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Authors: Yodi Soebadi, Marko Bakula, Lukman Hakim, Robert Puers, Dirk De Ridder
Summary: This protocol provides information for the invasive urodynamic measurement of bladder pressure, by urethral catheter as well as wireless device (bladder pill).
Proper citation: Yodi Soebadi, Marko Bakula, Lukman Hakim, Robert Puers, Dirk De Ridder 2019. KU Leuven Exp Urology - Urodynamics in Female MInipigs. protocols.io dx.doi.org/10.17504/protocols.io.3eggjbw Copy
Authors: Niwanda Yogiswara, Yusuf Azmi, Farapti farapti, Yufi Aulia Azmi
Summary: Several studies have demonstrated that vitamin D deficiency was associated with an increased incidence of infectious disease, including urinary tract diseases. The present systematic review aims to investigate whether vitamin D deficiency is associated with an increased incidence of urinary tract infections (UTI) and whether supplementation could reduce the risk of UTI. This systematic review and meta-analysis will be carried out in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). The search will be performed using multiple databases, including MEDLINE, CENTRAL, ClinicalTrials.gov. We will screen observational studies and interventional studies with our inclusion criteria and assessed the quality with the Newcastle-Ottawa scale and Cochrane Risk of Bias tool. Currently we do not anticipate any problems with the implementation of the proposed protocol. The results of this study will explain the effects of vitamin D deficiency and the prevention role of vitamin D supplements on UTI.
Proper citation: Niwanda Yogiswara, Yusuf Azmi, Farapti farapti, Yufi Aulia Azmi 2020. Systematic review and meta-analysis protocol examining the effect of vitamin D status and supplementation on urinary tract infection. protocols.io dx.doi.org/10.17504/protocols.io.be2tjgen Copy
Authors: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia
Group: GigaScience Press, BGI
Summary: Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. Potential links between female urine and reproductive tract microbial communities is currently not clear. Here, we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated, and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.
Proper citation: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia 2020. Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota.". protocols.io dx.doi.org/10.17504/protocols.io.bpyumpww Copy
Authors: Janet Keast, Peregrine Osborne
Group: SPARC
Summary: This collection describes the procedures required to label, visualise, characterise and quantify neurons that innervate the lower urinary tract tissues of adult male and female Sprague-Dawley rats. This collection includes protocols for:STAGE 1: Surgery to micro-inject fluorescent retrograde tracer dyes into one or more sites within the lower urinary tractSTAGE 2: Intracardiac perfusion with fixative to preserve neural tissues of interestSTAGE 3: Fluorescence immunohistochemistry of ganglion cryosections.
Proper citation: Janet Keast, Peregrine Osborne 2019. Immunohistochemical classification of sensory and autonomic neurons projecting to the lower urinary tract in rats [keast-001]. protocols.io dx.doi.org/10.17504/protocols.io.w3gfgjw Copy
Authors: Firuoz Danashgeri
Group: Diabetic Complications Consortium
Summary: This protocol describes the proper procedure for harvesting bladders from rats or mice for use by the DiaComp Uropathy group.Diabetic Complication:
Proper citation: Firuoz Danashgeri 2019. Removal and Preservation of the Urinary Bladder. protocols.io dx.doi.org/10.17504/protocols.io.8fahtie Copy
Authors: Janet Keast, Peregrine Osborne
Group: SPARC
Summary: This protocol is used to visualise sensory and autonomic neurons innervating the bladder body (dome), bladder trigone or proximal urethra in an experimental adult male or female rat. The protocol is performed under anesthesia and should incorporate all local requirements for standards of animal experimentation, including methods of anesthesia, surgical environment, and post-operative monitoring and care.
Proper citation: Janet Keast, Peregrine Osborne 2019. Use of tracer dyes to label neural projections to lower urinary tract organs [keast-001-stage01]. protocols.io dx.doi.org/10.17504/protocols.io.w3dfgi6 Copy
Authors: Janet Keast, Peregrine Osborne
Group: SPARC
Summary: This protocol is used to visualise sensory and autonomic neurons innervating the bladder body (dome), bladder trigone or proximal urethra in an experimental adult male or female rat. The protocol is performed under anesthesia and should incorporate all local requirements for standards of animal experimentation, including methods of anesthesia, surgical environment, and post-operative monitoring and care.
Proper citation: Janet Keast, Peregrine Osborne 2020. Use of tracer dyes to label neural projections to lower urinary tract organs. protocols.io dx.doi.org/10.17504/protocols.io.w2xfgfn Copy
Authors: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia
Group: GigaScience Press, BGI
Summary: Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. Potential links between female urine and reproductive tract microbial communities is currently not clear. Here, we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated, and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.
Proper citation: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia 2020. Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota.". protocols.io dx.doi.org/10.17504/protocols.io.bp3wmqpe Copy
Authors: Hsiao-Yu Yang
Summary: Prediction of pneumoconiosis by serum and urinary biomarkers in workers exposed to asbestos-contaminated mineralsPLOS One
Proper citation: Hsiao-Yu Yang 2019. Prediction of pneumoconiosis by serum and urinary biomarkers in workers exposed to asbestos-contaminated minerals. protocols.io dx.doi.org/10.17504/protocols.io.x8dfrs6 Copy
Authors: Lieven Van Meulebroek, Jella Wauters, Beata Pomian, Julie Vanden Bussche, Philippe Delahaut, Eric Fichant, Lynn Vanhaecke
Group: Metabolomics Protocols & Workflows
Summary: This protocol describes the untargeted polar analysis of urine samples from cows and calves, with special emphasis on the coverage of thyreostats. Extraction started with 3 mL urine and was in essence based on liquid-liquid extraction with ethyl acetate. Analysis of extracts was achieved by ultra-high performance liquid chromatography (UHPLC) using a Waters Acquity HSS T3 column (1.8 μm, 2.1 x 100 mm), HESI-II ionization, and Q-Exactive Orbitrap mass spectrometry.
Proper citation: Lieven Van Meulebroek, Jella Wauters, Beata Pomian, Julie Vanden Bussche, Philippe Delahaut, Eric Fichant, Lynn Vanhaecke 2018. Protocol for polar metabolomics (with emphasis on thyreostats) of urinary samples from cattle. protocols.io dx.doi.org/10.17504/protocols.io.ngmdbu6 Copy
Authors: Liam Broughton, Nicolas F. Villarino
Proper citation: Liam Broughton, Nicolas F. Villarino 2019. GC-MS protocol for the manuscript, "Urinary chemical fingerprint left behind by repeated NSAID administration: Discovery of putative biomarkers using artificial intelligence".. protocols.io dx.doi.org/10.17504/protocols.io.baqvidw6 Copy
Authors: Blue Lake, Elizabeth Duong, Dinh Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This document provides an overview of the protocols used by the Human Kidney, Urinary Tract, and Lung Mapping Center (KULMAP) for generation of spatially resolved mulitomic cell type organ maps within HuBMAP. This involves sequencing of the transcriptomes and epigenomes of dissociated single cells in a massively parallel manner, which will then inform on a highly multiplexed RNA in situ imaging method (DART-FISH) for spatial mapping of hundreds of molecular targets in the tissue sections, at a subcellular resolution. These spatial molecular maps will serve as scaffolds for computational registration of cell types and the associated transcriptome/chromatin maps to the tissue space.
Proper citation: Blue Lake, Elizabeth Duong, Dinh Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California 2020. Human Kidney, Urinary Tract, and Lung Cell Type Mapping Pipeline for the Human Biomolecular Atlas Program (HuBMAP). protocols.io dx.doi.org/10.17504/protocols.io.bj9wkr7e Copy
Authors: Yuan Hsu, Juraci A Cesar
Proper citation: Yuan Hsu, Juraci A Cesar 2020. Perinatal 2016 Rio Grande - Urinary Incontinence. protocols.io dx.doi.org/10.17504/protocols.io.bfxzjpp6 Copy
Authors: Janet Keast, Peregrine Osborne
Group: SPARC
Summary: This protocol is used for studies of neurons containing retrograde tracer dye in adult rat dorsal root ganglia (DRG) or pelvic ganglia (PG; synonym, major pelvic ganglia). Cryosections of ganglia are mounted directly on slides for immunohistochemical staining. Antibodies have been selected to distinguish different neurochemical classes of PG neurons or to specifically identify subclasses of sensory neurons that are myelinated (immunoreactive for NF200 [neurofilament, 200 kD]) or nociceptive (immunoreactive for TRPV1).
Proper citation: Janet Keast, Peregrine Osborne 2019. Immunohistochemical analysis of ganglion neurons innervating the lower urinary tract [keast-001-stage03]. protocols.io dx.doi.org/10.17504/protocols.io.w3efgje Copy
Authors: A. Lenore Ackerman, Jennifer Tash Anger, Muhammad Umair Khalique, James E. Ackerman, Jie Tang, Jayoung Kim, David M. Underhill, Michael R. Freeman
Summary: Introduction. Recent data suggest the urinary tract hosts a microbial community of varying composition, even in the absence of infection. Culture-independent methodologies, such as next-generation sequencing of conserved ribosomal DNA sequences, provide an expansive look at these communities, identifying both common commensals and fastidious organisms. A fundamental challenge has been the isolation of DNA representative of the entire resident microbial community, including fungi.
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Materials and Methods. We evaluated multiple modifications of commonly-used DNA extraction procedures using standardized male and female urine samples, comparing resulting overall, fungal and bacterial DNA yields by quantitative PCR. After identifying protocol modifications that increased DNA yields (lyticase/lysozyme digestion, bead beating, boil/freeze cycles, proteinase K treatment, and carrier DNA use), all modifications were combined for systematic confirmation of optimal protocol conditions. This optimized protocol was tested against commercially available methodologies to compare overall and microbial DNA yields, community representation and diversity by next-generation sequencing (NGS).
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Results. Overall and fungal-specific DNA yields from standardized urine samples demonstrated that microbial abundances differed significantly among the eight methods used. Methodologies that included multiple disruption steps, including enzymatic, mechanical, and thermal disruption and proteinase digestion, particularly in combination with small volume processing and pooling steps, provided more comprehensive representation of the range of bacterial and fungal species. Concentration of larger volume urine specimens at low speed centrifugation proved highly effective, increasing resulting DNA levels and providing greater microbial representation and diversity.
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Conclusions. Alterations in the methodology of urine storage, preparation, and DNA processing improve microbial community profiling using culture-independent sequencing methods. Our optimized protocol for DNA extraction from urine samples provided improved fungal community representation. Use of this technique resulted in equivalent representation of the bacterial populations as well, making this a useful technique for the concurrent evaluation of bacterial and fungal populations by NGS.
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Proper citation: A. Lenore Ackerman, Jennifer Tash Anger, Muhammad Umair Khalique, James E. Ackerman, Jie Tang, Jayoung Kim, David M. Underhill, Michael R. Freeman 2018. Protocol for DNA Extraction from Urine. protocols.io dx.doi.org/10.17504/protocols.io.wgsfbwe Copy
Authors: Juho Eineluoto, Petrus Järvinen, Anu Kenttämies, Tuomas Kilpeläinen, Hanna Vasarainen, Kevin Sandeman, Andrew Erickson, Tuomas Mirtti, Antti Rannikko
Summary: Introduction: This study was conducted to describe the repeat multiparametric MRI (mpMRI)
changes occurring in prostate cancer (PCa) patients during active surveillance (AS), and to study
possible associations between mpMRI-related parameters in predicting prostate biopsy (Bx)
Gleason score (GS) upgrading >3+3 (GU) and protocol-based treatment change (TC).
Materials and methods: The study cohort consisted of 76 AS patients with GS 3+3 PCa
and at least two consecutive mpMRIs of the prostate performed between 2006 and 2015. Patients
were followed according to the Prostate Cancer Research International Active Surveillance (PRIAS) protocol and additional mpMRIs. The primary end points were GS upgrading (GU) (>3+3) in protocol-based biopsies and protocol-based TC.
Results: 53/76 (69%) patients had progression (PIRADS upgrade, size increase or new
lesion[s]), 18/76 (24%) had radiologically stable disease, and 5/76 (7%) had regression
(PIRADS or size decrease, disappearance of lesion[s]) in repeat mpMRIs during AS. PIRADS
scores 4 to 5 in the initial mpMRI was associated with GU (p=0.008) and protocol-based TC
(p=0.009). Tumour progression on repeat mpMRIs was associated with TC (p=0.045) but not with
GU (p=1.00). PIRADS scores 4-5 predict GU (sensitivity 0.80 [95% confidence interval (CI);
0.51-0.95, specificity 0.62 [95% CI; 0.52-0.77]) with PPV and NPV values of 0.34 (95% CI;
0.21-0.55) and 0.93 (95% CI; 0.80-0.98), respectively.
Conclusion: mpMRI is a useful tool not only to select but also to monitor PCa
patients on AS.
Proper citation: Juho Eineluoto, Petrus Järvinen, Anu Kenttämies, Tuomas Kilpeläinen, Hanna Vasarainen, Kevin Sandeman, Andrew Erickson, Tuomas Mirtti, Antti Rannikko 2017. Repeat multiparametric MRI in prostate cancer patients on active surveillance. protocols.io dx.doi.org/10.17504/protocols.io.j5jcq4n Copy
Authors: Shankun Zhao, Ran Kang, Zhigang Zhao
Summary: Intracavernous pressure (ICP) measurement is a well-established technique for assessing the erectile function, which was performed by cannulating either crus or shaft of the penis. But yet, as far as we know, no consensus has reached on the ES parameters of frequency and voltage response.Moreover, the current technique for ICP measurement in the rat is difficult to perform, especially in the cannulation of the corpus cavernosum. It often leads to failure in the experiment and takes time to explore the optimum conditions for inexperienced investigators. In present study, we provided a detailed step-by-step procedure of ICP measurement.
Proper citation: Shankun Zhao, Ran Kang, Zhigang Zhao 2017. A protocol for assessment of intracavernosal pressure in a rat model. protocols.io dx.doi.org/10.17504/protocols.io.kwdcxa6 Copy
Authors: Juho Eineluoto, Petrus Järvinen, Anu Kenttämies, Tuomas Kilpeläinen, Hanna Vasarainen, Kevin Sandeman, Andrew Erickson, Tuomas Mirtti, Antti Rannikko
Summary: Introduction: This study was conducted to describe the repeat multiparametric MRI (mpMRI)
changes occurring in prostate cancer (PCa) patients during active surveillance (AS), and to study
possible associations between mpMRI-related parameters in predicting prostate biopsy (Bx)
Gleason score (GS) upgrading >3+3 (GU) and protocol-based treatment change (TC).
Materials and methods: The study cohort consisted of 76 AS patients with GS 3+3 PCa
and at least two consecutive mpMRIs of the prostate performed between 2006 and 2015. Patients
were followed according to the Prostate Cancer Research International Active Surveillance (PRIAS) protocol and additional mpMRIs. The primary end points were GS upgrading (GU) (>3+3) in protocol-based biopsies and protocol-based TC.
Results: 53/76 (69%) patients had progression (PIRADS upgrade, size increase or new
lesion[s]), 18/76 (24%) had radiologically stable disease, and 5/76 (7%) had regression
(PIRADS or size decrease, disappearance of lesion[s]) in repeat mpMRIs during AS. PIRADS
scores 4 to 5 in the initial mpMRI was associated with GU (p=0.008) and protocol-based TC
(p=0.009). Tumour progression on repeat mpMRIs was associated with TC (p=0.045) but not with
GU (p=1.00). PIRADS scores 4-5 predict GU (sensitivity 0.80 [95% confidence interval (CI);
0.51-0.95, specificity 0.62 [95% CI; 0.52-0.77]) with PPV and NPV values of 0.34 (95% CI;
0.21-0.55) and 0.93 (95% CI; 0.80-0.98), respectively.
Conclusion: mpMRI is a useful tool not only to select but also to monitor PCa
patients on AS.
Proper citation: Juho Eineluoto, Petrus Järvinen, Anu Kenttämies, Tuomas Kilpeläinen, Hanna Vasarainen, Kevin Sandeman, Andrew Erickson, Tuomas Mirtti, Antti Rannikko 2017. Repeat multiparametric MRI in prostate cancer patients on active surveillance. protocols.io dx.doi.org/10.17504/protocols.io.j66crhe Copy
Authors: Hyun Suk Yoon, Yong Tae Kim, Bong Suk Shim, Hana Yoon
Summary: This study aimed to investigate the effects of lactic acid bacterial fermentation extract (LABEF) on cystitis induced by Escherichia coli lipopolysaccharide (LPS) in the mouse bladder by pathological analyses and measurement of the levels of tumor necrosis factor-alpha (TNF-α) and interleukin-18 (IL-18). LABEF was administered orally (5 μg/L) to mice for 10 days following which, the study group (n = 12) was injected intravesically with 5 μg/L LPS. The bladder tissue was then harvested after 24 hours and subjected to hematoxylin and eosin (H-E) staining. A semiquantative score was used to evaluate inflammation (bladder inflammation index; BII). TNF-α immunohistochemical staining and multiplex cytokine assay were also performed. TNF-α and IL-18 levels were determined. The results were compared with those of the control group (n = 12). The BII in the control and study groups was 2.7 ± 0.5 and 1.1 ± 0.7, respectively, with the control group scores significantly differing from the study group scores (p value
Proper citation: Hyun Suk Yoon, Yong Tae Kim, Bong Suk Shim, Hana Yoon 2017. Preventive effect of Lactobacillus mixture on inflammation and cytokines in lipopolysaccharide-induced cystitis in mice. protocols.io dx.doi.org/10.17504/protocols.io.meyc3fw Copy
Authors: Daniel Uysal, Philipp Erben
Proper citation: Daniel Uysal, Philipp Erben 2021. In silico and RT-qPCR analysis of the 8q22.2 region in muscle invasive bladder cancer. protocols.io dx.doi.org/10.17504/protocols.io.bmewk3fe Copy
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