Search

Objective: Study the mechanism of Mulberry Root Bark Decoction in the treatment of COPD based on network pharmacology. Methods: The active components and predictive targets of Mulberry Root Bark Decoction were screened by TCMSP database. The disease targets of COPD were collected by searching GeneCards, DisGeNET, PhamGKB and TTD databases. Using R language to draw Venn diagram, and get the key target of Mulberry Root Bark Decoction in the treatment of COPD. Cytoscape was used to construct the regulatory network of drug active ingredient disease target. The key targets were imported into string database to construct protein-protein interaction network, and the core targets were obtained by network topology analysis with Cytoscape software. Finally, the Bioconductor platform and R language were used for GO and KEGG enrichment analysis. Results: There were 142 active components and 255 drug targets in Mulberry Root Bark Decoction. 1941 COPD targets were retrieved. There were 129 common targets of Mulberry Root Bark Decoction and COPD; Eight core targets of PPI network were obtained. GO function analysis is involved in oxidative stress, cellular chemical stress and other biological processes. Cell components such as cell membrane raft and membrane region involve molecular functions such as ubiquitin like protein ligase and DNA binding transcription factor. KEGG mainly includes PI3K-Akt signal pathway, tumor necrosis factor signal pathway, IL-17 signal pathway, etc. Conclusion: Quercetin, luteolin, kaempferol, wogonin and other active components in Mulberry Root Bark Decoction act on PI3K / Akt, TNF, IL-17, TCR and other signal pathways through Jun, TP53, MAPK1, IL6 and other targets to play an anti-inflammatory and reduce oxidative stress response role. The results of this study can provide a reference for further study on the mechanism of Mulberry Root Bark Decoction in the treatment of chronic obstructive pulmonary disease.

The sensor kinase DcuS of Escherichia coli perceives extracellular fumarate by a periplasmic PASP sensor domain. Transmembrane (TM) helix TM2, present as TM2-TM2′ homo-dimer, transmits fumarate activation in a piston-slide across the membrane. The second TM helix of DcuS, TM1, is known to lack piston movement. Structural and functional properties of TM1 were analyzed. Oxidative Cys-crosslinking (CL) revealed homo-dimerization of TM1 over the complete membrane, but only the central part showed α-helical +3/+4 spacing of the CL maxima. The GALLEX bacterial two-hybrid system indicates TM1/TM1′ interaction, and the presence of a TM1-TM1′ homo-dimer is suggested. The peripheral TM1 regions presented CL in a spacing atypical for α-helical arrangement. On the periplasmic side the deviation extended over 11 AA residues (V32-S42) between the α-helical part of TM1 and the onset of PASP. In the V32-S42 region, CL efficiency decreased in the presence of fumarate. Therefore, TM1 exists as a homo-dimer with α-helical arrangement in the central membrane region, and non-α-helical arrangement in the connector to PASP. The fumarate induced structural response in the V32-S42 region is suggested to represent a structural adaptation to the shift of TM2 in the TM1-TM1′/TM2-TM2′ four-helical bundle.

Membranes surrounding cells or organelles represent barriers to proteins and other molecules. However, specific proteins can cross membranes by different translocation systems, the best studied being the Sec61/SecY channel. This channel forms a hydrophilic, hourglass-shaped membrane channel, with a lateral gate towards the surrounding lipid. However, recent studies show that an aqueous pore is not required in other cases of protein translocation. The Hrd1 complex, mediating the retro-translocation of misfolded proteins from the endoplasmic reticulum (ER) lumen into the cytosol, contains multi-spanning proteins with aqueous luminal and cytosolic cavities and lateral gates juxtaposed in a thinned membrane region. A locally thinned, distorted lipid bilayer also allows protein translocation in other systems, suggesting a new paradigm to overcome the membrane barrier.

Proteomic information revealed approximately 3,923 proteins in Mycobacterium tuberculosis H37 Rv genome of which around ∼25% of proteins are hypothetical proteins (HPs). The present work comprises computational approaches to identify and characterize the HPs of M. tuberculosis that symbolize the putative target for rationale development of a drug or antituberculosis strategy. Proteins were primarily classified based on motif and domain information, which were further analyzed for the presence of virulence factors (VFs), determination of localization, and signal peptide/enzymatic cleavage sites. 863 HPs were found, and 599 HPs were finalized based on motifs, that is, GTP (525), Trx (47), SAM (14), PE-PGRS (5), and CBD (8). 80 HPs contain virulence factor (VF), 24 HPs localized in membrane region, and 4 HPs contain signal peptide/enzymatic cleavage sites. The overall parametric study finalizes four HPs Rv0679c, Rv0906, Rv3627c, and Rv3811 that also comprise GTPase domain. Structure prediction, structure-based function prediction, molecular docking and mutation analysis of selected proteins were done. Docking studies revealed that GTP and GTPase inhibitor (mac0182344) were docked with all four proteins with high affinities. In silico point mutation studies showed that substitution of aspartate with glycine within a GTPase motif showed the largest decrease in stability and pH differentiation also affects protein's stability. This analysis thus fixes a roadmap in the direction of finding potential target of this bacterium for drug development and enlightens the efficacy of GTP as a major regulator of Mycobacterial cellular pathways.

Orta kulak iltihabından dolayı kulak zarında çeşitli deformasyonlar meydana gelmektedir. Hastalığın teşhis edilebilmesi için otoskop cihazı ile kulağa bakıldığı zaman zar bölgesine erişilmesi ve detaylı bir şekilde kulak zarının incelenmesi gerekmektedir. Son yıllarda derin öğrenme birçok alanda uygulanmış ve oldukça etkili sonuçlar elde edilmiştir. Derin öğrenmenin biyomedikal alanda da sık bir şekilde kullanıldığı ve oldukça iyi neticelere varıldığı bilinmektedir. Otomatik nesne tanımlamada da derin öğrenme tabanlı yöntemler başarılı bir şekilde kullanılmaktadır. Bu çalışmada otoskop cihazı ile elde edilen orta kulak imgelerinde zar bölgesinin otomatik tespiti için derin öğrenme tabanlı nesne algılama yöntemi olan YOLO kullanılmıştır. YOLO yöntemi ile ilgili alanın otomatik olarak tespit edilmesini sağlamak üzere, nesne önerileri için evrişimsel sinir ağı mimarilerinden olan AlexNet, VGGNet, GoogLeNet, ve ResNet ile deneysel çalışmalar yapılmıştır. Performans sonuçlarına göre ResNet ve VGGNet mimarileri ile en verimli sonuçlar elde edilmiştir. YOLO ile zar bölgesinin tespiti %93 başarı oranı ile tespit edildi., Due to inflammation of the middle ear, various deformations occur in the eardrum. In order to diagnose the disease, it is necessary to examine the tympanic membrane in detail with an otoscope. In recent years, deep learning has been applied in many areas including biomedical field and very effective results have been achieved. Deep learning based methods are used successfully in automatic object detection. In this study, a deep learning based object detection method namely You Only Look Once (YOLO), is used for automatic detection of tympanic membrane in eardrum images obtained using otoscope device. To enable automatic detection of tympanic membrane by YOLO, experimental studies were conducted with AlexNet, VGGNet, GoogLeNet and ResNet. According to the performance results, the most efficient results were obtained with ResNet and VGGNet architectures. Tympanic membrane region detection with YOLO, was performed with an accuracy rate of 93%.

Objective To explore the potential molecular targets of Cang Fu Dao Tan Formula (CFDTF) in the treatment of obese polycystic ovary syndrome (PCOS) using network pharmacology and bioinformatic approaches. Methods The potential blood-entry active compounds and targets of CFDTF were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and obese PCOS related gene targets were retrieved from GeneCard databases. A protein-protein interaction (PPI) network of CFDTF component-targets and obese PCOS disease- targets was constructed using STRING. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the intersection network were conducted using a Bioconductor database. Results In total, 114 active compounds were screened according to oral bioavailability (OB) and drug similarity (DL), and 328 targets related to these constituents were obtained. Further, 2 559 target genes directly related to obese PCOS were obtained from the GeneCard databases, and 82 genes were obtained from the intersection of the component-target and disease-target PPI network. These genes were mainly involved in response to steroid hormones, nutrient levels and lipopolysaccharide as well as in other biological processes. Their molecular functions were mainly related to nuclear receptor activity, phosphatase binding and cytokine activity, and they were enriched in the cytoplasm, cell membrane and membrane region. Conclusions CFDTF consists of 114 active compounds that are responsible for its pharmacodynamic effects. It mainly regulates the AGE-RAGE signaling pathway in diabetic complications, bladder cancer, and hepatitis B and in other signaling networks. These findings provide certain theoretical and scientific basis for the treatment of obese PCOS with Chinese medicine.

Human epidermal growth factor receptor 2 (HER2) is one of the widely used Immunohistochemical (IHC) markers for prognostic evaluation amongst the patient of breast cancer. Accurate quantification of cell membrane is essential for HER2 scoring in therapeutic decision making. In modern laboratory practice, expert pathologist visually assesses the HER2-stained tissue sample under the bright field microscope for cell membrane assessment. This manual assessment is time consuming, tedious and quite often results in interobserver variability. Further, the burden of increasing number of patients is a challenge for the pathologists. To address these challenges, there is an urgent need with a rapid HER2 cell membrane extraction method. The proposed study aims at developing an automated IHC scoring system, termed as AutoIHC-Analyzer, for automated cell membrane extraction followed by HER2 molecular expression assessment from stained tissue images. A series of image processing approaches have been used to automatically extract the stained cells and membrane region, followed by automatic assessment of complete and broken membrane. Finally, a set of features are used to automatically classify the tissue under observation for the quantitative scoring as 0/1+, 2+ and 3+. In a set of surgically extracted cases of HER2-stained tissues, obtained from collaborative hospital for the testing and validation of the proposed approach AutoIHC-Analyzer and publicly available open source ImmunoMembrane software are compared for 90 set of randomly acquired images with the scores by expert pathologist where significant correlation is observed [(r = 0.9448; p < 0.001) and (r = 0.8521; p < 0.001)] respectively. The output shows promising quantification in automated scoring. LAY DESCRIPTION: In cancer prognosis amongst the patient of breast cancer, human epidermal growth factor receptor 2 (HER2) is used as Immunohistochemical (IHC) biomarker. The correct assessment of HER2 leads to the therapeutic decision making. In regular practice, the stained tissue sample is observed under a bright microscope and the expert pathologists score the sample as negative (0/1+), equivocal (2+) and positive (3+) case. The scoring is based on the standard guidelines relating the complete and broken cell membrane as well as intensity of staining in the membrane boundary. Such evaluation is time consuming, tedious and quite often results in interobserver variability. To assist in rapid HER2 cell membrane assessment, the proposed study aims at developing an automated IHC scoring system, termed as AutoIHC-Analyzer, for automated cell membrane extraction followed by HER2 molecular expression assessment from stained tissue images. The input image is preprocessed using modified white patch and CMYK and RGB colour space were used in extracting the haematoxylin (negatively stained cells) and diaminobenzidine (DAB) stain observed in the tumour cell membrane. Segmentation and postprocessing are applied to create the masks for each of the stain channels. The membrane mask is then quantified as complete or broken using skeletonisation and morphological operations. Six set of features were assessed for the classification from a set of 180 training images. These features are: complete to broken membrane ratio, amount of stain using area of Blue and Saturation channels to the image size, DAB to haematoxylin ratio from segmented masks and average R, G and B from five largest blobs in segmented DAB-masked image. These features are then used in training the SVM classifier with Gaussian kernel using 5-fold cross-validation. The accuracy in the training sample is found to be 88.3%. The model is then used for 90 set of unknown test sample images and the final labelling of stained cells and HER2 scores (as 0/1+, 2+ and 3+) are compared with the ground truth, that is expert pathologists' score from the collaborative hospital. The test sample images were also fed to ImmunoMembrane software for a comparative assessment. The results from the proposed AutoIHC-Analyzer and ImmunoMembrane software were compared with the expert pathologists' score where significant agreement using Pearson's correlation coefficient [(r = 0.9448; p < 0.001) and (r = 0.8521; p < 0.001) respectively] is observed. The results from AutoIHC-Analyzer show promising quantitative assessment of HER2 scoring.

Triacylglycerols store metabolic energy in organisms and have industrial uses as foods and fuels. Excessive accumulation of triacylglycerols in humans causes obesity and is associated with metabolic diseases1. Triacylglycerol synthesis is catalysed by acyl-CoA diacylglycerol acyltransferase (DGAT) enzymes2–4, the structures and catalytic mechanisms of which remain unknown. Here we determined the structure of dimeric human DGAT1, a member of the membrane-bound O-acyltransferase (MBOAT) family, by cryo-electron microscopy at approximately 3.0 A resolution. DGAT1 forms a homodimer through N-terminal segments and a hydrophobic interface, with putative active sites within the membrane region. A structure obtained with oleoyl-CoA substrate resolved at approximately 3.2 A shows that the CoA moiety binds DGAT1 on the cytosolic side and the acyl group lies deep within a hydrophobic channel, positioning the acyl-CoA thioester bond near an invariant catalytic histidine residue. The reaction centre is located inside a large cavity, which opens laterally to the membrane bilayer, providing lipid access to the active site. A lipid-like density—possibly representing an acyl-acceptor molecule—is located within the reaction centre, orthogonal to acyl-CoA. Insights provided by the DGAT1 structures, together with mutagenesis and functional studies, provide the basis for a model of the catalysis of triacylglycerol synthesis by DGAT. Cryo-electron microscopy structures and functional and mutagenesis studies provide insights into the catalysis of triacylglycerol synthesis by human acyl-CoA diacylglycerol acyltransferase at its intramembrane active site.

Snapshots of a rotary pump Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-hydrolysis–driven proton pumps. In neurons, V-ATPase activity generates a proton gradient across the membrane of synaptic vesicles so that neurotransmitters can be loaded into the vesicles. Abbas et al. developed a method to purify V-ATPase from rat brain and determined the structure of the entire complex by cryo–electron microscopy. Native mass spectrometry showed that the preparation was homogeneous and complemented structural studies by confirming the subunit composition. Three rotational states were resolved at better than 4-angstrom resolution, providing insight into the conformational changes that couple ATP hydrolysis to proton pumping. Science , this issue p. 1240

Crosslinking is a well-established technique to enhance chemical stability of polymer membranes but at the expense of lower flux. We previously demonstrated that this trade-off between chemical stability and separation performance can be overcome through the judicious selection of a crosslinking agent, 4-sulfophthalic acid (SPTA), which also functioned as a fixed carrier site. The mechanism underpinning this breakthrough remained unknown. Through molecular dynamic simulations and a series of complementary experiments, here we reveal that higher crosslinking degree can increase local water concentration close to the sulfonic acid groups, and enhance both long-distance water-sulfonic acid-interactions and water molecule mobility. These underpinned the significant increase in water flux of crosslinked pervaporation membranes during desalination. These results show that the dependence of water diffusivity on water concentration is reduced with higher crosslinking degree. More importantly, water diffusivity at the “dry membrane region” determined the overall water transport behaviour. These findings can potentially impact on the design of pervaporation membranes for production of potable water from brackish, sea and brine water.

Many of the mutations in GJB2 and GJB6, which encode connexins 26 and 30 (Cx26 and Cx30), impair the formation of membrane channels and cause autosomal syndromic and non-syndromic hearing loss. In cochlear non-sensory supporting cells, Cx26 and Cx30 form two types of homomeric and heteromeric gap junctions. The biogenesis processes of these channels occurring in situ remain largely unknown. Here we show that Cx30 homomeric and Cx26/Cx30 heteromeric gap junctions exhibit distinct assembly mechanisms in the cochlea. When expressed as homomeric channels, Cx30 preferentially interacts with β-actin in the peripheral non-junctional membrane region, called perinexus, and strongly relies on the actin network for gap junction plaque assembly. In contrast, we found that Cx26/Cx30 heteromeric gap junction plaques are devoid of perinexus and associated actin network, and resist to actin-depolymerizating drug. This supports that Cx26/Cx30 oligomers could be directly delivered from the interior of the cell to the junctional plaque. Altogether, our data provide a novel insight in homomeric and heteromeric gap junction plaque assembly in the cochlea.

Proteinase inhibitors (PIs) are polypeptides that occur naturally in a wide range of plants and are considered to be an essential part of the plant’s natural defense system. The aims of this study were to determine effect of PI2-N. tabacum in nematode (Meloidogyne incognita) resistance and its characterize. Resistant (KY9) and susceptible (Ergo) genotypes were inoculated by M. incognita race 2 and total RNA were extracted from roots. Exclusive primers were used for PI2 (Q40561) and EF1α (reference gene) in qPCR to determine PI2 level changes in two, three and four days after inoculation. Results showed significant difference of PI2 expression in resistant and susceptible genotypes in two-four days after inoculation. Bioinformatics analysis revealed PI2 is an unstable protein and has three proteinase inhibitory domains with a trance membrane region. Proteinase inhibitory domains are trypsin and chymotrypsin inhibitor. Alignment and phylogenetic relationship of inhibitor precursor-repeats in Nicotiana sp. revealed seven groups that were variable in sequence. However, they had conserved residues including eight cysteines, a single proline and three Glycine.

Tetraspanin membrane proteins form physical complexes with signaling molecules and have been suggested to influence the signaling events of associated molecules. Of the tetraspanin proteins, CD82 has been shown to promote homotypic cell-cell adhesion, which partially accounts for its role in suppressing cancer invasion and metastasis. We found here that CD82-induced cell-cell adhesion is attributed to increased E-cadherin expression through CD82-mediated downregulation of the E-cadherin repressor Snail. The Snail repression by CD82 resulted from the reduced binding of the Sp1 transcription factor to the Snail gene promoter. Notably, high CD82 expression did not allow the fibronectin matrix to induce Sp1 phosphorylation, implicating CD82 inhibition of the fibronectin-integrin signaling-dependent Sp1 activation. Meanwhile, E-cadherin upregulated by CD82 pulled β-catenin up to the membrane region, and consequently reduced the amount of cytoplasmic β-catenin that was able to move into to the nucleus. The Wnt signal-induced nuclear translocation of β-catenin was also inhibited by the CD82 function of upregulating E-cadherin. Overall, high CD82 expression was likely to suppress fibronectin adhesion-induced Sp1 activation signaling for Snail expression, resulting in continuous E-cadherin expression, which contributed not only to the maintenance of strong cell-cell adhesion but also to the blockage of nuclear β-catenin signaling.

Breast cancer is the most important and frequently diagnosed cancer among women worldwide. The CTLA 4 is a member of Immunoglobulin super family and binds to the CD80 and CD86 co-stimulatory molecules.(binds to CD80/86 on APCs with a higher affinity than CD28, thereby inhibiting co-stimulatory signals.CTLA-4 (Gene ID:1493, MIM number: 123890) is a new member of the immunoglobulin super family known as insulin-dependent diabetes mellitus 12 (IDDM 12) ,and cluster of differentiation 152 (CD152).The CTLA-4 protein consists of a 37 amino acid leader peptide, an extracellular immunoglobulin (Ig) V like domain or the ligand-binding domain (116 amino acid), a hydrophobic trans membrane region (37 amino acid), and a cytoplasmic domain. The aim of the present study of the association of CTLA-4 serum level and polymorphism with breast cancer in Iraqi women suffers from breast cancer. Materials and Methods: peripheral Blood samples were collected from 45 Iraqi patients women diagnosed with breast cancer patient, and 45 healthy women were matched with patients as a control. ELISA technique has been used to determine the serum level of sCTLA-4.The polymerase chain reaction (PCR) performed on 45 patients and 45 control, to determine the genetic variation in the +49 exon 1 region of CTLA-4 gene. Results: the serum level of understudying groups recorded an non-significant difference increasing in the serum level of CTLA-4 under (p>0.05). in mean ± SE (3.17 ± 0.82 ng/ml) patients as compared to control (2.72 ± 0.29 ng/ml) under (p>0.05). Genetic polymorphism of CTLA.4 gene (rs231775) which illustrated the distribution of genotypes of CTLA.4 in patients and control. The heterozygous genotype AG recorded high frequency in patients (35.56%) than control (0.00%) with a highly significant difference under (P

Piezo1 is a mechanosensitive channel involved in many cellular functions and responsible for sensing shear stress and pressure forces in cells. Piezo1 has a unique trilobed topology with a curved membrane region in the closed state. It has been suggested that upon activation Piezo1 adopts a flattened conformation, but the molecular and structural changes underpinning the Piezo1 gating and opening mechanisms and how the channel senses forces in the membrane remain elusive. Here, we used molecular dynamics simulations to reveal the structural rearrangements that occur when Piezo1 moves from a closed to an open state in response to increased mechanical tension applied to a model membrane. We find that membrane stretching causes Piezo1 to flatten and expand its blade region, resulting in tilting and lateral movement of the pore-lining transmembrane helices 37 and 38. This is associated with the opening of the channel and movement of lipids out of the pore region. Our results reveal that because of the rather loose packing of Piezo1 pore region, movement of the lipids outside the pore region is critical for the opening of the pore. Our simulations also suggest synchronous flattening of the Piezo1 blades during Piezo1 activation. The flattened structure lifts the C-terminal extracellular domain up, exposing it more to the extracellular space. Our studies support the idea that it is the blade region of Piezo1 that senses tension in the membrane because pore opening failed in the absence of the blades. Additionally, our simulations reveal that upon opening, water molecules occupy lateral fenestrations in the cytosolic region of Piezo1, which might be likely paths for ion permeation. Our results provide a model for how mechanical force opens the Piezo1 channel and thus how it might couple mechanical force to biological response.

The impact of the EphA2 receptor on cancer malignancy hinges on the two different ways it can be activated. EphA2 induces anti-oncogenic signaling after ligand binding, but ligand-independent activation of EphA2 is pro-oncogenic. It is believed that the transmembrane (TM) domain of EphA2 adopts two alternate conformations in the ligand-dependent and the ligand-independent states. However, it is poorly understood how the difference in TM helical crossing angles found in the two conformations impacts the activity and regulation of EphA2. We devised a method that uses hydrophobic matching to stabilize two conformations of a peptide comprising the EphA2 TM domain and a portion of the intracellular juxtamembrane (JM) segment. The two conformations exhibit different TM crossing angles, resembling the ligand-dependent and ligand-independent states. We developed a single-molecule technique using SMALPs to measure dimerization in membranes. We observed that the signaling lipid PIP2promotes TM dimerization, but only in the small crossing angle state, which we propose corresponds to the ligand-independent conformation. In this state the two TM are almost parallel, and the positively charged JM segments are expected to be close to each other, causing electrostatic repulsion. The mechanism PIP2uses to promote dimerization might involve alleviating this repulsion due to its high density of negative charges. Our data reveal a conformational coupling between the TM and JM regions, and suggest that PIP2might directly exert a regulatory effect on EphA2 activation in cells that is specific to the ligand-independent conformation of the receptor.

Pollen tube growth requires coordination of cytoskeletal dynamics and apical secretion. The regulatory phospholipid, phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) is enriched in the subapical plasma membrane of pollen tubes and can influence both actin dynamics and secretion. How alternative PtdIns(4,5)P2-effects are specified is unclear. Spinning disc microscopy (SD) reveals dual distribution of a fluorescent PtdIns(4,5)P2-reporter in dynamic plasma membrane nanodomains vs. apparent diffuse membrane labelling, consistent with spatially distinct coexisting pools of PtdIns(4,5)P2. Several PI4P 5-kinases (PIP5Ks) can generate PtdIns(4,5)P2in pollen tubes. Despite localizing to one membrane region, AtPIP5K2 and NtPIP5K6 display distinctive overexpression effects on cell morphologies, respectively related to altered actin dynamics or membrane trafficking. When analyzed by SD, AtPIP5K2-EYFP associated with nanodomains, whereas NtPIP5K6-EYFP localized diffusely. Chimeric AtPIP5K2 and NtPIP5K6 variants with reciprocally swapped membrane-associating domains evoked reciprocally shifted effects on cell morphology upon overexpression. Overall, PI4P 5-kinase variants targeted to nanodomains stabilized actin, suggesting a specific function of PtdIns(4,5)P2-nanodomains. A distinct role of nanodomain-associated AtPIP5K2 in actin regulation is further supported by proximity to and interaction with the Rho-GTPase NtRac5, and by functional interplay with elements of ROP-signalling. Plasma membrane nano-organization may thus aid the specification of PtdIns(4,5)P2-functions to coordinate cytoskeletal dynamics and secretion in pollen tubes.

Pollen tube growth requires coordination of cytoskeletal dynamics and apical secretion. The regulatory phospholipid phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) is enriched in the subapical plasma membrane of pollen tubes of Arabidopsis thaliana and tobacco (Nicotiana tabacum) and can influence both actin dynamics and secretion. How alternative PtdIns(4,5)P2 effects are specified is unclear. In tobacco pollen tubes, spinning disc microscopy (SD) reveals dual distribution of a fluorescent PtdIns(4,5)P2-reporter in dynamic plasma membrane nanodomains vs. apparent diffuse membrane labeling, consistent with spatially distinct coexisting pools of PtdIns(4,5)P2. Several PI4P 5-kinases (PIP5Ks) can generate PtdIns(4,5)P2 in pollen tubes. Despite localizing to one membrane region, the PIP5Ks AtPIP5K2-EYFP and NtPIP5K6-EYFP display distinctive overexpression effects on cell morphologies, respectively related to altered actin dynamics or membrane trafficking. When analyzed by SD, AtPIP5K2-EYFP associated with nanodomains, whereas NtPIP5K6-EYFP localized diffusely. Chimeric AtPIP5K2-EYFP and NtPIP5K6-EYFP variants with reciprocally swapped membrane-associating domains evoked reciprocally shifted effects on cell morphology upon overexpression. Overall, active PI4P 5-kinase variants stabilized actin when targeted to nanodomains, suggesting a role of nanodomain-associated PtdIns(4,5)P2 in actin regulation. This notion is further supported by interaction and proximity of nanodomain-associated AtPIP5K2 with the Rho-GTPase NtRac5, and by its functional interplay with elements of Rho of plants signaling. Plasma membrane nano-organization may thus aid the specification of PtdIns(4,5)P2 functions to coordinate cytoskeletal dynamics and secretion.

Heterogeneities (e.g., membrane proteins and lipid domains) and deformations (e.g., highly curved membrane regions) in biological lipid membranes cause lipid packing defects that may trigger functional sorting of lipids and membrane-associated proteins. To study these phenomena in a controlled and efficient way within molecular simulations, we developed an external field protocol that artificially enhances packing defects in lipid membranes by enforcing local thinning of a flat membrane region. For varying lipid compositions, we observed strong thinning-induced depletion or enrichment, depending on the lipid's intrinsic shape and its effect on a membrane's elastic modulus. In particular, polyunsaturated and lysolipids are strongly attracted to regions high in packing defects, whereas phosphatidylethanolamine (PE) lipids and cholesterol are strongly repelled from it. Our results indicate that externally imposed changes in membrane thickness, area, and curvature are underpinned by shared membrane elastic principles. The observed sorting toward the thinner membrane region is in line with the sorting expected for a positively curved membrane region. Furthermore, we have demonstrated that the amphipathic lipid packing sensor (ALPS) protein motif, a known curvature and packing defect sensor, is effectively attracted to thinner membrane regions. By extracting the force that drives amphipathic molecules toward the thinner region, our thinning protocol can directly quantify and score the lipid packing sensing of different amphipathic molecules. In this way, our protocol paves the way toward high-throughput exploration of potential defect- and curvature-sensing motifs, making it a valuable addition to the molecular simulation toolbox.

Vesicle associated membrane protein 2 (VAMP2/synaptobrevin2), a core SNARE protein residing on synaptic vesicles (SVs), forms helix bundles with syntaxin-1 and SNAP25 for the SNARE assembly. Prior to the SNARE assembly, the structure of VAMP2 is unclear. Here, by using in-cell NMR spectroscopy, we describe the dynamic membrane association of VAMP2 SNARE motif in mammalian cells, and the structural change of VAMP2 upon the change of intracellular lipid environment. We analyze the lipid compositions of the SV membrane by mass-spectrometry-based lipidomic profiling, and further reveal that VAMP2 forms distinctive conformations in different membrane regions. In contrast to the non-raft region, the membrane region of cholesterol-rich lipid raft markedly weakens the membrane association of VAMP2 SNARE motif, which releases the SNARE motif and facilitates the SNARE assembly. Our work reveals the regulation of different membrane regions on VAMP2 structure and sheds light on the spatial regulation of SNARE assembly., Vesicle associated membrane protein 2 (VAMP2) contains a conserved SNARE motif that interacts with syntaxin-1 and SNAP25 for SNARE complex assembly. Here authors use in-cell NMR spectroscopy to describe the dynamic membrane association of VAMP2 SNARE motif in mammalian cells at the atomic resolution.

International audience; Control of cell death/survival balance is an important feature to maintain tissue homeostasis. Dependence receptors are able to induce either survival or cell death in presence or absence of their ligand, respectively. However, their precise mechanism of action and their physiological importance are still elusive for most of them including the MET receptor. We evidence that pro-apoptotic fragment generated by caspase cleavage of MET localizes to the mitochondria-associated membrane region. This fragment triggers a calcium transfer from endoplasmic reticulum to mitochondria, which is instrumental for the apoptotic action of the receptor. Knock-in mice bearing a mutation of MET caspase cleavage site highlighted that p40MET production is important for FAS-driven hepatocyte apoptosis, and demonstrate that MET acts as a dependence receptor in vivo. Our data shed light on new signaling mechanisms for dependence receptors' control of cell survival/death balance, which may offer new clues for the pathophysiology of epithelial structures.

Summary Obinutuzumab is thought to exert its effects through its high antibody-dependent cellular cytotoxicity (ADCC) via glyco-engineering of the Fc region. In addition, obinutuzumab causes direct binding-induced cell death (DCD) only by specifically binding to its target CD20, a Ca2+ channel. However, the specific features of CD20 related to obinutuzumab binding-induction of cell death are not clearly understood. In this study, we evaluated the relationship between the Ca2+ channel features of CD20 as a store-operated Ca2+ channel (SOC) and obinutuzumab binding-induced cell death. Ca2+ channel function and biochemical analysis revealed that CD20 is an Orai1- and stromal interaction molecule (STIM1)-dependent Ca2+ pore. However, binding of obinutuzumab on CD20 did not have any effect on Ca2+ influx activity of CD20; the direct cell death rate mediated by obinutuzumab binding was almost equivalent with or without the extracellular Ca2+ condition. Given the apparent interaction between STIM1 and CD20, we observed Triton-X solubilized obinutuzumab-bound CD20 accompanied by STIM1. Subsequently, obinutuzumab binding and cell death were decreased by STIM1 knock-down in Ramos B cells. Thus, STIM1 directly contributes to cell death by increasing the affinity of cells for obinutuzumab by transferring CD20 to the Triton-soluble membrane region.

A major challenge to plant growth and survival are changes in temperature and diminishing water supply. During acute temperature and water stress, plants often express stress proteins, such as dehydrins, which are intrinsically disordered hydrophilic proteins. In this article, we investigated how the dehydrin Lti30 from Arabidopsis thaliana stabilizes membrane systems that are exposed to large changes in hydration. We also compared the effects of Lti30 on membranes with those of the simple osmolytes urea and trimethylamine N-oxide. Using X-ray diffraction and solid-state NMR, we studied lipid-protein self-assembly at varying hydration levels. We made the following observations: 1) the association of Lti30 with anionic membranes relies on electrostatic attraction, and the protein is located in the bilayer interfacial membrane region; 2) Lti30 can stabilize the lamellar multilayer structure, making it insensitive to variations in water content; 3) in lipid systems with a composition similar to those present in some seeds and plants, dehydrin can prevent the formation of nonlamellar phases upon drying, which may be crucial for maintaining membrane integrity; and 4) Lti30 stabilizes bilayer structures both at high and low water contents, whereas the small osmolyte molecules mainly prevent dehydration-induced transitions. These results corroborate the idea that dehydrins are part of a sensitive and multifaceted regulatory mechanism that protects plant cells against stress.

Sequence variants of the microglial expressed TREM2 (triggering receptor expressed on myeloid cells 2) are a major risk factor for late onset Alzheimer's disease. TREM2 requires a stable interaction with DAP12 in the membrane to initiate signaling, which is terminated by TREM2 ectodomain shedding and subsequent intramembrane cleavage by γ‐secretase. To understand the structural basis for the specificity of the intramembrane cleavage event, we determined the solution structure of the TREM2 transmembrane helix (TMH). Caused by the presence of a charged amino acid in the membrane region, the TREM2‐TMH adopts a kinked structure with increased flexibility. Charge removal leads to TMH stabilization and reduced dynamics, similar to its structure in complex with DAP12. Strikingly, these dynamical features match with the site of the initial γ‐secretase cleavage event. These data suggest an unprecedented cleavage mechanism by γ‐secretase where flexible TMH regions act as key determinants of substrate cleavage specificity., NMR analyses of the TREM2 transmembrane helix in its native lipid environments reveal the structural basis for site‐specific intramembrane proteolysis of this disease‐associated microglial signaling receptor.

In previous studies we had reported that the immunosuppressive cell membrane bound molecule CD200 is released from the cell following cleavage by matrix metalloproteases, with the released soluble CD200 acting as an immunosuppressant following binding to, and signaling through, its cognate receptor CD200R expressed on target cells. We now show that although the intracellular cytoplasmic tail (CD200C-tail) of CD200 has no consensus sites for adapter molecules which might signal the CD200+ cell directly, cleavage of the CD200C-tail from the membrane region of CD200 by a consensus γ-secretase, leads to nuclear translocation and DNA binding (identified by chromatin immunoprecipitation followed by sequencing, Chip-sequencing) of the CD200C-tail. Subsequently there occurs an altered expression of a limited number of genes, many of which are transcription factors (TFs) known to be associated with regulation of cell proliferation. Altered expression of these TFs was also prominent following transfection of CD200+ B cell lines and fresh patient CLL cells with a vector construct containing the CD200C-tail. Artificial transfection of non CD200+ Hek293 cells with this CD200C-tail construct resulted in altered expression of most of these same genes. Introduction of a siRNA for one of these TFs, POTEA, reversed CD200C-tail regulation of altered cell proliferation.

Placenta-specific 1 (Plac1) has been found to be essential for placentation, and abnormal Plac1 expression and distribution is highly correlated with preeclampsia and implantation failure; however, its function in mammalian oocytes has not been elucidated. Here, we report that Plac1 was more prominent in mouse oocytes and enriched at the membrane region throughout meiosis. On the one hand, Plac1 knockdown severely disrupted microvillus organization; however, on the other hand, Plac1 significantly decreased oocyte maturation and increased aneuploidy, consequently disrupting normal fertilization. On the basis of immunoprecipitate matrix-assisted laser desorption/ionization, we established a working model, then verified and suggested that, at the germinal vesicle stage, Plac1 enriches the membrane to activate furin, and active furin subsequently activates IGF-1 receptor to maintain regular microvillus organization. Upon meiosis onset, active furin/IGF-1 receptor relocates into the cytoplasm to activate (phosphorylate) Akt to promote meiosis. In summary, our finding suggests that Plac1, a protein that is crucial for placentation, is also essential for oocyte meiosis and fertilization.-Shi, L.-Y., Ma, Y., Zhu, G.-Y., Liu, J.-W., Zhou, C.-X., Chen, L.-J., Wang, Y., Li, R.-C., Yang, Z.-X., Zhang, D. Placenta-specific 1 regulates oocyte meiosis and fertilization through furin.

Background This study was performed to determine the hemodynamic changes of Budd-Chiari syndrome when the inferior vena vein membrane is developing. Methods A patient-specific Budd-Chiari syndrome vascular model was reconstructed based on magnetic resonance images using Mimics software and different degrees (16%, 37%, and 54%) of idealized membrane were built based on the Budd-Chiari syndrome vascular model using Geomagic software. Three membrane obstruction Budd-Chiari syndrome vascular models were established successfully and fluent software was used to simulate hemodynamic parameters, including blood velocity and wall shear stress. Findings The simulation results showed that there is low velocity and a low wall shear stress region at the junction of the inferior vena cava and the branches of the hepatic veins, and swirl may occur in this area. As the membrane develops, the size of the low velocity and low wall shear stress regions enlarged and the wall shear stress was increased at the membrane region. There was a significant difference in the mean values of wall shear stress between the different obstruction membrane models (P Interpretation Hemodynamic parameters play an important role in vascular disease and there may be a correlation between inferior vena cava wall shear force changes and the slow development process of the inferior vena cava membrane.

Store-operated calcium entry (SOCE) is triggered by assembly of Orai1 with STIM proteins in ER-PM junctions. Plasma membrane PIP2 as well as PIP2-binding protein, SEPT4, significantly impact Orai1-STIM1 interaction. While septins and PIP2 can organize the actin cytoskeleton, it is unclear whether the status of actin within the junctions contributes to SOCE. We report herein that actin remodeling modulates STIM1 clustering. Our findings show that a PIP2- and SEPT4-dependent mechanism involving CDC42, WASP/WAVE, and ARP2 regulates actin remodeling into a ring-like structure around STIM1 puncta. CDC42 localization in the ER-plasma membrane region is enhanced following ER-Ca2+ store depletion. PIP2 depletion or knockdown of SEPT4 attenuate the recruitment of CDC42 to the ER-PM region. Importantly, knockdown of SEPT4, or CDC42+ARP2, disrupts the organization of actin as well as STIM1 clustering. Consequently, Orai1 recruitment to STIM1 puncta, SOCE, and NFAT translocation to the nucleus are all attenuated. Ca2+ influx induced by STIM1-C terminus is not affected by CDC42 knockdown. In aggregate, our findings reveal that PIP2 and SEPT4 affect Orai1/STIM1 clustering by coordinating actin remodeling within ER-PM junctions. This dynamic reorganization of actin has an important role in regulation of SOCE and downstream Ca2+-dependent effector functions.

Chronic kidney disease (CKD) is defined as a decrease in renal function or glomerular filtration rate (GFR), and proteinuria is often present. Proteinuria increases with age and can be caused by glomerular and/or proximal tubule (PT) alterations. PT cells have an apical brush border membrane (BBM), which is a highly dynamic, organized, and specialized membrane region containing multiple glycoproteins required for its functions including regulating uptake, secretion, and signaling dependent upon the physiologic state. PT disorders contribute to the dysfunction observed in CKD. Many glycoprotein functions have been attributed to their N- and O-glycans, which are highly regulated and complex. In this study, the O-glycans present in rat BBMs from animals with different levels of kidney disease and proteinuria were characterized and analyzed using liquid chromatography tandem mass spectrometry (LC–MS/MS). A principal component analysis (PCA) documented that each group has distinct O-glycan distributions. Higher fucosylation levels were observed in the CKD and diabetic groups, which may contribute to PT dysfunction by altering physiologic glycoprotein interactions. Fucosylated O-glycans such as 1-1-1-0 exhibited higher abundance in the severe proteinuric groups. These glycomic results revealed that differential O-glycan expressions in CKD progressions has the potential to define the mechanism of proteinuria in kidney disease and to identify potential therapeutic interventions.

The glycoprotein Prominin-1 and the carbohydrate Lewis X stage-specific embryonic antigen 1 (LeX-SSEA1) both have been extensively used as cell surface markers to purify neural stem cells (NSCs). While Prominin-1 labels a specialized membrane region in NSCs and ependymal cells, the specificity of LeX-SSEA1 expression and its biological significance are still unknown. To address these issues, we have here monitored the expression of the carbohydrate in neonatal and adult NSCs and in their progeny. Our results show that the percentage of immunopositive cells and the levels of LeX-SSEA1 immunoreactivity both increase with postnatal age across all stages of the neural lineage. This is associated with decreased proliferation in precursors including NSCs, which accumulate the carbohydrate at the cell surface while remaining quiescent. Exposure of precursors to bone morphogenetic protein (BMP) increases LEX-SSEA1 expression, which promotes cell cycle withdrawal by a mechanism involving LeX-SSEA1-mediated interaction at the cell surface. Conversely, interference with either BMP signaling or with LeX-SSEA1 promotes proliferation to a similar degree. Thus, in the postnatal germinal niche, the expression of LeX-SSEA1 increases with age and exposure to BMP signaling, thereby downregulating the proliferation of subependymal zone precursors including NSCs.

We have developed and characterized a novel photoswitchable phospholipid analog termed N-nitroBIPS-DPPG. The fluorescence can be switched on and off repeatedly with minimal photobleaching by UV or visible light exposure, respectively. The rather large photochromic head group is inserted deeply into the interfacial membrane region conferring a conical overall lipid shape, preference for a positive curvature and only minimal intermembrane transfer. Utilizing the switchable NBD fluorescence quenching ability of N-nitroBIPS-DPPG, a detergent free intermembrane transfer assay system for NBD modified lipids was demonstrated and validated. As NBD quenching can be turned off, total NBD associated sample fluorescence can be determined without the need of detergents. This not only reduces detergent associated systematic errors, but also simplifies assay handling and allows assay extension to detergent insoluble lipid species.

The effect of four general anesthetics, namely chloroform, halothane, diethyl ether, and enflurane on the free volume fraction and lateral pressure profiles in a fully hydrated dipalmitoylphosphatidylcholime (DPPC) membrane is investigated by means of computer simulation. In order to find changes that can be related to the molecular mechanism of anesthesia as well as its pressure reversal, the simulations are performed both at atmospheric and high (1000 bar) pressures. The obtained results show that the additional free volume occurring in the membrane is localized around the anesthetic molecules themselves. Correspondingly, the fraction of the free volume is increased in the outer of the two membrane regions (i.e., at the outer edge of the hydrocarbon phase) where anesthetic molecules prefer to stay in every case. As a consequence, the presence of anesthetics decreases the lateral pressure in the nearby region of the lipid chain ester groups, in which the anesthetic molecules themselves do not penetrate. Both of these changes, occurring upon introducing anesthetics in the membrane, are clearly reverted by the increase of the global pressure. These findings are in accordance both with the more than 60 years old "critical volume hypothesis" of Mullins, and with the more recent "lateral pressure hypothesis" of Cantor. Our results suggest that if anesthesia is indeed caused by conformational changes of certain membrane-bound proteins, induced by changes in the lateral pressure profile, as proposed by Cantor, the relevant conformational changes are expected to occur in the membrane region where the ester groups are located.

Based on recent theoretical studies, we designed a multistep experimental protocol to understand the impact of environmental conditions around Pt nanodeposits on Membrane chemical degradation. The first experiment probes the local potential at a Pt microelectrode for different rates of permeation of hydrogen and oxygen gases from anode and cathode side. The subsequent degradation experiment utilizes the local conditions taken from the first experiment to analyze local rates of ionomer degradation. The rate of ionomer decomposition is significantly enhanced in the anodic H2-rich membrane region, which can be explained with the markedly increased amount of H2O2 formation at Pt nanodeposits in this region.

Sequence variants of the microglial expressed TREM2 (triggering receptor expressed on myeloid cells 2) are a major risk factor for late onset Alzheimer’s disease. TREM2 requires a stable interaction with DAP12 in the membrane to initiate signaling, which is terminated by TREM2 ectodomain shedding and subsequent intramembrane cleavage by γ-secretase. To understand the structural basis for the specificity of the intramembrane cleavage event, we determined the solution structure of the TREM2 transmembrane helix (TMH). Due to the presence of a charged amino acid in the membrane region the TREM2-TMH adopts a kinked structure with increased flexibility. Charge removal leads to TMH stabilization and reduced dynamics, similar to its structure in complex with DAP12. Strikingly, these dynamical features perfectly correlate with the site of the initial γ-secretase cleavage event. These data suggest an unprecedented cleavage mechanism by γ-secretase where flexible TMH regions are identified to initiate substrate cleavage.

The heterodimeric eukaryotic Drs2p-Cdc50p complex is a lipid flippase that maintains cell membrane asymmetry. The enzyme complex exists in an autoinhibited form in the absence of an activator and is specifically activated by phosphatidylinositol-4-phosphate (PI4P), although the underlying mechanisms have been unclear. Here we report the cryo-EM structures of intact Drs2p-Cdc50p isolated from S. cerevisiae in apo form and in the PI4P-activated form at 2.8 Å and 3.3 Å resolution, respectively. The structures reveal that the Drs2p C-terminus lines a long groove in the cytosolic regulatory region to inhibit the flippase activity. PIP4 binding in a cytosol-proximal membrane region triggers a 90° rotation of a cytosolic helix switch that is located just upstream of the inhibitory C-terminal peptide. The rotation of the helix switch dislodges the C-terminus from the regulatory region, activating the flippase., The heterodimeric eukaryotic Drs2p-Cdc50p complex is a lipid flippase that maintains cell membrane asymmetry and its autoinhibition is released by PI4P binding. Here authors show cryo-EM structures of Drs2p-Cdc50p in apo and PI4P-activated form which reveal the structural changes upon PI4P binding.

Although integrin α9 (ITGA9) is known to be involved in cell adhesion and motility, its expression in cancer and its role in tumor growth and metastasis remain largely unknown. This study was designed to investigate the role of ITGA9 in triple negative breast cancer (TNBC). ITGA9 expression in TNBC cells were knocked out (KO) using CRISPR/Cas9 technology. Four orthotopic mouse mammary xenograft tumor models coupled with cell culture studies were performed to determine the effect of ITGA9 depletion on TNBC tumor growth and metastasis and the underlying mechanism. Bioinformatics analysis showed that ITGA9 level is significantly higher in TNBC than other breast cancer subtypes; and higher ITGA9 level is associated with significantly worse distant metastasis free survival and recurrence free survival in TNBC patients. Experimentally, ITGA9 KO significantly reduced TNBC cell cancer stem cell (CSC)-like property, tumor angiogenesis, tumor growth and metastasis by promoting β-catenin degradation. Further mechanistic studies revealed that ITGA9 KO causes integrin-linked kinase (ILK) relocation from the membrane region to the cytoplasm, where it interacts with protein kinase A (PKA) and inhibits PKA activity leading to increased activity of glycogen synthase kinase 3 (GSK3) and subsequent β-catenin degradation. Overexpressing β-catenin in ITGA9 KO cells reversed the inhibitory effect of ITGA9 KO on tumor growth and metastasis. Furthermore, ITGA9 down-regulation in TNBC tumors by nanoparticle-mediated delivery of ITGA9 siRNA drastically decreased tumor angiogenesis, tumor growth and metastasis. These findings indicate that ITGA9 depletion suppresses TNBC tumor growth and metastasis by promoting β-catenin degradation through the ILK/PKA/GSK3 pathway.

Phosphatidylcholine (PC)-specific phospholipase D (PLD) hydrolyzes the phosphodiester bond of the PC to generate phosphatidic acid (PA) and regulates several subcellular functions. Mammalian genomes contain two genes encoding distinct isoforms of PLD in contrast with invertebrate genomes that include a single PLD gene. However, the significance of two genes within a genome encoding the same biochemical activity remains unclear. Recently, loss of function in the only PLD gene in Drosophila was reported to result in reduced PA levels and a PA-dependent collapse of the photoreceptor plasma membrane due to defects in vesicular transport. Phylogenetic analysis reveals that human PLD1 (hPLD1) is evolutionarily closer to dPLD than human PLD2 (hPLD2). In the present study, we expressed hPLD1 and hPLD2 in Drosophila and found that while reconstitution of hPLD1 is able to completely rescue retinal degeneration in a loss of function dPLD mutant, hPLD2 was less effective in its ability to mediate a rescue. Using a newly developed analytical method, we determined the acyl chain composition of PA species produced by each enzyme. While dPLD was able to restore the levels of most PA species in dPLD3.1 cells, hPLD1 and hPLD2 each were unable to restore the levels of a subset of unique species of PA. Finally, we found that in contrast with hPLD2, dPLD and hPLD1 are uniquely distributed to the subplasma membrane region in photoreceptors. In summary, hPLD1 likely represents the ancestral PLD in mammalian genomes while hPLD2 represents neofunctionalization to generate PA at distinct subcellular membranes.

We report ionic current and double-stranded DNA (dsDNA) translocation measurements through solid-state membranes with two TEM-drilled ∼3-nm diameter silicon nitride nanopores in parallel. Nanopores are fabricated with similar diameters but varying in effective thicknesses (from 2.6 to 10 nm) ranging from a thickness ratio of 1:1 to 1:3.75, producing distinct conductance levels. This was made possible by locally thinning the silicon nitride membrane to shape the desired topography with nanoscale precision using electron beam lithography (EBL). Two nanopores are engineered and subsequently drilled in either the EBL-thinned or the surrounding membrane region. By designing the interpore separation a few orders of magnitude larger than the pore diameter (e.g., ∼900 vs 3 nm), we show analytically, numerically, and experimentally that the total conductance of the two pores is the sum of the individual pore conductances. For a two-pore device with similar diameters yet thicknesses in the ratio of 1:3, a ratio of ∼1:2.2 in open-pore conductances and translocation current signals is expected, as if they were measured independently. Introducing dsDNA as analytes to both pores simultaneously, we detect more than 12 000 events within 2 min and trace them back with a high likelihood to which pore the dsDNA translocated through. Moreover, we monitor translocations through one active pore only when the other pore is clogged. This work demonstrates how two-pore devices can fundamentally open up a parallel translocation reading system for solid-state nanopores. This approach could be creatively generalized to more pores with desired parameters given a sufficient signal-to-noise ratio.

The impact of the EphA2 receptor on cancer malignancy hinges on the two different ways it can be activated. EphA2 induces antioncogenic signaling after ligand binding, but ligand-independent activation of EphA2 is pro-oncogenic. It is believed that the transmembrane (TM) domain of EphA2 adopts two alternate conformations in the ligand-dependent and the ligand-independent states. However, it is poorly understood how the difference in TM helical crossing angles found in the two conformations impacts the activity and regulation of EphA2. We devised a method that uses hydrophobic matching to stabilize two conformations of a peptide comprising the EphA2 TM domain and a portion of the intracellular juxtamembrane (JM) segment. The two conformations exhibit different TM crossing angles, resembling the ligand-dependent and ligand-independent states. We developed a single-molecule technique using styrene maleic acid lipid particles to measure dimerization in membranes. We observed that the signaling lipid PIP2 promotes TM dimerization, but only in the small crossing angle state, which we propose corresponds to the ligand-independent conformation. In this state the two TMs are almost parallel, and the positively charged JM segments are expected to be close to each other, causing electrostatic repulsion. The mechanism PIP2 uses to promote dimerization might involve alleviating this repulsion due to its high density of negative charges. Our data reveal a conformational coupling between the TM and JM regions and suggest that PIP2 might directly exert a regulatory effect on EphA2 activation in cells that is specific to the ligand-independent conformation of the receptor.

In this work, we studied the mechanical behavior of commercial thin-film composite membranes and measured water and salt transport through membranes that were subjected to known degrees of strain. Our aim was to correlate linear strain with transport properties. Firstly, we showed that the global transport properties of the membranes did not change significantly after being subjected to linear strain values that are typical of pressure-retarded osmosis (PRO) operations. Secondly, using a newly developed osmotically-driven burst pressure test for flat sheet membranes, we theorized that the increased salt passage through the membranes was attributable to local deformation and defect formation in the membrane region along the border of the feed spacer opening. Using laser microscopy, we were able to pinpoint the area on the membrane with increased deformation, and to measure the deformation profile. We defined a deformability coefficient to estimate the membrane strain at a known pressure in terms of easily attainable characteristics like opening size, membrane thickness and secant modulus and used it to postulate a solution-diffusion model that accounts for defects by considering the deformability of the membrane in the experimental setup. By incorporating membrane deformation into the boundary layer equations used to describe water and salt flux in osmotic processes (OP), the model can describe the observed dependence of salt flux with applied pressure. The model was used to fit our PRO experimental data and numerous data reported in the literature, which revealed that salt passage increases as membrane deformation increases. Along with this effect, there is a lowered mass-transfer resistance, which constitutes the trade-off between mechanical deformation and mass-transfer resistance observed in pressurized OP. Our findings show that the deformability coefficient and our solution-diffusion model with defects can serve as guidelines for the design of membranes and modules for pressurized OP such as PRO.

The oval shape of pneumococci results from a combination of septal and lateral peptidoglycan synthesis. The septal cross-wall is synthesized by the divisome, while the elongasome drives cell elongation by inserting new peptidoglycan into the lateral cell wall. Each of these molecular machines contains penicillin-binding proteins (PBPs), which catalyze the final stages of peptidoglycan synthesis, plus a number of accessory proteins. Much effort has been made to identify these accessory proteins and determine their function. In the present paper we have used a novel approach to identify members of the pneumococcal elongasome that are functionally closely linked to PBP2b. We discovered that cells depleted in PBP2b, a key component of the elongasome, display several distinct phenotypic traits. We searched for proteins that, when depleted or deleted, display the same phenotypic changes. Four proteins, RodA, MreD, DivIVA and Spr0777, were identified by this approach. Together with PBP2b these proteins are essential for the normal function of the elongasome. Furthermore, our findings suggest that DivIVA, which was previously assigned as a divisomal protein, is required to correctly localize the elongasome at the negatively curved membrane region between the septal and lateral cell wall.

Membrane distillation is an emerging technology to separate non-volatile components from an aqueous feed stream. Mathematical models have proven useful to pursue breakthrough in the economics of the technology and for further improvement through module design and operational optimization. However, before this can be done, all of the resistances in the system must be identified correctly and the model must be carefully calibrated to ensure its predictive power. In this work the typical structure of a direct contact membrane distillation (DCMD) model is studied, where the mass transfer inside the membrane is simulated using the Dusty Gas Model and Nusselt type equations are used to simulate the heat transfer inside the channels. We demonstrate that an off-the-shelf Nusselt equation cannot directly be applied to simulate the heat transfer in the spacer filled channels. Instead, the equations should be calibrated to match the behaviour of the particular spacer. A Monte Carlo filtering method was applied to calibrate and study the structure of the DCMD model for the membrane region. The method proved useful to identify which parameters need to be included in the calibration as it highlighted parameter correlations. Additionally, a submodel selection was performed for the heat and mass transfer inside the membrane. A simple, yet physical method for the simulation of supported membranes was tested and validated on 3 supported membranes, resulting in an excellent fit.

The orifice drilled in the membrane as a channel for drug delivery is the key functional part of the osmotic pumps for a controlled drug release system. Reported conventional microscopic evaluations of these orifices have been limited to measurement of two-dimensional cross-section diameters. This study was aimed at establishing a novel method to measure quantitatively the three-dimensional architectures of orifices based on synchrotron radiation X-ray microcomputed tomography (SR-μCT). Quantitative analysis of architectures extracted from captopril osmotic pumps drilled by a range of operating parameters indicated that laser power correlated with the cross section area, volume, surface area and depth of the orifices, while scanning speed of laser beam showed inverse relationships with the above structure characters. The synchrotron radiation based Fourier transform infrared microspectroscopy mapping showed that there was no apparent chemical change in the surrounding area of the orifice compared with the normal membrane region. Thus SR-μCT was successfully applied to marketed felodipine osmotic pumps for architectural evaluation of the orifices. In conclusion, the first three-dimensional structural insight of orifices in osmotic pump tablets by SR-μCT and structural reconstruction for the architectures has provided deeper insight into improving the design of advanced osmotic pumps for controlled drug release.

Objective— Thiol isomerases facilitate protein folding in the endoplasmic reticulum, and several of these enzymes, including protein disulfide isomerase and ERp57, are mobilized to the surface of activated platelets, where they influence platelet aggregation, blood coagulation, and thrombus formation. In this study, we examined the synthesis and trafficking of thiol isomerases in megakaryocytes, determined their subcellular localization in platelets, and identified the cellular events responsible for their movement to the platelet surface on activation. Approach and Results— Immunofluorescence microscopy imaging was used to localize protein disulfide isomerase and ERp57 in murine and human megakaryocytes at various developmental stages. Immunofluorescence microscopy and subcellular fractionation analysis were used to localize these proteins in platelets to a compartment distinct from known secretory vesicles that overlaps with an inner cell-surface membrane region defined by the endoplasmic/sarcoplasmic reticulum proteins calnexin and sarco/endoplasmic reticulum calcium ATPase 3. Immunofluorescence microscopy and flow cytometry were used to monitor thiol isomerase mobilization in activated platelets in the presence and absence of actin polymerization (inhibited by latrunculin) and in the presence or absence of membrane fusion mediated by Munc13-4 (absent in platelets from Unc13d Jinx mice). Conclusions— Platelet-borne thiol isomerases are trafficked independently of secretory granule contents in megakaryocytes and become concentrated in a subcellular compartment near the inner surface of the platelet outer membrane corresponding to the sarco/endoplasmic reticulum of these cells. Thiol isomerases are mobilized to the surface of activated platelets via a process that requires actin polymerization but not soluble N-ethylmaleimide–sensitive fusion protein attachment receptor/Munc13-4–dependent vesicular–plasma membrane fusion.

Location, location, location. The Na-K pump of skeletal muscle is regulated differently at neuromuscular junctions., The Na,K-ATPase is essential for the contractile function of skeletal muscle, which expresses the α1 and α2 subunit isoforms of Na,K-ATPase. The α2 isozyme is predominant in adult skeletal muscles and makes a greater contribution in working compared with noncontracting muscles. Hindlimb suspension (HS) is a widely used model of muscle disuse that leads to progressive atrophy of postural skeletal muscles. This study examines the consequences of acute (6–12 h) HS on the functioning of the Na,K-ATPase α1 and α2 isozymes in rat soleus (disused) and diaphragm (contracting) muscles. Acute disuse dynamically and isoform-specifically regulates the electrogenic activity, protein, and mRNA content of Na,K-ATPase α2 isozyme in rat soleus muscle. Earlier disuse-induced remodeling events also include phospholemman phosphorylation as well as its increased abundance and association with α2 Na,K-ATPase. The loss of α2 Na,K-ATPase activity results in reduced electrogenic pump transport and depolarized resting membrane potential. The decreased α2 Na,K-ATPase activity is caused by a decrease in enzyme activity rather than by altered protein and mRNA content, localization in the sarcolemma, or functional interaction with the nicotinic acetylcholine receptors. The loss of extrajunctional α2 Na,K-ATPase activity depends strongly on muscle use, and even the increased protein and mRNA content as well as enhanced α2 Na,K-ATPase abundance at this membrane region after 12 h of HS cannot counteract this sustained inhibition. In contrast, additional factors may regulate the subset of junctional α2 Na,K-ATPase pool that is able to recover during HS. Notably, acute, low-intensity muscle workload restores functioning of both α2 Na,K-ATPase pools. These results demonstrate that the α2 Na,K-ATPase in rat skeletal muscle is dynamically and acutely regulated by muscle use and provide the first evidence that the junctional and extrajunctional pools of the α2 Na,K-ATPase are regulated differently.

A new scheme for parallelization of microchannels for ion concentration polarization-based seawater desalination is proposed. In the proposed system, microchannels/micropores are paralleled only in ion-selective membrane region and all other parts are simply merged. A two-dimensional simulation model is developed to study performances of such a system, by calculating the salt removal ratio (SRR) and the average velocity of fluid, under varied working conditions. Our results show that SRR >98% for seawater salinity (realizing drinkable water) is achievable. It is found that a stronger cross membrane voltage strengthens electrokinetic flow of the second kind (EOF2) and increases both SRR and flow velocity. Increasing pressure promotes fluid flow but decrease SRR and EOF2 significantly when the ion depletion zone is destroyed. Volumetric energy consumption and energy per ion removal (EPIR) were also characterized under varied electric field and pressure conditions. Energy consumption as low as 12.82 kWh/m3 was realized to convert seawater (salinity ~500 mM) to the desalinated water (salinity ~10 mM) at a flow speed of 0.56 mm/s. The overall cost of water for such a process was estimated as 2.08 $/m3, which is competitive for small-scale desalination applications.

ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed theBacillusPS3 ATP synthase inEschericia coli, purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunitεshows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.