Formation of regulatory patterns during signal propagation in a Mammalian cellular network

We developed a model of 545 components (nodes) and 1259 interactions representing signaling pathways and cellular machines in the hippocampal CA1 neuron. Using graph theory methods, we analyzed ligand-induced signal flow through the system. Specification of input and output nodes allowed us to identify functional modules. Networking resulted in the emergence of regulatory motifs, such as positive and negative feedback and feedforward loops, that process information. Key regulators of plasticity were highly connected nodes required for the formation of regulatory motifs, indicating the potential importance of such motifs in determining cellular choices between homeostasis and plasticity.     

Silica-on-silicon waveguide quantum circuits

Quantum technologies based on photons will likely require an integrated optics architecture for improved performance, miniaturization, and scalability. We demonstrate high-fidelity silica-on-silicon integrated optical realizations of key quantum photonic circuits, including two-photon quantum interference with a visibility of 94.8 +/- 0.5%; a controlled-NOT gate with an average logical basis fidelity of 94.3 +/- 0.2%; and a path-entangled state of two photons with fidelity of >92%. These results show that it is possible to directly "write" sophisticated photonic quantum circuits onto a silicon chip, which will be of benefit to future quantum technologies based on photons, including information processing, communication, metrology, and lithography, as well as the fundamental science of quantum optics.     

The rise of the rhizosolenid diatoms

The 18S ribosomal DNA molecular phylogeny and lipid composition of over 120 marine diatoms showed that the capability to biosynthesize highly branched isoprenoid (HBI) alkenes is restricted to two specific phylogenetic clusters, which independently evolved in centric and pennate diatoms. The molecular record of C25 HBI chemical fossils in a large suite of well-dated marine sediments and petroleum revealed that the older cluster, composed of rhizosolenid diatoms, evolved 91.5 +/- 1.5 million years ago (Upper Turonian), enabling an accurate dating of the pace of diatom evolution that is unprecedented. The rapid rise of the rhizosolenid diatoms probably resulted from a major reorganization of the nutrient budget in the mid-Cretaceous oceans, triggered by plate tectonics.     

Effects of fire and fire intensity on the germination and establishment of Acacia karroo, Acacia nilotica, Acacia luederitzii and Dichrostachys cinerea in the field

Background

The native annual tobacco, Nicotiana attenuata, is found primarily in large ephemeral populations (typically for less than 3 growing seasons) after fires in sagebrush and pinyon-juniper ecosystems and in small persistent populations (for many growing seasons) in isolated washes typically along roadsides throughout the Great Basin Desert of the SW USA. This distribution pattern is due to its unusual germination behavior. Ephemeral populations are produced by the germination of dormant seeds from long-lived seed banks which are stimulated to germinate by a combination of unidentified positive cues found in wood smoke and the removal of inhibitors leached from the unburned litter of the dominant vegetation. Persistent populations may result where these inhibitors do not exist, as in washes or along disturbed roadsides. To determine if this germination behavior has influenced population structure, we conducted an AFLP (244 individuals), ISSR (175 individuals) and ISSR+ AFLP (175 individuals) analysis on plants originating from seed collected from populations growing in 11 wash and burns over 11 years from the SW USA.

Results

Genetic variance as measured by both ISSR and AFLP markers was low among sites and comparatively higher within populations. Cluster analysis of the Utah samples with samples collected from Arizona, California, and Oregon as out-groups also did not reveal patterns. AMOVA analysis of the combined AFLP and ISSR data sets yielded significantly low genetic differentiation among sites (Φct), moderate among populations within sites (Φsc) and higher genetic differentiation within populations (Φst).

Conclusions

We conclude that the seed dormancy of this post-fire annual and its resulting age structure in conjunction with natural selection processes are responsible for significantly low among sites and comparatively high within-population genetic variation observed in this species.     

Assessment of bovine mammary chemokine gene expression in response to lipopolysaccharide, lipotechoic acid + peptidoglycan, and CpG oligodeoxynucleotide 2135

During intramammary infections pathogen associated molecular patterns (PAMPs) induce an inflammatory response, recognized clinically as mastitis. Recognition of PAMPs by mammary cells leads to the production of the pro-inflammatory cytokines, TNF-α and IL-1β. These cytokines augment the secretion of various chemokines that are responsible for directing the host cellular immune response, and consequently the outcome of infection. Previous research has shown that gram-negative and gram-positive bacteria elicit different types of innate immune responses. The purpose of this study, therefore, was to characterize the expression of various chemokine genes in bovine mammary gland explants in response to lipopolysaccharide (LPS), peptidoglycan (PTG) combined with lipotechoic acid (LTA), and CpG oligodeoxynucleotide (CpG-ODN) 2135 representing gram-negative bacteria, gram-positive bacteria, and bacterial DNA, respectively, to determine if these PAMPs induce different chemokine gene expression patterns. Explants from 3 Holstein cows were cultured with 10 μg/mL of LPS, LTA + PTG, or CpG-ODN 2135 for 6 and 24 h. Total RNA was extracted and the expression of CXCL8, MCP-1, MCP-2, MCP-3, MIP1-α, and RANTES genes was measured by real-time polymerase chain reaction (RT-PCR). Lipopolysaccharide significantly induced MCP-1, MCP-2, and MCP-3 expression, and slightly increased CXCL8 gene expression. The combined PAMPs, LTA + PTG, on the other hand, significantly induced MCP-1 gene expression, and slightly increased MCP-3 expression. No significant expression differences for any of the chemokine genes were observed in explants stimulated with CpG-ODN 2135. These results demonstrate that PAMPs associated with different mastitis-causing pathogens induce chemokine-specific gene expression patterns that may contribute to different innate immune responses to bacteria.     

A comparison of new in-pond grading technology to live-car grading for food-sized channel catfish (Ictalurus punctatus)

Grading trials were performed in experimental and commercial catfish ponds to compare an in-pond horizontal floating bar grader to current live-car grading. Three replicate trials were conducted in experimental ponds at three different temperature ranges (warm, >26 °C; cool, 13–26 °C; cold, <13 °C) with catfish size groups stocked in ratios of either 75:25, 50:50, or 25:75 sub-marketable (<0.57 kg) to marketable fish (≥0.57 kg). Commercial pond trials were replicated three times at each temperature range with a fish size range typical of ponds ready to harvest. Stress experienced by fish during harvest and grading was measured by mean serum glucose and cortisol levels. Grading speed was greater (P < 0.05) with the UAPB grader (105–449 kg/min) than the traditional live-car grader (0.5–0.6 kg/min). The UAPB grader decreased (P < 0.05) the proportion of sub-marketable fish during all trials. In contrast, the live car did not reduce the proportion of sub-marketable fish with the experimental methods used in this study during commercial trials or in the 25:75 distributions during warm and cold temperature trials in experimental ponds. The UAPB grader returned an average two to four times (range of 2–52) more sub-marketable fish by weight to the pond than the traditional live car method. Glucose and cortisol levels in fish graded with the two technologies were not significantly different. The UAPB grader sorted fish more accurately, consistently, and quickly than the live car at all temperatures in both experimental and commercial trials.     

DNA barcoding reveals clear delineation between spawning sites for neritic versus oceanic fishes in the Gulf of Mexico

We combined research‐vessel cruises of opportunity with DNA barcoding to survey planktonic, percomorph fish eggs at 40 stations distributed across and around the Gulf of Mexico (GoM). The objectives were (a) to determine whether eggs of fishes that are potential candidates for the daily egg production method (DEPM) can be readily barcoded, (b) to identify taxa that are spawning in the GoM, (c) to determine encounter rates for eggs of economically valuable taxa, and (d) to characterize individual egg taxa as being primarily neritic, primarily oceanic, or primarily mixed (i.e., both neritic and oceanic). Of the 1,144 eggs that were individually barcoded, 709 (62%) were definitively identified to species (62 species from 42 families), with an additional 20 taxa identified to genus or subfamily level. The eggs of 15 economically important species were identified, most of which had intermediate encounter rates and moderately dispersed spatial distributions, as indicated by an index of aggregation. SIMPROF analysis of stationwise cluster analysis identified eight significant groups within the 35 stations that yielded percomorph eggs; a corresponding specieswise analysis identified six groups of stations as having a neritic egg community and two groups as having an oceanic community, with a community transition located at the shelf break. Although the neritic and oceanic stations did not share important species, it remains possible that coastal pelagic species have mixed neritic–oceanic distributions. Together, these results indicate DEPM fish‐egg surveys based on DNA barcoding are feasible at the large marine ecosystem scale.