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At least 703 records · Page 39Linked to original sources
PubMed2003

Isolation of Halobacterium salinarum retrieved directly from halite brine inclusions.

Halite crystals were selected from a 186 m subsurface core taken from the Badwater salt pan, Death Valley, California to ascertain if halophilic Archaea and their associated 16S rDNA can survive over several tens of thousands of years. Using a combined microscope microdrill/micropipette system, fluids from brine inclusions were aseptically extracted from primary, hopper texture, halite crystals from 8 and 85 metres below the surface (mbls). U-Th disequilibrium dating indicates that these halite layers were deposited at 9,600 and 97,000 years before present (ybp) respectively. Extracted inclusions were used for polymerase chain reaction (PCR) analysis with haloarchaea-specific 16S rDNA primers or placed into haloarchaea culture medium. Enrichment cultures were obtained from 97 kyr halite crystal inclusion fluid and haloarchaea-containing prepared crystals (positive controls), whereas inclusions from crystals of 9.6 kyr halite and the haloarchaea-free halite crystals (negative controls) resulted in no growth. Phylogenetic analysis (16S rDNA) of the 97 kyr isolate, designated BBH 001, revealed a homology of 100% with Halobacterium salinarum. DNA-DNA hybridization experiments confirmed that BBH 001 was closely related to H. salinarum (81-75% hybridization) and its ascription to this haloarchaea species. The described method of retrieving particle-containing brine from fluid inclusions offers a robust approach for assessing the antiquity of microorganisms associated with evaporites.

Base Composition↗
PubMed2025

Inclusion of Physical-Chemical Water Quality Measurements Can Improve Associations between SARS-CoV-2 RNA Levels in Wastewater and COVID-19 Cases within Smaller Sewersheds.

Measurements of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in wastewater can be used to understand the prevalence of COVID-19 cases within a community. Environmental conditions inclusive of physical-chemical water quality characteristics are known to impact wastewater SARS-CoV-2 signals, but they are rarely measured within the sewer infrastructure in areas upstream of wastewater treatment plants (WWTPs). The objectives of this study were to report on measurements of environmental parameters [flow and physical-chemical water quality (water temperature, pH, specific conductivity, dissolved oxygen, and turbidity)] upstream of a WWTP and to evaluate whether the inclusion of these environmental parameters improves correlations between SARS-CoV-2 RNA levels in wastewater, and COVID-19 prevalence in the sewershed community. Measurements of environmental parameters and SARS-CoV-2 RNA in wastewater spanned different time scales (minutes, hours and weeks) and population scales (building, campus, community). For short time scales, water quality parameters did not improve correlations between SARS-CoV-2 in wastewater and COVID-19 prevalence due to high variability of water quality and flows within the sewer system. When averaging data over weekly time scales, regressions showed that inclusion of pH improved correlations between RNA and COVID-19 prevalence. At the cluster scale, for the entire data set, the root mean square error decreased from 6.9 cases per week to 6.5 cases per week. At the community scale benefits were observed only for the delta wave with a decrease in root mean square error from 539 cases per week to 430 cases per week. The inclusion of pH improved correlations between wastewater SARS-CoV-2 and COVID-19 prevalence more frequently when evaluating the cluster sewershed scale (populations of a few thousand) in comparison to the community scale (populations of several 100,000). Given the simplicity of measuring pH and other physical-chemical water quality parameters, their inclusion should be considered as part of wastewater-based epidemiology programs.

COVID-19↗
PubMed2005

Prolyl-isomerase Pin1 accumulates in lewy bodies of parkinson disease and facilitates formation of alpha-synuclein inclusions.

Parkinson disease (PD) is a relatively common neurodegenerative disorder that is characterized by the loss of dopaminergic neurons and by the formation of Lewy bodies (LBs), which are cytoplasmic inclusions containing aggregates of alpha-synuclein. Although certain post-translational modifications of alpha-synuclein and its related proteins are implicated in the genesis of LBs, the specific molecular mechanisms that both regulate these processes and initiate subsequent inclusion body formation are not yet well understood. We demonstrate in our current study, however, that the prolyl-isomerase Pin1 localizes to the LBs in PD brain tissue and thereby enhances the formation of alpha-synuclein immunoreactive inclusions. Immunohistochemical analysis of brain tissue from PD patients revealed that Pin1 localizes to 50-60% of the LBs that show an intense halo pattern resembling that of alpha-synuclein. By utilizing a cellular model of alpha-synuclein aggregation, we also demonstrate that, whereas Pin1 overexpression facilitates the formation of alpha-synuclein inclusions, dominant-negative Pin1 expression significantly suppresses this process. Consistent with these observations, Pin1 overexpression enhances the protein half-life and insolubility of alpha-synuclein. Finally, we show that Pin1 binds synphilin-1, an alpha-synuclein partner, via its Ser-211-Pro and Ser-215-Pro motifs, and enhances its interaction with alpha-synuclein, thus likely facilitating the formation of alpha-synuclein inclusions. These results indicate that Pin1-mediated prolyl-isomerization plays a pivotal role in a post-translational modification pathway for alpha-synuclein aggregation and in the resultant Lewy body formations in PD.

Amino Acid Sequence↗
PubMed2006

RBM4 interacts with an intronic element and stimulates tau exon 10 inclusion.

Tau protein, which binds to and stabilizes microtubules, is critical for neuronal survival and function. In the human brain, tau pre-mRNA splicing is regulated to maintain a delicate balance of exon 10-containing and exon 10-skipping isoforms. Splicing mutations affecting tau exon 10 alternative splicing lead to tauopathies, a group of neurodegenerative disorders including dementia. Molecular mechanisms regulating tau alternative splicing remain to be elucidated. In this study, we have developed an expression cloning strategy to identify splicing factors that stimulate tau exon 10 inclusion. Using this expression cloning approach, we have identified a previously unknown tau exon 10 splicing regulator, RBM4 (RNA binding motif protein 4). In cells transfected with a tau minigene, RBM4 overexpression leads to an increased inclusion of exon 10, whereas RBM4 down-regulation decreases exon 10 inclusion. The activity of RBM4 in stimulating tau exon 10 inclusion is abolished by mutations in its RNA-binding domain. A putative intronic splicing enhancer located in intron 10 of the tau gene is required for the splicing stimulatory activity of RBM4. Immunohistological analyses reveal that RBM4 is expressed in the human brain regions affected in tauopathy, including the hippocampus and frontal cortex. Our study demonstrates that RBM4 is involved in tau exon 10 alternative splicing. Our work also suggests that down-regulating tau exon 10 splicing activators, such as RBM4, may be of therapeutic potential in tauopathies involving excessive tau exon 10 inclusion.

Adult↗
PubMed2002

Omental malignant fibrous histiocytoma with a unique rough endoplasmic reticulum inclusion.

The laminated inclusions in the rough endoplasmic reticulum (RER) are peculiar structures seen only in some cases of chondrocytes of pseudoachondroplasia. These ultrastructurally unique organelles have not yet been reported in inflammatory malignant fibrous histiocytoma (MFH). We describe an omental mass showing unique laminated inclusions in the RER in a young man with intra-abdominal inflammatory MFH. The most striking ultrastructural feature was a dilated RER containing a fine granular substance and a more electron-dense material exhibiting an onion skin-like lamellated or maze-like pattern, mimicking that of so-called laminated inclusions. These lamellated inclusions occupied most of the cytoplasm of the tumor cells. We speculate that the ultrastructural finding of the laminated RER inclusion is not specific for cartilage cells, but may represent abnormal accumulation of some kind of glycoprotein material or matrix protein. This granular material may undergo organization to form a peculiar laminated structure, probably due to a metabolic or fixation process. Further study is needed to elucidate the nature of this material.

Adult↗
PubMed1999

Considerations in educating deaf and hard-of-hearing students in inclusive settings.

This article provides an overview of key issues pertinent to an inclusive approach to the education of deaf students in order to establish a context for interpreting and integrating the articles in this issue. It discusses definitions of inclusion, integration, and mainstreaming from placement-related, philosophical, and pragmatic perspectives. The article provides demographic information pertinent to an inclusive approach. It also compares perspectives on inclusion in the general field of special education with those in the education of deaf and hard-of-hearing students. It considers the challenges of using an inclusive approach to achieve academic and social integration of students, as based on research on the learning and adjustment of deaf and hard-of-hearing students in regular classes. The article concludes with an overview of the topics addressed in the issue.

Journal Article↗
PubMed2000

Some mullerian inclusion cysts in lymph nodes may sometimes be metastases from serous borderline tumors of the ovary.

Glandular inclusions that appear morphologically benign are occasionally found in lymph nodes as well as in peritoneal and omental biopsies. In patients with gynecologic malignancies, the nature and significance of these mullerian inclusion cysts (MIC) present a diagnostic challenge with regard to whether they are benign and incidental or are related to the coincident tumor for which surgery is being performed. Sixty-two cases of MIC were prospectively identified during a 6-year period. The frequencies were calculated and stratified by lymph node chain distribution, primary tumor site, and primary tumor type. MIC appeared as small cysts lined by a serous (mullerian)-type, cytologically bland, cuboidal to columnar epithelium with a simple architecture. Among 62 women, MIC was found in lymph nodes (27 cases), pelvic peritoneum (19 cases), omentum (16 cases), bowel serosa (9 cases), uterine serosa (8 cases), and parametrial connective tissues (4 cases). Among a set of 417 consecutive cases in which lymphadenectomy was performed, 46 (11%) women had MIC. The MIC involved multiple sites (26 cases in the peritoneum/omentum and 27 in lymph nodes). The primary tumor was in the ovary in 32 of the 46 women with MIC (70%) and of these, 17 were borderline serous (53%). Sixty-two of 6,154 lymph nodes examined contained MIC (1.0%). 3.2% of nodes contained MIC in which the primary tumor arose in the ovary, but only 0.1% with either endometrial or cervical tumors (chi2, p <0.00001). The lymph nodes most often involved by MIC were from para-aortic sites (40%), which reflect the primary drainage route from the ovary. Not uncommonly, neighboring areas in the same lymph node group with MIC disclosed separate foci of obvious metastatic borderline tumor (4 of 10; 40%). In summary, the increased frequency of MIC in lymph nodes sampled for primary ovarian malignancies suggests that MIC in some cases, rather than being benign, incidental inclusions, are more likely bland-appearing forms of metastatic tumor. The preponderance of inclusions occurs with serous ovarian tumors of borderline malignancy, and the inclusions are overrepresented in the lymph nodes that primarily receive drainage from the ovary.

Cysts↗
PubMed1982

Inclusions in ovaries of females aged day 1-30 years.

This study was an examination of ovaries in the age group day 1-30 years. One hundred eight cystic epithelial inclusions cysts were found in 40 ovaries in the age group of day 1-7 years. All were lined by cuboidal and low columnar epithelium. A total of 81 cystic epithelial inclusions were found in 58 ovaries in individuals aged 12-30 years. Thirty four were lined by endosalpingeal cells, reflecting metaplasia of the epithelium. Metaplasia may be induced hormonally as none of the inclusions in premenarchal ovaries showed similar changes. In two cases in which an ectopic pregnancy was present in the fallopian tube, inclusions were lined by cells resembling those described by Arias-Stella, further strengthening the view that surface epithelium covering the ovary and lining cystic epithelial inclusions is responsive hormonally.

Adolescent↗
PubMed1995

Borderline and malignant serous tumor arising in pelvic lymph nodes: evidence of origin in benign glandular inclusions.

This report describes two cases of malignant serous cancers with areas of borderline malignancy, which appear to have arisen within benign glandular inclusions of coelomic origin in pelvic or para-aortic lymph nodes. The patients were 44 and 62 years of age. In both cases the nodes contained benign glandular inclusions lined by a single layer of epithelium which resembled that of tubal epithelium. The location of the glandular epithelium varied from within the fat near the node to intracapsular, subcapsular, or interfollicular positions. The number of glands ranged from few to extensive. In both cases the glandular inclusions disclosed epithelial proliferations, ranging from minor degrees of stratification with formation of small papillae of atypical cells (borderline serous tumor) to almost solid tumor typical of serous cancer. In both cases, the borderline and cancerous tumors exhibited areas of transition which appeared to arise from benign glands. Although benign glandular inclusions of coelomic origin are well documented to occur in pelvic or para-aortic lymph nodes of 5-20% of women and have been considered to be of significance only because of the possibility of the misdiagnosis of cancer, it should now be recognized that the glandular inclusion cysts themselves can become neoplastic.

Adult↗
PubMed1998

Abnormal expression of brush-border membrane transporters in the duodenal mucosa of two patients with microvillus inclusion disease.

BACKGROUND: Microvillus inclusion disease is a congenital disorder characterized by secretory diarrhea. Patients demonstrate villus atrophy, loss of microvilli, and internalized inclusions of microvilli within the cytoplasm of small intestinal enterocytes. The exact molecular defect in these patients is not known. Two infants are described in this report with microvillus inclusion disease. Case 1 was a 3-month-old boy who developed secretory diarrhea shortly after birth. Case 2 was a 9-month-old boy who had abrupt onset diarrhea at 2 weeks of age resulting in weight loss and dehydration. Light microscopy revealed total villus atrophy with minimal crypt hyperplasia, and electron microscopic examination revealed variably shortened microvilli and cytoplasmic microvillus inclusions in both patients. METHODS: Poly (A)+ RNA was purified from duodenal biopsies and RT-PCR reactions were performed. Normal human intestinal RNA was used as a positive control. Primers specific for human NHE-1, NHE-2, NHE-3 (2 sets), sodium-glucose transporter (SGLT1), and beta-actin were used. RESULTS: Results showed that NHE-1 and beta-actin cDNAs amplified to similar levels in both patient and control samples. However, the expression of NHE-2 and SGLT1 was much higher in the control sample than in the patient samples. Additionally, NHE-3 mRNA was not detected in the patient samples using two sets of NHE-3 specific primers. CONCLUSIONS: The patients with microvillus inclusion disease have defects in apical but not basolateral membrane transport systems, and these defects are related to the pathogenesis of the disease.

Diarrhea↗
PubMed2006

Social inclusion in workplaces where people with intellectual disabilities are employed: implications for supported employment professionals.

This research investigated elements of workplace culture across eight New Zealand workplaces where people with intellectual disability were employed. Using a semi-structured interview format, eight employers were surveyed, and variations in job entry procedures, orientation and training, company policies, job design, customs and practice, and social opportunities were examined. Factors influencing inclusion in the workplace culture of a total of 16 employees, eight supported employees and eight co-workers without disabilities, were identified and compared. The findings indicated that supported workers had a lower level of inclusion than co-workers. Several factors influencing inclusion of employees in the workplace culture were identified; full-time vs. part-time, level of employment support, limiting expectations and employer/co-worker attitudes. The use of a workplace culture survey by supported employment professionals has several benefits, including the identification of potentially inclusive workplaces, the facilitation of a good person and workplace environment match, the possibility of monitoring inclusion levels, encouragement of full work shift placements, and the provision of effective support on the job.

Humans↗
PubMed1990

How to measure inclusive fitness.

Although inclusive fitness (Hamilton 1964) is regarded as the basic currency of natural selection, difficulty in applying inclusive fitness theory to field studies persists, a quarter-century after its introduction (Grafen 1982, 1984; Brown 1987). For instance, strict application of the original (and currently accepted) definition of inclusive fitness predicts that no one should ever attempt to breed among obligately cooperative breeders. Much of this confusion may have arisen because Hamilton's (1964) original verbal definition of inclusive fitness was not in complete accord with his justifying model. By re-examining Hamilton's original model, a modified verbal definition of inclusive fitness can be justified.

Animals↗
PubMed1999

From neuronal inclusions to neurodegeneration: neuropathological investigation of a transgenic mouse model of Huntington's disease.

Huntington's disease (HD) is an inherited progressive neurodegenerative disease caused by the expansion of a polyglutamine repeat sequence within a novel protein. Recent work has shown that abnormal intranuclear inclusions of aggregated mutant protein within neurons is a characteristic feature shared by HD and several other diseases involving glutamine repeat expansion. This suggests that in each of the these disorders the affected nerve cells degenerate as a result of these abnormal inclusions. A transgenic mouse model of HD has been generated by introducing exon 1 of the HD gene containing a highly expanded CAG sequence into the mouse germline. These mice develop widespread neuronal intranuclear inclusions and neurodegeneration specifically within those areas of the brain known to degenerate in HD. We have investigated the sequence of pathological changes that occur after the formation of nuclear inclusions and that precede neuronal cell death in these cells. Although the relation between inclusion formation and neurodegeneration has recently been questioned, a full characterization of the pathways linking protein aggregation and cell death will resolve some of these controversies and will additionally provide new targets for potential therapies.

Animals↗
PubMed2006

Director configuration and self-organization of inclusions in two-dimensional smectic membranes.

The behavior of isolated inclusions (nematic droplets, smectic islands) and formation of chains and clusters from inclusions in oriented smectic membranes have been studied. Investigations of inclusions were performed in membranes in which the molecular ordering was oriented by an external magnetic field. At planar boundary conditions on the interface between the membrane and inclusions different configurations of the c-director field were observed: Coulombic, dipolar, quadrupolar, and mixed. The observed orientation of inclusions and their interactions and self-organization correlate with the predictions of the theory based on the electromagnetic analogy. Chaining and formation of superstructures differ in oriented and nonoriented membranes.

Journal Article↗
PubMed2006

Finite-element simulation of the depolarization factor of arbitrarily shaped inclusions.

An understanding of the polarization characteristics is a prevailing issue in electrostatics and scattering theory and is also vital to the rational design of future dielectric nanostructures. In this work, a finite-element methodology has been applied to simulate two-phase heterostructures containing a polarizable dielectric inclusion. The inclusions investigated can be considered as arbitrarily shaped cross sections of infinite three-dimensional objects, where the properties and characteristics are invariant along the perpendicular cross-sectional plane. Given the paucity of experimental and numerical data, we set out to systematically investigate the trends that shape and permittivity contrast between the inclusion and the host matrix have on the depolarization factor (DF). The effect of the first-versus second-order concentration virial coefficient on the value of the DF is considered for a variety of inclusion shapes and a large set of material properties. Our findings suggest that the DF for such inclusions is highly tunable depending on the choice of these parameters. These results can provide a useful insight for the design of artificial two-phase heterostructures with specific polarization properties.

Journal Article↗
PubMed2003

Inclusion compounds of 2,5-diphenylhydroquinone.

The crystal structures of three 1:2 inclusion compounds that consist of host molecule 2,5-diphenylhydroquinone (C(18)H(14)O(2)) and the guest molecules 2-pyridone (C(5)H(5)NO), 1,3-diphenyl-2-propen-1-one (chalcone, C(15)H(12)O) and 1-(4-methoxyphenyl)-3-phenyl-2-propen-1-one (4'-methoxychalcone, C(16)H(14)O(2)) were determined in order to study the ability of guest molecules in inclusion compounds to undergo photoreaction. All of the crystals were found to be photoresistant. The three inclusion compounds crystallize in triclinic space group P1. In each case, the host/guest ratio is 1:2, with the host molecules occupying crystallographic centers of symmetry and the guest molecules occupying general positions. The guest molecules in each of the inclusion compounds are linked to the host molecules by hydrogen bonds. In the inclusion compound where the guest molecule is pyridone, the host molecule is disordered so that the hydroxy groups are distributed between two different sites, with occupancies of 0.738 (3) and 0.262 (3). The pyridone molecules form dimers via N-H...O hydrogen bonds.

Journal Article↗
PubMed2005

Inclusion filters: a class of self-dual connected operators.

In this paper, we define a connected operator that either fills or retains the holes of the connected sets depending on application-specific criteria that are increasing in the set theoretic sense. We refer to this class of connected operators as inclusion filters, which are shown to be increasing, idempotent, and self dual (gray-level inversion invariance). We demonstrate self duality for 8-adjacency on a discrete Cartesian grid. Inclusion filters are defined first for binary-valued images, and then the definition is extended to grayscale imagery. It is also shown that inclusion filters are levelings, a larger class of connected operators. Several important applications of inclusion filters are demonstrated-automatic segmentation of the lung cavities from magnetic resonance imagery, user interactive shape delineation in content-based image retrieval, registration of intravital microscopic video sequences, and detection and tracking of cells from these sequences. The numerical performance measures on 100-cell tracking experiments show that the use of inclusion filter improves the total number of frames successfully tracked by five times and provides a threefold reduction in the overall position error.

Algorithms↗
PubMed1994

Characterization of NTPase, RNA-binding and RNA-helicase activities of the cytoplasmic inclusion protein of tamarillo mosaic potyvirus.

The 66-kDa cytoplasmic inclusion protein of tamarillo mosaic potyvirus was purified to near homogeneity using organic solvent clarification, differential centrifugation and sucrose density gradient centrifugation. ATPase and GTPase activities were shown to co-purify with the 66-kDa protein. ATPase activity was stimulated up to fivefold in the presence of 20 microM poly(A). The Km value for ATP hydrolysis (18 microM), was minimally affected upon addition of poly(A). In contrast, the Vmax value for ATP hydrolysis was increased fivefold by the addition of poly(A). Binding of RNA by the cytoplasmic inclusion protein was demonstrated by gel electrophoresis of ultraviolet cross-linked enzyme-RNA complexes. In the absence of added NTP, complexes between the cytoplasmic inclusion protein and single-stranded RNA species formed rapidly in the pH range 3-7, but not at pH 8 or 9. Binding to single-stranded RNA was markedly decreased by the addition of NaCl (10 mM), suggesting a weak association between RNA and enzyme. The cytoplasmic inclusion protein bound single-stranded RNA or partially double-stranded RNA duplexes with single-stranded overhangs of 35 bases and 81 bases, respectively, but did not bind 16-bp blunt-ended double-stranded RNA. RNA binding occurred in the absence of NTP (ATP, GTP, CTP or UTP), whereas dissociation of bound RNA occurred only in the presence of NTP. RNA duplex unwinding (helicase) activity of the enzyme was demonstrated in the presence of any of the above four NTPs using partially double-stranded RNA duplexes with 3' single-stranded overhangs. We propose that the cytoplasmic inclusion protein of tamarillo mosaic virus is an RNA helicase, which translocates in the 3' to 5' direction in an energy-dependent manner, unwinding double-stranded regions.

Acid Anhydride Hydrolases↗