Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons

UAV-based LiDAR for high-throughput determination of plant height and above‐ground biomass of the bioenergy grass arundo donax

Replacing fossil fuels with cellulosic biofuels is a valuable component of reducing the drivers of climate change. This leads to a requirement to develop more productive bioenergy crops, such as Arundo donax with the aim of increasing above-ground biomass (AGB). However, direct measurement of AGB is time consuming, destructive, and labor-intensive. Phenotyping of plant height and biomass production is a bottleneck in genomics- and phenomics-assisted breeding. Here, an unmanned aerial vehicle (UAV) for remote sensing equipped with light detection and ranging (LiDAR) was tested for remote plant height and biomass determination in A. donax. Experiments were conducted on three A. donax ecotypes grown in well-watered and moderate drought stress conditions. A novel UAV-LiDAR data collection and processing workflow produced a dense three-dimensional (3D) point cloud for crop height estimation through a normalized digital surface model (DSM) that acts as a crop height model (CHM). Manual measurements of crop height and biomass were taken in parallel and compared to LiDAR CHM estimates. Stepwise multiple regression was used to estimate biomass. Analysis of variance (ANOVA) tests and pairwise comparisons were used to determine differences between ecotypes and drought stress treatments. We found a significant relationship between the sensor readings and manually measured crop height and biomass, with determination coefficients of 0.73 and 0.71 for height and biomass, respectively. Differences in crop heights were detected more precisely from LiDAR estimates than from manual measurement. Crop biomass differences were also more evident in LiDAR estimates, suggesting differences in ecotypes’ productivity and tolerance to drought. Based on these results, application of the presented UAV-LiDAR workflow will provide new opportunities in assessing bioenergy crop morpho-physiological traits and in delivering improved genotypes for biorefining.</jats:p

Flexible Over-the-Tube Device for Soft-Tethered Colonoscopy

Soft-tethered colonoscopes were proposed for safe and effective colon navigation, yet the deployment of front-wheel actuated colonoscopes is hindered by contact interactions with the lumen along the entire soft tether. To mitigate this problem, this study introduces an over-the-tube flexible device aimed to assist colonoscope deployment. The device is composed of three pneumatically driven actuators devised to repeatedly perform a two-phase operation: (phase I) to advance along the tether up to a working position relatively close to the colonoscope’s tip; (phase II) to clamp and drag the tether forward, upon anchoring to colonic wall. This way, a distal tether portion is freed, thus reducing the aforementioned limitations and fostering effective front-wheel navigation. Considering anatomical/clinical constraints and a 2N resistive force, we designed and prototyped a system with an inner and outer diameter of 12 and 26 mm, respectively, a length of 91 mm, and operating pressures equal to 150, 50 and 15 kPa for clamping the tether, elongating the device and safely anchoring to the colonic wall, respectively. The device was successfully tested, achieving locomotion speeds up to 4.9 and 2.2 mm/s, and tether freeing rates up to 2.9 and 1.8 mm/s, in tabletop conditions and in a colon phantom, respectively

Growth enhancement and drought tolerance of hybrid poplar upon inoculation with endophyte consortia

With increasing effects of global climate change, there is a strong interest in developing biofuels from trees such as poplar (Populus sp.) that have high C sequestration rates and relatively low chemical inputs. Using plant-microbe symbiosis to maximize plant growth and increase host stress tolerance may play an important role in improving the economic viability and environmental sustainability of poplar as a feedstock. Based on our previous research, a total of ten endophyte strains were selected as a consortium to investigate the effects of inoculation on commercial hardwood cuttings of Populus deltoides x P. nigra clone OP-367. After one and a half months of growth under non-stress conditions followed by one month under water stress, there was substantial growth promotion with improved leaf physiology of poplar plants in response to the endophyte inoculation. Furthermore, inoculated plants demonstrated reduced damage by reactive oxygen species (ROS) indicating a possible mechanism for symbiosis-mediated drought tolerance. Production of important phytohormones by these endophytes and identification of microbial genes involved in conferring drought tolerance suggests their potential roles in the modulation of the plant host stress response.Fil: Khan, Zareen. University of Washington; Estados UnidosFil: Rho, Hyungmin. University of Washington; Estados UnidosFil: Firrincieli, Andrea. Università degli Studi della Tuscia; ItaliaFil: Hung, Shang Han. University of Washington; Estados UnidosFil: Luna, Maria Virginia. Universidad Nacional de Rio Cuarto. Facultad de Cs.exactas Fisicoquimicas y Naturales. Instituto de Investigaciones Agrobiotecnologicas. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Cordoba. Instituto de Investigaciones Agrobiotecnologicas.; ArgentinaFil: Masciarelli, Oscar Alberto. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Ciencias Naturales; ArgentinaFil: Kim, Soo-Hyung. University of Washington; Estados UnidosFil: Doty, Sharon L.. University of Washington; Estados Unido

Heterogeneous Integration and Fabrication of III-V MOS Devices in a 200mm Processing Environment

We report on the fabrication of MOS capacitors on 200 mm virtual GaAs substrates using a Si CMOS processing environment. The fabricated capacitors were comparable to those processed on bulk GaAs material. Topside contact was made to the GaAs using a novel CMOS compatible self-aligned NiGe contact scheme resulting in a measured contact resistance of 0.26 [ohm sign].cm. Cross-contamination from various III-V substrates was investigated and it was found that by limiting the thermal budget to <= 300C cross-contamination from the outgassing of In, Ga and As could be eliminated. For wet processing the judicious choice of recipe and processing conditions resulted in no significant cross-contamination being detected as determined by TXRF monitoring. This achievement enables III-V device production using state-of-the-art Si processing equipment.Peer reviewe

Ultra-thin biocompatible implantable chip for bidirectional communication with peripheral nerves

To realize optimal recording and stimulation of peripheral nerve cells, a CMOS chip is made with a multitude of electrodes which can be individually addressed in order to select after implantation the 16 best positioned electrodes. Since the Foreign Body Reaction should be minimal for optimum electrode-nerve contact, the CMOS chip is thinned down to 35um and fully packaged resulting in a 75um thin encapsulated chip. The chip is embedded in a biocompatible stack consisting of polymers and inorganic diffusion barriers deposited using atomic layer deposition (ALD). A biocompatible metallization is realized using gold and platinum sandwiched between polymers and ALD layers for flexible interconnects, and iridium oxide (IrOx) is selected as electrode material for optimal charge injection during stimulation. After this dedicated packaging based on the FITEP technology platform (Flexible Implantable Thin Electronic Package), the CMOS chip is still fully functional, which was tested dry (in air) as well as during submersion in saline. The form factor of the packaged chip is optimized for intra-fascicular implantation with minimum tissue damage. First acute in vivo stimulation tests proved that the stimulation capabilities of the IrOx electrodes are very good

Corrigendum: An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes

[This corrects the article DOI: 10.3389/fmicb.2017.00386.]