Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides.

Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-molecule biology. The Pacific Biosciences RS2 sequencer utilizes sequencing by synthesis within nanophotonic zero mode waveguides. A number of years ago this instrument was unlocked by Pacific Biosciences for custom use by researchers allowing them to monitor biological interactions at the single-molecule level with high throughput. In this capability letter we demonstrate the use of the RS2 sequencer for real-time observation of DNA-to-RNA transcription and RNA-protein interactions. We use a relatively complex model-transcription of structured ribosomal RNA fromE. coliand interactions of ribosomal RNA with ribosomal proteins. We also show evidence of observation of transcriptional pausing without the application of an external force (as is required for single-molecule pausing studies using optical traps). Overall, in the unlocked, custom mode, the RS2 sequencer can be used to address a wide variety of biological assembly and interaction questions at the single-molecule level with high throughput. This instrument is available for use at the Center for Integrated Nanotechnologies Gateway located at Los Alamos National Laboratory.

Clinical course of pain and disability following primary lumbar discectomy: systematic review and meta-analysis.

PURPOSE: To conduct a meta-analysis to describe clinical course of pain and disability in adult patients post-lumbar discectomy (PROSPERO: CRD42015020806). METHODS: Sensitive topic-based search strategy designed for individual databases was conducted. Patients (> 16 years) following first-time lumbar discectomy for sciatica/radiculopathy with no complications, investigated in inception (point of surgery) prospective cohort studies, were included. Studies including revision surgery or not published in English were excluded. Two reviewers independently searched information sources, assessed eligibility at title/abstract and full-text stages, extracted data, assessed risk of bias (modified QUIPs) and assessed GRADE. Authors were contacted to request raw data where data/variance data were missing. Meta-analyses evaluated outcomes at all available time points using the variance-weighted mean in random-effect meta-analyses. Means and 95% CIs were plotted over time for measurements reported on outcomes of leg pain, back pain and disability. RESULTS: A total of 87 studies (n = 31,034) at risk of bias (49 moderate, 38 high) were included. Clinically relevant improvements immediately following surgery (> MCID) for leg pain (0-10, mean before surgery 7.04, 50 studies, n = 14,910 participants) and disability were identified (0-100, mean before surgery 53.33, 48 studies, n = 15,037). Back pain also improved (0-10, mean before surgery 4.72, 53 studies, n = 14,877). Improvement in all outcomes was maintained (to 7 years). Meta-regression analyses to assess the relationship between outcome data and a priori potential covariates found preoperative back pain and disability predictive for outcome. CONCLUSION: Moderate-level evidence supports clinically relevant immediate improvement in leg pain and disability following lumbar discectomy with accompanying improvements in back pain. These slides can be retrieved under Electronic Supplementary Material.

De-escalating and escalating treatments for early-stage breast cancer: the St. Gallen International Expert Consensus Conference on the Primary Therapy of Early Breast Cancer 2017.

The 15th St. Gallen International Breast Cancer Conference 2017 in Vienna, Austria reviewed substantial new evidence on loco-regional and systemic therapies for early breast cancer. Treatments were assessed in light of their intensity, duration and side-effects, seeking where appropriate to escalate or de-escalate therapies based on likely benefits as predicted by tumor stage and tumor biology. The Panel favored several interventions that may reduce surgical morbidity, including acceptance of 2 mm margins for DCIS, the resection of residual cancer (but not baseline extent of cancer) in women undergoing neoadjuvant therapy, acceptance of sentinel node biopsy following neoadjuvant treatment of many patients, and the preference for neoadjuvant therapy in HER2 positive and triple-negative, stage II and III breast cancer. The Panel favored escalating radiation therapy with regional nodal irradiation in high-risk patients, while encouraging omission of boost in low-risk patients. The Panel endorsed gene expression signatures that permit avoidance of chemotherapy in many patients with ER positive breast cancer. For women with higher risk tumors, the Panel escalated recommendations for adjuvant endocrine treatment to include ovarian suppression in premenopausal women, and extended therapy for postmenopausal women. However, low-risk patients can avoid these treatments. Finally, the Panel recommended bisphosphonate use in postmenopausal women to prevent breast cancer recurrence. The Panel recognized that recommendations are not intended for all patients, but rather to address the clinical needs of the majority of common presentations. Individualization of adjuvant therapy means adjusting to the tumor characteristics, patient comorbidities and preferences, and managing constraints of treatment cost and access that may affect care in both the developed and developing world.

Fast, super resolution imaging via Bessel-beam stimulated emission depletion microscopy.

A substantial advantage of stimulated emission depletion (STED) microscopy over other super-resolution methods is that images can be acquired in real-time without any post-processing. However imaging speed and photodamage are two major concerns for STED imaging of whole cells. Here we propose a new microscopy method we have termed Bessel-Beam STED (or BB-STED) that overcomes both of these limitations of conventional STED microscopy. In the proposed method, rather than exciting a single STED spot in the sample, an entire line of the sample is illuminated. This line-scanning technique dramatically increases the speed of STED. In addition, plane-illumination by scanning of the line across the focal plane of a detection objective limits the light to a thin layer of the sample and thus significantly reduces photobleaching and photodamage above and below the focal plane compared to epi-illumination. Using the organic dye Atto647N as an example, we calculated the STED power required to break the diffraction limit. The results presented here will be used to guide future experimental designs.

Confocal line scanning of a Bessel beam for fast 3D imaging.

We have developed a light-sheet illumination microscope that can perform fast 3D imaging of transparent biological samples with inexpensive visible lasers and a single galvo mirror (GM). The light-sheet is created by raster scanning a Bessel beam with a GM, with this same GM also being used to rescan the fluorescence across a chip of a camera to construct an image in real time. A slit is used to reject out-of-focus fluorescence such that the image formed in real time has minimal contribution from the sidelobes of the Bessel beam. Compared with two-photon Bessel beam excitation or other confocal line-scanning approaches, our method is of lower cost, is simpler, and does not require calibration and synchronization of multiple GMs. We demonstrated the optical sectioning and out-of-focus background rejection capabilities of this microscope by imaging fluorescently labeled actin filaments in fixed 3T3 cells.

Interferometric three-dimensional single molecule localization microscopy using a single high-numerical-aperture objective.

Interferometric detection of the fluorescence emission from a single molecule [interferometric photoactivated localization microscopy (iPALM)] enables a localization accuracy of nanometers in axial localization for 3D superresolution imaging. However, iPALM uses two high-numerical-aperture (NA) objectives in juxtaposition for fluorescence collection (a 4Pi microscope geometry), increasing expense and limiting samples that can be studied. Here, we propose an interferometric single molecule localization microscopy method using a single high-NA objective. The axial position of single molecules can be unambiguously determined from the phase-shifted interference signals with nanometer precision and over a range of 2λ. The use of only one objective simplifies the system configuration and sample mounting. In addition, due to the use of wavefront-splitting interference in our approach, the two parts of the wavefront that eventually merge and interfere with each other travel along nearly equivalent optical paths, which should minimize the effect of drift for long-term 3D superresolution imaging.

A randomized double-blind placebo-controlled cross-over trial of the impact on quality of life of continuing dexamethasone beyond 24 h following adjuvant chemotherapy for breast cancer.

Uncertainty remains about the optimal anti-emetic regimen for control of delayed nausea and vomiting after adjuvant chemotherapy for breast cancer. Many patients receive dexamethasone but complain of insomnia, anxiety/agitation, and indigestion. The aim was to determine if patients receiving chemotherapy for breast cancer prefer treatment with dexamethasone or placebo for prophylaxis against delayed nausea and vomiting, and to compare quality of life (QOL) between the two treatments. In this randomized, double-blind, cross-over trial, we compared oral dexamethasone (4 mg twice daily for 2 days) versus placebo for chemotherapy-naïve patients with breast cancer. All patients received intravenous granisetron and dexamethasone pre-chemotherapy and oral granisetron on day 2. Primary endpoints were: (i) patient preference; (ii) difference between cycles in change of QOL from days 1 to 8. Median age of the 94 women was 51 years (range 27-76): 79 received fluorouracil/epirubicin/cyclophosphamide and 15 received doxorubicin/cyclophosphamide. Thirteen withdrew pre-cycle 2 with no differences between arms. Of 80 patients stating a preference, 31 preferred placebo (39 %, 95 % CI: 28-50 %) and 37 (46 %, 95 % CI: 35-58 %) preferred dexamethasone; 12 had no preference. There were no differences in intensity of vomiting, nausea, or time to onset of vomiting. There was greater decrease in global QOL (p = 0.06) when patients received dexamethasone. No other symptom/QOL domains differed significantly. In conclusion, no significant difference was found in patient preference, QOL, or symptoms regardless of whether dexamethasone or placebo was used after adjuvant chemotherapy.

Prognosis of BRCA-associated breast cancer: a summary of evidence.

The purpose of the study is to review the clinical studies relevant to the prognosis and prognostic associations of BRCA1- and BRCA2-associated breast cancers. Reports of relevant studies obtained from a MEDLINE search and references from these articles were critically reviewed. A number of methodologic limitations have been identified in the early studies. More recent studies have failed to demonstrate, for the most part, a significant overall survival difference between BRCA-associated breast cancers and sporadic breast cancers. The risk of in-breast tumor recurrence also appears to be similar in the first 5 years following a breast cancer diagnosis with apparent increase in the risk after 5 years in one study. Many in-breast tumor recurrences are now considered to be second primary breast cancers. There is a significant increase in the risk of contralateral breast cancers in BRCA mutation carriers with an estimated 10-year risk ranging from 20-40%. The prognosis of BRCA-associated breast cancers appears to be similar to that of sporadic breast cancers based on the current literature. Future data from large prospective cohort studies will be of interest.

A comparison of two class 10 pathogenesis-related genes from alfalfa and their activation by multiple stresses and stress-related signaling molecules.

A collection of 29 pathogenesis-related 10 (PR10) genes of Medicago sativa and Medicago truncatula showed that they were almost all obtained from cDNA libraries of tissues undergoing abiotic or biotic stresses. The predicted proteins could be divided into two subclasses, PR10.1 and PR10.2, but in silico predicted models of their three-dimensional structures revealed that they could be further divided based on size of the hydrophobic internal cavity and number of ß-bulges. A comparison of the expression of two highly similar M. sativa subclass PR10.1 genes, MsPR10.1A and MsPR10.1B, predicted to have similar sized hydrophobic internal cavities, but a different number of ß-bulges revealed differences in their expression patterns. MsPR10.1A was induced faster than MsPR10.1B by ABA, ethylene, and X. campestris pv. alfalfae, but slower than MsPR10.1B by harvesting and wounding. Unlike MsPR10.1A, MsPR10.1B expression was induced in non-harvested tissues following harvesting, but was not induced by heat treatment. Histochemical observations of Nicotiana benthamiana transformed with 657 bp of the MsPR10.1A promoter fused to the ß-glucuronidase (GUS) gene showed that GUS expression was wound-inducible in leaves, which was consistent with MsPR10.1A expression in alfalfa leaves. GUS expression in stems and leaves was mostly in vascular tissue. The MsPR10.1A promoter may be valuable in controlling the expression in vascular tissues and disease resistance.

Rehabilitation of Watson-Jones proximal tibial avulsion injury in elite academy level football: A report of two separate cases in one season.

OBJECTIVES: Watson-Jones proximal tibial avulsion injuries occur more frequently in athletic and muscular adolescent males. However, they are rare and therefore infrequently described in the medical literature. Two of these injuries occurred in a Category 1 football academy in the same season within a six-month period. We have described the cases with the hope of better informing other clinicians should they encounter this injury. METHODS: This case report describes the injury mechanism, surgical management and rehabilitation for the two cases [Players A and B]. Outcomes measures including player speed, agility and power were compared with scores from players of the same age group at the time of injury in the Premier League academies. Risk factors are also discussed. RESULTS: Both players were managed surgically, initially. Player B had the surgical fixation removed during rehabilitation. Player A still has the fixation in situ. Post-surgery, player A returned to full play at thirty-two weeks and thirty-eight weeks for player B. No critical incidents occurred during rehabilitation. CONCLUSION: Watson-Jones avulsion fractures, although rare, can be managed successfully. Athletes can achieve a successful return to play at their previous level.

Mitochondrial participation in the intracellular Ca2+ network.

Calcium can activate mitochondrial metabolism, and the possibility that mitochondrial Ca2+ uptake and extrusion modulate free cytosolic [Ca2+] (Cac) now has renewed interest. We use whole-cell and perforated patch clamp methods together with rapid local perfusion to introduce probes and inhibitors to rat chromaffin cells, to evoke Ca2+ entry, and to monitor Ca2+-activated currents that report near-surface [Ca2+]. We show that rapid recovery from elevations of Cac requires both the mitochondrial Ca2+ uniporter and the mitochondrial energization that drives Ca2+ uptake through it. Applying imaging and single-cell photometric methods, we find that the probe rhod-2 selectively localizes to mitochondria and uses its responses to quantify mitochondrial free [Ca2+] (Cam). The indicated resting Cam of 100-200 nM is similar to the resting Cac reported by the probes indo-1 and Calcium Green, or its dextran conjugate in the cytoplasm. Simultaneous monitoring of Cam and Cac at high temporal resolution shows that, although Cam increases less than Cac, mitochondrial sequestration of Ca2+ is fast and has high capacity. We find that mitochondrial Ca2+ uptake limits the rise and underlies the rapid decay of Cac excursions produced by Ca2+ entry or by mobilization of reticular stores. We also find that subsequent export of Ca2+ from mitochondria, seen as declining Cam, prolongs complete Cac recovery and that suppressing export of Ca2+, by inhibition of the mitochondrial Na+/ Ca2+ exchanger, reversibly hastens final recovery of Cac. We conclude that mitochondria are active participants in cellular Ca2+ signaling, whose unique role is determined by their ability to rapidly accumulate and then release large quantities of Ca2+.

Alterations of single molecule fluorescence lifetimes in near-field optical microscopy.

Fluorescence lifetimes of single Rhodamine 6G molecules on silica surfaces were measured with pulsed laser excitation, time-correlated single photon counting, and near-field scanning optical microscopy (NSOM). The fluorescence lifetime varies with the position of a molecule relative to a near-field probe. Qualitative features of lifetime decreases are consistent with molecular excited state quenching effects near metal surfaces. The technique of NSOM provides a means of altering the environment of a single fluorescent molecule and its decay kinetics in a repeatable fashion.

Differential expression of eight defensin genes of N. benthamiana following biotic stress, wounding, ethylene, and benzothiadiazole treatments.

Eight Nicotiana benthamiana defensin genes were identified that could be divided into two classes with class II defensins being longer than class I defensins due to an additional acidic C-terminal domain. Class I defensins were NbDef1.1, NbDef1.2, NbDef1.3, NbDef1.4, NbDef1.5, and NbDef1.6, and class II were Nbdef2.1 and NbDef2.2. Relative RT-PCR showed that NbDef1.1, NbDef1.2, and NbDef1.4 had relatively similar expression levels in healthy leaves, stems, roots, flowers, and seeds. However, Nbdef1.3, NbDef1.5, and NbDef1.6 had varying degrees of tissue specific expression, and Nbdef2.1 and NbDef2.2 had strictly flower-specific expression. None of the defensins were significantly induced by infection by Colletotrichum destructivum or C. orbiculare. However, infection by Pseudomonas syringae pv. tabaci resulted in increased expression of Nbdef1.2 and Nbdef2.2, and decreased expression of NbDef1.1, NbDef1.4, and NbDef1.6. In the hypersensitive response of N. benthamiana containing Pto with P. syringae pv. tabaci containing AvrPto, only NbDef2.2 was significantly up-regulated. Expression of the genes was also affected by abiotic treatments. Both wounding and ethylene treatments resulted in a strong induction of NbDef2.2 and a moderate to weak induction of NbDef1.1, NbDef1.2, and NbDef1.4. Only weak or no induction was observed with treatment with benzothiadiazole. The expression of these eight defensin genes demonstrates that only a small fraction of the members of a defensin gene family will respond to a particular hemibiotrophic pathogen as well as to abiotic stress or signaling molecules.

Review: Molecular techniques to assess genetic variation within and between Panax ginseng and Panax quinquefolius.

A variety of methods have been used to examine genetic differences in P. ginseng and P. quinquefolius. They have shown genetic differences within populations of P. ginseng (within and between elite cultivars, landraces and wild accessions), within populations of P. quinquefolius (within and between wild and cultivated accessions) and between P. ginseng and P. quinquefolius as well as other Panax species. Some examples of their applications have been to show that some elite cultivars are not uniform, there are possible founder effects in certain populations, there has been the spread of cultivated types into wild populations, relative diversity differs between different populations and identification of the source and purity of commercial samples. More work in the use of molecular markers for ginseng are needed, however, particularly the use of Next Generation Sequencing. Potential applications are the use of sequence analysis for genetic selection, breeding to develop new cultivars and providing traceability from field to consumer. Research on molecular markers in ginseng has lagged compared to other crops probably because of less of an emphasis on breeding for cultivar development and relatively small areas of production. The many potential benefits for ginseng production have yet to be realized.

Quantifying fungal infection of plant leaves by digital image analysis using Scion Image software.

A digital image analysis method previously used to evaluate leaf color changes due to nutritional changes was modified to measure the severity of several foliar fungal diseases. Images captured with a flatbed scanner or digital camera were analyzed with a freely available software package, Scion Image, to measure changes in leaf color caused by fungal sporulation or tissue damage. High correlations were observed between the percent diseased leaf area estimated by Scion Image analysis and the percent diseased leaf area from leaf drawings. These drawings of various foliar diseases came from a disease key previously developed to aid in visual estimation of disease severity. For leaves of Nicotiana benthamiana inoculated with different spore concentrations of the anthracnose fungus Colletotrichum destructivum, a high correlation was found between the percent diseased tissue measured by Scion Image analysis and the number of leaf spots. The method was adapted to quantify percent diseased leaf area ranging from 0 to 90% for anthracnose of lily-of-the-valley, apple scab, powdery mildew of phlox and rust of golden rod. In some cases, the brightness and contrast of the images were adjusted and other modifications were made, but these were standardized for each disease. Detached leaves were used with the flatbed scanner, but a method using attached leaves with a digital camera was also developed to make serial measurements of individual leaves to quantify symptom progression. This was successfully applied to monitor anthracnose on N. benthamiana leaves. Digital image analysis using Scion Image software is a useful tool for quantifying a wide variety of fungal interactions with plant leaves.

Exploring the disclosure decisions made by physiotherapists with a specific learning difficulty.

OBJECTIVES: To explore the disclosure decisions made in the workplace by physiotherapy staff with a specific learning difficulty (SpLD). DESIGN & SETTING: An exploratory qualitative design was used, which was informed by the social model of disability. The research was undertaken in North West England. It is presented according to the Consolidated Criteria for Reporting Qualitative Research. PARTICIPANTS: A purposive sample of eight physiotherapists recognised as having a SpLD were recruited. All participants had studied on one of two programmes at a university in England between 2004-2012. Their NHS workplace experience was from across the UK. DATA GENERATION: In-depth, semi-structured interviews were undertaken within the university setting or via telephone. Interviews lasted 40 to 70minutes and were digitally recorded. An interview guide was used to direct the interview. DATA ANALYSIS: Interview data were transcribed verbatim and analysed using thematic analysis. FINDINGS: Four participants were female. The mean number of years qualified as a physiotherapist was 4.5years (SD=2.27). Three themes were identified: 'Disclosing during the workplace application'; 'Positive about disabled people scheme'; 'Disclosing in the workplace'. CONCLUSIONS: Disclosure of dyslexia is a selective process and is a central dilemma in the lives of individuals who have a concealable stigmatised identity. As a consequence, physiotherapy staff with dyslexia may choose to conceal their disability and not disclose to their employer. In order for staff with dyslexia to get the support they need in the workplace, disclosure is recommended. A number of recommendations have been made to facilitate the disclosure process.

Radiocarbon constraints on the glacial ocean circulation and its impact on atmospheric CO2.

While the ocean's large-scale overturning circulation is thought to have been significantly different under the climatic conditions of the Last Glacial Maximum (LGM), the exact nature of the glacial circulation and its implications for global carbon cycling continue to be debated. Here we use a global array of ocean-atmosphere radiocarbon disequilibrium estimates to demonstrate a ∼689±53 14C-yr increase in the average residence time of carbon in the deep ocean at the LGM. A predominantly southern-sourced abyssal overturning limb that was more isolated from its shallower northern counterparts is interpreted to have extended from the Southern Ocean, producing a widespread radiocarbon age maximum at mid-depths and depriving the deep ocean of a fast escape route for accumulating respired carbon. While the exact magnitude of the resulting carbon cycle impacts remains to be confirmed, the radiocarbon data suggest an increase in the efficiency of the biological carbon pump that could have accounted for as much as half of the glacial-interglacial CO2 change.