Unraveling biochemical spatial patterns: Machine learning approaches to the inverse problem of stationary Turing patterns.

The diffusion-driven Turing instability is a potential mechanism for spatial pattern formation in numerous biological and chemical systems. However, engineering these patterns and demonstrating that they are produced by this mechanism is challenging. To address this, we aim to solve the inverse problem in artificial and experimental Turing patterns. This task is challenging since patterns are often corrupted by noise and slight changes in initial conditions can lead to different patterns. We used both least squares to explore the problem and physics-informed neural networks to build a noise-robust method. We elucidate the functionality of our network in scenarios mimicking biological noise levels and showcase its application using an experimentally obtained chemical pattern. The findings reveal the significant promise of machine learning in steering the creation of synthetic patterns in bioengineering, thereby advancing our grasp of morphological intricacies within biological systems while acknowledging existing limitations.

Differences in imaging biomarkers between patients with intermediate and advanced non-neovascular age-related macular degeneration (AMD) in the University of Colorado AMD registry.

PURPOSE: To quantify and compare the different prevalence rates of specific retinal imaging biomarkers in patients with intermediate AMD (iAMD) and advanced non-neovascular AMD (nnAMD). METHODS: Cross-sectional study of patients with iAMD and advanced nnAMD. Imaging studies were reviewed for qualitative imaging biomarkers. Choroidal thickness measurements were obtained subfoveally and in 1000 um and 2000 um intervals away from the fovea. The Chi-squared test and Fisher's exact test were used to compare rates of imaging biomarkers among the two cohorts. P-value of <0.05 was considered significant. RESULTS: 376 eyes of 197 patients with iAMD and 187 eyes of 97 patients with advanced nnAMD were recruited. There were significantly lower rates of the following imaging biomarkers in the iAMD compared with the advanced nnAMD cohorts: soft drusen (66.0% vs. 84.2%, p = 0.001), calcified drusen (4.3% vs. 40.0%, p < 0.0001), RPD (26.2% vs. 53.3%, p < 0.0001), ORT (0.5% vs. 46.9%, p < 0.0001), RP (1.1% vs. 46.3%, p < 0.0001), pigment migration (53.2% vs. 100%, p < 0.0001), and iRORA (17.9% vs. 80.2%, p < 0.0001). In the iAMD cohort, choroidal thickness was significantly greater at 188 µm (SD: 60) and 194 µm (SD: 69), compared to the advanced nnAMD with measurements of 153 µm (SD: 68), and 161 µm (SD: 76). This difference was statistically significant (p < 0.0001 and p = 0.0002). CONCLUSIONS: Our results highlight significant differences in imaging biomarkers between both cohorts. Key biomarkers, such as iRORA, RPD, pigment migration, and thinner choroidal thickness, were associated with advanced nnAMD. Identifying these biomarkers early may help target patients who could benefit from new treatments, potentially delaying vision loss.

Development and assessment of a virtual escape-room game for teaching industrial bioprocesses.

This article presents a study on the implementation of a virtual escape-room game as a novel teaching methodology in biochemistry education. The game aimed to engage students in producing monoclonal antibodies against SARS-CoV-2 while reinforcing theoretical concepts and fostering teamwork. Three versions of the game were tested, incorporating modifications to address student feedback on and improve the overall experience. The study employed a satisfaction survey to gather insights from students regarding their perception of the game. Results showed that the implementation of answer flexibility using RegEx had a significant positive impact on student satisfaction and motivation. The introduction of RegEx allowed for a more realistic and immersive gaming experience, as students could provide varied answers while still being evaluated correctly. Overall, the findings highlight the effectiveness of the game's design, the suitability of the Google Forms platform for distance learning, and the importance of incorporating answer flexibility through RegEx. These results provide valuable guidance for educators seeking to enhance student engagement and satisfaction through the use of escape-room games in biochemistry education.

Systemic phospho-defective and phospho-mimetic Drp1 mice exhibit normal growth and development with altered anxiety-like behavior.

Mitochondrial division controls the size, distribution, and turnover of this essential organelle. A dynamin-related GTPase, Drp1, drives membrane division as a force-generating mechano-chemical enzyme. Drp1 is regulated by multiple mechanisms, including phosphorylation at two primary sites: serine 579 and serine 600. While previous studies in cell culture systems have shown that Drp1 S579 phosphorylation promotes mitochondrial division, its physiological functions remained unclear. Here, we generated phospho-mimetic Drp1 S579D and phospho-defective Drp1 S579R mice using the CRISPR-Cas system. Both mouse models exhibited normal growth, development, and breeding. We found that Drp1 is highly phosphorylated at S579 in brain neurons. Notably, the Drp1 S579D mice showed decreased anxiety-like behaviors, whereas the Drp1 S579R mice displayed increased anxiety-like behaviors. These findings suggest a critical role for Drp1 S579 phosphorylation in brain function. The Drp1 S579D and S579R mice thus offer valuable in vivo models for specific analysis of Drp1 S579 phosphorylation.

Baseline physiological data from anesthetized pigs in a VX intoxication model.

Over the past fifty years, swine models have been used for organophosphorus intoxication studies. Among these studies and others on the swine model in general, some physiological data, especially cholinesterase activity highly impacted by organophosphorus compounds like nerve agent VX, still need to be completed. To support and compare our model to others, we have published the experimental protocol, the physiological values of 31 juvenile anesthetized pigs, and the 6 h-follow-up of six supplementary anesthetized control animals and 7 VX-intoxicated pigs. We reported hemodynamics and respiratory parameters, blood levels in several biochemical parameters, blood gas, and complete blood count and compared them to the literature. We also focused on tissue and blood cholinesterase activities and detailed them for acetylcholinesterase and butyrylcholinesterase. After establishing a broad physiological data set consistent with the literature, we reported several cardio-respiratory parameters that seem more affected by an organophosphate intoxication, like heart rate, arterial blood pressure, cardiac output, and respiratory rate. Within the blood, oxygen saturation (SpO2), lactatemia, base excess, and glycemia can also be measured and associated with the other parameters to evaluate the life-threatening status. This swine model is currently used to develop and evaluate medical countermeasures against organophosphate nerve agent intoxications.

Feeling the Stress: Salivary Cortisol Responses of Softball Umpires during National Championships.

Stress research in sports tends to focus on athletes, with sports officials typically being overlooked. In the current study, baseline, pre-game, and post-game cortisol levels among a sample of softball umpires were measured to assess the pattern of stress responses and determine if umpire performance (pass/fail) and position on the diamond (plate/field) could be predicted from cortisol levels. Nine male and four female participants aged 25-68 years (N = 13, M = 47.06 ± 15.65 years) each provided saliva samples on multiple occasions prior to and after officiating games at two Australian National Softball Championships. Data from 65 games were analysed. Performance was assessed using Softball Australia's official umpire assessment tool. Cortisol levels increased significantly from baseline to pre-game (p < 0.001, d = -0.69) and declined significantly from pre-game to post-game (p < 0.001, d = 0.47). Umpiring performances were correctly classified as pass or fail from baseline and pre-game cortisol levels in 61.5% of cases and umpire position on the diamond from pre-game cortisol in 63.1% of cases. Findings suggest that stress management strategies should be recommended to softball umpires for performance enhancement and to safeguard their mental health.

Hematologic and Serum Biochemical Characteristics of Belgian Blue Cattle.

Belgian blue (BB) cattle have an 11-bp deletion in myostatin that causes skeletal muscle hyperplasia and increased muscle mass, leading to a 'double-muscled' phenotype. Preliminary data suggest that this phenotype may be associated with breed-specific hematologic and biochemical values. Therefore, in this study, we sought to compare hematologic and serum biochemical parameters in healthy BB and Holstein Friesian (HF) cows and to propose breed-specific reference intervals for BB cows. Hematologic parameters, total protein, creatinine, creatine kinase (CK) and aspartate transaminase (AST) activities, albumin, and globulins were measured in 183 clinically healthy adult BB and HF cows. There were significant differences between BB and HF cows in 17 of 27 measured parameters. BB cows had significantly higher creatinine concentration and CK and AST activities (p < 0.001). RBCs, hemoglobin, hematocrit (p < 0.001), MCV and lymphocytes (p < 0.05) were also significantly higher in BB cows compared with HF cows. The average N/L ratio was greater than 1 in both breeds. These results suggest that BB and HF cows have significantly different clinically relevant hematologic and serum biochemical values, and, therefore, breed-specific reference intervals should be used.

Age-specific analysis of anti-müllerian hormone and liver biochemical parameters in freemartin holstein calves and heifers: A pilot study.

Freemartinism is the most common congenital anomaly among sexual disorders in dairy cows. This syndrome typically occurs in different-sex twin pregnancies and causes vascular anastomoses to form with the placenta in the early stages of fetal development. The study aims to determine the effectiveness of Anti-müllerian hormone (AMH) levels in calves and heifers of different age groups for diagnostic factors and to investigate the potential consequences of different hormone levels in different age groups on some liver biochemical parameters. The study involved 50 cattle from diverse age categories, divided into the freemartin group (FM Group, n=25) and the control group (C Group, n=25). Both FM and control groups were further divided into early-age (3-5 months), middle-aged (5-9 months), and older-aged groups (9-12 months). Serum AMH levels, along with total protein, albumin, and total cholesterol levels, were measured. While no statistically significant difference in AMH levels was observed in the early-age group (P:0.53), significant differences were determined in the middle (P:0.015) and older-age groups (P:0.01), where the FM group exhibited significantly decreased AMH levels compared to the control group. The evaluation of liver biochemistry revealed a statistically significant difference in total protein levels between the FM and control groups in the older age group (P:0.033). Consequently, it is reasonable to suggest that AMH levels may serve as a valid parameter for diagnosing freemartin syndrome in calves aged older than five months. Conversely, particularly in young calves, no significant differences in liver functionality were observed between freemartin-affected and healthy calves.

Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus.

To date, all major modes of monoclonal antibody therapy targeting SARS-CoV-2 have lost significant efficacy against the latest circulating variants. As SARS-CoV-2 omicron sublineages account for over 90% of COVID-19 infections, evasion of immune responses generated by vaccination or exposure to previous variants poses a significant challenge. A compelling new therapeutic strategy against SARS-CoV-2 is that of single-domain antibodies, termed nanobodies, which address certain limitations of monoclonal antibodies. Here, we demonstrate that our high-affinity nanobody repertoire, generated against wild-type SARS-CoV-2 spike protein (Mast et al., 2021), remains effective against variants of concern, including omicron BA.4/BA.5; a subset is predicted to counter resistance in emerging XBB and BQ.1.1 sublineages. Furthermore, we reveal the synergistic potential of nanobody cocktails in neutralizing emerging variants. Our study highlights the power of nanobody technology as a versatile therapeutic and diagnostic tool to combat rapidly evolving infectious diseases such as SARS-CoV-2.

Human pannexin 1 channel is not phosphorylated by Src tyrosine kinase at Tyr199 and Tyr309.

Protein phosphorylation is one of the major molecular mechanisms regulating protein activity and function throughout the cell. Pannexin 1 (PANX1) is a large-pore channel permeable to ATP and other cellular metabolites. Its tyrosine phosphorylation and subsequent activation have been found to play critical roles in diverse cellular conditions, including neuronal cell death, acute inflammation, and smooth muscle contraction. Specifically, the non-receptor kinase Src has been reported to phosphorylate Tyr198 and Tyr308 of mouse PANX1 (equivalent to Tyr199 and Tyr309 of human PANX1), resulting in channel opening and ATP release. Although the Src-dependent PANX1 activation mechanism has been widely discussed in the literature, independent validation of the tyrosine phosphorylation of PANX1 has been lacking. Here, we show that commercially available antibodies against the two phosphorylation sites mentioned above-which were used to identify endogenous PANX1 phosphorylation at these two sites-are nonspecific and should not be used to interpret results related to PANX1 phosphorylation. We further provide evidence that neither tyrosine residue is a major phosphorylation site for Src kinase in heterologous expression systems. We call on the field to re-examine the existing paradigm of tyrosine phosphorylation-dependent activation of the PANX1 channel.

Albumin levels in malaria patients: a systematic review and meta-analysis of their association with disease severity.

Albumin, a key protein in human blood plasma, has been linked to various health conditions. However, its association with malaria, particularly in assessing disease severity, remains inadequately understood. This comprehensive systematic review and meta-analysis aimed to elucidate the relationship between albumin levels and malaria severity. A comprehensive literature search was conducted across multiple databases, including Embase, Scopus, PubMed, MEDLINE, Ovid, and Google Scholar, to identify studies examining albumin levels in malaria patients. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed. Data were pooled using a random-effects model, and heterogeneity was assessed using I2 statistics. Subgroup and meta-regression analyses were performed based on publication year, study location, and Plasmodium species. A total of 37 studies were included in this review. The thematic synthesis indicated that albumin levels in malaria patients varied significantly based on geographical location. A meta-analysis of 28 studies found that albumin levels were significantly lower in malaria patients compared with non-malarial controls (P < 0.001, standardized mean differences [SMD] = -2.23, 95% CI - 3.25 to - 1.20, I2: 98%, random effects model, 28 studies). Additionally, subgroup analysis revealed variations in albumin levels based on geographical location and Plasmodium species. Regarding the association with disease severity, thematic synthesis showed that severe malaria cases generally had decreased albumin levels across various regions. However, one Brazilian study reported higher albumin levels in severe cases. A separate meta-analysis of five studies found significantly lower albumin levels in patients experiencing severe malaria relative to those with less severe forms of the disease (P < 0.001, SMD = -0.66, 95% CI - 1.07 to - 0.25), I2: 73%, random effects model, 5 studies). This study underscores the clinical significance of albumin as a potential biomarker for Plasmodium infection and the severity of malaria. The findings suggest that albumin level monitoring could be crucial in managing malaria patients, especially in assessing disease severity and tailoring treatment approaches. Additional studies are required to investigate the underlying mechanisms driving these associations and validate the clinical utility of albumin levels in malaria patient management.

Popeye domain containing proteins modulate the voltage-gated cardiac sodium channel Nav1.5.

Popeye domain containing (POPDC) proteins are predominantly expressed in the heart and skeletal muscle, modulating the K2P potassium channel TREK-1 in a cAMP-dependent manner. POPDC1 and POPDC2 variants cause cardiac conduction disorders with or without muscular dystrophy. Searching for POPDC2-modulated ion channels using a functional co-expression screen in Xenopus oocytes, we found POPDC proteins to modulate the cardiac sodium channel Nav1.5. POPDC proteins downregulate Nav1.5 currents in a cAMP-dependent manner by reducing the surface expression of the channel. POPDC2 and Nav1.5 are both expressed in different regions of the murine heart and consistently POPDC2 co-immunoprecipitates with Nav1.5 from native cardiac tissue. Strikingly, the knock-down of popdc2 in embryonic zebrafish caused an increased upstroke velocity and overshoot of cardiac action potentials. The POPDC modulation of Nav1.5 provides a new mechanism to regulate cardiac sodium channel densities under sympathetic stimulation, which is likely to have a functional impact on cardiac physiology and inherited arrhythmias.

Ubiquitin-specific protease 7 inhibitors reveal a differentiated mechanism of p53-driven anti-cancer activity.

The USP7 deubiquitinase regulates proteins involved in the cell cycle, DNA repair, and epigenetics and has been implicated in cancer progression. USP7 inhibition has been pursued for the development of anti-cancer therapies. Here, we describe the discovery of potent and specific USP7 inhibitors exemplified by FX1-5303. FX1-5303 was used as a chemical probe to study the USP7-mediated regulation of p53 signaling in cells. It demonstrates mechanistic differences compared to MDM2 antagonists, a related class of anti-tumor agents that act along the same pathway. FX1-5303 synergizes with the clinically approved BCL2 inhibitor venetoclax in acute myeloid leukemia (AML) cell lines and ex vivo patient samples and leads to strong tumor growth inhibition in in vivo mouse xenograft models of multiple myeloma and AML. This work introduces new USP7 inhibitors, differentiates their mechanism of action from MDM2 inhibition, and identifies specific opportunities for their use in the treatment of AML.

CircMEF2C(2, 3) modulates proliferation and adipogenesis of porcine intramuscular preadipocytes by miR-383/671-3p/MEF2C axis.

Circular RNA is a special category of non-coding RNA that has emerged as epigenetic regulator of adipose tissue development. However, the mechanism governing intramuscular adipogenesis of circRNA remains largely uncharted. In this study, circMEF2C(2, 3), looped by MEF2C exons 2 and 3, was identified from the pig MEF2C gene. Expression of circMEF2C(2, 3) is upregulated in early stage of intramuscular adipogenesis and muscular tissue of lean pigs (DLY pig). Subsequently, overexpression or knockdown of circMEF2C(2, 3) reflected that it participates in promoting proliferation and inhibiting adipogenic differentiation in porcine intramuscular preadipocytes and murine C3H10T1/2 cells. Mechanically, circMEF2C(2, 3) competitively combined with miR-383 and miR-671-3p to the 3'-UTR of MEF2C, which maintains MEF2C expression in regulating proliferation and adipogenesis. In summary, circMEF2C(2, 3) is a key regulator in the proliferation and adipogenic differentiation of intramuscular adipogenesis, suggesting its potential as a multi-target strategy for adipose development and associated diseases.

Enhancing complex bioprocess learning through simulation technology and hybrid teaching: A case study in university education.

The utilization of computer simulators in university education is progressively being embraced to offer students a practical exposure to industrial bioprocesses. Bioreactor computer simulators hold various advantages over conventional laboratory experiments, such as cost-effectiveness and enhanced safety. The research objective is to assess the effectiveness of integrating bioreactor computer simulators into hybrid teaching to promote active and collaborative learning experiences and evaluate their impact on student participation and understanding. A hybrid strategy combining synchronous, face-to-face, and online teaching has been implemented to enhance the teaching-learning processes in the Industrial Bioprocesses course for Biochemistry students. The simulation software BIOSTAT®T Yeast was used. This software models the production of ethanol with Saccharomyces cerevisiae through batch cultivation and the determination of the kLa value of a bioreactor. In the first simulation activity, students analyzed the software response based on parameter values input by the instructor, while in the second simulation activity, students autonomously used the computer simulator under the primary oversight of the instructor. The survey results indicate that the pedagogical innovation was positively received and significantly motivating for the students. Comparing student satisfaction surveys between the two simulation activities suggests that fostering student autonomy and engagement through simulation technology can improve satisfaction and learning outcomes in bioprocess education.

Stable measurement of chemistry, immunochemistry, and hematology analytes in a heparin-based anticoagulant with iloprost additive: A promising candidate for the polyvalent blood collection tube.

INTRODUCTION: A polyvalent blood collection tube could potentially reduce the number and volume of blood samples drawn from patients and reduce the risk of tube mix-ups in a point-of-care setting in the emergency department and the intensive care unit. METHODS: Four different concentrations of our experimental heparin anticoagulant with iloprost additive (HEP-ILOP 50 nM, 150 nM, 1000 nM, and 10 µM, respectively) were tested for significant differences and bias performance specifications against EDTA for 29 hematology analytes, and the highest concentration (HEP-ILOP 10 µM) against lithium heparin for 14 chemistry and immunochemistry analytes. Samples were drawn from 79 consenting subjects from the Oncology Department (n = 38) and the Intensive and Intermediary Care Unit (n = 41). RESULTS: For hematology analytes, the HEP-ILOP formulation generally provided stable measurement within optimal requirements within 5 h after sampling (mean 104 ± 56 min), with very little difference between the four HEP-ILOP concentrations. Because of differences in platelet and red blood cell swelling between EDTA and HEP-ILOP, all size-dependent analytes required proportional factorization to produce similar results. Platelet count by impedance similarly required factorization, whereas the fluorescent method provided results identical with EDTA. Chemistry and immunochemistry analytes were within optimal requirements except for potassium, lactate dehydrogenase, and glucose, indicating a cytoprotective effect of iloprost reducing cell metabolism and rupture, thereby producing results closer to in vivo conditions. CONCLUSIONS: Our novel dry-sprayed anticoagulant formulation, HEP-ILOP, is a promising candidate for a polyvalent blood collection tube, enabling the analysis of hematology, chemistry, and immunochemistry analytes in the same tube.

The distribution and sequestration of cercosporin by Cercospora cf. flagellaris.

Plant pathogenic fungi produce toxins as virulence factors in many plant diseases. In Cercospora leaf blight (CLB) of soybean caused by Cercospora cf. flagellaris, symptoms are a consequence of the production of a perylenequinone toxin, cercosporin, which is light-activated to produce damaging reactive oxygen species (ROS). Cercosporin is universally toxic to cells, except to the cells of the producer. The current model of self-resistance to cercosporin is largely attributed to the maintenance of cercosporin in a chemically-reduced state inside hyphae, unassociated with cellular organelles. However, in another perylenequinone-producing fungus, Phaeosphaeria sp., the toxin was specifically sequestered inside lipid droplets (LDs) to prevent ROS production. This study hypothesized that LD-based sequestration of cercosporin occurred in C. cf. flagellaris and that lipid-inhibiting fungicides could inhibit toxin production. Confocal microscopy using light-cultured C. cf. flagellaris indicated that 3-day old hyphae contained two forms of cercosporin distributed in two types of hyphae. Reduced cercosporin was uniformly distributed in the cytoplasm of thick, primary hyphae, and contrary to previous studies, active cercosporin was observed specifically in LDs of thin, secondary hyphae. The production of hyphae of two different thicknesses, a characteristic of hemibiotrophic plant pathogens, has not been documented in C. cf. flagellaris. No correlation was observed between cercosporin production and total lipid extracted, and two lipid-inhibiting fungicides had little effect on fungal growth in growth-inhibition assays. The study lays a foundation to explore the importance of pathogen lifestyle, toxin production, and LD content in pathogenicity and symptomology of Cercospora.

Phytophotodermatitis From Lime Margaritas on a Mexico Vacation.

Phytophotodermatitis is a type of contact dermatitis that occurs upon skin exposure to certain plant chemicals, known as furocoumarins, along with simultaneous sun exposure. This case details a 34-year-old patient who presented to the office with an asymptomatic, irregularly shaped, and hyperpigmented patch located on the left inferior middle back that had been present since a recent beach vacation in Mexico. Upon gathering the history, clinicians should inquire about recent sunlight exposure while consuming and/or touching phytotoxic plant derivatives found in most citrus plants. The history should correspond with the skin examination findings and conclude that a cutaneous phytotoxic reaction had occurred when a lime margarita contacted the hand, which was subsequently rubbed onto the patient's back. This case highlights the importance of both taking a thorough history and physical examination and being aware of the broad range of skin manifestations to prevent unnecessary treatment, such as topical corticosteroids, for other skin disorders (the irregular presentation of atopic dermatitis, allergic contact dermatitis, and dermatitis unspecified) or improperly suspected child abuse in younger patient presentations.

Mitochondrial F0F1-ATP synthase governs the induction of mitochondrial fission.

Mitochondrial dynamics is a process that balances fusion and fission events, the latter providing a mechanism for segregating dysfunctional mitochondria. Fission is controlled by the mitochondrial membrane potential (ΔΨm), optic atrophy 1 (OPA1) cleavage, and DRP1 recruitment. It is thought that this process is closely linked to the activity of the mitochondrial respiratory chain (MRC). However, we report here that MRC inhibition does not decrease ΔΨm nor increase fission, as evidenced by hyperconnected mitochondria. Conversely, blocking F0F1-ATP synthase activity induces fragmentation. We show that the F0F1-ATP synthase is sensing the inhibition of MRC activity by immediately promoting its reverse mode of action to hydrolyze matrix ATP and restoring ΔΨm, thus preventing fission. While this reverse mode is expected to be inhibited by the ATPase inhibitor ATPIF1, we show that this sensing is independent of this factor. We have unraveled an unexpected role of F0F1-ATP synthase in controlling the induction of fission by sensing and maintaining ΔΨm.

Fluid dynamics of life: exploring the physiology and importance of water in the critical illness.

Water acknowledged as a vital component for life and the universal solvent, is crucial for diverse physiological processes in the human body. While essential for survival, the human body lacks the capacity to produce water, emphasizing the need for regular ingestion to maintain a homeostatic environment. The human body, predominantly composed of water, exhibits remarkable biochemical properties, playing a pivotal role in processes such as protein transport, thermoregulation, the cell cycle, and acid­base balance. This review delves into comprehending the molecular characteristics of water and its interactions within the human body. The article offers valuable insights into the intricate relationship between water and critical illness. Through a comprehensive exploration, it seeks to enhance our understanding of water's pivotal role in sustaining overall human health.