Maximum likelihood estimation of natural mortality and quantification of temperature effects on catchability of brown tiger prawn (Penaeus esculentus) in Moreton Bay (Australia) using logbook data

It is common to model the dynamics of fisheries using natural and fishing mortality rates estimated independently using two separate analyses. Fishing mortality is routinely estimated from widely available logbook data, whereas natural mortality estimations have often required more specific, less frequently available, data. However, in the case of the fishery for brown tiger prawn (Penaeus esculentus) in Moreton Bay, both fishing and natural mortality rates have been estimated from logbook data. The present work extended the fishing mortality model to incorporate an eco-physiological response of tiger prawn to temperature, and allowed recruitment timing to vary from year to year. These ecological characteristics of the dynamics of this fishery were ignored in the separate model that estimated natural mortality. Therefore, we propose to estimate both natural and fishing mortality rates within a single model using a consistent set of hypotheses. This approach was applied to Moreton Bay brown tiger prawn data collected between 1990 and 2010. Natural mortality was estimated by maximum likelihood to be equal to 0.032 ± 0.002 week−1, approximately 30% lower than the fixed value used in previous models of this fishery (0.045 week−1).

Habitat use and population dynamics of brown bears (Ursus arctos) in Scandinavia

Large carnivore populations are currently recovering from past extirpation efforts and expanding back into their original habitats. At the same time human activities have resulted in very few wilderness areas left with suitable habitats and size large enough to maintain populations of large carnivores without human contact. Consequently the long-term future of large carnivores depends on their successful integration into landscapes where humans live. Thus, understanding their behaviour and interaction with surrounding habitats is of utmost importance in the development of management strategies for large carnivores. This applies also to brown bears (Ursus arctos) that were almost exterminated from Scandinavia and Finland at the turn of the century, but are now expanding their range with the current population estimates being approximately 2600 bears in Scandinavia and 840 in Finland. This thesis focuses on the large-scale habitat use and population dynamics of brown bears in Scandinavia with the objective to develop modelling approaches that support the management of bear populations. Habitat analysis shows that bear home ranges occur mainly in forested areas with a low level of human influence relative to surrounding areas. Habitat modelling based on these findings allows identification and quantification of the potentially suitable areas for bears in Scandinavia. Additionally, this thesis presents novel improvements to home range estimation that enable realistic estimates of the effective area required for the bears to establish a home range. This is achieved through fitting to the radio-tracking data to establish the amount of temporal autocorrelation and the proportion of time spent in different habitat types. Together these form a basis for the landscape-level management of the expanding population. Successful management of bears requires also assessment of the consequences of harvest on the population viability. An individual-based simulation model, accounting for the sexually selected infanticide, was used to investigate the possibility of increasing the harvest using different hunting strategies, such as trophy harvest of males. The results indicated that the population can sustain twice the current harvest rate. However, harvest should be changed gradually while carefully monitoring the population growth as some effects of increased harvest may manifest themselves only after a time-delay. The results and methodological improvements in this thesis can be applied to the Finnish bear population and to other large carnivores. They provide grounds for the further development of spatially-realistic management-oriented models of brow bear dynamics that can make projections of the future distribution of bears while accounting for the development of human activities.

Brown adipose tissue mitochondria are cytochrome c — subsaturated

The oxidative activity of mitochondria freshly isolated from brown adipose tissue of rats was stimulated two-fold on the addition of small concentrations of exogenous cytochrome c to the reaction medium. Loss of membrane-bound cytochrome c did not occur during isolation of mitochondria. Estimation of the high-affinity binding sites on the organelle membrane indicated that less than a third of these sites remained saturated with cytochrome c. The pigment is thus shown to be a functionally limiting electron transport component in brown adipose tissue.

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

Regulation of respiratory activity of brown adipose tissue mitochondria through changes in cytochromes.

Exposure of cold-acclimatized rats to heat (37 degrees C) for a short period decreased brown adipose tissue (BAT) mitochondrial substrate-dependent oxygen uptake and H2O2 generation. Both the concentration and substrate-dependent rate of cytochrome b reduction decreased as early as 3 h of heat exposure. These results identify cytochrome b as the locus of regulation of electron transport in BAT mitochondria under conditions of heat stress.

Microsomal redox systems in brown adipose tissue: high lipid peroxidation, low cholesterol biosynthesis and no detectable cytochrome P-450

The presence of redox systems in microsomes of brown adipose tissue (BAT) in cold exposed rats was investigated and compared with liver. BAT microsomes showed high activity of lipid peroxidation measured both by the formation of malondialdehyde (MDA) and by oxygen uptake. NADH and NADPH dependent cytochrome c reductase activity were present in both BAT and liver microsomes. Aminopyrine demethylase and aniline hydroxylase activities, the characteristic detoxification enzymes in liver microsomes could not be detected in BAT microsomes. BAT minces showed very poor incorporation of [1-14C]acetate and [2-14C]-mevalonate in unsaponifiable lipid fraction compared to liver. Biosynthesis of cholesterol and ubiquinone, but not fatty acids, and the activity of 3-hydroxy-3-methyl glutaryl CoA reductase appear to be very low in BAT. Examination of difference spectra showed the presence of only cytochrome b 5 in BAT microsomes. In addition to the inability to detect the enzyme activities dependent on cytochrome P-450, a protein with the characteristic spectrum, molecular size in SDS-PAGE and interaction with antibodies in double diffusion test, also could not be detected in BAT microsomes. The high activity of lipid peroxidation in microsomes, being associated with large oxygen uptake and oxidation of NADPH, will also contribute to the energy dissipation as heat in BAT, considered important in thermogenesis.

Evaluación de pollitas Hy-Line variedad Brown, en etapa de inicio a rompimiento de postura, bajo manejo tradicional

Se evaluó el comportamiento productivo de pollitas Hy- Line var. Brown, durante las primeras diecisiete semanas de desarrollo con la guía de manejo comercial para estas aves. Se utilizó un lote de 4,591 aves distribuidas en dos galeras. Se muestreó el 4% de la población de forma aleatoria y sin reemplazo, registrando peso, alimento consumido y mortalidad. Se realizaron los cálculos de consumo, uniformidad de peso, mortalidad de lote y se registraron las prácticas sanitarias de la granja. El consumo total obtenido fue un 15.6% inferior al reportado por la guía de manejo (803 g), viéndose afectado por cambios en el manejo del alimento, el que fue suministrado de acuerdo al peso vivo y no a la edad de las aves. El peso de las aves resultó 9.3% inferior al estipulado por la guía de manejo. La uniformidad del lote fue del 80% con una variación de ±10% igual al esperado para este tipo de aves. La mortalidad de la granja fue inferior al 0.04% expresado por la guía de manejo comercial. La aplicación del plan sanitario sufrió alteración en el tiempo de ejecución, sin embargo no tuvo efecto sobre la mortalidad de la granja. El manejo zootécnico de la granja está dentro de lo esperado en granjas de pequeños productores avícolas en condiciones tropicales.

Development of kelp rockfish, Sebastes atrovirens (Jordan and Gilbert 1880), and brown rockfish, S. auriculatus (Girard 1854), from birth to pelagic juvenile stage, with notes on early larval development of black-and-yellow rockfish, S. chrysomelas (Jordan and Gilbert 1880), reared in the laboratory (Pisces: Sebastidae).

Larval kelp (Sebastes atrovirens), brown (S. auriculatus), and blackand-yellow (S. chrysomelas) rockfish were reared from known adults, to preflexion stage, nine days after birth for S. chrysomelas, to late postflexion stage for S. atrovirens, and to pelagic juvenile stage for S. auriculatus. Larval S. atrovirens and S. chrysomelas were about 4.6 mm body length (BL) and S. auriculatus about 5.2 mm BL at birth. Both S. atrovirens and S. auriculatus underwent notochord flexion at about 6–9 mm BL. Sebastes atrovirens transform to the pelagic juvenile stage at about 14–16 mm BL and S. auriculatus transformed at ca. 25 mm BL. Early larvae of all three species were characterized by melanistic pigment dorsally on the head, on the gut, on most of the ventral margin of the tail, and in a long series on the dorsal margin of the tail. Larval S. atrovirens and S. auriculatus developed a posterior bar on the tail during the flexion or postflexion stage. In S. atrovirens xanthic pigment resembled the melanistic pattern throughout larval development. Larval S. auriculatus lacked xanthophores except on the head until late preflexion stage, when a pattern much like the melanophore pattern gradually developed. Larval S. chrysomelas had extensive xanthic pigmentation dorsally, but none ventrally, in preflexion stage. All members of the Sebastes subgenus Pteropodus (S. atrovirens, S. auriculatus, S. carnatus, S. caurinus, S. chrysomelas, S. dalli, S. maliger, S. nebulosus, S. rastrelliger) are morphologically similar and all share the basic melanistic pigment pattern described here. Although the three species reared in this study can be distinguished on the basis of xanthic pigmentation, it seems unlikely that it will be possible to reliably identify field-collected larvae to species using traditional morphological and melanistic pigmentation characters. (PDF file contains 36 pages.)

Survival, growth, and yield of brown trout stocked as fingerlings in Hot Creek, California

Four groups of fin clipped brown trout (Salmo trutta) fingerlings were planted in Hot Creek over a six year period. Survival and growth were estimated by fall and/or spring mark-and-recapture surveys. Yield to the angler for two of the tour groups stocked was estimated by stratified random creel surveys. Fingerling survival from the midsummer stocking period to fall averaged 51 %. Overwinter survival from young-of-the-year to yearling fish averaged 49%. Angler harvest of two groups of fingerlings stocked at densities of 16,082 fish/mile averaged 1,704 trout/mile (10.6%) and 194 lbs/acre. Abundant cover and microhabitat suitable tor young trout, ice-free winters, and rapid growth were factors viewed as contributing to high yields. Results do not suggest a change is needed in the general policy of not stocking brown trout fingerlings in California streams. Results do show that fingerlings stocked in Hot Creek, and presumably other productive streams with abundant cover, can effectively fill a void created by limited recruitment. (PDF contains 24 pages.)

A decade of studies at Loch Fleet, Galloway (Scotland): A catchment liming project and restoration of a brown trout fishery

Loch Fleet is a small upland lake in the hills of Galloway in southwest Scotland. In the 1970s the waters of the loch became more acidic and a brown trout fishery failed. This account summarises an experimental project, the "Loch Fleet Project" initiated in 1984, designed to reverse acidification of the loch by liming parts of the catchment. Liming about 40% of the catchment in 1986 and 1987 raised the pH and calcium levels, and reduced toxic aluminium concentrations. The improved conditions had been maintained up to 1994, but water in the loch, and its principal inflow stream, is now falling close to the desired threshold of quality. After liming, restocking with local strains of trout in 1987 was successful, and a self-recruiting population became established within 2 years. Recruitment is highly variable, however, and was attributed to severe spring conditions and the limited spawning capacity of the nursery stream, rather than to water quality.