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Article ; Online: Thermomechanical And Morphological Properties of Loligo Vulgaris Squid Sucker Ring Teeth.

Helft, Margot / Zhang, Zenghao / Kinane, Cecelia / Black, Noah / Pena-Francesch, Abdon

2024

Abstract: Climate change is accelerating the increase of temperatures across the planet and resulting in the warming of oceans. Ocean warming threatens the survival of many aquatic species, including squids, and has introduced physiological, behavioral, and ... ...

Abstract	Climate change is accelerating the increase of temperatures across the planet and resulting in the warming of oceans. Ocean warming threatens the survival of many aquatic species, including squids, and has introduced physiological, behavioral, and developmental changes, as well as physical changes in their biological materials composition, structure, and properties. Here, we characterize and analyze how the structure, morphology, and mechanical properties of European common squid Loligo vulgaris sucker ring teeth (SRT) are affected by temperature. SRT are predatory teethed structures located inside the suction cups of squids, which are used to capture prey, and are composed of semicrystalline structural proteins that give rise to high mechanical strength (GPa-range modulus). We observe here that this biological material reversibly softens with temperature, undergoing a glass transition at ∼35°C, to a MPa-range modulus. We analyze the SRT protein nanostructures as a function of temperature, as well as microscale and macroscale morphological changes, to understand their impact in the material properties. The results suggest that even small deviations from their habitat temperatures can result in significant softening of the material (up to 40% in modulus loss). Temperature changes following recent global climate trends and predictions might affect environmental adaptation in squid species, and pose emerging survival challenges to adapt to increasing ocean temperatures.
Language	English
Publishing date	2024-03-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2159110-6
ISSN	1557-7023 ; 1540-7063
ISSN (online)	1557-7023
ISSN	1540-7063
DOI	10.1093/icb/icae005
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Article ; Online: Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression.

Peña-Cearra, Ainize / Song, Deguang / Castelo, Janire / Palacios, Ainhoa / Lavín, Jose Luis / Azkargorta, Mikel / Elortza, Felix / Fuertes, Miguel / Pascual-Itoiz, Miguel Angel / Barriales, Diego / Martín-Ruiz, Itziar / Fullaondo, Asier / Aransay, Ana M / Rodríguez, Hector / Palm, Noah W / Anguita, Juan / Abecia, Leticia

NPJ biofilms and microbiomes

2023 Volume 9, Issue 1, Page(s) 74

Abstract: Recent evidence demonstrates potential links between mitochondrial dysfunction and inflammatory bowel diseases (IBD). In addition, bidirectional interactions between the intestinal microbiota and host mitochondria may modulate intestinal inflammation. We ...

Abstract	Recent evidence demonstrates potential links between mitochondrial dysfunction and inflammatory bowel diseases (IBD). In addition, bidirectional interactions between the intestinal microbiota and host mitochondria may modulate intestinal inflammation. We observed previously that mice deficient in the mitochondrial protein MCJ (Methylation-controlled J protein) exhibit increased susceptibility to DSS colitis. However, it is unclear whether this phenotype is primarily driven by MCJ
MeSH term(s)	Humans ; Animals ; Mice ; Colitis, Ulcerative/genetics ; Colitis, Ulcerative/microbiology ; RNA, Ribosomal, 16S/genetics ; Colitis ; Inflammatory Bowel Diseases ; Immunoglobulin A ; Mitochondria/genetics ; Disease Progression
Chemical Substances	RNA, Ribosomal, 16S ; Immunoglobulin A
Language	English
Publishing date	2023-10-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2817021-0
ISSN	2055-5008 ; 2055-5008
ISSN (online)	2055-5008
ISSN	2055-5008
DOI	10.1038/s41522-023-00443-y
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Article ; Online: Diagnostic and Management Strategies for Patients with Chronic Prostatitis and Chronic Pelvic Pain Syndrome.

Pena, Vanessa N / Engel, Noah / Gabrielson, Andrew T / Rabinowitz, Matthew J / Herati, Amin S

Drugs & aging

2021 Volume 38, Issue 10, Page(s) 845–886

Abstract: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a common and often heterogenous condition that can have severe consequences on patient quality of life. In this review, we describe the pathophysiology, diagnostic work-up, and treatment of ... ...

Abstract	Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a common and often heterogenous condition that can have severe consequences on patient quality of life. In this review, we describe the pathophysiology, diagnostic work-up, and treatment of patients with CP/CPPS incorporating the most recent literature. Studies have demonstrated that CP/CPPS involves a complex pathophysiology, including infectious, immunologic, neurologic, endocrinologic, and psychologic etiologies, with frequent intersections between the different entities. Despite robust research assessing a variety of therapeutics targeting these etiologies, clinical trials have failed to identify an empiric treatment strategy applicable specifically to older adult male patients with CP/CPPS. As such, it can be challenging to manage older male patients with this condition. The advent of clinical phenotyping of patients with CP/CPPS has led to advances in tailored management strategies. Monomodal therapy has been largely unsuccessful because of the unclear and complex etiology of CPPS. As a result, CP/CPPS therapy has transitioned to a multimodal approach, including both pharmacologic and non-pharmacologic therapies. The best studied pharmacologic therapies include antibiotics, alpha-blockers, anti-inflammatory and immunomodulatory agents, phytotherapies, phosphodiesterase inhibitors, hormonal agents, neuromodulatory agents, and antidepressants. The best studied non-pharmacological therapies include pelvic floor physical therapy, myofascial trigger point release, acupuncture and electroacupuncture, psychological support and biofeedback, and electrocorporeal shockwave therapy and local thermotherapy.
MeSH term(s)	Aged ; Chronic Disease ; Chronic Pain ; Humans ; Male ; Pelvic Pain/diagnosis ; Pelvic Pain/etiology ; Pelvic Pain/therapy ; Prostatitis/diagnosis ; Prostatitis/therapy ; Quality of Life
Language	English
Publishing date	2021-09-29
Publishing country	New Zealand
Document type	Journal Article ; Review
ZDB-ID	1075770-3
ISSN	1179-1969 ; 1170-229X
ISSN (online)	1179-1969
ISSN	1170-229X
DOI	10.1007/s40266-021-00890-2
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Zs.A 3481: Show issues

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Article ; Online: Engineered mischarged transfer RNAs for correcting pathogenic missense mutations.

Hou, Yichen / Zhang, Wen / McGilvray, Philip T / Sobczyk, Marek / Wang, Tianxin / Weng, Shao Huan Samuel / Huff, Allen / Huang, Sihao / Pena, Noah / Katanski, Christopher D / Pan, Tao

Molecular therapy : the journal of the American Society of Gene Therapy

2023 Volume 32, Issue 2, Page(s) 352–371

Abstract: Missense mutations account for approximately 50% of pathogenic mutations in human genetic diseases, and most lack effective treatments. Gene therapies, gene editing, and RNA therapies, including transfer RNA (tRNA) modalities, are common strategies for ... ...

Abstract	Missense mutations account for approximately 50% of pathogenic mutations in human genetic diseases, and most lack effective treatments. Gene therapies, gene editing, and RNA therapies, including transfer RNA (tRNA) modalities, are common strategies for genetic disease treatments. However, reported tRNA therapies are for nonsense mutations only. It has not been explored how tRNAs can be engineered to correct missense mutations. Here, we describe missense-correcting tRNAs (mc-tRNAs) as a potential therapeutic for correcting pathogenic missense mutations. Mc-tRNAs are engineered tRNAs charged with one amino acid, but read codons of another in translation. We first developed a series of fluorescent protein-based reporters that indicate the successful correction of missense mutations via restoration of fluorescence. We engineered mc-tRNAs that effectively corrected serine and arginine missense mutations in the reporters and confirmed the amino acid substitution by mass spectrometry and mc-tRNA expression by sequencing. We examined the transcriptome response to mc-tRNA expression and found some mc-tRNAs induced minimum transcriptomic changes. Furthermore, we applied an mc-tRNA to rescue a pathogenic CAPN3 Arg-to-Gln mutant involved in LGMD2A. These results establish a versatile pipeline for mc-tRNA engineering and demonstrate the potential of mc-tRNA as an alternative therapeutic platform for the treatment of genetic disorders.
MeSH term(s)	Humans ; Mutation, Missense ; RNA, Transfer/genetics ; Codon ; Mutation ; Amino Acids
Chemical Substances	RNA, Transfer (9014-25-9) ; Codon ; Amino Acids
Language	English
Publishing date	2023-12-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2023.12.014
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Zs.A 5640: Show issues

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Article: Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations.

Peña, Noah / Zhang, Wen / Watkins, Christopher / Halucha, Mateusz / Alshammary, Hala / Hernandez, Matthew M / Liu, Wen-Chun / Albrecht, Randy A / Garcia-Sastre, Adolfo / Simon, Viviana / Katanski, Christopher / Pan, Tao

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 768356

Abstract: Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at ... ...

Abstract	Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.
Language	English
Publishing date	2022-02-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.768356
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Article ; Online: Pediatric Pulmonology year in review 2018: Asthma, physiology/pulmonary function testing, and respiratory infections.

Loughlin, Ceila E / Muston, Heather N / Pena, Michael A / Ren, Clement L / Yilmaz, Ozge / Noah, Terry L

Pediatric pulmonology

2019 Volume 54, Issue 10, Page(s) 1508–1515

Abstract: Pediatric Pulmonology publishes original research, reviews, and case reports related to a wide range of children's respiratory disorders. In our "Year in Review" series, we summarize publications in our major topic areas from 2018, in the context of ... ...

Abstract	Pediatric Pulmonology publishes original research, reviews, and case reports related to a wide range of children's respiratory disorders. In our "Year in Review" series, we summarize publications in our major topic areas from 2018, in the context of selected literature in these areas from other journals relevant to our discipline. This review covers selected articles on asthma, physiology/lung function testing, and respiratory infections.
MeSH term(s)	Asthma/drug therapy ; Asthma/epidemiology ; Asthma/physiopathology ; Child ; Humans ; Pulmonary Medicine ; Respiratory Function Tests ; Respiratory Tract Infections/drug therapy ; Respiratory Tract Infections/epidemiology
Language	English
Publishing date	2019-06-25
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	632784-9
ISSN	1099-0496 ; 8755-6863
ISSN (online)	1099-0496
ISSN	8755-6863
DOI	10.1002/ppul.24420
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Zs.A 2143: Show issues

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Article ; Online: Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression

Ainize Peña-Cearra / Deguang Song / Janire Castelo / Ainhoa Palacios / Jose Luis Lavín / Mikel Azkargorta / Felix Elortza / Miguel Fuertes / Miguel Angel Pascual-Itoiz / Diego Barriales / Itziar Martín-Ruiz / Asier Fullaondo / Ana M. Aransay / Hector Rodríguez / Noah W. Palm / Juan Anguita / Leticia Abecia

npj Biofilms and Microbiomes, Vol 9, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract Recent evidence demonstrates potential links between mitochondrial dysfunction and inflammatory bowel diseases (IBD). In addition, bidirectional interactions between the intestinal microbiota and host mitochondria may modulate intestinal ... ...

Abstract	Abstract Recent evidence demonstrates potential links between mitochondrial dysfunction and inflammatory bowel diseases (IBD). In addition, bidirectional interactions between the intestinal microbiota and host mitochondria may modulate intestinal inflammation. We observed previously that mice deficient in the mitochondrial protein MCJ (Methylation-controlled J protein) exhibit increased susceptibility to DSS colitis. However, it is unclear whether this phenotype is primarily driven by MCJ−/− associated gut microbiota dysbiosis or by direct effects of MCJ-deficiency. Here, we demonstrate that fecal microbiota transplantation (FMT) from MCJ-deficient into germ-free mice was sufficient to confer increased susceptibility to colitis. Therefore, an FMT experiment by cohousing was designed to alter MCJ-deficient microbiota. The phenotype resulting from complex I deficiency was reverted by FMT. In addition, we determined the protein expression pathways impacted by MCJ deficiency, providing insight into the pathophysiology of IBD. Further, we used magnetic activated cell sorting (MACS) and 16S rRNA gene sequencing to characterize taxa-specific coating of the intestinal microbiota with Immunoglobulin A (IgA-SEQ) in MCJ-deficient mice. We show that high IgA coating of fecal bacteria observed in MCJ-deficient mice play a potential role in disease progression. This study allowed us to identify potential microbial signatures in feces associated with complex I deficiency and disease progression. This research highlights the importance of finding microbial biomarkers, which might serve as predictors, permitting the stratification of ulcerative colitis (UC) patients into distinct clinical entities of the UC spectrum.
Keywords	Microbial ecology ; QR100-130
Subject code	570
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations

Noah Peña / Wen Zhang / Christopher Watkins / Mateusz Halucha / Hala Alshammary / Matthew M. Hernandez / Wen-Chun Liu / Randy A. Albrecht / Adolfo Garcia-Sastre / Viviana Simon / Christopher Katanski / Tao Pan

Frontiers in Cell and Developmental Biology, Vol

2022 Volume 10

Abstract	Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.
Keywords	SARS-CoV-2 ; tRNA ; modification ; SRP RNA ; packaging ; Biology (General) ; QH301-705.5
Subject code	630
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Intranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract.

Mao, Tianyang / Kim, Jooyoung / Peña-Hernández, Mario A / Valle, Gabrielee / Moriyama, Miyu / Luyten, Sophia / Ott, Isabel M / Gomez-Calvo, Maria Luisa / Gehlhausen, Jeff R / Baker, Emily / Israelow, Benjamin / Slade, Martin / Sharma, Lokesh / Liu, Wei / Ryu, Changwan / Korde, Asawari / Lee, Chris J / Silva Monteiro, Valter / Lucas, Carolina /

Dong, Huiping / Yang, Yi / Gopinath, Smita / Wilen, Craig B / Palm, Noah / Dela Cruz, Charles S / Iwasaki, Akiko

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 18, Page(s) e2319566121

Abstract: Respiratory virus infections in humans cause a broad-spectrum of diseases that result in substantial morbidity and mortality annually worldwide. To reduce the global burden of respiratory viral diseases, preventative and therapeutic interventions that ... ...

Abstract	Respiratory virus infections in humans cause a broad-spectrum of diseases that result in substantial morbidity and mortality annually worldwide. To reduce the global burden of respiratory viral diseases, preventative and therapeutic interventions that are accessible and effective are urgently needed, especially in countries that are disproportionately affected. Repurposing generic medicine has the potential to bring new treatments for infectious diseases to patients efficiently and equitably. In this study, we found that intranasal delivery of neomycin, a generic aminoglycoside antibiotic, induces the expression of interferon-stimulated genes (ISGs) in the nasal mucosa that is independent of the commensal microbiota. Prophylactic or therapeutic administration of neomycin provided significant protection against upper respiratory infection and lethal disease in a mouse model of COVID-19. Furthermore, neomycin treatment protected Mx1 congenic mice from upper and lower respiratory infections with a highly virulent strain of influenza A virus. In Syrian hamsters, neomycin treatment potently mitigated contact transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In healthy humans, intranasal application of neomycin-containing Neosporin ointment was well tolerated and effective at inducing ISG expression in the nose in a subset of participants. These findings suggest that neomycin has the potential to be harnessed as a host-directed antiviral strategy for the prevention and treatment of respiratory viral infections.
MeSH term(s)	Animals ; Neomycin/pharmacology ; Neomycin/administration & dosage ; Administration, Intranasal ; Mice ; Humans ; Antiviral Agents/pharmacology ; Antiviral Agents/administration & dosage ; SARS-CoV-2/immunology ; SARS-CoV-2/drug effects ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19/virology ; Respiratory Tract Infections/immunology ; Respiratory Tract Infections/drug therapy ; Respiratory Tract Infections/virology ; Respiratory Tract Infections/prevention & control ; Nasal Mucosa/immunology ; Nasal Mucosa/virology ; Nasal Mucosa/drug effects ; Disease Models, Animal ; COVID-19 Drug Treatment ; Mesocricetus ; Female ; Influenza A virus/drug effects ; Influenza A virus/immunology
Chemical Substances	Neomycin (I16QD7X297) ; Antiviral Agents
Language	English
Publishing date	2024-04-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2319566121
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Zs.A 1148: Show issues

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Article ; Online: Characterization and structure determination of prolyl-tRNA synthetase from Pseudomonas aeruginosa and development as a screening platform.

Pena, Noah / Dranow, David M / Hu, Yanmei / Escamilla, Yaritza / Bullard, James M

Protein science : a publication of the Protein Society

2019 Volume 28, Issue 4, Page(s) 727–737

Abstract: Pseudomonas aeruginosa is an opportunistic multi-drug resistant pathogen implicated as a causative agent in nosocomial and community acquired bacterial infections. The gene encoding prolyl-tRNA synthetase (ProRS) from P. aeruginosa was overexpressed in ... ...

Abstract	Pseudomonas aeruginosa is an opportunistic multi-drug resistant pathogen implicated as a causative agent in nosocomial and community acquired bacterial infections. The gene encoding prolyl-tRNA synthetase (ProRS) from P. aeruginosa was overexpressed in Escherichia coli and the resulting protein was characterized. ProRS was kinetically evaluated and the K
MeSH term(s)	Amino Acyl-tRNA Synthetases/antagonists & inhibitors ; Amino Acyl-tRNA Synthetases/chemistry ; Amino Acyl-tRNA Synthetases/metabolism ; Bacterial Proteins/antagonists & inhibitors ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Crystallography, X-Ray ; Humans ; Microbial Sensitivity Tests ; Models, Molecular ; Protein Conformation ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/chemistry ; Pseudomonas aeruginosa/metabolism
Chemical Substances	Bacterial Proteins ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-) ; prolyl T RNA synthetase (EC 6.1.1.15)
Language	English
Publishing date	2019-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3579
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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