Connected Dominating Set (CDS) has been proposed as the virtual backbone to alleviate the broadca... more Connected Dominating Set (CDS) has been proposed as the virtual backbone to alleviate the broadcasting storm in wireless ad hoc networks. Most recent research has extensively focused on the construction of 1-Connected 1-Dominating Set (1-CDS) in homogeneous networks. However, the nodes in the CDS need to carry other node’s traffic and nodes in wireless networks are subject to failure. Therefore, it is desirable to construct a fault tolerant CDS. In this paper, we study a general fault tolerant CDS problem, called kk-Connected mm-Dominating Set (kk-mm-CDS), in heterogeneous networks. We first present two approximation algorithms for 1-mm-CDS and kk-kk-CDS problems. Using disk graphs to model heterogeneous networks, we show that our algorithms have a constant approximation ratio. Based on these two algorithms, we further develop a general algorithm for kk-mm-CDS. We also provide an interesting analysis for a special case of kk-mm-CDS, where k=m+1k=m+1.
• Medicago truncatula (barrel medic) A17 is currently being sequenced as a model legume, compleme... more • Medicago truncatula (barrel medic) A17 is currently being sequenced as a model legume, complementing the sequenced root nodule bacterial strain Sinorhizobium meliloti 1021 (Sm1021). In this study, the effectiveness of the Sm1021–M. truncatula symbiosis at fixing N2 was evaluated.• N2 fixation effectiveness was examined with eight Medicago species and three accessions of M. truncatula with Sm1021 and two other Sinorhizobium strains. Plant shoot dry weights, plant nitrogen content and nodule distribution, morphology and number were analysed.• Compared with nitrogen-fed controls, Sm1021 was ineffective or partially effective on all hosts tested (excluding M. sativa), as measured by reduced dry weights and shoot N content. Against an effective strain, Sm1021 on M. truncatula accessions produced more nodules, which were small, pale, more widely distributed on the root system and with fewer infected cells.• The Sm1021–M. truncatula symbiosis is poorly matched for N2 fixation and the strain could possess broader N2 fixation deficiencies. A possible origin for this reduction in effectiveness is discussed. An alternative sequenced strain, effective at N2 fixation on M. truncatula A17, is Sinorhizobium medicae WSM419.Medicago truncatula (barrel medic) A17 is currently being sequenced as a model legume, complementing the sequenced root nodule bacterial strain Sinorhizobium meliloti 1021 (Sm1021). In this study, the effectiveness of the Sm1021–M. truncatula symbiosis at fixing N2 was evaluated.N2 fixation effectiveness was examined with eight Medicago species and three accessions of M. truncatula with Sm1021 and two other Sinorhizobium strains. Plant shoot dry weights, plant nitrogen content and nodule distribution, morphology and number were analysed.Compared with nitrogen-fed controls, Sm1021 was ineffective or partially effective on all hosts tested (excluding M. sativa), as measured by reduced dry weights and shoot N content. Against an effective strain, Sm1021 on M. truncatula accessions produced more nodules, which were small, pale, more widely distributed on the root system and with fewer infected cells.The Sm1021–M. truncatula symbiosis is poorly matched for N2 fixation and the strain could possess broader N2 fixation deficiencies. A possible origin for this reduction in effectiveness is discussed. An alternative sequenced strain, effective at N2 fixation on M. truncatula A17, is Sinorhizobium medicae WSM419.
Journal of Molecular Microbiology and Biotechnology, 2004
The low pH sensitivity of Sinorhizobium species is one of the major causes of reduced productivit... more The low pH sensitivity of Sinorhizobium species is one of the major causes of reduced productivity of Medicago species (such as lucerne) sown in acidic soils. To investigate the pH response of an acid-tolerant Sinorhizobium medicae strain, a pool of random promoter fusions to gusA was created using minitransposon insertional mutagenesis. Acid-activated expression was identified in 11 mutants; rhizobial DNA flanking insertions in 10 mutants could be cloned and the DNA sequences obtained were used to interrogate the genome database of Sinorhizobium meliloti strain 1021. Acid activated expression was detected for fixNO, kdpC, lpiA, and phrR and for genes encoding a putative lipoprotein, two ABC-transporter components, a putative DNA ligase and a MPA1-family protein. These findings implicate cytochrome synthesis, potassium ion cycling, lipid biosynthesis and transport processes as key components of pH response in S. medicae.
The multi-billion dollar asset attributed to symbiotic nitrogen fixation is often threatened by t... more The multi-billion dollar asset attributed to symbiotic nitrogen fixation is often threatened by the nodulation of legumes by rhizobia that are ineffective or poorly effective in N2 fixation. This study investigated the development of rhizobial diversity for the pasture legume Biserrula pelecinus L., 6 years after its introduction, and inoculation with Mesorhizobium ciceri bv. biserrulae strain WSM1271, to Western Australia. Molecular fingerprinting of 88 nodule isolates indicated seven were distinctive. Two of these were ineffective while five were poorly effective in N2 fixation on B. pelecinus. Three novel isolates had wider host ranges for nodulation than WSM1271, and four had distinct carbon utilization patterns. Novel isolates were identified as Mesorhizobium sp. using 16S rRNA, dnaK and GSII phylogenies. In a second study, a large number of nodules were collected from commercially grown B. pelecinus from a broader geographical area. These plants were originally inoculated with M. c bv. biserrulae WSM1497 5–6 years prior to isolation of strains for this study. Nearly 50% of isolates from these nodules had distinct molecular fingerprints. At two sites diverse strains dominated nodule occupancy indicating recently evolved strains are highly competitive. All isolates tested were less effective and six were ineffective in N2 fixation. Twelve randomly selected diverse isolates clustered together, based on dnaK sequences, within Mesorhizobium and distantly to M. c bv. biserrulae. All 12 had identical sequences for the symbiosis island insertion region with WSM1497. This study shows the rapid evolution of competitive, yet suboptimal strains for N2 fixation on B. pelecinus following the lateral transfer of a symbiosis island from inoculants to other soil bacteria.
The rhizobia strain R. gallicum bv. gallicum 8a3 was isolated from root nodules of Phaseolus vulg... more The rhizobia strain R. gallicum bv. gallicum 8a3 was isolated from root nodules of Phaseolus vulgaris cultivated in Tunisian soils. This strain was selected on the basis of its high symbiotic effectiveness in laboratory conditions. In order to assess its ability to compete indigenous rhizobia, this strain was labelled with gusA gene. Conservation of initial effectiveness and competitiveness by transconjugants was tested. A transconjugant was introduced in three soil-core microcosms originating from different geographical and agronomic regions. Nodulation monitoring showed that the labelled transconjugant was able to occupy more than 90% of nodules at 30 days after inoculation. The nodule occupancy by the introduced strain was high even in the soil sample of Mateur which showed an MPN value of 103 rhizobia/g of dry soil. A significant improvement of plant productivity by inoculation was observed with the three soil samples in green house. Field inoculation with the parental strain showed a significant increase in nodule number, pod number and seed dry weight. The improvement of plant productivity in green house or in field conditions was equal or better than nitrogen fertilisation.
Two ‘calcium-irreparable’ acid-sensitive mutants were identified after mutagenizing Rhizobium leg... more Two ‘calcium-irreparable’ acid-sensitive mutants were identified after mutagenizing Rhizobium leguminosarum bv. viciae and Sinorhizobium meliloti with Tn5. Each mutant contains a single copy of the transposon which, inserted within the actP gene, prevents expression of a P-type ATPase that belongs to the CPx heavy metal-transporting subfamily. Here, we show that both actP-knockout mutants show sensitivity to copper; omission of this heavy metal from low pH-buffered media restores acid tolerance to these strains. Furthermore, complementation of the mutant phenotype requires only the actP gene. An actP–gusA fusion in R. leguminosarum was transcriptionally regulated by copper in a pH-dependent manner. Downstream to actP in both organisms is the hmrR gene that encodes a heavy metal-responsive regulator (HmrR) that belongs to the merR class of regulatory genes. Insertional inactivation of hmrR abolished transcriptional activation of actP by copper ions and increased the basal level of its expression in their absence. These observations suggest that HmrR can regulate actP transcription positively and negatively. We show that copper homeostasis is an essential mechanism for the acid tolerance of these root nodule bacteria since it prevents this heavy metal from becoming overtly toxic in acidic conditions.
Journal of Molecular Microbiology and Biotechnology, 2004
To elucidate the mechanisms of pH response in an acid-tolerant Sinorhizobium medicae strain we ha... more To elucidate the mechanisms of pH response in an acid-tolerant Sinorhizobium medicae strain we have identified acid-activated gene transcription and now complement this approach by using a proteomic analysis to identify the changes that occur following exposure to acidity. Protein profiles of persistently or transiently acid-stressed S. medicae cells were compared to those grown in pH neutral, buffered media. Fifty pH-regulated proteins were identified; N-terminal sequences for 15 of these were obtained using the Edman degradation. Transient acid exposure downregulated GlnA and GlnK and upregulated a hypothetical protein. Continuing acid exposure downregulated ClpP, an ABC transporter, a hypothetical protein, a lipoprotein, the Trp-like repressor WrbA1 and upregulated DegP, fructose bisphosphate aldolase, GroES, malate dehydrogenase and two hypothetical proteins. These findings implicate proteolytic, chaperone and transport processes as key components of pH response in S. medicae.
Connected Dominating Set (CDS) has been proposed as the virtual backbone to alleviate the broadca... more Connected Dominating Set (CDS) has been proposed as the virtual backbone to alleviate the broadcasting storm in wireless ad hoc networks. Most recent research has extensively focused on the construction of 1-Connected 1-Dominating Set (1-CDS) in homogeneous networks. However, the nodes in the CDS need to carry other node’s traffic and nodes in wireless networks are subject to failure. Therefore, it is desirable to construct a fault tolerant CDS. In this paper, we study a general fault tolerant CDS problem, called kk-Connected mm-Dominating Set (kk-mm-CDS), in heterogeneous networks. We first present two approximation algorithms for 1-mm-CDS and kk-kk-CDS problems. Using disk graphs to model heterogeneous networks, we show that our algorithms have a constant approximation ratio. Based on these two algorithms, we further develop a general algorithm for kk-mm-CDS. We also provide an interesting analysis for a special case of kk-mm-CDS, where k=m+1k=m+1.
• Medicago truncatula (barrel medic) A17 is currently being sequenced as a model legume, compleme... more • Medicago truncatula (barrel medic) A17 is currently being sequenced as a model legume, complementing the sequenced root nodule bacterial strain Sinorhizobium meliloti 1021 (Sm1021). In this study, the effectiveness of the Sm1021–M. truncatula symbiosis at fixing N2 was evaluated.• N2 fixation effectiveness was examined with eight Medicago species and three accessions of M. truncatula with Sm1021 and two other Sinorhizobium strains. Plant shoot dry weights, plant nitrogen content and nodule distribution, morphology and number were analysed.• Compared with nitrogen-fed controls, Sm1021 was ineffective or partially effective on all hosts tested (excluding M. sativa), as measured by reduced dry weights and shoot N content. Against an effective strain, Sm1021 on M. truncatula accessions produced more nodules, which were small, pale, more widely distributed on the root system and with fewer infected cells.• The Sm1021–M. truncatula symbiosis is poorly matched for N2 fixation and the strain could possess broader N2 fixation deficiencies. A possible origin for this reduction in effectiveness is discussed. An alternative sequenced strain, effective at N2 fixation on M. truncatula A17, is Sinorhizobium medicae WSM419.Medicago truncatula (barrel medic) A17 is currently being sequenced as a model legume, complementing the sequenced root nodule bacterial strain Sinorhizobium meliloti 1021 (Sm1021). In this study, the effectiveness of the Sm1021–M. truncatula symbiosis at fixing N2 was evaluated.N2 fixation effectiveness was examined with eight Medicago species and three accessions of M. truncatula with Sm1021 and two other Sinorhizobium strains. Plant shoot dry weights, plant nitrogen content and nodule distribution, morphology and number were analysed.Compared with nitrogen-fed controls, Sm1021 was ineffective or partially effective on all hosts tested (excluding M. sativa), as measured by reduced dry weights and shoot N content. Against an effective strain, Sm1021 on M. truncatula accessions produced more nodules, which were small, pale, more widely distributed on the root system and with fewer infected cells.The Sm1021–M. truncatula symbiosis is poorly matched for N2 fixation and the strain could possess broader N2 fixation deficiencies. A possible origin for this reduction in effectiveness is discussed. An alternative sequenced strain, effective at N2 fixation on M. truncatula A17, is Sinorhizobium medicae WSM419.
Journal of Molecular Microbiology and Biotechnology, 2004
The low pH sensitivity of Sinorhizobium species is one of the major causes of reduced productivit... more The low pH sensitivity of Sinorhizobium species is one of the major causes of reduced productivity of Medicago species (such as lucerne) sown in acidic soils. To investigate the pH response of an acid-tolerant Sinorhizobium medicae strain, a pool of random promoter fusions to gusA was created using minitransposon insertional mutagenesis. Acid-activated expression was identified in 11 mutants; rhizobial DNA flanking insertions in 10 mutants could be cloned and the DNA sequences obtained were used to interrogate the genome database of Sinorhizobium meliloti strain 1021. Acid activated expression was detected for fixNO, kdpC, lpiA, and phrR and for genes encoding a putative lipoprotein, two ABC-transporter components, a putative DNA ligase and a MPA1-family protein. These findings implicate cytochrome synthesis, potassium ion cycling, lipid biosynthesis and transport processes as key components of pH response in S. medicae.
The multi-billion dollar asset attributed to symbiotic nitrogen fixation is often threatened by t... more The multi-billion dollar asset attributed to symbiotic nitrogen fixation is often threatened by the nodulation of legumes by rhizobia that are ineffective or poorly effective in N2 fixation. This study investigated the development of rhizobial diversity for the pasture legume Biserrula pelecinus L., 6 years after its introduction, and inoculation with Mesorhizobium ciceri bv. biserrulae strain WSM1271, to Western Australia. Molecular fingerprinting of 88 nodule isolates indicated seven were distinctive. Two of these were ineffective while five were poorly effective in N2 fixation on B. pelecinus. Three novel isolates had wider host ranges for nodulation than WSM1271, and four had distinct carbon utilization patterns. Novel isolates were identified as Mesorhizobium sp. using 16S rRNA, dnaK and GSII phylogenies. In a second study, a large number of nodules were collected from commercially grown B. pelecinus from a broader geographical area. These plants were originally inoculated with M. c bv. biserrulae WSM1497 5–6 years prior to isolation of strains for this study. Nearly 50% of isolates from these nodules had distinct molecular fingerprints. At two sites diverse strains dominated nodule occupancy indicating recently evolved strains are highly competitive. All isolates tested were less effective and six were ineffective in N2 fixation. Twelve randomly selected diverse isolates clustered together, based on dnaK sequences, within Mesorhizobium and distantly to M. c bv. biserrulae. All 12 had identical sequences for the symbiosis island insertion region with WSM1497. This study shows the rapid evolution of competitive, yet suboptimal strains for N2 fixation on B. pelecinus following the lateral transfer of a symbiosis island from inoculants to other soil bacteria.
The rhizobia strain R. gallicum bv. gallicum 8a3 was isolated from root nodules of Phaseolus vulg... more The rhizobia strain R. gallicum bv. gallicum 8a3 was isolated from root nodules of Phaseolus vulgaris cultivated in Tunisian soils. This strain was selected on the basis of its high symbiotic effectiveness in laboratory conditions. In order to assess its ability to compete indigenous rhizobia, this strain was labelled with gusA gene. Conservation of initial effectiveness and competitiveness by transconjugants was tested. A transconjugant was introduced in three soil-core microcosms originating from different geographical and agronomic regions. Nodulation monitoring showed that the labelled transconjugant was able to occupy more than 90% of nodules at 30 days after inoculation. The nodule occupancy by the introduced strain was high even in the soil sample of Mateur which showed an MPN value of 103 rhizobia/g of dry soil. A significant improvement of plant productivity by inoculation was observed with the three soil samples in green house. Field inoculation with the parental strain showed a significant increase in nodule number, pod number and seed dry weight. The improvement of plant productivity in green house or in field conditions was equal or better than nitrogen fertilisation.
Two ‘calcium-irreparable’ acid-sensitive mutants were identified after mutagenizing Rhizobium leg... more Two ‘calcium-irreparable’ acid-sensitive mutants were identified after mutagenizing Rhizobium leguminosarum bv. viciae and Sinorhizobium meliloti with Tn5. Each mutant contains a single copy of the transposon which, inserted within the actP gene, prevents expression of a P-type ATPase that belongs to the CPx heavy metal-transporting subfamily. Here, we show that both actP-knockout mutants show sensitivity to copper; omission of this heavy metal from low pH-buffered media restores acid tolerance to these strains. Furthermore, complementation of the mutant phenotype requires only the actP gene. An actP–gusA fusion in R. leguminosarum was transcriptionally regulated by copper in a pH-dependent manner. Downstream to actP in both organisms is the hmrR gene that encodes a heavy metal-responsive regulator (HmrR) that belongs to the merR class of regulatory genes. Insertional inactivation of hmrR abolished transcriptional activation of actP by copper ions and increased the basal level of its expression in their absence. These observations suggest that HmrR can regulate actP transcription positively and negatively. We show that copper homeostasis is an essential mechanism for the acid tolerance of these root nodule bacteria since it prevents this heavy metal from becoming overtly toxic in acidic conditions.
Journal of Molecular Microbiology and Biotechnology, 2004
To elucidate the mechanisms of pH response in an acid-tolerant Sinorhizobium medicae strain we ha... more To elucidate the mechanisms of pH response in an acid-tolerant Sinorhizobium medicae strain we have identified acid-activated gene transcription and now complement this approach by using a proteomic analysis to identify the changes that occur following exposure to acidity. Protein profiles of persistently or transiently acid-stressed S. medicae cells were compared to those grown in pH neutral, buffered media. Fifty pH-regulated proteins were identified; N-terminal sequences for 15 of these were obtained using the Edman degradation. Transient acid exposure downregulated GlnA and GlnK and upregulated a hypothetical protein. Continuing acid exposure downregulated ClpP, an ABC transporter, a hypothetical protein, a lipoprotein, the Trp-like repressor WrbA1 and upregulated DegP, fructose bisphosphate aldolase, GroES, malate dehydrogenase and two hypothetical proteins. These findings implicate proteolytic, chaperone and transport processes as key components of pH response in S. medicae.
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Papers by Ravi Tiwari