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Surgical Pathology Clinics Mar 2018Lobular carcinoma in situ (LCIS) is a risk factor and a nonobligate precursor of breast carcinoma. The relative risk of invasive carcinoma after classic LCIS diagnosis... (Review)
Review
Lobular carcinoma in situ (LCIS) is a risk factor and a nonobligate precursor of breast carcinoma. The relative risk of invasive carcinoma after classic LCIS diagnosis is approximately 9 to 10 times that of the general population. Classic LCIS diagnosed on core biopsy with concordant imaging and pathologic findings does not mandate surgical excision, and margin status is not reported. The identification of variant LCIS in a needle core biopsy specimen mandates surgical excision, regardless of radiologic-pathologic concordance. The presence of variant LCIS close to the surgical margin of a resection specimen is reported, and reexcision should be considered.
Topics: Biopsy, Large-Core Needle; Breast Carcinoma In Situ; Carcinoma, Lobular; Disease Management; Female; Humans; Margins of Excision; Mastectomy, Segmental; Precancerous Conditions; Unnecessary Procedures; Watchful Waiting
PubMed: 29413653
DOI: 10.1016/j.path.2017.09.009 -
Anatomical Record (Hoboken, N.J. : 2007) Aug 2014In situ hybridization is a technique that is used to detect nucleotide sequences in cells, tissue sections, and even whole tissue. This method is based on the... (Review)
Review
In situ hybridization is a technique that is used to detect nucleotide sequences in cells, tissue sections, and even whole tissue. This method is based on the complementary binding of a nucleotide probe to a specific target sequence of DNA or RNA. These probes can be labeled with either radio-, fluorescent-, or antigen-labeled bases. Depending on the probe used, autoradiography, fluorescence microscopy, or immunohistochemistry, respectively, are used for visualization. In situ hybridization is extensively used in research, as well as clinical applications, especially for diagnostic purposes. This review discusses the basic technique of in situ hybridization. The standard in situ hybridization process is reviewed, and different types of in situ hybridization, their applications, and advantages and disadvantages are discussed.
Topics: Autoradiography; Humans; In Situ Hybridization; Isotope Labeling; Microscopy, Fluorescence; Paraffin Embedding; RNA Probes; Tissue Fixation
PubMed: 24810158
DOI: 10.1002/ar.22944 -
Methods in Enzymology 2016Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single cells could revolutionize our understanding...
Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single cells could revolutionize our understanding of a variety of cellular and tissue behaviors in both healthy and diseased states. Single-molecule fluorescence in situ hybridization (smFISH)-an approach where individual RNAs are labeled with fluorescent probes and imaged in their native cellular and tissue context-provides both the copy number and spatial context of RNAs but has been limited in the number of RNA species that can be measured simultaneously. Here, we describe multiplexed error-robust fluorescence in situ hybridization (MERFISH), a massively parallelized form of smFISH that can image and identify hundreds to thousands of different RNA species simultaneously with high accuracy in individual cells in their native spatial context. We provide detailed protocols on all aspects of MERFISH, including probe design, data collection, and data analysis to allow interested laboratories to perform MERFISH measurements themselves.
Topics: Animals; Base Sequence; Fluorescent Dyes; Humans; In Situ Hybridization, Fluorescence; Oligonucleotide Probes; RNA; Single-Cell Analysis; Transcriptome
PubMed: 27241748
DOI: 10.1016/bs.mie.2016.03.020 -
Biomedicines Oct 2021Understanding the processes of inflammation and tissue regeneration after injury is of great importance. For a long time, macrophages have been known to play a central... (Review)
Review
Understanding the processes of inflammation and tissue regeneration after injury is of great importance. For a long time, macrophages have been known to play a central role during different stages of inflammation and tissue regeneration. However, the molecular and cellular mechanisms by which they exert their effects are as yet mostly unknown. While in vitro macrophages have been characterized, recent progress in macrophage biology studies revealed that macrophages in vivo exhibited distinctive features. Actually, the precise characterization of the macrophages in vivo is essential to develop new healing treatments and can be approached via in situ analyses. Nowadays, the characterization of macrophages in situ has improved significantly using antigen surface markers and cytokine secretion identification resulting in specific patterns. This review aims for a comprehensive overview of different tools used for in situ macrophage identification, reporter genes, immunolabeling and in situ hybridization, discussing their advantages and limitations.
PubMed: 34680510
DOI: 10.3390/biomedicines9101393 -
Cell Reports Methods Apr 2022We describe a cost-effective, highly sensitive, and quantitative method for detection of RNA molecules in tissue sections. This method, dubbed Yn-situ, standing for...
We describe a cost-effective, highly sensitive, and quantitative method for detection of RNA molecules in tissue sections. This method, dubbed Yn-situ, standing for Y-branched probe hybridization, uses a single-strand DNA preamplifier with multiple initiation sites that trigger a hybridization chain reaction (HCR) to detect polynucleotides. By characterizing the performance of this method, we show that the Yn-situ method, in conjunction with an improved fixation step, is sensitive enough to allow detection of RNA molecules using fewer probes targeting short nucleotide sequences than existing methods. A set of five probes can produce quantitative results with smaller puncta and higher signal-to-noise ratio than the 20-probe sets commonly required for HCR and RNAscope. We show that the high sensitivity and wide dynamic range allow quantification of genes expressed at different levels in the olfactory sensory neurons. We describe key steps of this method to enable broad utility by individual laboratories.
Topics: RNA; In Situ Hybridization; Signal-To-Noise Ratio; Base Sequence
PubMed: 35497500
DOI: 10.1016/j.crmeth.2022.100201 -
Frontiers in Chemistry 2022Nanomedicines provide distinct clinical advantages over traditional monomolecular therapeutic and diagnostic agents. Supramolecular nanomedicines made from... (Review)
Review
Nanomedicines provide distinct clinical advantages over traditional monomolecular therapeutic and diagnostic agents. Supramolecular nanomedicines made from self-assembling peptides have emerged as a promising strategy in designing and fabricating nanomedicines. self-assambly (SA) allows the combination of nanomedicines approach with prodrug approach, which exhibited both advantages of these strategies while addressed the problems of both and thus receiving more and more research attention. In this review, we summarized recently designed supramolecular nanomedicines of SA peptides in the manner of applications and design principles, and the interaction between the materials and biological environments was also discussed.
PubMed: 35186883
DOI: 10.3389/fchem.2022.815551 -
Transplantation May 2023Ischemia-free liver transplantation (IFLT) has been innovated to avoid graft ischemia during organ procurement, preservation, and implantation. However, the metabolism...
BACKGROUND
Ischemia-free liver transplantation (IFLT) has been innovated to avoid graft ischemia during organ procurement, preservation, and implantation. However, the metabolism activity of the donor livers between in the in situ and ex situ normothermic machine perfusion (NMP) conditions, and between standard criteria donor and extend criteria donor remains unknown.
METHODS
During IFLT, plasma samples were collected both at the portal vein and hepatic vein of the donor livers in situ during procurement and ex situ during NMP. An ultra-high performance liquid chromatography-mass spectrometry was conducted to investigate the common and distinct intraliver metabolite exchange.
RESULTS
Profound cysteine and methionine metabolism, and aminoacyl-tRNA biosynthesis were found in both in situ and ex situ conditions. However, obvious D-arginine and D-ornithine metabolism, arginine and proline metabolism were only found in the in situ condition. The suppressed activities of the urea cycle pathway during ex situ condition were confirmed in an RNA expression level. In addition, compared with extend criteria donor group, standard criteria donor group had more active intraliver metabolite exchange in metabonomics level. Furthermore, we found that the relative concentration of p-cresol, allocystathionine, L-prolyl-L-proline in the ex situ group was strongly correlated with peak alanine aminotransferase and aspartate aminotransferase at postoperative days 1-7.
CONCLUSIONS
In the current study, we show the common and distinct metabolism activities during IFLT. These findings might provide insights on how to modify the design of NMP device, improve the perfusate components, and redefine the criteria of graft viability.
Topics: Humans; Liver Transplantation; Organ Preservation; Living Donors; Tissue and Organ Procurement; Perfusion; Liver
PubMed: 36857152
DOI: 10.1097/TP.0000000000004529 -
Nanomaterials (Basel, Switzerland) Jun 2023Metal halide perovskite materials have demonstrated significant potential in various optoelectronic applications, such as photovoltaics, light emitting diodes,... (Review)
Review
Metal halide perovskite materials have demonstrated significant potential in various optoelectronic applications, such as photovoltaics, light emitting diodes, photodetectors, and lasers. However, the stability issues of perovskite materials continue to impede their widespread use. Many studies have attempted to understand the complex degradation mechanism and dynamics of these materials. Among them, in situ and/or operando approaches have provided remarkable insights into the degradation process by enabling precise control of degradation parameters and real-time monitoring. In this review, we focus on these studies utilizing in situ and operando approaches and demonstrate how these techniques have contributed to reveal degradation details, including structural, compositional, morphological, and other changes. We explore why these two approaches are necessary in the study of perovskite degradation and how they can be achieved by upgrading the corresponding ex situ techniques. With recent stability improvements of halide perovskite using various methods (compositional engineering, surface engineering, and structural engineering), the degradation of halide perovskite materials is greatly retarded. However, these improvements may turn into new challenges during the investigation into the retarded degradation process. Therefore, we also highlight the importance of enhancing the sensitivity and probing range of current in situ and operando approaches to address this issue. Finally, we identify the challenges and future directions of in situ and operando approaches in the stability research of halide perovskites. We believe that the advancement of in situ and operando techniques will be crucial in supporting the journey toward enhanced perovskite stability.
PubMed: 37446498
DOI: 10.3390/nano13131983 -
Frontiers in Microbiology 2022Environmental microorganisms are important sources of biotechnology innovations; however, the discovery process is hampered by the inability to culture the overwhelming...
Environmental microorganisms are important sources of biotechnology innovations; however, the discovery process is hampered by the inability to culture the overwhelming majority of microbes. To drive the discovery of new biotechnology products from previously unculturable microbes, several methods such as modification of media composition, incubation conditions, single-cell isolation, and incubation, have been employed to improve microbial recovery from environmental samples. To improve microbial recovery, we examined the effect of microencapsulation followed by incubation on the abundance, viability, and diversity of bacteria recovered from marine sediment. Bacteria from marine sediment samples were resuspended or encapsulated in agarose and half of each sample was directly plated on agar and the other half inserted into modified Slyde-A-Lyzer™ dialysis cassettes. The cassettes were incubated in their natural environment () for a week, after which they were retrieved, and the contents plated. Colony counts indicated that bacterial abundance increased during incubation and that cell density was significantly higher in cassettes containing non-encapsulated sediment bacteria. Assessment of viability indicated that a higher proportion of cells in encapsulated samples were viable at the end of the incubation period, suggesting that agarose encapsulation promoted higher cell viability during incubation. One hundred and 46 isolates were purified from the study (32-38 from each treatment) to assess the effect of the four treatments on cultivable bacterial diversity. In total, 58 operational taxonomic units (OTUs) were identified using a 99% 16S rRNA gene sequence identity threshold. The results indicated that encapsulation recovered greater bacterial diversity from the sediment than simple resuspension (41 vs. 31 OTUs, respectively). While the cultivable bacterial diversity decreased by 43%-48% after incubation, difficult-to-culture () and obligate marine () taxa were only recovered after incubation. These results suggest that agarose encapsulation coupled with incubation in commercially available, low-cost, diffusion chambers facilitates the cultivation and improved recovery of bacteria from marine sediments. This study provides another tool that microbiologists can use to access microbial dark matter for environmental, biotechnology bioprospecting.
PubMed: 36071955
DOI: 10.3389/fmicb.2022.958660 -
International Journal of Bioprinting 2023bioprinting has emerged as a promising technology for tissue and organ engineering based on the precise positioning of living cells, growth factors, and biomaterials.... (Review)
Review
bioprinting has emerged as a promising technology for tissue and organ engineering based on the precise positioning of living cells, growth factors, and biomaterials. Rather than traditional reconstruction and recapitulation of tissue or organ models, the technology can directly print on specific anatomical positions in living bodies. The requirements for biological activity, function, and mechanical property in an setting are more complex. By combining progressive innovations of biomaterials, tissue engineering, and digitalization, especially robotics, bioprinting has gained significant interest from the academia and industry, demonstrating its prospect for clinical studies. This article reviews the progress of bioprinting, with an emphasis on robotic-assisted studies. The main modalities for three-dimensional bioprinting, which include extrusion-based printing, inkjet printing, laser-based printing, and their derivatives, are briefly introduced. These modalities have been integrated with various custom-tailored printers (.., end effectors) mounted on robotic arms for dexterous and precision biofabrication. The typical prototypes based on various robot configurations, including Cartesian, articulated, and parallel mechanisms, for bioprinting are discussed and compared. The conventional and most recent applications of robotic-assisted methods for fabrication of tissue and organ models, including cartilage, bone, and skin, are also elucidated, followed by a discussion on the existing challenges in this field with their corresponding suggestions.
PubMed: 36636132
DOI: 10.18063/ijb.v9i1.629