41 results on '"Fernandez, JJ"'
Search Results
2. Three-dimensional real-space crystallography of MCM-48 mesoporous silica revealed by scanning transmission electron tomography
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Yates, TJV, Thomas, JM, Fernandez, JJ, Terasaki, O, Ryoo, R, Midgley, PA, Yates, TJV, Thomas, JM, Fernandez, JJ, Terasaki, O, Ryoo, R, and Midgley, PA
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- 2006
3. Reagentless carbon paste phosphate biosensors: preliminary studies
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Enginyeria Química, Eng. Electrònica, Elèctrica i Automàtica, Universitat Rovira i Virgili, Katakis, I, Correig, X, Lopez, JR, Fernandez, JJ, Enginyeria Química, Eng. Electrònica, Elèctrica i Automàtica, Universitat Rovira i Virgili, Katakis, I, Correig, X, Lopez, JR, and Fernandez, JJ
- Abstract
The development of a reagentless phosphate biosensor with potential applications in continuous monitoring of environmental samples is described. The sensor is based on a biorecognition sequence of three enzymes: phosphorylase A, phosphoglucomutase and glucose 6-phosphate dehydrogenase. The incorporation of these enzymes, the substrate glycogen, the cofactor NAD(+), and Os(1,10-phenanthroline-5,6-dione)(2)Cl-2 mediator in a carbon paste electrode covered with in situ formed hydrogels was the fundamental base for the development of an amperometric enzyme electrode for the detection of inorganic phosphate. A study of the effects on the response of enzymatic cofactors, and the operating conditions and the optimisation of the biosensor response were carried out with dialysis membrane-covered glassy carbon electrodes, achieving a maximum current density of 2 mu A cm(-2) a detection limit of 6 mu M of phosphate with an extended linear dynamic range up to 2 mM, and sensitivity in the linear region of 4.5 mu A cm(-2) mM(-1) with a useful pH operational range between 6.5 and 7.5. The preliminary results with carbon paste phosphate electrodes showed a maximum current density of 30 mu A cm(-2), a detection limit of 2 mM of phosphate with linearity up to 250 mM, and sensitivity in the linear region of 0.1 mu A cm(-2) mM(-1). (C) 1998 Elsevier Science S.A. All rights reserved.
- Published
- 1998
4. Evolution of a large periplasmic disk in Campylobacterota flagella enables both efficient motility and autoagglutination.
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Cohen EJ, Drobnič T, Ribardo DA, Yoshioka A, Umrekar T, Guo X, Fernandez JJ, Brock EE, Wilson L, Nakane D, Hendrixson DR, and Beeby M
- Abstract
The flagellar motors of Campylobacter jejuni (C. jejuni) and related Campylobacterota (previously epsilonproteobacteria) feature 100-nm-wide periplasmic "basal disks" that have been implicated in scaffolding a wider ring of additional motor proteins to increase torque, but the size of these disks is excessive for a role solely in scaffolding motor proteins. Here, we show that the basal disk is a flange that braces the flagellar motor during disentanglement of its flagellar filament from interactions with the cell body and other filaments. We show that motor output is unaffected when we shrink or displace the basal disk, and suppressor mutations of debilitated motors occur in flagellar-filament or cell-surface glycosylation pathways, thus sidestepping the need for a flange to overcome the interactions between two flagellar filaments and between flagellar filaments and the cell body. Our results identify unanticipated co-dependencies in the evolution of flagellar motor structure and cell-surface properties in the Campylobacterota., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
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- 2024
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5. The Structure of Cilium Inner Junctions Revealed by Electron Cryo-tomography.
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Li S, Fernandez JJ, Ruehle MD, Howard-Till RA, Fabritius A, Pearson CG, Agard DA, and Winey ME
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The cilium is a microtubule-based organelle critical for many cellular functions. Its assembly initiates at a basal body and continues as an axoneme that projects out of the cell to form a functional cilium. This assembly process is tightly regulated. However, our knowledge of the molecular architecture and the mechanism of assembly is limited. By applying electron cryotomography and subtomogram averaging, we obtained subnanometer resolution structures of the inner junction in three distinct regions of the cilium: the proximal region of the basal body, the central core of the basal body, and the flagellar axoneme. The structures allowed us to identify several basal body and axoneme components. While a few proteins are distributed throughout the entire length of the organelle, many are restricted to particular regions of the cilium, forming intricate local interaction networks and bolstering local structural stability. Finally, by knocking out a critical basal body inner junction component Poc1, we found the triplet MT was destabilized, resulting in a defective structure. Surprisingly, several axoneme-specific components were found to "infiltrate" into the mutant basal body. Our findings provide molecular insight into cilium assembly at its inner Junctions, underscoring its precise spatial regulation.
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- 2024
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6. Disruption of the mitochondrial network in a mouse model of Huntington's disease visualized by in-tissue multiscale 3D electron microscopy.
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Martin-Solana E, Casado-Zueras L, Torres TE, Goya GF, Fernandez-Fernandez MR, and Fernandez JJ
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- Animals, Mice, Mice, Transgenic, Brain pathology, Brain ultrastructure, Brain metabolism, Microscopy, Electron methods, Male, Neurons pathology, Neurons ultrastructure, Neurons metabolism, Huntington Disease pathology, Huntington Disease genetics, Huntington Disease metabolism, Disease Models, Animal, Mitochondria ultrastructure, Mitochondria pathology, Mitochondria metabolism, Imaging, Three-Dimensional methods
- Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the coding sequence of huntingtin protein. Initially, it predominantly affects medium-sized spiny neurons (MSSNs) of the corpus striatum. No effective treatment is still available, thus urging the identification of potential therapeutic targets. While evidence of mitochondrial structural alterations in HD exists, previous studies mainly employed 2D approaches and were performed outside the strictly native brain context. In this study, we adopted a novel multiscale approach to conduct a comprehensive 3D in situ structural analysis of mitochondrial disturbances in a mouse model of HD. We investigated MSSNs within brain tissue under optimal structural conditions utilizing state-of-the-art 3D imaging technologies, specifically FIB/SEM for the complete imaging of neuronal somas and Electron Tomography for detailed morphological examination, and image processing-based quantitative analysis. Our findings suggest a disruption of the mitochondrial network towards fragmentation in HD. The network of interlaced, slim and long mitochondria observed in healthy conditions transforms into isolated, swollen and short entities, with internal cristae disorganization, cavities and abnormally large matrix granules., (© 2024. The Author(s).)
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- 2024
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7. Progressive alterations in polysomal architecture and activation of ribosome stalling relief factors in a mouse model of Huntington's disease.
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Martin-Solana E, Diaz-Lopez I, Mohamedi Y, Ventoso I, Fernandez JJ, and Fernandez-Fernandez MR
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- Animals, Mice, Corpus Striatum metabolism, Corpus Striatum pathology, Mice, Transgenic, Disease Progression, Huntingtin Protein genetics, Huntingtin Protein metabolism, Peptide Initiation Factors metabolism, Peptide Initiation Factors genetics, Huntington Disease metabolism, Huntington Disease pathology, Huntington Disease genetics, Disease Models, Animal, Polyribosomes metabolism, Ribosomes metabolism
- Abstract
Given their highly polarized morphology and functional singularity, neurons require precise spatial and temporal control of protein synthesis. Alterations in protein translation have been implicated in the development and progression of a wide range of neurological and neurodegenerative disorders, including Huntington's disease (HD). In this study we examined the architecture of polysomes in their native brain context in striatal tissue from the zQ175 knock-in mouse model of HD. We performed 3D electron tomography of high-pressure frozen and freeze-substituted striatal tissue from HD models and corresponding controls at different ages. Electron tomography results revealed progressive remodelling towards a more compacted polysomal architecture in the mouse model, an effect that coincided with the emergence and progression of HD related symptoms. The aberrant polysomal architecture is compatible with ribosome stalling phenomena. In fact, we also detected in the zQ175 model an increase in the striatal expression of the stalling relief factor EIF5A2 and an increase in the accumulation of eIF5A1, eIF5A2 and hypusinated eIF5A1, the active form of eIF5A1. Polysomal sedimentation gradients showed differences in the relative accumulation of 40S ribosomal subunits and in polysomal distribution in striatal samples of the zQ175 model. These findings indicate that changes in the architecture of the protein synthesis machinery may underlie translational alterations associated with HD, opening new avenues for understanding the progression of the disease., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2023. Published by Elsevier Inc.)
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- 2024
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8. The incidence and decompression rates of median and ulnar neuropathies following shoulder surgery.
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Dua K, Kazi O, Hoy J, Xu B, Verma NN, Wysocki RW, Fernandez JJ, Cohen MS, and Simcock XC
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Background: Upper extremity peripheral neuropathy is a known, but uncommon complication that can occur after shoulder surgery. The incidence rate is well documented, and most of these cases historically have been treated conservatively. However, we hypothesize peripheral compression neuropathy requires a much higher need for surgical decompression than originally reported. The purpose of this study was to evaluate the incidence, decompression rates, and prognostic factors for developing median and ulnar neuropathies following shoulder surgery., Methods: A retrospective chart review was performed examining patients who underwent open and arthroscopic shoulder surgery from a multisurgeon, single-institution database. Perioperative data and functional outcomes were recorded. Symptom resolution was assessed with both conservative and surgical management of compression peripheral neuropathy. Further analysis was made to compare open and arthroscopic procedures, the type of neuropathy developed, and electromyographic (EMG) severity., Results: The incidence rates of compression peripheral neuropathy following open arthroplasty and arthroscopic procedures was 1.80% (31/1722) and 0.54% (44/8150), respectively. 73.33% (55/75) of patients developed ipsilateral disease, while 20.00% (15/75) of patients had bilateral disease. Amongst the 75 included patients, there were 99 cases of neuropathy. Carpal tunnel syndrome was more common than cubital tunnel syndrome, comprising 61.61% (61/99) cases of neuropathy. 12.00% (9/75) of patients developed both carpal tunnel syndrome and cubital tunnel syndrome. Four patients were lost to follow-up. Decompression surgery was performed for 36.84% (35/95) cases of neuropathy with >90% obtaining symptom resolution with surgery. 63.16% (60/95) cases of neuropathy were managed conservatively, 71.67% (43/60) of which had persistent symptoms. When comparing arthroscopic versus open procedures, patients who underwent open procedures were significantly older (68.62 vs. 49.78 years, P < .001) and developed peripheral neuropathy significantly faster after the index procedure (87.24 vs. 125.58 days, P = .008). EMG severity did not correlate with decompression rates or symptom resolution. There were no differences in the subgroup analyses between beach chair and lateral positioning in regard to the type of neuropathy, laterality of symptoms, and/or treatment received., Conclusion: The overall incidence of peripheral neuropathy after shoulder surgery was 0.76% (75/9872). The development of peripheral neuropathy is multifactorial, with older patients undergoing open arthroplasty more at risk. Neuropathy symptoms were refractory to conservative management despite the type of shoulder surgery, type of neuropathy, or EMG severity. Decompression consistently led to resolution of symptoms., (© 2024 The Authors.)
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- 2024
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9. Carpal Joint Malalignment With Distal Radius Malunion and Factors in Correction After Distal Radius Osteotomy.
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Doarn M, Xu B, Winterton M, Fernandez JJ, Cohen MS, and Wysocki RW
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Purpose: There is a paucity of data regarding recommendations on when to correct for distal radius malunions and if the initial severity of the radiographic outcomes is correlated with the ability to correct to baseline. We evaluated the effects of distal radius corrective osteotomy on preoperative carpal joint malalignment resulting from distal radius malunions, correlated injury severity and osteotomy timing to radiographic outcomes, and developed a straightforward classification system for predicting radiocarpal and midcarpal maladaptive patterns., Methods: A retrospective review included 26 patients (27 wrists) who reported initial closed treatment for a distal radius fracture and who subsequently underwent a corrective osteotomy for malunion. Data included patient demographics, range of motion, preoperative fracture deformity, fracture deformity correction, and preoperative and postoperative radiographic measurements of the radiocarpal and midcarpal alignment patterns., Results: Of 27 dorsally angulated malunions, 16 were classified as type 1 midcarpal adaptation and 11 as type 2 radiocarpal adaptation. The midcarpal group showed significant improvements in distal radius and carpal alignment parameters after surgery, except for the ulnar variance. The radiocarpal group showed significant improvements in distal radius and carpal alignment parameters, except for the radiolunate angle, radioscaphoid angle, and capitolunate angle. The radiocarpal group exhibited an overall decrease in range of motion compared with that of the midcarpal group. Severity of the fracture and time taken from injury to corrective osteotomy correlated with the ability to correct carpal radiographic parameters in dorsally angulated malunions of the distal radius, especially beyond 40 weeks., Conclusions: The severity of the initial fracture and time taken from injury to corrective osteotomy correlate with the ability to correct radiographic parameters in dorsally angulated malunions of the distal radius. Early correction of distal radius malunions is recommended, especially in radiocarpal malalignment patterns. A useful analysis for predicting midcarpal and radiocarpal adaptation patterns is the direct measurement of the distal articular surface of the radius to the lunate, termed the relative-radiolunate angle., Type of Study/level of Evidence: Therapeutic IV., (© 2023 The Authors.)
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- 2023
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10. Patient Perspectives on Telemedicine During the COVID-19 Pandemic.
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Ahmad F, Wysocki RW, Fernandez JJ, Cohen MS, and Simcock XC
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- Humans, Pandemics, Emotions, Pain Measurement, COVID-19 epidemiology, Telemedicine
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Background: Patients received care over telemedicine during the COVID-19 pandemic, and their perspective is useful for hand surgeons., Methods: Online surveys were sent October-November 2020 to 497 patients who received telemedicine care. Questions were free-response and multi-item Likert scales asking about telehealth in general, limitations, benefits, comparisons to in-person visits, and opinions on future use., Results: The response rate was 26% (n = 130). Prior to the pandemic, 55% had not used telemedicine for hand surgery consultation. Patients liked their telemedicine visit and felt their provider spent enough time with them (means = 9/10). In all, 48% would have preferred in-person visits despite the pandemic, and 69% would prefer in-person visits once the pandemic concludes. While 43% had no concerns with telemedicine, 36% had difficulties explaining their symptoms. Telemedicine was easy to access and navigate (M = 9/10). However, 23% saw telemedicine of limited value due to the need for an in-person visit soon afterward. Of these patients, 46% needed an in-person visit due to inadequate physical examination. Factors that make telemedicine more favorable to patients included convenience, lack of travel, scheduling ease, and time saved. Factors making telemedicine less favorable included need for in-person examination or procedure, pain assessment, and poor connectivity. There was no specific appointment time the cohort preferred. Patient recommendations to improve telemedicine included decreasing wait times and showing patient queue, wait time, or physician status online., Conclusions: Telemedicine was strongly liked by patients during the COVID-19 pandemic. However, nearly 70% of patients still preferred in-person visits for the future.
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- 2023
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11. Avascular Necrosis of an Adolescent Distal Radius: A Literature Review.
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Ahmad F, Torres-Gonzalez L, Sabet A, Simcock X, and Fernandez JJ
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A 12-year-old boy was tackled mid-air, resulting in a fall on the outstretched hand without fracture. The patient was treated conservatively but developed sharp pain and stiffness 6 months later. Imaging revealed distal radius avascular necrosis with physeal involvement. Owing to the injury chronicity and location, we treated the patient conservatively with hand therapy. After 1 year of therapy, the patient returned to normal activities without pain and with a resolution of findings on imaging. Avascular necrosis is more frequent in carpal bones (eg, Kienböck disease of the lunate and Preiser disease of the scaphoid). Growth arrest at the distal radius can lead to ulnocarpal impaction, triangular fibrocartilage complex injury, or distal radioulnar joint injury. In this case report, we discuss our treatment rationale and review the literature on pediatric avascular necrosis for hand surgeons., (© 2023 The Authors.)
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- 2023
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12. The use of tranexamic acid in open elbow release surgery.
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Goyal N, Wilson DJ, Wysocki RW, Fernandez JJ, and Cohen MS
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Background: Tranexamic acid (TXA) has been effective in reducing perioperative blood loss in hip, knee, and shoulder arthroplasty. Our purpose was to assess the effect of TXA on perioperative blood loss for open elbow release., Methods: Consecutive open elbow releases performed between October 2016 and March 2020 were identified. Patients were included if both anterior and posterior joint releases with a single medial approach was performed. From November 2018 onward, intravenous TXA and topical TXA infused through a deep hemovac drain were administered as part of the perioperative protocol. Drain output, intraoperative blood loss, postoperative aspiration rate, and postoperative transfusion frequency were assessed., Results: Fifty patients (25 TXA, 25 non-TXA) were included. Drain output was significantly lower in the TXA-treated group compared to the non-treated group (121 mL vs. 221 mL; p = 0.003). There was no significant difference in intraoperative blood loss and the incidence of postoperative aspiration between groups. None of the patients received a blood transfusion or had a documented thromboembolic event., Discussion: The use of tranexamic acid with open elbow release surgeries resulted in decreased drain output, with no thromboembolic events. Perioperative tranexamic acid can be a safe and effective modality in reducing perioperative blood loss for open elbow release surgery., Competing Interests: Declaration of Conflicting Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© 2020 The British Elbow & Shoulder Society.)
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- 2022
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13. Effects of Foam Rolling vs. Manual Therapy in Patients with Tension-Type Headache: A Randomized Pilot Study.
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Espi-Lopez GV, Ingles M, Carrasco-Fernandez JJ, Serra-Añó P, Copete-Fajardo L, Gonzalez-Gerez JJ, Saavedra-Hernandez M, and Marques-Sule E
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Background: This study compares the effect of foam rolling (FR) vs. manual therapy (MT) on pain, pressure pain threshold (PPT), headache disability (HDI) and impact of headache (HIT-6) in patients with tension-type headache (TTH)., Methods: A total of 38 participants with TTH were randomly assigned to an FR group (FRG, n = 13), an MT group (MTG, n = 13) or a control group (CG, n = 12). FRG received FR treatment; MTG received MT techniques; CG received a placebo treatment. The treatment lasted one month. Outcome measures were assessed at baseline, post-intervention and follow-up., Results: Both FRG and MTG showed significant improvements in all variables after the treatment, but the intervention effect was maintained only for functional disability ( p = 0.002 and p = 0.005, respectively), overall disability ( p = 0.007; p = 0.030) and HIT-6 ( p = 0.002; p = 0.001) at follow-up. After treatment, FRG and MTG presented a significantly higher PPT in right ( p = 0.044; p = 0.009) and left suboccipital ( p = 0.004; p = 0.021). MTG showed a significantly lower HIT-6 than CG ( p = 0.008). No differences between FRG and MTG were found in any variable., Conclusions: Both FR and MT are effective treatments for the improvement of clinical symptoms in TTH. Further studies are needed to confirm our findings in a larger population.
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- 2022
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14. Electron cryo-tomography structure of axonemal doublet microtubule from Tetrahymena thermophila .
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Li S, Fernandez JJ, Fabritius AS, Agard DA, and Winey M
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- Binding Sites, Microtubule Proteins genetics, Models, Molecular, Mutation, Protein Binding, Protein Conformation, Protozoan Proteins chemistry, Protozoan Proteins genetics, Protozoan Proteins metabolism, Structure-Activity Relationship, Axoneme metabolism, Microtubule Proteins chemistry, Microtubule Proteins metabolism, Microtubules metabolism, Tetrahymena thermophila
- Abstract
Doublet microtubules (DMTs) provide a scaffold for axoneme assembly in motile cilia. Aside from α/β tubulins, the DMT comprises a large number of non-tubulin proteins in the luminal wall of DMTs, collectively named the microtubule inner proteins (MIPs). We used cryoET to study axoneme DMT isolated from Tetrahymena We present the structures of DMT at nanometer and sub-nanometer resolution. The structures confirm that MIP RIB72A/B binds to the luminal wall of DMT by multiple DM10 domains. We found FAP115, an MIP-containing multiple EF-hand domains, located at the interface of four-tubulin dimers in the lumen of A-tubule. It contacts both lateral and longitudinal tubulin interfaces and playing a critical role in DMT stability. We observed substantial structure heterogeneity in DMT in an FAP115 knockout strain, showing extensive structural defects beyond the FAP115-binding site. The defects propagate along the axoneme. Finally, by comparing DMT structures from Tetrahymena and Chlamydomonas , we have identified a number of conserved MIPs as well as MIPs that are unique to each organism. This conservation and diversity of the DMT structures might be linked to their specific functions. Our work provides structural insights essential for understanding the roles of MIPs during motile cilium assembly and function, as well as their relationships to human ciliopathies., (© 2021 Li et al.)
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- 2021
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15. Clinical Outcomes After Revision Distal Biceps Tendon Surgery.
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Grewal G, Bernardoni ED, Cohen MS, Fernandez JJ, Verma NN, Romeo AA, and Frank RM
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Background: Little is known about the clinical indications of performing a revision distal biceps tendon repair/reconstruction, and there is even less data available on the clinical outcomes of patients after revision surgery., Purpose: To determine the clinical outcomes of patients undergoing revision distal biceps tendon repair/reconstruction and evaluate the causes of primary repair failure., Study Design: Case series; Level of evidence, 4., Methods: We performed a retrospective review of patients undergoing ipsilateral primary and revision distal biceps tendon repair/reconstruction at a single institution. Between 2011 and 2016, a total of 277 patients underwent distal biceps tendon repair, with 8 patients requiring revision surgery. Patient characteristics, surgical technique, and patient-reported outcome scores (shortened version of Disabilities of Arm, Shoulder and Hand [QuickDASH], 12-Item Short Form Health Survey [SF-12], visual analog scale [VAS] for pain, and Mayo Elbow Performance Score [MEPS]), were assessed. Complications as well as indications for reoperation after primary and revision surgery were examined., Results: The overall revision rate was 2.9%. The number of single- and double-incision techniques utilized were similar among the primary repairs (50% single-incision, 50% double-incision) and revision repairs/reconstructions (62.5% single-incision, 37.5% double-incision). Reasons for reoperation included continued pain and weakness (n = 7), limited range of motion (n = 2), and acute traumatic re-rupture (n = 1). The median duration between primary and revision surgery was 9.5 months (interquartile range [IQR], 5.8-12.8 months). Intraoperatively, the most common finding during revision was a partially ruptured, fibrotic distal tendon with extensive adhesions. At a median of 33.7 months after revision surgery (IQR, 21.7-40.7 months), the median QuickDASH was 12.5 (IQR, 1.7-23.3), MEPS was 92.5 (IQR, 80.0-100), SF-12 mental component measure was 53.4 (IQR, 47.6-58.2), SF-12 physical component measure was 52.1 (IQR, 36.9-55.4), and VAS for elbow pain was 1.0 (IQR, 0-2.0). Revision surgery had a complication rate of 37.5% (3 of 8 patients), consisting of persistent pain and weakness (2 patients; 25%) and numbness over the dorsal radial sensory nerve (1 patient; 12.5%). Two patients required reoperation (25% reoperation rate)., Conclusion: The overall revision distal biceps repair/reconstruction rate was approximately 3%. While patients undergoing revision distal biceps repair demonstrated improved outcomes after revision surgery, these outcomes remained inferior to previously reported outcomes of patients undergoing only primary distal biceps repair., Competing Interests: One or more of the authors has declared the following potential conflict of interest or source of funding: M.S.C. has received faculty/speaker fees from Synthes, consulting fees from Acumed, and royalties from Acumed and Integra LifeSciences. J.J.F. has received education payments from Arthrex. N.N.V. has received research support from Arthrex, Arthrosurface, Athletico, ConMed Linvatec, DJO, Miomed, Mitek, and Ossur; consulting fees from Minivasive, Smith & Nephew, Medacta, Orthospace, and Arthrex; nonconsulting fees from Arthrex; royalties from Smith & Nephew and Vindico Medical–Orthopedics Hyperguide; and stock/stock options from Cymedica, Minivasive, and Omeros. A.A.R. has received research support from Aesculap/B.Braun, Arthrex, Histogenics, Medipost, NuTech, OrthoSpace, Smith & Nephew, and Zimmer; consulting fees and speaking fees from Arthrex; and royalties from Arthrex, Saunders/Mosby-Elsevier, and SLACK. R.M.F. has received grant support from Arthrex, educational payments from Arthrex/Medwest and Smith & Nephew, and royalties from Elsevier. AOSSM checks author disclosures against the Open Payments Database (OPD). AOSSM has not conducted an independent investigation on the OPD and disclaims any liability or responsibility relating thereto., (© The Author(s) 2021.)
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- 2021
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16. PolishEM: image enhancement in FIB-SEM.
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Fernandez JJ, Torres TE, Martin-Solana E, Goya GF, and Fernandez-Fernandez MR
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- Computers, Image Enhancement, Microscopy, Software
- Abstract
Summary: We have developed a software tool to improve the image quality in focused ion beam-scanning electron microscopy (FIB-SEM) stacks: PolishEM. Based on a Gaussian blur model, it automatically estimates and compensates for the blur affecting each individual image. It also includes correction for artifacts commonly arising in FIB-SEM (e.g. curtaining). PolishEM has been optimized for an efficient processing of huge FIB-SEM stacks on standard computers., Availability and Implementation: PolishEM has been developed in C. GPL source code and binaries for Linux, OSX and Windows are available at http://www.cnb.csic.es/%7ejjfernandez/polishem., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2020
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17. Clinical and functional correlations of the difference between slow vital capacity and FVC.
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Fernandez JJ, Castellano MVCO, Vianna FAF, Nacif SR, Rodrigues Junior R, and Rodrigues SCS
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- Adult, Aged, Cross-Sectional Studies, Female, Humans, Male, Middle Aged, Plethysmography, Respiratory Function Tests, Spirometry, Statistics, Nonparametric, Surveys and Questionnaires, Forced Expiratory Volume physiology, Lung Diseases, Obstructive physiopathology, Vital Capacity physiology
- Abstract
Objective: To evaluate the relationship that the difference between slow vital capacity (SVC) and FVC (ΔSVC-FVC) has with demographic, clinical, and pulmonary function data., Methods: This was an analytical cross-sectional study in which participants completed a respiratory health questionnaire, as well as undergoing spirometry and plethysmography. The sample was divided into two groups: ΔSVC-FVC ≥ 200 mL and ΔSVC-FVC < 200 mL. The intergroup correlations were analyzed, and binomial logistic regression analysis was performed., Results: The sample comprised 187 individuals. In the sample as a whole, the mean ΔSVC-FVC was 0.17 ± 0.14 L, and 61 individuals (32.62%) had a ΔSVC-FVC ≥ 200 mL. The use of an SVC maneuver reduced the prevalence of nonspecific lung disease and of normal spirometry results by revealing obstructive lung disease (OLD). In the final logistic regression model (adjusted for weight and body mass index > 30 kg/m2), OLD and findings of air trapping (high functional residual capacity and a low inspiratory capacity/TLC ratio) were predictors of a ΔSVC-FVC ≥ 200 mL. The chance of a bronchodilator response was found to be greater in the ΔSVC-FVC ≥ 200 mL group: for FEV1 (OR = 4.38; 95% CI: 1.45-13.26); and for FVC (OR = 3.83; 95% CI: 1.26-11.71)., Conclusions: The use of an SVC maneuver appears to decrease the prevalence of nonspecific lung disease and of normal spirometry results. Individuals with a ΔSVC-FVC ≥ 200 mL, which is probably the result of OLD and air trapping, are apparently more likely to respond to bronchodilator administration.
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- 2019
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18. Saline Load Test for Detecting Traumatic Arthrotomy in the Wrist.
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Goyal N, Bohl DD, Frank RM, Slikker W 3rd, Fernandez JJ, Cohen MS, and Wysocki RW
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Background Open injuries communicating with the wrist joint are essential to detect to facilitate timely, appropriate treatment. While the saline load test to detect traumatic arthrotomy has been well studied in the knee and ankle, it has not been studied in the wrist, and therefore the appropriate volume of saline infusion to detect traumatic arthrotomy is not known. Purpose The purpose of this study was to utilize wrist arthroscopy to determine the saline infusion volume necessary to achieve 99% sensitivity in detecting traumatic arthrotomy. Methods Twenty consecutive patients undergoing elective wrist arthroscopy were prospectively enrolled. A 5-mm arthrotomy was established between the third and fourth dorsal extensor compartments. An 18-gauge needle was inserted into the 6R portal on the radial side of the extensor carpi ulnaris. Sterile normal saline was injected into the wrist joint through the needle at a rate of 0.1 mL per second until extravasation from the 3-4 portal was visualized. Saline volumes required for extravasation were analyzed. Results The mean saline volume required for extravasation was 0.8 mL. The volume of saline needed to achieve sensitivities of 50, 90, 95, and 99% were 0.4, 2.2, 2.3, and 2.5 mL respectively. Conclusions The saline infusion volume required to detect a dorsal radiocarpal arthrotomy with 99% sensitivity was 2.5 mL. We recommend using at least 2.5 mL when performing the saline load test to rule out a potential arthrotomy to the wrist in the traumatic setting. Level of Evidence: This is a Level II, diagnostic study.
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- 2019
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19. Surgical Repair of Distal Triceps Tendon Injuries: Short-term to Midterm Clinical Outcomes and Risk Factors for Perioperative Complications.
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Waterman BR, Dean RS, Veera S, Cole BJ, Romeo AA, Wysocki RW, Cohen MS, Fernandez JJ, and Verma NN
- Abstract
Background: Few large-scale series have described functional outcomes after distal triceps tendon repair. Predictors for operative success and a comparative analysis of surgical techniques are limited in the reported literature., Purpose: To evaluate short-term to midterm functional outcomes after distal triceps tendon repair in a broad patient population and to comparatively evaluate patient-reported outcomes in patients with and without pre-existing olecranon enthesopathy while also assessing for modifiable risk factors associated with adverse patient outcomes and/or revision surgery., Study Design: Case series; Level of evidence, 4., Methods: This study was a retrospective analysis of 69 consecutive patients who underwent surgical repair of distal triceps tendon injuries at a single institution. Demographic information, time from injury to surgery, mechanism of injury, extent of the tear, pre-existing enthesopathy, perioperative complications, and validated patient-reported outcome scores were included in the analysis. Patients with a minimum of 1-year follow-up were included., Results: The most common mechanisms of injury were direct elbow trauma (44.9%), extension/lifting exercises (20.3%), overuse (17.4%), and hyperflexion or hyperextension (17.4%). Eighteen patients were identified with pre-existing symptomatic enthesopathy, and 51 tears were caused by an acute injury. A total of 36 complete and 33 partial tendon tears were identified. Bone tunnels were most commonly used (n = 30; 43.5%), while direct sutures (n = 23; 33.3%) and suture anchors (n = 13; 18.8%) were also used. Perioperative complications occurred in 21.7% of patients, but no patients experienced a rerupture at the time of final follow-up. No statistically significant relationship was found between patient age ( P = .750), degree of the tear ( P = .613), or surgical technique employed ( P = .608) and the presence of perioperative complications., Conclusion: Despite the heightened risk of perioperative complications after primary repair of distal triceps tendon injuries, the current series found favorable functional outcomes and no cases of reruptures at short-term to midterm follow-up. Furthermore, age, surgical technique, extent of the tear, and mechanism of injury were not associated with adverse patient outcomes in this investigation. Pre-existing triceps enthesopathy was shown to be associated with increased complication rates., Competing Interests: One or more of the authors has declared the following potential conflict of interest or source of funding: B.R.W. has received research support from Arthrex and Encore Medical; educational support from Arthrex, Desert Mountain Medical, Medwest, and Smith & Nephew; honoraria from Vericel; speaking fees from Genzyme; hospitality payments from DePuy and Wright Medical; and publishing royalties from Elsevier. B.J.C. has received research support from Aesculap/B. Braun, Arthrex, Geistlich, Medipost, Novartis, Sanofi-Aventis, and Zimmer; consulting fees from Anika Therapeutics, Arthrex, Bioventus, Flexion, Genzyme, Regentis, Pacira, Smith & Nephew, Zimmer, and Vericel; speaking fees from Carticept and Pacira; has stock/stock options in Aqua Boom, Biomerix, GiteliScope, Ossio, and Regentis; receives royalties from Arthrex, DJ Orthopedics, Encore Medical, and Saunders/Mosby-Elsevier; and has received hospitality payments from Athletico, DePuy, JRF Ortho, LifeNet Health, and Tornier. A.A.R. has received research support from Aesculap/B. Braun, Arthrex, Histogenics, Medipost, NuTech, OrthoSpace, Smith & Nephew, and Zimmer; consulting fees from Arthrex; royalties from Arthrex, Saunders/Mosby-Elsevier, SLACK, and Wolters Kluwer Health; and is a board or committee member for Atreon Orthopedics. R.W.W. has received speaking fees from Synthes. M.S.C. has received consulting fees from Acumed and Integra LifeSciences, speaking fees from Synthes, and royalties from Acumed and Integra LifeSciences. N.N.V. has received research support from Arthrex, Arthrosurface, DJ Orthopedics, Ossur, and Smith & Nephew; educational support from Medwest; consulting fees from Arthrex, Medacta, Minivasive, OrthoSpace, and Smith & Nephew; speaking fees from Pacira; hospitality payments from Stryker and Wright Medical; royalties from Smith & Nephew and Vindico Medical Education–Orthopedics Hyperguide; and has stock/stock options in CyMedica Orthopedics, Minivasive, and Omeros. AOSSM checks author disclosures against the Open Payments Database (OPD). AOSSM has not conducted an independent investigation on the OPD and disclaims any liability or responsibility relating thereto.
- Published
- 2019
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20. Electron cryo-tomography provides insight into procentriole architecture and assembly mechanism.
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Li S, Fernandez JJ, Marshall WF, and Agard DA
- Subjects
- Cell Cycle genetics, Cell Cycle Proteins chemistry, Cell Cycle Proteins genetics, Centrioles genetics, Microtubules ultrastructure, Centrioles ultrastructure, Chlamydomonas reinhardtii ultrastructure, Cryoelectron Microscopy, Electron Microscope Tomography
- Abstract
Centriole is an essential structure with multiple functions in cellular processes. Centriole biogenesis and homeostasis is tightly regulated. Using electron cryo-tomography (cryoET) we present the structure of procentrioles from Chlamydomonas reinhardtii . We identified a set of non-tubulin components attached to the triplet microtubule (MT), many are at the junctions of tubules likely to reinforce the triplet. We describe structure of the A-C linker that bridges neighboring triplets. The structure infers that POC1 is likely an integral component of A-C linker. Its conserved WD40 β-propeller domain provides attachment sites for other A-C linker components. The twist of A-C linker results in an iris diaphragm-like motion of the triplets in the longitudinal direction of procentriole. Finally, we identified two assembly intermediates at the growing ends of procentriole allowing us to propose a model for the procentriole assembly. Our results provide a comprehensive structural framework for understanding the molecular mechanisms underpinning procentriole biogenesis and assembly., Competing Interests: SL, JF, WM, DA No competing interests declared, (© 2019, Li et al.)
- Published
- 2019
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21. Full Factorial Microfluidic Designs and Devices for Parallelizing Human Pluripotent Stem Cell Differentiation.
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Chadly DM, Oleksijew AM, Coots KS, Fernandez JJ, Kobayashi S, Kessler JA, and Matsuoka AJ
- Subjects
- Humans, Immunohistochemistry, Microscopy, Confocal, Pluripotent Stem Cells cytology, Cell Culture Techniques instrumentation, Cell Culture Techniques methods, Cell Differentiation, Microfluidics instrumentation, Microfluidics methods, Pluripotent Stem Cells physiology
- Abstract
Human pluripotent stem cells (hPSCs) are promising therapeutic tools for regenerative therapies and disease modeling. Differentiation of cultured hPSCs is influenced by both exogenous factors added to the cultures and endogenously secreted molecules. Optimization of protocols for the differentiation of hPSCs into different cell types is difficult because of the many variables that can influence cell fate. We present microfluidic devices designed to perform three- and four-factor, two-level full factorial experiments in parallel for investigating and directly optimizing hPSC differentiation. These devices feature diffusion-isolated, independent culture wells that allow for control of both exogenous and endogenous cellular signals and that allow for immunocytochemistry (ICC) and confocal microscopy in situ. These devices are fabricated by soft lithography in conjunction with 3D-printed molds and are operable with a single syringe pump, eliminating the need for specialized equipment or cleanroom facilities. Their utility was demonstrated by on-chip differentiation of hPSCs into the auditory neuron lineage. More broadly, these devices enable multiplexing for experimentation with any adherent cell type or even multiple cell types, allowing efficient investigation of the effects of medium conditions, pharmaceuticals, or other soluble reagents.
- Published
- 2019
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22. Physician Extenders in Hand Surgery: The Patient's Perspective.
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Manning BT, Bohl DD, Luchetti TJ, Christian DR, Fernandez JJ, Cohen MS, and Wysocki RW
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- Adult, Clinical Competence, Female, Hand surgery, Humans, Insurance, Health, Reimbursement, Male, Professional Role, Quality of Health Care, Surveys and Questionnaires, United States, Nurse Practitioners, Orthopedics, Patient Satisfaction, Physician Assistants
- Abstract
Background: Physician extenders, such as physician assistants (PAs) and nurse practitioners (NPs), have been incorporated into health systems in response to the rising demand for care. There is a paucity of literature regarding patient perspectives toward physician extenders in hand surgery., Methods: We anonymously surveyed 939 consecutive new patients before their clinic visit. Our questionnaire assessed patient perspectives toward physician extenders, including optimal scope of practice, the effect of the extender when choosing a hand surgeon, and pay equity for the same clinical services., Results: Of 939 patients, 784 (84%) responded: 54% were male and 46% were female with a mean age of 44.1 years. Most (65%) patients consider the extender's training background when choosing a hand surgeon, with 31% of all patients considering PAs to have higher training than NPs and 17% the reverse. Patients responded that certain services should be physician-provided, including determining the need for advanced imaging (eg, magnetic resonance imaging), follow-up for abnormal diagnostics, and new patient visits. Patients were amenable to services being extender-provided, including minor in-office procedures, preoperative teaching, and postoperative clinic visits. Patients lacked a consensus toward reimbursement equity for hand surgeons and physician extenders providing the same clinical services., Conclusions: Our data suggest that patients presenting to a hand surgeon are comfortable receiving direct care from a physician extender in many, but not all, circumstances. Hand surgeons can use these data when deciding how to use extenders to optimize patient satisfaction and practice efficiency as health care systems become increasingly consumer-focused and value-based.
- Published
- 2019
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23. 3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons.
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Fernandez-Fernandez MR, Ruiz-Garcia D, Martin-Solana E, Chichon FJ, Carrascosa JL, and Fernandez JJ
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- Animals, Cryopreservation, Mice, Inbred C57BL, Brain ultrastructure, Electron Microscope Tomography methods, Golgi Apparatus metabolism, Golgi Apparatus ultrastructure, Imaging, Three-Dimensional, Neurons metabolism, Neurons ultrastructure
- Abstract
Macroautophagy is morphologically characterized by autophagosome formation. Autophagosomes are double-membraned vesicles that sequester cytoplasmic components for further degradation in the lysosome. Basal autophagy is paramount for intracellular quality control in post-mitotic cells but, surprisingly, the number of autophagosomes in post-mitotic neurons is very low, suggesting that alternative degradative structures could exist in neurons. To explore this possibility, we have examined neuronal subcellular architecture by performing three-dimensional (3D) electron tomography analysis of mouse brain tissue that had been preserved through high-pressure freezing. Here, we report that sequestration of neuronal cytoplasmic contents occurs at the Golgi complex in distinct and dynamic structures that coexist with autophagosomes in the brain. These structures are composed of several concentric double-membraned layers that appear to be formed simultaneously by the direct bending and sealing of discrete Golgi stacks. These structures are labelled for proteolytic enzymes, and lysosomes and late endosomes are found in contact with them, leading to the possibility that the sequestered material could be degraded inside them. Our findings highlight the key role that 3D electron tomography, together with tissue rapid-freezing techniques, will have in gaining new knowledge about subcellular architecture., (© 2017. Published by The Company of Biologists Ltd.)
- Published
- 2017
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24. Removing Contamination-Induced Reconstruction Artifacts from Cryo-electron Tomograms.
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Fernandez JJ, Laugks U, Schaffer M, Bäuerlein FJ, Khoshouei M, Baumeister W, and Lucic V
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- Animals, Fiducial Markers, HeLa Cells, Humans, Male, Neurons cytology, Phantoms, Imaging, Rats, Rats, Wistar, Vitrification, Artifacts, Electron Microscope Tomography methods, Image Processing, Computer-Assisted
- Abstract
Imaging of fully hydrated, vitrified biological samples by electron tomography yields structural information about cellular protein complexes in situ. Here we present a computational procedure that removes artifacts of three-dimensional reconstruction caused by contamination present in samples during imaging by electron microscopy. Applying the procedure to phantom data and electron tomograms of cellular samples significantly improved the resolution and the interpretability of tomograms. Artifacts caused by surface contamination associated with thinning by focused ion beam, as well as those arising from gold fiducial markers and from common, lower contrast contamination, could be removed. Our procedure is widely applicable and is especially suited for applications that strive to reach a higher resolution and involve the use of recently developed, state-of-the-art instrumentation., (Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
- Published
- 2016
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25. Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy.
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Arnold J, Mahamid J, Lucic V, de Marco A, Fernandez JJ, Laugks T, Mayer T, Hyman AA, Baumeister W, and Plitzko JM
- Subjects
- Electron Microscope Tomography instrumentation, Fiducial Markers, HeLa Cells, Humans, Imaging, Three-Dimensional instrumentation, Microscopy, Fluorescence, Electron Microscope Tomography methods, Imaging, Three-Dimensional methods
- Abstract
The development of cryo-focused ion beam (cryo-FIB) for the thinning of frozen-hydrated biological specimens enabled cryo-electron tomography (cryo-ET) analysis in unperturbed cells and tissues. However, the volume represented within a typical FIB lamella constitutes a small fraction of the biological specimen. Retaining low-abundance and dynamic subcellular structures or macromolecular assemblies within such limited volumes requires precise targeting of the FIB milling process. In this study, we present the development of a cryo-stage allowing for spinning-disk confocal light microscopy at cryogenic temperatures and describe the incorporation of the new hardware into existing workflows for cellular sample preparation by cryo-FIB. Introduction of fiducial markers and subsequent computation of three-dimensional coordinate transformations provide correlation between light microscopy and scanning electron microscopy/FIB. The correlative approach is employed to guide the FIB milling process of vitrified cellular samples and to capture specific structures, namely fluorescently labeled lipid droplets, in lamellas that are 300 nm thick. The correlation procedure is then applied to localize the fluorescently labeled structures in the transmission electron microscopy image of the lamella. This approach can be employed to navigate the acquisition of cryo-ET data within FIB-lamellas at specific locations, unambiguously identified by fluorescence microscopy., (Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
- Published
- 2016
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26. Hibernomas of the upper extremity: a case report and literature review.
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Cipriano CA, Gray RR, and Fernandez JJ
- Abstract
Hibernomas are rare, benign tumors of brown adipose tissue. While they have been found in a variety of locations, they are rare in the upper extremity and not previously described in the hand. Diagnosis is most often made histologically, and treatment consists of surgical resection. We present an unusual case of hibernoma in the hand treated with marginal excision, resulting in good function, cosmesis, and no recurrence.
- Published
- 2015
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27. Ring closure activates yeast γTuRC for species-specific microtubule nucleation.
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Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, and Agard DA
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- Protein Binding, Protein Structure, Quaternary, Protein Structure, Secondary, Microtubules metabolism, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins chemistry, Saccharomyces cerevisiae Proteins metabolism, Tubulin chemistry, Tubulin metabolism
- Abstract
The γ-tubulin ring complex (γTuRC) is the primary microtubule nucleator in cells. γTuRC is assembled from repeating γ-tubulin small complex (γTuSC) subunits and is thought to function as a template by presenting a γ-tubulin ring that mimics microtubule geometry. However, a previous yeast γTuRC structure showed γTuSC in an open conformation that prevents matching to microtubule symmetry. By contrast, we show here that γ-tubulin complexes are in a closed conformation when attached to microtubules. To confirm the functional importance of the closed γTuSC ring, we trapped the closed state and determined its structure, showing that the γ-tubulin ring precisely matches microtubule symmetry and providing detailed insight into γTuRC architecture. Importantly, the closed state is a stronger nucleator, thus suggesting that this conformational switch may allosterically control γTuRC activity. Finally, we demonstrate that γTuRCs have a strong preference for tubulin from the same species.
- Published
- 2015
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28. Tuning the cache memory usage in tomographic reconstruction on standard computers with Advanced Vector eXtensions (AVX).
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Agulleiro JI and Fernandez JJ
- Abstract
Cache blocking is a technique widely used in scientific computing to minimize the exchange of information with main memory by reusing the data kept in cache memory. In tomographic reconstruction on standard computers using vector instructions, cache blocking turns out to be central to optimize performance. To this end, sinograms of the tilt-series and slices of the volumes to be reconstructed have to be divided into small blocks that fit into the different levels of cache memory. The code is then reorganized so as to operate with a block as much as possible before proceeding with another one. This data article is related to the research article titled Tomo3D 2.0 - Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction (Agulleiro and Fernandez, 2015) [1]. Here we present data of a thorough study of the performance of tomographic reconstruction by varying cache block sizes, which allows derivation of expressions for their automatic quasi-optimal tuning.
- Published
- 2015
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29. Three-dimensional structure of basal body triplet revealed by electron cryo-tomography.
- Author
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Li S, Fernandez JJ, Marshall WF, and Agard DA
- Subjects
- Models, Molecular, Molecular Structure, Electron Microscope Tomography methods, Microtubules ultrastructure
- Abstract
Basal bodies and centrioles play central roles in microtubule (MT)-organizing centres within many eukaryotes. They share a barrel-shaped cylindrical structure composed of nine MT triplet blades. Here, we report the structure of the basal body triplet at 33 Å resolution obtained by electron cryo-tomography and 3D subtomogram averaging. By fitting the atomic structure of tubulin into the EM density, we built a pseudo-atomic model of the tubulin protofilaments at the core of the triplet. The 3D density map reveals additional densities that represent non-tubulin proteins attached to the triplet, including a large inner circular structure in the basal body lumen, which functions as a scaffold to stabilize the entire basal body barrel. We found clear longitudinal structural variations along the basal body, suggesting a sequential and coordinated assembly mechanism. We propose a model in which δ-tubulin and other components participate in the assembly of the basal body.
- Published
- 2012
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30. Fast tomographic reconstruction on multicore computers.
- Author
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Agulleiro JI and Fernandez JJ
- Subjects
- Algorithms, Electron Microscope Tomography, Image Processing, Computer-Assisted methods, Software
- Abstract
Summary: Tomo3D implements a multithreaded vectorized approach to tomographic reconstruction that takes full advantage of the computer power in modern multicore computers. Full resolution tomograms are generated at high speed on standard computers with no special system requirements. Tomo3D has the most common reconstruction methods implemented, namely weighted Back-projection (WBP) and simultaneous iterative reconstruction technique (SIRT). It proves to be competitive with current graphic processor unit solutions in terms of processing time, in the order of a few seconds with WBP or minutes with SIRT. The program is compatible with standard packages, which easily allows integration in the electron tomography workflow.
- Published
- 2011
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31. Oxaliplatin-Related Ocular Toxicity.
- Author
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Mesquida M, Sanchez-Dalmau B, Ortiz-Perez S, Pelegrín L, Molina-Fernandez JJ, Figueras-Roca M, Casaroli-Marano R, and Adán A
- Abstract
We report the case of a 52-year-old woman with advanced colorectal cancer who was treated with oxaliplatin on a FOLFOX schedule. After 3 cycles of chemotherapy, she started to complain of visual loss, altered color vision and neurological symptoms. Due to the suspicion of ocular and neurological toxicity, antineoplastic treatment was stopped. Her visual field showed a concentric bilateral scotoma and the electrooculogram test revealed severe impairment of the retinal pigment epithelium. Visual acuity, color vision and visual field recovered completely 8 months later, although electrooculogram remained abnormal. Ocular toxicity has been reported as an infrequent adverse event of oxaliplatin. Findings in this case indicate toxicity of this chemotherapeutic agent on the retinal pigment epithelium, which has not been reported before. This damage could be permanent, and it thus differs from previously described oxaliplatin-induced ocular toxicities, which are usually transient and reversible. With increasing use of oxaliplatin as first-line treatment in advanced colorectal cancer, we have to be aware of this possible toxicity.
- Published
- 2010
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32. TOMOBFLOW: feature-preserving noise filtering for electron tomography.
- Author
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Fernandez JJ
- Subjects
- Algorithms, Image Processing, Computer-Assisted methods, Sensitivity and Specificity, Electron Microscope Tomography, Imaging, Three-Dimensional methods
- Abstract
Background: Noise filtering techniques are needed in electron tomography to allow proper interpretation of datasets. The standard linear filtering techniques are characterized by a tradeoff between the amount of reduced noise and the blurring of the features of interest. On the other hand, sophisticated anisotropic nonlinear filtering techniques allow noise reduction with good preservation of structures. However, these techniques are computationally intensive and are difficult to be tuned to the problem at hand., Results: TOMOBFLOW is a program for noise filtering with capabilities of preservation of biologically relevant information. It is an efficient implementation of the Beltrami flow, a nonlinear filtering method that locally tunes the strength of the smoothing according to an edge indicator based on geometry properties. The fact that this method does not have free parameters hard to be tuned makes TOMOBFLOW a user-friendly filtering program equipped with the power of diffusion-based filtering methods. Furthermore, TOMOBFLOW is provided with abilities to deal with different types and formats of images in order to make it useful for electron tomography in particular and bioimaging in general., Conclusion: TOMOBFLOW allows efficient noise filtering of bioimaging datasets with preservation of the features of interest, thereby yielding data better suited for post-processing, visualization and interpretation. It is available at the web site (http://www.ual.es/%7ejjfdez/SW/tomobflow.html).
- Published
- 2009
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33. Zidovudine induces S-phase arrest and cell cycle gene expression changes in human cells.
- Author
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Olivero OA, Tejera AM, Fernandez JJ, Taylor BJ, Das S, Divi RL, and Poirier MC
- Subjects
- Anti-HIV Agents administration & dosage, Base Sequence, DNA genetics, DNA Adducts metabolism, Gene Expression drug effects, HeLa Cells, Humans, Lamivudine administration & dosage, Lamivudine toxicity, Mutagens administration & dosage, Mutagens toxicity, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Reverse Transcriptase Inhibitors administration & dosage, Reverse Transcriptase Inhibitors toxicity, Zidovudine administration & dosage, Anti-HIV Agents toxicity, Cell Cycle drug effects, Cell Cycle genetics, S Phase drug effects, Zidovudine toxicity
- Abstract
Antiretroviral therapy for the human immunodeficiency virus-1 (HIV-1) typically includes two nucleoside reverse transcriptase inhibitors (NRTIs). 3'-Azido-3'-deoxythymidine (AZT, Zidovudine) plus 2'-deoxy-3'-thiacytidine (3TC, Lamivudine) is a combination that is used frequently. The NRTIs are mutagenic nucleoside analogs that become incorporated into DNA and terminate replication. We therefore hypothesized that exposure to this class of drug may alter cell cycle parameters. We used flow cytometry to examine the cell cycle in human epithelioid carcinoma (HeLa) cells exposed to AZT and 3TC alone, as well as a series of AZT/3TC dose combinations: (A) 125.0 microM AZT/12.5 microM 3TC; (B) 250.0 microM AZT/25.0 microM 3TC; and (C) 500 microM AZT/50 microM 3TC. At 24 h, at all doses, there was a good cell viability (>/=68%), and incorporation of AZT into nuclear DNA. Using flow cytometry, a dose-related increase in the percentage of cells in S phase, from 9.5% with no drug, to 36.0% with dose C, was observed in cells exposed for 24 h (P = 0.001, ANOVA). A concomitant decrease in the percentage of cells in G(1) phase, from 82.6% with no drug to 58.5% with dose C, was observed in cells exposed for 24 h (P = 0.017, ANOVA). A similar S phase arrest was seen in cells exposed to 125, 250 and 500 microM AZT alone, but there was no S phase alteration with 50 microM 3TC alone, suggesting that AZT is responsible for the accumulation of cells in S phase. To elucidate the accumulation of cells in S phase and explore the cell cycle gene expression changes induced by AZT and 3TC, we used c-DNA microarray, Cell Cycle Super Array and real-time PCR. There was a strong upregulation of the DNA damage-inducible transcript 3 (DDIT3 or GADD153) in NRTI-exposed cells. In addition, AZT induced an upregulation of cyclin D1 accompanied by a downregulation of the cyclin D1-associated inhibitors P18 and P57, and the G(1)-S check point gene P21, the net effect of which would be to foster a cell progression into S phase. Cyclin A2 was down-regulated in cells exposed to AZT, suggesting a block in S-G(2)-M progression that would also be consistent with the accumulation of cells in S phase. Overall, the study demonstrates that AZT, but not 3TC, causes an arrest of cells in S phase with a consistent alteration in the expression of several cell cycle genes.
- Published
- 2005
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34. Transplacental genotoxicity of combined antiretroviral nucleoside analogue therapy in Erythrocebus patas monkeys.
- Author
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Olivero OA, Fernandez JJ, Antiochos BB, Wagner JL, St Claire ME, and Poirier MC
- Subjects
- Animals, Anti-HIV Agents metabolism, Antiretroviral Therapy, Highly Active, DNA drug effects, DNA metabolism, Erythrocebus patas, Female, HIV Infections drug therapy, HIV-1 drug effects, Humans, Infectious Disease Transmission, Vertical prevention & control, Lamivudine metabolism, Placenta drug effects, Pregnancy, Reverse Transcriptase Inhibitors metabolism, Telomere drug effects, Zidovudine metabolism, Anti-HIV Agents toxicity, DNA Damage, Fetus drug effects, Lamivudine toxicity, Maternal-Fetal Exchange, Reverse Transcriptase Inhibitors toxicity, Zidovudine toxicity
- Abstract
Antiretroviral nucleoside analogue drugs are a major constituent of highly active antiretroviral therapy (HAART), the most advanced form of treatment for HIV-1 infection. Currently, HAART combinations that include zidovudine (ZDV) and lamivudine (3TC) are highly effective in preventing HIV-1 vertical transmission; most children are born with no evident adverse clinical effects. However, ZDV is a moderately strong transplacental carcinogen in mice, and potential long-term consequences of fetal exposure to most HAART combinations remain unknown. To model human transplacental ZDV and 3TC exposures, experiments were performed in Erythrocebus patas monkeys given human-equivalent drug exposure protocols. Pregnant monkeys were dosed with either no drug (n = 2), 40.0 mg ZDV/d (about 6 mg/kg body weight/d) for the last 50% (10 weeks) of gestation (n = 3), or with the same regimen of ZDV plus 24.0 mg 3TC/d (about 3.6 mg/kg body weight/d) for the last 20% (4 weeks) of gestation (n = 3). Multiple fetal organs were examined at term for DNA incorporation of ZDV and 3TC using two separate radioimmunoassays (RIAs). Values for ZDV-DNA incorporation were similar in fetuses exposed to ZDV alone and those exposed to ZDV plus 3TC. Values for 3TC-DNA in fetal organs were greater than or equal to values for ZDV-DNA, indicating that the total DNA damage sustained by fetuses exposed to both drugs was at least double that observed in fetuses exposed to ZDV alone. Telomere shortening, determined by Southern blot with a telomeric probe, was observed in most organs of the three animals exposed in utero to ZDV plus 3TC. No telomere shortening was evident in the unexposed fetuses, and occasional telomere shortening was found in fetuses exposed to ZDV alone. Overall, these studies demonstrate that monkey fetuses exposed in utero to the combination ZDV plus 3TC sustain a higher level of drug-DNA incorporation and show evidence of more telomere damage than monkey fetuses exposed to ZDV alone.
- Published
- 2002
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35. Eukaryotic type II chaperonin CCT interacts with actin through specific subunits.
- Author
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Llorca O, McCormack EA, Hynes G, Grantham J, Cordell J, Carrascosa JL, Willison KR, Fernandez JJ, and Valpuesta JM
- Subjects
- Actins chemistry, Actins genetics, Animals, Binding Sites, Chaperonin Containing TCP-1, Cloning, Molecular, Escherichia coli, Humans, Models, Molecular, Protein Conformation, Rats, Recombinant Fusion Proteins metabolism, Actins metabolism, Chaperonins metabolism
- Abstract
Chaperonins assist the folding of other proteins. Type II chaperonins, such as chaperonin containing TCP-1(CCT), are found in archaea and in the eukaryotic cytosol. They are hexadecameric or nonadecameric oligomers composed of one to eight different polypeptides. Whereas type I chaperonins like GroEL are promiscuous, assisting in the folding of many other proteins, only a small number of proteins, mainly actin and tubulin, have been described as natural substrates of CCT. This specificity may be related to the divergence of the eight CCT subunits. Here we have obtained a three-dimensional reconstruction of the complex between CCT and alpha-actin by cryo-electron microscopy and image processing. This shows that alpha-actin interacts with the apical domains of either of two CCT subunits. Immunolabelling of CCT-substrate complexes with antibodies against two specific CCT subunits showed that actin binds to CCT using two specific and distinct interactions: the small domain of actin binds to CCTdelta and the large domain to CCTbeta or CCTepsilon (both in position 1,4 with respect to delta). These results indicate that the binding of actin to CCT is both subunit-specific and geometry-dependent. Thus, the substrate recognition mechanism of eukaryotic CCT may differ from that of prokaryotic GroEL.
- Published
- 1999
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36. Malt lymphoma as first clinical presentation of a celiac disease.
- Author
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Alcalde M, Carro J, Rivero M, Fernandez JJ, and Saenz De Santamaria JS
- Subjects
- Adult, Celiac Disease pathology, Diagnosis, Differential, Female, Humans, Lymphoma, B-Cell, Marginal Zone pathology, Celiac Disease complications, Celiac Disease diagnosis, Lymphoma, B-Cell, Marginal Zone complications, Lymphoma, B-Cell, Marginal Zone diagnosis
- Abstract
We report a case of a 35 year-old-woman who suffered from abdominal pain and weight loss. Asymptomatic celiac disease was discovered and complicated with a MALT Lymphoma in the jejunum. This is an uncommon combination because lymphoma that arises in the presence of enteropathy is commonly from T lymphocytes. Also because it normally appears in patients with long standing celiac disease who report a recrudescence of the abdominal symptoms.
- Published
- 1998
37. Biomechanical study of the Grosse-Kempf femoral nail.
- Author
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Sánchez Gimeno M, Albareda Albareda J, Cardona Vernet JM, Fuentelsalz Gallego J, Fernandez JJ, and Seral Iñigo F
- Subjects
- Compressive Strength, Equipment Failure, Femoral Fractures diagnostic imaging, Humans, Materials Testing, Numerical Analysis, Computer-Assisted, Pliability, Radiography, Torque, Weight-Bearing, Bone Nails standards, Femoral Fractures surgery, Fracture Fixation, Intramedullary instrumentation
- Abstract
We have carried out a biomechanical study of the forces acting on the Grosse-Kempf intramedullary nail to determine those which most affect its structure. We have used finite element analysis to assess the distribution of compression, flexion and torsion forces. The qualitative and quantitative distribution of the tension on the surface of the nail has been observed. We have shown that the torsional force is most important and it is exerted in the posterior part of the nail where there is a change from the unslotted to the slotted section.
- Published
- 1997
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38. SIGNIFICANCE OF ANGIOGRAPHIC ABSENCE OF LEFT ANTERIOR DESCENDING CORONARY ARTERY IN A LEFT VENTRICLE WITH INTACT ANTERIOR WALL.
- Author
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Sabbagh AH, Schocket LI, Dexter RL, Fernandez JJ, and O'Hare JE
- Abstract
Fifteen patients having total occlusion of the proximal left anterior descending coronary artery were studied. All fifteen had normal left ventricular anterior walls. The electrocardiogram was normal in eight patients; old inferior wall infarction was evident in one; anterior ischemia in five; and left anterior hemiblock in one. Collateral circulation was found in twelve patients (80%). These findings suggest that an angiographically non-visualized left anterior descending (LAD) vessel is patent and bypassable in patients where the anterior ventricular wall is intact, thus representing an additional criterion for aortocoronary bypass surgery.
- Published
- 1978
39. Echocardiographic detection of tricuspid valve prolapse.
- Author
-
Chandraratna PN, Lopez JM, Fernandez JJ, and Cohen LS
- Subjects
- Adolescent, Adult, Aged, Angiography, Child, Coronary Disease complications, Ebstein Anomaly complications, Female, Heart Septal Defects, Atrial complications, Heart Valve Diseases complications, Humans, Male, Middle Aged, Mitral Valve Insufficiency diagnosis, Phonocardiography, Echocardiography, Tricuspid Valve Insufficiency diagnosis
- Abstract
The echocardiographic findings in 12 patients with tricuspid valve prolapse are presented. Eight of these patients had associated mitral valve prolapse. Only one of the above patients had the characteristic physical signs of tricuspid incompetence. Two types of abnormality were noted on the echocardiogram of the tricuspid valve. In eight patients, the systolic segment of the tricuspid valve showed an initial horizontal motion followed by a posterior motion in midsystole. Four patients exhibited posterior motion of the tricuspid valve in early systole, which reached a maximum in midsystole, and this was followed by an anterior motion, thus producing a hammock-like configuration. We conclude that echocardiography is useful in the diagnosis of tricuspid valve prolapse. Since this condition may be associated with clinically significant tricuspid incompetence or bacterial endocarditis, its recognition is of clinical importance.
- Published
- 1975
- Full Text
- View/download PDF
40. SURGICAL CORRECTION OF COMBINED DOUBLE-OUTLET RIGHT VENTRICLE AND TAUSSIG-BING SYNDROME.
- Author
-
Sabbagh AH, Strug BS, O'Hare JE, Schocket LI, and Fernandez JJ
- Abstract
Total surgical correction of a Taussig-Bing type double outlet right ventricle (DORV) was successfully performed in a severely cyanotic 3-year-old girl. The malformation was associated with bilateral conus, d-transposition of the great arteries, d-loop, and a subpulmonary ventricular septal defect (VSD) without significant pulmonary stenosis in situs solitus. It was impossible to create a tunnel repair by resecting the markedly hypertrophied muscular conus that separated the aortic valve from the subpulmonary ventricular septal defect. Therefore, the VSD was repaired with a Dacron patch, transforming the double outlet right ventricle into a transposition, after which total correction was achieved by means of a Mustard procedure.
- Published
- 1979
41. Family planning in El Salvador.
- Author
-
Fernandez JJ
- Subjects
- Curriculum, Demography, Education, Medical, El Salvador, Physicians supply & distribution, Population, Family Planning Services
- Published
- 1969
- Full Text
- View/download PDF
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