Historical and recent processes shaping the geographic range of a rocky intertidal gastropod: phylogeography, ecology, and habitat availability

Factors shaping the geographic range of a species can be identified when phylogeographic patterns are combined with data on contemporary and historical geographic distribution, range-wide abundance, habitat / food availability and through comparisons with co-distributed taxa. Here, we evaluate range dynamism and phylogeography of the rocky intertidal gastropod Mexacanthina lugubris lugubris across its geographic range - the Pacific coast of the Baja peninsula and southern California. We sequenced mitochondrial DNA (CO1) from ten populations and compliment these data with museum records, habitat availability and range-wide field surveys of the distribution and abundance of M. l. lugubris and its primary prey (the barnacle Chthamalus fissus). The geographic range of M. l. lugubris can be characterized by three different events in its history: an old sundering in the mid-peninsular region of Baja (~ 417,000 years ago) and more recent northern range expansion and southern range contraction. The mid-peninsular break is shared with many terrestrial and marine species, although M. l. lugubris represents the first mollusc to show it. This common break is often attributed to a hypothesized ancient seaway bisecting the peninsula, but for M. l. lugubris it may result from large habitat gaps in the southern clade. Northern clade populations, particularly near the historical northern limit (prior to the 1970’s) have high local abundances and reside in a region with plentiful food and habitat – which makes its northern range conducive to expansion. The observed southern range contraction may result from the opposite scenario, with little food or habitat nearby. Our study highlights the importance of taking an integrative approach to understanding the processes that shape the geographic range of a species via combining range-wide phylogeography data with temporal geographic distributions and spatial patterns of habitat / food availability

Entanglement Generation of Nearly-Random Operators

We study the entanglement generation of operators whose statistical properties approach those of random matrices but are restricted in some way. These include interpolating ensemble matrices, where the interval of the independent random parameters are restricted, pseudo-random operators, where there are far fewer random parameters than required for random matrices, and quantum chaotic evolution. Restricting randomness in different ways allows us to probe connections between entanglement and randomness. We comment on which properties affect entanglement generation and discuss ways of efficiently producing random states on a quantum computer.Comment: 5 pages, 3 figures, partially supersedes quant-ph/040505

Use of the Mitochondrial Control Region as a Potential DNA Mini-Barcoding Target for the Identification of Canned Tuna Species

In this study, a DNA mini-barcoding methodology was developed for the differentiation of species commonly found in canned tuna. Primers were designed to target a 236-base pair (bp) fragment of the mitochondrial control region (CR) and a 179-bp fragment of the first internal transcribed spacer region (ITS1). Phylogenetic analysis revealed the ability to differentiate 13 tuna species on the basis of the CR mini-barcode, except in a few cases of species introgression. Supplementary use of ITS1 allowed for differentiation of introgressed Atlantic bluefin tuna (Thunnus thynnus) and albacore tuna (Thunnus alalunga), while differentiation of introgressed Atlantic bluefin tuna and Pacific bluefin tuna (Thunnus orientalis) requires a longer stretch of the CR. After primer design, a market sample of 53 commercially canned tuna products was collected for testing. This mini-barcoding system was able to successfully identify species in 23 of the products, including albacore tuna, yellowfin tuna (Thunnus albacares), and skipjack tuna (Katsuwonus pelamis). One instance of mislabeling was detected, in which striped bonito (Sarda orientalis) was identified in a product labeled as tongol tuna (Thunnus tonggol). PCR amplification and sequencing was unsuccessful in a number of products, likely due to factors such as the presence of PCR inhibitors and DNA fragmentation during the canning process. Overall, CR and ITS1 show high potential for use in identification of canned tuna products; however, further optimization of the assay may be necessary in order to improve amplification and sequencing success rates

Neutrophil-mediated post-ischemic tubular leakage in the rat kidney

Neutrophil-mediated post-ischemic tubular leakage in the rat kidney. Neutropenia was induced in male Sprague-Dawley rats by administration of antineutrophil serum (ANS). A control group received an equal volume of inactive serum. After 45 minutes of unilateral complete renal ischemia the renal blood flow (RBF) was measured by an electromagnetic flow meter. The net filtration force (NFF) in glomerular capillaries, single nephron filtration rate (SNGFR) and frequency of tubular obstructions were estimated by a micropuncture technique. Tubular leakage was measured from the fractional recovery in the normal contralateral kidney of 3H- or 14C-inulin injected into surface proximal and distal tubules of the post-ischemic kidney. Neither ANS nor inactive serum had any influence on inulin clearance (CIn) in the normal kidney. In the post-ischemic kidney, CIn was four times higher in ANS-treated than in control animals. There was no difference in RBF, NFF, SNGFR or the frequency of tubular obstructions between neutrophil-depleted and control animals. The transtubular leakage of inulin injected into proximal tubules was substantially less in the ANS-treated than in the control group (11.3 ± 1.5% vs. 35.1 ± 6.5%; P < 0.01). But distal tubular leakage was equal in the two groups. The control group showed isosthenuria (350 ± 29mOsm · kg-1), while ANS-treated animals produced hyperosmolar urine (555 ± 60mOsm · kg-1; P < 0.05). It is concluded that neutrophil granulocytes mediate post-ischemic tubular leakage, which contributes to the depression in renal clearance parameters and the inability to produce hyperosmolar urine

Matrix Element Distribution as a Signature of Entanglement Generation

We explore connections between an operator's matrix element distribution and its entanglement generation. Operators with matrix element distributions similar to those of random matrices generate states of high multi-partite entanglement. This occurs even when other statistical properties of the operators do not conincide with random matrices. Similarly, operators with some statistical properties of random matrices may not exhibit random matrix element distributions and will not produce states with high levels of multi-partite entanglement. Finally, we show that operators with similar matrix element distributions generate similar amounts of entanglement.Comment: 7 pages, 6 figures, to be published PRA, partially supersedes quant-ph/0405053, expands quant-ph/050211

Microplate Immunocapture Coupled with the 3M Molecular Detection System and Selective Plating for the Rapid Detection of \u3cem\u3eSalmonella\u3c/em\u3e infantis in Dry Dog Food and Treats

The objective of this study was to use microplate immunocapture (IC) to reduce the enrichment time required for detection of Salmonella in pet food with the 3 M Molecular Detection System (MDS) or selective plating on XLD. Dog food and pig ear treats were inoculated with Salmonella Infantis at concentrations of 100–104 CFU/25 g, followed by a 3-h enrichment, then microplate IC and 3 M MDS or microplate IC and selective plating on XLD. Another set of samples underwent a traditional 24-h enrichment followed by 3 M MDS or selective plating. Based on the results of three independent trials, microplate IC followed by selective plating enabled detection of Salmonella in 100% of dog food and treat samples tested, including at levels as low as 100 CFU/25 g. Microplate IC coupled with 3 M MDS enabled detection of Salmonella in dog food and treat samples down to levels of 100 CFU/25 g, with an overall detection rate of 92%. These results indicate high potential for microplate IC to be used in place of the traditional 24-h enrichment step, enabling detection of Salmonella in complex matrices when coupled with 3 M MDS or selective plating

Pseudo-random operators of the circular ensembles

We demonstrate quantum algorithms to implement pseudo-random operators that closely reproduce statistical properties of random matrices from the three universal classes: unitary, symmetric, and symplectic. Modified versions of the algorithms are introduced for the less experimentally challenging quantum cellular automata. For implementing pseudo-random symplectic operators we provide gate sequences for the unitary part of the time-reversal operator.Comment: 5 pages, 4 figures, to be published PR

The breakdown of the Nagaoka phase in the 2D t-J model

In the limit of weak exchange, J, at low hole concentration, the ground state of the 2D t-J model is believed to be ferromagnetic. We study the leading instability of this Nagaoka state, which emerges with increasing J. Both exact diagonalization of small clusters, and a semiclassical analytical calculation of larger systems show that above a certain critical value of the exchange, Nagaoka's state is unstable to phase separation. In a finite-size system a bubble of antiferromagnetic Mott insulator appears in the ground state above this threshold. The size of this bubble depends on the hole concentration and scales as a power of the system size, N