Unraveling membrane properties at the organelle-level with LipidDyn

Cellular membranes are formed from many different lipids in various amounts and proportions depending on the subcellular localization. The lipid composition of membranes is sensitive to changes in the cellular environment, and their alterations are linked to several diseases, including cancer. Lipids not only form lipid-lipid interactions but also interact with other biomolecules, including proteins, profoundly impacting each other. Molecular dynamics (MD) simulations are a powerful tool to study the properties of cellular membranes and membrane-protein interactions on different timescales and at varying levels of resolution. Over the last few years, software and hardware for biomolecular simulations have been optimized to routinely run long simulations of large and complex biological systems. On the other hand, high-throughput techniques based on lipidomics provide accurate estimates of the composition of cellular membranes at the level of subcellular compartments. The community needs computational tools for lipidomics and simulation data effectively interacting to better understand how changes in lipid compositions impact membrane function and structure. Lipidomic data can be analyzed to design biologically relevant models of membranes for MD simulations. Similar applications easily result in a massive amount of simulation data where the bottleneck becomes the analysis of the data to understand how membrane properties and membrane-protein interactions are changing in the different conditions. In this context, we developed LipidDyn, an in silico pipeline to streamline the analyses of MD simulations of membranes of different compositions. Once the simulations are collected, LipidDyn provides average properties and time series for several membrane properties such as area per lipid, thickness, diffusion motions, the density of lipid bilayers, and lipid enrichment/depletion. The calculations exploit parallelization and the pipelines include graphical outputs in a publication-ready form. We applied LipidDyn to different case studies to illustrate its potential, including membranes from cellular compartments and transmembrane protein domains. LipidDyn is implemented in Python and relies on open-source libraries. LipidDyn is available free of charge under the GNU General Public License from https://github.com/ELELAB/LipidDyn.

Unveiling the Membrane and Cell Wall Action of Antimicrobial Cyclic Lipopeptides: Modulation of the Spectrum of Activity

Antibiotic resistance is a major public health challenge, and Gram-negative multidrug-resistant bacteria are particularly dangerous. The threat of running out of active molecules is accelerated by the extensive use of antibiotics in the context of the COVID-19 pandemic, and new antibiotics are urgently needed. Colistin and polymyxin B are natural antibiotics considered as last resort drugs for multi-resistant infections, but their use is limited because of neuro- and nephrotoxicity. We previously reported a series of synthetic analogues inspired in natural polymyxins with a flexible scaffold that allows multiple modifications to improve activity and reduce toxicity. In this work, we focus on modifications in the hydrophobic domains, describing analogues that broaden or narrow the spectrum of activity including both Gram-positive and Gram-negative bacteria, with MICs in the low µM range and low hemolytic activity. Using biophysical methods, we explore the interaction of the new molecules with model membranes that mimic the bacterial inner and outer membranes, finding a selective effect on anionic membranes and a mechanism of action based on the alteration of membrane function. Transmission electron microscopy observation confirms that polymyxin analogues kill microbial cells primarily by damaging membrane integrity. Redistribution of the hydrophobicity within the polymyxin molecule seems a plausible approach for the design and development of safer and more selective antibiotics.

Assessing Mechanical Catheter Dysfunction in Peritoneal Dialysis Patients: A Case Control, Proof-of-Concept Study

New guidelines on evaluation of peritoneal membrane function recommend ruling out catheter dysfunction when evaluating patients with low ultrafiltration capacity. We introduce the use of a combination of parameters obtained from daily measurements of the cycler software for predicting catheter dysfunction in automated peritoneal dialysis patients. Out of 117 patients treated between 2015 and 2021, all patients with verified catheter dysfunction (n=14) were identified and compared to controls (n=19). We retrieved cycler data for seven days each and tested parameters predictive capability of catheter dysfunction. Total number of alarms/week >7 as single predictive parameter of catheter dislocation identified 85.7% (sensitivity) of patients with dislocated catheter and 31.6% (1-specificity) of control patients. A combination of parameters (number of alarms/week >7, drain time >22 min, ultrafiltration of last fill <150 mL) where at least two of three parameters appeared identified the same proportion of patients with catheter dislocation, but was more accurate in identifying controls (21% false positive). An easily applicable combination of daily cycler readout parameters, also available in remote monitoring platforms can be used as predictor of inadequate catheter function during routine follow-up with potential for earlier diagnosis of this frequent complication in the future.

Fundamentals of Membrane Lipid Replacement: A Natural Medicine Approach to Repairing Cellular Membranes and Reducing Fatigue, Pain, and Other Symptoms While Restoring Function in Chronic Illnesses and Aging

Membrane Lipid Replacement (MLR) uses natural membrane lipid supplements to safely replace damaged, oxidized lipids in membranes in order to restore membrane function, decrease symptoms and improve health. Oral MLR supplements contain mixtures of cell membrane glycerolphospholipids, fatty acids, and other lipids, and can be used to replace and remove damaged cellular and intracellular membrane lipids. Membrane injury, caused mainly by oxidative damage, occurs in essentially all chronic and acute medical conditions, including cancer and degenerative diseases, and in normal processes, such as aging and development. After ingestion, the protected MLR glycerolphospholipids and other lipids are dispersed, absorbed, and internalized in the small intestines, where they can be partitioned into circulating lipoproteins, globules, liposomes, micelles, membranes, and other carriers and transported in the lymphatics and blood circulation to tissues and cellular sites where they are taken in by cells and partitioned into various cellular membranes. Once inside cells, the glycerolphospholipids and other lipids are transferred to various intracellular membranes by lipid carriers, globules, liposomes, chylomicrons, or by direct membrane–membrane interactions. The entire process appears to be driven by ‘bulk flow’ or mass action principles, where surplus concentrations of replacement lipids can stimulate the natural exchange and removal of damaged membrane lipids while the replacement lipids undergo further enzymatic alterations. Clinical studies have demonstrated the advantages of MLR in restoring membrane and organelle function and reducing fatigue, pain, and other symptoms in chronic illness and aging patients.

Effect of Glutathione on Sperm Quality in Guanzhong Dairy Goat Sperm During Cryopreservation

In the process of cryopreservation of dairy goat semen, it will face many threats such as oxidative damage, which will affect the motility and plasma membrane function of sperm. As an endogenous antioxidant in animals, glutathione (GSH) can significantly improve the quality of thawed sperm when added to the frozen diluent of semen of pigs and cattle. In this study, different concentration gradients of GSH [0 mmol/L (control), 1, 2, 3, 4 mmol/L] were added to the frozen diluent of Guanzhong dairy goat semen. By detecting the sperm motility parameters, acrosome intact rate and plasma membrane intact rate after thawing, the effect of GSH on the cryopreservation of dairy goat semen was explored. Sperm motility parameters were measured with the computer-aided sperm analysis (CASA) system (total power, TM; forward power, PM; linearity, LIN; average path speed, VAP; straight line speed, VSL; curve speed, VCL; beat cross frequency, BCF). The sperm acrosome integrity rate after thawing was detected by a specific fluorescent probe (isothiocyanate-labeled peanut agglutinin, FITC-PNA), and the sperm plasma membrane integrity rate after thawing was detected by the hypotonic sperm swelling (HOST) method. Reactive oxygen species (ROS) kit, malondialdehyde (MDA) kit, superoxide dismutase (SOD) kit, glutathione peroxidase (GSH-PX) kit were used to detect various antioxidant indicators of thawed sperm. in vitro fertilization experiment was used to verify the effect of adding glutathione on sperm fertilization and embryo development. The results showed that when the concentration of glutathione was 2 mmol/l, the sperm viability, plasma membrane intact rate, and acrosome intact rate were the highest after thawing, reaching 62.14, 37.62, and 70.87% respectively, and they were all significantly higher. In terms of antioxidant indexes; the values of SOD and GSH-PX were 212.60 U/ml and 125.04 U/L, respectively, which were significantly higher than those of the control group; The values of ROS and MDA were 363.05 U/ml and 7.02 nmol/L, respectively, which were significantly lower than the control group. The addition of 2 mmol/L glutathione significantly improves the fertilization ability of sperm. In short, adding 2 mmol/l glutathione to the semen diluent can improve the quality of frozen Guanzhong dairy goat sperm.

Abstract 11710: Poloxamer 188 Protects Coronary Artery Endothelial Cells After Extended Hypoxia and Reoxygenation in an in vitro Model of Simulated Ischemia/Reperfusion Injury

Reperfusion restores blood flow after myocardial ischemia but can cause additional cellular injury by the sudden reintroduction of oxygen and nutrients. There is still no effective remedy for myocardial ischemia/reperfusion (IR) injury. Our previous study using cardiomyocytes (CMs) found that, after 3 hrs hypoxia followed by 2 hrs reoxygenation, viability decreased, and release of lactate dehydrogenase (LDH), calcium influx, membrane leakage (insertion of fluorescent probe FM1-43) significantly increased, indicating that cell membrane function was negatively affected. This was attenuated by the triblock copolymer Poloxamer (P)188. Here, we first hypothesized that endothelial cells are also susceptible to simulated IR injury, albeit requiring longer hypoxia times. We further hypothesized that P188 can also attenuate simulated IR injury in endothelial cells when given upon reoxygenation. Mouse coronary artery endothelial cells (MCAECs) were exposed to different durations of hypoxia (2, 3, 12 and 24 hrs) in serum- and glucose-free media +/- reoxygenation for 2 hrs in regular media. P188 was administered upon reoxygenation at 0, 100, 300 or 1,000 μM in experiments of 24 hrs hypoxia / 2 hrs reoxygenation. LDH release was measured and compared to appropriately timed normoxic control experiments. Reoxygenation and hypoxia times significantly longer than 3 hrs were required to elicit sufficient injury (panel A). When P188 was given upon reoxygenation after 24 hrs hypoxia, it dose-dependently attenuated LDH release (panel B). These findings contrast to the higher susceptibility of CMs to IR injury that only allowed shorter hypoxia durations. They also confirm a protective effect of P188 on the endothelium, not just on CMs. These findings have important implications for co-culture models with MCAECs and CMs to elucidate the interplay of both cell types on each other when studying mechanisms of cardioprotective strategies and compounds like P188.

Melatonin enhances SIRT1 to ameliorate mitochondrial membrane damage by activating PDK1/Akt in granulosa cells of PCOS

Mitochondrial injury in granulosa cells (GCs) is associated with the pathophysiological mechanism of polycystic ovary syndrome (PCOS). Melatonin reduces the mitochondrial injury by enhancing SIRT1 (NAD-dependent deacetylase sirtuin-1), while the mechanism remains unclear. Mitochondrial membrane potential is a universal selective indicator of mitochondrial function. In this study, mitochondrial swelling and membrane defect mitochondria in granulosa cells were observed from PCOS patients and DHT-induced PCOS-like mice, and the cytochrome C level in the cytoplasm and the expression of BAX (BCL2-associated X protein) in mitochondria were significantly increased in GCs, with p-Akt decreased, showing mitochondrial membrane was damaged in GCs of PCOS. Melatonin treatment decreased mitochondrial permeability transition pore (mPTP) opening and increased the JC-1 (5,5′,6,6′-tetrachloro1,1′,3,3′-tetramethylbenzimidazolylcarbocyanine iodide) aggregate/monomer ratio in the live KGN cells treated with DHT, indicating melatonin mediates mPTP to increase mitochondrial membrane potential. Furthermore, we found melatonin decreased the levels of cytochrome C and BAX in DHT-induced PCOS mice. PDK1/Akt played an essential role in improving the mitochondrial membrane function, and melatonin treatment increased p-PDK 1 and p-Akt in vivo and in vitro. The SIRT1 was also increased with melatonin treatment, while knocking down SIRT1 mRNA inhibiting the protective effect of melatonin to activate PDK1/Akt. In conclusion, melatonin enhances SIRT1 to ameliorate mitochondrial membrane damage by activating PDK1/Akt in granulosa cells of PCOS.

Stress- and metabolic responses of Candida albicans require Tor1 kinase N-terminal HEAT repeats

Whether to commit limited cellular resources toward growth and proliferation, or toward survival and stress responses, is an essential determination made by Target of Rapamycin Complex 1 (TORC1) for a eukaryotic cell in response to favorable or adverse conditions. Loss of TORC1 function is lethal. The TORC1 inhibitor rapamycin that targets the highly conserved Tor kinase domain kills fungal pathogens like Candida albicans, but is also severely toxic to human cells. The least conserved region of fungal and human Tor kinases are the N-terminal HEAT domains. We examined the role of the 8 most N-terminal HEAT repeats of C. albicans Tor1. We compared nutritional- and stress responses of cells expressing a message for N-terminally truncated Tor1 from repressible tetO, with cells expressing a wild type TOR1 allele from tetO or from the native promoter. Some but not all stress responses were significantly impaired by loss of Tor1 N-terminal HEAT repeats, including those to oxidative-, cell wall-, and heat stress; in contrast, plasma membrane stress and antifungal agents that disrupt plasma membrane function were tolerated by cells lacking this Tor1 region. Translation was inappropriately upregulated during oxidative stress in cells lacking N-terminal Tor1 HEAT repeats despite simultaneously elevated Gcn2 activity, while activation of the oxidative stress response MAP kinase Hog1 was weak. Conversely, these cells were unable to take advantage of favorable nutritional conditions by accelerating their growth. While consuming oxygen more slowly than cells containing wild type TOR1 alleles during growth in glucose, cells lacking N-terminal Tor1 HEAT repeats were capable of utilizing non-fermentable as well as fermentable carbon sources and of growth during severe acid stress, but were uniquely unable to grow on lactate. Genome-wide expression analysis showed paradoxical simultaneous activation of anabolic- and starvation responses in cells lacking Tor1 N-terminal HEAT repeats, with misregulation of carbon metabolism and of translational machinery biosynthesis. Targeting fungal-specific Tor1 N-terminal HEAT repeats with small molecules might abrogate fungal viability, especially when during infection multiple stresses are imposed by the host immune system.

Effect of Boron Application On Growth, Yield Parameters, Nutrient Uptake, Quality and Economics of Groundnut (Arachis hypogaea L.); A Review

Groundnut is an important crop cultivated all over world owing to its versatile nature of adaptation to different agro-climatic and soil conditions. In India groundnut gains momentum as an edible oil and India next to food grain. Nutritionally groundnut contains 50 % oil, 25-30 % protein, 20% carbohydrate and 5%fiber. The productivity is lower due to different factors among which nutrient management especially boron that plays pivot role in governing the growth, yield and quality of groundnut. Boron plays various role in the physiological processes of plants, such as cell elongation, cell maturation, meristematic tissue development and protein synthesis, cellular membrane function, reproductive structures and anti- oxidative defence system. It induces flowering, fertilization, hormonal metabolism and translocation of sugars from source to sink. Extensive investigations of research on boron levels were critically reviewed. Application of boron at 10-15 kg ha-1 of soil application and foliar application of 0.5 percent at critical stage was found to increase the growth and yield attributes, yield, quality as well as higher benefit cost ratio sustaining the livelihood of groundnut growers.