Genetic variability,management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis

Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as Bothrops insularis, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (a) characterize the genetic diversity of ex situ and in situ populations of B. insularis using heterologous microsatellites; (b) investigate genetic structure among and within these populations; and (c) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the B. neuwiedi group were used to access genetic diversity indexes of ex situ and in situ populations. Low‐to‐medium genetic diversity parameters were found. Both populations showed low—albeit significant—values of system of mating inbreeding coefficient, whereas only the in situ population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the in situ one, which is crucial for considering a reintroduction process into the island.     

What Is Stochastic Resonance? Definitions, Misconceptions, Debates, and Its Relevance to Biology

Stochastic resonance is said to be observed when increases in levels of unpredictable fluctuations—e.g., random noise—cause an increase in a metric of the quality of signal transmission or detection performance, rather than a decrease. This counterintuitive effect relies on system nonlinearities and on some parameter ranges being “suboptimal”. Stochastic resonance has been observed, quantified, and described in a plethora of physical and biological systems, including neurons. Being a topic of widespread multidisciplinary interest, the definition of stochastic resonance has evolved significantly over the last decade or so, leading to a number of debates, misunderstandings, and controversies. Perhaps the most important debate is whether the brain has evolved to utilize random noise in vivo, as part of the “neural code”. Surprisingly, this debate has been for the most part ignored by neuroscientists, despite much indirect evidence of a positive role for noise in the brain. We explore some of the reasons for this and argue why it would be more surprising if the brain did not exploit randomness provided by noise—via stochastic resonance or otherwise—than if it did. We also challenge neuroscientists and biologists, both computational and experimental, to embrace a very broad definition of stochastic resonance in terms of signal-processing “noise benefits”, and to devise experiments aimed at verifying that random variability can play a functional role in the brain, nervous system, or other areas of biology.     

Helical coherence of DNA in crystals and solution

The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however, is obscured by poorly understood variations in the stacking geometry of the same adjoining base pairs within different sequence contexts. In this article, we approach the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers. We evaluate the corresponding helical coherence length—a cumulative parameter quantifying sequence-dependent deviations from the ideal double helix geometry. We find, e.g. that the solution structure of synthetic oligomers is characterized by 100–200 Å coherence length, which is similar to ~150 Å coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800–1200 Å, consistent with its theoretically predicted role in interactions between DNA at close separations.     

Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity

Enzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filament-forming sequence-specific DNA endonuclease SgrAI, the process of filamentation both accelerates its DNA cleavage activity and expands its DNA sequence specificity, thus allowing for many additional DNA sequences to be rapidly cleaved. Both outcomes—the acceleration of DNA cleavage and the expansion of sequence specificity—are proposed to regulate critical processes in bacterial innate immunity. However, the mechanistic bases underlying these events remain unclear. Herein, we describe two new structures of the SgrAI enzyme that shed light on its catalytic function. First, we present the cryo-EM structure of filamentous SgrAI bound to intact primary site DNA and Ca²⁺ resolved to ∼2.5 Å within the catalytic center, which represents the trapped enzyme–DNA complex prior to the DNA cleavage reaction. This structure reveals important conformational changes that contribute to the catalytic mechanism and the binding of a second divalent cation in the enzyme active site, which is expected to contribute to increased DNA cleavage activity of SgrAI in the filamentous state. Second, we present an X-ray crystal structure of DNA-free (apo) SgrAI resolved to 2.0 Å resolution, which reveals a disordered loop involved in DNA recognition. Collectively, these multiple new observations clarify the mechanism of expansion of DNA sequence specificity of SgrAI, including the indirect readout of sequence-dependent DNA structure, changes in protein–DNA interactions, and the disorder-to-order transition of a crucial DNA recognition element.     

Advanced Beamformers for Cochlear Implant Users: Acute Measurement of Speech Perception in Challenging Listening Conditions

Objective

To investigate the performance of monaural and binaural beamforming technology with an additional noise reduction algorithm, in cochlear implant recipients.

Method

This experimental study was conducted as a single subject repeated measures design within a large German cochlear implant centre. Twelve experienced users of an Advanced Bionics HiRes90K or CII implant with a Harmony speech processor were enrolled. The cochlear implant processor of each subject was connected to one of two bilaterally placed state-of-the-art hearing aids (Phonak Ambra) providing three alternative directional processing options: an omnidirectional setting, an adaptive monaural beamformer, and a binaural beamformer. A further noise reduction algorithm (ClearVoice) was applied to the signal on the cochlear implant processor itself. The speech signal was presented from 0° and speech shaped noise presented from loudspeakers placed at ±70°, ±135° and 180°. The Oldenburg sentence test was used to determine the signal-to-noise ratio at which subjects scored 50% correct.

Results

Both the adaptive and binaural beamformer were significantly better than the omnidirectional condition (5.3 dB±1.2 dB and 7.1 dB±1.6 dB (p<0.001) respectively). The best score was achieved with the binaural beamformer in combination with the ClearVoice noise reduction algorithm, with a significant improvement in SRT of 7.9 dB±2.4 dB (p<0.001) over the omnidirectional alone condition.

Conclusions

The study showed that the binaural beamformer implemented in the Phonak Ambra hearing aid could be used in conjunction with a Harmony speech processor to produce substantial average improvements in SRT of 7.1 dB. The monaural, adaptive beamformer provided an averaged SRT improvement of 5.3 dB.     

Features of Large Hinge-Bending Conformational Transitions. Prediction of Closed Structure from Open State

We performed a detailed analysis of conformational transition pathways for a set of 10 proteins, which undergo large hinge-bending-type motions with 4–12 Å RMSD (root mean-square distance) between open and closed crystal structures. Anisotropic network model-Monte Carlo (ANM-MC) algorithm generates a targeted pathway between two conformations, where the collective modes from the ANM are used for deformation at each iteration and the conformational energy of the deformed structure is minimized via an MC algorithm. The target structure was approached successfully with an RMSD of 0.9–4.1 Å when a relatively low cutoff radius of 10 Å was used in ANM. Even though one predominant mode (first or second) directed the open-to-closed conformational transition, changes in the dominant mode character were observed for most cases along the transition. By imposing radius of gyration constraint during mode selection, it was possible to predict the closed structure for eight out of 10 proteins (with initial 4.1–7.1 Å and final 1.7–2.9 Å RMSD to target). Deforming along a single mode leads to most successful predictions. Based on the previously reported free energy surface of adenylate kinase, deformations along the first mode produced an energetically favorable path, which was interestingly facilitated by a change in mode shape (resembling second and third modes) at key points. Pathway intermediates are provided in our database of conformational transitions (http://safir.prc.boun.edu.tr/anmmc/method/1).     

Anterior Lamina Cribrosa Insertion in Primary Open-Angle Glaucoma Patients and Healthy Subjects

PurposeTo determine using swept-source optical coherence tomography (SS-OCT) whether there are differences in the location of the anterior lamina cribrosa insertion (ALI) in primary open-angle glaucoma (POAG) patients and healthy subjects.MethodsFifty three eyes from 53 patients with POAG, and 53 eyes from 53 age-matched healthy subjects were included prospectively in Seoul National University Bundang Hospital. Twelve radial line B-scans centered on the optic disc in every half-clock-hour meridian were acquired using SS-OCT. The ALI position was assessed by measuring two parameters: (1) ALI distance (ALID)—the distance from the anterior scleral canal opening (ASCO) to the ALI; and (2) marginal anterior lamina cribrosa surface depth (mALCSD)—the perpendicular distance from the ASCO plane to the anterior lamina cribrosa surface. These parameters were compared between the two groups for each meridian.ResultsBoth ALID (256±54 vs. 209±37 µm, mean ± SD, p<0.001) and mALCSD (232±63 vs. 187±40 µm, p<0.001) were significantly greater in the POAG group than in the normal group. The largest difference was observed at the 6.5 o′clock and 11.5 o′clock meridians for both ALID and mALCSD. Multiple regression analysis revealed a negative correlation between age and both ALID and mALCSD in the control group, and a negative correlation between mean deviation of the visual field test and both ALID and mALCSD in the POAG group.ConclusionsThe ALI was displaced posteriorly in eyes with POAG compared to those of healthy controls. This finding suggests that the posteriorly located lamina cribrosa insertion is an important component of glaucomatous optic nerve excavation.     

Adaptive search space pruning in complex strategic problems

People have limited computational resources, yet they make complex strategic decisions over enormous spaces of possibilities. How do people efficiently search spaces with combinatorially branching paths? Here, we study players’ search strategies for a winning move in a “k-in-a-row” game. We find that players use scoring strategies to prune the search space and augment this pruning by a “shutter” heuristic that focuses the search on the paths emanating from their previous move. This strong pruning has its costs—both computational simulations and behavioral data indicate that the shutter size is correlated with players’ blindness to their opponent’s winning moves. However, simulations of the search while varying the shutter size, complexity levels, noise levels, branching factor, and computational limitations indicate that despite its costs, a narrow shutter strategy is the dominant strategy for most of the parameter space. Finally, we show that in the presence of computational limitations, the shutter heuristic enhances the performance of deep learning networks in these end-game scenarios. Together, our findings suggest a novel adaptive heuristic that benefits search in a vast space of possibilities of a strategic game.     

Maternal Lineage of Warmblood Mares Contributes to Variation of Gestation Length and Bias of Foal Sex Ratio

Maternal lineage influences performance traits in horses. This is probably caused by differences in mitochondrial DNA (mtDNA) transferred to the offspring via the oocyte. In the present study, we investigated if reproductive traits with high variability—gestation length and fetal sex ratio—are influenced by maternal lineage. Data from 142 Warmblood mares from the Brandenburg State Stud at Neustadt (Dosse), Germany, were available for the study. Mares were grouped according to their maternal lineage. Influences on the reproduction parameters gestation length and sex ratio of offspring were analyzed by simple and multiple analyses of variance. A total of 786 cases were included. From the 142 mares, 119 were assigned to six maternal lineages with n≥10 mares per lineage, and 23 mares belonged to smaller maternal lineages. The mean number of live foals produced per mare was 4.6±3.6 (±SD). Live foal rate was 83.5%. Mean gestation length was 338.5±8.9 days (±SD) with a range of 313 to 370 days. Gestation length was affected by maternal lineage (p<0.001). Gestation length was also significantly influenced by the individual mare, age of the mare, year of breeding, month of breeding and sex of the foal (p<0.05). Of the 640 foals born alive at term, 48% were male and 52% female. Mare age group and maternal lineage significantly influenced the sex ratio of the foals (p<0.05). It is concluded that maternal lineage influences reproductive parameters with high variation such as gestation length and foal sex ratio in horses. In young primiparous and aged mares, the percentage of female offspring is higher than the expected 1:1 ratio.     

Movement Demands of Elite U20 International Rugby Union Players

The purpose of this study was to quantify movement demands of elite international age grade (U20) rugby union players during competitive tournament match play. Forty elite professional players from an U20 international performance squad were monitored using 10Hz global positioning systems (GPS) during 15 international tournament matches during the 2014/15 and 2015/16 seasons. Data on distances, velocities, accelerations, decelerations, high metabolic load (HML) distance and efforts, and number of sprints were derived. Data files from players who played over 60 min (n = 161) were separated firstly into Forwards and Backs, and more specifically into six positional groups; FR—Front Row (prop & hooker), SR—Second Row, BR—Back Row (Flankers & No.8), HB—Half Backs (scrum half & outside half), MF—Midfield (centres), B3 –Back Three (wings & full back) for match analysis. Analysis revealed significant differences between forwards and backs positions. Backs scored higher on all variables measured with the exception of number of moderate accelerations, decelerations (no difference). The centres covered the greatest total distance with the front row covering the least (6.51 ± 0.71 vs 4.97 ± 0.75 km, p < 0.001). The front row also covered the least high speed running (HSR) distance compared to the back three (211.6 ± 112.7 vs 728.4 ± 150.2 m, p < 0.001) who covered the most HSR distance, affirming that backs cover greater distances but forwards have greater contact loads. These findings highlight for the first time differences in the movement characteristics of elite age grade rugby union players specific to positional roles.     

The Positive Effects of Priming Exercise on Oxygen Uptake Kinetics and High-Intensity Exercise Performance Are Not Magnified by a Fast-Start Pacing Strategy in Trained Cyclists

The purpose of this study was to determine both the independent and additive effects of prior heavy-intensity exercise and pacing strategies on the VO2 kinetics and performance during high-intensity exercise. Fourteen endurance cyclists (VO₂max  = 62.8±8.5 mL.kg⁻¹.min⁻¹) volunteered to participate in the present study with the following protocols: 1) incremental test to determine lactate threshold and VO₂max; 2) four maximal constant-load tests to estimate critical power; 3) six bouts of exercise, using a fast-start (FS), even-start (ES) or slow-start (SS) pacing strategy, with and without a preceding heavy-intensity exercise session (i.e., 90% critical power). In all conditions, the subjects completed an all-out sprint during the final 60 s of the test as a measure of the performance. For the control condition, the mean response time was significantly shorter (p<0.001) for FS (27±4 s) than for ES (32±5 s) and SS (32±6 s). After the prior exercise, the mean response time was not significantly different among the paced conditions (FS = 24±5 s; ES = 25±5 s; SS = 26±5 s). The end-sprint performance (i.e., mean power output) was only improved (∼3.2%, p<0.01) by prior exercise. Thus, in trained endurance cyclists, an FS pacing strategy does not magnify the positive effects of priming exercise on the overall VO2 kinetics and short-term high-intensity performance.     

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions.     

Macular Bruch′s Membrane Length and Axial Length. The Beijing Eye Study

Purpose

To assess whether macular Bruch´s membrane gets lengthened in axial myopia.

Methods

Using the enhanced depth imaging mode of spectral-domain optical coherence tomography and examining a subgroup of participants of the population-based cross-sectional Beijing Eye Study, we measured the length of Bruch´s membrane (“MacBMLength”) from the fovea to the temporal edge of parapapillary gamma zone, and the distance between the fovea and the temporal optic disc border. Parapapillary gamma zone was defined as the parapapillary region without Bruch´s membrane. We additionally measured ocular biometric parameters and assessed non-ophthalmologic variables.

Results

Measurements of MacBMLength were performed on 322 individuals. MacBMLength (mean: 3.99±0.33 mm; range: 3.17–4.93 mm) was not significantly associated with any systemic parameter or ocular biometric parameter. Gamma zone width (mean: 0.18±0.30mm; range: 0.00–2.61mm) was associated (multivariate analysis; correlation coefficient r:0.80) with longer axial length (P<0.001; standardized correlation coefficient beta: 0.60; non-standardized correlation coefficient B:0.11; 95%CI: 0.09,0.14) and with longer fovea-optic disc border distance (P<0.001; beta:0.28; B:0.19; 95%CI:0.14,0.25), but not with MacBMLength (P = 0.42). Fovea-temporal disc border distance (mean: 4.16±0.44mm; range: 3.17–5.86mm) was associated (overall correlation coefficient: 0.68) with longer axial length (P<0.001; beta: 0.36; B: 0.10; 95%CI: 0.06, 0.13), after adjusting for flatter anterior chamber depth (P = 0.003; beta:-0.14; B:-0.14; 95%CI: -0.23,-0.05) and wider parapapillary gamma zone (P<0.001; beta:0.42; B:0.62; 95%CI:0.44,0.81).

Conclusions

In contrast to parapapillary gamma zone width and fovea-disc border distance, MacBMLength was not significantly associated with axial length. Axial elongation associated increase in fovea-disc distance may predominantly occur through development or elongation of parapapillary gamma zone, while macular Bruch´s membrane may mostly be independent of axial elongation.     

Profile of the GSK Published Protein Kinase Inhibitor Set Across ATP-Dependent and-Independent Luciferases: Implications for Reporter-Gene Assays

A library of 367 protein kinase inhibitors, the GSK Published Kinase Inhibitor Set (PKIS), which has been annotated for protein kinase family activity and is available for public screening efforts, was assayed against the commonly used luciferase reporter enzymes from the firefly, Photinus pyralis (FLuc) and marine sea pansy, Renilla reniformis (RLuc). A total of 22 compounds (∼6% of the library) were found to inhibit FLuc with 10 compounds showing potencies ≤1 µM. Only two compounds were found to inhibit RLuc, and these showed relatively weak potency values (∼10 µM). An inhibitor series of the VEGFR2/TIE2 protein kinase family containing either an aryl oxazole or benzimidazole-urea core illustrate the different structure activity relationship profiles FLuc inhibitors can display for kinase inhibitor chemotypes. Several FLuc inhibitors were broadly active toward the tyrosine kinase and CDK families. These data should aid in interpreting the results derived from screens employing the GSK PKIS in cell-based assays using the FLuc reporter. The study also underscores the general need for strategies such as the use of orthogonal reporters to identify kinase or non-kinase mediated cellular responses.     

Androgen Function in “Psychogenic” and “Constitutional” Types of Impotence

Androgen function was studied in twenty-five physically healthy “primarily” impotent males classified on clinical criteria into “psychogenic” or “constitutional” groups. The mean urinary testosterone level in the former was significantly higher than in the latter group (P<0·005). Important variables associated significantly with higher urinary testosterone levels (P<0·05) were (a) “late onset” impotence, (b) shorter duration than two years, (c) stronger “sex drive,” and (d) an alternative sexual outlet to orgasm and ejaculation in the three months preceding referral; the last-mentioned appeared to be the single most important discriminatory feature.It is suggested that testosterone excretion patterns—namely, high, average, and low—may be one method of classifying impotence.     

Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain

Vancomycin response regulator (VncR) is a pneumococcal response regulator of the VncRS two-component signal transduction system (TCS) of Streptococcus pneumoniae. VncRS regulates bacterial autolysis and vancomycin resistance. VncR contains two different functional domains, the N-terminal receiver domain and C-terminal effector domain. Here, we investigated VncR C-terminal DNA binding domain (VncRc) structure using a crystallization approach. Crystallization was performed using the micro-batch method. The crystals diffracted to a 1.964 _Å resolution and belonged to space group P212121. The crystal unit-cell parameters were a = 25.71 _Å, b = 52.97 _Å, and c = 60.61 _Å. The structure of VncRc had a helix-turn-helix motif highly similar to the response regulator PhoB of Escherichia coli. In isothermal titration calorimetry and size exclusion chromatography results, VncR formed a complex with VncS, a sensor histidine kinase of pneumococcal TCS. Determination of VncR structure will provide insight into the mechanism by how VncR binds to target genes.     

Coronary Stent Artifact Reduction with an Edge-Enhancing Reconstruction Kernel – A Prospective Cross-Sectional Study with 256-Slice CT

PurposeMetallic artifacts can result in an artificial thickening of the coronary stent wall which can significantly impair computed tomography (CT) imaging in patients with coronary stents. The objective of this study is to assess in vivo visualization of coronary stent wall and lumen with an edge-enhancing CT reconstruction kernel, as compared to a standard kernel.MethodsThis is a prospective cross-sectional study involving the assessment of 71 coronary stents (24 patients), with blinded observers. After 256-slice CT angiography, image reconstruction was done with medium-smooth and edge-enhancing kernels. Stent wall thickness was measured with both orthogonal and circumference methods, averaging thickness from diameter and circumference measurements, respectively. Image quality was assessed quantitatively using objective parameters (noise, signal to noise (SNR) and contrast to noise (CNR) ratios), as well as visually using a 5-point Likert scale.ResultsStent wall thickness was decreased with the edge-enhancing kernel in comparison to the standard kernel, either with the orthogonal (0.97 ± 0.02 versus 1.09 ± 0.03 mm, respectively; p<0.001) or the circumference method (1.13 ± 0.02 versus 1.21 ± 0.02 mm, respectively; p = 0.001). The edge-enhancing kernel generated less overestimation from nominal thickness compared to the standard kernel, both with the orthogonal (0.89 ± 0.19 versus 1.00 ± 0.26 mm, respectively; p<0.001) and the circumference (1.06 ± 0.26 versus 1.13 ± 0.31 mm, respectively; p = 0.005) methods. The edge-enhancing kernel was associated with lower SNR and CNR, as well as higher background noise (all p < 0.001), in comparison to the medium-smooth kernel. Stent visual scores were higher with the edge-enhancing kernel (p<0.001).ConclusionIn vivo 256-slice CT assessment of coronary stents shows that the edge-enhancing CT reconstruction kernel generates thinner stent walls, less overestimation from nominal thickness, and better image quality scores than the standard kernel.     

Dimensionless parameter predicts bacterial prodrug success

Understanding mechanisms of antibiotic failure is foundational to combating the growing threat of multidrug‐resistant bacteria. Prodrugs—which are converted into a pharmacologically active compound after administration—represent a growing class of therapeutics for treating bacterial infections but are understudied in the context of antibiotic failure. We hypothesize that strategies that rely on pathogen‐specific pathways for prodrug conversion are susceptible to competing rates of prodrug activation and bacterial replication, which could lead to treatment escape and failure. Here, we construct a mathematical model of prodrug kinetics to predict rate‐dependent conditions under which bacteria escape prodrug treatment. From this model, we derive a dimensionless parameter we call the Bacterial Advantage Heuristic (BAH) that predicts the transition between prodrug escape and successful treatment across a range of time scales (1–10⁴ h), bacterial carrying capacities (5 × 10⁴–10⁵ CFU/µl), and Michaelis constants (K_M  = 0.747–7.47 mM). To verify these predictions in vitro, we use two models of bacteria‐prodrug competition: (i) an antimicrobial peptide hairpin that is enzymatically activated by bacterial surface proteases and (ii) a thiomaltose‐conjugated trimethoprim that is internalized by bacterial maltodextrin transporters and hydrolyzed by free thiols. We observe that prodrug failure occurs at BAH values above the same critical threshold predicted by the model. Furthermore, we demonstrate two examples of how failing prodrugs can be rescued by decreasing the BAH below the critical threshold via (i) substrate design and (ii) nutrient control. We envision such dimensionless parameters serving as supportive pharmacokinetic quantities that guide the design and administration of prodrug therapeutics.     

Deletion of CD73 increases exercise power in mice

Ecto-5′-nucleotidase or CD73 is the main source of extracellular adenosine involved in the activation of adenosine A_2A receptors, responsible for the ergogenic effects of caffeine. We now investigated the role of CD73 in exercise by comparing female wild-type (WT) and CD73 knockout (KO) mice in a treadmill-graded test to evaluate running power, oxygen uptake (V̇O₂), and respiratory exchange ratio (RER) — the gold standards characterizing physical performance. Spontaneous locomotion in the open field and submaximal running power and V̇O₂ in the treadmill were similar between CD73-KO and WT mice; V̇O₂max also demonstrated equivalent aerobic power, but CD73-KO mice displayed a 43.7 ± 4.2% larger critical power (large effect size, P < 0.05) and 3.8 ± 0.4% increase of maximum RER (small effect size, P < 0.05). Thus, KO of CD73 was ergogenic; i.e., it increased physical performance.     

Cavities and Atomic Packing in Protein Structures and Interfaces

A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues) lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 ų of cavity volume is found to accommodate single water, with another 40–45 ų needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface), residues in β-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein–protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein–protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure.