Backbone resonance assignments for the SET domain of the human methyltransferase NSD2

Aberrant NSD2 methyltransferase activity is implicated as the oncogenic driver in multiple myeloma, suggesting opportunities for novel therapeutic intervention. The methyltransferase activity of NSD2 resides in its catalytic SET domain, which is conserved among most lysine methyltransferases. Here we report the backbone \(\hbox {H}^{\mathrm{N}}\), N, C\(^{\prime }\), \(\hbox {C}^\alpha\) and side-chain \(\hbox {C}^\beta\) assignments of a 25 kDa NSD2 SET domain construct, spanning residues 991–1203. A chemical shift analysis of C\(^{\prime }\), \(\hbox {C}^\alpha\) and \(\hbox {C}^\beta\) resonances predicts a secondary structural pattern that is in agreement with homology models.     

A Mathematical Model Supports a Key Role for Ae4 (Slc4a9) in Salivary Gland Secretion

We develop a mathematical model of a salivary gland acinar cell with the objective of investigating the role of two \(\mathrm{Cl}^-/\mathrm{HCO}_3^-\) exchangers from the solute carrier family 4 (Slc4), Ae2 (Slc4a2) and Ae4 (Slc4a9), in fluid secretion. Water transport in this type of cell is predominantly driven by \(\mathrm{Cl}^-\) movement. Here, a basolateral \(\mathrm{Na}^+/ \mathrm{K}^+\) adenosine triphosphatase pump (NaK-ATPase) and a \(\mathrm{Na}^+\)–\(\mathrm{K}^+\)–\(2 \mathrm{Cl}^-\) cotransporter (Nkcc1) are primarily responsible for concentrating the intracellular space with \(\mathrm{Cl}^-\) well above its equilibrium potential. Gustatory and olfactory stimuli induce the release of \(\mathrm{Ca}^{2+}\) ions from the internal stores of acinar cells, which triggers saliva secretion. \(\mathrm{Ca}^{2+}\)-dependent \(\mathrm{Cl}^-\) and \(\mathrm{K}^+\) channels promote ion secretion into the luminal space, thus creating an osmotic gradient that promotes water movement in the secretory direction. The current model for saliva secretion proposes that \(\mathrm{Cl}^-/ \mathrm{HCO}_3^-\) anion exchangers (Ae), coupled with a basolateral \(\mathrm{Na}^+/\hbox {proton}\) (\(\hbox {H}^+\)) (Nhe1) antiporter, regulate intracellular pH and act as a secondary \(\mathrm{Cl}^-\) uptake mechanism (Nauntofte in Am J Physiol Gastrointest Liver Physiol 263(6):G823–G837, 1992; Melvin et al. in Annu Rev Physiol 67:445–469, 2005.  https://doi.org/10.1146/annurev.physiol.67.041703.084745). Recent studies demonstrated that Ae4 deficient mice exhibit an approximate \(30\%\) decrease in gland salivation (Peña-Münzenmayer et al. in J Biol Chem 290(17):10677–10688, 2015). Surprisingly, the same study revealed that absence of Ae2 does not impair salivation, as previously suggested. These results seem to indicate that the Ae4 may be responsible for the majority of the secondary \(\mathrm{Cl}^-\) uptake and thus a key mechanism for saliva secretion. Here, by using ‘in-silico’ Ae2 and Ae4 knockout simulations, we produced mathematical support for such controversial findings. Our results suggest that the exchanger’s cotransport of monovalent cations is likely to be important in establishing the osmotic gradient necessary for optimal transepithelial fluid movement.     

A finite-element model of mechanosensation by a Pacinian corpuscle cluster in human skin

The Pacinian corpuscle (PC) is the cutaneous mechanoreceptor responsible for sensation of high-frequency (20–1000 Hz) vibrations. PCs lie deep within the skin, often in multicorpuscle clusters with overlapping receptive fields. We developed a finite-element mechanical model of one or two PCs embedded within human skin, coupled to a multiphysics PC model to simulate action potentials elicited by each PC. A vibration was applied to the skin surface, and the resulting mechanical signal was analyzed using two metrics: the deformation amplitude ratio (\({\rho }_{\mathrm{1S}} \), \({\rho }_{\mathrm{2S}} )\) and the phase shift of the vibration (\({\delta }_{\mathrm{S}1}^{\mathrm{mech}} \), \({\delta }_{\mathrm{S}2}^{\mathrm{mech}} )\) between the stimulus and the PC. Our results showed that the amplitude attenuation and phase shift at a PC increased with distance from the stimulus to the PC. Differences in amplitude (\(\rho _{12} )\) and phase shift (\({\delta }_{12}^{\mathrm{mech}} )\) between the two PCs in simulated clusters directly affected the interspike interval between the action potentials elicited by each PC (\({\delta }_{12}^{\mathrm{spike}} )\). While \({\delta }_{12}^{\mathrm{mech}} \) had a linear relationship with \({\delta }_{12}^{\mathrm{spike}} \), \(\rho _{12} \)’s effect on \({\delta }_{12}^{\mathrm{spike}} \) was greater for lower values of \(\rho _{12} \). In our simulations, the separation between PCs and the distance of each PC from the stimulus location resulted in differences in amplitude and phase shift at each PC that caused \({\delta }_{12}^{\mathrm{spike}} \) to vary with PC location. Our results suggest that PCs within a cluster receive different mechanical stimuli which may enhance source localization of vibrotactile stimuli, drawing parallels to sound localization in binaural hearing.     

Performance and kinetics of ANAMMOX granular sludge with pH shock in a sequencing batch reactor

As an efficient and cost-effective nitrogen removal process, anaerobic ammonium oxidation (ANAMMOX) could be well operated at suitable pH condition. However, pH shock occurred in different kinds of wastewater and affected ANANNOX process greatly. The present research aimed at studying the performance and kinetics of ANAMMOX granular sludge with pH shock. When influent pH was below 7.5, effluent \({\text{NH}}_{4}^{ + }\)–N and \({\text{NO}}_{2}^{ - }\)–N increased with decreasing pH. At Ph 6.0, effluent \({\text{NO}}_{2}^{ - }\)–N approached 100 mg/L, and the ratios of \(\Delta {\text{NO}}_{2}^{ - } - {\text{N}}:\Delta {\text{NH}}_{4}^{ + } - {\text{N and }}\Delta {\text{NO}}_{3}^{ - } - {\text{N}}:\Delta {\text{NH}}_{4}^{ + } - {\text{N}}\) approached 2.2 and 1.3, respectively. Both greatly deviated from theoretical values. When influent pH was above 7.5, effluent \({\text{NH}}_{4}^{ + }\)–N and \({\text{NO}}_{2}^{ - }\)–N increased with increasing pH. At pH 9.0, ammonium removal rate (ARR) and nitrite removal rate (NRR) decreased to 0.011 ± 0.004 and 0.035 ± 0.004 kg/(m³·d), respectively. Besides, \(\Delta {\text{NO}}_{2}^{ - }\)–N:\(\Delta {\text{NH}}_{4}^{ + }\)–N deviated from theoretical value. Longer recovery time from pH 9.0 than from pH 6.0 indicated that alkaline surroundings inhibited anaerobic ammonium oxidizing bacteria (AAOB) greater. The sludge settling velocity was 2.15 cm/s at pH 7.5. However, it decreased to 2.02 cm/s when pH was 9.0. Acidic pH had little effect on sludge size, but disintegration of ANAMMOX granule was achieved with pH of 9.0. The Bell-shaped (A) model and the Ratkowsky model were more applicable to simulate the effect resulting from pH shock on ANAMMOX activity (R² > 0.95), and both could describe ANAMMOX activity well with pH shock. They indicated that q_max was 0.37 kg \(\Delta {\text{NH}}_{4}^{ + }\)–N/(kgMLSS·d) at the optimum pH value (7.47) in present study. The minimum pH during which ANAMMOX occurred was 5.68 while the maximum pH for ANAMMOX reaction was 9.26. Based on nitrogen removal performance with different pH, strongly acidic (pH ≤ 6.5) or alkaline (pH ≥ 8.5) inhibited ANAMMOX process. Besides, ANAMMOX appeared to be more susceptible to alkaline wastewater. Compared to extremely acidic condition (low pH), extremely alkaline condition (high pH) affected ANAMMOX granules much more.     

Potential use of sulfite as a supplemental electron donor for wastewater denitrification

Biological denitrification typically requires the addition of a supplemental electron donor, which can add a significant operating expense to wastewater treatment facilities. Most common electron donors are organic, but reduced inorganic sulfur compounds (RISCs), such as sulfide (HS^?) and elemental sulfur (S⁰), may be more cost-effective. S⁰ is an inexpensive and well characterized electron donor, but it provides slow denitrification rates due to its low solubility. A lesser-known RISC is sulfite (\({\text{SO}}_{3}^{2 - }\)), which can be easily produced from S⁰ by a simple combustion process. Unlike S⁰, \({\text{SO}}_{3}^{2 - }\) is highly soluble, and therefore may provide higher denitrification rates. However, very little is known about microbial denitrification with \({\text{SO}}_{3}^{2 - }\). Also, \({\text{SO}}_{3}^{2 - }\) is a strong reductant that reacts abiotically with oxygen and has toxic effects on microorganisms. This paper reviews \({\text{SO}}_{3}^{2 - }\) in the environment, \({\text{SO}}_{3}^{2 - }\) chemistry, microbiology, toxicity, and its potential use for denitrification. Since \({\text{SO}}_{3}^{2 - }\) is an intermediate in the sulfur oxidation pathway of most sulfur-oxidizing microorganisms, it is an energetic electron donor and it should select for a \({\text{SO}}_{3}^{2 - }\)-oxidizing community. Our review of the literature, as well as our own lab experience, suggests that \({\text{SO}}_{3}^{2 - }\) can effectively serve as an electron donor for denitrification. Further research is needed to determine the kinetics of \({\text{SO}}_{3}^{2 - }\)-based denitrification, its toxic threshold for sulfur-oxidizing microorganisms, and its potential inhibition of sensitive species such as nitrifying microorganisms and potential formation of nitrous oxide. Its effect on sludge settling efficiency also should be explored.     

Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs

Despite major strides in the treatment of cancer, the development of drug resistance remains a major hurdle. One strategy which has been proposed to address this is the sequential application of drug therapies where resistance to one drug induces sensitivity to another drug, a concept called collateral sensitivity. The optimal timing of drug switching in these situations, however, remains unknown. To study this, we developed a dynamical model of sequential therapy on heterogeneous tumors comprised of resistant and sensitive cells. A pair of drugs (DrugA, DrugB) are utilized and are periodically switched during therapy. Assuming resistant cells to one drug are collaterally sensitive to the opposing drug, we classified cancer cells into two groups, \(A_\mathrm{R}\) and \(B_\mathrm{R}\), each of which is a subpopulation of cells resistant to the indicated drug and concurrently sensitive to the other, and we subsequently explored the resulting population dynamics. Specifically, based on a system of ordinary differential equations for \(A_\mathrm{R}\) and \(B_\mathrm{R}\), we determined that the optimal treatment strategy consists of two stages: an initial stage in which a chosen effective drug is utilized until a specific time point, T, and a second stage in which drugs are switched repeatedly, during which each drug is used for a relative duration (i.e., \(f \Delta t\)-long for DrugA and \((1-f) \Delta t\)-long for DrugB with \(0 \le f \le 1\) and \(\Delta t \ge 0\)). We prove that the optimal duration of the initial stage, in which the first drug is administered, T, is shorter than the period in which it remains effective in decreasing the total population, contrary to current clinical intuition. We further analyzed the relationship between population makeup, \(\mathcal {A/B} = A_\mathrm{R}/B_\mathrm{R}\), and the effect of each drug. We determine a critical ratio, which we term \(\mathcal {(A/B)}^{*}\), at which the two drugs are equally effective. As the first stage of the optimal strategy is applied, \(\mathcal {A/B}\) changes monotonically to \(\mathcal {(A/B)}^{*}\) and then, during the second stage, remains at \(\mathcal {(A/B)}^{*}\) thereafter. Beyond our analytic results, we explored an individual-based stochastic model and presented the distribution of extinction times for the classes of solutions found. Taken together, our results suggest opportunities to improve therapy scheduling in clinical oncology.     

Cell Volume Regulation in the Proximal Tubule of Rat Kidney

We developed a dynamic model of a rat proximal convoluted tubule cell in order to investigate cell volume regulation mechanisms in this nephron segment. We examined whether regulatory volume decrease (RVD), which follows exposure to a hyposmotic peritubular solution, can be achieved solely via stimulation of basolateral K\(^+\) and \(\hbox {Cl}^-\) channels and \(\hbox {Na}^+\)–\(\hbox {HCO}_3^-\) cotransporters. We also determined whether regulatory volume increase (RVI), which follows exposure to a hyperosmotic peritubular solution under certain conditions, may be accomplished by activating basolateral \(\hbox {Na}^+\)/H\(^+\) exchangers. Model predictions were in good agreement with experimental observations in mouse proximal tubule cells assuming that a 10% increase in cell volume induces a fourfold increase in the expression of basolateral K\(^+\) and \(\hbox {Cl}^-\) channels and \(\hbox {Na}^+\)–\(\hbox {HCO}_3^-\) cotransporters. Our results also suggest that in response to a hyposmotic challenge and subsequent cell swelling, \(\hbox {Na}^+\)–\(\hbox {HCO}^-_3\) cotransporters are more efficient than basolateral K\(^+\) and \(\hbox {Cl}^-\) channels at lowering intracellular osmolality and reducing cell volume. Moreover, both RVD and RVI are predicted to stabilize net transcellular \(\hbox {Na}^+\) reabsorption, that is, to limit the net \(\hbox {Na}^+\) flux decrease during a hyposmotic challenge or the net \(\hbox {Na}^+\) flux increase during a hyperosmotic challenge.     

Comparison of the Functional Activities of Xanthine Oxidases Isolated from Microorganisms and from Cow’s Milk

The characteristics of the formation of the superoxide radical anion (\(\rm{O}_2^{\bullet-}\)) and hydrogen peroxide by xanthine oxidases isolated from microorganisms and from cow’s milk were investigated. The increase in pH led to an increase in the rate of xanthine oxidation with oxygen by both xanthine oxidases. The functioning of xanthine oxidase from milk along with the two-electron reduction of O₂ to H₂O₂ carries through the one-electron reduction of O₂ to \(\rm{O}_2^{\bullet-}\), and the rate and the fraction of generation of \(\rm{O}_2^{\bullet-}\) increased with increasing pH. Under operation of the microbial xanthine oxidase, the \(\rm{O}_2^{\bullet-}\) radical was not detected in the medium. The results suggest a difference in the operation of active centers of enzyme from different sources.     

Uptake of ammonium and soluble reactive phosphorus in forested streams: influence of dissolved organic matter composition

Many microbes responsible for inorganic nutrient uptake and transformation utilize dissolved organic matter (DOM) as a nutrient or energy source, but little is known about whether DOM composition is an important driver of nutrient uptake in streams. Our goal was to determine whether incorporating DOM composition metrics with other more commonly considered biological, physical, and chemical variables improved our ability to explain patterns of ammonium (\({\text{NH}}_{4}^{ + }\)–N) and soluble reactive phosphorus (SRP) uptake across 11 Lake Superior tributaries. Nutrient uptake velocities (V_f) ranged from undetectable to 14.6 mm min^?1 for \({\text{NH}}_{4}^{ + }\)–N and undetectable to 7.2 mm min^?1 for SRP. Logistic regressions suggested that DOM composition was a useful predictor of where SRP uptake occurred (4/11 sites) and \({\text{NH}}_{4}^{ + }\)–N concentration was a useful predictor of where \({\text{NH}}_{4}^{ + }\)–N uptake occurred (9/11 sites). Multiple regression analysis revealed that the best models included temperature, specific discharge, and canopy cover, and DOM composition as significant predictors of \({\text{NH}}_{4}^{ + }\)–N V_f. Partial least squares revealed fluorescence index (describing the source of aquatic fulvic acids), specific ultraviolet absorbance at 254 nm (an indicator of DOM aromaticity), temperature, and conductivity were highly influential predictors of \({\text{NH}}_{4}^{ + }\)–N V_f. Therefore, streams with higher temperatures, lower solute concentrations, more terrestrial DOM signal and greater aromaticity had greater \({\text{NH}}_{4}^{ + }\)–N V_f. Our results suggest that DOM composition may be an important, yet often overlooked, predictor of \({\text{NH}}_{4}^{ + }\)–N and SRP uptake in deciduous forest streams that should be considered along with commonly measured predictors.     

Isolation and characterization of microsatellite markers in the spiny lobster, <Emphasis Type="Italic">Panulirus echinatus</Emphasis> Smith, 1869 (Decapoda: Palinuridae) by Illumina MiSeq sequencing

Okra’s (Abelmoschus esculentus (L.) Moench) commercial cultivation is threatened in the tropics due to high incidence of yellow vein mosaic virus (YVMV) disease. Okra geneticists across the world tried to understand the inheritance pattern of YVMV disease tolerance without much success. Therefore, the inheritance pattern of YVMV disease in okra was revisited by employing six generations (\(\hbox {P}_{1}\), \(\hbox {P}_{2}\), \(\hbox {F}_{1}\), \(\hbox {F}_{2}\), \(\hbox {BC}_{1}\) and \(\hbox {BC}_{2}\)) of four selected crosses (one tolerant \(\times \) tolerant, two tolerant \(\times \) susceptible and one susceptible \(\times \) susceptible) using two tolerant (BCO-1 and Lal Bhendi) and two susceptible (Japanese Jhar Bhendi and PAN 2127) genotypes. Qualitative genetic analysis was done on the basis of segregation pattern of tolerant and susceptible plants in \(\hbox {F}_{2}\) and backcross generations of all the four crosses. It revealed that a single dominant gene along with some minor factors governed the disease tolerant trait in both the tolerant parents used. However, it was observed that genes governing disease tolerance identified in both the tolerant variety used was different. It could be concluded that the gene governing YVMV disease tolerance in okra was genotype specific. Further, duplicate gene action as evident from an approximate ratio of 15 : 1 (tolerant : susceptible) in the \(\hbox {F}_{2}\) population in the cross of two tolerant varieties gave a scope of increasing the tolerance level of the hybrid plants when both the tolerant genes are brought together. However, generation mean analysis revealed involvement of both additive and nonadditive effects in the inheritance of disease tolerance. Thus, the present study confirms that a complicated genetic inheritance pattern is involved in the disease tolerance against YVMV trait. The major tolerance genes could be transferred to other okra varieties, but the tolerance breaking virus strains might not allow them to achieve tolerance in stable condition. Therefore, accumulation of additional genes may be needed for a sustainable tolerance phenotype in okra.     

Resolving the viscoelasticity and anisotropy dependence of the mechanical properties of skin from a porcine model

The mechanical response of skin to external loads is influenced by anisotropy and viscoelasticity of the tissue, but the underlying mechanisms remain unclear. Here, we report a study of the main effects of tissue orientation (TO, which is linked to anisotropy) and strain rate (SR, a measure of viscoelasticity), as well as the interaction effects between the two factors, on the tensile properties of skin from a porcine model. Tensile testing to rupture of porcine skin tissue was conducted to evaluate the sensitivity of the tissue modulus of elasticity (E) and fracture-related properties, namely maximum stress \((\sigma _{U})\) and strain \((\varepsilon _{U})\) at \(\sigma _{U}\), to varying SR and TO. Specimens were excised from the abdominal skin in two orientations, namely parallel (P) and right angle (R) to the torso midline. Each TO was investigated at three SR levels, namely 0.007–0.015 \(\hbox {s}^{-1}\) (low), 0.040 \(\hbox {s}^{-1}\) (mid) and 0.065 \(\hbox {s}^{-1}\) (high). Two-factor analysis of variance revealed that the respective parameters responded differently to varying SR and TO. Significant changes in the \(\sigma _{U}\) were observed with different TOs but not with SR. The \(\varepsilon _{U}\) decreased significantly with increasing SR, but no significant variation was observed for different TOs. Significant changes in E were observed with different TOs; E increased significantly with increasing SR. More importantly, the respective mechanical parameters were not significantly influenced by interactions between SR and TO. These findings suggest that the trends associated with the changes in the skin mechanical properties may be attributed partly to differences in the anisotropy and viscoelasticity but not through any interaction between viscoelasticity and anisotropy.     

Trend analysis of variations in carbon stock using stock big data

Changes in land use affect the terrestrial carbon stock through changes in the land cover. Research on land use and analysis of variations in carbon stock have practical applications in the optimization of land use and the mitigation of climate change effects. This study was conducted in Baixiang and Julu counties in the Taihang Piedmont by employing the trend analysis method to characterize the variation in county land use and carbon stock. The findings show that in both counties, agricultural and unused land areas decreased while built-up land area increased, and the reduction in cropland was the main reason behind the agricultural land reduction. An inflection point appeared on the cropland curves of Julu, because the cropland area decreased by 1576.97 hm\(^{2}\) from 2004 to 2006. Cropland area in Baixiang decreased from 1996 to 1998 by a total of 129.89 hm\(^{2}\) and then remained relatively stable after 1998. The total carbon storage and variation in land use in the two counties displayed similar trends. Total carbon reserves in Julu increased by 2.76 \(\times \) 10\(^{4}\) tC (carbon equivalent), while those in Baixiang decreased by 0.63 \(\times \) 10\(^{4}\) tC. Carbon stock of built-up land in Julu and Baixiang increased by 2.44 \(\times \) 10\(^{4}\) and 1.22 \(\times \) 10\(^{4}\) tC, respectively.     

Calcium signaling as a novel method to optimize the biosynthetic response of chondrocytes to dynamic mechanical loading

Chondrocyte sensitization and desensitization to mechanical stimuli are complex phenomena that have not been fully described. In this study, we investigated the temporal response of chondrocytes to dynamic mechanical loading and whether changes in calcium signaling could be used a predictor of the biosynthetic response. Cell-seeded agarose gels pre-incubated with an intracellular \(\hbox {Ca}^{2+}\) dye (Fluo-4) were subjected to dynamic compressive loading under varying conditions (amplitude and duration). Induced changes in \(\hbox {Ca}^{2+}\) signaling were determined by confocal imaging and matrix biosynthesis by radioisotope incorporation. It was observed that chondrocytes required a minimum amount of stimulation in order to elicit an anabolic response and they quickly became insensitive to the imposed stimulus. The response appeared to be amplitude dependent and could be predicted by measuring resultant changes in \(\hbox {Ca}^{2+}\) signaling. A positive correlation between \(\hbox {Ca}^{2+}\) signaling and matrix synthesis was achieved when changes in \(\hbox {Ca}^{2+}\) signaling was expressed as a relative number of cells experiencing multiple transients. In addition, these changes in \(\hbox {Ca}^{2+}\) signaling were effective at determining optimal recovery period between successive applications of intermittent mechanical loading, in which full mechanosensitivity was achieved when \(\hbox {Ca}^{2+}\) signaling was allowed to return to baseline (control) levels. The use of \(\hbox {Ca}^{2+}\) signaling to predict the effectiveness of a particular mechanical stimulus as well as to determine optimal refractory periods appears to be advantageous over empirical-based approaches. Future work will investigate the process of \(\hbox {Ca}^{2+}\) ion sequestration into intracellular stores to elucidate potential desensitization mechanisms to dynamic mechanical loading.     

Towards the prediction of flow-induced shear stress distributions experienced by breast cancer cells in the lymphatics

Tumour metastasis in the lymphatics is a crucial step in the progression of breast cancer. The dynamics by which breast cancer cells (BCCs) travel in the lymphatics remains poorly understood. The goal of this work is to develop a model capable of predicting the shear stresses metastasising BCCs experience using numerical and experimental techniques. This paper models the fluidic transport of large particles (\(\eta =d_{\mathrm{p}}/W=0.1-0.4\) where \(d_{\mathrm{p}}\) is the particle diameter and W is the channel width) subjected to lymphatic flow conditions (\({ Re}=0.04\)), in a \(100\times 100\,\upmu \hbox {m}\) microchannel. The feasibility of using the dynamic fluid body interaction (DFBI) method to predict particle motion was assessed, and particle tracking experiments were performed. The experiments found that particle translational velocity decreased from the undisturbed fluid velocity with increasing particle size (5–14% velocity lag for \(\eta =0.1-0.3\)). DFBI simulations were found to better predict particle behaviour than theoretical predictions; however, mesh restrictions in the near-wall region (\(0.2\,\mathrm{W}>y>0.8\,\mathrm{W}\)) result in computationally expensive models. The simulations were in good agreement with the experiments (\(<12\%\) difference) across the channel (\(0.2\,\mathrm{W}\le y\le 0.8\,\mathrm{W}\)), with differences up to 25% in the near-wall region. Particles experience a range of shear stresses (0.002–0.12 Pa) and spatial shear gradients (\(0.004-0.137\,\hbox {Pa}/\upmu \hbox {m}\)) depending on their size and radial position. The predicted shear gradients are far in excess of values associated with BCC apoptosis (\(0.004-0.023\,\hbox {Pa}/\upmu \hbox {m}\)). Increasing our understanding of the shear stress magnitudes and gradients experienced by BCCs could be leveraged to elucidate whether a particular BCC size or location exists that encourages metastasis within the lymphatics.     

Computational modelling of local calcium ions release from calcium phosphate-based scaffolds

A variety of natural or synthetic calcium phosphate (CaP)-based scaffolds are currently produced for dental and orthopaedic applications. These scaffolds have been shown to stimulate bone formation due to their biocompatibility, osteoconductivity and osteoinductivity. The release of the \(\hbox {Ca}^{2+}\) ions from these scaffolds is of great interest in light of the aforementioned properties. It can depend on a number of biophysicochemical phenomena such as dissolution, diffusion and degradation, which in turn depend on specific scaffold characteristics such as composition and morphology. Achieving an optimal release profile can be challenging when relying on traditional experimental work alone. Mathematical modelling can complement experimentation. In this study, the in vitro dissolution behaviour of four CaP-based scaffold types was investigated experimentally. Subsequently, a mechanistic finite element method model based on biophysicochemical phenomena and specific scaffold characteristics was developed to predict the experimentally observed behaviour. Before the model could be used for local \(\hbox {Ca}^{2+}\) ions release predictions, certain parameters such as dissolution constant (\(k_{\mathrm{dc}}\)) and degradation constant (\(k_\mathrm{sc}\)) for each type of scaffold were determined by calibrating the model to the in vitro dissolution data. The resulting model showed to yield release characteristics in satisfactory agreement with those observed experimentally. This suggests that the mathematical model can be used to investigate the local \(\hbox {Ca}^{2+}\) ions release from CaP-based scaffolds.     

Measuring the signs of the methyl <Superscript>1</Superscript>H chemical shift differences between major and ‘invisible’ minor protein conformational states using methyl <Superscript>1</Superscript>H multi-quantum spectroscopy

Carr–Purcell–Meiboom–Gill (CPMG) type relaxation dispersion experiments are now routinely used to characterise protein conformational dynamics that occurs on the μs to millisecond (ms) timescale between a visible major state and ‘invisible’ minor states. The exchange rate(s) (\( k_{{{\text{ex}}}} \)), population(s) of the minor state(s) and the absolute value of the chemical shift difference \(|{\Delta \varpi }|\) (ppm) between different exchanging states can be extracted from the CPMG data. However the sign of \({\Delta \varpi }\) that is required to reconstruct the spectrum of the ‘invisible’ minor state(s) cannot be obtained from CPMG data alone. Building upon the recently developed triple quantum (TQ) methyl \( ^{1} {\text{H}} \) CPMG experiment (Yuwen in Angew Chem 55:11490–11494, 2016) we have developed pulse sequences that use carbon detection to generate and evolve single quantum (SQ), double quantum (DQ) and TQ coherences from methyl protons in the indirect dimension to measure the chemical exchange-induced shifts of the SQ, DQ and TQ coherences from which the sign of \({\Delta \varpi }\) is readily obtained for two state exchange. Further a combined analysis of the CPMG data and the difference in exchange induced shifts between the SQ and DQ resonances and between the SQ and TQ resonances improves the estimates of exchange parameters like the population of the minor state. We demonstrate the use of these experiments on two proteins undergoing exchange: (1) the ~ 18 kDa cavity mutant of T4 Lysozyme (\( k_{{{\text{ex}}}} \sim\,3500{\text{ s}}^{{ - 1}} \)) and (2) the \(\sim\,4.7\) kDa Peripheral Sub-unit Binding Domain (PSBD) from the acetyl transferase of Bacillus stearothermophilus (\(k_{ex} \sim\,13,000\hbox { s}^{-1}\)).