Micki Kuhlmann - Academia.edu (original) (raw)

Papers by Micki Kuhlmann

Research paper thumbnail of <i>Murraya paniculata</i> and Related Species as Potential Hosts and Inoculum Reservoirs of ‘<i>Candidatus</i> Liberibacter asiaticus’, Causal Agent of Huanglongbing

Plant Disease, May 1, 2010

Huanglongbing (HLB), considered to be the most serious insect-vectored bacterial disease of citru... more Huanglongbing (HLB), considered to be the most serious insect-vectored bacterial disease of citrus, is transmitted in nature by the Asian citrus psyllid Diaphorina citri and the African citrus psyllid Trioza erytreae. D. citri was discovered in southern Florida in 1998 and the HLB disease in 2005. Both have become established throughout citrus-producing areas of Florida. Murraya species are widely grown in southern Florida as ornamental hedges and are readily colonized by D. citri vectors. Colonies of D. citri, isolates of 'Candidatus Liberibacter asiaticus' from Taiwan and Florida, and the Murraya species were established in the BSL-3 biosecurity facility at Fort Detrick. In controlled inoculation experiments, D. citri transmitted 'Ca. L. asiaticus' into M. paniculata (34/36 plants) and M. exotica (22/23 plants), but not into Bergera (Murraya) koenigii. Disease symptoms rarely developed in Murraya plants; however, positive infections were determined by conventional and real-time polymerase chain reaction (PCR). Back-inoculations of 'Ca. L. asiaticus' from M. paniculata to Madam Vinous sweet orange resulted in disease development in 25% of the inoculated plants. Considerable variability was observed in infection rates, titer, and persistence of 'Ca. L. asiaticus' in infected Murraya.

Research paper thumbnail of Molecular analysis of soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination

Virology, Mar 1, 2011

Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as ... more Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as a growing problem in the Midwestern United States. The majority of research on SbDV had been limited to four lab maintained strains from Japan. SbDV had been found in clover in the eastern United States, but these isolates rarely emerged into soybeans. These isolates were analyzed by multiplex PCR and sequencing, revealing that some were infections of both Y and D components, including a recombinant subisolate. Phylogenetic analyses for the US isolates revealed a broad diversity of SbDV, with selection pressure greater on the movement protein than the coat protein. The field isolates from the Eastern United States showed differences in symptoms, aphid transmission and host range, demonstrating that a study of field isolates is an important complement to laboratory maintained strains in understanding the biology and evolution of plant viruses.

Research paper thumbnail of Molecular analysis of soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination

Virology, 2011

Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as ... more Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as a growing problem in the Midwestern United States. The majority of research on SbDV had been limited to four lab maintained strains from Japan. SbDV had been found in clover in the eastern United States, but these isolates rarely emerged into soybeans. These isolates were analyzed by multiplex PCR and sequencing, revealing that some were infections of both Y and D components, including a recombinant subisolate. Phylogenetic analyses for the US isolates revealed a broad diversity of SbDV, with selection pressure greater on the movement protein than the coat protein. The field isolates from the Eastern United States showed differences in symptoms, aphid transmission and host range, demonstrating that a study of field isolates is an important complement to laboratory maintained strains in understanding the biology and evolution of plant viruses.

Research paper thumbnail of Acquisition and Transmissibility of U.S. Soybean dwarf virus Isolates by the Soybean Aphid, Aphis glycines

Plant Disease, 2011

Soybean dwarf virus (SbDV) exists as several distinct strains based on symptomatology, vector spe... more Soybean dwarf virus (SbDV) exists as several distinct strains based on symptomatology, vector specificity, and host range. Originally characterized Japanese isolates of SbDV were specifically transmitted by Aulacorthum solani. More recently, additional Japanese isolates and endemic U.S. isolates have been shown to be transmitted by several different aphid species. The soybean aphid, Aphis glycines, the only aphid that colonizes soybean, has been shown to be a very inefficient vector of some SbDV isolates from Japan and the United States. Transmission experiments have shown that the soybean aphid can transmit certain isolates of SbDV from soybean to soybean and clover species and from clover to clover and soybean with long acquisition and inoculation access periods. Although transmission of SbDV by the soybean aphid is very inefficient, the large soybean aphid populations that develop on soybean may have epidemiological potential to produce serious SbDV-induced yield losses.

Research paper thumbnail of An RNA Element that Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations

Journal of virology, Oct 20, 2016

Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past term... more Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past termination codons for synthesis of extension products. Recoding sites along with downstream Recoding Stimulatory Elements (RSEs) have long been studied in reporter constructs as these fragments alone mediate customary levels of recoding and are thus assumed to contain complete instructions for establishment of the proper ratio of termination to recoding. RSEs from the Tombusviridae and Luteoviridae are thought to be exceptions, as they contain a long-distance RNA:RNA connection with the 3' end. This interaction has been suggested to substitute for pseudoknots thought to be missing in Tombusvirid RSEs. We provide evidence that the phylogenetically conserved RSE of carmovirus Turnip crinkle virus (TCV) adopts an alternative, smaller structure that extends an upstream conserved hairpin and this alternative structure is the predominant form of the RSE within nascent viral RNA in plant cells...

Research paper thumbnail of Requirement for Host RNA Silencing Components and the Virus Silencing Suppressor when Second-Site Mutations Compensate For Structural Defects in the 3' UTR

Journal of virology, Jan 9, 2015

Turnip crinkle virus (TCV) contains a structured 3' region with hairpins and pseudoknots that... more Turnip crinkle virus (TCV) contains a structured 3' region with hairpins and pseudoknots that form a complex network of non-canonical RNA:RNA interactions supporting higher order structure critical for translation and replication. We investigated several second-site mutations in the p38 coat protein ORF that arose in response to a mutation in the asymmetric loop of a critical 3' UTR hairpin that disrupts local higher order structure. All tested second-site mutations improved accumulation of TCV in conjunction with a partial reversion of the primary mutation (TCV-rev1) but had neutral or a negative effect on wt TCV or TCV with the primary mutation. SHAPE structure probing indicated that these second-site mutations reside in an RNA domain that includes most of p38 (Domain 2), and evidence for RNA:RNA interactions between Domain 2 and 3' UTR-containing Domain 1 was found. However, second-site mutations were not compensatory in the absence of p38, which is also the TCV silen...

Research paper thumbnail of Position of the kissing-loop interaction associated with PTE-type 3′CITEs can affect enhancement of cap-independent translation

Virology, 2014

The Panicum mosaic virus-like translation enhancer (PTE) functions as a cap-independent translati... more The Panicum mosaic virus-like translation enhancer (PTE) functions as a cap-independent translation enhancer (3 0 CITE) in members of several Tombusviridae genera including 7/19 carmoviruses. For nearly all PTE, a kissing-loop connects the element with a hairpin found in several conserved locations in the genomic RNA (5 0 terminal hairpin or $ 100 nt from the 5 0 end) and small subgenomic RNA ($ 63 nt from the 5 0 end). Moving the interaction closer to the 5 0 end in reporter mRNAs using Saguaro cactus virus (SCV) sequences had either a minimal or substantial negative effect on translation. Movement of the kissing loop from position 104 to the SCV 5 0 terminal hairpin also reduced translation by 4-fold. These results suggest that relocating the PTE kissing loop closer to the 5 0 end reduces PTE efficiency, in contrast to results for the Barley yellow dwarf BTE and Tomato bushy stunt virus Y-shaped 3 0 CITEs, suggesting that different 3 0 CITEs have different bridging requirements.

Research paper thumbnail of Alternate Conformations Regulate Ribosomal Recoding in a Positive-sense RNA Virus

Title of Document: ALTERNATE CONFORMATIONS REGULATE RIBOSOMAL RECODING IN A POSITIVESENSE RNA VIR... more Title of Document: ALTERNATE CONFORMATIONS REGULATE RIBOSOMAL RECODING IN A POSITIVESENSE RNA VIRUS Michelle Kuhlmann Doctor of Philosophy, 2016 Directed By: Professor Anne E. Simon Cell Biology and Molecular Genetics Positive-sense RNA viruses are important animal, plant, insect and bacteria pathogens and constitute the largest group of RNA viruses. Due to the relatively small size of their genomes, these viruses have evolved a variety of non-canonical translation mechanisms to optimize coding capacity expanding their proteome diversity. One such strategy is codon redefinition or recoding. First described in viruses, recoding is a programmed translation event in which codon alterations are context dependent. Recoding takes place in a subset of messenger RNA (mRNAs) with some products reflecting new, and some reflecting standard, meanings. The ratio between the two is both critical and highly regulated. While a variety of recoding mechanisms have been documented, (ribosome shunting,...

Research paper thumbnail of <i>Murraya paniculata</i> and Related Species as Potential Hosts and Inoculum Reservoirs of ‘<i>Candidatus</i> Liberibacter asiaticus’, Causal Agent of Huanglongbing

Plant Disease, May 1, 2010

Huanglongbing (HLB), considered to be the most serious insect-vectored bacterial disease of citru... more Huanglongbing (HLB), considered to be the most serious insect-vectored bacterial disease of citrus, is transmitted in nature by the Asian citrus psyllid Diaphorina citri and the African citrus psyllid Trioza erytreae. D. citri was discovered in southern Florida in 1998 and the HLB disease in 2005. Both have become established throughout citrus-producing areas of Florida. Murraya species are widely grown in southern Florida as ornamental hedges and are readily colonized by D. citri vectors. Colonies of D. citri, isolates of 'Candidatus Liberibacter asiaticus' from Taiwan and Florida, and the Murraya species were established in the BSL-3 biosecurity facility at Fort Detrick. In controlled inoculation experiments, D. citri transmitted 'Ca. L. asiaticus' into M. paniculata (34/36 plants) and M. exotica (22/23 plants), but not into Bergera (Murraya) koenigii. Disease symptoms rarely developed in Murraya plants; however, positive infections were determined by conventional and real-time polymerase chain reaction (PCR). Back-inoculations of 'Ca. L. asiaticus' from M. paniculata to Madam Vinous sweet orange resulted in disease development in 25% of the inoculated plants. Considerable variability was observed in infection rates, titer, and persistence of 'Ca. L. asiaticus' in infected Murraya.

Research paper thumbnail of Molecular analysis of soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination

Virology, Mar 1, 2011

Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as ... more Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as a growing problem in the Midwestern United States. The majority of research on SbDV had been limited to four lab maintained strains from Japan. SbDV had been found in clover in the eastern United States, but these isolates rarely emerged into soybeans. These isolates were analyzed by multiplex PCR and sequencing, revealing that some were infections of both Y and D components, including a recombinant subisolate. Phylogenetic analyses for the US isolates revealed a broad diversity of SbDV, with selection pressure greater on the movement protein than the coat protein. The field isolates from the Eastern United States showed differences in symptoms, aphid transmission and host range, demonstrating that a study of field isolates is an important complement to laboratory maintained strains in understanding the biology and evolution of plant viruses.

Research paper thumbnail of Molecular analysis of soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination

Virology, 2011

Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as ... more Soybean dwarf virus (SbDV), first identified as an agricultural problem in Japan, has emerged as a growing problem in the Midwestern United States. The majority of research on SbDV had been limited to four lab maintained strains from Japan. SbDV had been found in clover in the eastern United States, but these isolates rarely emerged into soybeans. These isolates were analyzed by multiplex PCR and sequencing, revealing that some were infections of both Y and D components, including a recombinant subisolate. Phylogenetic analyses for the US isolates revealed a broad diversity of SbDV, with selection pressure greater on the movement protein than the coat protein. The field isolates from the Eastern United States showed differences in symptoms, aphid transmission and host range, demonstrating that a study of field isolates is an important complement to laboratory maintained strains in understanding the biology and evolution of plant viruses.

Research paper thumbnail of Acquisition and Transmissibility of U.S. Soybean dwarf virus Isolates by the Soybean Aphid, Aphis glycines

Plant Disease, 2011

Soybean dwarf virus (SbDV) exists as several distinct strains based on symptomatology, vector spe... more Soybean dwarf virus (SbDV) exists as several distinct strains based on symptomatology, vector specificity, and host range. Originally characterized Japanese isolates of SbDV were specifically transmitted by Aulacorthum solani. More recently, additional Japanese isolates and endemic U.S. isolates have been shown to be transmitted by several different aphid species. The soybean aphid, Aphis glycines, the only aphid that colonizes soybean, has been shown to be a very inefficient vector of some SbDV isolates from Japan and the United States. Transmission experiments have shown that the soybean aphid can transmit certain isolates of SbDV from soybean to soybean and clover species and from clover to clover and soybean with long acquisition and inoculation access periods. Although transmission of SbDV by the soybean aphid is very inefficient, the large soybean aphid populations that develop on soybean may have epidemiological potential to produce serious SbDV-induced yield losses.

Research paper thumbnail of An RNA Element that Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations

Journal of virology, Oct 20, 2016

Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past term... more Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past termination codons for synthesis of extension products. Recoding sites along with downstream Recoding Stimulatory Elements (RSEs) have long been studied in reporter constructs as these fragments alone mediate customary levels of recoding and are thus assumed to contain complete instructions for establishment of the proper ratio of termination to recoding. RSEs from the Tombusviridae and Luteoviridae are thought to be exceptions, as they contain a long-distance RNA:RNA connection with the 3' end. This interaction has been suggested to substitute for pseudoknots thought to be missing in Tombusvirid RSEs. We provide evidence that the phylogenetically conserved RSE of carmovirus Turnip crinkle virus (TCV) adopts an alternative, smaller structure that extends an upstream conserved hairpin and this alternative structure is the predominant form of the RSE within nascent viral RNA in plant cells...

Research paper thumbnail of Requirement for Host RNA Silencing Components and the Virus Silencing Suppressor when Second-Site Mutations Compensate For Structural Defects in the 3' UTR

Journal of virology, Jan 9, 2015

Turnip crinkle virus (TCV) contains a structured 3' region with hairpins and pseudoknots that... more Turnip crinkle virus (TCV) contains a structured 3' region with hairpins and pseudoknots that form a complex network of non-canonical RNA:RNA interactions supporting higher order structure critical for translation and replication. We investigated several second-site mutations in the p38 coat protein ORF that arose in response to a mutation in the asymmetric loop of a critical 3' UTR hairpin that disrupts local higher order structure. All tested second-site mutations improved accumulation of TCV in conjunction with a partial reversion of the primary mutation (TCV-rev1) but had neutral or a negative effect on wt TCV or TCV with the primary mutation. SHAPE structure probing indicated that these second-site mutations reside in an RNA domain that includes most of p38 (Domain 2), and evidence for RNA:RNA interactions between Domain 2 and 3' UTR-containing Domain 1 was found. However, second-site mutations were not compensatory in the absence of p38, which is also the TCV silen...

Research paper thumbnail of Position of the kissing-loop interaction associated with PTE-type 3′CITEs can affect enhancement of cap-independent translation

Virology, 2014

The Panicum mosaic virus-like translation enhancer (PTE) functions as a cap-independent translati... more The Panicum mosaic virus-like translation enhancer (PTE) functions as a cap-independent translation enhancer (3 0 CITE) in members of several Tombusviridae genera including 7/19 carmoviruses. For nearly all PTE, a kissing-loop connects the element with a hairpin found in several conserved locations in the genomic RNA (5 0 terminal hairpin or $ 100 nt from the 5 0 end) and small subgenomic RNA ($ 63 nt from the 5 0 end). Moving the interaction closer to the 5 0 end in reporter mRNAs using Saguaro cactus virus (SCV) sequences had either a minimal or substantial negative effect on translation. Movement of the kissing loop from position 104 to the SCV 5 0 terminal hairpin also reduced translation by 4-fold. These results suggest that relocating the PTE kissing loop closer to the 5 0 end reduces PTE efficiency, in contrast to results for the Barley yellow dwarf BTE and Tomato bushy stunt virus Y-shaped 3 0 CITEs, suggesting that different 3 0 CITEs have different bridging requirements.

Research paper thumbnail of Alternate Conformations Regulate Ribosomal Recoding in a Positive-sense RNA Virus

Title of Document: ALTERNATE CONFORMATIONS REGULATE RIBOSOMAL RECODING IN A POSITIVESENSE RNA VIR... more Title of Document: ALTERNATE CONFORMATIONS REGULATE RIBOSOMAL RECODING IN A POSITIVESENSE RNA VIRUS Michelle Kuhlmann Doctor of Philosophy, 2016 Directed By: Professor Anne E. Simon Cell Biology and Molecular Genetics Positive-sense RNA viruses are important animal, plant, insect and bacteria pathogens and constitute the largest group of RNA viruses. Due to the relatively small size of their genomes, these viruses have evolved a variety of non-canonical translation mechanisms to optimize coding capacity expanding their proteome diversity. One such strategy is codon redefinition or recoding. First described in viruses, recoding is a programmed translation event in which codon alterations are context dependent. Recoding takes place in a subset of messenger RNA (mRNAs) with some products reflecting new, and some reflecting standard, meanings. The ratio between the two is both critical and highly regulated. While a variety of recoding mechanisms have been documented, (ribosome shunting,...