Optimization of the nutritional environment for differentiation of human-induced pluripotent stem cells using design of experiments—A proof of concept

The utilization of human-induced pluripotent stem cells (hiPSCs) in cell therapy has a tremendous potential but faces many practical challenges, including costs associated with cell culture media and growth factors. There is an immediate need to establish an optimized culture platform to direct the differentiation of hiPSCs into germ layers in a defined nutritional microenvironment to generate cost-effective and robust therapeutics. The aim of this study was to identify the optimal nutritional environment by mimicking the in vivo concentrations of three key factors (glucose, pyruvate, and oxygen) during the spontaneous differentiation of hiPSCs derived from cord blood, which greatly differ from the in vitro expansion and differentiation scenarios. Moreover, we hypothesized that the high glucose, pyruvate, and oxygen concentrations found in typical growth media could inhibit the differentiation of certain lineages. A design of experiments was used to investigate the interaction between these three variables during the spontaneous differentiation of hiPSCs. We found that lower oxygen and glucose concentrations enhance the expression of mesodermal (Brachyury, KIF1A) and ectodermal (Nestin, β-Tubulin) markers. Our findings present a novel approach for efficient directed differentiation of hiPSCs through the manipulation of media components while simultaneously avoiding the usage of growth factors thus reducing costs.     

Enhancing the sensitivity of multidimensional NMR experiments by using triply-compensated π pulses

An improved expression protocol is proposed for amino acid type-specific [¹³C], [¹⁵N]-isotope labeling of proteins in baculovirus-infected (BV) insect cell cultures. This new protocol modifies the methods published by Gossert et al. (J Biomol NMR 51(4):449–456, 2011) and provides efficient incorporation of isotopically labeled amino acids, with similar yields per L versus unlabeled expression in rich media. Gossert et al. identified the presence of unlabeled amino acids in the yeastolate of the growth medium as a major limitation in isotope labeling using BV-infected insect cells. By reducing the amount of yeastolate in the growth medium ten-fold, a significant improvement in labeling efficiency was demonstrated, while maintaining good protein expression yield. We report an alternate approach to improve isotope labeling efficiency using BV-infected insect cells namely by replacing the yeast extracts in the medium with dialyzed yeast extracts to reduce the amount of low molecular weight peptides and amino acids. We report the residual levels of amino acids in various media formulations and the amino acid consumption during fermentation, as determined by NMR. While direct replacement of yeastolate with dialyzed yeastolate delivered moderately lower isotope labeling efficiencies compared to the use of ten-fold diluted undialized yeastolate, we show that the use of dialyzed yeastolate combined with a ten-fold dilution delivered enhanced isotope labeling efficiency and at least a comparable level of protein expression yield, all at a scale which economizes use of these costly reagents.     

Modeling of the structure of protein–DNA complexes using the data from FRET and footprinting experiments

We discuss the question of constructing three-dimensional models of DNA in complex with proteins using computer modeling and indirect methods of studying the conformation of macromolecules. We consider the methods of interpreting the experimental data obtained by indirect methods of studying the three-dimensional structure of biomolecules. We discuss some aspects of integrating such data into the process of constructing the molecular models of DNA–protein complexes based on the geometric characteristics of DNA. We propose an algorithm for estimating conformations of such complexes based on the information about the local flexibility of DNA and on the experimental data obtained by Forster resonance energy transfer (FRET) and hydroxyl footprinting. Finally, we use this algorithm to predict the hypothetical configuration of DNA in a nucleosome bound with histone H1.     

The possibilities for control of two‐spotted spider mite Tetranychus urticae on field‐grown strawberries in the UK by predatory mites

The potential of two species of predatory phytoseiid mites to control the two‐spotted spider mite, Tetranychus urticae, on unprotected field‐grown strawberries in the UK was investigated. Typhlodromus pyri, a native species, was able to control T. urticae in some circumstances, but was less effective under hot, dry conditions. Natural colonization by this species is likely to be too slow in plantations of 1–2 years life. Attempts to introduce this predator to strawberry fields on cut apple shoots were unsuccessful. The exotic predator Phytoseiulus persimilis, which is available from commercial sources, gave very good control of T. urticae when released onto strawberry plants in June. A release earlier in the year was less successful, so to prevent early build‐up of mites and possible plant damage it may sometimes be necessary to reduce spider mite numbers early in the year with an acaricide, before a later release of P. persimilis. The success of this integrated control strategy was demonstrated.     

The possibilities for control of two‐spotted spider mite tetranychus urticae on field‐grown strawberries in the UK by predatory mites

Numerous field trials have been undertaken in order to obtain a deeper understanding of the behavior (persistence, dispersion, etc.) of Bacillus thuringiensis serovar. israelensis (B.t.i.) formulations when treating rivers or streams for blackfly control. After an extensive sampling of water and natural substrates (periphyton, sediments, moss), freezing is a useful procedure to prevent enzymatic deterioration or bacterial growth in samples before bioassays are to be performed. Using Aedes triseriatus neonate larvae, we quantified the effect on potency of freezing and thawing of B.t.i. suspensions at operational field concentrations. In addition, as samples varied in their content of natural substrates we tested the hypothesis that the presence of such suspended solids affected the mortality response of larvae. Our results showed that these parameters are of significant importance and should be accounted for when comparing bioassays performed on previously frozen or turbid samples.     

Animal definition: a necessity for the validity of animal experiments?

In most scientific journals, experimental animals are described poorly. Whether this is scientifically justified is discussed in this article. It was concluded that when laboratory animals are used in scientific experiments, which almost always are of a quantitative nature, a detailed animal definition is imperative.     

How does a carabid predator find aggregations of slugs in the field? Electroantennograms and behavioural assays suggest chemical cues

Field studies suggest that the generalist carabid predator and scavenger Pterostichus melanarius Illiger aggregates to patches with a higher density of slug prey. The mechanisms behind such aggregation are unknown. Experiments were conducted to test the hypothesis that they are responding to chemical cues. Electroantennograms (EAGs) showed no response by P. melanarius antennae to live, nematode-infected, injured or freshly killed slugs, but a strong response to dead slugs that had been allowed to decay for up to 48 h. Such a response would enable the beetles to find carrion in the field and may also, as dead prey are likely to be spatially correlated with live ones, provide a mechanism by which P. melanarius finds patches with a higher density of live slugs. Subsequent video analyses of P. melanarius responses to patches of slug mucus within arenas showed that beetles with intact antennae could detect these patches because they spent more time, and moved greater distances, within them and increased their rate of turning. Thus, at close range, P. melanarius used their antennae to detect slug mucus and hence, by implication, live slugs. The apparent contradiction between EAG data and behavioural experiments is discussed. Together these result confirm that P. melanariusdoes respond to chemical cues from its slug prey in ways that could lead to aggregation in areas of higher slug density in the field.     

How well do laboratory experiments explain field patterns of zooplankton emergence?

1. We conducted a laboratory experiment to explore potential mechanisms driving variation in zooplankton emergence from diapausing eggs observed in Oneida Lake, NY, U.S.A. We hypothesized that variation in timing of ice-out (date of thawing of ice) between 1994 and 1995, which resulted in variation in photoperiod–temperature cues, contributed to the differences in the observed field patterns. Environmental chambers were used to establish weekly photoperiod–temperature combinations that reproduced natural conditions in Oneida Lake in 1994 and 1995. In addition, a third treatment ('dark') exposed eggs only to the changes in temperature. We recorded zooplankton emergence for 2.5 simulated ice-free seasons.
2. Nine cladoceran taxa were found to hatch, but only Daphnia pulicaria in large numbers. Hatching of D. pulicaria was recorded throughout the season in the two light treatments and sporadically in the dark treatment. The early ice-out treatment had the highest emergence, followed by the late ice-out and dark treatments. Among taxa, there was temporal segregation with five hatching in the early weeks of sampling and two taxa hatching during the middle weeks. Alona hatched late in the first year, but earlier in the second year.
3. We compared our laboratory results of D. pulicaria hatching with the field data obtained by Cáceres (1998) . Hatching was continuous in the laboratory, whereas a synchronous spring emergence was found in the field. However, in both the laboratory and the field, more D. pulicaria hatched under conditions reflecting ice-out occurring in March as opposed to April. Because differences in rates and timing of emergence can affect the population and community dynamics of pelagic systems, we suggest caution when applying laboratory results to field populations.     

A method for the determination of confidence limits for the P/2e − ratio for chosen values of Y ATP max from the results of continuous culture experiments

A model is described, which allows the determination of 95% confidence limits for the maintenance coefficient and the efficiency of oxidative phosphorylation for chosen values of the growth yield for ATP corrected for energy maintenance (Y _ATP ^max ). As experimental data the specific rates of substrate consumption, product formation and oxygen uptake in chemostat cultures at various growth rates are used.     

Analytical basis for the determination of the lacunar–canalicular permeability of bone using cyclic loading

An analytical model for the determination of the permeability in the lacunar-canalicular porosity of bone using cyclic loading is described in this contribution. The objective of the analysis presented is to relate the lacunar-canalicular permeability to a particular phase angle that is measurable when the bone is subjected to infinitesimal cyclic strain. The phase angle of interest is the lag angle between the applied strain and the resultant stress. Cyclic strain causes the interstitial fluid to move. This movement is essential for the viability of osteocytes and is believed to play a major role in the bone mechanotransduction mechanism. However, certain bone fluid flow properties, notably the permeability of the lacunar-canalicular porosity, are still not accurately determined. In this paper, formulas for the phase angle as a function of permeability for infinitesimal cyclic strain are presented and mathematical expressions for the storage modulus, loss modulus, and loss tangent are obtained. An accurate determination of the PLC permeability will improve our ability to understand mechanotransduction and mechanosensory mechanisms, which are fundamental to the understanding of how to treat osteoporosis, how to cope with microgravity in long-term manned space flights, and how to increase the longevity of prostheses that are implanted in bone tissue.     

Poincaré plot interpretation using a physiological model of HRV based on a network of oscillators

In this paper, we develop a physiological oscillator model of which the output mimics the shape of the R-R interval Poincaré plot. To validate the model, simulations of various nervous conditions are compared with heart rate variability (HRV) data obtained from subjects under each prescribed condition. For a variety of sympathovagal balances, our model generates Poincaré plots that undergo alterations strongly resembling those of actual R-R intervals. By exploiting the oscillator basis of our model, we detail the way that low- and high-frequency modulation of the sinus node translates into R-R interval Poincaré plot shape by way of simulations and analytic results. With the use of our model, we establish that the length and width of a Poincaré plot are a weighted combination of low- and high-frequency power. This provides a theoretical link between frequency-domain spectral analysis techniques and time-domain Poincaré plot analysis. We ascertain the degree to which these principles apply to real R-R intervals by testing the mathematical relationships on a set of data and establish that the principles are clearly evident in actual HRV records.     

Linkage analysis by genotyping of sibling populations: a genetic map for the potato cyst nematode constructed using a “pseudo-F2” mapping strategy

A mapping strategy is described for the construction of a linkage map of a non-inbred species in which individual offspring genotypes are not amenable to marker analysis. After one extra generation of random mating, the segregating progeny was propagated, and bulked populations of offspring were analyzed. Although the resulting population structure is different from that of commonly used mapping populations, we show that the maximum likelihood formula for a normal F2 is applicable for the estimation of recombination. This “pseudo-F2” mapping strategy, in combination with the development of an AFLP assay for single cysts, facilitated the construction of a linkage map for the potato cyst nematode Globodera rostochiensis. Using 12 pre-selected AFLP primer combinations, a total of 66 segregating markers were identified, 62 of which were mapped to nine linkage groups. These 62 AFLP markers are randomly distributed and cover about 65% of the genome. An estimate of the physical size of the Globodera genome was obtained from comparisons of the number of AFLP fragments obtained with the values for Caenorhabditis elegans. The methodology presented here resulted in the first genomic map for a cyst nematode. The low value of the kilobase/centimorgan (kb/cM) ratio for the Globodera genome will facilitate map-based cloning of genes that mediate the interaction between the nematode and its host plant. Received: 7 January 1999 / Accepted: 16 April 1999     

Alterations of the Characteristics of the Circadian Rest‐Activity Rhythm of Cancer In‐Patients

The aim of the present study was to evaluate the characteristics of the circadian rest‐activity rhythm of cancer patients. Thirty‐one in‐patients, consisting of 19 males and 12 females, were randomly selected from the Regional Cancer Center, Pandit Jawaharlal Nehru Medical College, Raipur, India. The rest‐activity rhythm was studied non‐invasively by wrist actigraphy, and compared with 35 age‐matched apparently healthy subjects (22 males and 13 females). All subjects wore an Actiwatch (AW64, Mini Mitter Co. Inc., USA) for at least 4–7 consecutive days. Fifteen‐second epoch length was selected for gathering actigraphy data. In addition, several sleep parameters, such as time in bed, assumed sleep, actual sleep time, actual wake time, sleep efficiency, sleep latency, sleep bouts, wake bouts, and fragmentation index, were also recorded. Data were analyzed using several statistical techniques, such as cosinor rhythmometry, spectral analysis, ANOVA, Duncan's multiple‐range test, and t‐test. Dichotomy index (I<O) and autocorrelation coefficient (r24) were also computed. The results validated a statistically significant circadian rhythm in rest‐activity with a prominent period of 24 h for most cancer patients and control subjects. Results of this study further revealed that cancer patients do experience a drastic alteration in the circadian rest‐activity rhythm parameters. Both the dichotomy index and r24 declined in the group of cancer patients. The occurrence of the peak (acrophase, Ø) of the rest‐activity rhythm was earlier (p<0.001) in cancer patients than age‐ and gender‐matched control subjects. Results of sleep parameters revealed that cancer patients spent longer time in bed, had longer assumed and actual sleep durations, and a greater number of sleep and wake bouts compared to control subjects. Further, nap frequency, total nap duration, average nap, and total nap duration per 1 h awake span were statistically significantly higher in cancer patients than control subjects. In conclusion, the results of the present study document the disruption of the circadian rhythm in rest‐activity of cancer in‐patients, with a dampening of amplitude, lowering of mean level of activity, and phase advancement. These alterations of the circadian rhythm characteristics could be attributed to disease, irrespective of variability due to gender, sites of cancer, and timings of therapies. These results might help in designing patient‐specific chronotherapeutic protocols.     

Validity of the Morningness‐Eveningness Scale for Children among Spanish Adolescents

Adolescents tend to be much later chronotypes than other age groups. This circadian phase delay is attributed as much to biological as psychosocial factors. Because the consequences of this change on performance and health have been documented, questionnaires to identify morning and evening‐type adolescents are necessary. The aim of the present study was to validate a Spanish version of the Morningness‐Eveningness Scale for Children (MESC) by means of several relevant psychological variables as external criteria. A sample of 623 urban high school students completed the MESC and self‐reported measures of sleep behaviors, subjective alertness, physical performance, and mood. On the whole, results indicate a good validity of MESC. Significant differences in the self‐reported ratings between morning and evening types were obtained by time‐of‐day. These results provide preliminary support for the Spanish version of MESC.     

Deciphering the origin of Aspergillus flavus NRRL21882, the active biocontrol agent of Afla-Guard®

Single nucleotide polymorphisms (SNPs) of genome sequences of eight Aspergillus flavus and seven Aspergillus oryzae strains were extracted with Mauve, a multiple-genome alignment programme. A phylogenetic analysis with sequences comprised of concatenated total SNPs by the unweighted pair group method with arithmetic mean (UPGMA) of MAFFT adequately separated them into three groups, A. flavus S-morphotype, A. flavus L-morphotype and A. oryzae. Divergence time inferred for A. flavus NRRL21882, the active agent of the biocontrol product Afla-Guard^®, and S-morphotype was about 5·1 mya. Another biocontrol strain, A. flavus AF36, diverged from aflatoxigenic L-morphotype about 2·6–3·0 mya. Despite the close relatedness of A. oryzae to A. flavus, A. oryzae strains likely evolved from aflatoxigenic Aspergillus aflatoxiformans (=A. parvisclerotigenus). A survey of A. flavus populations implies that prior Afla-Guard^® applications are associated with prevalence of NRRL21882-type isolates in Mississippi fields. In addition, a few NRRL21882 relatives were identified. A. flavus Og0222, a biocontrol ingredient of Aflasafe™, was verified as a NRRL21882-type strain, having identical sequence breakpoints that led to deletion of aflatoxin and cyclopiazonic acid gene clusters. A similar UPGMA analysis suggests that the occurrence of NRRL21882-type strains is a more recent event.     

Assessment of the efficacy of parasiticides for the control of tick infection in dogs under field conditions: what's new?

For their biological and ecological characteristics, ticks are vectors of the widest variety of pathogens causing tick-borne diseases (TBDs). Little information is available about the ways in which time spent by ticks to feed on hosts, transmission times and TBD prevention are related and it is exclusively limited to laboratory reports on adult stages. In particular, the time required by immature stages to transmit pathogens has not been determined for most TBDs. Considering their importance for animal and human health, effective control of immature ticks is advisable to reduce the damage ticks cause. Recently, the efficacy of a combination of imidacloprid 10%/permethrin 50% was compared with that of fipronil 10%/S-methoprene 9% against ticks when administered to naturally infected dogs. A semi-quantitative method was used to assess the methodological parameters to calculate drug efficacy on immature stages. On adult ticks, the efficacy of both products was high and overall very similar, whereas for the immature stages the combination of imidacloprid 10% and permethrin 50% had a higher efficacy than fipronil 10% and methoprene 9% throughout the observation period (statistically significant difference on day + 28 only). The semi-quantitative method proposed for the evaluation of immature stages can be considered a useful tool for calculating the efficacy of a drug in the field. Due the important role of immatures in the spread of TBDs, the immature tick load should be calculated to assess the efficacy of acaricidal products both under laboratory and field conditions.