The demography of ovenbirds (<i>Seiurus aurocapillus</i>) was compared in landscapes highly fragmented by agriculture, moderately fragmented by commercial harvesting, and in contiguous boreal forest of Saskatchewan. Various survey techniques demonstrated that ovenbirds were less common in small, isolated forest patches in fragmented landscapes relative to contiguous forest. Male ovenbirds in fragmented landscapes (84 to 87% paired) had a lower probability of attracting females relative to males in contiguous forest (97%). Competition for territories was intense, as removal experiments demonstrated the presence of non-territorial male floaters. However, floaters were more common in contiguous forest, indicating this habitat was most preferred. Nesting success was lower in small farm fragments (29%) than the other landscapes (43 to 58%), due to high nest predation. Apparent annual survival of males was lower in small farm fragments (30%) relative to the other landscapes (57 to 60%). The difference in adult survival among landscapes was not caused by increased mortality in small farm fragments, but likely occurred because failed breeders (20% annual return rate) dispersed more than successful breeders (50%). Overall, small farm fragments were population sinks, where the number of adult birds lost to mortality and emigration exceeded the number of young produced. However, population size was constant over the length of the study indicating that populations in small farm fragments were rescued from extinction by immigration of birds from contiguous forest, where excess juveniles were produced. Populations in farm fragments were more likely to be rescued from local extinction by first time breeders (95% first time breeders) than the other landscapes (65 to 75%). <p>Increased turnover in small farm fragments, also resulted in a greater proportion of first time breeders (60%) in small farm fragments than the other landscapes (44 to 46%). These results support the idea that forest songbirds select habitat in a ideal preemptive manner. Younger individuals seem to be forced to settle in low-quality farm fragments, due to competition from older birds in the more optimal contiguous forest. Forest fragmentation bad a negative impact on ovenbirds and likely is an important factor influencing the decline of this and other Neotropical migrant species.

The avian influenza virus can be transmitted from sick birds to other birds by fecal and oral secretion. Therefore, when birds with avian influenza virus enter domestic bird farms and make contacts, it is possible to carry the virus in and transmit it to domestic birds. Since the outbreak of the avian influenza in Taiwan, most bird farms had set up the screen. Yet, the actual effectiveness of screen coverage rate has not been researched. This study will discuss further regarding the results of different screen coverage rate in preventing wild birds¡¦ entering to poultry farms in Kaohsiung area. Field observations were carried out at the wetlands in Kaohsiung county, including Old Railroad Bridge artificial wetland, Fongshan reservoir and 20 poultry farms which were less than five kilometers away from wetlands from September 2008 to October 2009. Chicken and duck farms were analyzed respectively, and the screen coverage rate was categorized into full, partial and no coverage, respectively. The aims of the study were to investigate the effect of screen coverage on the entrance of wild birds to the farms, and found out the potential bridge species near poultry farms. By observing different levels of screen coverage in poultry farms, migratory birds¡¦ activity, and the contact situation between wild and domestic birds, we can analyze the contact level of high risk species and speculate possible transmission path of the avian influenza, and understand the effectiveness of the screens. Also, showing the correlation between the density of domestic poultry and the number of wild bird enterance. The result showed, in terms of screen with different coverage rates, the number of bird species within the duck farms had significant different in full and no coverage. The number of total birds within the duck and chicken farms with full coverage was significant less than partial coverage. Both in chicken and farms, screen had a great effectively in preventing small sized birds entering, yet not on big sized birds. The density of domestic poultry and the number of wild bird enterance showed negative correlation only in chicken farms with partial coverage. In terms of the wild land birds entering poultry farms, Passeer montanus is the largest species, followed by Hirundo rustica and Streptopelia tranquebarica. As for aquatic birds, it is mainly of Ardeidae, Scolopacidae, Charadriidae and Rallidae. Among all, Passeer montanus, Hirundo rustica, Streptopelia tranquebarica, and Bubulcus ibis are not migratory birds and highly pathogenic avian influenza virus species which move between poultry farms and wetlands. Therefore, they were considered bridge species. Due to the bridge species makes direct contacts with poultry, it might be the spreader of the virus. Decreasing the possibility of wild birds¡¦ contact with poultry is an important mechanism for avian influenza control. Also, based on the model of European Food Safety Authority (ESFA), risk assessments will be conducted on Kaohsiung County wetland¡¦s migratory birds¡¦ highly pathogenic avian influenza virus H5N1 transmission to poultry farms.

We collected 6,823 cloacal swabs over four years (2005–2006: 1,460; 2006– 2007: 2,171; 2007–2008: 2,424; and 2008–2009: 768) from 30 potential avian host species. Most samples (88.3 percent) were from dabbling ducks (genus Anas), while diving ducks (genus Aythya) accounted for 5.0 percent, and geese (genera Anser, Chen, and Branta) 3.0 percent of the samples tested. Waterfowl (Anatidae) comprised 98.7 percent of samples, with 1.8 percent from non-migratory dabbling ducks (genus Anas). All samples were screened for avian influenza virus (AIV) by AIV-matrix real-time RT-PCR (rRT-PCR); all rRT-PCR positive samples (541) were processed for virus isolation as well as 4,473 rRT-PCR negative samples. Differences were observed in apparent prevalence estimates over the four years between virus isolation (0.5, 1.3, 3.9, and 0.7 percent) and rRT-PCR (5.9, 6.5, 11.2, and 5.5 percent). We isolated 138 AIVs, of which two were obtained from rRT-PCR negative samples. Unlike previous reports of seasonal variation in AIV prevalence, we documented differences in prevalence estimates among months using rRT-PCR only during 2008–2009 and by virus isolation only during 2006–2007 and 2007–2008. Several of the AIV subtypes we identified are common in North America (e.g., H3, H4, and H6); H3N8 and H4N6 were the most common subtype combinations isolated. Similar to most surveillance studies, we found no significant difference in AIV infection based on host sex, but did find that juveniles were more likely to be positive for AIV than adults. We also documented that dabbling ducks were more likely to be positive for AIV than diving ducks, although not all dabbling ducks are equally likely to be positive. Molecular sequence analysis revealed no insertions of multiple basic amino acids at the cleavage site, which supported the identification of low pathogenic AIV. Phylogenetic anlyses performed on H5, H6, H7, N1, N2, N3, and N4 subtypes sequenced indicated similarity to other North American isolates with the exception of seven H6 which were more similar in amino acid translation to an isolate from Japan. In sum, this is the first multiyear study of avian influenza viruses on waterfowl wintering grounds of the Central Flyway, a historically understudied area of North America.

Avian Influenza (AI) has made hundreds of people dead in Europe. The hospital system of Taiwan, standing in the first line of prevention and treatment, has to effectively employ the experience of SARS in order to tackle the new serious challenge of AI. Though Taiwan is not yet an epidemic area of AI, it is important for us to be well prepared to confront it. Given that prevention is more important than treatment. It is essential that we try our best to build up an efficiently preventive system for AI. This study aims to investigate what is most important and critical in the preventive system. More specifically, what is a priority to do in such a preventive system, especially in a limited condition of budgets and human resources? According to the five stages of crisis management proposed by Mitroff (1988) (see page 35), the current study focuses mainly on operations in the second stage, preparation and prevention of crisis. In terms of analytic hierarchy process (AHP), it designs a questionnaire to systematically interview 12 doctors. Since four of them are outliers when the consistency test is considered, results are based primarily on the opinions of the remaining 8 doctors. The results are summarized as follows. 1. Before the crisis comes, both ¡§the training of doctors and nurses¡¨ (weighted value = 0.3195) and ¡§the regularization of preventive process¡¨ (weighted value = 0.2978) are most important. 2. The regularization of preventive process (weighted value = 0.3066) is most economic in the limited condition of budgets that is available to the preventive operations. Accordingly, it is a best way to regularize the individual operations and spread the concept of the regularization. 3. The training of doctors and nurses (weighted value = 0.3513) is most important in the limited condition of human resources, that recently appears gradual reduction among hospitals. That is, by means of rehearsal of related operations and of training courses, the crew in a hospital can have an understanding of AI spreading in a short period of time. 4. In consideration of hard equipments, the doctors to be questioned hold similar opinions, as mentioned above. Apparently, the mastery of various preventive operations in the preventive system plays a critical role in that whether the AI crisis will continue to develop. 5. Only in consideration of the effects of prevention, the training of doctors and nurses is also most important. In conclusion, the experts all think that the training of doctors and nurses is a priority, regardless of in what conditions. The findings of the study hope to provide references for other hospitals by manifesting the order of the importance of different preventive operations in the preventive system.

In the first phase of this study, the diversity of methanogenic bacteria in avian ceca was found to be minimal. Based on 16S rDNA clone libraries, a common phylotype, designated CH101, ranged between 92.86 to 100 % of the total clones whereas less than 1% of the other phylotypes were found. On the basis of the sequence identity, all of the sequences, except sequence CH1270, are related from 98.97 to 99.45% to 16S rDNA Methanobrevibacter woesei GS. Sequence CH1270 is 97.62% homologous to the sequence identified to uncultured archaeon clone ConP1-11F. Clearly, the predominant methanogen found to reside in the chicken ceca was M. woesei. By using a MPN enumeration method, methanogen counts were found to be in the range of 6.38 to 8.23 log10 organisms per gram wet weight. The 16S rDNA copy number per gram wet weight in the samples was between log10 5.50 and 7.19. The second phase of the study was conducted to observe the effects of selected nitrocompounds and two different feedstuffs on in vitro methane production in chicken cecal contents and rumen fluid. Initially, one of the three nitrocompounds was added to incubations containing cecal contents from laying hens supplemented with either alfalfa or layer feed. Both feed materials influenced volatile fatty acids (VFA) production and also fostered methane production in the incubations although methane was lower (P < 0.05) in incubations with added nitrocompound, particularly nitroethane. Secondly, nitroethane was examined in incubations of bovine or ovine rumen fluid or cecal contents containing either alfalfa or layer feed. Unlike cecal contents, layer feed significantly (P < 0.05) supported in vitro methane production in incubations of both rumen fluids. The results show that nitroethane impedes methane production, especially in incubations of chicken cecal contents. The final phase of this study was carried out to determine the methanogenic establishment in the chicken ceca by the cultural method with the quantitative PCR. The results suggested that methanogens colonized in chicken ceca at a few days after birth. Litter and house flies could be potential sources for methanogenic colonization in broiler chicks.

Surface mining often changes the native landscape and vegetation of an area. Reclamation is used to counter this change, with the goal of restoring the land to its original pre-mined state. The process of reclamation creates early successional-stage lands, such as grasslands, shrublands, and wetlands, attracting new plant and animal species to the area. I compared avian species density (number of individuals/ha), diversity (H'), and richness (number of species/ha) on reclaimed and non-mined lands at TXU's Big Brown Mine in Fairfield, Texas. I also compared my results to those of a previous study conducted 25 years earlier. Avian counts were conducted using a fixedradius point-count method on 240 points placed in four different vegetation types and in four land-age groups (time since being reclaimed). Vegetation was measured both locally, and at a landscape level. Overall bird species density did not exhibit a clear relationship on non-mined versus reclaimed land. Overall bird species diversity was greater on non-mined lands, whereas overall species richness was greater on reclaimed lands. My results demonstrated a lower mean/point bird density and higher mean/point bird diversity than were found 25 years earlier. Different nesting guilds occurred on the reclaimed lands than occurred on the non-mined lands. Results suggested different species were attracted to the several successional stages of reclaimed lands over the nonmined lands, which consisted of climax vegetation. The different successional stages of reclaimed lands increased overall diversity and richness of the landscape as a whole. Five bird species of conservation concern were observed in the study, all of which occurred on reclaimed land. Four of the five species primarily occurred on reclaimed lands. Future land management should include conserving different successional-stage lands to increase overall biotic diversity and richness of mined land, preserving reclaimed habitat for species of concern, and educating future private landowners on the importance of maintaining vegetative and bird species diversity.

published_or_final_version / Microbiology / Doctoral / Doctor of Philosophy

Continually reported human cases of highly pathogenic avian influenza (HPAI) H5N1 virus infection create heightened threat to public health, due to the disease severity and high lethality. Acute respiratory syndrome (ARDS) has been found to be the most severe form of acute lung injury caused by H5N1 virus infection. Studies have highlighted that the unusually high virulence of H5N1 virus infection is associated with the cytokine dysregulation and enhanced viral replication in the host. In reference to the past experience during Spanish 1918 influenza pandemic and SARS, it is crucial that a novel therapeutic target is explored and employed in time for the effective control of emerging diseases. The pandemic potential of H5N1 influenza virus urges well preparedness not only in terms of containment measures, but also in the treatment aspect of the severe human H5N1 disease. To date, therapeutic approaches are limited to the use of vaccine, antiviral drugs and corticosteroids. It has been suggested that commercially available antiviral drugs are prone to induce resistance mutations; and are effective in the protection against influenza virus infection only if administered during the early course of disease development. Moreover, vaccine development does not grant a promising therapeutic strategy at the time of a pandemic as it takes time for the development and distribution of safe and reliable vaccine. In attempts to search for a novel adjunctive therapy in addition to currently available agents, indirubin-3’-oxime (IDO) and indirubin derivative, E804 have been tested to show the effect in cytokine suppression and antiviral activity against H5N1 influenza virus infection in vitro. These compounds have been extracted and purified from a natural herb called Isatis tinctoria which is frequently used for herbal remedy in treating respiratory symptoms in traditional Chinese medicine. In this study, it was demonstrated that IDO and E804 treatment in H5N1 influenza virus infected human alveolar epithelial cells effectively inhibit the proinflammatory cytokine induction and viral replication. This physiologically relevant in vitro alveolar epithelial cell model and the efficacy of IDO and E804 provide new insights to the development of new treatment option for severe human H5N1 disease. / published_or_final_version / Microbiology / Master / Master of Medical Sciences

The goal of this work was to characterize avian skeletal muscle (SKM) glucose and fatty acid uptake. English sparrows (Passer domesticus) were used for the following studies: 1. Characterization of glucose uptake, 2. Identification and localization of glucose transporters, 3. Characterization of free fatty acid uptake, and 4. Reciprocal inhibition of glucose and free fatty acids. The results are summarized as follows. Isolated SKM incubated for 60 minutes with insulin, IGF-1, caffeine or AICAR demonstrated no increase in glucose transport. Interestingly, uptake was decreased in the presence of incremental unlabeled glucose suggesting the presence of glucose transporters (GLUT) and by phloretin, an inhibitor of transport proteins, decreased transport. The SKM glycogen content was low, which is supportive of the observed minimal glucose uptake. These findings suggest that GLUT expression may differ in birds as compared to mammals. GLUT1 and GLUT3 gene expression, but not GLUT4, were found in all tissues examined and share a high degree of homology with published chicken sequences. In addition, GLUT3 and GLUT4 proteins were not detected, whereas GLUT1 protein was abundant in blood-tissue barriers. Sparrows have high plasma ketone body levels suggestive of a high rate of free fatty acid (FFA) oxidation. In vitro uptake of radiolabeled oleic acid (OA) was maximal at 60 minutes and competitively inhibited by unlabeled OA suggesting a facilitative process. Radiolabeled OA uptake was not increased by IGF-1, caffeine and AICAR, whereas insulin increased uptake at 60 minutes. Inhibitors of protein-mediated substrate transport increased OA uptake by 60 minutes (DIDS and phloretin) whereas a specific inhibitor of long chain FFA transport, sulfo-N-succinimidyl oleate, decreased its uptake at 2.5 min. In reciprocal inhibition studies, 20mM unlabeled glucose and OA inhibited the uptake of their radiolabeled counterparts. Glucose (20mM) significantly decreased labeled OA uptake 36% and 20mM OA significantly decreased labeled glucose transport by 49%. These data begin to elucidate why avian skeletal muscle may not take up glucose to an appreciable extent and further, why avian skeletal muscle is insulin resistant.

Differences in the expression of antimicrobial peptides in vivo have been proposed as underlying factors influencing susceptibility to infection. In this context, the role of avian b-defensins in inhibiting avian influenza infections is a study object in an ongoing collaboration with the Zoonotic Ecology and Epidemiology group at Lnu. In this report, an attempt to synthesize two variants of the peptide Anas Platyrhynchos AvBD-8, using Fmoc-based SPPS, is described. The length of AvBD-8 (43 aa) necessitated peptide synthesis in two segments to subsequently be ligated using native chemical ligation. The first component of a 19 aa segment was thus a Dbz-linker, which would allow to ligate this end with a second segment (24 aa). Halfway through the synthesis of this larger segment the batch was split into two pots, allowing the synthesis of two segments differing by one single amino acid (R for W). The composition of these segments were: Dbz-HDTSCTGGAQKCQVANNPA (Dbz-segment), SVVTRCCPIGQKCWGFARTNPPPC(boc) (W-segment), and  SVVTRCCPIGQKCRGFARTNPPPC(boc) (R-segment). Crude product yields were 284,5 mg; 67,6% (Dbz-segment), 137,6 mg; 52,3% (W-segment), and 166,3 mg; 64,2%. Preliminary mass spectrometric analysis on the crude products did not indicate the presence of the desired segments in major mass peaks. Further product purification is necessary in order to allow definite conclusions, but it appears as if the synthesis has not worked. Possible explanations are either impure or degraded reactant(-s), folding or shielding effects of the growing peptide chain at some point inhibiting synthesis, or experimental errors during one or more of the many steps involved in the synthesis.