Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure

Interdependence across time and length scales is common in biology, where atomic interactions can impact larger-scale phenomenon. Such dependence is especially true for a well-known cancer signaling pathway, where the membrane-bound RAS protein binds an effector protein called RAF. To capture the driving forces that bring RAS and RAF (represented as two domains, RBD and CRD) together on the plasma membrane, simulations with the ability to calculate atomic detail while having long time and large length- scales are needed. The Multiscale Machine-Learned Modeling Infrastructure (MuMMI) is able to resolve RAS/RAF protein-membrane interactions that identify specific lipid-protein fingerprints that enhance protein orientations viable for effector binding. MuMMI is a fully automated, ensemble-based multiscale approach connecting three resolution scales: (1) the coarsest scale is a continuum model able to simulate milliseconds of time for a 1 μm² membrane, (2) the middle scale is a coarse-grained (CG) Martini bead model to explore protein-lipid interactions, and (3) the finest scale is an all-atom (AA) model capturing specific interactions between lipids and proteins. MuMMI dynamically couples adjacent scales in a pairwise manner using machine learning (ML). The dynamic coupling allows for better sampling of the refined scale from the adjacent coarse scale (forward) and on-the-fly feedback to improve the fidelity of the coarser scale from the adjacent refined scale (backward). MuMMI operates efficiently at any scale, from a few compute nodes to the largest supercomputers in the world, and is generalizable to simulate different systems. As computing resources continue to increase and multiscale methods continue to advance, fully automated multiscale simulations (like MuMMI) will be commonly used to address complex science questions.

Bone mineral density, vertebral fractures and trabecular bone score in primary ovarian insufficiency

PURPOSE

Bone health in primary ovarian insufficiency (POI) is under-investigated. We assessed patients with spontaneous POI for vertebral fractures (VFs) and related parameters of bone health.

METHODS

70 cases with spontaneous POI (age 32.5 ± 7.0 years) and an equal number of controls were assessed for BMD, TBS, and VFs. BMD at the lumbar-spine (L1-L4), left hip, non-dominant forearm, and TBS (iNsight software) were measured on a dual-energy X-ray absorptiometry (DXA) machine. VFs were assessed by Genant's classification. Serum FSH, LH, estradiol, T4, TSH, iPTH, serum 25(OH)D, total calcium, and inorganic phosphorus were measured.

RESULTS

BMD at the lumbar-spine, hip and forearm was reduced by 11.5%, 11.4% and 9.1% in POI as compared to controls (P < 0.001). Degraded or partially degraded microarchitecture on TBS was observed in 66.7% of patients and 38.2% of controls (P = 0.001). 15.7% of the POI patients had VFs, compared to 4.3% of controls (P = 0.045). Age, duration of amenorrhea and duration of HRT use were the significant predictors of TBS (P < 0.01). Serum 25(OH)D was the significant determinant of VFs. TBS abnormalities were higher in patients with POI and VFs. BMD was not significantly different in patients with and without VFs.

CONCLUSION

Thus, lumbar-spine osteoporosis, impaired TBS and VFs were present in 35.7%, 66.7% and 15.7% of patients with spontaneous POI in their early third decade. This indicates need for rigorous investigations for impaired bone health in these young patients and management with HRT, vitamin-D, and possible need for bisphosphonate therapy.

Lifetime of actin-dependent protein nanoclusters

Protein nanoclusters (PNCs) are dynamic collections of a few proteins that spatially organize in nanometer-length clusters. PNCs are one of the principal forms of spatial organization of membrane proteins, and they have been shown or hypothesized to be important in various cellular processes, including cell signaling. PNCs show remarkable diversity in size, shape, and lifetime. In particular, the lifetime of PNCs can vary over a wide range of timescales. The diversity in size and shape can be explained by the interaction of the clustering proteins with the actin cytoskeleton or the lipid membrane, but very little is known about the processes that determine the lifetime of the nanoclusters. In this paper, using mathematical modeling of the cluster dynamics, we model the biophysical processes that determine the lifetime of actin-dependent PNCs. In particular, we investigated the role of actin aster fragmentation, which had been suggested to be a key determinant of the PNC lifetime, and we found that it is important only for a small class of PNCs. A simple extension of our model allowed us to investigate the kinetics of protein-ligand interaction near PNCs. We found an anomalous increase in the lifetime of ligands near PNCs, which agrees remarkably well with experimental data on RAS-RAF kinetics. In particular, analysis of the RAS-RAF data through our model provides falsifiable predictions and novel hypotheses that will not only shed light on the role of RAS-RAF kinetics in various cancers, but also will be useful in studying membrane protein clustering in general.

Abstract 238: Targeting glutaminolysis potentiates the efficacy of chemotherapy in RAS-driven pancreatic cancers

Pancreatic cancer is an extremely aggressive and deadly malignancy. Despite a detailed understanding of pancreatic ductal adenocarcinoma (PDAC)'s biology, the outcome of the current therapeutic regimen remains grim. Chemotherapeutic treatment is one of the first-line systemic treatments for PDAC. However, creating resistance against chemotherapy remains a major challenge. Oncogenic K-Ras mutation is one of the most common events responsible for the initiation and progression of PDAC. K-Ras mutation also promotes the activation of a transcription factor called NRF2 that is crucial for tumor development and pancreatic cancer proliferation. Our study detects differential basal levels of NRF2 in a panel of PDAC cell lines. We hypothesized that this phenomenon might reflect a greater intrinsic capacity of PDAC cells to become resistant to chemotherapy. We then demonstrated that up-regulation of NRF2 creates resistance against chemotherapy in PDAC cells. Consequently, NRF2 activation rewires metabolic pathway networks. Importantly, our metabolomics analysis revealed that, upon NRF2 activation, several metabolic pathways are reprogrammed. Recent advances in tumor metabolism signify the critical role of glutamine as a key regulator of cancer therapy. Moreover, we observed that inhibiting glutamine metabolism enhances the efficacy of chemotherapeutic drugs in PDAC cells. Taken together, our finding holds promise as a novel combination therapy for patients with pancreatic cancer marked by developed resistance against chemotherapy. Finally, this treatment strategy further establishes the potential for exploiting metabolic changes in RAS-driven cancer cells that confer novel therapeutic opportunities.

Citation Format: Suman Mukhopadhyay, Debanjan Goswami, Dwight V. Nissley, Frank McCormick. Targeting glutaminolysis potentiates the efficacy of chemotherapy in RAS-driven pancreatic cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 238.

Abstract A47: Targeting glutaminolysis potentiates the efficacy of chemotherapy in RAS-driven pancreatic cancers

Pancreatic cancer is an extremely aggressive and deadly malignancy. Despite a detailed understanding of pancreatic ductal adenocarcinoma (PDAC)’s biology, the outcome of the current therapeutic regimen remains grim. Chemotherapeutic treatment is one of the first-line systemic treatments for PDAC. However, creating resistance against chemotherapy remains a major challenge. Oncogenic K-Ras mutation is one of the most common events responsible for the initiation and progression of PDAC. K-Ras mutation also promotes the activation of a transcription factor called NRF2 that is crucial for tumor development and pancreatic cancer proliferation. Our study detects differential basal levels of NRF2 in a panel of PDAC cell lines. We hypothesized that this phenomenon might reflect a greater intrinsic capacity of PDAC cells to become resistant to chemotherapy. We then demonstrated that upregulation of NRF2 creates resistance against chemotherapy in PDAC cells. Consequently, NRF2 activation rewires metabolic pathway networks. Importantly, our metabolomics analysis revealed that, upon NRF2 activation, several metabolic pathways are reprogrammed. Recent advances in tumor metabolism signify the critical role of glutamine as a key regulator of cancer therapy. Moreover, we observed that inhibiting glutamine metabolism enhances the efficacy of chemotherapeutic drugs in PDAC cells. Taken together, our finding holds promise as a novel combination therapy for patients with pancreatic cancer marked by developed resistance against chemotherapy. Finally, this treatment strategy further establishes the potential for exploiting metabolic changes in RAS-driven cancer cells that confer novel therapeutic opportunities.

Citation Format: Suman Mukhopadhyay, Pavan Adiseshaiah, Debanjan Goswami, Dwight V. Nissley, Frank McCormick. Targeting glutaminolysis potentiates the efficacy of chemotherapy in RAS-driven pancreatic cancers [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A47.

Abstract A09: Cooperative membrane interaction between G-domain and HVR defines unique diffusion behavior of KRAS4b

Rat sarcoma (RAS) family of proteins function as GTP/GDP-dependent control switch to regulate Raf-MAPK effector pathway for cell proliferation and are frequently mutated in human cancer. RAS is anchored to the inner leaflet of the plasma membrane (PM) via C-terminal lipid-tether(s) and hypothesized to concentrate in distinct locations in membrane nano-domains to control the activation step. However, very little is known about the molecular dynamics of RAS on PM and the precise mechanism of activation. Here we characterize the molecular mobility of RAS variants by single-molecule tracking (SMT) method and estimate underlying mobility states. KRAS4b exhibit confined mobility with three diffusive states, a unique characteristic compared to all the other RAS isoforms (KRAS4a, NRAS, and HRAS). Although the major difference across RAS isoforms lies within the C-terminus HVR (hypervariable region) and its post-translational lipid modifications, the additional confinement for KRAS4b is contributed by the G-domain (globular domain) of the protein. Simulation of KRAS4b on membrane revealed a detailed atomistic mechanism that corroborates with the experimental results. Importantly, the oncogenic mutant of KRAS4b shows an altered mode of diffusion, implicating a plausible attribution to/from enhanced effector interaction. This study uncovers a novel underlying principle of KRAS4b functionality on living cell membrane with a potential for innovation in therapeutic strategies against its oncogenic variant.

Citation Format: Debanjan Goswami, De Chen, John Columbus, Thomas Turbyville. Cooperative membrane interaction between G-domain and HVR defines unique diffusion behavior of KRAS4b [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A09.

Abstract IA07: KRAS4b’s unique diffusion behavior is defined by plasma membrane and effector interactions

RAS proteins are GTP-dependent switches that control and regulate signaling pathways involved in cell fate and are frequently mutated in cancer. RAS association with the plasma membrane, or with certain endomembrane compartments, is a required step for its activity. Why precisely this is so remains an open question. One possibility is that RAS is merely required for recruitment of RAF and other effectors to the membrane where it can associate with key regulatory molecules that lead to signaling activation. However, four isoforms exist in humans (HRAS, NRAS, and two splice variants, KRAS4b and KRAS4a) and their differences lie within 22 amino acids in the C-terminal hypervariable region (HVR, aa 167-189). These differences in the domain responsible for membrane association result in the recruitment and organization of RAS into distinct membrane nanodomains, and it is thought that this results in differential signaling behavior from RAS isoforms. Isoform-specific RAS nanodomains are thought to both be highly dynamic, differentially composed of a variety of lipids and proteins, and supported by interactions with cytoskeletal structures. How these domains are regulated, and how they influence isoform-specific RAS signaling, remains unclear. Here, we report the molecular mobility of RAS variants in the plasma membrane of living cancer cells using single-molecule tracking methods. Detailed analysis of tracks revealed that KRAS4b molecules exhibit confined mobility with three diffusive states in the active plasma membrane of living cells. This diffusion characteristic was unique to KRAS4b and influenced by both the hypervariable region and globular domain of the protein, compared to all the other Ras isoforms. Importantly, the occupancy of each diffusive states was altered for the oncogenic mutant of KRAS4b, suggesting that the diffusive states we observe are related to signaling events. Our working hypothesis is that the HVR of KRAS4b may be directly involved in assembling the membrane lipid and protein nanodomain necessary for KRAS4b signaling activity. In addition, using two-color single-molecule tracking studies, we are beginning to characterize the interactions of KRAS4b with its major effector RAF. From these studies, we are learning about the kinetics of RAS/RAF interactions in the membrane of living cells. Understanding the underlying principle of KRAS4b functionality on cell membranes is useful for developing novel therapeutic strategies for targeting oncogenic KRAS4b.

Citation Format: Debanjan Goswami, De Chen, John Columbus, Yue Yang, Felice Lightstone, Thomas Turbyville. KRAS4b’s unique diffusion behavior is defined by plasma membrane and effector interactions [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr IA07.

Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior

The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable region side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here, we characterize RAS in live human and mouse cells using single-molecule-tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein’s globular domain. To understand the altered mobility of an oncogenic KRAS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a detailed mechanism.

Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers

Pancreatic cancer is a disease with limited therapeutic options. Resistance to chemotherapies poses a significant clinical challenge for patients with pancreatic cancer and contributes to a high rate of recurrence. Oncogenic KRAS, a critical driver of pancreatic cancer, promotes metabolic reprogramming and upregulates NRF2, a master regulator of the antioxidant network. Here, we show that NRF2 contributed to chemoresistance and was associated with a poor prognosis in patients with pancreatic cancer. NRF2 activation metabolically rewired and elevated pathways involved in glutamine metabolism. This curbed chemoresistance in KRAS-mutant pancreatic cancers. In addition, manipulating glutamine metabolism restrained the assembly of stress granules, an indicator of chemoresistance. Glutaminase inhibitors sensitized chemoresistant pancreatic cancer cells to gemcitabine, thereby improving the effectiveness of chemotherapy. This therapeutic approach holds promise as a novel therapy for patients with pancreatic cancer harboring KRAS mutation. SIGNIFICANCE: These findings illuminate the mechanistic features of KRAS-mediated chemoresistance and provide a rationale for exploiting metabolic reprogramming in pancreatic cancer cells to confer therapeutic opportunities that could be translated into clinical trials. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/8/1630/F1.large.jpg.

Abstract 3373: Identification of KRAS membrane bound states using an integrated computational and experimental approach

Driver mutations in KRAS occur in almost 30% of human tumors, primarily in pancreatic, colorectal and lung tumors. These mutations result in increased cell proliferation and survival predominantly mediated through the MAPK signaling pathway. MAPK signal transduction is initiated by the interaction of RAF kinase with active RAS at the plasma membrane. The precise molecular details of this process are currently unknown. The Frederick National Laboratory for Cancer Research has partnered with the Department of Energy to harness high-performance computing and experimental data to generate models and hypotheses of how KRAS engages with RAF kinase at the plasma membrane to initiate signal transduction. The initial phase of this work has focused on identifying membrane bound states of KRAS. We have used a variety of biophysical approaches (including NMR, protein foot-printing and neutron reflectivity) to investigate the structural orientation of KRAS at the membrane. In addition, large scale coarse-grained simulations of membrane bound KRAS spanning the millisecond time scale, have been completed. Three predominant membrane bound KRAS states were observed computationally: an exposed state (where switch 1 is available for RAF binding), an occluded state (where switch 1 is unavailable for RAF binding) and a transition state (where helix 5 is perpendicular to the membrane). These three states are also identified in the experimental data. Cumulatively, experimental and computational data predict KRAS exists in a dynamic equilibrium on the plasma membrane, interconverting between 3 states on the nanosecond time scale. The experimental data indicates the most populated conformation of KRAS is the transition state. Future efforts will address the significance of these three states for RAF interaction and signal transduction. This in depth understanding of RAS activation of RAF and the MAPK pathway is critically important for developing effective therapeutic interventions for cancers harboring mutant RAS.

Citation Format: Andrew G. Stephen, Animesh Agarwal, Angel E. Garcia, Gnana S. Gnanakaran, Jeevapani Hettige, Christopher Neale, Timothy Travers, Harsh Bhatia, Peer-Timo Bremer, Tim Carpenter, Jim Glosli, Helgi Ingolfsson, Piyush Karande, Felice Lightstone, Tomas Oppelstrup, Liam Stanton, Shiv Sundram, Xiaohua Zhang, Debsindhu Bhowmik, Arvind Ramanathan, Christopher Stanley, Debanjan Goswami, Gulcin Gulten, Frantz Jean-Francios, Dhirendra Simanshu, Tommy Turbyville, Rebika Shrestha, Que Van, Frank McCormick, Dwight Nissley, Fred Streitz, Constance Agamasu. Identification of KRAS membrane bound states using an integrated computational and experimental approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3373.

Postsynaptic synaptotagmins mediate AMPA receptor exocytosis during LTP

Strengthening of synaptic connections by NMDA-receptor-dependent long-term potentiation (LTP) shapes neural circuits and mediates learning and memory. During NMDA-receptor-dependent LTP induction, Ca²⁺-influx stimulates recruitment of synaptic AMPA-receptors, thereby strengthening synapses. How Ca²⁺ induces AMPA-receptor recruitment, however, remains unclear. Here we show that, in pyramidal neurons of the hippocampal CA1-region, blocking postsynaptic expression of both synaptotagmin-1 and synaptotagmin-7, but not of synaptotagmin-1 or synaptotagmin-7 alone, abolished LTP. LTP was rescued by wild-type but not by Ca²⁺-binding-deficient mutant synaptotagmin-7. Blocking postsynaptic synaptotagmin-1/7 expression did not impair basal synaptic transmission, synaptic or extrasynaptic AMPA-receptor levels, or other AMPA-receptor trafficking events. Moreover, expression of dominant-negative mutant synaptotagmin-1 that inhibited Ca²⁺-dependent presynaptic vesicle exocytosis also blocked Ca²⁺-dependent postsynaptic AMPA-receptor exocytosis, thereby abolishing LTP. Our results suggest that postsynaptic synaptotagmin-1 and synaptotagmin-7 act as redundant Ca²⁺-sensors for Ca²⁺-dependent exocytosis of AMPA-receptors during LTP, thus delineating a simple mechanism for the recruitment of AMPA-receptors that mediates LTP.

Modulation of excitation on parvalbumin interneurons by neuroligin-3 regulates the hippocampal network

Hippocampal network activity is generated by a complex interplay between excitatory pyramidal cells and inhibitory interneurons. Although much is known about the molecular properties of excitatory synapses on pyramidal cells, comparatively little is known about excitatory synapses on interneurons. Here we show that conditional deletion of the postsynaptic cell adhesion molecule neuroligin-3 in parvalbumin interneurons causes a decrease in NMDA-receptor-mediated postsynaptic currents and an increase in presynaptic glutamate release probability by selectively impairing the inhibition of glutamate release by presynaptic Group III metabotropic glutamate receptors. As a result, the neuroligin-3 deletion altered network activity by reducing gamma oscillations and sharp wave ripples, changes associated with a decrease in extinction of contextual fear memories. These results demonstrate that neuroligin-3 specifies the properties of excitatory synapses on parvalbumin-containing interneurons by a retrograde trans-synaptic mechanism and suggest a molecular pathway whereby neuroligin-3 mutations contribute to neuropsychiatric disorders.

Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors

During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

Typing of Plasmodium falciparum DNA from 2 years old Giemsa-stained dried blood spots using nested polymerase chain reaction assay

A panel of 129 Giemsa-stained thick blood spots (TBS) confirmed for Plasmodium falciparum infection having different levels of parasite density were collected from a malaria endemic area. DNA was extracted and nested polymerase chain reaction (PCR) assay was performed to amplify P. falciparum DNA. Nested PCR assay successfully amplified P. falciparum DNA at a very low parasitaemia of ~10 parasites/μl of blood. Current PCR assay is very simple and can be used retrospectively to monitor the invasion and prevalence of different Plasmodium species in endemic areas.

Central bronchial carcinoid: Management of a case and anesthetic perspectives

Obstructing lesions of the central airways present with a variety of symptoms and are often associated with pneumonia or asthma-like states. Anesthesia to these patients often presents challenges right from the preoperative stabilization of underlying lung condition, mask ventilation in the supine position to maintaining oxygenation and ventilation in the intraoperative and postoperative period. We present here a case of a young woman with a central bronchial tumor with significant airway obstruction with potential for major bleeding and subsequent anesthetic management without lung sacrificing measures and cardiopulmonary bypass assistance.

Generation of stable overlaps between antiparallel filaments

During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. Establishing a stable overlap region is essential for maintenance of bipolarity, but the underlying mechanisms are poorly understood. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can robustly generate partial overlaps between antiparallel filaments. In this situation, motors reduce the overlap in a length-dependent manner, whereas passive cross-linkers increase it independently of the length. In addition to maintaining structural integrity, passive cross-linkers can thus also have a dynamic role for overlap size regulation.

The Effect of Subchronic Dosing of Ciproxifan and Clobenpropit on Dopamine and Histamine Levels in Rats

The present study was designed to investigate the effect of once daily for 7-day (subchronic treatment) dosing of histamine H₃ receptor antagonists, ciproxifan (CPX) (3 mg/kg, i.p.), and clobenpropit (CBP) (15 mg/kg, i.p), including clozapine (CLZ) (3.0 mg/kg, i.p.) and chlorpromazine (CPZ) (3.0 mg/kg, i.p.), the atypical and typical antipsychotic, respectively, on MK-801(0.2 mg/kg, i.p.)-induced locomotor activity, and dopamine and histamine levels in rats. Dopamine and histamine levels were measured in striatum and hypothalamus, respectively, of rat brain. Atypical and typical antipsychotics were used to serve as clinically relevant reference agents to compare the effects of the H3 receptor antagonists. MK-801-induced increase of horizontal activity was reduced with CPX and CBP. The attenuation of MK-801-induced locomotor hyperactivity produced by CPX and CBP was comparable to CLZ and CPZ. MK-801 raised dopamine levels in the striatum, which was reduced in rats pretreated with CPX and CBP. CPZ also lowered striatal dopamine levels, though the decrease was less robust compared to CLZ, CPX and CBP. MK-801 increased histamine content although to a lesser degree. Subchronic treatment with CPX and CBP exhibited further increase in histamine levels in the hypothalamus compared to the MK-801 treatment alone. Histamine H₃ receptor agonist, R-α methylhistamine (10 mg/kg, i.p.) counteracted the effects of CPX and CBP. In conclusion, the subchronic dosing of CPX/CBP suggests some antipsychotic-like activities as CPX/CBP counteracts the modulatory effects of MK-801 on dopamine and histamine levels and prevents MK-801-induced hyperlocomotor behaviors.

Modeling effects of SGLT-2 inhibitor dapagliflozin treatment versus standard diabetes therapy on cardiovascular and microvascular outcomes

AIMS

Dapagliflozin, a sodium-glucose cotransporter 2 (SGLT-2) inhibitor, has been shown to lower glycated hemoglobin (HbA1c), weight, blood pressure and serum uric acid in clinical trials. Plasma lipids were also evaluated as exploratory variables. The goal of this study was to estimate the long-term cardiovascular (CV) and microvascular outcomes of dapagliflozin added to the standard of care (SOC) versus SOC using simulation methodology.

METHODS

The Archimedes Model, a validated model of human physiology, diseases and healthcare systems, was used to model a type 2 diabetes mellitus (T2DM) population derived from National Health and Nutrition Examination Survey (NHANES) with HbA1c 7-10%, taking a single oral antidiabetic agent [metformin, sulfonylureas SU or thiazolidinedione (TZD)] at the beginning of the trial. A 20-year trial was simulated comparing dapagliflozin 10 mg, given in addition to SOC, with SOC alone. SOC was based on American Diabetes Association (ADA)/European Association for the Study of Diabetes (EASD) 2012 guidelines and included diet, metformin, SU, TZD, dipeptidyl peptidase-4 (DPP-4), glucagon-like peptide-1 (GLP-1), and insulin therapies, with usage levels reflective of those in NHANES. Dapagliflozin effects were derived from phase 3 clinical trial results. End points included CV and microvascular outcomes.

RESULTS

Over a 20-year period, patients on dapagliflozin were projected to experience relative reductions in the incidence of myocardial infarction (MI), stroke, CV death, and all-cause death of 13.8, 9.1, 9.6 and 5.0%, respectively, and relative reductions in the incidence of end-stage renal disease (ESRD), foot amputation, and diabetic retinopathy of 18.7, 13.0 and 9.8%, respectively, when compared with SOC.

CONCLUSIONS

On the basis of simulation results, adding dapagliflozin to currently available treatment options is projected to further decrease the CV and microvascular complications associated with T2DM.

Segregation of diffusible and directionally moving particles on a polar filament

Directed transport in living cells relies on the action of motor proteins. These enzymes can transform chemical energy into mechanical work and move directionally along filamentous tracks. At the same time, these filaments serve as a substrate for the binding of proteins performing other functions, but that also obstruct the motors' motion. Motivated by the mobile cross-linker Ase1, we theoretically study a system of molecular motors in the presence of diffusible particles. Both the motors and the obstacles shuttle between the filament and its surrounding. Numerical simulations of this system show a segregation between motors and obstacles if the filament ends act as diffusion barriers for the obstacles. A phenomenological mean-field theory captures the essential effects observed in the simulations.

LTP requires a unique postsynaptic SNARE fusion machinery

Membrane fusion during exocytosis is mediated by assemblies of SNARE (soluble NSF-attachment protein receptor) and SM (Sec1/Munc18-like) proteins. The SNARE/SM proteins involved in vesicle fusion during neurotransmitter release are well understood, whereas little is known about the protein machinery that mediates activity-dependent AMPA receptor (AMPAR) exocytosis during long-term potentiation (LTP). Using direct measurements of LTP in acute hippocampal slices and an in vitro LTP model of stimulated AMPAR exocytosis, we demonstrate that the Q-SNARE proteins syntaxin-3 and SNAP-47 are required for regulated AMPAR exocytosis during LTP but not for constitutive basal AMPAR exocytosis. In contrast, the R-SNARE protein synaptobrevin-2/VAMP2 contributes to both regulated and constitutive AMPAR exocytosis. Both the central complexin-binding and the N-terminal Munc18-binding sites of syntaxin-3 are essential for its postsynaptic role in LTP. Thus, postsynaptic exocytosis of AMPARs during LTP is mediated by a unique fusion machinery that is distinct from that used during presynaptic neurotransmitter release.

Spectrally resolved photon-echo spectroscopy of Rhodamine-6G

Wavelength dependent study of a laser dye: Rhodamine-6G (Rh6G) by using spectrally resolved photon-echo spectroscopy is presented. The coherence and population dynamics of Rh6G solution in methanol changes as the excitation wavelength is tuned near its absorption maxima of 528 nm. Specifically, the central wavelength of the femtosecond laser pulse was set to 535 nm and to 560 nm while the respective spectra of the photon-echo signals were collected. This gives information on how the ultrafast dynamics of the Rh6G molecule changes with a change in the excitation wavelength.

Postsynaptic complexin controls AMPA receptor exocytosis during LTP

Long-term potentiation (LTP) is a compelling synaptic correlate of learning and memory. LTP induction requires NMDA receptor (NMDAR) activation, which triggers SNARE-dependent exocytosis of AMPA receptors (AMPARs). However, the molecular mechanisms mediating AMPAR exocytosis induced by NMDAR activation remain largely unknown. Here, we show that complexin, a protein that regulates neurotransmitter release via binding to SNARE complexes, is essential for AMPAR exocytosis during LTP but not for the constitutive AMPAR exocytosis that maintains basal synaptic strength. The regulated postsynaptic AMPAR exocytosis during LTP requires binding of complexin to SNARE complexes. In hippocampal neurons, presynaptic complexin acts together with synaptotagmin-1 to mediate neurotransmitter release. However, postsynaptic synaptotagmin-1 is not required for complexin-dependent AMPAR exocytosis during LTP. These results suggest a complexin-dependent molecular mechanism for regulating AMPAR delivery to synapses, a mechanism that is surprisingly similar to presynaptic exocytosis but controlled by regulators other than synaptotagmin-1.

Effect of zinc in animal models of anxiety, depression and psychosis

The role of zinc (Zn) in anxiety, depression and psychosis was studied in rodents. Zn was administered at doses of 15 and 20 mg/kg intraperitoneally for 7 days. Both doses of Zn reduced the immobility time and increased the swimming time in the modified forced swim test. In the elevated plus maze test, increases in the number of open arm entries and time spent in the open arms were observed with both doses of Zn. In the amphetamine (1 and 2 mg/kg subcutaneously) induced locomotor activity test both doses of Zn produced reduction in the total movement time, mean velocity and stereotypic movements. Extrapyramidal symptoms such as catalepsy in animals are usually observed with conventional antipsychotic agents; but in the present study, Zn at doses of 15 and 20 mg/kg did not produce any cataleptic state in mice. The results of the present study demonstrated the anxiolytic, antidepressant and antipsychotic-like effects of Zn metal ion, which may be due to its N-methyl d-aspartate receptor antagonistic activity. Concurrent administration of a lower dose of Zn with standard existing anxiolytic and antidepressant drugs in this study showed potentiating effect, suggesting that Zn could exert beneficial role when prescribed as add-on medicine in the psychiatric illnesses. The results obtained in this study are preliminary, as further research is required to confirm the exact role of Zn metal in the investigated central nervous system disorders.

Cooking fuel type, household ventilation, and the risk of acute lower respiratory illness in urban Bangladeshi children: a longitudinal study

Acute lower respiratory illnesses (ALRI) are the leading cause of death among children <5 years. Studies have found that biomass cooking fuels are an important risk factor for ALRI. However, few studies have evaluated the influence of natural household ventilation indicators on ALRI. The purpose of this study was to assess the association between cooking fuel, natural household ventilation, and ALRI. During October 17, 2004-September 30, 2005, children <5 years living in a low-income neighborhood of Dhaka, Bangladesh, were assessed weekly for ALRI and surveyed quarterly about biomass fuel use, electric fan ownership, and natural household ventilation (windows, ventilation grates, and presence of a gap between the wall and ceiling). Bivariate and multivariate analyses were performed using generalized estimating equations. Six thousand and seventy-nine children <5 years enrolled during the study period (99% participation) experienced 1291 ALRI. In the multivariate model, ≥2 windows [OR = 0.75, 95% CI = (0.58, 0.96)], ventilation grates [OR = 0.80, 95% CI = (0.65, 0.98)], and not owning an electric fan [OR = 1.50, 95% CI = (1.21, 1.88)] were associated with ALRI; gap presence and using biomass fuels were not associated with ALRI. Structural factors that might improve household air circulation and exchange were associated with decreased ALRI risk. Improved natural ventilation might reduce ALRI among children in low-income families.

PRACTICAL IMPLICATIONS

The World Health Organization has stated that controlling pneumonia is a priority for achieving the fourth Millennium Development Goal, which calls for a two-third reduction in mortality of children <5 years old compared to the 1990 baseline. Our study represents an important finding of a modifiable risk factor that might decrease the burden of respiratory illness among children living in Bangladesh and other low-income settings similar to our study site. We found that the existence of at least two windows in the child's sleeping room was associated with a 25% decreased ALRI risk. Increasing available natural ventilation within the household in similar settings has the potential to reduce childhood mortality because of acute lower respiratory illnesses.

Chirp and polarization control of femtosecond molecular fragmentation

We explore the simultaneous effect of chirp and polarization as the two control parameters for non-resonant photo-dissociation of n-propyl benzene. Experiments performed over a wide range of laser intensities show that these two control knobs behave mutually exclusively. Specifically, for the coherently enhanced fragments (C3H3+, C5H5+) with negatively chirped pulses and C6H5+ with positively chirped pulses, polarization effect is the same as compared to that in the case of transform-limited pulses. Though a change in polarization affects the overall fragmentation efficiency, the fragmentation pattern of n-propyl benzene molecule remains unaffected in contrast to the chirp case.

Epidemiology and Risk Analysis of Malaria among Pregnant Women

Malaria remains a complex problem during the pregnancy, which threatens > 35 millions pregnant women every year. Malaria pathogenesis in pregnancy results in accumulation of infected RBCs in the intervillous spaces causing severe alterations leading to the reduced materno-foetal exchanges. In this article we have revisited the current evidences of clinical implications and overall burden of malaria in pregnancy. Many adverse aftermaths including, low birth weight, intrauterine growth retardation, preterm delivery, stillbirth and anemia were found associated with malaria in pregnant women. Despite of worldwide comprehensive control programmes for malaria in pregnancy, the disease control has been a daunting task everywhere. Socio cultural, economical, lack of awareness and various logistic problems compound the disease in developing countries. Thorough evidence based information and estimates, education and awareness and strengthening of prevention programmes are needed urgently to achieve success in malaria control in pregnancy.

A cross sectional investigation of malaria epidemiology among seven tea estates in Assam, India

In the present investigation, the epidemiology of malaria among seven tea estates of Nagaon and Udalguri districts of Assam, India has been described. A cross-sectional open study was carried out to understand the malaria epidemiology and associated risk factors among the tea tribes during March to September 2009. Out of 1,182 peripheral blood smears examined, 506 found positive for malaria (slide positivity rate, SPR = 42.8) with Plasmodium falciparum as predominant species. Dimakuchi tea estate was having highest SPR (P = 0.0275) and contributed more number of P. falciparum cases (P < 0.00001). Tea estates studied in both Udalguri and Nagaon districts were equally affected and the SPR recorded were 41.75 and 43.32% respectively. 154 malaria cases detected were having 'O' blood group but each blood group was found to have similar susceptibility of acquiring malaria infection (χ(2 ) = 3.603; P = 0.3076) and P. falciparum infection (χ(2 ) = 1.818; P = 0.6110). The SPR was highest among children more than 2 years of age group and variation in SPR among the age groups was statistically significant (χ(2 ) = 17.186; P = 0.0018). No gender biasing was observed in malaria distribution. Anemia was found associated with the infection among both the sexes. The findings suggest that tea estates are endemic for stable malaria transmission primarily due to P. falciparum and the prevalence rate decline with age, suggesting the development of protective immunity. Promising intervention measures could be able to reduce the malaria prevalence effectively in the study areas.

A simple twist for signal enhancement in non-linear optical microscopy

We describe a very simple but elegant approach to two-photon fluorescence signal enhancement by intensity modulation with immediate application in two-photon laser-scanning fluorescence microscopy. This method of enhancement shows potential application in any microscopic technique that result from non-linear photon absorption and plays a pivotal role in live cell imaging.

Insecticide resistance and detoxifying enzyme activity in the principal bancroftian filariasis vector, Culex quinquefasciatus, in northeastern India

The insecticide resistance status of Culex quinquefasciatus Say (Diptera: Culicidae) to DDT and deltamethrin across army cantonments and neighbouring villages in northeastern India was investigated. In India, DDT is still the insecticide of choice for public health programmes. In military stations, pyrethroids, especially deltamethrins, are used for insecticide-treated nets (ITNs). Recent information on the levels of resistance to DDT and deltamethrin in mosquito populations of northeastern India is scare. Continued monitoring of insecticide resistance status, identification of the underlying mechanisms of resistance in local mosquito populations and the establishment of a baseline data bank of this information are of prime importance. Insecticide susceptibility assays were performed on wild-caught adult female Cx. quinquefasciatus mosquitoes to the discriminating doses recommended by the World Health Organisation (WHO) to DDT (4%) and deltamethrin (0.05%). Across all study sites, mortality as a result of DDT varied from 11.9 to 50.0%, as compared with 91.2% in the susceptible laboratory strain (S-Lab), indicating that Cx. quinquefasciatus is resistant to DDT. The species was found to be 100% susceptible to deltamethrin in all study sites except Benganajuli and Rikamari. Knock-down times (KDT) in response to deltamethrin varied significantly between study sites (P < 0.01) from 8.3 to 17.8 min for KDT(50) and 37.4 to 69.5 min for KDT(90). All populations exceeded the threshold level of alpha-esterase, beta-esterase and glutathion S-transferase (GST) established for the S-Lab susceptible strain, and all populations had 100% elevated esterase and GST activity, except Missamari and Solmara. Beta-esterase activity in Field Unit II (96.9%) was less than in any of the other populations. Benganajuli had the highest activity level for all the enzymes tested. There was a significant correlation between all enzyme activity levels and insecticide resistance phenotype by populations (P < 0.05). The results presented here provide the first report and baseline information of the insecticide resistance status of Cx. quinquefasciatus in northeastern India, and associated information about biochemical mechanisms that are essential for monitoring the development of insecticide resistance in the area.

A DNA nanomachine that maps spatial and temporal pH changes inside living cells

DNA nanomachines are synthetic assemblies that switch between defined molecular conformations upon stimulation by external triggers. Previously, the performance of DNA devices has been limited to in vitro applications. Here we report the construction of a DNA nanomachine called the I-switch, which is triggered by protons and functions as a pH sensor based on fluorescence resonance energy transfer (FRET) inside living cells. It is an efficient reporter of pH from pH 5.5 to 6.8, with a high dynamic range between pH 5.8 and 7. To demonstrate its ability to function inside living cells we use the I-switch to map spatial and temporal pH changes associated with endosome maturation. The performance of our DNA nanodevices inside living systems illustrates the potential of DNA scaffolds responsive to more complex triggers in sensing, diagnostics and targeted therapies in living systems.

Adding new dimensions to laser-scanning fluorescence microscopy

We describe a novel method of optical imaging by exploiting simple ideas borrowed from pulsed optics. We show that the use of ultrafast pulsed one-photon excitation in laser-scanning fluorescence microscopy dramatically brings together several advantages offered by two widely used present day microscopic techniques, confocal and multi-photon fluorescence microscopy. The method appears as a novel tool in the context of laser-scanning fluorescence microscopy by having a 'built-in' 3D spatial resolution.

Nanoclusters of GPI-anchored proteins are formed by cortical actin-driven activity

Several cell-surface lipid-tethered proteins exhibit a concentration-independent, cholesterol-sensitive organization of nanoscale clusters and monomers. To understand the mechanism of formation of these clusters, we investigate the spatial distribution and steady-state dynamics of fluorescently tagged GPI-anchored protein nanoclusters using high-spatial and temporal resolution FRET microscopy. These studies reveal a nonrandom spatial distribution of nanoclusters, concentrated in optically resolvable domains. Monitoring the dynamics of recovery of fluorescence intensity and anisotropy, we find that nanoclusters are immobile, and the dynamics of interconversion between nanoclusters and monomers, over a range of temperatures, is spatially heterogeneous and non-Arrhenius, with a sharp crossover coinciding with a reduction in the activity of cortical actin. Cholesterol depletion perturbs cortical actin and the spatial scale and interconversion dynamics of nanoclusters. Direct perturbations of cortical actin activity also affect the construction, dynamics, and spatial organization of nanoclusters. These results suggest a unique mechanism of complexation of cell-surface molecules regulated by cortical actin activity.

Comparison of bone mineral density and body proportions between women with complete androgen insensitivity syndrome and women with gonadal dysgenesis

OBJECTIVES

To compare bone mineral density (BMD) and body proportions between women with complete androgen insensitivity syndrome (CAIS) and with gonadal dysgenesis (GD).

SETTING

Adult Disorders of Sexual Development and Ovarian Failure Clinics at University College London Hospitals.

DESIGN

Retrospective cross-sectional study of three groups of women aged 17-58 years with varying degrees of exposure to sex hormones and different combinations of sex chromosomes. Forty-six subjects had CAIS, 18 had GD and 46,XY (GD(XY)), and 25 had GD and 46,XX (GD(XX)). In addition, body proportions of subgroups of these women were analysed.

OUTCOME MEASURES

Oestrogen therapy, karyotype, anthropometry and BMD.

RESULTS

Height differed between groups (F ratio 5.2, P=0.007)), with GD(XX) women being the shortest (mean+/-s.d.: 1.66+/-0.10 m), GD(XY) women the tallest (1.74+/-0.09 m) and CAIS women were in-between (1.70+/-0.07 m). Delayed gonadectomy resulted in taller stature in CAIS women (P=0.011). The ratio of lower to upper body length in GD(XY) women was significantly (P=0.001) greater than that of CAIS women. Multivariate logistic regression analysis (adjusted for age and height) showed that among women with XY karyotype, GD(XY) women were 5.2 times (95% confidence interval (CI): 1.3-20.1, P=0.018) more likely than CAIS women to have a low hip BMD. This difference was not evident among women with GD of different karyotypes (P=0.938). Spinal BMD did not differ between subject groups. Further adjustment for oestrogen replacement did not alter these relationships.

CONCLUSIONS

Taller stature in late gonadectomised CAIS women suggests an oestrogen deficiency in these women prior to gonadectomy. Increased lower to upper body ratio in GD(XY) women compared with the other groups implies that these subjects have the greatest degree of oestrogen deficiency in puberty. Androgen rather than sex chromosomes may play an important role in cortical bone mineralisation in CAIS women, probably via estrogen receptor-alpha either directly or via aromatisation during critical periods of growth prior to gonadectomy.

Nanoscale organization of hedgehog is essential for long-range signaling

Hedgehog (Hh) plays crucial roles in tissue-patterning and activates signaling in Patched (Ptc)-expressing cells. Paracrine signaling requires release and transport over many cell diameters away by a process that requires interaction with heparan sulfate proteoglycans (HSPGs). Here, we examine the organization of functional, fluorescently tagged variants in living cells by using optical imaging, FRET microscopy, and mutational studies guided by bioinformatics prediction. We find that cell-surface Hh forms suboptical oligomers, further concentrated in visible clusters colocalized with HSPGs. Mutation of a conserved Lys in a predicted Hh-protomer interaction interface results in an autocrine signaling-competent Hh isoform--incapable of forming dense nanoscale oligomers, interacting with HSPGs, or paracrine signaling. Thus, Hh exhibits a hierarchical organization from the nanoscale to visible clusters with distinct functions.

Precise positioning of myosin VI on endocytic vesicles in vivo

Myosin VI has been studied in both a monomeric and a dimeric form in vitro. Because the functional characteristics of the motor are dramatically different for these two forms, it is important to understand whether myosin VI heavy chains are brought together on endocytic vesicles. We have used fluorescence anisotropy measurements to detect fluorescence resonance energy transfer between identical fluorophores (homoFRET) resulting from myosin VI heavy chains being brought into close proximity. We observed that, when associated with clathrin-mediated endocytic vesicles, myosin VI heavy chains are precisely positioned to bring their tail domains in close proximity. Our data show that on endocytic vesicles, myosin VI heavy chains are brought together in an orientation that previous in vitro studies have shown causes dimerization of the motor. Our results are therefore consistent with vesicle-associated myosin VI existing as a processive dimer, capable of its known trafficking function.

Faecal contamination of drinking water sources of Dhaka city during the 2004 flood in Bangladesh and use of disinfectants for water treatment

AIMS

To describe the extent of faecal pollution and point of use water treatment strategy during and after the 2004 flood in Dhaka.

METHODS

A total of 300 water samples were collected from 20 different drinking water sources in Kamalapur, Dhaka city from August 2004 to January 2005. The level of faecal contamination was estimated using measurements of faecal indicator bacteria (total coliforms, faecal coliforms and faecal streptococci) and isolation of Vibrio cholerae was carried out following standard procedures. Total dissolved solids, dissolved oxygen, hardness, chloride and pH were also monitored. The efficacy of four disinfectants including Halotab, Zeoline-200, alum potash and bleaching powder were tested as point of use water treatment agents. The unacceptable level of contamination of total coliforms (TC), faecal coliforms (FC) and faecal streptococci (FS) ranged from 23.8% to 95.2%, 28.6% to 95.2% and 33.3% to 90.0%, respectively. The isolation rates of V. cholerae O1 and O139 were both 0.33%, and non-O1/non-O139 was 7.0%.

CONCLUSION

Water collected during and after floods was contaminated with TC, FC, FS and V. cholerae. Although alum potash, bleaching powder, Halotab and Zeoline-200 were all effective general disinfectants, Halotab and Zeoline-200 were superior to bleaching powder and alum potash against FC.

SIGNIFICANCE AND IMPACT OF THE STUDY

During and after floods, point of use water treatment could reduce waterborne diseases among flood-affected people.