Mechanisms of nucleation from electrolyte solutions have been debated for more than a century. Recent discoveries of amorphous precursors and evidence for cluster aggregation and liquid-liquid separation contradict common assumptions of classical nucleation theory. Using in situ transmission electron microscopy (TEM) to explore calcium carbonate (CaCO3) nucleation in a cell that enables reagent mixing, we demonstrate that multiple nucleation pathways are simultaneously operative, including formation both directly from solution and indirectly through transformation of amorphous and crystalline precursors. However, an amorphous-to-calcite transformation is not observed. The behavior of amorphous calcium carbonate upon dissolution suggests that it encompasses a spectrum of structures, including liquids and solids. These observations of competing direct and indirect pathways are consistent with classical predictions, whereas the behavior of amorphous particles hints at an underlying commonality among recently proposed precursor-based mechanisms.
Polycystic ovary syndrome (PCOS) is associated with insulin resistance and increased risk of type 2 diabetes. Skeletal muscle is the major site of insulin mediated glucose disposal and the skeletal muscle tissue is capable to synthesize, convert and degrade androgens. Insulin sensitivity is conserved in cultured myotubes (in vitro) from patients with PCOS, but the effect of testosterone on this insulin sensitivity is unknown. We investigated the effect of 7days testosterone treatment (100nmol/l) on glucose transport and gene expression levels of hormone receptors and enzymes involved in the synthesis and conversion of testosterone (HSD17B1, HSD17B2, CYP19A1, SRD5A1-2, AR, ER-?, HSD17B6 and AKR1-3) in myotubes from ten patients with PCOS and ten matched controls. Testosterone treatment significantly increased aromatase and androgen receptor gene expression levels in patients and controls. Glucose transport in myotubes was comparable in patients with PCOS vs. controls and was unchanged by testosterone treatment (p=0.21 PCOS vs. controls). These results suggest that testosterone treatment of myotubes increases the aromatase and androgen receptor gene expression without affecting insulin sensitivity and if testosterone is implicated in muscular insulin resistance in PCOS, this is by and indirect mechanism.
The vector velocity method Transverse Oscillation (TO) implemented on a conventional ultrasound (US) scanner (ProFocus, BK Medical, Herlev, Denmark) can provide real-time, angle-independent estimates of the cardiac blood flow. During cardiac surgery, epicardial US examination using TO was performed on (A) 3 patients with healthy aortic valve and (B) 3 patients with aortic valve stenosis. In group B, the systolic flow of the ascending aorta had higher velocities, was more aliased and chaotic. The jet narrowed to 44% of the lumen compared to 75% in group A and with a vector concentration, a measure of flow complexity, of 0.41 compared to 0.87 in group A. The two groups had similar secondary flow of the ascending aorta with an average rotation frequency of 4.8Hz. Simultaneous measurements were obtained with spectral Doppler (SD) and a thermodilution technique (TD). The mean difference in peak systolic velocity compared to SD in group A was 22% and 45% in B, while the mean difference in volume flow compared to TD in group A was 30% and 32% in B. TO can potentially reveal new information of cardiac blood flow, and may become a valuable diagnostic tool in the evaluation of patients with cardiovascular diseases.
A MHz-bandwidth thermo-optical (TO) plasmonic switch operating at telecommunication wavelengths and based on a hybrid solid-state silicon-loaded surface plasmon polariton waveguide design is demonstrated numerically. The nanosecond (ns) TO response of the switch is due to the high thermal conductivities of the employed materials and we demonstrate specifically a 10 dB extinction ratio in the time-dependent switch transmission which features a pulsed 1 ns rise time followed by a 25 ns fall time when the switch is photo-thermally activated by a ns pulse at 532 nm wavelength.
Chromosome breakage elicits transient silencing of ribosomal RNA synthesis, but the mechanisms involved remained elusive. Here we discover an in trans signalling mechanism that triggers pan-nuclear silencing of rRNA transcription in response to DNA damage. This is associated with transient recruitment of the Nijmegen breakage syndrome protein 1 (NBS1), a central regulator of DNA damage responses, into the nucleoli. We further identify TCOF1 (also known as Treacle), a nucleolar factor implicated in ribosome biogenesis and mutated in Treacher Collins syndrome, as an interaction partner of NBS1, and demonstrate that NBS1 translocation and accumulation in the nucleoli is Treacle dependent. Finally, we provide evidence that Treacle-mediated NBS1 recruitment into the nucleoli regulates rRNA silencing in trans in the presence of distant chromosome breaks.
CD8??(+) intraepithelial lymphocytes (IELs) are instrumental in maintaining the epithelial barrier in the intestine. Similar to natural killer cells and other innate lymphoid cells, CD8??(+) IELs constitutively express the T-box transcription factor T-bet. However, the precise role of T-bet for the differentiation or function of IELs is unknown. Here we show that mice genetically deficient for T-bet lacked both TCR??(+) and TCR??(+) CD8??(+) IELs and thus are more susceptible to chemically induced colitis. Although T-bet was induced in thymic IEL precursors (IELPs) as a result of agonist selection and interleukin-15 (IL-15) receptor signaling, it was dispensable for the generation of IELPs. Subsequently, T-bet was required for the IL-15-dependent activation, differentiation, and expansion of IELPs in the periphery. Our study reveals a function of T-bet as a central transcriptional regulator linking agonist selection and IL-15 signaling with the emergence of CD8??(+) IELs.
Unambiguous identification of tandem mass spectra is a cornerstone in mass-spectrometry-based proteomics. As the study of post-translational modifications (PTMs) by means of shotgun proteomics progresses in depth and coverage, the ability to correctly identify PTM-bearing peptides is essential, increasing the demand for advanced data interpretation. Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. Although such ions offer tremendous analytical advantages, algorithms to decipher MS/MS spectra for the presence of diagnostic ions in an unbiased manner are currently lacking. Here, we present a systematic spectral-pattern-based approach for the discovery of diagnostic ions and new fragmentation mechanisms in shotgun proteomics datasets. The developed software tool is designed to analyze large sets of high-resolution peptide fragmentation spectra independent of the fragmentation method, instrument type, or protease employed. To benchmark the software tool, we analyzed large higher-energy collisional activation dissociation datasets of samples containing phosphorylation, ubiquitylation, SUMOylation, formylation, and lysine acetylation. Using the developed software tool, we were able to identify known diagnostic ions by comparing histograms of modified and unmodified peptide spectra. Because the investigated tandem mass spectra data were acquired with high mass accuracy, unambiguous interpretation and determination of the chemical composition for the majority of detected fragment ions was feasible. Collectively we present a freely available software tool that allows for comprehensive and automatic analysis of analogous product ions in tandem mass spectra and systematic mapping of fragmentation mechanisms related to common amino acids.
Targeted endonucleases including zinc finger nucleases (ZFNs) and clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas9 are increasingly being used for genome editing in higher species. We therefore devised a broadly applicable and versatile method for increasing editing efficiencies by these tools. Briefly, 2A peptide-coupled co-expression of fluorescent protein and nuclease was combined with fluorescence-activated cell sorting (FACS) to allow for efficient isolation of cell populations with increasingly higher nuclease expression levels, which translated into increasingly higher genome editing rates. For ZFNs, this approach, combined with delivery of donors as single-stranded oligodeoxynucleotides and nucleases as messenger ribonucleic acid, enabled high knockin efficiencies in demanding applications, including biallelic codon conversion frequencies reaching 30-70% at high transfection efficiencies and ? 2% at low transfection efficiencies, simultaneous homozygous knockin mutation of two genes with ? 1.5% efficiency as well as generation of cell pools with almost complete codon conversion via three consecutive targeting and FACS events. Observed off-target effects were minimal, and when occurring, our data suggest that they may be counteracted by selecting intermediate nuclease levels where off-target mutagenesis is low, but on-target mutagenesis remains relatively high. The method was also applicable to the CRISPR/Cas9 system, including CRISPR/Cas9 mutant nickase pairs, which exhibit low off-target mutagenesis compared to wild-type Cas9.
Volume flow in arteriovenous fistulas for hemodialysis was measured using the angle-independent ultrasound technique Vector Flow Imaging and compared with flow measurements using the ultrasound dilution technique during dialysis. Using an UltraView 800 ultrasound scanner (BK Medical, Herlev, Denmark) with a linear transducer, 20 arteriovenous fistulas were scanned directly on the most superficial part of the fistula just before dialysis. Vector Flow Imaging volume flow was estimated with two different approaches, using the maximum and the average flow velocities detected in the fistula. Flow was estimated to be 242 mL/min and 404 mL/min lower than the ultrasound dilution technique estimate, depending on the approach. The standard deviations of the two Vector Flow Imaging approaches were 175.9 mL/min and 164.8 mL/min compared with a standard deviation of 136.9 mL/min using the ultrasound dilution technique. The study supports that Vector Flow Imaging is applicable for volume flow measurements.
Abnormal blood flow is usually assessed using spectral Doppler estimation of the peak systolic velocity. The technique, however, only estimates the axial velocity component, and therefore the complexity of blood flow remains hidden in conventional ultrasound examinations. With the vector ultrasound technique transverse oscillation the blood velocities of both the axial and the transverse directions are obtained and the complexity of blood flow can be visualized. The aim of the study was to determine the technical performance and interpretation of vector concentration as a tool for estimation of flow complexity. A secondary aim was to establish accuracy parameters to detect flow changes/patterns in the common carotid artery (CCA) and the carotid bulb (CB). The right carotid bifurcation including the CCA and CB of eight healthy volunteers were scanned in a longitudinal plane with vector flow ultrasound (US) using a commercial vector flow ultrasound scanner (ProFocus, BK Medical, Denmark) with a linear 5 MHz transducer transverse oscillation vector flow software. CCA and CB areas were marked in one cardiac cycle from each volunteer. The complex flow was assessed by medical expert evaluation and by vector concentration calculation. A vortex with complex flow was found in all carotid bulbs, whereas the CCA had mainly laminar flow. The medical experts evaluated the flow to be mainly laminar in the CCA (0.82 ± 0.14) and mainly complex (0.23 ± 0.22) in the CB. Likewise, the estimated vector concentrations in CCA (0.96 ± 0.16) indicated mainly laminar flow and in CB (0.83 ± 0.07) indicated mainly turbulence. Both methods were thus able to clearly distinguish the flow patterns of CCA and CB in systole. Vector concentration from angle-independent vector velocity estimates is a quantitative index, which is simple to calculate and can differentiate between laminar and complex flow.
Recent ex situ observations of crystallization in both natural and synthetic systems indicate that the classical models of nucleation and growth are inaccurate. However, in situ observations that can provide direct evidence for alternative models have been lacking due to the limited temporal and spatial resolution of experimental techniques that can observe dynamic processes in a bulk solution. Here we report results from liquid cell transmission electron microscopy studies of nucleation and growth of Au, CaCO3, and iron oxide nanoparticles. We show how these in situ data can be used to obtain direct evidence for the mechanisms underlying nanoparticle crystallization as well as dynamic information that provide constraints on important energetic parameters not available through ex situ methods.
Arthrodesis is a common procedure indicated for surgical treatment of end-stage degenerative joint disease of the foot and ankle. Many published studies have reviewed the union rate, focusing on specific technique or fixation. However, studies reporting on the average period required to achieve fusion, irrespective of the type of fixation or surgical method used, have been lacking. We report on the union rate and interval to fusion in patients who had undergone primary arthrodesis of various joints of the foot and ankle. A retrospective review of the medical records of 135 patients was performed. The specific joints studied were ankle, and the subtalar, triple, first tarsometatarsal, first metatarsophalangeal, and hallux interphalangeal joints. Our results showed that the average interval for complete fusion was significantly less for the joints in the forefoot, with the subtalar joint, ankle, and triple arthrodesis requiring a longer period to achieve complete fusion. The nonunion rate was also greater when the fusion involved the joints of the rearfoot. Our results have refuted the idea that 6 weeks is the minimum period required to achieve fusion in the foot and ankle. The results of our study support the need for additional education of the patients and surgeons that the interval required for recovery after foot and ankle fusion depends on the location and surface area that has been fused.
The covalent attachment of methyl groups to the side-chain of arginine residues is known to play essential roles in regulation of transcription, protein function, and RNA metabolism. The specific N-methylation of arginine residues is catalyzed by a small family of gene products known as protein arginine methyltransferases; however, very little is known about which arginine residues become methylated on target substrates. Here we describe a proteomics methodology that combines single-step immunoenrichment of methylated peptides with high-resolution mass spectrometry to identify endogenous arginine mono-methylation (MMA) sites. We thereby identify 1027 site-specific MMA sites on 494 human proteins, discovering numerous novel mono-methylation targets and confirming the majority of currently known MMA substrates. Nuclear RNA-binding proteins involved in RNA processing, RNA localization, transcription, and chromatin remodeling are predominantly found modified with MMA. Despite this, MMA sites prominently are located outside RNA-binding domains as compared with the proteome-wide distribution of arginine residues. Quantification of arginine methylation in cells treated with Actinomycin D uncovers strong site-specific regulation of MMA sites during transcriptional arrest. Interestingly, several MMA sites are down-regulated after a few hours of transcriptional arrest. In contrast, the corresponding di-methylation or protein expression levels are not altered, confirming that MMA sites contain regulated functions on their own. Collectively, we present a site-specific MMA data set in human cells and demonstrate for the first time that MMA is a dynamic post-translational modification regulated during transcriptional arrest by a hitherto uncharacterized arginine demethylase.
Medical ultrasound imaging using synthetic aperture sequential beamforming (SASB) has for the first time been used for clinical patient scanning. Nineteen patients with cancer of the liver (hepatocellular carcinoma or colorectal liver metastases) were scanned simultaneously with conventional ultrasound and SASB using a commercial ultrasound scanner and abdominal transducer. SASB allows implementation of the synthetic aperture technique on systems with restricted data handling capabilities due to a reduction in the data rate in the scanner by a factor of 64. The image quality is potentially maintained despite the data reduction. A total of 117 sequences were recorded and evaluated blinded by five radiologists from a clinical perspective. Forty-eight percent of the evaluations were in favor of SASB, 33% in favor of conventional ultrasound and 19 % were equal, that is, a clear, but non-significant trend favoring SASB over conventional ultrasound (p = 0.18), despite the substantial data reduction.
During DNA replication, nucleosomes are rapidly assembled on newly synthesized DNA to restore chromatin organization. Asf1, a key histone H3-H4 chaperone required for this process, is phosphorylated by Tousled-like kinases (TLKs). Here, we identify TLK phosphorylation sites by mass spectrometry and dissect how phosphorylation has an impact on human Asf1 function. The divergent C-terminal tail of Asf1a is phosphorylated at several sites, and this is required for timely progression through S phase. Consistent with this, biochemical analysis of wild-type and phospho-mimetic Asf1a shows that phosphorylation enhances binding to histones and the downstream chaperones CAF-1 and HIRA. Moreover, we find that TLK phosphorylation of Asf1a is induced in cells experiencing deficiency of new histones and that TLK interaction with Asf1a involves its histone-binding pocket. We thus propose that TLK signalling promotes histone supply in S phase by targeting histone-free Asf1 and stimulating its ability to shuttle histones to sites of chromatin assembly.
Citrullination is the post-translational conversion of an arginine residue within a protein to the non-coded amino acid citrulline. This modification leads to the loss of a positive charge and reduction in hydrogen-bonding ability. It is carried out by a small family of tissue-specific vertebrate enzymes called peptidylarginine deiminases (PADIs) and is associated with the development of diverse pathological states such as autoimmunity, cancer, neurodegenerative disorders, prion diseases and thrombosis. Nevertheless, the physiological functions of citrullination remain ill-defined, although citrullination of core histones has been linked to transcriptional regulation and the DNA damage response. PADI4 (also called PAD4 or PADV), the only PADI with a nuclear localization signal, was previously shown to act in myeloid cells where it mediates profound chromatin decondensation during the innate immune response to infection. Here we show that the expression and enzymatic activity of Padi4 are also induced under conditions of ground-state pluripotency and during reprogramming in mouse. Padi4 is part of the pluripotency transcriptional network, binding to regulatory elements of key stem-cell genes and activating their expression. Its inhibition lowers the percentage of pluripotent cells in the early mouse embryo and significantly reduces reprogramming efficiency. Using an unbiased proteomic approach we identify linker histone H1 variants, which are involved in the generation of compact chromatin, as novel PADI4 substrates. Citrullination of a single arginine residue within the DNA-binding site of H1 results in its displacement from chromatin and global chromatin decondensation. Together, these results uncover a role for citrullination in the regulation of pluripotency and provide new mechanistic insights into how citrullination regulates chromatin compaction.
Phosphoinositides (PIPs) play key roles in signaling and disease. Using high-resolution quantitative mass spectrometry, we identified PIP-interacting proteins and profiled their binding specificities toward all seven PIP variants. This analysis revealed 405 PIP-binding proteins, which is greater than the total number of phospho- or ubiquitin-binding domains. Translocation and inhibitor assays of identified PIP-binding proteins confirmed that our methodology targets direct interactors. The PIP interactome encompasses proteins from diverse cellular compartments, prominently including the nucleus. Our data set revealed a consensus motif for PI(3,4,5)P3-interacting pleckstrin homology (PH) domains, which enabled in silico identification of phosphoinositide interactors. Members of the dedicator of cytokinesis family C exhibited specificity toward both PI(3,4,5)P3 and PI(4,5)P2. Structurally, this dual specificity is explained by a decreased number of positively charged residues in the L1 subdomain compared with DOCK1. The presented PIP-binding proteome and its specificity toward individual PIPs should be a valuable resource for the community.
The solar wind (SW), composed of predominantly ?1-keV H(+) ions, produces amorphous rims up to ?150 nm thick on the surfaces of minerals exposed in space. Silicates with amorphous rims are observed on interplanetary dust particles and on lunar and asteroid soil regolith grains. Implanted H(+) may react with oxygen in the minerals to form trace amounts of hydroxyl (-OH) and/or water (H2O). Previous studies have detected hydroxyl in lunar soils, but its chemical state, physical location in the soils, and source(s) are debated. If -OH or H2O is generated in rims on silicate grains, there are important implications for the origins of water in the solar system and other astrophysical environments. By exploiting the high spatial resolution of transmission electron microscopy and valence electron energy-loss spectroscopy, we detect water sealed in vesicles within amorphous rims produced by SW irradiation of silicate mineral grains on the exterior surfaces of interplanetary dust particles. Our findings establish that water is a byproduct of SW space weathering. We conclude, on the basis of the pervasiveness of the SW and silicate materials, that the production of radiolytic SW water on airless bodies is a ubiquitous process throughout the solar system.
The younger an individual starts smoking, the greater the likelihood that addiction to nicotine will develop, suggesting that neurobiological responses vary across age to the addictive component of cigarettes. Cholinergic neurons of the laterodorsal tegmental nucleus (LDT) are importantly involved in the development of addiction, however, the effects of nicotine on LDT neuronal excitability across ontogeny are unknown. Nicotinic effects on LDT cells across different age groups were examined using calcium imaging and whole-cell patch clamping. Within the youngest age group (P7-P15), nicotine induced larger intracellular calcium transients and inward currents. Nicotine induced a greater number of excitatory synaptic currents in the youngest animals, whereas larger amplitude inhibitory synaptic events were induced in cells from the oldest animals (P15-P34). Nicotine increased neuronal firing of cholinergic cells to a greater degree in younger animals, possibly linked to development associated differences found in nicotinic effects on action potential shape and afterhyperpolarization. We conclude that in addition to age-associated alterations of several properties expected to affect resting cell excitability, parameters affecting cell excitability are altered by nicotine differentially across ontogeny. Taken together, our data suggest that nicotine induces a larger excitatory response in cholinergic LDT neurons from the youngest animals, which could result in a greater excitatory output from these cells to target regions involved in development of addiction. Such output would be expected to be promotive of addiction; therefore, ontogenetic differences in nicotine-mediated increases in the excitability of the LDT could contribute to the differential susceptibility to nicotine addiction seen across age.
Clinical staging of patients with oral squamous cell carcinoma (OSCC) is crucial for the choice of treatment. Computed tomography (CT) and/or magnetic resonance imaging (MRI) are typically recommended and used for staging of the cervical lymph nodes (LNs). Although ultrasonography (US) is a non-expensive, accessible and non-ionising imaging modality this method is not consistently used. This study aimed to investigate if addition of US of patients classified as clinically LN negative (cN0) by CT and/or MRI, increases the detection of LN metastases. Also, we aimed to identify which of the sonographic characteristics: echogenicity, border, shape, appearance of hilum and nodal blood-flow pattern best detect metastases in this patient group.
The aim of this study was to evaluate the performance of strain elastography in an elasticity phantom and to assess which factors influenced visual scoring, strain histograms and strain ratios. Furthermore this study aimed to evaluate the effect of observer experience on visual scorings.
The Ankyrin and SOCS (Suppressor of Cytokine Signaling) box (ASB) family of proteins function as the substrate recognition subunit in a subset of Elongin-Cullin-SOCS (ECS) E3 ubiquitin ligases. Despite counting with 18 members in humans, the identity of the physiological targets of the Asb proteins remain largely unexplored. To increase our understanding of the ASB proteins function, we conducted a family-wide SILAC (Stable Isotope Labeling by Amino acids in Cell Culture)-based protein-protein interaction analysis. This investigation led to the identification of novel as well as known ASB associated proteins like Cullin 5, and Elongins B/C. We observed that several proteins can be bound by more than one Asb protein. The additional exploration of this phenomena demonstrated that ASB/Cullin 5 complexes can oligomerize and provide evidence that Cullin 5 forms heterodimeric complexes with the Cullin 4a/DDB1 complex. We also demonstrated that ASB11 is a novel ER associated ubiquitin ligase with the ability to interact and promote the ubiquitination of Ribophorin 1, an integral protein of the OST glycosylation complex. Moreover, expression of ASB11 can increase Ribophorin 1 protein turnover in vivo. In summary, we provide a comprehensive protein-protein interaction data resource that can aid the biological and functional characterization of ASB ubiquitin ligases.
BACKGROUND:An injury to the hamstring muscle complex is the most common injury in soccer. Ultrasound of acute hamstring injuries is often used as a clinical tool for diagnosing hamstring injuries and guiding players in when they can return to play. PURPOSE:To (1) investigate the characteristic sonographic findings of acute hamstring injuries in soccer players, (2) compare the mean injury severity (time to return to play) in injured players with and without sonographically verified abnormalities, and (3) correlate the length of the injured area and absence from soccer play (time to return to play) to investigate if ultrasonography can be used as a prognostic indicator of time to return to play. STUDY DESIGN:Case series; Level of evidence, 4. METHODS:Players from 50 teams participating in 1 of the top 5 Danish soccer divisions were followed in the period from January to December 2008. Of 67 players with acute hamstring injuries, 51 underwent ultrasonographic examination of the injured thigh and were included in this study. RESULTS:Ultrasonographic examinations were performed 1 to 10 days after injury (mean, 5.2 ± 3.0 days), and sonographic findings were present in 31 of 51 cases (61%). Two thirds of the injuries were to the biceps femoris muscle and one third to the semitendinosus muscle. No total ruptures were documented. The 51 acute hamstring injuries resulted in absence from soccer of a mean 25.4 ± 15.7 days per injury, with no significant difference between players with and without sonographically verified abnormalities (P = .41). No correlation existed between the length of the injured area and injury severity (r = 0.19, P = .29). CONCLUSION:The biceps femoris is the most commonly injured hamstring muscle detected by ultrasound, and more than half of the injuries are intramuscular. Because neither the presence of sonographic findings nor the size of the findings was correlated with time to return to play in injured soccer players, the prognosis of hamstring injuries should not be guided by these findings alone.
Organothiol self-assembled monolayers (SAMs) have garnered much interest as templates for oriented crystallization of biominerals. While, on the surface, SAM preparation appears to be straightforward, there are many subtleties that may yield films that lack the desired effect on the mineral component in subsequent use for templated mineralization. Herein, we discuss literature that uses organothiol SAMs to understand various principles in biomineralization, to motivate the following discussion of preparation procedures and pitfalls that may arise while working with SAMs. We provide a range of parameters for each element of a SAM-forming process, which have been shown in the literature to produce monolayers suitable for mineralization experiments, and close with a step-by-step procedure, based on findings in the cited literature, that yields functional SAMs with very high fidelity.
Self-assembled monolayers (SAMs) of organothiol molecules prepared on noble metal substrates are known to exert considerable influence over biomineral nucleation and growth and, as such, offer model templates for investigation of the processes of directed biomineralization. Identifying the structural evolution of SAM/crystal systems is essential for a more comprehensive understanding of the mechanisms by which organic monolayers mediate mineral growth. X-ray absorption spectroscopy (XAS) provides the attractive ability to study SAM structure at critical stages throughout the processes of crystallization in SAM/mineral systems. Here, we discuss important theoretical and experimental considerations for designing and implementing XAS studies of SAM/mineral systems.
In situ fluid cell TEM is a powerful new tool for understanding dynamic processes during liquid phase chemical reactions, including mineral formation. This technique, which operates in the high vacuum of a TEM chamber, provides information on crystal structure, phase, morphology, size, aggregation/segregation, and crystal growth mechanisms in real time. In situ TEM records both crystal structure and morphology at spatial resolutions down to the atomic level with high temporal resolution of up to 10(-6)s per image, giving it distinct advantages over other in situ techniques such as optical microscopy, AFM, or X-ray scattering or diffraction. This chapter addresses the design, fabrication, and assembly of TEM fluid cells and applications of fluid cell TEM to understanding mechanisms of mineralization.
Authentication of food is a major concern worldwide to ensure that food products are correctly labeled in terms of which animals are actually processed for consumption. Normally authentication is based on species recognition by comparison of selected sequences of DNA or protein. We here present a new robust, proteome-wide tandem mass spectrometry method for species recognition and food product authentication. The method does not use or require any genome sequences or selection of tandem mass spectra but uses all acquired data. The experimental steps were performed in a simple, standardized workflow including protein extraction, digestion, and data analysis. First, a set of reference spectral libraries was generated using unprocessed muscle tissue from 22 different fish species. Query tandem mass spectrometry data sets from "unknown" fresh muscle tissue samples were then searched against the reference libraries. The number of matching spectra could unambiguously identify the origin of all fresh samples. A number of processed samples were also analyzed to further test the robustness and applicability of the method. The results clearly show that the method is also able to correctly identify heavily processed samples.
Conventional ultrasound (US) methods for blood velocity estimation only provide one-dimensional and angle-dependent velocity estimates; thus, the complexity of cardiac flow has been difficult to measure. To circumvent these limitations, the Transverse Oscillation (TO) vector flow method has been proposed. The vector flow method implemented on a commercial scanner provided real-time, angle-independent estimates of cardiac blood flow. Epicardiac and epiaortic, intraoperative US examinations were performed on three patients with stenosed coronary arteries scheduled for bypass surgery. Repeating cyclic beat-to-beat flow patterns were seen in the ascending aorta and pulmonary artery of each patient, but these patterns varied between patients. Early systolic retrograde flow filling the aortic sinuses was seen in the ascending aorta as well as early systolic retrograde flow in the pulmonary artery. In diastole, stable vortices in aortic sinuses of the ascending aorta created central antegrade flow. A stable vortex in the right atrium was seen during the entire heart cycle. The measurements were compared with estimates obtained intraoperatively with conventional spectral Doppler US using a transesophageal and an epiaortic approach. Mean differences in peak systole velocity of 11% and 26% were observed when TO was compared with transesophageal echocardiography and epiaortic US, respectively. In one patient, the cardiac output derived from vector velocities was compared with pulmonary artery catheter thermodilution technique and showed a difference of 16%. Vector flow provides real-time, angle-independent vector velocities of cardiac blood flow. The technique can potentially reveal new information of cardiovascular physiology and give insight into blood flow dynamics.
The total lymph node yield in neck dissection is highly variable and depends on anatomical, surgical and pathological parameters. A minimum yield of six lymph nodes for a selective neck dissection (SND) as recommended in guidelines lies in the lower range of the reported clinical nodal yields. A future application of a lymph node ratio may improve the risk stratification of head and neck cancer patients. However, this will require a higher number of retrieved lymph nodes.
Centriolar satellites are small, granular structures that cluster around centrosomes, but whose biological function and regulation are poorly understood. We show that centriolar satellites undergo striking reorganization in response to cellular stresses such as UV radiation, heat shock, and transcription blocks, invoking acute and selective displacement of the factors AZI1/CEP131, PCM1, and CEP290 from this compartment triggered by activation of the stress-responsive kinase p38/MAPK14. We demonstrate that the E3 ubiquitin ligase MIB1 is a new component of centriolar satellites, which interacts with and ubiquitylates AZI1 and PCM1 and suppresses primary cilium formation. In response to cell stress, MIB1 is abruptly inactivated in a p38-independent manner, leading to loss of AZI1, PCM1, and CEP290 ubiquitylation and concomitant stimulation of ciliogenesis, even in proliferating cells. Collectively, our findings uncover a new two-pronged signalling response, which by coupling p38-dependent phosphorylation with MIB1-catalysed ubiquitylation of ciliogenesis-promoting factors plays an important role in controlling centriolar satellite status and key centrosomal functions in a cell stress-regulated manner.
Adductor-related groin pain and bony morphology such as femoroacetabular impingement (FAI) or hip dysplasia can coexist clinically. A previous randomised controlled trial in which athletes with adductor-related groin pain underwent either passive treatment (PT) or active treatment (AT) showed good results in the AT group. The primary purpose of the present study was to evaluate if radiological signs of FAI or hip dysplasia seem to affect the clinical outcome, initially and at 8-12 years of follow-up.
The aim of this study was to investigate the possibility of predicting the type and concentration level of astaxanthin coating of aquaculture feed pellets using multispectral image analysis. We used both natural and synthetic astaxanthin, and we used several different concentration levels of synthetic astaxanthin in combination with four different recipes of feed pellets. We used a VideometerLab with 20 spectral bands in the range of 385-1050 nm. We used linear discriminant analysis and sparse linear discriminant analysis for classification and variable selection. We used partial least squares regression (PLSR) for prediction of the concentration level. The results show that it is possible to predict the level of synthetic astaxanthin coating using PLSR on either the same recipe, or when calibrating on all recipes. The concentration prediction is adequate for screening for all recipes. Moreover, it shows that it is possible to predict the type of astaxanthin used in the coating using only ten spectral bands. Finally, the most selected spectral bands for astaxanthin prediction are in the visible range of the spectrum.
CD36 is a scavenger receptor involved in lipid uptake and inflammation. Recently, non-cell-bound CD36 (sCD36) was identified in plasma and suggested to be a marker of lipid accumulation in the vessel wall. Marine n-3 polyunsaturated fatty acids (PUFA) may have cardioprotective effects. This study evaluated the effect of marine n-3 PUFA on sCD36 levels in overweight subjects. Fifty overweight subjects were randomized to 1.1 g of n-3 PUFA or 2 g of olive oil daily for six weeks. Neutrophils were isolated at baseline and after six weeks of treatment while an adipose tissue biopsy was obtained at baseline. The content of n-3 PUFA in adipose tissue and neutrophils was analyzed by gas chromatography, while plasma levels of sCD36 were determined using an enzyme-linked immunosorbent assay (ELISA). After six weeks of supplement plasma sCD36 did not differ between supplements (P = 0.18). There was no significant correlation between plasma sCD36 levels and n-3 PUFA in neutrophils at baseline (r = -0.02, P = 0.88), after six weeks supplement (r = -0.03, P = 0.85) or in adipose tissue (r = 0.14, P = 0.34). This study therefore does not provide evidence for a cardioprotective effect of n-3 PUFA acting through a CD36-dependent mechanism.
We investigated the effect of full-thickness incisional wounding on expression of genes related to the immune system in larvae and juveniles of common carp (Cyprinus carpio). The wounds were inflicted by needle puncture immediately below the anterior part of the dorsal fin on days 7, 14, 28 and 49 after fertilization. We followed the local gene expression 1, 3 and 7days after wounding by removing head and viscera before extracting RNA from the remaining part of the fish, including the wound area. In addition, we visually followed wound healing. Overall the wounds had regenerated to a point where they were microscopically indistinguishable from normal tissue by day 3 post-wounding in all but the juvenile carp wounded on day 49 post-fertilization. In these juveniles the wounded area was still visible even 7days post-wounding. On the transcriptional level a very limited response was observed in the investigated genes as a result of the wounding. HSP70 was downregulated 1 and 3days post-wounding in the smallest larvae. However, HSP70 was differentially expressed at different time-points in a similar manner in wounded and mock-wounded groups, thus suggesting a stress effect of the handling, which may have overshadowed some transcriptional effects of the wounding. MMP-9, TGF-?1 and IgZ1 were slightly but significantly upregulated at few time-points, while no effect of wounding was detected on the expression of IgM, C3, IL-1? and IL-6 family member M17.
SCF (Skp1/Cul1/F-box) ubiquitin ligases act as master regulators of cellular homeostasis by targeting key proteins for ubiquitylation. Here, we identified a hitherto uncharacterized F-box protein, FBXO28 that controls MYC-dependent transcription by non-proteolytic ubiquitylation. SCF(FBXO28) activity and stability are regulated during the cell cycle by CDK1/2-mediated phosphorylation of FBXO28, which is required for its efficient ubiquitylation of MYC and downsteam enhancement of the MYC pathway. Depletion of FBXO28 or overexpression of an F-box mutant unable to support MYC ubiquitylation results in an impairment of MYC-driven transcription, transformation and tumourigenesis. Finally, in human breast cancer, high FBXO28 expression and phosphorylation are strong and independent predictors of poor outcome. In conclusion, our data suggest that SCF(FBXO28) plays an important role in transmitting CDK activity to MYC function during the cell cycle, emphasizing the CDK-FBXO28-MYC axis as a potential molecular drug target in MYC-driven cancers, including breast cancer.
Poly(ADP-ribos)ylation (PARylation) is a reversible posttranslational modification found in higher eukaryotes. However, little is known about PARylation acceptor proteins. Here, we describe a sensitive proteomics approach based on high-accuracy quantitative mass spectrometry for the identification of PARylated proteins induced under different cellular stress conditions. While confirming the majority of known PARylated substrates, our screen identifies numerous additional PARylation targets. In vivo and in vitro validation of acceptor proteins confirms that our methodology targets covalent PARylation. Nuclear proteins encompassing nucleic acid binding properties are prominently PARylated upon genotoxic stress, consistent with the nuclear localization of ARTD1/PARP1 and ARTD2/PARP2. Distinct differences in proteins becoming PARylated upon various genotoxic insults are observed, exemplified by the PARylation of RNA-processing factors THRAP3 and TAF15 under oxidative stress. High-content imaging reveals that PARylation affects the nuclear relocalization of THRAP3 and TAF15, demonstrating the potential of our approach to uncover hitherto unappreciated processes being controlled by specific genotoxic-stress-induced PARylation.
Transfer of a biosynthetic pathway between evolutionary distant organisms can create a metabolic shunt capable of bypassing the native regulation of the host organism, hereby improving the production of secondary metabolite precursor molecules for important natural products. Here, we report the engineering of Escherichia coli genes encoding the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway into the genome of Saccharomyces cerevisiae and the characterization of intermediate metabolites synthesized by the MEP pathway in yeast. Our UPLC-MS analysis of the MEP pathway metabolites from engineered yeast showed that the pathway is active until the synthesis of 2-C-methyl-D-erythritol-2,4-cyclodiphosphate, but appears to lack functionality of the last two steps of the MEP pathway, catalyzed by the [4Fe-4S] iron sulfur cluster proteins encoded by ispG and ispH. In order to functionalize the last two steps of the MEP pathway, we co-expressed the genes for the E. coli iron sulfur cluster (ISC) assembly machinery. By deleting ERG13, thereby incapacitating the mevalonate pathway, in conjunction with labeling experiments with U-¹³C? glucose and growth experiments, we found that the ISC assembly machinery was unable to functionalize ispG and ispH. However, we have found that leuC and leuD, encoding the heterodimeric iron-sulfur cluster protein, isopropylmalate isomerase, can complement the S. cerevisiae leu1 auxotrophy. To our knowledge, this is the first time a bacterial iron-sulfur cluster protein has been functionally expressed in the cytosol of S. cerevisiae under aerobic conditions and shows that S. cerevisiae has the capability to functionally express at least some bacterial iron-sulfur cluster proteins in its cytosol.
We report on monitoring the mode power in dielectric-loaded surface plasmon polariton waveguides (DLSPPWs) by measuring the resistance of gold electrodes, supporting the DLSPPW mode propagation, with internal (on-chip) Wheatstone bridges. The investigated DLSPPW configuration consisted of 1-?m-thick and 10-?m-wide cycloaliphatic acrylate polymer ridges tapered laterally to a 1-?m-wide ridge placed on a 50-nm-thin and 4-um wide gold stripe, all supported by a ~1.7-µm-thick Cytop layer deposited on a Si wafer. The fabricated DLSPPW power monitors were characterized at telecom wavelengths, showing very high responsivities reaching up to ~6.4 ?V/?W (for a bias voltage of 245 mV) and the operation bandwidth exceeding 40 kHz.
We demonstrate, both numerically and experimentally, that metal-insulator-metal configurations in which the top metal layer consists of a periodic arrangement of nanobricks, thus supporting gap-surface plasmon resonances, can be designed to function as reflective broadband half-wave plates. Using gold as the metal, the constructed wave plates in the near-infrared regime show scalability, bandwidth of ~20% of the design wavelength, and theoretical reflectivity above 85%, while a reflectivity of ~50% is experimentally measured.
The aim of our article is to give an overview of the current and future possibilities of real-time image fusion involving ultrasound. We present a review of the existing English-language peer-reviewed literature assessing this technique, which covers technical solutions (for ultrasound and endoscopic ultrasound), image fusion in several anatomic regions, and electromagnetic needle tracking.
The response to tissue damage is a complex process, which involves the coordinated regulation of multiple proteins to ensure tissue repair. In order to investigate the effect of tissue damage in a lower vertebrate, samples were taken from rainbow trout (Oncorhynchus mykiss) at day 7 after damage and proteins were separated using 2DE. The experimental design included two groups of rainbow trout, which were fed organic feed either with or without astaxanthin. In total, 96 proteins were found to be affected by tissue damage, clearly demonstrating in this lower vertebrate the complexity and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes such as apoptosis, iron homeostasis, and regulation of muscular structure. Interestingly, it was established that exclusively within the astaxanthin feed group, three members of the annexin protein family (annexin IV, V, and VI) were regulated in response to tissue damage.
Long-standing symphyseal and adductor-related groin pain is a common problem for many athletes, and requires a multidisciplinary approach. Radiological evaluation of symptomatic individuals is a cornerstone in the diagnostic workup, and should be based on precise and reliable diagnostic terms and imaging techniques. The authors performed a review of the existing original evidence-based radiological literature involving radiography, ultrasonography and MRI in athletes with long-standing symphyseal and adductor-related groin pain. Our search yielded 17 original articles, of which 12 were dedicated to MRI, four to radiography and one to ultrasonography. Four main radiological findings seem to consistently appear: degenerative changes at the pubic symphyseal joint, pathology at the adductor muscle insertions, pubic bone marrow oedema and the secondary cleft sign. However, the existing diagnostic terminology is confusing, and the interpretation of radiological findings would benefit from imaging studies using a more systematic approach.
We demonstrate that metal-insulator-metal configurations, with the top metal layer consisting of a periodic arrangement of differently sized nanobricks, can be designed to function as broadband focusing flat mirrors. Using 50-nm-high gold nanobricks arranged in a 240-nm-period lattice on the top of a 50-nm-thick layer of silicon dioxide deposited on a continuous 100-nm-thick gold film, we realize a 17.3 × 17.3 ?m(2) flat mirror that efficiently reflects (experiment: 14-27%; theory: 50-78%) and focuses a linearly polarized (along the direction of nanobrick size variation) incident beam in the plane of its polarization with the focal length, which changes from ~15 to 11 ?m when tuning the light wavelength from 750 to 950 nm, respectively. Our approach can easily be extended to realize the radiation focusing in two dimensions as well as other optical functionalities by suitably controlling the phase distribution of reflected light.
Hypercoagulability evaluated with thrombelastography (TEG) has been reported to be associated to thrombembolic events in patients undergoing coronary artery bypass graft surgery (CABG). The objective of this study was to test the hypothesis that graft patency and post-CABG thrombembolic events are related to the pre-surgical TEG status.
The primary aim of the study was to evaluate the association between adipose tissue arachidonic acid (AA) content and the risk of myocardial infarction (MI). The secondary aim was to assess the correlation between adipose tissue AA and dietary intake of AA and linoleic acid (LA).
Nucleosomes are decorated with numerous post-translational modifications capable of influencing many DNA processes. Here we describe a new class of histone modification, methylation of glutamine, occurring on yeast histone H2A at position 105 (Q105) and human H2A at Q104. We identify Nop1 as the methyltransferase in yeast and demonstrate that fibrillarin is the orthologue enzyme in human cells. Glutamine methylation of H2A is restricted to the nucleolus. Global analysis in yeast, using an H2AQ105me-specific antibody, shows that this modification is exclusively enriched over the 35S ribosomal DNA transcriptional unit. We show that the Q105 residue is part of the binding site for the histone chaperone FACT (facilitator of chromatin transcription) complex. Methylation of Q105 or its substitution to alanine disrupts binding to FACT in vitro. A yeast strain mutated at Q105 shows reduced histone incorporation and increased transcription at the ribosomal DNA locus. These features are phenocopied by mutations in FACT complex components. Together these data identify glutamine methylation of H2A as the first histone epigenetic mark dedicated to a specific RNA polymerase and define its function as a regulator of FACT interaction with nucleosomes.
BACKGROUND: Non-operative treatment of acute hip adductor longus ruptures in athletes has been described in the literature. However, very limited information concerning the recovery of this type of injury exists. This case represented a unique possibility to study the recovery of two acute adductor longus ruptures, using novel, reliable and validated assessment methods. CASE PRESENTATION: A 22-year old male soccer player (Caucasian) sustained two subsequent acute adductor longus ruptures, one in each leg. The injuries occurred 10 months apart, and were treated non-surgically in both situations. He was evaluated using hip-strength assessments, self-report and ultrasonography until complete muscle-strength recovery of the hip adductors had occurred. The player was able to participate in a full soccer training session without experiencing pain 15 weeks after the first rupture, and 12 weeks after the second rupture. Full hip adductor muscle-strength recovery was obtained 52 weeks after the first rupture and 10 weeks after the second rupture. The adductor longus injuries, as verified by initial ultrasonography (10 days post-injury), showed evidence of a complete tendon rupture in both cases, with an almost identical imaging appearance. It was only at 6 and 10 weeks ultrasonographic follow-up that the first rupture was found to include a larger anatomical area than the second rupture. CONCLUSION: From this case we can conclude that two apparently similar hip adductor longus ruptures, verified by initial ultrasonography (10 days post-injury), can have very different hip adductor strength recovery times. Assessment of adductor strength recovery may therefore in the future be a useful and important additional measure for determining when soccer players with hip adductor longus ruptures can return safely to play.
The content of arachidonic acid in adipose tissue is positively associated with the risk of myocardial infarction, whereas the content of eicosapentaenoic acid in adipose tissue has been reported to be negatively associated with the risk of myocardial infarction. Both arachidonic acid and eicosapentaenoic acid are substrates for the synthesis of pro-inflammatory leukotrienes and leukotrienes derived from eicosapentaenoic acid are generally much less potent. In this study we hypothesized that a high content of arachidonic acid in adipose tissue would reflect a high formation of arachidonic acid derived leukotrienes and a high expression of 5-lipoxygenase in atherosclerotic plaques. Likewise, we hypothesized that a high content of eicosapentaenoic acid in adipose tissue would reflect a low formation of arachidonic acid derived leukotrienes and a low expression of 5-lipoxygenase in plaques.
Formation of biominerals commonly occurs within the context of an organic matrix composed of proteins, polysaccharides, and other macromolecules. Much has been learned about the structure of matrices and the spatial and molecular relationships between matrix and mineral. Only recently has quantitative study of matrix organization and subsequent mineralization been pursued. Here, we review findings from physical studies of matrix assembly in the system of microbial S-layer proteins and of calcium carbonate nucleation on organic templates composed of organothiol self-assembled monolayers on noble metals. Studies on S-layers reveal the importance of multistage assembly pathways and kinetic traps associated with the conformational transformations required to build the basic oligomeric building blocks of the matrix. Experimental investigations of calcium carbonate nucleation on carboxyl-terminated self-assembled monolayers combined with theoretical analyses demonstrate the applicability of classical concepts of nucleation, even when cluster-aggregation pathways are considered, and reveal the underlying energetic and structural source of matrix control over the process. Taken together, these studies highlight the ways in which matrix assembly and mineralization deviate from our classical concepts of crystallization but clearly demonstrate that the concepts of physical chemistry that date back to the days of Gibbs and Ostwald still serve us well in understanding the nucleation and growth of organic matrices and mineral phases.
The attachment of one or more ubiquitin moieties to proteins plays a central regulatory mechanism in eukaryotic cells. Protein ubiquitylation regulates numerous cellular processes, including protein degradation, signal transduction, DNA repair and cell division. The characterization of ubiquitylation is a two-fold challenge that involves the mapping of ubiquitylation sites and the determination of ubiquitin chain topology. This review focuses on the technical advances in the mass spectrometry-based characterization of ubiquitylation sites, which have recently involved the large-scale identification of ubiquitylation sites by peptide-level enrichment strategies. The discovery that ubiquitylation is a widespread modification similar to phosphorylation and acetylation suggests cross-talk may also occur at the post translational modification level.
Polycystic ovary syndrome (PCOS), the most common endocrine disease among premenopausal women, is caused by both genes and environment. We and others previously reported association between single nucleotide polymorphisms (SNPs) in the DENND1A gene and PCOS. We therefore sequenced the DENND1A gene in white patients with PCOS to identify possible alterations that may be implicated in the PCOS pathogenesis. Patients were referred with PCOS and/or hirsutism between 1998 and 2011 (n = 261). PCOS was diagnosed according to the Rotterdam criteria (n = 165). Sequence analysis was performed in 10 patients with PCOS. Additional patients (n = 251) and healthy female controls (n = 248) were included for SNP genotyping. Patients underwent clinical examination including Ferriman-Gallwey score (FG-score), biochemical analyses and transvaginal ultrasound. Mutation analysis was carried out by bidirectional sequencing. SNP genotyping was tested by allelic discrimination in real-time PCR in the additional patients and controls. Sequencing of the DENND1A gene identified eight SNPs; seven were not known to be associated with any diseases. One missense SNP was detected (rs189947178, A/C), potentially altering the structural conformation of the DENND1A protein. SNP genotyping of rs189947178 showed significantly more carriers among patients with PCOS and moderate hirsutism compared to controls. However, due to small sample size and lack of multiple regression analysis supporting an association between rs189947178 and FG-score or PCOS diagnosis, this could be a false positive finding. In conclusion, sequence analysis of the DENND1A gene of patients with PCOS did not identify alterations that alone could be responsible for the PCOS pathogenesis, but a missense SNP (rs189947178) was identified in one patient and significantly more carriers of rs189947178 were found among patients with PCOS and moderate hirsutism vs. controls. Additional studies with independent cohort are needed to confirm this due to the small sample size of this study.
ATAF1, an Arabidopsis thaliana NAC transcription factor, plays important roles in plant adaptation to environmental stress and development. To search for ATAF1 target genes, we used protein binding microarrays and chromatin-immunoprecipitation (ChIP). This identified T[A,C,G]CGT[A,G] and TT[A,C,G]CGT as ATAF1 consensus binding sequences. Co-expression analysis across publicly available microarray experiments identified 25 genes co-expressed with ATAF1. The promoter regions of ATAF1 co-expressors were significantly enriched for ATAF1 binding sites, and TTGCGTA was identified in the promoter of the key abscisic acid (ABA) phytohormone biosynthetic gene NCED3. ChIP-qPCR and expression analysis showed that ATAF1 binding to the NCED3 promoter correlated with increased NCED3 expression and ABA hormone levels. These results indicate that ATAF1 regulates ABA biosynthesis.
We propose and investigate theoretically and experimentally L-shaped gap surface plasmon waveguides (L-GSPWs) formed by a dielectric film (strip) partially enclosed between two metal films. The proposed L-GSPWs combine the benefits of strong plasmon localization in a nanogap, significant propagation distance, low cross-talk between two neighboring waveguides, high transmission through a sharp 90° bend, and simplicity of fabrication by means of the standard lithography combined with the thin film deposition.
Fast and accurate work-up is crucial to ensure the best possible treatment and prognosis for patients with head and neck cancer. The presence or absence of neck lymph node metastases is important for the prognosis and the choice of treatment. Clinical lymph node (N)-staging is done by palpation and diagnostic imaging of the neck. We investigated the current practice of the initial radiological work-up of patients with oral squamous cell carcinomas (OSCC) in the Nordic countries.
We report on the realization of long-range dielectric-loaded surface plasmon polariton waveguides (LR-DLSPPWs) consisting of straight and bent subwavelength dielectric ridges deposited on thin and narrow metal stripes supported by a dielectric buffer layer covering a low-index substrate. Using imaging with a near-field optical microscope and end-fire coupling with a tapered fiber connected to a tunable laser at telecommunication wavelengths (1425-1545?nm), we demonstrate low-loss (propagation length ?500??m) and well-confined (mode width ?1??m) LR-DLSPPW mode guiding and determine the propagation and bend loss.
We demonstrate both theoretically and experimentally that a gold nanostrip supported by a thin dielectric (silicon dioxide) film and a gold underlay forms an efficient (Fabry-Perot) resonator for gap surface plasmons. Periodic nanostrip arrays are shown to exhibit strong and narrow resonances with nearly complete absorption and quality factors of ~15-20 in the near-infrared. Two-photon luminescence microscopy measurements reveal intensity enhancement factors of ~120 in the 400-nm-period array of 85-nm-wide gold strips atop a 23-nm-thick silica film at the resonance wavelength of ~770 nm. Excellent resonant characteristics, the simplicity of tuning the resonance wavelength by adjusting the nanostrip width and/or the dielectric film thickness and the ease of fabrication with (only) one lithography step required make the considered plasmonic configuration very attractive for a wide variety of applications, ranging from surface sensing to photovoltaics.
Post-translational modification of proteins by ubiquitin is a fundamentally important regulatory mechanism. However, proteome-wide analysis of endogenous ubiquitylation remains a challenging task, and almost always has relied on cells expressing affinity tagged ubiquitin. Here we combine single-step immunoenrichment of ubiquitylated peptides with peptide fractionation and high-resolution mass spectrometry to investigate endogenous ubiquitylation sites. We precisely map 11,054 endogenous putative ubiquitylation sites (diglycine-modified lysines) on 4,273 human proteins. The presented data set covers 67% of the known ubiquitylation sites and contains 10,254 novel sites on proteins with diverse cellular functions including cell signaling, receptor endocytosis, DNA replication, DNA damage repair, and cell cycle progression. Our method enables site-specific quantification of ubiquitylation in response to cellular perturbations and is applicable to any cell type or tissue. Global quantification of ubiquitylation in cells treated with the proteasome inhibitor MG-132 discovers sites that are involved in proteasomal degradation, and suggests a nonproteasomal function for almost half of all sites. Surprisingly, ubiquitylation of about 15% of sites decreased more than twofold within four hours of MG-132 treatment, showing that inhibition of proteasomal function can dramatically reduce ubiquitylation on many sites with non-proteasomal functions. Comparison of ubiquitylation sites with acetylation sites reveals an extensive overlap between the lysine residues targeted by these two modifications. However, the crosstalk between these two post-translational modifications is significantly less frequent on sites that show increased ubiquitylation upon proteasome inhibition. Taken together, we report the largest site-specific ubiquitylation dataset in human cells, and for the first time demonstrate proteome-wide, site-specific quantification of endogenous putative ubiquitylation sites.
Fungi possess an advanced secondary metabolism that is regulated and coordinated in a complex manner depending on environmental challenges. To understand this complexity, a holistic approach is necessary. We initiated such an analysis in the important model fungus Aspergillus nidulans by systematically deleting all 32 individual genes encoding polyketide synthases. Wild-type and all mutant strains were challenged on different complex media to provoke induction of the secondary metabolism. Screening of the mutant library revealed direct genetic links to two austinol meroterpenoids and expanded the current understanding of the biosynthetic pathways leading to arugosins and violaceols. We expect that the library will be an important resource towards a systemic understanding of polyketide production in A. nidulans.
The left internal thoracic artery (LITA) undergoes vascular remodelling when used for coronary artery bypass grafting. In this study we tested the hypothesis that the extent of the LITA remodelling late after coronary artery bypass grafting assessed by multidetector computed tomography is related to the severity of stenosis in the native coronary vessel. One hundred and forty-two patients who had undergone coronary artery bypass grafting including implantation of LITA as conduit to the left anterior descending artery were studied 5 years after surgery. Arterial graft patency and geometry was assessed with 64-slice multidetector computed tomography. Quantitative volumetric assessment of the LITA was performed to measure the average vessel lumen area (mm(2)/m(2)). The native coronary vessel subtended by the LITA was evaluated by multidetector computed tomography and defined as a high-grade stenosis patient group, when the diameter stenosis was >70% and an intermediate grade stenosis patient group when <70%. Among patients with intermediate-grade stenosis of the native vessel 11 out of 65 patients (17%) had a totally occluded LITA, as opposed to none among the 77 patients with a high-grade stenosis. In patients with intermediate-grade stenosis of the proximal native vessel, the LITA lumen area was 4.9 compared to 5.3 mm(2)/m(2) in patients with a high-grade stenosis of the proximal native vessel (P = 0.0043). Lumen area of the LITA when used as a conduit in patients with coronary artery disease seems to be inversely correlated with the severity of disease in the native coronary vessel proximal to the anastomosis. Volumetric vessel multidetector computed tomography appears to be useful for evaluation of coronary bypass remodelling.
The purpose of this study is to show whether a newly introduced vector flow method is equal to conventional spectral estimation. Thirty-two common carotid arteries of 16 healthy volunteers were scanned using a BK Medical ProFocus scanner (DK-2730, Herlev, Denmark) and a linear transducer at 5 MHz. A triplex imaging sequence yields both the conventional velocity spectrum and a two-dimensional vector velocity image. Several clinical parameters were estimated and compared for the two methods: Flow angle, peak systole velocity (PS), end diastole velocity (ED) and resistive index (RI). With a paired t-test, the spectral and vector angles did not differ significantly (p = 0.658), whereas PS (p = 0.034), ED (p = 0.004) and RI (p < 0.0001) differed significantly. Vector flow can measure the angle for spectral angle correction, thus eliminating the bias from the radiologist performing the angle setting with spectral estimation. The flow angle limitation in velocity estimation is also eliminated, so that flow at any angle can be measured.
Growth Hormone is essential for the regulation of growth and the homeostatic control of intermediary metabolism. GH actions are mediated by the Growth Hormone Receptor; a member of the cytokine receptor super family that signals chiefly through the JAK2/STAT5 pathway. Target tissue responsiveness to GH is under regulatory control to avoid excessive and off-target effects upon GHR activation. The suppressor of cytokine signalling 2 (SOCS) is a key regulator of GHR sensitivity. This is clearly shown in mice where the SOCS2 gene has been inactivated, which show 30-40% increase in body length, a phenotype that is dependent on endogenous GH secretion. SOCS2 is a GH-stimulated, STAT5b-regulated gene that acts in a negative feedback loop to downregulate GHR signalling. Since the biochemical basis for these actions is poorly understood, we studied the molecular function of SOCS2. We demonstrated that SOCS2 is part of a multimeric complex with intrinsic ubiquitin ligase activity. Mutational analysis shows that the interaction with Elongin B/C controls SOCS2 protein turnover and affects its molecular activity. Increased GHR levels were observed in livers from SOCS2?/? mice and in the absence of SOCS2 in in vitro experiments. We showed that SOCS2 regulates cellular GHR levels through direct ubiquitination and in a proteasomally dependent manner. We also confirmed the importance of the SOCS-box for the proper function of SOCS2. Finally, we identified two phosphotyrosine residues in the GHR to be responsible for the interaction with SOCS2, but only Y487 to account for the effects of SOCS2. The demonstration that SOCS2 is an ubiquitin ligase for the GHR unveils the molecular basis for its physiological actions.
When producing aquaculture fish feed pellets, the size of the output product is of immense importance. As the production method cannot produce pellets of constant and uniform size using constant machine settings, there is a demand for size control. Fish fed with feed pellets of improper size are prone to not grow as expected, which is undesirable to the aquaculture industry. In this paper an image analysis method is proposed for automatic size-monitoring of pellets. This is called granulometry and the method used here is based on the mathematical morphological opening operation. In the proposed method, no image object segmentation is needed. The results show that it is possible to extract a general size distribution from an image of piled disordered pellets representing both length and diameter of the pellets in combination as an area.
We demonstrate that a pair of perpendicular electrical dipolar scatterers resonating at different frequencies can be used as a metamaterial unit cell to construct a nanometer-thin retarder in reflection, designing nanocross and nanobrick plasmonic configurations to function as reflecting quarter-wave plates at ~1520 and 770 nm, respectively. The design is corroborated experimentally with a monolayer of gold nanobricks, transforming linearly polarized incident radiation into circularly polarized radiation at ~780 nm.
The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
The imaging modalities computed tomography (CT) and the ultrasonography (US) examination focused assessment with sonography for trauma (FAST) in relation to damage control in traumas are discussed. CT has the advantage of high sensitivity and specificity for detection of organ specific lesions. FAST ultrasound is a good screening tool for intraperitoneal bleeding, but the sensitivity and specificity is lower than by CT. We recommend FAST-US prehospitally or early in the trauma room resuscitation. Haemodynamically stable patients with relevant traumas should undergo CT.
A recent paper in Science by Li et al. 2011(1) reports widespread sequence differences in the human transcriptome between RNAs and their encoding genes termed RNA-DNA differences (RDDs). The findings could add a new layer of complexity to gene expression but the study has been criticized.
Related JoVE Video
Journal of Visualized Experiments
What is Visualize?
JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.
How does it work?
We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.
Video X seems to be unrelated to Abstract Y...
In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.