Synthetic Biology Guides Biofuel Production

The advancement of microbial processes for the production of renewable liquid fuels has increased with concerns about the current fuel economy. The development of advanced biofuels in particular has risen to address some of the shortcomings of ethanol. These advanced fuels have chemical properties similar to petroleum-based liquid fuels, thus removing the need for engine modification or infrastructure redesign. While the productivity and titers of each of these processes remains to be improved, progress in synthetic biology has provided tools to guide the engineering of these processes through present and future challenges

The khmer software package: enabling efficient nucleotide sequence analysis

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

Detection of cancer cells in the cerebrospinal fluid: current methods and future directions

The spread of cancer into the central nervous system is a serious problem leading to neurological symptoms and rapid mortality. The current tools available for detecting the spread of cancer into the cerebrospinal fluid (CSF) are cytology, neurologic examination, and neuroimaging. All three of these methods can be applied in concert to reach a diagnosis, but they all suffer from a lack of sensitivity, leading to delays in treatment in many cases. An overview of research tools in the field of CSF cancer detection reveals a variety of promising technologies that can be used to answer questions about the biology of metastatic cancer and to develop more powerful clinical detection methods. Methods currently under investigation include new immunocytochemistry methods and flow cytometry for the in vitro detection of cells. Additionally, polymerase chain reaction, fluorescence in situ hybridization, capillary electrophoresis with laser-induced fluorescence, and mass spectrometry using matrix-assisted laser absorption-deionization time-of-flight and surface-enhanced laser desorption/ionization time-of-flight techniques are being tested for in vitro assessment of the non-cellular biomarkers in CSF. For in vivo detection of cancer in the CSF, research techniques include certain quantum dot platforms as well as magnetic iron oxide nanoparticles. As systemic therapies for cancer improve, the CNS is becoming a more common site of disease recurrence. This increases the importance of effective detection methods in the CSF, since early intervention can maximize therapeutic benefit. Furthermore, many cell-based detection methods can be combined with therapeutic agents to serve multiple medical functions through a common targeting system

Novel use of stir bar sorptive extraction (SBSE) as a tool for isolation of oviposition site attractants for gravid Culex quinquefasciatus

Mosquitoes such as Culex quinquefasciatus Say (Diptera: Culicidae) are important vectors of organisms that cause disease in humans. Research into the development of effective standardized odour baits for blood-fed females (oviposition attractants), to enable entomological monitoring of vector populations, is hampered by complex protocols for extraction of physiologically active volatile chemicals from natural breeding site water samples, which have produced inconsistent results. Air entrainment and solvent extraction are technically demanding methods and are impractical for use in resource poor environments where mosquito-borne disease is most prevalent. This study reports the first use of a simple, robust extraction technique, stir bar sorptive extraction (SBSE), to extract behaviourally active small lipophilic molecules (SLMs) present in water samples collected from Cx. quinquefasciatus breeding sites in Tanzania. Extracts from a pit latrine and from a cess pool breeding site attracted more gravid Cx. quinquefasciatus in pair choice bioassays than control extracts, and coupled gas chromatography-electroantennography (GC-EAG) allowed tentative identification of 15 electrophysiologically active chemicals, including the known oviposition attractant, skatole (3-methylindole). Here, we have demonstrated, using simple pair choice bioassays in controlled laboratory conditions, that SBSE is effective for the extraction of behaviourally and electrophysiologically active semiochemicals from mosquito breeding site waters. Further research is required to confirm that SBSE is an appropriate technique for use in field surveys in the search for oviposition cues for Cx. quinquefasciatus

Study of Beauty Hadron Decays into Pairs of Charm Hadrons

First observations of the decays Λ[0 over b] → Λ[+ over c]D[− over (s)] are reported using data corresponding to an integrated luminosity of 3  fb[superscript −1] collected at 7 and 8 TeV center-of-mass energies in proton-proton collisions with the LHCb detector. In addition, the most precise measurement of the branching fraction B(B[0 over s] → D[superscript +]D[− over s]) is made and a search is performed for the decays B[0 over (s)] → Λ[+ over c]Λ[− over c]. The results obtained are B(Λ[0 over b] → Λ[+ over c]D[superscript −])/B(Λ[0 over b] → Λ[+ over c]D[− over s]) = 0.042 ± 0.003(stat) ± 0.003(syst), ⎡⎣B(Λ[0 over b] → Λ[+ over c]D[− over s]) over B([¯ over B[superscript 0] → D[superscript +]D[− over s])⎤⎦/⎡⎣B(Λ[0 over b] → Λ[+ over c]π[superscript −]) over B([¯ over B[superscript 0] → D[superscript +]π[superscript −])⎤⎦ = 0.96 ± 0.02(stat) ± 0.06(syst), B(B[0 over s] → D[superscript +]D[− over s])/B([¯ over B][superscript 0] → D[superscript +]D[− over s]) = 0.038 ± 0.004(stat) ± 0.003(syst), B([¯ over B][superscript 0] → Λ[+ over c]Λ[− over c])/B([¯ over B][superscript 0] → D[superscript +]D[− over s]) < 0.0022[95%  C.L.], B(B[0 over s] → Λ[+ over c]Λ[− over c])/B(B[0 over s] → D[superscript +]D[− over s]) < 0.30[95%  C.L.]. Measurement of the mass of the Λ[0 over b] baryon relative to the [¯ over B][superscript 0] meson gives M(Λ[0 over b]) − M([¯ over B][superscript 0]) = 339.72 ± 0.24(stat) ± 0.18(syst)  MeV/c[superscript 2]. This result provides the most precise measurement of the mass of the Λ[0 over b] baryon to date.National Science Foundation (U.S.

Large Scale Signal and Interconnect FDTD Modeling for BGA Package

This paper introduces a Finite-Difference Time-Domain (FDTD) approach to modeling portions of Ball Grid Array (BGA) package interconnect circuits. A fullwave circuit model including vias, trace segments, and ground vias was generated, using a computer gridding tool, and fed into the FDTD (Taflove and Hagness, 2005) program. The simulated results were correlated with TDR measurements

Habitat Characteristics of Eastern Wild Turkey Nest and Ground-roost Sites in 2 Longleaf Pine Forests

Managing and restoring longleaf pine forests throughout the Southeast is a conservation priority. Prescribed fire is an integral part of these activities, as it is the primary means of controlling hardwood encroachment and maintaining native groundcover. Nest site and preflight brood groundroost site selection of eastern wild turkeys (Meleagris gallopavo silvestris) has not been well studied in longleaf pine systems. Therefore, we determined habitat characteristics associated with wild turkey nests and ground-roosts in 2 longleaf pine forests in southwestern Georgia. We radio-tagged 45 female turkeys and evaluated habitat characteristics associated with 84 nests and 51 ground-roosts during the 2011–2013 nesting seasons. Nests were located farther from mature pine and mature pine-hardwood stands and closer to shrub/scrub habitats than expected. Nests were also negatively associated with percent canopy closure and positively associated with percent woody ground cover and vegetation height. Ground-roosts were closer to mature pine-hardwood stands and open water than were random sites. We suggest that management of longleaf pine forests should focus on maintaining open-canopied forests with adequate understory vegetation to serve as nesting and brood-rearing cover. Our findings suggest that frequent prescribed fire (≤ 2 years), when the management goal is to optimize restoration of longleaf ecosystems, is conducive to maintaining wild turkey populations

Modelflow Estimates of Stroke Volume Do Not Correlate With Doppler Ultrasound Estimates During Upright Posture

Orthostatic intolerance affects 6080% of astronauts returning from longduration missions, representing a significant risk to completing missioncritical tasks. While likely multifactorial, a reduction in stroke volume (SV) represents one factor contributing to orthostatic intolerance during stand and head up tilt (HUT) tests. Current measures of SV during stand or HUT tests use Doppler ultrasound and require a trained operator and specialized equipment, restricting its use in the field. BeatScope (Finapres Medical Systems BV, The Netherlands) uses a modelflow algorithm to estimate SV from continuous blood pressure waveforms in supine subjects; however, evidence supporting the use of Modelflow to estimate SV in subjects completing stand or HUT tests remain scarce. Furthermore, because the blood pressure device is held extended at heart level during HUT tests, but allowed to rest at the side during stand tests, changes in the finger arterial pressure waveform resulting from arm positioning could alter modelflow estimated SV. The purpose of this project was to compare Doppler ultrasound and BeatScope estimations of SV to determine if BeatScope can be used during stand or HUT tests. Finger photoplethysmography was used to acquire arterial pressure waveforms corrected for hydrostatic fingertoheart height using the Finometer (FM) and Portapres (PP) arterial pressure devices in 10 subjects (5 men and 5 women) during a stand test while simultaneous estimates of SV were collected using Doppler ultrasound. Measures were made after 5 minutes of supine rest and while subjects stood for 5 minutes. Next, SV estimates were reacquired while each arm was independently raised to heart level, a position similar to tilt testing. Supine SV estimates were not significantly different between all three devices (FM: 68+/-20, PP: 71+/-21, US: 73+/-21 ml/beat). Upon standing, the change in SV estimated by FM (18+/-8 ml) was not different from PP (21+/-12), but both were significantly less than US (37+/-16 ml, p<.05). Raising finger BP devices to heart level caused no significant change in SV measured with any of the devices (FM: 1.5+/-19, PP: 1.7+/-26, US: 0.5+/-6), although variability was 36x greater as assessed by both blood pressure devices compared to US. Retrospective analysis of blood pressure data to assess SV in 11 supine subjects revealed significantly different estimates between methods (FM: 95+/-17, US: 75+/-32, p<.05), but the change in SV resulting from HUT was similar between methods (FM: 37+/-9, US: 40+/-18 ml). However, the correlation coefficient determined from pairs of SV estimated by US and FM was weak (r2=0.03). These data suggest Modelflow cannot be used in lieu of Doppler ultrasound to estimate SV during stand or HUT tests. Further investigation should focus on identifying factors contributing to differences between these measurement techniques in order to make use of a simple method for assessing beatbybeat changes in SV during postural changes, especially during field testing

Male aggression varies with consortship rate and habitat in a dolphin social network

Coalitions and alliances exemplify the core elements of conflict and cooperation in animal societies. Ecological influences on alliance formation are more readily attributed to within-species variation where phylogenetic signals are muted. Remarkably, male Indo-Pacific bottlenose dolphins in Shark Bay, Western Australia, exhibit systematic spatial variation in alliance behavior, not simply within a species or population, but within a single social network. Moving SE-NW along Peron Peninsula in Shark Bay, males ally more often in trios than pairs, consort females more often, and exhibit greater seasonal movements. Ecological models predict more male-male conflict in the north, but sufficient observations of aggression are lacking. However, dolphins often incur marks, in the form of tooth rakes, during conflicts. Here we report that the incidence of new tooth rake marks varies systematically in the predicted pattern, with greater marking in the north, where males form more trios and consort females at a higher rate. While our previous work demonstrated that alliance complexity has an ecological component, we can now infer that ecological variation impacts the level of alliance-related conflict in Shark Bay