Molecular Threading: Mechanical Extraction,Stretching and Placement of DNA Molecules from a Liquid-Air Interface

We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers.     

Chest Radiographic Patterns and the Transmission of Tuberculosis: Implications for Automated Systems

BackgroundComputer-aided detection to identify and diagnose pulmonary tuberculosis is being explored. While both cavitation on chest radiograph and smear-positivity on microscopy are independent risk factors for the infectiousness of pulmonary tuberculosis it is unknown which radiographic pattern, were it detectable, would provide the greatest public health benefit; i.e. reduced transmission. Herein we provide that evidence.Objectives1) to determine whether pulmonary tuberculosis in a high income, low incidence country is more likely to present with “typical” adult-type pulmonary tuberculosis radiographic features and 2) to determine whether those with “typical” radiographic features are more likely than those without such features to transmit the organism and/or cause secondary cases.MethodsOver a three-year period beginning January 1, 2006 consecutive adults with smear-positive pulmonary tuberculosis in the Province of Alberta, Canada, were identified and their pre-treatment radiographs scored by three independent readers as “typical” (having an upper lung zone predominant infiltrate, with or without cavitation but no discernable adenopathy) or “atypical” (all others). Each patient’s pre-treatment bacillary burden was carefully documented and, during a 30-month transmission window, each patient’s transmission events were recorded. Mycobacteriology, radiology and transmission were compared in those with “typical” versus “atypical” radiographs.FindingsA total of 97 smear-positive pulmonary tuberculosis cases were identified, 69 (71.1%) with and 28 (28.9%) without “typical” chest radiographs. “Typical” cases were more likely to have high bacillary burdens and cavitation (Odds Ratios and 95% Confidence Intervals: 2.75 [1.04–7.31] and 9.10 [2.51–32.94], respectively). Typical cases were also responsible for most transmission events—78% of tuberculin skin test conversions (p<0.002) and 95% of secondary cases in reported close contacts (p<0.01); 94% of secondary cases in “unreported” contacts (p<0.02).ConclusionAs a group, smear-positive pulmonary tuberculosis patients with typical radiographic features constitute the greatest public health risk. This may have implications for automated detection systems.     

Composition and Function of Thylakoid Membranes from Grana-rich and Grana-deficient Chloroplast Mutants of Barley

Chlorophyll-deficient barley (Hordeum vulgare) mutants were studied that had chlorophyll a/b ratios either higher or lower than the wild type. Mutants with high ratios (>5.2) had a reduced proportion of their photosynthetic lamellae appressed into grana (“grana-deficient” mutants) compared with wild type (chlorophyll a/b = 3.2), while the majority of lamellae in the chloroplasts with low chlorophyll a/b ratios (2.0-2.4) were organized into grana (“grana-rich” mutants).     

The Control of Growth Habit of Marquillo x Kenya Farmer Wheat Dwarf I by Temperature

The Marquillo × Kenya Farmer 1 “grass-clump” dwarf selection of Triticum aestivum L. was grown under continuous 2000 foot candle light and several regimes of alternating 16° and 26° temperatures combined in total cycle lengths of 6, 12, 24, or 48 hr. Plants at 26° grew as normal wheat. Those exposed to 0.25 to 2 hr of 16° per cycle showed typical “grass-clump” dwarf characteristics which were independent of the cycle length. Treatments with 16° exposures of 4 to 8 hr per 24 hr and 12 to 16 hr per 48 hr exhibited vegetative “grass-clump” dwarfness for 40 days but later displayed extensive reproductive development. Longer 16° treatments killed the plants at a very early stage of vegetative development before floral initiation. The data supported an hypothesis that all 4 growth habits were related to the temperature sensitivity of the vegetative meristem. The cessation of meristem development was possibly due to the accumulation of a stable inhibitory substance produced at low temperatures.     

A dynamic formin-dependent deep F-actin network in axons

Although actin at neuronal growth cones is well-studied, much less is known about actin organization and dynamics along axon shafts and presynaptic boutons. Using probes that selectively label filamentous-actin (F-actin), we found focal “actin hotspots” along axons—spaced ∼3–4 µm apart—where actin undergoes continuous assembly/disassembly. These foci are a nidus for vigorous actin polymerization, generating long filaments spurting bidirectionally along axons—a phenomenon we call “actin trails.” Super-resolution microscopy reveals intra-axonal deep actin filaments in addition to the subplasmalemmal “actin rings” described recently. F-actin hotspots colocalize with stationary axonal endosomes, and blocking vesicle transport diminishes the actin trails, suggesting mechanistic links between vesicles and F-actin kinetics. Actin trails are formin—but not Arp2/3—dependent and help enrich actin at presynaptic boutons. Finally, formin inhibition dramatically disrupts synaptic recycling. Collectively, available data suggest a two-tier F-actin organization in axons, with stable “actin rings” providing mechanical support to the plasma membrane and dynamic "actin trails" generating a flexible cytoskeletal network with putative physiological roles.     

Heat Generation/Absorption Effects in a Boundary Layer Stretched Flow of Maxwell Nanofluid: Analytic and Numeric Solutions

Analysis has been done to investigate the heat generation/absorption effects in a steady flow of non-Newtonian nanofluid over a surface which is stretching linearly in its own plane. An upper convected Maxwell model (UCM) has been utilized as the non-Newtonian fluid model in view of the fact that it can predict relaxation time phenomenon which the Newtonian model cannot. Behavior of the relaxations phenomenon has been presented in terms of Deborah number. Transport phenomenon with convective cooling process has been analyzed. Brownian motion “D_b” and thermophoresis effects “D_t” occur in the transport equations. The momentum, energy and nanoparticle concentration profiles are examined with respect to the involved rheological parameters namely the Deborah number, source/sink parameter, the Brownian motion parameters, thermophoresis parameter and Biot number. Both numerical and analytic solutions are presented and found in nice agreement. Comparison with the published data is also made to ensure the validity. Stream lines for Maxwell and Newtonian fluid models are presented in the analysis.     

Pathological States and Criminal Responsibility

The doctor is embarrassed in court when asked to testify to the effects of illness on a defendant''s capability “of appreciating the nature and quality of an act or omission or of knowing that an act or omission is wrong”. The source of his difficulty is traced to the legal concepts of “guilt”, “crime” and “punishment” which imply a legal view of man at variance with our modern biological view. To abolish this discrepancy we need not accept a medical model for criminal law where “crime” is analogous to “disease”, and “punishment” to “treatment”. A pragmatic approach to the handling of the criminal could exclude the notions of “guilt” and “punishment” and yet fulfil the rational goals of protecting society from the criminal and of compensating his victims.     

Influence of Water and Temperature Stress on the Temperature Dependence of the Reappearance of Variable Fluorescence following Illumination

The temperature dependence of the rate and magnitude of the reappearance of photosystem II (PSII) variable fluorescence following illumination has been used to determine plant temperature optima. The present study was designed to determine the effect of a plant's environmental history on the thermal dependency of the reappearance of PSII variable fluorescence. In addition, this study further evaluated the usefulness of this fluorescence technique in identifying plant temperature optima. Laboratory and greenhouse grown potato (Solanum tuberosum L. cv “Norgold M”) plants had a thermal kinetic window between 15 and 25°C. The minimum apparent K_m of NADH hydroxypyruvate reductase for NADH occurred at 20°C. This temperature was also the temperature providing maximal reappearance of variable fluorescence. Soybean (Glycine max [L.] Merrill cv “Wayne”) plants had a thermal kinetic window between 15 and 30°C with a minimum apparent K_m at 25°C. Maximal reappearance of variable fluorescence was seen between 20 and 30°C. To determine if increasing environmental temperatures increased the temperature optimum provided from the fluorescence response curves, potato and soybean leaves from irrigated and dryland field grown plants were evaluated. Although the absolute levels of PSII variable fluorescence declined with increasing thermal stress, the temperature optimum of the dryland plants did not increase with increased exposure to elevated temperatures. Because of variability in the daily period of high temperature stress in the field, studies were initiated with tobacco plants grown in controlled environment chambers. The reappearance of PSII variable fluorescence in tobacco (Nicotiana tabacum L. cv “Wisconsin 38”) leaves that had experienced continuous leaf temperatures of 35°C for 8 days had the same 20°C optima as leaves from plants grown at room temperature. The results of this study suggest that the temperature optimum for the reappearance of variable fluorescence following illumination is not altered by the plant's previous exposure to variable environmental temperatures. These findings support the usefulness of this procedure for the rapid identification of a plant's temperature optimum.     

Niche theory‐based modeling of assembly processes of viral communities in bats

Understanding the assembly processes of symbiont communities, including viromes and microbiomes, is important for improving predictions on symbionts’ biogeography and disease ecology. Here, we use phylogenetic, functional, and geographic filters to predict the similarity between symbiont communities, using as a test case the assembly process in viral communities of Mexican bats. We construct generalized linear models to predict viral community similarity, as measured by the Jaccard index, as a function of differences in host phylogeny, host functionality, and spatial co‐occurrence, evaluating the models using the Akaike information criterion. Two model classes are constructed: a “known” model, where virus–host relationships are based only on data reported in Mexico, and a “potential” model, where viral reports of all the Americas are used, but then applied only to bat species that are distributed in Mexico. Although the “known” model shows only weak dependence on any of the filters, the “potential” model highlights the importance of all three filter types—phylogeny, functional traits, and co‐occurrence—in the assemblage of viral communities. The differences between the “known” and “potential” models highlight the utility of modeling at different “scales” so as to compare and contrast known information at one scale to another one, where, for example, virus information associated with bats is much scarcer.     

Intrakinetochore stretch is associated with changes in kinetochore phosphorylation and spindle assembly checkpoint activity

Cells have evolved a signaling pathway called the spindle assembly checkpoint (SAC) to increase the fidelity of chromosome segregation by generating a “wait anaphase” signal until all chromosomes are properly aligned within the mitotic spindle. It has been proposed that tension generated by the stretch of the centromeric chromatin of bioriented chromosomes stabilizes kinetochore microtubule attachments and turns off SAC activity. Although biorientation clearly causes stretching of the centromeric chromatin, it is unclear whether the kinetochore is also stretched. To test whether intrakinetochore stretch occurs and is involved in SAC regulation, we developed a Drosophila melanogaster S2 cell line expressing centromere identifier–mCherry and Ndc80–green fluorescent protein to mark the inner and outer kinetochore domains, respectively. We observed stretching within kinetochores of bioriented chromosomes by monitoring both inter- and intrakinetochore distances in live cell assays. This intrakinetochore stretch is largely independent of a 30-fold variation in centromere stretch. Furthermore, loss of intrakinetochore stretch is associated with enhancement of 3F3/2 phosphorylation and SAC activation.     

Network Effects of Risk Behavior Change Following Prophylactic Interventions

We formulated a network-based model to understand how risk behavior change in conjunction with failure of prophylactic interventions can lead to unintended outcomes where “less (intervention) is more (effective).” Our model captures the distinction between one- and two-sided risk behavior change. In one-sided situations (e.g. influenza/H1N1) it is sufficient for either individual in an interaction to exhibit risk behavior change whereas in two-sided situations (e.g. AIDS/HIV) it is necessary for both individuals in the interaction to exhibit risk behavior change, for a potential transmission of the disease. A central discovery is that this phenomenon occurs at differing levels of intervention coverage depending upon the “sidedness” of the interaction. We find that for one-sided interactions, sufficiently high vaccination coverage is necessary for mitigating the effects of risk behavior; for two-sided interactions, it is essential to combine prophylactic treatments with programs aimed at reducing risky behavior. Furthermore, again dependent on the “sidedness,” targeting highly connected nodes can be strictly worse than uniformly random interventions at the same level of coverage.     

Do Pressures to Publish Increase Scientists' Bias? An Empirical Support from US States Data

The growing competition and “publish or perish” culture in academia might conflict with the objectivity and integrity of research, because it forces scientists to produce “publishable” results at all costs. Papers are less likely to be published and to be cited if they report “negative” results (results that fail to support the tested hypothesis). Therefore, if publication pressures increase scientific bias, the frequency of “positive” results in the literature should be higher in the more competitive and “productive” academic environments. This study verified this hypothesis by measuring the frequency of positive results in a large random sample of papers with a corresponding author based in the US. Across all disciplines, papers were more likely to support a tested hypothesis if their corresponding authors were working in states that, according to NSF data, produced more academic papers per capita. The size of this effect increased when controlling for state''s per capita R&D expenditure and for study characteristics that previous research showed to correlate with the frequency of positive results, including discipline and methodology. Although the confounding effect of institutions'' prestige could not be excluded (researchers in the more productive universities could be the most clever and successful in their experiments), these results support the hypothesis that competitive academic environments increase not only scientists'' productivity but also their bias. The same phenomenon might be observed in other countries where academic competition and pressures to publish are high.     

Permissive Summer Temperatures of the 2010 European West Nile Fever Upsurge

Background

In the summer of 2010, Europe experienced outbreaks of West Nile Fever (WNF) in humans, which was preceded by hot spells. The objective of this study was to identify potential drivers of these outbreaks, such as spring and summer temperatures, relative humidity (RH), and precipitation.

Methods

Pearson and lag correlations, binary and multinomial logistic regressions were used to assess the relationship between the climatic parameters and these outbreaks.

Results

For human morbidity, significant (<0.05) positive correlations were observed between a number of WNF cases and temperature, with a geographic latitude gradient: northern (“colder”) countries displayed strong correlations with a lag of up to four weeks, in contrast to southern (“warmer”) countries, where the response was immediate. The correlations with RH were weaker, while the association with precipitation was not consistent. Horse morbidity started three weeks later than in humans where integrated surveillance was conducted, and no significant associations with temperature or RH were found for lags of 0 to 4 weeks.

Conclusions

Significant temperature deviations during summer months might be considered environmental precursors of WNF outbreaks in humans, particularly at more northern latitudes. These insights can guide vector abatement strategies by health practitioners in areas at risk for persistent transmission cycles.     

Phenotypic plasticity in life‐history traits of Daphnia galeata in response to temperature – a comparison across clonal lineages separated in time

Climatic changes are projected to result in rapid adaptive events with considerable phenotypic shifts. In order to reconstruct the impact of increased mean water temperatures during past decades and to reveal possible thermal micro‐evolution, we applied a resurrection ecology approach using dormant eggs of the freshwater keystone species Daphnia galeata. To this end, we compared the adaptive response of D. galeata clones from Lake Constance of two different time periods, 1965–1974 (“historical”) versus 2000–2009 (“recent”), to experimentally increased temperature regimes. In order to distinguish between genetic versus environmentally induced effects, we performed a common garden experiment in a flow‐through system and measured variation in life‐history traits. Experimental thermal regimes were chosen according to natural temperature conditions during the reproductive period of D. galeata in Central European lakes, with one additional temperature regime exceeding the currently observable maximum (+2°C). Increased water temperatures were shown to significantly affect measured life‐history traits, and significant “temperature × clonal age” interactions were revealed. Compared to historical clones, recent clonal lineages exhibited a shorter time to first reproduction and a higher survival rate, which may suggest temperature‐driven micro‐evolution over time but does not allow an explicit conclusion on the adaptive nature of such responses.     

Predictive Habitat Modelling as a Tool to Assess the Change in Distribution and Extent of an OSPAR Priority Habitat under an Increased Ocean Temperature Scenario: Consequences for Marine Protected Area Networks and Management

The aims of this study were to determine the extent and distribution of an OSPAR priority habitat under current baseline ocean temperatures; to illustrate the prospect for habitat loss under a changing ocean temperature scenario; and to demonstrate the potential application of predictive habitat mapping in “future-proofing” conservation and biodiversity management.Maxent modelling and GIS environmental envelope analysis of the biogenic bed forming species, Modiolus modiolus was carried out. The Maxent model was tested and validated using 75%/25% training/test occurrence records and validated against two sampling biases (the whole study area and a 20km buffer). The model was compared to the envelope analysis and the area under the receiver operating characteristic curve (Area Under the curve; AUC) was evaluated.The performance of the Maxent model was rated as ‘good’ to ‘excellent’ on all replicated runs and low variation in the runs was recorded from the AUC values. The extent of “most suitable”, “less suitable” and “unsuitable” habitat was calculated for the baseline year (2009) and the projected increased ocean temperature scenarios (2030, 2050, 2080 and 2100). A loss of 100% of “most suitable” habitat was reported by 2080.Maintaining a suitable level of protection of marine habitats/species of conservation importance may require management of the decline and migration rather than maintenance of present extent. Methods applied in this study provide the initial application of a plausible “conservation management tool”.     

ThermoSpots to Detect Hypothermia in Children with Severe Acute Malnutrition

Introduction

Hypothermia is a risk factor for increased mortality in children with severe acute malnutrition (SAM). Yet frequent temperature measurement remains unfeasible in under-resourced units in developing countries. ThermoSpot is a continuous temperature monitoring sticker designed originally for neonates. When applied to skin, its liquid crystals are designed to turn black with hypothermia and remain green with normothermia.

Aims

To (i) estimate the diagnostic accuracy of ThermoSpots for detecting WHO-defined hypothermia (core temperature <35.5°C or peripheral temperature <35.0°C) in children with SAM and (ii) determine their acceptability amongst mothers.

Methods

Children with SAM in a malnutrition unit in Malawi were enrolled during March-July 2010. The sensitivity and specificity of ThermoSpots were calculated by comparing the device colour against ‘gold standard’ rectal temperatures taken on admission and follow up peripheral temperatures taken until discharge. Guardians completed a questionnaire to assess acceptability.

Results

Hypothermia was uncommon amongst the 162 children enrolled. ThermoSpot successfully detected the one rectal temperature and two peripheral temperatures recorded that met the WHO definition of hypothermia. Overall, 3/846 (0.35%) temperature measurements were in the WHO-defined hypothermia range. Interpreting the brown transition colour (between black and green) as hypothermia improved sensitivities. For milder hypothermia definitions, sensitivities declined (<35.4°C, 50.0%; <35.9°C, 39.2%). Specificity was consistently above 94%. From questionnaires, 40/43 (93%) mothers reported they were 90–100% happy with the device overall. Free-text answers revealed themes of “Skin Rashes”, “User-satisfaction” and “Empowerment".

Conclusion

Although hypothermia was uncommon in this study, ThermoSpots successfully detected these episodes in malnourished children and were acceptable to mothers. Research in settings where hypothermia is common is needed to determine performance with certainty. Instructing users to act when the device’s transition colour appears could improve accuracy. If reliable, ThermoSpots may offer simple, acceptable and continuous temperature measurement for high-burden areas and reduce the workload of over-stretched staff.     

Behavioral and Emotional Dynamics of Two People Struggling to Reach Consensus about a Topic on Which They Disagree

We studied the behavioral and emotional dynamics displayed by two people trying to resolve a conflict. 59 groups of two people were asked to talk for 20 minutes to try to reach a consensus about a topic on which they disagreed. The topics were abortion, affirmative action, death penalty, and euthanasia. Behavior data were determined from audio recordings where each second of the conversation was assessed as proself, neutral, or prosocial. We determined the probability density function of the durations of time spent in each behavioral state. These durations were well fit by a stretched exponential distribution, with an exponent, , of approximately 0.3. This indicates that the switching between behavioral states is not a random Markov process, but one where the probability to switch behavioral states decreases with the time already spent in that behavioral state. The degree of this “memory” was stronger in those groups who did not reach a consensus and where the conflict grew more destructive than in those that did. Emotion data were measured by having each person listen to the audio recording and moving a computer mouse to recall their negative or positive emotional valence at each moment in the conversation. We used the Hurst rescaled range analysis and power spectrum to determine the correlations in the fluctuations of the emotional valence. The emotional valence was well described by a random walk whose increments were uncorrelated. Thus, the behavior data demonstrated a “memory” of the duration already spent in a behavioral state while the emotion data fluctuated as a random walk whose steps did not have a “memory” of previous steps. This work demonstrates that statistical analysis, more commonly used to analyze physical phenomena, can also shed interesting light on the dynamics of processes in social psychology and conflict management.     

Ethylene Oxide Gaseous Sterilization: I. Concentration and Temperature Effects

The relationships of reaction temperature and concentration of gaseous ethylene oxide to the time required for inactivation of air-dried Bacillus subtilis var. niger spores are more complex than previously reported. A plot of temperature vs. the logarithm of “thermochemical death time” (TCDT) resulted in a straight line between 18 and 57 C for systems of “high” ethylene oxide concentration. The TCDT values were independent of ethylene oxide concentrations above certain temperature-dependent limits. A given ethylene oxide concentration produced a TCDT curve identical in the upper temperature regions with that for higher concentrations. As the temperature was lowered beyond a critical point, this curve diverged from that for higher concentrations, as a straight line of lesser slope. Thus, a series of curves exists for a range of ethylene oxide concentrations. They are characterized by two segments, both logarithmic, intersecting at a critical temperature for each concentration. The intersecting point is at a temperature inversely related to the ethylene oxide gas concentration. The temperature quotient for the high temperature segments of all systems was 1.8. This value was characteristic for ethylene oxide concentrations of 440 and 880 mg/liter at temperatures above 40.6 and 33.4 C, respectively. Below these critical temperatures, the Q₁₀ values for the respective systems were 3.2 and 2.3.