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Biochemistry, Biophysics, and Structural Biology Commons™
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Articles 31 - 60 of 1105
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Development Of Self-Assembled Polymeric Polyplexes For Microrna Delivery: Toward Treatment Of Alcohol-Associated Liver Disease, Marjina Akter Kalpana
Development Of Self-Assembled Polymeric Polyplexes For Microrna Delivery: Toward Treatment Of Alcohol-Associated Liver Disease, Marjina Akter Kalpana
Theses & Dissertations
Self-assembled polymeric polyplexes have the potential to serve as an RNA interference (RNAi) delivery platform for the combined inhibition of CXCR4 and miR-155 in the treatment of alcohol-associated liver disease (AALD). A central challenge in RNA delivery is balancing the extracellular stability of polyplexes, cellular uptake, and intracellular release of RNA cargo. We developed polymeric polyplexes using the CXCR4-antagonist polymer PAMD, designed to target CXCR4 on activated hepatic stellate cells (HSCs) and deliver therapeutic miRNA to activated Kupffer cells (KCs) in fibrotic liver. We improved the polyplexes by cholesterol modification of PAMD and by PEGylation of PAMD-Ch. The cholesterol modification …
Context Dependent Regulation Of Dicer Function During Oocyte-To-Embryo Transition, Nick A. Newkirk
Context Dependent Regulation Of Dicer Function During Oocyte-To-Embryo Transition, Nick A. Newkirk
Dissertations and Theses (Open Access)
Over two decades ago, Dicer was discovered as the primary enzyme responsible for the generation of small RNAs known as the microRNAs (miRNAs) and short interfering RNAs (siRNAs). Spatiotemporal regulation of Dicer-dependent small-RNA biogenesis affects many aspects of biology, including aging, disease progression, fertility, and cancer. Interestingly, a distinct population of Dicer-dependent small RNAs, known as the endogenous siRNAs (endo-siRNAs), are uniquely abundant in the germ cells and gametes, and are critical for normal fertility. Despite their function regulating new life, the mechanisms controlling their biogenesis and subsequent germ cell functions remain poorly defined. Work to parse these mechanisms in …
Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte
Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte
Faculty Publications
Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD …
Losing Focus In The Age Of Tik Tok: Clinical Evidence For Policy Action On Social Media Use, Megan Conefrey, Robert Griffin
Losing Focus In The Age Of Tik Tok: Clinical Evidence For Policy Action On Social Media Use, Megan Conefrey, Robert Griffin
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Tracking Livestock Heart Rate & Location Using Long-Range Radio Networks. An Immediate Solution For Farms Without Reliable Wi-Fi, Dermott Harkin, Martin Bradley
Tracking Livestock Heart Rate & Location Using Long-Range Radio Networks. An Immediate Solution For Farms Without Reliable Wi-Fi, Dermott Harkin, Martin Bradley
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Voices Matter: Tackling Accentism In Ireland. A Study Addressing Accent-Based Discrimination Awareness In Education, Sadhbh Reddington, Victoria Graham, Holly Jordan, Mairead Moriarty
Voices Matter: Tackling Accentism In Ireland. A Study Addressing Accent-Based Discrimination Awareness In Education, Sadhbh Reddington, Victoria Graham, Holly Jordan, Mairead Moriarty
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Income Inequality And Attitudes Towards Immigrants – How Increased Inequality Drives Division, Niamh Anderson, Vincent O'Sullivan
Income Inequality And Attitudes Towards Immigrants – How Increased Inequality Drives Division, Niamh Anderson, Vincent O'Sullivan
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Supporting Single Parents: How Loneliness And Self-Stigma Can Impact Single Parents And Their Quality Of Life, Alana Powell, David Mothersill
Supporting Single Parents: How Loneliness And Self-Stigma Can Impact Single Parents And Their Quality Of Life, Alana Powell, David Mothersill
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Unheard And Underserved: Exploring Support For Male Victims Of Partner Abuse, Michael Keenan, Colletta Dalikeni
Unheard And Underserved: Exploring Support For Male Victims Of Partner Abuse, Michael Keenan, Colletta Dalikeni
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Ireland Blossoms Through Multiculturalism - Designing For Community Connection, Julia Kuczera, Shirley Casey, Hilary Kenna
Ireland Blossoms Through Multiculturalism - Designing For Community Connection, Julia Kuczera, Shirley Casey, Hilary Kenna
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Assessing Demand And Simulating Feasibility For Commuter Rail In Lagging Regional Areas. Case Study: Sligo, Holly Briere-Edney, Brian Mccann
Assessing Demand And Simulating Feasibility For Commuter Rail In Lagging Regional Areas. Case Study: Sligo, Holly Briere-Edney, Brian Mccann
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Ireland's Infrastructure: From Delays To Deliveries!, Conor Barnett, Keren Goodman
Ireland's Infrastructure: From Delays To Deliveries!, Conor Barnett, Keren Goodman
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
A Fast-Track Way To Identify Derelict And Vacant Homes For Refurbishment, Dylan O'Donnell, Enda Dunican
A Fast-Track Way To Identify Derelict And Vacant Homes For Refurbishment, Dylan O'Donnell, Enda Dunican
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Making Buildings Smarter And More Sustainable With Ai, Anthony Lowe, Martin Klepal
Making Buildings Smarter And More Sustainable With Ai, Anthony Lowe, Martin Klepal
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Solving The Bed Crisis - Predicting 30-Day Hospital Readmissions In Elderly Patients Using Ai, Mark Mckeon, Thoa Pham
Solving The Bed Crisis - Predicting 30-Day Hospital Readmissions In Elderly Patients Using Ai, Mark Mckeon, Thoa Pham
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
The Impact Of Chronic Pain On Income And Employment, Jordan Vaarsi, Amber Jolly, Karim S. Ladha
The Impact Of Chronic Pain On Income And Employment, Jordan Vaarsi, Amber Jolly, Karim S. Ladha
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Living The Life: A Community Approach To Men’S Health And Longevity, Paul Anders, Aisling Mcgrath
Living The Life: A Community Approach To Men’S Health And Longevity, Paul Anders, Aisling Mcgrath
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
When Care Can’T Move Forward – The Human And Social Cost Of Freezing Of Gait In Parkinson’S Disease, Padraig Cronin, Lucy M. Collins, Aideen M. Sullivan
When Care Can’T Move Forward – The Human And Social Cost Of Freezing Of Gait In Parkinson’S Disease, Padraig Cronin, Lucy M. Collins, Aideen M. Sullivan
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Sticky Genes: Can Repeated Dna Sequences Trigger Motor Neurone Disease?, Guste Venslovaite, Russell Mclaughlin
Sticky Genes: Can Repeated Dna Sequences Trigger Motor Neurone Disease?, Guste Venslovaite, Russell Mclaughlin
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Life Under Pressure: How Doubling The Genome Affects The Memory Of Environmental Stress In Worms, Aisling Phelan, Emma Bazzani, Clément Verdier, Laetitia Chauve, Aoife Mclysaght
Life Under Pressure: How Doubling The Genome Affects The Memory Of Environmental Stress In Worms, Aisling Phelan, Emma Bazzani, Clément Verdier, Laetitia Chauve, Aoife Mclysaght
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Pause For Policy - The Cognitive Cost Of Cannabis Use In Adolescence, Michael O'Connor, Linda Kelly, Emma O'Hora, Claire O'Doherty, Ciaran Brown, An Hsu, Sahar Riaz, Frank Crosson, Darren Roddy, Mary Cannon
Pause For Policy - The Cognitive Cost Of Cannabis Use In Adolescence, Michael O'Connor, Linda Kelly, Emma O'Hora, Claire O'Doherty, Ciaran Brown, An Hsu, Sahar Riaz, Frank Crosson, Darren Roddy, Mary Cannon
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
The Future Of Metabolic Health: A Needle-Free Alternative For Blood Sugar Monitoring, Conor Cleary, Martin Bradley, Christopher Crosson, John Wade
The Future Of Metabolic Health: A Needle-Free Alternative For Blood Sugar Monitoring, Conor Cleary, Martin Bradley, Christopher Crosson, John Wade
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
From Recognition To Action: Advancing Nutrition Care In Irish Healthcare, Aoife Gillane, Sarah Donovan, Lisa Ryan
From Recognition To Action: Advancing Nutrition Care In Irish Healthcare, Aoife Gillane, Sarah Donovan, Lisa Ryan
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Transforming Plastic For A Sustainable Planet: Next-Generation Materials That Biodegrade Naturally, Kristof Racz, Clement Higginbotham
Transforming Plastic For A Sustainable Planet: Next-Generation Materials That Biodegrade Naturally, Kristof Racz, Clement Higginbotham
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
The Dock Beetle: Reducing Costs And Pesticides In Irish Agriculture, Bianca Araujo, Daniel P. Fitzpatrick
The Dock Beetle: Reducing Costs And Pesticides In Irish Agriculture, Bianca Araujo, Daniel P. Fitzpatrick
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Implementation Of The Nature Restoration Law In The Eu - Pros, Cons And Impossibilities, Emma Mcdonagh, Liam Sunner
Implementation Of The Nature Restoration Law In The Eu - Pros, Cons And Impossibilities, Emma Mcdonagh, Liam Sunner
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Ireland’S Energy Transition: Unlocking The Potential Of Offshore Renewables, Caoimhe O'Hare, Madjid Karimirad, Gautam Baruah
Ireland’S Energy Transition: Unlocking The Potential Of Offshore Renewables, Caoimhe O'Hare, Madjid Karimirad, Gautam Baruah
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
From Conflict To Connection: Educators Leading The Shift Towards Restorative Practices (Rp) In Deis Primary Schools, Ellen Slattery, Clara Hoyne
From Conflict To Connection: Educators Leading The Shift Towards Restorative Practices (Rp) In Deis Primary Schools, Ellen Slattery, Clara Hoyne
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Bridging The Gap From Preschool To Primary: From Policy To Practice, Aimee O'Connor, Cóilín O’ Braonáin
Bridging The Gap From Preschool To Primary: From Policy To Practice, Aimee O'Connor, Cóilín O’ Braonáin
SURE Journal: Science Undergraduate Research Experience Journal
No abstract provided.
Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy
Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy
Makara Journal of Science
Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …