Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data

Analyses of somatic hypermutation (SHM) patterns in B cell immunoglobulin (Ig) sequences contribute to our basic understanding of adaptive immunity, and have broad applications not only for understanding the immune response to pathogens, but also to determining the role of SHM in autoimmunity and B cell cancers. Although stochastic, SHM displays intrinsic biases that can confound statistical analysis, especially when combined with the particular codon usage and base composition in Ig sequences. Analysis of B cell clonal expansion, diversification, and selection processes thus critically depends on an accurate background model for SHM micro-sequence targeting (i.e., hot/cold-spots) and nucleotide substitution. Existing models are based on small numbers of sequences/mutations, in part because they depend on data from non-coding regions or non-functional sequences to remove the confounding influences of selection. Here, we combine high-throughput Ig sequencing with new computational analysis methods to produce improved models of SHM targeting and substitution that are based only on synonymous mutations, and are thus independent of selection. The resulting “S5F” models are based on 806,860 Synonymous mutations in 5-mer motifs from 1,145,182 Functional sequences and account for dependencies on the adjacent four nucleotides (two bases upstream and downstream of the mutation). The estimated profiles can explain almost half of the variance in observed mutation patterns, and clearly show that both mutation targeting and substitution are significantly influenced by neighboring bases. While mutability and substitution profiles were highly conserved across individuals, the variability across motifs was found to be much larger than previously estimated. The model and method source code are made available at http://clip.med.yale.edu/SH

Isolation of a euryhaline microalgal strain, Tetraselmis sp CTP4, as a robust feedstock for biodiesel production

Bioprospecting for novel microalgal strains is key to improving the feasibility of microalgae-derived biodiesel production. Tetraselmis sp. CTP4 (Chlorophyta, Chlorodendrophyceae) was isolated using fluorescence activated cell sorting (FACS) in order to screen novel lipid-rich microalgae. CTP4 is a robust, euryhaline strain able to grow in seawater growth medium as well as in non-sterile urban wastewater. Because of its large cell size (9-22 mu m), CTP4 settles down after a six-hour sedimentation step. This leads to a medium removal efficiency of 80%, allowing a significant decrease of biomass dewatering costs. Using a two-stage system, a 3-fold increase in lipid content (up to 33% of DW) and a 2-fold enhancement in lipid productivity (up to 52.1 mg L-1 d(-1)) were observed upon exposure to nutrient depletion for 7 days. The biodiesel synthesized from the lipids of CTP4 contained high levels of oleic acid (25.67% of total fatty acids content) and minor amounts of polyunsaturated fatty acids with >= 4 double bonds (< 1%). As a result, this biofuel complies with most of the European (EN14214) and American (ASTM D6751) specifications, which commonly used microalgal feedstocks are usually unable to meet. In conclusion, Tetraselmis sp. CTP4 displays promising features as feedstock with lower downstream processing costs for biomass dewatering and biodiesel refining

Optimization of insect cell based protein production processes - online monitoring, expression systems, scale-up

Due to the increasing use of insect cell based expression systems in research and industrial recombinant protein production, the development of efficient and reproducible production processes remains a challenging task. In this context, the application of online monitoring techniques is intended to ensure high and reproducible product qualities already during the early phases of process development. In the following chapter, the most common transient and stable insect cell based expression systems are briefly introduced. Novel applications of insect cell based expression systems for the production of insect derived antimicrobial peptides/proteins (AMPs) are discussed using the example of G. mellonella derived gloverin. Suitable in situ sensor techniques for insect cell culture monitoring in disposable and common bioreactor systems are outlined with respect to optical and capacitive sensor concepts. Since scale-up of production processes is one of the most critical steps in process development, a conclusive overview is given about scale up aspects for industrial insect cell culture processes

Gene Expression Analysis of Forskolin Treated Basilar Papillae Identifies MicroRNA181a as a Mediator of Proliferation

Auditory hair cells spontaneously regenerate following injury in birds but not mammals. A better understanding of the molecular events underlying hair cell regeneration in birds may allow for identification and eventually manipulation of relevant pathways in mammals to stimulate regeneration and restore hearing in deaf patients.Gene expression was profiled in forskolin treated (i.e., proliferating) and quiescent control auditory epithelia of post-hatch chicks using an Affymetrix whole-genome chicken array after 24 (n = 6), 48 (n = 6), and 72 (n = 12) hours in culture. In the forskolin-treated epithelia there was significant (p<0.05; >two-fold change) upregulation of many genes thought to be relevant to cell cycle control and inner ear development. Gene set enrichment analysis was performed on the data and identified myriad microRNAs that are likely to be upregulated in the regenerating tissue, including microRNA181a (miR181a), which is known to mediate proliferation in other systems. Functional experiments showed that miR181a overexpression is sufficient to stimulate proliferation within the basilar papilla, as assayed by BrdU incorporation. Further, some of the newly produced cells express the early hair cell marker myosin VI, suggesting that miR181a transfection can result in the production of new hair cells.These studies have identified a single microRNA, miR181a, that can cause proliferation in the chicken auditory epithelium with production of new hair cells

Use of systemic steroids in management of a pregnant patient with ARDS.

Learning Objectives: Steroids have been used in the management of ARDS. All studies which have shown the benefit of using steroids in ARDS excluded pregnant patients and there is no data to support the use of steroids in pregnant patients with ARDS. Methods: 16 y/o female with a past medical history of childhood asthma, pregnant in her 33rd week, who failed outpatient mild UTI treatment with Nitrofurantoin presented to the ER with fever, chills and worsening back pain. She was found to be febrile, tachycardic with leukocytosis. She was admitted for sepsis secondary to pyelonephritis due to pan-susceptible E Coli and was started on Ceftriaxone. The following day, she had worsening respiratory distress with increasing oxygen requirements. Imaging showed complete consolidation of the almost entire right lung. She required 12L HFNC. Antibiotics were escalated and she was transferred to a tertiary care center for escalation of care. Blood cultures and tests for respiratory pathogens remained negative. She was intubated after 2 days for worsening respiratory distress and hypoxic respiratory failure. Despite 5 days of broad spectrum antibiotics, her respiratory status was unchanged. Repeat imaging now showed diffuse airspace opacities in the left lung. She had no evidence of cardiogenic pulmonary edema and a diagnosis of ARDS was made. Her ventilator settings were then managed per ARDSNet protocol. 2 days later she was started on Methylprednisolone per Meduri protocol for ARDS. After 7 days of broad spectrum antibiotics, she was continued on Ceftriaxone to complete total 14 days of antibiotics for pyelonephritis. 3 days after starting corticosteroid, she underwent cesarean section due to pre-eclampsia. She required high FiO2 and PEEP to maintain oxygenation. Weaning her ventilator settings was a gradual process. She was extubated to HFNC after 17 days of intubation. Hospital course complicated by pneumomediastinum and pneumothorax requiring drainage catheter and mood disorder. Clinical status then improved and the patient was transferred to a general medical floor. After 1 month of hospitalization, she was discharged home on 2L NC and a tapering dose of prednisone. PFTs done a week after her discharge showed severe restriction with severely reduced DLCO at 24% with 92%oxygen saturation on room air. Results: This case demonstrated successful use of steroids in a pregnant patient with ARDS. Adverse effects like pregnancy induced hypertension, muscle weakness, mood disorder should be kept in mind

Microalgae dewatering: Technology advancement using electrocoagulation

With growing sustainable development and environmental protection concerns, it islogical that renewable fuels are becoming more important. Biodiesel is an alternative topetroleum based transport fuels and it has many advantages such as a low emissionprofile. Microalgae have gained interest as a source of biomass for biodiesel production,due to the advantages of high lipid content and fast growth rates with negligiblecompetition with human food production. A major limitation with microalgae is the highenergy consumption and cost associated with current dewatering processes, and thismakes microalgae bioprocess engineering economically unattractive. Electrocoagulationis a promising dewatering process that has the potential to reduce the overall energydemand of the process.In this chapter, a batch electrocoagulation process with two marine microalgaespecies (Chlorococcum sp. and Tetraselmis sp.) and three different anode materials(aluminum, ferritic stainless steel, and carbon) is examined. The flocculation andflotation efficiency of each electrode was investigated and optimum electrocoagulationparameters were determined. A mass balance of the system was performed and thepolarity of the dissolving metal cation was determined. Power consumption and carbondioxide emissions analysis were also conducted in order to evaluate the feasibility ofcommercially applying electrocoagulation to the biodiesel production process. Resultsfrom the power consumption and carbon dioxide emission analysis showed thatelectrocoagulation requires little energy for operation, but the overall process was highlyenergy intensive due to the energy demand associated with aluminum production.However, in order to make the method more feasible for commercial use, theconsumption of electrode material has to be minimized. © 2013 by Nova Science Publishers, Inc. All rights reserved