MyMedR

Displaying all 5 publications

Abstract:

Sort:

Fulltext Characterisation of Drosophila Ubx CPTI000601 and hth CPTI000378 protein trap lines

Choo SW, Beh CY, Russell S, White R

ScientificWorldJournal, 2014;2014:191535.
PMID: 25389534 DOI: 10.1155/2014/191535

In Drosophila, protein trap strategies provide powerful approaches for the generation of tagged proteins expressed under endogenous control. Here, we describe expression and functional analysis to evaluate new Ubx and hth protein trap lines generated by the Cambridge Protein Trap project. Both protein traps exhibit spatial and temporal expression patterns consistent with the reported endogenous pattern in the embryo. In imaginal discs, Ubx-YFP is expressed throughout the haltere and 3rd leg imaginal discs, while Hth-YFP is expressed in the proximal regions of haltere and wing discs but not in the pouch region. The Ubx (CPTI000601) line is semilethal as a homozygote. No T3/A1 to T2 transformations were observed in the embryonic cuticle or the developing midgut. The homozygous survivors, however, exhibit a weak haltere phenotype with a few wing-like marginal bristles on the haltere capitellum. Although hth (CPTI000378) is completely lethal as a homozygote, the hth (CPTI000378) /hth (C1) genotype is viable. Using a hth deletion (Df(3R)BSC479) we show that hth (CPTI000378) /Df(3R)BSC479 adults are phenotypically normal. No transformations were observed in hth (CPTI000378), hth (CPTI000378) /hth (C1), or hth (CPTI000378) /Df(3R)BSC479 embryonic cuticles. We have successfully characterised the Ubx-YFP and Hth-YFP protein trap lines demonstrating that the tagged proteins show appropriate expression patterns and produce at least partially functional proteins.
Fulltext Roles of cofactors and chromatin accessibility in Hox protein target specificity

Beh CY, El-Sharnouby S, Chatzipli A, Russell S, Choo SW, White R

Epigenetics Chromatin, 2016;9:1.
PMID: 26753000 DOI: 10.1186/s13072-015-0049-x

The regulation of specific target genes by transcription factors is central to our understanding of gene network control in developmental and physiological processes yet how target specificity is achieved is still poorly understood. This is well illustrated by the Hox family of transcription factors as their limited in vitro DNA-binding specificity contrasts with their clear in vivo functional specificity.
Fulltext Detection of mitochondrial COII DNA sequences in ant guts as a method for assessing termite predation by ants

Fayle TM, Scholtz O, Dumbrell AJ, Russell S, Segar ST, Eggleton P

PLoS One, 2015;10(4):e0122533.
PMID: 25853549 DOI: 10.1371/journal.pone.0122533

Termites and ants contribute more to animal biomass in tropical rain forests than any other single group and perform vital ecosystem functions. Although ants prey on termites, at the community level the linkage between these groups is poorly understood. Thus, assessing the distribution and specificity of ant termitophagy is of considerable interest. We describe an approach for quantifying ant-termite food webs by sequencing termite DNA (cytochrome c oxidase subunit II, COII) from ant guts and apply this to a soil-dwelling ant community from tropical rain forest in Gabon. We extracted DNA from 215 ants from 15 species. Of these, 17.2 % of individuals had termite DNA in their guts, with BLAST analysis confirming the identity of 34.1 % of these termites to family level or better. Although ant species varied in detection of termite DNA, ranging from 63 % (5/7; Camponotus sp. 1) to 0 % (0/7; Ponera sp. 1), there was no evidence (with small sample sizes) for heterogeneity in termite consumption across ant taxa, and no evidence for species-specific ant-termite predation. In all three ant species with identifiable termite DNA in multiple individuals, multiple termite species were represented. Furthermore, the two termite species that were detected on multiple occasions in ant guts were in both cases found in multiple ant species, suggesting that ant-termite food webs are not strongly compartmentalised. However, two ant species were found to consume only Anoplotermes-group termites, indicating possible predatory specialisation at a higher taxonomic level. Using a laboratory feeding test, we were able to detect termite COII sequences in ant guts up to 2 h after feeding, indicating that our method only detects recent feeding events. Our data provide tentative support for the hypothesis that unspecialised termite predation by ants is widespread and highlight the use of molecular approaches for future studies of ant-termite food webs.
Fulltext Regions of very low H3K27me3 partition the Drosophila genome into topological domains

El-Sharnouby S, Fischer B, Magbanua JP, Umans B, Flower R, Choo SW, et al.

PLoS One, 2017;12(3):e0172725.
PMID: 28282436 DOI: 10.1371/journal.pone.0172725

It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4/Putzig. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the transcription start sites of housekeeping genes than with the H3K27me3 domain boundaries. While we have not demonstrated causality, we suggest that the D domain chromatin state, characterised by very low or absent H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.
Fulltext Centering and collaborating with community knowledge systems: piloting a novel participatory modeling approach

Shaikh Y, Jeelani M, Gibbons MC, Livingston D, Williams DR, Wijesinghe S, et al.

Int J Equity Health, 2023 Mar 13;22(1):45.
PMID: 36915080 DOI: 10.1186/s12939-023-01839-0

BACKGROUND: Systems science approaches like simulation modeling can offer an opportunity for community voice to shape policies. In the episteme of many communities there are elders, leaders, and researchers who are seen as bearers of historic knowledge and can contextualize and interpret contemporary research using knowledge systems of the community. There is a need for a systematic methodology to collaborate with community Knowledge Bearers and Knowledge Interpreters. In this paper we report the results of piloting a systematic methodology for collaborating with a community Knowledge-Bearer and Knowledge-Interpreter to develop a conceptual model revealing the local-level influences and architecture of systems shaping community realities. The use case for this pilot is 'persistent poverty' in the United States, specifically within the inner-city African American community in Baltimore City.
METHODS: This pilot of a participatory modeling approach was conducted over a span of 7 sessions and included the following steps, each with an associated script: Step 1: Knowledge-Bearer and Knowledge-Interpreter recruitment Step 2: Relationship building Step 3: Session introduction, Vignette development & enrichment Step 4: Vignette analysis & constructing architecture of systems map Step 5: Augmenting architecture of systems map RESULTS: Each step of the participatory modeling approach resulted in artifacts that were valuable for both the communities and the research effort. Vignette construction resulted in narratives representing a spectrum of lived experiences, trajectories, and outcomes within a community. The collaborative analysis of vignettes yielded the Architecture of Systemic Factors map, that revealed how factors inter-relate to form a system in which lived experience of poverty occurs. A literature search provided an opportunity for the community to contextualize existing research about them using realities of lived experience.
CONCLUSION: This methodology showed that a community Knowledge Bearer can function as communicators and interpreters of their community's knowledge base, can develop coherent narratives of lived experiences within which research and knowledge is contextualized, and can collaboratively construct conceptual mappings necessary for simulation modeling. This participatory modeling approach showed that even if there already exists a vast body of research about a community, collaborating with community gives context to that research and brings together disparate findings within narratives of lived experience.