A video method for quantifying size distribution, density, and three-dimensional spatial structure of reef fish spawning aggregations

There is a clear need to develop fisheries independent methods to quantify individual sizes, density, and three dimensional characteristics of reef fish spawning aggregations for use in population assessments and to provide critical baseline data on reproductive life history of exploited populations. We designed, constructed, calibrated, and applied an underwater stereo-video system to estimate individual sizes and three dimensional (3D) positions of Nassau grouper (Epinephelus striatus) at a spawning aggregation site located on a reef promontory on the western edge of Little Cayman Island, Cayman Islands, BWI, on 23 January 2003. The system consists of two free-running camcorders mounted on a meter-long bar and supported by a SCUBA diver. Paired video “stills” were captured, and nose and tail of individual fish observed in the field of view of both cameras were digitized using image analysis software. Conversion of these two dimensional screen coordinates to 3D coordinates was achieved through a matrix inversion algorithm and calibration data. Our estimate of mean total length (58.5 cm, n = 29) was in close agreement with estimated lengths from a hydroacoustic survey and from direct measures of fish size using visual census techniques. We discovered a possible bias in length measures using the video method, most likely arising from some fish orientations that were not perpendicular with respect to the optical axis of the camera system. We observed 40 individuals occupying a volume of 33.3 m3, resulting in a concentration of 1.2 individuals m–3 with a mean (SD) nearest neighbor distance of 70.0 (29.7) cm. We promote the use of roving diver stereo-videography as a method to assess the size distribution, density, and 3D spatial structure of fish spawning aggregations.

Nassau grouper (Epinephelus striatus) spawning aggregations: hydroacoustic surveys and geostatistical analysis

With the near extinction of many spawning aggregations of large grouper and snapper throughout the Caribbean, Gulf of Mexico, and tropical Atlantic, we need to provide baselines for their conservation. Thus, there is a critical need to develop techniques for rapidly assessing the remaining known (and unknown) aggregations. To this end we used mobile hydroacoustic surveys to estimate the density, spatial extent, and total abundance of a Nassau grouper spawning aggregation at Little Cayman Island, Cayman Islands, BWI. Hydroacoustic estimates of abundance, density, and spatial extent were similar on two sampling occasions. The location and approximate spatial extent of the Nassau grouper spawning aggregation near the shelf-break was corroborated by diver visual observations. Hydroacoustic density estimates were, overall, three-times higher than the average density observed by divers; however, we note that in some instances diver-estimated densities in localized areas were similar to hydroacoustic density estimates. The resolution of the hydroacoustic transects and geostatistical interpolation may have resulted in over-estimates in fish abundance, but still provided reasonable estimates of total spatial extent of the aggregation. Limitations in bottom time for scuba and visibility resulted in poor coverage of the entire Nassau grouper aggregation and low estimates of abundance when compared to hydroacoustic estimates. Although the majority of fish in the aggregation were well off bottom, fish that were sometimes in close proximity to the seafloor were not detected by the hydroacoustic survey. We conclude that diver observations of fish spawning aggregations are critical to interpretations of hydroacoustic surveys, and that hydroacoustic surveys provide a more accurate estimate of overall fish abundance and spatial extent than diver observations. Thus, hydroacoustics is an emerging technology that, when coupled with diver observations, provides a comprehensive survey method for monitoring spawning aggregations of fish.

Anatomical and developmental patterns of interleukin-2 gene expression in the mouse: analysis of IL-2 expressing cells and partial characterization of interactions involved in mediating IL-2 gene expression in vivo

Interleukin-2 (IL-2) is an important mediator in the vertebrate immune system. IL-2 is a potent growth factor that mature T lymphocytes use as a proliferation signal and the production of IL-2 is crucial for the clonal expansion of antigen-specific T cells in the primary immune response. IL-2 driven proliferation is dependent on the interaction of the lymphokine with its cognate multichain receptor. IL-2 expression is induced only upon stimulation and transcriptional activation of the IL-2 gene relies extensively on the coordinate interaction of numerous inducible and constitutive trans-acting factors. Over the past several years, thousands of papers have been published regarding molecular and cellular aspects of IL-2 gene expression and IL-2 function. The vast majority of these reports describe work that has been carried out in vitro. However, considerably less is known about control of IL-2 gene expression and IL-2 function in vivo.

To gain new insight into the regulation of IL-2 gene expression in vivo, anatomical and developmental patterns of IL-2 gene expression in the mouse were established by employing in situ hybridization and immunohistochemical staining methodologies to tissue sections generated from normal mice and mutant animals in which T -cell development was perturbed. Results from these studies revealed several interesting aspects of IL-2 gene expression, such as (1) induction of IL-2 gene expression and protein synthesis in the thymus, the primary site of T-cell development in the body, (2) cell-type specificity of IL-2 gene expression in vivo, (3) participation of IL-2 in the extrathymic expansion of mature T cells in particular tissues, independent of an acute immune response to foreign antigen, (4) involvement of IL-2 in maintaining immunologic balance in the mucosal immune system, and (5) potential function of IL-2 in early events associated with hematopoiesis.

Extensive analysis of IL-2 mRNA accumulation and protein production in the murine thymus at various stages of development established the existence of two classes of intrathymic IL-2 producing cells. One class of intrathymic IL-2 producers was found exclusively in the fetal thymus. Cells belonging to this subset were restricted to the outermost region of the thymus. IL-2 expression in the fetal thymus was highly transient; a dramatic peak ofiL-2 mRNA accumulation was identified at day 14.5 of gestation and maximal IL-2 protein production was observed 12 hours later, after which both IL-2 mRNA and protein levels rapidly decreased. Significantly, the presence of IL-2 expressing cells in the day 14-15 fetal thymus was not contingent on the generation of T-cell receptor (TcR) positive cells. The second class of IL-2 producing cells was also detectable in the fetal thymus (cells found in this class represented a minority subset of IL-2 producers in the fetal thymus) but persist in the thymus during later stages of development and after birth. Intrathymic IL-2 producers in postnatal animals were located in the subcapsular region and cortex, indicating that these cells reside in the same areas where immature T cells are consigned. The frequency of IL-2 expressing cells in the postnatal thymus was extremely low, indicating that induction of IL-2 expression and protein synthesis are indicative of a rare activation event. Unlike the fetal class of intrathymic IL-2 producers, the presence of IL-2 producing cells in the postnatal thymus was dependent on to the generation of TcR+ cells. Subsequent examination of intrathymic IL-2 production in mutant postnatal mice unable to produce either αβ or γδ T cells showed that postnatal IL-2 producers in the thymus belong to both αβ and γδ lineages. Additionally, further studies indicated that IL-2 synthesis by immature αβ -T cells depends on the expression of bonafide TcR αβ-heterodimers. Taken altogether, IL-2 production in the postnatal thymus relies on the generation of αβ or γδ-TcR^+ cells and induction of IL-2 protein synthesis can be linked to an activation event mediated via the TcR.

With regard to tissue specificity of IL-2 gene expression in vivo, analysis of whole body sections obtained from normal neonatal mouse pups by in situ hybridization demonstrated that IL-2 mRNA^+ cells were found in both lymphoid and nonlymphoid tissues with which T cells are associated, such as the thymus (as described above), dermis and gut. Tissues devoid of IL-2 mRNA^+ cells included brain, heart, lung, liver, stomach, spine, spinal cord, kidney, and bladder. Additional analysis of isolated tissues taken from older animals revealed that IL-2 expression was undetectable in bone marrow and in nonactivated spleen and lymph nodes. Thus, it appears that extrathymic IL-2 expressing cells in nonimmunologically challenged animals are relegated to particular epidermal and epithelial tissues in which characterized subsets of T cells reside and thatinduction of IL-2 gene expression associated with these tissues may be a result of T-cell activation therein.

Based on the neonatal in situ hybridization results, a detailed investigation into possible induction of IL-2 expression resulting in IL-2 protein synthesis in the skin and gut revealed that IL-2 expression is induced in the epidermis and intestine and IL-2 protein is available to drive cell proliferation of resident cells and/or participate in immune function in these tissues. Pertaining to IL-2 expression in the skin, maximal IL-2 mRNA accumulation and protein production were observed when resident Vγ_3^+ T-cell populations were expanding. At this age, both IL-2 mRNA^+ cells and IL-2 protein production were intimately associated with hair follicles. Likewise, at this age a significant number of CD3ε^+ cells were also found in association with follicles. The colocalization of IL-2 expression and CD3ε^+ cells suggests that IL-2 expression is induced when T cells are in contact with hair follicles. In contrast, neither IL-2 mRNA nor IL-2 protein were readily detected once T-cell density in the skin reached steady-state proportions. At this point, T cells were no longer found associated with hair follicles but were evenly distributed throughout the epidermis. In addition, IL-2 expression in the skin was contingent upon the presence of mature T cells therein and induction of IL-2 protein synthesis in the skin did not depend on the expression of a specific TcR on resident T cells. These newly disclosed properties of IL-2 expression in the skin indicate that IL-2 may play an additional role in controlling mature T-cell proliferation by participating in the extrathymic expansion of T cells, particularly those associated with the epidermis.

Finally, regarding IL-2 expression and protein synthesis in the gut, IL-2 producing cells were found associated with the lamina propria of neonatal animals and gut-associated IL-2 production persisted throughout life. In older animals, the frequency of IL-2 producing cells in the small intestine was not identical to that in the large intestine and this difference may reflect regional specialization of the mucosal immune system in response to enteric antigen. Similar to other instances of IL-2 gene expression in vivo, a failure to generate mature T cells also led to an abrogation of IL-2 protein production in the gut. The presence of IL-2 producing cells in the neonatal gut suggested that these cells may be generated during fetal development. Examination of the fetal gut to determine the distribution of IL-2 producing cells therein indicated that there was a tenfold increase in the number of gut-associated IL-2 producers at day 20 of gestation compared to that observed four days earlier and there was little difference between the frequency of IL-2 producing cells in prenatal versus neonatal gut. The origin of these fetally-derived IL-2 producing cells is unclear. Prior to the immigration of IL-2 inducible cells to the fetal gut and/or induction of IL-2 expression therein, IL-2 protein was observed in the fetal liver and fetal omentum, as well as the fetal thymus. Considering that induction of IL-2 protein synthesis may be an indication of future functional capability, detection of IL-2 producing cells in the fetal liver and fetal omentum raises the possibility that IL-2 producing cells in the fetal gut may be extrathymic in origin and IL-2 producing cells in these fetal tissues may not belong solely to the T lineage. Overall, these results provide increased understanding of the nature of IL-2 producing cells in the gut and how the absence of IL-2 production therein and in fetal hematopoietic tissues can result in the acute pathology observed in IL-2 deficient animals.

An analysis of Nigerian freshwater fishes: those under threat and conservation options

The study assessed qualitatively the threat status of all nigerian freshwater fishes using such criteria as rarity, size at maturity, mode of reproduction, human population density, habitat degradation, pollution and range of each species among others. The biology of 48% (129n) of nigerian freshwater species is not well known. Of the 266 known freshwater fishes, 47 species represented 17% are critically endangered, 15 (5%) are endangered , 8(3%), are vulnerable while 23(8%) are near threatened. The paper suggests increased basic knowledge of threatened species and conservation policy along three lines public awareness, legislation and creation of national parks, aquaria and reserves as measures needed to ensure the conservation of the fishes

On the Role of Delays in Biological Systems : Analysis and Design

This work quantifies the nature of delays in genetic regulatory networks and their effect on system dynamics. It is known that a time lag can emerge from a sequence of biochemical reactions. Applying this modeling framework to the protein production processes, delay distributions are derived in a stochastic (probability density function) and deterministic setting (impulse function), whilst being shown to be equivalent under different assumptions. The dependence of the distribution properties on rate constants, gene length, and time-varying temperatures is investigated. Overall, the distribution of the delay in the context of protein production processes is shown to be highly dependent on the size of the genes and mRNA strands as well as the reaction rates. Results suggest longer genes have delay distributions with a smaller relative variance, and hence, less uncertainty in the completion times, however, they lead to larger delays. On the other hand large uncertainties may actually play a positive role, as broader distributions can lead to larger stability regions when this formalization of the protein production delays is incorporated into a feedback system.

Furthermore, evidence suggests that delays may play a role as an explicit design into existing controlling mechanisms. Accordingly, the reccurring dual-feedback motif is also investigated with delays incorporated into the feedback channels. The dual-delayed feedback is shown to have stabilizing effects through a control theoretic approach. Lastly, a distributed delay based controller design method is proposed as a potential design tool. In a preliminary study, the dual-delayed feedback system re-emerges as an effective controller design.

Effects of density differences on lateral mixing in open-channel flows

This study investigates lateral mixing of tracer fluids in turbulent open-channel flows when the tracer and ambient fluids have different densities. Longitudinal dispersion in flows with longitudinal density gradients is investigated also.

Lateral mixing was studied in a laboratory flume by introducing fluid tracers at the ambient flow velocity continuously and uniformly across a fraction of the flume width and over the entire depth of the ambient flow. Fluid samples were taken to obtain concentration distributions in cross-sections at various distances, x, downstream from the tracer source. The data were used to calculate variances of the lateral distributions of the depth-averaged concentration. When there was a difference in density between the tracer and the ambient fluids, lateral mixing close to the source was enhanced by density-induced secondary flows; however, far downstream where the density gradients were small, lateral mixing rates were independent of the initial density difference. A dimensional analysis of the problem and the data show that the normalized variance is a function of only three dimensionless numbers, which represent: (1) the x-coordinate, (2) the source width, and (3) the buoyancy flux from the source.

A simplified set of equations of motion for a fluid with a horizontal density gradient was integrated to give an expression for the density-induced velocity distribution. The dispersion coefficient due to this velocity distribution was also obtained. Using this dispersion coefficient in an analysis for predicting lateral mixing rates in the experiments of this investigation gave only qualitative agreement with the data. However, predicted longitudinal salinity distributions in an idealized laboratory estuary agree well with published data.

Phase interpretation for polarization-dependent near-field images of high-density gratings

It has been described that the near-field images of a high-density grating at the half self-imaging distance could be different for TE and TM polarization states. We propose that the phases of the diffraction orders play an important role in such polarization dependence. The view is verified through the coincidence of the numerical result of finite-difference time-domain method and the reconstructed results from the rigorous coupled-wave analysis. Field distributions of TE and TM polarizations are given numerically for a grating with period d = 2.3 lambda, which are verified through experiments with the scanning near-field optical microscopy technique. The concept of phase interpretation not only explains the polarization dependence at the half self-imaging distance of gratings with a physical view, but also, it could be widely used to describe the near-field diffraction of a variety of periodic diffractive optical elements whose feature size comparable to the wavelength. (C) 2008 Elsevier B.V. All rights reserved.

Talbot effect of a high-density grating under femtosecond laser illumination

The Talbot effect of a high-density grating under femtosecond laser illumination is analyzed with rigorous electromagnetic theory which is based on the Fourier decomposition and the rigorous coupled-wave analysis (RCWA). Numerical simulations show that the contrast of the Talbot images steadily decreases as the transmitted femtosecond laser pulses propagate forward and with wider spectrum width of the femtosecond laser pulses. The Talbot images of high-density gratings have much higher sensitivity of the spectrum widths of the incident laser pulses than those of the traditional low-density gratings. In experiments, the spectrums and the pulse widths of the incident pulses are measured with a frequency-resolved optical grating (FROG) apparatus. The Talbot images are detected by using a Talbot scanning near-field optical microscopy (Talbot-SNOM) technique, which are in coincidence with the numerical simulations. This effect should be useful for developing new femtosecond laser techniques and devices. (C) 2008 Elsevier B.V. All rights reserved.

Trapping success and population analysis of Siren lacertina and Amphiuma means

Siren and Amphiuma are two poorly known genera of aquatic salamanders that occur in the Southeastern United States. A primarily bottom-dwelling existence makes these salamanders difficult to detect with conventional sampling methodologies. Therefore, the current status of their populations is unknown. I compared the capture success of modified crayfish traps and plastic minnow traps in capturing these salamanders. In addition, a mark-recapture study of S. lacertina (Greater siren) and A. means (Two-toed amphiuma) was conducted at Okefenokee National Wildlife Refuge (southern Georgia) and at Katharine Ordway Preserve (north-central Florida) from August 2001 until September 2002. Crayfish traps were much more successful than minnow traps in catching siren and amphiuma. Crayfish traps yielded 270 captures for an overall capture success of 16%, whereas minnow traps yielded only 13 captures for an overall success rate of 0.05%. In addition, several marking techniques were evaluated, and of these, only passive integrated transponder (PIT) tags were retained for the duration of the study. Therefore, I recommend this marking technique for long-term monitoring of S. lacertina and A. means. Several variables were found to have significant effects on capture rates of salamanders. A. means were most often captured in summer and the number of captures was positively correlated with water temperature, water level, and rainfall. S. lacertina were most often captured during winter and spring. Number of captures was negatively correlated with water temperature, while no relationship was found with water level or rainfall. Trap day and baiting had no significant effect on number of A. means or S. lacertina captured. Recapture probabilities of both species were low, 0.025-0.03 for S. lacertina and 0.08-0.11 for A. means. Monthly survival rates were high, 0.77-0.97 for A. means and 0.88-1.00 for S. lacertina. Density estimates of 1.3 salamanders/m2 (S. lacertina) and 0.28 salamanders/m2 (A. means) were obtained for Lake Suggs using Jolly-Seber models. Siren and amphiuma make up a substantial part of wetland biomass and can impact many other wetland species. Thus, more attention must be focused on evaluating and monitoring their populations.

Osteometric analysis of the scapula and humerus of Rangifer tarandus and Cervus elaphus : A contribution to the discrimination of Late Pleistocene cervids

Fossil remains of reindeer (Rangifer tarandus) occurring outside their present range are an important indicator of formerly cold climatic conditions, but are easily confused with those of the red deer (Cervus elaphus). The locality of Kiputz IX has yielded one of the best-preserved Late Pleistocene reindeer populations of the southern Pyrenees, occurring in association with Bison priscus and the much more abundant Cervus elaphus. Fossil remains from this site are mostly complete and not affected by human intervention, thus creating the perfect conditions for reliable osteometric analyses. Here, we quantify diagnostic morphological features of the scapula and the humerus of Cervus elaphus and Rangifer tarandus to establish the potential of these bones to aid in interspecific discrimination. In the case of the scapula, the best species discriminator is the ratio of the minimum anteroposterior diameter of the scapular neck and the development of the articular process, while the breadth of the trochlea is the best discriminator in the case of the humerus.

Rare earth doped beta-diketone complexes as promising high-density optical recording materials for blue optoelectronics

Some kinds of rare earth beta-diketone complexes with blue-violet light absorption edge were synthesized using the ligands of thenoyltrifluoroacctone (HTTA), 2, 2'-dipyridyl (BIPY) and different metal ions (Gd3+, Sm3+ and La3+). Their contents, structures and optoelectronic parameters were monitored by elemental analysis, MS, IR and UV spectra. The solubility of rare earth beta-diketone complexes in 2, 2, 3, 3-tetrafluoro-1-propanol (TFP) and absorption properties of their films in the region 300-800 nm were measured. The influence on the difference of absorption maximum from rare earth beta-diketone complexes to beta-diketone ligand by different metal ions was studied. In addition, the thermal stability of rare earth beta-diketone complexes was also reported. (C) 2005 Elsevier B.V. All rights reserved.

High-density holographic recording parameters under different wavelength of a two dyes-sensitized photopolymer

The high-density holographic recording parameters of a novel two dyes-sensitized photopolymer under different exposure wavelengths are studied. The results show that the maximum diffraction efficiency, exposure sensitivity, maximum refraction index modulation, dynamic range, and the exposure time constant increases with the increase of the exposure wavelength. The analysis indicates that the scattering has an important role in the forming of the holographic grating. (c) 2005 Elsevier GmbH. All rights reserved.