universal probe set Dotaz Zobrazit nápovědu
PREMISE: Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. METHODS: To evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony-informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance. RESULTS: Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony-informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. DISCUSSION: A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large-scale systematic studies, where financially possible.
- Klíčová slova
- Angiosperms353, Malinae, customized probe set, target enrichment, universal probe set,
- Publikační typ
- časopisecké články MeSH
PREMISE: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. METHODS AND RESULTS: Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%). CONCLUSIONS: High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.
- Klíčová slova
- Brassicaceae, Hyb‐Seq, combining probes, enrichment, phylogenomics, phylogeny, population biology, target enrichment,
- Publikační typ
- časopisecké články MeSH
The development of a diagnostic polymerase chain reaction (PCR) or quantitative PCR (qPCR) assay for universal detection of highly variable viral genomes is always a difficult task. The purpose of this chapter is to provide a guideline on how to align, process, and evaluate a huge set of homologous nucleotide sequences in order to reveal the evolutionarily most conserved positions suitable for universal qPCR primer and hybridization probe design. Attention is paid to the quantification and clear graphical visualization of the sequence variability at each position of the alignment. In addition, specific problems related to the processing of the extremely large sequence pool are highlighted. All of these steps are performed using an ordinary desktop computer without the need for extensive mathematical or computational skills.
- MeSH
- DNA primery genetika MeSH
- polymerázová řetězová reakce metody MeSH
- sekvenční seřazení metody MeSH
- teoretické modely MeSH
- virus chřipky A genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA primery MeSH
Compartmentalization was likely essential for primitive chemical systems during the emergence of life, both for preventing leakage of important components, i.e., genetic materials, and for enhancing chemical reactions. Although life as we know it uses lipid bilayer-based compartments, the diversity of prebiotic chemistry may have enabled primitive living systems to start from other types of boundary systems. Here, we demonstrate membraneless compartmentalization based on prebiotically available organic compounds, α-hydroxy acids (αHAs), which are generally coproduced along with α-amino acids in prebiotic settings. Facile polymerization of αHAs provides a model pathway for the assembly of combinatorially diverse primitive compartments on early Earth. We characterized membraneless microdroplets generated from homo- and heteropolyesters synthesized from drying solutions of αHAs endowed with various side chains. These compartments can preferentially and differentially segregate and compartmentalize fluorescent dyes and fluorescently tagged RNA, providing readily available compartments that could have facilitated chemical evolution by protecting, exchanging, and encapsulating primitive components. Protein function within and RNA function in the presence of certain droplets is also preserved, suggesting the potential relevance of such droplets to various origins of life models. As a lipid amphiphile can also assemble around certain droplets, this further shows the droplets' potential compatibility with and scaffolding ability for nascent biomolecular systems that could have coexisted in complex chemical systems. These model compartments could have been more accessible in a "messy" prebiotic environment, enabling the localization of a variety of protometabolic and replication processes that could be subjected to further chemical evolution before the advent of the Last Universal Common Ancestor.
- Klíčová slova
- membraneless compartments, origins of life, polyesters, prebiotic chemistry, self-assembly,
- MeSH
- fluorescenční barviva chemie MeSH
- FRAP MeSH
- koncentrace vodíkových iontů MeSH
- kyseliny karboxylové chemie MeSH
- membrány umělé * MeSH
- polyestery chemická syntéza chemie MeSH
- původ života * MeSH
- RNA chemie MeSH
- velikost částic MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- fluorescenční barviva MeSH
- kyseliny karboxylové MeSH
- membrány umělé * MeSH
- polyestery MeSH
- RNA MeSH
OBJECTIVE: To develop guidelines for the ultrasound examination of cervical cancer, including a unified ultrasound terminology. SUBJECT: Original paper. SETTING: Gynecological Oncology Center, Department of Obstetrics and Gynecology, Masaryk University and General Faculty Hospital Brno, and Gynecological Oncology Center, Department of Obstetrics and Gynecology, Charles University in Prague - First Faculty of Medicine and General Faculty Hospital Prague. SUBJECT AND METHOD: The standard diagnostic algo-rithm for examination of cervical cancer in oncogynecology centers in the Czech Republic is based on published studies, own experience (Oncogynecological Center, Department of Gynecology and Obstetrics,1st Medical Faculty, Charles University) and the experiences of a group of ultrasonographers involved in the grant project IGA MZ ČR NT13070 focused on the implementation of an oncogynecological ultrasound into clinical practice. Standard ultrasound examination includes two-dimensional real-time ultrasound examination (sagittal and transverse views). Transrectal or transvaginal ultrasound examination is combined with transabdominal ultrasound. Prerequisites are quality ultrasound equipment, a high frequency microconvex linear probe and abdominal convex and linear probe. The examination is performed by an experienced sonographer (level 2 or 3 according to the recommendations of the Ultrasound division of the Czech Society of Obstetrics and Gynecology and the Czech Society of Ultrasound in Obstetrics and Gynecology). Intravenous administration of contrast material or three-dimensional ultrasound examination do not influence accuracy of the examination and is not a prerequisite. CONCLUSION: Based on the consensus of experienced sonographers and a review of the literature, guidelines were created for ultrasound staging of cervical cancer.
The authors present a review of various techniques of long-term intubation of efferent lacrimal pathways by a silicone fibre. They use an original way of intubation and intubate the insertion probes of the intubation set from the lower nasal outlet by means of a titanium loop under direct optic control by means of an endoscope. The use of the endoscope makes it possible to reduce the number of complications and iatrogenic damage of the mucosa and it enhances the effectiveness of the procedure. The authors prefer the use of special intubations sets; for young children intubation sets made from soft metal are preferable. At present all their demands are met by the intubation set they developed in collaboration with the Technical University, Prague. During the period between April 1994 and August 1996 the authors used the described technique for bicanalicular intubation of the efferent lacrimal pathways in 127 children and in adult patients 6x. In 86 instances they used an intubation set of Geuder Co., 44 times their own intubation set.
- MeSH
- dítě MeSH
- dospělí MeSH
- endoskopie MeSH
- intubace přístrojové vybavení metody MeSH
- lidé MeSH
- obstrukce slzovodu terapie MeSH
- slzné ústrojí * MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- lidé MeSH
- Publikační typ
- anglický abstrakt MeSH
- časopisecké články MeSH
The aim of this study was to evaluate the use of solid hydrogel as a probe for the drug delivery to the rabbit eye upon application of low current iontophoresis. Hydroxyethyl methacrylate (HEMA), cross-linked with ethylenglycol dimethacrylate (EGDMA) were prepared to form solid hydrogels. The concentrations of gentamicin sulfate in different segments of rabbit eye after transconjunctival and transscleral iontophoresis were also studied. For iontophoresis we used a portable Mini Ion device (designed at Hebrew University of Jerusalem) and applied a current from 0 mA to 1.5 mA for pre-set period from 30 to 120 seconds and after application the concentrations of gentamicin in cornea were assayed. The rabbits in control group were treated with fortified gentamicin eye-drops (concentration 1.4 %). The highest concentration of gentamicin sulfate was reached after iontophoresis with current intensity of 1.5 mA applied for 60 s. High gentamicin concentration were found in the retina and in the sclera four hours after transscleral iontophoresis, the lowest concentration was obtained in vitreous. The delivery of gentamicin to the eye via iontophoresis with solid HEMA/EGDMA hydrogels seems to be promising method achieving high concentrations of the drug in the eye tissue.
- MeSH
- antibakteriální látky aplikace a dávkování farmakokinetika MeSH
- gentamiciny aplikace a dávkování farmakokinetika MeSH
- iontoforéza * MeSH
- králíci MeSH
- methakryláty MeSH
- nosiče léků * MeSH
- oči * MeSH
- PEG-DMA hydrogel * MeSH
- rohovka metabolismus MeSH
- zvířata MeSH
- Check Tag
- králíci MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antibakteriální látky MeSH
- ethylene dimethacrylate MeSH Prohlížeč
- gentamiciny MeSH
- hydroxyethyl methacrylate MeSH Prohlížeč
- methakryláty MeSH
- nosiče léků * MeSH
- PEG-DMA hydrogel * MeSH
OBJECTIVE: To present our experience with ultrasound-guided minimally invasive interventions in gynecologic oncology. SUBJECT: Original paper. SETTING: Oncogynecological Center, Department of Obstetrics and Gynecology, Charles University in Prague - First Faculty of Medicine and General Faculty Hospital, Prague. SUBJECT AND METHOD: We provide minimally invasive punction interventions under ultrasound guidance using either abdominal or vaginal probe in three indication groups - diagnostics (tru-cut biopsy), therapy (punction drainage of lymphocyst) and palliation (insertion of permanent peritoneal catheter). CONCLUSION: Ultrasound-guided minimally invasive interventions represent a group of accessible and relatively simple methods useful in many indications, not only in gynecologic oncology. Adoption of these methods allows to broadening the spectrum of interventions offered and decreasing patient's stress.
OBJECTIVE: The aim of this study was to evaluate the feasibility of pre-operative lymphoscintigraphy and radio-guided surgery in endometrial cancer patients after intramyometrial administration of labelled colloid. DESIGN: Prospective study. SETTING: Department of Obstetrics and Gynaecology of the Palacký University Medical School and University Hospital, Olomouc, Czech Republic. PATIENTS AND METHODS: Between April 2002 and March 2005, thirty three patients with endometrial cancer received pre-operatively 50 MBq of 99mTc-nanocolloid. The radiopharmaceutical agent was administered by a 25 Gauge needle transcervically into the myometrium. Subsequently, series of static lymphoscintigrams were made 20 to 90 min after injection. Two hours after injection the surgery started. Twenty eight patients underwent total abdominal hysterectomy, bilateral salpingo-oophorectomy and pelvic lymphadenectomy. Five patients were scheduled for laparoscopically assisted vaginal hysterectomy, bilateral salpingo-oophorectomy and pelvic lymphadenectomy. Paraaortal lymphadenectomy was performed in 11 cases. A gamma detecting probe was used to locate radioactive lymph nodes during operation. Each hot lymph node was removed separately. RESULTS: Sentinel lymph nodes (SLN) were identified in 26 (79%) of 33 patients. The mean number of sentinel nodes detected was 2.9 (range 1-10). Seventy two (15.3%) of 472 nodes obtained in total, were identified as radioactive-colloid positive. Histopathological analysis revealed five (7%) of 72 lymphonodes to be positive of metastases. Sentinel nodes in paraaortic area were identified in 11 (33%) patients. No false negative sentinel lymphonodes were observed. CONCLUSION: The preoperative lymphoscintigraphy and intraoperative gamma probe guided biopsy may be useful in identifying sentinel nodes in endometrial cancer. No false negative sentinel lymphonodes were observed if representative SLNs were diagnosed with tumor.
- MeSH
- adenokarcinom patologie sekundární chirurgie MeSH
- biopsie sentinelové lymfatické uzliny * MeSH
- lidé středního věku MeSH
- lidé MeSH
- lymfatické metastázy MeSH
- lymfatické uzliny diagnostické zobrazování MeSH
- nádory endometria patologie chirurgie MeSH
- peroperační doba MeSH
- radiofarmaka * MeSH
- radioisotopová scintigrafie MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- technecium 99mTc-agregovaný albumin * MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- radiofarmaka * MeSH
- technecium 99mTc-agregovaný albumin * MeSH
- technetium Tc 99m nanocolloid MeSH Prohlížeč
OBJECTIVE: The aim of our study was to analyze whether transabdominal and introital ultrasonography can accurately identify paravaginal defect associated with GSI (Genuine stress urinary incontinence) and to determine the changes after paravaginal defect repair. DESIGN: Prospective randomised clinical study. SETTING: Department of Obstetrics and Gynecology, Charles University, Prague, Czech Republic. METHODS: Sixteen women with GSI, who had previously not undergone anti-incontinence surgery were involved. Their average age was 52 years, average weight 71 kg and average parity 2.0. Within vaginal examination our attention was focussed on the diminution of sulsus superioris vaginae during Valsalva maneuver. The bladder of a patient in supine position was filled with 300 ml of sterile saline. Than a 5 MHz curved array probe was used to assess the bladder neck mobility from the perineal approach, and the same probe was used from the abdominal approach to determine paravaginal defect and subsequently a vaginal probe from introital approach was used for the rest of the examination. After Burch colposuspension and paravaginal defect repair US scanning was performed 6 till 8 days and 5 or 6 weeks after operation. RESULTS: We found significant differences in bladder neck position and mobility before and after the operation. In women with symptoms of GSI we found from abdominal approach unilateral or bilateral paravaginal defect in fifteen women. Unilateral defect was found on the right side six times and on the left side only once. In eight women the defect was bilateral. The introital approach obtained similar results, only in two patients with bilateral defect the examination concluded unilateral right defect. After the operation we did not find PVD in patients after paravaginal defect repair. We obtained worse results from vaginal examination, where preoperatively PVD was correctly determined (sensitivity) only in 82.6%. CONCLUSION: From our preliminary results we can suggest performing US scanning to conform paravaginal defect before anti-incontinence surgery and possibly adding to the Burch colposuspension paravaginal defect repair to correct cystourethrocele.
- MeSH
- lidé středního věku MeSH
- lidé MeSH
- močový měchýř diagnostické zobrazování MeSH
- prospektivní studie MeSH
- stresová inkontinence moči diagnostické zobrazování chirurgie MeSH
- ultrasonografie MeSH
- uretra diagnostické zobrazování MeSH
- vagina diagnostické zobrazování MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- klinické zkoušky MeSH
- práce podpořená grantem MeSH
- randomizované kontrolované studie MeSH
