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Fungal Diversity Dec 2011In this paper we revisit the Capnodiaceae with notes on selected genera. Type specimens of the ascomycetous genera Aithaloderma, Anopeltis, Callebaea, Capnodaria,...
In this paper we revisit the Capnodiaceae with notes on selected genera. Type specimens of the ascomycetous genera Aithaloderma, Anopeltis, Callebaea, Capnodaria, Echinothecium, Phragmocapnias and Scorias were re-examined, described and illustrated. Leptoxyphium is anamorphic Capnodiaceae and Polychaeton is a legitimate and earlier name for Capnodium, but in order to maintain nomenclatural stability we propose that the teleomorphic name should be conisdered for the approved lists of names currently in preparation for fungi. Notes are provided on the ascomycetous genus Scoriadopsis. However, we were unable to locate the type of this genus during the time frame of this study. The ascomycetous genera Aithaloderma, Ceramoclasteropsis, Hyaloscolecostroma and Trichomerium are excluded from Capnodiaceae on the basis of having ascostromata and trans-septate hyaline ascospores and should be accommodated in Chaetothyriaceae. Callebaea is excluded as the ascomata are thyriothecia and the genus is placed in Micropeltidaceae. Echinothecium is excluded as synonym of Sphaerellothecium and is transferred to Mycosphaerellaceae. The type specimen of Capnophaeum is lost and this should be considered as a doubtful genus. The coelomycetous Microxiphium is polyphyletic, while the status of Fumiglobus, Polychaetella and Tripospermum is unclear. Fourteen new collections of sooty moulds made in Thailand were isolated and sequenced. The nuclear large and small rDNA was partially sequenced and compared in a phylogeny used to build a more complete understanding of the relationships of genera in Capnodiaceae. Four new species are described and illustrated, while Phragmocapnias and Scorias are epitypified with fresh collections.
PubMed: 22737101
DOI: 10.1007/s13225-011-0145-6 -
Indian Journal of Plastic Surgery :... May 2019Landsmeer ligaments play a significant role in synchronizing the movements of the two distal phalanges of the fingers. However, there is considerable controversy in...
Landsmeer ligaments play a significant role in synchronizing the movements of the two distal phalanges of the fingers. However, there is considerable controversy in descriptions of its anatomy, function, presence, and clinical applications. To ascertain and redefine the detailed anatomy of Oblique Retinacular (ORL) and Transverse Retinacular ligaments (TRL) and their applied features. Anatomical dissection study was conducted in 100 cadaveric fingers in 42 cadavers (28 fresh specimens and remaining preserved specimens) under loupe magnification. The whole dorsal digital expansion with attached fibrous flexor sheath was dissected and specimen was examined after thorough saline wash. The dimensions, course, attachment, and configuration were noted in each specimen. The statistical mean was obtained for thickness of the ligaments. The measurements were made using a caliper at the level of the mid proximal phalanx, volar to the proximal interphalangeal (PIP) joint, and dorsal to the distal interphalangeal (DIP) joint. By anatomical dissection we have found the following: • The ORL was deep to the TRL. • The ORL had got a check rein effect at the PIP joint, in such a way that extension of the PIP joint causes extension of the DIP joint. • The ORL criss-crossed volar to the A3 pulley of fibrous flexor sheath and formed a good hammock for the PIP joint. This criss-crossing anatomical feature was found in all dissected fingers as an additional normal anatomical feature complementing the classical description of Landsmeer. • Variations in configuration of the Landsmeer ligaments were observed among various fingers. • The Landsmeer ligament was never absent as reported by several studies. Contrary to several studies, the ORL was omnipresent in all dissected fingers with considerable variations in dimensions. Complementing the classical description of Landsmeer, we found that there was an additional normal criss-cross anatomical feature of the ORL in all fingers volar to A3 pulley and deep to the TRL. Also, the TRL was present in all the fingers.
PubMed: 31602135
DOI: 10.1055/s-0039-1695802 -
Journal of Pathology Informatics 2023Structured light three-dimensional (3D) scanning is a ubiquitous mainstay of object inspection and quality control in industrial manufacturing, and has recently been...
Structured light three-dimensional (3D) scanning is a ubiquitous mainstay of object inspection and quality control in industrial manufacturing, and has recently been integrated into various medical disciplines. Photorealistic 3D scans can readily be acquired from fresh or formalin-fixed tissue and have potential for use within anatomic pathology (AP) in a variety of scenarios, ranging from direct clinical care to documentation and education. Methods for scanning and post-processing of fresh surgical specimens rely on relatively low-cost and technically simple procedures. Here, we demonstrate potential use of 3D scanning in surgical pathology in the form of a mixed media pathology report with a novel post-scan virtual inking and marking technique to precisely demarcate areas of tissue sectioning and details of final tumor and margin status. We display a sample mixed-media pathology report (3D specimen map) which integrates 3D and conventional pathology reporting methods. Finally, we describe the potential utility of 3D specimen modeling in both didactic and experiential teaching of gross pathology lab procedures.
PubMed: 36687529
DOI: 10.1016/j.jpi.2022.100186 -
BMC Plant Biology Nov 2021Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland...
BACKGROUND
Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882-2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species.
RESULTS
We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin.
CONCLUSIONS
While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.
Topics: Phalaris; Poaceae; Polymerase Chain Reaction; Polymorphism, Single Nucleotide
PubMed: 34742253
DOI: 10.1186/s12870-021-03284-z -
Cancer Cytopathology Jun 2017With increasing requests for the evaluation of prognostic and predictive molecular biomarkers, great attention must be paid to the preanalytical issues regarding sample... (Review)
Review
With increasing requests for the evaluation of prognostic and predictive molecular biomarkers, great attention must be paid to the preanalytical issues regarding sample quality and DNA/RNA yield from all different types of cytological preparations. The objectives of this review were: 1) to provide an update regarding the importance of specimen triage as well as specimen handling and collection; 2) to discuss the different cell preparations that can be used for molecular testing, their advantages and limitations; and 3) to highlight the strategies for biobanking cytology samples. Good-quality DNA/RNA can be harvested from fresh cells in cell suspensions, formalin-fixed paraffin-embedded cell blocks, archival stained smears, archival unstained cytospin preparations, liquid-based cytology slides, FTA cards, and cryopreserved cells. In contrast to formalin-fixed paraffin-embedded tissue specimens (small biopsies and surgical resections), the multitude of types of sample preparations as well as the diversity in sample collection and processing procedures make cytology an ideal specimen for most genomic platforms, with less DNA and RNA degradation and a purer sample, usually with a higher concentration of tumor cells. The broad incorporation of cytological specimens into clinical practice. A should increase the number of samples potentially available for molecular tests and avoid repeat invasive procedures for tissue procurement, thereby increasing patient safety. In this context, it is of utmost importance that cytopathologists become familiar with the variables that can affect test results and embrace the goal of excellence in sample quality. Cancer Cytopathol 2017;125(6 suppl):455-64. © 2017 American Cancer Society.
Topics: Biopsy; Cryopreservation; Humans; Molecular Diagnostic Techniques; Neoplasms; Papanicolaou Test; Paraffin Embedding; Sequence Analysis, DNA; Sequence Analysis, RNA; Specimen Handling; Triage
PubMed: 28609003
DOI: 10.1002/cncy.21850 -
Current Fungal Infection Reports 2018The expanding population of immunocompromised patients coupled with the recognition of a growing number of different species of fungi responsible for diseases in such... (Review)
Review
PURPOSE OF REVIEW
The expanding population of immunocompromised patients coupled with the recognition of a growing number of different species of fungi responsible for diseases in such hosts makes the diagnosis of invasive fungal infection (IFI) a challenging task. The recent advances and challenges in the diagnosis of IFI in the setting of immunocompromised hosts are reviewed. The advantages and limitations of histopathology and the role of culture-independent methods, such as those based on the use of nucleic acids applied to fresh and formalin-fixed, paraffin-embedded sections, besides culture- and non-culture-based diagnostic methods, to obtain a timely and correct diagnosis of IFI are highlighted.
RECENT FINDINGS
The therapeutic implications of identifying the genus and species of the fungus present in the specimen with the molecular diagnostics applied to tissue specimens are reviewed. No method alone is efficient in correctly identifying fungi and it is essential to combine the traditional histochemical staining with molecular methods to achieve a rapid and genus-/species-specific diagnosis of IFI.
SUMMARY
We review the recent findings and challenges in the hystopathologic diagnosis of IFI in the setting of immunocompromised hosts. Non method alone is efficient in correctly identify fungi and pathologists should combine classic staining with molecular methods to achieve a rapid and genus/species fungal diagnosis.
PubMed: 32288934
DOI: 10.1007/s12281-018-0306-0 -
Archives of Razi Institute Apr 2022serovar Typhi () and paratyphi () bacteria exclusively found in humans, cause typhoid fever, an acute, and possibly deadly systemic infection. Typhoid fever is caused...
serovar Typhi () and paratyphi () bacteria exclusively found in humans, cause typhoid fever, an acute, and possibly deadly systemic infection. Typhoid fever is caused by a species of rod-shaped, Gram-negative Enterobacteriaceae called . The present study aimed to examine the gene and investigate the possible relation between this gene and multi-drug resistance in . A total of 30 blood samples were obtained from patients who were suspicious of typhoid fever using the direct strategy of inoculation. Each specimen was injected into a culture of a selective medium, such as XLD and SS agar, and then incubated at 37°C for 24 h. The genomic DNA was extracted through a boiling process. Tris-EDTA was used to suspend bacterial colonies cultured on MacConkey agar plates. The suspension of bacterial colonies was centrifuged for 5 min at 8000×g and for 20 min at -20°C which lyses the organisms and extracts the DNA from the buffer. The supernatant is then transferred to a fresh Eppendorf tube. Gel electrophoresis was carried out utilizing a UV transilluminator. The gene for was found using a PCR test. The antibiotic sensitivity testing showed that the isolates were classed as multi-resistant. These results were confirmed using the polymerase chain reaction (PCR) technique using gene where twenty specimens isolated from typhoid patients were positive for .
Topics: Humans; Agar; Anti-Bacterial Agents; Drug Resistance, Bacterial; Edetic Acid; Integrons; Salmonella paratyphi A; Salmonella typhi; Typhoid Fever
PubMed: 36284974
DOI: 10.22092/ARI.2021.356953.1944 -
Journal of the American Society of... Aug 2021Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a... (Review)
Review
Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. This review provides an overview of the technical challenges that should be addressed when designing single-cell transcriptomics experiments that focus on glomerulopathies. The isolation of glomerular cells from core needle biopsy specimens for single-cell transcriptomics remains difficult and depends upon five major factors. First, core needle biopsies generate little tissue material, and several samples are required to identify glomerular cells. Second, both fresh and frozen tissue samples may yield glomerular cells, although every experimental pipeline has different (dis)advantages. Third, enrichment for glomerular cells in human tissue before single-cell analysis is challenging because no effective standardized pipelines are available. Fourth, the current warm cell-dissociation protocols may damage glomerular cells and induce transcriptional artifacts, which can be minimized by using cold dissociation techniques at the cost of less efficient cell dissociation. Finally, snRNA-seq methods may be superior to scRNA-seq in isolating glomerular cells; however, the efficacy of snRNA-seq on core needle biopsy specimens remains to be proven. The field of single-cell omics is rapidly evolving, and the integration of these techniques in multiomics assays will undoubtedly create new insights in the complex pathophysiology of glomerular diseases.
Topics: Biopsy, Large-Core Needle; Cell Nucleus; Cell Separation; Flow Cytometry; Freezing; Gene Expression Profiling; Humans; Kidney Diseases; Kidney Glomerulus; Mesangial Cells; Podocytes; RNA; Sequence Analysis, RNA; Single-Cell Analysis
PubMed: 34140401
DOI: 10.1681/ASN.2021020157 -
Cancer Research Apr 2015Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it... (Review)
Review
Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.
Topics: Case-Control Studies; Formaldehyde; Frozen Sections; Gene Expression Profiling; Genomics; Genotyping Techniques; Humans; Oligonucleotide Array Sequence Analysis; Paraffin Embedding; Reproducibility of Results; Specimen Handling; Tissue Fixation
PubMed: 25836717
DOI: 10.1158/0008-5472.CAN-14-2378 -
Materials (Basel, Switzerland) Dec 2022This study will investigate the effect of non-woven PET plastic tissue on the fresh, physical, mechanical, acoustic, thermal, and microstructural behaviors of concrete....
This study will investigate the effect of non-woven PET plastic tissue on the fresh, physical, mechanical, acoustic, thermal, and microstructural behaviors of concrete. Including reference specimens, non-woven fabrics were considered in two ways: (a) as a layer with four various configurations of 1-layer, 2-sides, 3-sides, and full wrapping (4-sides) to strengthen specimens, and (b) as (10 × 10) mm cut pieces with three different incorporated percentages of 0.25%, 0.50%, and 0.75%. Based on the experimental results, mechanical properties (compressive, split tensile, and flexural strengths) were remarkably improved by applying non-woven sheets as a layer. For instance, the cylindrical compressive and split tensile strengths were improved by 13.40% and 15.12% for the strengthened specimens compared to the reference specimens, respectively. Moreover, control specimens were damaged to many fragments after mechanical testing, but the samples strengthened by such fabrics or containing cut pieces were maintained and not separated into many small parts. The acoustic behavior and thermal conductivity declined by 9.83% and 19.67% with the attachment of tissue on one side and 2-sides, respectively. Acoustic behaviors decreased by 10.0%, 17.60%, and 26.30% and thermal conductivity decreased by 6.60%, 12.10%, and 15.50%, with the incorporation of 0.25%, 0.50%, and 0.75% of cut pieces, respectively. Finally, it was discovered that non-woven tissue is advised to enhance particular properties of concrete.
PubMed: 36556586
DOI: 10.3390/ma15248766