The unreasonable effectiveness of equilibrium gene regulation through the cell cycle.

Systems like the prototypical lac operon can reliably hold repression of transcription upon DNA replication across cell cycles with just 10 repressor molecules per cell and behave as if they were at equilibrium. The origin of this phenomenology is still an unresolved question. Here, we develop a general theory to analyze strong perturbations in quasi-equilibrium systems and use it to quantify the effects of DNA replication in gene regulation. We find a scaling law linking actual with predicted equilibrium transcription via a single kinetic parameter. We show that even the lac operon functions beyond the physical limits of naive regulation through compensatory mechanisms that suppress non-equilibrium effects. Synthetic systems without adjuvant activators, such as the cAMP receptor protein (CRP), lack this reliability. Our results provide a rationale for the function of CRP, beyond just being a tunable activator, as a mitigator of cell cycle perturbations.

Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites.

The prevalent one-dimensional alignment of genomic signals to a reference landmark is a cornerstone of current methods to study transcription and its DNA-dependent processes but it is prone to mask potential relations among multiple DNA elements. We developed a systematic approach to align genomic signals to multiple locations simultaneously by expanding the dimensionality of the genomic-coordinate space. We analyzed transcription in human and uncovered a complex dependence on the relative position of neighboring transcription start sites (TSSs) that is consistently conserved among cell types. The dependence ranges from enhancement to suppression of transcription depending on the relative distances to the TSSs, their intragenic position, and the transcriptional activity of the gene. Our results reveal a conserved hierarchy of alternative TSS usage within a previously unrecognized level of genomic organization and provide a general methodology to analyze complex functional relationships among multiple types of DNA elements.

Dynamics-informed deconvolutional neural networks for super-resolution identification of regime changes in epidemiological time series.

The ability to infer the timing and amplitude of perturbations in epidemiological systems from their stochastically spread low-resolution outcomes is crucial for multiple applications. However, the general problem of connecting epidemiological curves with the underlying incidence lacks the highly effective methodology present in other inverse problems, such as super-resolution and dehazing from computer vision. Here, we develop an unsupervised physics-informed convolutional neural network approach in reverse to connect death records with incidence that allows the identification of regime changes at single-day resolution. Applied to COVID-19 data with proper regularization and model-selection criteria, the approach can identify the implementation and removal of lockdowns and other nonpharmaceutical interventions (NPIs) with 0.93-day accuracy over the time span of a year.

Robustness of DNA looping across multiple cell divisions in individual bacteria.

DNA looping has emerged as a central paradigm of transcriptional regulation, as it is shared across many living systems. One core property of DNA looping-based regulation is its ability to greatly enhance repression or activation of genes with only a few copies of transcriptional regulators. However, this property based on a small number of proteins raises the question of the robustness of such a mechanism with respect to the large intracellular perturbations taking place during growth and division of the cell. Here we address the issue of sensitivity to variations of intracellular parameters of gene regulation by DNA looping. We use the lac system as a prototype to experimentally identify the key features of the robustness of DNA looping in growing Escherichia coli cells. Surprisingly, we observe time intervals of tight repression spanning across division events, which can sometimes exceed 10 generations. Remarkably, the distribution of such long time intervals exhibits memoryless statistics that is mostly insensitive to repressor concentration, cell division events, and the number of distinct loops accessible to the system. By contrast, gene regulation becomes highly sensitive to these perturbations when DNA looping is absent. Using stochastic simulations, we propose that the observed robustness to division emerges from the competition between fast, multiple rebinding events of repressors and slow initiation rate of the RNA polymerase. We argue that fast rebinding events are a direct consequence of DNA looping that ensures robust gene repression across a range of intracellular perturbations.

Ascertaining the initiation of epidemic resurgences: an application to the COVID-19 second surges in Europe and the Northeast United States.

Assessing a potential resurgence of an epidemic outbreak with certainty is as important as it is challenging. The low number of infectious individuals after a long regression, and the randomness associated with it, makes it difficult to ascertain whether the infectious population is growing or just fluctuating. We have developed an approach to compute confidence intervals for the switching time from decay to growth and to compute the corresponding multiple-location aggregated quantities over a region to increase the precision of the determination. We estimated the aggregate prevalence over time for Europe and the northeast United States to characterize the COVID-19 second surge in these regions during year 2020. We find a starting date as early as 3 July (95% confidence interval (CI): 1-6 July) for Europe and 19 August (95% CI: 16-23 August) for the northeast United States; subsequent infectious populations that, as of 31 December, have always increased or remained stagnant; and the resurgences being the collective effect of each overall region with no location, either country or state, dominating the regional dynamics by itself.

Reliably quantifying the evolving worldwide dynamic state of the COVID-19 outbreak from death records, clinical parametrization, and demographic data.

The dynamic characterization of the COVID-19 outbreak is critical to implement effective actions for its control and eradication but the information available at a global scale is not sufficiently reliable to be used directly. Here, we develop a quantitative approach to reliably quantify its temporal evolution and controllability through the integration of multiple data sources, including death records, clinical parametrization of the disease, and demographic data, and we explicitly apply it to countries worldwide, covering 97.4% of the human population, and to states within the United States (US). The validation of the approach shows that it can accurately reproduce the available prevalence data and that it can precisely infer the timing of nonpharmaceutical interventions. The results of the analysis identified general patterns of recession, stabilization, and resurgence. The diversity of dynamic behaviors of the outbreak across countries is paralleled by those of states and territories in the US, converging to remarkably similar global states in both cases. Our results offer precise insights into the dynamics of the outbreak and an efficient avenue for the estimation of the prevalence rates over time.

All-or-none amyloid disassembly via chaperone-triggered fibril unzipping favors clearance of α-synuclein toxic species.

α-synuclein aggregation is present in Parkinson's disease and other neuropathologies. Among the assemblies that populate the amyloid formation process, oligomers and short fibrils are the most cytotoxic. The human Hsc70-based disaggregase system can resolve α-synuclein fibrils, but its ability to target other toxic assemblies has not been studied. Here, we show that this chaperone system preferentially disaggregates toxic oligomers and short fibrils, while its activity against large, less toxic amyloids is severely impaired. Biochemical and kinetic characterization of the disassembly process reveals that this behavior is the result of an all-or-none abrupt solubilization of individual aggregates. High-speed atomic force microscopy explicitly shows that disassembly starts with the destabilization of the tips and rapidly progresses to completion through protofilament unzipping and depolymerization without accumulation of harmful oligomeric intermediates. Our data provide molecular insights into the selective processing of toxic amyloids, which is critical to identify potential therapeutic targets against increasingly prevalent neurodegenerative disorders.

Extraction and Refolding Determinants of Chaperone-Driven Aggregated Protein Reactivation.

Reactivation of protein aggregates plays a fundamental role in numerous situations, including essential cellular processes, hematological and neurological disorders, and biotechnological applications. The molecular details of the chaperone systems involved are known to a great extent but how the overall reactivation process is achieved has remained unclear. Here, we quantified reactivation over time through a predictive mechanistic model and identified the key parameters that control the overall dynamics. We performed new targeted experiments and analyzed classical data, covering multiple types of non-ordered aggregates, chaperone combinations, and experimental conditions. We found that, irrespective of the behavior observed, the balance of surface disaggregation and refolding in solution universally determines the reactivation dynamics, which is broadly described by two characteristic times. This characterization makes it possible to use activity measurements to accurately infer the underlying loss of aggregated protein and to quantify, for the first time, the refolding rates of the soluble intermediates.

Pedobarography: a novel approach to test the efficacy of treatments for lameness; an experience with mavacoxib in dogs with elbow osteoarthritis.

BACKGROUND: Pedobarographic analyses detect pressure redistribution among limbs and within limbs in humans, equids and dogs. The main objective of this study was to assess the usefulness of a set of pedobarographic parameters for the detection of lameness, as well as for its suitability for assessing the effects of therapies against osteoarthritis in dogs. With this purpose, eleven large-breed lame dogs with unilateral osteoarthritis due to elbow dysplasia were evaluated using a pressure platform prior to (D0) and after 3 months (D90) of treatment with mavacoxib, a COX-2 selective NSAID. The obtained parameters were: pressure distribution between lame and sound limbs, as well as paw area, mean pressure, and peak pressure of both lame and sound limbs. RESULTS: The results showed statistical differences in all these parameters between lame and sound limbs at D0; however, at D90, differences were significantly decreased as result of the treatment, indicating a substantial functional recovery under the study design conditions. CONCLUSIONS: The provided data prove the suitability of this novel technique in canine models for the quantitative and objective assessment of lameness, but also for the evaluation of treatments for lameness caused by articular pain.

Center of pressure limb path differences for the detection of lameness in dogs: a preliminary study.

BACKGROUND: The limb center of pressure (COP) path measures and quantifies the load distribution within a limb in a still or moving subject. Under this premise, the aim of this study was to test whether data derived from this parameter could detect the differences between sound and lame limbs in unilaterally lame dogs with elbow dysplasia. To accomplish this purpose, ten unilaterally lame dogs of similar conformation were walked over a pressure platform. Next, the COP path, in relation to the position of sound and lame limbs, was measured in a coordinate system over a standard paw template obtained by pedobarography during the whole support phase. To compare variables, force platform data (peak vertical force and vertical impulse) from the same animals were obtained. Sound and lame limb statokinesiograms were also obtained while the animals stood still. RESULTS: The statistical analysis clearly showed that COP in lame limbs start cranially and were shorter than sound limbs. In addition, the value of the COP excursion index was lower in lame limbs. Finally, the area of statokinesiograms was greater in lame limbs. CONCLUSION: This methodology based in limb COP characteristics serves to discriminate between sound and lame limbs in dogs with elbow dysplasia.

Photoluminescent Cu(i) vs. Ag(i) complexes: slowing down emission in Cu(i) complexes by pentacoordinate low-lying excited states.

This work describes the synthesis, and structural, spectroscopic, and theoretical studies of a mononuclear silver(i) complex with the formula [Ag(Xantphos)(4,4'-(MeO)2-2,2'-bipy)]BF4·DCM (1·BF4) [Xantphos: 4,5-bis(diphenylphosphino)-9,9'-dimethylxanthene]. We provide meaningful insights into the enhancement of the photoluminescence features of this silver(i) complex compared to its copper(i) analogue.

Assessment of the Efficacy of Platelet-Rich Plasma in the Treatment of Traumatic Canine Fractures.

The role of platelet-rich plasma (PRP) in promoting the healing of bone fractures has not yet been clearly stated. The aim of this prospective clinical study was to evaluate the effectiveness of plasma rich in growth factors (PRGF, a PRP derivate) in the treatment of naturally-occurring bone fractures in dogs. With this objective, sixty-five dogs with radius/ulna or tibia/fibula bone fractures were randomly divided into two groups (PRGF and saline solution (SS) groups) and checked at days 0, 7, 14, 21, 28, 35, 42, 49, 56, 60, 63, 70, 120, and 180. All the fractures were treated with an external skeletal fixation, and pain was controlled with Carprofen. Healing was evaluated by physical examination, limb function, radiography, and by a Likert-type owner satisfaction questionnaire. A faster fracture healing was observed in the PRGF group, with statistically significant differences with respect to the SS group. Swelling at the fracture site was significantly greater at day 14 and 28 in animals injected with PRGF, and more pain on palpation was found in the area at day 28. The injection of PRGF in acute bone fractures accelerates bone healing.

Regulation of Human Hsc70 ATPase and Chaperone Activities by Apg2: Role of the Acidic Subdomain.

Protein aggregate reactivation in metazoans is accomplished by the combined activity of Hsp70, Hsp40 and Hsp110 chaperones. Hsp110s support the refolding of aggregated polypeptides acting as specialized nucleotide exchange factors of Hsp70. We have studied how Apg2, one of the three human Hsp110s, regulates the activity of Hsc70 (HspA8), the constitutive Hsp70 in our cells. Apg2 shows a biphasic behavior: at low concentration, it stimulates the ATPase cycle of Hsc70, binding of the chaperone to protein aggregates and the refolding activity of the system, while it inhibits these three processes at high concentration. When the acidic subdomain of Apg2, a characteristic sequence present in the substrate binding domain of all Hsp110s, is deleted, the detrimental effects occur at lower concentration and are more pronounced, which concurs with an increase in the affinity of the Apg2 mutant for Hsc70. Our data support a mechanism in which Apg2 arrests the chaperone cycle through an interaction with Hsc70(ATP) that might lead to premature ATP dissociation before hydrolysis. In this line, the acidic subdomain might serve as a conformational switch to support dissociation of the Hsc70:Apg2 complex.

Combined plasma rich in growth factors and adipose-derived mesenchymal stem cells promotes the cutaneous wound healing in rabbits.

BACKGROUND: The use of Plasma Rich in Growth Factors (PRGF) and Adipose Derived Mesenchymal Stem Cells (ASCs) are today extensively studied in the field of regenerative medicine. In recent years, human and veterinary medicine prefer to avoid using traumatic techniques and choose low or non-invasive procedures. The objective of this study was to evaluate the efficacy of PRGF, ASCs and the combination of both in wound healing of full-thickness skin defects in rabbits. With this purpose, a total of 144 rabbits were used for this study. The animals were divided in three study groups of 48 rabbits each depending on the administered treatment: PRGF, ASCs, and PGRF+ASCs. Two wounds of 8 mm of diameter and separated from each other by 20 mm were created on the back of each rabbit: the first was treated with saline solution, and the second with the treatment assigned for each group. Macroscopic and microscopic evolution of wounds was assessed at 1, 2, 3, 5, 7 and 10 days post-surgery. With this aim, 8 animals from each treatment group and at each study time were euthanized to collect wounds for histopathological study. RESULTS: Wounds treated with PRGF, ASCs and PRGF+ASCs showed significant higher wound healing and epithelialization rates, more natural aesthetic appearance, significant lower inflammatory response, significant higher collagen deposition and angiogenesis compared with control wounds. The combined treatment PRGF+ASCs showed a significant faster cutaneous wound healing process. CONCLUSIONS: The combined treatment PRGF+ASCs showed the best results, suggesting this is the best choice to enhance wound healing and improve aesthetic results in acute wounds.

Clearly Detectable, Kinetically Restricted Solid-Solid Phase Transition in cis-Ceramide Monolayers.

Sphingosine [(2 S,3 R,4 E)-2-amino-4-octadecene-1,3-diol] is the most common sphingoid base in mammals. Ceramides are N-acyl sphingosines. Numerous small variations on this canonical structure are known, including the 1-deoxy, the 4,5-dihydro, and many others. However, whenever there is a Δ4 double bond, it adopts the trans (or E) configuration. We synthesized a ceramide containing 4 Z-sphingosine and palmitic acid ( cis-pCer) and studied its behavior in the form of monolayers extended on an air-water interface. cis-pCer acted very differently from the trans isomer in that, upon lateral compression of the monolayer, a solid-solid transition was clearly observed at a mean molecular area ≤44 Å2·molecule-1, whose characteristics depended on the rate of compression. The solid-solid transition, as well as states of domain coexistence, could be imaged by atomic force microscopy and by Brewster-angle microscopy. Atomistic molecular dynamics simulations provided results compatible with the experimentally observed differences between the cis and trans isomers. The data can help in the exploration of other solid-solid transitions in lipids, both in vitro and in vivo, that have gone up to now undetected because of their less obvious change in surface properties along the transition, as compared to cis-pCer.

Assessment of static posturography and pedobarography for the detection of unilateral forelimb lameness in ponies.

BACKGROUND: Static posturography and pedobarography are based on the detection of postural imbalance and, consequently, the pressure redistribution between limbs in lame subjects. These techniques have proven to be useful for the detection of lameness in humans and dogs. The main objective of this study was to test the suitability of static posturography and pedobarography in diagnosing lameness in ponies. A pressure platform was used to obtain postural data (statokinesiograms, mean X and Y, length, LFS ratio, and mean velocity) from 10 sound ponies and 7 ponies with unilateral forelimb lameness. Static pedobarographic data (pressure distribution, mean pressure, and peak pressure) were also collected and compared with force plate data (peak vertical force and vertical impulse) obtained from the same animals at the walk. RESULTS: Significant differences were seen between lame and sound ponies for almost all evaluated parameters. With this sample size, differences between lame and sound limbs/groups were detected with a statistical power of 90%, except for mean X and Y. CONCLUSIONS: Static posturography and pedobarography provide a complementary approach for lameness detection in equids.

Effect of leukocyte-reduced platelet-rich plasma on osteoarthritis caused by cranial cruciate ligament rupture: A canine gait analysis model.

The goal of this study was to objectively assess the effect of a platelet-rich plasma (PRP) derivate in English bulldogs with stifle degenerative joint disease secondary to cranial cruciate ligament rupture (CCLR). We used a force platform and affixed electrogoniometers to measure peak vertical force (PVF), vertical impulse (VI), stance time (ST), and angular range of motion (AROM), from 12 lame client-owned English bulldogs with post-CCLR stifle joint abnormalities. The 12 affected subjects were treated with 4 intra-articular injections of PRP, at 30-day intervals. Ten untreated, sound English bulldogs were used as a reference group. Clinical outcomes were evaluated using a linear mixed effects model. Mean values of PVF, VI, ST, and AROM were improved within the first 3 months post-treatment in the CCLR group, with mean measured changes increasing to maximum 4.56% body weight gain, 1.5% body weight/second, 0.07 seconds, and 6.18 degrees, respectively. The effects declined progressively after the treatment interval, ending at nearly initial levels after 6 months. This study demonstrates that dogs with CCLR treated with intra-articular PRP had improved PVF, VI, ST, and AROM over time; the duration of effect was waning by the end of the post-treatment period.

Posturography and dynamic pedobarography in lame dogs with elbow dysplasia and cranial cruciate ligament rupture.

BACKGROUND: The usefulness of studying posture and its modifications due to locomotor deficiencies of multiple origins has been widely proven in humans. To assess its suitability in the canine species, static posturography and dynamic pedobarography were performed on lame dogs affected with unilateral elbow dysplasia and cranial cruciate ligament rupture by using a pressure platform. With this objective, statokinesiograms and stabilograms, the percentage of pressure distribution between limbs, paw area, mean pressure, and peak pressure, were obtained from lame and sound dogs. These data were compared with Peak Vertical Force values originated from a force platform in the same recording sessions. RESULTS: Significant differences were found in the parameters mentioned above between sound and lame dogs and limbs. CONCLUSIONS: Posturography and pedobarography are useful and reliable for the monitoring of fore and hindlimb lameness in dogs, providing a new set of parameters for lameness detection.

Comparison of 3 anesthetic protocols for the elective cesarean-section in the dog: Effects on the bitch and the newborn puppies.

This study assessed the influence of 3 different anesthetic protocols based on the quality of anesthesia induction and maintenance in four dog breeds (French Bulldog, n = 13; Yorkshire terrier, n = 12; Chihuahua, n = 10; Bull Terrier, n = 10) subjected to cesarean section. Neonatal mortality, birth defects and newborn viability were assessed. All females were pre-medicated with morphine (IM), and then were assigned to three different anesthetic protocols: group P (n = 17), anesthesia was induced with propofol (IV) and then also maintained with propofol until the complete delivery of puppies and then anesthesia was maintained afterwards with sevoflurane; group PS (n = 14), anesthesia was induced with IV propofol, and maintenance of the anesthesic plan was performed with sevoflurane; group PES (n = 14) the females were induced by propofol and an epidural anesthesia was then performed, anesthesia was then maintained with propofol until the complete extraction of all puppies and then anesthesia was maintained afterwards with sevoflurane. Throughout the surgery, group PES required a lower concentration of sevoflurane (p < 0.05), and extra doses of propofol or fentanyl during inhalatory anesthesia were not required. Mean values of heart rate (p < 0.01) were higher in females from groups P and PS. Mean values of blood pressure values were lower (p < 0.01) in group PES as compared with the other two groups. Birth defects were detected in 3.1% (5/162) of the neonates, with a significantly higher incidence (p < 0.05) in French bulldog puppies. Neonatal viability was assessed using a modified Apgar score model; Apgar score was defined immediately after delivery (Apgar0) and a second score was assessed 60 min after delivery (Apgar60). Apgar0 scores were significantly different between the groups, showing neonates of group PES the highest values (p < 0.05). In Apgar60, more than 94% of puppies were already classified as normal viability neonates (7-10 score) and no differences were observed between groups. This study confirmed that females of group PES showed a higher quality of anesthesia during surgery and a vitality of puppies immediately after delivery. Regardless of the anesthetic protocol used, French bulldog females and puppies required more clinical care than other breeds.

Determinants of population responses to environmental fluctuations.

Environmental fluctuations, such as changing conditions and variable nutrient availability, are an unavoidable component of the dynamics of virtually all populations. They affect populations in ways that are often difficult to predict and sometimes lead to paradoxical outcomes. Here, we present a general analytical approach to examine how populations respond to fluctuations. We show that there exist general explicit conditions that determine to what extent fluctuations propagate to the variability of the responses and how they change the behavior of the system, including whether they promote proliferation or death and whether they facilitate coexistence or exclusion of competing species. These conditions depend on linear and nonlinear terms of the growth rate and on the characteristic times of the fluctuations. We validated our general approach through computational experiments for both stochastic and chaotic fluctuations and for multiple types of systems. From an applied point of view, our results provide an avenue for the precise control of the population behavior through fluctuations in addition to just through average properties.