi Sun, Margaret R. Starostik, Samuel S. Hunter, Milton A. English, Audrey Duncan, Abirami Santhanam, Eyad Shihabeddin, John O'Brien, Anand Swaroop, Deborah L. Stenkamp
Summary: This study aimed to investigate the transcriptional heterogeneity and regulation of differentially expressed tandemly-replicated opsins using zebrafish as a model. The results showed additional transcriptional differences beyond opsin expression between LWS1 and LWS2 cones, which are likely controlled by multiple signals.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Jun Seo Ha, Hyundoo Jeong
Summary: Recent advances in single-cell sequencing techniques have allowed for gene expression profiling at the individual cell level, accelerating biomedical research for complex disease treatment. In this study, we introduce a novel single-cell clustering algorithm, GRACE, which employs ensemble similarity learning and graph autoencoders to accurately classify cells. Through evaluations using real-world single-cell sequencing datasets, we demonstrate that GRACE achieves high assessment metric scores and yields accurate single-cell clustering results.
Article
Medicine, Research & Experimental
Mei-li Wei, Shi-min He, An-qi Chen, Zi-xuan Fan, Wei Liu, Ling Zhang, Shi-jie Lv, Cheng-zeng Qiu, Hui-ru Liu, Mu-xian Hao, Zong-jun Yin, Da-long Ren
Summary: This study investigated the effects of FLX on circadian rhythm using zebrafish as a model. The results showed that FLX treatment led to down-regulation of clock genes expression, reduction in amplitude and phase shift of circadian rhythms, as well as inhibition of melatonin secretion. These findings provide valuable insights into the impact of FLX exposure on circadian rhythm and locomotor activity, and may have implications for its clinical application.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Cell Biology
Ashley C. Kramer, Katherine Gurdziel, Ryan Thummel
Summary: The study revealed that adult zebrafish have the ability to completely regenerate their retinas through the re-entry of Muller glia into the cell cycle and differentiation into new photoreceptors after intense light exposure. Additionally, the research identified two peaks of MG gliosis, a distinct transcriptional shift between 5- and 10-days post lesion, and different patterns of transcriptional recovery of photoreceptor opsins at 28 days post lesion.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Plant Sciences
Ce Chen, Yining Ge, Lingli Lu
Summary: Single-cell and spatial transcriptomics have shifted researchers' focus from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into transcriptomes at the single-cell level, while spatial transcriptomes help preserve spatial information. Though these two omics technologies are mature and helpful, further research is needed to ensure their widespread applicability in plant studies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biology
Alexandra J. Trott, Ben J. Greenwell, Tejas R. Karhadkar, Natali N. Guerrero-Vargas, Carolina Escobar, Ruud M. Buijs, Jerome S. Menet
Summary: Shift work has been shown to have impacts on the heart transcriptome in rats, independent of food consumption. Restricting food intake during shift work affects the expression of hundreds of genes related to extracellular matrix components and inflammatory markers in the heart. While maintaining food access during shift work has less effects on gene expression, it still leads to cardiac fibrosis without inflammation.
Article
Environmental Sciences
Graciela Lopez-Soop, Trine Husoy, Marcin Wlodzimierz Wojewodzic, Hege Hjertholm, Anastasia Spyropoulou, Effrosyni S. Katsanou, Petros Batakis, Katerina Kyriakopoulou, Kyriaki Machera, Hubert Dirven, Birgitte Lindeman, Nur Duale
Summary: Exposure to phthalates is common in Europe, and their effects on the human transcriptome are largely unknown. A study conducted on blood samples from the Norwegian EuroMix cohort revealed that phthalate exposure led to differential gene expression, with DINCH showing the highest number of differentially expressed genes. Gene ontology analysis indicated that the differentially expressed genes were mainly associated with cellular metabolism, while phthalate metabolites MnBP and DINCH showed enrichment in immunological function pathways. The study also found associations between phthalates and genes involved in the PPAR signaling pathway. Overall, DINCH had similar effects on gene expression as phthalates, despite being considered a substitute for them.
ENVIRONMENTAL RESEARCH
(2023)
Article
Forestry
Fabiano Sillo, Cecilia Brunetti, Fabio Marroni, Federico Vita, Luana Beatriz dos Santos Nascimento, Alfredo Vizzini, Antonietta Mello, Raffaella Balestrini
Summary: The European hazelnut forms a symbiotic relationship with ectomycorrhizal fungi, and this study suggests that this symbiosis can help plants adapt to stress and regulate defense responses. This research has important implications for understanding novel aspects of ectomycorrhizal symbiosis.
Article
Environmental Sciences
Rui F. O. Silva, Brigida R. Pinho, Miguel M. Santos, Jorge M. A. Oliveira
Summary: Behavioural disruptions can serve as sensitive indicators of abnormal animal physiology and are valuable for toxicity assessment. Zebrafish, a small vertebrate, is a commonly used model organism for toxicological studies. This study validates the use of an infrared-based Locomotor Activity Monitor (LAM) to assess zebrafish behaviour, and demonstrates the feasibility of using this method to evaluate multi parameter behavioural disruptions in zebrafish. The findings have broad applicability and may contribute to the development of standard methods for toxicity testing.
Article
Engineering, Environmental
Sahar Daer, Joseph E. Goodwill, Kaoru Ikuma
Summary: Disinfection mechanisms vary by disinfectant, with monochloramine potentially inducing viable but non-culturable state through reduced protein synthesis and metabolism, while ferrate does not have this effect. Both disinfectants upregulate oxidative stress response genes, with monochloramine showing slower disinfection kinetics compared to ferrate.
Article
Medicine, General & Internal
Maria Tio-Coma, Szymon M. Kielbasa, Susan J. F. van den Eeden, Hailiang Mei, Johan Chandra Roy, Jacco Wallinga, Marufa Khatun, Sontosh Soren, Abu Sufian Chowdhury, Khorshed Alam, Anouk van Hooij, Jan Hendrik Richardus, Annemieke Geluk
Summary: The study identified a prospective transcriptional risk signature in blood that can predict the development of leprosy 4 to 61 months before clinical diagnosis. Using a machine learning approach, a leprosy signature was identified and validation showed potential value in confirming leprosy risk.
Article
Plant Sciences
Gust Bilcke, Cristina Maria Osuna-Cruz, Marta Santana Silva, Nicole Poulsen, Sofie D'hondt, Petra Bulankova, Wim Vyverman, Lieven De Veylder, Klaas Vandepoele
Summary: Coastal regions, occupying only 0.03% of ocean surface area, contribute around 20% of annual gross primary production in the oceans. Diatoms dominate coastal sediments and exhibit significant expression oscillations at night with a 24-hour periodicity.
Letter
Medicine, General & Internal
Debojyoti Chakraborty, Anurag Agrawal, Souvik Maiti
Article
Multidisciplinary Sciences
Toni M. Delorey, Carly G. K. Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Asa Segerstolpe, Domenic Abbondanza, Stephen J. Fleming, Ayshwarya Subramanian, Daniel T. Montoro, Karthik A. Jagadeesh, Kushal K. Dey, Pritha Sen, Michal Slyper, Yered H. Pita-Juarez, Devan Phillips, Jana Biermann, Zohar Bloom-Ackermann, Nikolaos Barkas, Andrea Ganna, James Gomez, Johannes C. Melms, Igor Katsyv, Erica Normandin, Pourya Naderi, Yury V. Popov, Siddharth S. Raju, Sebastian Niezen, Linus T. -Y. Tsai, Katherine J. Siddle, Malika Sud, Victoria M. Tran, Shamsudheen K. Vellarikkal, Yiping Wang, Liat Amir-Zilberstein, Deepak S. Atri, Joseph Beechem, Olga R. Brook, Jonathan Chen, Prajan Divakar, Phylicia Dorceus, Jesse M. Engreitz, Adam Essene, Donna M. Fitzgerald, Robin Fropf, Steven Gazal, Joshua Gould, John Grzyb, Tyler Harvey, Jonathan Hecht, Tyler Hether, Judit Jane-Valbuena, Michael Leney-Greene, Hui Ma, Cristin McCabe, Daniel E. McLoughlin, Eric M. Miller, Christoph Muus, Mari Niemi, Robert Padera, Liuliu Pan, Deepti Pant, Carmel Pe'er, Jenna Pfiffner-Borges, Christopher J. Pinto, Jacob Plaisted, Jason Reeves, Marty Ross, Melissa Rudy, Erroll H. Rueckert, Michelle Siciliano, Alexander Sturm, Ellen Todres, Avinash Waghray, Sarah Warren, Shuting Zhang, Daniel R. Zollinger, Lisa Cosimi, Rajat M. Gupta, Nir Hacohen, Hanina Hibshoosh, Winston Hide, Alkes L. Price, Jayaraj Rajagopal, Purushothama Rao Tata, Stefan Riedel, Gyongyi Szabo, Timothy L. Tickle, Patrick T. Ellinor, Deborah Hung, Pardis C. Sabeti, Richard Novak, Robert Rogers, Donald E. Ingber, Z. Gordon Jiang, Dejan Juric, Mehrtash Babadi, Samouil L. Farhi, Benjamin Izar, James R. Stone, Ioannis S. Vlachos, Isaac H. Solomon, Orr Ashenberg, Caroline B. M. Porter, Bo Li, Alex K. Shalek, Alexandra-Chloe Villani, Orit Rozenblatt-Rosen, Aviv Regev
Summary: This study using single-cell and spatial atlases revealed the impact of COVID-19 infection on lung, kidney, liver, and heart tissues, showing structural remodeling and viral RNA enrichment. Differences in lung inflammatory responses and transcriptional alterations in heart tissue of COVID-19 patients were also identified, along with cell types and genes associated with disease severity.
Article
Genetics & Heredity
Mayank Bansal, Sundaram Acharya, Saumya Sharma, Rhythm Phutela, Riya Rauthan, Souvik Maiti, Debojyoti Chakraborty
Summary: Precision genome engineering targeting patient-specific mutations is the future of personalized medicine, with ophthalmology leading the way as an accessible organ for therapy and monitoring. Increasing evidence supports the role of genomic editing in retinal dystrophies, with CRISPR-Cas9 system revolutionizing genome editing and drug discovery in this field.
OPHTHALMIC GENETICS
(2021)
Article
Critical Care Medicine
Paul B. Dieffenbach, Christina Mallarino Haeger, Rakhshinda Rehman, Alexis M. Corcoran, Anna Maria F. Coronata, Shamsudheen K. Vellarikkal, Izabela Chrobak, Aaron B. Waxman, Sally H. Vitali, Lynette M. Sholl, Robert F. Padera, David Lagares, Francesca Polverino, Caroline A. Owen, Laura E. Fredenburgh
Summary: MMP-8 is upregulated in the pulmonary vasculature during PAH pathogenesis and acts as a protective factor by altering matrix composition and disrupting integrin-beta 3/FAK and YAP/TAZ-dependent mechanical signaling in PASMCs.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Paras Sehgal, Samatha Mathew, Ambily Sivadas, Arjun Ray, Jyoti Tanwar, Sushma Vishwakarma, Gyan Ranjan, K. Shamsudheen, Rahul C. Bhoyar, Abhishek Pateria, Elvin Leonard, Mukesh Lalwani, Archana Vats, Rajeev R. Pappuru, Mudit Tyagi, Saumya Jakati, Shantanu Sengupta, B. K. Binukumar, Subhabrata Chakrabarti, Inderjeet Kaur, Rajender K. Motiani, Vinod Scaria, Sridhar Sivasubbu
Summary: The study identified a novel vascular endothelial-associated lncRNA named VEAL2, which regulates endothelial permeability and function through interaction with PRKCB2, and is implicated in diabetic retinopathy.
Article
Biology
Manoj Kumar, Sneha Gulati, Asgar H. Ansari, Rhythm Phutela, Sundaram Acharya, Mohd Azhar, Jayaram Murthy, Poorti Kathpalia, Akshay Kanakan, Ranjeet Maurya, Janani Srinivasa Vasudevan, S. Aparna, Rajesh Pandey, Souvik Maiti, Debojyoti Chakraborty
Summary: The COVID-19 pandemic has led to increased mortality rates among elderly and patients with comorbid conditions. A lateral flow assay using FnCas9 was developed for simultaneous detection of SARS-CoV-2 infection and identification of point mutations in the virus sequence with high sensitivity and specificity, showing potential for rapid CRISPR diagnostics.
Article
Genetics & Heredity
James P. Pirruccello, Mark D. Chaffin, Elizabeth L. Chou, Stephen J. Fleming, Honghuang Lin, Mahan Nekoui, Shaan Khurshid, Samuel F. Friedman, Alexander G. Bick, Alessandro Arduini, Lu-Chen Weng, Seung Hoan Choi, Amer-Denis Akkad, Puneet Batra, Nathan R. Tucker, Amelia W. Hall, Carolina Roselli, Emelia J. Benjamin, Shamsudheen K. Vellarikkal, Rajat M. Gupta, Christian M. Stegmann, Dejan Juric, James R. Stone, Ramachandran S. Vasan, Jennifer E. Ho, Udo Hoffmann, Steven A. Lubitz, Anthony A. Philippakis, Mark E. Lindsay, Patrick T. Ellinor
Summary: Genome-wide association analyses identified variants associated with thoracic aortic diameter and polygenic score for ascending aortic diameter was correlated with a diagnosis of thoracic aortic aneurysm. Enlargement or aneurysm of the aorta predisposes to dissection, and a deep learning model along with genome-wide association studies successfully identified loci associated with ascending and descending thoracic aortic diameter, highlighting the potential for rapidly defining quantitative traits with deep learning in biomedical images.
Article
Biochemistry & Molecular Biology
Arpita Ghosh, Satya Prakash Pandey, Asgar Hussain Ansari, Jennifer Seematti Sundar, Praveen Singh, Yasmeen Khan, Mary Krishna Ekka, Debojyoti Chakraborty, Souvik Maiti
Summary: The study identified three conserved and stable rG4 structures in the 3' region of MALAT1 that regulate alternative splicing, and demonstrated the importance of rG4s in the localization of NCL and NPM to nuclear speckles. Disruption of rG4 in MALAT1 resulted in altered pre-mRNA splicing of endogenous genes, similar to NCL knockdown.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Soundhar Ramasamy, Shubham Mishra, Surbhi Sharma, Sangamithirai Subramanian Parimalam, Thangavel Vaijayanthi, Yoto Fujita, Basavaraj Kovi, Hiroshi Sugiyama, Ganesh N. Pandian
Summary: This study introduces an internal comparison strategy, IndoC, for detecting RNA modifications, which can analyze modification sites without the need for matched knockout controls. The results show that by comparing the features of modification sites on different sequences, it is possible to effectively distinguish between SNPs and true modifications. The purpose of this research is to address the limitations of current RNA modification detection methods.
Meeting Abstract
Cardiac & Cardiovascular Systems
Rakhshinda Rehman, Shamsudheen Karuthedath Vellarikkal, Paul B. Dieffenbach, Hilaire C. Lam, Charilaos Filippakis, Laura E. Fredenburgh
Meeting Abstract
Cardiac & Cardiovascular Systems
Shamsudheen Vellarikkal, Deepak Atri, Vivian Lee-Kim, Ankith Reddy, Tsuyoshi Kaneko, Hari R. Mallidi, Rakhshinda Rehman, Prem S. Shekar, Laura E. Fredenburgh, Oscar Sias-Garcia, J. Daniel D. Muehlschlegel, Rajat Gupta
Meeting Abstract
Cardiac & Cardiovascular Systems
Vivian Lee-Kim, Deepak Atri, Shamsudheen Vellarikkal, Pierre Paradis, Ernesto L. Schiffrin, Rajat Gupta
Letter
Multidisciplinary Sciences
Poorti Kathpalia, Arpita Konar, Beena Pillai
Article
Chemistry, Multidisciplinary
Love Panchariya, Wajahat Ali Khan, Shobhan Kuila, Kirtishila Sonkar, Sibasis Sahoo, Archita Ghoshal, Ankit Kumar, Dileep Kumar Verma, Abdul Hasan, Mohd Azeem Khan, Niyati Jain, Amit Kumar Mohapatra, Shubhashis Das, Jitendra K. Thakur, Souvik Maiti, Ranjan Kumar Nanda, Rajkumar Halder, Sujatha Sunil, Arulandu Arockiasamy
Summary: Research shows that zinc can inhibit the SARS-CoV-2 main protease and viral replication, increasing antiviral potency. The crystal structure of the complex formed by zinc and Mpro provides important structural basis for further study of viral replication.
CHEMICAL COMMUNICATIONS
(2021)
Article
Evolutionary Biology
Aniket Bhattacharya, Vineet Jha, Khushboo Singhal, Mahar Fatima, Dayanidhi Singh, Gaura Chaturvedi, Dhwani Dholakia, Rintu Kutum, Rajesh Pandey, Trygve E. Bakken, Pankaj Seth, Beena Pillai, Mitali Mukerji
Summary: Alu repeats play a role in phylogenetic novelties in conserved regulatory networks in primates. An exonized Alu transcript isoform, CYP20A1_Alu-LT, with 23 Alus in its 3'UTR has been characterized. This transcript is widely expressed and potentially acts as a multi-miRNA sponge with cytosolic localization.
GENOME BIOLOGY AND EVOLUTION
(2021)