Biology subjects

Davies, S. J.

Publications and source records attributed to Davies, S. J..

12 recordsLinked to original sources

bioRxiv2026

A scalable in vitro cell competition model identifies preleukemic super competitor clones

Preleukemic and leukemic conditions are frequently characterized by the acquisition of recurrent genetic mutations in hematopoietic stem cells (HSCs). One of the most frequently mutated genes in both clonal hematopoiesis and myeloid malignancies is the ten-eleven translocation 2 (TET2) gene, which encodes an epigenetic enzyme with a critical role in the regulation of gene transcription. While substantial work has shown that TET2 loss-of-function mutations lead to a clonal advantage, the underpinning cellular mechanism remains unclear, especially with respect to the early interactions with other cells. To study these early cell interactions of mutant and non-mutant cells, we developed an in vitro clonal competition platform where single-cell derived cultures are split into subclonal fractions which can be simultaneously cross-competed against multiple different clones of an opposing genotype. We identify a novel preleukemic cell phenotype that parallels the developmental biology phenomenon of super-competition, whereby ~10% of TET2-mutant clones actively and selectively suppress wild type (WT) cell expansion and, in some cases, completely eliminate WT clones. Molecular profiling and functional assays point to RAC1-GEF signalling inhibition as a specific WT cell vulnerability that is promoted, and tolerated, by neighbouring TET2-mutated clones. In addition to pinpointing selective drivers of non-mutant cell suppression, this clonal competition platform offers a broadly applicable new approach to study cell competition dynamics at an unprecedented scale.

cancer biology↗

bioRxiv2024

Apparent digestibility and nutritional performance of bakery waste produced in Punjab Pakistan for Labeo rohita fingerlings

This study aimed to examine the impact of bakery waste supplementation on the nutrient digestibility and performance metrics of rohu (Labeo rohita) juveniles. Fish were fed with seven different diets containing bakery waste products (biscuits, cream cake, bread, and dry rusk) in combination with rice polish and wheat flour. Chromic oxide (1%) was added to the diet as an inert marker to measure nutrient digestibility. The results indicated a significant difference (p < 0.05) in the digestibility of crude protein, lipid, gross energy, and dry matter among the dietary groups. Fish fed with rice polish had the lowest apparent digestibility value of protein (16.13 {+/-} 1.86), whereas fish fed wheat flour had the highest (77.70 {+/-} 0.05). Moreover, it was shown that fish fed rusk waste had better growth. It has been concluded that bakery wastes could be used as a cheaper fish feed ingredient source for the manufacturing of cost-effective feed for L. rohita. This investigation was discussed within the context of providing cost effective ingredients for sustainable aquaculture production in Pakistan.

zoology↗

bioRxiv2024

Coated crystalline essential amino acid supplementation supports high soybean meal inclusion in diets for Nile tilapia (Oreochromis niloticus) with improved protein retention and nutrient assimilation

The aquaculture industry has previously relied on high-quality fishmeal (FM) to produce diets of excellent standards. However, plant-based proteins such as soybean are more cost-effective for low-value fish species, for example, tilapia and carp, and fishmeal use has been significantly diminished. Previous studies have mainly addressed standard soybean meal (SBM) sources in aquafeeds. A 55-day feeding trial was conducted to investigate the replacement of fish meal with soybean meal concentrate in Nile tilapia (Oreochromis niloticus) using a semi-purified diet approach against a Low Temperature (LT) fishmeal as a primary reference protein. Four diets with different levels of soybean meal were evaluated and compared to a control diet of 100 % fish meal. Three diets containing 20, 40, and 80 % soybean protein concentrate (SBPC) were examined. The fourth diet consisted of 80 % SBPC and two essential amino acids: lysine and methionine (80SBPCAA) in a coated form. The average daily growth values highlight similar daily growth rates when tilapia was fed 100FM and 40SBPC. No significant differences were observed in the final mean weight for all soybean-fed tilapia, but they were marginally lower than the 100FM control diet group. The 80SBPC diet showed the poorest feed conversion ratio (FCR) at 1.31 and protein efficiency ratio (PER) at 2.19. However, the 80SBPCAA diet showed a significantly improved result for per cent weight gain compared to the 80SBPC-fed tilapia. Also, protein efficiency ratio was significantly higher at 2.47 and had a better Apparent Net Protein Utilization (ANPU) value of 28.51 % compared to un-supplemented 80SBPC-fed tilapia (25.48 %). These results confirmed that high-quality fishmeal can be substituted by up to 40 % SBPC alone and without any detrimental effects on growth or carcass composition. Further studies on plant proteins and supplementary amino acids as a suitable alternative for replacing high-quality fishmeal may promote a more sustainable aquaculture industry.

developmental biology↗

bioRxiv2023

Nutritional value of extracted soybean, full fat soya and maize gluten meal proteins in comparison to a fishmeal-based reference diet for fingerling tilapia (Oreochromis mossambicus)

A two-month investigation evaluated potential selected plant protein sources compared to fish meal protein in scientifically formulated diets for fingerling tilapia (Oreochromis mossambicus). Six nutritionally balanced diets: one reference (control) diet (fish-meal-based diet), three selected plant proteins (solvent extracted soybean, full fat soybean, and maize gluten) were substituted in the LT (Low Temperature dried) fish-meal-based control diet protein at 50% respectively, and the remaining diets were replaced with 75% inclusion of solvent extracted soybean and maize gluten meals. Results showed that SESB50, FFSB50 and MG50 fed tilapia did not appreciably differ in their growthperformance (final mean weights of 12.07, 10.75 and 9.18% respectively) with a final mean weight of 14.95g being significantly superior for the fish meal control (CO) group. Substitution of fish meal diet with solvent-extracted soybean and maize gluten at levels of 75% gave the poorest growth performance and Feed Efficiency (FE) (7.01g final weight, 51% FE). However, the MG50 diet also showed some inferior feed utilisation performance. However, tilapia fed on a full fat soybean diet (FFSB50) did not vary significantly from the control (CON) diet in terms of Apparent Net Protein Utilisation (ANPU) at 34.20 and 37.53% respectively. Whilst this preliminary study concluded that limitations on the use of the selected plant proteins in diets for tilapia are apparent, several approaches that could result in the future improvement of the nutritional value of soybean and maize gluten products for use in fish diets are also stated. HighlightsA scientifically formulated reference diet using a Low Temperature dried (LT) fish meal produced superior growth performance for fingerling tilapia compared to selected oilseed (soybean) and grain (maize gluten) derived protein concentrates. Soybean and full fat soybean meals were effective in contributing to 50% inclusion in experimental diets, but 75% of soybean and maize gluten meal was not able to support similar growth of tilapia over eight weeks. Feed utilisation parameters such as Protein Efficiency Ratio (PER), Apparent Net Protein Utilisation (ANPU), Net Energy Utilisation (NEU) and Feed Efficiency (FE) gave supporting evidence and conclusions for optimal threshold inclusions of the test plant ingredients for tilapia.

developmental biology↗

bioRxiv2023

Enhancing farmed striped catfish (Pangasianodon hypophthalmus) robustness using dietary β-glucan

{beta}-glucan is a well-documented feed additive for its potent immunostimulatory properties in many farmed fish species. This study examined how it can also be a promising growth promoter, modulate antioxidant enzyme activities, and act as an anti-stress agent in striped catfish (Pangasianodon hypophthalmus). A 12-week feeding experiment was untaken to determine the effects of dietary {beta}-glucan supplementation at graded levels (0, 0.5, 1.0, and 1.5 g kg-1). Measured indicators suggest that a dietary inclusion level of 1.5 g kg-1 {beta}-glucan gave the highest positive responses: weight gain (120.10 g fish-1), survival (98.30 %), and lower FCR (1.70) (P<0.05). Whole body proximate analysis had only revealed that crude protein was significantly affected by the dietary inclusion of {beta}-glucan (P<0.05), with the highest protein content (19.70 %) being in fish that were fed with 1.5 g kg-1 {beta}-glucan. Although other inclusion levels (i.e., 0.5 and 1 g kg-1) of {beta}-glucan did not enhance body protein content (P>0.05). The assessment of fatty acid composition in muscle, liver, and adipose tissues showed modifications with the inclusion of {beta}-glucan. Antioxidative-related enzyme activities (inc. catalase, glutathione peroxidase, and superoxide dismutase) that were measured in the liver had higher levels when fed with {beta}-glucan inclusion diets (P<0.05). Following the feed trial, fish were subjected to crowding stress treatment. It was subsequently found that catfish fed with {beta}-glucan-based diet groups had lower levels of blood stress-related indicators compared to the control group with no dietary {beta}-glucan. The use of 1.5 g kg-1 of dietary {beta}-glucan resulted in the lowest measured levels of cortisol (43.13 ng mL-1) and glucose (50.16 mg dL-1). This study has demonstrated that the dietary inclusion of {beta}-glucan can have functional benefits beyond the immunological enhancements in striped catfish. Furthermore, its use can increase production levels and mitigate the stress associated with intensive farming practices.

zoology↗

bioRxiv2023

Influence of pseudo-green water on growth, colouration, and survival in European lobster (Homarus gammarus) larvae

With the depletion of European lobster (Homarus gammarus) wild stocks from historic overexploitation, the attention has turned towards restocking, stock enhancement programs and farming potential. The early life larval stages of the European lobster present a major barrier to hatchery production efforts due to low survival rates. Green water techniques are rapidly growing due to their ability to improve nutrition quality. This study explores the potential benefits of using pseudo-green water. This is determined by adding microalgae to the rearing environment of larvae by analysing the effects on growth and survival. The commonly used algal species: Tetraselmis suecica (TS), Dunaliella salina (DS), and Nannochloropsis sp. (N) were added as monoculture or mixture treatments to a controlled European lobster larvae-rearing environment over thirteen days. The trial consisted of seven permutations of algal treatments (TS, DS, N, TS+DS, TS+N, DS+N, and TS+DS+N) and one control group, with clear water conditions using length measurements, survival rates and colouration to determine treatment impacts at the end of the trial. Results indicate that mixtures of algal species outperformed monocultures and clear water regarding growth performance. Nannochloropsis sp. is of significant benefit to growth performance. Algal mixes containing Nannochloropsis sp. resulted in significantly better growth than D. salina monoculture treatment. There were no significant differences in survival rates between treatment groups.

developmental biology↗

bioRxiv2023

Major axes of variation in tree demography across global forests

The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatial-temporal patterns in tree population dynamics. While historical research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach is to group mechanisms according to their shared effects on the variability of tree vital rates and to quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in tree growth, mortality, and recruitment to variation in species, space, and time, and their interactions, categories we refer to as organising principles (OPs). We applied the framework to data from 21 forest plots covering more than 2.9 million trees of approximately 6,500 species. We found that differences among species, the species OP, proved a major source of variability in tree vital rates, explaining 28-33% of demographic variance alone, and in interaction with space 14-17%, totalling 40-43%. The average variability among species declined with species richness across forests, indicating that diverse forests featured smaller interspecific differences in vital rates supporting the theory that the range of vital rates is similar across global forests. Decomposing the variance in vital rates into the proposed OPs showed that taxonomy is crucial to predicting and understanding tree demography on large forest plots. A focus on how variance is organized in forests can facilitate the construction of more targeted models with clearer expectations of which covariates might drive a vital rate. This study therefore highlights the most promising avenues for future research, both in terms of understanding the relative contributions of groups of mechanisms to forest demography and diversity, and for improving projections of forest ecosystems.

ecology↗

bioRxiv2022

Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech.

Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33,042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the SNP-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-fall transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologs we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed GO terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech (Fagus grandifolia).

ecology↗

bioRxiv2021

Key Drivers of Ecological Assembly in the Hindgut of Atlantic Cod (Gadus morhua) when Fed with a Macroalgal Supplemented diet - How Robust Is the Gut to Taxonomic Perturbation?

The microbiota in the gastrointestinal tract of any species is shaped by internal and external cues in addition to random events which can be difficult to disentangle from a range of interacting variables. Estimating ecological assembly processes can help elucidate these factors. In our study, farmed Atlantic cod (Gadus morhua) were fed a diet of 10% macroalgae supplement (Ulva rigida species [ULVA] or Ascophyllum nodosum [ASCO] or a non-amended control diet [CTRL]) over a 12-week period and the ecological assembly processes quantified. The CTRL samples showed selection (variable selection - divergence in communities related to selective environmental conditions) as a key assembly process, while dispersal limitation (limited movement results in divergent communities through stochastic processes) was a driver of the gut microbiome for fish fed the macroalgae supplemented diet at Week 12 (i.e., ASCO and ULVA). Fish from the ASCO grouping diverged into ASCO_N (normal) and ASCO_LG (lower growth), where ASCO_LG individuals found the diet unpalatable. The recruitment of new taxa over time was altered in the ASCO_LG fish, with the gut microbiome showing phylogenetic under dispersion (nepotistic recruitment of species). Finally, the gut microbiome (CTRL and ULVA only) showed increasing robustness to taxonomic disturbance over time and an increase in functional redundancy. This study advances our understanding of the ecological assembly and succession in the hindgut of juvenile Atlantic cod across dietary regimes. Understanding the processes driving ecological assembly in the gut microbiome, in fish research specifically, could allow us to manipulate the microbiome for improved health or resilience to disease for improved aquaculture production.

microbiology↗

bioRxiv2021

Comparative Transcriptomics of Tropical Woody Plants Supports Fast and Furious Strategy along the Leaf Economics Spectrum in Lianas.

Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, include upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. All together, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance.

plant biology↗

bioRxiv2020

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae.

BackgroundAquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is modest in comparison to market demand. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. ResultsThe results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time-point. This contrasts with the A. nodosum treatment. Fish within this group were further categorised as either Normal or Lower Growth. Lower Growth individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium). ConclusionsOur study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet.

microbiology↗

bioRxiv2018

Positive and negative plant-soil feedbacks are caused by mycorrhizal type, soil fertility, and phylogenetic relatedness in a mixed Dipterocarp rain forest

While work in temperate forests suggests that there may be consistent differences in plant-soil feedback (PSF) between plants with arbuscular and ectomycorrhizal associations, it is unclear whether this is compatible with the high diversity of tropical rainforests. To examine this, we tested the effect of mycorrhizal type, phylogenetic distance, and soil fertility on variation in PSF strength in a mixed-tropical rainforest with a uniquely high diversity of ectomycorrhizal and arbuscular mycorrhizal trees. We found positive phylogenetic PSFs for ectomycorrhizal tree species that were insensitive to soil fertility. By contrast, PSFs for arbuscular mycorrhizal tree species were negative, and increasingly so with greater soil fertility. Our results demonstrate consistent effects of mycorrhizal types on plant population dynamics across biomes, and help explain biogeographic variation across tropical forests, such as familial dominance of the Dipterocarpaceae in SE Asia. However, they also raise questions about the role of PSFs in maintaining tropical diversity.\n\nStatement of authorshipRMS, SER, SJD and KGP designed the experiment. RMS conducted the experiment and collected data. RMS analyzed data with input from KGP and SER. RMS wrote the first draft of the manuscript, and all authors contributed to subsequent revision and preparation of the manuscript.

ecology↗