Membrane lipids and morphology of brain cortex synaptosomes isolated from hibernating Yakutian ground squirrel

Synaptosomes were isolated from Yakutian ground squirrel brain cortex of summer and winter hibernating animals in active and torpor states. Synaptosomal membrane cholesterol and phospholipids were determined. The seasonal changes of synaptosomal lipid composition were found. Synaptosomes isolated from hibernating Yakutian ground squirrel brain cortex maintained the cholesterol sphingomyelin, phosphatidylethanolamine, lysophosphatidylcholine, cardiolipin, phosphatidylinositol and phosphatidylserine contents 2.5, 1.8, 2.6, 1.8, 1.6, and 1.3 times less, respectively, and the content of phosphatidylcholine twice as much as the one in summer season. The synaptosomal membrane lipid composition of summer animals was shown to be markedly different from that as hibernating ground squirrels and non-hibernating rodents. It is believed that phenotypic changes of synaptosomal membrane lipid composition in summer Yakutian ground squirrel are the important preparation step for hibernation. The phosphatidylethanolamine content was increased in torpor state compared with winter-active state and the molar ratio of cholesterol/phospholipids in synaptosomal membrane of winter torpor ground squirrels was lower than that in active winter and summer animals. These events were supposed to lead to increase of the synaptosomal membrane fluidity during torpor. Synaptosomes isolated from torpor animals have larger sizes and contain a greater number of synaptic vesicles on the synaptosomal profile area. The synaptosomal membrane lipid composition and synaptosome morphology were involved in phenotypic adaptation of Yakutian ground squirrel to hibernation.     

Strategic deployment of CHO expression platforms to deliver Pfizer's Monoclonal Antibody Portfolio

Development of stable cell lines for expression of large‐molecule therapeutics represents a significant portion of the time and effort required to advance a molecule to enabling regulatory toxicology studies and clinical evaluation. Our development strategy employs two different approaches for cell line development based on the needs of a particular project: a random integration approach for projects where high‐level expression is critical, and a site‐specific integration approach for projects in which speed and reduced employee time spend is a necessity. Here we describe both our random integration and site‐specific integration platforms and their applications in support of monoclonal antibody development and production. We also compare product quality attributes of monoclonal antibodies produced with a nonclonal cell pool or clonal cell lines derived from the two platforms. Our data suggests that material source (pools vs. clones) does not significantly alter the examined product quality attributes. Our current practice is to leverage this observation with our site‐specific integration platform, where material generated from cell pools is used for an early molecular assessment of a given candidate to make informed decisions around development strategy. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1463–1467, 2017     

Microbial transformation of styrene by anaerobic consortia

Methanogenic microbial consortia, originally enriched from anaerobic sewage sludge with ferulic acid or styrene (vinylbenzene) as sole organic carbon and energy sources, were used to study transformation of styrene under strictly anaerobic conditions. Styrene, which was added as the substrate in a range of concentrations from 0.1 to 10 mmol/l, was extensively degraded but no methane production was observed during incubation for eight months. The addition of yeast extract during the enrichment stage completely inhibited degradation of styrene. Gas chromatog-raphy (GC), gas chromatography/mass spectrometry (GC/MS), high performance liquid chromatography (HPLC) analyses of the culture fluid, and GC analyses of the anaerobic headspace, indicated that the transformation of this arylalkene was initiated through an oxidation-reduction reaction and that the favoured mechanism was most likely the addition of water across the double bond in the alkenyl side-chain. The degradation proceeded through to carbon dioxide, the final product. Benzoic acid and phenol were transient compounds found in highest concentrations in the spent culture fluid and are suggested as the key intermediates of the transformation process. The tentative routes of anaerobic transformation partially overlap with those previously proposed for aromatic hydrocarbons such as toluene. Several pure cultures, which were tentatively identified as Clostridium spp. and Enterobacter spp., were isolated from the styrene-degrading consortia. Two of these cultures were demonstrated to grow on styrene as sole carbon and energy source. Additionally, a pure culture of Enterobacter cloacae DG-6 (ATCC 35929) which had been isolated previously from the ferulate-degrading consortium, was shown to degrade styrene through to carbon dioxide.     

Changes in Photosynthetic Characteristics Induced by Transferring Air-Grown Cells of Chlorococcum littorale to High-CO2 Conditions

When air-grown cells of Chlorococcum littorale was enrichedwith CO₂, growth was enhanced after a lag period of one to twodays at 20% CO₂, and 3 to 6 days at 40% CO₂. Changes in therate of photosynthesis measured as oxygen evolution and CO₂fixation, were similar to those observed for growth. Duringthe initial inhibition of photosynthesis in 40% CO₂, the activityof PSII was suppressed. In contrast, PSI activity was greatlyenhanced. Air-grown cells of C. littorale possessed comparatively highcarbonic anhydrase (CA) activity which was localized insidethe cells and on the cell surface. Under high CO₂ concentrationsextracellular CA activity was greatly suppressed and intracellularactivity almost completely abolished. Phosphoenol pyruvate carboxylaseactivity was also suppressed in high CO₂-grown cells. Ribulose-l,5-bisphosphatecarboxylase activity was higher in high-CO₂ grown cells thanin air-grown cells. The above results indicated that the lagphase induced by 40% CO₂ was due to suppression of PSII activity. ¹Part of this work was reported in the International PhotosynthesisCongress, Nagoya, 1992.     

Optimizing I/O forwarding techniques for extreme-scale event tracing

Programming development tools are a vital component for understanding the behavior of parallel applications. Event tracing is a principal ingredient to these tools, but new and serious challenges place event tracing at risk on extreme-scale machines. As the quantity of captured events increases with concurrency, the additional data can overload the parallel file system and perturb the application being observed. In this work we present a solution for event tracing on extreme-scale machines. We enhance an I/O forwarding software layer to aggregate and reorganize log data prior to writing to the storage system, significantly reducing the burden on the underlying file system. Furthermore, we introduce a sophisticated write buffering capability to limit the impact. To validate the approach, we employ the Vampir tracing toolset using these new capabilities. Our results demonstrate that the approach increases the maximum traced application size by a factor of 5× to more than 200,000 processes.     

The genome of African yam (Dioscorea cayenensis‐rotundata complex) hosts endogenous sequences from four distinct badnavirus species

Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis‐rotundata complex. We propose that these sequences should be termed ‘endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.     

Middleware support for many-task computing

Many-task computing aims to bridge the gap between two computing paradigms, high throughput computing and high performance computing. Many-task computing denotes high-performance computations comprising multiple distinct activities, coupled via file system operations. The aggregate number of tasks, quantity of computing, and volumes of data may be extremely large. Traditional techniques found in production systems in the scientific community to support many-task computing do not scale to today’s largest systems, due to issues in local resource manager scalability and granularity, efficient utilization of the raw hardware, long wait queue times, and shared/parallel file system contention and scalability. To address these limitations, we adopted a “top-down” approach to building a middleware called Falkon, to support the most demanding many-task computing applications at the largest scales. Falkon (Fast and Light-weight tasK executiON framework) integrates (1) multi-level scheduling to enable dynamic resource provisioning and minimize wait queue times, (2) a streamlined task dispatcher able to achieve orders-of-magnitude higher task dispatch rates than conventional schedulers, and (3) data diffusion which performs data caching and uses a data-aware scheduler to co-locate computational and storage resources. Micro-benchmarks have shown Falkon to achieve over 15K+ tasks/s throughputs, scale to hundreds of thousands of processors and to millions of queued tasks, and execute billions of tasks per day. Data diffusion has also shown to improve applications scalability and performance, with its ability to achieve hundreds of Gb/s I/O rates on modest sized clusters, with Tb/s I/O rates on the horizon. Falkon has shown orders of magnitude improvements in performance and scalability than traditional approaches to resource management across many diverse workloads and applications at scales of billions of tasks on hundreds of thousands of processors across clusters, specialized systems, Grids, and supercomputers. Falkon’s performance and scalability have enabled a new class of applications called Many-Task Computing to operate at previously so-believed impossible scales with high efficiency.     

Mice Lacking NMDA Receptors in Parvalbumin Neurons Display Normal Depression-Related Behavior and Response to Antidepressant Action of NMDAR Antagonists

The underlying circuit imbalance in major depression remains unknown and current therapies remain inadequate for a large group of patients. Discovery of the rapid antidepressant effects of ketamine - an NMDA receptor (NMDAR) antagonist – has linked the glutamatergic system to depression. Interestingly, dysfunction in the inhibitory GABAergic system has also been proposed to underlie depression and deficits linked to GABAergic neurons have been found with human imaging and in post-mortem material from depressed patients. Parvalbumin-expressing (PV) GABAergic interneurons regulate local circuit function through perisomatic inhibition and their activity is NMDAR-dependent, providing a possible link between NMDAR and the inhibitory system in the antidepressant effect of ketamine. We have therefore investigated the role of the NMDAR-dependent activity of PV interneurons for the development of depression-like behavior as well as for the response to rapid antidepressant effects of NMDAR antagonists. We used mutant mice lacking NMDA neurotransmission specifically in PV neurons (PV-Cre+/NR1f/f) and analyzed depression-like behavior and anhedonia. To study the acute and sustained effects of a single NMDAR antagonist administration, we established a behavioral paradigm of repeated exposure to forced swimming test (FST). We did not observe altered behavioral responses in the repeated FST or in a sucrose preference test in mutant mice. In addition, the behavioral response to administration of NMDAR antagonists was not significantly altered in mutant PV-Cre+/NR1f/f mice. Our results show that NMDA-dependent neurotransmission in PV neurons is not necessary to regulate depression-like behaviors, and in addition that NMDARs on PV neurons are not a direct target for the NMDAR-induced antidepressant effects of ketamine and MK801.     

NK and CD4+ T Cell Cooperative Immune Responses Correlate with Control of Disease in a Macaque Simian Immunodeficiency Virus Infection Model

Control of infectious disease may be accomplished by successful vaccination or by complex immunologic and genetic factors favoring Ag-specific multicellular immune responses. Using a rhesus macaque model, we evaluated Ag-specific T cell-dependent NK cell immune responses in SIV-infected macaques, designated "controlling" or "noncontrolling" based on long-term chronic viremia levels, to determine whether NK cell effector functions contribute to control of SIV infection. We observed that Gag stimulation of macaque PBMCs induced subset-specific NK cell responses in SIV-controlling but not SIV-noncontrolling animals, as well as that circulatory NK cell responses were dependent on Ag-specific IL-2 production by CD4(+) central memory T cells. NK cell activation was blocked by anti-IL-2-neutralizing Ab and by CD4(+) T cell depletion, which abrogated the Gag-specific responses. Among tissue-resident cells, splenic and circulatory NK cells displayed similar activation profiles, whereas liver and mucosal NK cells displayed a decreased activation profile, similar in SIV-controlling and -noncontrolling macaques. Lack of T cell-dependent NK cell function was rescued in SIV-noncontrolling macaques through drug-mediated control of viremia. Our results indicate that control of disease progression in SIV-controlling macaques is associated with cooperation between Ag-specific CD4(+) T cells and NK cell effector function, which highlight the importance of such cell-to-cell cooperativity in adaptive immunity and suggest that this interaction should be further investigated in HIV vaccine development and other prophylactic vaccine approaches.