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> Anatomy > Body Part > Vagina

Vagina

The vagina is a muscular tubular organ that connects the cervix of the uterus to the exterior of the female body.
It serves as a passageway for menstrual flow, sexual intercourse, and childbirth.
The vaginna is lined with a mucous membrane that maintains a slightly acidic pH, which helps protect against infection.
Vaginal research is essential for understanding female reproductive health and developing new treatments for conditions affecting this important anatomical structure.

Most cited protocols related to «Vagina»

1
Validating PICRUSt's Metagenome Prediction Accuracy
Cited 1640 times
Several microbiome studies that included both 16S sequencing and WGS metagenome sequencing for the same samples were used to test the accuracy of PICRUSt. These included 530 paired human microbiome samples22 (link), 39 paired mammal gut samples24 (link), 14 paired soil samples34 (link), 10 paired hypersaline microbial mats23 (link), 24 (link) and two even/staggered synthetic mock communities from the HMP33 (link). We additionally used PICRUSt to make predictions on three 16S-only microbiome studies, specifically 6,431 HMP samples (http://hmpdacc.org/HMQCP), 993 vaginal time course samples43 and 335 coral mucus samples(http://www.microbio.me/qiime/; Study ID 1854).
For 16S data, PICRUSt-compatible OTU tables were constructed using the closed-reference OTU picking protocol in QIIME 1.5.0-dev (pick_reference_otus_through_otu_table.py) against Greengenes+IMG using ‘uclust’48 (link). For paired metagenomes, WGS reads were annotated to KOs using v0.98 of HUMAnN30 (link). Expected KO counts for the HMP mock communities were obtained by multiplying the mixing proportions of community members by the annotated KO counts of their respective reference genomes in IMG. PICRUSt was used to predict the metagenomes using the 16S-based OTU tables, and predictions were compared to the annotated WGS metagenome across all KOs using Spearman rank correlation. In addition, KOs were mapped to KEGG Module abundances, following the conjugative normal form as implemented in HUMAnN script “pathab.py” for the HMP and vaginal datasets to compare modules and pathways. Bray-Curtis distances (for Beta-diversity comparison between OTU or PICRUSt KO abundances across samples) were calculated using as implemented in the QIIME “beta_diversity.py” script. The PCA plot and identification of KEGG modules with significant mean proportion differences for both the HMP and vaginal datasets was created using STAMP v2.036 (link).
The Nearest Sequenced Taxon Index (NSTI) was developed as an evaluation measure describing the novelty of organisms within an OTU table with respect to previously sequenced genomes. For every OTU in a sample, the sum of branch lengths between that OTU in the Greengenes tree to the nearest tip in the tree with a sequenced genome is weighted by the relative abundance of that OTU. All OTU scores are then summed to give a single NSTI value per microbial community sample. PICRUSt calculates NSTI values for every sample in the given OTU table, and we compared NSTI scores and PICRUSt accuracies for all of the metagenome validation datasets.
In the metagenome rarefaction analysis (Fig. 4), a given number of counts were randomly selected from either the collection of microbial OTUs for each sample (i.e. the 16S rRNA OTU table) or the collection of sequenced genes in that sample using the multiple_rarefactions.py script in QIIME 1.5.0-dev29 (link). To estimate the number of raw reads at which PICRUSt outperforms metagenomic sequencing the annotated shotgun reads were transformed to total sequenced reads by dividing by the mean annotation rates from the original manuscript (17.3%), while 16S rRNA reads were transformed using the success rate for closed-reference OTU picking at a 97% 16S rRNA identity threshold (68.9%). Both the subsampled metagenome and the PICRUSt predictions from the subsampled OTU table were compared for accuracy using Spearman rank correlation versus the non-subsampled metagenome.
Langille M.G., Zaneveld J., Caporaso J.G., McDonald D., Knights D., Reyes J.A., Clemente J.C., Burkepile D.E., Vega Thurber R.L., Knight R., Beiko R.G, & Huttenhower C. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature biotechnology, 31(9), 814-821.
Publication 2013
Coral Genes Genome Human Microbiome Mammals Metagenome Microbial Community Microbiome Mucus RNA, Ribosomal, 16S Trees Vagina
2
Microbiome Analysis of Human Vaginal and Mouse Fecal Samples
Cited 1517 times
The 16S rRNA gene amplicon data from human vaginal samples in [19 (link)] (2.13M paired-end Illumina Miseq reads in 157 samples) and from mouse feces in [17 (link)] (3.65M paired-end Illumina Miseq reads in 362 samples) were analyzed with the DADA2 pipeline outlined above. First the demultiplexed fastq files were filtered and trimmed in the same manner as the test datasets. Each sample was dereplicated, a portion of the dataset was used to estimate the error parameters, and dada() was applied to the full pooled dataset using those inferred error parameters. isBimeraDenovo() was used to remove chimeras.
For the human vaginal samples, output sequences that appeared in at least two samples and at least 0.3% of the total reads were taxonomically identified by BLAST. Further analysis focused on the six L. crispatus sequence variants identified by this procedure.
Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J, & Holmes S.P. (2016). DADA2: High resolution sample inference from Illumina amplicon data. Nature methods, 13(7), 581-583.
Publication 2016
Chimera Feces Genes Genetic Diversity Homo sapiens Mice, House RNA, Ribosomal, 16S Vagina
3
16S rRNA Phylometagenomic Analysis of Normal Human Microbiome
Cited 805 times
The 16S rRNA-based phylometagenomic dataset of the normal (healthy) human microbiome was made available through the Human Microbiome Project [13 (link)], and consists of 454 FLX Titanium sequences spanning the V3 to V5 variable regions obtained for 301 samples from 24 healthy subjects (12 male, 12 female) enrolled at a single clinical site in Houston, TX. These samples cover 18 different body sites, including 6 main body site categories: the oral cavity (9 samples), the gut (1 sample), the vagina (3 samples), the retroauricular crease (2 samples), the nasal cavity (1 sample) and the skin (2 samples). Detailed protocols used for enrollment, sampling, DNA extraction, 16S amplification and sequencing are available on the Human Microbiome Project Data Analysis and Coordination Center website [103 ], and are also described elsewhere [55 ,56 (link)]. In brief, genomic DNA was isolated using the Mo Bio PowerSoil kit [104 ] and subjected to 16S amplifications using primers designed incorporating the FLX Titanium adapters and a sample barcode sequence, allowing directional sequencing covering variable regions V5 to partial V3 (primers: 357F 5'-CCTACGGGAGGCAGCAG-3' and 926R 5'-CCGTCAATTCMTTTRAGT-3'). Resulting sequences were processed using a data curation pipeline implemented in mothur [41 (link)], which reduces the sequencing error rate to less than 0.06% as validated on a mock community. As part of the pipeline parameters, to pass the initial quality control step, one unambiguous mismatch to the sample barcode and two mismatches to the PCR amplification primers were allowed. Sequences with an ambiguous base call or a homopolymer longer than eight nucleotides were removed from subsequent analyses, as suggested previously [105 (link)]. Based on the supplied quality scores, all sequences were trimmed when a base call with a score below 20 was encountered. All sequences were aligned using a NAST-based sequence aligner to a custom reference based on the SILVA alignment [106 (link),107 (link)]. Sequences that were shorter than 200 bp or that did not align to the anticipated region of the reference alignment were removed from further analysis. Chimeric sequences were identified using the mothur implementation of the ChimeraSlayer algorithm [108 (link)]. Unique reads were classified with the MSU RDP classifier v2.2 [58 (link)] using the taxonomy proposed by [109 ], maintained at the RDP (RDP 10 database, version 6). The 16S rRNA reads are available in the Sequence Read Archive at [110 ].
Segata N., Izard J., Waldron L., Gevers D., Miropolsky L., Garrett W.S, & Huttenhower C. (2011). Metagenomic biomarker discovery and explanation. Genome Biology, 12(6), R60.
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Publication 2011
Base Sequence Chimera Females Genome Healthy Volunteers Human Body Human Microbiome Males Nasal Cavity Nucleotides Oligonucleotide Primers Oral Cavity RNA, Ribosomal, 16S Skin Titanium Vagina
4
Amplification and Sequencing of 16S rRNA V3-V4 Region
Cited 265 times
The 16S rRNA gene consists of nine hypervariable regions flanked by regions of more conserved sequence. To maximize the effective length of the MiSeq’s 250PE and 300PE sequencing reads, a region of approximately 469 bp encompassing the V3 and V4 hypervariable regions of the 16S rRNA gene was targeted for sequencing. This region provides ample information for taxonomic classification of microbial communities from specimens associated with human microbiome studies and was used by the Human Microbiome Project [5 (link)], however, the approach described could be adapted to any primer pairs.
To amplify and sequence the V3-V4 hypervariable region of the 16S rRNA gene, primers were designed that contained: 1) a linker sequence allowing amplicons to bind to the flow cell and be sequenced using the standard Illumina HP10 or HP11 (Illumina, San Diego, CA, USA) sequencing primers; 2) a 12 bp index sequence; 3) a 0 to 7 bp “heterogeneity spacer” that we designed in this study to mitigate the issues caused by low sequence diversity amplicons (Additional file 1: Figure S1C); and 4) 16S rRNA gene universal primers (Figure 1A and Additional file 2). Genomic DNA extracted from clinical vaginal and anal swabs were amplified, normalized using the SequalPrep Normalization Kit (Life Technologies, Carlsbad, CA, USA) and pooled (11 pools with 271 to 426 samples per pool) prior to sequencing on the MiSeq platform (see Additional file 3 and Table 1 for number of samples per pools). The amplicon pools were prepared for sequencing with AMPure XT beads (Beckman Coulter Genomics, Danvers, MA, USA) and the size and quantity of the amplicon library were assessed on the LabChip GX (Perkin Elmer, Waltham, MA, USA) and with the Library Quantification Kit for Illumina (Kapa Biosciences, Woburn, MA, USA), respectively. PhiX Control library (v3) (Illumina) was combined with the amplicon library (expected at 20%). The library was clustered to a density of approximately 570 K/mm2. The libraries were sequenced either on 250PE or 300PE MiSeq runs and one library was sequenced with both protocols using the standard Illumina sequencing primers (Figure 1A), eliminating the need for a third (or fourth) index read. Sequencing data was available within approximately 48 hours. Image analysis, base calling and data quality assessment were performed on the MiSeq instrument.
Fadrosh D.W., Ma B., Gajer P., Sengamalay N., Ott S., Brotman R.M, & Ravel J. (2014). An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome, 2, 6.
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Publication 2014
Anus Cells Conserved Sequence DNA Library Genes Genetic Heterogeneity Genome Human Microbiome Microbial Community Oligonucleotide Primers Ribosomal RNA Genes RNA, Ribosomal, 16S Vagina
5
Vaginal Microbiome Analysis via RNA-Seq
Cited 203 times
Vaginal swabs were collected from four women: two with BV and two considered to have a non-BV vaginal biota as diagnosed by Nugent scoring[55] (link), and vaginal pH. Nurses obtained vaginal samples for RNA-seq using a Dacron polyester-tipped swab rolled against the mid-vaginal wall and immediately suspended in RNAprotect (Qiagen) containing 100 µg/ml rifampicin. Vaginal pH was measured using the pHem-alert applicator (Gynex). Samples for RNA extraction were incubated at room temperature for at least 10 minutes (to a maximum of 3 hours), and then centrifuged before discarding the supernatant and freezing the remaining pellet at 80 C. Lysis and RNA extraction were performed within 3 weeks of storage. RNA was isolated as for the B. cereus samples.
Reference sequence clustering and mapping. A total of 110 accessions representing 103 organisms (of 31 genera, and 63 species) isolated from or detected in the vagina were included in a reference sequence set for mapping. These 234,991 sequences (including 230,031 coding sequences) were clustered by sequence identity (95% nucleotide identity over 90% sequence length) using CD-HIT[56] (link) to remove redundancy in the reference mapping set. A representative sequence (''refseq'') from each of the resulting 163,014 clusters was used to build a Bowtie[32] colorspace reference library for mapping the RNA-seq reads. Reads mapped uniquely by Bowtie to a coding refseq were included in the differential expression analysis (all other unmapped reads were discarded). Reads were trimmed from the 3 end to 40 nt, and up to 2 mismatches were allowed.
ALDEX version 1.0.3 was used. It can be accessed at: http://code.google.com/p/aldex/. DESeq version 1.6.1 was used for these analyses using the per-gene dispersion estimates. The edgeR version 2.4.6 package was used. A false discovery rate of 0.1 was used to identify putative differentially-expressed transcripts as recommended by the documentation. Cuffdiff version 1.3.0 was used with a mean fragment length of 200 bp and the default false discovery rate of 0.05.
Fernandes A.D., Macklaim J.M., Linn T.G., Reid G, & Gloor G.B. (2013). ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq. PLoS ONE, 8(7), e67019.
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Publication 2013
Base Sequence Biological Community Dacron DNA Library Exons Genes Nurses Polyesters Rifampin RNA-Seq Vagina Woman

Most recents protocols related to «Vagina»

1
Diagnosis and Significance of Bacterial Vaginosis
Not available on PMC !

Example 5

Bacterial Vaginosis (BV) is an infection caused when too much of certain bacteria change the normal balance of bacteria in the vagina. Bacterial vaginosis (BV) is one of the most common lower genital tract conditions, occurring in 35% of women attending sexually transmitted infection (STI) clinics, 15% to 20% of pregnant women, and 5% to 15% of women attending gynecology clinics (Eschenbach D A, Am J Obstet Gynecol 1993). Pregnant women with BV are more likely to have babies who are born premature (early) or with low birth weight than women who do not have BV while pregnant. Low birth weight means having a baby that weighs less than 5.5 pounds at birth (CDC fact sheet, 2015).

Diagnosis of BV is typically done through a vaginal swab to assess the presence and balance of certain bacteria within the vaginal flora through PCR. A wet mount, whiff test, or pH test can also be performed in order to diagnose a possible bacterial infection.

In some embodiments, the disclosed device can be used to detect bacterial vaginosis from menstrual blood or cervicovaginal fluids.

US11864740B2. Sample collection and preservation devices, systems and methods (2024-01-09). NextGen Jane, Inc. [US]. Inventors: Ridhi Tariyal [US], Stephen K. Gire [US].
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Patent 2024
Bacteria Bacterial Infections Bacterial Vaginosis Blood Childbirth Diagnosis Hereditary Diseases Infant Infection Medical Devices Menstruation Pregnant Women Premature Birth Sexually Transmitted Diseases Vagina Vaginal Diseases Woman
2
Chlamydia: Diagnosis, Transmission, and Impacts
Not available on PMC !

Example 2

Chlamydia is a common STI that is caused by the bacterium Chlamydia trachomatis. Transmission occurs during vaginal, anal, or oral sex, but the bacterium can also be passed from an infected mother to her baby during vaginal childbirth. It is estimated that about 1 million individuals in the United States are infected with this bacterium, making chlamydia one of the most common STIs worldwide. Like gonorrhea, chlamydial infection is asymptomatic for a majority of women. If symptoms are present, they include unusual vaginal bleeding or discharge, pain in the abdomen, painful sexual intercourse, fever, painful urination or the urge to urinate more frequently than usual. Of those who develop asymptomatic infection, approximately half may develop PID. Infants born to mothers with chlamydia may suffer from pneumonia and conjunctivitis, which may lead to blindness. They may also be subject to spontaneous abortion or premature birth.

Diagnosis of chlamydial infection is usually done by nucleic acid amplification techniques, such as PCR, using samples collected from cervical swabs or urine specimens (Gaydos et al., J. Clin. Microbio., 42:3041-3045; 2004). Treatment involves various antibiotic regimens.

In some embodiments, the disclosed device can be used to detect chlamydial infections from menstrual blood or cervicovaginal fluids.

US11864740B2. Sample collection and preservation devices, systems and methods (2024-01-09). NextGen Jane, Inc. [US]. Inventors: Ridhi Tariyal [US], Stephen K. Gire [US].
Full text: Click here
Patent 2024
Abdominal Pain Antibiotics Anus Asymptomatic Infections Bacteria Blindness Blood Childbirth Chlamydia Chlamydia Infections Chlamydia trachomatis Coitus Conjunctivitis Diagnosis Dysuria Fever Gonorrhea Infant Medical Devices Menstruation Mothers Neck Nucleic Acid Amplification Techniques Pain Patient Discharge Pneumonia Premature Birth Sexually Transmitted Diseases Spontaneous Abortion Transmission, Communicable Disease Treatment Protocols Urine Vagina Woman
3
Vaginal Dryness and Pain Alleviation
Not available on PMC !

Example 5

10 women were surveyed using The Yale Visual Analogue Scale before and after using the vaginal care composition. The women rated their experience on dryness and pain from 0-10 (0 being no dryness/no pain; 10 being most dry/most painful).

The following inclusion and exclusion criteria were used in selecting the subjects: Perimenopausal and menopausal women, women showing symptoms of vulvovaginal dryness, women showing symptoms of painful sex due to dryness or atrophy, women with no treatments of symptoms for the past year, women with no use of estrogen based devices, and women with no use of vaginal Hyaluronic acid (HA), collagen, platelet-rich plasma (prp), carboxytherapy in the past year were included in the study. In contrast, women who received treatments for vaginal dryness or pain symptoms for past year, women who used estrogens locally, women who used vaginal HA, collagen, prp, or carboxytherapy in the past year were excluded from the study.

The subjects intra-vaginally applied intra-vaginal capsules comprising 5 mg exosomes, mg L-carnosine, and 75 mg magnesium citrate twice a week for 60 days.

Results: Women included in the study reported a significant decrease in vaginal dryness (FIG. 3A) and vaginal pain (FIG. 3B) when they used the vaginal care composition for 60 days.

US11878036B2. Vaginal care compositions and methods of improving vaginal health (2024-01-23). Neuvian LLC [US]. Inventors: Spencer Bouhadir [US], Jacob Miguel [US].
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Patent 2024
Administration, Intravaginal Atrophy Capsule Carnosine Collagen Day Care, Medical Estrogens Exosomes Hyaluronic acid Magnesium magnesium citrate Medical Devices Menopause Pain Platelet-Rich Plasma Vagina Visual Analog Pain Scale Woman
4
Semen Analysis for DNA Profiling
Not available on PMC !

Example 23

In many cases of sexual assault, traces of semen are left behind in the vagina, allowing for later collection and analysis. Semen consists of a variety of proteins, vitamins, nutrients, blood group antigens, and DNA. The preservation and/or analysis of semen can facilitate later development of a DNA profile. In some embodiments, the disclosed kit allows for at-home detection of analytes from semen.

Devices, systems and methods of the present disclosure can be combined with or modified by other devices, systems and methods, such as, for example, those described in International Patent Publication No. WO/2016/025332, which is entirely incorporated herein by reference.

US11864740B2. Sample collection and preservation devices, systems and methods (2024-01-09). NextGen Jane, Inc. [US]. Inventors: Ridhi Tariyal [US], Stephen K. Gire [US].
Full text: Click here
Patent 2024
Biologic Preservation Blood Group Antigens Medical Devices Nutrients Plant Embryos Semen Analysis Sexual Assault Staphylococcal Protein A Vagina Vitamins
5
Urine and Vaginal Candidiasis Profiles
The urine and HVS samples were collected and analyzed for candidiasis and candidiasis profiles from patients who visited the Outpatients department of the University of Cape Coast Hospital from January 2013 to December 2020. The patients who provided urine samples were given a screw-cap plastic container to collect 25 to 30 ml of midstream urine samples. For vaginal swabs, patients were instructed verbally on how to collect high vagina swabs (HVS) samples by asking them to insert the swab into the vagina approximately 4 to 5 cm and then rotate it several times before placing it into a capped tube. Again, they were given a diagram showing the procedure for HVS sample collection.
Asare K.K., Bentil H.A., Gyesi E., Amoah S., Bentsi-Enchill F, & Opoku Y.K. (2023). Candidiasis profile at the outpatient department of the university of cape coast hospital in the central region of Ghana: a retrospective study. BMC Women's Health, 23, 101.
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Publication 2023
Candidiasis Outpatients Patients Urine Vagina

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1
Tamoxifen by Merck Group
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Tamoxifen is a drug used in the treatment of certain types of cancer, primarily breast cancer. It is a selective estrogen receptor modulator (SERM) that can act as both an agonist and antagonist of the estrogen receptor. Tamoxifen is used to treat and prevent breast cancer in both men and women.
2
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CD-1 mice are a widely used outbred mouse strain that exhibit genetic diversity. They are suitable for a variety of research applications due to their adaptability and lack of specific genetic modifications.
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Human chorionic gonadotropin (hcg) by Merck Group
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The HCG (Human Chorionic Gonadotropin) is a laboratory equipment product by Merck Group. It is a hormone typically used in various diagnostic and research applications. The core function of HCG is to detect and measure the levels of this hormone in biological samples.
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Qiaamp dna mini kit by Qiagen
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M2 medium by Merck Group
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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Gonal-F is a recombinant human follicle-stimulating hormone (r-hFSH) produced by recombinant DNA technology. It is used as a fertility medication to stimulate follicular development and maturation in the ovary as part of an assisted reproductive technology (ART) program.

More about "Vagina"

The vagina is a versatile and essential part of the female reproductive system.
This muscular, tubular organ connects the cervix of the uterus to the exterior of the body, serving as a passageway for menstrual flow, sexual intercourse, and childbirth.
Lined with a mucous membrane, the vagina maintains a slightly acidic pH, which helps protect against infection.
Vaginal research is crucial for understanding female reproductive health and developing new treatments for conditions affecting this important anatomical structure.
From studying the effects of drugs like Tamoxifen to examining the role of hormones like HCG (human chorionic gonadotropin) and Gonal-F, researchers rely on animal models like C57BL/6J, C57BL/6, and CD-1 mice to gain invaluable insights.
Obtaining high-quality genetic material from vaginal samples is crucial for various analyses.
The QIAamp DNA Mini Kit is a widely used tool for extracting and purifying DNA from these samples.
Similarly, the TRIzol reagent is employed for effective RNA isolation, enabling deeper exploration of gene expression patterns.
To maintain a healthy vaginal environment, antimicrobial agents like Streptomycin play a vital role, helping to prevent infection and support overall reproductive well-being.
Culturing vaginal cells in specialized media, such as M2 medium, allows researchers to study their behavior and responses in controlled settings.
Unlocking the power of vaginal research with innovative tools and techniques is essential for advancing our understanding of female reproductive health and driving the development of groundbreaking treatments.
PubCompare.ai, the AI-driven platform, can help optimize protocols, enhance reproducibility, and identify the most effective products and procedures to support your vaginal research journey.