Biology subjects

Hammer, T.

Publications and source records attributed to Hammer, T..

5 recordsLinked to original sources

bioRxiv2026

A dermal-epidermal junction-inclusive skin model enabled by controllable hydrogel swelling

Tissue engineered skin models are important tools for the in vitro study of physiological and pathophysiological processes as well as the evaluation of therapeutic strategies and the efficacy of pharmaceutical and cosmetic compounds. Replicating the functional anatomy of cutaneous tissue is a crucial aspect in ensuring that observations made using these models are translatable to the actual situation in native skin. However, most contemporary full-thickness skin models neglect the reconstruction of the undulated microtopography of the dermal-epidermal junction (DEJ), which not only contributes to the biological functionality of the skin (e.g. stem cell niches), but also affects tissue mechanics and drug diffusion. Herein, we fabricated bilayer skin models with DEJ-like microtopographies introduced by interfacial wrinkling between a hydrogel and a nanofibrous membrane through a controllable swelling-deswelling approach. The interfacial wrinkles contributed to the structural integrity of the bilayer models. Their formation could be induced in the presence of living cells through mechanical stress-driven buckling instabilities, thus differentiating the process from commonly used pre-patterning techniques. Bilayer models supported the co-culture of human dermal fibroblasts and human epidermal keratinocytes, and the formation of stratified epithelia. Our findings provide a potential alternative method to introduce DEJ-like anatomical features into full-thickness skin tissue models.

bioengineering↗

bioRxiv2026

Gain and loss of gut symbionts during stingless bee diversification is linked to host group size

Microbiomes typically vary between closely related host species, but how and why they diverge during host diversification remain poorly understood. Bees provide a well-established model for the role of sociality in microbiome evolution: solitary species have generalist gut bacterial symbionts, while eusocial honey bees and bumble bees have host-specific "core" gut bacterial symbionts. Curiously however, some species of stingless bees--the most diverse clade of eusocial bees--lack the core symbionts Snodgrassella and Gilliamella. Here, we tested whether group size, a fundamental trait of social organisms, explains symbiont gain and loss in stingless bees. Using specimens from a global collection, we performed 16S rRNA gene sequencing and qPCR on 187 adult workers representing 29 species and 18 genera. Maximum reported colony sizes for these species range from [~]100 to over [~]100,000 individuals. Our phylogenetic models indicate positive feedbacks between group size and the symbionts Snodgrassella and Gilliamella. We suggest that challenges faced by large groups (e.g., disease risk) may select for symbionts that supply needed functionality (e.g., pathogen protection). Our findings highlight group size as a potentially widespread driver of microbiome evolution in social hosts.

evolutionary biology↗

bioRxiv2025

A comparison of two universal angiosperm bait sets and the phylogenomics of Alismatales

High throughput sequencing of hybridisation capture libraries provides an efficient approach for assembling large scale phylogenomic data. These include universal bait sets that aim to generate comparable data from any lineage within the taxon of interest. Here, we present the OzBaits v2 bait set, which targets a set of low copy nuclear loci for angiosperms. Using published genomic data, we design a set of RNA baits targeting a single exon in each of 98 putatively orthologous nuclear protein coding genes. We tested the efficiency of this bait set for a diverse range of angiosperms and recovered, on average, 93 (95%) genes per sample. We compared a common set of samples for the monocot order Alismatales enriched using OzBaits and the Angiosperms353 (A353) bait set, a widely used universal probe set targeting up to 353 nuclear genes in angiosperms. Gene recovery was, on average, c. 1.7 times higher for OzBaits relative to A353. Using proxies for signal and bias to rank gene alignments by their phylogenetic usefulness, we found that on average, the OzBaits data had higher phylogenetic utility. Both data sets resolved largely congruent, well-supported phylogenies for Alismatales although measures of internal discordance where higher for the A353 data. We discuss the implications of these findings for the design universal baits sets.

evolutionary biology↗

bioRxiv2024

Blanking on Blanks: Few Insect Microbiota Studies Control for Contaminants - A Systematic Review

Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial biomass. Such low-biomass samples are common across insect taxa, developmental stages, and tissue types. Identifying putative contaminants is essential to distinguish between true microbiota and introduced contaminant DNA. It is therefore important that studies control for contamination, but how often this is done is unknown. To investigate the status quo of contamination control, we undertook a systematic literature review to quantify the prevalence of negative control usage and contamination control across the literature on insect microbiota (specifically bacterial communities) over the past 20 years. Two-thirds of the 243 insect microbiota studies evaluated did not include blanks (negative controls), and only 13.6% of the studies sequenced these blanks to control for contamination in their samples. Our findings highlight a major lack of contamination control in the field of insect microbiota research. This result suggests that a large number of microbes reported in the literature may be contaminants as opposed to insect-associated microbiota, and that more rigorous contamination control is needed to improve research reliability, validity and reproducibility. Based on our findings, we recommend a modified version of the guidelines outlined in the RIDES checklist: Report methodology, Include negative controls, Determine the level of contamination, Explore contamination downstream, and State the amount of off-target amplification. IMPORTANCEOur systematic review reveals a major lack of methodological rigour within the field of research on insect-associated microbiota. The small percentage of studies that control for contamination suggests that a considerable proportion of bacteria reported in the literature could be contaminants. The implication of this finding is that true microbiota may be masked or misrepresented, especially in insects with low microbial biomass.

microbiology↗

bioRxiv2017

Structure and function of the bacterial and fungal gut flora of Neotropical butterflies

The relationship between animals and their gut flora is simultaneously one of the most common and most complex symbioses on Earth. Despite its ubiquity, our understanding of this invisible but often critical relationship is still in its infancy. We employed adult Neotropical butterflies as a study system to ask three questions: First, how does gut microbial community composition vary across host individuals, species and dietary guilds? Second, how do gut flora compare to food microbial communities? Finally, are gut flora functionally adapted to the chemical makeup of host foods? To answer these questions we captured nearly 300 Costa Rican butterflies representing over 50 species, six families and two feeding guilds: frugivores and nectivores. We characterized the bacteria and fungi in guts, wild fruits and wild nectars via amplicon sequencing and assessed the catabolic abilities of the gut flora via culture-based assays.\n\nGut communities were distinct from food communities, suggesting that the gut environment acts as a strong filter on potential colonists. Nevertheless, gut flora varied widely among individuals and species. On average, a pair of butterflies shared 21% of their bacterial species and 6% of their fungi. Host species explained 25-30% of total variation in microbial communities while host diet explained 4%. However, diet was still relevant at the individual microbe level--half of the most abundant microbial species differed in abundance between frugivores and nectivores. Diet was also related to the functional profile of gut flora: compared to frugivores, nectivores gut flora exhibited increased catabolism of sugars and sugar alcohols and decreased catabolism of amino acids, carboxylic acids and dicarboxylic acids. Since fermented juice contains more amino acids and less sugar than nectar, it appears that host diet filters the gut flora by favoring microbes that digest compounds abundant in foods.\n\nBy quantifying the degree to which gut communities vary among host individuals, species and dietary guilds and evaluating how gut microbial composition and catabolic potential are related to host diet, this study deepens our understanding of the structure and function of one of the most complex and ubiquitous symbioses in the animal kingdom.

ecology↗