Use of PCR Cloning Combined with DNA Barcoding to Identify Fish in a Mixed-Species Product

DNA barcoding is a valuable tool for fish species identification by food regulators, however, it does not perform well when multiple species are present within the same food product. PCR cloning has high potential to be used in combination with DNA barcoding to overcome this challenge. The objective of this study was to examine the use of PCR cloning combined with DNA barcoding to identify fish in a mixed-species product that cannot be identified with standard DNA barcoding. A total of 15 fish ball mixtures were prepared with known amounts of Nile tilapia (Oreochromis niloticus), Pacific cod (Gadus macrocephalus), and walleye pollock (Gadus chalcogrammus). The fish balls underwent DNA extraction in triplicate, followed by DNA barcoding across the full barcode (655 bp) and SH-E mini-barcode (226 bp) of the cytochrome c oxidase subunit 1 (CO1) region. Samples that did not pass sequencing according to regulatory standards were further analyzed with PCR cloning. Full barcoding enabled identification of at least one species in 80% of the fish ball mixtures compared to 51% for minibarcoding. The results of PCR cloning with samples that did not pass DNA barcoding showed identification success rates of 61% for clones (54 of 90) that underwent full barcoding and 51% for clones (111 of 220) that underwent mini-barcoding. All fish balls made of just one species tested positive for that species (i.e., tilapia, cod, or pollock).. The combination of standard full barcoding and PCR cloning enabled identification of Nile tilapia in all 12 mixed-species fish balls and Pacific cod in 6 of 12 (50%) of mixed-species fish balls. In comparison, the combination of standard mini-barcoding and PCR cloning enabled identification of Nile tilapia in all 12 mixed-species fish balls and Pacific cod in 9 of 12 (75%) of mixed-species fish balls. Overall, the results of this study show that PCR cloning may be an effective method to identify certain fish in mixed-species products when standard DNA barcoding fails. However, additional research is needed to understand the limitations associated with primer bias

Thermodynamics of quantum systems with multiple conserved quantities

We consider a generalisation of thermodynamics that deals with multiple conserved quantities at the level of individual quantum systems. Each conserved quantity, which, importantly, need not commute with the rest, can be extracted and stored in its own battery. Unlike in standard thermodynamics, where the second law places a constraint on how much of the conserved quantity (energy) that can be extracted, here, on the contrary, there is no limit on how much of any individual conserved quantity that can be extracted. However, other conserved quantities must be supplied, and the second law constrains the combination of extractable quantities and the trade-offs between them which are allowed. We present explicit protocols which allow us to perform arbitrarily good trade-offs and extract arbitrarily good combinations of conserved quantities from individual quantum systems.Comment: 16 pages, 3 figure

Subsequence Rational Ergodicity of Rank-One Transformations

We show that all rank-one transformations are subsequence boundedly rationally ergodic and that there exist rank-one transformations that are not weakly rationally ergodic.Comment: Added references, minor update

Sexual dimorphism in bite performance drives morphological variation in chameleons

Phenotypic performance in different environments is central to understanding the evolutionary and ecological processes that drive adaptive divergence and, ultimately, speciation. Because habitat structure can affect an animal's foraging behaviour, anti-predator defences, and communication behaviour, it can influence both natural and sexual selection pressures. These selective pressures, in turn, act upon morphological traits to maximize an animal's performance. For performance traits involved in both social and ecological activities, such as bite force, natural and sexual selection often interact in complex ways, providing an opportunity to understand the adaptive significance of morphological variation with respect to habitat. Dwarf chameleons within the Bradypodion melanocephalum-Bradypodion thamnobates species complex have multiple phenotypic forms, each with a specific head morphology that could reflect its use of either open-or closed-canopy habitats. To determine whether these morphological differences represent adaptations to their habitats, we tested for differences in both absolute and relative bite performance. Only absolute differences were found between forms, with the closed-canopy forms biting harder than their open-canopy counterparts. In contrast, sexual dimorphism was found for both absolute and relative bite force, but the relative differences were limited to the closed-canopy forms. These results indicate that both natural and sexual selection are acting within both habitat types, but to varying degrees. Sexual selection seems to be the predominant force within the closed-canopy habitats, which are more protected from aerial predators, enabling chameleons to invest more in ornamentation for communication. In contrast, natural selection is likely to be the predominant force in the open-canopy habitats, inhibiting the development of conspicuous secondary sexual characteristics and, ultimately, enforcing their overall diminutive body size and constraining performance

Exploring the limits of no backward in time signalling

We present an operational and model-independent framework to investigate the concept of no-backwards-in-time signaling. We define no-backwards-in-time signaling conditions, closely related to the spatial no-signaling conditions. These allow for theoretical possibilities in which the future affects the past, nevertheless without signaling backwards in time. This is analogous to non-local but no-signaling spatial correlations. Furthermore, our results shed new light on situations with indefinite causal structure and their connection to quantum theory.Comment: 10 pages, 3 figures, v2: reference adde

Pre- and post-selected quantum states: density matrices, tomography, and Kraus operators

We present a general formalism for charecterizing 2-time quantum states, describing pre- and post-selected quantum systems. The most general 2-time state is characterized by a `density vector' that is independent of measurements performed between the preparation and post-selection. We provide a method for performing tomography of an unknown 2-time density vector. This procedure, which cannot be implemented by weak or projective measurements, brings new insight to the fundamental role played by Kraus operators in quantum measurements. Finally, after showing that general states and measurements are isomorphic, we show that any measurement on a 2-time state can be mapped to a measurement on a preselected bipartite state.Comment: 7 page

The Nature and Extent of Species Interactions With the United States Gulf Menhaden Fishery.

I employed categorical techniques to explain patchy data on the releasable bycatch in the U.S. Gulf of Mexico menhaden fishery looking for species and areas of potential concern and potential solutions. For fishing grounds east of the Mississippi River, the odds of observing sets with high bycatch in spring and summer were greater than in the fall. Furthermore, spring bycatch rates were higher east of 89°W than in areas west of 93°W. Correspondence analysis indicated that the fate of the releasable bycatch could be classified into three major species-fate groupings. Two distinct bycatch species assemblages from April through August that separated the fishery at a longitude of 91°W were observed. From September through October there was a shift in the species assemblage. The assemblage west of 93°W appeared distinct from the rest of the fishery. From these analyses, bull sharks emerged as a species for potential concern. A shark-specific analysis of the bycatch revealed an annual take of approximately 30,000 sharks. Logit analysis indicated that the odds of observing shark bycatch were significantly greater in June--August than September--October. The odds of observing shark bycatch during April--May were also significantly different from September--October, however, these differences were only apparent east of 93°W. Stomach analyses of sharks and a consideration of size at age suggests that the fishery is impacting an important nursery ground for a complex assemblage of sharks, for which menhaden is an important forage base. I describe the spatial and temporal patterns of bottlenose dolphins and brown pelicans associated with the fishery. Dolphins were observed around 19% of fishing sets and diving and circling pelicans were observed in 23% of sets. These associations are described by a loglinear model with pelican-season-dolphin, dolphin-season-area, and prelican-season-area terms. Results suggest that while the incidental capture of dolphins in the fishery is extremely low, they are far more frequently observed in the immediate vicinity of the fishing operation. This suggests dolphins may have learned to avoid being captured. However, the extremely low rates of incidental capture may be biologically important given the low population estimates

Properties of the open cluster Tombaugh 1 from high resolution spectroscopy and uvbyCaHβ\beta photometry

Open clusters can be the key to deepen our knowledge on various issues involving the structure and evolution of the Galactic disk and details of stellar evolution because a cluster's properties are applicable to all its members. However the number of open clusters with detailed analysis from high resolution spectroscopy and/or precision photometry imposes severe limitation on studies of these objects. To expand the number of open clusters with well-defined chemical abundances and fundamental parameters, we investigate the poorly studied, anticenter open cluster Tombaugh 1. Using precision uvbyCaH$\beta$ photometry and high resolution spectroscopy, we derive the cluster's properties and, for the first time, present detailed abundance analysis of 10 potential cluster stars. Using radial position from the cluster center and multiple color indices, we have isolated a sample of unevolved probable, single-star members of Tombaugh 1. The weighted photometric metallicity from $m_1$ and $hk$ is [Fe/H] = -0.10 $\pm$ 0.02, while a match to the Victoria-Regina Str\"{o}mgren isochrones leads to an age of 0.95 $\pm$ 0.10 Gyr and an apparent modulus of $(m-M)$ = 13.10 $\pm$ 0.10. Radial velocities identify 6 giants as probable cluster members and the elemental abundances of Fe, Na, Mg, Al, Si, Ca, Ti, Cr, Ni, Y,Ba, Ce, and Nd have been derived for both the cluster and the field stars. Tombaugh 1 appears to be a typical inner thin disk, intermediate-age open cluster of slightly subsolar metallicity, located just beyond the solar circle, with solar elemental abundance ratios except for the heavy s-process elements, which are a factor of two above solar. Its metallicity is consistent with a steep metallicity gradient in the galactocentric region between 9.5 and 12 kpc. Our study also shows that Cepheid XZ CMa is not a member of Tombaugh 1, and reveals that this Cepheid presents signs of barium enrichment.Comment: 74 pages, 15 figures, 13 tables; Accepted for publication in A