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Sample records for revealed granular cell

  1. Cell-Targeted Optogenetics and Electrical Microstimulation Reveal the Primate Koniocellular Projection to Supra-granular Visual Cortex.

    Science.gov (United States)

    Klein, Carsten; Evrard, Henry C; Shapcott, Katharine A; Haverkamp, Silke; Logothetis, Nikos K; Schmid, Michael C

    2016-04-06

    Electrical microstimulation and more recently optogenetics are widely used to map large-scale brain circuits. However, the neuronal specificity achieved with both methods is not well understood. Here we compare cell-targeted optogenetics and electrical microstimulation in the macaque monkey brain to functionally map the koniocellular lateral geniculate nucleus (LGN) projection to primary visual cortex (V1). Selective activation of the LGN konio neurons with CamK-specific optogenetics caused selective electrical current inflow in the supra-granular layers of V1. Electrical microstimulation targeted at LGN konio layers revealed the same supra-granular V1 activation pattern as the one elicited by optogenetics. Taken together, these findings establish a selective koniocellular LGN influence on V1 supra-granular layers, and they indicate comparable capacities of both stimulation methods to isolate thalamo-cortical circuits in the primate brain. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Granular Cell Tumor

    African Journals Online (AJOL)

    1). Her packed cell volume was 40%, she was system, gastro-intestinal tract, brain, heart, and negative to human immunodeficiency virus. 2 female reproductive . ... histocytes and neurons at various times. They granules. The granules are probably of lysosmal were consequently termed granular cell origin and contain ...

  3. Paediatric laryngeal granular cell tumour

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    Dauda Ayuba

    2009-01-01

    Full Text Available Granular cell tumour (GCT affecting the larynx is not common, especially in children. Most cases are apt to be confused with respiratory papilloma and may even be mistaken for a malignant neoplasia. We present a case of laryngeal GCT in a 12-year-old child to emphasize that the tumour should be regarded in the differential of growths affecting the larynx in children.

  4. Periurethral granular cell tumor: a case report

    International Nuclear Information System (INIS)

    Kim, Jeong Kon; Choi, Hyo Gyeong; Cho, Kyoung Sik

    1998-01-01

    Granular cell tumors are uncommon soft tissue tumors which arise as solitary or multiple masses. Lesions commonly arise in the head, neck, and chest wall, but can occur in any part of the body. To our knowledge, periurethral granular cell tumor has not been previously reported. We report one such case

  5. Granular cell tumor: An uncommon benign neoplasm

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    Tirthankar Gayen

    2015-01-01

    Full Text Available Granular cell tumor is a distinctly rare neoplasm of neural sheath origin. It mainly presents as a solitary asymptomatic swelling in the oral cavity, skin, and rarely internal organs in the middle age. Histopathology is characteristic, showing polyhedral cells containing numerous fine eosinophilic granules with indistinct cell margins. We present a case of granular cell tumor on the back of a 48-year-old woman which was painful, mimicking an adnexal tumor.

  6. Granular cells Tumor in the gastrointestinal tract

    International Nuclear Information System (INIS)

    Castano LL, Rodrigo; Gaitan B, Maria H; Juliao E, Fabian

    2005-01-01

    Granular cells tumors are ubiquitous lesions in the gastrointestinal tract, are rare and asymptomatic and they are generally an incidental discovery at gastroduodenoscopy or colonoscopy. In the gastrointestinal tract they are more frequently located in the esophagus, right colon and rectum, stomach, appendix, small intestine or biliopancreatic tract. This article describes three patients with four tumors of granular cells in rectum, esophagus (2 lesions) and appendix. It becomes special emphasis in their neural origin, their benign behavior that justifies the endoscopic resections or limited surgical excisions and the necessity of a pursuit for the possibility, although little, of malignant transformation

  7. Granular cell tumour of the urinary bladder

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    Christoph von Klot

    2012-04-01

    Full Text Available With only 16 cases reported in the literature, the mostly benign granular cell tumour of the urinary bladder is exceptionally rare. We present the case of a 68-year old patient with one of these lesions demonstrating our histological findings including several immunohistochemical stainings used to differentiate between other more common entities.

  8. Granular cell tumors of the urinary bladder

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    Kayani Naila

    2007-03-01

    Full Text Available Abstract Background Granular cell tumors (GCTs are extremely rare lesions of the urinary bladder with only nine cases being reported in world literature of which one was malignant. Generally believed to be of neural origin based on histochemical, immunohistochemical, and ultrastructural studies; they mostly follow a clinically benign course but are commonly mistaken for malignant tumors since they are solid looking, ulcerated tumors with ill-defined margins. Materials and methods We herein report two cases of GCTs, one benign and one malignant, presenting with gross hematuria in a 14- and a 47-year-old female, respectively. Results Histopathology revealed characteristic GCTs with positive immunostaining for neural marker (S-100 and negative immunostaining for epithelial (cytokeratin, Cam 5.2, AE/A13, neuroendocrine (neuron specific enolase, chromogranin A, and synaptophysin and sarcoma (desmin, vimentin markers. The benign tumor was successfully managed conservatively with transurethral resection alone while for the malignant tumor, radical cystectomy, hysterectomy with bilateral salpingo-oophorectomy, anterior vaginectomy, plus lymph node dissection was done. Both cases show long-term disease free survival. Conclusion We recommend careful pathologic assessment for establishing the appropriate diagnosis and either a conservative or aggressive surgical treatment for benign or localized malignant GCT of the urinary bladder, respectively.

  9. Tumor of granular cells of esophagus

    International Nuclear Information System (INIS)

    Gonzalez Fabian, Licet; Diaz Anaya, Amnia; Perez de la Torre, Georgina

    2010-01-01

    Granular cells tumors are rare and asymptomatic lesions and by general, it is an incidental finding en high or low endoscopy. They were described for the first time by Abrikossoff in 1926. The more frequent locations are the buccal mucosa, dermis and subcutaneous cellular tissue, most of these tumors has a benign origin. This is the case of a woman aged 44 with a pyrosis history from a year ago; by high endoscopy it is noted a 8 mm lesion distal to esophagus and confirmed by histological study of granular cells tumor. Elective treatment of this lesion is the endoscopic polypectomy. Despite that the malign potential is low; we suggested a close clinical and endoscopic follow-up.

  10. Large mid-esophageal granular cell tumor: benign versus malignant

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    Prarthana Roselil Christopher

    2015-06-01

    Full Text Available Granular cell tumors are rare soft tissue neoplasms, among which only 2% are malignant, arising from nervous tissue. Here we present a case of a large esophageal granular cell tumor with benign histopathological features which metastasized to the liver, but showing on positron emission tomography-computerized tomography standardized uptake value suggestive of a benign lesion.

  11. A Therapeutic and Diagnostic Dilemma: Granular Cell Tumor of the Breast

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    Ahmet Pergel

    2011-01-01

    Full Text Available Six to eight percent of granular cell tumors are seen in the breast. Although mostly benign, they rarely have malignant features clinically and radiologically reminding of breast cancer. This may lead to a potential misdiagnosis of breast carcinoma and overtreatment of patients. The final diagnosis is made by immunohistochemical examination. We performed excisional biopsy on a patient who was diagnosed to have a breast mass. The histopathological examination of the mass revealed granular cell tumor.

  12. A therapeutic and diagnostic dilemma: granular cell tumor of the breast.

    Science.gov (United States)

    Pergel, Ahmet; Yucel, Ahmet Fikret; Karaca, A Serdar; Aydin, Ibrahim; Sahin, Dursun Ali; Demirbag, Nilgun

    2011-01-01

    Six to eight percent of granular cell tumors are seen in the breast. Although mostly benign, they rarely have malignant features clinically and radiologically reminding of breast cancer. This may lead to a potential misdiagnosis of breast carcinoma and overtreatment of patients. The final diagnosis is made by immunohistochemical examination. We performed excisional biopsy on a patient who was diagnosed to have a breast mass. The histopathological examination of the mass revealed granular cell tumor.

  13. Massive granular cell ameloblastoma with dural extension and atypical morphology

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    Vandana Raghunath

    2014-01-01

    Full Text Available Ameloblastomas are rare histologically benign, locally aggressive tumors arising from the oral ectoderm that occasionally reach a gigantic size. Giant ameloblastomas are a rarity these days with the advent of panoramic radiography in routine dental practice. Furthermore, the granular cell variant is an uncommon histological subtype of ameloblastoma where the central stellate reticulum like cells in tumor follicles is replaced by granular cells. Although granular cell ameloblastoma (GCA is considered to be a destructive tumor with a high recurrence rate, the significance of granular cells in predicting its biologic behavior is debatable. However, we present a rare case of giant GCA of remarkable histomorphology showing extensive craniofacial involvement and dural extension that rendered a good prognosis following treatment.

  14. Granular cell tumor of the esophagus. Report of three cases.

    Science.gov (United States)

    Cohle, S D; McKechnie, J C; Truong, L; Jurco, S

    1981-06-01

    Granular cell tumors, (formerly called myoblastomas) involving the esophagus were encountered in three patients. In all three the tumors were asymptomatic and in two they were multiple. The first published endoscopic photographs of such a tumor are presented. The successful total removal of this neoplasm using the endoscope is described. The pathologic, radiologic and therapeutic aspects of previously reported cases of granular cell tumor of the esophagus are reviewed and compared with the three reported herein.

  15. Granular Cell Tumor of the Neurohypophysis: A Case Report with Magnetic Resonance and CT Imaging Findings

    Energy Technology Data Exchange (ETDEWEB)

    Choo, Ka Yeon; Lee, Sun Jin; Ahn, Kook Jin; Jung, So Lyung; Kim, Bum Soo [Dept. of Radiology, Seoul St.Mary' s Hospital, The Catholic University of Korea College of Medicine, Seoul (Korea, Republic of); Lee, Yeon Soo [Dept. of Pathology, Seoul St.Mary' s Hospital, The Catholic University of Korea College of Medicine, Seoul (Korea, Republic of); Jeun, Shin Soo [Dept. of Neurosurgery, Seoul St.Mary' s Hospital, The Catholic University of Korea College of Medicine, Seoul (Korea, Republic of)

    2011-11-15

    A granular cell tumor (GCT) usually occurs as a small, solitary, nodular tumor and is more prevalent in adult females. The authors report the magnetic resonance (MR) and CT imaging findings in a 61-year-old woman with GCT of the neurohypophysis presenting with a history of reduced visual acuity in her right eye. MR images showed a suprasellar mass with an isointense signal on a T1-weighted image and an hypointense signal on a T2-weighted image. The histopathological examination revealed a granular cell tumor. In this article, the MR and CT imaging findings of GCT of the neurohypophysis with the literature reviews are discussed.

  16. Granular Cell Tumor of the Neurohypophysis: A Case Report with Magnetic Resonance and CT Imaging Findings

    International Nuclear Information System (INIS)

    Choo, Ka Yeon; Lee, Sun Jin; Ahn, Kook Jin; Jung, So Lyung; Kim, Bum Soo; Lee, Yeon Soo; Jeun, Shin Soo

    2011-01-01

    A granular cell tumor (GCT) usually occurs as a small, solitary, nodular tumor and is more prevalent in adult females. The authors report the magnetic resonance (MR) and CT imaging findings in a 61-year-old woman with GCT of the neurohypophysis presenting with a history of reduced visual acuity in her right eye. MR images showed a suprasellar mass with an isointense signal on a T1-weighted image and an hypointense signal on a T2-weighted image. The histopathological examination revealed a granular cell tumor. In this article, the MR and CT imaging findings of GCT of the neurohypophysis with the literature reviews are discussed.

  17. Neurohypophysis granular cell tumours. Upon neurohypophysis rare tumours

    International Nuclear Information System (INIS)

    Barrande, G.; Kujas, M.; Gancel, A.; Turpin, G.; Bruckert, E.; Kuhn, J.M.; Luton, J.P.

    1995-01-01

    Granular cell tumours of neurohypophysis are rare. These tumours are more often encountered as incidental autopsy findings seen in up to 17 % of unselected adult autopsy cases. There are few reports of para-sellar granular cell tumours large enough to cause symptoms. We present three cases of neurohypophysis granular cell tumour and a review of the literature. In one patient, the asymptomatic granular cell tumour was incidentally discovered at surgical removal of a corticotrophic micro-adenoma. The remaining 2 patients had a symptomatic tumour which caused neurological symptoms such as visual disturbance and headaches and endocrine disorders such as hypopituitarism or hyper-prolactinaemia. In these 2 cases, computerized tomography showed a well-circumscribed, contrast-enhanced, intra-sellar and supra-sellar mass. Magnetic resonance imaging demonstrated an isointense gadolinium-enhanced mass in T1-weighted-images. Trans-sphenoidal partial resection was performed and histology was interpreted as a granular cell tumour. The immunohistochemical study was positive for glial fibrillary acidic protein (GEAP) and neuron specific enolase (NSE) in 1 of the 2 tumours and positive for S100 protein and vimentin in both tumours but negative for CD68. The histogenesis of neurohypophysis granular cell tumours is still controversial but ultrastructural and immunohistochemical studies support the theory that may arise from pituicytes, the glial cells of neurohypophysis. Management of these benign, slow growing, tumours is based mainly on neurosurgical resection. Data from the literature do not support a beneficial effect of post operative radiation therapy on postoperative recurrences. (authors). 23 refs., 4 figs., 1 tab

  18. Dermatofibroma-like granular cell tumour: a potential diagnostic pitfall

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    Jiri Soukup

    2016-11-01

    Full Text Available Dermatofibroma-like granular cell tumour (GCT is a rare entity, with only two cases having been described so far. We report another case in a 62-year-old woman, discuss histopathological features, and review other tumours in which granular changes have been observed. Our tumour was composed predominantly of oval-to-spindle granular cells with prominent nucleoli, arranged in short fascicles and storiform pattern, infiltrating around collagen bundles. Immunohistochemical analysis with antibodies against CD31, CD56, CD68, CD117, S-100 protein, inhibin, calretinin, EMA, p53 and MIB-1 was performed, showing expression of CD56, CD68, S-100 protein, inhibin and calretinin. The diagnosis of atypical dermatofibroma-like GCT was made.

  19. Granular cell tumor with orbital involvement in a child

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Fabiano [Universidade Estadual de Campinas (FCM/UNICAMP), SP (Brazil). Fac. de Ciencias Medicas. Dept. de Radiologia; Iyeyasu, Josie Naomi; Carvalho, Keila Monteiro de [Universidade Estadual de Campinas (FCM/UNICAMP), SP (Brazil). Fac. de Ciencias Medicas. Dept. de Oftalmo-Otorrinolaringologia; Altemani, Albina Messias [Universidade Estadual de Campinas (FCM/UNICAMP), SP (Brazil). Fac. de Ciencias Medicas. Dept. de Anatomia Patologica

    2011-09-15

    The authors report a rare case of granular cell tumor in the left medial rectus muscle of a seven-year-old boy. Clinical, pathologic and radiologic findings of the present case are described and a brief literature review is undertaken. (author)

  20. Multifocal Synchronous Granular Cell Tumors of the Gastrointestinal Tract

    OpenAIRE

    Lipkin-Moore, Zachary; Thomas, Rebecca M.; Rothstein, Robin D.

    2014-01-01

    Granular cell tumors (GCT) are rare and unusual tumors, which are usually benign and asymptomatic. Only 5?10% of cases involve the gastrointestinal tract, most commonly as singular, non-cancerous lesions in the esophagus. We report a rare case of symptomatic, multifocal, synchronous GCT involving the esophagus, stomach, and cecum.

  1. Granular cell tumor with orbital involvement in a child

    International Nuclear Information System (INIS)

    Reis, Fabiano; Iyeyasu, Josie Naomi; Carvalho, Keila Monteiro de; Altemani, Albina Messias

    2011-01-01

    The authors report a rare case of granular cell tumor in the left medial rectus muscle of a seven-year-old boy. Clinical, pathologic and radiologic findings of the present case are described and a brief literature review is undertaken. (author)

  2. Multifocal Abrikossoff's granular cell tumor of the oesophagus: Case report

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    Ranđelović Tomislav D.

    2008-01-01

    Full Text Available INTRODUCTION Granular cell tumors, relatively uncommon soft tissue tumors, have been a matter of debate among pathologists regarding histogenesis for a long time. Less common locations are in the aerodigestive tract including the oesophagus. CASE OUTLINE We have recently treated a rare case, a 37-year old male, who was admitted due to dysphagia and a painful swallow with occasional pharyngo-nasal regurgitation followed with a mild loss of weight. Standard clinical examination including X-ray chest, ECG and laboratory tests did not show pathological findings. Barium contrast oesophagography demonstrated multiple ovoid defects in the wall of the oesophagus. CT scan of the chest confirmed luminal narrowing owing to the tumor of the upper oesophagus. Upper endoscopy showed unusual multifocal nodular lesions alongside the oesophageal axis covered by smooth mucosa. A primary biopsy specimen taken from the largest nodules confirmed an unusual pathological finding of the granular cell tumor. Subtotal, transpleural oesophagectomy was performed and reconstruction was derived by long colon segment interposition through the posterior mediastinum. The postoperative course was uneventful. The operative specimen consisted of four ovoid tumors alongside the oesophagus (the greatest diameter 0.5-1.8, average 1.25. All verified tumors histologicaly consisted of a spindle-shaped or polygonal cells containing small and large eosinophilic granules and central nuclei. Most tumor cells showed strongly positive immunohistochemical staining for S-100 protein. These tumor cells were partially positive for p-53 and Ki-67. No lymph node metastases were detected histologically. CONCLUSION Multifocal granular cell tumor of the oesophagus is an unusual finding with low incidence, and rarely caused symptoms. Pathological features and multiplicity of such tumors emphasized malignant predisposition requiring surgical resection of the oesophagus.

  3. Ulcerative Granular Cell Tumor: A Clinico pathological and Immunohistochemical Study

    International Nuclear Information System (INIS)

    El-Khalawan, M.; Mosbeh, A.; Abd-Al Salam, F.; Abou-Bakr, A.

    2011-01-01

    Granular cell tumor (GCT) is uncommonly presented with cutaneous ulcer. We examined the clinico pathological and immunohistochemical features of this ulcerative form in fourteen cases that may raise the awareness of this variant. The study included 11 males and 3 females with a mean age 31.5± 7.42 years. All cases were presented with large solitary ulcer with indurated base, elevated border, skin colored margin, and necrotic floor. Twelve lesions were located on the extremities and two lesions on the genital region. Histologically, the lesions showed dermal infiltrate composed of large polygonal cells with granular cytoplasm and characteristic infiltration of the dermal muscles in all cases. Immunostaining showed positive reaction for S100 (14/14), NSE (14/14), CD68 (5/14), and Vimentin (7/14) while HMB45, CK, EMA, and Desmin were negative. We hope that this paper increases the awareness of ulcerative GCT and consider it in the differential diagnosis of ulcerative lesions

  4. Diagnosis and Treatment of Esophageal Granular Cell Tumor: A Case Report and Review of the Literature

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    Ramin Niknam

    2017-01-01

    Full Text Available Gastrointestinal granular cell tumors are uncommon. The most common site of gastrointestinal granular cell tumor (GCT is esophagus. We report a case of esophageal GCT incidentally diagnosed by endoscopy. The lesion was evaluated by endoscopic ultrasonography and resected using the endoscopic technique without complication.

  5. Granular cell tumor in an endangered Puerto Rican Amazon parrot (Amazon vittata)

    Science.gov (United States)

    Quist, C.F.; Latimer, K.S.; Goldade, S.L.; Rivera, A.; Dein, F.J.

    1999-01-01

    A 3 cm diameter mass from the metacarpus of a Puerto Rican Amazon parrot was diagnosed as a granular cell tumour based on light microscopy. The cytoplasmic granules were periodic-acid Schiff positive and diastase resistant. Ultrastructural characteristics of the cells included convoluted nuclei and the presence of numerous cytoplasmic tertiary lysosomes. This is only the second granular cell tumour reported in a bird. We speculate that most granular cell tumours are derived from cells that are engaged in some type of cellular degradative process, creating a similar morphologic appearance, but lacking a uniform histogenesis.

  6. Amelanotic Melanoma Masquerading as a Granular Cell Lesion

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    Deepak Pandiar

    2013-01-01

    Full Text Available Amelanotic melanoma (AM presents a diagnostic challenge due to its wide clinical presentations, lack of pigmentation, and varied histological appearances. Immunohistochemistry plays a crucial role in the diagnosis of these lesions. Amelanotic melanoma of oral mucosa is an uncommon lesion. We report a case of a 50-year-old male patient with a growth on the anterior mandibular gingiva of seven-month duration. In the present case, histologically, the tumour resembled a granular cell lesion, which has not been reported previously in AM. Diagnosis was possible by a sequential panel of immunohistochemical markers, of which finally vimentin, S100, HMB45, and Melan-A were positive. The tumor was surgically excised, and postsurgical radiotherapy was given.

  7. Granular cell tumor on perianal region: a case report.

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    Kesici Ugur

    2013-07-01

    Full Text Available Granular cell tumor (GCT was first described by Abrikossoff in 1926. GCT is a rarely seen soft tissue tumor and is generally benign. While the tumor can be seen in all parts of the body it is generally located on the head and neck region, and especially on the tongue. GCT is rarely seen in the anal-perianal region. In accordance with literature this case was reported because it was thought to be the 27th anal-perianal located GCT case. In this case report, approximately 0,5-1 cm pedunculated polypoid lesion was determined in the perianal region during the physical examination of a 23 year old female patient who applied with palpable mass complaint in the perianal region. Lesion in the patient was totally excited with healthy skin-subcutaneous tissue under local anesthesia. A benign granular cell tumor was detected in the histopathological examination. Positive staining was monitored immunohistochemically with S-100 and neuron specific enolase (NSE. GCT is a rarely seen tumor in the anal-perianal region and its malign transformation rate is very low. Even lesions seen in the perianal region have clinically a benign appearance, a histopathological examination should be conducted and also GCT should be kept in mind during diagnosis. Malign-benign separation of these lesions is difficult so histopathological examination should be conducted with great care. Large local excision in the treatment provides curative treatment. But for those presenting malign transformation further examination must be performed for metastasis. After the treatment local recurrence and metastasis should be considered carefully. Prognosis of metastatic disease is very bad.

  8. Association of inclusion body myositis with T cell large granular lymphocytic leukaemia

    DEFF Research Database (Denmark)

    Greenberg, Steven A; Pinkus, Jack L; Amato, Anthony A

    2016-01-01

    SEE HOHLFELD AND SCHULZE-KOOPS DOI101093/BRAIN/AWW053 FOR A SCIENTIFIC COMMENTARY ON THIS ARTICLE: Inclusion body myositis and T cell large granular lymphocytic leukaemia are rare diseases involving pathogenic cytotoxic CD8+ T cells. After encountering four patients with both disorders, we...... prospectively screened 38 patients with inclusion body myositis for the presence of expanded large granular lymphocyte populations by standard clinical laboratory methods (flow cytometry, examination of blood smears, and T cell receptor gene rearrangements), and performed muscle immunohistochemistry for CD8, CD......57, and TIA1. Most (22/38; 58%) patients with inclusion body myositis had aberrant populations of large granular lymphocytes in their blood meeting standard diagnostic criteria for T cell large granular lymphocytic leukaemia. These T cell populations were clonal in 20/20 patients and stably present...

  9. Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib

    Science.gov (United States)

    Wei, Lei; Liu, Song; Conroy, Jeffrey; Wang, Jianmin; Papanicolau-Sengos, Antonios; Glenn, Sean T.; Murakami, Mitsuko; Liu, Lu; Hu, Qiang; Conroy, Jacob; Miles, Kiersten Marie; Nowak, David E.; Liu, Biao; Qin, Maochun; Bshara, Wiam; Omilian, Angela R.; Head, Karen; Bianchi, Michael; Burgher, Blake; Darlak, Christopher; Kane, John; Merzianu, Mihai; Cheney, Richard; Fabiano, Andrew; Salerno, Kilian; Talati, Chetasi; Khushalani, Nikhil I.; Trump, Donald L.; Johnson, Candace S.; Morrison, Carl D.

    2015-01-01

    Granular cell tumors are an uncommon soft tissue neoplasm. Malignant granular cell tumors comprise T transitions, particularly when immediately preceded by a 5′ G. A loss-of-function mutation was detected in a newly recognized tumor suppressor candidate, BRD7. No mutations were found in known targets of pazopanib. However, we identified a receptor tyrosine kinase pathway mutation in GFRA2 that warrants further evaluation. To the best of our knowledge, this is only the second reported case of a malignant granular cell tumor exhibiting a response to pazopanib, and the first whole-genome sequencing of this uncommon tumor type. The findings provide insight into the genetic basis of malignant granular cell tumors and identify potential targets for further investigation. PMID:27148567

  10. Congenital granular cell epulis—a case report

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    Alexander Aresdahl, DDS

    2015-03-01

    Full Text Available Congenital granular cell epulis (CGCE is an uncommon benign lesion found in newborns. It has predominance for females with an 8:1 ratio in relation to males and is exclusively encountered in the oral cavity. The most affected oral site is located around the canine/incisor region of the maxillary alveolar ridge, where the lesion arises from the soft tissue as a solitary pedunculated mass. CGCE's histogenesis remains obscure and controversial. We present a rare case of 2 separate CGCE lesions adjacent to each other measuring 23 × 18 × 10 and 15 × 10 mm, positioned facially on the right maxillary alveolar process. The patient, a 2-day-old female newborn, did not experience any serious difficulty regarding breathing or deglutition. Complete surgical excision was the treatment of choice in this case, and the procedure was performed under both general and local anesthesia. Histologic and immunohistochemical analysis confirmed the diagnosis of CGCE. The patient showed satisfactory postoperative healing and excellent health at both the 10-day recall appointment and the 6-month follow-up.

  11. Esophageal Granular Cell Tumor and Eosinophilic Esophagitis: Two Interesting Entities Identified in the Same Patient

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    Alfredo J. Lucendo

    2008-02-01

    Full Text Available We illustrate the case of a 41-year-old male with allergic manifestations since childhood. He sought medical attention for intermittent, progressive dysphagia from which he had been suffering for a number of years, having felt the sensation of a retrosternal lump and a self-limited obstruction to the passage of food. Endoscopy detected a submucosal tumor in the upper third of the esophagus, which was typified, via biopsy, as a granular cell tumor with benign characteristics and probably responsible for the symptoms. Two years later, the patient sought medical attention once again as these symptoms had not abated, hence digestive endoscopy was repeated. This revealed stenosis of the junction between the middle and lower thirds of the organ which had not been detected previously but was passable under gentle pressure. Eosinophilic esophagitis was detected after biopsies were taken. Esophageal manometry identified a motor disorder affecting the esophageal body. Following three months of treatment using fluticasone propionate applied topically, the symptoms went into remission, esophageal stenosis disappeared and the esophageal biopsies returned to normal. This is the first documented case of the link between granular cell tumors and Eosinophilic esophagitis, two different disorders which could cause dysphagia in young patients.

  12. Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor

    KAUST Repository

    Bagchi, Samik

    2016-06-20

    Granules enriched with anammox bacteria are essential in enhancing the treatment of ammonia-rich wastewater, but little is known about how anammox bacteria grow and multiply inside granules. Here, we combined metatranscriptomics, quantitative PCR and 16S rRNA gene sequencing to study the changes in community composition, metabolic gene content and gene expression in a granular anammox reactor with the objective of understanding the molecular mechanism of anammox growth and multiplication that led to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all the essential transcripts for anammox metabolism. During the later stage of reactor operation, higher expression of ammonia and nitrite transport proteins and key metabolic enzymes mainly in the bottom large granules facilitated anammox bacteria activity. The high activity resulted in higher growth and multiplication of anammox bacteria and expanded the size of the granules. This conceptual model for large granule formation proposed here may assist in the future design of anammox processes for mainstream wastewater treatment.

  13. Stem cell heterogeneity revealed

    DEFF Research Database (Denmark)

    Andersen, Marianne S; Jensen, Kim B

    2016-01-01

    The skin forms a protective, water-impermeable barrier consisting of heavily crosslinked epithelial cells. However, the specific role of stem cells in sustaining this barrier remains a contentious issue. A detailed analysis of the interfollicular epidermis now proposes a model for how a composite...... of cells with different properties are involved in its maintenance....

  14. Granular cell tumour of the neurohypophysis: an unusual cause of hypopituitarism

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    Carlos Tavares Bello

    2018-04-01

    Full Text Available Granular cell tumours (GCT are rare, slow-growing, benign neoplasms that are usually located in the head and neck. They are more frequent in the female gender and typically have an asymptomatic clinical course, being diagnosed only at autopsy. Symptomatic GCT of the neurohypophysis are exceedingly rare, being less than 70 cases described so far. The authors report on a case of a 28-year-old male that presented to the Endocrinology clinic with clinical and biochemical evidence of hypogonadism. He also reported minor headaches without any major visual symptoms. Further laboratory tests confirmed hypopituitarism (hypogonadotrophic hypogonadism, central hypothyroidism and hypocortisolism and central nervous system imaging revealed a pituitary macroadenoma. The patient underwent transcranial pituitary adenoma resection and the pathology report described a GCT of the neurohypophysis with low mitotic index. The reported case is noteworthy for the rarity of the clinicopathological entity.

  15. The specificity of immune priming in silkworm, Bombyx mori, is mediated by the phagocytic ability of granular cells.

    Science.gov (United States)

    Wu, Gongqing; Li, Mei; Liu, Yi; Ding, Ying; Yi, Yunhong

    2015-10-01

    In the past decade, the phenomenon of immune priming was documented in many invertebrates in a large number of studies; however, in most of these studies, behavioral evidence was used to identify the immune priming. The underlying mechanism and the degree of specificity of the priming response remain unclear. We studied the mechanism of immune priming in the larvae of the silkworm, Bombyx mori, and analyzed the specificity of the priming response using two closely related Gram-negative pathogenic bacteria (Photorhabdus luminescens TT01 and P. luminescens H06) and one Gram-positive pathogenic bacterium (Bacillus thuringiensis HD-1). Primed with heat-killed bacteria, the B. mori larvae were more likely to survive subsequent homologous exposure (the identical bacteria used in the priming and in the subsequent challenge) than heterologous (different bacteria used in the priming and subsequent exposure) exposure to live bacteria. This result indicated that the B. mori larvae possessed a strong immune priming response and revealed a degree of specificity to TT01, H06 and HD-1 bacteria. The degree of enhanced immune protection was positively correlated with the level of phagocytic ability of the granular cells and the antibacterial activity of the cell-free hemolymph. Moreover, the granular cells of the immune-primed larvae increased the phagocytosis of a previously encountered bacterial strain compared with other bacteria. Thus, the enhanced immune protection of the B. mori larvae after priming was mediated by the phagocytic ability of the granular cells and the antibacterial activity of the hemolymph; the specificity of the priming response was primarily attributed to the phagocytosis of bacteria by the granular cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Cell percolation model for electrical conduction of granular superconducting composites. 2

    International Nuclear Information System (INIS)

    Horvath, G.; Bankuti, J.

    1990-01-01

    The percolation of the electrical conductivity of the uniform cells is studied in an in-situ elongated granular superconducting composite on the basis of the uniform cell model improved previously. The critical temperatures are determined in the macroscopic superconducting state of the two- and the three-dimensional composites. (author)

  17. Cytological and histological correlation of granular cell tumor in a series of three cases

    Directory of Open Access Journals (Sweden)

    Soutrik Das

    2018-01-01

    Full Text Available Granular cell tumor (GCT is an uncommon soft tissue tumor characterized by proliferation of cells with granular eosinophilic cytoplasm. We came across three such tumors, one in the tongue, one in the chest wall, and one in the right deltoid region, which were referred for fine-needle aspiration cytology. On cytological examination, the first two cases were diagnosed as GCT, and the mass in deltoid region was suggestive of proliferative myositis. The cytological details of these cases are discussed. The excision biopsies of the first two cases and Tru-cut biopsy of the deltoid mass confirmed the diagnosis of GCT.

  18. Coexistence of Granular Cell Tumor with Squamous Cell Carcinoma on the Tongue: A Case Report

    Directory of Open Access Journals (Sweden)

    Recep Bedir

    2015-01-01

    Full Text Available Introduction: Granular cell tumors (GCTs are rare and mostly benign soft tissue tumors. Though they have been reported in all parts of body, they are generally located in the head and neck region, especially on the tongue. Some malign forms exist, but these have been rarely reported. Granular cell tumors have a neural origin and, in immunohistochemical evaluations, they express S-100 and neuron specific enolase (NSE. The treatment of these tumors is bulky surgical excision.   Case Report:   In this case, a cauliflower shaped lesion with a 1 cm diameter was excised from the midline tongue of a 65 year old woman. The histopathological evaluation indicated that it was squamous cell carcinoma (SCC covering GCT. Herein, the coexistence of GCT and SCC we describe on the same region of the tongue, in accordance with literature review, since this is a very rare condition.   Conclusion: Pseudoepitheliomatous hyperplasia may accompany GCTs on the tongue and this condition may mimic well-differentiated SCC. For this reason, with the help of Ki-67 and p63 expression, in addition to immunohistochemical markers, well-differentiated SCC should be differentiated from pseudoepitheliomatous hyperplasia through careful investigation.

  19. MR imaging findings in granular cell tumor of the neurohypophysis: a difficult preoperative diagnosis

    Energy Technology Data Exchange (ETDEWEB)

    Iglesias, A.; Arias, M.; Brasa, J. [Unidad de Resonancia Magnetica (MEDTEC), Hospital Xeral-Cies, Vigo (Spain); Paramo, C. [Servicio de Endocrinologia, Hospital Xeral-Cies, Vigo (Spain); Conde, C. [Servicio de Neurocirugia, Hospital Xeral-Cies, Vigo (Spain); Fernandez, R. [Servicio de Anatomia Patologica, Hospital Xeral-Cies, Vigo (Spain)

    2000-12-01

    Granular cell tumor is a rare neoplasm arising within the neurohypophysis. We describe the MR imaging findings in two symptomatic patients. In one patient with history of panhypopituitarism, MR images showed a large sellar and suprasellar mass. The other patient presented with acute loss of vision in her left eye, and MR images showed a suprasellar mass with compression of the optic chiasm. (orig.)

  20. MR imaging findings in granular cell tumor of the neurohypophysis: a difficult preoperative diagnosis

    International Nuclear Information System (INIS)

    Iglesias, A.; Arias, M.; Brasa, J.; Paramo, C.; Conde, C.; Fernandez, R.

    2000-01-01

    Granular cell tumor is a rare neoplasm arising within the neurohypophysis. We describe the MR imaging findings in two symptomatic patients. In one patient with history of panhypopituitarism, MR images showed a large sellar and suprasellar mass. The other patient presented with acute loss of vision in her left eye, and MR images showed a suprasellar mass with compression of the optic chiasm. (orig.)

  1. Malignant Granular Cell Tumor of the Back: A Case Report and Review of the Literature

    Directory of Open Access Journals (Sweden)

    Laura Stone McGuire

    2014-01-01

    Full Text Available Malignant granular cell tumors are rare, intensely aggressive entities. This paper presents a case of a large rapidly recurrent malignant granular cell tumor with regional and distal metastases on the back of a 54-year-old Cuban man. The primary tumor recurred within six months of the original wide local excision and with satellite lesions apparent at twelve months, and the mass was diagnosed using the histological criteria established by Fanburg-Smith et al. for malignant granular cell tumors. By fifteen months, right axillary lymphadenopathy, multiple satellite lesions, pulmonary nodules, and distant metastasis in the right thigh were present. At sixteen months, wide local excision of recurrent mass and local satellite masses along with right axillary dissection and placement of Integra with subsequent split-thickness skin graft were performed by surgical oncology and plastic surgery teams. The surgical specimen measured 32.0 × 13.5 × 5.5 cm, containing multiple homogeneous masses with the largest mass 22.0 × 9.0 × 4.6 cm. Following surgery, patient was started on Pazopanib 800 mg/day based on phase III randomized trial data in the treatment of soft tissue sarcomas showing this as a potential novel therapy for malignant granular cell tumors.

  2. Granular cell tumour of the neurohypophysis: a rare sellar tumour with specific radiological and operative features.

    LENUS (Irish Health Repository)

    Aquilina, K

    2012-02-03

    Symptomatic granular cell tumours of the neurohypophysis are rare sellar lesions. Preoperative prediction of the diagnosis on the basis of radiological appearance is useful as these tumours carry specific surgical difficulties. This is possible when the tumour arises from the pituitary stalk, rostral to a normal pituitary gland. This has not been emphasized previously.

  3. The cerebellar Golgi cell and spatiotemporal organization of granular layer activity

    Directory of Open Access Journals (Sweden)

    Egidio eD‘Angelo

    2013-05-01

    Full Text Available The cerebellar granular layer has been suggested to perform a complex spatiotemporal reconfiguration of incoming mossy fiber signals. Central to this role is the inhibitory action exerted by Golgi cells over granule cells: Golgi cells inhibit granule cells through double feedforward and feedback inhibitory loops and generate a broad lateral inhibition that extends beyond the afferent synaptic field. This characteristic connectivity has recently been investigated in great detail and been correlated with specific functional properties of the neuron. These include theta-frequency pacemaking, network entrainment into coherent oscillations and phase resetting. Important advances have also been made in terms of determining the membrane and synaptic properties of the neuron, and clarifying the mechanisms of activation by input bursts. Moreover, voltage sensitive dye imaging and multi-electrode array recordings, combined with mathematical simulations based on realistic computational models, have improved our understanding of the impact of Golgi cell activity on granular layer circuit computations. These investigations have highlighted the critical role of Golgi cells in: generating dense clusters of granule cell activity organized in center-surround structures, implementing combinatorial operations on multiple mossy fiber inputs, regulating transmission gain and cut-off frequency, controlling spike timing and burst transmission, and determining the sign, intensity and extension of long-term synaptic plasticity at the mossy fiber-granule cell relay. This review considers recent advances in the field, highlighting the functional implications of Golgi cells for granular layer network computation and indicating new challenges for cerebellar research.

  4. Pyramid-like basket cells in the granular layer of the dentate gyrus in the rat.

    Science.gov (United States)

    Seress, L

    1978-01-01

    Basket cells of the dentate gyrus were identified using Nissl (cresyl violet) staining. It has been found that the ratio between basket and granule cells is 1:150--210. Only a few glial cells, mainly astroglia, were found in the granular layer of the dentate gyrus. In accordance with earlier data it was found that the granule cells and glial cells originate mainly postnatally, but the basket cells, like the pyramidal cells of the hippocampus, originate prenatally. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:701192

  5. Novel somatic mutations in large granular lymphocytic leukemia affecting the STAT-pathway and T-cell activation

    International Nuclear Information System (INIS)

    Andersson, E I; Rajala, H L M; Eldfors, S; Ellonen, P; Olson, T; Jerez, A; Clemente, M J; Kallioniemi, O; Porkka, K; Heckman, C; Loughran, T P Jr; Maciejewski, J P; Mustjoki, S

    2013-01-01

    T-cell large granular lymphocytic (T-LGL) leukemia is a clonal disease characterized by the expansion of mature CD3+CD8+ cytotoxic T cells. It is often associated with autoimmune disorders and immune-mediated cytopenias. Our recent findings suggest that up to 40% of T-LGL patients harbor mutations in the STAT3 gene, whereas STAT5 mutations are present in 2% of patients. In order to identify putative disease-causing genetic alterations in the remaining T-LGL patients, we performed exome sequencing from three STAT mutation-negative patients and validated the findings in 113 large granular lymphocytic (LGL) leukemia patients. On average, 11 CD8+ LGL leukemia cell-specific high-confidence nonsynonymous somatic mutations were discovered in each patient. Interestingly, all patients had at least one mutation that affects either directly the STAT3-pathway (such as PTPRT) or T-cell activation (BCL11B, SLIT2 and NRP1). In all three patients, the STAT3 pathway was activated when studied by RNA expression or pSTAT3 analysis. Screening of the remaining 113 LGL leukemia patients did not reveal additional patients with same mutations. These novel mutations are potentially biologically relevant and represent rare genetic triggers for T-LGL leukemia, and are associated with similar disease phenotype as observed in patients with mutations in the STAT3 gene

  6. The angle of repose of spherical grains in granular Hele–Shaw cells: a molecular dynamics study

    International Nuclear Information System (INIS)

    Maleki, Hamed; Ebrahimi, Fatemeh; Oskoee, Ehsan Nedaaee

    2008-01-01

    We report the results of three-dimensional molecular dynamic simulations on the angle of repose of a sandpile formed by pouring mono-sized cohesionless spherical grains into a granular Hele–Shaw cell. In particular, we are interested in investigating the effects of those variables which may have a significant impact on the pattern formation of granular mixtures in Hele–Shaw cells. The results indicate that the frictional forces influence the formation of piles on the grain level remarkably. Furthermore, we see that increasing grain insertion rate decreases the angle of repose slightly. We also find that the cell thickness is a significant factor and the angle of repose decays when the size of the gap between the lateral walls increases. In addition to agreeing with the experimental exponential decay law, our results are in accordance with a recently proposed model which takes into account the arching effects. Using grains with different sizes reveals that the behaviour of the angle of repose when both size and cell thickness are varied is controlled by a scaled function of the ratio of these two variables

  7. Movement of beta-irradiated epidermal basal cells to the spinous-granular layers in the absence of cell division

    International Nuclear Information System (INIS)

    Etoh, H.; Taguchi, Y.H.; Tabachnick, J.

    1975-01-01

    Guinea-pig epidermis was irradiated with 3000 rad of beta rays 1 hr after two injections of [ 3 H]thymidine 5 hr apart (labeled cells in S phase and G 2 phase) or 18 hr after injection (labeled early G 1 cells). In nonirradiated epidermis labeled basal cells divided within 24 hr with daughter cells remaining in the basal layer, and approximately 50 percent of the labeled cells moved into the spinal layer by the 3rd day. Cell division in nonirradiated epidermis diluted the number of silver grains/nucleus, and lightly labeled cells were found in the granular layer by day 7. Beta irradiation inhibited cell division but it did not slow the rate of transit (ca 8 days) of irradiated labeled cells from basal to granular layer, some of these remaining heavily labeled. Although cell division may play some role in upward movement of basal cells in normal epidermis detachment of a basal cell from the basement membrane and its transit to the granular layer is unimpaired in the absence of cell division. These findings suggest that some radioresistant metabolic function(s), not cell division, is responsible for upward movement of basal cells. (auth)

  8. Oral Granular Cell Tumor: Report of Case Series and a Brief Review of the Literature

    Directory of Open Access Journals (Sweden)

    Karakostas Panayiotis

    2017-07-01

    Full Text Available Background/Aim: The present analysis focuses on examining a case series of eight patients diagnosed with a granular cell tumor located in the oral cavity. Case series: The patients’ clinical states were thoroughly studied, along with the histopathological and immunohistochemical examinations findings. Their surgical treatment and postoperative course are also within the scope of this analysis. Numerous histogenesis theories and the appropriate tumor treatment are mentioned within the article being always in accordance with the relative literature. Conclusions: Oral granular cell tumor is a benign oral disease of possible neural origin commonly located on the tongue. Surgical excision is the treatment of choice. In any case, histological and immunohistochemical examination confirm both the clinical diagnosis and the differential diagnosis between oral squamous cell carcinoma.

  9. A forgotten facial nerve tumour: granular cell tumour of the parotid and its implications for treatment.

    Science.gov (United States)

    Lerut, B; Vosbeck, J; Linder, T E

    2011-04-01

    We present a rare case of a facial nerve granular cell tumour in the right parotid gland, in a 10-year-old boy. A parotid or neurogenic tumour was suspected, based on magnetic resonance imaging. Intra-operatively, strong adhesions to surrounding structures were found, and a midfacial nerve branch had to be sacrificed for complete tumour removal. Recent reports verify that granular cell tumours arise from Schwann cells of peripheral nerve branches. The rarity of this tumour within the parotid gland, its origin from peripheral nerves, its sometimes misleading imaging characteristics, and its rare presentation with facial weakness and pain all have considerable implications on the surgical strategy and pre-operative counselling. Fine needle aspiration cytology may confirm the neurogenic origin of this lesion. When resecting the tumour, the surgeon must anticipate strong adherence to the facial nerve and be prepared to graft, or sacrifice, certain branches of this nerve.

  10. [Granular cell tumor of the larynx in the child. Case report].

    Science.gov (United States)

    Cuestas, Giselle; Rodríguez, Verónica; Doormann, Flavia; Bellia Munzón, Patricio; Bellia Munzón, Gastón

    2018-02-01

    Laryngeal tumors are uncommon in children, accounting only for 2% of the laryngeal anomalies. Ninety-eight percent are benign; the most frequent ones are recurrent respiratory papillomatosis and haemangioma. Granular cell tumor, also called Abrikossoff tumor, is an unusual benign neoplasm, especially in the larynx. Clinical manifestations depend on the size and location of the tumor. Dysphonia is the main presenting symptom. The diagnosis is confirmed by the biopsy. The treatment of choice is surgery. We present a 9-year-old girl with dysphonia and exertion dyspnea due to a granular cell tumor of the larynx, and we emphasize the importance of considering the endoscopic evaluation of the airway in every child with progressive or persistent dysphonia in order to determine the etiology. Sociedad Argentina de Pediatría.

  11. Suitability of granular carbon as an anode material for sediment microbial fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Arends, Jan B.A.; Blondeel, Evelyne; Boon, Nico; Verstraete, Willy [Ghent Univ. (Belgium). Faculty of Bioscience Engineering; Tennison, Steve R. [Mast Carbon International Ltd., Basingstoke, Hampshire (United Kingdom)

    2012-08-15

    Purpose: Sediment microbial fuel cells (S-MFCs) are bio-electrochemical devices that are able to oxidize organic matter directly into harvestable electrical power. The flux of organic matter into the sediment is rather low; therefore, other researchers have introduced plants for a continuous supply of organic matter to the anode electrode. Until now only interconnected materials have been considered as anode materials in S-MFCs. Here, granular carbon materials were investigated for their suitability as an anode material in S-MFCs. Materials and methods: Laboratory microcosms with eight different electrode materials (granules, felts and cloths) were examined with controlled organic matter addition under brackish conditions. Current density, organic matter removal and microbial community composition were monitored using 16S rRNA gene PCR followed by denaturing gradient gel electrophoresis (DGGE). The main parameters investigated were the influence of the amount of electrode material applied to the sediment, the size of the granular material and the electrode configuration. Results and discussion: Felt material had an overall superior performance in terms of current density per amount of applied electrode material; felt and granular anode obtained similar current densities (approx. 50-60 mA m{sup -2}), but felt materials required 29 % less material to be applied. Yet, when growing plants, granular carbon is more suited because it is considered to restore, upon disturbance, the electrical connectivity within the anode compartment. Small granules (0.25-0.5 mm) gave the highest current density compared to larger granules (1-5 mm) of the same material. Granules with a rough surface had a better performance compared to smooth granules of the same size. The different granular materials lead to a selection of distinct microbial communities for each material, as shown by DGGE. Conclusions: Granular carbon is suitable as an anode material for S-MFCs. This opens the possibility

  12. Granular cell tumor of the scrotum: A case report and literature review

    Directory of Open Access Journals (Sweden)

    Ko-Hung Chen

    2013-01-01

    Full Text Available Granular cell tumors (GCTs on the male genitalia are exceedingly rare. Solitary tumors have been reported on the penile shaft, prepuce, corpus cavernosum, glans penis, and scrotum. According to the latest serial analysis by using a MEDLINE search of the literature from January 1970 to December 2011, we identified seven reported GCTs involving the scrotum. We present a new case and perform a brief literature review.

  13. Malignant granular cell tumour on the thoracic wall: a case report and literature review

    International Nuclear Information System (INIS)

    Perez, E.; Esteban, R.; Alcalaya, R.; Albors, L.; Jimenez, C.; Ovelar, Y.; Cantera, M.G.

    1993-01-01

    A case is presented of a malignant granular cell tumour in a 52-year-old patient the initial location of which was the thoracic wall. After the tumour's removal there was recurrence in the lymph nodes, retroperitoneum, bone, lung and orbits. The important features of this case are its extraordinary rarity, the unusual location in the thoracic wall, and the tumour's infrequent malignancy. The radiological and histological findings are discussed, and the literature on the subject is reviewed. (orig.)

  14. Atrial granular cells of the snail Achatina fulica release proteins into hemolymph after stimulation of the heart nerve.

    Science.gov (United States)

    Shabelnikov, Sergej V; Bystrova, Olga A; Ivanov, Vadim A; Margulis, Boris A; Martynova, Marina

    2009-10-01

    The atrium of the gastropod mollusc Achatina fulica receives rich innervation and contains numerous granular cells (GCs). We studied the atrial innervation and discovered that axon profiles typical in appearance of peptidergic neurons form close unspecialized membrane contacts with GCs. Then, we investigated, at both morphological and biochemical levels, the effect of electrical stimulation of the heart nerve on GCs of Achatina heart perfused in situ. The ultrastructural study demonstrated changes in granule morphology consistent with secretion. These events included alteration of granule content, intracellular granule fusion and formation of complex degranulation channels, within which the granule matrix solubilized. It was shown that electrical stimulation resulted in a significant increase of the total protein concentration in the perfusate. Furthermore, SDS-PAGE analysis of the perfusate revealed three new proteins with molecular masses of 16, 22, and 57 kDa. Affinity-purified polyclonal antibodies against the 16 kDa protein were obtained; the whole-mount immunofluorescence technique revealed the presence of this protein in the granules of atrial GCs. In GCs of the stimulated atrium, a progressive loss of their granular content was observed. The results suggest that the central nervous system can modulate the secretory activity of the atrial GCs through non-synaptic pathways.

  15. M cells and granular mononuclear cells in Peyer's patch domes of mice depleted of their lymphocytes by total lymphoid irradiation

    International Nuclear Information System (INIS)

    Ermak, T.H.; Steger, H.J.; Strober, S.; Owen, R.L.

    1989-01-01

    The cytoarchitecture of Peyer's patches that were depleted of their lymphocytes by total lymphoid irradiation (TLI) was examined with particular attention to the effects on M cells in the follicle epithelium and on mononuclear cells in follicle domes underlying the epithelium. Five-month-old, specific pathogen-free Balb/c mice were irradiated with 200-250 rad/day, five times a week to a total dose of 3400-4250, and their Peyer's patches were either fixed for electron microscopy or frozen for immunohistochemistry 1-4 days after completion of irradiation. Control mice were examined at the same time intervals. Follicle domes of TLI mice had approximately one fourth the epithelial surface area of domes of control mice. Within the epithelium, lymphoid cells were virtually depleted after TLI, and yet the epithelium contained M cells. In control mice, most M cells were accompanied by lymphoid cells in invaginations of the apical-lateral cell membrane. In TLI mice, most M cells did not have such apical-lateral invaginations and were columnar shaped. Other than lacking lymphocytes, these cells appeared to be mature M cells. Some M cells did have lymphoid cells or granular mononuclear cells below their basal membranes, adjacent to the basal lamina. Below the epithelium, the proportion of granular mononuclear cells was greatly increased following TLI. The retention of M cells and the increase in proportion of granular mononuclear cells in follicle domes are consistent with selective depletion of lymphocytes following TLI. Persistence of M cells without lymphocytic invaginations after TLI suggests that M cells can differentiate in the absence of, or at least in the presence of very few, lymphocytes, and that invagination by lymphocytes is not necessary to maintain mature M cell morphology

  16. Effect of Substrate Friction in a Two-Dimensional Granular Couette Shearing Cell

    Science.gov (United States)

    Templeman, Chris; Garg, Shila

    2001-03-01

    An investigation of the effect of substrate friction on the kinematics of rigid granular material in a two-dimensional granular Couette shearing cell was conducted. Cylindrical disks resting on a substrate were packed between a stationary outer ring and a rotating inner wheel. Previous work reports the velocity and particle rotation rates as a function of packing fraction and shearing rates [1]. The authors report the existence of a stick-slip condition of the disks in contact with the shearing wheel. The focus of our study is to investigate the impact of the substrate friction on the stick-slip condition as well as the kinematics of the system in general. [1] C.T. Veje, Daniel W. Howell, and R.P Behringer, Phys. Rev. E 59, 739 (1999). This research was partially supported by the Copeland Fund, administered by The College of Wooster. C.T. received support from NASA GRC LERCIP internship program.

  17. The pattern of distribution of laminin in neurogenic tumors, granular cell tumors, and nevi of the oral mucosa

    DEFF Research Database (Denmark)

    Reibel, J; Wewer, U; Albrechtsen, R

    1985-01-01

    . Accentuated staining was seen in Verocay bodies. In granular cell myoblastomas (GCM), small groups of tumor cells were encircled by laminin-positive material, whereas individual tumor cells were unstained. In nevi, diffusely spread nevus cells were surrounded by a rim of laminin, whereas when arranged...

  18. GRANULAR CELL TUMOUR OF THE LARYNX – A CASE REPORT

    African Journals Online (AJOL)

    2015-12-01

    Dec 1, 2015 ... cell tumour involving the right vocal cord diagnosed after direct laryngoscopy and biopsy. She was treated ... She had no associated weight loss, dysphagia, odynophagia or dyspnoea. She occasionally took ... A provisional diagnosis of a right vocal cord tumour was made and patient worked up for direct.

  19. Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor

    KAUST Repository

    Bagchi, Samik; Lamendella, Regina; Strutt, Steven; Van Loosdrecht, Mark C. M.; Saikaly, Pascal

    2016-01-01

    to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all

  20. Cell-specific expression of the glucocorticoid receptor within granular convoluted tubules of the rat submaxillary gland

    International Nuclear Information System (INIS)

    Antakly, T.; Zhang, C.X.; Sarrieau, A.; Raquidan, D.

    1991-01-01

    The submaxillary gland, a heterogeneous tissue composed essentially of two functionally distinct cell types (tubular epithelial and acinar), offers an interesting system in which to study the mechanisms of steroid-dependent growth and differentiation. One cell type, the granular convoluted tubular (GCT) cell, secretes a large number of physiologically important polypeptides, including epidermal and nerve growth factors. Two steroids, androgens and glucocorticoids, greatly influence the growth, differentiation, and secretory activity of GCT cells. Because glucocorticoids can partially mimic or potentiate androgen effects, it has been thought that glucocorticoids act via androgen receptors. Since the presence of glucocorticoid receptors is a prerequisite for glucocorticoid action, we have investigated the presence and cellular distribution of glucocorticoid receptors within the rat submaxillary gland. Binding experiments using [3H]dexamethasone revealed the presence of high affinity binding sites in rat submaxillary tissue homogenates. Most of these sites were specifically competed by dexamethasone, corticosterone, and a pure glucocorticoid agonist RU 28362. Neither testosterone nor dihydrotestosterone competed for glucocorticoid binding. The cellular distribution of glucocorticoid receptors within the submaxillary gland was investigated by immunocytochemistry, using two highly specific glucocorticoid receptor antibodies. The receptor was localized in the GCT cells, but not in the acinar cells of rat and mouse submaxillary tissue sections. In GCT cells, the glucocorticoid receptor colocalized with several secretory polypeptides, including epidermal growth factor, nerve growth factor, alpha 2u-globulin, and atrial natriuretic factor

  1. Granular cell tumor of the breast: a report of the three cases

    International Nuclear Information System (INIS)

    Mellado, M.; Pina, L.; Cojo, R.; Arias-Camison, I.

    2000-01-01

    Granular cell tumors (GCT) of the breast are uncommon benign neoplasms that are usually indistinguishable from breast cancer with respect to their clinical and radiological presentation. FNAB can be a usefull diagnostic tool, but histological examination is essential for the correct diagnosis. This benign tumor should be considered among the diagnostic possibilities in the presence of a lesion with mammographic and ultrasonographic indications of highly probable malignancy. We present three cases of breast GCT that mimicked primary breast cancer. Benign neoplasm was diagnosed and local excision was carried out rather than mastectomy and lymphadenectomy. (Author) 9 refs

  2. Central Granular Cell Odontogenic Tumor: Report of a Case with CBCT Features.

    Directory of Open Access Journals (Sweden)

    Najmeh Anbiaee

    2014-06-01

    Full Text Available Central granular cell odontogenic tumor CGCOT of the jaw is an exceedingly rare benign odontogenic neoplasm with 35 reported cases in the literature. Among these, very few studies have focused on the cone-beam CT features of CGCOT. Here, we report a case of an asymptomatic CGCOT in a 16-year-old girl and focus on the cone-beam CT features. Only 36 cases of this lesion, including this one, have been reported so far. The case presented is of special importance due to the young age of the patient, the posterior location of the lesion and the multilocular pattern in the cone beam CT images.

  3. Granular flow

    DEFF Research Database (Denmark)

    Mitarai, Namiko; Nakanishi, Hiizu

    2012-01-01

    Granular material is a collection of macroscopic particles that are visible with naked eyes. The non-equilibrium nature of the granular materials makes their rheology quite different from that of molecular systems. In this minireview, we present the unique features of granular materials focusing...... on the shear flow of dry granular materials and granule-liquid mixture....

  4. Malignant granular cell tumor of the abdominal wall mimicking desmoid tumor: A case report with CT imaging findings and literature review

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Je Hong; Ahn, Sung Eun; Lee, Dong Ho; Park, Seong Jin; Moon, Sung Kyoung; Lim, Joo Won [Dept. Radiology, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul (Korea, Republic of)

    2016-08-15

    Granular cell tumors (GCTs) are extremely rare mesenchymal neoplasms of Schwann cell origin. Malignant GCTs (MGCTs) comprise 0.5-2% of all GCTs. In the present report, we describe a case of a 66-year-old man with MGCT of the abdominal wall. The patient visited our hospital due to a recently growing palpable soft tissue mass in the abdominal wall. Computed tomography scan revealed a 4.3 × 4.1 × 2.9 cm sized mass arising from the left abdominal wall, which was contemplated as a desmoid tumor before surgical excision. Histopathological examination confirmed MGCT.

  5. Is fine needle aspiration cytology a useful diagnostic tool for granular cell tumors? A cytohistological review with emphasis on pitfalls

    Directory of Open Access Journals (Sweden)

    Jason Koshy

    2014-01-01

    Full Text Available Background: Granular cell tumors (GCT formerly known as Abrikossoff tumor or granular cell myoblastoma, are rare neoplasms encountered in the fine needle aspiration (FNA service. Named because of their highly granular cytoplasm which is invariably positive for the S-100 antibody, the classic GCT is thought to be of neural origin. The cytomorphological features range from highly cellular to scanty cellular smears with dispersed polygonal tumor cells. The cells have abundant eosinophilic granular cytoplasm, eccentric round to oval vesicular nuclei with small inconspicuous nucleoli. The fragility of the cells can result in many stripped nuclei in a granular background. The differential diagnosis occasionally can range from a benign or reactive process to features that are suspicious for malignancy. Some of the concerning cytologic features include necrosis, mitoses and nuclear pleomorphism. Methods: We identified 6 cases of suspected GCT on cytology within the last 10 years and compared them to their final histologic diagnoses. Results: Four had histologic correlation of GCT including one case that was suspicious for GCT on cytology and called atypical with features concerning for a malignant neoplasm. Of the other two cases where GCT was suspected, one showed breast tissue with fibrocystic changes, and the other was a Hurthle cell adenoma of the thyroid. Conclusions: These results imply that FNA has utility in the diagnosis of GCT, and should be included in the differential diagnoses when cells with abundant granular cytoplasm are seen on cytology. Careful attention to cytologic atypia, signs of reactive changes, use of immunohistochemistry, and clinical correlation are helpful in arriving at a definite diagnosis on FNA cytology.

  6. Neurohypophysis granular cell tumours. Upon neurohypophysis rare tumours; Les tumeurs a cellules granuleuses. Des tumeurs rares de la neurohypophyse

    Energy Technology Data Exchange (ETDEWEB)

    Barrande, G.; Kujas, M.; Gancel, A.; Turpin, G.; Bruckert, E.; Kuhn, J.M.; Luton, J.P. [Hopital Cochin, 75 - Paris (France)

    1995-10-01

    Granular cell tumours of neurohypophysis are rare. These tumours are more often encountered as incidental autopsy findings seen in up to 17 % of unselected adult autopsy cases. There are few reports of para-sellar granular cell tumours large enough to cause symptoms. We present three cases of neurohypophysis granular cell tumour and a review of the literature. In one patient, the asymptomatic granular cell tumour was incidentally discovered at surgical removal of a corticotrophic micro-adenoma. The remaining 2 patients had a symptomatic tumour which caused neurological symptoms such as visual disturbance and headaches and endocrine disorders such as hypopituitarism or hyper-prolactinaemia. In these 2 cases, computerized tomography showed a well-circumscribed, contrast-enhanced, intra-sellar and supra-sellar mass. Magnetic resonance imaging demonstrated an isointense gadolinium-enhanced mass in T1-weighted-images. Trans-sphenoidal partial resection was performed and histology was interpreted as a granular cell tumour. The immunohistochemical study was positive for glial fibrillary acidic protein (GEAP) and neuron specific enolase (NSE) in 1 of the 2 tumours and positive for S100 protein and vimentin in both tumours but negative for CD68. The histogenesis of neurohypophysis granular cell tumours is still controversial but ultrastructural and immunohistochemical studies support the theory that may arise from pituicytes, the glial cells of neurohypophysis. Management of these benign, slow growing, tumours is based mainly on neurosurgical resection. Data from the literature do not support a beneficial effect of post operative radiation therapy on postoperative recurrences. (authors). 23 refs., 4 figs., 1 tab.

  7. Study of budding yeast colony formation and its characterizations by using circular granular cell

    Science.gov (United States)

    Aprianti, D.; Haryanto, F.; Purqon, A.; Khotimah, S. N.; Viridi, S.

    2016-03-01

    Budding yeast can exhibit colony formation in solid substrate. The colony of pathogenic budding yeast can colonize various surfaces of the human body and medical devices. Furthermore, it can form biofilm that resists drug effective therapy. The formation of the colony is affected by the interaction between cells and with its growth media. The cell budding pattern holds an important role in colony expansion. To study this colony growth, the molecular dynamic method was chosen to simulate the interaction between budding yeast cells. Every cell was modelled by circular granular cells, which can grow and produce buds. Cohesion force, contact force, and Stokes force govern this model to mimic the interaction between cells and with the growth substrate. Characterization was determined by the maximum (L max) and minimum (L min) distances between two cells within the colony and whether two lines that connect the two cells in the maximum and minimum distances intersect each other. Therefore, it can be recognized the colony shape in circular, oval, and irregular shapes. Simulation resulted that colony formation are mostly in oval shape with little branch. It also shows that greater cohesion strength obtains more compact colony formation.

  8. Effects of adult dysthyroidism on the morphology of hippocampal granular cells in rats.

    Science.gov (United States)

    Martí-Carbonell, Maria Assumpció; Garau, Adriana; Sala-Roca, Josefina; Balada, Ferran

    2012-01-01

    Thyroid hormones are essential for normal brain development and very important in the normal functioning of the brain. Thyroid hormones action in the adult brain has not been widely studied. The effects of adult hyperthyroidism are not as well understood as adult hypothyroidism, mainly in hippocampal granular cells. The purpose of the present study is to assess the consequences of adult hormone dysthyroidism (excess/deficiency of TH) on the morphology of dentate granule cells in the hippocampus by performing a quantitative study of dendritic arborizations and dendritic spines using Golgi impregnated material. Hypo-and hyperthyroidism were induced in rats by adding 0.02 percent methimazole and 1 percent L-thyroxine, respectively, to drinking water from 40 days of age. At 89 days, the animals' brains were removed and stained by a modified Golgi method and blood samples were collected in order to measure T4 serum levels. Neurons were selected and drawn using a camera lucida. Our results show that both methimazole and thyroxine treatment affect granule cell morphology. Treatments provoke alterations in the same direction, namely, reduction of certain dendritic-branching parameters that are more evident in the methimazole than in the thyroxine group. We also observe a decrease in spine density in both the methimazole and thyroxine groups.

  9. Transformations to granular zircon revealed: Twinning, reidite, and ZrO2 in shocked zircon from Meteor Crater (Arizona, USA)

    Science.gov (United States)

    Cavosie, Aaron; Timms, Nicholas E.; Erickson, Timmons M.; Hagerty, Justin J.; Hörz, Friedrich

    2016-01-01

    Granular zircon in impact environments has long been recognized but remains poorly understood due to lack of experimental data to identify mechanisms involved in its genesis. Meteor Crater in Arizona (United States) contains abundant evidence of shock metamorphism, including shocked quartz, the high pressure polymorphs coesite and stishovite, diaplectic SiO2 glass, and lechatelierite (fused SiO2). Here we report the presence of granular zircon, a new shocked mineral discovery at Meteor Crater, that preserve critical orientation evidence of specific transformations that occurred during its formation at extreme impact conditions. The zircon grains occur as aggregates of sub-µm neoblasts in highly shocked Coconino Formation Sandstone (CFS) comprised of lechatelierite. Electron backscatter diffraction shows that each grain consists of multiple domains, some with boundaries disoriented by 65°, a known {112} shock-twin orientation. Other domains have crystallographic c-axes in alignment with {110} of neighboring domains, consistent with the former presence of the high pressure ZrSiO4 polymorph reidite. Additionally, nearly all zircon preserve ZrO2 + SiO2, providing evidence of partial dissociation. The genesis of CFS granular zircon started with detrital zircon that experienced shock-twinning and reidite formation from 20 to 30 GPa, ultimately yielding a phase that retained crystallographic memory; this phase subsequently recrystallized to systematically oriented zircon neoblasts, and in some areas partially dissociated to ZrO2. The lechatelierite matrix, experimentally constrained to form at >2000 °C, provided an ultra high-temperature environment for zircon dissociation (~1670 °C) and neoblast formation. The capacity of granular zircon to preserve a cumulative P-T record has not been recognized previously, and provides a new method for retrieving histories of impact-related mineral transformations in the crust at conditions far beyond which most rocks melt.

  10. Altered expression of the cell cycle regulatory protein cyclin D1 in the rat dentate gyrus after adrenalectomy-induced granular cell lass

    NARCIS (Netherlands)

    Postigo, JA; Van der Werf, YD; Korf, J; Krugers, HJ

    1998-01-01

    The loss of dentate gyrus (DG) granular cells after removal of the rat adrenal glands (ADX) is mediated by a process that is apoptotic in nature. The present study was initiated to compare changes in the immunocytochemical distribution of the cell-cycle regulatory protein cyclin D1, which has been

  11. Effect of pre-acclimation of granular activated carbon on microbial electrolysis cell startup and performance.

    Science.gov (United States)

    LaBarge, Nicole; Yilmazel, Yasemin Dilsad; Hong, Pei-Ying; Logan, Bruce E

    2017-02-01

    Microbial electrolysis cells (MECs) can generate methane by fixing carbon dioxide without using expensive catalysts, but the impact of acclimation procedures on subsequent performance has not been investigated. Granular activated carbon (GAC) was used to pre-enrich electrotrophic methanogenic communities, as GAC has been shown to stimulate direct transfer of electrons between different microbial species. MEC startup times using pre-acclimated GAC were improved compared to controls (without pre-acclimation or without GAC), and after three fed batch cycles methane generation rates were similar (P>0.4) for GAC acclimated to hydrogen (22±9.3nmolcm -3 d -1 ), methanol (25±9.7nmolcm -3 d -1 ), and a volatile fatty acid (VFA) mix (22±11nmolcm -3 d -1 ). However, MECs started with GAC but no pre-acclimation had lower methane generation rates (13±4.1nmolcm -3 d -1 ), and MECs without GAC had the lowest rates (0.7±0.8nmolcm -3 d -1 after cycle 2). Microbes previously found in methanogenic MECs, or previously shown to be capable of exocellular electron transfer, were enriched on the GAC. Pre-acclimation using GAC is therefore a simple approach to enrich electroactive communities, improve methane generation rates, and decrease startup times in MECs. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. IS MAGNETIC RECONNECTION THE CAUSE OF SUPERSONIC UPFLOWS IN GRANULAR CELLS?

    Energy Technology Data Exchange (ETDEWEB)

    Borrero, J. M.; Schmidt, W. [Kiepenheuer-Institut fuer Sonnenphysik, Schoeneckstr. 6, D-79110, Freiburg (Germany); Martinez Pillet, V.; Quintero Noda, C.; Bonet, J. A. [Instituto de Astrofisica de Canarias, Avd. Via Lactea s/n, E-38200 La Laguna (Spain); Del Toro Iniesta, J. C.; Bellot Rubio, L. R., E-mail: borrero@kis.uni-freiburg.de, E-mail: wolfgang@kis.uni-freiburg.de, E-mail: vmp@ll.iac.es, E-mail: cqn@ll.iac.es, E-mail: jab@ll.iac.es, E-mail: jti@iaa.es, E-mail: lbellot@iaa.es [Instituto de Astrofisica de Andalucia (CSIC), Apdo. de Correos 3004, E-18080 Granada (Spain)

    2013-05-01

    In a previous work, we reported on the discovery of supersonic magnetic upflows on granular cells in data from the SUNRISE/IMaX instrument. In the present work, we investigate the physical origin of these events employing data from the same instrument but with higher spectral sampling. By means of the inversion of Stokes profiles we are able to recover the physical parameters (temperature, magnetic field, line-of-sight velocity, etc.) present in the solar photosphere at the time of these events. The inversion is performed in a Monte-Carlo-like fashion, that is, repeating it many times with different initializations and retaining only the best result. We find that many of the events are characterized by a reversal in the polarity of the magnetic field along the vertical direction in the photosphere, accompanied by an enhancement in the temperature and by supersonic line-of-sight velocities. In about half of the studied events, large blueshifted and redshifted line-of-sight velocities coexist above/below each other. These features can be explained in terms of magnetic reconnection, where the energy stored in the magnetic field is released in the form of kinetic and thermal energy when magnetic field lines of opposite polarities coalesce. However, the agreement with magnetic reconnection is not perfect and, therefore, other possible physical mechanisms might also play a role.

  13. Solitary, multiple, benign, atypical, or malignant: the "Granular Cell Tumor" puzzle.

    Science.gov (United States)

    Machado, Isidro; Cruz, Julia; Lavernia, Javier; Llombart-Bosch, Antonio

    2016-05-01

    The clinical evolution and biology of granular cell tumors (GCT) are poorly understood and treatment remains an issue of discussion. The majority of GCT are benign, although some display malignant behavior. The distinction between benign, atypical, and malignant GCT is controversial due to morphological and immunohistochemical overlap and lack of consistent histological and phenotypic criteria that predict behavior. Although histological criteria may indicate increased risk of malignant evolution, some GCT with evident benign appearance exceptionally progress towards metastatic disease. In this review, we discuss current knowledge on GCT, including histologic, immunophenotypic, and molecular characteristics and differential diagnosis. We focus on the following problematic items in GCT: (1) evolution of classification, (2) neural versus non-neural GCT, (3) neoplastic versus reactive disease, (4) malignant transformation of benign GCT, and (5) multiple versus metastatic GCT. We conclude that although a Ki-67 index >10 % and the presence of mitoses and/or of necrosis are frequently associated with malignant behavior, metastasis remains the only unequivocal sign of malignancy in GCT. An infiltrative growth pattern and vascular and/or perineural invasion are not indicative of malignancy. GCT with atypical/uncertain features almost never metastasize, and many of these tumors either behave in a benign fashion or only recur locally (similar to incompletely excised benign tumors). We therefore propose that classical and atypical histological variants form a single group of GCT. GCT with various unfavorable histological features might be labeled as "GCT with increased risk of metastasis" rather than malignant GCT.

  14. Granular patterns

    CERN Document Server

    Aranson, Igor S

    2009-01-01

    This title presents a review of experiments and novel theoretical concepts needed to understand the mechanisms of pattern formation in granular materials. An effort is made to connect concepts and ideas developed in granular physics with new emergent fields, especially in biology, such as cytoskeleton dynamics.

  15. Effect of pre-acclimation of granular activated carbon on microbial electrolysis cell startup and performance

    KAUST Repository

    LaBarge, Nicole

    2016-09-09

    Microbial electrolysis cells (MECs) can generate methane by fixing carbon dioxide without using expensive catalysts, but the impact of acclimation procedures on subsequent performance has not been investigated. Granular activated carbon (GAC) was used to pre-enrich electrotrophic methanogenic communities, as GAC has been shown to stimulate direct transfer of electrons between different microbial species. MEC startup times using pre-acclimated GAC were improved compared to controls (without pre-acclimation or without GAC), and after three fed batch cycles methane generation rates were similar (P > 0.4) for GAC acclimated to hydrogen (22 ± 9.3 nmol cm− 3 d− 1), methanol (25 ± 9.7 nmol cm− 3 d− 1), and a volatile fatty acid (VFA) mix (22 ± 11 nmol cm− 3 d− 1). However, MECs started with GAC but no pre-acclimation had lower methane generation rates (13 ± 4.1 nmol cm− 3 d− 1), and MECs without GAC had the lowest rates (0.7 ± 0.8 nmol cm− 3 d− 1 after cycle 2). Microbes previously found in methanogenic MECs, or previously shown to be capable of exocellular electron transfer, were enriched on the GAC. Pre-acclimation using GAC is therefore a simple approach to enrich electroactive communities, improve methane generation rates, and decrease startup times in MECs. © 2016 Elsevier B.V.

  16. Transcriptome differentiation along the dorso-ventral axis in laser-captured microdissected rat hippocampal granular cell layer

    DEFF Research Database (Denmark)

    Christensen, T.; Bisgaard, C.F.; Nielsen, Henrik Bjørn

    2010-01-01

    Several findings suggest a functional and anatomical differentiation along the dorso-ventral axis of the hippocampus. Lesion studies in rats have indicated that the dorsal hippocampus preferentially plays a role in spatial learning and memory, while the ventral hippocampus is involved in anxiety...... and ventral granular cell layer with a false discovery rate below 5% and with a relative change in gene expression level of 20% or more. From this pool of genes 45 genes were more than two-fold regulated, 13 genes being dorsally enriched and 32 genes being ventrally enriched. Moreover, cluster analysis based...

  17. Biophysics Model of Heavy-Ion Degradation of Neuron Morphology in Mouse Hippocampal Granular Cell Layer Neurons.

    Science.gov (United States)

    Alp, Murat; Cucinotta, Francis A

    2018-03-01

    Exposure to heavy-ion radiation during cancer treatment or space travel may cause cognitive detriments that have been associated with changes in neuron morphology and plasticity. Observations in mice of reduced neuronal dendritic complexity have revealed a dependence on radiation quality and absorbed dose, suggesting that microscopic energy deposition plays an important role. In this work we used morphological data for mouse dentate granular cell layer (GCL) neurons and a stochastic model of particle track structure and microscopic energy deposition (ED) to develop a predictive model of high-charge and energy (HZE) particle-induced morphological changes to the complex structures of dendritic arbors. We represented dendrites as cylindrical segments of varying diameter with unit aspect ratios, and developed a fast sampling method to consider the stochastic distribution of ED by δ rays (secondary electrons) around the path of heavy ions, to reduce computational times. We introduce probabilistic models with a small number of parameters to describe the induction of precursor lesions that precede dendritic snipping, denoted as snip sites. Predictions for oxygen ( 16 O, 600 MeV/n) and titanium ( 48 Ti, 600 MeV/n) particles with LET of 16.3 and 129 keV/μm, respectively, are considered. Morphometric parameters to quantify changes in neuron morphology are described, including reduction in total dendritic length, number of branch points and branch numbers. Sholl analysis is applied for single neurons to elucidate dose-dependent reductions in dendritic complexity. We predict important differences in measurements from imaging of tissues from brain slices with single neuron cell observations due to the role of neuron death through both soma apoptosis and excessive dendritic length reduction. To further elucidate the role of track structure, random segment excision (snips) models are introduced and a sensitivity study of the effects of the modes of neuron death in predictions

  18. From cell extracts to fish schools to granular layers: the universal hydrodynamics of self-driven systems

    Science.gov (United States)

    Ramaswamy, Sriram

    2007-03-01

    Collections of self-driven or ``active'' particles are now recognised as a distinct kind of nonequilibrium matter, and an understanding of their phases, hydrodynamics, mechanical response, and correlations is a vital and rapidly developing part of the statistical physics of soft-matter systems far from equilibrium. My talk will review our recent results, from theory, simulation and experiment, on order, fluctuations, and flow instabilities in collections of active particles, in suspension or on a solid surface. Our work, which began by adapting theories of flocking to include the hydrodynamics of the ambient fluid, provides the theoretical framework for understanding active matter in all its diversity: contractile filaments in cell extracts, crawling or dividing cells, collectively swimming bacteria, fish schools, and agitated monolayers of orientable granular particles.

  19. Mesoscale simulations of shock compaction of a granular ceramic: effects of mesostructure and mixed-cell strength treatment

    Science.gov (United States)

    Derrick, J. G.; LaJeunesse, J. W.; Davison, T. M.; Borg, J. P.; Collins, G. S.

    2018-04-01

    The shock response of granular materials is important in a variety of contexts but the precise dynamics of grains during compaction is poorly understood. Here we use 2D mesoscale numerical simulations of the shock compaction of granular tungsten carbide to investigate the effect of internal structure within the particle bed and ‘stiction’ between grains on the shock response. An increase in the average number of contacts with other particles, per particle, tends to shift the Hugoniot to higher shock velocities, lower particle velocities and lower densities. This shift is sensitive to inter-particle shear resistance. Eulerian shock physics codes approximate friction between, and interlocking of, grains with their treatment of mixed cell strength (stiction) and here we show that this has a significant effect on the shock response. When studying the compaction of particle beds it is not common to quantify the pre-compaction internal structure, yet our results suggest that such differences should be taken into account, either by using identical beds or by averaging results over multiple experiments.

  20. An approach to discriminatively determine thoron and radon emanation rates for a granular material with a scintillation cell

    International Nuclear Information System (INIS)

    Sakoda, Akihiro; Meisenberg, Oliver; Tschiersch, Jochen

    2016-01-01

    A powder sandwich technique was applied to determine thoron ("2"2"0Rn) and radon ("2"2"2Rn) emanation rates for a granular material. The feature of this technique is the sample preparation, in which a granular material is put and fixed between two membrane filters. Airflow is directly given to this sandwich sample, will include thoron and radon emanated from the material, and then is transferred to the detector. This method makes sure that thoron and radon emanated are not retained in pore space within the sample volume, which is crucial for the appropriate emanation test. This technique was first introduced by Kanse et al. (2013) with the intention to measure the emanation of thoron - but not of radon - from materials having much higher "2"2"4Ra activity than "2"2"6Ra. In the present study, the methodology for the discriminative determination of thoron and radon emanation rates from a granular material has been examined using a flow-through scintillation cell and sandwich sample. The mathematical model was developed to differentiate total alpha counts into thoron- and radon-associated counts. With a sample of uranium ore, this model was experimentally validated by comparison between the scintillation cell and a reference detector that can discriminatively measure thoron and radon concentrations. Furthermore, the detection limits and uncertainties were evaluated to discuss the characteristics of this method. Key parameters for improving the determination of thoron and radon emanations were found to be the background radon concentration and the leakage of radon from the measurement system, respectively. It was concluded that the present method is advantageous to a sample that has much higher "2"2"6Ra activity than "2"2"4Ra. - Highlights: • The methodology of appropriate and discriminative measurement of thoron and radon emanation is presented. • Measurement of thoron and radon emanated from a sample was made using a scintillation cell. • Detection limits and

  1. HMB-45 and Melan-A are useful in the differential diagnosis between granular cell tumor and malignant melanoma.

    Science.gov (United States)

    Gleason, Briana C; Nascimento, Alessandra F

    2007-02-01

    Granular cell tumors (GCTs), especially if atypical or malignant, may share cytomorphologic and architectural features with malignant melanoma, when the latter shows granular cell change. In many cases, these neoplasms can be differentiated from each other on histologic grounds, but distinction may sometimes be challenging. By immunohistochemistry, both tumors are strongly positive for S-100 protein and frequently express other nonspecific markers such as CD68, NSE, and NKIC3. In the current study, we reviewed 60 cases of conventional cutaneous, mucosal, and visceral GCT and studied the use of immunoperoxidase staining for the differential diagnosis between malignant melanoma and GCT. Immunohistochemical stains for S-100 protein, A, HMB-45, and microphthalmia transcription factor (MITF) were performed in all cases. All of the tumors were positive for S-100 protein. MITF immunostaining was diffusely positive in 53 (88%) cases, focally positive in three (5%) cases, and negative in four (7%). Fifty-seven (95%) tumors were negative for Melan-A, one case was focally positive, and two cases showed rare positive tumor cells. None of the tumors expressed HMB-45. In conclusion, GCT and malignant melanoma can be reliably differentiated on the basis of immunohistochemical stains in the majority of cases. Although not always positive in malignant melanoma, in this context, HMB-45 expression seems to be 100% specific for the diagnosis of melanoma. Melan-A is slightly less specific, with rare cases of GCT showing focal positivity. MITF is not useful in this differential-93% of the GCTs in our series showed nuclear reactivity for this marker. The latter finding highlights the limited specificity of this antibody in the diagnosis of melanocytic tumors.

  2. Heterogeneous adsorption behavior of landfill leachate on granular activated carbon revealed by fluorescence excitation emission matrix (EEM)-parallel factor analysis (PARAFAC).

    Science.gov (United States)

    Lee, Sonmin; Hur, Jin

    2016-04-01

    Heterogeneous adsorption behavior of landfill leachate on granular activated carbon (GAC) was investigated by fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (PARAFAC). The equilibrium adsorption of two leachates on GAC was well described by simple Langmuir and Freundlich isotherm models. More nonlinear isotherm and a slower adsorption rate were found for the leachate with the higher values of specific UV absorbance and humification index, suggesting that the leachate containing more aromatic content and condensed structures might have less accessible sites of GAC surface and a lower degree of diffusive adsorption. Such differences in the adsorption behavior were found even within the bulk leachate as revealed by the dissimilarity in the isotherm and kinetic model parameters between two identified PARAFAC components. For both leachates, terrestrial humic-like fluorescence (C1) component, which is likely associated with relatively large sized and condensed aromatic structures, exhibited a higher isotherm nonlinearity and a slower kinetic rate for GAC adsorption than microbial humic-like (C2) component. Our results were consistent with size exclusion effects, a well-known GAC adsorption mechanism. This study demonstrated the promising benefit of using EEM-PARAFAC for GAC adsorption processes of landfill leachate through fast monitoring of the influent and treated leachate, which can provide valuable information on optimizing treatment processes and predicting further environmental impacts of the treated effluent. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Clinical relevance of sensitive and quantitative STAT3 mutation analysis using next-generation sequencing in T-cell large granular lymphocytic leukemia

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Larsen, Martin; Rewes, Annika

    2014-01-01

    Diagnosis of T-cell large granular lymphocytic leukemia (T-LGL) is often challenging because clinical and laboratory characteristics are overlapping with nonneoplastic conditions. Recently, mutation in the STAT3 gene has been identified as a recurrent genetic abnormality in T-LGL. STAT3 mutation...

  4. Granular cell tumor of the oral cavity; a case series including a case of metachronous occurrence in the tongue and the lung

    NARCIS (Netherlands)

    van de Loo, S.; Thunissen, E.; Postmus, P.; van der Waal, I.

    2015-01-01

    The granular cell tumor (GCT) is a rare, benign tumor that most commonly occurs in the oral cavity, particularly in the anterior part of the tongue. In this study the experience with 16 patients with a GCT observed in a single Institution will be discussed. Although no radicality has been obtained

  5. Elevated Systemic Levels of Eosinophil, Neutrophil, and Mast Cell Granular Proteins in Strongyloides Stercoralis Infection that Diminish following Treatment.

    Science.gov (United States)

    Rajamanickam, Anuradha; Munisankar, Saravanan; Bhootra, Yukthi; Dolla, Chandra Kumar; Nutman, Thomas B; Babu, Subash

    2018-01-01

    Infection with the helminth parasite Strongyloides stercoralis ( Ss ) is commonly clinically asymptomatic that is often accompanied by peripheral eosinophilia. Granulocytes are activated during helminth infection and can act as immune effector cells. Plasma levels of eosinophil and neutrophil granular proteins convey an indirect measure of granulocyte degranulation and are prominently augmented in numerous helminth-infected patients. In this study, we sought to examine the levels of eosinophil, neutrophil, and mast cell activation-associated granule proteins in asymptomatic Ss infection and to understand their kinetics following anthelmintic therapy. To this end, we measured the plasma levels of eosinophil cationic protein, eosinophil-derived neurotoxin, eosinophil peroxidase, eosinophil major basic protein, neutrophil elastase, myeloperoxidase, neutrophil proteinase-3, mast cell tryptase, leukotriene C4, and mast cell carboxypeptidase-A3 in individuals with asymptomatic Ss infection or without Ss infection [uninfected (UN)]. We also estimated the levels of all of these analytes in infected individuals following definitive treatment of Ss infection. We demonstrated that those infected individuals have significantly enhanced plasma levels of eosinophil cationic protein, eosinophil-derived neurotoxin, eosinophil peroxidase, eosinophil major basic protein, elastase, myeloperoxidase, mast cell tryptase, leukotriene C4, and carboxypeptidase-A3 compared to UN individuals. Following the treatment of Ss infection, each of these granulocyte-associated proteins drops significantly. Our data suggest that eosinophil, neutrophil, and mast cell activation may play a role in the response to Ss infection.

  6. Biodegradation of phenol in batch and continuous flow microbial fuel cells with rod and granular graphite electrodes.

    Science.gov (United States)

    Moreno, Lyman; Nemati, Mehdi; Predicala, Bernardo

    2018-01-01

    Phenol biodegradation was evaluated in batch and continuous flow microbial fuel cells (MFCs). In batch-operated MFCs, biodegradation of 100-1000 mg L -1 phenol was four to six times faster when graphite granules were used instead of rods (3.5-4.8 mg L -1  h -1 vs 0.5-0.9 mg L -1  h -1 ). Similarly maximum phenol biodegradation rates in continuous MFCs with granular and single-rod electrodes were 11.5 and 0.8 mg L -1  h -1 , respectively. This superior performance was also evident in terms of electrochemical outputs, whereby continuous flow MFCs with granular graphite electrodes achieved maximum current and power densities (3444.4 mA m -3 and 777.8 mW m -3 ) that were markedly higher than those with single-rod electrodes (37.3 mA m -3 and 0.8 mW m -3 ). Addition of neutral red enhanced the electrochemical outputs to 5714.3 mA m -3 and 1428.6 mW m -3 . Using the data generated in the continuous flow MFC, biokinetic parameters including μ m , K S , Y and K e were determined as 0.03 h -1 , 24.2 mg L -1 , 0.25 mg cell (mg phenol) -1 and 3.7 × 10 -4  h -1 , respectively. Access to detailed kinetic information generated in MFC environmental conditions is critical in the design, operation and control of large-scale treatment systems utilizing MFC technology.

  7. Comparisons of physical experiment and discrete element simulations of sheared granular materials in an annular shear cell

    Science.gov (United States)

    Ji, S.; Hanes, D.M.; Shen, H.H.

    2009-01-01

    In this study, we report a direct comparison between a physical test and a computer simulation of rapidly sheared granular materials. An annular shear cell experiment was conducted. All parameters were kept the same between the physical and the computational systems to the extent possible. Artificially softened particles were used in the simulation to reduce the computational time to a manageable level. Sensitivity study on the particle stiffness ensured such artificial modification was acceptable. In the experiment, a range of normal stress was applied to a given amount of particles sheared in an annular trough with a range of controlled shear speed. Two types of particles, glass and Delrin, were used in the experiment. Qualitatively, the required torque to shear the materials under different rotational speed compared well with those in the physical experiments for both the glass and the Delrin particles. However, the quantitative discrepancies between the measured and simulated shear stresses were nearly a factor of two. Boundary conditions, particle size distribution, particle damping and friction, including a sliding and rolling, contact force model, were examined to determine their effects on the computational results. It was found that of the above, the rolling friction between particles had the most significant effect on the macro stress level. This study shows that discrete element simulation is a viable method for engineering design for granular material systems. Particle level information is needed to properly conduct these simulations. However, not all particle level information is equally important in the study regime. Rolling friction, which is not commonly considered in many discrete element models, appears to play an important role. ?? 2009 Elsevier Ltd.

  8. Clinical response to a lomustine/cytarabine-based chemotherapy protocol in a case of canine large granular lymphocyte T-cell lymphoma with spinal involvement

    Directory of Open Access Journals (Sweden)

    Elisabetta Treggiari

    2018-05-01

    Full Text Available A 7-year-old, female neutered cross-breed dog was referred to our institution with a history of progressive hind limb weakness, which then progressed to paraplegia. An MRI of the spine revealed severe meningeal infiltrate consistent with lymphoma involvement, located at the level of L2-L7 with concurrent lymph node enlargement and abnormal bone marrow. Abdominal ultrasonography also identified changes in the spleen and confirmed enlargement of the lumbar aortic lymph node. Cytology of lymph nodes and spleen confirmed a high-grade lymphoma with features of a large granular lymphocyte (LGL variant; PCR for antigen receptor re-arrangements (PARR was positive for a clonal T-cell receptor rearrangement. The dog was started on a chemotherapy protocol with lomustine and cytarabine incorporation and had a rapid improvement in neurological status. Chemotherapy was continued until relapse and rescue treatment used at that time. The dog was euthanased at the time of recurrence of neurological signs, 195 days since medical treatment was started. This case report suggests that combination chemotherapy may be of use when treating LGL lymphoma with spinal involvement and survival time may potentially exceed 6 months.

  9. Granular activated carbon based microbial fuel cell for simultaneous decolorization of real dye wastewater and electricity generation.

    Science.gov (United States)

    Kalathil, Shafeer; Lee, Jintae; Cho, Moo Hwan

    2011-12-15

    Decolorization of dye wastewater before discharge is pivotal because of its immense color and toxicities. In this study, a granular activated carbon based microbial fuel cell (GACB-MFC) was used without using any expensive materials like Nafion membrane and platinum catalyst for simultaneous decolorization of real dye wastewater and bioelectricity generation. After 48 hours of GACB-MFC operation, 73% color was removed at anode and 77% color was removed at cathode. COD removal was 71% at the anode and 76% at the cathode after 48 hours. Toxicity measurements showed that cathode effluent was almost nontoxic after 24 hours. The anode effluent was threefold less toxic compared to original dye wastewater after 48 hours. The GACB-MFC produced a power density of 1.7 W/m(3) with an open circuit voltage 0.45 V. One of the advantages of the GACB-MFC system is that pH was automatically adjusted from 12.4 to 7.2 and 8.0 at the anode and cathode during 48 hours operation. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Computational investigation of the flow field contribution to improve electricity generation in granular activated carbon-assisted microbial fuel cells

    Science.gov (United States)

    Zhao, Lei; Li, Jian; Battaglia, Francine; He, Zhen

    2016-11-01

    Microbial fuel cells (MFCs) offer an alternative approach to treat wastewater with less energy input and direct electricity generation. To optimize MFC anodic performance, adding granular activated carbon (GAC) has been proved to be an effective way, most likely due to the enlarged electrode surface for biomass attachment and improved mixing of the flow field. The impact of a flow field on the current enhancement within a porous anode medium (e.g., GAC) has not been well understood before, and thus is investigated in this study by using mathematical modeling of the multi-order Butler-Volmer equation with computational fluid dynamics (CFD) techniques. By comparing three different CFD cases (without GAC, with GAC as a nonreactive porous medium, and with GAC as a reactive porous medium), it is demonstrated that adding GAC contributes to a uniform flow field and a total current enhancement of 17%, a factor that cannot be neglected in MFC design. However, in an actual MFC operation, this percentage could be even higher because of the microbial competition and energy loss issues within a porous medium. The results of the present study are expected to help with formulating strategies to optimize MFC with a better flow pattern design.

  11. SOLITARY T-CELL HEPATIC LYMPHOMA WITH LARGE GRANULAR LYMPHOCYTE MORPHOLOGY IN A CAPTIVE CHEETAH (ACINONYX JUBATUS).

    Science.gov (United States)

    Lindemann, Dana M; Carpenter, James W; Almes, Kelli M; Schumacher, Loni; Ryseff, Julia K; Hallman, Mackenzie

    2015-06-01

    A 13-yr-old male cheetah (Acinonyx jubatus) presented for an acute history of lateral recumbency and anorexia. Upon physical examination under general anesthesia, severe icterus was noted. A serum biochemical profile confirmed markedly elevated total bilirubin and alanine transaminase. Based on ultrasound-guided liver aspirates and cytology, a presumptive diagnosis of large granular lymphocyte hepatic lymphoma was reached. Abdominal and thoracic radiographs did not assist in reaching an antemortem diagnosis. Postmortem examination and histopathology provided a definitive diagnosis of hepatic lymphoma with acute massive hepatocelluar necrosis and hemorrhage, as well as concurrent lesions of gastric ulcers, ulcerative and sclerosing enteritis, myocardial hypertrophy, and splenic myelolipomas. Immunohistochemistry of the liver yielded CD-3 positive and CD-20 negative results, confirming lymphocytes of a T-cell lineage. Due to concern for possible retrovirus-associated disease, enzyme-linked immunosorbent assays for feline leukemia virus and feline immunodeficiency virus were performed retrospectively on a banked serum sample and yielded negative results, thus diminishing concern for the male conspecific housed in the same exhibit.

  12. Enhanced desalination performance of membrane capacitive deionization cells by packing the flow chamber with granular activated carbon.

    Science.gov (United States)

    Bian, Yanhong; Yang, Xufei; Liang, Peng; Jiang, Yong; Zhang, Changyong; Huang, Xia

    2015-11-15

    A new design of membrane capacitive deionization (MCDI) cell was constructed by packing the cell's flow chamber with granular activated carbon (GAC). The GAC packed-MCDI (GAC-MCDI) delivered higher (1.2-2.5 times) desalination rates than the regular MCDI at all test NaCl concentrations (∼ 100-1000 mg/L). The greatest performance enhancement by packed GAC was observed when treating saline water with an initial NaCl concentration of 100 mg/L. Several different GAC materials were tested and they all exhibited similar enhancement effects. Comparatively, packing the MCDI's flow chamber with glass beads (GB; non-conductive) and graphite granules (GG; conductive but with lower specific surface area than GAC) resulted in inferior desalination performance. Electrochemical impedance spectroscopy (EIS) analysis showed that the GAC-MCDI had considerably smaller internal resistance than the regular MCDI (∼ 19.2 ± 1.2 Ω versus ∼ 1222 ± 15 Ω at 100 mg/L NaCl). The packed GAC also decreased the ionic resistance across the flow chamber (∼ 1.49 ± 0.05 Ω versus ∼ 1130 ± 12 Ω at 100 mg/L NaCl). The electric double layer (EDL) formed on the GAC surface was considered to store salt ions during electrosorption, and facilitate the ion transport in the flow chamber because of the higher ion conductivity in the EDLs than in the bulk solution, thereby enhancing the MCDI's desalination rate. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Apoptosis of Purkinje and granular cells of the cerebellum following chronic ethanol intake.

    Science.gov (United States)

    Oliveira, Suelen A; Chuffa, Luiz Gustavo A; Fioruci-Fontanelli, Beatriz Aparecida; Lizarte Neto, Fermino Sanches; Novais, Paulo Cezar; Tirapelli, Luiz Fernando; Oishi, Jorge Camargo; Takase, Luiz Fernando; Stefanini, Maira Aparecida; Martinez, Marcelo; Martinez, Francisco Eduardo

    2014-12-01

    Ethanol alters motricity, learning, cognition, and cellular metabolism in the cerebellum. We evaluated the effect of ethanol on apoptosis in Golgi, Purkinje, and granule cells of the cerebellum in adult rats. There were two groups of 20 rats: a control group that did not consume ethanol and an experimental group of UChA rats that consumed ethanol at 10% (cerebellum of adult UChA rats.

  14. Successful treatment of cerebral aspergillosis: case report of a patient with T-cell large granular lymphocytic leukemia (T-LGL).

    Science.gov (United States)

    Turki, Amin T; Rashidi-Alavijeh, Jassin; Dürig, Jan; Gerken, Guido; Rath, Peter-Michael; Witzke, Oliver

    2017-12-28

    Invasive aspergillosis involving patients with neutropenia or severe immunosuppression, such as patients with hematologic malignancies is associated with high mortality. Patients with T-cell large granular lymphocytic leukemia (T-LGL) on the other hand are considered to be less vulnerable for severe opportunistic fungal infection as their course of disease is chronic and marked by less violent cytopenia then in e.g. Aplastic Anemia. Only neutropenia is regarded as independent risk factor for severe opportunistic infection in T-LGL patients. We report a case of a 53 year old patient with T-LGL, Immune-Thrombocytopenia (ITP) and combined antibody deficiency, who presented with fever and reduced general condition. The patient revealed a complicated infection involving the lungs and later the brain, with the presentation of vomiting and seizures. Broad microbiological testing of blood-, lung- and cerebrospinal fluid samples was inconclusive. In the absence of mycological proof, Aspergillus infection was confirmed by pathological examination of a brain specimen and finally successfully treated with liposomal amphotericin B and voriconazole, adopting a long-term treatment scheme. Beyond typical problems in the clinical practice involving fungal infections and hematologic malignancies, this case of invasive aspergillosis in a patient with T-LGL illustrates caveats in diagnosis, therapy and follow-up. Our data support careful ambulatory monitoring for patients with T-LGL, even in the absence of neutropenia. Especially those patients with combined hematologic malignancies and immune defects are at risk. Long-term treatment adhesion for 12 months with sufficient drug levels was necessary for sustained clearance from infection.

  15. Energy decay in a granular gas collapse

    International Nuclear Information System (INIS)

    Almazán, Lidia; Serero, Dan; Pöschel, Thorsten; Salueña, Clara

    2017-01-01

    An inelastic hard ball bouncing repeatedly off the ground comes to rest in finite time by performing an infinite number of collisions. Similarly, a granular gas under the influence of external gravity, condenses at the bottom of the confinement due to inelastic collisions. By means of hydrodynamical simulations, we find that the condensation process of a granular gas reveals a similar dynamics as the bouncing ball. Our result is in agreement with both experiments and particle simulations, but disagrees with earlier simplified hydrodynamical description. Analyzing the result in detail, we find that the adequate modeling of pressure plays a key role in continuum modeling of granular matter. (paper)

  16. High-frequency microrheology reveals cytoskeleton dynamics in living cells

    Science.gov (United States)

    Rigato, Annafrancesca; Miyagi, Atsushi; Scheuring, Simon; Rico, Felix

    2017-08-01

    Living cells are viscoelastic materials, dominated by an elastic response on timescales longer than a millisecond. On shorter timescales, the dynamics of individual cytoskeleton filaments are expected to emerge, but active microrheology measurements on cells accessing this regime are scarce. Here, we develop high-frequency microrheology experiments to probe the viscoelastic response of living cells from 1 Hz to 100 kHz. We report the viscoelasticity of different cell types under cytoskeletal drug treatments. On previously inaccessible short timescales, cells exhibit rich viscoelastic responses that depend on the state of the cytoskeleton. Benign and malignant cancer cells revealed remarkably different scaling laws at high frequencies, providing a unique mechanical fingerprint. Microrheology over a wide dynamic range--up to the frequency characterizing the molecular components--provides a mechanistic understanding of cell mechanics.

  17. The effects of early hypo- and hyperthyroidism on the development of rat cerebellar cortex. III. Kinetics of cell proliferation in the external granular layer.

    Science.gov (United States)

    Lauder, J M

    1977-04-22

    The effects of early hypo- and hyperthyroidism on the rates of cell acquisition and proliferation have been studied in the external granular layer (EGL) of the developing rat cerebellar cortex at 10 days of age using quantitative autoradiographic methods. Both altered thyroid states reduce the rate of cell acquisition in the EGL, but appear to do so for different reasons. Hyperthyroidism shortens the average length of the cell cycle by decreasing the duration of the pre-DNA synthetic phase (G1), indicating that excess thyroxine may exert a direct effect on the EGL. This action involves the early onset of neuronal differentiation (cessation of proliferation)46 which presumably leads to the observed decrease in the rate of cell acquisition (increased doubling time). Such differentiating cells do not, however, leave the proliferative zone or the EGL prematurely, resulting in a reduced labeling index, mitotic index, and growth fraction as non-dividing cells dilute the proliferating cell population. Hypothyroidism, on the other hand, leads to no significant change in the length of the cell cycle or in the mitotic index, but causes a decreased labeling index and growth fraction, as well as a reduced rate of cell acquisition (increased doubling time). No significant change in the amount of cell death in the EGL could be found to explain this apparent discrepancy between the rate of cell proliferation (cell cycle length) and cell acqusiition. The answer to this puzzle appears to lie in the mitotic index, which is not affected to the same extent as the labeling index, although it is also slightly reduced. If cells were to remain longer in mitosis, this could result in a decreased labeling index and growth fraction but nearly normal mitotic index and cell cycle length (as measured using the % labeled mitoses method), since those cells dropping out of the cycling population would be counted as mitoses...

  18. 'Big bang' of B-cell development revealed.

    Science.gov (United States)

    Murre, Cornelis

    2018-01-15

    Earlier studies have identified transcription factors that specify B-cell fate, but the underlying mechanisms remain to be revealed. Two new studies by Miyai and colleagues (pp. 112-126) and Li and colleagues (pp. 96-111) in this issue of Genes & Development provide new and unprecedented insights into the genetic and epigenetic mechanisms that establish B-cell identity. © 2018 Murre; Published by Cold Spring Harbor Laboratory Press.

  19. Cell kinetics of the marine sponge Halisarca caerulea reveal rapid cell turnover and shedding

    NARCIS (Netherlands)

    Goeij, de J.M.; Kluijver, de A.; Duyl, van F.C.; Vacelet, J.; Wijffels, R.H.; Goeij, de A.F.P.M.; Cleutjens, J.P.M.; Schutte, B.

    2009-01-01

    This study reveals the peculiar in vivo cell kinetics and cell turnover of the marine sponge Halisarca caerulea under steady-state conditions. The tropical coral reef sponge shows an extremely high proliferation activity, a short cell cycle duration and massive cell shedding. Cell turnover is

  20. Opto-acoustic microscopy reveals adhesion mechanics of single cells

    Science.gov (United States)

    Abi Ghanem, Maroun; Dehoux, Thomas; Liu, Liwang; Le Saux, Guillaume; Plawinski, Laurent; Durrieu, Marie-Christine; Audoin, Bertrand

    2018-01-01

    Laser-generated GHz-ultrasonic-based technologies have shown the ability to image single cell adhesion and stiffness simultaneously. Using this new modality, we here demonstrate quantitative indicators to investigate contact mechanics and adhesion processes of the cell. We cultured human cells on a rigid substrate, and we used an inverted pulsed opto-acoustic microscope to generate acoustic pulses containing frequencies up to 100 GHz in the substrate. We map the reflection of the acoustic pulses at the cell-substrate interface to obtain images of the acoustic impedance of the cell, Zc, as well as of the stiffness of the interface, K, with 1 μm lateral resolution. Our results show that the standard deviation ΔZc reveals differences between different cell types arising from the multiplicity of local conformations within the nucleus. From the distribution of K-values within the nuclear region, we extract a mean interfacial stiffness, Km, that quantifies the average contact force in areas of the cell displaying weak bonding. By analogy with classical contact mechanics, we also define the ratio of the real to nominal contact areas, Sr/St. We show that Km can be interpreted as a quantitative indicator of passive contact at metal-cell interfaces, while Sr/St is sensitive to active adhesive processes in the nuclear region. The ability to separate the contributions of passive and active adhesion processes should allow gaining insight into cell-substrate interactions, with important applications in tissue engineering.

  1. Granular gas dynamics

    CERN Document Server

    Brilliantov, Nikolai

    2003-01-01

    While there is not yet any general theory for granular materials, significant progress has been achieved for dilute systems, also called granular gases. The contributions in this book address both the kinetic approach one using the Boltzmann equation for dissipative gases as well as the less established hydrodynamic description. The last part of the book is devoted to driven granular gases and their analogy with molecular fluids. Care has been taken so as to present the material in a pedagogical and self-contained way and this volume will thus be particularly useful to nonspecialists and newcomers to the field.

  2. Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

    Science.gov (United States)

    Mueller, Nikola S.; Krumsiek, Jan; Theis, Fabian J.; Böhm, Christian; Meyer-Bäse, Anke

    2011-06-01

    Advances in high-throughput measurements of biological specimens necessitate the development of biologically driven computational techniques. To understand the molecular level of many human diseases, such as cancer, lipid quantifications have been shown to offer an excellent opportunity to reveal disease-specific regulations. The data analysis of the cell lipidome, however, remains a challenging task and cannot be accomplished solely based on intuitive reasoning. We have developed a method to identify a lipid correlation network which is entirely disease-specific. A powerful method to correlate experimentally measured lipid levels across the various samples is a Gaussian Graphical Model (GGM), which is based on partial correlation coefficients. In contrast to regular Pearson correlations, partial correlations aim to identify only direct correlations while eliminating indirect associations. Conventional GGM calculations on the entire dataset can, however, not provide information on whether a correlation is truly disease-specific with respect to the disease samples and not a correlation of control samples. Thus, we implemented a novel differential GGM approach unraveling only the disease-specific correlations, and applied it to the lipidome of immortal Glioblastoma tumor cells. A large set of lipid species were measured by mass spectrometry in order to evaluate lipid remodeling as a result to a combination of perturbation of cells inducing programmed cell death, while the other perturbations served solely as biological controls. With the differential GGM, we were able to reveal Glioblastoma-specific lipid correlations to advance biomedical research on novel gene therapies.

  3. Opto-acoustic microscopy reveals adhesion mechanics of single cells.

    Science.gov (United States)

    Abi Ghanem, Maroun; Dehoux, Thomas; Liu, Liwang; Le Saux, Guillaume; Plawinski, Laurent; Durrieu, Marie-Christine; Audoin, Bertrand

    2018-01-01

    Laser-generated GHz-ultrasonic-based technologies have shown the ability to image single cell adhesion and stiffness simultaneously. Using this new modality, we here demonstrate quantitative indicators to investigate contact mechanics and adhesion processes of the cell. We cultured human cells on a rigid substrate, and we used an inverted pulsed opto-acoustic microscope to generate acoustic pulses containing frequencies up to 100 GHz in the substrate. We map the reflection of the acoustic pulses at the cell-substrate interface to obtain images of the acoustic impedance of the cell, Z c , as well as of the stiffness of the interface, K, with 1 μm lateral resolution. Our results show that the standard deviation ΔZ c reveals differences between different cell types arising from the multiplicity of local conformations within the nucleus. From the distribution of K-values within the nuclear region, we extract a mean interfacial stiffness, K m , that quantifies the average contact force in areas of the cell displaying weak bonding. By analogy with classical contact mechanics, we also define the ratio of the real to nominal contact areas, S r /S t . We show that K m can be interpreted as a quantitative indicator of passive contact at metal-cell interfaces, while S r /S t is sensitive to active adhesive processes in the nuclear region. The ability to separate the contributions of passive and active adhesion processes should allow gaining insight into cell-substrate interactions, with important applications in tissue engineering.

  4. Study on Molasses Concentration from Sugarcanne Bagasse for Biohydrogen Production using Enriched Granular Activated Carbon (GAC) Immobilised Cells by Repeated Batch Cultivation

    Science.gov (United States)

    Idris, Norfatiha; Aminah Lutpi, Nabilah; Ruhaizul Che Ridzuan, Che Mohd; Shian, Wong Yee; Nuraiti Tengku Izhar, Tengku

    2018-03-01

    Repeated batch cultivation is known as most attractive method in improving hydrogen productivity, due to the facts that this approach could minimize the reuse of the cell and the inoculum preparation. In addition, with the combination of attach growth system during the fermentation processes to produce biohydrogen, the density of cells will be increased and the cell washout could be avoided. Therefore, this study aimed to examine the effectiveness of repeated batch cultivation for enrichment of anaerobic mixed culture onto granular activated carbon (GAC) and investigate the effect of molasses concentration during immobilization of mixed culture onto the GAC. The molasses concentration using 50 %, 40 %, 30 %, 20 % and 10 % of diluted molasses were used as feedstock in the fermentation process. The maximum hydrogen production of 60 ml was obtained at 30 % of molasses concentration with 831 ppm of hydrogen concentration. Thus, the kinetic parameter obtained from the batch profiling based on modified Gompertz equation are, Hm= 58 ml for the maximum hydrogen production and Rm= 2.02 ml/h representing the hydrogen production rate.

  5. Granular computing: perspectives and challenges.

    Science.gov (United States)

    Yao, JingTao; Vasilakos, Athanasios V; Pedrycz, Witold

    2013-12-01

    Granular computing, as a new and rapidly growing paradigm of information processing, has attracted many researchers and practitioners. Granular computing is an umbrella term to cover any theories, methodologies, techniques, and tools that make use of information granules in complex problem solving. The aim of this paper is to review foundations and schools of research and to elaborate on current developments in granular computing research. We first review some basic notions of granular computing. Classification and descriptions of various schools of research in granular computing are given. We also present and identify some research directions in granular computing.

  6. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.

    Science.gov (United States)

    Pei, Weike; Feyerabend, Thorsten B; Rössler, Jens; Wang, Xi; Postrach, Daniel; Busch, Katrin; Rode, Immanuel; Klapproth, Kay; Dietlein, Nikolaus; Quedenau, Claudia; Chen, Wei; Sauer, Sascha; Wolf, Stephan; Höfer, Thomas; Rodewald, Hans-Reimer

    2017-08-24

    Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure.

  7. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

    Science.gov (United States)

    Rössler, Jens; Wang, Xi; Postrach, Daniel; Busch, Katrin; Rode, Immanuel; Klapproth, Kay; Dietlein, Nikolaus; Quedenau, Claudia; Chen, Wei; Sauer, Sascha; Wolf, Stephan; Höfer, Thomas; Rodewald, Hans-Reimer

    2017-01-01

    Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping1 has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites2, viral barcodes3, and strategies based on transposons4 and CRISPR/Cas9 genome editing5; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system6,7. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs8–10. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure. PMID:28813413

  8. Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

    Directory of Open Access Journals (Sweden)

    Iain C. Macaulay

    2016-02-01

    Full Text Available The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree. The progression of cells along this continuum is characterized by a highly coordinated transcriptional program, displaying simultaneous suppression of genes involved in cell proliferation and ribosomal biogenesis as the expression of lineage specific genes increases. Within this program, there is substantial heterogeneity in the expression of the key lineage regulators. Overall, the total number of genes expressed, as well as the total mRNA content of the cell, decreases as the cells undergo lineage commitment.

  9. Impact of granular drops

    KAUST Repository

    Marston, J. O.

    2013-07-15

    We investigate the spreading and splashing of granular drops during impact with a solid target. The granular drops are formed from roughly spherical balls of sand mixed with water, which is used as a binder to hold the ball together during free-fall. We measure the instantaneous spread diameter for different impact speeds and find that the normalized spread diameter d/D grows as (tV/D)1/2. The speeds of the grains ejected during the “splash” are measured and they rarely exceed twice that of the impact speed.

  10. Impact of granular drops

    KAUST Repository

    Marston, J. O.; Mansoor, Mohammad M.; Thoroddsen, Sigurdur T

    2013-01-01

    We investigate the spreading and splashing of granular drops during impact with a solid target. The granular drops are formed from roughly spherical balls of sand mixed with water, which is used as a binder to hold the ball together during free-fall. We measure the instantaneous spread diameter for different impact speeds and find that the normalized spread diameter d/D grows as (tV/D)1/2. The speeds of the grains ejected during the “splash” are measured and they rarely exceed twice that of the impact speed.

  11. Characterization of dissolved organic matter during landfill leachate treatment by sequencing batch reactor, aeration corrosive cell-Fenton, and granular activated carbon in series

    International Nuclear Information System (INIS)

    Bu Lin; Wang Kun; Zhao Qingliang; Wei Liangliang; Zhang Jing; Yang Junchen

    2010-01-01

    Landfill leachate is generally characterized as a complex recalcitrant wastewater containing high concentration of dissolved organic matter (DOM). A combination of sequencing batch reactor (SBR) + aeration corrosive cell-Fenton (ACF) + granular activated carbon (GAC) adsorption in series was proposed for the purpose of removing pollutants in the leachate. Fractionation was also performed to investigate the composition changes and characteristics of the leachate DOM in each treatment process. Experimental results showed that organic matter, in terms of chemical oxygen demand (COD), 5-day biological oxygen demand (BOD 5 ), and dissolved organic carbon (DOC), was reduced by 97.2%, 99.1%, and 98.7%, respectively. To differentiate the DOM portions, leachates were separated into five fractions by XAD-8 and XAD-4 resins: hydrophobic acid (HPO-A), hydrophobic neutral (HPO-N), transphilic acid (TPI-A), transphilic neutral (TPI-N), and hydrophilic fraction (HPI). The predominant fraction in the raw leachate was HPO-A (36% of DOC), while the dominant fraction in the final effluent was HPI (53% of DOC). Accordingly, macromolecules were degraded to simpler ones in a relatively narrow range below 1000 Da. Spectral and chromatographic analyses also showed that most humic-like substances in all fractions were effectively removed during the treatments and led to a simultaneous decrease in aromaticity.

  12. Characterization of dissolved organic matter during landfill leachate treatment by sequencing batch reactor, aeration corrosive cell-Fenton, and granular activated carbon in series

    Energy Technology Data Exchange (ETDEWEB)

    Bu Lin [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wang Kun [State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090 (China); School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Zhao Qingliang, E-mail: zhql1962@yahoo.com.cn [State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), Harbin Institute of Technology, Harbin 150090 (China); School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wei Liangliang; Zhang Jing; Yang Junchen [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China)

    2010-07-15

    Landfill leachate is generally characterized as a complex recalcitrant wastewater containing high concentration of dissolved organic matter (DOM). A combination of sequencing batch reactor (SBR) + aeration corrosive cell-Fenton (ACF) + granular activated carbon (GAC) adsorption in series was proposed for the purpose of removing pollutants in the leachate. Fractionation was also performed to investigate the composition changes and characteristics of the leachate DOM in each treatment process. Experimental results showed that organic matter, in terms of chemical oxygen demand (COD), 5-day biological oxygen demand (BOD{sub 5}), and dissolved organic carbon (DOC), was reduced by 97.2%, 99.1%, and 98.7%, respectively. To differentiate the DOM portions, leachates were separated into five fractions by XAD-8 and XAD-4 resins: hydrophobic acid (HPO-A), hydrophobic neutral (HPO-N), transphilic acid (TPI-A), transphilic neutral (TPI-N), and hydrophilic fraction (HPI). The predominant fraction in the raw leachate was HPO-A (36% of DOC), while the dominant fraction in the final effluent was HPI (53% of DOC). Accordingly, macromolecules were degraded to simpler ones in a relatively narrow range below 1000 Da. Spectral and chromatographic analyses also showed that most humic-like substances in all fractions were effectively removed during the treatments and led to a simultaneous decrease in aromaticity.

  13. Comparison of two highly granular hadronic calorimeter concepts

    International Nuclear Information System (INIS)

    Neubueser, Coralie

    2016-11-01

    The CALICE collaboration develops hadron calorimeter technologies with high granularity for future electron-positron linear colliders. These technologies differ in active material, granularity and their readout and thus their energy reconstruction schemes. The Analogue Hadron Calorimeter (AHCAL), based on scintillator tiles with Silicon Photomultiplier readout, measures the signal amplitude of the energy deposition in the cells of at most 3 x 3 cm"2 size. The Digital, Resistive Plate Chamber (RPC) based, HCAL (DHCAL) detects hits above a certain threshold by firing pad sensors of 1 x 1 cm"2. A 2 bit readout is provided by the, also RPC based, Semi-Digital HCAL (SDHCAL), which counts hits above three different thresholds per 1 x 1 cm"2 pad. All three calorimeter concepts have been realised in 1 m"3 prototypes with interleaved steel absorber and tested at various test beams. The differences in active medium, granularity and readout have different impacts on the energy resolution and need to be studied independently. This analysis concentrates on the comparison between these technologies by investigating the impact of the different energy reconstruction schemes on the energy resolution of the AHCAL testbeam data and simulation. Additionally, a so-called software compensation algorithm is developed to weight hits dependent on their energy content and correct for the difference in the response to the electromagnetic and hadronic sub-showers (e/h≠1) and thus reduce the influence of fluctuations in the π"0 generation. The comparison of the energy resolutions revealed that it is mandatory for the AHCAL with 3 x 3 cm"2 cell size to have analogue signal readout, to apply the software compensation algorithm and thus achieve the best possible energy resolution. The effect of the granularity is studied with a simulation of the AHCAL with 1 x 1 cm"2 cell size, and it has been found that to achieve the best possible energy resolution the semi-digital energy reconstruction is

  14. [Prostatic granulomas revealing a peripheral T-cell lymphoma].

    Science.gov (United States)

    Foguem, C; Curlier, E; Rouamba, M-M; Regent, A; Philippe, P

    2009-02-01

    The presence of granulomas on tissue biopsie has been reported in a wide range of disorders. The clinical presentation and the diagnostic work-up of granulomatosis can be difficult as it is illustrated in the following report. A 59-year-old patient was referred in 2002 for a granulomatous prostatitis. Physical examination was normal. Except for the increase of prostate-specific antigen (which motivated a biopsy), the laboratory results were normal. Thoracic CT-scan disclosed mediastinal lymph nodes. A minor salivary gland biopsy was consistent with the diagnosis of sarcoidosis. In 2004, the patient presented an epidermal necrolysis, and in 2005 the deterioration of general status raised suspicion of a lymphoproliferative disorder. Liver and bone marrow biopsies revealed a granulomatous process. Despite steroid therapy, the patient died. Autopsy discloses a anaplasic T cell lymphoma. This report illustrates the relationship between sarcoidosis and lymphoma as a mode of presentation, a complication, or an accidental but misleading association? The association between anaplastic lymphoma and sarcoidosis is exceptional.

  15. Aerofractures in Confined Granular Media

    Science.gov (United States)

    Eriksen, Fredrik K.; Turkaya, Semih; Toussaint, Renaud; Måløy, Knut J.; Flekkøy, Eirik G.

    2015-04-01

    We will present the optical analysis of experimental aerofractures in confined granular media. The study of this generic process may have applications in industries involving hydraulic fracturing of tight rocks, safe construction of dams, tunnels and mines, and in earth science where phenomena such as mud volcanoes and sand injectites are results of subsurface sediment displacements driven by fluid overpressure. It is also interesting to increase the understanding the flow instability itself, and how the fluid flow impacts the solid surrounding fractures and in the rest of the sample. Such processes where previously studied numerically [Niebling 2012a, Niebling 2012b] or in circular geometries. We will here explore experimentally linear geometries. We study the fracturing patterns that form when air flows into a dense, non-cohesive porous medium confined in a Hele-Shaw cell - i.e. into a packing of dry 80 micron beads placed between two glass plates separated by ~1mm. The cell is rectangular and fitted with a semi-permeable boundary to the atmosphere - blocking beads but not air - on one short edge, while the other three edges are impermeable. The porous medium is packed inside the cell between the semi-permeable boundary and an empty volume at the sealed side where the air pressure can be set and kept at a constant overpressure (1-2bar). Thus, for the air trapped inside the cell to release the overpressure it has to move through the solid. At high enough overpressures the air flow deforms the solid and increase permeability in some regions along the air-solid interface, which results in unstable flow and aerofracturing. Aerofractures are thought to be an analogue to hydrofractures, and an advantage of performing aerofracturing experiments in a Hele-Shaw cell is that the fracturing process can easily be observed in the lab. Our experiments are recorded with a high speed camera with a framerate of 1000 frames per second. In the analysis, by using various image

  16. Distrofia corneal granular

    Directory of Open Access Journals (Sweden)

    Alexeide de la C Castillo Pérez

    Full Text Available Las distrofias corneales constituyen un conjunto de enfermedades que presentan, en su mayoría, una baja incidencia y se caracterizan por acúmulo de material hialino o amiloide que disminuyen la transparencia corneal. La distrofia granular es una enfermedad autosómica dominante que presenta opacidades grises en el estroma superficial central de la córnea y se hacen visibles en la primera y segunda décadas de la vida, lo que provoca disminución de la visión más significativa cerca de los 40 años de edad. Presentamos dos casos clínicos de distrofia granular en pacientes hermanos de diferentes sexos, quienes acudieron a la consulta y refirieron visión nublada. El estudio de la historia familiar nos ayuda en el correcto diagnóstico y la biomicroscopia constituye el elemento más importante.

  17. Microservices: Granularity vs. Performance

    OpenAIRE

    Shadija, Dharmendra; Rezai, Mo; Hill, Richard

    2017-01-01

    Microservice Architectures (MA) have the potential to increase the agility of software development. In an era where businesses require software applications to evolve to support emerging software requirements, particularly for Internet of Things (IoT) applications, we examine the issue of microservice granularity and explore its effect upon application latency. Two approaches to microservice deployment are simulated; the first with microservices in a single container, and the second with micr...

  18. Reproducible isolation of lymph node stromal cells reveals site-dependent differences in fibroblastic reticular cells

    Directory of Open Access Journals (Sweden)

    Anne L Fletcher

    2011-09-01

    Full Text Available Within lymph nodes, non-hematopoietic stromal cells organize and interact with leukocytes in an immunologically important manner. In addition to organizing T and B cell segregation and expressing lymphocyte survival factors, several recent studies have shown that lymph node stromal cells shape the naïve T cell repertoire, expressing self-antigens which delete self-reactive T cells in a unique and non-redundant fashion. A fundamental role in peripheral tolerance, in addition to an otherwise extensive functional portfolio, necessitates closer study of lymph node stromal cell subsets using modern immunological techniques; however this has not routinely been possible in the field, due to difficulties reproducibly isolating these rare subsets. Techniques were therefore developed for successful ex vivo and in vitro manipulation and characterization of lymph node stroma. Here we discuss and validate these techniques in mice and humans, and apply them to address several unanswered questions regarding lymph node composition. We explored the steady-state stromal composition of lymph nodes isolated from mice and humans, and found that marginal reticular cells and lymphatic endothelial cells required lymphocytes for their normal maturation in mice. We also report alterations in the proportion and number of fibroblastic reticular cells (FRCs between skin-draining and mesenteric lymph nodes. Similarly, transcriptional profiling of FRCs revealed changes in cytokine production from these sites. Together, these methods permit highly reproducible stromal cell isolation, sorting, and culture.

  19. Reproducible isolation of lymph node stromal cells reveals site-dependent differences in fibroblastic reticular cells.

    Science.gov (United States)

    Fletcher, Anne L; Malhotra, Deepali; Acton, Sophie E; Lukacs-Kornek, Veronika; Bellemare-Pelletier, Angelique; Curry, Mark; Armant, Myriam; Turley, Shannon J

    2011-01-01

    Within lymph nodes, non-hematopoietic stromal cells organize and interact with leukocytes in an immunologically important manner. In addition to organizing T and B cell segregation and expressing lymphocyte survival factors, several recent studies have shown that lymph node stromal cells shape the naïve T cell repertoire, expressing self-antigens which delete self-reactive T cells in a unique and non-redundant fashion. A fundamental role in peripheral tolerance, in addition to an otherwise extensive functional portfolio, necessitates closer study of lymph node stromal cell subsets using modern immunological techniques; however this has not routinely been possible in the field, due to difficulties reproducibly isolating these rare subsets. Techniques were therefore developed for successful ex vivo and in vitro manipulation and characterization of lymph node stroma. Here we discuss and validate these techniques in mice and humans, and apply them to address several unanswered questions regarding lymph node composition. We explored the steady-state stromal composition of lymph nodes isolated from mice and humans, and found that marginal reticular cells and lymphatic endothelial cells required lymphocytes for their normal maturation in mice. We also report alterations in the proportion and number of fibroblastic reticular cells (FRCs) between skin-draining and mesenteric lymph nodes. Similarly, transcriptional profiling of FRCs revealed changes in cytokine production from these sites. Together, these methods permit highly reproducible stromal cell isolation, sorting, and culture.

  20. Pneumatic fractures in confined granular media.

    Science.gov (United States)

    Eriksen, Fredrik K; Toussaint, Renaud; Turquet, Antoine L; Måløy, Knut J; Flekkøy, Eirik G

    2017-06-01

    We perform experiments where air is injected at a constant overpressure P_{in}, ranging from 5 to 250 kPa, into a dry granular medium confined within a horizontal linear Hele-Shaw cell. The setup allows us to explore compacted configurations by preventing decompaction at the outer boundary, i.e., the cell outlet has a semipermeable filter such that beads are stopped while air can pass. We study the emerging patterns and dynamic growth of channels in the granular media due to fluid flow, by analyzing images captured with a high speed camera (1000 images/s). We identify four qualitatively different flow regimes, depending on the imposed overpressure, ranging from no channel formation for P_{in} below 10 kPa, to large thick channels formed by erosion and fingers merging for high P_{in} around 200 kPa. The flow regimes where channels form are characterized by typical finger thickness, final depth into the medium, and growth dynamics. The shape of the finger tips during growth is studied by looking at the finger width w as function of distance d from the tip. The tip profile is found to follow w(d)∝d^{β}, where β=0.68 is a typical value for all experiments, also over time. This indicates a singularity in the curvature d^{2}d/dw^{2}∼κ∼d^{1-2β}, but not of the slope dw/dd∼d^{β-1}, i.e., more rounded tips rather than pointy cusps, as they would be for the case β>1. For increasing P_{in}, the channels generally grow faster and deeper into the medium. We show that the channel length along the flow direction has a linear growth with time initially, followed by a power-law decay of growth velocity with time as the channel approaches its final length. A closer look reveals that the initial growth velocity v_{0} is found to scale with injection pressure as v_{0}∝P_{in}^{3/2}, while at a critical time t_{c} there is a cross-over to the behavior v(t)∝t^{-α}, where α is close to 2.5 for all experiments. Finally, we explore the fractal dimension of the fully

  1. Inertial picobalance reveals fast mass fluctuations in mammalian cells

    Science.gov (United States)

    Martínez-Martín, David; Fläschner, Gotthold; Gaub, Benjamin; Martin, Sascha; Newton, Richard; Beerli, Corina; Mercer, Jason; Gerber, Christoph; Müller, Daniel J.

    2017-10-01

    The regulation of size, volume and mass in living cells is physiologically important, and dysregulation of these parameters gives rise to many diseases. Cell mass is largely determined by the amount of water, proteins, lipids, carbohydrates and nucleic acids present in a cell, and is tightly linked to metabolism, proliferation and gene expression. Technologies have emerged in recent years that make it possible to track the masses of single suspended cells and adherent cells. However, it has not been possible to track individual adherent cells in physiological conditions at the mass and time resolutions required to observe fast cellular dynamics. Here we introduce a cell balance (a ‘picobalance’), based on an optically excited microresonator, that measures the total mass of single or multiple adherent cells in culture conditions over days with millisecond time resolution and picogram mass sensitivity. Using our technique, we observe that the mass of living mammalian cells fluctuates intrinsically by around one to four per cent over timescales of seconds throughout the cell cycle. Perturbation experiments link these mass fluctuations to the basic cellular processes of ATP synthesis and water transport. Furthermore, we show that growth and cell cycle progression are arrested in cells infected with vaccinia virus, but mass fluctuations continue until cell death. Our measurements suggest that all living cells show fast and subtle mass fluctuations throughout the cell cycle. As our cell balance is easy to handle and compatible with fluorescence microscopy, we anticipate that our approach will contribute to the understanding of cell mass regulation in various cell states and across timescales, which is important in areas including physiology, cancer research, stem-cell differentiation and drug discovery.

  2. Single-cell RNA-Seq reveals cell heterogeneity and hierarchy within mouse mammary epithelia.

    Science.gov (United States)

    Sun, Heng; Miao, Zhengqiang; Zhang, Xin; Chan, Un In; Su, Sek Man; Guo, Sen; Wong, Chris Koon Ho; Xu, Xiaoling; Deng, Chu-Xia

    2018-04-17

    The mammary gland is very intricately and well organized into distinct tissues, including epithelia, endothelia, adipocytes, and stromal and immune cells. Many mammary gland diseases, such as breast cancer arise from abnormalities in the mammary epithelium, which is mainly composed of two distinct lineages, the basal and luminal cells. Because of the limitation of traditional transcriptome analysis of bulk mammary cells, the hierarchy and heterogeneity of mammary cells within these two lineages remain unclear. To this end, using single-cell RNA-Seq coupled with FACS analysis and principal component analysis, we determined gene expression profiles of mammary epithelial cells of virgin and pregnant mice. These analyses revealed a much higher heterogeneity among the mammary cells than has been previously reported and enabled cell classification into distinct subgroups according to signature gene markers present in each group. We also identified and verified a rare CDH5+ cell subpopulation within a basal cell lineage as quiescent mammary stem cells (MaSCs). Moreover, using pseudo-temporal analysis, we reconstructed the developmental trajectory of mammary epithelia and uncovered distinct changes in gene expression and in biological functions of mammary cells along the developmental process. In conclusion, our work greatly refines the resolution of the cellular hierarchy in developing mammary tissues. The discovery of CDH5+ cells as MaSCs in these tissues may have implications for our understanding of the initiation, development, and pathogenesis of mammary tumors. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Spinal cord injury reveals multilineage differentiation of ependymal cells.

    Directory of Open Access Journals (Sweden)

    Konstantinos Meletis

    2008-07-01

    Full Text Available Spinal cord injury often results in permanent functional impairment. Neural stem cells present in the adult spinal cord can be expanded in vitro and improve recovery when transplanted to the injured spinal cord, demonstrating the presence of cells that can promote regeneration but that normally fail to do so efficiently. Using genetic fate mapping, we show that close to all in vitro neural stem cell potential in the adult spinal cord resides within the population of ependymal cells lining the central canal. These cells are recruited by spinal cord injury and produce not only scar-forming glial cells, but also, to a lesser degree, oligodendrocytes. Modulating the fate of ependymal progeny after spinal cord injury may offer an alternative to cell transplantation for cell replacement therapies in spinal cord injury.

  4. Type-2 fuzzy granular models

    CERN Document Server

    Sanchez, Mauricio A; Castro, Juan R

    2017-01-01

    In this book, a series of granular algorithms are proposed. A nature inspired granular algorithm based on Newtonian gravitational forces is proposed. A series of methods for the formation of higher-type information granules represented by Interval Type-2 Fuzzy Sets are also shown, via multiple approaches, such as Coefficient of Variation, principle of justifiable granularity, uncertainty-based information concept, and numerical evidence based. And a fuzzy granular application comparison is given as to demonstrate the differences in how uncertainty affects the performance of fuzzy information granules.

  5. Mathematical models of granular matter

    CERN Document Server

    Mariano, Paolo; Giovine, Pasquale

    2008-01-01

    Granular matter displays a variety of peculiarities that distinguish it from other appearances studied in condensed matter physics and renders its overall mathematical modelling somewhat arduous. Prominent directions in the modelling granular flows are analyzed from various points of view. Foundational issues, numerical schemes and experimental results are discussed. The volume furnishes a rather complete overview of the current research trends in the mechanics of granular matter. Various chapters introduce the reader to different points of view and related techniques. New models describing granular bodies as complex bodies are presented. Results on the analysis of the inelastic Boltzmann equations are collected in different chapters. Gallavotti-Cohen symmetry is also discussed.

  6. Microtubule-Associated Proteins in Mesial Temporal Lobe Epilepsy with and without Psychiatric Comorbidities and Their Relation with Granular Cell Layer Dispersion

    Directory of Open Access Journals (Sweden)

    Ludmyla Kandratavicius

    2013-01-01

    Full Text Available Background. Despite strong association between epilepsy and psychiatric comorbidities, biological substrates are unknown. We have previously reported decreased mossy fiber sprouting in mesial temporal lobe epilepsy (MTLE patients with psychosis and increased in those with major depression. Microtubule associated proteins (MAPs are essentially involved in dendritic and synaptic sprouting. Methods. MTLE hippocampi of subjects without psychiatric history, MTLE + major depression, and MTLE + interictal psychosis derived from epilepsy surgery and control necropsies were investigated for neuronal density, granular layer dispersion, and MAP2 and tau immunohistochemistry. Results. Altered MAP2 and tau expression in MTLE and decreased tau expression in MTLE with psychosis were found. Granular layer dispersion correlated inversely with verbal memory scores, and with MAP2 and tau expression in the entorhinal cortex. Patients taking fluoxetine showed increased neuronal density in the granular layer and those taking haloperidol decreased neuronal density in CA3 and subiculum. Conclusions. Our results indicate relations between MAPs, granular layer dispersion, and memory that have not been previously investigated. Differential MAPs expression in human MTLE hippocampi with and without psychiatric comorbidities suggests that psychopathological states in MTLE rely on differential morphological and possibly neurochemical backgrounds. This clinical study was approved by our institution’s Research Ethics Board (HC-FMRP no. 1270/2008 and is registered under the Brazilian National System of Information on Ethics in Human Research (SISNEP no. 0423.0.004.000-07.

  7. Chronology of Islet Differentiation Revealed By Temporal Cell Labeling

    Science.gov (United States)

    Miyatsuka, Takeshi; Li, Zhongmei; German, Michael S.

    2009-01-01

    OBJECTIVE Neurogenin 3 plays a pivotal role in pancreatic endocrine differentiation. Whereas mouse models expressing reporters such as eGFP or LacZ under the control of the Neurog3 gene enable us to label cells in the pancreatic endocrine lineage, the long half-life of most reporter proteins makes it difficult to distinguish cells actively expressing neurogenin 3 from differentiated cells that have stopped transcribing the gene. RESEARCH DESIGN AND METHODS In order to separate the transient neurogenin 3 –expressing endocrine progenitor cells from the differentiating endocrine cells, we developed a mouse model (Ngn3-Timer) in which DsRed-E5, a fluorescent protein that shifts its emission spectrum from green to red over time, was expressed transgenically from the NEUROG3 locus. RESULTS In the Ngn3-Timer embryos, green-dominant cells could be readily detected by microscopy or flow cytometry and distinguished from green/red double-positive cells. When fluorescent cells were sorted into three different populations by a fluorescence-activated cell sorter, placed in culture, and then reanalyzed by flow cytometry, green-dominant cells converted to green/red double-positive cells within 6 h. The sorted cell populations were then used to determine the temporal patterns of expression for 145 transcriptional regulators in the developing pancreas. CONCLUSIONS The precise temporal resolution of this model defines the narrow window of neurogenin 3 expression in islet progenitor cells and permits sequential analyses of sorted cells as well as the testing of gene regulatory models for the differentiation of pancreatic islet cells. PMID:19478145

  8. Evaluating Energy Flux in Vibrofluidized Granular Bed

    Directory of Open Access Journals (Sweden)

    N. A. Sheikh

    2013-01-01

    Full Text Available Granular flows require sustained input of energy for fluidization. A level of fluidization depends on the amount of heat flux provided to the flow. In general, the dissipation of the grains upon interaction balances the heat inputs and the resultant flow patterns can be described using hydrodynamic models. However, with the increase in packing fraction, the heat fluxes prediction of the cell increases. Here, a comparison is made for the proposed theoretical models against the MD simulations data. It is observed that the variation of packing fraction in the granular cell influences the heat flux at the base. For the elastic grain-base interaction, the predictions vary appreciably compared to MD simulations, suggesting the need to accurately model the velocity distribution of grains for averaging.

  9. Ultrastructural observations reveal the presence of channels between cork cells.

    Science.gov (United States)

    Teixeira, Rita Teresa; Pereira, Helena

    2009-12-01

    The ultrastructure of phellem cells of Quercus suber L. (cork oak) and Calotropis procera (Ait) R. Br. were analyzed using electron transmission microscopy to determine the presence or absence of plasmodesmata (PD). Different types of Q. suber cork samples were studied: one year shoots; virgin cork (first periderm), reproduction cork (traumatic periderm), and wet cork. The channel structures of PD were found in all the samples crossing adjacent cell walls through the suberin layer of the secondary wall. Calotropis phellem also showed PD crossing the cell walls of adjacent cells but in fewer numbers compared to Q. suber. In one year stems of cork oak, it was possible to follow the physiologically active PD with ribosomic accumulation next to the aperture of the channel seen in the phellogen cells to the completely obstructed channels in the dead cells that characterize the phellem tissue.

  10. Using a Time Granularity Table for Gradual Granular Data Aggregation

    DEFF Research Database (Denmark)

    Iftikhar, Nadeem; Pedersen, Torben Bach

    2010-01-01

    solution for data reduction based on gradual granular data aggregation. With the gradual granular data aggregation mechanism, older data can be made coarse-grained while keeping the newest data fine-grained. For instance, when data is 3 months old aggregate to 1 minute level from 1 second level, when data...... and improve query performance, especially on resource-constrained systems with limited storage and query processing capabilities. A number of data reduction solutions have been developed, however an effective solution particularly based on gradual data reduction is missing. This paper presents an effective...... is 6 months old aggregate to 2 minutes level from 1 minute level and so on. The proposed solution introduces a time granularity based data structure, namely a relational time granularity table that enables long term storage of old data by maintaining it at different levels of granularity and effective...

  11. Similitude study of a moving bed granular filter

    Energy Technology Data Exchange (ETDEWEB)

    Robert C. Brown; Huawei Shi; Gerald Colver; Saw-Choon Soo [Iowa State University, IA (United States)

    2003-12-10

    The goal of this study was to evaluate the performance of a moving bed granular filter designed for hot gas clean up. This study used similitude theory to devise experiments that were conducted at near-ambient conditions while simulating the performance of filters operated at elevated temperatures and pressures (850{sup o}C and 1000 kPa). These experiments revealed that the proposed moving bed granular filter can operate at high collection efficiencies, typically exceeding 99%, and low pressure drops without the need for periodic regeneration through the use of a continuous flow of fresh granular filter media in the filter. In addition, important design constraints were discovered for the successful operation of the proposed moving bed granular filter.

  12. Granular corneal dystrophy

    OpenAIRE

    Castillo Pérez, Alexeide de la C; Vilches Lescaille, Daysi; Noriega, Justo Luis; Martínez Balido, Daneel; León Balbón, Bárbaro Ramón; León Bernal, Danysleidi

    2015-01-01

    Las distrofias corneales constituyen un conjunto de enfermedades que presentan, en su mayoría, una baja incidencia y se caracterizan por acúmulo de material hialino o amiloide que disminuyen la transparencia corneal. La distrofia granular es una enfermedad autosómica dominante que presenta opacidades grises en el estroma superficial central de la córnea y se hacen visibles en la primera y segunda décadas de la vida, lo que provoca disminución de la visión más significativa cerca de los 40 año...

  13. Sinking a Granular Raft

    Science.gov (United States)

    Protière, Suzie; Josserand, Christophe; Aristoff, Jeffrey M.; Stone, Howard A.; Abkarian, Manouk

    2017-03-01

    We report experiments that yield new insights on the behavior of granular rafts at an oil-water interface. We show that these particle aggregates can float or sink depending on dimensionless parameters taking into account the particle densities and size and the densities of the two fluids. We characterize the raft shape and stability and propose a model to predict its shape and maximum length to remain afloat. Finally we find that wrinkles and folds appear along the raft due to compression by its own weight, which can trigger destabilization. These features are characteristics of an elastic instability, which we discuss, including the limitations of our model.

  14. Biophysical characteristics reveal neural stem cell differentiation potential.

    Directory of Open Access Journals (Sweden)

    Fatima H Labeed

    Full Text Available Distinguishing human neural stem/progenitor cell (huNSPC populations that will predominantly generate neurons from those that produce glia is currently hampered by a lack of sufficient cell type-specific surface markers predictive of fate potential. This limits investigation of lineage-biased progenitors and their potential use as therapeutic agents. A live-cell biophysical and label-free measure of fate potential would solve this problem by obviating the need for specific cell surface markers.We used dielectrophoresis (DEP to analyze the biophysical, specifically electrophysiological, properties of cortical human and mouse NSPCs that vary in differentiation potential. Our data demonstrate that the electrophysiological property membrane capacitance inversely correlates with the neurogenic potential of NSPCs. Furthermore, as huNSPCs are continually passaged they decrease neuron generation and increase membrane capacitance, confirming that this parameter dynamically predicts and negatively correlates with neurogenic potential. In contrast, differences in membrane conductance between NSPCs do not consistently correlate with the ability of the cells to generate neurons. DEP crossover frequency, which is a quantitative measure of cell behavior in DEP, directly correlates with neuron generation of NSPCs, indicating a potential mechanism to separate stem cells biased to particular differentiated cell fates.We show here that whole cell membrane capacitance, but not membrane conductance, reflects and predicts the neurogenic potential of human and mouse NSPCs. Stem cell biophysical characteristics therefore provide a completely novel and quantitative measure of stem cell fate potential and a label-free means to identify neuron- or glial-biased progenitors.

  15. RNAi screen reveals host cell kinases specifically involved in Listeria monocytogenes spread from cell to cell.

    Directory of Open Access Journals (Sweden)

    Ryan Chong

    Full Text Available Intracellular bacterial pathogens, such as Listeria monocytogenes and Rickettsia conorii display actin-based motility in the cytosol of infected cells and spread from cell to cell through the formation of membrane protrusions at the cell cortex. Whereas the mechanisms supporting cytosolic actin-based motility are fairly well understood, it is unclear whether specific host factors may be required for supporting the formation and resolution of membrane protrusions. To address this gap in knowledge, we have developed high-throughput fluorescence microscopy and computer-assisted image analysis procedures to quantify pathogen spread in human epithelial cells. We used the approach to screen a siRNA library covering the human kinome and identified 7 candidate kinases whose depletion led to severe spreading defects in cells infected with L. monocytogenes. We conducted systematic validation procedures with redundant silencing reagents and confirmed the involvement of the serine/threonine kinases, CSNK1A1 and CSNK2B. We conducted secondary assays showing that, in contrast with the situation observed in CSNK2B-depleted cells, L. monocytogenes formed wild-type cytosolic tails and displayed wild-type actin-based motility in the cytosol of CSNK1A1-depleted cells. Furthermore, we developed a protrusion formation assay and showed that the spreading defect observed in CSNK1A1-depleted cells correlated with the formation of protrusion that did not resolve into double-membrane vacuoles. Moreover, we developed sending and receiving cell-specific RNAi procedures and showed that CSNK1A was required in the sending cells, but was dispensable in the receiving cells, for protrusion resolution. Finally, we showed that the observed defects were specific to Listeria monocytogenes, as Rickettsia conorii displayed wild-type cell-to-cell spread in CSNK1A1- and CSNK2B-depleted cells. We conclude that, in addition to the specific host factors supporting cytosolic actin

  16. Metabolic profiling of hypoxic cells revealed a catabolic signature required for cell survival.

    Directory of Open Access Journals (Sweden)

    Christian Frezza

    Full Text Available Hypoxia is one of the features of poorly vascularised areas of solid tumours but cancer cells can survive in these areas despite the low oxygen tension. The adaptation to hypoxia requires both biochemical and genetic responses that culminate in a metabolic rearrangement to counter-balance the decrease in energy supply from mitochondrial respiration. The understanding of metabolic adaptations under hypoxia could reveal novel pathways that, if targeted, would lead to specific death of hypoxic regions. In this study, we developed biochemical and metabolomic analyses to assess the effects of hypoxia on cellular metabolism of HCT116 cancer cell line. We utilized an oxygen fluorescent probe in anaerobic cuvettes to study oxygen consumption rates under hypoxic conditions without the need to re-oxygenate the cells and demonstrated that hypoxic cells can maintain active, though diminished, oxidative phosphorylation even at 1% oxygen. These results were further supported by in situ microscopy analysis of mitochondrial NADH oxidation under hypoxia. We then used metabolomic methodologies, utilizing liquid chromatography-mass spectrometry (LC-MS, to determine the metabolic profile of hypoxic cells. This approach revealed the importance of synchronized and regulated catabolism as a mechanism of adaptation to bioenergetic stress. We then confirmed the presence of autophagy under hypoxic conditions and demonstrated that the inhibition of this catabolic process dramatically reduced the ATP levels in hypoxic cells and stimulated hypoxia-induced cell death. These results suggest that under hypoxia, autophagy is required to support ATP production, in addition to glycolysis, and that the inhibition of autophagy might be used to selectively target hypoxic regions of tumours, the most notoriously resistant areas of solid tumours.

  17. Blockade of maitotoxin-induced oncotic cell death reveals zeiosis

    Directory of Open Access Journals (Sweden)

    Schilling William P

    2002-01-01

    Full Text Available Abstract Background Maitotoxin (MTX initiates cell death by sequentially activating 1 Ca2+ influx via non-selective cation channels, 2 uptake of vital dyes via formation of large pores, and 3 release of lactate dehydrogenase, an indication of cell lysis. MTX also causes formation of membrane blebs, which dramatically dilate during the cytolysis phase. To determine the role of phospholipase C (PLC in the cell death cascade, U73122, a specific inhibitor of PLC, and U73343, an inactive analog, were examined on MTX-induced responses in bovine aortic endothelial cells. Results Addition of either U73122 or U73343, prior to MTX, produced a concentration-dependent inhibition of the cell death cascade (IC50 ≈ 1.9 and 0.66 μM, respectively suggesting that the effect of these agents was independent of PLC. Addition of U73343 shortly after MTX, prevented or attenuated the effects of the toxin, but addition at later times had little or no effect. Time-lapse videomicroscopy showed that U73343 dramatically altered the blebbing profile of MTX-treated cells. Specifically, U73343 blocked bleb dilation and converted the initial blebbing event into "zeiosis", a type of membrane blebbing commonly associated with apoptosis. Cells challenged with MTX and rescued by subsequent addition of U73343, showed enhanced caspase-3 activity 48 hr after the initial insult, consistent with activation of the apoptotic program. Conclusions Within minutes of MTX addition, endothelial cells die by oncosis. Rescue by addition of U73343 shortly after MTX showed that a small percentage of cells are destined to die by oncosis, but that a larger percentage survive; cells that survive the initial insult exhibit zeiosis and may ultimately die by apoptotic mechanisms.

  18. Heightened systemic levels of neutrophil and eosinophil granular proteins in pulmonary tuberculosis and reversal following treatment.

    Science.gov (United States)

    Moideen, Kadar; Kumar, Nathella Pavan; Nair, Dina; Banurekha, Vaithilingam V; Bethunaickan, Ramalingam; Babu, Subash

    2018-04-09

    Granulocytes are activated during tuberculosis (TB) infection and act as immune effector cells and granulocyte responses are implicated in TB pathogenesis. Plasma levels of neutrophil and eosinophil granular proteins provide an indirect measure of degranulation. In this study, we wanted to examine the levels of neutrophil and eosinophil granular proteins in individuals with pulmonary tuberculosis (PTB) and to compare them with the levels in latent TB (LTB) individuals. Hence, we measured the plasma levels of myeloperoxidase (MPO), neutrophil elastase, and proteinase-3; major basic protein (MBP), eosinophil derived neurotoxin (EDN), eosinophil cationic protein (ECP) and eosinophil peroxidase (EPX) in these individuals. Finally, we also measured the levels of all of these parameters in PTB individuals following anti-tuberculosis (ATT) treatment. Our data reveal that PTB individuals are characterized by significantly higher plasma levels of MPO, elastase, human proteinase 3 as well as MBP and EDN in comparison to LTB individuals. Our data also reveal that ATT resulted in reversal of all of these changes, indicating an association with TB disease. Finally, our data show that the systemic levels of MPO and proteinase-3 can significantly discriminate PTB from LTB individuals. Thus, our data suggest that neutrophil and eosinophil granular proteins could play a potential role in the innate immune response and therefore, the pathogenesis of pulmonary TB. Copyright © 2018 American Society for Microbiology.

  19. Live cell imaging reveals at novel view of DNA

    International Nuclear Information System (INIS)

    Moritomi-Yano, Keiko; Yano, Ken-ichi

    2010-01-01

    Non-homologous end-joining (NHEJ) is the major repair pathway for DNA double-strand breaks (DSBs) that are the most severe form of DNA damages. Recently, live cell imaging techniques coupled with laser micro-irradiation were used to analyze the spatio-temporal behavior of the NHEJ core factors upon DSB induction in living cells. Based on the live cell imaging studies, we proposed a novel two-phase model for DSB sensing and protein assembly in the NHEJ pathway. This new model provides a novel view of the dynamic protein behavior on DSBs and broad implications for the molecular mechanism of NHEJ. (author)

  20. Granularity controlled irradiation response of cuprate superconductors

    International Nuclear Information System (INIS)

    Mishra, N.C.; Behera, D.; Mohanty, T.; Mohanta, D.; Kanjilal, D.; Mehta, G.K.; Pinto, R.

    1999-01-01

    Confining to an energy range where ions can neither create defects through elastic energy loss nor they can create defects through latent track formation, we study the effect of 140 MeV Si-ion irradiation in YBa 2 Cu 3 O 7-x (YBCO). We show that the evolution of superconducting and normal state properties in such situation is largely governed by the initial defects structure, particularly the grain boundary characteristics of the YBCO system. Both intra- and inter-granular defect structure in films of two batches were made widely different by having Ag as composite and substituent in one and by aging the other prior to irradiation. Evolution of the resistivity vs temperature characteristics in these films with ion fluence reveals the importance of Ag in bringing about both inter- and intra-granular modifications and making the films insensitive to ion irradiation

  1. Spreading of a granular droplet

    Science.gov (United States)

    Clement, Eric; Sanchez, Ivan; Raynaud, Franck; Lanuza, Jose; Andreotti, Bruno; Aranson, Igor

    2008-03-01

    The influence of controlled vibrations on the granular rheology is investigated in a specifically designed experiment in which a granular film spreads under the action of horizontal vibrations. A nonlinear diffusion equation is derived theoretically that describes the evolution of the deposit shape. A self-similar parabolic shape (the``granular droplet'') and a spreading dynamics are predicted that both agree quantitatively with the experimental results. The theoretical analysis is used to extract effective friction coefficients between the base and the granular layer under sustained and controlled vibrations. A shear thickening regime characteristic of dense granular flows is evidenced at low vibration energy, both for glass beads and natural sand. Conversely, shear thinning is observed at high agitation.

  2. Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.

    Science.gov (United States)

    Shah, Prajay T; Stratton, Jo A; Stykel, Morgan Gail; Abbasi, Sepideh; Sharma, Sandeep; Mayr, Kyle A; Koblinger, Kathrin; Whelan, Patrick J; Biernaskie, Jeff

    2018-05-03

    Ependymal cells are multi-ciliated cells that form the brain's ventricular epithelium and a niche for neural stem cells (NSCs) in the ventricular-subventricular zone (V-SVZ). In addition, ependymal cells are suggested to be latent NSCs with a capacity to acquire neurogenic function. This remains highly controversial due to a lack of prospective in vivo labeling techniques that can effectively distinguish ependymal cells from neighboring V-SVZ NSCs. We describe a transgenic system that allows for targeted labeling of ependymal cells within the V-SVZ. Single-cell RNA-seq revealed that ependymal cells are enriched for cilia-related genes and share several stem-cell-associated genes with neural stem or progenitors. Under in vivo and in vitro neural-stem- or progenitor-stimulating environments, ependymal cells failed to demonstrate any suggestion of latent neural-stem-cell function. These findings suggest remarkable stability of ependymal cell function and provide fundamental insights into the molecular signature of the V-SVZ niche. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Phase resetting reveals network dynamics underlying a bacterial cell cycle.

    Science.gov (United States)

    Lin, Yihan; Li, Ying; Crosson, Sean; Dinner, Aaron R; Scherer, Norbert F

    2012-01-01

    Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS).

  4. Single cell Hi-C reveals cell-to-cell variability in chromosome structure

    Science.gov (United States)

    Schoenfelder, Stefan; Yaffe, Eitan; Dean, Wendy; Laue, Ernest D.; Tanay, Amos; Fraser, Peter

    2013-01-01

    Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. PMID:24067610

  5. Large granular lymphocyte leukemia

    OpenAIRE

    Terra, Bruno; Maia, Amanda M.

    2010-01-01

    O presente estudo tem como objetivo o estabelecimento de fundamentação teórica atualizada baseada em revisão bibliográfica sobre a leucemia de grandes linfócitos granulares (LGLG), doença onco-hematológica, que, devido à sua relativa raridade, é pouco conhecida e subdiagnosticada. A LGLG é caracterizada pela proliferação clonal de linfócitos T ou NK na medula óssea e/ou no sangue periférico. Dentre as manifestações clínico-laboratoriais, podem ocorrer citopenias (anemia e/ou neutropenia e/ou ...

  6. Ten cases of severe oral lichen planus showing granular C3 deposition in oral mucosal basement membrane zone.

    Science.gov (United States)

    Hashimoto, Takashi; Fukuda, Aoi; Himejima, Akio; Morita, Shosuke; Tsuruta, Daisuke; Koga, Hiroshi; Krol, Rafal P; Ishii, Norito

    2015-01-01

    Oral lichen planus (OLP) may show depositions of immunoglobulins and complement components in oral mucosal basement membrane zone (BMZ) in direct immunofluorescence, although these finding are not frequently seen. We collected and examined ten cases of severe OLP showing granular C3 deposition in BMZ. In addition to clinical, histopathological and direct immunofluorescence assessments, we performed various immune-serological tests, including indirect immunofluorescence of normal human skin and 1M NaCl-split skin, immunoblotting of normal human epidermal and dermal extracts, recombinant proteins of BP180 NC16a and C-terminal domains, concentrated culture supernatant of HaCaT cells and purified human laminin-332, and enzyme-linked immunosorbent assays for BP230 and BP180. Direct immunofluorescence showed C3 deposition in BMZ exclusively of granular pattern in 7 cases and of both granular and linear patterns in 3 cases. The 10 cases showed no positive reactivity for either IgG or IgA antibodies in any immuno-serological tests. Detailed analyses of clinical, histopathological and immunological findings revealed striking female prevalence, although other parameters were in general characteristic of OLP. Granular C3 deposition in oral BMZ may be one of the characteristic features of severe OLP, although mechanisms for C3 deposition and its pathogenic role in OLP are currently unknown.

  7. Revealing new mouse epicardial cell markers through transcriptomics.

    Directory of Open Access Journals (Sweden)

    Lars Bochmann

    2010-06-01

    Full Text Available The epicardium has key functions during myocardial development, by contributing to the formation of coronary endothelial and smooth muscle cells, cardiac fibroblasts, and potentially cardiomyocytes. The epicardium plays a morphogenetic role by emitting signals to promote and maintain cardiomyocyte proliferation. In a regenerative context, the adult epicardium might comprise a progenitor cell population that can be induced to contribute to cardiac repair. Although some genes involved in epicardial function have been identified, a detailed molecular profile of epicardial gene expression has not been available.Using laser capture microscopy, we isolated the epicardial layer from the adult murine heart before or after cardiac infarction in wildtype mice and mice expressing a transgenic IGF-1 propeptide (mIGF-1 that enhances cardiac repair, and analyzed the transcription profile using DNA microarrays.Expression of epithelial genes such as basonuclin, dermokine, and glycoprotein M6A are highly enriched in the epicardial layer, which maintains expression of selected embryonic genes involved in epicardial development in mIGF-1 transgenic hearts. After myocardial infarct, a subset of differentially expressed genes are down-regulated in the epicardium representing an epicardium-specific signature that responds to injury.This study presents the description of the murine epicardial transcriptome obtained from snap frozen tissues, providing essential information for further analysis of this important cardiac cell layer.

  8. Thermal conductivity of granular materials

    Energy Technology Data Exchange (ETDEWEB)

    Buyevich, Yu A

    1974-01-01

    Stationary heat transfer in a granular material consisting of a continuous medium containing spherical granules of other substances is considered under the assumption that the spatial distribution of granules is random. The effective thermal conductivity characterizing macroscopic heat transfer in such a material is expressed as a certain function of the conductivities and volume fractions of the medium and dispersed substances. For reasons of mathematical analogy, all the results obtained for the thermal conductivity are valid while computing the effective diffusivity of some admixture in granular materials as well as for evaluation of the effective electric conductivity or the mean dielectric and magnetic permeabilities of granular conductors and dielectrics. (23 refs.)

  9. 3T3 fibroblasts induce cloned interleukin 3-dependent mouse mast cells to resemble connective tissue mast cells in granular constituency

    International Nuclear Information System (INIS)

    Dayton, E.T.; Pharr, P.; Ogawa, M.; Serafin, W.E.; Austen, K.F.; Levi-Schaffer, F.; Stevens, R.L.

    1988-01-01

    As assessed by ultrastructure, histochemical staining, and T-cell dependency, in vitro-differentiated interleukin 3-dependent mouse mast cells are comparable to the mast cells that reside in the gastrointestinal mucosa but not in the skin or the serosal cavity of the mouse. The authors now demonstrate that when cloned interleukin 3-dependent mast cells are cocultured with mouse skin-derived 3T3 fibroblasts in the presence of WEHI-3 conditioned medium for 28 days, the mast cells acquire the ability to stain with safranin, increase their histamine content ∼ 50-fold and their carboxypeptidase. A content ∼ 100-fold, and augment ∼ their biosynthesis of proteoglycans bearing 35 S-labeled haparin relative to 35 S-labeled chondroitin sulfate glycosaminoglycans. Thus, fibroblasts induce interleukin 3-dependent mouse mast cells to change phenotype from mucosal-like to connective tissue-like, indicating that the biochemical and functional characteristics of this mast cell type are strongly influenced by the connective tissue microenvironment

  10. Superconductivity effects near metal-insulator transition in granular idnium films

    International Nuclear Information System (INIS)

    Belevtsev, B.I.; Komnik, Yu.F.; Fomin, A.V.

    1986-01-01

    The influence of granules superconductivity on the electric properties of granular indium films is investigated under the conditions of partial or full granular localization of electrons. At temperatures below 5 K a minimum of electric resistance and negative magnetoresistance are revealed which are attributed to the competition of hopping conductivity and Josephson intergranular tunneling of electrons

  11. Large granular lymphocytic leukaemia pathogenesis and management.

    Science.gov (United States)

    Dearden, Claire

    2011-02-01

    The WHO classification recognises three distinct disorders of large granular lymphocytes: T-cell large granular lymphocytic leukaemia (T-LGL), chronic lymphoproliferative disorders of NK-cells (CLPD-NK) and agressive NK-cell leukaemia. Despite the different cell of origin, there is considerable overlap between T-LGL and CLPD-NK in terms of clinical presentation and therapy. Many patients are asymptomatic and do not require treatment. Therapy, with immunosuppressant agents such as low dose methotrexate or ciclosporin, is usually indicated to correct cytopenias. In contrast, aggressive NK-cell leukaemia and the rare CD56(+) aggressive T-LGL leukaemia follow a fulminant clinical course, affect younger individuals and require more intensive combination chemotherapy followed by allogeneic stem cell transplant in eligible patients. The relative rarity of these disorders means that there have been few clinical trials to inform management. However, there is now considerable interest in the pathogenesis of the chronic LGL leukaemias and this has stimulated early trials to evaluate novel agents which target the dysregulated apoptotic pathways characteristic of this disease. © 2010 Blackwell Publishing Ltd.

  12. Characterization of microbial consortia in a terephthalate-degrading anaerobic granular sludge system.

    Science.gov (United States)

    Wu, J H; Liu, W T; Tseng, I C; Cheng, S S

    2001-02-01

    The microbial composition and spatial distribution in a terephthalate-degrading anaerobic granular sludge system were characterized using molecular techniques. 16S rDNA clone library and sequence analysis revealed that 78.5% of 106 bacterial clones belonged to the delta subclass of the class Proteobacteria; the remaining clones were assigned to the green non-sulfur bacteria (7.5%), Synergistes (0.9%) and unidentified divisions (13.1%). Most of the bacterial clones in the delta-Proteobacteria formed a novel group containing no known bacterial isolates. For the domain Archaea, 81.7% and 18.3% of 72 archaeal clones were affiliated with Methanosaeta and Methanospirillum, respectively. Spatial localization of microbial populations inside granules was determined by transmission electron microscopy and fluorescent in situ hybridization with oligonucleotide probes targeting the novel delta-proteobacterial group, the acetoclastic Methanosaeta, and the hydrogenotrophic Methanospirillum and members of Methanobacteriaceae. The novel group included at least two different populations with identical rod-shape morphology, which made up more than 87% of the total bacterial cells, and were closely associated with methanogenic populations to form a nonlayered granular structure. This novel group was presumed to be the primary bacterial population involved in the terephthalate degradation in the methanogenic granular consortium.

  13. Granular flows: fundamentals and applications

    Science.gov (United States)

    Cleary, Paul W.

    DEM allows the prediction of complex industrial and geophysical particle flows. The importance of particle shape is demonstrated through a series of simple examples. Shape controls resistance to shear, the magnitude of collision stress, dilation and the angle of repose. We use a periodic flow of a bed of particles to demonstrate the different states of granular matter, the generation of dilute granular flow when granular temperature is high and the flow dependent nature of the granular thermodynamic boundary conditions. A series of industrial case studies examines how DEM can be used to understand and improve processes such as separation, mixing, grinding, excavation, hopper discharge, metering and conveyor interchange. Finally, an example of landslide motion over real topography is presented.

  14. Kinetic Theory of Granular Gases

    Energy Technology Data Exchange (ETDEWEB)

    Trizac, Emmanuel [Center of Theoretical Biological Physics, UC San Diego, La Jolla, CA 92093-0374 (United States); Laboratoire de Physique Theorique et Modeles Statistiques, Campus Universitaire, 91405 Orsay (France)

    2005-11-25

    tangential and normal restitution coefficients, that are again velocity dependent. Th is seems to be the price of a consistent approach, which does not lend itself to much insight. In addition, the behaviour of driven systems is not addressed, whereas in the realm of granular media, force-free systems are the exception rather than the rule. The differences between constant {epsilon} and visco-elastic models is presumably less pronounced in the driven case. Study of driven systems also reveals that the rheology of granular gases is intrinsically non-Newtonian, which is a key feature. Finally, the powerful direct simulation Monte Carlo technique is not described, whereas it is an important tool, particularly relevant for the physics of the Boltzmann equation, and straightforward to implement in its simplest version. N Brilliantov and T Poeschel concentrate on the (equally relevant) molecular dynamics method instead. In conclusion, the book fills a gap in the field. The companion webpage from where molecular dynamics and symbolic algebra programs can be downloaded is also useful. (book review)

  15. Kinetic Theory of Granular Gases

    International Nuclear Information System (INIS)

    Trizac, Emmanuel

    2005-01-01

    coefficients, that are again velocity dependent. Th is seems to be the price of a consistent approach, which does not lend itself to much insight. In addition, the behaviour of driven systems is not addressed, whereas in the realm of granular media, force-free systems are the exception rather than the rule. The differences between constant ε and visco-elastic models is presumably less pronounced in the driven case. Study of driven systems also reveals that the rheology of granular gases is intrinsically non-Newtonian, which is a key feature. Finally, the powerful direct simulation Monte Carlo technique is not described, whereas it is an important tool, particularly relevant for the physics of the Boltzmann equation, and straightforward to implement in its simplest version. N Brilliantov and T Poeschel concentrate on the (equally relevant) molecular dynamics method instead. In conclusion, the book fills a gap in the field. The companion webpage from where molecular dynamics and symbolic algebra programs can be downloaded is also useful. (book review)

  16. Superconductivity in inhomogeneous granular metals

    International Nuclear Information System (INIS)

    McLean, W.L.

    1980-01-01

    A model of elongated metal ellipsoids imbedded in a granular metal is treated by an effective medium approach to explain the observed temperature dependence of the normal-state conductivity of superconducting granular aluminum. Josephson tunneling is thus still required to account for the superconductivity. The model predicts the same kind of contrasting behavior on opposite sides of the metal-insulator transition as is found in the recent scaling treatment of Anderson localization

  17. Microfabricated microbial fuel cell arrays reveal electrochemically active microbes.

    Directory of Open Access Journals (Sweden)

    Huijie Hou

    Full Text Available Microbial fuel cells (MFCs are remarkable "green energy" devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated.

  18. Microfluidics of soft granular gels

    Science.gov (United States)

    Nixon, Ryan; Bhattacharjee, Tapomoy; Sawyer, W. Gregory; Angelini, Thomas E.

    Microfluidic methods for encapsulating cells and particles typically involve drop making with two immiscible fluids. The main materials constraint in this approach is surface tension, creating inherent instability between the two fluids. We can eliminate this instability by using miscible inner and outer phases. This is achieved by using granular micro gels which are chemically miscible but physically do not mix. These microgels are yield stress materials, so they flow as solid plugs far from shear gradients, and fluidize where gradients are generated - near an injection nozzle for example. We have found that tuning the yield stress of the material by varying polymer concentration, device performance can be controlled. The solid like behavior of the gel allows us to produces infinitely stable jets that maintain their integrity and configuration over long distances and times. These properties can be combined and manipulated to produce discrete particulate bunches of an inner phase, flowing inside of an outer phase, well enough even to print a Morse code message suspended within flow chambers about a millimeter in diameter moving at millimeters a second.

  19. Granular Superconductors and Gravity

    Science.gov (United States)

    Noever, David; Koczor, Ron

    1999-01-01

    As a Bose condensate, superconductors provide novel conditions for revisiting previously proposed couplings between electromagnetism and gravity. Strong variations in Cooper pair density, large conductivity and low magnetic permeability define superconductive and degenerate condensates without the traditional density limits imposed by the Fermi energy (approx. 10(exp -6) g cu cm). Recent experiments have reported anomalous weight loss for a test mass suspended above a rotating Type II, YBCO superconductor, with a relatively high percentage change (0.05-2.1%) independent of the test mass' chemical composition and diamagnetic properties. A variation of 5 parts per 104 was reported above a stationary (non-rotating) superconductor. In experiments using a sensitive gravimeter, bulk YBCO superconductors were stably levitated in a DC magnetic field and exposed without levitation to low-field strength AC magnetic fields. Changes in observed gravity signals were measured to be less than 2 parts in 108 of the normal gravitational acceleration. Given the high sensitivity of the test, future work will examine variants on the basic magnetic behavior of granular superconductors, with particular focus on quantifying their proposed importance to gravity.

  20. Raman spectrum reveals Mesenchymal stem cells inhibiting HL60 cells growth

    Science.gov (United States)

    Su, Xin; Fang, Shaoyin; Zhang, Daosen; Zhang, Qinnan; Lu, Xiaoxu; Tian, Jindong; Fan, Jinping; Zhong, Liyun

    2017-04-01

    Though some research results reveals that Mesenchymal stem cells (MSCs) have the ability of inhibiting tumor cells proliferation, it remains controversial about the precise interaction mechanism during MSCs and tumor cells co-culture. In this study, combing Raman spectroscopic data and principle component analysis (PCA), the biochemical changes of MSCs or Human promyelocytic leukemia (HL60) cells during their co-culture were presented. The obtained results showed that some main Raman peaks of HL60 assigned to nucleic acids or proteins were greatly higher in intensity in the late stage of co-culture than those in the early stage of co-culture while they were still lower relative to the control group, implicating that the effect of MSCs inhibiting HL60 proliferation appeared in the early stage but gradually lost the inhibiting ability in the late stage of co-culture. Moreover, some other peaks of HL60 assigned to proteins were decreased in intensity in the early stage of co-culture relative to the control group but rebounded to the level similar to the control group in the late stage, showing that the content and structure changes of these proteins might be generated in the early stage but returned to the original state in the late stage of co-culture. As a result, in the early stage of MSCs-HL60 co-culture, along with the level of Akt phosphorylation of HL60 was lowered relative to its control group, the proliferation rate of HL60 cells was decreased. And in the late stage of co-culture, along with the level of Akt phosphorylation was rebounded, the reverse transfer of Raman peaks within 875-880 cm- 1 appeared, thus MSCs lost the ability to inhibit HL60 growth and HL60 proliferation was increased. In addition, it was observed that the peak at 811 cm- 1, which is a marker of RNA, was higher in intensity in the late stage than that in the control group, indicating that MSCs might be differentiated into myofibroblast-like MSCs. In addition, PCA results also exhibited

  1. Enhanced selection of micro-aerobic pentachlorophenol degrading granular sludge

    International Nuclear Information System (INIS)

    Lv, Yuancai; Chen, Yuancai; Song, Wenzhe; Hu, Yongyou

    2014-01-01

    Graphical abstract: In this work, an aerobic column reactor was placed before the USB to maintain micro-oxygen condition in the reactor and the micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L −1 ) was successfully obtained. PCP degradation by the micro-aerobic system was studied and the variance of microbial community was also discussed by using PCR-DGGE analysis. - Highlights: • Micro-aerobic granular sludge was cultivated in column-type combined reactors. • PCP biodegradation, VFA accumulation and biogas production were studied. • The function of Methanogenic archaeon in the system was investigated. • Fluctuation and diversity of microbial community were discussed by DGGE analysis. • The dominated microorganisms were identified by 16S rDNA sequences. - Abstract: Column-type combined reactors were designed to cultivate micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L −1 ) over 39-day experimental period. Micro-aerobic granular had both anaerobic activity (SMA: 2.34 mMCH 4 /h g VSS) and aerobic activity (SOUR: 2.21 mMO 2 /h g VSS). Metabolite analysis results revealed that PCP was sequentially dechlorinated to TCP, DCP, and eventually to MCP. Methanogens were not directly involved in the dechlorination of PCP, but might played a vital role in stabilizing the overall structure of the granule sludge. For Eubacteria, the Shannon Index (2.09 in inoculated granular sludge) increased both in micro-aerobic granular sludge (2.61) and PCP-degradation granular sludge (2.55). However, for Archaea, it decreased from 2.53 to 1.85 and 1.84, respectively. Although the Shannon Index demonstrated slight difference between micro-aerobic granular sludge and PCP-degradation granular sludge, the Principal Component Analysis (PCA) indicated obvious variance of the microbial composition, revealing significant effect of micro-aerobic condition and

  2. Enhanced selection of micro-aerobic pentachlorophenol degrading granular sludge

    Energy Technology Data Exchange (ETDEWEB)

    Lv, Yuancai, E-mail: donkey1204@hotmail.com [State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640 (China); Chen, Yuancai, E-mail: chenyc@scut.edu.cn [State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640 (China); Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); Song, Wenzhe, E-mail: songwenzhe007@126.com [Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); Hu, Yongyou, E-mail: ppyyhu@scut.edu.cn [State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Science, South China University of Technology, Guangzhou 510640 (China); Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, College of Environment and Energy, South China University of Technology, Guangzhou 510006 (China)

    2014-09-15

    Graphical abstract: In this work, an aerobic column reactor was placed before the USB to maintain micro-oxygen condition in the reactor and the micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L{sup −1}) was successfully obtained. PCP degradation by the micro-aerobic system was studied and the variance of microbial community was also discussed by using PCR-DGGE analysis. - Highlights: • Micro-aerobic granular sludge was cultivated in column-type combined reactors. • PCP biodegradation, VFA accumulation and biogas production were studied. • The function of Methanogenic archaeon in the system was investigated. • Fluctuation and diversity of microbial community were discussed by DGGE analysis. • The dominated microorganisms were identified by 16S rDNA sequences. - Abstract: Column-type combined reactors were designed to cultivate micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1–0.2 mg L{sup −1}) over 39-day experimental period. Micro-aerobic granular had both anaerobic activity (SMA: 2.34 mMCH{sub 4}/h g VSS) and aerobic activity (SOUR: 2.21 mMO{sub 2}/h g VSS). Metabolite analysis results revealed that PCP was sequentially dechlorinated to TCP, DCP, and eventually to MCP. Methanogens were not directly involved in the dechlorination of PCP, but might played a vital role in stabilizing the overall structure of the granule sludge. For Eubacteria, the Shannon Index (2.09 in inoculated granular sludge) increased both in micro-aerobic granular sludge (2.61) and PCP-degradation granular sludge (2.55). However, for Archaea, it decreased from 2.53 to 1.85 and 1.84, respectively. Although the Shannon Index demonstrated slight difference between micro-aerobic granular sludge and PCP-degradation granular sludge, the Principal Component Analysis (PCA) indicated obvious variance of the microbial composition, revealing significant effect of micro

  3. Granular flows in constrained geometries

    Science.gov (United States)

    Murthy, Tejas; Viswanathan, Koushik

    Confined geometries are widespread in granular processing applications. The deformation and flow fields in such a geometry, with non-trivial boundary conditions, determine the resultant mechanical properties of the material (local porosity, density, residual stresses etc.). We present experimental studies of deformation and plastic flow of a prototypical granular medium in different nontrivial geometries- flat-punch compression, Couette-shear flow and a rigid body sliding past a granular half-space. These geometries represent simplified scaled-down versions of common industrial configurations such as compaction and dredging. The corresponding granular flows show a rich variety of flow features, representing the entire gamut of material types, from elastic solids (beam buckling) to fluids (vortex-formation, boundary layers) and even plastically deforming metals (dead material zone, pile-up). The effect of changing particle-level properties (e.g., shape, size, density) on the observed flows is also explicitly demonstrated. Non-smooth contact dynamics particle simulations are shown to reproduce some of the observed flow features quantitatively. These results showcase some central challenges facing continuum-scale constitutive theories for dynamic granular flows.

  4. Assessing continuum postulates in simulations of granular flow

    Energy Technology Data Exchange (ETDEWEB)

    Rycroft, Chris; Kamrin, Ken; Bazant, Martin

    2008-08-26

    Continuum mechanics relies on the fundamental notion of a mesoscopic volume"element" in which properties averaged over discrete particles obey deterministic relationships. Recent work on granular materials suggests a continuum law may be inapplicable, revealing inhomogeneities at the particle level, such as force chains and slow cage breaking. Here, we analyze large-scale three-dimensional Discrete-Element Method (DEM) simulations of different granular flows and show that an approximate"granular element" defined at the scale of observed dynamical correlations (roughly three to five particle diameters) has a reasonable continuum interpretation. By viewing all the simulations as an ensemble of granular elements which deform and move with the flow, we can track material evolution at a local level. Our results confirm some of the hypotheses of classical plasticity theory while contradicting others and suggest a subtle physical picture of granular failure, combining liquid-like dependence on deformation rate and solid-like dependence on strain. Our computational methods and results can be used to guide the development of more realistic continuum models, based on observed local relationships betweenaverage variables.

  5. Characteristics and performance of aerobic algae-bacteria granular consortia in a photo-sequencing batch reactor.

    Science.gov (United States)

    Liu, Lin; Zeng, Zhichao; Bee, Mingyang; Gibson, Valerie; Wei, Lili; Huang, Xu; Liu, Chaoxiang

    2018-05-05

    The characteristics and performance of algae-bacteria granular consortia which cultivated with aerobic granules and targeted algae (Chlorella and Scenedesmus), and the essential difference between granular consortia and aerobic granules were investigated in this experiment. The result indicated that algae-bacteria granular consortia could be successfully developed, and the algae present in the granular consortia were mainly Chlorella and Scenedesmus. Although the change of chlorophyll composition revealed the occurrence of light limitation for algal growth, the granular consortia could maintain stable granular structure, and even showed better settling property than aerobic granules. Total nitrogen and phosphate in the algal-bacterial granular system showed better removal efficiencies (50.2% and 35.7%) than those in the aerobic granular system (32.8% and 25.6%) within one cycle (6 h). The biodiesel yield of aerobic granules could be significantly improved by algal coupled process, yet methyl linolenate and methyl palmitoleate were the dominant composition of biodiesel obtained from granular consortia and aerobic granules, respectively. Meanwhile, the difference of dominant bacterial communities in the both granules was found at the order level and family level, and alpha diversity indexes revealed the granular consortia had a higher microbial diversity. Copyright © 2018. Published by Elsevier B.V.

  6. Why granular media are thermal after all

    Science.gov (United States)

    Liu, Mario; Jiang, Yimin

    2017-06-01

    Two approaches exist to account for granular behavior. The thermal one considers the total entropy, which includes microscopic degrees of freedom such as phonons; the athermal one (as with the Edward entropy) takes grains as elementary. Granular solid hydrodynamics (GSH) belongs to the first, DEM, granular kinetic theory and athermal statistical mechanics (ASM) to the second. A careful discussion of their conceptual differences is given here. Three noteworthy insights or results are: (1) While DEM and granular kinetic theory are well justified to take grains as elementary, any athermal entropic consideration is bound to run into trouble. (2) Many general principles are taken as invalid in granular media. Yet within the thermal approach, energy conservation and fluctuation-dissipation theorem remain valid, granular temperatures equilibrate, and phase space is well explored in a grain at rest. Hence these are abnormalities of the athermal approximation, not of granular media as such. (3) GSH is a wide-ranged continuum mechanical description of granular dynamics.

  7. Live cell imaging reveals marked variability in myoblast proliferation and fate

    Science.gov (United States)

    2013-01-01

    Background During the process of muscle regeneration, activated stem cells termed satellite cells proliferate, and then differentiate to form new myofibers that restore the injured area. Yet not all satellite cells contribute to muscle repair. Some continue to proliferate, others die, and others become quiescent and are available for regeneration following subsequent injury. The mechanisms that regulate the adoption of different cell fates in a muscle cell precursor population remain unclear. Methods We have used live cell imaging and lineage tracing to study cell fate in the C2 myoblast line. Results Analyzing the behavior of individual myoblasts revealed marked variability in both cell cycle duration and viability, but similarities between cells derived from the same parental lineage. As a consequence, lineage sizes and outcomes differed dramatically, and individual lineages made uneven contributions toward the terminally differentiated population. Thus, the cohort of myoblasts undergoing differentiation at the end of an experiment differed dramatically from the lineages present at the beginning. Treatment with IGF-I increased myoblast number by maintaining viability and by stimulating a fraction of cells to complete one additional cell cycle in differentiation medium, and as a consequence reduced the variability of the terminal population compared with controls. Conclusion Our results reveal that heterogeneity of responses to external cues is an intrinsic property of cultured myoblasts that may be explained in part by parental lineage, and demonstrate the power of live cell imaging for understanding how muscle differentiation is regulated. PMID:23638706

  8. Disinfection of bacteria attached to granular activated carbon.

    Science.gov (United States)

    LeChevallier, M W; Hassenauer, T S; Camper, A K; McFeters, G A

    1984-01-01

    Heterotrophic plate count bacteria, coliform organisms, and pathogenic microorganisms attached to granular activated carbon particles were examined for their susceptibility to chlorine disinfection. When these bacteria were grown on carbon particles and then disinfected with 2.0 mg of chlorine per liter (1.4 to 1.6 mg of free chlorine residual per liter after 1 h) for 1 h, no significant decrease in viable counts was observed. Washed cells attached to the surface of granular activated carbon particles showed similar resistance to chlorine, but a progressive increase in sublethal injury was found. Observations made by scanning electron microscope indicated that granular activated carbon was colonized by bacteria which grow in cracks and crevices and are coated by an extracellular slime layer. These data suggest a possible mechanism by which treatment and disinfection barriers can be penetrated and pathogenic bacteria may enter drinking water supplies. Images PMID:6508306

  9. Traffic and Granular Flow '11

    CERN Document Server

    Buslaev, Alexander; Bugaev, Alexander; Yashina, Marina; Schadschneider, Andreas; Schreckenberg, Michael; TGF11

    2013-01-01

    This book continues the biannual series of conference proceedings, which has become a classical reference resource in traffic and granular research alike. It addresses new developments at the interface between physics, engineering and computational science. Complex systems, where many simple agents, be they vehicles or particles, give rise to surprising and fascinating phenomena.   The contributions collected in these proceedings cover several research fields, all of which deal with transport. Topics include highway, pedestrian and internet traffic, granular matter, biological transport, transport networks, data acquisition, data analysis and technological applications. Different perspectives, i.e. modeling, simulations, experiments and phenomenological observations, are considered.

  10. Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.

    Science.gov (United States)

    Hochgerner, Hannah; Zeisel, Amit; Lönnerberg, Peter; Linnarsson, Sten

    2018-02-01

    The dentate gyrus of the hippocampus is a brain region in which neurogenesis persists into adulthood; however, the relationship between developmental and adult dentate gyrus neurogenesis has not been examined in detail. Here we used single-cell RNA sequencing to reveal the molecular dynamics and diversity of dentate gyrus cell types in perinatal, juvenile, and adult mice. We found distinct quiescent and proliferating progenitor cell types, linked by transient intermediate states to neuroblast stages and fully mature granule cells. We observed shifts in the molecular identity of quiescent and proliferating radial glia and granule cells during the postnatal period that were then maintained through adult stages. In contrast, intermediate progenitor cells, neuroblasts, and immature granule cells were nearly indistinguishable at all ages. These findings demonstrate the fundamental similarity of postnatal and adult neurogenesis in the hippocampus and pinpoint the early postnatal transformation of radial glia from embryonic progenitors to adult quiescent stem cells.

  11. Uniform shock waves in disordered granular matter

    NARCIS (Netherlands)

    Gómez, L.R.; Turner, A.M.; Vitelli, V.

    2012-01-01

    The confining pressure P is perhaps the most important parameter controlling the properties of granular matter. Strongly compressed granular media are, in many respects, simple solids in which elastic perturbations travel as ordinary phonons. However, the speed of sound in granular aggregates

  12. Radioresistance of intermediate TCR cells and their localization in the body of mice revealed by irradiation

    International Nuclear Information System (INIS)

    Kimura, Motohiko; Watanabe, Hisami; Ohtsuka, Kazuo; Iiai, Tsuneo; Tsuchida, Masanori; Sato, Shotaro; Abo, Toru

    1993-01-01

    Extrathymic generation of T cells in the liver and in the intestine was recently demonstrated. We investigated herein whether such T cells, especially those in the liver, are present in other organs of mice. This investigation is possible employing our recently introduced method with which even a minor proportion of extrathymic, intermediate T-cell receptor (TCR) cells in organs other than the liver can be identified. Intermediate TCR cells expressed higher levels of IL-2Rβ and lymphocyte function-associated antigen-1 (LFA-1) than bright TCR cells (i.e., T cells of thymic origin) as revealed by two-color staining. Although intermediate TCR cells were present at a small proportion in the spleen and thymus, they predominated in these organs after irradiation (9 Gy) and bone marrow reconstitution, or after low dose irradiation (6 Gy). This was due to that intermediate TCR cells were relatively radioresistant, whereas bright TCR cells were radiosensitive. Microscopic observation and immunochemical staining showed that intermediate TCR cells in the spleen localized in the red pulp and those in the thymus localized in the medulla. These intermediate TCR cells displayed a large light scatter, similar to such cells in the liver. The present results suggest that intermediate TCR cells may proliferate at multiple sites in the body. (author)

  13. Acoustic waves in granular materials

    NARCIS (Netherlands)

    Mouraille, O.J.P.; Luding, Stefan

    2008-01-01

    Dynamic simulations with discrete elements are used to obtain more insight into the wave propagation in dense granular media. A small perturbation is created on one side of a dense, static packing and examined during its propagation until it arrives at the opposite side. The influence of

  14. Standardized orthotopic xenografts in zebrafish reveal glioma cell-line-specific characteristics and tumor cell heterogeneity

    Directory of Open Access Journals (Sweden)

    Alessandra M. Welker

    2016-02-01

    Full Text Available Glioblastoma (GBM is a deadly brain cancer, for which few effective drug treatments are available. Several studies have used zebrafish models to study GBM, but a standardized approach to modeling GBM in zebrafish was lacking to date, preventing comparison of data across studies. Here, we describe a new, standardized orthotopic xenotransplant model of GBM in zebrafish. Dose-response survival assays were used to define the optimal number of cells for tumor formation. Techniques to measure tumor burden and cell spread within the brain over real time were optimized using mouse neural stem cells as control transplants. Applying this standardized approach, we transplanted two patient-derived GBM cell lines, serum-grown adherent cells and neurospheres, into the midbrain region of embryonic zebrafish and analyzed transplanted larvae over time. Progressive brain tumor growth and premature larval death were observed using both cell lines; however, fewer transplanted neurosphere cells were needed for tumor growth and lethality. Tumors were heterogeneous, containing both cells expressing stem cell markers and cells expressing markers of differentiation. A small proportion of transplanted neurosphere cells expressed glial fibrillary acidic protein (GFAP or vimentin, markers of more differentiated cells, but this number increased significantly during tumor growth, indicating that these cells undergo differentiation in vivo. By contrast, most serum-grown adherent cells expressed GFAP and vimentin at the earliest times examined post-transplant. Both cell types produced brain tumors that contained Sox2+ cells, indicative of tumor stem cells. Transplanted larvae were treated with currently used GBM therapeutics, temozolomide or bortezomib, and this resulted in a reduction in tumor volume in vivo and an increase in survival. The standardized model reported here facilitates robust and reproducible analysis of glioblastoma tumor cells in real time and provides a

  15. Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.

    Science.gov (United States)

    Yu, Tao; Wang, Yongtao; Zhang, Huizhen; Johnson, Caroline H; Jiang, Yiming; Li, Xiangjun; Wu, Zeming; Liu, Tian; Krausz, Kristopher W; Yu, Aiming; Gonzalez, Frank J; Huang, Min; Bi, Huichang

    2016-06-01

    Mycoplasma contamination is a common problem in cell culture and can alter cellular functions. Since cell metabolism is either directly or indirectly involved in every aspect of cell function, it is important to detect changes to the cellular metabolome after mycoplasma infection. In this study, liquid chromatography mass spectrometry (LC/MS)-based metabolomics was used to investigate the effect of mycoplasma contamination on the cellular metabolism of human pancreatic carcinoma cells (PANC-1). Multivariate analysis demonstrated that mycoplasma contamination induced significant metabolic changes in PANC-1 cells. Twenty-three metabolites were identified and found to be involved in arginine and purine metabolism and energy supply. This study demonstrates that mycoplasma contamination significantly alters cellular metabolite levels, confirming the compelling need for routine checking of cell cultures for mycoplasma contamination, particularly when used for metabolomics studies. Graphical abstract Metabolomics reveals mycoplasma contamination changes the metabolome of PANC-1 cells.

  16. Naturally death-resistant precursor cells revealed as the origin of retinoblastoma

    DEFF Research Database (Denmark)

    Trinh, Emmanuelle; Lazzerini Denchi, Eros; Helin, Kristian

    2004-01-01

    The molecular mechanisms and the cell-of-origin leading to retinoblastoma are not well defined. In this issue of Cancer Cell, Bremner and colleagues describe the first inheritable model of retinoblastoma, revealing that loss of the pocket proteins pRb and p107 deregulates cell cycle exit in retinal...... precursors. The authors show that a subset of these precursors contain an inherent resistance to apoptosis, and that while most terminally differentiate, some are likely to acquire additional mutations, leading to tumor formation. Thus, this work defines the cell-of-origin of retinoblastoma and suggests...... that mutations giving increased proliferative capacity are required for retinoblastoma development....

  17. Granular boycott effect: How to mix granulates

    Science.gov (United States)

    Duran, J.; Mazozi, T.

    1999-11-01

    Granular material can display the basic features of the Boycott effect in sedimentation. A simple experiment shows that granular material falls faster in an inclined tube than in a vertical tube, in analogy with the Boycott effect. As long as the inclination of the tube is above the avalanche threshold, descent of granular material in the tube causes internal convection which in turn results in an efficient mixture of the granular components. By contrast, as in analogous experiments in two dimensions, a vertical fall of granular material occurs via successive block fragmentation, resulting in poor mixing.

  18. Lizard locomotion in heterogeneous granular media

    Science.gov (United States)

    Schiebel, Perrin; Goldman, Daniel

    2014-03-01

    Locomotion strategies in heterogeneous granular environments (common substrates in deserts), are relatively unexplored. The zebra-tailed lizard (C. draconoides) is a useful model organism for such studies owing to its exceptional ability to navigate a variety of desert habitats at impressive speed (up to 50 body-lengths per second) using both quadrapedal and bidepal gaits. In laboratory experiments, we challenge the lizards to run across a field of boulders (2.54 cm diameter glass spheres or 3.8 cm 3D printed spheres) placed in a lattice pattern and embedded in a loosely packed granular medium of 0.3 mm diameter glass particles. Locomotion kinematics of the lizard are recorded using high speed cameras, with and without the scatterers. The data reveals that unlike the lizard's typical quadrupedal locomotion using a diagonal gait, when scatterers are present the lizard is most successful when using a bipedal gait, with a raised center of mass (CoM). We propose that the kinematics of bipedal running in conjunction with the lizard's long toes and compliant hind foot are the keys to this lizard's successful locomotion in the presence of such obstacles. NSF PoLS

  19. Endometrial natural killer (NK) cells reveal a tissue-specific receptor repertoire.

    Science.gov (United States)

    Feyaerts, D; Kuret, T; van Cranenbroek, B; van der Zeeuw-Hingrez, S; van der Heijden, O W H; van der Meer, A; Joosten, I; van der Molen, R G

    2018-02-13

    Is the natural killer (NK) cell receptor repertoire of endometrial NK (eNK) cells tissue-specific? The NK cell receptor (NKR) expression profile in pre-pregnancy endometrium appears to have a unique tissue-specific phenotype, different from that found in NK cells in peripheral blood, suggesting that these cells are finely tuned towards the reception of an allogeneic fetus. NK cells are important for successful pregnancy. After implantation, NK cells encounter extravillous trophoblast cells and regulate trophoblast invasion. NK cell activity is amongst others regulated by C-type lectin heterodimer (CD94/NKG2) and killer cell immunoglobulin-like (KIR) receptors. KIR expression on decidual NK cells is affected by the presence of maternal HLA-C and biased towards KIR2D expression. However, little is known about NKR expression on eNK cells prior to pregnancy. In this study, matched peripheral and menstrual blood (a source of endometrial cells) was obtained from 25 healthy females with regular menstrual cycles. Menstrual blood was collected during the first 36 h of menstruation using a menstrual cup, a non-invasive technique to obtain endometrial cells. KIR and NKG2 receptor expression on eNK cells was characterized by 10-color flow cytometry, and compared to matched pbNK cells of the same female. KIR and HLA-C genotypes were determined by PCR-SSOP techniques. Anti-CMV IgG antibodies in plasma were measured by chemiluminescence immunoassay. KIR expression patterns of eNK cells collected from the same female do not differ over consecutive menstrual cycles. The percentage of NK cells expressing KIR2DL2/L3/S2, KIR2DL3, KIR2DL1, LILRB1 and/or NKG2A was significantly higher in eNK cells compared to pbNK cells, while no significant difference was observed for NKG2C, KIR2DL1/S1, and KIR3DL1. The NKR repertoire of eNK cells was clearly different from pbNK cells, with eNK cells co-expressing more than three NKR simultaneously. In addition, outlier analysis revealed 8 and 15 NKR

  20. Granular Corneal Dystrophy Manifesting after Radial Keratotomy

    Directory of Open Access Journals (Sweden)

    Sepehr Feizi

    2008-12-01

    Full Text Available

    PURPOSE: To report manifestation of granular corneal dystrophy after radial keratotomy (RK. CASE REPORT: A 32-year-old man presented with white radial lines in both corneas. He had undergone uncomplicated RK in both eyes 8 years ago. Preoperative refraction had been OD: -3.5 -0.75@180 and OS: -3.0 -0.5@175. Uncorrected visual acuity was OD: 8/10 and OS: 7/10; best corrected visual acuity was 9/10 in both eyes with OD: -0.5 -0.5@60 and OS: -0.75 -0.5@80. Slit lamp examination revealed discrete well-demarcated whitish lesions with clear intervening stroma in the central anterior cornea consistent with granular dystrophy. Similar opacities were present within the RK incisions. CONCLUSION: Granular dystrophy deposits may appear within RK incisions besides other previously reported locations.

  1. Single-cell cloning of colon cancer stem cells reveals a multi-lineage differentiation capacity

    NARCIS (Netherlands)

    Vermeulen, L.; Todaro, M.; de Sousa E Melo, F.; Sprick, M. R.; Kemper, K.; Alea, M. Perez; Richel, D. J.; Stassi, G.; Medema, J. P.

    2008-01-01

    Colon carcinoma is one of the leading causes of death from cancer and is characterized by a heterogenic pool of cells with distinct differentiation patterns. Recently, it was reported that a population of undifferentiated cells from a primary tumor, so-called cancer stem cells (CSC), can

  2. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

    DEFF Research Database (Denmark)

    Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas

    2016-01-01

    to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially...... kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified...... as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human...

  3. Microspectroscopic Study of Liposome-to-cell Interaction Revealed by Förster Resonance Energy Transfer.

    Science.gov (United States)

    Yefimova, Svetlana L; Kurilchenko, Irina Yu; Tkacheva, Tatyana N; Kavok, Nataliya S; Todor, Igor N; Lukianova, Nataliya Yu; Chekhun, Vasyl F; Malyukin, Yuriy V

    2014-03-01

    We report the Förster resonance energy transfer (FRET)-labeling of liposomal vesicles as an effective approach to study in dynamics the interaction of liposomes with living cells of different types (rat hepatocytes, rat bone marrow, mouse fibroblast-like cells and human breast cancer cells) and cell organelles (hepatocyte nuclei). The in vitro experiments were performed using fluorescent microspectroscopic technique. Two fluorescent dyes (DiO as the energy donor and DiI as an acceptor) were preloaded in lipid bilayers of phosphatidylcholine liposomes that ensures the necessary distance between the dyes for effective FRET. The change in time of the donor and acceptor relative fluorescence intensities was used to visualize and trace the liposome-to-cell interaction. We show that FRET-labeling of liposome vesicles allows one to reveal the differences in efficiency and dynamics of these interactions, which are associated with composition, fluidity, and metabolic activity of cell plasma membranes.

  4. Calcium Imaging Reveals Coordinated Simple Spike Pauses in Populations of Cerebellar Purkinje Cells

    Directory of Open Access Journals (Sweden)

    Jorge E. Ramirez

    2016-12-01

    Full Text Available The brain’s control of movement is thought to involve coordinated activity between cerebellar Purkinje cells. The results reported here demonstrate that somatic Ca2+ imaging is a faithful reporter of Na+-dependent “simple spike” pauses and enables us to optically record changes in firing rates in populations of Purkinje cells in brain slices and in vivo. This simultaneous calcium imaging of populations of Purkinje cells reveals a striking spatial organization of pauses in Purkinje cell activity between neighboring cells. The source of this organization is shown to be the presynaptic gamma-Aminobutyric acid producing (GABAergic network, and blocking ionotropic gamma-Aminobutyric acid receptor (GABAARs abolishes the synchrony. These data suggest that presynaptic interneurons synchronize (inactivity between neighboring Purkinje cells, and thereby maximize their effect on downstream targets in the deep cerebellar nuclei.

  5. Single-cell analysis reveals early manifestation of cancerous phenotype in pre-malignant esophageal cells.

    Directory of Open Access Journals (Sweden)

    Jiangxin Wang

    Full Text Available Cellular heterogeneity plays a pivotal role in a variety of functional processes in vivo including carcinogenesis. However, our knowledge about cell-to-cell diversity and how differences in individual cells manifest in alterations at the population level remains very limited mainly due to the lack of appropriate tools enabling studies at the single-cell level. We present a study on changes in cellular heterogeneity in the context of pre-malignant progression in response to hypoxic stress. Utilizing pre-malignant progression of Barrett's esophagus (BE as a disease model system we studied molecular mechanisms underlying the progression from metaplastic to dysplastic (pre-cancerous stage. We used newly developed methods enabling measurements of cell-to-cell differences in copy numbers of mitochondrial DNA, expression levels of a set of mitochondrial and nuclear genes involved in hypoxia response pathways, and mitochondrial membrane potential. In contrast to bulk cell studies reported earlier, our study shows significant differences between metaplastic and dysplastic BE cells in both average values and single-cell parameter distributions of mtDNA copy numbers, mitochondrial function, and mRNA expression levels of studied genes. Based on single-cell data analysis, we propose that mitochondria may be one of the key factors in pre-malignant progression in BE.

  6. Live cell linear dichroism imaging reveals extensive membrane ruffling within the docking structure of natural killer cell immune synapses

    DEFF Research Database (Denmark)

    Benninger, Richard K P; Vanherberghen, Bruno; Young, Stephen

    2009-01-01

    We have applied fluorescence imaging of two-photon linear dichroism to measure the subresolution organization of the cell membrane during formation of the activating (cytolytic) natural killer (NK) cell immune synapse (IS). This approach revealed that the NK cell plasma membrane is convoluted...... into ruffles at the periphery, but not in the center of a mature cytolytic NK cell IS. Time-lapse imaging showed that the membrane ruffles formed at the initial point of contact between NK cells and target cells and then spread radialy across the intercellular contact as the size of the IS increased, becoming...... absent from the center of the mature synapse. Understanding the role of such extensive membrane ruffling in the assembly of cytolytic synapses is an intriguing new goal....

  7. HYPERELASTIC MODELS FOR GRANULAR MATERIALS

    Energy Technology Data Exchange (ETDEWEB)

    Humrickhouse, Paul W; Corradini, Michael L

    2009-01-29

    A continuum framework for modeling of dust mobilization and transport, and the behavior of granular systems in general, has been reviewed, developed and evaluated for reactor design applications. The large quantities of micron-sized particles expected in the international fusion reactor design, ITER, will accumulate into piles and layers on surfaces, which are large relative to the individual particle size; thus, particle-particle, rather than particle-surface, interactions will determine the behavior of the material in bulk, and a continuum approach is necessary and justified in treating the phenomena of interest; e.g., particle resuspension and transport. The various constitutive relations that characterize these solid particle interactions in dense granular flows have been discussed previously, but prior to mobilization their behavior is not even fluid. Even in the absence of adhesive forces between particles, dust or sand piles can exist in static equilibrium under gravity and other forces, e.g., fluid shear. Their behavior is understood to be elastic, though not linear. The recent “granular elasticity” theory proposes a non-linear elastic model based on “Hertz contacts” between particles; the theory identifies the Coulomb yield condition as a requirement for thermodynamic stability, and has successfully reproduced experimental results for stress distributions in sand piles. The granular elasticity theory is developed and implemented in a stand- alone model and then implemented as part of a finite element model, ABAQUS, to determine the stress distributions in dust piles subjected to shear by a fluid flow. We identify yield with the onset of mobilization, and establish, for a given dust pile and flow geometry, the threshold pressure (force) conditions on the surface due to flow required to initiate it. While the granular elasticity theory applies strictly to cohesionless granular materials, attractive forces are clearly important in the interaction of

  8. Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility

    Science.gov (United States)

    Seumois, Grégory; Chavez, Lukas; Gerasimova, Anna; Lienhard, Matthias; Omran, Nada; Kalinke, Lukas; Vedanayagam, Maria; Ganesan, Asha Purnima V; Chawla, Ashu; Djukanović, Ratko; Ansel, K Mark; Peters, Bjoern; Rao, Anjana; Vijayanand, Pandurangan

    2014-01-01

    A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce type 2 cytokines (TH2 cells). By mapping genome-wide histone modification profiles for subsets of T cells isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human TH1 cells and TH2 cells. We discovered disease-specific enhancers in T cells that differ between healthy and asthmatic individuals. Enhancers that gained the histone H3 Lys4 dimethyl (H3K4me2) mark during TH2 cell development showed the highest enrichment for asthma-associated single nucleotide polymorphisms (SNPs), which supported a pathogenic role for TH2 cells in asthma. In silico analysis of cell-specific enhancers revealed transcription factors, microRNAs and genes potentially linked to human TH2 cell differentiation. Our results establish the feasibility and utility of enhancer profiling in well-defined populations of specialized cell types involved in disease pathogenesis. PMID:24997565

  9. B-Cell-Specific Diversion of Glucose Carbon Utilization Reveals a Unique Vulnerability in B Cell Malignancies.

    Science.gov (United States)

    Xiao, Gang; Chan, Lai N; Klemm, Lars; Braas, Daniel; Chen, Zhengshan; Geng, Huimin; Zhang, Qiuyi Chen; Aghajanirefah, Ali; Cosgun, Kadriye Nehir; Sadras, Teresa; Lee, Jaewoong; Mirzapoiazova, Tamara; Salgia, Ravi; Ernst, Thomas; Hochhaus, Andreas; Jumaa, Hassan; Jiang, Xiaoyan; Weinstock, David M; Graeber, Thomas G; Müschen, Markus

    2018-04-05

    B cell activation during normal immune responses and oncogenic transformation impose increased metabolic demands on B cells and their ability to retain redox homeostasis. While the serine/threonine-protein phosphatase 2A (PP2A) was identified as a tumor suppressor in multiple types of cancer, our genetic studies revealed an essential role of PP2A in B cell tumors. Thereby, PP2A redirects glucose carbon utilization from glycolysis to the pentose phosphate pathway (PPP) to salvage oxidative stress. This unique vulnerability reflects constitutively low PPP activity in B cells and transcriptional repression of G6PD and other key PPP enzymes by the B cell transcription factors PAX5 and IKZF1. Reflecting B-cell-specific transcriptional PPP-repression, glucose carbon utilization in B cells is heavily skewed in favor of glycolysis resulting in lack of PPP-dependent antioxidant protection. These findings reveal a gatekeeper function of the PPP in a broad range of B cell malignancies that can be efficiently targeted by small molecule inhibition of PP2A and G6PD. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

    NARCIS (Netherlands)

    Semrau, Stefan; Goldmann, Johanna E; Soumillon, Magali; Mikkelsen, Tarjei S; Jaenisch, Rudolf; van Oudenaarden, Alexander

    2017-01-01

    Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measure the gene expression

  11. Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.

    Science.gov (United States)

    Zheng, Chunhong; Zheng, Liangtao; Yoo, Jae-Kwang; Guo, Huahu; Zhang, Yuanyuan; Guo, Xinyi; Kang, Boxi; Hu, Ruozhen; Huang, Julie Y; Zhang, Qiming; Liu, Zhouzerui; Dong, Minghui; Hu, Xueda; Ouyang, Wenjun; Peng, Jirun; Zhang, Zemin

    2017-06-15

    Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8 + T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8 + T cells and Tregs and represses the CD8 + T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Genetically induced cell death in bulge stem cells reveals their redundancy for hair and epidermal regeneration.

    Science.gov (United States)

    Driskell, Iwona; Oeztuerk-Winder, Feride; Humphreys, Peter; Frye, Michaela

    2015-03-01

    Adult mammalian epidermis contains multiple stem cell populations in which quiescent and more proliferative stem and progenitor populations coexist. However, the precise interrelation of these populations in homeostasis remains unclear. Here, we blocked the contribution of quiescent keratin 19 (K19)-expressing bulge stem cells to hair follicle formation through genetic ablation of the essential histone methyltransferase Setd8 that is required for the maintenance of adult skin. Deletion of Setd8 eliminated the contribution of bulge cells to hair follicle regeneration through inhibition of cell division and induction of cell death, but the growth and morphology of hair follicles were unaffected. Furthermore, ablation of Setd8 in the hair follicle bulge blocked the contribution of K19-postive stem cells to wounded epidermis, but the wound healing process was unaltered. Our data indicate that quiescent bulge stem cells are dispensable for hair follicle regeneration and epidermal injury in the short term and support the hypothesis that quiescent and cycling stem cell populations are equipotent. © 2014 AlphaMed Press.

  13. Surface-enhanced Raman scattering reveals adsorption of mitoxantrone on plasma membrane of living cells

    International Nuclear Information System (INIS)

    Breuzard, G.; Angiboust, J.-F.; Jeannesson, P.; Manfait, M.; Millot, J.-M.

    2004-01-01

    Surface-enhanced Raman scattering (SERS) spectroscopy was applied to analyze mitoxantrone (MTX) adsorption on the plasma membrane microenvironment of sensitive (HCT-116 S) or BCRP/MXR-type resistant (HCT-116 R) cells. The addition of silver colloid to MTX-treated cells revealed an enhanced Raman scattering of MTX. Addition of extracellular DNA induced a total extinction of MTX Raman intensity for both cell lines, which revealed an adsorption of MTX on plasma membrane. A threefold higher MTX Raman intensity was observed for HCT-116 R, suggesting a tight MTX adsorption in the plasma membrane microenvironment. Fluorescence confocal microscopy confirmed a relative MTX emission around plasma membrane for HCT-116 R. After 30 min at 4 deg. C, a threefold decrease of the MTX Raman scattering was observed for HCT-116 R, contrary to HCT-116 S. Permeation with benzyl alcohol revealed a threefold decrease of membrane MTX adsorption on HCT-116 R, exclusively. This additional MTX adsorption should correspond to the drug bound to an unstable site on the HCT-116 R membrane. This study showed that SERS spectroscopy could be a direct method to reveal drug adsorption to the membrane environment of living cells

  14. Survey reveals public open to ban on hand-held cell phone use and texting.

    Science.gov (United States)

    2013-01-01

    A study performed by the Bureau of Transportation Statistics (BTS) reveals that the public is open to a ban on hand-held cell phone use while driving. The study is based on data from 2009s Omnibus Household Survey (OHS), which is administered by B...

  15. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Resch, Michael G.; Donohoe, Byron; Ciesielski, Peter; Nill, Jennifer; McKinney, Kellene; Mittal, Ashutosh; Katahira, Rui; Himmel, Michael; Biddy, Mary; Beckham, Gregg; Decker, Steve

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution.

  16. Sorption of metaldehyde using granular activated carbon

    Directory of Open Access Journals (Sweden)

    S. Salvestrini

    2017-09-01

    Full Text Available In this work, the ability of granular activated carbon (GAC to sorb metaldehyde was evaluated. The kinetic data could be described by an intra-particle diffusion model, which indicated that the porosity of the sorbent strongly influenced the rate of sorption. The analysis of the equilibrium sorption data revealed that ionic strength and temperature did not play any significant role in the metaldehyde uptake. The sorption isotherms were successfully predicted by the Freundlich model. The GAC used in this paper exhibited a higher affinity and sorption capacity for metaldehyde with respect to other GACs studied in previous works, probably as a result of its higher specific surface area and high point of zero charge.

  17. NMRI Measurements of Flow of Granular Mixtures

    Science.gov (United States)

    Nakagawa, Masami; Waggoner, R. Allen; Fukushima, Eiichi

    1996-01-01

    We investigate complex 3D behavior of granular mixtures in shaking and shearing devices. NMRI can non-invasively measure concentration, velocity, and velocity fluctuations of flows of suitable particles. We investigate origins of wall-shear induced convection flow of single component particles by measuring the flow and fluctuating motion of particles near rough boundaries. We also investigate if a mixture of different size particles segregate into their own species under the influence of external shaking and shearing disturbances. These non-invasive measurements will reveal true nature of convecting flow properties and wall disturbance. For experiments in a reduced gravity environment, we will design a light weight NMR imager. The proof of principle development will prepare for the construction of a complete spaceborne system to perform experiments in space.

  18. Bubbling in vibrated granular films.

    Science.gov (United States)

    Zamankhan, Piroz

    2011-02-01

    With the help of experiments, computer simulations, and a theoretical investigation, a general model is developed of the flow dynamics of dense granular media immersed in air in an intermediate regime where both collisional and frictional interactions may affect the flow behavior. The model is tested using the example of a system in which bubbles and solid structures are produced in granular films shaken vertically. Both experiments and large-scale, three-dimensional simulations of this system are performed. The experimental results are compared with the results of the simulation to verify the validity of the model. The data indicate evidence of formation of bubbles when peak acceleration relative to gravity exceeds a critical value Γ(b). The air-grain interfaces of bubblelike structures are found to exhibit fractal structure with dimension D=1.7±0.05.

  19. Single-cell analysis reveals a link between CD3- and CD59-mediated signaling pathways in Jurkat T cells

    International Nuclear Information System (INIS)

    Lipp, A. M.

    2012-01-01

    Elevation of intracellular free calcium concentration ([Ca2+]i) is a key signal during T cell activation and is commonly used as a read-out parameter for stimulation of T cell signaling. Upon T cell stimulation a variety of calcium signals is produced by individual cells of the T cell population and the type of calcium signal strongly influences cell fate decisions. The heterogeneous nature of T cells is masked in ensemble measurements, which highlights the need for single-cell measurements. In this study we used single-cell calcium measurements in Jurkat cells to investigate signaling pathways, which are triggered by different proteins, namely CD3 and CD59. By application of an automated cluster algorithm the presented assay provides unbiased analysis of a large data set of individual calcium time traces generated by the whole cell population. By using this method we could demonstrate that the Jurkat population generates heterogeneous calcium signals in a stimulus-dependent manner. Furthermore, our data revealed the existence of a link between CD3- and CD59-mediated signaling pathways. Single-cell calcium measurements in Jurkat cells expressing different levels of the T cell receptor (TCR) complex indicated that CD59-mediated calcium signaling is critically dependent on TCR surface expression levels. In addition, triggering CD59-mediated calcium signaling resulted in down-regulation of TCR surface expression levels, which is known to happen upon direct TCR triggering too. Moreover, by using siRNA-mediated protein knock-downs and protein knock-out Jurkat mutants we could show that CD3- and CD59-mediated calcium signaling require identical key proteins. We therefore explored by which mechanism CD59-mediated signaling couples into TCR-mediated signaling. Fluorescence recovery after photobleaching (FRAP) experiments and live-cell protein-protein interaction assays provided no evidence of a direct physical interaction between CD3- and CD59-mediated signaling pathways

  20. Strain localisation in granular media

    OpenAIRE

    Desrues , Jacques

    1984-01-01

    This study is devoted to strain localisation in Granular materials. Both experimental and theoretical results have been obtained.The first part of the thesis is a review of the methods and theories about rupture in sols mechanics and more generally, in solid mechanics. The classical framework of Shear Band analysis is presented, and the main results available for different classes of materials are discussed.The second part describes an experimental study of strain localisation in sand specime...

  1. Robophysical study of jumping dynamics on granular media

    Science.gov (United States)

    Aguilar, Jeffrey; Goldman, Daniel I.

    2016-03-01

    Characterizing forces on deformable objects intruding into sand and soil requires understanding the solid- and fluid-like responses of such substrates and their effect on the state of the object. The most detailed studies of intrusion in dry granular media have revealed that interactions of fixed-shape objects during free impact (for example, cannonballs) and forced slow penetration can be described by hydrostatic- and hydrodynamic-like forces. Here we investigate a new class of granular interactions: rapid intrusions by objects that change shape (self-deform) through passive and active means. Systematic studies of a simple spring-mass robot jumping on dry granular media reveal that jumping performance is explained by an interplay of nonlinear frictional and hydrodynamic drag as well as induced added mass (unaccounted by traditional intrusion models) characterized by a rapidly solidified region of grains accelerated by the foot. A model incorporating these dynamics reveals that added mass degrades the performance of certain self-deformations owing to a shift in optimal timing during push-off. Our systematic robophysical experiment reveals both new soft-matter physics and principles for robotic self-deformation and control, which together provide principles of movement in deformable terrestrial environments.

  2. Pneumatic fractures in Confined Granular Media

    Science.gov (United States)

    Eriksen, Fredrik K.; Toussaint, Renaud; Jørgen Måløy, Knut; Grude Flekkøy, Eirik; Turkaya, Semih

    2016-04-01

    We will present our ongoing study of the patterns formed when air flows into a dry, non-cohesive porous medium confined in a horizontal Hele-Shaw cell. This is an optically transparent system consisting of two glass plates separated by 0.5 to 1 mm, containing a packing of dry 80 micron beads in between. The cell is rectangular and has an air-permeable boundary (blocking beads) at one short edge, while the other three edges are completely sealed. The granular medium is loosely packed against the semi-permeable boundary and fills about 80 % of the cell volume. This leaves an empty region at the sealed side, where an inlet allows us to set and maintain the air at a constant overpressure (0.1 - 2 bar). For the air trapped inside the cell to relax its overpressure it has to move through the deformable granular medium. Depending on the applied overpressure and initial density of the medium, we observe a range of different behaviors such as seepage through the pore-network with or without an initial compaction of the solid, formation of low density bubbles with rearrangement of particles, granular fingering/fracturing, and erosion inside formed channels/fractures. The experiments are recorded with a high-speed camera at a framerate of 1000 images/s and a resolution of 1024x1024 pixels. We use various image processing techniques to characterize the evolution of the air invasion patterns and the deformations in the surrounding material. The experiments are similar to deformation processes in porous media which are driven by pore fluid overpressure, such as mud volcanoes and hydraulic or pneumatic (gas-induced) fracturing, and the motivation is to increase the understanding of such processes by optical observations. In addition, this setup is an experimental version of the numerical models analyzed by Niebling et al. [1,2], and is useful for comparison with their results. In a directly related project [3], acoustic emissions from the cell plate are recorded during

  3. Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

    Directory of Open Access Journals (Sweden)

    Dmitri Papatsenko

    2015-08-01

    Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

  4. Granular nanocrystalline zirconia electrolyte layers deposited on porous SOFC cathode substrates

    International Nuclear Information System (INIS)

    Seydel, Johannes; Becker, Michael; Ivers-Tiffee, Ellen; Hahn, Horst

    2009-01-01

    Thin granular yttria-stabilized zirconia (YSZ) electrolyte layers were prepared by chemical vapor synthesis and deposition (CVD/CVS) on a porous substoichiometric lanthanum-strontium-manganite (ULSM) solid oxide fuel cell cathode substrate. The substrate porosity was optimized with a screen printed fine porous buffer layer. Structural analysis by scanning electron microscopy showed a homogeneous, granular nanocrystalline layer with a microstructure that was controlled via reactor settings. The CVD/CVS gas-phase process enabled the deposition of crack-free granular YSZ films on porous ULSM substrates. The electrolyte layers characterized with impedance spectroscopy exhibited enhanced grain boundary conductivity.

  5. The Molecular Architecture of Cell Adhesion: Dynamic Remodeling Revealed by Videonanoscopy

    Directory of Open Access Journals (Sweden)

    Arnauld eSergé

    2016-05-01

    Full Text Available The plasma membrane delimits the cell, which is the basic unit of living organisms, and is also a privileged site for cell communication with the environment. Cell adhesion can occur through cell-cell and cell-matrix contacts. Adhesion proteins such as integrins and cadherins also constitute receptors for inside-out and outside-in signaling within proteolipidic platforms. Adhesion molecule targeting and stabilization relies on specific features such as preferential segregation by the sub-membrane cytoskeleton meshwork and within membrane proteolipidic microdomains. This review presents an overview of the recent insights brought by the latest developments in microscopy, to unravel the molecular remodeling occurring at cell contacts. The dynamic aspect of cell adhesion was recently highlighted by super-resolution videomicroscopy, also named videonanoscopy. By circumventing the diffraction limit of light, nanoscopy has allowed the monitoring of molecular localization and behavior at the single-molecule level, on fixed and living cells. Accessing molecular-resolution details such as quantitatively monitoring components entering and leaving cell contacts by lateral diffusion and reversible association has revealed an unexpected plasticity. Adhesion structures can be highly specialized, such as focal adhesion in motile cells, as well as immune and neuronal synapses. Spatiotemporal reorganization of adhesion molecules, receptors and adaptors directly relates to structure/function modulation. Assembly of these supramolecular complexes is continuously balanced by dynamic events, remodeling adhesions on various timescales, notably by molecular conformation switches, lateral diffusion within the membrane and endo/exocytosis. Pathological alterations in cell adhesion are involved in cancer evolution, through cancer stem cell interaction with stromal niches, growth, extravasation and metastasis.

  6. Cell Wall Remodeling by a Synthetic Analog Reveals Metabolic Adaptation in Vancomycin Resistant Enterococci.

    Science.gov (United States)

    Pidgeon, Sean E; Pires, Marcos M

    2017-07-21

    Drug-resistant bacterial infections threaten to overburden our healthcare system and disrupt modern medicine. A large class of potent antibiotics, including vancomycin, operate by interfering with bacterial cell wall biosynthesis. Vancomycin-resistant enterococci (VRE) evade the blockage of cell wall biosynthesis by altering cell wall precursors, rendering them drug insensitive. Herein, we reveal the phenotypic plasticity and cell wall remodeling of VRE in response to vancomycin in live bacterial cells via a metabolic probe. A synthetic cell wall analog was designed and constructed to monitor cell wall structural alterations. Our results demonstrate that the biosynthetic pathway for vancomycin-resistant precursors can be hijacked by synthetic analogs to track the kinetics of phenotype induction. In addition, we leveraged this probe to interrogate the response of VRE cells to vancomycin analogs and a series of cell wall-targeted antibiotics. Finally, we describe a proof-of-principle strategy to visually inspect drug resistance induction. Based on our findings, we anticipate that our metabolic probe will play an important role in further elucidating the interplay among the enzymes involved in the VRE biosynthetic rewiring.

  7. An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development

    Science.gov (United States)

    Benitez, Cecil M.; Qu, Kun; Sugiyama, Takuya; Pauerstein, Philip T.; Liu, Yinghua; Tsai, Jennifer; Gu, Xueying; Ghodasara, Amar; Arda, H. Efsun; Zhang, Jiajing; Dekker, Joseph D.; Tucker, Haley O.; Chang, Howard Y.; Kim, Seung K.

    2014-01-01

    The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus. PMID:25330008

  8. An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.

    Directory of Open Access Journals (Sweden)

    Cecil M Benitez

    2014-10-01

    Full Text Available The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus.

  9. Impact Compaction of a Granular Material

    Science.gov (United States)

    Fenton, Gregg; Asay, Blaine; Todd, Steve; Grady, Dennis

    2017-06-01

    The dynamic behavior of granular materials has importance to a variety of engineering applications. Although, the mechanical behavior of granular materials have been studied extensively for several decades, the dynamic behavior of these materials remains poorly understood. High-quality experimental data are needed to improve our general understanding of granular material compaction physics. This paper describes how an instrumented plunger impact system can be used to measure the compaction process for granular materials at high and controlled strain rates and subsequently used for computational modelling. The experimental technique relies on a gas-gun driven plunger system to generate a compaction wave through a volume of granular material. This volume of material has been redundantly instrumented along the bed length to track the progression of the compaction wave, and the piston displacement is measured with Photon Doppler Velocimetry (PDV). Using the gathered experimental data along with the initial material tap density, a granular material equation of state can be determined.

  10. Quantitative Proteomics Reveals the Regulatory Networks of Circular RNA CDR1as in Hepatocellular Carcinoma Cells.

    Science.gov (United States)

    Yang, Xue; Xiong, Qian; Wu, Ying; Li, Siting; Ge, Feng

    2017-10-06

    Circular RNAs (circRNAs), a class of widespread endogenous RNAs, play crucial roles in diverse biological processes and are potential biomarkers in diverse human diseases and cancers. Cerebellar-degeneration-related protein 1 antisense RNA (CDR1as), an oncogenic circRNA, is involved in human tumorigenesis and is dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying CDR1as functions in HCC remain unclear. Here we explored the functions of CDR1as and searched for CDR1as-regulated proteins in HCC cells. A quantitative proteomics strategy was employed to globally identify CDR1as-regulated proteins in HCC cells. In total, we identified 330 differentially expressed proteins (DEPs) upon enhanced CDR1as expression in HepG2 cells, indicating that they could be proteins regulated by CDR1as. Bioinformatic analysis revealed that many DEPs were involved in cell proliferation and the cell cycle. Further functional studies of epidermal growth factor receptor (EGFR) found that CDR1as exerts its effects on cell proliferation at least in part through the regulation of EGFR expression. We further confirmed that CDR1as could inhibit the expression of microRNA-7 (miR-7). EGFR is a validated target of miR-7; therefore, CDR1as may exert its function by regulating EGFR expression via targeting miR-7 in HCC cells. Taken together, we revealed novel functions and underlying mechanisms of CDR1as in HCC cells. This study serves as the first proteome-wide analysis of a circRNA-regulated protein in cells and provides a reliable and highly efficient method for globally identifying circRNA-regulated proteins.

  11. In vivo fluorescence imaging reveals the promotion of mammary tumorigenesis by mesenchymal stromal cells.

    Directory of Open Access Journals (Sweden)

    Chien-Chih Ke

    Full Text Available Mesenchymal stromal cells (MSCs are multipotent adult stem cells which are recruited to the tumor microenvironment (TME and influence tumor progression through multiple mechanisms. In this study, we examined the effects of MSCs on the tunmorigenic capacity of 4T1 murine mammary cancer cells. It was found that MSC-conditioned medium increased the proliferation, migration, and efficiency of mammosphere formation of 4T1 cells in vitro. When co-injected with MSCs into the mouse mammary fat pad, 4T1 cells showed enhanced tumor growth and generated increased spontaneous lung metastasis. Using in vivo fluorescence color-coded imaging, the interaction between GFP-expressing MSCs and RFP-expressing 4T1 cells was monitored. As few as five 4T1 cells could give rise to tumor formation when co-injected with MSCs into the mouse mammary fat pad, but no tumor was formed when five or ten 4T1 cells were implanted alone. The elevation of tumorigenic potential was further supported by gene expression analysis, which showed that when 4T1 cells were in contact with MSCs, several oncogenes, cancer markers, and tumor promoters were upregulated. Moreover, in vivo longitudinal fluorescence imaging of tumorigenesis revealed that MSCs created a vascularized environment which enhances the ability of 4T1 cells to colonize and proliferate. In conclusion, this study demonstrates that the promotion of mammary cancer progression by MSCs was achieved through the generation of a cancer-enhancing microenvironment to increase tumorigenic potential. These findings also suggest the potential risk of enhancing tumor progression in clinical cell therapy using MSCs. Attention has to be paid to patients with high risk of breast cancer when considering cell therapy with MSCs.

  12. A Single-Cell Biochemistry Approach Reveals PAR Complex Dynamics during Cell Polarization.

    Science.gov (United States)

    Dickinson, Daniel J; Schwager, Francoise; Pintard, Lionel; Gotta, Monica; Goldstein, Bob

    2017-08-21

    Regulated protein-protein interactions are critical for cell signaling, differentiation, and development. For the study of dynamic regulation of protein interactions in vivo, there is a need for techniques that can yield time-resolved information and probe multiple protein binding partners simultaneously, using small amounts of starting material. Here we describe a single-cell protein interaction assay. Single-cell lysates are generated at defined time points and analyzed using single-molecule pull-down, yielding information about dynamic protein complex regulation in vivo. We established the utility of this approach by studying PAR polarity proteins, which mediate polarization of many animal cell types. We uncovered striking regulation of PAR complex composition and stoichiometry during Caenorhabditis elegans zygote polarization, which takes place in less than 20 min. PAR complex dynamics are linked to the cell cycle by Polo-like kinase 1 and govern the movement of PAR proteins to establish polarity. Our results demonstrate an approach to study dynamic biochemical events in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Cell metabolomics reveals the neurotoxicity mechanism of cadmium in PC12 cells.

    Science.gov (United States)

    Zong, Li; Xing, Junpeng; Liu, Shu; Liu, Zhiqiang; Song, Fengrui

    2018-01-01

    The heavy metals such as cadmium (Cd) can induce neurotoxicity. Extensive studies about the effects of Cd on human health have been reported, however, a systematic investigation on the molecular mechanisms of the effects of Cd on central nervous system is still needed. In this paper, the neuronal PC-12 cells were treated with a series of concentrations of CdCl 2 for 48h. Then the cytotoxicity was evaluated by MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. The IC 15 value (15% inhibiting concentration) was selected for further mechanism studies. After PC-12 cells incubated with CdCl 2 at a dose of IC 15 for 48h, the intracellular and extracellular metabolites were profiled using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS)-based cell metabolomics approach. As found, the effects of the heavy metal Cd produced on the PC-12 cell viability were dose-dependent. The metabolic changes were involved in the glycolysis and gluconeogenesis, biopterin metabolism, tryptophan metabolism, tyrosine metabolism, glycerophospholipid metabolism, and fatty acids beta-oxidation. These could cause the perturbation of cell membrane, redox balance, energy supply, cellular detoxification, further affecting the cellular proliferation and apoptosis and other cellular activities. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. RNAi screen reveals an Abl kinase-dependent host cell pathway involved in Pseudomonas aeruginosa internalization.

    Directory of Open Access Journals (Sweden)

    Julia F Pielage

    2008-03-01

    Full Text Available Internalization of the pathogenic bacterium Pseudomonas aeruginosa by non-phagocytic cells is promoted by rearrangements of the actin cytoskeleton, but the host pathways usurped by this bacterium are not clearly understood. We used RNAi-mediated gene inactivation of approximately 80 genes known to regulate the actin cytoskeleton in Drosophila S2 cells to identify host molecules essential for entry of P. aeruginosa. This work revealed Abl tyrosine kinase, the adaptor protein Crk, the small GTPases Rac1 and Cdc42, and p21-activated kinase as components of a host signaling pathway that leads to internalization of P. aeruginosa. Using a variety of complementary approaches, we validated the role of this pathway in mammalian cells. Remarkably, ExoS and ExoT, type III secreted toxins of P. aeruginosa, target this pathway by interfering with GTPase function and, in the case of ExoT, by abrogating P. aeruginosa-induced Abl-dependent Crk phosphorylation. Altogether, this work reveals that P. aeruginosa utilizes the Abl pathway for entering host cells and reveals unexpected complexity by which the P. aeruginosa type III secretion system modulates this internalization pathway. Our results furthermore demonstrate the applicability of using RNAi screens to identify host signaling cascades usurped by microbial pathogens that may be potential targets for novel therapies directed against treatment of antibiotic-resistant infections.

  15. Nonlinear optical microscopy reveals invading endothelial cells anisotropically alter three-dimensional collagen matrices

    International Nuclear Information System (INIS)

    Lee, P.-F.; Yeh, Alvin T.; Bayless, Kayla J.

    2009-01-01

    The interactions between endothelial cells (ECs) and the extracellular matrix (ECM) are fundamental in mediating various steps of angiogenesis, including cell adhesion, migration and sprout formation. Here, we used a noninvasive and non-destructive nonlinear optical microscopy (NLOM) technique to optically image endothelial sprouting morphogenesis in three-dimensional (3D) collagen matrices. We simultaneously captured signals from collagen fibers and endothelial cells using second harmonic generation (SHG) and two-photon excited fluorescence (TPF), respectively. Dynamic 3D imaging revealed EC interactions with collagen fibers along with quantifiable alterations in collagen matrix density elicited by EC movement through and morphogenesis within the matrix. Specifically, we observed increased collagen density in the area between bifurcation points of sprouting structures and anisotropic increases in collagen density around the perimeter of lumenal structures, but not advancing sprout tips. Proteinase inhibition studies revealed membrane-associated matrix metalloproteinase were utilized for sprout advancement and lumen expansion. Rho-associated kinase (p160ROCK) inhibition demonstrated that the generation of cell tension increased collagen matrix alterations. This study followed sprouting ECs within a 3D matrix and revealed that the advancing structures recognize and significantly alter their extracellular environment at the periphery of lumens as they progress

  16. Granular packing as model glass formers

    International Nuclear Information System (INIS)

    Wang Yujie

    2017-01-01

    Static granular packings are model hard-sphere glass formers. The nature of glass transition has remained a hotly debated issue. We review recent experimental progresses in using granular materials to study glass transitions. We focus on the growth of glass order with five-fold symmetry in granular packings and relate the findings to both geometric frustration and random first-order phase transition theories. (paper)

  17. Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells.

    Science.gov (United States)

    Breuer, Rebecca J; Bandyopadhyay, Arpan; O'Brien, Sofie A; Barnes, Aaron M T; Hunter, Ryan C; Hu, Wei-Shou; Dunny, Gary M

    2017-07-01

    In Enterococcus faecalis, sex pheromone-mediated transfer of antibiotic resistance plasmids can occur under unfavorable conditions, for example, when inducing pheromone concentrations are low and inhibiting pheromone concentrations are high. To better understand this paradox, we adapted fluorescence in situ hybridization chain reaction (HCR) methodology for simultaneous quantification of multiple E. faecalis transcripts at the single cell level. We present direct evidence for variability in the minimum period, maximum response level, and duration of response of individual cells to a specific inducing condition. Tracking of induction patterns of single cells temporally using a fluorescent reporter supported HCR findings. It also revealed subpopulations of rapid responders, even under low inducing pheromone concentrations where the overall response of the entire population was slow. The strong, rapid induction of small numbers of cells in cultures exposed to low pheromone concentrations is in agreement with predictions of a stochastic model of the enterococcal pheromone response. The previously documented complex regulatory circuitry controlling the pheromone response likely contributes to stochastic variation in this system. In addition to increasing our basic understanding of the biology of a horizontal gene transfer system regulated by cell-cell signaling, demonstration of the stochastic nature of the pheromone response also impacts any future efforts to develop therapeutic agents targeting the system. Quantitative single cell analysis using HCR also has great potential to elucidate important bacterial regulatory mechanisms not previously amenable to study at the single cell level, and to accelerate the pace of functional genomic studies.

  18. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

    Science.gov (United States)

    Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

    2017-03-03

    Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6  cells/mm 3 . Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

  19. Stem cell-like differentiation potentials of endometrial side population cells as revealed by a newly developed in vivo endometrial stem cell assay.

    Directory of Open Access Journals (Sweden)

    Kaoru Miyazaki

    Full Text Available Endometrial stem/progenitor cells contribute to the cyclical regeneration of human endometrium throughout a woman's reproductive life. Although the candidate cell populations have been extensively studied, no consensus exists regarding which endometrial population represents the stem/progenitor cell fraction in terms of in vivo stem cell activity. We have previously reported that human endometrial side population cells (ESP, but not endometrial main population cells (EMP, exhibit stem cell-like properties, including in vivo reconstitution of endometrium-like tissues when xenotransplanted into immunodeficient mice. The reconstitution efficiency, however, was low presumably because ESP cells alone could not provide a sufficient microenvironment (niche to support their stem cell activity. The objective of this study was to establish a novel in vivo endometrial stem cell assay employing cell tracking and tissue reconstitution systems and to examine the stem cell properties of ESP through use of this assay.ESP and EMP cells isolated from whole endometrial cells were infected with lentivirus to express tandem Tomato (TdTom, a red fluorescent protein. They were mixed with unlabeled whole endometrial cells and then transplanted under the kidney capsule of ovariectomized immunodeficient mice. These mice were treated with estradiol and progesterone for eight weeks and nephrectomized. All of the grafts reconstituted endometrium-like tissues under the kidney capsules. Immunofluorescence revealed that TdTom-positive cells were significantly more abundant in the glandular, stromal, and endothelial cells of the reconstituted endometrium in mice transplanted with TdTom-labeled ESP cells than those with TdTom-labeled EMP cells.We have established a novel in vivo endometrial stem cell assay in which multi-potential differentiation can be identified through cell tracking during in vivo endometrial tissue reconstitution. Using this assay, we demonstrated that ESP

  20. Biofilm growth program and architecture revealed by single-cell live imaging

    Science.gov (United States)

    Yan, Jing; Sabass, Benedikt; Stone, Howard; Wingreen, Ned; Bassler, Bonnie

    Biofilms are surface-associated bacterial communities. Little is known about biofilm structure at the level of individual cells. We image living, growing Vibrio cholerae biofilms from founder cells to ten thousand cells at single-cell resolution, and discover the forces underpinning the architectural evolution of the biofilm. Mutagenesis, matrix labeling, and simulations demonstrate that surface-adhesion-mediated compression causes V. cholerae biofilms to transition from a two-dimensional branched morphology to a dense, ordered three-dimensional cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture, and this growth pattern is controlled by a single gene. Competition analyses reveal the advantages of the dense growth mode in providing the biofilm with superior mechanical properties. We will further present continuum theory to model the three-dimensional growth of biofilms at the solid-liquid interface as well as solid-air interface.

  1. Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination

    OpenAIRE

    Li, Xi; Miao, Hongyu; Henn, Alicia; Topham, David J.; Wu, Hulin; Zand, Martin S.; Mosmann, Tim R.

    2012-01-01

    Although previous studies have found minimal changes in CD4 T cell responses after vaccination of adults with trivalent inactivated influenza vaccine, daily sampling and monitoring of the proliferation marker Ki-67 have now been used to reveal that a substantial fraction of influenza-specific CD4 T cells respond to vaccination. At 4–6 days after vaccination, there is a sharp rise in the numbers of Ki-67-expressing PBMC that produce IFNγ, IL-2 and/or TNFα in vitro in response to influenza vacc...

  2. Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells

    DEFF Research Database (Denmark)

    Pines, Alex; Kelstrup, Christian D; Vrouwe, Mischa G

    2011-01-01

    (stable isotope labeling by amino acids in cell culture)-labeled murine embryonic stem cells with the anticancer drug cisplatin. Network and pathway analyses indicated that processes related to the DNA damage response and cytoskeleton organization were significantly affected. Although the ATM (ataxia...... rearrangements. Integration of transcriptomic and proteomic data revealed a poor correlation between changes in the relative levels of transcripts and their corresponding proteins, but a large overlap in affected pathways at the levels of mRNA, protein, and phosphoprotein. This study provides an integrated view...

  3. Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells

    DEFF Research Database (Denmark)

    Hattori, Naoko; Niwa, Tohru; Kimura, Kana

    2013-01-01

    . Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell......Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which...... population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination...

  4. Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation.

    Science.gov (United States)

    Yu, Bingfei; Zhang, Kai; Milner, J Justin; Toma, Clara; Chen, Runqiang; Scott-Browne, James P; Pereira, Renata M; Crotty, Shane; Chang, John T; Pipkin, Matthew E; Wang, Wei; Goldrath, Ananda W

    2017-05-01

    Dynamic changes in the expression of transcription factors (TFs) can influence the specification of distinct CD8 + T cell fates, but the observation of equivalent expression of TFs among differentially fated precursor cells suggests additional underlying mechanisms. Here we profiled the genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8 + T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that the expression and binding of TFs contributed to the establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal key TFs that influence the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8 + T cell differentiation, regulated the formation of terminal-effector cell fates and memory-precursor cell fates, respectively. Our data define the epigenetic landscape of differentiation intermediates and facilitate the identification of TFs with previously unappreciated roles in CD8 + T cell differentiation.

  5. Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination.

    Science.gov (United States)

    Li, Xi; Miao, Hongyu; Henn, Alicia; Topham, David J; Wu, Hulin; Zand, Martin S; Mosmann, Tim R

    2012-06-29

    Although previous studies have found minimal changes in CD4 T cell responses after vaccination of adults with trivalent inactivated influenza vaccine, daily sampling and monitoring of the proliferation marker Ki-67 have now been used to reveal that a substantial fraction of influenza-specific CD4 T cells respond to vaccination. At 4-6 days after vaccination, there is a sharp rise in the numbers of Ki-67-expressing PBMC that produce IFNγ, IL-2 and/or TNFα in vitro in response to influenza vaccine or peptide. Ki-67(+) cell numbers then decline rapidly, and 10 days after vaccination, both Ki-67(+) and overall influenza-specific cell numbers are similar to pre-vaccination levels. These results provide a tool for assessing the quality and quantity of CD4 T cell responses to different influenza vaccines, and raise the possibility that the anti-influenza T cell memory response may be qualitatively altered by vaccination, even if the overall memory cell numbers do not change significantly. Copyright © 2012. Published by Elsevier Ltd.

  6. Quantitative proteomics reveals middle infrared radiation-interfered networks in breast cancer cells.

    Science.gov (United States)

    Chang, Hsin-Yi; Li, Ming-Hua; Huang, Tsui-Chin; Hsu, Chia-Lang; Tsai, Shang-Ru; Lee, Si-Chen; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2015-02-06

    Breast cancer is one of the leading cancer-related causes of death worldwide. Treatment of triple-negative breast cancer (TNBC) is complex and challenging, especially when metastasis has developed. In this study, we applied infrared radiation as an alternative approach for the treatment of TNBC. We used middle infrared (MIR) with a wavelength range of 3-5 μm to irradiate breast cancer cells. MIR significantly inhibited cell proliferation in several breast cancer cells but did not affect the growth of normal breast epithelial cells. We performed iTRAQ-coupled LC-MS/MS analysis to investigate the MIR-triggered molecular mechanisms in breast cancer cells. A total of 1749 proteins were identified, quantified, and subjected to functional enrichment analysis. From the constructed functionally enriched network, we confirmed that MIR caused G2/M cell cycle arrest, remodeled the microtubule network to an astral pole arrangement, altered the actin filament formation and focal adhesion molecule localization, and reduced cell migration activity and invasion ability. Our results reveal the coordinative effects of MIR-regulated physiological responses in concentrated networks, demonstrating the potential implementation of infrared radiation in breast cancer therapy.

  7. Chick embryo xenograft model reveals a novel perineural niche for human adipose-derived stromal cells

    Directory of Open Access Journals (Sweden)

    Ingrid R. Cordeiro

    2015-09-01

    Full Text Available Human adipose-derived stromal cells (hADSC are a heterogeneous cell population that contains adult multipotent stem cells. Although it is well established that hADSC have skeletal potential in vivo in adult organisms, in vitro assays suggest further differentiation capacity, such as into glia. Thus, we propose that grafting hADSC into the embryo can provide them with a much more instructive microenvironment, allowing the human cells to adopt diverse fates or niches. Here, hADSC spheroids were grafted into either the presumptive presomitic mesoderm or the first branchial arch (BA1 regions of chick embryos. Cells were identified without previous manipulations via human-specific Alu probes, which allows efficient long-term tracing of heterogeneous primary cultures. When grafted into the trunk, in contrast to previous studies, hADSC were not found in chondrogenic or osteogenic territories up to E8. Surprisingly, 82.5% of the hADSC were associated with HNK1+ tissues, such as peripheral nerves. Human skin fibroblasts showed a smaller tropism for nerves. In line with other studies, hADSC also adopted perivascular locations. When grafted into the presumptive BA1, 74.6% of the cells were in the outflow tract, the final goal of cardiac neural crest cells, and were also associated with peripheral nerves. This is the first study showing that hADSC could adopt a perineural niche in vivo and were able to recognize cues for neural crest cell migration of the host. Therefore, we propose that xenografts of human cells into chick embryos can reveal novel behaviors of heterogeneous cell populations, such as response to migration cues.

  8. Single cell amperometry reveals curcuminoids modulate the release of neurotransmitters during exocytosis from PC12 cells

    Science.gov (United States)

    Li, Xianchan; Mohammadi, Amir Saeid; Ewing, Andrew G.

    2016-01-01

    We used single cell amperometry to examine whether curcumin and bisdemethoxycurcumin (BDMC), substances that are suggested to affect learning and memory, can modulate monoamine release from PC12 cells. Our results indicate both curcumin and BDMC need long-term treatment (72 h in this study) to influence exocytosis effectively. By analyzing the parameters calculated from single exocytosis events, it can be concluded that curcumin and BDMC affect exocytosis through different mechanisms. Curcumin accelerates the event dynamics with no significant change of the monoamine amount released from single exocytotic events, whereas BDMC attenuates the amount from single exocytotic event with no significant change of the event dynamics. This comparison of the effect of curcumin and BDMC on exocytosis at the single cell level brings insight into their different mechanisms, which might lead to different biological actions. The effect of curcumin and BDMC on the opening and closing of the exocytotic fusion pore were also investigated. These results might be helpful for understanding the improvement of learning and memory and the anti-depression properties of curcuminoids. PMID:28579928

  9. Single-cell tracking reveals antibiotic-induced changes in mycobacterial energy metabolism.

    Science.gov (United States)

    Maglica, Željka; Özdemir, Emre; McKinney, John D

    2015-02-17

    ATP is a key molecule of cell physiology, but despite its importance, there are currently no methods for monitoring single-cell ATP fluctuations in live bacteria. This is a major obstacle in studies of bacterial energy metabolism, because there is a growing awareness that bacteria respond to stressors such as antibiotics in a highly individualistic manner. Here, we present a method for long-term single-cell tracking of ATP levels in Mycobacterium smegmatis based on a combination of microfluidics, time-lapse microscopy, and Förster resonance energy transfer (FRET)-based ATP biosensors. Upon treating cells with antibiotics, we observed that individual cells undergo an abrupt and irreversible switch from high to low intracellular ATP levels. The kinetics and extent of ATP switching clearly discriminate between an inhibitor of ATP synthesis and other classes of antibiotics. Cells that resume growth after 24 h of antibiotic treatment maintain high ATP levels throughout the exposure period. In contrast, antibiotic-treated cells that switch from ATP-high to ATP-low states never resume growth after antibiotic washout. Surprisingly, only a subset of these nongrowing ATP-low cells stains with propidium iodide (PI), a widely used live/dead cell marker. These experiments also reveal a cryptic subset of cells that do not resume growth after antibiotic washout despite remaining ATP high and PI negative. We conclude that ATP tracking is a more dynamic, sensitive, reliable, and discriminating marker of cell viability than staining with PI. This method could be used in studies to evaluate antimicrobial effectiveness and mechanism of action, as well as for high-throughput screening. New antimicrobials are urgently needed to stem the rising tide of antibiotic-resistant bacteria. All antibiotics are expected to affect bacterial energy metabolism, directly or indirectly, yet tools to assess the impact of antibiotics on the ATP content of individual bacterial cells are lacking. The

  10. Dynamics of crater formations in immersed granular materials

    Science.gov (United States)

    Varas, G.; Vidal, V.; Géminard, J.

    2009-12-01

    Craters are part of the widespread phenomena observed in nature. Among the main applications to natural phenomena, aside from meteorite impact craters, are the formation and growth of volcanic edifices, by successive ejecta emplacement and/or erosion. The time evolution and dynamics play a crucial role here, as the competition between volcanic-jet mass-flux (degassing and ejecta) and crater-size evolution may control directly the eruptive regime. Crater morphology in dry granular material has been extensively studied, both experimentally and theoretically. Most of these studies investigate the final, steady crater shape resulting from the collision of solid bodies with the material surface and scaling laws are derived. In immersed granular material, craters generated by an underwater vortex ring, or underwater impact craters generated by landslide, have been reported. In a previous experimental study, Gostiaux et al. [Gran. Matt., 2002] have investigated the dynamics of air flowing through an immersed granular layer. They reported that, depending on the flow rate, the system exhibits two qualitatively different regimes: At small flow rate, the bubbling regime during which bubbles escape the granular layer independently one from another; At large flow rate, the open-channel regime which corresponds to the formation of a channel crossing the whole thickness of the granular bed through which air escapes almost continuously. At intermediate flow rate, a spontaneous alternation between these two regimes is observed. Here, we report the dynamics of crater formations at the free surface of an immersed granular bed, locally crossed by an ascending gas flow. We reproduce the experimental conditions of Gostiaux et al. (2002) in two dimensions: In a vertical Hele-Shaw cell, the crater consists of two sand piles which develop around the location of the gas emission. We observe that the typical size of the crater increases logarithmically with time, independently of the gas

  11. Modeling chronic myeloid leukemia in immunodeficient mice reveals expansion of aberrant mast cells and accumulation of pre-B cells

    International Nuclear Information System (INIS)

    Askmyr, M; Ågerstam, H; Lilljebjörn, H; Hansen, N; Karlsson, C; Palffy, S von; Landberg, N; Högberg, C; Lassen, C; Rissler, M; Richter, J; Ehinger, M; Järås, M; Fioretos, T

    2014-01-01

    Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm that, if not treated, will progress into blast crisis (BC) of either myeloid or B lymphoid phenotype. The BCR-ABL1 fusion gene, encoding a constitutively active tyrosine kinase, is thought to be sufficient to cause chronic phase (CP) CML, whereas additional genetic lesions are needed for progression into CML BC. To generate a humanized CML model, we retrovirally expressed BCR-ABL1 in the cord blood CD34 + cells and transplanted these into NOD-SCID (non-obese diabetic/severe-combined immunodeficient) interleukin-2-receptor γ-deficient mice. In primary mice, BCR-ABL1 expression induced an inflammatory-like state in the bone marrow and spleen, and mast cells were the only myeloid lineage specifically expanded by BCR-ABL1. Upon secondary transplantation, the pronounced inflammatory phenotype was lost and mainly human mast cells and macrophages were found in the bone marrow. Moreover, a striking block at the pre-B-cell stage was observed in primary mice, resulting in an accumulation of pre-B cells. A similar block in B-cell differentiation could be confirmed in primary cells from CML patients. Hence, this humanized mouse model of CML reveals previously unexplored features of CP CML and should be useful for further studies to understand the disease pathogenesis of CML

  12. Confocal Microscopy of Jammed Matter: From Elasticity to Granular Thermodynamics

    Science.gov (United States)

    Jorjadze, Ivane

    Packings of particles are ubiquitous in nature and are of interest not only to the scientific community but also to the food, pharmaceutical, and oil industries. In this thesis we use confocal microscopy to investigate packing geometry and stress transmission in 3D jammed particulate systems. By introducing weak depletion attraction we probe the accessible phase-space and demonstrate that a microscopic approach to jammed matter gives validity to statistical mechanics framework, which is intriguing because our particles are not thermally activated. We show that the fluctuations of the local packing parameters can be successfully captured by the recently proposed 'granocentric' model, which generates packing statistics according to simple stochastic processes. This model enables us to calculate packing entropy and granular temperature, the so-called 'compactivity', therefore, providing a basis for a statistical mechanics of granular matter. At a jamming transition point at which there are formed just enough number of contacts to guarantee the mechanical stability, theoretical arguments suggest a singularity which gives rise to the surprising scaling behavior of the elastic moduli and the microstructure, as observed in numerical simulations. Since the contact network in 3D is typically hidden from view, experimental test of the scaling law between the coordination number and the applied pressure is lacking in the literature. Our data show corrections to the linear scaling of the pressure with density which takes into account the creation of contacts. Numerical studies of vibrational spectra, in turn, reveal sudden features such as excess of low frequency modes, dependence of mode localization and structure on the pressure. Chapter four describes the first calculation of vibrational density of states from the experimental 3D data and is in qualitative agreement with the analogous computer simulations. We study the configurational role of the pressure and demonstrate

  13. The Granular Blasius Problem: High inertial number granular flows

    Science.gov (United States)

    Tsang, Jonathan; Dalziel, Stuart; Vriend, Nathalie

    2017-11-01

    The classical Blasius problem considers the formation of a boundary layer through the change at x = 0 from a free-slip to a no-slip boundary beneath an otherwise steady uniform flow. Discrete particle model (DPM) simulations of granular gravity currents show that a similar phenomenon exists for a steady flow over a uniformly sloped surface that is smooth upstream (allowing slip) but rough downstream (imposing a no-slip condition). The boundary layer is a region of high shear rate and therefore high inertial number I; its dynamics are governed by the asymptotic behaviour of the granular rheology as I -> ∞ . The μ(I) rheology asserts that dμ / dI = O(1 /I2) as I -> ∞ , but current experimental evidence is insufficient to confirm this. We show that `generalised μ(I) rheologies', with different behaviours as I -> ∞ , all permit the formation of a boundary layer. We give approximate solutions for the velocity profile under each rheology. The change in boundary condition considered here mimics more complex topography in which shear stress increases in the streamwise direction (e.g. a curved slope). Such a system would be of interest in avalanche modelling. EPSRC studentship (Tsang) and Royal Society Dorothy Hodgkin Fellowship (Vriend).

  14. Theoretical model of granular compaction

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E. [Los Alamos National Lab., NM (United States); Knight, J.B. [Princeton Univ., NJ (United States). Dept. of Physics; Nowak, E.R. [Univ. of Illinois, Urbana, IL (United States). Dept. of Physics]|[Univ. of Chicago, IL (United States). James Franck Inst.; Jaeger, H.M.; Nagel, S.R. [Univ. of Chicago, IL (United States). James Franck Inst.

    1997-11-01

    Experimental studies show that the density of a vibrated granular material evolves from a low density initial state into a higher density final steady state. The relaxation towards the final density follows an inverse logarithmic law. As the system approaches its final state, a growing number of beads have to be rearranged to enable a local density increase. A free volume argument shows that this number grows as N = {rho}/(1 {minus} {rho}). The time scale associated with such events increases exponentially e{sup {minus}N}, and as a result a logarithmically slow approach to the final state is found {rho} {infinity} {minus}{rho}(t) {approx_equal} 1/lnt.

  15. Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation.

    Directory of Open Access Journals (Sweden)

    Hongkai Ji

    Full Text Available The functions of key oncogenic transcription factors independent of context have not been fully delineated despite our richer understanding of the genetic alterations in human cancers. The MYC oncogene, which produces the Myc transcription factor, is frequently altered in human cancer and is a major regulatory hub for many cancers. In this regard, we sought to unravel the primordial signature of Myc function by using high-throughput genomic approaches to identify the cell-type independent core Myc target gene signature. Using a model of human B lymphoma cells bearing inducible MYC, we identified a stringent set of direct Myc target genes via chromatin immunoprecipitation (ChIP, global nuclear run-on assay, and changes in mRNA levels. We also identified direct Myc targets in human embryonic stem cells (ESCs. We further document that a Myc core signature (MCS set of target genes is shared in mouse and human ESCs as well as in four other human cancer cell types. Remarkably, the expression of the MCS correlates with MYC expression in a cell-type independent manner across 8,129 microarray samples, which include 312 cell and tissue types. Furthermore, the expression of the MCS is elevated in vivo in Eμ-Myc transgenic murine lymphoma cells as compared with premalignant or normal B lymphocytes. Expression of the MCS in human B cell lymphomas, acute leukemia, lung cancers or Ewing sarcomas has the highest correlation with MYC expression. Annotation of this gene signature reveals Myc's primordial function in RNA processing, ribosome biogenesis and biomass accumulation as its key roles in cancer and stem cells.

  16. Epigenetic landscapes reveal transcription factors regulating CD8+ T cell differentiation

    Science.gov (United States)

    Yu, Bingfei; Zhang, Kai; Milner, J. Justin; Toma, Clara; Chen, Runqiang; Scott-Browne, James P.; Pereira, Renata M.; Crotty, Shane; Chang, John T.; Pipkin, Matthew E.; Wang, Wei; Goldrath, Ananda W.

    2017-01-01

    Dynamic changes in the expression of transcription factors (TFs) can influence specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TF among differentially-fated precursor cells suggests additional underlying mechanisms. Here, we profiled genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that TF expression and binding contributed to establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal novel TFs influencing the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8+ T cell differentiation, regulated the formation of terminal-effector and memory-precursor cell-fates, respectively. Our data define the epigenetic landscape of differentiation intermediates, facilitating identification of TFs with previously unappreciated roles in CD8+ T cell differentiation. PMID:28288100

  17. Changes in chromatin structure during the aging of cell cultures as revealed by differential scanning calorimetry

    International Nuclear Information System (INIS)

    Almagor, M.; Cole, R.D.

    1989-01-01

    Nuclei from cultured human cells were examined by differential scanning calorimetry. Their melting profiles revealed four structural transitions at 60, 76, 88, and 105 degrees C (transitions I-IV, respectively). In immortalized (i.e., tumor) cell cultures and in normal cell cultures of low passage number, melting profiles were dominated by the 105 degrees C transition (transition IV), but in vitro aging of normal and Werner syndrome cells was associated with a marked decrease in transition IV followed by an increase in transition III at the expense of transition IV. At intermediate times in the aging process, much DNA melted at a temperature range (95-102 degrees C) intermediate between transitions III and IV, and this is consistent with the notion that aging of cell cultures is accompanied by an increase in single-strand character of the DNA. Calorimetric changes were observed in the melting profile of nuclei from UV-irradiated tumor cells that resembled the age-induced intermediate melting of chromatin. It is suggested that aging is accompanied by an increase in single-stranded character of the DNA in chromatin, which lowers its melting temperature, followed by strand breaks in the DNA that destroy its supercoiling potential

  18. [Revealing the chemical changes of tea cell wall induced by anthracnose with confocal Raman microscopy].

    Science.gov (United States)

    Li, Xiao-li; Luo, Liu-bin; Hu, Xiao-qian; Lou, Bing-gan; He, Yong

    2014-06-01

    Healthy tea and tea infected by anthracnose were first studied by confocal Raman microscopy to illustrate chemical changes of cell wall in the present paper. Firstly, Raman spectra of both healthy and infected sample tissues were collected with spatial resolution at micron-level, and ultrastructure of healthy and infected tea cells was got from scanning electron microscope. These results showed that there were significant changes in Raman shift and Raman intensity between healthy and infected cell walls, indicating that great differences occurred in chemical compositions of cell walls between healthy and infected samples. In details, intensities at many Raman bands which were closely associated with cellulose, pectin, esters were reduced after infection, revealing that the content of chemical compounds such as cellulose, pectin, esters was decreased after infection. Subsequently, chemical imaging of both healthy and infected tea cell walls were realized based on Raman fingerprint spectra of cellulose and microscopic spatial structure. It was found that not only the content of cellulose was reduced greatly after infection, but also the ordered structure of cellulose was destroyed by anthracnose infection. Thus, confocal Raman microscopy was shown to be a powerful tool to detect the chemical changes in cell wall of tea caused by anthracnose without any chemical treatment or staining. This research firstly applied confocal Raman microscopy in phytopathology for the study of interactive relationship between host and pathogen, and it will also open a new way for intensive study of host-pathogen at cellular level.

  19. Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

    Science.gov (United States)

    Liu, Mingshan; Liu, Yang; Di, Jiabo; Su, Zhe; Yang, Hong; Jiang, Beihai; Wang, Zaozao; Zhuang, Meng; Bai, Fan; Su, Xiangqian

    2017-11-23

    Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-region whole-exome sequencing and single-cell whole-genome sequencing to examine the genomic intratumor heterogeneity (ITH) of rectal tumors. We sequenced nine tumor regions and 88 single cells from two rectal cancer patients with tumors of the same molecular classification and characterized their mutation profiles and somatic copy number alterations (SCNAs) at the multi-region and the single-cell levels. A variable extent of genomic heterogeneity was observed between the two patients, and the degree of ITH increased when analyzed on the single-cell level. We found that major SCNAs were early events in cancer development and inherited steadily. Single-cell sequencing revealed mutations and SCNAs which were hidden in bulk sequencing. In summary, we studied the ITH of rectal cancer at regional and single-cell resolution and demonstrated that variable heterogeneity existed in two patients. The mutational scenarios and SCNA profiles of two patients with treatment naïve from the same molecular subtype are quite different. Our results suggest each tumor possesses its own architecture, which may result in different diagnosis, prognosis, and drug responses. Remarkable ITH exists in the two patients we have studied, providing a preliminary impression of ITH in rectal cancer.

  20. Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis.

    Science.gov (United States)

    Kuang, Siyun; Zheng, Jun; Yang, Hui; Li, Suhua; Duan, Shuyan; Shen, Yanfang; Ji, Chaoneng; Gan, Jianhua; Xu, Xue-Wei; Li, Jixi

    2017-10-03

    Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD. Substitution of this region by a short linker sequence increased levels of cell death. Mutants F283A and F283R can increase protein heterogeneity in vitro and are capable of undergoing cell pyroptosis in 293T cells. The small-angle X-ray-scattering envelope of human GSDMD is consistent with the modeled GSDMD structure and mouse GSDMA3 structure, which suggests that GSDMD adopts an autoinhibited conformation in solution. The positive potential surface of GSDMD-N covered by GSDMD-C is exposed after being released from the autoinhibition state and can form high-order oligomers via a charge-charge interaction. Furthermore, by mapping different regions of GSDMD, we determined that one short segment is sufficient to kill bacteria in vitro and can efficiently inhibit cell growth in Escherichia coli and Mycobacterium Smegmatis These findings reveal that GSDMD-C acts as an auto-inhibition executor and GSDMD-N could form pore structures via a charge-charge interaction upon cleavage by caspases during cell pyroptosis.

  1. Storage and discharge of a granular fluid

    NARCIS (Netherlands)

    Pacheco-Martinez, Hector; van Gerner, H.J.; Ruiz-Suarez, J.C.

    2008-01-01

    Experiments and computational simulations are carried out to study the behavior of a granular column in a silo whose walls are able to vibrate horizontally. The column is brought to a steady fluidized state and it behaves similar to a hydrostatic system. We study the dynamics of the granular

  2. Characterization of Unbound Granular Materials for Pavements

    NARCIS (Netherlands)

    Araya, A.A.

    2011-01-01

    This research is focused on the characterization of the mechanical behavior of unbound granular road base materials (UGMs). An extensive laboratory investigation is described, in which various methods for determination of the mechanical properties of granular materials are examined for their

  3. Viscosity evolution of anaerobic granular sludge

    NARCIS (Netherlands)

    Pevere, A.; Guibaud, G.; Hullebusch, van E.D.; Lens, P.N.L.; Baudu, M.

    2006-01-01

    The evolution of the apparent viscosity at steady shear rate of sieved anaerobic granular sludge (20¿315 ¿m diameter) sampled from different full-scale anaerobic reactors was recorded using rotation tests. The ¿limit viscosity¿ of sieved anaerobic granular sludge was determined from the apparent

  4. V-ATPase-mediated granular acidification is regulated by the V-ATPase accessory subunit Ac45 in POMC-producing cells.

    NARCIS (Netherlands)

    Jansen, E.J.S.; Hafmans, T.G.M.; Martens, G.J.

    2010-01-01

    The vacuolar (H(+))-ATPase (V-ATPase) is an important proton pump, and multiple critical cell-biological processes depend on the proton gradient provided by the pump. Yet, the mechanism underlying the control of the V-ATPase is still elusive but has been hypothesized to involve an accessory subunit

  5. R&D for a highly granular silicon tungsten electromagnetic calorimeter

    CERN Document Server

    Pöschl, R

    2015-01-01

    This article reports on first experience with the technological prototype of a highly- granular silicon-tungsten electromagnetic calorimeter as envisaged for the detectors at a future lepton collider. In the focus of the analysis is the performance of a highly integrated Application Specific Integrated Circuit designed to meet the requirements in terms of dynamic range, compactness and power consumption. The beam test results show that the circuit will allow a future detector with a signal over noise ratio of at least 10:1. To minimise the power dissipation the ASIC will be operated in a power pulsed mode. So far no conceptual problem was revealed but the studies show the way for further work. The prototype is read out by a DAQ system conceived to meet the needs of a trigger less system with a huge number of readout cells.

  6. Traffic and Granular Flow ’03

    CERN Document Server

    Luding, Stefan; Bovy, Piet; Schreckenberg, Michael; Wolf, Dietrich

    2005-01-01

    These proceedings are the fifth in the series Traffic and Granular Flow, and we hope they will be as useful a reference as their predecessors. Both the realistic modelling of granular media and traffic flow present important challenges at the borderline between physics and engineering, and enormous progress has been made since 1995, when this series started. Still the research on these topics is thriving, so that this book again contains many new results. Some highlights addressed at this conference were the influence of long range electric and magnetic forces and ambient fluids on granular media, new precise traffic measurements, and experiments on the complex decision making of drivers. No doubt the “hot topics” addressed in granular matter research have diverged from those in traffic since the days when the obvious analogies between traffic jams on highways and dissipative clustering in granular flow intrigued both c- munities alike. However, now just this diversity became a stimulating feature of the ...

  7. Traffic and Granular Flow’05

    CERN Document Server

    Pöschel, Thorsten; Kühne, Reinhart; Schreckenberg, Michael; Wolf, Dietrich

    2007-01-01

    The conference series Tra?c and Granular Flow has been established in 1995 and has since then been held biannually. At that time, the investigation of granular materials and tra?c was still somewhat exotic and was just starting to become popular among physicists. Originally the idea behind this conference series was to facilitate the c- vergence of the two ?elds, inspired by the similarities of certain phenomena and the use of similar theoretical methods. However, in recent years it has become clear that probably the di?erences between the two systems are much more interesting than the similarities. Nevertheless, the importance of various interrelations among these ?elds is still growing. The workshop continues to o?er an opportunity to stimulate this interdisciplinary research. Over the years the spectrum of topics has become much broader and has included also problems related to topics ranging from social dynamics to - ology. The conference manages to bring together people with rather di?erent background, r...

  8. Centrifuge modelling of granular flows

    Science.gov (United States)

    Cabrera, Miguel Angel; Wu, Wei

    2015-04-01

    A common characteristic of mass flows like debris flows, rock avalanches and mudflows is that gravity is their main driving force. Gravity defines the intensity and duration of the main interactions between particles and their surrounding media (particle-particle, particle-fluid, fluid-fluid). At the same time, gravity delimits the occurrence of phase separation, inverse segregation, and mass consolidation, among other phenomena. Therefore, in the understanding of the flow physics it is important to account for the scaling of gravity in scaled models. In this research, a centrifuge model is developed to model free surface granular flows down an incline at controlled gravity conditions. Gravity is controlled by the action of an induced inertial acceleration field resulting from the rotation of the model in a geotechnical centrifuge. The characteristics of the induced inertial acceleration field during flow are discussed and validated via experimental data. Flow heights, velocity fields, basal pressure and impact forces are measured for a range of channel inclinations and gravity conditions. Preliminary results enlighten the flow characteristics at variable gravity conditions and open a discussion on the simulation of large scale processes at a laboratory scale. Further analysis on the flow physics brings valuable information for the validation of granular flows rheology.

  9. A novel immunotoxin reveals a new role for CD321 in endothelial cells.

    Directory of Open Access Journals (Sweden)

    Takeshi Fukuhara

    Full Text Available There are currently several antibody therapies that directly target tumors, and antibody-drug conjugates represent a novel moiety as next generation therapeutics. Here, we used a unique screening probe, DT3C, to identify functional antibodies that recognized surface molecules and functional epitopes, and which provided toxin delivery capability. Accordingly, we generated the 90G4 antibody, which induced DT3C-dependent cytotoxicity in endothelial cells. Molecular analysis revealed that 90G4 recognized CD321, a protein localized at tight junctions. Although CD321 plays a pivotal role in inflammation and lymphocyte trans-endothelial migration, little is known about its mechanism of action in endothelial cells. Targeting of CD321 by the 90G4 immunotoxin induced cell death. Moreover, 90G4 immunotoxin caused cytotoxicity primarily in migratory endothelial cells, but not in those forming sheets, suggesting a critical role for CD321 in tumor angiogenesis. We also found that hypoxia triggered redistribution of CD321 to a punctate localization on the basal side of cells, resulting in functional impairment of tight junctions and increased motility. Thus, our findings raise the intriguing possibility that endothelial CD321 presented cellular localization in tight junction as well as multifunctional dynamics in several conditions, leading to illuminate the importance of widely-expressed CD321 as a potential target for antitumor therapy.

  10. Live cell CRISPR-imaging in plants reveals dynamic telomere movements

    KAUST Repository

    Dreissig, Steven

    2017-05-16

    Elucidating the spatio-temporal organization of the genome inside the nucleus is imperative to understand the regulation of genes and non-coding sequences during development and environmental changes. Emerging techniques of chromatin imaging promise to bridge the long-standing gap between sequencing studies which reveal genomic information and imaging studies that provide spatial and temporal information of defined genomic regions. Here, we demonstrate such an imaging technique based on two orthologues of the bacterial CRISPR-Cas9 system. By fusing eGFP/mRuby2 to the catalytically inactive version of Streptococcus pyogenes and Staphylococcus aureus Cas9, we show robust visualization of telomere repeats in live leaf cells of Nicotiana benthamiana. By tracking the dynamics of telomeres visualized by CRISPR-dCas9, we reveal dynamic telomere movements of up to 2 μm within 30 minutes during interphase. Furthermore, we show that CRISPR-dCas9 can be combined with fluorescence-labelled proteins to visualize DNA-protein interactions in vivo. By simultaneously using two dCas9 orthologues, we pave the way for imaging of multiple genomic loci in live plants cells. CRISPR-imaging bears the potential to significantly improve our understanding of the dynamics of chromosomes in live plant cells.

  11. Effects of Noise and Vibration on the Solid to Liquid Fluidization Transition in Small Dense Granular Systems Under Shear

    Science.gov (United States)

    Melhus, Martin Frederic

    2011-07-01

    Granular materials exhibit bulk properties that are distinct from conventional solids, liq- uids, and gases, due to the dissipative nature of the inter-granular forces. Understanding the fundamentals of granular materials draws upon and gives insight into many fields at the current frontiers of physics, such as plasticity of solids, fracture and friction, com- plex systems such as colloids, foams and suspensions, and a variety of biological systems. Particulate flows are widespread in geophysics, and are also essential to many industries. Despite the importance of these phenomena, we lack a theoretical model that explains most behaviors of granular materials. Since granular assemblies are highly dissipative, they are often far from mechanical equilibrium, making most classical analyses inappli- cable. A theory for dilute granular systems exists, but for dense granular systems (by far the majority of granular systems in the real world) no comparable theory is accepted. We approach this problem by examining the fluidization, or transition from solid to liquid, in dense granular systems. In this study, the separate effects of random noise and vibration on the static to flowing transition of a dense granular assembly under planar shear is studied numerically using soft contact particle dynamics simulations in two dimensions. We focus on small systems in a thin planar Couette cell, examining the bistable region while increasing shear, with varying amounts of random noise or vibration, and determine the statistics of the shear required for the onset of flow. We find that the applied power is the key parameter in determining the magnitude of the effects of the noise or vibration, with vibration frequency also having an influence. Similarities and differences between noise and vibration are determined, and the results compare favorably with a two phase model for dense granular flow.

  12. Granular deformation mechanisms in semi-solid alloys

    International Nuclear Information System (INIS)

    Gourlay, C.M.; Dahle, A.K.; Nagira, T.; Nakatsuka, N.; Nogita, K.; Uesugi, K.; Yasuda, H.

    2011-01-01

    Deformation mechanisms in equiaxed, partially solid Al-15 wt.% Cu are studied in situ by coupling shear-cell experiments with synchrotron X-ray radiography. Direct evidence is presented for granular deformation mechanisms in both globular and equiaxed-dendritic samples at solid fractions shortly after crystal impingement. It is demonstrated that dilatancy, arching and jamming occur at the crystal scale, and that these can cause stick-slip flow due to periodic dilation and compaction at low displacement rate. Granular deformation is found to be similar in globular and equiaxed-dendritic samples if length is scaled by the crystal size and packing is considered to occur among crystal envelopes. Rheological differences between the morphologies are discussed in terms of the competition between crystal rearrangement and crystal deformation.

  13. Electromagnetic response of a highly granular hadronic calorimeter

    Energy Technology Data Exchange (ETDEWEB)

    Adloff, C.; Blaha, J.; Blaising, J.J. [Savoie Univ., CNRS/IN2P3, Annecy-le-Vieux (FR). Lab. d' Annecy-le-Vieux de Physique des Particules] (and others)

    2010-12-15

    The CALICE collaboration is studying the design of high performance electromagnetic and hadronic calorimeters for future International Linear Collider detectors. For the hadronic calorimeter, one option is a highly granular sampling calorimeter with steel as absorber and scintillator layers as active material. High granularity is obtained by segmenting the scintillator into small tiles individually read out via silicon photo-multipliers (SiPM). A prototype has been built, consisting of thirty-eight sensitive layers, segmented into about eight thousand channels. In 2007 the prototype was exposed to positrons and hadrons using the CERN SPS beam, covering a wide range of beam energies and incidence angles. The challenge of cell equalization and calibration of such a large number of channels is best validated using electromagnetic processes. The response of the prototype steel-scintillator calorimeter, including linearity and uniformity, to electrons is investigated and described. (orig.)

  14. Electromagnetic response of a highly granular hadronic calorimeter

    International Nuclear Information System (INIS)

    Adloff, C.; Blaha, J.; Blaising, J.J.

    2010-12-01

    The CALICE collaboration is studying the design of high performance electromagnetic and hadronic calorimeters for future International Linear Collider detectors. For the hadronic calorimeter, one option is a highly granular sampling calorimeter with steel as absorber and scintillator layers as active material. High granularity is obtained by segmenting the scintillator into small tiles individually read out via silicon photo-multipliers (SiPM). A prototype has been built, consisting of thirty-eight sensitive layers, segmented into about eight thousand channels. In 2007 the prototype was exposed to positrons and hadrons using the CERN SPS beam, covering a wide range of beam energies and incidence angles. The challenge of cell equalization and calibration of such a large number of channels is best validated using electromagnetic processes. The response of the prototype steel-scintillator calorimeter, including linearity and uniformity, to electrons is investigated and described. (orig.)

  15. Erosion of a wet/dry granular interface

    Science.gov (United States)

    Jop, Pierre; Lefebvre, Gautier

    2013-04-01

    To model the dynamic of landslides, the evolution of the interface between the erodible ground and the flowing material is still studied experimentally or numerically (ie. Mangeney et al. 2010, Iverson 2012). In some cases, the basal material is more cohesive than the flowing one. Such situation arises for example due to cementation or humidity. What are the exchange rates between these phases? What is the coupling between the evolution of the interface and the flow? We studied the erosion phenomenon and performed laboratory experiments to focus on the interaction between a cohesive unsaturated granular material and a dry granular flow. Both materials were spherical grains, the cohesion being induced by adding a given mass of liquid to the grains. Two configurations were explored: a circular aggregate submitted to a dry flow in a rotating drum, and a granular flow eroding a wet granular pile. First, we focused on the influence of the cohesion, controlled by the liquid properties, such as the surface tension and the viscosity. Then the flow characteristics were modified by varying the grain size and density. These results allowed us to present a model for the erosion mechanisms, based on the flow and fluid properties. The main results are the need to take into account the whole probability distribution the stress applied on the wet grains and that both the surface tension and the viscosity are important since they play a different roles. The latter is mainly responsible of the time scale of the dynamic of a wet grain, while the former acts as a threshold on the force distribution. In the second configuration, we could also control the inclination of the slope. This system supported the previous model and moreover revealed an interface instability, leading the formation of steep steps, which is a reminiscence of the cyclic-steps observed during river-channel incision (Parker and Izumi 2000). We will present the dynamics of such granular steps. [1] Mangeney, A., O

  16. Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

    Science.gov (United States)

    Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

    2011-01-01

    As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

  17. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2011-11-01

    Full Text Available As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium and prototrophic (minimal medium culture conditions. The differential patterns of genetic interactions detected among > 235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens and an important target.

  18. Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics.

    Directory of Open Access Journals (Sweden)

    Andreas Sagner

    2018-02-01

    Full Text Available During tissue development, multipotent progenitors differentiate into specific cell types in characteristic spatial and temporal patterns. We addressed the mechanism linking progenitor identity and differentiation rate in the neural tube, where motor neuron (MN progenitors differentiate more rapidly than other progenitors. Using single cell transcriptomics, we defined the transcriptional changes associated with the transition of neural progenitors into MNs. Reconstruction of gene expression dynamics from these data indicate a pivotal role for the MN determinant Olig2 just prior to MN differentiation. Olig2 represses expression of the Notch signaling pathway effectors Hes1 and Hes5. Olig2 repression of Hes5 appears to be direct, via a conserved regulatory element within the Hes5 locus that restricts expression from MN progenitors. These findings reveal a tight coupling between the regulatory networks that control patterning and neuronal differentiation and demonstrate how Olig2 acts as the developmental pacemaker coordinating the spatial and temporal pattern of MN generation.

  19. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill

    Energy Technology Data Exchange (ETDEWEB)

    Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon; Chain, Patrick S. G.; Dubinsky, Eric A.; Fortney, Julian L.; Han, James; Holman, Hoi-Ying N.; Hultman, Jenni; Lamendella, Regina; Mackelprang, Rachel; Malfatti, Stephanie; Tom, Lauren M.; Tringe, Susannah G.; Woyke, Tanja; Zhou, Jizhong; Rubin, Edward M.; Jansson, Janet K.

    2012-06-12

    The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

  20. Electrical transport properties in Fe-Cr nanocluster-assembled granular films

    Science.gov (United States)

    Wang, Xiong-Zhi; Wang, Lai-Sen; Zhang, Qin-Fu; Liu, Xiang; Xie, Jia; Su, A.-Mei; Zheng, Hong-Fei; Peng, Dong-Liang

    2017-09-01

    The Fe100-xCrx nanocluster-assembled granular films with Cr atomic fraction (x) ranging from 0 to 100 were fabricated by using a plasma-gas-condensation cluster deposition system. The TEM characterization revealed that the uniform Fe clusters were coated with a Cr layer to form a Fe-Cr core-shell structure. Then, the as-prepared Fe100-xCrx nanoclusters were randomly assembled into a granular film in vacuum environments with increasing the deposition time. Because of the competition between interfacial resistance and shunting effect of Cr layer, the room temperature resistivity of the Fe100-xCrx nanocluster-assembled granular films first increased and then decreased with increasing the Cr atomic fraction (x), and revealed a maximum of 2 × 104 μΩ cm at x = 26 at.%. The temperature-dependent longitudinal resistivity (ρxx), magnetoresistance (MR) effect and anomalous Hall effect (AHE) of these Fe100-xCrx nanocluster-assembled granular films were also studied systematically. As the x increased from 0 to 100, the ρxx of all samples firstly decreased and then increased with increasing the measuring temperature. The dependence of ρxx on temperature could be well addressed by a mechanism incorporated for the fluctuation-induced-tunneling (FIT) conduction process and temperature-dependent scattering effect. It was found that the anomalous Hall effect (AHE) had no legible scaling relation in Fe100-xCrx nanocluster-assembled granular films. However, after deducting the contribution of tunneling effect, the scaling relation was unambiguous. Additionally, the Fe100-xCrx nanocluster-assembled granular films revealed a small negative magnetoresistance (MR), which decreased with the increase of x. The detailed physical mechanism of the electrical transport properties in these Fe100-xCrx nanocluster-assembled granular films was also studied.

  1. CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Yue Hu

    Full Text Available We analyzed the gene expression patterns of 138 Non-Small Cell Lung Cancer (NSCLC samples and developed a new algorithm called Coverage Analysis with Fisher's Exact Test (CAFET to identify molecular pathways that are differentially activated in squamous cell carcinoma (SCC and adenocarcinoma (AC subtypes. Analysis of the lung cancer samples demonstrated hierarchical clustering according to the histological subtype and revealed a strong enrichment for the Wnt signaling pathway components in the cluster consisting predominantly of SCC samples. The specific gene expression pattern observed correlated with enhanced activation of the Wnt Planar Cell Polarity (PCP pathway and inhibition of the canonical Wnt signaling branch. Further real time RT-PCR follow-up with additional primary tumor samples and lung cancer cell lines confirmed enrichment of Wnt/PCP pathway associated genes in the SCC subtype. Dysregulation of the canonical Wnt pathway, characterized by increased levels of β-catenin and epigenetic silencing of negative regulators, has been reported in adenocarcinoma of the lung. Our results suggest that SCC and AC utilize different branches of the Wnt pathway during oncogenesis.

  2. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

    Directory of Open Access Journals (Sweden)

    Liang-Hui Chu

    Full Text Available Angiogenesis involves stimulation of endothelial cells (EC by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome" could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A. We used the Short Time-series Expression Miner (STEM to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC and human microvascular EC (MEC. The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

  3. Suicide Gene-Engineered Stromal Cells Reveal a Dynamic Regulation of Cancer Metastasis

    Science.gov (United States)

    Shen, Keyue; Luk, Samantha; Elman, Jessica; Murray, Ryan; Mukundan, Shilpaa; Parekkadan, Biju

    2016-02-01

    Cancer-associated fibroblasts (CAFs) are a major cancer-promoting component in the tumor microenvironment (TME). The dynamic role of human CAFs in cancer progression has been ill-defined because human CAFs lack a unique marker needed for a cell-specific, promoter-driven knockout model. Here, we developed an engineered human CAF cell line with an inducible suicide gene to enable selective in vivo elimination of human CAFs at different stages of xenograft tumor development, effectively circumventing the challenge of targeting a cell-specific marker. Suicide-engineered CAFs were highly sensitive to apoptosis induction in vitro and in vivo by the addition of a simple small molecule inducer. Selection of timepoints for targeted CAF apoptosis in vivo during the progression of a human breast cancer xenograft model was guided by a bi-phasic host cytokine response that peaked at early timepoints after tumor implantation. Remarkably, we observed that the selective apoptosis of CAFs at these early timepoints did not affect primary tumor growth, but instead increased the presence of tumor-associated macrophages and the metastatic spread of breast cancer cells to the lung and bone. The study revealed a dynamic relationship between CAFs and cancer metastasis that has counter-intuitive ramifications for CAF-targeted therapy.

  4. Granular metamaterials for vibration mitigation

    Science.gov (United States)

    Gantzounis, G.; Serra-Garcia, M.; Homma, K.; Mendoza, J. M.; Daraio, C.

    2013-09-01

    Acoustic metamaterials that allow low-frequency band gaps are interesting for many practical engineering applications, where vibration control and sound insulation are necessary. In most prior studies, the mechanical response of these structures has been described using linear continuum approximations. In this work, we experimentally and theoretically address the formation of low-frequency band gaps in locally resonant granular crystals, where the dynamics of the system is governed by discrete equations. We investigate the quasi-linear behavior of such structures. The analysis shows that a stopband can be introduced at about one octave lower frequency than in materials without local resonances. Broadband and multi-frequency stopband characteristics can also be achieved by strategically tailoring the non-uniform local resonance parameters.

  5. Fracture surfaces of granular pastes.

    Science.gov (United States)

    Mohamed Abdelhaye, Y O; Chaouche, M; Van Damme, H

    2013-11-01

    Granular pastes are dense dispersions of non-colloidal grains in a simple or a complex fluid. Typical examples are the coating, gluing or sealing mortars used in building applications. We study the cohesive rupture of thick mortar layers in a simple pulling test where the paste is initially confined between two flat surfaces. After hardening, the morphology of the fracture surfaces was investigated, using either the box counting method to analyze fracture profiles perpendicular to the mean fracture plane, or the slit-island method to analyze the islands obtained by cutting the fracture surfaces at different heights, parallel to the mean fracture plane. The fracture surfaces were shown to exhibit scaling properties over several decades. However, contrary to what has been observed in the brittle or ductile fracture of solid materials, the islands were shown to be mass fractals. This was related to the extensive plastic flow involved in the fracture process.

  6. Shear failure of granular materials

    Science.gov (United States)

    Degiuli, Eric; Balmforth, Neil; McElwaine, Jim; Schoof, Christian; Hewitt, Ian

    2012-02-01

    Connecting the macroscopic behavior of granular materials with the microstructure remains a great challenge. Recent work connects these scales with a discrete calculus [1]. In this work we generalize this formalism from monodisperse packings of disks to 2D assemblies of arbitrarily shaped grains. In particular, we derive Airy's expression for a symmetric, divergence-free stress tensor. Using these tools, we derive, from first-principles and in a mean-field approximation, the entropy of frictional force configurations in the Force Network Ensemble. As a macroscopic consequence of the Coulomb friction condition at contacts, we predict shear failure at a critical shear stress, in accordance with the Mohr-Coulomb failure condition well known in engineering. Results are compared with numerical simulations, and the dependence on the microscopic geometric configuration is discussed. [4pt] [1] E. DeGiuli & J. McElwaine, PRE 2011. doi: 10.1103/PhysRevE.84.041310

  7. Mechanics of a granular skin

    Science.gov (United States)

    Karmakar, Somnath; Sane, Anit; Bhattacharya, S.; Ghosh, Shankar

    2017-04-01

    Magic sand, a hydrophobic toy granular material, is widely used in popular science instructions because of its nonintuitive mechanical properties. A detailed study of the failure of an underwater column of magic sand shows that these properties can be traced to a single phenomenon: the system self-generates a cohesive skin that encapsulates the material inside. The skin, consisting of pinned air-water-grain interfaces, shows multiscale mechanical properties: they range from contact-line dynamics in the intragrain roughness scale, to plastic flow at the grain scale, all the way to sample-scale mechanical responses. With decreasing rigidity of the skin, the failure mode transforms from brittle to ductile (both of which are collective in nature) to a complete disintegration at the single-grain scale.

  8. Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells

    KAUST Repository

    Joshi, Rubin N.

    2017-09-25

    Regulatory T cells (Tregs) control key events of immune tolerance, primarily by suppression of effector T cells. We previously revealed that Tregs rapidly suppress T cell receptor (TCR)-induced calcium store depletion in conventional CD4CD25 T cells (Tcons) independently of IP levels, consequently inhibiting NFAT signaling and effector cytokine expression. Here, we study Treg suppression mechanisms through unbiased phosphoproteomics of primary human Tcons upon TCR stimulation and Treg-mediated suppression, respectively. Tregs induced a state of overall decreased phosphorylation as opposed to TCR stimulation. We discovered novel phosphosites (T595_S597) in the DEF6 (SLAT) protein that were phosphorylated upon TCR stimulation and conversely dephosphorylated upon coculture with Tregs. Mutation of these DEF6 phosphosites abrogated interaction of DEF6 with the IP receptor and affected NFAT activation and cytokine transcription in primary Tcons. This novel mechanism and phosphoproteomics data resource may aid in modifying sensitivity of Tcons to Treg-mediated suppression in autoimmune disease or cancer.

  9. Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

    KAUST Repository

    Simone, Giuseppina

    2013-02-11

    Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction\\'s strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

    KAUST Repository

    Simone, Giuseppina; Malara, Natalia Maria; Trunzo, Valentina; Perozziello, Gerardo; Neužil, Pavel; Francardi, Marco; Roveda, Laura; Renne, Maria; Prati, Ubaldo; Mollace, Vincenzo; Manz, Andreas; Di Fabrizio, Enzo M.

    2013-01-01

    Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction's strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Storage and discharge of a granular fluid.

    Science.gov (United States)

    Pacheco-Martinez, Hector; van Gerner, Henk Jan; Ruiz-Suárez, J C

    2008-02-01

    Experiments and computational simulations are carried out to study the behavior of a granular column in a silo whose walls are able to vibrate horizontally. The column is brought to a steady fluidized state and it behaves similar to a hydrostatic system. We study the dynamics of the granular discharge through openings at the bottom of the silo in order to search for a Torricelli-like behavior. We show that the flow rate scales with the wall induced shear rate, and at high rates, the granular bed indeed discharges similar to a viscous fluid.

  12. On inconsistency in frictional granular systems

    Science.gov (United States)

    Alart, Pierre; Renouf, Mathieu

    2018-04-01

    Numerical simulation of granular systems is often based on a discrete element method. The nonsmooth contact dynamics approach can be used to solve a broad range of granular problems, especially involving rigid bodies. However, difficulties could be encountered and hamper successful completion of some simulations. The slow convergence of the nonsmooth solver may sometimes be attributed to an ill-conditioned system, but the convergence may also fail. The prime aim of the present study was to identify situations that hamper the consistency of the mathematical problem to solve. Some simple granular systems were investigated in detail while reviewing and applying the related theoretical results. A practical alternative is briefly analyzed and tested.

  13. Shock waves in weakly compressed granular media.

    Science.gov (United States)

    van den Wildenberg, Siet; van Loo, Rogier; van Hecke, Martin

    2013-11-22

    We experimentally probe nonlinear wave propagation in weakly compressed granular media and observe a crossover from quasilinear sound waves at low impact to shock waves at high impact. We show that this crossover impact grows with the confining pressure P0, whereas the shock wave speed is independent of P0-two hallmarks of granular shocks predicted recently. The shocks exhibit surprising power law attenuation, which we model with a logarithmic law implying that shock dissipation is weak and qualitatively different from other granular dissipation mechanisms. We show that elastic and potential energy balance in the leading part of the shocks.

  14. Granular-relational data mining how to mine relational data in the paradigm of granular computing ?

    CERN Document Server

    Hońko, Piotr

    2017-01-01

    This book provides two general granular computing approaches to mining relational data, the first of which uses abstract descriptions of relational objects to build their granular representation, while the second extends existing granular data mining solutions to a relational case. Both approaches make it possible to perform and improve popular data mining tasks such as classification, clustering, and association discovery. How can different relational data mining tasks best be unified? How can the construction process of relational patterns be simplified? How can richer knowledge from relational data be discovered? All these questions can be answered in the same way: by mining relational data in the paradigm of granular computing! This book will allow readers with previous experience in the field of relational data mining to discover the many benefits of its granular perspective. In turn, those readers familiar with the paradigm of granular computing will find valuable insights on its application to mining r...

  15. Identification of colonic fibroblast secretomes reveals secretory factors regulating colon cancer cell proliferation.

    Science.gov (United States)

    Chen, Sun-Xia; Xu, Xiao-En; Wang, Xiao-Qing; Cui, Shu-Jian; Xu, Lei-Lei; Jiang, Ying-Hua; Zhang, Yang; Yan, Hai-Bo; Zhang, Qian; Qiao, Jie; Yang, Peng-Yuan; Liu, Feng

    2014-10-14

    Stromal microenvironment influences tumor cell proliferation and migration. Fibroblasts represent the most abundant stromal constituents. Here, we established two pairs of normal fibroblast (NF) and cancer-associated fibroblast (CAF) cultures from colorectal adenocarcinoma tissues and the normal counterparts. The NFs and CAFs were stained positive for typical fibroblast markers and inhibited colon cancer (CC) cell proliferation in in vitro cocultures and in xenograft mouse models. The fibroblast conditioned media were analyzed using LC-MS and 227 proteins were identified at a false discovery rate of 1.3%, including 131 putative secretory and 20 plasma membrane proteins. These proteins were enriched for functional categories of extracellular matrix, adhesion, cell motion, inflammatory response, redox homeostasis and peptidase inhibitor. Secreted protein acidic and rich in cysteine, transgelin, follistatin-related protein 1 (FSTL1) and decorin was abundant in the fibroblast secretome as confirmed by Western blot. Silencing of FSTL1 and transgelin in colonic fibroblast cell line CCD-18Co induced an accelerated proliferation of CC cells in cocultures. Exogenous FSTL1 attenuates CC cell proliferation in a negative fashion. FSTL1 was upregulated in CC patient plasma and cancerous tissues but had no implication in prognosis. Our results provided novel insights into the molecular signatures and modulatory role of CC associated fibroblasts. In this study, a label-free LC-MS was performed to analyze the secretomes of two paired primary fibroblasts, which were isolated from fresh surgical specimen of colorectal adenocarcinoma and adjacent normal colonic tissues and exhibited negative modulatory activity for colon cancer cell growth in in vitro cocultures and in vivo xenograph mouse models. Follistatin-related protein 1 was further revealed to be one of the stroma-derived factors of potential suppression role for colon cancer cell proliferation. Our results provide novel

  16. Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins

    Directory of Open Access Journals (Sweden)

    Kahlem Pascal

    2006-06-01

    Full Text Available Abstract Background Trisomy of human chromosome 21 (Chr21 results in Down's syndrome, a complex developmental and neurodegenerative disease. Molecular analysis of Down's syndrome, however, poses a particular challenge, because the aneuploid region of Chr21 contains many genes of unknown function. Subcellular localization of human Chr21 proteins may contribute to further understanding of the functions and regulatory mechanisms of the genes that code for these proteins. Following this idea, we used a transfected-cell array technique to perform a rapid and cost-effective analysis of the intracellular distribution of Chr 21 proteins. Results We chose 89 genes that were distributed over the majority of 21q, ranging from RBM11 (14.5 Mb to MCM3AP (46.6 Mb, with part of them expressed aberrantly in the Down's syndrome mouse model. Open reading frames of these genes were cloned into a mammalian expression vector with an amino-terminal His6 tag. All of the constructs were arrayed on glass slides and reverse transfected into HEK293T cells for protein expression. Co-localization detection using a set of organelle markers was carried out for each Chr21 protein. Here, we report the subcellular localization properties of 52 proteins. For 34 of these proteins, their localization is described for the first time. Furthermore, the alteration in cell morphology and growth as a result of protein over-expression for claudin-8 and claudin-14 genes has been characterized. Conclusion The cell array-based protein expression and detection approach is a cost-effective platform for large-scale functional analyses, including protein subcellular localization and cell phenotype screening. The results from this study reveal novel functional features of human Chr21 proteins, which should contribute to further understanding of the molecular pathology of Down's syndrome.

  17. Human mast cell tryptase: Multiple cDNAs and genes reveal a multigene serine protease family

    International Nuclear Information System (INIS)

    Vanderslice, P.; Ballinger, S.M.; Tam, E.K.; Goldstein, S.M.; Craik, C.S.; Caughey, G.H.

    1990-01-01

    Three different cDNAs and a gene encoding human skin mast cell tryptase have been cloned and sequenced in their entirety. The deduced amino acid sequences reveal a 30-amino acid prepropeptide followed by a 245-amino acid catalytic domain. The C-terminal undecapeptide of the human preprosequence is identical in dog tryptase and appears to be part of a prosequence unique among serine proteases. The differences among the three human tryptase catalytic domains include the loss of a consensus N-glycosylation site in one cDNA, which may explain some of the heterogeneity in size and susceptibility to deglycosylation seen in tryptase preparations. All three tryptase cDNAs are distinct from a recently reported cDNA obtained from a human lung mast cell library. A skin tryptase cDNA was used to isolate a human tryptase gene, the exons of which match one of the skin-derived cDNAs. The organization of the ∼1.8-kilobase-pair tryptase gene is unique and is not closely related to that of any other mast cell or leukocyte serine protease. The 5' regulatory regions of the gene share features with those of other serine proteases, including mast cell chymase, but are unusual in being separated from the protein-coding sequence by an intron. High-stringency hybridization of a human genomic DNA blot with a fragment of the tryptase gene confirms the presence of multiple tryptase genes. These findings provide genetic evidence that human mast cell tryptases are the products of a multigene family

  18. Functional malignant cell heterogeneity in pancreatic neuroendocrine tumors revealed by targeting of PDGF-DD.

    Science.gov (United States)

    Cortez, Eliane; Gladh, Hanna; Braun, Sebastian; Bocci, Matteo; Cordero, Eugenia; Björkström, Niklas K; Miyazaki, Hideki; Michael, Iacovos P; Eriksson, Ulf; Folestad, Erika; Pietras, Kristian

    2016-02-16

    Intratumoral heterogeneity is an inherent feature of most human cancers and has profound implications for cancer therapy. As a result, there is an emergent need to explore previously unmapped mechanisms regulating distinct subpopulations of tumor cells and to understand their contribution to tumor progression and treatment response. Aberrant platelet-derived growth factor receptor beta (PDGFRβ) signaling in cancer has motivated the development of several antagonists currently in clinical use, including imatinib, sunitinib, and sorafenib. The discovery of a novel ligand for PDGFRβ, platelet-derived growth factor (PDGF)-DD, opened the possibility of a previously unidentified signaling pathway involved in tumor development. However, the precise function of PDGF-DD in tumor growth and invasion remains elusive. Here, making use of a newly generated Pdgfd knockout mouse, we reveal a functionally important malignant cell heterogeneity modulated by PDGF-DD signaling in pancreatic neuroendocrine tumors (PanNET). Our analyses demonstrate that tumor growth was delayed in the absence of signaling by PDGF-DD. Surprisingly, ablation of PDGF-DD did not affect the vasculature or stroma of PanNET; instead, we found that PDGF-DD stimulated bulk tumor cell proliferation by induction of paracrine mitogenic signaling between heterogeneous malignant cell clones, some of which expressed PDGFRβ. The presence of a subclonal population of tumor cells characterized by PDGFRβ expression was further validated in a cohort of human PanNET. In conclusion, we demonstrate a previously unrecognized heterogeneity in PanNET characterized by signaling through the PDGF-DD/PDGFRβ axis.

  19. Immunolocalization of 7-2-ribonucleoprotein in the granular component of the nucleolus

    International Nuclear Information System (INIS)

    Reimer, G.; Raska, I.; Scheer, U.; Tan, E.M.

    1988-01-01

    Certain autoimmune sera contain antibodies against a nucleolar ribonucleotprotein particle associated with 7-2-RNA. In this study, the authors showed by immunofluorescence microscopy that antibodies reactive with 7-2-ribonucleoprotein immunolocalized in the granular regions of actinomycin D and 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB)--segregated nucleoli from Vero cells. By electron microscopic immunocytochemistry, antigen-antibody complexes were located in the granular component of transcriptionally active nucleoli from rat liver hepatocytes and HeLa cells. Anti-7-2-RNP antibodies from two autoimmune sera immunoprecipitated a major protein of M r 40,000 from [ 35 S] methionine-labeled HeLa cell extract. The immunolocalization data suggest that 7-2-ribonucleoprotein may be involved in stages of ribosome biogenesis which take place in the granular component of the nucleolus, i.e., assembly, maturation, and/or transport of preribosomes

  20. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  1. Jamming and chaotic dynamics in different granular systems

    Science.gov (United States)

    Maghsoodi, Homayoon; Luijten, Erik

    Although common in nature and industry, the jamming transition has long eluded a concrete, mechanistic explanation. Recently, Banigan et al. (Nat. Phys. 9, 288-292, 2013) proposed a method for characterizing this transition in a granular system in terms of the system's chaotic properties, as quantified by the largest Lyapunov exponent. They demonstrated that in a two-dimensional shear cell the jamming transition coincides with the bulk density at which the system's largest Lyapunov exponent changes sign, indicating a transition between chaotic and non-chaotic regimes. To examine the applicability of this observation to realistic granular systems, we study a model that includes frictional forces within an expanded phase space. Furthermore, we test the generality of the relation between chaos and jamming by investigating the relationship between jamming and the chaotic properties of several other granular systems, notably sheared systems (Howell, D., Behringer R. P., Veje C., Phys. Rev. Lett. 82, 5241-5244, 1999) and systems with a free boundary. Finally, we quantify correlations between the largest Lyapunov vector and collective rearrangements of the system to demonstrate the predictive capabilities enabled by adopting this perspective of jamming.

  2. Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells.

    Science.gov (United States)

    Sun, Rui; Fu, Ling; Liu, Keke; Tian, Caiping; Yang, Yong; Tallman, Keri A; Porter, Ned A; Liebler, Daniel C; Yang, Jing

    2017-10-01

    4-Oxo-2-nonenal (ONE) derived from lipid peroxidation modifies nucleophiles and transduces redox signaling by its reactions with proteins. However, the molecular interactions between ONE and complex proteomes and their dynamics in situ remain largely unknown. Here we describe a quantitative chemoproteomic analysis of protein adduction by ONE in cells, in which the cellular target profile of ONE is mimicked by its alkynyl surrogate. The analyses reveal four types of ONE-derived modifications in cells, including ketoamide and Schiff-base adducts to lysine, Michael adducts to cysteine, and a novel pyrrole adduct to cysteine. ONE-derived adducts co-localize and exhibit crosstalk with many histone marks and redox sensitive sites. All four types of modifications derived from ONE can be reversed site-specifically in cells. Taken together, our study provides much-needed mechanistic insights into the cellular signaling and potential toxicities associated with this important lipid derived electrophile. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Single-Cell Analysis of SMN Reveals Its Broader Role in Neuromuscular Disease

    Directory of Open Access Journals (Sweden)

    Natalia Rodriguez-Muela

    2017-02-01

    Full Text Available The mechanism underlying selective motor neuron (MN death remains an essential question in the MN disease field. The MN disease spinal muscular atrophy (SMA is attributable to reduced levels of the ubiquitous protein SMN. Here, we report that SMN levels are widely variable in MNs within a single genetic background and that this heterogeneity is seen not only in SMA MNs but also in MNs derived from controls and amyotrophic lateral sclerosis (ALS patients. Furthermore, cells with low SMN are more susceptible to cell death. These findings raise the important clinical implication that some SMN-elevating therapeutics might be effective in MN diseases besides SMA. Supporting this, we found that increasing SMN across all MN populations using an Nedd8-activating enzyme inhibitor promotes survival in both SMA and ALS-derived MNs. Altogether, our work demonstrates that examination of human neurons at the single-cell level can reveal alternative strategies to be explored in the treatment of degenerative diseases.

  4. Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells.

    Science.gov (United States)

    Rusin, Scott F; Schlosser, Kate A; Adamo, Mark E; Kettenbach, Arminja N

    2015-10-13

    Protein phosphorylation is an important regulatory mechanism controlling mitotic progression. Protein phosphatase 6 (PP6) is an essential enzyme with conserved roles in chromosome segregation and spindle assembly from yeast to humans. We applied a baculovirus-mediated gene silencing approach to deplete HeLa cells of the catalytic subunit of PP6 (PP6c) and analyzed changes in the phosphoproteome and proteome in mitotic cells by quantitative mass spectrometry-based proteomics. We identified 408 phosphopeptides on 272 proteins that increased and 298 phosphopeptides on 220 proteins that decreased in phosphorylation upon PP6c depletion in mitotic cells. Motif analysis of the phosphorylated sites combined with bioinformatics pathway analysis revealed previously unknown PP6c-dependent regulatory pathways. Biochemical assays demonstrated that PP6c opposed casein kinase 2-dependent phosphorylation of the condensin I subunit NCAP-G, and cellular analysis showed that depletion of PP6c resulted in defects in chromosome condensation and segregation in anaphase, consistent with dysregulation of condensin I function in the absence of PP6 activity. Copyright © 2015, American Association for the Advancement of Science.

  5. Live-cell microscopy reveals small molecule inhibitor effects on MAPK pathway dynamics.

    Directory of Open Access Journals (Sweden)

    Daniel J Anderson

    Full Text Available Oncogenic mutations in the mitogen activated protein kinase (MAPK pathway are prevalent in human tumors, making this pathway a target of drug development efforts. Recently, ATP-competitive Raf inhibitors were shown to cause MAPK pathway activation via Raf kinase priming in wild-type BRaf cells and tumors, highlighting the need for a thorough understanding of signaling in the context of small molecule kinase inhibitors. Here, we present critical improvements in cell-line engineering and image analysis coupled with automated image acquisition that allow for the simultaneous identification of cellular localization of multiple MAPK pathway components (KRas, CRaf, Mek1 and Erk2. We use these assays in a systematic study of the effect of small molecule inhibitors across the MAPK cascade either as single agents or in combination. Both Raf inhibitor priming as well as the release from negative feedback induced by Mek and Erk inhibitors cause translocation of CRaf to the plasma membrane via mechanisms that are additive in pathway activation. Analysis of Erk activation and sub-cellular localization upon inhibitor treatments reveals differential inhibition and activation with the Raf inhibitors AZD628 and GDC0879 respectively. Since both single agent and combination studies of Raf and Mek inhibitors are currently in the clinic, our assays provide valuable insight into their effects on MAPK signaling in live cells.

  6. Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement

    OpenAIRE

    Herranz, M. Carmen; Sánchez Navarro, Jesús A.; Saurí Peris, Ana; Mingarro Muñoz, Ismael; Pallás Benet, Vicente

    2005-01-01

    The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive c...

  7. Diagnosis of large granular lymphocytic leukemia in a patient previously treated for acute myeloblastic leukemia

    OpenAIRE

    Sinem Civriz Bozdag; Sinem Namdaroglu; Omur Kayikci; Gülsah Kaygusuz; Itir Demiriz; Murat Cinarsoy; Emre Tekgunduz; Fevzi Altuntas

    2013-01-01

    Large granular lymphocytic (LGL) leukemia is a lymphoproliferative disease characterized by the clonal expansion of cytotoxic T or natural killer cells. We report on a patient diagnosed with T-cell LGL leukemia two years after the achievement of hematologic remission for acute myeloblastic leukemia.

  8. Optimization of low energy sonication treatment for granular activated carbon colonizing biomass assessment.

    Science.gov (United States)

    Saccani, G; Bernasconi, M; Antonelli, M

    2014-01-01

    This study is aimed at optimizing a low energy sonication (LES) treatment for granular activated carbon (GAC)-colonizing biomass detachment and determination, evaluating detachment efficiency and the effects of ultrasound exposure on bacterial cell viability. GAC samples were collected from two filters fed with groundwater. Conventional heterotrophic plate count (HPC) and fluorescence microscopy with a double staining method were used to evaluate cell viability, comparing two LES procedures, without and with periodical bulk substitution. A 20 min LES treatment, with bulk substitution after cycles of 5 min as maximum treatment time, allowed to recover 87%/100% of attached biomass, protecting detached bacteria from ultrasound damaging effects. Observed viable cell inactivation rate was 6.5/7.9% cell/min, with membrane-compromised cell damage appearing to be even higher (11.5%/13.1% cell/min). Assessing bacterial detachment and damaging ultrasound effects, fluorescence microscopy turned out to be more sensitive compared to conventional HPC. The optimized method revealed a GAC-colonizing biomass of 9.9 x 10(7) cell/gGAC for plant 1 and 8.8 x 10(7) cell/gGAC for plant 2, 2 log lower than reported in literature. The difference between the two GAC-colonizing biomasses is higher in terms of viable cells (46.3% of total cells in plant 1 GAC-colonizing biomass compared to the 33.3% in plant 2). Studying influent water contamination through multivariate statistical analyses, apossible combined toxic and genotoxic effect of chromium VI and trichloroethylene was suggested as a reason for the lower viable cell fraction observed in plant 2 GAC-colonizing population.

  9. Ultrastructural and functional characterization of circulating hemocytes from Galleria mellonella larva: Cell types and their role in the innate immunity.

    Science.gov (United States)

    Wu, Gongqing; Liu, Yi; Ding, Ying; Yi, Yunhong

    2016-08-01

    Galleria mellonella larvae have been widely used as a model to study the virulence of various human pathogens. Hemocytes play important roles in the innate immune response of G. mellonella. In this study, the hemocytes of G. mellonella larvae were analyzed by transmission electron microscope, light microscope, and cytochemistry. The cytological and morphological analyses revealed four types of hemocytes; Plasmatocytes, granular cells, spherule cells and oenocytoids. Differential hemocyte counts showed that under our conditions plasmatocytes and granular cells were the most abundant circulating cell types in the hemolymph. We also investigated the role of different types of hemocytes in the cellular and humoral immune defenses. The in-vivo experiment showed that plasmatocytes, granular cells and oenocytoids phagocytized FITC-labelled Escherichia coli bacteria in larvae of G. mellonella, whereas the granular cells exhibited the strongest phagocytic ability against these microbial cells. After incubation with L-DOPA, plasmatocytes, granular cells and oenocytoids are stained brown, indicating the presence of phenoloxidase activity. These results shed new light on our understanding of the immune function of G. mellonella hemocytes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Spatial correlations in compressible granular flows

    NARCIS (Netherlands)

    van Noije, T.P.C.; Ernst, M.H.; Brito, R.

    The clustering instability in freely evolving granular fluids manifests itself in the density-density correlation function and structure factor. These functions are calculated from fluctuating hydrodynamics. As time increases, the structure factor of density fluctuations develops a maximum, which

  11. Granular Gases: Probing the Boundaries of Hydrodynamics

    International Nuclear Information System (INIS)

    Goldhirsch, I.

    1999-01-01

    The dissipative nature of the particle interactions in granular systems renders granular gases mesoscopic and bearing some similarities to regular gases in the ''continuum transition regime'' where shear rates and/or thermal gradients are very large). The following properties of granular gases support the above claim: (i). Mean free times are of the same order as macroscopic time scales (inverse shear rates); (ii). Mean free paths can be macroscopic and comparable to the system's dimensions; (iii). Typical flows are supersonic; (iv). Shear rates are typically ''large''; (v). Stress fields are scale (resolution) dependent; (vi). Burnett and super-Burnett corrections to both the constitutive relations and the boundary conditions are of importance; (vii). Single particle distribution functions can be far from Gaussian. It is concluded that while hydrodynamic descriptions of granular gases are relevant, they are probing the boundaries of applicability of hydrodynamics and perhaps slightly beyond

  12. Advanced Granular System Modeling, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Spaceports of the future will utilize new granular materials in unique applications including insulation for cryogenic tanks and Lunar regolith processing for usable...

  13. Resistance capability of microaerobic granular sludge for ...

    African Journals Online (AJOL)

    enoh

    2012-02-08

    Feb 8, 2012 ... The resistance capability to pH shock of microaerobic granular sludge for pentachlorophenol (PCP) ... process with chlorine gas in pulp and paper, leather and spinning ... nitrifying bacteria in the aerobic zone, and then trans-.

  14. Microbiological aspects of granular methanogenic sludge

    NARCIS (Netherlands)

    Dolfing, J.

    1987-01-01

    The settling characteristics of anaerobic sludge are enhanced by the formation of microbial conglomerates. Various types of conglomerates having different structures, were distinguished in the present study, viz. granules, pellets and flocs (chapter 1). Granular methanogenic sludge, often

  15. NMR Measurements of Granular Flow and Compaction

    Science.gov (United States)

    Fukushima, Eiichi

    1998-03-01

    Nuclear magnetic resonance (NMR) can be used to measure statistical distributions of granular flow velocity and fluctuations of velocity, as well as spatial distributions of particulate concentration, flow velocity, its fluctuations, and other parameters that may be derived from these. All measurements have been of protons in liquid-containing particles such as mustard seeds or pharmaceutical pills. Our favorite geometry has been the slowly rotating partially filled rotating drum with granular flow taking place along the free surface of the particles. All the above-mentioned parameters have been studied as well as a spatial distribution of particulate diffusion coefficients, energy dissipation due to collisions, as well as segregation of non-uniform mixtures of granular material. Finally, we describe some motions of granular material under periodic vibrations.

  16. Uniform shock waves in disordered granular matter.

    Science.gov (United States)

    Gómez, Leopoldo R; Turner, Ari M; Vitelli, Vincenzo

    2012-10-01

    The confining pressure P is perhaps the most important parameter controlling the properties of granular matter. Strongly compressed granular media are, in many respects, simple solids in which elastic perturbations travel as ordinary phonons. However, the speed of sound in granular aggregates continuously decreases as the confining pressure decreases, completely vanishing at the jamming-unjamming transition. This anomalous behavior suggests that the transport of energy at low pressures should not be dominated by phonons. In this work we use simulations and theory to show how the response of granular systems becomes increasingly nonlinear as pressure decreases. In the low-pressure regime the elastic energy is found to be mainly transported through nonlinear waves and shocks. We numerically characterize the propagation speed, shape, and stability of these shocks and model the dependence of the shock speed on pressure and impact intensity by a simple analytical approach.

  17. Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

    Science.gov (United States)

    Tsang, Jason C H; Yu, Yong; Burke, Shannon; Buettner, Florian; Wang, Cui; Kolodziejczyk, Aleksandra A; Teichmann, Sarah A; Lu, Liming; Liu, Pentao

    2015-09-21

    Hematopoietic stem cells (HSCs) are a rare cell type with the ability of long-term self-renewal and multipotency to reconstitute all blood lineages. HSCs are typically purified from the bone marrow using cell surface markers. Recent studies have identified significant cellular heterogeneities in the HSC compartment with subsets of HSCs displaying lineage bias. We previously discovered that the transcription factor Bcl11a has critical functions in the lymphoid development of the HSC compartment. In this report, we employ single-cell transcriptomic analysis to dissect the molecular heterogeneities in HSCs. We profile the transcriptomes of 180 highly purified HSCs (Bcl11a (+/+) and Bcl11a (-/-)). Detailed analysis of the RNA-seq data identifies cell cycle activity as the major source of transcriptomic variation in the HSC compartment, which allows reconstruction of HSC cell cycle progression in silico. Single-cell RNA-seq profiling of Bcl11a (-/-) HSCs reveals abnormal proliferative phenotypes. Analysis of lineage gene expression suggests that the Bcl11a (-/-) HSCs are constituted of two distinct myeloerythroid-restricted subpopulations. Remarkably, similar myeloid-restricted cells could also be detected in the wild-type HSC compartment, suggesting selective elimination of lymphoid-competent HSCs after Bcl11a deletion. These defects are experimentally validated in serial transplantation experiments where Bcl11a (-/-) HSCs are myeloerythroid-restricted and defective in self-renewal. Our study demonstrates the power of single-cell transcriptomics in dissecting cellular process and lineage heterogeneities in stem cell compartments, and further reveals the molecular and cellular defects in the Bcl11a-deficient HSC compartment.

  18. Mouse model of chromosome mosaicism reveals lineage-specific depletion of aneuploid cells and normal developmental potential.

    Science.gov (United States)

    Bolton, Helen; Graham, Sarah J L; Van der Aa, Niels; Kumar, Parveen; Theunis, Koen; Fernandez Gallardo, Elia; Voet, Thierry; Zernicka-Goetz, Magdalena

    2016-03-29

    Most human pre-implantation embryos are mosaics of euploid and aneuploid cells. To determine the fate of aneuploid cells and the developmental potential of mosaic embryos, here we generate a mouse model of chromosome mosaicism. By treating embryos with a spindle assembly checkpoint inhibitor during the four- to eight-cell division, we efficiently generate aneuploid cells, resulting in embryo death during peri-implantation development. Live-embryo imaging and single-cell tracking in chimeric embryos, containing aneuploid and euploid cells, reveal that the fate of aneuploid cells depends on lineage: aneuploid cells in the fetal lineage are eliminated by apoptosis, whereas those in the placental lineage show severe proliferative defects. Overall, the proportion of aneuploid cells is progressively depleted from the blastocyst stage onwards. Finally, we show that mosaic embryos have full developmental potential, provided they contain sufficient euploid cells, a finding of significance for the assessment of embryo vitality in the clinic.

  19. Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells

    Directory of Open Access Journals (Sweden)

    Yener Bülent

    2007-10-01

    Full Text Available Abstract Background Recently, we demonstrated that human mesenchymal stem cells (hMSC stimulated with dexamethazone undergo gene focusing during osteogenic differentiation (Stem Cells Dev 14(6: 1608–20, 2005. Here, we examine the protein expression profiles of three additional populations of hMSC stimulated to undergo osteogenic differentiation via either contact with pro-osteogenic extracellular matrix (ECM proteins (collagen I, vitronectin, or laminin-5 or osteogenic media supplements (OS media. Specifically, we annotate these four protein expression profiles, as well as profiles from naïve hMSC and differentiated human osteoblasts (hOST, with known gene ontologies and analyze them as a tensor with modes for the expressed proteins, gene ontologies, and stimulants. Results Direct component analysis in the gene ontology space identifies three components that account for 90% of the variance between hMSC, osteoblasts, and the four stimulated hMSC populations. The directed component maps the differentiation stages of the stimulated stem cell populations along the differentiation axis created by the difference in the expression profiles of hMSC and hOST. Surprisingly, hMSC treated with ECM proteins lie closer to osteoblasts than do hMSC treated with OS media. Additionally, the second component demonstrates that proteomic profiles of collagen I- and vitronectin-stimulated hMSC are distinct from those of OS-stimulated cells. A three-mode tensor analysis reveals additional focus proteins critical for characterizing the phenotypic variations between naïve hMSC, partially differentiated hMSC, and hOST. Conclusion The differences between the proteomic profiles of OS-stimulated hMSC and ECM-hMSC characterize different transitional phenotypes en route to becoming osteoblasts. This conclusion is arrived at via a three-mode tensor analysis validated using hMSC plated on laminin-5.

  20. Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation.

    Science.gov (United States)

    Löffler, Markus W; Kowalewski, Daniel J; Backert, Linus; Bernhardt, Jörg; Adam, Patrick; Schuster, Heiko; Dengler, Florian; Backes, Daniel; Kopp, Hans-Georg; Beckert, Stefan; Wagner, Silvia; Königsrainer, Ingmar; Kohlbacher, Oliver; Kanz, Lothar; Königsrainer, Alfred; Rammensee, Hans-Georg; Stevanovic, Stefan; Haen, Sebastian P

    2018-05-22

    Immune cell infiltrates have proven highly relevant for colorectal carcinoma (CRC) prognosis, making CRC a promising candidate for immunotherapy. Since tumors interact with the immune system via HLA-presented peptide ligands, exact knowledge of the peptidome constitution is fundamental for understanding this relationship. Here we comprehensively describe the naturally presented HLA-ligandome of CRC and corresponding non-malignant colon (NMC) tissue. Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands on CRC and NMC, attributable to 7,684 and 6,312 distinct source proteins, respectively. Cancer-exclusive peptides were assessed on source protein level using Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein analysis through evolutionary relationships (PANTHER), revealing pathognomonic CRC-associated pathways including Wnt, TGF-β, PI3K, p53, and RTK-RAS. Relative quantitation of peptide presentation on paired CRC and NMC tissue further identified source proteins from cancer- and infection-associated pathways to be over-represented merely within the CRC ligandome. From the pool of tumor-exclusive peptides, a selected HLA-ligand subset was assessed for immunogenicity, with the majority exhibiting an existing T cell repertoire. Overall, these data show that the HLA-ligandome reflects cancer-associated pathways implicated in CRC oncogenesis, suggesting that alterations in tumor cell metabolism could result in cancer-specific, albeit not mutation-derived tumor-antigens. Hence, a defined pool of unique tumor peptides, attributable to complex cellular alterations that are exclusive to malignant cells might comprise promising candidates for immunotherapeutic applications. Copyright ©2018, American Association for Cancer Research.

  1. Granular materials flow like complex fluids

    Science.gov (United States)

    Kou, Binquan; Cao, Yixin; Li, Jindong; Xia, Chengjie; Li, Zhifeng; Dong, Haipeng; Zhang, Ang; Zhang, Jie; Kob, Walter; Wang, Yujie

    2017-11-01

    Granular materials such as sand, powders and foams are ubiquitous in daily life and in industrial and geotechnical applications. These disordered systems form stable structures when unperturbed, but in the presence of external influences such as tapping or shear they `relax', becoming fluid in nature. It is often assumed that the relaxation dynamics of granular systems is similar to that of thermal glass-forming systems. However, so far it has not been possible to determine experimentally the dynamic properties of three-dimensional granular systems at the particle level. This lack of experimental data, combined with the fact that the motion of granular particles involves friction (whereas the motion of particles in thermal glass-forming systems does not), means that an accurate description of the relaxation dynamics of granular materials is lacking. Here we use X-ray tomography to determine the microscale relaxation dynamics of hard granular ellipsoids subject to an oscillatory shear. We find that the distribution of the displacements of the ellipsoids is well described by a Gumbel law (which is similar to a Gaussian distribution for small displacements but has a heavier tail for larger displacements), with a shape parameter that is independent of the amplitude of the shear strain and of the time. Despite this universality, the mean squared displacement of an individual ellipsoid follows a power law as a function of time, with an exponent that does depend on the strain amplitude and time. We argue that these results are related to microscale relaxation mechanisms that involve friction and memory effects (whereby the motion of an ellipsoid at a given point in time depends on its previous motion). Our observations demonstrate that, at the particle level, the dynamic behaviour of granular systems is qualitatively different from that of thermal glass-forming systems, and is instead more similar to that of complex fluids. We conclude that granular materials can relax

  2. Small-signal analysis of granular semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Varpula, Aapo; Sinkkonen, Juha; Novikov, Sergey, E-mail: aapo.varpula@tkk.f [Department of Micro and Nanosciences, Aalto University, PO Box 13500, FI-00076 Aalto, Espoo (Finland)

    2010-11-01

    The small-signal ac response of granular n-type semiconductors is calculated analytically using the drift-diffusion theory when electronic trapping at grain boundaries is present. An electrical equivalent circuit (EEC) model of a granular n-type semiconductor is presented. The analytical model is verified with numerical simulation performed by SILVACO ATLAS. The agreement between the analytical and numerical results is very good in a broad frequency range at low dc bias voltages.

  3. Small-signal analysis of granular semiconductors

    International Nuclear Information System (INIS)

    Varpula, Aapo; Sinkkonen, Juha; Novikov, Sergey

    2010-01-01

    The small-signal ac response of granular n-type semiconductors is calculated analytically using the drift-diffusion theory when electronic trapping at grain boundaries is present. An electrical equivalent circuit (EEC) model of a granular n-type semiconductor is presented. The analytical model is verified with numerical simulation performed by SILVACO ATLAS. The agreement between the analytical and numerical results is very good in a broad frequency range at low dc bias voltages.

  4. A constitutive law for dense granular flows.

    Science.gov (United States)

    Jop, Pierre; Forterre, Yoël; Pouliquen, Olivier

    2006-06-08

    A continuum description of granular flows would be of considerable help in predicting natural geophysical hazards or in designing industrial processes. However, the constitutive equations for dry granular flows, which govern how the material moves under shear, are still a matter of debate. One difficulty is that grains can behave like a solid (in a sand pile), a liquid (when poured from a silo) or a gas (when strongly agitated). For the two extreme regimes, constitutive equations have been proposed based on kinetic theory for collisional rapid flows, and soil mechanics for slow plastic flows. However, the intermediate dense regime, where the granular material flows like a liquid, still lacks a unified view and has motivated many studies over the past decade. The main characteristics of granular liquids are: a yield criterion (a critical shear stress below which flow is not possible) and a complex dependence on shear rate when flowing. In this sense, granular matter shares similarities with classical visco-plastic fluids such as Bingham fluids. Here we propose a new constitutive relation for dense granular flows, inspired by this analogy and recent numerical and experimental work. We then test our three-dimensional (3D) model through experiments on granular flows on a pile between rough sidewalls, in which a complex 3D flow pattern develops. We show that, without any fitting parameter, the model gives quantitative predictions for the flow shape and velocity profiles. Our results support the idea that a simple visco-plastic approach can quantitatively capture granular flow properties, and could serve as a basic tool for modelling more complex flows in geophysical or industrial applications.

  5. Diversity of Neuropeptide Cell-Cell Signaling Molecules Generated by Proteolytic Processing Revealed by Neuropeptidomics Mass Spectrometry

    Science.gov (United States)

    Hook, Vivian; Lietz, Christopher B.; Podvin, Sonia; Cajka, Tomas; Fiehn, Oliver

    2018-04-01

    Neuropeptides are short peptides in the range of 3-40 residues that are secreted for cell-cell communication in neuroendocrine systems. In the nervous system, neuropeptides comprise the largest group of neurotransmitters. In the endocrine system, neuropeptides function as peptide hormones to coordinate intercellular signaling among target physiological systems. The diversity of neuropeptide functions is defined by their distinct primary sequences, peptide lengths, proteolytic processing of pro-neuropeptide precursors, and covalent modifications. Global, untargeted neuropeptidomics mass spectrometry is advantageous for defining the structural features of the thousands to tens of thousands of neuropeptides present in biological systems. Defining neuropeptide structures is the basis for defining the proteolytic processing pathways that convert pro-neuropeptides into active peptides. Neuropeptidomics has revealed that processing of pro-neuropeptides occurs at paired basic residues sites, and at non-basic residue sites. Processing results in neuropeptides with known functions and generates novel peptides representing intervening peptide domains flanked by dibasic residue processing sites, identified by neuropeptidomics. While very short peptide products of 2-4 residues are predicted from pro-neuropeptide dibasic processing sites, such peptides have not been readily identified; therefore, it will be logical to utilize metabolomics to identify very short peptides with neuropeptidomics in future studies. Proteolytic processing is accompanied by covalent post-translational modifications (PTMs) of neuropeptides comprising C-terminal amidation, N-terminal pyroglutamate, disulfide bonds, phosphorylation, sulfation, acetylation, glycosylation, and others. Neuropeptidomics can define PTM features of neuropeptides. In summary, neuropeptidomics for untargeted, global analyses of neuropeptides is essential for elucidation of proteases that generate diverse neuropeptides for cell-cell

  6. Diversity of Neuropeptide Cell-Cell Signaling Molecules Generated by Proteolytic Processing Revealed by Neuropeptidomics Mass Spectrometry

    Science.gov (United States)

    Hook, Vivian; Lietz, Christopher B.; Podvin, Sonia; Cajka, Tomas; Fiehn, Oliver

    2018-05-01

    Neuropeptides are short peptides in the range of 3-40 residues that are secreted for cell-cell communication in neuroendocrine systems. In the nervous system, neuropeptides comprise the largest group of neurotransmitters. In the endocrine system, neuropeptides function as peptide hormones to coordinate intercellular signaling among target physiological systems. The diversity of neuropeptide functions is defined by their distinct primary sequences, peptide lengths, proteolytic processing of pro-neuropeptide precursors, and covalent modifications. Global, untargeted neuropeptidomics mass spectrometry is advantageous for defining the structural features of the thousands to tens of thousands of neuropeptides present in biological systems. Defining neuropeptide structures is the basis for defining the proteolytic processing pathways that convert pro-neuropeptides into active peptides. Neuropeptidomics has revealed that processing of pro-neuropeptides occurs at paired basic residues sites, and at non-basic residue sites. Processing results in neuropeptides with known functions and generates novel peptides representing intervening peptide domains flanked by dibasic residue processing sites, identified by neuropeptidomics. While very short peptide products of 2-4 residues are predicted from pro-neuropeptide dibasic processing sites, such peptides have not been readily identified; therefore, it will be logical to utilize metabolomics to identify very short peptides with neuropeptidomics in future studies. Proteolytic processing is accompanied by covalent post-translational modifications (PTMs) of neuropeptides comprising C-terminal amidation, N-terminal pyroglutamate, disulfide bonds, phosphorylation, sulfation, acetylation, glycosylation, and others. Neuropeptidomics can define PTM features of neuropeptides. In summary, neuropeptidomics for untargeted, global analyses of neuropeptides is essential for elucidation of proteases that generate diverse neuropeptides for cell-cell

  7. Proteomics investigation reveals cell death-associated proteins of basidiomycete fungus Trametes versicolor treated with Ferruginol.

    Science.gov (United States)

    Chen, Yu-Han; Yeh, Ting-Feng; Chu, Fang-Hua; Hsu, Fu-Lan; Chang, Shang-Tzen

    2015-01-14

    Ferruginol has antifungal activity against wood-rot fungi (basidiomycetes). However, specific research on the antifungal mechanisms of ferruginol is scarce. Two-dimensional gel electrophoresis and fluorescent image analysis were employed to evaluate the differential protein expression of wood-rot fungus Trametes versicolor treated with or without ferruginol. Results from protein identification of tryptic peptides via liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI-MS/MS) analyses revealed 17 protein assignments with differential expression. Downregulation of cytoskeleton β-tubulin 3 indicates that ferruginol has potential to be used as a microtubule-disrupting agent. Downregulation of major facilitator superfamily (MFS)–multiple drug resistance (MDR) transporter and peroxiredoxin TSA1 were observed, suggesting reduction in self-defensive capabilities of T. versicolor. In addition, the proteins involved in polypeptide sorting and DNA repair were also downregulated, while heat shock proteins and autophagy-related protein 7 were upregulated. These observations reveal that such cellular dysfunction and damage caused by ferruginol lead to growth inhibition and autophagic cell death of fungi.

  8. Harmonic generation and flux quantization in granular superconductors

    International Nuclear Information System (INIS)

    Lam, Q.H.; Jeffries, C.D.

    1989-01-01

    Simple dynamical models of granular superconductors are used to compute the generation of harmonic power in ac and dc magnetic fields. In zero order, the model is a single superconducting loop, with or without a weak link. The sample-average power is predicted by averaging over suitable distribution functions for loop areas and orientations in a dc magnetic field. In a first-order model, inductance and resistance are also included. In all models the power at high harmonics shows strikingly sharp dips periodic in the dc field, revealing flux quantization in the prototype loops

  9. Phenotypic diversity of diploid and haploid Emiliania huxleyi cells and of cells in different growth phases revealed by comparative metabolomics.

    Science.gov (United States)

    Mausz, Michaela A; Pohnert, Georg

    2015-01-01

    In phytoplankton a high species diversity of microalgae co-exists at a given time. But diversity is not only reflected by the species composition. Within these species different life phases as well as different metabolic states can cause additional diversity. One important example is the coccolithophore Emiliania huxleyi. Diploid cells play an important role in marine ecosystems since they can form massively abundant algal blooms but in addition the less abundant haploid life phase of E. huxleyi occurs in lower quantities. Both life phases may fulfill different functions in the plankton. We hypothesize that in addition to the functional diversity caused by this life phase transition the growth stage of cells can also influence the metabolic composition and thus the ecological impact of E. huxleyi. Here we introduce a metabolomic survey in dependence of life phases as well as different growth phases to reveal such changes. The comparative metabolomic approach is based on the extraction of intracellular metabolites from intact microalgae, derivatization and analysis by gas chromatography coupled to mass spectrometry (GC-MS). Automated data processing and statistical analysis using canonical analysis of principal coordinates (CAP) revealed unique metabolic profiles for each life phase. Concerning the correlations of metabolites to growth phases, complex patterns were observed. As for example the saccharide mannitol showed its highest concentration in the exponential phase, whereas fatty acids were correlated to stationary and sterols to declining phase. These results are indicative for specific ecological roles of these stages of E. huxleyi and are discussed in the context of previous physiological and ecological studies. Copyright © 2014 Elsevier GmbH. All rights reserved.

  10. 3-D Imaging Reveals Participation of Donor Islet Schwann Cells and Pericytes in Islet Transplantation and Graft Neurovascular Regeneration.

    Science.gov (United States)

    Juang, Jyuhn-Huarng; Kuo, Chien-Hung; Peng, Shih-Jung; Tang, Shiue-Cheng

    2015-02-01

    The primary cells that participate in islet transplantation are the endocrine cells. However, in the islet microenvironment, the endocrine cells are closely associated with the neurovascular tissues consisting of the Schwann cells and pericytes, which form sheaths/barriers at the islet exterior and interior borders. The two cell types have shown their plasticity in islet injury, but their roles in transplantation remain unclear. In this research, we applied 3-dimensional neurovascular histology with cell tracing to reveal the participation of Schwann cells and pericytes in mouse islet transplantation. Longitudinal studies of the grafts under the kidney capsule identify that the donor Schwann cells and pericytes re-associate with the engrafted islets at the peri-graft and perivascular domains, respectively, indicating their adaptability in transplantation. Based on the morphological proximity and cellular reactivity, we propose that the new islet microenvironment should include the peri-graft Schwann cell sheath and perivascular pericytes as an integral part of the new tissue.

  11. Dynamic Deformation and Collapse of Granular Columns

    Science.gov (United States)

    Uenishi, K.; Tsuji, K.; Doi, S.

    2009-12-01

    Large dynamic deformation of granular materials may be found in nature not only in the failure of slopes and cliffs — due to earthquakes, rock avalanches, debris flows and landslides — but also in earthquake faulting itself. Granular surface flows often consist of solid grains and intergranular fluid, but the effect of the fluid may be usually negligible because the volumetric concentration of grains is in many cases high enough for interparticle forces to dominate momentum transport. Therefore, the investigation of dry granular flow of a mass might assist in further understanding of the above mentioned geophysical events. Here, utilizing a high-speed digital video camera system, we perform a simple yet fully-controlled series of laboratory experiments related to the collapse of granular columns. We record, at an interval of some microseconds, the dynamic transient granular mass flow initiated by abrupt release of a tube that contains dry granular materials. The acrylic tube is partially filled with glass beads and has a cross-section of either a fully- or semi-cylindrical shape. Upon sudden removal of the tube, the granular solid may fragment under the action of its own weight and the particles spread on a rigid horizontal plane. This study is essentially the extension of the previous ones by Lajeunesse et al. (Phys. Fluids 2004) and Uenishi and Tsuji (JPGU 2008), but the striped layers of particles in a semi-cylindrical tube, newly introduced in this contribution, allow us to observe the precise particle movement inside the granular column: The development of slip lines inside the column and the movement of particles against each other can be clearly identified. The major controlling parameters of the spreading dynamics are the initial aspect ratio of the granular (semi-)cylindrical column, the frictional properties of the horizontal plane (substrate) and the size of beads. We show the influence of each parameter on the average flow velocity and final radius

  12. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2014-01-01

    . Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Conclusions Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity. PMID:24422981

  13. Leucemia de grandes linfócitos granulares Large granular lymphocyte leukemia

    Directory of Open Access Journals (Sweden)

    Bruno Terra

    2010-01-01

    Full Text Available O presente estudo tem como objetivo o estabelecimento de fundamentação teórica atualizada baseada em revisão bibliográfica sobre a leucemia de grandes linfócitos granulares (LGLG, doença onco-hematológica, que, devido à sua relativa raridade, é pouco conhecida e subdiagnosticada. A LGLG é caracterizada pela proliferação clonal de linfócitos T ou NK na medula óssea e/ou no sangue periférico. Dentre as manifestações clínico-laboratoriais, podem ocorrer citopenias (anemia e/ou neutropenia e/ou plaquetopenia, linfocitose (não costuma ser acentuada, linfadenomegalia, hepatoesplenomegalia, alterações imunológicas e sintomas constitucionais (emagrecimento, febre e sudorese. O curso clínico da LGLG é bastante variável, sendo que no subtipo T costuma ser indolente ou oligossintomática, enquanto no subtipo NK a evolução costuma ser desfavorável. O diagnóstico é firmado através de imunofenotipagem por citometria de fluxo e estudo de clonalidade por métodos de biologia molecular. Seu tratamento é bastante diversificado e é definido de acordo com a apresentação clínica da doença.This is a literature review about large granular lymphocyte leukemia (LGLL, a rare and misdiagnosed oncohematological disease, characterized by a clonal expansion of T-cells (T-LGLL or NK-cells (NK-LGLL in the bone marrow and/or peripheral blood. The clinical features of LGLL include cytopenias (anemia, neutropenia and thrombocytopenia, lymphocytosis (usually discrete, lymphadenopathy, hepatomegaly, splenomegaly, immune abnormalities and constitutional symptoms (fever, night sweats and weight loss. The diagnosis is based on the confirmation of the clonality of T-cells or NK-cells (polymerase chain reaction and Southern blot are the two methods most commonly used and typical findings of the immunophenotypic analysis of peripheral blood lymphocytes (flow cytometry analyses for specific surface antigens. In contrast to the chronic and indolent

  14. Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states

    Science.gov (United States)

    Toan, Ngo Minh; Thirumalai, D.

    2018-03-01

    Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling experiments using atomic force spectroscopy on leukocyte function-associated antigen-1 (LFA-1), expressed in T-cells, bound to intercellular adhesion molecules (ICAM), we performed constant loading rate (rf) and constant force (F) simulations using the self-organized polymer model to describe the mechanism of ligand rupture from CACs. The simulations reproduce the major experimental finding on the kinetics of the rupture process, namely, the dependence of the most probable rupture forces (f*s) on ln rf (rf is the loading rate) exhibits two distinct linear regimes. The first, at low rf, has a shallow slope, whereas the slope at high rf is much larger, especially for a LFA-1/ICAM-1 complex with the transition between the two occurring over a narrow rf range. Locations of the two transition states (TSs) extracted from the simulations show an abrupt change from a high value at low rf or constant force, F, to a low value at high rf or F. This unusual behavior in which the CACs switch from one brittle (TS position is a constant over a range of forces) state to another brittle state is not found in forced-rupture in other protein complexes. We explain this novel behavior by constructing the free energy profiles, F(Λ)s, as a function of a collective reaction coordinate (Λ), involving many key charged residues and a critical metal ion (Mg2+). The TS positions in F(Λ), which quantitatively agree with the parameters extracted using the Bell-Evans model, change abruptly at a critical force, demonstrating that it, rather than the molecular extension, is a good reaction coordinate. Our combined analyses using simulations performed in both the pulling modes (constant rf and F) reveal a new mechanism for the two loading regimes observed in the

  15. Partition instability in water-immersed granular systems.

    Science.gov (United States)

    Clement, C P; Pacheco-Martinez, H A; Swift, Michael R; King, P J

    2009-07-01

    It is well known that a system of grains, vibrated vertically in a cell divided into linked columns, may spontaneously move into just one of the columns due to the inelastic nature of their collisions. Here we study the behavior of a water-immersed system of spherical barium titanate particles in a rectangular cell which is divided into two columns, linked by two connecting holes, one at the top and one at the bottom of the cell. Under vibration the grains spontaneously move into just one of the columns via a gradual transfer of grains through the connecting hole at the base of the cell. We have developed numerical simulations that are able to reproduce this behavior and provide detailed information on the instability mechanism. We use this knowledge to propose a simple analytical model for this fluid-driven partition instability based on two coupled granular beds vibrated within an incompressible fluid.

  16. An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas.

    Directory of Open Access Journals (Sweden)

    Priscila Daniele Ramos Cirilo

    Full Text Available Uterine Leiomyomas (ULs are the most common benign tumours affecting women of reproductive age. ULs represent a major problem in public health, as they are the main indication for hysterectomy. Approximately 40-50% of ULs have non-random cytogenetic abnormalities, and half of ULs may have copy number alterations (CNAs. Gene expression microarrays studies have demonstrated that cell proliferation genes act in response to growth factors and steroids. However, only a few genes mapping to CNAs regions were found to be associated with ULs.We applied an integrative analysis using genomic and transcriptomic data to identify the pathways and molecular markers associated with ULs. Fifty-one fresh frozen specimens were evaluated by array CGH (JISTIC and gene expression microarrays (SAM. The CONEXIC algorithm was applied to integrate the data.The integrated analysis identified the top 30 significant genes (P<0.01, which comprised genes associated with cancer, whereas the protein-protein interaction analysis indicated a strong association between FANCA and BRCA1. Functional in silico analysis revealed target molecules for drugs involved in cell proliferation, including FGFR1 and IGFBP5. Transcriptional and protein analyses showed that FGFR1 (P = 0.006 and P<0.01, respectively and IGFBP5 (P = 0.0002 and P = 0.006, respectively were up-regulated in the tumours when compared with the adjacent normal myometrium.The integrative genomic and transcriptomic approach indicated that FGFR1 and IGFBP5 amplification, as well as the consequent up-regulation of the protein products, plays an important role in the aetiology of ULs and thus provides data for potential drug therapies development to target genes associated with cellular proliferation in ULs.

  17. Improved flow cytometric assessment reveals distinct microvesicle (cell-derived microparticle signatures in joint diseases.

    Directory of Open Access Journals (Sweden)

    Bence György

    Full Text Available INTRODUCTION: Microvesicles (MVs, earlier referred to as microparticles, represent a major type of extracellular vesicles currently considered as novel biomarkers in various clinical settings such as autoimmune disorders. However, the analysis of MVs in body fluids has not been fully standardized yet, and there are numerous pitfalls that hinder the correct assessment of these structures. METHODS: In this study, we analyzed synovial fluid (SF samples of patients with osteoarthritis (OA, rheumatoid arthritis (RA and juvenile idiopathic arthritis (JIA. To assess factors that may confound MV detection in joint diseases, we used electron microscopy (EM, Nanoparticle Tracking Analysis (NTA and mass spectrometry (MS. For flow cytometry, a method commonly used for phenotyping and enumeration of MVs, we combined recent advances in the field, and used a novel approach of differential detergent lysis for the exclusion of MV-mimicking non-vesicular signals. RESULTS: EM and NTA showed that substantial amounts of particles other than MVs were present in SF samples. Beyond known MV-associated proteins, MS analysis also revealed abundant plasma- and immune complex-related proteins in MV preparations. Applying improved flow cytometric analysis, we demonstrate for the first time that CD3(+ and CD8(+ T-cell derived SF MVs are highly elevated in patients with RA compared to OA patients (p=0.027 and p=0.009, respectively, after Bonferroni corrections. In JIA, we identified reduced numbers of B cell-derived MVs (p=0.009, after Bonferroni correction. CONCLUSIONS: Our results suggest that improved flow cytometric assessment of MVs facilitates the detection of previously unrecognized disease-associated vesicular signatures.

  18. Granular Materials and Risks In ISRU

    Science.gov (United States)

    Behringer, Robert P.; Wilkinson, R. Allen

    2004-01-01

    Working with soil, sand, powders, ores, cement and sintered bricks, excavating, grading construction sites, driving off-road, transporting granules in chutes and pipes, sifting gravel, separating solids from gases, and using hoppers are so routine that it seems straightforward to execute these operations on the Moon and Mars as we do on Earth. We discuss how little these processes are understood and point out the nature of trial-and-error practices that are used in today's massive over-design. Nevertheless, such designs have a high failure rate. Implementation and extensive incremental scaling up of industrial processes are routine because of the inadequate predictive tools for design. We present a number of pragmatic scenarios where granular materials play a role, the risks involved, what some of the basic issues are, and what understanding is needed to greatly reduce the risks. This talk will focus on a particular class of granular flow issues, those that pertain to dense materials, their physics, and the failure problems associated with them. In particular, key issues where basic predictability is lacking include stability of soils for the support of vehicles and facilities, ability to control the flow of dense materials (jamming and flooding/unjamming at the wrong time), the ability to predict stress profiles (hence create reliable designs) for containers such as bunkers or silos. In particular, stress fluctuations, which are not accounted for in standard granular design models, can be very large as granular materials flows, and one result is frequent catastrophic failure of granular devices.

  19. Collapse of tall granular columns in fluid

    Science.gov (United States)

    Kumar, Krishna; Soga, Kenichi; Delenne, Jean-Yves

    2017-06-01

    Avalanches, landslides, and debris flows are geophysical hazards, which involve rapid mass movement of granular solids, water, and air as a multi-phase system. In order to describe the mechanism of immersed granular flows, it is important to consider both the dynamics of the solid phase and the role of the ambient fluid. In the present study, the collapse of a granular column in fluid is studied using 2D LBM - DEM. The flow kinematics are compared with the dry and buoyant granular collapse to understand the influence of hydrodynamic forces and lubrication on the run-out. In the case of tall columns, the amount of material destabilised above the failure plane is larger than that of short columns. Therefore, the surface area of the mobilised mass that interacts with the surrounding fluid in tall columns is significantly higher than the short columns. This increase in the area of soil - fluid interaction results in an increase in the formation of turbulent vortices thereby altering the deposit morphology. It is observed that the vortices result in the formation of heaps that significantly affects the distribution of mass in the flow. In order to understand the behaviour of tall columns, the run-out behaviour of a dense granular column with an initial aspect ratio of 6 is studied. The collapse behaviour is analysed for different slope angles: 0°, 2.5°, 5° and 7.5°.

  20. Proteomics analysis of dendritic cell activation by contact allergens reveals possible biomarkers regulated by Nrf2

    Energy Technology Data Exchange (ETDEWEB)

    Mussotter, Franz, E-mail: franz.mussotter@bfr.bund.de [German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Berlin (Germany); Tomm, Janina Melanie [Helmholtz Centre for Environmental Research (UFZ), Department of Molecular Systems Biology, Leipzig (Germany); El Ali, Zeina; Pallardy, Marc; Kerdine-Römer, Saadia [INSERM UMR 996, Univ Paris-Sud, Université Paris-Saclay, Chátenay-Malabry (France); Götz, Mario [German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Berlin (Germany); Bergen, Martin von [Helmholtz Centre for Environmental Research (UFZ), Department of Molecular Systems Biology, Leipzig (Germany); University of Leipzig, Institute of Biochemistry, Leipzig (Germany); Aalborg University, Department of Chemistry and Bioscience, Aalborg (Denmark); Haase, Andrea; Luch, Andreas [German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Berlin (Germany)

    2016-12-15

    Allergic contact dermatitis is a widespread disease with high clinical relevance affecting approximately 20% of the general population. Typically, contact allergens are low molecular weight electrophilic compounds which can activate the Keap1/Nrf2 pathway. We performed a proteomics study to reveal possible biomarkers for dendritic cell (DC) activation by contact allergens and to further elucidate the role of Keap1/Nrf2 signaling in this process. We used bone marrow derived dendritic cells (BMDCs) of wild-type (nrf2{sup +/+}) and Nrf2 knockout (nrf2{sup −/−}) mice and studied their response against the model contact sensitizers 2,4-dinitrochlorobenzene (DNCB), cinnamaldehyde (CA) and nickel(II) sulfate by 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE) in combination with electrospray ionization tandem mass spectrometry (ESI-MS/MS). Sodium dodecyl sulfate (SDS, 100 μM) served as irritant control. While treatment with nickel(II) sulfate and SDS had only little effects, CA and DNCB led to significant changes in protein expression. We found 18 and 30 protein spots up-regulated in wild-type cells treated with 50 and 100 μM CA, respectively. For 5 and 10 μM DNCB, 32 and 37 spots were up-regulated, respectively. Almost all of these proteins were not differentially expressed in nrf2{sup −/−} BMDCs, indicating an Nrf2-dependent regulation. Among them proteins were detected which are involved in oxidative stress and heat shock responses, as well as in signal transduction or basic cellular pathways. The applied approach allowed us to differentiate between Nrf2-dependent and Nrf2-independent cellular biomarkers differentially regulated upon allergen-induced DC activation. The data presented might contribute to the further development of suitable in vitro testing methods for chemical-mediated sensitization. - Highlights: • Contact allergens induce proteins involved in DC maturation Nrf2-dependently. • Induction of these proteins points to a functional

  1. Low dose irradiation of thyroid cells reveals a unique transcriptomic and epigenetic signature in RET/PTC-positive cells

    Energy Technology Data Exchange (ETDEWEB)

    Abou-El-Ardat, Khalil, E-mail: kabouela@sckcen.be [Radiobiology Unit, Molecular and Cellular Biology, GKD Building, Studiecentrum voor Kernenergie - Centre d' Etude de l' Energie Nucleaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); Monsieurs, Pieter [Radiobiology Unit, Molecular and Cellular Biology, GKD Building, Studiecentrum voor Kernenergie - Centre d' Etude de l' Energie Nucleaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Anastasov, Natasa; Atkinson, Mike [Department of Radiation Sciences, Helmholtz Zentrum Muenchen, Munich (Germany); Derradji, Hanane [Radiobiology Unit, Molecular and Cellular Biology, GKD Building, Studiecentrum voor Kernenergie - Centre d' Etude de l' Energie Nucleaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); De Meyer, Tim [Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); Department of Applied Mathematics, Biometrics and Process Control, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); Bekaert, Sofie [Clinical Research Center, Faculty for Medicine and Health Sciences, Universiteit Gent, 185 De Pintelaan, 9000 Ghent (Belgium); Van Criekinge, Wim [Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); and others

    2012-03-01

    The high doses of radiation received in the wake of the Chernobyl incident and the atomic bombing of Hiroshima and Nagasaki have been linked to the increased appearance of thyroid cancer in the children living in the vicinity of the site. However, the data gathered on the effect of low doses of radiation on the thyroid remain limited. We have examined the genome wide transcriptional response of a culture of TPC-1 human cell line of papillary thyroid carcinoma origin with a RET/PTC1 translocation to various doses (0.0625, 0.5, and 4 Gy) of X-rays and compared it to response of thyroids with a RET/PTC3 translocation and against wild-type mouse thyroids irradiated with the same doses using Affymetrix microarrays. We have found considerable overlap at a high dose of 4 Gy in both RET/PTC-positive systems but no common genes at 62.5 mGy. In addition, the response of RET/PTC-positive system at all doses was distinct from the response of wild-type thyroids with both systems signaling down different pathways. Analysis of the response of microRNAs in TPC-1 cells revealed a radiation-responsive signature of microRNAs in addition to dose-responsive microRNAs. Our results point to the fact that a low dose of X-rays seems to have a significant proliferative effect on normal thyroids. This observation should be studied further as opposed to its effect on RET/PTC-positive thyroids which was subtle, anti-proliferative and system-dependent.

  2. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

    Science.gov (United States)

    Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

    2017-11-06

    Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

  3. Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.

    Science.gov (United States)

    Klopffleisch, Karsten; Phan, Nguyen; Augustin, Kelsey; Bayne, Robert S; Booker, Katherine S; Botella, Jose R; Carpita, Nicholas C; Carr, Tyrell; Chen, Jin-Gui; Cooke, Thomas Ryan; Frick-Cheng, Arwen; Friedman, Erin J; Fulk, Brandon; Hahn, Michael G; Jiang, Kun; Jorda, Lucia; Kruppe, Lydia; Liu, Chenggang; Lorek, Justine; McCann, Maureen C; Molina, Antonio; Moriyama, Etsuko N; Mukhtar, M Shahid; Mudgil, Yashwanti; Pattathil, Sivakumar; Schwarz, John; Seta, Steven; Tan, Matthew; Temp, Ulrike; Trusov, Yuri; Urano, Daisuke; Welter, Bastian; Yang, Jing; Panstruga, Ralph; Uhrig, Joachim F; Jones, Alan M

    2011-09-27

    The heterotrimeric G-protein complex is minimally composed of Gα, Gβ, and Gγ subunits. In the classic scenario, the G-protein complex is the nexus in signaling from the plasma membrane, where the heterotrimeric G-protein associates with heptahelical G-protein-coupled receptors (GPCRs), to cytoplasmic target proteins called effectors. Although a number of effectors are known in metazoans and fungi, none of these are predicted to exist in their canonical forms in plants. To identify ab initio plant G-protein effectors and scaffold proteins, we screened a set of proteins from the G-protein complex using two-hybrid complementation in yeast. After deep and exhaustive interrogation, we detected 544 interactions between 434 proteins, of which 68 highly interconnected proteins form the core G-protein interactome. Within this core, over half of the interactions comprising two-thirds of the nodes were retested and validated as genuine in planta. Co-expression analysis in combination with phenotyping of loss-of-function mutations in a set of core interactome genes revealed a novel role for G-proteins in regulating cell wall modification.

  4. Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures.

    Directory of Open Access Journals (Sweden)

    Moon Young Lee

    Full Text Available Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC, which serve as slow-wave electrical pacemakers for gastrointestinal (GI smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies.

  5. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  6. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-09

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  7. Biomarker screening of oral cancer cell lines revealed sub-populations of CD133-, CD44-, CD24- and ALDH1- positive cancer stem cells

    Directory of Open Access Journals (Sweden)

    Kendall K

    2013-05-01

    Full Text Available Head and neck squamous cell carcinoma (HNSCC ranks sixth worldwide for cancer-related mortality. For the past several decades the mainstay of treatment for HNSCC has been surgery and external beam radiation, although more recent trials combining chemotherapy and radiation have demonstrated improvements. However, cancer recurrence and treatment failures continue to occur in a significant percentage of patients. Recent advances in tumor biology have led to the discovery that many cancers, including HNSCC, may contain subpopulations of cells with stem cell-like properties that may explain relapse and recurrence. The objective of this study was to screen existing oral cancer cell lines for biomarkers specific for cells with stem cell-like properties. RNA was isolated for RT-PCR screening using primers for specific mRNA of the biomarkers: CD44, CD24, CD133, NANOG, Nestin, ALDH1, and ABCG2 in CAL27, SCC25 and SCC15 cells. This analysis revealed that some oral cancer cell lines (CAL27 and SCC25 may contain small subpopulations of adhesion- and contact-independent cells (AiDC that also express tumor stem cell markers, including CD44, CD133, and CD24. In addition, CAL27 cells also expressed the intracellular tumor stem cell markers, ALDH1 and ABCG2. Isolation and culture of the adhesion- and contact-independent cells from CAL27 and SCC25 populations revealed differential proliferation rates and more robust inhibition by the MEK inhibitor PD98059, as well as the chemotherapeutic agents Cisplatin and Paclitaxel, within the AiDC CAL27 cells. At least one oral cancer cell line (CAL27 contained subpopulations of cells that express specific biomarkers associated with tumor stem cells which were morphologically and phenotypically distinct from other cells within this cell line.

  8. Single cell time-lapse analysis reveals that podoplanin enhances cell survival and colony formation capacity of squamous cell carcinoma cells.

    Science.gov (United States)

    Miyashita, Tomoyuki; Higuchi, Youichi; Kojima, Motohiro; Ochiai, Atsushi; Ishii, Genichiro

    2017-01-06

    Tumor initiating cells (TICs) are characterized by high clonal expansion capacity. We previously reported that podoplanin is a TIC-specific marker for the human squamous cell carcinoma cell line A431. The aim of this study is to explore the molecular mechanism underlying the high clonal expansion potential of podoplanin-positive A431cells using Fucci imaging. Single podoplanin-positive cells created large colonies at a significantly higher frequency than single podoplanin-negative cells, whereas no difference was observed between the two types of cells with respect to cell cycle status. Conversely, the cell death ratio of progenies derived from podoplanin-positive single cell was significantly lower than that of cells derived from podoplanin-negative cells. Single A431 cells, whose podoplanin expression was suppressed by RNA interference, exhibited increased cell death ratios and decreased frequency of large colony forming. Moreover, the frequency of large colony forming decreased significantly when podoplanin-positive single cells was treated with a ROCK (Rho-associated coiled-coil kinase) inhibitor, whereas no difference was observed in single podoplanin-negative cells. Our current study cleared that high clonal expansion capacity of podoplanin-positive TICs populations was the result of reduced cell death by podoplanin-mediated signaling. Therefore, podoplanin activity may be a therapeutic target in the treatment of squamous cell carcinomas.

  9. Wet granular matter a truly complex fluid

    CERN Document Server

    Herminghaus, Stephan

    2013-01-01

    This is a monograph written for the young and advanced researcher who is entering the field of wet granular matter and keen to understand the basic physical principles governing this state of soft matter. It treats wet granulates as an instance of a ternary system, consisting of the grains, a primary, and a secondary fluid. After addressing wetting phenomena in general and outlining the basic facts on dry granular systems, a chapter on basic mechanisms and their effects is dedicated to every region of the ternary phase diagram. Effects of grain shape and roughness are considered as well. Rather than addressing engineering aspects such as existing books on this topic do, the book aims to provide a generalized framework suitable for those who want to understand these systems on a more fundamental basis. Readership: For the young and advanced researcher entering the field of wet granular matter.

  10. 11th Traffic and Granular Flow Conference

    CERN Document Server

    Daamen, Winnie

    2016-01-01

    The Conference on Traffic and Granular Flow brings together international researchers from different fields ranging from physics to computer science and engineering to discuss the latest developments in traffic-related systems. Originally conceived to facilitate new ideas by considering the similarities of traffic and granular flow, TGF'15, organised by Delft University of Technology, now covers a broad range of topics related to driven particle and transport systems. Besides the classical topics of granular flow and highway traffic, its scope includes data transport (Internet traffic), pedestrian and evacuation dynamics, intercellular transport, swarm behaviour and the collective dynamics of other biological systems. Recent advances in modelling, computer simulation and phenomenology are presented, and prospects for applications, for example to traffic control, are discussed. The conference explores the interrelations between the above-mentioned fields and offers the opportunity to stimulate interdisciplinar...

  11. Granular Silo collapse: an experimental study

    Science.gov (United States)

    Clement, Eric; Gutierriez, Gustavo; Boltenhagen, Philippe; Lanuza, Jose

    2008-03-01

    We present an experimental work that develop some basic insight into the pre-buckling behavior and the buckling transition toward plastic collapse of a granular silo. We study different patterns of deformation generated on thin paper cylindrical shells during granular discharge. We study the collapse threshold for different bed height, flow rates and grain sizes. We compare the patterns that appear during the discharge of spherical beads, with those obtained in the axially compressed cylindrical shells. When the height of the granular column is close to the collapse threshold, we describe a ladder like pattern that rises around the cylinder surface in a spiral path of diamond shaped localizations, and develops into a plastic collapsing fold that grows around the collapsing silo.

  12. Statistical mechanics of dense granular media

    International Nuclear Information System (INIS)

    Coniglio, A; Fierro, A; Nicodemi, M; Ciamarra, M Pica; Tarzia, M

    2005-01-01

    We discuss some recent results on the statistical mechanics approach to dense granular media. In particular, by analytical mean field investigation we derive the phase diagram of monodisperse and bidisperse granular assemblies. We show that 'jamming' corresponds to a phase transition from a 'fluid' to a 'glassy' phase, observed when crystallization is avoided. The nature of such a 'glassy' phase turns out to be the same as found in mean field models for glass formers. This gives quantitative evidence for the idea of a unified description of the 'jamming' transition in granular media and thermal systems, such as glasses. We also discuss mixing/segregation transitions in binary mixtures and their connections to phase separation and 'geometric' effects

  13. Lift on side by side intruders of various geometries within a granular flow

    Science.gov (United States)

    Acevedo-Escalante, M. F.; Caballero-Robledo, G. A.

    2017-06-01

    Obstacles within fluids have been widely used in engineering and in physics to study hydrodynamic interactions. In granular matter, objects within a granular flow have helped to understand fundamental features of drag and lift forces. In our group, we have studied numerically the flow mediated interaction between two static disks within a vertical granular flow in a two-dimensional container where the flow velocity and the distance between obstacles were varied. Attractive and repulsive forces were found depending on flow velocity and separation between intruders. The simulations evidenced a relationship between the average flow velocity in a specific section ahead of the obstacles and the attractive-repulsive lift. On the other hand, it was showed that the lift force on an object dragged within a granular medium depends on the shape of the intruder. Here we present experimental results of the interaction between two side-by-side intruders of different shapes within a vertical granular flow. We built a quasi-two-dimensional container in which we placed the intruders and using load cells we measured lift and drag forces during the discharge process for different flow velocities.

  14. 76 FR 8774 - Granular Polytetrafluoroethylene Resin From Japan

    Science.gov (United States)

    2011-02-15

    ... INTERNATIONAL TRADE COMMISSION [Investigation No. 731-TA-386 (Third Review)] Granular Polytetrafluoroethylene Resin From Japan AGENCY: United States International Trade Commission. ACTION: Termination of five... revocation of the antidumping duty order on granular polytetrafluoroethylene resin from Japan would be likely...

  15. Surface instabilities in shock loaded granular media

    Science.gov (United States)

    Kandan, K.; Khaderi, S. N.; Wadley, H. N. G.; Deshpande, V. S.

    2017-12-01

    The initiation and growth of instabilities in granular materials loaded by air shock waves are investigated via shock-tube experiments and numerical calculations. Three types of granular media, dry sand, water-saturated sand and a granular solid comprising PTFE spheres were experimentally investigated by air shock loading slugs of these materials in a transparent shock tube. Under all shock pressures considered here, the free-standing dry sand slugs remained stable while the shock loaded surface of the water-saturated sand slug became unstable resulting in mixing of the shocked air and the granular material. By contrast, the PTFE slugs were stable at low pressures but displayed instabilities similar to the water-saturated sand slugs at higher shock pressures. The distal surfaces of the slugs remained stable under all conditions considered here. Eulerian fluid/solid interaction calculations, with the granular material modelled as a Drucker-Prager solid, reproduced the onset of the instabilities as seen in the experiments to a high level of accuracy. These calculations showed that the shock pressures to initiate instabilities increased with increasing material friction and decreasing yield strain. Moreover, the high Atwood number for this problem implied that fluid/solid interaction effects were small, and the initiation of the instability is adequately captured by directly applying a pressure on the slug surface. Lagrangian calculations with the directly applied pressures demonstrated that the instability was caused by spatial pressure gradients created by initial surface perturbations. Surface instabilities are also shown to exist in shock loaded rear-supported granular slugs: these experiments and calculations are used to infer the velocity that free-standing slugs need to acquire to initiate instabilities on their front surfaces. The results presented here, while in an idealised one-dimensional setting, provide physical understanding of the conditions required to

  16. Critical state flow rules for CFD simulations of wet granular flows

    NARCIS (Netherlands)

    Schwarze, R.; Gladkyy, A.; Luding, Stefan; E. Onate M. Bischoff, E. Ramm; P. Wriggers,

    2013-01-01

    First rheological investigation results of weakly wet granular media are presented. The materials have been examined experimentally and numerically in well- defined shear configurations in steady state, in the intermediate flow regime. For the experiments, a Searl-type ring shear cell with rotating

  17. Metabolic profiling reveals potential metabolic markers associated with Hypoxia Inducible Factor-mediated signalling in hypoxic cancer cells.

    Science.gov (United States)

    Armitage, Emily G; Kotze, Helen L; Allwood, J William; Dunn, Warwick B; Goodacre, Royston; Williams, Kaye J

    2015-10-28

    Hypoxia inducible factors (HIFs) plays an important role in oxygen compromised environments and therefore in tumour survival. In this research, metabolomics has been applied to study HIFs metabolic function in two cell models: mouse hepatocellular carcinoma and human colon carcinoma, whereby the metabolism has been profiled for a range of oxygen potentials. Wild type cells have been compared to cells deficient in HIF signalling to reveal its effect on cellular metabolism under normal oxygen conditions as well as low oxygen, hypoxic and anoxic environments. Characteristic responses to hypoxia that were conserved across both cell models involved the anti-correlation between 2-hydroxyglutarate, 2-oxoglutarate, fructose, hexadecanoic acid, hypotaurine, pyruvate and octadecenoic acid with 4-hydroxyproline, aspartate, cysteine, glutamine, lysine, malate and pyroglutamate. Further to this, network-based correlation analysis revealed HIF specific pathway responses to each oxygen condition that were also conserved between cell models. From this, 4-hydroxyproline was revealed as a regulating hub in low oxygen survival of WT cells while fructose appeared to be in HIF deficient cells. Pathways surrounding these hubs were built from the direct connections of correlated metabolites that look beyond traditional pathways in order to understand the mechanism of HIF response to low oxygen environments.

  18. Anaerobic granular sludge and biofilm reactors

    DEFF Research Database (Denmark)

    Skiadas, Ioannis V.; Gavala, Hariklia N.; Schmidt, Jens Ejbye

    2003-01-01

    by the immobilization of the biomass, which forms static biofilms, particle-supported biofilms, or granules depending on the reactor's operational conditions. The advantages of the high-rate anaerobic digestion over the conventional aerobic wastewater treatment methods has created a clear trend for the change......-rate anaerobic treatment systems based on anaerobic granular sludge and biofilm are described in this chapter. Emphasis is given to a) the Up-flow Anaerobic Sludge Blanket (UASB) systems, b) the main characteristics of the anaerobic granular sludge, and c) the factors that control the granulation process...

  19. Anisotropy in cohesive, frictional granular media

    International Nuclear Information System (INIS)

    Luding, Stefan

    2005-01-01

    The modelling of cohesive, frictional granular materials with a discrete particle molecular dynamics is reviewed. From the structure of the quasi-static granular solid, the fabric, stress, and stiffness tensors are determined, including both normal and tangential forces. The influence of the material properties on the flow behaviour is also reported, including relations between the microscopic attractive force and the macroscopic cohesion as well as the dependence of the macroscopic friction on the microscopic contact friction coefficient. Related to the dynamics, the anisotropy of both structure and stress are exponentially approaching the maximum

  20. International Workshop on Traffic and Granular Flow

    CERN Document Server

    Herrmann, Hans; Schreckenberg, Michael; Wolf, Dietrich; Social, Traffic and Granular Dynamics

    2000-01-01

    "Are there common phenomena and laws in the dynamic behavior of granular materials, traffic, and socio-economic systems?" The answers given at the international workshop "Traffic and Granular Flow '99" are presented in this volume. From a physical standpoint, all these systems can be treated as (self)-driven many-particle systems with strong fluctuations, showing multistability, phase transitions, non-linear waves, etc. The great interest in these systems is due to several unexpected new discoveries and their practical relevance for solving some fundamental problems of today's societies. This includes intelligent measures for traffic flow optimization and methods from "econophysics" for stabilizing (stock) markets.

  1. Granular contact dynamics using mathematical programming methods

    DEFF Research Database (Denmark)

    Krabbenhoft, K.; Lyamin, A. V.; Huang, J.

    2012-01-01

    granular contact dynamics formulation uses an implicit time discretization, thus allowing for large time steps. Moreover, in the limit of an infinite time step, the general dynamic formulation reduces to a static formulation that is useful in simulating common quasi-static problems such as triaxial tests...... is developed and it is concluded that the associated sliding rule, in the context of granular contact dynamics, may be viewed as an artifact of the time discretization and that the use of an associated flow rule at the particle scale level generally is physically acceptable. (C) 2012 Elsevier Ltd. All rights...

  2. Tracing Thermal Creep Through Granular Media

    Science.gov (United States)

    Steinpilz, Tobias; Teiser, Jens; Koester, Marc; Schywek, Mathias; Wurm, Gerhard

    2017-08-01

    A temperature gradient within a granular medium at low ambient pressure drives a gas flow through the medium by thermal creep. We measured the resulting air flow for a sample of glass beads with particle diameters between 290 μ m and 420 μ m for random close packing. Ambient pressure was varied between 1 Pa and 1000 Pa. The gas flow was quantified by means of tracer particles during parabolic flights. The flow varies systematically with pressure between 0.2 cm/s and 6 cm/s. The measured flow velocities are in quantitative agreement to model calculations that treat the granular medium as a collection of linear capillaries.

  3. Mitogenic activation of B cells in vitro: the properties of adherent accessory cells as revealed by partition analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kettman, J.R.; Soederberg, A.; Lefkovits, I.

    1986-08-15

    The requirement of B cells activated by mitogen (dextran sulfate plus lipopolysaccharide) for accessory cells was studied by partition analysis. Small numbers of splenic B cells were activated to clonal growth, as determined by visual inspection, and to immunoglobulin (Ig) synthesis, as determined by release of Ig into the culture fluid. By placing irradiated adherent cells in the periphery of the microculture wells and forcing responding cells to different areas of the well (slant experiments), it was observed that no cell contact was necessary for B cell activation, and that promoted contact (Rock and Roll experiments) does not increase the efficiency of activation. Sequential microcultures suggest that only some irradiated adherent cells act as accessory cells, but they can perform this function to more than one B cell. Attempts to perform limiting dilution analysis by varying irradiated adherent cell input showed non-single-hit behavior. When the data were rearranged, taking into account the distribution of irradiated adherent cells, then single-hit behavior with about 1 to 5% of irradiated adherent cells acting as an accessory cells for B cell clonal activation was observed. The evidence suggests that an uncommon irradiated adherent cell releases a soluble factor necessary for B cell activation and/or clonal proliferation.

  4. Mitogenic activation of B cells in vitro: the properties of adherent accessory cells as revealed by partition analysis

    International Nuclear Information System (INIS)

    Kettman, J.R.; Soederberg, A.; Lefkovits, I.

    1986-01-01

    The requirement of B cells activated by mitogen (dextran sulfate plus lipopolysaccharide) for accessory cells was studied by partition analysis. Small numbers of splenic B cells were activated to clonal growth, as determined by visual inspection, and to immunoglobulin (Ig) synthesis, as determined by release of Ig into the culture fluid. By placing irradiated adherent cells in the periphery of the microculture wells and forcing responding cells to different areas of the well (slant experiments), it was observed that no cell contact was necessary for B cell activation, and that promoted contact (Rock and Roll experiments) does not increase the efficiency of activation. Sequential microcultures suggest that only some irradiated adherent cells act as accessory cells, but they can perform this function to more than one B cell. Attempts to perform limiting dilution analysis by varying irradiated adherent cell input showed non-single-hit behavior. When the data were rearranged, taking into account the distribution of irradiated adherent cells, then single-hit behavior with about 1 to 5% of irradiated adherent cells acting as an accessory cells for B cell clonal activation was observed. The evidence suggests that an uncommon irradiated adherent cell releases a soluble factor necessary for B cell activation and/or clonal proliferation

  5. Electrical transport properties in Co nanocluster-assembled granular film

    Science.gov (United States)

    Zhang, Qin-Fu; Wang, Lai-Sen; Wang, Xiong-Zhi; Zheng, Hong-Fei; Liu, Xiang; Xie, Jia; Qiu, Yu-Long; Chen, Yuanzhi; Peng, Dong-Liang

    2017-03-01

    A Co nanocluster-assembled granular film with three-dimensional cross-connection paralleled conductive paths was fabricated by using the plasma-gas-condensation method in a vacuum environment. The temperature-dependent longitudinal resistivity and anomalous Hall effect of this new type granular film were systematically studied. The longitudinal resistivity of the Co nanocluster-assembled granular film first decreased and then increased with increasing measuring temperature, revealing a minimum value at certain temperature, T min . In a low temperature region ( T governed the electrical transport process, and the temperature coefficient of resistance (TCR) showed an insulator-type behavior. The thermal fluctuation-induced tunneling conduction progressively increased with increasing temperature, which led to a decrease in the longitudinal resistivity. In a high temperature region, the TCR showed a metallic-type behavior, which was primarily attributed to the temperature-dependent scattering. Different from the longitudinal resistivity behavior, the saturated anomalous Hall resistivity increased monotonically with increasing measuring temperature. The value of the anomalous Hall coefficient ( R S ) reached 2.3 × 10-9 (Ω cm)/G at 300 K, which was about three orders of magnitude larger than previously reported in blocky single-crystal Co [E. N. Kondorskii, Sov. Phys. JETP 38, 977 (1974)]. Interestingly, the scaling relation ( ρx y A ∝ ρx x γ ) between saturated anomalous Hall resistivity ( ρx y A ) and longitudinal resistivity ( ρ x x ) was divided into two regions by T min . However, after excluding the contribution of tunneling, the scaling relation followed the same rule. The corresponding physical mechanism was also proposed to explain these phenomena.

  6. Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

    Directory of Open Access Journals (Sweden)

    Beverly E. Flood

    2016-05-01

    Full Text Available The genus Thiomargarita includes the world’s largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria.Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence transposable elements and miniature inverted-repeat transposable elements (MITEs. In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsr

  7. Multi-Anode Photomultplier (MAPMT) readout for High Granularity Calorimeters

    CERN Document Server

    Mkrtchyan, Tigran; The ATLAS collaboration

    2017-01-01

    Hadron calorimeter high performance in jet sub-structure measurements can be achieved for objects with $p_{T}$ greater than 1 TeV if the readout geometry is finely segmented in $\\Delta\\eta \\times \\Delta\\phi$. A feasibility study to increase the readout granularity of TileCal, the central hadron calorimeter of the ATLAS detector, is presented. We show a preliminary study exploring the possibility to increase by a factor 4 the present readout granularity of the inner layer cells of TileCal (0.1->0.025 in $\\Delta\\eta$) and to split into two layers the intermediate section of TileCal. The proposed solution is designed to cope with mechanical and readout bandwidth and power constraints. Assuming that the mechanics of the Tile modules cannot be changed, Multi-Anode PMTs with same boundary geometry of the present single-anode PMTs are considered to readout WLS bers, ideally one per pixel, carrying the signals from the individual scintillating tiles of each detector cells. The discussed challenges of the design are: ...

  8. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland.

    Science.gov (United States)

    Lilja, Anna M; Rodilla, Veronica; Huyghe, Mathilde; Hannezo, Edouard; Landragin, Camille; Renaud, Olivier; Leroy, Olivier; Rulands, Steffen; Simons, Benjamin D; Fre, Silvia

    2018-06-01

    Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.

  9. Single-Cell Gene Expression Analysis of a Human ESC Model of Pancreatic Endocrine Development Reveals Different Paths to β-Cell Differentiation.

    Science.gov (United States)

    Petersen, Maja Borup Kjær; Azad, Ajuna; Ingvorsen, Camilla; Hess, Katja; Hansson, Mattias; Grapin-Botton, Anne; Honoré, Christian

    2017-10-10

    The production of insulin-producing β cells from human embryonic stem cells (hESCs) in vitro represents a promising strategy for a cell-based therapy for type 1 diabetes mellitus. To explore the cellular heterogeneity and temporal progression of endocrine progenitors and their progeny, we performed single-cell qPCR on more than 500 cells across several stages of in vitro differentiation of hESCs and compared them with human islets. We reveal distinct subpopulations along the endocrine differentiation path and an early lineage bifurcation toward either polyhormonal cells or β-like cells. We uncover several similarities and differences with mouse development and reveal that cells can take multiple paths to the same differentiation state, a principle that could be relevant to other systems. Notably, activation of the key β-cell transcription factor NKX6.1 can be initiated before or after endocrine commitment. The single-cell temporal resolution we provide can be used to improve the production of functional β cells. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  10. Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness.

    Science.gov (United States)

    Bogeas, Alexandra; Morvan-Dubois, Ghislaine; El-Habr, Elias A; Lejeune, François-Xavier; Defrance, Matthieu; Narayanan, Ashwin; Kuranda, Klaudia; Burel-Vandenbos, Fanny; Sayd, Salwa; Delaunay, Virgile; Dubois, Luiz G; Parrinello, Hugues; Rialle, Stéphanie; Fabrega, Sylvie; Idbaih, Ahmed; Haiech, Jacques; Bièche, Ivan; Virolle, Thierry; Goodhardt, Michele; Chneiweiss, Hervé; Junier, Marie-Pierre

    2018-02-01

    Although a growing body of evidence indicates that phenotypic plasticity exhibited by glioblastoma cells plays a central role in tumor development and post-therapy recurrence, the master drivers of their aggressiveness remain elusive. Here we mapped the changes in active (H3K4me3) and repressive (H3K27me3) histone modifications accompanying the repression of glioblastoma stem-like cells tumorigenicity. Genes with changing histone marks delineated a network of transcription factors related to cancerous behavior, stem state, and neural development, highlighting a previously unsuspected association between repression of ARNT2 and loss of cell tumorigenicity. Immunohistochemistry confirmed ARNT2 expression in cell sub-populations within proliferative zones of patients' glioblastoma. Decreased ARNT2 expression was consistently observed in non-tumorigenic glioblastoma cells, compared to tumorigenic cells. Moreover, ARNT2 expression correlated with a tumorigenic molecular signature at both the tissue level within the tumor core and at the single cell level in the patients' tumors. We found that ARNT2 knockdown decreased the expression of SOX9, POU3F2 and OLIG2, transcription factors implicated in glioblastoma cell tumorigenicity, and repressed glioblastoma stem-like cell tumorigenic properties in vivo. Our results reveal ARNT2 as a pivotal component of the glioblastoma cell tumorigenic signature, located at a node of a transcription factor network controlling glioblastoma cell aggressiveness.

  11. Long-Term Live Cell Imaging Reveals New Roles For Salmonella Effector Proteins SseG and SteA

    Science.gov (United States)

    McQuate, Sarah E.; Young, Alexandra M.; Silva-Herzog, Eugenia; Bunker, Eric; Hernandez, Mateo; de Chaumont, Fabrice; Liu, Xuedong; Detweiler, Corrella S.; Palmer, Amy E.

    2016-01-01

    Summary Salmonella Typhimurium is an intracellular bacterial pathogen that infects both epithelial cells and macrophages. Salmonella effector proteins, which are translocated into the host cell and manipulate host cell components, control the ability to replicate and/or survive in host cells. Due to the complexity and heterogeneity of Salmonella infections, there is growing recognition of the need for single cell and live-cell imaging approaches to identify and characterize the diversity of cellular phenotypes and how they evolve over time. Here we establish a pipeline for long-term (16 hours) live-cell imaging of infected cells and subsequent image analysis methods. We apply this pipeline to track bacterial replication within the Salmonella-containing vacuole in epithelial cells, quantify vacuolar replication versus survival in macrophages, and investigate the role of individual effector proteins in mediating these parameters. This approach revealed that dispersed bacteria can coalesce at later stages of infection, that the effector protein SseG influences the propensity for cytosolic hyperreplication in epithelial cells, and that while SteA only has a subtle effect on vacuolar replication in epithelial cells, it has a profound impact on infection parameters in immunocompetent macrophages, suggesting differential roles for effector proteins in different infection models. PMID:27376507

  12. In Situ Microscopy Analysis Reveals Local Innate Immune Response Developed around Brucella Infected Cells in Resistant and Susceptible Mice

    Science.gov (United States)

    Copin, Richard; Vitry, Marie-Alice; Hanot Mambres, Delphine; Machelart, Arnaud; De Trez, Carl; Vanderwinden, Jean-Marie; Magez, Stefan; Akira, Shizuo; Ryffel, Bernhard; Carlier, Yves; Letesson, Jean-Jacques; Muraille, Eric

    2012-01-01

    Brucella are facultative intracellular bacteria that chronically infect humans and animals causing brucellosis. Brucella are able to invade and replicate in a broad range of cell lines in vitro, however the cells supporting bacterial growth in vivo are largely unknown. In order to identify these, we used a Brucella melitensis strain stably expressing mCherry fluorescent protein to determine the phenotype of infected cells in spleen and liver, two major sites of B. melitensis growth in mice. In both tissues, the majority of primary infected cells expressed the F4/80 myeloid marker. The peak of infection correlated with granuloma development. These structures were mainly composed of CD11b+ F4/80+ MHC-II+ cells expressing iNOS/NOS2 enzyme. A fraction of these cells also expressed CD11c marker and appeared similar to inflammatory dendritic cells (DCs). Analysis of genetically deficient mice revealed that differentiation of iNOS+ inflammatory DC, granuloma formation and control of bacterial growth were deeply affected by the absence of MyD88, IL-12p35 and IFN-γ molecules. During chronic phase of infection in susceptible mice, we identified a particular subset of DC expressing both CD11c and CD205, serving as a reservoir for the bacteria. Taken together, our results describe the cellular nature of immune effectors involved during Brucella infection and reveal a previously unappreciated role for DC subsets, both as effectors and reservoir cells, in the pathogenesis of brucellosis. PMID:22479178

  13. Fluorescent labelling of intestinal epithelial cells reveals independent long-lived intestinal stem cells in a crypt

    International Nuclear Information System (INIS)

    Horita, Nobukatsu; Tsuchiya, Kiichiro; Hayashi, Ryohei; Fukushima, Keita; Hibiya, Shuji; Fukuda, Masayoshi; Kano, Yoshihito; Mizutani, Tomohiro; Nemoto, Yasuhiro; Yui, Shiro; Okamoto, Ryuichi; Nakamura, Tetsuya; Watanabe, Mamoru

    2014-01-01

    Highlights: • Lentivirus mixed with Matrigel enables direct infection of intestinal organoids. • Our original approach allows the marking of a single stem cell in a crypt. • Time-lapse imaging shows the dynamics of a single stem cell. • Our lentivirus transgene system demonstrates plural long-lived stem cells in a crypt. - Abstract: Background and aims: The dynamics of intestinal stem cells are crucial for regulation of intestinal function and maintenance. Although crypt stem cells have been identified in the intestine by genetic marking methods, identification of plural crypt stem cells has not yet been achieved as they are visualised in the same colour. Methods: Intestinal organoids were transferred into Matrigel® mixed with lentivirus encoding mCherry. The dynamics of mCherry-positive cells was analysed using time-lapse imaging, and the localisation of mCherry-positive cells was analysed using 3D immunofluorescence. Results: We established an original method for the introduction of a transgene into an organoid generated from mouse small intestine that resulted in continuous fluorescence of the mCherry protein in a portion of organoid cells. Three-dimensional analysis using confocal microscopy showed a single mCherry-positive cell in an organoid crypt that had been cultured for >1 year, which suggested the presence of long-lived mCherry-positive and -negative stem cells in the same crypt. Moreover, a single mCherry-positive stem cell in a crypt gave rise to both crypt base columnar cells and transit amplifying cells. Each mCherry-positive and -negative cell contributed to the generation of organoids. Conclusions: The use of our original lentiviral transgene system to mark individual organoid crypt stem cells showed that long-lived plural crypt stem cells might independently serve as intestinal epithelial cells, resulting in the formation of a completely functional villus

  14. Fluorescent labelling of intestinal epithelial cells reveals independent long-lived intestinal stem cells in a crypt

    Energy Technology Data Exchange (ETDEWEB)

    Horita, Nobukatsu [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan); Tsuchiya, Kiichiro, E-mail: kii.gast@tmd.ac.jp [Department of Advanced Therapeutics for Gastrointestinal Diseases, Graduate School, Tokyo Medical and Dental University (Japan); Hayashi, Ryohei [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan); Department of Gastroenterology and Metabolism, Hiroshima University (Japan); Fukushima, Keita; Hibiya, Shuji; Fukuda, Masayoshi; Kano, Yoshihito; Mizutani, Tomohiro; Nemoto, Yasuhiro; Yui, Shiro [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan); Okamoto, Ryuichi; Nakamura, Tetsuya [Department of Advanced Therapeutics for Gastrointestinal Diseases, Graduate School, Tokyo Medical and Dental University (Japan); Watanabe, Mamoru [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan)

    2014-11-28

    Highlights: • Lentivirus mixed with Matrigel enables direct infection of intestinal organoids. • Our original approach allows the marking of a single stem cell in a crypt. • Time-lapse imaging shows the dynamics of a single stem cell. • Our lentivirus transgene system demonstrates plural long-lived stem cells in a crypt. - Abstract: Background and aims: The dynamics of intestinal stem cells are crucial for regulation of intestinal function and maintenance. Although crypt stem cells have been identified in the intestine by genetic marking methods, identification of plural crypt stem cells has not yet been achieved as they are visualised in the same colour. Methods: Intestinal organoids were transferred into Matrigel® mixed with lentivirus encoding mCherry. The dynamics of mCherry-positive cells was analysed using time-lapse imaging, and the localisation of mCherry-positive cells was analysed using 3D immunofluorescence. Results: We established an original method for the introduction of a transgene into an organoid generated from mouse small intestine that resulted in continuous fluorescence of the mCherry protein in a portion of organoid cells. Three-dimensional analysis using confocal microscopy showed a single mCherry-positive cell in an organoid crypt that had been cultured for >1 year, which suggested the presence of long-lived mCherry-positive and -negative stem cells in the same crypt. Moreover, a single mCherry-positive stem cell in a crypt gave rise to both crypt base columnar cells and transit amplifying cells. Each mCherry-positive and -negative cell contributed to the generation of organoids. Conclusions: The use of our original lentiviral transgene system to mark individual organoid crypt stem cells showed that long-lived plural crypt stem cells might independently serve as intestinal epithelial cells, resulting in the formation of a completely functional villus.

  15. Whole-organ cell shape analysis reveals the developmental basis of ascidian notochord taper

    OpenAIRE

    Veeman, Michael T.; Smith, William C.

    2013-01-01

    Here we use in toto imaging together with computational segmentation and analysis methods to quantify the shape of every cell at multiple stages in the development of a simple organ: the notochord of the ascidian Ciona savignyi. We find that cell shape in the intercalated notochord depends strongly on anterior-posterior (AP) position, with cells in the middle of the notochord consistently wider than cells at the anterior or posterior. This morphological feature of having a tapered notochord i...

  16. Dental pulp stem cells differentiation reveals new insights in Oct4A dynamics.

    Directory of Open Access Journals (Sweden)

    Federico Ferro

    Full Text Available Although the role played by the core transcription factor network, which includes c-Myc, Klf4, Nanog, and Oct4, in the maintenance of embryonic stem cell (ES pluripotency and in the reprogramming of adult cells is well established, its persistence and function in adult stem cells are still debated. To verify its persistence and clarify the role played by these molecules in adult stem cell function, we investigated the expression pattern of embryonic and adult stem cell markers in undifferentiated and fully differentiated dental pulp stem cells (DPSC. A particular attention was devoted to the expression pattern and intracellular localization of the stemness-associated isoform A of Oct4 (Oct4A. Our data demonstrate that: Oct4, Nanog, Klf4 and c-Myc are expressed in adult stem cells and, with the exception of c-Myc, they are significantly down-regulated following differentiation. Cell differentiation was also associated with a significant reduction in the fraction of DPSC expressing the stem cell markers CD10, CD29 and CD117. Moreover, a nuclear to cytoplasm shuttling of Oct4A was identified in differentiated cells, which was associated with Oct4A phosphorylation. The present study would highlight the importance of the post-translational modifications in DPSC stemness maintenance, by which stem cells balance self-renewal versus differentiation. Understanding and controlling these mechanisms may be of great importance for stemness maintenance and stem cells clinical use, as well as for cancer research.

  17. Bioluminescence Imaging of Olig2-Neural Stem Cells Reveals Improved Engraftment in a Demyelination Mouse Model

    NARCIS (Netherlands)

    Sher, Falak; van Dam, Go; Boddeke, Erik; Copray, Sjef

    2009-01-01

    A major issue in the potential application of neural stem cell (NSC)-based cell replacement therapy for demyelinating diseases is the question of the survival, functional behavior, and stability of implanted NSC-derived oligodendrocyte precursor cells (OPCs) over an extended period. To address this

  18. Computational models reveal a passive mechanism for cell migration in the crypt.

    Directory of Open Access Journals (Sweden)

    Sara-Jane Dunn

    Full Text Available Cell migration in the intestinal crypt is essential for the regular renewal of the epithelium, and the continued upward movement of cells is a key characteristic of healthy crypt dynamics. However, the driving force behind this migration is unknown. Possibilities include mitotic pressure, active movement driven by motility cues, or negative pressure arising from cell loss at the crypt collar. It is possible that a combination of factors together coordinate migration. Here, three different computational models are used to provide insight into the mechanisms that underpin cell movement in the crypt, by examining the consequence of eliminating cell division on cell movement. Computational simulations agree with existing experimental results, confirming that migration can continue in the absence of mitosis. Importantly, however, simulations allow us to infer mechanisms that are sufficient to generate cell movement, which is not possible through experimental observation alone. The results produced by the three models agree and suggest that cell loss due to apoptosis and extrusion at the crypt collar relieves cell compression below, allowing cells to expand and move upwards. This finding suggests that future experiments should focus on the role of apoptosis and cell extrusion in controlling cell migration in the crypt.

  19. A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

    Science.gov (United States)

    Labbé, Roselyne M.; Irimia, Manuel; Currie, Ko W.; Lin, Alexander; Zhu, Shu Jun; Brown, David D.R.; Ross, Eric J.; Voisin, Veronique; Bader, Gary D.; Blencowe, Benjamin J.; Pearson, Bret J.

    2014-01-01

    Many long-lived species of animals require the function of adult stem cells throughout their lives. However, the transcriptomes of stem cells in invertebrates and vertebrates have not been compared, and consequently, ancestral regulatory circuits that control stem cell populations remain poorly defined. In this study, we have used data from high-throughput RNA sequencing to compare the transcriptomes of pluripotent adult stem cells from planarians with the transcriptomes of human and mouse pluripotent embryonic stem cells. From a stringently defined set of 4,432 orthologs shared between planarians, mice and humans, we identified 123 conserved genes that are ≥5-fold differentially expressed in stem cells from all three species. Guided by this gene set, we used RNAi screening in adult planarians to discover novel stem cell regulators, which we found to affect the stem cell-associated functions of tissue homeostasis, regeneration, and stem cell maintenance. Examples of genes that disrupted these processes included the orthologs of TBL3, PSD12, TTC27, and RACK1. From these analyses, we concluded that by comparing stem cell transcriptomes from diverse species, it is possible to uncover conserved factors that function in stem cell biology. These results provide insights into which genes comprised the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency. PMID:22696458

  20. Analysis of chlorophyll fluorescence reveals stage specific patterns of chloroplast-containing cells during Arabidopsis embryogenesis

    Directory of Open Access Journals (Sweden)

    RICARDO I TEJOS

    2010-01-01

    Full Text Available The basic body plan of a plant is established early in embryogenesis when cells differentiate, giving rise to the apical and basal regions of the embryo. Using chlorophyll fluorescence as a marker for chloroplasts, we have detected specific patterns of chloroplast-containing cells at specific stages of embryogenesis. Non-randomly distributed chloroplast-containing cells are seen as early as the globular stage of embryogenesis in Arabidopsis. In the heart stage of embryogenesis, chloroplast containing cells are detected in epidermal cells as well as a central region of the heart stage embryo, forming a triangular septum of chloroplast-containing cells that divides the embryo into three equal sectors. Torpedo stage embryos have chloroplast-containing epidermal cells and a central band of chloroplast-containing cells in the cortex layer, just below the shoot apical meristem. In the walking-stick stage of embryogenesis, chloroplasts are present in the epidermal, cortex and endodermal cells. The chloroplasts appear reduced or absent from the provascular and columella cells of walking-stick stage embryos. These results suggest that there is a tight regulation of plastid differentiation during embryogenesis that generates specific patterns of chloroplast-containing cells in specific cell layers at specific stages of embryogenesis.

  1. Granular Gas in a Periodic Lattice

    Science.gov (United States)

    Dorbolo, S.; Brandenbourger, M.; Damanet, F.; Dister, H.; Ludewig, F.; Terwagne, D.; Lumay, G.; Vandewalle, N.

    2011-01-01

    Glass beads are placed in the compartments of a horizontal square grid. This grid is then vertically shaken. According to the reduced acceleration [image omitted] of the system, the granular material exhibits various behaviours. By counting the number of beads in each compartment after shaking, it is possible to define three regimes. At low…

  2. Pion showers in highly granular calorimeters

    Indian Academy of Sciences (India)

    New results on properties of hadron showers created by pion beam at 8–80 GeV in high granular electromagnetic and hadron calorimeters are presented. Data were used for the first time to investigate the separation of the neutral and charged hadron showers. The result is important to verify the prediction of the PFA ...

  3. Anomalous infrared absorption in granular superconductors

    International Nuclear Information System (INIS)

    Carr, G.L.; Garland, J.C.; Tanner, D.B.

    1983-01-01

    Granular superconductors are shown to have a far-infrared absorption that is larger when the samples are superconducting than when they are normal. By constrast, theoretical models for these materials predict that when the samples become superconducting, the absorption should decrease

  4. Vortex jamming in superconductors and granular rheology

    International Nuclear Information System (INIS)

    Yoshino, Hajime; Nogawa, Tomoaki; Kim, Bongsoo

    2009-01-01

    We demonstrate that a highly frustrated anisotropic Josephson junction array (JJA) on a square lattice exhibits a zero-temperature jamming transition, which shares much in common with those in granular systems. Anisotropy of the Josephson couplings along the horizontal and vertical directions plays roles similar to normal load or density in granular systems. We studied numerically static and dynamic response of the system against shear, i.e. injection of external electric current at zero temperature. Current-voltage curves at various strength of the anisotropy exhibit universal scaling features around the jamming point much as do the flow curves in granular rheology, shear-stress versus shear-rate. It turns out that at zero temperature the jamming transition occurs right at the isotropic coupling and anisotropic JJA behaves as exotic fragile vortex matter: it behaves as a superconductor (vortex glass) in one direction, whereas it is a normal conductor (vortex liquid) in the other direction even at zero temperature. Furthermore, we find a variant of the theoretical model for the anisotropic JJA quantitatively reproduces universal master flow-curves of the granular systems. Our results suggest an unexpected common paradigm stretching over seemingly unrelated fields-the rheology of soft materials and superconductivity.

  5. Random packing of colloids and granular matter

    NARCIS (Netherlands)

    Wouterse, A.

    2008-01-01

    This thesis deals with the random packing of colloids and granular matter. A random packing is a stable disordered collection of touching particles, without long-range positional and orientational order. Experimental random packings of particles with the same shape but made of different materials

  6. Deposition and shaking of dry granular piles

    NARCIS (Netherlands)

    Hasan, M.

    2003-01-01

    A friction force model describing reversible stick-slip transition during contact has been developed with the special purpose to simulate the deposition of granular material. A test with a mass on a conveyor belt kept in position by a spring shows that a numerical simulation of the dynamics of such

  7. ENGINEERING BULLETIN: GRANULAR ACTIVATED CARBON TREATMENT

    Science.gov (United States)

    Granular activated carbon (GAC) treatment is a physicochemical process that removes a wide variety of contaminants by adsorbing them from liquid and gas streams [1, p. 6-3]. This treatment is most commonly used to separate organic contaminants from water or air; however, it can b...

  8. Velocity distributions in dilute granular systems

    NARCIS (Netherlands)

    van Zon, J.S.; Mac Kintosh, F.C.

    2005-01-01

    We investigate the idea that velocity distributions in granular gases are determined mainly by η, the coefficient of restitution and q, which measures the relative importance of heating (or energy input) to collisions. To this end, we study by numerical simulation the properties of inelastic gases

  9. Nonlinear coherent structures in granular crystals

    Science.gov (United States)

    Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

    2017-10-01

    The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

  10. The critical current of granular superconductor

    International Nuclear Information System (INIS)

    Ignat'ev, V.K.

    1998-01-01

    A mechanism of hyper vortex pinning in granular superconductors is proposed to describe the field dependence of the critical current density and pinning potential. The results are in a good agreement with the experiment. The model represents the peak effect and the percolation mechanism of conductivity in ceramic superconductors

  11. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.

    Directory of Open Access Journals (Sweden)

    Artémis Llamosi

    2016-02-01

    Full Text Available Significant cell-to-cell heterogeneity is ubiquitously observed in isogenic cell populations. Consequently, parameters of models of intracellular processes, usually fitted to population-averaged data, should rather be fitted to individual cells to obtain a population of models of similar but non-identical individuals. Here, we propose a quantitative modeling framework that attributes specific parameter values to single cells for a standard model of gene expression. We combine high quality single-cell measurements of the response of yeast cells to repeated hyperosmotic shocks and state-of-the-art statistical inference approaches for mixed-effects models to infer multidimensional parameter distributions describing the population, and then derive specific parameters for individual cells. The analysis of single-cell parameters shows that single-cell identity (e.g. gene expression dynamics, cell size, growth rate, mother-daughter relationships is, at least partially, captured by the parameter values of gene expression models (e.g. rates of transcription, translation and degradation. Our approach shows how to use the rich information contained into longitudinal single-cell data to infer parameters that can faithfully represent single-cell identity.

  12. Human Monoclonal Islet Cell Antibodies From a Patient with Insulin- Dependent Diabetes Mellitus Reveal Glutamate Decarboxylase as the Target Antigen

    Science.gov (United States)

    Richter, Wiltrud; Endl, Josef; Eiermann, Thomas H.; Brandt, Michael; Kientsch-Engel, Rosemarie; Thivolet, Charles; Jungfer, Herbert; Scherbaum, Werner A.

    1992-09-01

    The autoimmune phenomena associated with destruction of the β cell in pancreatic islets and development of type 1 (insulin-dependent) diabetes mellitus (IDDM) include circulating islet cell antibodies. We have immortalized peripheral blood lymphocytes from prediabetic individuals and patients with newly diagnosed IDDM by Epstein-Barr virus transformation. IgG-positive cells were selected by anti-human IgG-coupled magnetic beads and expanded in cell culture. Supernatants were screened for cytoplasmic islet cell antibodies using the conventional indirect immunofluorescence test on cryostat sections of human pancreas. Six islet cell-specific B-cell lines, originating from a patient with newly diagnosed IDDM, could be stabilized on a monoclonal level. All six monoclonal islet cell antibodies (MICA 1-6) were of the IgG class. None of the MICA reacted with human thyroid, adrenal gland, anterior pituitary, liver, lung, stomach, and intestine tissues but all six reacted with pancreatic islets of different mammalian species and, in addition, with neurons of rat cerebellar cortex. MICA 1-6 were shown to recognize four distinct antigenic epitopes in islets. Islet cell antibody-positive diabetic sera but not normal human sera blocked the binding of the monoclonal antibodies to their target epitopes. Immunoprecipitation of 35S-labeled human islet cell extracts revealed that a protein of identical size to the enzyme glutamate decarboxylase (EC 4.1.1.15) was a target of all MICA. Furthermore, antigen immunotrapped by the MICA from brain homogenates showed glutamate decarboxylase enzyme activity. MICA 1-6 therefore reveal glutamate decarboxylase as the predominant target antigen of cytoplasmic islet cell autoantibodies in a patient with newly diagnosed IDDM.

  13. Real-time motion analysis reveals cell directionality as an indicator of breast cancer progression.

    Directory of Open Access Journals (Sweden)

    Michael C Weiger

    Full Text Available Cancer cells alter their migratory properties during tumor progression to invade surrounding tissues and metastasize to distant sites. However, it remains unclear how migratory behaviors differ between tumor cells of different malignancy and whether these migratory behaviors can be utilized to assess the malignant potential of tumor cells. Here, we analyzed the migratory behaviors of cell lines representing different stages of breast cancer progression using conventional migration assays or time-lapse imaging and particle image velocimetry (PIV to capture migration dynamics. We find that the number of migrating cells in transwell assays, and the distance and speed of migration in unconstrained 2D assays, show no correlation with malignant potential. However, the directionality of cell motion during 2D migration nicely distinguishes benign and tumorigenic cell lines, with tumorigenic cell lines harboring less directed, more random motion. Furthermore, the migratory behaviors of epithelial sheets observed under basal conditions and in response to stimulation with epidermal growth factor (EGF or lysophosphatitic acid (LPA are distinct for each cell line with regard to cell speed, directionality, and spatiotemporal motion patterns. Surprisingly, treatment with LPA promotes a more cohesive, directional sheet movement in lung colony forming MCF10CA1a cells compared to basal conditions or EGF stimulation, implying that the LPA signaling pathway may alter the invasive potential of MCF10CA1a cells. Together, our findings identify cell directionality as a promising indicator for assessing the tumorigenic potential of breast cancer cell lines and show that LPA induces more cohesive motility in a subset of metastatic breast cancer cells.

  14. Nitrate adsorption from aqueous solution using granular chitosan-Fe{sup 3+} complex

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Qili [School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083 (China); Key Laboratory of Groundwater Cycle and Environment Evolution,China University of Geosciences (Beijing), Ministry of Education, Beijing, 100083 (China); Chen, Nan, E-mail: chennan@cugb.edu.cn [School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083 (China); Key Laboratory of Groundwater Cycle and Environment Evolution, China University of Geosciences (Beijing), Ministry of Education, Beijing, 100083 (China); Feng, Chuanping [School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083 (China); Key Laboratory of Groundwater Cycle and Environment Evolution, China University of Geosciences (Beijing), Ministry of Education, Beijing, 100083 (China); Hu, WeiWu [The Journal Center, China University of Geosciences (Beijing), Beijing, 100083 (China)

    2015-08-30

    Highlights: • Granular chitosan-Fe{sup 3+} complex had high performance for nitrate adsorption. • Granular chitosan-Fe{sup 3+} complex had shorter equilibrium time (1.5 h). • Nitrate adsorption was ascribed to ion exchange and electrostatic attraction. • Granular chitosan-Fe{sup 3+} complex could be regenerated using NaCl solution. - Abstract: In the present study, In order to efficiently remove nitrate, granular chitosan-Fe{sup 3+} complex with high chemical stability and good environmental adaptation was synthesized through precipitation method and characterized using SEM, XRD, BET and FTIR. The nitrate adsorption performance was evaluated by batch experiments. The results indicated that granular chitosan-Fe{sup 3+} complex was an amorphous and mesoporous material. The BET specific surface area and average pore size were 8.98 m{sup 2} g{sup −1} and 56.94 Å, respectively. The point of zero charge was obtained at pH 5. The maximum adsorption capacity reached 8.35 mg NO{sub 3}{sup −}-N g{sup −1} based on Langmuir–Freundlich model. Moreover, no significant change in the nitrate removal efficiency was observed in the pH range of 3.0–10.0. The adverse influence of sulphate on nitrate removal was the most significant, followed by bicarbonate and fluoride, whereas chloride had slightly adverse effect. Adsorption process followed the pseudo-second-order kinetic model, and the experimental equilibrium data were fitted well with the Langmuir–Freundlich and D–R isotherm models. Thermodynamic parameters revealed that nitrate adsorption was a spontaneous and exothermic process. Granular chitosan-Fe{sup 3+} complex could be effectively regenerated by NaCl solution.

  15. KSHV cell attachment sites revealed by ultra sensitive tyramide signal amplification (TSA) localize to membrane microdomains that are up-regulated on mitotic cells.

    Science.gov (United States)

    Garrigues, H Jacques; Rubinchikova, Yelena E; Rose, Timothy M

    2014-03-01

    Cell surface structures initiating attachment of Kaposi's sarcoma-associated herpesvirus (KSHV) were characterized using purified hapten-labeled virions visualized by confocal microscopy with a sensitive fluorescent enhancement using tyramide signal amplification (TSA). KSHV attachment sites were present in specific cellular domains, including actin-based filopodia, lamellipodia, ruffled membranes, microvilli and intercellular junctions. Isolated microdomains were identified on the dorsal surface, which were heterogeneous in size with a variable distribution that depended on cellular confluence and cell cycle stage. KSHV binding domains ranged from scarce on interphase cells to dense and continuous on mitotic cells, and quantitation of bound virus revealed a significant increase on mitotic compared to interphase cells. KSHV also bound to a supranuclear domain that was distinct from microdomains in confluent and interphase cells. These results suggest that rearrangement of the cellular membrane during mitosis induces changes in cell surface receptors implicated in the initial attachment stage of KSHV entry. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Immunogold scanning electron microscopy can reveal the polysaccharide architecture of xylem cell walls

    Science.gov (United States)

    Sun, Yuliang; Juzenas, Kevin

    2017-01-01

    Abstract Immunofluorescence microscopy (IFM) and immunogold transmission electron microscopy (TEM) are the two main techniques commonly used to detect polysaccharides in plant cell walls. Both are important in localizing cell wall polysaccharides, but both have major limitations, such as low resolution in IFM and restricted sample size for immunogold TEM. In this study, we have developed a robust technique that combines immunocytochemistry with scanning electron microscopy (SEM) to study cell wall polysaccharide architecture in xylem cells at high resolution over large areas of sample. Using multiple cell wall monoclonal antibodies (mAbs), this immunogold SEM technique reliably localized groups of hemicellulosic and pectic polysaccharides in the cell walls of five different xylem structures (vessel elements, fibers, axial and ray parenchyma cells, and tyloses). This demonstrates its important advantages over the other two methods for studying cell wall polysaccharide composition and distribution in these structures. In addition, it can show the three-dimensional distribution of a polysaccharide group in the vessel lateral wall and the polysaccharide components in the cell wall of developing tyloses. This technique, therefore, should be valuable for understanding the cell wall polysaccharide composition, architecture and functions of diverse cell types. PMID:28398585

  17. Expression weighted cell type enrichments reveal genetic and cellular nature of major brain disorders

    Directory of Open Access Journals (Sweden)

    Nathan Gerald Skene

    2016-01-01

    Full Text Available The cell types that trigger the primary pathology in many brain diseases remain largely unknown. One route to understanding the primary pathological cell type for a particular disease is to identify the cells expressing susceptibility genes. Although this is straightforward for monogenic conditions where the causative mutation may alter expression of a cell type specific marker, methods are required for the common polygenic disorders. We developed the Expression Weighted Cell Type Enrichment (EWCE method that uses single cell transcriptomes to generate the probability distribution associated with a gene list having an average level of expression within a cell type. Following validation, we applied EWCE to human genetic data from cases of epilepsy, Schizophrenia, Autism, Intellectual Disability, Alzheimer’s disease, Multiple Sclerosis and anxiety disorders. Genetic susceptibility primarily affected microglia in Alzheimer’s and Multiple Sclerosis; was shared between interneurons and pyramidal neurons in Autism and Schizophrenia; while intellectual disabilities and epilepsy were attributable to a range of cell-types, with the strongest enrichment in interneurons. We hypothesised that the primary cell type pathology could trigger secondary changes in other cell types and these could be detected by applying EWCE to transcriptome data from diseased tissue. In Autism, Schizophrenia and Alzheimer’s disease we find evidence of pathological changes in all of the major brain cell types. These findings give novel insight into the cellular origins and progression in common brain disorders. The methods can be applied to any tissue and disorder and have applications in validating mouse models.

  18. Cell proliferation in the Drosophila adult brain revealed by clonal analysis and bromodeoxyuridine labelling

    Directory of Open Access Journals (Sweden)

    Brand Andrea H

    2009-03-01

    Full Text Available Abstract Background The production of new neurons during adulthood and their subsequent integration into a mature central nervous system have been shown to occur in all vertebrate species examined to date. However, the situation in insects is less clear and, in particular, it has been reported that there is no proliferation in the Drosophila adult brain. Results We report here, using clonal analysis and 5'-bromo-2'-deoxyuridine (BrdU labelling, that cell proliferation does occur in the Drosophila adult brain. The majority of clones cluster on the ventrolateral side of the antennal lobes, as do the BrdU-positive cells. Of the BrdU-labelled cells, 86% express the glial gene reversed polarity (repo, and 14% are repo negative. Conclusion We have observed cell proliferation in the Drosophila adult brain. The dividing cells may be adult stem cells, generating glial and/or non-glial cell types.

  19. Kinetics and mass-transfer phenomena in anaerobic granular sludge.

    Science.gov (United States)

    Gonzalez-Gil, G; Seghezzo, L; Lettinga, G; Kleerebezem, R

    2001-04-20

    The kinetic properties of acetate-degrading methanogenic granular sludge of different mean diameters were assessed at different up-flow velocities (V(up)). Using this approach, the influence of internal and external mass transfer could be estimated. First, the apparent Monod constant (K(S)) for each data set was calculated by means of a curve-fitting procedure. The experimental results revealed that variations in the V(up) did not affect the apparent K(S)-value, indicating that external mass-transport resistance normally can be neglected. With regard to the granule size, a clear increase in K(S) was found at increasing granule diameters. The experimental data were further used to validate a dynamic mathematical biofilm model. The biofilm model was able to describe reaction-diffusion kinetics in anaerobic granules, using a single value for the effective diffusion coefficient in the granules. This suggests that biogas formation did not influence the diffusion-rates in the granular biomass. Copyright 2001 John Wiley & Sons, Inc.

  20. Jamming of three-dimensional prolate granular materials.

    Science.gov (United States)

    Desmond, K; Franklin, Scott V

    2006-03-01

    We have found that the ability of long thin rods to jam into a solidlike state in response to a local perturbation depends upon both the particle aspect ratio and the container size. The dynamic phase diagram in this parameter space reveals a broad transition region separating granular stick-slip and solidlike behavior. In this transition region the pile displays both solid and stick-slip behavior. We measure the force on a small object pulled through the pile, and find the fluctuation spectra to have power law tails with an exponent characteristic of the region. The exponent varies from beta=-2 in the stick-slip region to beta=-1 in the solid region. These values reflect the different origins--granular rearrangements vs dry friction--of the fluctuations. Finally, the packing fraction shows only a slight dependence on container size, but depends on aspect ratio in a manner predicted by mean-field theory and implies an aspect-ratio-independent contact number of =5.25 +/- 0.03.

  1. Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

    Science.gov (United States)

    Macovei, Anca; Faè, Matteo; Biggiogera, Marco; de Sousa Araújo, Susana; Carbonera, Daniela; Balestrazzi, Alma

    2018-01-01

    The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2) involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively) and a control (CTRL) line carrying the empty vector were investigated. Transmission electron microscopy (TEM) revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL), the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL) and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells. PMID:29868059

  2. Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

    Directory of Open Access Journals (Sweden)

    Anca Macovei

    2018-05-01

    Full Text Available The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2 involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively and a control (CTRL line carrying the empty vector were investigated. Transmission electron microscopy (TEM revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL, the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells.

  3. Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.

    Science.gov (United States)

    Enge, Martin; Arda, H Efsun; Mignardi, Marco; Beausang, John; Bottino, Rita; Kim, Seung K; Quake, Stephen R

    2017-10-05

    As organisms age, cells accumulate genetic and epigenetic errors that eventually lead to impaired organ function or catastrophic transformation such as cancer. Because aging reflects a stochastic process of increasing disorder, cells in an organ will be individually affected in different ways, thus rendering bulk analyses of postmitotic adult cells difficult to interpret. Here, we directly measure the effects of aging in human tissue by performing single-cell transcriptome analysis of 2,544 human pancreas cells from eight donors spanning six decades of life. We find that islet endocrine cells from older donors display increased levels of transcriptional noise and potential fate drift. By determining the mutational history of individual cells, we uncover a novel mutational signature in healthy aging endocrine cells. Our results demonstrate the feasibility of using single-cell RNA sequencing (RNA-seq) data from primary cells to derive insights into genetic and transcriptional processes that operate on aging human tissue. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Diversity in cell motility reveals the dynamic nature of the formation of zebrafish taste sensory organs.

    Science.gov (United States)

    Soulika, Marina; Kaushik, Anna-Lila; Mathieu, Benjamin; Lourenço, Raquel; Komisarczuk, Anna Z; Romano, Sebastian Alejo; Jouary, Adrien; Lardennois, Alicia; Tissot, Nicolas; Okada, Shinji; Abe, Keiko; Becker, Thomas S; Kapsimali, Marika

    2016-06-01

    Taste buds are sensory organs in jawed vertebrates, composed of distinct cell types that detect and transduce specific taste qualities. Taste bud cells differentiate from oropharyngeal epithelial progenitors, which are localized mainly in proximity to the forming organs. Despite recent progress in elucidating the molecular interactions required for taste bud cell development and function, the cell behavior underlying the organ assembly is poorly defined. Here, we used time-lapse imaging to observe the formation of taste buds in live zebrafish larvae. We found that tg(fgf8a.dr17)-expressing cells form taste buds and get rearranged within the forming organs. In addition, differentiating cells move from the epithelium to the forming organs and can be displaced between developing organs. During organ formation, tg(fgf8a.dr17) and type II taste bud cells are displaced in random, directed or confined mode relative to the taste bud they join or by which they are maintained. Finally, ascl1a activity in the 5-HT/type III cell is required to direct and maintain tg(fgf8a.dr17)-expressing cells into the taste bud. We propose that diversity in displacement modes of differentiating cells acts as a key mechanism for the highly dynamic process of taste bud assembly. © 2016. Published by The Company of Biologists Ltd.

  5. Metabolomics reveals metabolic changes in male reproductive cells exposed to thirdhand smoke

    Science.gov (United States)

    Xu, Bo; Chen, Minjian; Yao, Mengmeng; Ji, Xiaoli; Mao, Zhilei; Tang, Wei; Qiao, Shanlei; Schick, Suzaynn F.; Mao, Jian-Hua; Hang, Bo; Xia, Yankai

    2015-10-01

    Thirdhand smoke (THS) is a new term for the toxins in cigarette smoke that linger in the environment long after the cigarettes are extinguished. The effects of THS exposure on male reproduction have not yet been studied. In this study, metabolic changes in male germ cell lines (GC-2 and TM-4) were analyzed after THS treatment for 24 h. THS-loaded chromatography paper samples were generated in a laboratory chamber system and extracted in DMEM. At a paper: DMEM ratio of 50 μg/ml, cell viability in both cell lines was normal, as measured by the MTT assay and markers of cytotoxicity, cell cycle, apoptosis and ROS production were normal as measured by quantitative immunofluorescence. Metabolomic analysis was performed on methanol extracts of GC-2 and TM-4 cells. Glutathione metabolism in GC-2 cells, and nucleic acid and ammonia metabolism in TM-4 cells, was changed significantly by THS treatment. RT-PCR analyses of mRNA for enzyme genes Gss and Ggt in GC-2 cells, and TK, SMS and Glna in TM-4 cells reinforced these findings, showing changes in the levels of enzymes involved in the relevant pathways. In conclusion, exposure to THS at very low concentrations caused distinct metabolic changes in two different types of male reproductive cell lines.

  6. Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement.

    Science.gov (United States)

    Carmen Herranz, Ma; Sanchez-Navarro, Jesús-Angel; Saurí, Ana; Mingarro, Ismael; Pallás, Vicente

    2005-08-15

    The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive charges prevented the cell-to-cell movement even though all mutants showed a similar accumulation level in protoplasts to those observed with the wild-type (wt) MP. Synthetic peptides representing the mutants and wild-type RBDs were used to study RNA-binding affinities by EMSA assays being approximately 20-fold lower in the mutants. Circular dichroism analyses revealed that the secondary structure of the peptides was not significantly affected by mutations. The involvement of the affinity changes between the viral RNA and the MP in the viral cell-to-cell movement is discussed.

  7. Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement

    International Nuclear Information System (INIS)

    Carmen Herranz, Ma; Sanchez-Navarro, Jesus-Angel; Sauri, Ana; Mingarro, Ismael; Pallas, Vicente

    2005-01-01

    The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive charges prevented the cell-to-cell movement even though all mutants showed a similar accumulation level in protoplasts to those observed with the wild-type (wt) MP. Synthetic peptides representing the mutants and wild-type RBDs were used to study RNA-binding affinities by EMSA assays being approximately 20-fold lower in the mutants. Circular dichroism analyses revealed that the secondary structure of the peptides was not significantly affected by mutations. The involvement of the affinity changes between the viral RNA and the MP in the viral cell-to-cell movement is discussed

  8. Atomic force microscopy stiffness tomography on living Arabidopsis thaliana cells reveals the mechanical properties of surface and deep cell-wall layers during growth.

    Science.gov (United States)

    Radotić, Ksenija; Roduit, Charles; Simonović, Jasna; Hornitschek, Patricia; Fankhauser, Christian; Mutavdžić, Dragosav; Steinbach, Gabor; Dietler, Giovanni; Kasas, Sandor

    2012-08-08

    Cell-wall mechanical properties play a key role in the growth and the protection of plants. However, little is known about genuine wall mechanical properties and their growth-related dynamics at subcellular resolution and in living cells. Here, we used atomic force microscopy (AFM) stiffness tomography to explore stiffness distribution in the cell wall of suspension-cultured Arabidopsis thaliana as a model of primary, growing cell wall. For the first time that we know of, this new imaging technique was performed on living single cells of a higher plant, permitting monitoring of the stiffness distribution in cell-wall layers as a function of the depth and its evolution during the different growth phases. The mechanical measurements were correlated with changes in the composition of the cell wall, which were revealed by Fourier-transform infrared (FTIR) spectroscopy. In the beginning and end of cell growth, the average stiffness of the cell wall was low and the wall was mechanically homogenous, whereas in the exponential growth phase, the average wall stiffness increased, with increasing heterogeneity. In this phase, the difference between the superficial and deep wall stiffness was highest. FTIR spectra revealed a relative increase in the polysaccharide/lignin content. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  9. Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm

    Directory of Open Access Journals (Sweden)

    Junjie Lu

    2018-04-01

    Full Text Available Differentiation of human pluripotent stem cells towards definitive endoderm (DE is the critical first step for generating cells comprising organs such as the gut, liver, pancreas and lung. This in-vitro differentiation process generates a heterogeneous population with a proportion of cells failing to differentiate properly and maintaining expression of pluripotency factors such as Oct4. RNA sequencing of single cells collected at four time points during a 4-day DE differentiation identified high expression of metallothionein genes in the residual Oct4-positive cells that failed to differentiate to DE. Using X-ray fluorescence microscopy and multi-isotope mass spectrometry, we discovered that high intracellular zinc level corresponds with persistent Oct4 expression and failure to differentiate. This study improves our understanding of the cellular heterogeneity during in-vitro directed differentiation and provides a valuable resource to improve DE differentiation efficiency. Keywords: hPSC, Differentiation, Definitive endoderm, Heterogeneity, Single cell, RNA sequencing

  10. Cell membrane conformation at vertical nanowire array interface revealed by fluorescence imaging

    International Nuclear Information System (INIS)

    Berthing, Trine; Bonde, Sara; Rostgaard, Katrine R; Martinez, Karen L; Madsen, Morten Hannibal; Sørensen, Claus B; Nygård, Jesper

    2012-01-01

    The perspectives offered by vertical arrays of nanowires for biosensing applications in living cells depend on the access of individual nanowires to the cell interior. Recent results on electrical access and molecular delivery suggest that direct access is not always obtained. Here, we present a generic approach to directly visualize the membrane conformation of living cells interfaced with nanowire arrays, with single nanowire resolution. The method combines confocal z-stack imaging with an optimized cell membrane labelling strategy which was applied to HEK293 cells interfaced with 2–11 μm long and 3–7 μm spaced nanowires with various surface coatings (bare, aminosilane-coated or polyethyleneimine-coated indium arsenide). We demonstrate that, for all commonly used nanowire lengths, spacings and surface coatings, nanowires generally remain enclosed in a membrane compartment, and are thereby not in direct contact with the cell interior. (paper)

  11. 3-D Imaging Reveals Participation of Donor Islet Schwann Cells and Pericytes in Islet Transplantation and Graft Neurovascular Regeneration

    Directory of Open Access Journals (Sweden)

    Jyuhn-Huarng Juang

    2015-02-01

    Full Text Available The primary cells that participate in islet transplantation are the endocrine cells. However, in the islet microenvironment, the endocrine cells are closely associated with the neurovascular tissues consisting of the Schwann cells and pericytes, which form sheaths/barriers at the islet exterior and interior borders. The two cell types have shown their plasticity in islet injury, but their roles in transplantation remain unclear. In this research, we applied 3-dimensional neurovascular histology with cell tracing to reveal the participation of Schwann cells and pericytes in mouse islet transplantation. Longitudinal studies of the grafts under the kidney capsule identify that the donor Schwann cells and pericytes re-associate with the engrafted islets at the peri-graft and perivascular domains, respectively, indicating their adaptability in transplantation. Based on the morphological proximity and cellular reactivity, we propose that the new islet microenvironment should include the peri-graft Schwann cell sheath and perivascular pericytes as an integral part of the new tissue.

  12. Differential growth of pavement cells of Arabidopsis thaliana leaf epidermis as revealed by microbead labeling.

    Science.gov (United States)

    Elsner, Joanna; Lipowczan, Marcin; Kwiatkowska, Dorota

    2018-02-01

    In numerous vascular plants, pavement cells of the leaf epidermis are shaped like a jigsaw-puzzle piece. Knowledge about the subcellular pattern of growth that accompanies morphogenesis of such a complex shape is crucial for studies of the role of the cytoskeleton, cell wall and phytohormones in plant cell development. Because the detailed growth pattern of the anticlinal and periclinal cell walls remains unknown, our aim was to measure pavement cell growth at a subcellular resolution. Using fluorescent microbeads applied to the surface of the adaxial leaf epidermis of Arabidopsis thaliana as landmarks for growth computation, we directly assessed the growth rates for the outer periclinal and anticlinal cell walls at a subcellular scale. We observed complementary tendencies in the growth pattern of the outer periclinal and anticlinal cell walls. Central portions of periclinal walls were characterized by relatively slow growth, while growth of the other wall portions was heterogeneous. Local growth of the periclinal walls accompanying lobe development after initiation was relatively fast and anisotropic, with maximal extension usually in the direction along the lobe axis. This growth pattern of the periclinal walls was complemented by the extension of the anticlinal walls, which was faster on the lobe sides than at the tips. Growth of the anticlinal and outer periclinal walls of leaf pavement cells is heterogeneous. The growth of the lobes resembles cell elongation via diffuse growth rather than tip growth. © 2018 Botanical Society of America.

  13. Cell-Specific PEAR1 Methylation Studies Reveal a Locus that Coordinates Expression of Multiple Genes

    Directory of Open Access Journals (Sweden)

    Benedetta Izzi

    2018-04-01

    Full Text Available Chromosomal interactions connect distant enhancers and promoters on the same chromosome, activating or repressing gene expression. PEAR1 encodes the Platelet-Endothelial Aggregation Receptor 1, a contact receptor involved in platelet function and megakaryocyte and endothelial cell proliferation. PEAR1 expression during megakaryocyte differentiation is controlled by DNA methylation at its first CpG island. We identified a PEAR1 cell-specific methylation sensitive region in endothelial cells and megakaryocytes that showed strong chromosomal interactions with ISGL20L2, RRNAD1, MRLP24, HDGF and PRCC, using available promoter capture Hi-C datasets. These genes are involved in ribosome processing, protein synthesis, cell cycle and cell proliferation. We next studied the methylation and expression profile of these five genes in Human Umbilical Vein Endothelial Cells (HUVECs and megakaryocyte precursors. While cell-specific PEAR1 methylation corresponded to variability in expression for four out of five genes, no methylation change was observed in their promoter regions across cell types. Our data suggest that PEAR1 cell-type specific methylation changes may control long distance interactions with other genes. Further studies are needed to show whether such interaction data might be relevant for the genome-wide association data that showed a role for non-coding PEAR1 variants in the same region and platelet function, platelet count and cardiovascular risk.

  14. Temporal fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle.

    Science.gov (United States)

    Ahn, Eunyong; Kumar, Praveen; Mukha, Dzmitry; Tzur, Amit; Shlomi, Tomer

    2017-11-06

    Cellular metabolic demands change throughout the cell cycle. Nevertheless, a characterization of how metabolic fluxes adapt to the changing demands throughout the cell cycle is lacking. Here, we developed a temporal-fluxomics approach to derive a comprehensive and quantitative view of alterations in metabolic fluxes throughout the mammalian cell cycle. This is achieved by combining pulse-chase LC-MS-based isotope tracing in synchronized cell populations with computational deconvolution and metabolic flux modeling. We find that TCA cycle fluxes are rewired as cells progress through the cell cycle with complementary oscillations of glucose versus glutamine-derived fluxes: Oxidation of glucose-derived flux peaks in late G1 phase, while oxidative and reductive glutamine metabolism dominates S phase. These complementary flux oscillations maintain a constant production rate of reducing equivalents and oxidative phosphorylation flux throughout the cell cycle. The shift from glucose to glutamine oxidation in S phase plays an important role in cell cycle progression and cell proliferation. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

  15. Dynamic single-cell NAD(P)H measurement reveals oscillatory metabolism throughout the E. coli cell division cycle.

    Science.gov (United States)

    Zhang, Zheng; Milias-Argeitis, Andreas; Heinemann, Matthias

    2018-02-01

    Recent work has shown that metabolism between individual bacterial cells in an otherwise isogenetic population can be different. To investigate such heterogeneity, experimental methods to zoom into the metabolism of individual cells are required. To this end, the autofluoresence of the redox cofactors NADH and NADPH offers great potential for single-cell dynamic NAD(P)H measurements. However, NAD(P)H excitation requires UV light, which can cause cell damage. In this work, we developed a method for time-lapse NAD(P)H imaging in single E. coli cells. Our method combines a setup with reduced background emission, UV-enhanced microscopy equipment and optimized exposure settings, overall generating acceptable NAD(P)H signals from single cells, with minimal negative effect on cell growth. Through different experiments, in which we perturb E. coli's redox metabolism, we demonstrated that the acquired fluorescence signal indeed corresponds to NAD(P)H. Using this new method, for the first time, we report that intracellular NAD(P)H levels oscillate along the bacterial cell division cycle. The developed method for dynamic measurement of NAD(P)H in single bacterial cells will be an important tool to zoom into metabolism of individual cells.

  16. Adventitial SCA-1+ Progenitor Cell Gene Sequencing Reveals the Mechanisms of Cell Migration in Response to Hyperlipidemia

    Directory of Open Access Journals (Sweden)

    Ioannis Kokkinopoulos

    2017-08-01

    Full Text Available Adventitial progenitor cells, including SCA-1+ and mesenchymal stem cells, are believed to be important in vascular remodeling. It has been shown that SCA-1+ progenitor cells are involved in neointimal hyperplasia of vein grafts, but little is known concerning their involvement in hyperlipidemia-induced atherosclerosis. We employed single-cell sequencing technology on primary adventitial mouse SCA-1+ cells from wild-type and atherosclerotic-prone (ApoE-deficient mice and found that a group of genes controlling cell migration and matrix protein degradation was highly altered. Adventitial progenitors from ApoE-deficient mice displayed an augmented migratory potential both in vitro and in vivo. This increased migratory ability was mimicked by lipid loading to SCA-1+ cells. Furthermore, we show that lipid loading increased miRNA-29b expression and induced sirtuin-1 and matrix metalloproteinase-9 levels to promote cell migration. These results provide direct evidence that blood cholesterol levels influence vascular progenitor cell function, which could be a potential target cell for treatment of vascular disease.

  17. Reconfiguration of a flexible fiber immersed in a 2D dense granular flow close to the jamming transition

    Science.gov (United States)

    Kolb, Evelyne; Algarra, Nicolas; Vandembroucq, Damien; Lazarus, Arnaud

    2015-11-01

    We propose a new fluid/structure interaction in the unusual case of a dense granular medium flowing against an elastic fibre acting as a flexible intruder. We experimentally studied the deflection of a mylar flexible beam clamped at one side, the other free side facing a 2D granular flow in a horizontal cell moving at a constant velocity. We investigated the reconfiguration of the fibre as a function of the fibre's rigidity and of the granular packing fraction close but below the jamming in 2D. Imposing the fibre geometry like its length or thickness sets the critical buckling force the fibre is able to resist if it was not supported by lateral grains, while increasing the granular packing fraction might laterally consolidate the fibre and prevent it from buckling. But on the other side, the approach to jamming transition by increasing the granular packing fraction will be characterized by a dramatically increasing size of the cluster of connected grains forming a solid block acting against the fibre, which might promote the fibre's deflection. Thus, we investigated the granular flow fields, the fibre's deflexion as well as the forces experienced by the fibre and compared them with theoretical predictions from elastica for different loadings along the fibre. PMMH, CNRS UMR 7636, UPMC, ESPCI-ParisTech, 10 rue Vauquelin, 75231 Paris Cedex 05, France.

  18. Comparative Analysis Between Flaviviruses Reveals Specific Neural Stem Cell Tropism for Zika Virus in the Mouse Developing Neocortex

    Directory of Open Access Journals (Sweden)

    Jean-Baptiste Brault

    2016-08-01

    Full Text Available The recent Zika outbreak in South America and French Polynesia was associated with an epidemic of microcephaly, a disease characterized by a reduced size of the cerebral cortex. Other members of the Flavivirus genus, including West Nile virus (WNV, can cause encephalitis but were not demonstrated to cause microcephaly. It remains unclear whether Zika virus (ZIKV and other flaviviruses may infect different cell populations in the developing neocortex and lead to distinct developmental defects. Here, we describe an assay to infect mouse E15 embryonic brain slices with ZIKV, WNV and dengue virus serotype 4 (DENV-4. We show that this tissue is able to support viral replication of ZIKV and WNV, but not DENV-4. Cell fate analysis reveals a remarkable tropism of ZIKV infection for neural stem cells. Closely related WNV displays a very different tropism of infection, with a bias towards neurons. We further show that ZIKV infection, but not WNV infection, impairs cell cycle progression of neural stem cells. Both viruses inhibited apoptosis at early stages of infection. This work establishes a powerful comparative approach to identify ZIKV-specific alterations in the developing neocortex and reveals specific preferential infection of neural stem cells by ZIKV.

  19. Assessment of Membrane Fluidity Fluctuations during Cellular Development Reveals Time and Cell Type Specificity

    KAUST Repository

    Noutsi, Bakiza Kamal; Gratton, Enrico; Chaieb, Saharoui

    2016-01-01

    Cell membrane is made up of a complex structure of lipids and proteins that diffuse laterally giving rise to what we call membrane fluidity. During cellular development, such as differentiation cell membranes undergo dramatic fluidity changes induced by proteins such as ARC and Cofilin among others. In this study we used the generalized polarization (GP) property of fluorescent probe Laurdan using two-photon microscopy to determine membrane fluidity as a function of time and for various cell lines. A low GP value corresponds to a higher fluidity and a higher GP value is associated with a more rigid membrane. Four different cell lines were monitored such as hN2, NIH3T3, HEK293 and L6 cells. Membrane fluidity was measured at 12h, 72h and 92 h. Our results show significant changes in membrane fluidity among all cell types at different time points. GP values tend to increase significantly within 92 h in hN2 cells and 72 h in NIH3T3 cells and only at 92 h in HEK293 cells. L6 showed a marked decrease in membrane fluidity at 72 h and starts to increase at 92 h. As expected, NIH3T3 cells have more rigid membrane at earlier time points. On the other hand, neurons tend to have the highest membrane fluidity at early time points emphasizing its correlation with plasticity and the need for this malleability during differentiation. This study sheds light on the involvement of membrane fluidity during neuronal differentiation and development of other cell lines.

  20. Assessment of Membrane Fluidity Fluctuations during Cellular Development Reveals Time and Cell Type Specificity

    KAUST Repository

    Noutsi, Bakiza Kamal

    2016-06-30

    Cell membrane is made up of a complex structure of lipids and proteins that diffuse laterally giving rise to what we call membrane fluidity. During cellular development, such as differentiation cell membranes undergo dramatic fluidity changes induced by proteins such as ARC and Cofilin among others. In this study we used the generalized polarization (GP) property of fluorescent probe Laurdan using two-photon microscopy to determine membrane fluidity as a function of time and for various cell lines. A low GP value corresponds to a higher fluidity and a higher GP value is associated with a more rigid membrane. Four different cell lines were monitored such as hN2, NIH3T3, HEK293 and L6 cells. Membrane fluidity was measured at 12h, 72h and 92 h. Our results show significant changes in membrane fluidity among all cell types at different time points. GP values tend to increase significantly within 92 h in hN2 cells and 72 h in NIH3T3 cells and only at 92 h in HEK293 cells. L6 showed a marked decrease in membrane fluidity at 72 h and starts to increase at 92 h. As expected, NIH3T3 cells have more rigid membrane at earlier time points. On the other hand, neurons tend to have the highest membrane fluidity at early time points emphasizing its correlation with plasticity and the need for this malleability during differentiation. This study sheds light on the involvement of membrane fluidity during neuronal differentiation and development of other cell lines.

  1. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

    DEFF Research Database (Denmark)

    Lewis, Nathan E; Liu, Xin; Li, Yuxiang

    2013-01-01

    stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages...

  2. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

    DEFF Research Database (Denmark)

    Lewis, Nathan E; Liu, Xin; Li, Yuxiang

    2013-01-01

    Chinese hamster ovary (CHO) cells, first isolated in 1957, are the preferred production host for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has been well documented, a systematic, nucleotide-resolution characterization of their genotypic differences has been st...

  3. Ultra-deep sequencing reveals the subclonal structure and genomic evolution of oral squamous cell carcinoma

    DEFF Research Database (Denmark)

    Tabatabaeifar, Siavosh; Thomassen, Mads; Larsen, Martin Jakob

    Background: Oral squamous cell carcinoma (OSCC), a subgroup of head and neck squamous cell carcinoma (HNSCC), is primarily caused by alcohol consumption and tobacco use. Recent DNA sequencing studies suggests that HNSCC are very heterogeneous between patients; however the intra-patient subclonal...

  4. Deep RNA-Seq analysis reveals unexpected features of human prostate basal epithelial cells

    Directory of Open Access Journals (Sweden)

    Dingxiao Zhang

    2016-03-01

    Full Text Available Prostate cancer is the second leading cause of cancer-related deaths among American men [1]. The prostate gland mainly contains basal and luminal cells, which are constructed as a pseudostratified epithelium. Annotation of prostate epithelial transcriptomes provides a foundation for discoveries that can impact disease understanding and treatment. Here, for the first time, we describe a whole-genome transcriptome analysis of human benign prostatic basal and luminal populations by using deep RNA sequencing (GSE67070 [2]. Combined with comprehensive molecular and biological characterizations, we show that the differential gene expression profiles account for their distinct functional phenotypes. Strikingly, in contrast to luminal cells, basal cells preferentially express gene categories associated with stem cells, neural and neuronal development, and RNA processing. Of clinical relevance, the treatment failed castration-resistant and anaplastic prostate cancers molecularly resemble a basal-like phenotype. We also identified genes associated with patient clinical outcome. Therefore, we provide a gene expression resource for understanding human prostate epithelial lineages, and link the cell-type specific gene signatures to subtypes of prostate cancer development. Keywords: Prostate epithelial cells, Basal cells, Luminal cells, RNA-seq

  5. Whole-organ cell shape analysis reveals the developmental basis of ascidian notochord taper.

    Science.gov (United States)

    Veeman, Michael T; Smith, William C

    2013-01-15

    Here we use in toto imaging together with computational segmentation and analysis methods to quantify the shape of every cell at multiple stages in the development of a simple organ: the notochord of the ascidian Ciona savignyi. We find that cell shape in the intercalated notochord depends strongly on anterior-posterior (AP) position, with cells in the middle of the notochord consistently wider than cells at the anterior or posterior. This morphological feature of having a tapered notochord is present in many chordates. We find that ascidian notochord taper involves three main mechanisms: Planar Cell Polarity (PCP) pathway-independent sibling cell volume asymmetries that precede notochord cell intercalation; the developmental timing of intercalation, which proceeds from the anterior and posterior towards the middle; and the differential rates of notochord cell narrowing after intercalation. A quantitative model shows how the morphology of an entire developing organ can be controlled by this small set of cellular mechanisms. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation

    DEFF Research Database (Denmark)

    Klochendler, Agnes; Weinberg-Corem, Noa; Moran, Maya

    2012-01-01

    Most adult mammalian tissues are quiescent, with rare cell divisions serving to maintain homeostasis. At present, the isolation and study of replicating cells from their in vivo niche typically involves immunostaining for intracellular markers of proliferation, causing the loss of sensitive biolo...

  7. Revealing organization of cellulose in wood cell walls by Raman imaging

    Science.gov (United States)

    Umesh P. Agarwal; Sally A. Ralph

    2007-01-01

    Anisotropy of cellulose organization in mature black spruce wood cell wall was investigated by Raman imaging using a 1 [mu]m lateral-resolution capable confocal Raman microscope. In these studies, wood cross sections (CS) and radial longitudinal sections (LS) that were partially delignified by acid chlorite treatment were used. In the case of CS where latewood cells...

  8. Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

    Directory of Open Access Journals (Sweden)

    Bidesh Mahata

    2014-05-01

    Full Text Available T helper 2 (Th2 cells regulate helminth infections, allergic disorders, tumor immunity, and pregnancy by secreting various cytokines. It is likely that there are undiscovered Th2 signaling molecules. Although steroids are known to be immunoregulators, de novo steroid production from immune cells has not been previously characterized. Here, we demonstrate production of the steroid pregnenolone by Th2 cells in vitro and in vivo in a helminth infection model. Single-cell RNA sequencing and quantitative PCR analysis suggest that pregnenolone synthesis in Th2 cells is related to immunosuppression. In support of this, we show that pregnenolone inhibits Th cell proliferation and B cell immunoglobulin class switching. We also show that steroidogenic Th2 cells inhibit Th cell proliferation in a Cyp11a1 enzyme-dependent manner. We propose pregnenolone as a “lymphosteroid,” a steroid produced by lymphocytes. We speculate that this de novo steroid production may be an intrinsic phenomenon of Th2-mediated immune responses to actively restore immune homeostasis.

  9. Flavivirus infection from mosquitoes in vitro reveals cell entry at the plasma membrane

    International Nuclear Information System (INIS)

    Vancini, Ricardo; Kramer, Laura D.; Ribeiro, Mariana; Hernandez, Raquel; Brown, Dennis

    2013-01-01

    Dengue and West Nile viruses are enveloped RNA viruses that belong to genus Flavivirus (family Flaviviridae) and are considered important mosquito-borne viral pathogenic agents worldwide. A potential target for intervention strategies is the virus cell entry mechanism. Previous studies of flavivirus entry have focused on the effects of biochemical and molecular inhibitors on viral entry leading to controversial conclusions suggesting that the process is dependent upon endocytosis and low pH mediated membrane fusion. In this study we analyzed the early events in the infection process by means of electron microscopy and immuno-gold labeling of viral particles during cell entry, and used as a new approach for infecting cells with viruses obtained directly from mosquitoes. The results show that Dengue and West Nile viruses may infect cells by a mechanism that involves direct penetration of the host cell plasma membrane as proposed for alphaviruses.

  10. Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria.

    Science.gov (United States)

    Wheeler, Richard; Mesnage, Stéphane; Boneca, Ivo G; Hobbs, Jamie K; Foster, Simon J

    2011-12-01

    Cell morphology and viability in Eubacteria is dictated by the architecture of peptidoglycan, the major and essential structural component of the cell wall. Although the biochemical composition of peptidoglycan is well understood, how the peptidoglycan architecture can accommodate the dynamics of growth and division while maintaining cell shape remains largely unknown. Here, we elucidate the peptidoglycan architecture and dynamics of bacteria with ovoid cell shape (ovococci), which includes a number of important pathogens, by combining biochemical analyses with atomic force and super-resolution microscopies. Atomic force microscopy analysis showed preferential orientation of the peptidoglycan network parallel to the short axis of the cell, with distinct architectural features associated with septal and peripheral wall synthesis. Super-resolution three-dimensional structured illumination fluorescence microscopy was applied for the first time in bacteria to unravel the dynamics of peptidoglycan assembly in ovococci. The ovococci have a unique peptidoglycan architecture and growth mode not observed in other model organisms. © 2011 Blackwell Publishing Ltd.

  11. Flavivirus infection from mosquitoes in vitro reveals cell entry at the plasma membrane

    Energy Technology Data Exchange (ETDEWEB)

    Vancini, Ricardo [Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC (United States); Kramer, Laura D. [Wadsworth Center, New York State Department of Health, and School of Public Health, State University of New York at Albany, Albany, NY (United States); Ribeiro, Mariana; Hernandez, Raquel [Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC (United States); Brown, Dennis, E-mail: dennis_brown@ncsu.edu [Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC (United States)

    2013-01-20

    Dengue and West Nile viruses are enveloped RNA viruses that belong to genus Flavivirus (family Flaviviridae) and are considered important mosquito-borne viral pathogenic agents worldwide. A potential target for intervention strategies is the virus cell entry mechanism. Previous studies of flavivirus entry have focused on the effects of biochemical and molecular inhibitors on viral entry leading to controversial conclusions suggesting that the process is dependent upon endocytosis and low pH mediated membrane fusion. In this study we analyzed the early events in the infection process by means of electron microscopy and immuno-gold labeling of viral particles during cell entry, and used as a new approach for infecting cells with viruses obtained directly from mosquitoes. The results show that Dengue and West Nile viruses may infect cells by a mechanism that involves direct penetration of the host cell plasma membrane as proposed for alphaviruses.

  12. Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutans.

    Science.gov (United States)

    Li, Y; Liu, Z; Zhang, Y; Su, Q P; Xue, B; Shao, S; Zhu, Y; Xu, X; Wei, S; Sun, Y

    2015-10-01

    Streptococcus mutans is a primary pathogen responsible for dental caries. It has an outstanding ability to form biofilm, which is vital for virulence. Previous studies have shown that knockout of Wall-associated protein A (WapA) affects cell chain and biofilm formation of S. mutans. As a surface protein, the distribution of WapA remains unknown, but it is important to understand the mechanism underlying the function of WapA. This study applied the fluorescence protein mCherry as a reporter gene to characterize the dynamic distribution of WapA in S. mutans via time-lapse and super-resolution fluorescence imaging. The results revealed interesting subcellular distribution patterns of WapA in single, dividing and long chains of S. mutans cells. It appears at the middle of the cell and moves to the poles as the cell grows and divides. In a cell chain, after each round of cell division, such dynamic relocation results in WapA distribution at the previous cell division sites, resulting in a pattern where WapA is located at the boundary of two adjacent cell pairs. This WapA distribution pattern corresponds to the breaking segmentation of wapA deletion cell chains. The dynamic relocation of WapA through the cell cycle increases our understanding of the mechanism of WapA in maintaining cell chain integrity and biofilm formation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  13. Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates.

    Directory of Open Access Journals (Sweden)

    Yaron E Antebi

    2013-07-01

    Full Text Available Cell differentiation is typically directed by external signals that drive opposing regulatory pathways. Studying differentiation under polarizing conditions, with only one input signal provided, is limited in its ability to resolve the logic of interactions between opposing pathways. Dissection of this logic can be facilitated by mapping the system's response to mixtures of input signals, which are expected to occur in vivo, where cells are simultaneously exposed to various signals with potentially opposing effects. Here, we systematically map the response of naïve T cells to mixtures of signals driving differentiation into the Th1 and Th2 lineages. We characterize cell state at the single cell level by measuring levels of the two lineage-specific transcription factors (T-bet and GATA3 and two lineage characteristic cytokines (IFN-γ and IL-4 that are driven by these transcription regulators. We find a continuum of mixed phenotypes in which individual cells co-express the two lineage-specific master regulators at levels that gradually depend on levels of the two input signals. Using mathematical modeling we show that such tunable mixed phenotype arises if autoregulatory positive feedback loops in the gene network regulating this process are gradual and dominant over cross-pathway inhibition. We also find that expression of the lineage-specific cytokines follows two independent stochastic processes that are biased by expression levels of the master regulators. Thus, cytokine expression is highly heterogeneous under mixed conditions, with subpopulations of cells expressing only IFN-γ, only IL-4, both cytokines, or neither. The fraction of cells in each of these subpopulations changes gradually with input conditions, reproducing the continuous internal state at the cell population level. These results suggest a differentiation scheme in which cells reflect uncertainty through a continuously tuneable mixed phenotype combined with a biased

  14. Live Imaging of Influenza Infection of the Trachea Reveals Dynamic Regulation of CD8+ T Cell Motility by Antigen.

    Science.gov (United States)

    Lambert Emo, Kris; Hyun, Young-Min; Reilly, Emma; Barilla, Christopher; Gerber, Scott; Fowell, Deborah; Kim, Minsoo; Topham, David J

    2016-09-01

    During a primary influenza infection, cytotoxic CD8+ T cells need to infiltrate the infected airways and engage virus-infected epithelial cells. The factors that regulate T cell motility in the infected airway tissue are not well known. To more precisely study T cell infiltration of the airways, we developed an experimental model system using the trachea as a site where live imaging can be performed. CD8+ T cell motility was dynamic with marked changes in motility on different days of the infection. In particular, significant changes in average cell velocity and confinement were evident on days 8-10 during which the T cells abruptly but transiently increase velocity on day 9. Experiments to distinguish whether infection itself or antigen affect motility revealed that it is antigen, not active infection per se that likely affects these changes as blockade of peptide/MHC resulted in increased velocity. These observations demonstrate that influenza tracheitis provides a robust experimental foundation to study molecular regulation of T cell motility during acute virus infection.

  15. Live Imaging of Influenza Infection of the Trachea Reveals Dynamic Regulation of CD8+ T Cell Motility by Antigen.

    Directory of Open Access Journals (Sweden)

    Kris Lambert Emo

    2016-09-01

    Full Text Available During a primary influenza infection, cytotoxic CD8+ T cells need to infiltrate the infected airways and engage virus-infected epithelial cells. The factors that regulate T cell motility in the infected airway tissue are not well known. To more precisely study T cell infiltration of the airways, we developed an experimental model system using the trachea as a site where live imaging can be performed. CD8+ T cell motility was dynamic with marked changes in motility on different days of the infection. In particular, significant changes in average cell velocity and confinement were evident on days 8-10 during which the T cells abruptly but transiently increase velocity on day 9. Experiments to distinguish whether infection itself or antigen affect motility revealed that it is antigen, not active infection per se that likely affects these changes as blockade of peptide/MHC resulted in increased velocity. These observations demonstrate that influenza tracheitis provides a robust experimental foundation to study molecular regulation of T cell motility during acute virus infection.

  16. The functional micro-organization of grid cells revealed by cellular-resolution imaging.

    Science.gov (United States)

    Heys, James G; Rangarajan, Krsna V; Dombeck, Daniel A

    2014-12-03

    Establishing how grid cells are anatomically arranged, on a microscopic scale, in relation to their firing patterns in the environment would facilitate a greater microcircuit-level understanding of the brain's representation of space. However, all previous grid cell recordings used electrode techniques that provide limited descriptions of fine-scale organization. We therefore developed a technique for cellular-resolution functional imaging of medial entorhinal cortex (MEC) neurons in mice navigating a virtual linear track, enabling a new experimental approach to study MEC. Using these methods, we show that grid cells are physically clustered in MEC compared to nongrid cells. Additionally, we demonstrate that grid cells are functionally micro-organized: the similarity between the environment firing locations of grid cell pairs varies as a function of the distance between them according to a "Mexican hat"-shaped profile. This suggests that, on average, nearby grid cells have more similar spatial firing phases than those further apart. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer.

    Science.gov (United States)

    Francavilla, Chiara; Lupia, Michela; Tsafou, Kalliopi; Villa, Alessandra; Kowalczyk, Katarzyna; Rakownikow Jersie-Christensen, Rosa; Bertalot, Giovanni; Confalonieri, Stefano; Brunak, Søren; Jensen, Lars J; Cavallaro, Ugo; Olsen, Jesper V

    2017-03-28

    Our understanding of the molecular determinants of cancer is still inadequate because of cancer heterogeneity. Here, using epithelial ovarian cancer (EOC) as a model system, we analyzed a minute amount of patient-derived epithelial cells from either healthy or cancerous tissues by single-shot mass-spectrometry-based phosphoproteomics. Using a multi-disciplinary approach, we demonstrated that primary cells recapitulate tissue complexity and represent a valuable source of differentially expressed proteins and phosphorylation sites that discriminate cancer from healthy cells. Furthermore, we uncovered kinase signatures associated with EOC. In particular, CDK7 targets were characterized in both EOC primary cells and ovarian cancer cell lines. We showed that CDK7 controls cell proliferation and that pharmacological inhibition of CDK7 selectively represses EOC cell proliferation. Our approach defines the molecular landscape of EOC, paving the way for efficient therapeutic approaches for patients. Finally, we highlight the potential of phosphoproteomics to identify clinically relevant and druggable pathways in cancer. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Chiara Francavilla

    2017-03-01

    Full Text Available Our understanding of the molecular determinants of cancer is still inadequate because of cancer heterogeneity. Here, using epithelial ovarian cancer (EOC as a model system, we analyzed a minute amount of patient-derived epithelial cells from either healthy or cancerous tissues by single-shot mass-spectrometry-based phosphoproteomics. Using a multi-disciplinary approach, we demonstrated that primary cells recapitulate tissue complexity and represent a valuable source of differentially expressed proteins and phosphorylation sites that discriminate cancer from healthy cells. Furthermore, we uncovered kinase signatures associated with EOC. In particular, CDK7 targets were characterized in both EOC primary cells and ovarian cancer cell lines. We showed that CDK7 controls cell proliferation and that pharmacological inhibition of CDK7 selectively represses EOC cell proliferation. Our approach defines the molecular landscape of EOC, paving the way for efficient therapeutic approaches for patients. Finally, we highlight the potential of phosphoproteomics to identify clinically relevant and druggable pathways in cancer.

  19. Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation.

    Science.gov (United States)

    Zhyvoloup, Alexander; Melamed, Anat; Anderson, Ian; Planas, Delphine; Lee, Chen-Hsuin; Kriston-Vizi, Janos; Ketteler, Robin; Merritt, Andy; Routy, Jean-Pierre; Ancuta, Petronela; Bangham, Charles R M; Fassati, Ariberto

    2017-07-01

    HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D) in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism. Analysis of >400,000 unique integration sites showed that WT virus integrated more frequently than N74D mutant within or near genes susceptible to repression by digoxin and involved in T-cell activation and cell metabolism. Two main gene networks down-regulated by the drug were CD40L and CD38. Blocking CD40L by neutralizing antibodies selectively inhibited WT virus infection, phenocopying digoxin. Thus the selectivity of digoxin depends on a combination of integration targeting and repression of specific gene networks. The drug unmasked a functional connection between HIV-1 integration and T-cell activation. Our results suggest that HIV-1 evolved integration site selection to couple its early gene expression with the status of target CD4+ T-cells, which may affect latency and viral reactivation.

  20. Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation.

    Directory of Open Access Journals (Sweden)

    Alexander Zhyvoloup

    2017-07-01

    Full Text Available HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism. Analysis of >400,000 unique integration sites showed that WT virus integrated more frequently than N74D mutant within or near genes susceptible to repression by digoxin and involved in T-cell activation and cell metabolism. Two main gene networks down-regulated by the drug were CD40L and CD38. Blocking CD40L by neutralizing antibodies selectively inhibited WT virus infection, phenocopying digoxin. Thus the selectivity of digoxin depends on a combination of integration targeting and repression of specific gene networks. The drug unmasked a functional connection between HIV-1 integration and T-cell activation. Our results suggest that HIV-1 evolved integration site selection to couple its early gene expression with the status of target CD4+ T-cells, which may affect latency and viral reactivation.

  1. Positive cell-free fetal DNA testing for trisomy 13 reveals confined placental mosaicism.

    Science.gov (United States)

    Hall, April L; Drendel, Holli M; Verbrugge, Jennifer L; Reese, Angela M; Schumacher, Katherine L; Griffith, Christopher B; Weaver, David D; Abernathy, Mary P; Litton, Christian G; Vance, Gail H

    2013-09-01

    We report on a case in which cell-free fetal DNA was positive for trisomy 13 most likely due to confined placental mosaicism. Cell-free fetal DNA testing analyzes DNA derived from placental trophoblast cells and can lead to incorrect results that are not representative of the fetus. We sought to confirm commercial cell-free fetal DNA testing results by chorionic villus sampling and amniocentesis. These results were followed up by postnatal chromosome analysis of cord blood and placental tissue. First-trimester cell-free fetal DNA test results were positive for trisomy 13. Cytogenetic analysis of chorionic villus sampling yielded a mosaic karyotype of 47,XY,+13[10]/46,XY[12]. G-banded analysis of amniotic fluid was normal, 46,XY. Postnatal cytogenetic analysis of cord blood was normal. Karyotyping of tissues from four quadrants of the placenta demonstrated mosaicism for trisomy 13 in two of the quadrants and a normal karyotype in the other two. Our case illustrates several important aspects of this new testing methodology: that cell-free fetal DNA may not be representative of the fetal karyotype; that follow-up with diagnostic testing of chorionic villus sampling and/or amniotic fluid for abnormal test results should be performed; and that pretest counseling regarding the full benefits, limitations, and possible testing outcomes of cell-free fetal DNA screening is important.

  2. Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-Like Cells.

    Science.gov (United States)

    Kondo, Yuki; Nurani, Alif Meem; Saito, Chieko; Ichihashi, Yasunori; Saito, Masato; Yamazaki, Kyoko; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Fukuda, Hiroo

    2016-06-01

    Cell differentiation is a complex process involving multiple steps, from initial cell fate specification to final differentiation. Procambial/cambial cells, which act as vascular stem cells, differentiate into both xylem and phloem cells during vascular development. Recent studies have identified regulatory cascades for xylem differentiation. However, the molecular mechanism underlying phloem differentiation is largely unexplored due to technical challenges. Here, we established an ectopic induction system for phloem differentiation named Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL). Our results verified similarities between VISUAL-induced Arabidopsis thaliana phloem cells and in vivo sieve elements. We performed network analysis using transcriptome data with VISUAL to dissect the processes underlying phloem differentiation, eventually identifying a factor involved in the regulation of the master transcription factor gene APL Thus, our culture system opens up new avenues not only for genetic studies of phloem differentiation, but also for future investigations of multidirectional differentiation from vascular stem cells. © 2016 American Society of Plant Biologists. All rights reserved.

  3. Synthetic Strigolactone Analogues Reveal Anti-Cancer Activities on Hepatocellular Carcinoma Cells

    KAUST Repository

    Hasan, Mohammed Nihal

    2018-02-09

    Hepatocellular carcinoma (HCC) remains one of the leading causes of death worldwide. The complex etiology is attributed to many factors like heredity, cirrhosis, hepatitis infections or the dysregulation of the different molecular pathways. Nevertheless, the current treatment regimens have either severe side effects or tumors gradually acquire resistance upon prolonged use. Thus, developing a new selective treatment for HCC is the need of the hour. Many anticancer agents derived from plants have been evaluated for their cytotoxicity towards many human cancer cell lines. Strigolactones (SLs)-a newly discovered class of phytohormones, play a crucial role in the development of plant-root and shoot. Recently, many synthetic analogues of SLs have demonstrated pro-apoptotic effects on different cancer cell lines like prostate, breast, colon and lung. In this study, we tested synthetic SLs analogues on HCC cell line-HepG2 and evaluated their capability to induce cell proliferation inhibition and apoptosis. Primary WST-1 assays, followed by annexin-V/7AAD staining, demonstrated the anti-proliferative effects. The SLs analogues TIT3 and TIT7 were found to significantly reduce HepG2 cell viability in a dose- and time-dependent manner and induce apoptosis. Interestingly, though TIT3 and TIT7 strongly affected cancer cell proliferation, both compounds showed moderate anti-proliferative effect on normal cells. Further, migration of cancer cells was suppressed upon treatment with TIT3 and TIT7 in a wound healing assay. In summary, these findings suggest that two SLs analogues TIT3 and TIT7 exert selective inhibitory effects on cancer cells most likely through targeting microtubules. SLs analogues could be used in future as potential anti-cancer candidates in chemotherapy.

  4. Synthetic Strigolactone Analogues Reveal Anti-Cancer Activities on Hepatocellular Carcinoma Cells

    KAUST Repository

    Hasan, Mohammed Nihal; Choudhry, Hani; Razvi, Syed Shoeb; Moselhy, Said Salama; Kumosani, Taha Abduallah; Zamzami, Mazin A.; Omran, Ziad; Halwani, Majed A.; Al-Babili, Salim; Abualnaja, Khalid Omer; Al-Malki, Abdulrahman Labeed; Alhosin, Mahmoud; Asami, Tadao

    2018-01-01

    Hepatocellular carcinoma (HCC) remains one of the leading causes of death worldwide. The complex etiology is attributed to many factors like heredity, cirrhosis, hepatitis infections or the dysregulation of the different molecular pathways. Nevertheless, the current treatment regimens have either severe side effects or tumors gradually acquire resistance upon prolonged use. Thus, developing a new selective treatment for HCC is the need of the hour. Many anticancer agents derived from plants have been evaluated for their cytotoxicity towards many human cancer cell lines. Strigolactones (SLs)-a newly discovered class of phytohormones, play a crucial role in the development of plant-root and shoot. Recently, many synthetic analogues of SLs have demonstrated pro-apoptotic effects on different cancer cell lines like prostate, breast, colon and lung. In this study, we tested synthetic SLs analogues on HCC cell line-HepG2 and evaluated their capability to induce cell proliferation inhibition and apoptosis. Primary WST-1 assays, followed by annexin-V/7AAD staining, demonstrated the anti-proliferative effects. The SLs analogues TIT3 and TIT7 were found to significantly reduce HepG2 cell viability in a dose- and time-dependent manner and induce apoptosis. Interestingly, though TIT3 and TIT7 strongly affected cancer cell proliferation, both compounds showed moderate anti-proliferative effect on normal cells. Further, migration of cancer cells was suppressed upon treatment with TIT3 and TIT7 in a wound healing assay. In summary, these findings suggest that two SLs analogues TIT3 and TIT7 exert selective inhibitory effects on cancer cells most likely through targeting microtubules. SLs analogues could be used in future as potential anti-cancer candidates in chemotherapy.

  5. A germ cell determinant reveals parallel pathways for germ line development in Caenorhabditis elegans.

    Science.gov (United States)

    Mainpal, Rana; Nance, Jeremy; Yanowitz, Judith L

    2015-10-15

    Despite the central importance of germ cells for transmission of genetic material, our understanding of the molecular programs that control primordial germ cell (PGC) specification and differentiation are limited. Here, we present findings that X chromosome NonDisjunction factor-1 (XND-1), known for its role in regulating meiotic crossover formation, is an early determinant of germ cell fates in Caenorhabditis elegans. xnd-1 mutant embryos display a novel 'one PGC' phenotype as a result of G2 cell cycle arrest of the P4 blastomere. Larvae and adults display smaller germ lines and reduced brood size consistent with a role for XND-1 in germ cell proliferation. Maternal XND-1 proteins are found in the P4 lineage and are exclusively localized to the nucleus in PGCs, Z2 and Z3. Zygotic XND-1 turns on shortly thereafter, at the ∼300-cell stage, making XND-1 the earliest zygotically expressed gene in worm PGCs. Strikingly, a subset of xnd-1 mutants lack germ cells, a phenotype shared with nos-2, a member of the conserved Nanos family of germline determinants. We generated a nos-2 null allele and show that nos-2; xnd-1 double mutants display synthetic sterility. Further removal of nos-1 leads to almost complete sterility, with the vast majority of animals without germ cells. Sterility in xnd-1 mutants is correlated with an increase in transcriptional activation-associated histone modification and aberrant expression of somatic transgenes. Together, these data strongly suggest that xnd-1 defines a new branch for PGC development that functions redundantly with nos-2 and nos-1 to promote germline fates by maintaining transcriptional quiescence and regulating germ cell proliferation. © 2015. Published by The Company of Biologists Ltd.

  6. T Cell Receptor Vβ Staining Identifies the Malignant Clone in Adult T cell Leukemia and Reveals Killing of Leukemia Cells by Autologous CD8+ T cells.

    Directory of Open Access Journals (Sweden)

    Aileen G Rowan

    2016-11-01

    Full Text Available There is growing evidence that CD8+ cytotoxic T lymphocyte (CTL responses can contribute to long-term remission of many malignancies. The etiological agent of adult T-cell leukemia/lymphoma (ATL, human T lymphotropic virus type-1 (HTLV-1, contains highly immunogenic CTL epitopes, but ATL patients typically have low frequencies of cytokine-producing HTLV-1-specific CD8+ cells in the circulation. It remains unclear whether patients with ATL possess CTLs that can kill the malignant HTLV-1 infected clone. Here we used flow cytometric staining of TCRVβ and cell adhesion molecule-1 (CADM1 to identify monoclonal populations of HTLV-1-infected T cells in the peripheral blood of patients with ATL. Thus, we quantified the rate of CD8+-mediated killing of the putative malignant clone in ex vivo blood samples. We observed that CD8+ cells from ATL patients were unable to lyse autologous ATL clones when tested directly ex vivo. However, short in vitro culture restored the ability of CD8+ cells to kill ex vivo ATL clones in some donors. The capacity of CD8+ cells to lyse HTLV-1 infected cells which expressed the viral sense strand gene products was significantly enhanced after in vitro culture, and donors with an ATL clone that expressed the HTLV-1 Tax gene were most likely to make a detectable lytic CD8+ response to the ATL cells. We conclude that some patients with ATL possess functional tumour-specific CTLs which could be exploited to contribute to control of the disease.

  7. Live-cell FRET imaging reveals clustering of the prion protein at the cell surface induced by infectious prions.

    Science.gov (United States)

    Tavares, Evandro; Macedo, Joana A; Paulo, Pedro M R; Tavares, Catarina; Lopes, Carlos; Melo, Eduardo P

    2014-07-01

    Prion diseases are associated to the conversion of the prion protein into a misfolded pathological isoform. The mechanism of propagation of protein misfolding by protein templating remains largely unknown. Neuroblastoma cells were transfected with constructs of the prion protein fused to both CFP-GPI-anchored and to YFP-GPI-anchored and directed to its cell membrane location. Live-cell FRET imaging between the prion protein fused to CFP or YFP was measured giving consistent values of 10±2%. This result was confirmed by fluorescence lifetime imaging microscopy and indicates intermolecular interactions between neighbor prion proteins. In particular, considering that a maximum FRET efficiency of 17±2% was determined from a positive control consisting of a fusion CFP-YFP-GPI-anchored. A stable cell clone expressing the two fusions containing the prion protein was also selected to minimize cell-to-cell variability. In both, stable and transiently transfected cells, the FRET efficiency consistently increased in the presence of infectious prions - from 4±1% to 7±1% in the stable clone and from 10±2% to 16±1% in transiently transfected cells. These results clearly reflect an increased clustering of the prion protein on the membrane in the presence of infectious prions, which was not observed in negative control using constructs without the prion protein and upon addition of non-infected brain. Our data corroborates the recent view that the primary site for prion conversion is the cell membrane. Since our fluorescent cell clone is not susceptible to propagate infectivity, we hypothesize that the initial event of prion infectivity might be the clustering of the GPI-anchored prion protein. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Live cell imaging reveals different modes of cytotoxic action of extracts derived from commonly used luting cements.

    Science.gov (United States)

    Trumpaitė-Vanagienė, Rita; Čebatariūnienė, Alina; Tunaitis, Virginijus; Pūrienė, Alina; Pivoriūnas, Augustas

    2018-02-01

    To compare cytotoxicity of extracts derived from commonly used luting cements: Hoffmann's Zinc Phosphate (ZPC), GC Fuji Plus Resin Modified Glass Ionomer (RMGIC) and 3M ESPE RelyX Unicem Resin Cement (RC) on primary human gingival fibroblasts (HGFs). HGFs were exposed to different concentrations of the ZPC, RMGIC and RC extracts. The cytotoxicity was assessed with the PrestoBlue Cell Viability Reagent and viable cells were counted by a haemocytometer using the trypan blue exclusion test. In order to determine the primary mechanism of the cell death induced by extracts from different luting cements, the real-time monitoring of caspase-3/-7 activity and membrane integrity of cells was employed. The extracts from the RMGIC and ZPC decreased the metabolic activity and numbers of viable cells. Unexpectedly, the extracts from the RC evoked only small effects on the metabolic activity of HGFs with a decreasing number of viable cells in a dose-and time-dependent manner. The live cell imaging revealed that the apoptosis was the primary mechanism of a cell death induced by the extracts derived from the RMGIC, whereas the extracts from the RC and ZPC induced a cell death through a necrotic and caspase-independent pathway. The apoptosis was the primary mechanism of the cell death induced by the extracts derived from the RMGIC, whereas the extracts from the RC and ZPC induced a cell death via a necrotic pathway. We suggest that metabolic assays commonly used to assess the cytotoxicity of luting cements should be validated by alternative methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Genomic analysis reveals a potential role for cell cycle perturbation in HCV-mediated apoptosis of cultured hepatocytes.

    Directory of Open Access Journals (Sweden)

    Kathie-Anne Walters

    2009-01-01

    Full Text Available The mechanisms of liver injury associated with chronic HCV infection, as well as the individual roles of both viral and host factors, are not clearly defined. However, it is becoming increasingly clear that direct cytopathic effects, in addition to immune-mediated processes, play an important role in liver injury. Gene expression profiling during multiple time-points of acute HCV infection of cultured Huh-7.5 cells was performed to gain insight into the cellular mechanism of HCV-associated cytopathic effect. Maximal induction of cell-death-related genes and appearance of activated caspase-3 in HCV-infected cells coincided with peak viral replication, suggesting a link between viral load and apoptosis. Gene ontology analysis revealed that many of the cell-death genes function to induce apoptosis in response to cell cycle arrest. Labeling of dividing cells in culture followed by flow cytometry also demonstrated the presence of significantly fewer cells in S-phase in HCV-infected relative to mock cultures, suggesting HCV infection is associated with delayed cell cycle progression. Regulation of numerous genes involved in anti-oxidative stress response and TGF-beta1 signaling suggest these as possible causes of delayed cell cycle progression. Significantly, a subset of cell-death genes regulated during in vitro HCV infection was similarly regulated specifically in liver tissue from a cohort of HCV-infected liver transplant patients with rapidly progressive fibrosis. Collectively, these data suggest that HCV mediates direct cytopathic effects through deregulation of the cell cycle and that this process may contribute to liver disease progression. This in vitro system could be utilized to further define the cellular mechanism of this perturbation.

  10. Characterization of a null allelic mutant of the rice NAL1 gene reveals its role in regulating cell division.

    Directory of Open Access Journals (Sweden)

    Dan Jiang

    Full Text Available Leaf morphology is closely associated with cell division. In rice, mutations in Narrow leaf 1 (NAL1 show narrow leaf phenotypes. Previous studies have shown that NAL1 plays a role in regulating vein patterning and increasing grain yield in indica cultivars, but its role in leaf growth and development remains unknown. In this report, we characterized two allelic mutants of NARROW LEAF1 (NAL1, nal1-2 and nal1-3, both of which showed a 50% reduction in leaf width and length, as well as a dwarf culm. Longitudinal and transverse histological analyses of leaves and internodes revealed that cell division was suppressed in the anticlinal orientation but enhanced in the periclinal orientation in the mutants, while cell size remained unaltered. In addition to defects in cell proliferation, the mutants showed abnormal midrib in leaves. Map-based cloning revealed that nal1-2 is a null allelic mutant of NAL1 since both the whole promoter and a 404-bp fragment in the first exon of NAL1 were deleted, and that a 6-bp fragment was deleted in the mutant nal1-3. We demonstrated that NAL1 functions in the regulation of cell division as early as during leaf primordia initiation. The altered transcript level of G1- and S-phase-specific genes suggested that NAL1 affects cell cycle regulation. Heterogeneous expression of NAL1 in fission yeast (Schizosaccharomyces pombe further supported that NAL1 affects cell division. These results suggest that NAL1 controls leaf width and plant height through its effects on cell division.

  11. Single-cell duplex RT-LATE-PCR reveals Oct4 and Xist RNA gradients in 8-cell embryos

    Directory of Open Access Journals (Sweden)

    Hartung Odelya

    2007-12-01

    Full Text Available Abstract Background The formation of two distinctive cell lineages in preimplantation mouse embryos is characterized by differential gene expression. The cells of the inner cell mass are pluripotent and express high levels of Oct4 mRNA, which is down-regulated in the surrounding trophectoderm. In contrast, the trophectoderm of female embryos contains Xist mRNA, which is absent from cells of the inner mass. Prior to blastocyst formation, all blastomeres of female embryos still express both of these RNAs. We, thus, postulated that simultaneous quantification of Oct4 and Xist transcripts in individual blastomeres at the 8-cell stage could be informative as to their subsequent fate. Testing this hypothesis, however, presented numerous technical challenges. We overcame these difficulties by combining PurAmp, a single-tube method for RNA preparation and quantification, with LATE-PCR, an advanced form of asymmetric PCR. Results We constructed a duplex RT-LATE-PCR assay for real-time measurement of Oct4 and Xist templates and confirmed its specificity and quantitative accuracy with different methods. We then undertook analysis of sets of blastomeres isolated from embryos at the 8-cell stage. At this stage, all cells in the embryo are still pluripotent and morphologically equivalent. Our results demonstrate, however, that both Oct4 and Xist RNA levels vary in individual blastomeres comprising the same embryo, with some cells having particularly elevated levels of either transcript. Analysis of multiple embryos also shows that Xist and Oct4 expression levels are not correlated at the 8-cell stage, although transcription of both genes is up-regulated at this time in development. In addition, comparison of data from males and females allowed us to determine that the efficiency of the Oct4/Xist assay is unaffected by sex-related differences in gene expression. Conclusion This paper describes the first example of multiplex RT-LATE-PCR and its utility, when

  12. Mapping organelle motion reveals a vesicular conveyor belt spatially replenishing secretory vesicles in stimulated chromaffin cells.

    Science.gov (United States)

    Maucort, Guillaume; Kasula, Ravikiran; Papadopulos, Andreas; Nieminen, Timo A; Rubinsztein-Dunlop, Halina; Meunier, Frederic A

    2014-01-01

    How neurosecretory cells spatially adjust their secretory vesicle pools to replenish those that have fused and released their hormonal content is currently unknown. Here we designed a novel set of image analyses to map the probability of tracked organelles undergoing a specific type of movement (free, caged or directed). We then applied our analysis to time-lapse z-stack confocal imaging of secretory vesicles from bovine Chromaffin cells to map the global changes in vesicle motion and directionality occurring upon secretagogue stimulation. We report a defined region abutting the cortical actin network that actively transports secretory vesicles and is dissipated by actin and microtubule depolymerizing drugs. The directionality of this "conveyor belt" towards the cell surface is activated by stimulation. Actin and microtubule networks therefore cooperatively probe the microenvironment to transport secretory vesicles to the periphery, providing a mechanism whereby cells globally adjust their vesicle pools in response to secretagogue stimulation.

  13. Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

    DEFF Research Database (Denmark)

    Ding, Li; Paszkowski-Rogacz, Maciej; Winzi, Maria

    2015-01-01

    We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression...... of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell...... identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide...

  14. Single-cell Raman and fluorescence microscopy reveal the association of lipid bodies with phagosomes in leukocytes

    Science.gov (United States)

    van Manen, Henk-Jan; Kraan, Yvonne M.; Roos, Dirk; Otto, Cees

    2005-01-01

    Cellular imaging techniques based on vibrational spectroscopy have become powerful tools in cell biology because the molecular composition of subcellular compartments can be visualized without the need for labeling. Using high-resolution, nonresonant confocal Raman microscopy on individual cells, we demonstrate here that lipid bodies (LBs) rich in arachidonate as revealed by their Raman spectra associate with latex bead-containing phagosomes in neutrophilic granulocytes. This finding was corroborated in macrophages and in PLB-985 cells, which can be induced to differentiate into neutrophil-like cells, by selective staining of LBs and visualization by confocal fluorescence microscopy. We further show that the accumulation of LBs near phagosomes is mediated at least in part by the flavohemoprotein gp91phox (in which “phox” is phagocyte oxidase), because different LB distributions around phagocytosed latex beads were observed in WT and gp91phox-deficient PLB-985 cells. gp91phox, which accumulates in the phagosomal membrane, is the catalytic subunit of the leukocyte NADPH oxidase, a critical enzyme in the innate immune response. Finally, time-lapse fluorescence microscopy experiments on neutrophils revealed that the LB-phagosome association is transient, similar to the “kiss-and-run” behavior displayed by endosomes involved in phagosome maturation. Because arachidonic acid (AA) has been shown to be involved in NADPH oxidase activation and phagosome maturation in neutrophils and macrophages, respectively, the findings reported here suggest that LBs may provide a reservoir of AA for local activation of these essential leukocyte functions. PMID:16002471

  15. Papillary Renal Cell Carcinoma Revealed by Renal Traumatism: A Case Report in Lomé

    Directory of Open Access Journals (Sweden)

    Tchilabalo Matchonna Kpatcha

    2017-07-01

    Full Text Available This study is a report on a case of papillary carcinoma of the kidney revealed by an abdominal contusion. The results of radiological investigations were discordant with the low intensity of the shock. The treatment consisted of radical nephrectomy because of the suspicion of a pre-existing malignancy. Histological analysis revealed a papillary carcinoma pT3N0M0. We focus on the need for performing diagnostic tests in order to avoid missing a pre-existing anomaly to the kidney trauma.

  16. Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling

    DEFF Research Database (Denmark)

    Almstrup, Kristian; Hoei-Hansen, Christina E; Wirkner, Ute

    2004-01-01

    in their stoichiometry on progression into embryonic carcinoma. We compared the CIS expression profile with patterns reported in embryonic stem cells (ESCs), which revealed a substantial overlap that may be as high as 50%. We also demonstrated an over-representation of expressed genes in regions of 17q and 12, reported......Carcinoma in situ (CIS) is the common precursor of histologically heterogeneous testicular germ cell tumors (TGCTs), which in recent decades have markedly increased and now are the most common malignancy of young men. Using genome-wide gene expression profiling, we identified >200 genes highly...

  17. Optical Bistability in Graded Core-Shell Granular Composites

    International Nuclear Information System (INIS)

    Wu Ya-Min; Chen Guo-Qing; Xue Si-Zhong; Zhu Zhuo-Wei; Ma Chao-Qun

    2012-01-01

    The intrinsic optical bistability (OB) of graded core-shell granular composites is investigated. The coated particles are made of cores with gradient dielectric function in c (r) = A(r/a) k and nonlinear shells. In view of the exponential distribution of the core dielectric constant, the potential functions of each region are obtained by solving the Maxwell equations, and the mathematical expressions of electric field in the shells and cores are determined. Numerical study reveals that the optical bistable threshold and the threshold width of the composite medium are dependent on the shell thickness, core dielectric exponent, and power function coefficient. The optical bistable width increases with the decreasing shell thickness and the power exponent and with the increasing power function coefficient

  18. Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.

    Science.gov (United States)

    Golumbeanu, Monica; Cristinelli, Sara; Rato, Sylvie; Munoz, Miguel; Cavassini, Matthias; Beerenwinkel, Niko; Ciuffi, Angela

    2018-04-24

    Despite effective treatment, HIV can persist in latent reservoirs, which represent a major obstacle toward HIV eradication. Targeting and reactivating latent cells is challenging due to the heterogeneous nature of HIV-infected cells. Here, we used a primary model of HIV latency and single-cell RNA sequencing to characterize transcriptional heterogeneity during HIV latency and reactivation. Our analysis identified transcriptional programs leading to successful reactivation of HIV expression. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. Constitutive law of dense granular matter

    International Nuclear Information System (INIS)

    Hatano, Takahiro

    2010-01-01

    The frictional properties of dense granular matter under steady shear flow are investigated using numerical simulation. Shear flow tends to localize near the driving boundary unless the coefficient of restitution is close to zero and the driving velocity is small. The bulk friction coefficient is independent of shear rate in dense and slow flow, whereas it is an increasing function of shear rate in rapid flow. The coefficient of restitution affects the friction coefficient only in such rapid flow. Contrastingly, in dense and slow regime, the friction coefficient is independent of the coefficient of restitution and mainly determined by the elementary friction coefficient and the rotation of grains. It is found that the mismatch between the vorticity of flow and the angular frequency of grains plays a key role to the frictional properties of sheared granular matter.

  20. An automata model of granular materials

    International Nuclear Information System (INIS)

    Gutt, G.M.; Haff, P.K.

    1990-01-01

    In this paper a new modeling technique (the Lattice Grain Model) is presented for the simulation of two-dimensional granular systems involving large numbers of grains. These granular systems may include both high shear rate regions as well as static plugs of grains and cannot easily be handled within the framework of existing continuum theories such as soil mechanics. The Lattice Grain Model (LGrM) is similar to the Lattice Gas Model (LBM). This allows large simulations to be programmed onto a hypercube concurrent processor in a straightforward manner. However, it differs from LBM in that it includes the inelastic collisions and volume-filling properties of macroscopic grains. Examples to be presented will include Couette flow, flow through an hourglass, and gravity-driven flows around obstacles

  1. Submammary Granular Parakeratosis Treated With Mastopexy.

    Science.gov (United States)

    Nelson, Garrett; Lien, Mary H; Messina, Jane L; Ranjit, Sonali; Fenske, Neil Alan

    2017-08-01

    Granular parakeratosis, originally named axillary granular parakeratosis, is an uncommon disease with an unclear etiology. It is thought to result from defective processing of profillagrin to fillagrin, causing retention of keratohyaline granules in the epidermis. A myriad of causative factors has been proposed, including friction, moisture, heat, and contact irritants such as deodorants. We present a case in the inframammary area that resolved with mastopexy, further supporting the role of friction, moisture, and heat. Furthermore, we present electron microscopic evidence demonstrating non-degraded keratohyaline granules upon epidermal maturation. This entity, we believe, is reactive and represents a protective response of the body to moisture and heat. J Drugs Dermatol. 2017;16(8):810-812..

  2. Granular flow down a flexible inclined plane

    Directory of Open Access Journals (Sweden)

    Sonar Prasad

    2017-01-01

    Full Text Available Discrete and continuous systems are commonly studied individually, but seldom together. Indeed, granular flows are typically studied through flows over a rigid base. Here, we investigate the behaviour of granular flows over an inclined, flexible base. The flexible base is modeled as a rigid platform mounted on springs and has one degree of freedom. The base vibrations are introduced by the flow. We simulate such flows through a discrete element method and compare with experiments. We find that a flexible base increased the upper limit of the inclination up to which a steady flow is possible by at least 3 degrees. This stabilized zone may have important implications in applications such as conveyor belts and chutes.

  3. Memory effect in uniformly heated granular gases

    Science.gov (United States)

    Trizac, E.; Prados, A.

    2014-07-01

    We evidence a Kovacs-like memory effect in a uniformly driven granular gas. A system of inelastic hard particles, in the low density limit, can reach a nonequilibrium steady state when properly forced. By following a certain protocol for the drive time dependence, we prepare the gas in a state where the granular temperature coincides with its long time value. The temperature subsequently does not remain constant but exhibits a nonmonotonic evolution with either a maximum or a minimum, depending on the dissipation and on the protocol. We present a theoretical analysis of this memory effect at Boltzmann-Fokker-Planck equation level and show that when dissipation exceeds a threshold, the response can be called anomalous. We find excellent agreement between the analytical predictions and direct Monte Carlo simulations.

  4. Traffic and Granular Flow ’07

    CERN Document Server

    Chevoir, François; Gondret, Philippe; Lassarre, Sylvain; Lebacque, Jean-Patrick; Schreckenberg, Michael

    2009-01-01

    This book covers several research fields, all of which deal with transport. Three main topics are treated: road traffic, granular matter, and biological transport. Different points of view, i.e. modelling, simulations, experiments, and phenomenological observations, are considered. Sub-topics include: highway or urban vehicular traffic (dynamics of traffic, macro/micro modelling, measurements, data analysis, security issues, psychological issues), pedestrian traffic, animal traffic (e.g. social insects), collective motion in biological systems (molecular motors...), granular flow (dense flows, intermittent flows, solid/liquid transition, jamming, force networks, fluid and solid friction), networks (biological networks, urban traffic, the internet, vulnerability of networks, optimal transport networks) and cellular automata applied to the various aforementioned fields.

  5. Mathematics and Mechanics of Granular Materials

    CERN Document Server

    Hill, James M

    2005-01-01

    Granular or particulate materials arise in almost every aspect of our lives, including many familiar materials such as tea, coffee, sugar, sand, cement and powders. At some stage almost every industrial process involves a particulate material, and it is usually the cause of the disruption to the smooth running of the process. In the natural environment, understanding the behaviour of particulate materials is vital in many geophysical processes such as earthquakes, landslides and avalanches. This book is a collection of current research from some of the major contributors in the topic of modelling the behaviour of granular materials. Papers from every area of current activity are included, such as theoretical, numerical, engineering and computational approaches. This book illustrates the numerous diverse approaches to one of the outstanding problems of modern continuum mechanics.

  6. Slow creep in soft granular packings.

    Science.gov (United States)

    Srivastava, Ishan; Fisher, Timothy S

    2017-05-14

    Transient creep mechanisms in soft granular packings are studied numerically using a constant pressure and constant stress simulation method. Rapid compression followed by slow dilation is predicted on the basis of a logarithmic creep phenomenon. Characteristic scales of creep strain and time exhibit a power-law dependence on jamming pressure, and they diverge at the jamming point. Microscopic analysis indicates the existence of a correlation between rheology and nonaffine fluctuations. Localized regions of large strain appear during creep and grow in magnitude and size at short times. At long times, the spatial structure of highly correlated local deformation becomes time-invariant. Finally, a microscale connection between local rheology and local fluctuations is demonstrated in the form of a linear scaling between granular fluidity and nonaffine velocity.

  7. Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes.

    Science.gov (United States)

    Clark, David J; Fondrie, William E; Yang, Austin; Mao, Li

    2016-02-05

    Exosomes are 30-100 nm sized membrane vesicles released by cells into the extracellular space that mediate intercellular communication via transfer of proteins and other biological molecules. To better understand the role of these microvesicles in lung carcinogenesis, we employed a Triple SILAC quantitative proteomic strategy to examine the differential protein abundance between exosomes derived from an immortalized normal bronchial epithelial cell line and two non-small cell lung cancer (NSCLC) cell lines harboring distinct activating mutations in the cell signaling molecules: Kirsten rat sarcoma viral oncogene homolog (KRAS) or epidermal growth factor receptor (EGFR). In total, we were able to quantify 721 exosomal proteins derived from the three cell lines. Proteins associated with signal transduction, including EGFR, GRB2 and SRC, were enriched in NSCLC exosomes, and could actively regulate cell proliferation in recipient cells. This study's investigation of the NSCLC exosomal proteome has identified enriched protein cargo that can contribute to lung cancer progression, which may have potential clinical implications in biomarker development for patients with NSCLC. The high mortality associated with lung cancer is a result of late-stage diagnosis of the disease. Current screening techniques used for early detection of lung cancer lack the specificity for accurate diagnosis. Exosomes are nano-sized extracellular vesicles, and the increased abundance of select protein cargo in exosomes derived from cancer cells may be used for diagnostic purposes. In this paper, we applied quantitative proteomic analysis to elucidate abundance differences in exosomal protein cargo between two NSCLC cell lines with distinctive oncogene mutations and an immortalized normal bronchial epithelial cell line. This study revealed proteins associated with cell adhesion, the extracellular matrix, and a variety of signaling molecules were enriched in NSCLC exosomes. The present data reveals

  8. Transport measurements in superconductors: critical current of granular high TC ceramic superconductor samples; Medidas de transporte em supercondutores: corrente critica de supercondutores granulares de alta temperatura critica

    Energy Technology Data Exchange (ETDEWEB)

    Passos, W.A.C., E-mail: wagner.passos@univasf.edu.br [Universidade Federal do Vale do Sao Francisco (IPCM/UNIVASF), Juazeiro do Norte, BA (Brazil). Instituto de Pesquisas em Ciencia dos Materiais; Silva, E.B. [Companhia Energetica do Sao Francisco (CHESF), Recife, PE (Brazil)

    2016-07-01

    This work presents a method to obtain critical current of granular superconductors. We have carried out transport measurements (ρxT curves and VxI curves) in a YBa{sub 2}Cu{sub 3}O{sub 7-δ} sample to determine critical current density of it. Some specimens reveal a 'semiconductor-like' behavior (electrical resistivity decreases with increasing temperatures above critical temperature T{sub c} of material) competing with superconductor behavior. Due to high granular fraction of the sample, these competition is clearly noted in ρxT curves. Measurements carried out from 0 to 8500 Oe of applied field show the same behavior, and the critical current density of the samples is shown. (author)

  9. Quantifying non-ergodic dynamics of force-free granular gases.

    Science.gov (United States)

    Bodrova, Anna; Chechkin, Aleksei V; Cherstvy, Andrey G; Metzler, Ralf

    2015-09-14

    Brownian motion is ergodic in the Boltzmann-Khinchin sense that long time averages of physical observables such as the mean squared displacement provide the same information as the corresponding ensemble average, even at out-of-equilibrium conditions. This property is the fundamental prerequisite for single particle tracking and its analysis in simple liquids. We study analytically and by event-driven molecular dynamics simulations the dynamics of force-free cooling granular gases and reveal a violation of ergodicity in this Boltzmann-Khinchin sense as well as distinct ageing of the system. Such granular gases comprise materials such as dilute gases of stones, sand, various types of powders, or large molecules, and their mixtures are ubiquitous in Nature and technology, in particular in Space. We treat-depending on the physical-chemical properties of the inter-particle interaction upon their pair collisions-both a constant and a velocity-dependent (viscoelastic) restitution coefficient ε. Moreover we compare the granular gas dynamics with an effective single particle stochastic model based on an underdamped Langevin equation with time dependent diffusivity. We find that both models share the same behaviour of the ensemble mean squared displacement (MSD) and the velocity correlations in the limit of weak dissipation. Qualitatively, the reported non-ergodic behaviour is generic for granular gases with any realistic dependence of ε on the impact velocity of particles.

  10. Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association.

    Directory of Open Access Journals (Sweden)

    William Cenens

    2015-12-01

    Full Text Available Monitoring the complex transmission dynamics of a bacterial virus (temperate phage P22 throughout a population of its host (Salmonella Typhimurium at single cell resolution revealed the unexpected existence of a transiently immune subpopulation of host cells that emerged from peculiarities preceding the process of lysogenization. More specifically, an infection event ultimately leading to a lysogen first yielded a phage carrier cell harboring a polarly tethered P22 episome. Upon subsequent division, the daughter cell inheriting this episome became lysogenized by an integration event yielding a prophage, while the other daughter cell became P22-free. However, since the phage carrier cell was shown to overproduce immunity factors that are cytoplasmically inherited by the P22-free daughter cell and further passed down to its siblings, a transiently resistant subpopulation was generated that upon dilution of these immunity factors again became susceptible to P22 infection. The iterative emergence and infection of transiently resistant subpopulations suggests a new bet-hedging strategy by which viruses could manage to sustain both vertical and horizontal transmission routes throughout an infected population without compromising a stable co-existence with their host.

  11. Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters.

    Science.gov (United States)

    Kumar, Vibhor; Rayan, Nirmala Arul; Muratani, Masafumi; Lim, Stefan; Elanggovan, Bavani; Xin, Lixia; Lu, Tess; Makhija, Harshyaa; Poschmann, Jeremie; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam

    2016-05-01

    Although over 35 different histone acetylation marks have been described, the overwhelming majority of regulatory genomics studies focus exclusively on H3K27ac and H3K9ac. In order to identify novel epigenomic traits of regulatory elements, we constructed a benchmark set of validated enhancers by performing 140 enhancer assays in human T cells. We tested 40 chromatin signatures on this unbiased enhancer set and identified H2BK20ac, a little-studied histone modification, as the most predictive mark of active enhancers. Notably, we detected a novel class of functionally distinct enhancers enriched in H2BK20ac but lacking H3K27ac, which was present in all examined cell lines and also in embryonic forebrain tissue. H2BK20ac was also unique in highlighting cell-type-specific promoters. In contrast, other acetylation marks were present in all active promoters, regardless of cell-type specificity. In stimulated microglial cells, H2BK20ac was more correlated with cell-state-specific expression changes than H3K27ac, with TGF-beta signaling decoupling the two acetylation marks at a subset of regulatory elements. In summary, our study reveals a previously unknown connection between histone acetylation and cell-type-specific gene regulation and indicates that H2BK20ac profiling can be used to uncover new dimensions of gene regulation. © 2016 Kumar et al.; Published by Cold Spring Harbor Laboratory Press.

  12. Cytogenetic analyses of Azadirachtin reveal absence of genotoxicity but marked antiproliferative effects in human lymphocytes and CHO cells in vitro.

    Science.gov (United States)

    Mosesso, Pasquale; Bohm, Lothar; Pepe, Gaetano; Fiore, Mario; Carpinelli, Alice; Gäde, Gerd; Nagini, Siddavaram; Ottavianelli, Alessandro; Degrassi, Francesca

    2012-09-18

    In this work we have examined the genotoxic potential of the bioinsecticide Azadirachtin A (AZA) and its influence on cell proliferation on human lymphocytes and Chinese Hamster ovary (CHO) cells. AZA genotoxicity was assessed by the analysis of chromosomal aberrations and sister chromatid exchanges (SCEs) in the absence and presence of rat liver S9 metabolism. Primary DNA damage was also investigated by means of the comet assay. The results obtained clearly indicate that AZA is not genotoxic in mammalian cells. On the other hand, AZA proved to interfere with cell cycle progression as shown by modulation of frequencies of first (M1) and second division (M2) metaphases detected by 5-Bromo-2'-deoxyuridine labeling. Accumulation of M1 metaphases were more pronounced in human lymphocytes. In the transformed CHO cell line, however, significant increases of multinucleated interphases and polyploid cells were observed at long treatment time. At higher dose-levels, the incidence of polyploidy was close to 100%. Identification of spindle structure and number of centrosomes by fluorescent immunostaining with α- and γ-tubulin antibodies revealed aberrant mitoses exhibiting multipolar spindles with several centrosomal signals. These findings suggest that AZA can act either through a stabilizing activity of microtubules or by inhibition of Aurora A, since both mechanisms are able to generate genetically unstable polyploid cells with multipolar spindles and multinucleated interphases. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  13. Fuzzy batch controller for granular materials

    OpenAIRE

    Zamyatin Nikolaj; Smirnov Gennadij; Fedorchuk Yuri; Rusina Olga

    2018-01-01

    The paper focuses on batch control of granular materials in production of building materials from fluorine anhydrite. Batching equipment is intended for smooth operation and timely feeding of supply hoppers at a required level. Level sensors and a controller of an asynchronous screw drive motor are used to control filling of the hopper with industrial anhydrite binders. The controller generates a required frequency and ensures required productivity of a feed conveyor. Mamdani-type fuzzy infer...

  14. Arching Structures in Granular Sedimentary Deposits

    Czech Academy of Sciences Publication Activity Database

    Kulaviak, Lukáš; Hladil, Jindřich; Růžička, Marek; Drahoš, Jiří; Saint-Lary, L.

    2013-01-01

    Roč. 246, SEP (2013), s. 269-277 ISSN 0032-5910 R&D Projects: GA ČR GA104/07/1110; GA AV ČR IAAX00130702; GA MŠk(CZ) LG11014 Institutional support: RVO:67985858 ; RVO:67985831 Keywords : wet granulars * deposit * arching structure Subject RIV: CI - Industrial Chemistry, Chemical Engineering; DB - Geology ; Mineralogy (GLU-S) Impact factor: 2.269, year: 2013

  15. Seismic wave propagation in granular media

    Science.gov (United States)

    Tancredi, Gonzalo; López, Francisco; Gallot, Thomas; Ginares, Alejandro; Ortega, Henry; Sanchís, Johnny; Agriela, Adrián; Weatherley, Dion

    2016-10-01

    Asteroids and small bodies of the Solar System are thought to be agglomerates of irregular boulders, therefore cataloged as granular media. It is a consensus that many asteroids might be considered as rubble or gravel piles.Impacts on their surface could produce seismic waves which propagate in the interior of these bodies, thus causing modifications in the internal distribution of rocks and ejections of particles and dust, resulting in a cometary-type comma.We present experimental and numerical results on the study of propagation of impact-induced seismic waves in granular media, with special focus on behavior changes by increasing compression.For the experiment, we use an acrylic box filled with granular materials such as sand, gravel and glass spheres. Pressure inside the box is controlled by a movable side wall and measured with sensors. Impacts are created on the upper face of the box through a hole, ranging from free-falling spheres to gunshots. We put high-speed cameras outside the box to record the impact as well as piezoelectic sensors and accelerometers placed at several depths in the granular material to detect the seismic wave.Numerical simulations are performed with ESyS-Particle, a software that implements the Discrete Element Method. The experimental setting is reproduced in the numerical simulations using both individual spherical particles and agglomerates of spherical particles shaped as irregular boulders, according to rock models obtained with a 3D scanner. The numerical experiments also reproduces the force loading on one of the wall to vary the pressure inside the box.We are interested in the velocity, attenuation and energy transmission of the waves. These quantities are measured in the experiments and in the simulations. We study the dependance of these three parameters with characteristics like: impact speed, properties of the target material and the pressure in the media.These results are relevant to understand the outcomes of impacts in

  16. Simulation of 2D Granular Hopper Flow

    Science.gov (United States)

    Li, Zhusong; Shattuck, Mark

    2012-02-01

    Jamming and intermittent granular flow are big problems in industry, and the vertical hopper is a canonical example of these difficulties. We simulate gravity driven flow and jamming of 2D disks in a vertical hopper and compare with identical companion experiments presented in this session. We measure and compare the flow rate and probability for jamming as a function of particle properties and geometry. We evaluate the ability of standard Hertz-Mindlin contact mode to quantitatively predict the experimental flow.

  17. Spatial correlations in compressible granular flows

    OpenAIRE

    Van Noije, T. P. C.; Ernst, M. H.; Brito López, Ricardo

    1998-01-01

    The clustering instability in freely evolving granular fluids manifests itself in the density-density correlation function and structure factor. These functions are calculated from fluctuating hydrodynamics. As time increases, the structure factor of density fluctuations develops a maximum, which shifts to smaller wave numbers (growing correlation length). Furthermore, the inclusion of longitudinal velocity fluctuations changes long-range correlations in the flow field qualitatively and exten...

  18. Zebrafish model of tuberous sclerosis complex reveals cell-autonomous and non-cell-autonomous functions of mutant tuberin

    Directory of Open Access Journals (Sweden)

    Seok-Hyung Kim

    2011-03-01

    Tuberous sclerosis complex (TSC is an autosomal dominant disease caused by mutations in either the TSC1 (encodes hamartin or TSC2 (encodes tuberin genes. Patients with TSC have hamartomas in various organs throughout the whole body, most notably in the brain, skin, eye, heart, kidney and lung. To study the development of hamartomas, we generated a zebrafish model of TSC featuring a nonsense mutation (vu242 in the tsc2 gene. This tsc2vu242 allele encodes a truncated Tuberin protein lacking the GAP domain, which is required for inhibition of Rheb and of the TOR kinase within TORC1. We show that tsc2vu242 is a recessive larval-lethal mutation that causes increased cell size in the brain and liver. Greatly elevated TORC1 signaling is observed in tsc2vu242/vu242 homozygous zebrafish, and is moderately increased in tsc2vu242/+ heterozygotes. Forebrain neurons are poorly organized in tsc2vu242/vu242 homozygous mutants, which have extensive gray and white matter disorganization and ectopically positioned cells. Genetic mosaic analyses demonstrate that tsc2 limits TORC1 signaling in a cell-autonomous manner. However, in chimeric animals, tsc2vu242/vu242 mutant cells also mislocalize wild-type host cells in the forebrain in a non-cell-autonomous manner. These results demonstrate a highly conserved role of tsc2 in zebrafish and establish a new animal model for studies of TSC. The finding of a non-cell-autonomous function of mutant cells might help explain the formation of brain hamartomas and cortical malformations in human TSC.

  19. Raman chemical mapping reveals site of action of HIV protease inhibitors in HPV16 E6 expressing cervical carcinoma cells.

    Science.gov (United States)

    Kim, Dong-Hyun; Jarvis, Roger M; Allwood, J William; Batman, Gavin; Moore, Rowan E; Marsden-Edwards, Emma; Hampson, Lynne; Hampson, Ian N; Goodacre, Royston

    2010-12-01

    It has been shown that the HIV protease inhibitors indinavir and lopinavir may have activity against the human papilloma virus (HPV) type 16 inhibiting HPV E6-mediated proteasomal degradation of p53 in cultured cervical carcinoma cells. However, their mode and site of action is unknown. HPV-negative C33A cervical carcinoma cells and the same cells stably transfected with E6 (C33AE6) were exposed to indinavir and lopinavir at concentrations of 1 mM and 30 μM, respectively. The intracellular distribution of metabolites and metabolic changes induced by these treatments were investigated by Raman microspectroscopic imaging combined with the analysis of cell fractionation products by liquid chromatography-mass spectrometry (LC-MS). A uniform cellular distribution of proteins was found in drug-treated cells irrespective of cell type. Indinavir was observed to co-localise with nucleic acid in the nucleus, but only in E6 expressing cells. Principal components analysis (PCA) score maps generated on the full Raman hypercube and the corresponding PCA loadings plots revealed that the majority of metabolic variations influenced by the drug exposure within the cells were associated with changes in nucleic acids. Analysis of cell fractionation products by LC-MS confirmed that the level of indinavir in nuclear extracts was approximately eight-fold greater than in the cytoplasm. These data demonstrate that indinavir undergoes enhanced nuclear accumulation in E6-expressing cells, which suggests that this is the most likely site of action for this compound against HPV.

  20. Mammalian knock out cells reveal prominent roles for atlastin GTPases in ER network morphology

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Guohua; Zhu, Peng-Peng; Renvoisé, Benoît; Maldonado-Báez, Lymarie; Park, Seong Hee; Blackstone, Craig, E-mail: blackstc@ninds.nih.gov

    2016-11-15

    Atlastins are large, membrane-bound GTPases that participate in the fusion of endoplasmic reticulum (ER) tubules to generate the polygonal ER network in eukaryotes. They also regulate lipid droplet size and inhibit bone morphogenetic protein (BMP) signaling, though mechanisms remain unclear. Humans have three atlastins (ATL1, ATL2, and ATL3), and ATL1 and ATL3 are mutated in autosomal dominant hereditary spastic paraplegia and hereditary sensory neuropathies. Cellular investigations of atlastin orthologs in most yeast, plants, flies and worms are facilitated by the presence of a single or predominant isoform, but loss-of-function studies in mammalian cells are complicated by multiple, broadly-expressed paralogs. We have generated mouse NIH-3T3 cells lacking all three mammalian atlastins (Atl1/2/3) using CRISPR/Cas9-mediated gene knockout (KO). ER morphology is markedly disrupted in these triple KO cells, with prominent impairment in formation of three-way ER tubule junctions. This phenotype can be rescued by expression of distant orthologs from Saccharomyces cerevisiae (Sey1p) and Arabidopsis (ROOT HAIR DEFECTIVE3) as well as any one of the three human atlastins. Minimal, if any, changes are observed in the morphology of mitochondria and the Golgi apparatus. Alterations in BMP signaling and increased sensitivity to ER stress are also noted, though effects appear more modest. Finally, atlastins appear required for the proper differentiation of NIH-3T3 cells into an adipocyte-like phenotype. These findings have important implications for the pathogenesis of hereditary spastic paraplegias and sensory neuropathies associated with atlastin mutations. - Highlights: • NIH-3T3 cells lacking all three atlastin paralogs were generated using CRISPR/Cas9. • Cells lacking all atlastin GTPases exhibit far fewer 3-way ER tubule junctions. • ER morphology defects in atlastin knockout cells are rescued by distant plant and yeast orthologs. • Atlastin knock out cells also

  1. Mammalian knock out cells reveal prominent roles for atlastin GTPases in ER network morphology

    International Nuclear Information System (INIS)

    Zhao, Guohua; Zhu, Peng-Peng; Renvoisé, Benoît; Maldonado-Báez, Lymarie; Park, Seong Hee; Blackstone, Craig

    2016-01-01

    Atlastins are large, membrane-bound GTPases that participate in the fusion of endoplasmic reticulum (ER) tubules to generate the polygonal ER network in eukaryotes. They also regulate lipid droplet size and inhibit bone morphogenetic protein (BMP) signaling, though mechanisms remain unclear. Humans have three atlastins (ATL1, ATL2, and ATL3), and ATL1 and ATL3 are mutated in autosomal dominant hereditary spastic paraplegia and hereditary sensory neuropathies. Cellular investigations of atlastin orthologs in most yeast, plants, flies and worms are facilitated by the presence of a single or predominant isoform, but loss-of-function studies in mammalian cells are complicated by multiple, broadly-expressed paralogs. We have generated mouse NIH-3T3 cells lacking all three mammalian atlastins (Atl1/2/3) using CRISPR/Cas9-mediated gene knockout (KO). ER morphology is markedly disrupted in these triple KO cells, with prominent impairment in formation of three-way ER tubule junctions. This phenotype can be rescued by expression of distant orthologs from Saccharomyces cerevisiae (Sey1p) and Arabidopsis (ROOT HAIR DEFECTIVE3) as well as any one of the three human atlastins. Minimal, if any, changes are observed in the morphology of mitochondria and the Golgi apparatus. Alterations in BMP signaling and increased sensitivity to ER stress are also noted, though effects appear more modest. Finally, atlastins appear required for the proper differentiation of NIH-3T3 cells into an adipocyte-like phenotype. These findings have important implications for the pathogenesis of hereditary spastic paraplegias and sensory neuropathies associated with atlastin mutations. - Highlights: • NIH-3T3 cells lacking all three atlastin paralogs were generated using CRISPR/Cas9. • Cells lacking all atlastin GTPases exhibit far fewer 3-way ER tubule junctions. • ER morphology defects in atlastin knockout cells are rescued by distant plant and yeast orthologs. • Atlastin knock out cells also

  2. A Tendon Cell Specific RNAi Screen Reveals Novel Candidates Essential for Muscle Tendon Interaction.

    Directory of Open Access Journals (Sweden)

    Prabhat Tiwari

    Full Text Available Tendons are fibrous connective tissue which connect muscles to the skeletal elements thus acting as passive transmitters of force during locomotion and provide appropriate body posture. Tendon-derived cues, albeit poorly understood, are necessary for proper muscle guidance and attachment during development. In the present study, we used dorsal longitudinal muscles of Drosophila and their tendon attachment sites to unravel the molecular nature of interactions between muscles and tendons. We performed a genetic screen using RNAi-mediated knockdown in tendon cells to find out molecular players involved in the formation and maintenance of myotendinous junction and found 21 candidates out of 2507 RNAi lines screened. Of these, 19 were novel molecules in context of myotendinous system. Integrin-βPS and Talin, picked as candidates in this screen, are known to play important role in the cell-cell interaction and myotendinous junction formation validating our screen. We have found candidates with enzymatic function, transcription activity, cell adhesion, protein folding and intracellular transport function. Tango1, an ER exit protein involved in collagen secretion was identified as a candidate molecule involved in the formation of myotendinous junction. Tango1 knockdown was found to affect development of muscle attachment sites and formation of myotendinous junction. Tango1 was also found to be involved in secretion of Viking (Collagen type IV and BM-40 from hemocytes and fat cells.

  3. Tracking of plus-ends reveals microtubule functional diversity in different cell types

    Science.gov (United States)

    Shaebani, M. Reza; Pasula, Aravind; Ott, Albrecht; Santen, Ludger

    2016-07-01

    Many cellular processes are tightly connected to the dynamics of microtubules (MTs). While in neuronal axons MTs mainly regulate intracellular trafficking, they participate in cytoskeleton reorganization in many other eukaryotic cells, enabling the cell to efficiently adapt to changes in the environment. We show that the functional differences of MTs in different cell types and regions is reflected in the dynamic properties of MT tips. Using plus-end tracking proteins EB1 to monitor growing MT plus-ends, we show that MT dynamics and life cycle in axons of human neurons significantly differ from that of fibroblast cells. The density of plus-ends, as well as the rescue and catastrophe frequencies increase while the growth rate decreases toward the fibroblast cell margin. This results in a rather stable filamentous network structure and maintains the connection between nucleus and membrane. In contrast, plus-ends are uniformly distributed along the axons and exhibit diverse polymerization run times and spatially homogeneous rescue and catastrophe frequencies, leading to MT segments of various lengths. The probability distributions of the excursion length of polymerization and the MT length both follow nearly exponential tails, in agreement with the analytical predictions of a two-state model of MT dynamics.

  4. Novel effects of edaravone on human brain microvascular endothelial cells revealed by a proteomic approach.

    Science.gov (United States)

    Onodera, Hidetaka; Arito, Mitsumi; Sato, Toshiyuki; Ito, Hidemichi; Hashimoto, Takuo; Tanaka, Yuichiro; Kurokawa, Manae S; Okamoto, Kazuki; Suematsu, Naoya; Kato, Tomohiro

    2013-10-09

    Edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one) is a free radical scavenger used for acute ischemic stroke. However, it is not known whether edaravone works only as a free radical scavenger or possess other pharmacological actions. Therefore, we elucidated the effects of edaravone on human brain microvascular endothelial cells (HBMECs) by 2 dimensional fluorescence difference gel electrophoresis (2D-DIGE). We found 38 protein spots the intensity of which was significantly altered 1.3 fold on average (pedaravone treatment and successfully identified 17 proteins of those. Four of those 17 proteins were cytoskeleton proteins or cytoskeleton-regulating proteins. Therefore, we subsequently investigated the change of size and shape of the cells, the actin network, and the tight junction of HBMEC by immunocytochemistry. As a result, most edaravone-treated HBMECs became larger and rounder compared with those that were not treated. Furthermore, edaravone-treated HBMECs formed gathering zona occludens (ZO)-1, a tight junction protein, along the junction of the cells. In addition, we found that edaravone suppressed interleukin (IL)-1β-induced secretion of monocyte chemoattractant protein-1 (MCP-1), which was reported to increase cell permeability. We found a novel function of edaravone is the promotion of tight junction formations of vascular endothelial cells partly via the down-regulation of MCP-1 secretion. These data provide fundamental and useful information in the clinical use of edaravone in patients with cerebral vascular diseases. © 2013 Elsevier B.V. All rights reserved.

  5. Expression of basal cell marker revealed by RAM11 antibody during epithelial regeneration in rabbits.

    Directory of Open Access Journals (Sweden)

    Tadeusz Cichocki

    2010-06-01

    Full Text Available RAM11 is a mouse monoclonal anti-rabbit macrophage antibody recognizing connective tissue and vascular macrophages. Our previous report showed that RAM11 reacted with basal cells of stratified squamous epithelia of rabbit skin, oral mucosa and esophagus. The aim of the present study was to follow the appearance of RAM11 immunoreactivity in basal cells of regenerating oral epithelium in rabbits. No RAM11 immunostaining was observed in the regenerating epithelium examined on days 1 and 3 of wound healing. A weak immunofluorescence first appeared on day 7 in single basal cells and 32% of RAM11- positive basal cells were observed on day 14. These findings indicate that expression of the antigen recognized by RAM11 antibody is a transient event in the differentiation of oral keratinocytes which not always occurs during epithelial repair, although it is a constant feature of epithelial turnover in mature epithelium. Therefore this antigen can be regarded as basal cell marker only in mature stratified squamous epithelia.

  6. Variability in surface antigen expression on neuroblastoma cells as revealed by monoclonal antibodies

    International Nuclear Information System (INIS)

    Malpas, J.S.; Kemshead, J.T.; Pritchard, J.; Greaves, M.F.

    1982-01-01

    In treatment programmes for neuroblastoma involving autologous bone marrow transplantation, a problem exists in the identification of small numbers of metastatic tumour cells present in the marrow aspirates. Reinfusion of tumour cells along with normal bone marrow may reseed the tumour within a patient who has received high dose chemotherapy. Formalin-induced fluorescence in neuroblastoma is a possible diagnostic aid, but this method has no therapeutic potential. Other methods of detecting tumour relying on gross physiological changes in the patient are not suitable for diagnosis of minimal metastatic disease. As an immunological approach to the problem, rabbit antisera to neuroblastoma have been raised but these reagents suffer from low titre after absorption to make them specific. The authors have used the technique of somatic cell hybridisation to raise monoclonal antibodies which bind to neuroblastoma cells and not to normal haemopoietic progenitors. A panel of such reagents to demonstrate heterogeneity in antigen expression amongst metastatic neuroblastoma cells was employed in a radioimmunoassay as diagnostic aid for this problem. (Auth.)

  7. Small solar system bodies as granular systems

    Science.gov (United States)

    Hestroffer, Daniel; Campo Bagatín, Adriano; Losert, Wolfgang; Opsomer, Eric; Sánchez, Paul; Scheeres, Daniel J.; Staron, Lydie; Taberlet, Nicolas; Yano, Hajime; Eggl, Siegfried; Lecomte, Charles-Edouard; Murdoch, Naomi; Radjai, Fahrang; Richardson, Derek C.; Salazar, Marcos; Schwartz, Stephen R.; Tanga, Paolo

    2017-06-01

    Asteroids and other Small Solar System Bodies (SSSBs) are currently of great scientific and even industrial interest. Asteroids exist as the permanent record of the formation of the Solar System and therefore hold many clues to its understanding as a whole, as well as insights into the formation of planetary bodies. Additionally, SSSBs are being investigated in the context of impact risks for the Earth, space situational awareness and their possible industrial exploitation (asteroid mining). In all these aspects, the knowledge of the geophysical characteristics of SSSB surface and internal structure are of great importance. Given their size, constitution, and the evidence that many SSSBs are not simple monoliths, these bodies should be studied and modelled as self-gravitating granular systems in general, or as granular systems in micro-gravity environments in particular contexts. As such, the study of the geophysical characteristics of SSSBs is a multi-disciplinary effort that lies at the crossroads between Granular Mechanics, Celestial Mechanics, Soil Mechanics, Aerospace Engineering and Computer Sciences.

  8. Iodine Gas Trapping using Granular Porous Bismuth

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jae Hwan; Shin, Jin Myeong; Park, Jang Jin; Park, Geun Il [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Yim, Mansung [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2014-05-15

    {sup 129}I is a radionuclide with a very long half-life of 1.57 Χ 10{sup 7} years and has negative health effects to the human body. Therefore, the emission of {sup 129}I into the air is closely regulated by the Environmental Protection Agency (EPA). Many methods for trapping gaseous {sup 129}I have been developed thus far, including wet scrubbing and adsorption using silver loaded zeolites. Although wet scrubbing can effectively remove iodine, it suffers from corrosion of the vessel due to high concentration of the scrubbing solution. Silver loaded zeolites also show effectiveness in capturing {sup 129}I gas, yet weak thermal stability of physisorbed iodine remains a challenge. We studied a novel and facile method to trap iodine gas using bismuth. Granular bismuth having many pores was synthesized using bismuth nitrate and polyvinyl alcohol as a bismuth precursor and pore forming agent, respectively. Reaction of iodine and our samples resulted in an iodine capturing capacity of more than 2 times that of the commercial grade silver exchanged zeolite (AgX). Granular porous bismuths synthesized using bismuth nitrate and PVA show a promising performance in capturing iodine gas. The use of bismuth in trapping {sup 129}I gas can reduce the process cost as bismuth is cheap. Further study is going on to improve the mechanical property of granular porous bismuths for their easy handling.

  9. Iodine Gas Trapping using Granular Porous Bismuth

    International Nuclear Information System (INIS)

    Yang, Jae Hwan; Shin, Jin Myeong; Park, Jang Jin; Park, Geun Il; Yim, Mansung

    2014-01-01

    129 I is a radionuclide with a very long half-life of 1.57 Χ 10 7 years and has negative health effects to the human body. Therefore, the emission of 129 I into the air is closely regulated by the Environmental Protection Agency (EPA). Many methods for trapping gaseous 129 I have been developed thus far, including wet scrubbing and adsorption using silver loaded zeolites. Although wet scrubbing can effectively remove iodine, it suffers from corrosion of the vessel due to high concentration of the scrubbing solution. Silver loaded zeolites also show effectiveness in capturing 129 I gas, yet weak thermal stability of physisorbed iodine remains a challenge. We studied a novel and facile method to trap iodine gas using bismuth. Granular bismuth having many pores was synthesized using bismuth nitrate and polyvinyl alcohol as a bismuth precursor and pore forming agent, respectively. Reaction of iodine and our samples resulted in an iodine capturing capacity of more than 2 times that of the commercial grade silver exchanged zeolite (AgX). Granular porous bismuths synthesized using bismuth nitrate and PVA show a promising performance in capturing iodine gas. The use of bismuth in trapping 129 I gas can reduce the process cost as bismuth is cheap. Further study is going on to improve the mechanical property of granular porous bismuths for their easy handling

  10. Propulsion via flexible flapping in granular media

    Science.gov (United States)

    Peng, Zhiwei; Ding, Yang; Pietrzyk, Kyle; Elfring, Gwynn; Pak, On Shun

    2017-11-01

    Biological locomotion in nature is often achieved by the interaction between a flexible body and its surrounding medium. The interaction of a flexible body with granular media is less understood compared with viscous fluids partially due to its complex rheological properties. In this work, we explore the effect of flexibility on granular propulsion by considering a simple mechanical model in which a rigid rod is connected to a torsional spring that is under a displacement actuation using a granular resistive force theory. Through a combined numerical and asymptotic investigation, we characterize the propulsive dynamics of such a flexible flapper in relation to the actuation amplitude and spring stiffness, and we compare these dynamics with those observed in a viscous fluid. In addition, we demonstrate that the maximum possible propulsive force can be obtained in the steady propulsion limit with a finite spring stiffness and large actuation amplitude. These results may apply to the development of synthetic locomotive systems that exploit flexibility to move through complex terrestrial media. Funding for Z.P. and Y.D. was partially provided by NSFC 394 Grant No. 11672029 and NSAF-NSFC Grant No. U1530401.

  11. Rough – Granular Computing knowledge discovery models

    Directory of Open Access Journals (Sweden)

    Mohammed M. Eissa

    2016-11-01

    Full Text Available Medical domain has become one of the most important areas of research in order to richness huge amounts of medical information about the symptoms of diseases and how to distinguish between them to diagnose it correctly. Knowledge discovery models play vital role in refinement and mining of medical indicators to help medical experts to settle treatment decisions. This paper introduces four hybrid Rough – Granular Computing knowledge discovery models based on Rough Sets Theory, Artificial Neural Networks, Genetic Algorithm and Rough Mereology Theory. A comparative analysis of various knowledge discovery models that use different knowledge discovery techniques for data pre-processing, reduction, and data mining supports medical experts to extract the main medical indicators, to reduce the misdiagnosis rates and to improve decision-making for medical diagnosis and treatment. The proposed models utilized two medical datasets: Coronary Heart Disease dataset and Hepatitis C Virus dataset. The main purpose of this paper was to explore and evaluate the proposed models based on Granular Computing methodology for knowledge extraction according to different evaluation criteria for classification of medical datasets. Another purpose is to make enhancement in the frame of KDD processes for supervised learning using Granular Computing methodology.

  12. Revealing chemical processes and kinetics of drug action within single living cells via plasmonic Raman probes.

    Science.gov (United States)

    Li, Shan-Shan; Guan, Qi-Yuan; Meng, Gang; Chang, Xiao-Feng; Wei, Ji-Wu; Wang, Peng; Kang, Bin; Xu, Jing-Juan; Chen, Hong-Yuan

    2017-05-23

    Better understanding the drug action within cells may extend our knowledge on drug action mechanisms and promote new drugs discovery. Herein, we studied the processes of drug induced chemical changes on proteins and nucleic acids in human breast adenocarcinoma (MCF-7) cells via time-resolved plasmonic-enhanced Raman spectroscopy (PERS) in combination with principal component analysis (PCA). Using three popular chemotherapy drugs (fluorouracil, cisplatin and camptothecin) as models, chemical changes during drug action process were clearly discriminated. Reaction kinetics related to protein denaturation, conformational modification, DNA damage and their associated biomolecular events were calculated. Through rate constants and reaction delay times, the different action modes of these drugs could be distinguished. These results may provide vital insights into understanding the chemical reactions associated with drug-cell interactions.

  13. [Pulmonary Langerhans' cell histiocytosis (PLCH) revealed by pneumothorax: about a case].

    Science.gov (United States)

    Sajiai, Hafsa; Rachidi, Mariam; Serhane, Hind; Aitbatahar, Salma; Amro, Lamyae

    2016-01-01

    Langerhans cell histiocytosis is a rare disease of unknown etiology characterized by the infiltration of Langerhans cells in one or more organs. It has a polymorphic clinical presentation. We report the case of Mr R.Y, age 22, with 8 pack year history of smoking, admitted to hospital with complete spontaneous right-sided pneumothorax. Chest drainage was performed with good evolution. Control chest CT scan showed multiple diffuse cyst formations, predominant in the upper lobes. Lab and imaging tests were performed in order to detect systemic histiocytosis with negative results. Patient's evolution was marked by pneumothorax recurrence; pleurodesis and lung biopsy were performed which confirmed the diagnosis. The diagnosis of Langerhans cell histiocytosis should be evoked in front of pneumothorax associated with lung cystic. The diagnosis is easy in front of a suggestive clinical and radiological picture. Nevertheless, therapeutic options are limited and pneumothorax recurrence is common.

  14. Chromosome 2 short arm translocations revealed by M-FISH analysis of neuroblastoma cell lines.

    Science.gov (United States)

    Van Roy, N; Van Limbergen, H; Vandesompele, J; Van Gele, M; Poppe, B; Laureys, G; De Paepe, A; Speleman, F

    2000-12-01

    M-FISH analysis was performed on 18 neuroblastoma cell lines, which were previously studied with cytogenetic, standard FISH and CGH data. One of the most striking findings of this study was the detection of chromosome 2 short arm rearrangements in 61% of the investigated cell lines. These rearrangements resulted from translocations with various partner chromosomes. All translocations, except one were unbalanced, leading to the consistent gain of chromosome segment 2pter-p22. A cryptic balanced translocation t(2;4) was observed with a breakpoint located in the vicinity of MYCN in cell line NBL-S. Combination of M-FISH results together with cytogenetic, standard FISH and CGH data yielded the most comprehensive description of chromosome 2 short arm rearrangements, leading to a consistent gain of chromosome 2 short arm material. Copyright 2000 Wiley-Liss, Inc.

  15. Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes.

    Science.gov (United States)

    Ofran, Yanay; Schlessinger, Avner; Rost, Burkhard

    2008-11-01

    Exact identification of complementarity determining regions (CDRs) is crucial for understanding and manipulating antigenic interactions. One way to do this is by marking residues on the antibody that interact with B cell epitopes on the antigen. This, of course, requires identification of B cell epitopes, which could be done by marking residues on the antigen that bind to CDRs, thus requiring identification of CDRs. To circumvent this vicious circle, existing tools for identifying CDRs are based on sequence analysis or general biophysical principles. Often, these tools, which are based on partial data, fail to agree on the boundaries of the CDRs. Herein we present an automated procedure for identifying CDRs and B cell epitopes using consensus structural regions that interact with the antigens in all known antibody-protein complexes. Consequently, we provide the first comprehensive analysis of all CDR-epitope complexes of known three-dimensional structure. The CDRs we identify only partially overlap with the regions suggested by existing methods. We found that the general physicochemical properties of both CDRs and B cell epitopes are rather peculiar. In particular, only four amino acids account for most of the sequence of CDRs, and several types of amino acids almost never appear in them. The secondary structure content and the conservation of B cell epitopes are found to be different than previously thought. These characteristics of CDRs and epitopes may be instrumental in choosing which residues to mutate in experimental search for epitopes. They may also assist in computational design of antibodies and in predicting B cell epitopes.

  16. Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

    Science.gov (United States)

    Jankowski, Aleksander; Szczurek, Ewa; Jauch, Ralf; Tiuryn, Jerzy; Prabhakar, Shyam

    2013-01-01

    The binding of transcription factors (TFs) to their specific motifs in genomic regulatory regions is commonly studied in isolation. However, in order to elucidate the mechanisms of transcriptional regulation, it is essential to determine which TFs bind DNA cooperatively as dimers and to infer the precise nature of these interactions. So far, only a small number of such dimeric complexes are known. Here, we present an algorithm for predicting cell-type–specific TF–TF dimerization on DNA on a large scale, using DNase I hypersensitivity data from 78 human cell lines. We represented the universe of possible TF complexes by their corresponding motif complexes, and analyzed their occurrence at cell-type–specific DNase I hypersensitive sites. Based on ∼1.4 billion tests for motif complex enrichment, we predicted 603 highly significant cell-type–specific TF dimers, the vast majority of which are novel. Our predictions included 76% (19/25) of the known dimeric complexes and showed significant overlap with an experimental database of protein–protein interactions. They were also independently supported by evolutionary conservation, as well as quantitative variation in DNase I digestion patterns. Notably, the known and predicted TF dimers were almost always highly compact and rigidly spaced, suggesting that TFs dimerize in close proximity to their partners, which results in strict constraints on the structure of the DNA-bound complex. Overall, our results indicate that chromatin openness profiles are highly predictive of cell-type–specific TF–TF interactions. Moreover, cooperative TF dimerization seems to be a widespread phenomenon, with multiple TF complexes predicted in most cell types. PMID:23554463

  17. Proteomic analysis of BmN cell lipid rafts reveals roles in Bombyx mori nucleopolyhedrovirus infection.

    Science.gov (United States)

    Hu, Xiaolong; Zhu, Min; Liang, Zi; Kumar, Dhiraj; Chen, Fei; Zhu, Liyuan; Kuang, Sulan; Xue, Renyu; Cao, Guangli; Gong, Chengliang

    2017-04-01

    The mechanism of how Bombyx mori nucleopolyhedrovirus (BmNPV) enters cells is unknown. The primary components of membrane lipid rafts are proteins and cholesterol, and membrane lipid rafts are thought to be an active region for host-viral interactions. However, whether they contribute to the entry of BmNPV into silkworm cells remains unclear. In this study, we explored the membrane protein components of lipid rafts from BmN cells with mass spectrometry (MS). Proteins and cholesterol were investigated after establishing infection with BmNPV in BmN cells. In total, 222 proteins were identified in the lipid rafts, and Gene Ontology (GO) annotation analysis showed that more than 10% of these proteins had binding and catalytic functions. We then identified proteins that potentially interact between lipid rafts and BmNPV virions using the Virus Overlay Protein Blot Assay (VOPBA). A total of 65 proteins were analyzed with MS, and 7 were predicted to be binding proteins involved in BmNPV cellular invasion, including actin, kinesin light chain-like isoform X2, annexin B13, heat-shock protein 90, barrier-to-autointegration factor B-like and serine/arginine-rich splicing factor 1 A-like. When the cholesterol of the lipid rafts from the membrane was depleted by methyl-β-cyclodextrin (MβCD), BmNPV entry into BmN cells was blocked. However, supplying cholesterol into the medium rescued the BmNPV infection ability. These results show that membrane lipid rafts may be the active regions for the entry of BmNPV into cells, and the components of membrane lipid rafts may be candidate targets for improving the resistance of the silkworm to BmNPV.

  18. Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential.

    Directory of Open Access Journals (Sweden)

    Stéphane Bellafiore

    2008-10-01

    Full Text Available The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. Infection is associated with secretion of proteins surrounded by proliferating cells. Many parasites are known to secrete effectors that interfere with plant innate immunity, enabling infection to occur; they can also release pathogen-associated molecular patterns (PAMPs, e.g., flagellin that trigger basal immunity through the nematode stylet into the plant cell. This leads to suppression of innate immunity and reprogramming of plant cells to form a feeding structure containing multinucleate giant cells. Effectors have generally been discovered using genetics or bioinformatics, but M. incognita is non-sexual and its genome sequence has not yet been reported. To partially overcome these limitations, we have used mass spectrometry to directly identify 486 proteins secreted by M. incognita. These proteins contain at least segmental sequence identity to those found in our 3 reference databases (published nematode proteins; unpublished M. incognita ESTs; published plant proteins. Several secreted proteins are homologous to plant proteins, which they may mimic, and they contain domains that suggest known effector functions (e.g., regulating the plant cell cycle or growth. Others have regulatory domains that could reprogram cells. Using in situ hybridization we observed that most secreted proteins were produced by the subventral glands, but we found that phasmids also secreted proteins. We annotated the functions of the secreted proteins and classified them according to roles they may play in the development of root knot disease. Our results show that parasite secretomes can be partially characterized without cognate genomic DNA sequence. We observed that the M. incognita secretome overlaps the reported secretome of mammalian parasitic nematodes (e.g., Brugia malayi, suggesting a common parasitic behavior and a possible

  19. Large granular lymphocytosis in a patient infected with HTLV-II.

    Science.gov (United States)

    Martin, M P; Biggar, R J; Hamlin-Green, G; Staal, S; Mann, D

    1993-08-01

    HTLV-II has been associated with a variety of lymphoproliferative disorders, including atypical hairy cell leukemia, chronic T cell leukemia, T prolymphocytic leukemia, and large granular lymphocytic leukemia. However, a direct or indirect role for HTLV-II in these disorders is not yet firmly established. We studied a patient diagnosed as having leukemia of the large granular lymphocyte (LGL) type who was HTLV-II seropositive, to determine if the expanded cell population was infected. Two populations of CD3-CD16+ LGL were identified; one was CD8+, the other CD8-. Populations of cells with these surface markers as well as normal CD3+CD4+ and CD3+CD8+ cells were separated by flow cytometric methods, DNA extracted, and gene regions of HTLV-II pol and tax amplified, using the polymerase chain reaction, and probed after Southern blotting. HTLV-II was detected in the CD3+CD8+ population, and not in the CD3-CD16+ large granular lymphocyte population. This finding indicates that the role of HTLV-II, if any, in LGL proliferation is indirect.

  20. Isolation and Characterization of Current Human Coronavirus Strains in Primary Human Epithelial Cell Cultures Reveal Differences in Target Cell Tropism

    Science.gov (United States)

    Dijkman, Ronald; Jebbink, Maarten F.; Koekkoek, Sylvie M.; Deijs, Martin; Jónsdóttir, Hulda R.; Molenkamp, Richard; Ieven, Margareta; Goossens, Herman; Thiel, Volker

    2013-01-01

    The human airway epithelium (HAE) represents the entry port of many human respiratory viruses, including human coronaviruses (HCoVs). Nowadays, four HCoVs, HCoV-229E, HCoV-OC43, HCoV-HKU1, and HCoV-NL63, are known to be circulating worldwide, causing upper and lower respiratory tract infections in nonhospitalized and hospitalized children. Studies of the fundamental aspects of these HCoV infections at the primary entry port, such as cell tropism, are seriously hampered by the lack of a universal culture system or suitable animal models. To expand the knowledge on fundamental virus-host interactions for all four HCoVs at the site of primary infection, we used pseudostratified HAE cell cultures to isolate and characterize representative clinical HCoV strains directly from nasopharyngeal material. Ten contemporary isolates were obtained, representing HCoV-229E (n = 1), HCoV-NL63 (n = 1), HCoV-HKU1 (n = 4), and HCoV-OC43 (n = 4). For each strain, we analyzed the replication kinetics and progeny virus release on HAE cell cultures derived from different donors. Surprisingly, by visualizing HCoV infection by confocal microscopy, we observed that HCoV-229E employs a target cell tropism for nonciliated cells, whereas HCoV-OC43, HCoV-HKU1, and HCoV-NL63 all infect ciliated cells. Collectively, the data demonstrate that HAE cell cultures, which morphologically and functionally resemble human airways in vivo, represent a robust universal culture system for isolating and comparing all contemporary HCoV strains. PMID:23427150

  1. Elastic Nonlinear Response in Granular Media Under Resonance Conditions

    Science.gov (United States)

    Jia, X.; Johnson, P. A.

    2004-12-01

    We are studying the elastic linear and nonlinear behavior of granular media using dynamic wave methods. In the work presented here, our goal is to quantify the elastic nonlinear response by applying wave resonance. Resonance studies are desirable because they provide the means to easily study amplitude dependencies of elastic nonlinear behavior and thus to characterize the physical nature of the elastic nonlinearity. This work has implications for a variety of topics, in particular, the in situ nonlinear response of surface sediments. For this work we constructed an experimental cell in which high sensitivity dynamic resonance studies were conducted using granular media under controlled effective pressure. We limit our studies here to bulk modes but have the capability to employ shear waves as well. The granular media are composed of glass beads held under pressure by a piston, while applying resonance waves from transducers as both the excitation and the material probe. The container is closed with two fitted pistons and a normal load is applied to the granular sample across the top piston. Force and displacement are measured directly. Resonant frequency sweeps with frequencies corresponding to the fundamental bulk mode are applied to the longitudinal source transducer. The pore pressure in the system is 1 atm. The glass beads used in our experiments are of diameter 0.5 mm, randomly deposited in a duralumin cylinder of diameter 30 mm and height of 15 mm. This corresponds to a granular skeleton acoustic wave velocity of v ª 750m/s under 50 N of force [0.07 Mpa]. The loaded system gives fundamental mode resonances in the audio frequency band at half a wavelength where resonance frequency is effective-pressure dependent. The volume fraction of glass beads thus obtained is found to be 0.63 ± 0.01. Plane-wave generating and detecting transducers of diameter 30 mm are placed on axis at the top and bottom of the cylindrical container in direct contact with the glass

  2. Settling properties of aerobic granular sludge (AGS) and aerobic granular sludge molasses (AGSM)

    Science.gov (United States)

    Mat Saad, Azlina; Aini Dahalan, Farrah; Ibrahim, Naimah; Yasina Yusuf, Sara; Aqlima Ahmad, Siti; Khalil, Khalilah Abdul

    2018-03-01

    Aerobic granulation technology is applied to treat domestic and industrial wastewater. The Aerobic granular sludge (AGS) cultivated has strong properties that appears to be denser and compact in physiological structure compared to the conventional activated sludge. It offers rapid settling for solid:liquid separation in wastewater treatment. Aerobic granules were developed using sequencing batch reactor (SBR) with intermittent aerobic - anaerobic mode with 8 cycles in 24 hr. This study examined the settling velocity performance of cultivated aerobic granular sludge (AGS) and aerobic granular sludge molasses (AGSM). The elemental composition in both AGS and AGSM were determined using X-ray fluorescence (XRF). The results showed that AGSM has higher settling velocity 30.5 m/h compared to AGS.

  3. Rheological Modeling of Macro Viscous Flows of Granular Suspension of Regular and Irregular Particles

    Directory of Open Access Journals (Sweden)

    Anna Maria Pellegrino

    2017-12-01

    Full Text Available This paper refers to complex granular-fluid mixtures involved into geophysical flows, such as debris and hyper-concentrated flows. For such phenomena, the interstitial fluids play a role when they are in the viscous regime. Referring to experiments on granular-fluid mixture carried out with pressure imposed annular shear cell, we study the rheological behaviour of dense mixture involving both spheres and irregular-shaped particles. For the case of viscous suspensions with irregular grains, a significant scatter of data from the trend observed for mixtures with spherical particles was evident. In effect, the shape of the particles likely plays a fundamental role in the flow dynamics, and the constitutive laws proposed by the frictional theory for the spheres are no longer valid. Starting from the frictional approach successfully applied to suspension of spheres, we demonstrate that also in case of irregular particles the mixture rheology may be fully characterized by the two relationships involving friction coefficient µ and volume concentration Ф as a function of the dimensionless viscous number Iv. To this goal, we provided a new consistent general model, referring to the volume fraction law and friction law, which accounts for the particle shape. In this way, the fitting parameters reduce just to the static friction angle µ1, and the two parameters, k and fs related to the grain shape. The resulting general model may apply to steady fully developed flows of saturated granular fluid mixture in the viscous regime, no matter of granular characteristics.

  4. Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

    DEFF Research Database (Denmark)

    Rennie, Sarah; Dalby, Maria; van Duin, Lucas

    2018-01-01

    Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it is unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone and how this impacts disease...... proportion of total levels and is highly informative of topological associating domain activities and organisation, revealing boundaries and chromatin compartments. Furthermore, expression data alone accurately predict individual enhancer-promoter interactions, drawing features from expression strength...... between transcription and chromatin architecture....

  5. The CMS High Granularity Calorimeter for HL-LHC

    CERN Document Server

    Mastrolorenzo, Luca

    2017-01-01

    The High Luminosity LHC (HL-LHC) will integrate 10 times more luminosity than the LHC, posing significant challenges for radiation tolerance and event pileup on detectors, especially for forward calorimetry, and hallmarks the issue for future colliders. As part of its HL-LHC upgrade program, the CMS collaboration is designing a High Granularity Calorimeter to replace the existing endcap calorimeters. It features unprecedented transverse and longitudinal segmentation for both electromagnetic (ECAL) and hadronic (HCAL) compartments. This will facilitate particle-flow calorimetry, where the fine structure of showers can be measured and used to enhance pileup rejection and particle identification, whilst still achieving good energy resolution. The ECAL and a large fraction of HCAL will be based on hexagonal silicon sensors of 0.5 - 1 cm$^2$ cell size, with the remainder of the HCAL based on highly-segmented scintillators with SiPM readout. The intrinsic high-precision timing capabilities of the silicon sensors wi...

  6. The CMS High Granularity Calorimeter for the High Luminosity LHC

    CERN Document Server

    Sauvan, Jean-baptiste

    2017-01-01

    The High Luminosity LHC (HL-LHC) will integrate 10 times more luminosity than the LHC, posing significant challenges for radiation tolerance and event pileup on detectors, especially for forward calorimetry, and hallmarks the issue for future colliders. As part of its HL-LHC upgrade program, the CMS collaboration is designing a High Granularity Calorimeter to replace the existing endcap calorimeters. It features unprecedented transverse and longitudinal segmentation for both electromagnetic (ECAL) and hadronic (HCAL) compartments. This will facilitate particle-flow calorimetry, where the fine structure of showers can be measured and used to enhance pileup rejection and particle identification, whilst still achieving good energy resolution. The ECAL and a large fraction of HCAL will be based on hexagonal silicon sensors of 0.5 - 1 cm$^2$ cell size, with the remainder of the HCAL based on highly-segmented scintillators with silicon photomultiplier (SiPM) readout. The intrinsic high-precision timing capabilities...

  7. Coexistence and transition between shear zones in slow granular flows.

    Science.gov (United States)

    Moosavi, Robabeh; Shaebani, M Reza; Maleki, Maniya; Török, János; Wolf, Dietrich E; Losert, Wolfgang

    2013-10-04

    We report experiments on slow granular flows in a split-bottom Couette cell that show novel strain localization features. Nontrivial flow profiles have been observed which are shown to be the consequence of simultaneous formation of shear zones in the bulk and at the boundaries. The fluctuating band model based on a minimization principle can be fitted to the experiments over a large variation of morphology and filling height with one single fit parameter, the relative friction coefficient μ(rel) between wall and bulk. The possibility of multiple shear zone formation is controlled by μ(rel). Moreover, we observe that the symmetry of an initial state, with coexisting shear zones at both side walls, breaks spontaneously below a threshold value of the shear velocity. A dynamical transition between two asymmetric flow states happens over a characteristic time scale which depends on the shear strength.

  8. The role of fluid viscosity in an immersed granular collapse

    Science.gov (United States)

    Yang, Geng Chao; Kwok, Chung Yee; Sobral, Yuri Dumaresq

    2017-06-01

    Instabilities of immersed slopes and cliffs can lead to catastrophic events that involve a sudden release of huge soil mass. The scaled deposit height and runout distance are found to follow simple power laws when a granular column collapses on a horizontal plane. However, if the granular column is submerged in a fluid, the mobility of the granular collapse due to high inertia effects will be reduced by fluid-particle interactions. In this study, the effects of fluid viscosity on granular collapse is investigated qualitatively by adopting a numerical approach based on the coupled lattice Boltzmann method (LBM) and discrete element method (DEM). It is found that the granular collapse can be dramatically slowed down due to the presence of viscous fluids. For the considered granular configuration, when the fluid viscosity increases. the runout distance decreases and the final deposition shows a larger deposit angle.

  9. The role of fluid viscosity in an immersed granular collapse

    Directory of Open Access Journals (Sweden)

    Yang Geng Chao

    2017-01-01

    Full Text Available Instabilities of immersed slopes and cliffs can lead to catastrophic events that involve a sudden release of huge soil mass. The scaled deposit height and runout distance are found to follow simple power laws when a granular column collapses on a horizontal plane. However, if the granular column is submerged in a fluid, the mobility of the granular collapse due to high inertia effects will be reduced by fluid-particle interactions. In this study, the effects of fluid viscosity on granular collapse is investigated qualitatively by adopting a numerical approach based on the coupled lattice Boltzmann method (LBM and discrete element method (DEM. It is found that the granular collapse can be dramatically slowed down due to the presence of viscous fluids. For the considered granular configuration, when the fluid viscosity increases. the runout distance decreases and the final deposition shows a larger deposit angle.

  10. Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations.

    Science.gov (United States)

    Reem, Nathan T; Chen, Han-Yi; Hur, Manhoi; Zhao, Xuefeng; Wurtele, Eve Syrkin; Li, Xu; Li, Ling; Zabotina, Olga

    2018-03-01

    This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.

  11. Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis.

    Science.gov (United States)

    Cochain, Clément; Vafadarnejad, Ehsan; Arampatzi, Panagiota; Jaroslav, Pelisek; Winkels, Holger; Ley, Klaus; Wolf, Dennis; Saliba, Antoine-Emmanuel; Zernecke, Alma

    2018-03-15

    Rationale: It is assumed that atherosclerotic arteries contain several macrophage subsets endowed with specific functions. The precise identity of these subsets is poorly characterized as they ha ve been defined by the expression of a restricted number of markers. Objective: We have applied single-cell RNA-seq as an unbiased profiling strategy to interrogate and classify aortic macrophage heterogeneity at the single-cell level in atherosclerosis. Methods and Results: We performed single-cell RNA sequencing of total aortic CD45 + cells extracted from the non-diseased (chow fed) and atherosclerotic (11 weeks of high fat diet) aorta of Ldlr -/- mice. Unsupervised clustering singled out 13 distinct aortic cell clusters. Among the myeloid cell populations, Resident-like macrophages with a gene expression profile similar to aortic resident macrophages were found in healthy and diseased aortae, whereas monocytes, monocyte-derived dendritic cells (MoDC), and two populations of macrophages were almost exclusively detectable in atherosclerotic aortae, comprising Inflammatory macrophages showing enrichment in I l1b , and previously undescribed TREM2 hi macrophages. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these three macrophage subsets and MoDC, and uncovered putative functions of each cell type. Notably, TREM2 hi macrophages appeared to be endowed with specialized functions in lipid metabolism and catabolism, and presented a gene expression signature reminiscent of osteoclasts, suggesting a role in lesion calcification. TREM2 expression was moreover detected in human lesional macrophages. Importantly, these macrophage populations were present also in advanced atherosclerosis and in Apoe -/- aortae, indicating relevance of our findings in different stages of atherosclerosis and mouse models. Conclusions: These data unprecedentedly uncovered the transcriptional landscape and phenotypic

  12. Phylogenetic analysis of the Neks reveals early diversification of ciliary-cell cycle kinases.

    Directory of Open Access Journals (Sweden)

    Jeremy D K Parker

    2007-10-01

    Full Text Available NIMA-related kinases (Neks have been studied in diverse eukaryotes, including the fungus Aspergillus and the ciliate Tetrahymena. In the former, a single Nek plays an essential role in cell cycle regulation; in the latter, which has more than 30 Neks in its genome, multiple Neks regulate ciliary length. Mammalian genomes encode an intermediate number of Neks, several of which are reported to play roles in cell cycle regulation and/or localize to centrosomes. Previously, we reported that organisms with cilia typically have more Neks than organisms without cilia, but were unable to establish the evolutionary history of the gene family.We have performed a large-scale analysis of the Nek family using Bayesian techniques, including tests of alternate topologies. We find that the Nek family had already expanded in the last common ancestor of eukaryotes, a ciliated cell which likely expressed at least five Neks. We suggest that Neks played an important role in the common ancestor in regulating cilia, centrioles, and centrosomes with respect to mitotic entry, and that this role continues today in organisms with cilia. Organisms that lack cilia generally show a reduction in the number of Nek clades represented, sometimes associated with lineage specific expansion of a single clade, as has occurred in the plants.This is the first rigorous phylogenetic analysis of a kinase family across a broad array of phyla. Our findings provide a coherent framework for the study of Neks and their roles in coordinating cilia and cell cycle progression.

  13. Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance

    DEFF Research Database (Denmark)

    Du, Peina; Huang, Peide; Huang, Xuanlin

    2017-01-01

    Oesophageal carcinoma is the fourth leading cause of cancer-related death in China, and more than 90% of these tumours are oesophageal squamous cell carcinoma (ESCC). Although several ESCC genomic sequencing studies have identified mutated somatic genes, the number of samples in each study...

  14. Assessment of synergistic antibacterial activity of combined biosurfactants revealed by bacterial cell envelop damage.

    Science.gov (United States)

    Sana, Santanu; Datta, Sriparna; Biswas, Dipa; Sengupta, Dipanjan

    2018-02-01

    Besides potential surface activity and some beneficial physical properties, biosurfactants express antibacterial activity. Bacterial cell membrane disrupting ability of rhamnolipid produced by Pseudomonas aeruginosa C2 and a lipopeptide type biosurfactant, BS15 produced by Bacillus stratosphericus A15 was examined against Staphylococcus aureus ATCC 25923 and Escherichia coli K8813. Broth dilution technique was followed to examine minimum inhibitory concentration (MIC) of both the biosurfactants. The combined effect of rhamnolipid and BS15 against S. aureus and E. coli showed synergistic activity by expressing fractional inhibitory concentration (F