Multiple Sequence Alignment Using ClustalW and ClustalX

Thompson, Julie; Gibson, Toby J.; Higgins, Desmond G.

doi:10.1002/0471250953.bi0203s00

Cited by 2,026 publications

(1,584 citation statements)

References 22 publications

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“…Chimeric sequences were detected and removed by ChimeraSlayer using the identify_chimeric_seqs.py pipeline implemented in QIIME 1.6 (Haas et al 2011;Caporaso et al 2010). Nucleotide sequences were aligned with the ClustalW2 software package (Thompson et al, 2002;Larkin et al 2007). The phylogeny of the sequences was analyzed by calculating a distance matrix according to the Jukes-Cantor model (Jukes and Cantor, 1969) followed by the construction of a phylogenetic tree using the neighbour-joining method (Saitou and Nei, 1987) as implemented in the program Treecon ( Van de Peer and De Wachter, 1995).…”

Section: Phylogenetic Analysis Of 16s Rdna Sequencesmentioning

confidence: 99%

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems

Babatunde

Miranda-CasoLuengo

Imtiaz

et al. 2016

Journal of Environmental Sciences

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Section: Phylogenetic Analysis Of 16s Rdna Sequencesmentioning

confidence: 99%

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems

Babatunde

Miranda-CasoLuengo

Imtiaz

et al. 2016

Journal of Environmental Sciences

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“…The fragment sequences were aligned using ClustalW (Thompson et al, 2002). Gene specific primers were then used to amplify 5'-and 3'-ends by the Generacer RACE-PCR kit (Invitrogen) according to kit protocol including nested PCR.…”

Section: )And Glossina Morsitans Morsitans (Genbank Accessimentioning

confidence: 99%

“…Bold residues indicate phosphorylation sites. Alignment was produced using ClustalW (Thompson et al, 2002).…”

Section: Figure 5 the Nucleotide And Deduced Amino Acid Sequence Ofmentioning

confidence: 99%

Nutritional sensitivity of fifth instar prothoracic glands in the tobacco hornworm, Manduca sexta

Walsh

Smith

2011

Journal of Insect Physiology

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The tobacco hornworm, Manduca sexta, has been a useful model for studying insect endocrinology. In M. sexta the majority of growth occurs during the fifth (final) larval stage. This growth is concurrent with endocrine changes that lead to a metamorphic molt. Past research has focused on the interplay of three growth hormones: juvenile hormone (JH), prothoracicotropic hormone (PTTH) and ecdysone, in regulating metamorphosis. The prothoracic glands, source of ecdysteroid molting hormones in insects, play a crucial role in coordinating growth. Insulin/insulin-like growth factor (IGF) signaling has been shown to regulate growth and secretion of steroidogenic tissues in both vertebrates and invertebrates, but it had yet to be well-characterized in M. sexta.In this dissertation I examined the role of insulin-directed growth in prothoracic glands during both normal larval development and in response to nutrient deprivation. In particular, I predicted that in response to a reduction in nutrients, the prothoracic glands would stop growing and ecdysone secretion would be reduced. Changes were assessed in actin abundance and in two nutritionally sensitive transcripts, insulin receptor and 4EBP.Actin abundance in prothoracic glands increased in the first four days of this stage, demo nstrating significant growth. Actin decreased in glands from starved larvae, indicating a cessation of growth. Both insulin receptor and 4EBP transcript were present during normal larval development. As expected, both insulin receptor and 4EBP transcript increased in response to starvation. This research was the first demonstration of insulin signaling in prothoracic glands of fifth instar M. sexta larvae, and revealed nutritional sensitivity of the prothoracic glands. 5Finally, ecdysone assays were conducted to determine the impact of nutrition on glandular secretory capacity. Starved larvae were unable to secrete as much ecdysone as fed controls. Injections of insulin were unable to rescue the ability of the glands to secrete high levels of ecdysone. This demonstrated that although insulin signaling was correlated with normal growth of the glands, insulin is not sufficient to impact the ability of the glands to secrete ecdysone in the absence of nutrie nts. 6 This thesis is dedicated to my parents,Robert and Angela Walsh, whose love and support made this dissertation possible.

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“…COI sequences were aligned with ClustalW (Thompson, Gibson, & Higgins, 2002) using default parameter settings, and obviously misaligned positions were adjusted manually in Bioedit v7.0 (Hall, 1999). Homogeneity of base frequencies among COI sequences was checked with the χ 2 ‐ test implemented in PAUP* v4.0b10 (Swofford, 2002).…”

Section: Methodsmentioning

confidence: 99%

Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa

Greve

Haase

Hutterer

et al. 2017

Ecology and Evolution

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The spatial subdivision of species often plays a pivotal role in speciation. Across their entire range, species are rarely panmictic and crucial consequences of spatial subdivision are (1) random genetic drift including historical factors, (2) uniform selection, and (3) divergent selection. Each of these consequences may result in geographic variation and eventually reproductive isolation, but their relative importance in speciation is still unclear. In this study, we used a combination of genetic, morphological, and climatic data to obtain a comprehensive picture of differentiation among three closely related, parapatrically distributed taxa of the land snail genus Theba occurring along the Atlantic coasts of South Morocco and Western Sahara. We conducted Mantel and partial Mantel tests to relate phenotypic and genotypic variation of these species to geography and/or climate. As null hypothesis for an evolutionary scenario, we assumed nonadaptive speciation and expected a pattern of isolation by distance among taxa. Rejection of the null hypothesis would indicate isolation by environment due to adaptation. Generally, genetic drift plays an important role but is rarely considered as sole driver of speciation. It is the combination of drift and selection that predominantly drives speciation. This study, however, provides a potential example, in which nonadaptive speciation, that is, genetic drift, is apparently the main driver of shaping the diversity of Theba in NW Africa. Restriction of gene flow between populations caused by geographic isolation probably has played an important role. Climate oscillations during the Plio‐ and Pleistocene may have led to repeated ecological changes in NW Africa and disruptions of habitats promoting differentiation by geographic isolation. The inferred evolutionary scenario, however, did not fully explain the incongruence between the AFLP‐ and mtDNA‐tree topologies. This incongruence might indicate past hybridization among the studied Theba forms.

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Multiple Sequence Alignment Using ClustalW and ClustalX

Cited by 2,026 publications

References 22 publications

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems

Nutritional sensitivity of fifth instar prothoracic glands in the tobacco hornworm, Manduca sexta

Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa

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