Genomic Pathogen Typing Using Solid-State Nanopores

In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based “fingerprints” of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.     

High-Bandwidth Protein Analysis Using Solid-State Nanopores

High-bandwidth measurements of the ion current through hafnium oxide and silicon nitride nanopores allow the analysis of sub-30 kD protein molecules with unprecedented time resolution and detection efficiency. Measured capture rates suggest that at moderate transmembrane bias values, a substantial fraction of protein translocation events are detected. Our dwell-time resolution of 2.5 μs enables translocation time distributions to be fit to a first-passage time distribution derived from a 1D diffusion-drift model. The fits yield drift velocities that scale linearly with voltage, consistent with an electrophoretic process. Further, protein diffusion constants (D) are lower than the bulk diffusion constants (D₀) by a factor of ∼50, and are voltage-independent in the regime tested. We reason that deviations of D from D₀ are a result of confinement-driven pore/protein interactions, previously observed in porous systems. A straightforward Kramers model for this inhibited diffusion points to 9- to 12-kJ/mol interactions of the proteins with the nanopore. Reduction of μ and D are found to be material-dependent. Comparison of current-blockage levels of each protein yields volumetric information for the two proteins that is in good agreement with dynamic light scattering measurements. Finally, detection of a protein-protein complex is achieved.     

High-Bandwidth Protein Analysis Using Solid-State Nanopores

High-bandwidth measurements of the ion current through hafnium oxide and silicon nitride nanopores allow the analysis of sub-30 kD protein molecules with unprecedented time resolution and detection efficiency. Measured capture rates suggest that at moderate transmembrane bias values, a substantial fraction of protein translocation events are detected. Our dwell-time resolution of 2.5 μs enables translocation time distributions to be fit to a first-passage time distribution derived from a 1D diffusion-drift model. The fits yield drift velocities that scale linearly with voltage, consistent with an electrophoretic process. Further, protein diffusion constants (D) are lower than the bulk diffusion constants (D₀) by a factor of ∼50, and are voltage-independent in the regime tested. We reason that deviations of D from D₀ are a result of confinement-driven pore/protein interactions, previously observed in porous systems. A straightforward Kramers model for this inhibited diffusion points to 9- to 12-kJ/mol interactions of the proteins with the nanopore. Reduction of μ and D are found to be material-dependent. Comparison of current-blockage levels of each protein yields volumetric information for the two proteins that is in good agreement with dynamic light scattering measurements. Finally, detection of a protein-protein complex is achieved.     

Chain Assembly and Disassembly Processes Differently Affect the Conformational Space of Ubiquitin Chains

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Using Protein Motion to Read,Write, and Erase Ubiquitin Signals

Eukaryotes use a tiny protein called ubiquitin to send a variety of signals, most often by post-translationally attaching ubiquitins to substrate proteins and to each other, thereby forming polyubiquitin chains. A combination of biophysical, biochemical, and biological studies has shown that complex macromolecular dynamics are central to many aspects of ubiquitin signaling. This review focuses on how equilibrium fluctuations and coordinated motions of ubiquitin itself, the ubiquitin conjugation machinery, and deubiquitinating enzymes enable activity and regulation on many levels, with implications for how such a tiny protein can send so many signals.     

Taste Discrimination Using Alternative Solvents for PTC and NaCl

Better discrimination was possible between threshold PTC solutionsand pure solvent when the solvent was a tasteless, low concentrationNaCl solution to which the subject had adapted, than when thesolvent was purified water. The reverse was true for thresholdNaCl stimuli. Subjective reports indicated this to be due tothe absence or presence of taste cues from the solvent and stimulusafter-effects. Interstimulus rinsing with the appropriate solventimproved discrimination. Chem. Senses 20: 299–304, 1995.     

Discrimination of Six Pratylenchus Species Using PCR and Species-Specific Primers

A PCR-based assay for identification of six species of Pratylenchus common in California is described. In this assay, five forward species-specific primers were designed from the internal variable portion of the D3 expansion region of the 26S rDNA and were each used with a single, common reverse primer. The optimized species-specific primers produced unique amplicons from their respective target and did not amplify DNA from other Pratylenchus species. With this assay we were able to identify single females to species level. This method obviates the need for subsequent RFLP or sequence analysis of the PCR product and can be used as a rapid diagnostic tool in epidemiological and management studies.     

Sensitivity and Specificity of Cardiac Tissue Discrimination Using Fiber-Optics Confocal Microscopy

Disturbances of the cardiac conduction system constitute a major risk after surgical repair of complex cases of congenital heart disease. Intraoperative identification of the conduction system may reduce the incidence of these disturbances. We previously developed an approach to identify cardiac tissue types using fiber-optics confocal microscopy and extracellular fluorophores. Here, we applied this approach to investigate sensitivity and specificity of human and automated classification in discriminating images of atrial working myocardium and specialized tissue of the conduction system. Two-dimensional image sequences from atrial working myocardium and nodal tissue of isolated perfused rodent hearts were acquired using a fiber-optics confocal microscope (Leica FCM1000). We compared two methods for local application of extracellular fluorophores: topical via pipette and with a dye carrier. Eight blinded examiners evaluated 162 randomly selected images of atrial working myocardium (n = 81) and nodal tissue (n = 81). In addition, we evaluated the images using automated classification. Blinded examiners achieved a sensitivity and specificity of 99.2±0.3% and 98.0±0.7%, respectively, with the dye carrier method of dye application. Sensitivity and specificity was similar for dye application via a pipette (99.2±0.3% and 94.0±2.4%, respectively). Sensitivity and specificity for automated methods of tissue discrimination were similarly high. Human and automated classification achieved high sensitivity and specificity in discriminating atrial working myocardium and nodal tissue. We suggest that our findings facilitate clinical translation of fiber-optics confocal microscopy as an intraoperative imaging modality to reduce the incidence of conduction disturbances during surgical correction of congenital heart disease.     

Discrimination Between Paraffin-Embedded and Frozen Skin Sections Using Synchrotron Infrared Microspectroscopy

The difference between paraffin-embedded and frozen skin sections is always questionable. Ten patients of early stage mycosis fungoides, ten patients with psoriasis and ten normal controls were included in this study. Aim of this study is to differentiate between paraffin-embedded and frozen skin sections in inflammatory and malignant dermatoses using synchrotron infrared microspectroscopy (SIRM). It was found that epidermal beta sheets in paraffin-embedded sections were higher in a highly significant manner than frozen sections (P < 0.001). Also, epidermal nucleic acids in paraffin-embedded sections were lower in a highly significant manner than frozen sections (P < 0.001). However, when various skin diseases were compared with the control. It was found that the difference between paraffin-embedded and frozen skin sections were almost similar. In conclusion SIRM is a unique promising diagnostic technique and it seems that frozen processing preserve skin tissue more, this was represented by less apoptosis (beta sheets) and more nucleic acids than paraffin processing. However, there are still many advantages of both approaches over the other depending on the goal of the study.     

Calcium Sensing Receptor Absence Delays Postnatal Brain Development via Direct and Indirect Mechanisms

Calcium sensing receptor (CaSR) is implicated in the establishment of neural connections and myelin formation. However, its contribution to brain development remains unclear. We addressed this issue by analyzing brain phenotype in postnatal CaSR null mice, a model of human neonatal severe hyperparathyroidism. One- and 2-week-old CaSR null mice exhibited decreased brain weight and size with a developmental delay in expression of proliferating cell nuclear antigen. Neuronal and glial differentiation markers, neuronal specific nuclear protein, glial fibrillary acidic protein, and myelin basic protein, were also decreased compared with age-matched wild-type littermates. Moreover, deletion of the parathyroid hormone gene that corrects hyperparathyroidism, hypercalcemia, hypophosphatemia, and whole-body growth retardation normalized brain cell proliferation, but not differentiation, in CaSR null mice. Cultured neural stem cells (NSCs) derived from the subventricular zones of CaSR null neonatal mice exhibited normal proliferation capacity but decreased differentiation capacity, compared with wild-type controls. These results demonstrate that direct effects of CaSR absence impair NSC differentiation, while secondary effects of parathyroid hormone-related endocrine abnormalities impair NSC proliferation, both of which contribute to delayed brain development in CaSR null newborn mice.     

Perceived Racial Discrimination in the Workplace and Body Weight among the Unemployed

This study investigates the association between body weight and the likelihood that people perceive that they have been the victims of racial discrimination in the workplace among the unemployed. I find that unemployed obese men and women are 8.4 percentage points and 7.7 percentage points, respectively, more likely to have experienced racial discrimination before becoming unemployed than their non-obese counterparts. For unemployed men, the relationship between body weight and perceived racial discrimination does not seem to be associated with race. For unemployed women, being black and obese significantly increases the likelihood of perceiving racial discrimination.     

Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code

The nature of the neural codes for pitch and loudness, two basic auditory attributes, has been a key question in neuroscience for over century. A currently widespread view is that sound intensity (subjectively, loudness) is encoded in spike rates, whereas sound frequency (subjectively, pitch) is encoded in precise spike timing. Here, using information-theoretic analyses, we show that the spike rates of a population of virtual neural units with frequency-tuning and spike-count correlation characteristics similar to those measured in the primary auditory cortex of primates, contain sufficient statistical information to account for the smallest frequency-discrimination thresholds measured in human listeners. The same population, and the same spike-rate code, can also account for the intensity-discrimination thresholds of humans. These results demonstrate the viability of a unified rate-based cortical population code for both sound frequency (pitch) and sound intensity (loudness), and thus suggest a resolution to a long-standing puzzle in auditory neuroscience.     

Quantification and Size-profiling of Extracellular Vesicles Using Tunable Resistive Pulse Sensing

Extracellular vesicles (EVs), including ‘microvesicles’ and ‘exosomes’, are highly abundant in bodily fluids. Recent years have witnessed a tremendous increase in interest in EVs. EVs have been shown to play important roles in various physiological and pathological processes, including coagulation, immune responses, and cancer. In addition, EVs have potential as therapeutic agents, for instance as drug delivery vehicles or as regenerative medicine. Because of their small size (50 to 1,000 nm) accurate quantification and size profiling of EVs is technically challenging.This protocol describes how tunable resistive pulse sensing (tRPS) technology, using the qNano system, can be used to determine the concentration and size of EVs. The method, which relies on the detection of EVs upon their transfer through a nano sized pore, is relatively fast, suffices the use of small sample volumes and does not require the purification and concentration of EVs. Next to the regular operation protocol an alternative approach is described using samples spiked with polystyrene beads of known size and concentration. This real-time calibration technique can be used to overcome technical hurdles encountered when measuring EVs directly in biological fluids.     

Discrimination of American Cranberry Cultivars and Assessment of Clonal Heterogeneity Using Microsatellite Markers

Cranberries (Vaccinium macrocarpon Ait.) are an economically important fruit crop derived from a North American native species. We report the application of 12 simple sequence repeats (SSR) or microsatellite markers to assess the genetic diversity of cranberry cultivars. We studied 164 samples of 21 different cranberry cultivars, 11 experimental hybrids, and 6 representative accessions of wild species. Genetic cluster analysis, based on 117 SSR alleles, differentiated the major cranberry cultivars. However, some cranberry cultivar subclone variants and mislabeled samples were observed. Consensus genetic profiles identified the most likely clonal representatives of several important cranberry cultivars (e.g., “Ben Lear,” “Howes,” and “Stevens”). The markers were further used to confirm putative parents of several hybrid progenies. The long-term goal of our studies is to identify, preserve, and utilize unique genetic materials to breed improved cranberries. Attaining this goal will help growers maintain sustainability under changing economic and environmental conditions.     

Single-Base-Pair Discrimination of Terminal Mismatches by Using Oligonucleotide Microarrays and Neural Network Analyses

The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T_d) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5′ terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T_d and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T_d and signal intensity, and it decreased the variability of the signal. Although T_ds of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T_ds than those with mismatches in the first or second position. The trained NNs predicted the T_d with high accuracies (R² = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R² = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T_ds, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5′ terminus plays a greater role in determining the T_d and signal intensity of duplexes than the type of mismatch.     

Colorimetric and Fiber Optic Sensing of Cysteine Using Green Synthesized Gold Nanoparticles

Plasmonics - In the present study, simple green synthesis of stable gold nanoparticles (green AuNPs) in an aqueous medium using flower extract of Acmella oleracea is reported. In addition,...     

Discrimination of Unrewarding Flowers by Bees; Direct Detection of Rewards and Use of Repellent Scent Marks

Bumblebees and honeybees deposit short-lived scent marks on flowers that they visit when foraging. Conspecifics use these marks to distinguish those flowers that have recently been emptied and, so, avoid them. The aim of this study was to assess how widespread this behavior is. Evidence for direct detection of reward levels was found in two bee species: Agapostemon nasutus was able to detect directly pollen availability in flowers with exposed anthers, while Apis mellifera appeared to be able to detect nectar levels of tubular flowers. A third species, Trigona fulviventris, avoided flowers that had recently been visited by conspecifies, regardless of reward levels, probably by using scent marks. Three further bee/flower systems were examined in which there was no detectable discrimination among flowers. We argue that bees probably rely on direct detection of rewards where this is allowed by the structure of the flower and on scent marks when feeding on flowers where the rewards are hidden. However, discrimination does not always occur. We suggest that discrimination may not always make economic sense; when visiting flowers with a low handling time, or flowers that are scarce, it may be more efficient to visit every flower that is encountered.     

HTLV-1 Tax Stimulates Ubiquitin E3 Ligase,Ring Finger Protein 8, to Assemble Lysine 63-Linked Polyubiquitin Chains for TAK1 and IKK Activation

Human T lymphotropic virus type 1 (HTLV-1) trans-activator/oncoprotein, Tax, impacts a multitude of cellular processes, including I-κB kinase (IKK)/NF-κB signaling, DNA damage repair, and mitosis. These activities of Tax have been implicated in the development of adult T-cell leukemia (ATL) in HTLV-1-infected individuals, but the underlying mechanisms remain obscure. IKK and its upstream kinase, TGFβ-activated kinase 1 (TAK1), contain ubiquitin-binding subunits, NEMO and TAB2/3 respectively, which interact with K63-linked polyubiquitin (K63-pUb) chains. Recruitment to K63-pUb allows cross auto-phosphorylation and activation of TAK1 to occur, followed by TAK1-catalyzed IKK phosphorylation and activation. Using cytosolic extracts of HeLa and Jurkat T cells supplemented with purified proteins we have identified ubiquitin E3 ligase, ring finger protein 8 (RNF8), and E2 conjugating enzymes, Ubc13:Uev1A and Ubc13:Uev2, to be the cellular factors utilized by Tax for TAK1 and IKK activation. In vitro, the combination of Tax and RNF8 greatly stimulated TAK1, IKK, IκBα and JNK phosphorylation. In vivo, RNF8 over-expression augmented while RNF8 ablation drastically reduced canonical NF-κB activation by Tax. Activation of the non-canonical NF-κB pathway by Tax, however, is unaffected by the loss of RNF8. Using purified components, we further demonstrated biochemically that Tax greatly stimulated RNF8 and Ubc13:Uev1A/Uev2 to assemble long K63-pUb chains. Finally, co-transfection of Tax with increasing amounts of RNF8 greatly induced K63-pUb assembly in a dose-dependent manner. Thus, Tax targets RNF8 and Ubc13:Uev1A/Uev2 to promote the assembly of K63-pUb chains, which signal the activation of TAK1 and multiple downstream kinases including IKK and JNK. Because of the roles RNF8 and K63-pUb chains play in DNA damage repair and cytokinesis, this mechanism may also explain the genomic instability of HTLV-1-transformed T cells and ATL cells.     

Direct Administration and Gene Modulation Using Antisense Oligonucleotides Within the CNS

Besides his vast contribution to the opioid receptor studies, Dr. G. W. Pasternak was among the early pioneers in the antisense oligonucleotide (ASO) field at the time when the crucial in vivo studies using ASO-mediated gene knockdown in the CNS were still impeded by the ASO’s inability to cross the blood–brain barrier. This changed at the start of 1990s, when administration of oligonucleotides through intracerebroventricular or, later, intrathecal injection was undertaken at Cornell University Medical College and further developed in close collaboration with Pasternak lab. These early studies eventually led to the practical realization of the significant therapeutic potential of ASO-based drugs we see today.