Verenium Corporation

About: Verenium Corporation is a based out in . It is known for research contribution in the topics: Cellulase & Phytase. The organization has 290 authors who have published 184 publications receiving 10153 citations.

A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics

Abstract: Proteomic analysis of complex protein mixtures using proteolytic digestion and liquid chromatography in combination with tandem mass spectrometry is a standard approach in biological studies. Data-dependent acquisition is used to automatically acquire tandem mass spectra of peptides eluting into the mass spectrometer. In more complicated mixtures, for example, whole cell lysates, data-dependent acquisition incompletely samples among the peptide ions present rather than acquiring tandem mass spectra for all ions available. We analyzed the sampling process and developed a statistical model to accurately predict the level of sampling expected for mixtures of a specific complexity. The model also predicts how many analyses are required for saturated sampling of a complex protein mixture. For a yeast-soluble cell lysate 10 analyses are required to reach a 95% saturation level on protein identifications based on our model. The statistical model also suggests a relationship between the level of sampling observed for a protein and the relative abundance of the protein in the mixture. We demonstrate a linear dynamic range over 2 orders of magnitude by using the number of spectra (spectral sampling) acquired for each protein.

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.

Abstract: From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding ‘higher’ Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H_2 metabolism, CO_2-reductive acetogenesis and N_2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-μl environment can be.

Ambulatory drug delivery device

Abstract: A device for infusing a drug into an ambulatory patient, the drug being contained in a transparent spiral conduit which is embedded in a disposable flexible casting conformingly adhered to the patient's body, includes a reusable micropump module which is detachably mounted in a collar valve on the casting and forces oxygen into the conduit under pressure to expel the drug into a semi-pivoting cannula inserted into the patient's body. A colored oil drop between the oxygen and the drug in the conduit provides a visual indication of drug quantity, while a filter with hydrophobic and hydrophylic membranes keeps the oxygen and oil substantially out of the cannula. A test button sounds an alarm when the device is ready for use and a pressure sensitive switch automatically sounds an alarm and shuts off the pump if the drug becomes completely discharged from the conduit or if the drug delivery system becomes occluded and an interlock switch completes the circuit between the pump and a power source when the reusable module and disposable casting are joined.

Syringe plunger driver

Abstract: A plunger driver system which engages a plurality of different sizes of syringes A pushing surface includes a detector to determine syringe plunger presence In the event that the plunger is not present and the pump is operating, a processor provides an alarm and may stop the pump motor Arms retain the plunger flange in a fixed position in relation to the plunger driver The arms have anti-siphon flanges to prevent too rapid movement of the plunger into the syringe barrel A shelf for opposing downward movement of the syringe plunger and a ramp to guide the syringe plunger into position in relation to the plunger driver are included in the plunger driver A cradle for containing all sizes of syringe barrels yet aligning the syringes with the plunger driver is included with a clamp to hold the syringe barrel in position in the cradle The detector button includes a bevel at its top edge to facilitate loading the plunger in the driver The plunger driver arms are biased independently from the screw drive disengagement mechanism A ramp is also formed with the shelf to assist in guiding the syringe plunger into position during syringe installation

Mechanism for screw drive and syringe plunger engagement/disengagement

Abstract: A mechanism for screw drive and syringe plunger engagement and disengagement for a syringe infusion pump, wherein a split-nut pair are moveable into and out of engagement with a lead screw by means of rotary cam control, the rotary cam being keyed with a crank disk that is coupled to a crank arm, which operates as the syringe plunger mover. The crank arm is rotatable into and out of engagement with the syringe plunger, such rotation also causing the split-nut pair to move into and out of engagement with the lead screw. Index and cam means are carried by the crank arm to aid in proper alignment with the syringe plunger, and a sensor is provided for monitoring proper engagement of the crank arm with the plunger.