Martini 3: a general purpose force field for coarse-grained molecular dynamics.

The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.

Microanatomy of the human tunnel of Corti structures and cochlear partition-tonotopic variations and transcellular signaling.

Auditory sensitivity and frequency resolution depend on the optimal transfer of sound-induced vibrations from the basilar membrane (BM) to the inner hair cells (IHCs), the principal auditory receptors. There remains a paucity of information on how this is accomplished along the frequency range in the human cochlea. Most of the current knowledge is derived either from animal experiments or human tissue processed after death, offering limited structural preservation and optical resolution. In our study, we analyzed the cytoarchitecture of the human cochlear partition at different frequency locations using high-resolution microscopy of uniquely preserved normal human tissue. The results may have clinical implications and increase our understanding of how frequency-dependent acoustic vibrations are carried to human IHCs. A 1-micron-thick plastic-embedded section (mid-modiolar) from a normal human cochlea uniquely preserved at lateral skull base surgery was analyzed using light and transmission electron microscopy (LM, TEM). Frequency locations were estimated using synchrotron radiation phase-contrast imaging (SR-PCI). Archival human tissue prepared for scanning electron microscopy (SEM) and super-resolution structured illumination microscopy (SR-SIM) were also used and compared in this study. Microscopy demonstrated great variations in the dimension and architecture of the human cochlear partition along the frequency range. Pillar cell geometry was closely regulated and depended on the reticular lamina slope and tympanic lip angle. A type II collagen-expressing lamina extended medially from the tympanic lip under the inner sulcus, here named "accessory basilar membrane." It was linked to the tympanic lip and inner pillar foot, and it may contribute to the overall compliance of the cochlear partition. Based on the findings, we speculate on the remarkable microanatomic inflections and geometric relationships which relay different sound-induced vibrations to the IHCs, including their relevance for the evolution of human speech reception and electric stimulation with auditory implants. The inner pillar transcellular microtubule/actin system's role of directly converting vibration energy to the IHC cuticular plate and ciliary bundle is highlighted.

Synchrotron Phase-Contrast Imaging and Cochlear Otosclerosis: A Case Report.

INTRODUCTION: Otosclerosis is a bone disorder affecting the labyrinthine capsule that leads to conductive and occasionally sensorineural hearing loss. The etiology of otosclerosis remains unknown; factors such as infection, hormones, inflammation, genetics, and autoimmunity have been discussed. Treatment consists primarily of surgical stapes replacement and cochlear implantation. High-resolution computed tomography is routinely used to visualize bone pathology. In the present study, we used synchrotron radiation phase-contrast imaging (SR-PCI) to examine otosclerosis plaques in a temporal bone for the first time. The primary aim was to study their three-dimensional (3D) outline, vascular interrelationships, and connections to the middle ear. METHODS: A donated ear from a patient with otosclerosis who had undergone partial stapedectomy with the insertion of a stapes wire prosthesis was investigated using SR-PCI and compared with a control ear. Otosclerotic lesions were 3D rendered using the composite with shading technique. Scalar opacity and color mapping were adjusted to display volume properties with the removal of bones to enhance surfaces. Vascular bone channels were segmented, and the communications between lesions and the middle ear were established. RESULTS: Fenestral, cochlear, meatal, and vestibular lesions were outlined three-dimensionally. Vascular bone channels were found to be frequently connected to the middle ear mucosa, perilabyrinthine air spaces, and facial nerve vessels. Round window lesions partly embedded the cochlear aqueduct which was pathologically narrowed, while the inferior cochlear vein was significantly dilated in its proximal part. CONCLUSION: Otosclerotic/otospongiotic lesions were imaged for the first time using SR-PCI and 3D rendering. The presence of shunts and abnormal vascular connections to the labyrinth appeared to result in hyper-vascularization, overloading the venous system, and leading to sensorineural hearing loss. We speculate about possible local treatments to alleviate the impact of such critical lesions on the labyrinthine microcirculation.

Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage.

Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the ß clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in ß clade toxins vary and include preference for substrates containing ethanolamine headgroups (Sicarius terrosus, St_ßIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the ß clade, St_ßIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_ßIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and ß clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments.

Factors Associated with 30-day Major Adverse Cardiovascular Event in Acute Coronary Syndrome Patients with Non-Dialysis Chronic Kidney Disease: A Retrospective Cohort Study.

BACKGROUND: Acute coronary syndrome (ACS) accounts for the majority of ischemic heart disease-related deaths. It is known that ACS patients with chronic kidney disease (CKD) tend to have worse clinical outcomes, including major adverse coronary events (MACE) compared to patients without CKD.  Some studies suggested that several determinant factors may be involved in this condition. Until now, research on determinant factors of MACE in ACS patients with CKD in Indonesia is still limited. Thus, we aimed to investigate the relationship of various factors to MACE in ACS patients with non-dialysis CKD who underwent percutaneous coronary intervention (PCI), in the form of neutrophile leukocyte ratio (NLR) as a factor describing chronic inflammation, left ventricular hypertrophy (LVH) as a factor describing cardiac remodeling, Gensini score may represent coronary severity, whereas GRACE was used to evaluate the severity and clinical risk of ACS patients. METHODS: This study is a retrospective cohort study using secondary data from the medical records of 117 ACS patients who underwent percutaneous coronary intervention (PCI) at Cipto Mangunkusumo General Hospital Jakarta from January 2018 to June 2018 . Patients were classified based on the stage of CKD and assessed for 30-day MACE. Data were recorded on GRACE score, Gensini score, LVH, and neutrophil-lymphocyte ratio (NLR). Analysis of the relationship between these factors was carried out using the chi-square test. RESULTS: Of the 117 patients, 62.3% were STEMI. At the end of hospital treatment, 67.5% were in the normal-stage 2 CKD group, 17.1% in the CKD stage 3a-3b group, and 15.4% in the CKD stage 4-5 group. MACE occurred in 47 (40.2%) patients with 17 (14.5%) dying. There was a significant relationship between GRACE scores and MACE (54.8% MACE at high GRACE scores vs. 32% MACE at low-moderate GRACE scores, p = 0.016, OR: 2,57 CI 95%, 1,18-5,59), while no significant relationship was found for the Gensini score, LVH, and NLR scores even though there was an increase in the proportion of MACE. CONCLUSION: The incidence of MACE is higher than in the previous studies conducted in the same place, i.e. Cipto Mangunkusumo General Hospital, no significant relationship is found in NLR, LVH, and Gensini score with the 30-day MACE of ACS patients with non-dialysis CKD, meanwhile the GRACE score correlates with the 30-day MACE of ACS in non-dialysis CKD patients as is the known theory regarding this score.

The voltage-sensing domain of a hERG1 mutant is a cation-selective channel.

A cationic leak current known as an "omega current" may arise from mutations of the first charged residue in the S4 of the voltage sensor domains of sodium and potassium voltage-gated channels. The voltage-sensing domains (VSDs) in these mutated channels act as pores allowing nonspecific passage of cations, such as Li+, K+, Cs+, and guanidinium. Interestingly, no omega currents have been previously detected in the nonswapped voltage-gated potassium channels such as the human-ether-a-go-go-related (hERG1), hyperpolarization-activated cyclic nucleotide-gated, and ether-a-go-go channels. In this work, we discovered a novel omega current by mutating the first charged residue of the S4 of the hERG1, K525 to serine. To characterize this omega current, we used various probes, including the hERG1 pore domain blocker, dofetilide, to show that the omega current does not require cation flux via the canonical pore domain. In addition, the omega flux does not cross the conventional selectivity filter. We also show that the mutated channel (K525S hERG1) conducts guanidinium. These data are indicative of the formation of an omega current channel within the VSD. Using molecular dynamics simulations with replica-exchange umbrella sampling simulations of the wild-type hERG1 and the K525S hERG1, we explored the molecular underpinnings governing the cation flow in the VSD of the mutant. We also show that the wild-type hERG1 may form water crevices supported by the biophysical surface accessibility data. Overall, our multidisciplinary study demonstrates that the VSD of hERG1 may act as a cation-selective channel wherein a mutation of the first charged residue in the S4 generates an omega current. Our simulation uncovers the atomistic underpinning of this mechanism.

Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C.

Peripheral membrane proteins (PMPs) bind temporarily to cellular membranes and play important roles in signaling, lipid metabolism, and membrane trafficking. Obtaining accurate membrane-PMP affinities using experimental techniques is more challenging than for protein-ligand affinities in an aqueous solution. At the theoretical level, calculation of the standard protein-membrane binding free energy using molecular dynamics simulations remains a daunting challenge owing to the size of the biological objects at play, the slow lipid diffusion, and the large variation in configurational entropy that accompanies the binding process. To overcome these challenges, we used a computational framework relying on a series of potential-of-mean-force (PMF) calculations including a set of geometrical restraints on collective variables. This methodology allowed us to determine the standard binding free energy of a PMP to a phospholipid bilayer using an all-atom force field. Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) was chosen due to its importance as a virulence factor and owing to the host of experimental affinity data available. We computed a standard binding free energy of -8.2 ± 1.4 kcal/mol in reasonable agreement with the reported experimental values (-6.6 ± 0.2 kcal/mol). In light of the 2.3-µs separation PMF calculation, we investigated the mechanism whereby BtPI-PLC disengages from interactions with the lipid bilayer during separation. We describe how a short amphipathic helix engages in transitory interactions to ease the passage of its hydrophobes through the interfacial region upon desorption from the bilayer.

Refinement of a cryo-EM structure of hERG: Bridging structure and function.

The human-ether-a-go-go-related gene (hERG) encodes the voltage-gated potassium channel (KCNH2 or Kv11.1, commonly known as hERG). This channel plays a pivotal role in the stability of phase 3 repolarization of the cardiac action potential. Although a high-resolution cryo-EM structure is available for its depolarized (open) state, the structure surprisingly did not feature many functionally important interactions established by previous biochemical and electrophysiology experiments. Using molecular dynamics flexible fitting (MDFF), we refined the structure and recovered the missing functionally relevant salt bridges in hERG in its depolarized state. We also performed electrophysiology experiments to confirm the functional relevance of a novel salt bridge predicted by our refinement protocol. Our work shows how refinement of a high-resolution cryo-EM structure helps to bridge the existing gap between the structure and function in the voltage-sensing domain (VSD) of hERG.

Micro-CT of the human ossicular chain: Statistical shape modeling and implications for otologic surgery.

The ossicular chain is a middle ear structure consisting of the small incus, malleus and stapes bones, which transmit tympanic membrane vibrations caused by sound to the inner ear. Despite being shown to be highly variable in shape, there are very few morphological studies of the ossicles. The objective of this study was to use a large sample of cadaveric ossicles to create a set of three-dimensional models and study their statistical variance. Thirty-three cadaveric temporal bone samples were scanned using micro-computed tomography (µCT) and segmented. Statistical shape models (SSMs) were then made for each ossicle to demonstrate the divergence of morphological features. Results revealed that ossicles were most likely to vary in overall size, but that more specific feature variability was found at the manubrium of the malleus, the long process and lenticular process of the incus, and the crura and footplate of the stapes. By analyzing samples as whole ossicular chains, it was revealed that when fixed at the malleus, changes along the chain resulted in a wide variety of final stapes positions. This is the first known study to create high-quality, three-dimensional SSMs of the human ossicles. This information can be used to guide otological surgical training and planning, inform ossicular prosthesis development, and assist with other ossicular studies and applications by improving automated segmentation algorithms. All models have been made publicly available.

Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes.

Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes from Gram-positive bacteria are secreted virulence factors that aid in downregulating host immunity. These PI-PLCs are minimalist peripheral membrane enzymes with a distorted (ßα)8 TIM barrel fold offering a conserved and stable scaffold for the conserved catalytic amino acids while membrane recognition is achieved mostly through variable loops. Decades of experimental and computational research on these enzymes have revealed the subtle interplay between molecular mechanisms of catalysis and membrane binding, leading to a semiquantitative model for how they find, bind, and cleave their respective substrates on host cell membranes. Variations in sequence and structure of their membrane binding sites may correlate with how enzymes from different Gram-positive bacteria search for their particular targets on the membrane. Detailed molecular characterization of protein-lipid interactions have been aided by cutting-edge methods ranging from 31P field-cycling NMR relaxometry to monitor protein-induced changes in phospholipid dynamics to molecular dynamics simulations to elucidate the roles of electrostatic and cation-π interactions in lipid binding to single molecule fluorescence measurements of dynamic interactions between PI-PLCs and vesicles. This toolkit is readily applicable to other peripheral membrane proteins including orthologues in Gram-negative bacteria and more recently discovered eukaryotic minimalist PI-PLCs.

Synchrotron Radiation-Based Reconstruction of the Human Spiral Ganglion: Implications for Cochlear Implantation.

OBJECTIVE: To three-dimensionally reconstruct Rosenthal's canal (RC) housing the human spiral ganglion (SG) using synchrotron radiation phase-contrast imaging (SR-PCI). Straight cochlear implant electrode arrays were inserted to better comprehend the electro-cochlear interface in cochlear implantation (CI). DESIGN: SR-PCI was used to reconstruct the human cochlea with and without cadaveric CI. Twenty-eight cochleae were volume rendered, of which 12 underwent cadaveric CI with a straight electrode via the round window (RW). Data were input into the 3D Slicer software program and anatomical structures were modeled using a threshold paint tool. RESULTS: The human RC and SG were reproduced three-dimensionally with artefact-free imaging of electrode arrays. The anatomy of the SG and its relationship to the sensory organ (Corti) and soft and bony structures were assessed. CONCLUSIONS: SR-PCI and computer-based three-dimensional reconstructions demonstrated the relationships among implanted electrodes, angular insertion depths, and the SG for the first time in intact, unstained, and nondecalcified specimens. This information can be used to assess stimulation strategies and future electrode designs, as well as create place-frequency maps of the SG for optimal stimulation strategies of the human auditory nerve in CI.

Three-dimensional imaging of the human internal acoustic canal and arachnoid cistern: a synchrotron study with clinical implications.

A thorough knowledge of the gross and micro-anatomy of the human internal acoustic canal (IAC) is essential in vestibular schwannoma removal, cochlear implantation (CI) surgery, vestibular nerve section, and decompression procedures. Here, we analyzed the acoustic-facial cistern of the human IAC, including nerves and anastomoses using synchrotron phase contrast imaging (SR-PCI). A total of 26 fresh human temporal bones underwent SR-PCI. Data were processed using volume-rendering software to create three-dimensional (3D) reconstructions allowing soft tissue analyses, orthogonal sectioning, and cropping. A scalar opacity mapping tool was used to enhance tissue surface borders, and anatomical structures were color-labeled for improved 3D comprehension of the soft tissues. SR-PCI reproduced, for the first time, the variable 3D anatomy of the human IAC, including cranial nerve complexes, anastomoses, and arachnoid membrane invagination (acoustic-facial cistern; an extension of the cerebellopontine cistern) in unprocessed, un-decalcified specimens. An unrecognized system of arachnoid pillars and trabeculae was found to extend between the arachnoid and cranial nerves. We confirmed earlier findings that intra-meatal vestibular schwannoma may grow unseparated from adjacent nerves without duplication of the arachnoid layers. The arachnoid pillars may support and stabilize cranial nerves in the IAC and could also play a role in local fluid hydrodynamics.

Effects of object-to-detector distance and beam energy on synchrotron radiation phase-contrast imaging of implanted cochleae.

OBJECTIVES: To demonstrate that synchrotron radiation phase-contrast imaging (SR-PCI) can be used to visualize the intrascalar structures in implanted human cochleae and to find the optimal combination of the parameters object-to-detector distance (ODD) and beam energy (E) for visualization. MATERIALS AND METHODS: Three cadaveric implanted human temporal bones underwent SR-PCI with varying combinations of parameters ODD (3, 2 and 1 m) and E (47, 60 and 72 keV). All images were then reconstructed to a three-dimensional (3D) stack of slices. The acquired 3D images were compared using contrast-to-noise ratios (CNRs) of the basilar membrane ( CNRBM ) and the electrode array (CNRE ) and the standard deviation of the beam streaks ( σS ). Postprocessing calculations were performed using Matlab (Version 2017b, MathWorks Inc., Natick, MA, U.S.A.) with a standard significance level p < 0.05 to determine the most optimal combination of parameters. RESULTS: SR-PCI with computed tomography reconstruction provided good visualization of the anatomical features of the implanted cochleae, specifically the exact location of the electrode with respect to the BM. A single-factor ANOVA revealed a significant difference of variance for both CNRE and CNRBM , but failed to show significance for σS . A two-sample t-test failed to show any significant difference between CNRE columns of (3 m, 72 keV) and (2 m, 60 keV). The CNRBM was significantly different only at two pairs of columns, when (1 m, 72 keV) was compared against (2 m, 72 keV) and (3 m, 72 keV). CONCLUSIONS: The results of this study show that SR-PCI is a viable method to visualize implanted human cochleae. SR-PCI is less invasive, less labour intensive and is associated with a much lower acquisition time compared to other methods for postimplantation imaging in humans, such as histological sectioning. We found that the optimal combination of E and ODD parameters was 72 keV and 2 m, respectively. These parameters resulted in high-contrast images of the electrode as well as all internal structures of the cochleae. LAY DESCRIPTION: Cochlear implants (CI) are currently the preferred method of treatment for hearing loss. Cochlear implantation surgery involves placement of a metallic, wire-shaped electrode inside the cochlea, the main organ of the human hearing system. Knowledge of the exact location of the electrode after implantation is beneficial in improving the extent of restored hearing. Common clinical imaging modalities such as computed-tomography (CT) are not ideal for providing such information, due to lack of resolution and streaking caused by the metallic electrode. Recent studies have developed algorithms to extract the electrode location from clinical computed-tomography images and have been validated using histology or micro computed-tomography (micro-CT). Synchrotron radiation phase contrast imaging (SR-PCI) is a high-resolution imaging technique used to visualize small structures in three dimensions. Recently, SR-PCI has been shown to be an alternative to histology or micro-CT for imaging the human cochlea. However, it has not been optimized for imaging implanted human cochleae. The main objective of the present work was to find the optimal organization of imaging parameters (i.e., object-to-detector distance and beam energy) for using SR-PCI to image implanted human cochleae. Three cadaveric human cochleae were imaged using five different combinations of imaging parameters at the Canadian Light Source Inc., Saskatoon, SK, Canada. The resulting images were compared both quantitatively and qualitatively. An optimal combination of parameters was found to produce high-contrast images of the both the CI electrode and all internal structures of the cochlea with minimal streaking. SR-PCI is therefore a viable alternative to histological or micro-CT studies for post-surgical imaging of implanted human cochleae.

Effects of Various Trajectories on Tissue Preservation in Cochlear Implant Surgery: A Micro-Computed Tomography and Synchrotron Radiation Phase-Contrast Imaging Study.

OBJECTIVES: The purpose of this study was to evaluate the three-dimensional (3D) anatomy and potential damage to the hook region of the human cochlea following various trajectories at cochlear implantation (CI). The goal was to determine which of the approaches can avoid lesions to the soft tissues, including the basilar membrane and its suspension to the lateral wall. Currently, there is increased emphasis on conservation of inner ear structures, even in nonhearing preservation CI surgery. DESIGN: Micro-computed tomography and various CI approaches were made in an archival collection of macerated and freshly fixed human temporal bones. Furthermore, synchrotron radiation phase-contrast imaging was used to reproduce the soft tissues. The 3D anatomy was investigated using bony and soft tissue algorithms, and influences on inner ear structures were examined. RESULTS: Micro-computed tomography with 3D rendering demonstrated the topography of the round window (RW) and osseous spiral laminae, while synchrotron imaging allowed reproduction of soft tissues such as the basilar membrane and its suspension around the RW membrane. Anterior cochleostomies and anteroinferior cochleostomies invariably damaged the intracochlear soft tissues while inferior cochleostomies sporadically left inner ear structures unaffected. CONCLUSIONS: Results suggest that cochleostomy approaches often traumatize the soft tissues at the hook region at CI surgery. For optimal structural preservation, the RW approach is, therefore, recommended.

Inelastic scattering of photoelectrons from He nanodroplets.

We present a detailed study of inelastic energy-loss collisions of photoelectrons emitted from He nanodroplets by tunable extreme ultraviolet (XUV) radiation. Using coincidence imaging detection of electrons and ions, we probe the lowest He droplet excited states up to the electron impact ionization threshold. We find significant signal contributions from photoelectrons emitted from free He atoms accompanying the He nanodroplet beam. Furthermore, signal contributions from photoionization and electron impact excitation/ionization occurring in pairs of nearest-neighbor atoms in the He droplets are detected. This work highlights the importance of inelastic electron scattering in the interaction of nanoparticles with XUV radiation.

In-vitro antibacterial and antioxidant potential of winged prickly ash, green tea and thyme.

Herbs and plants are mostly used as antimicrobials and antioxidants owing to the harmfulness and linked side-effects of synthetic chemical constituents. Plants and spices produce various metabolites with antibacterial and antioxidant potential. These metabolites are principally revealed as encouraging healing components or mediators which control ailments in human beings. The present study was aimed to characterize the extracts from selected medicinal plants through in-vitro activities. Winged prickly ash, green tea and thyme were selected and extracted through ethanol and methanol solutions. The extracts were assessed for antibacterial and antioxidant activities. The antibacterial potential of extracts showed the significant extent of the activity against Bacillus subtilis and E. coli. The maximum activity was noted in 80% methanolic fraction of Thymus vulgaris (15.20±0.64 mm) against Bacillus subtilis. Antioxidant potential exhibited the highest phenolic and flavonoid content in Camellia sinensis . The total phenolic content was significantly higher (1456.26±12.05 mg gallic acid) in 80% ethanolic fraction of Camellia sinensis. The flavonoid content in different plant extracts ranged from 8.17±2.02 to 376.29±7.11 mg/g. The radical scavenging DPPH assay also showed the significant antioxidant capacity of selected plants with the methanolic (50%) extract of Camellia sinensis found to be the most potent (78.95±7.12%). It was concluded that the alcoholic extracts of selected medicinal plants revealed the effective antibacterial and antioxidant activity, showing protective prospective against oxidative injury.

Penning Ionization of Acene Molecules by Helium Nanodroplets.

Acene molecules (anthracene, tetracene, pentacene) and fullerene (C60) are embedded in He nanodroplets (HeN) and probed by EUV synchrotron radiation. When resonantly exciting the He nanodroplets, the embedded molecules M are efficiently ionized by the Penning reaction HeN* + M → HeN + M+ + e-. However, the Penning electron spectra are all broad and structureless, largely differing from those measured by binary Penning collisions, as well as from those measured for dopants bound to the He droplet surface. Simulations based on elastic binary electron-He collisions qualitatively reproduce the measured spectra only when assuming unexpectedly large He droplets, indicating that electron spectra of molecules embedded in helium nanodroplets are severely affected by collective electron-helium interactions.

Role of pRIFLE Criteria in Early Diagnosis of Severity Staging of Neonatal AKI and its Impact on Management.

Mortality is high among sick neonates who have concomitant acute kidney injury (AKI). This observational study was done at Special Care Baby Unit (SCABU) of Dhaka Medical College Hospital (DMCH), Bangladesh from October 2013 to March 2014 to find out the role of pRIFLE criteria in prediction of severity stages of AKI in neonate and early intervention to see the immediate outcome. A total of 44 neonates with AKI were included, all were treated conservatively and with intermittent peritoneal dialysis (IPD) as needed. The neonate of ≤7 days old comprised the main bulk (n=28) and M: F = 21: 23. The diagnosis was based on eCCL criteria of pRIFLE showed that 40.9% neonates were at risk of AKI, 20.5% have had already injured. Higher proportions of neonates were classified as failure (38.6%). The distribution of biochemical parameters among three stages of AKI showed serum potassium was significantly higher in failure group (p<0.001). The serum creatinine both at baseline and at next evaluations were significantly raised in the failure group (p<0.001). However, failure group had a significantly longer hospital stay compared to risk and injury group (p<0.001). Multiorgan failure was found to be lower in the risk group compared to other two groups (p=0.026). Majority of the failure group needed dialysis as compared to the risk and injury group (p<0.001). The mortality was progressively higher from risk to failure groups (p=0.106). Overall 27% of the neonates diagnosed AKI by pRIFLE were died of the disease. The study concluded that pRIFLE staging in AKI is useful and sensitive in the diagnosis and management of AKI in neonates.

A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding.

Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that binds specifically to phosphatidylcholine (PC) bilayers containing negatively charged phospholipids. BtPI-PLC carries a negative net charge and its interfacial binding site has no obvious cluster of basic residues. Continuum electrostatic calculations show that, as expected, nonspecific electrostatic interactions between BtPI-PLC and membranes vary as a function of the fraction of anionic lipids present in the bilayers. Yet they are strikingly weak, with a calculated ΔGel below 1 kcal/mol, largely due to a single lysine (K44). When K44 is mutated to alanine, the equilibrium dissociation constant for small unilamellar vesicles increases more than 50 times (∼2.4 kcal/mol), suggesting that interactions between K44 and lipids are not merely electrostatic. Comparisons of molecular-dynamics simulations performed using different lipid compositions reveal that the bilayer composition does not affect either hydrogen bonds or hydrophobic contacts between the protein interfacial binding site and bilayers. However, the occupancies of cation-π interactions between PC choline headgroups and protein tyrosines vary as a function of PC content. The overall contribution of basic residues to binding affinity is also context dependent and cannot be approximated by a rule-of-thumb value because these residues can contribute to both nonspecific electrostatic and short-range protein-lipid interactions. Additionally, statistics on the distribution of basic amino acids in a data set of membrane-binding domains reveal that weak electrostatics, as observed for BtPI-PLC, might be a less unusual mechanism for peripheral membrane binding than is generally thought.