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1.
Appl Opt ; 63(14): 3863-3875, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38856349

ABSTRACT

Segmented-aperture systems, such as the James Webb Space Telescope (JWST), require fine piston alignment between primary mirror segments. Computer simulation experiments show that using a broadband long-wavelength channel, illustrated with the Mid Infrared Instrument (MIRI) onboard the JWST, can extend the capture range of segment piston phase retrieval significantly (in the case of JWST with MIRI, up to hundreds of microns), greatly reducing the requirements on coarse phasing.

2.
J Neurooncol ; 166(3): 431-440, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38310157

ABSTRACT

PURPOSE: Upfront dual checkpoint blockade with immune checkpoint inhibitors (ICI) has demonstrated efficacy for treating melanoma brain metastases (MBM) in asymptomatic patients. Whether the combination of stereotactic radiosurgery (SRS) with dual checkpoint blockade improves outcomes over dual-checkpoint blockade alone is unknown. We evaluated clinical outcomes of patients with MBM receiving ICI with nivolumab and ipilimumab, with and without SRS. METHODS: 49 patients with 158 MBM receiving nivolumab and ipilimumab for untreated MBM between 2015 and 2022 were identified at our institution. Patient and tumor characteristics including age, Karnofsky Performance Status (KPS), presence of symptoms, cancer history, MBM burden, and therapy course were recorded. Outcomes measured from initiation of MBM-directed therapy included overall survival (OS), local control (LC), and distant intracranial control (DIC). Time-to-event analysis was conducted with the Kaplan-Meier method. RESULTS: 25 patients with 74 MBM received ICI alone, and 24 patients with 84 MBM received concurrent SRS. Median follow-up was 24 months. No differences in age (p = 0.96), KPS (p = 0.85), presence of symptoms (p = 0.79), prior MBM (p = 0.68), prior MBM-directed surgery (p = 0.96) or SRS (p = 0.68), MBM size (p = 0.67), or MBM number (p = 0.94) were seen. There was a higher rate of nivolumab and ipilimumab course completion in the SRS group (54% vs. 24%; p = 0.029). The SRS group received prior immunotherapy more often than the ICI alone group (54% vs. 8.0%; p < 0.001). There was no significant difference in 1-year OS (72% vs. 71%, p = 0.20) and DIC (63% v 51%, p = 0.26) between groups. The SRS group had higher 1-year LC (92% vs. 64%; p = 0.002). On multivariate analysis, LC was improved with combination therapy (AHR 0.38, p = 0.01). CONCLUSION: In our analysis, patients who received SRS with nivolumab and ipilimumab had superior LC without increased risk of toxicity or compromised immunotherapy treatment completion despite the SRS cohort having higher rates of prior immunotherapy. Further prospective study of combination nivolumab and ipilimumab with SRS is warranted.


Subject(s)
Antineoplastic Agents, Immunological , Brain Neoplasms , Melanoma , Radiosurgery , Humans , Ipilimumab/therapeutic use , Melanoma/pathology , Nivolumab/therapeutic use , Radiosurgery/methods , Prospective Studies , Antineoplastic Agents, Immunological/therapeutic use , Brain Neoplasms/drug therapy , Brain Neoplasms/secondary , Retrospective Studies
3.
Eur J Cancer ; 192: 113287, 2023 10.
Article in English | MEDLINE | ID: mdl-37657227

ABSTRACT

BACKGROUND: Immunotherapy and targeted BRAF/MEK inhibitors (i) have revolutionised the systemic management of advanced melanoma. Given the role of stereotactic radiosurgery (SRS) in the local management of brain metastases, we sought to evaluate clinical outcomes in patients with melanoma brain metastases (MBM) treated with SRS and various systemic therapies. METHODS: Patients were included if MBM were diagnosed and treated with SRS within 3 months of receiving anti-PD-1+CTLA-4 therapy, anti-PD-1 therapy, anti-CTLA-4 therapy, BRAF/MEK-i, BRAF-i, or conventional chemotherapy. Comparisons between groups were made for overall survival (OS), distant MBM control, local MBM, systemic progression-free survival (sPFS), and neurotoxicity. RESULTS: In total, 257 patients with 1048 MBM treated over 368 SRS sessions between 2011 and 2020 were identified. On MVA, treatment with anti-PD1+anti-CTLA-4, anti-PD-1, and BRAF/MEK-i improved distant intracranial control over conventional chemotherapy. No significant differences were noted in local control (LC) between groups (p = 0.78). Kaplan-Meier OS at 12 months for anti-PD-1 + CTLA-4 therapy, anti-PD-1 therapy, anti-CTLA-4 therapy, BRAF/MEK-i, BRAF-i, and conventional chemotherapy was 68%, 59%, 45%, 62%, 21%, and 15%, respectively (p = <0.0001). The sPFS rates at 12 months were 57%, 53%, 42%, 45%, 14%, and 6% (p = <0.0001). No significant differences were noted in rates of radiation necrosis (p = 0.93). CONCLUSIONS: This is among the largest series evaluating MBM treated with SRS and various systemic therapy regimens. Our analysis noted significant differences in OS, distant MBM control, and sPFS by systemic therapy. No differences in LC or radiation necrosis risk were noted.


Subject(s)
Brain Neoplasms , Melanoma , Radiation Injuries , Radiosurgery , Humans , Proto-Oncogene Proteins B-raf/genetics , Radiosurgery/adverse effects , Brain Neoplasms/therapy , Melanoma/therapy , Protein Kinase Inhibitors/adverse effects , Necrosis , Mitogen-Activated Protein Kinase Kinases
4.
Sci Rep ; 13(1): 13192, 2023 08 14.
Article in English | MEDLINE | ID: mdl-37580360

ABSTRACT

Nature offers many examples of materials which exhibit exceptional properties due to hierarchical assembly of their constituents. In well-studied multi-cellular systems, such as the morpho butterfly, a visible indication of having ordered submicron features is given by the display of structural color. Detailed investigations of nature's designs have yielded mechanistic insights and led to the development of biomimetic materials at laboratory scales. However, the manufacturing of hierarchical assemblies at industrial scales remains difficult. Biomanufacturing aims to leverage the autonomy of biological systems to produce materials at lower cost and with fewer carbon emissions. Earlier reports documented that some bacteria, particularly those with gliding motility, self-assemble into biofilms with polycrystalline structures and exhibit glittery, iridescent colors. The current study demonstrates the potential of using one of these bacteria, Cellulophaga lytica, as a platform for the large scale biomanufacturing of ordered materials. Specific approaches for controlling C. lytica biofilm optical, spatial and temporal properties are reported. Complementary microscopy-based studies reveal that biofilm color variations are attributed to changes in morphology induced by cellular responses to the local environment. Incorporation of C. lytica biofilms into materials is also demonstrated, thereby facilitating their handling and downstream processing, as would be needed during manufacturing processes. Finally, the utility of C. lytica as a self-printing, photonic ink is established by this study. In summary, autonomous surface assembly of C. lytica under ambient conditions and across multiple length scales circumvent challenges that currently hinder production of ordered materials in industrial settings.


Subject(s)
Flavobacteriaceae , Flavobacteriaceae/chemistry , Biofilms , Photons , Iridescence
5.
Am Surg ; 89(5): 1485-1496, 2023 May.
Article in English | MEDLINE | ID: mdl-34920671

ABSTRACT

BACKGROUND: Malnutrition is under-recognized in cancer patients and can lead to poor treatment outcomes. We aim to develop an outpatient-focused score based on the Malnutrition Screening Tool (MST) to help identify colorectal cancer (CRC) profiles at high risk for malnutrition. METHODS: 506 CRC patients during initial outpatient oncology consultation at our tertiary referral outpatient oncology clinic completed the MST. Objective and subjective data were collected through chart review. Data gathered are as follows: demographics, anthropometrics, laboratory values, patient-reported symptoms, MST score, cancer history, performance status, socioeconomic status, and Charlson Comorbidity. Predictors of malnutrition were identified by logistic regression. Receiver operating curve (ROC), area under the curve (AUC), and our model's predictability were determined. RESULTS: Significant predictors of malnutrition are as follows: younger age (20-39 vs >40 years) (P = .007), normal-to-low body mass index at presentation (P = .019), Eastern Cooperative Oncology Group classification 2-3 (P = .012), metastatic disease (P = .046), albumin <3.0 g/dL (P = .033), fatigue (P < .001), and change in stool/bowel habits (P = .002). In our derived malnutrition score, risk of malnutrition increased from 11% for score 0, to 100% for scores 9-10. Receiver operating curve showed AUC .745 (95% CI, .697-.793). DISCUSSION: An outpatient clinic-derived malnutrition score obtained from objective and patient-reported variables may facilitate identification of CRC patients at highest risk for malnutrition. Rapid identification and intervention in high-risk patients may improve treatment recovery, therapy tolerance, and quality of life. Our tool requires external validation before application in clinical practice.


Subject(s)
Colorectal Neoplasms , Malnutrition , Humans , Adult , Nomograms , Nutrition Assessment , Quality of Life , Malnutrition/diagnosis , Malnutrition/etiology , Colorectal Neoplasms/complications , Colorectal Neoplasms/diagnosis , Nutritional Status
6.
Otolaryngol Head Neck Surg ; 168(3): 282-290, 2023 03.
Article in English | MEDLINE | ID: mdl-35763364

ABSTRACT

OBJECTIVE: Endolymphatic sac tumors are rare neoplasms originating in the endolymphatic sac. Current literature is limited to case reports and small case series. The objective of this study was to systematically review the literature to better describe clinical presentation, treatment options, and outcomes in endolymphatic sac tumors. DATA SOURCE: PubMed, Embase, and Cochrane Library. REVIEW METHODS: A systematic review was performed following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines describing human endolymphatic sac tumors. Risk of bias was assessed using a validated critical appraisal checklist for case series. Studies without inclusion of individual patient characteristics, corresponding treatments, and outcomes were excluded. Heterogeneity of data precluded meta-analysis. RESULTS: A total of 82 studies met inclusion criteria, and 253 discrete tumors were analyzed. A total of 23.4% of patients had von Hippel-Lindau disease. Von Hippel-Lindau-associated tumors affected females to males in a 2.4:1 ratio. Patients with von Hippel-Lindau disease displayed earlier average age at diagnosis compared to the sporadic cohort. Surgery was the primary treatment modality and was performed in 88.9% of cases. Adjuvant radiation therapy was employed in 18.7% of cases; 16.2% cases recurred, and 10.6% had progression of residual disease after treatment. Mean time to recurrence or progression was 53.1 ± 52.4 months with a range of 3 to 240 months. CONCLUSION: Endolymphatic sac tumors require a high degree of suspicion for early diagnosis. Complete resection is the standard of care. No strong evidence supports routine use of adjuvant radiation therapy. Given the high rate of recurrence and wide-ranging time to recurrence, long-term follow-up is necessary.


Subject(s)
Adenoma , Bone Neoplasms , Ear Neoplasms , Endolymphatic Sac , von Hippel-Lindau Disease , Male , Female , Humans , von Hippel-Lindau Disease/complications , von Hippel-Lindau Disease/diagnosis , von Hippel-Lindau Disease/pathology , Endolymphatic Sac/surgery , Early Detection of Cancer , Ear Neoplasms/surgery , Ear Neoplasms/diagnosis , Bone Neoplasms/pathology , Adenoma/pathology , Treatment Outcome
7.
Am J Physiol Gastrointest Liver Physiol ; 323(4): G306-G317, 2022 Oct 01.
Article in English | MEDLINE | ID: mdl-35916405

ABSTRACT

The alternative (noncanonical) nuclear factor-κB (NF-κB) signaling pathway predominantly regulates the function of the p52/RelB heterodimer. Germline Nfkb2 deficiency in mice leads to loss of p100/p52 protein and offers protection against a variety of gastrointestinal conditions, including azoxymethane/dextran sulfate sodium (DSS)-induced colitis-associated cancer and lipopolysaccharide (LPS)-induced small intestinal epithelial apoptosis. However, the common underlying protective mechanisms have not yet been fully elucidated. We applied high-throughput RNA-Seq and proteomic analyses to characterize the transcriptional and protein signatures of the small intestinal mucosa of naïve adult Nfkb2-/- mice. Those data were validated by immunohistochemistry and quantitative ELISA using both small intestinal tissue lysates and serum. We identified a B-lymphocyte defect as a major transcriptional signature in the small intestinal mucosa and immunoglobulin A as the most downregulated protein by proteomic analysis in Nfkb2-/- mice. Small intestinal immunoglobulins were dramatically dysregulated, with undetectable levels of immunoglobulin A and greatly increased amounts of immunoglobulin M being detected. The numbers of IgA-producing, cluster of differentiation (CD)138-positive plasma cells were also reduced in the lamina propria of the small intestinal villi of Nfkb2-/- mice. This phenotype was even more striking in the small intestinal mucosa of RelB-/- mice, although these mice were equally sensitive to LPS-induced intestinal apoptosis as their RelB+/+ wild-type counterparts. NF-κB2/p52 deficiency confers resistance to LPS-induced small intestinal apoptosis and also appears to regulate the plasma cell population and immunoglobulin levels within the gut.NEW & NOTEWORTHY Novel transcriptomic analysis of murine proximal intestinal mucosa revealed an unexpected B cell signature in Nfkb2-/- mice. In-depth analysis revealed a defect in the CD38+ B cell population and a gut-specific dysregulation of immunoglobulin levels.


Subject(s)
NF-kappa B p52 Subunit , Plasma Cells , Animals , Immunoglobulin A/metabolism , Immunoglobulins/metabolism , Intestinal Mucosa/metabolism , Lipopolysaccharides/pharmacology , Mice , NF-kappa B/metabolism , NF-kappa B p52 Subunit/genetics , NF-kappa B p52 Subunit/metabolism , Plasma Cells/metabolism , Proteomics
8.
J Neurosurg ; : 1-8, 2022 Nov 11.
Article in English | MEDLINE | ID: mdl-36681988

ABSTRACT

OBJECTIVE: Immune checkpoint inhibitors (ICIs) and epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) are commonly used in the systemic management of non-small cell lung cancer (NSCLC) brain metastases (BMs). However, optimizing control of NSCLC BM with stereotactic radiosurgery (SRS) and various systemic therapies remains an area of investigation. METHODS: Between 2016 and 2019, the authors identified 171 NSCLC BM patients with 646 BMs treated with single-fraction SRS within 3 months of receiving treatment with ICIs (n = 56; 33%), EGFR-TKI (n = 30; 18%), chemotherapy and ICIs (n = 23; 14%), or standard chemotherapy alone (n = 62; 36%). Time-to-event analysis was conducted, and outcomes included distant intracranial control (DIC), local control (LC), and overall survival from SRS. RESULTS: The median follow-up from BM diagnosis was 8.9 months (range 0.3-127 months). The 12-month Kaplan-Meier DIC rates were 37%, 53%, 41%, and 21% (p = 0.047) for the ICI, EGFR-TKI, ICI and chemotherapy, and chemotherapy-alone groups, respectively. On multivariate analysis, DIC was improved with EGFR-TKI (HR 0.4, 95% CI 0.3-0.8, p = 0.005) compared with conventional chemotherapy and treatment with SRS before systemic therapy (HR 0.5, 95% CI 0.3-0.9, p = 0.03) compared with after; and LC was improved with SRS before (HR 0.4, 95% CI 0.2-0.9, p = 0.03) or concurrently (HR 0.3, 95% CI 0.1-0.6, p = 0.003) compared with after. No differences in radionecrosis were noted by timing or type of systemic therapy. CONCLUSIONS: The authors' analysis showed significant differences in DIC based on receipt of systemic therapy and treatment with SRS before systemic therapy improved DIC. Prospective evaluation of the potential synergism between systemic therapy and SRS in NSCLC BM management is warranted.

9.
Radiographics ; 41(7): 2011-2028, 2021.
Article in English | MEDLINE | ID: mdl-34623945

ABSTRACT

Chest, abdominal, and groin pain are common patient complaints that can be due to a variety of causes. Once potentially life-threatening visceral causes of pain are excluded, the evaluation should include musculoskeletal sources of pain from the body wall and core muscles. Percutaneous musculoskeletal procedures play a key role in evaluating and managing pain, although most radiologists may be unfamiliar with applications for the body wall and core muscles. US is ideally suited to guide these less commonly performed procedures owing to its low cost, portability, lack of ionizing radiation, and real-time visualization of superficial soft-tissue anatomy. US provides the operator with added confidence that the needle will be placed at the intended location and will not penetrate visceral or vascular structures. The authors review both common and uncommon US-guided procedures targeting various portions of the chest wall, abdominal wall, and core muscles with the hope of familiarizing radiologists with these techniques. Procedures include anesthetic and corticosteroid injection as well as platelet-rich plasma injection to promote tendon healing. Specific anatomic structures discussed include the sternoclavicular joint, costochondral joint, interchondral joint, intercostal nerve, scapulothoracic bursa, anterior abdominal cutaneous nerve, ilioinguinal nerve, iliohypogastric nerve, genitofemoral nerve, pubic symphysis, common aponeurotic plate, and adductor tendon origin. Relevant US anatomy is depicted with MRI correlation, and steps to performing successful safe US-guided injections are discussed. Confidence in performing these procedures will allow radiologists to continue to play an important role in diagnosis and management of many musculoskeletal pathologic conditions. ©RSNA, 2021.


Subject(s)
Magnetic Resonance Imaging , Pain Management , Humans , Pelvic Pain , Peripheral Nerves
10.
Cureus ; 13(2): e13227, 2021 Feb 08.
Article in English | MEDLINE | ID: mdl-33728177

ABSTRACT

Sarcoidosis preceding a diagnosis of lymphoma has been a reported phenomenon termed sarcoidosis-lymphoma syndrome. Skeletal metastasis is extremely rare. Here, we detail a case of sarcoidosis-lymphoma syndrome presenting as a lumbar vertebral metastasis with suspected associated intracranial lesions. A 72-year-old man with a history of follicular lymphoma presented with symptomatic central nervous system (CNS) lesions with concurrent lumbar vertebral metastases visualized with CT and MRI. Rituximab, cyclophosphamide, doxorubicin hydrochloride, vincristine sulfate, and prednisone (R-CHOP) with dexamethasone treatment resulted in significant radiographic regression of his intracranial lesions with dramatic symptomatic improvement. Out of concern for compression fracture of his lytic lumbar lesions, kyphoplasty with biopsy was performed showing lymphocytes that were positive for cluster-of-differentiation 10 (CD10), CD20, and B-cell lymphoma 2 (Bcl2). The patient was diagnosed with CNS and vertebral sarcoidosis-lymphoma syndrome and began treatment with high-dose methotrexate. Including the present case, only four occurrences of sarcoidosis-lymphoma syndrome with bony involvement have been described. We detail our own experience and summarize all previous literature. While rare, sarcoidosis-lymphoma may present with CNS and lytic bone involvement; in these cases, symptomatic severity, as well as an effective response to steroid treatment, underscore the importance of an accurate and prompt diagnosis.

11.
J Biol Chem ; 295(40): 13914-13926, 2020 10 02.
Article in English | MEDLINE | ID: mdl-32796031

ABSTRACT

Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. Here we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD+ reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the "aromatic box" that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.


Subject(s)
Aldehyde Dehydrogenase/chemistry , Bacterial Proteins/chemistry , Plant Diseases/microbiology , Pseudomonas syringae/enzymology , Aldehyde Dehydrogenase/genetics , Bacterial Proteins/genetics , Crystallography, X-Ray , Pseudomonas syringae/genetics
12.
Sci Adv ; 6(30): eabb9379, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32832677

ABSTRACT

Van der Waals (VdW) materials have opened new directions in the study of low dimensional magnetism. A largely unexplored arena is the intrinsic tuning of VdW magnets toward new ground states. Chromium trihalides provided the first such example with a change of interlayer magnetic coupling emerging upon exfoliation. Here, we take a different approach to engineer previously unknown ground states, not by exfoliation, but by tuning the spin-orbit coupling (SOC) of the nonmagnetic ligand atoms (Cl, Br, I). We synthesize a three-halide series, CrCl3 - x - y Br x I y , and map their magnetic properties as a function of Cl, Br, and I content. The resulting triangular phase diagrams unveil a frustrated regime near CrCl3. First-principles calculations confirm that the frustration is driven by a competition between the chromium and halide SOCs. Furthermore, we reveal a field-induced change of interlayer coupling in the bulk of CrCl3 - x - y Br x I y crystals at the same field as in the exfoliation experiments.

13.
Article in English | MEDLINE | ID: mdl-31632702

ABSTRACT

Introduction: Spinal epidural abscesses are most commonly treated with surgical decompression and antibiotics or in specific instances managed medically with antibiotic therapy alone. Image-guided percutaneous aspiration as an alternative to surgery has only rarely been reported in the literature. Case presentation: We report two cases of successful fluoroscopy-guided needle aspiration of posterior epidural abscesses. Case 1 is a 48-year-old man who presented with several days of escalating back pain and constitutional symptoms with MRI showing a posterior epidural abscess at L2-L3 causing spinal stenosis. The patient remained neurologically intact. Percutaneous needle aspiration of the collection provided dramatic pain relief with the aspirate growing methicillin sensitive Staphylococcus aureus. The patient made a full recovery on antibiotic therapy. Case 2 is an 81-year-old man who presented with worsening upper back pain and was found to have osteomyelitis/discitis with a large posterior epidural abscess in the thoracic spine. Needle drainage was performed with the sample growing Bacteroides fragilis. This patient also responded successfully to nonsurgical management with full recovery after appropriate antibiotic therapy. Discussion: In carefully selected patients, image-guided needle aspiration of posterior epidural abscesses may be a viable and less invasive alternative to surgery.


Subject(s)
Biopsy, Needle , Epidural Abscess/surgery , Image-Guided Biopsy , Aged, 80 and over , Anti-Bacterial Agents/therapeutic use , Epidural Abscess/diagnosis , Epidural Abscess/drug therapy , Epidural Abscess/microbiology , Fluoroscopy , Humans , Male , Middle Aged
15.
Small ; 13(38)2017 10.
Article in English | MEDLINE | ID: mdl-28809455

ABSTRACT

Photosynthetic organisms rely on a series of self-assembled nanostructures with tuned electronic energy levels in order to transport energy from where it is collected by photon absorption, to reaction centers where the energy is used to drive chemical reactions. In the photosynthetic bacteria Chlorobaculum tepidum, a member of the green sulfur bacteria family, light is absorbed by large antenna complexes called chlorosomes to create an exciton. The exciton is transferred to a protein baseplate attached to the chlorosome, before migrating through the Fenna-Matthews-Olson complex to the reaction center. Here, it is shown that by placing living Chlorobaculum tepidum bacteria within a photonic microcavity, the strong exciton-photon coupling regime between a confined cavity mode and exciton states of the chlorosome can be accessed, whereby a coherent exchange of energy between the bacteria and cavity mode results in the formation of polariton states. The polaritons have energy distinct from that of the exciton which can be tuned by modifying the energy of the optical modes of the microcavity. It is believed that this is the first demonstration of the modification of energy levels within living biological systems using a photonic structure.


Subject(s)
Bacteria/metabolism , Nanoparticles/chemistry , Photons , Photosynthesis , Bacteria/ultrastructure , Optical Imaging , Thermodynamics
16.
Microorganisms ; 5(1)2017 Feb 21.
Article in English | MEDLINE | ID: mdl-28230808

ABSTRACT

Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3), but not light-harvesting complex 2 (LH2), were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment.

18.
Curr Protoc Pharmacol ; 69: 14.34.1-14.34.35, 2015 Jun 01.
Article in English | MEDLINE | ID: mdl-26344212

ABSTRACT

Gastric adenocarcinoma is the fifth most common cancer and third most common cause of cancer-related death in the world. The majority of these cancers develop in genetically susceptible individuals who are chronically infected with the Gram-negative bacterium Helicobacter pylori. Often these individuals have also been exposed to certain environmental factors that increase susceptibility, such as dietary components. Murine models of Helicobacter-induced gastric cancer are valuable tools for investigating the mechanisms responsible for the stepwise pathological changes of chronic atrophic gastritis, intestinal metaplasia, dysplasia and gastric adenocarcinoma. Helicobacter felis colonization greatly accelerates the development of gastric neoplasia in mice, and causes pathologies similar to those observed with Helicobacter pylori-associated gastric carcinogenesis in humans. These mouse models are therefore useful for investigating genetic and environmental factors that may be involved in the pathogenesis and treatment of gastric cancer. Detailed in these protocols are procedures for inducing Helicobacter-associated carcinogenesis in mice as well as the histological analysis and interpretation of gastric pathology in these animals.


Subject(s)
Adenocarcinoma/microbiology , Disease Models, Animal , Helicobacter Infections/microbiology , Helicobacter felis/pathogenicity , Helicobacter pylori/pathogenicity , Paraneoplastic Syndromes/microbiology , Stomach Neoplasms/microbiology , Adenocarcinoma/drug therapy , Adenocarcinoma/immunology , Adenocarcinoma/pathology , Animals , Anti-Bacterial Agents/therapeutic use , Antineoplastic Agents/therapeutic use , Carcinogenesis/drug effects , Carcinogenesis/immunology , Carcinogenesis/metabolism , Carcinogenesis/pathology , Gastric Mucosa/drug effects , Gastric Mucosa/immunology , Gastric Mucosa/microbiology , Gastric Mucosa/pathology , Helicobacter Infections/drug therapy , Helicobacter Infections/immunology , Helicobacter Infections/pathology , Helicobacter felis/drug effects , Helicobacter felis/immunology , Helicobacter pylori/drug effects , Helicobacter pylori/immunology , Humans , Mice , Paraneoplastic Syndromes/drug therapy , Paraneoplastic Syndromes/immunology , Paraneoplastic Syndromes/pathology , Stomach Neoplasms/drug therapy , Stomach Neoplasms/immunology , Stomach Neoplasms/pathology
19.
J Phys Chem Lett ; 6(14): 2702-7, 2015 Jul 16.
Article in English | MEDLINE | ID: mdl-26266851

ABSTRACT

In the photosynthetic green sulfur bacterium Chlorobaculum tepidum, the baseplate mediates excitation energy transfer from the light-harvesting chlorosome to the Fenna-Matthews-Olson (FMO) complex and subsequently toward the reaction center (RC). Literature data suggest that the baseplate is a 2D lattice of BChl a-CsmA dimers. However, recently, it has been proposed, using 2D electronic spectroscopy (2DES) at 77 K, that at least four excitonically coupled BChl a are in close contact within the baseplate structure [ Dostál , J. ; et al., J. Phys. Chem. Lett. 2014 , 5 , 1743 ]. This finding is tested via hole burning (HB) spectroscopy (5 K). Our results indicate that the four excitonic states identified by 2DES likely correspond to contamination of the baseplate with the FMO antenna and possibly the RC. In contrast, HB reveals a different excitonic structure of the baseplate chromophores, where excitation is transferred to a localized trap state near 818 nm via exciton hopping, which leads to emission near 826 nm.


Subject(s)
Bacterial Proteins/chemistry , Chlorobi/chemistry , Light-Harvesting Protein Complexes/chemistry , Chlorobi/cytology , Energy Transfer , Protein Conformation , Spectrum Analysis
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