Le corail rouge de Méditerranée (Corallium rubrum) fait l'objet d'un important commerce depuis des millénaires ; il est traditionnellement utilisé pour la confection de bijoux et d'objets d'art. L'étude de son squelette permet de mieux comprendre les procédés utilisés par la nature pour fabriquer des matériaux résistants avec un coût énergétique minimal (conditions de chimie douce). D'autre part, la caractérisation des taux de croissance vertical et radial est toute aussi importante pour établir des critères à des fins de conservation de l'espèce. Dans ce travail, C. rubrum a été comparé à d'autres espèces de coraux précieux de la même famille (C. elatius et Paracorallium japonicum). Ces espèces présentent deux modes de croissance distincts: (1) un mode 'bloc par bloc' à l'apex de la branche, associé à une croissance axiale rapide (~2 mm/an) et (2) un mode 'couche par couche' se produisant en dessous de l'apex, associé à une croissance radiale lente (~0,2 mm/an). Les structures physiques et chimiques des squelettes des coraux précieux aident à mieux comprendre les mécanismes complexes de la croissance cristalline bio-assistée. / The Mediterranean red coral (Corallium rubrum) has been harvested and traded for centuries; it is highly valued in jewelry. Studies of the skeletal structures are important to better understand how nature proceeds to synthetize resistant material at low-energy cost by soft chemistry. On the other hand, the determination of vertical and axial growth rates is important to establish criterions for the sustainable management of these precious species. In this work, the skeleton of C. rubrum has been compared to skeleton of other species belonging of the same family (C. elatius and P. japonicum). All species show two distinct growth modes: (1) a block-by-block mode at the branch apex associated with a fast axial growth rate (~2 mm/year) and (2) a layer-by-layer mode associated with a slow radial growth rate (~0,2 mm/year). The physical and chemical patterns of the skeleton of precious corals provide important constraints to better understand the complex mechanisms of in bio-assisted crystalline growth.

Master of Science / Department of Agronomy / Kraig Roozeboom / Nitrogen fixation by Bradyrhizobium japonicum in soybean [Glycine max] is highly beneficial in soybean crop production. Nodulation issues have been encountered on fields new to growing soybeans in recent years in Kansas. The purpose of this research was to evaluate soybean nodulation performance under various situations and seed handling practices in order to educate producers on how to achieve reliable nodulation consistency in the field. The objectives of the study were to: 1) compare inoculant products using single and double rates and in combination with one another on fields with varying soybean history; 2) determine if there was a negative interaction between inoculant products and common seed treatments; and 3) discover the influence of inoculated seed storage conditions before planting on the rhizobia’s ability to successfully nodulate soybean roots. Field experiments were conducted on diverse Kansas sites in 2011 and 2012. Inoculant treatment and seed treatment interaction trials had ten and seven experimental sites respectively. Inoculated seed storage conditions were evaluated in a greenhouse experiment during the spring of 2013. All studies used a randomized complete block design with four replications. The Novozymes inoculant products generally provided superior nodulation performance over other company products in the study where soybean had not been in recent rotation with an average increase of 167% in nodule number verses the control. The combination of dry and liquid inoculant products provided a significant increase in root nodule number at five of the environments out of recent rotation with a 76% increase over single inoculant rates. Although there were early season nodulation differences between treatments in new soybean ground, these did not carry through to seed yield differences in the majority of research sites. Hot and dry summer conditions reduced yields, making detection of treatment differences difficult. There were no negative effects on nodulation performance with any of the seed treatments. Although soybean seed yield was 634 kg ha[superscript]-[superscript]1 greater for the Novozyme combination treatment compared to the check at one location in 2011, the control yielded as well or better than all other treatment/inoculant combinations, implying that yield differences were likely not related to inoculant treatments. At other sites, yield was not influenced by seed treatment and inoculant combinations. Results indicate that seed treatment formulations did not significantly impact bacterial inoculant product performance, soybean nodulation, or yield. Storage conditions had no effect on nodulation performance in the greenhouse study, likely due to survival of Bradyrhizobium japonicum in the heat-treated growth medium.

No description available.

Schistosomiasis, a disease of humans caused by helminth parasites of the genus Schistosoma, kills 200 to 500 thousand people annually, endangering over 600 million people world-wide with 200 million people infected in 2003 [1, 2]. Three species of schistosome are primarily responsible for human infections, namely, Schistosoma haematobium, endemic to Africa, India, and the Middle East, S. mansoni, endemic to Africa / South America, and S. japonicum endemic to China and the Philippines [3]. The major pathological effects of schistosomiasis result from the deposition of parasite ova in human tissues and the subsequent intense granulomatous response induced by these eggs. There is a high priority to provide an effective sub-unit vaccine against these schistosome flukes, using proteins encoded by cDNAs expressed by the parasites at critical phases of their development. One technique that may expedite this gene identification is the use of microarrays for expression analysis. A 22,575 feature custom oligonucleotide DNA microarray designed from public domain databases of schistosome ESTs (Expressed Sequence Tags) was used to explore differential gene expression between the Philippine (SJP) and Chinese (SJC) strains of S. japonicum, and between males and females. It was found that 593, 664 and 426 probes were differentially expressed between the two geographical strains when mix sexed adults, male worms and female worms were compared respectively. Additionally, the study revealed that 1,163 male- and 1,016 female-associated probes were differentially expressed in SJP whereas 1,047 male- and 897 female-associated probes were differentially expressed in SJC [4]. Further to this, a detailed real time PCR expression study was used to explore the differential expression of eight genes of interest throughout the SJC life cycle, which showed that several of the genes were down-regulated in different life cycle stages. The study has greatly expanded previously published data of strain and gender-associated differential expression in S. japonicum. Further, the new data will provide a stepping stone for understanding the complexities of the biology, sexual differentiation, maturation, and development of human schistosomes, signaling new approaches for identifying novel intervention and diagnostic targets against schistosomiasis [4].

No description available.

Apios priceana is a native endangered species plant found in the Southeast United States. It is characterized as a leguminous species that bears wisteria like clusters with pea like flowers, a large tuberous root and four to six inch long seed pods. It is believed the Native Americans and early European settlers relied on this species as a source of protein and utilized the seeds for cultivation of the tuberous “potato” which formed. Apios priceana contains an average of 13% fiber, 6.9% protein, 71% carbohydrate and 9 of the 11 essential amino acids needed in human diets (Walter et al.,1986). In addition, A. priceanatuberous roots contain anti-carcinogenic properties known to be used to treat prostate and breast cancer as well as lowering blood pressure and cholesterol with an added use for diabetes. If removed from the endangered species list it could prove to be a valuable agronomic crop. Its use spans human and animal consumption, bio fuel, medicinal and horticultural purposes. This research was initiated to investigate a biological symbiosis between A. priceana and known beneficial soil bacteria which may indicate growth potential of known colonies. Experimental treatments were 1) no inoculation 2) Azospirillum brasilense inoculate 3) Bradyrhizobium japonicum inoculate and 4) Rhizobium leguminosarum biovar viceae inoculate. Specimens were evaluated at 30, 60 and 90 day’s growth from emergence for taproot length, number of lateral roots and taproot girth. Due to non-germination of seeds, data presented is for treatments 2 and 3. The correlation coefficient for average taproot length, number of lateral roots developed and taproot girth per treatment was as follows: taproot length to number of lateral roots, positive correlation coefficient 0.996; taproot length to taproot girth, positive correlation coefficient 0.999; and number of lateral roots to taproot girth, positive correlation coefficient 0.991. All correlation coefficients are significant at the 0.01 level.

Most members of the Rhizobiaceae possess single copies of the poly-3-hydroxybutyrate biosynthesis genes, phbA, phbB and phbC. Analysis of the genome sequence of Bradyrhizobium japonicum reveals the presence of five homologues of the PHB synthase gene phbC as well as two homologues of the biosynthesis operon, phbAB. The presence of multiple, seemingly redundant homologues may suggest a functional importance. Each B. japonicum phbC gene was cloned and used to complement the pleiotropic phenotype of a Sinorhizobium meliloti phbC mutant; this mutant is unable to synthesize PHB, grow on certain PHB cycle intermediates and forms non-mucoid colonies on yeast mannitol medium. Two of the five putative B. japonicum phbC genes were found to complement the S. meliloti phbC mutant phenotype on D-3-hydroxybutyrate although none of them could fully complement the phenotype on acetoacetate. Both complementing genes were also able to restore PHB accumulation and formation of mucoid colonies on yeast mannitol agar to phbC mutants. In-frame deletions were constructed in three of the five phbC open reading frames in B. japonicum, as well as in both phbAB operons, by allelic replacement. One of the phbC mutants was unable to synthesize PHB under free-living conditions; one of the two phbAB operons was shown to be necessary and sufficient for PHB production under free-living conditions. These mutants also demonstrated an exopolysaccharide phenotype that was comparable to S meliloti PHB synthesis mutants. These strains were non-mucoid when grown under PHB-inducing conditions and, in contrast to wild-type B. japonicum, formed a compact pellet upon centrifugation. Interestingly, none of the mutants exhibited carbon-utilization phenotypes similar to those exhibited by S. meliloti PHB mutants. Wild-type B. japonicum accumulates PHB during symbiosis, and plants inoculated with the phbC mutants demonstrate a reproducible reduction in shoot dry mass. Analysis of bacteroid PHB accumulation in the mutant strains suggests that the phbAB operons of B. japonicum are differently regulated relative to growth under free-living conditions; mutants of the second phbAB operon demonstrated a significant reduction in PHB accumulation during symbiosis. These data suggest that the first phbAB operon is required for PHB synthesis only under free-living conditions, but is able to partially substitute for the second operon during symbiosis. Deletion of both phbAB operons completely abolished PHB synthesis in bacteroids. Analysis of the upstream regions of these genes suggest the existence of putative RpoN binding sites, perhaps indicating a potential mode of regulation and highlighting the metabolic complexity that is characteristic of the Rhizobiaceae. PHB metabolism in S. meliloti has been studied in considerable detail with two notable exceptions. No reports of the construction of either a β-ketothiolase (phbA) or a PHB depolymerase (phaZ ) mutant have ever been documented. The phaZ gene, encoding the first enzyme of the catabolic half of the PHB cycle in S. meliloti, was identified and a phaZ mutant strain was generated by insertion mutagenesis. The phaZ mutant demonstrates a Fix+ symbiotic phenotype and, unlike other PHB cycle mutants, does not demonstrate reduced rhizosphere competitiveness. Bacteroids of this strain were shown to accumulate PHB, demonstrating for the first time that S. meliloti is able to synthesize and accumulate PHB during symbiosis. Interestingly, there is no significant difference in shoot dry mass of plants inoculated with the phaZ mutant, suggesting that PHB accumulation does not occur at the expense of nitrogen fixation. The phaZ mutant strain was also used to demonstrate roles for PhaZ in the control of PHB accumulation and exopolysaccharide production. When grown on high-carbon media, this mutant demonstrates a mucoid phenotype characteristic of exopolysaccharide production. Subsequent analyses of a phoA::exoF fusion confirmed elevated transcription levels in the phaZ mutant background. In contrast, mutants of the PHB biosynthesis gene, phbC, have a characteristically dry phenotype and demonstrate reduced exoF transcriptional activity. The phaZ mutant also demonstrates a significant increase in PHB accumulation relative to the wild-type strain. Previous work on phasin mutants in S. meliloti demonstrated that they lack the ability to synthesize PHB. Transduction of the phaZ lesion into the phasin mutant background was used to construct a phaZ-phasin mutant strain. Analysis of the PHB biosynthesis capacity of this strain showed that the lack of PHB synthesis exhibited by S. meliloti phasin mutants is due to loss of PHB biosynthesis activity and not due to an inherent instability in the PHB granules themselves. A recent study suggested that some bacteria may possess an alternate pathway for acetate assimilation that would bypass the need for the glyoxylate cycle in organisms that do not possess the enzyme, isocitrate lyase. In these organisms, acetate is assimilated through the ethylmalonyl-CoA pathway, which has significant overlap with the anabolic half of the PHB cycle, including reliance on the PHB intermediate 3-hydroxybutyryl-CoA. The observation that phbB and phbC mutants of S. meliloti are unable to grow well on acetoacetate -- coupled with previously unexplained data that show a class of mutants (designated bhbA-D) are able to grow on acetate, but not on hydroxybutyrate or acetoacetate -- made it tempting to speculate that an ethylmalonyl-CoA-like pathway might be present in S. meliloti, and that this pathway might overlap with the PHB cycle at the point of 3-hydroxybutyryl-CoA. An in-frame mutation of phbA was constructed by cross-over PCR and allelic replacement. This mutant exhibited a complete abolition of growth on acetoacetate, suggesting that PhbA represents the only exit point for carbon from the PHB cycle and that an alternative ethylmalonyl-CoA-like pathway is not present in this organism. During symbiosis, rhizobial cells are dependent on the provision of carbon from the host plant in order to fuel cellular metabolism. This carbon is transported into the bacteroids via the dicarboxylate transport protein, DctA. Most rhizobia possess single copies of the transporter gene dctA and its corresponding two-component regulatory system dctBD. The completed genome sequence of B. japonicum suggests that it possesses seven copies of dctA. Complementation of Sinorhizobium meliloti dct mutants using the cosmid bank of B. japonicum USDA110 led to the identification a dctA locus and a dctBD operon. Interestingly, the B. japonicum dctABD system carried on the complementing cosmid was not able to complement the symbiotic deficiency of S. meliloti strains carrying individual mutations in either dctA, dctB, or dctD suggesting that the B. japonicum dctBD is unable to recognize either DctB/DctD or the DctB/DctD-independent regulatory elements in S. meliloti. All seven B. japonicum dctA ORFs were cloned and an analysis of their capacity to complement the free-living phenotype of a S. meliloti dctA mutant demonstrated that they all possess some capacity for dicarboxylate transport. Mutants of all seven B. japonicum dctA ORFs were constructed and an analysis of their free-living phenotypes suggested that significant functional redundancy exists in B. japonicum DctA function. Given the large number of potential dctA genes in the genome, coupled with an apparent lack of dctBD regulators, it is tempting to speculate that different DctA isoforms may be used during free-living and symbiotic growth and may be subject to different regulatory mechanisms than those of better-studied systems. A comprehensive analysis of desiccation tolerance and ion sensitivity in S. meliloti was conducted. The results of these analyses suggest that genetic elements on both pSymA and pSymB may play a significant role in enhancing cell survival under conditions of osmotic stress. The S. meliloti expR+ strains SmUW3 and SmUW6 were both shown to exhibit considerably higher desiccation tolerance than Rm1021, suggesting a role for enhanced exopolysaccharide production in facilitating survival under adverse conditions. Furthermore, scanning electron microscopy of inoculated seeds suggests that S. meliloti cells initiate biofilm formation upon application to the surface of seeds. This finding has implications for the analysis of OSS and the development of desiccation assays and may explain some of the variability that is characteristic of desiccation studies.

Most members of the Rhizobiaceae possess single copies of the poly-3-hydroxybutyrate biosynthesis genes, phbA, phbB and phbC. Analysis of the genome sequence of Bradyrhizobium japonicum reveals the presence of five homologues of the PHB synthase gene phbC as well as two homologues of the biosynthesis operon, phbAB. The presence of multiple, seemingly redundant homologues may suggest a functional importance. Each B. japonicum phbC gene was cloned and used to complement the pleiotropic phenotype of a Sinorhizobium meliloti phbC mutant; this mutant is unable to synthesize PHB, grow on certain PHB cycle intermediates and forms non-mucoid colonies on yeast mannitol medium. Two of the five putative B. japonicum phbC genes were found to complement the S. meliloti phbC mutant phenotype on D-3-hydroxybutyrate although none of them could fully complement the phenotype on acetoacetate. Both complementing genes were also able to restore PHB accumulation and formation of mucoid colonies on yeast mannitol agar to phbC mutants. In-frame deletions were constructed in three of the five phbC open reading frames in B. japonicum, as well as in both phbAB operons, by allelic replacement. One of the phbC mutants was unable to synthesize PHB under free-living conditions; one of the two phbAB operons was shown to be necessary and sufficient for PHB production under free-living conditions. These mutants also demonstrated an exopolysaccharide phenotype that was comparable to S meliloti PHB synthesis mutants. These strains were non-mucoid when grown under PHB-inducing conditions and, in contrast to wild-type B. japonicum, formed a compact pellet upon centrifugation. Interestingly, none of the mutants exhibited carbon-utilization phenotypes similar to those exhibited by S. meliloti PHB mutants. Wild-type B. japonicum accumulates PHB during symbiosis, and plants inoculated with the phbC mutants demonstrate a reproducible reduction in shoot dry mass. Analysis of bacteroid PHB accumulation in the mutant strains suggests that the phbAB operons of B. japonicum are differently regulated relative to growth under free-living conditions; mutants of the second phbAB operon demonstrated a significant reduction in PHB accumulation during symbiosis. These data suggest that the first phbAB operon is required for PHB synthesis only under free-living conditions, but is able to partially substitute for the second operon during symbiosis. Deletion of both phbAB operons completely abolished PHB synthesis in bacteroids. Analysis of the upstream regions of these genes suggest the existence of putative RpoN binding sites, perhaps indicating a potential mode of regulation and highlighting the metabolic complexity that is characteristic of the Rhizobiaceae. PHB metabolism in S. meliloti has been studied in considerable detail with two notable exceptions. No reports of the construction of either a β-ketothiolase (phbA) or a PHB depolymerase (phaZ ) mutant have ever been documented. The phaZ gene, encoding the first enzyme of the catabolic half of the PHB cycle in S. meliloti, was identified and a phaZ mutant strain was generated by insertion mutagenesis. The phaZ mutant demonstrates a Fix+ symbiotic phenotype and, unlike other PHB cycle mutants, does not demonstrate reduced rhizosphere competitiveness. Bacteroids of this strain were shown to accumulate PHB, demonstrating for the first time that S. meliloti is able to synthesize and accumulate PHB during symbiosis. Interestingly, there is no significant difference in shoot dry mass of plants inoculated with the phaZ mutant, suggesting that PHB accumulation does not occur at the expense of nitrogen fixation. The phaZ mutant strain was also used to demonstrate roles for PhaZ in the control of PHB accumulation and exopolysaccharide production. When grown on high-carbon media, this mutant demonstrates a mucoid phenotype characteristic of exopolysaccharide production. Subsequent analyses of a phoA::exoF fusion confirmed elevated transcription levels in the phaZ mutant background. In contrast, mutants of the PHB biosynthesis gene, phbC, have a characteristically dry phenotype and demonstrate reduced exoF transcriptional activity. The phaZ mutant also demonstrates a significant increase in PHB accumulation relative to the wild-type strain. Previous work on phasin mutants in S. meliloti demonstrated that they lack the ability to synthesize PHB. Transduction of the phaZ lesion into the phasin mutant background was used to construct a phaZ-phasin mutant strain. Analysis of the PHB biosynthesis capacity of this strain showed that the lack of PHB synthesis exhibited by S. meliloti phasin mutants is due to loss of PHB biosynthesis activity and not due to an inherent instability in the PHB granules themselves. A recent study suggested that some bacteria may possess an alternate pathway for acetate assimilation that would bypass the need for the glyoxylate cycle in organisms that do not possess the enzyme, isocitrate lyase. In these organisms, acetate is assimilated through the ethylmalonyl-CoA pathway, which has significant overlap with the anabolic half of the PHB cycle, including reliance on the PHB intermediate 3-hydroxybutyryl-CoA. The observation that phbB and phbC mutants of S. meliloti are unable to grow well on acetoacetate -- coupled with previously unexplained data that show a class of mutants (designated bhbA-D) are able to grow on acetate, but not on hydroxybutyrate or acetoacetate -- made it tempting to speculate that an ethylmalonyl-CoA-like pathway might be present in S. meliloti, and that this pathway might overlap with the PHB cycle at the point of 3-hydroxybutyryl-CoA. An in-frame mutation of phbA was constructed by cross-over PCR and allelic replacement. This mutant exhibited a complete abolition of growth on acetoacetate, suggesting that PhbA represents the only exit point for carbon from the PHB cycle and that an alternative ethylmalonyl-CoA-like pathway is not present in this organism. During symbiosis, rhizobial cells are dependent on the provision of carbon from the host plant in order to fuel cellular metabolism. This carbon is transported into the bacteroids via the dicarboxylate transport protein, DctA. Most rhizobia possess single copies of the transporter gene dctA and its corresponding two-component regulatory system dctBD. The completed genome sequence of B. japonicum suggests that it possesses seven copies of dctA. Complementation of Sinorhizobium meliloti dct mutants using the cosmid bank of B. japonicum USDA110 led to the identification a dctA locus and a dctBD operon. Interestingly, the B. japonicum dctABD system carried on the complementing cosmid was not able to complement the symbiotic deficiency of S. meliloti strains carrying individual mutations in either dctA, dctB, or dctD suggesting that the B. japonicum dctBD is unable to recognize either DctB/DctD or the DctB/DctD-independent regulatory elements in S. meliloti. All seven B. japonicum dctA ORFs were cloned and an analysis of their capacity to complement the free-living phenotype of a S. meliloti dctA mutant demonstrated that they all possess some capacity for dicarboxylate transport. Mutants of all seven B. japonicum dctA ORFs were constructed and an analysis of their free-living phenotypes suggested that significant functional redundancy exists in B. japonicum DctA function. Given the large number of potential dctA genes in the genome, coupled with an apparent lack of dctBD regulators, it is tempting to speculate that different DctA isoforms may be used during free-living and symbiotic growth and may be subject to different regulatory mechanisms than those of better-studied systems. A comprehensive analysis of desiccation tolerance and ion sensitivity in S. meliloti was conducted. The results of these analyses suggest that genetic elements on both pSymA and pSymB may play a significant role in enhancing cell survival under conditions of osmotic stress. The S. meliloti expR+ strains SmUW3 and SmUW6 were both shown to exhibit considerably higher desiccation tolerance than Rm1021, suggesting a role for enhanced exopolysaccharide production in facilitating survival under adverse conditions. Furthermore, scanning electron microscopy of inoculated seeds suggests that S. meliloti cells initiate biofilm formation upon application to the surface of seeds. This finding has implications for the analysis of OSS and the development of desiccation assays and may explain some of the variability that is characteristic of desiccation studies.

Tez (Yüksek Lisans) - Süleyman Demirel Üniversitesi, Fen Bilimleri Enstitüsü, Toprak Anabilim Dalı, 2009. / Kaynakça var.

In the soybean nitrogen fixing symbiosis, suboptimal root zone temperatures (RZTs) inhibit the inception and development of nodules, leading to reduced nitrogen fixation and soybean yield. The purpose of this thesis was to evaluate the effects of selected with potential low temperature tolerant strains, originating from the northern areas of the USA, and mutants made from Bradyrhizobium japonicum USDA 110, on soybean nodulation, nitrogen fixation and yield in a short season area with cool spring conditions. Among the 40 B. japonicum strains evaluated, only USDA 30, USDA 31, 532 C and USDA 110 grew well at 15°C. USDA 30 and USDA 31 grew better than 532 C and USDA 110 at 15°C. Mutants Bj 30050--Bj 30059 could not produce lipo-chito-oligosaccharide (LCO) at measurable levels in the absence of genistein. All mutants produced more LCOs than 532 C and USDA 110 at the same temperature and genistein concentration. Temperature and genistein concentration did not affect LCO production dynamics for the following: mutant Bj 30055, 532 C and USDA 110. Both mutant production and identification of low temperature tolerant strains achieved the general objective of improved soybean nitrogen fixation in a cool climate. Inoculation with low temperature tolerant strains (USDA 30, USDA31), or mutants (Bj 30055 and Bj 30058) improved soybean development (increases in leaf area and shoot nitrogen content), nodulation (increases in nodule number and nodule weight), nitrogen fixation and yield relative to inoculation with B. japonicum strain 532 C, the strain currently included in most Canadian soybean inocula.