Biology subjects

Hoffmann, A.

Publications and source records attributed to Hoffmann, A..

6 recordsLinked to original sources

bioRxiv2018

Non-heritable variation in individual fitness adds stability to neutral theories in ecology and evolution

Neutral theories in ecology1 and evolution2 contend that high diversity of natural communities and high rates of molecular evolution conform to models where individuals have equal fitness and mutations have no effects. Demographic stochasticity makes community and population compositions inherently unstable under these models, with overall levels of diversity being maintained by random processes. This is in contrast with niche and adaptive theories which emphasize differences between species or genotypes as the key to their coexistence3. Here we show that non-heritable variation in individual fitness within species or genotypes can stabilize coexistence without evoking niche differentiation. We construct two classes of mathematical models based on experimental evidence: (1) bacterial growth with variation in cell longevity4,5; and (2) microbial transmission in a host population with variation in host susceptibility6-11. We find stable coexistence of 2 bacterial species in the first model under a single oscillating resource, and 3 or more in the second with independent distributions of host susceptibility to the various microbial species. We discuss the implications of these findings for the interpretation of common measures of relative fitness and for the maintenance of biodiversity.

ecology↗

bioRxiv2018

Climate, human influence, and the distribution limits of the invasive European earwig, Forficula auricularia, in Australia

BACKGROUNDBy modelling species-environment relationships of pest species, it is possible to understand potential limits to their distributions when they invade new regions, and their likely continued spread. The European earwig, Forficula auricularia, is a non-native invasive species in Australia that has been in the country for over 170 years. However, in the last few decades it has invaded new areas. Unlike in other countries, F. auricularia is a pest species of grains production in Australia. In this study we detail the Australian distribution of this species, adding new samples focussed around grain growing regions. Using this information we build global species distribution models for F. auricularia to better understand species-environment relationships.\n\nRESULTSOur models indicated that the distribution of F. auricularia is strongly associated with temperate through to semi-arid environments, a high winter rainfall and pronounced temperature seasonality. We identified regions that hold suitable, but as yet vacant, niche space for Australian populations, suggesting further potential for range expansion. Beyond climate, an index describing human influence on the landscape was important to understand the distribution limits of this pest. We identified regions where there was suitable climate space, but which F. auricularia has not occupied likely due to low levels of human impact.\n\nCONCLUSIONModelling the global distribution of a non-native pest species aided understanding of the regional distribution limits within Australia and highlighted the usefulness of human impact measures for modelling globally invasive insect species.

ecology↗

bioRxiv2018

Polypyrimidine Tract Binding Protein blocks microRNA-124 biogenesis to enforce its neuronal specific expression.

MicroRNA-124 is expressed in neurons, where it represses genes inhibitory for neuronal differentiation, including the RNA binding protein PTBP1. PTBP1 maintains non-neuronal splicing patterns of mRNAs that switch to neuronal isoforms upon neuronal differentiation. We find that pri-miR-124-1 is expressed in mouse embryonic stem cells (mESCs) where mature miR-124 is absent. PTBP1 binds to this precursor RNA upstream of the miRNA stem-loop to inhibit mature miR-124 expression in vivo, and DROSHA cleavage of pri-miR-124-1 in vitro. This new function for PTBP1 in repressing miR-124 biogenesis adds an additional regulatory loop to the already intricate interplay between these two molecules. Applying mathematical modeling to examine the dynamics of this regulation, we find that the pool of pri-miR-124 whose maturation is blocked by PTBP1 creates a robust and self-reinforcing transition in gene expression as PTBP1 is depleted during early neuronal differentiation. While interlocking regulatory loops are often modeled between miRNAs and transcriptional regulators, our results indicate that miRNA targeting of posttranscriptional regulators also reinforces developmental decisions. Notably, induction of neuronal differentiation observed upon PTBP1 knockdown likely results from direct de-repression of miR-124, in addition to indirect effects previously described.

molecular biology↗

bioRxiv2017

A molecular model of the mitochondrial genome segregation machinery in Trypanosoma brucei

In almost all eukaryotes mitochondria maintain their own genome. Despite the discovery more than 50 years ago still very little is known about how the genome is properly segregated during cell division. The protozoan parasite Trypanosoma brucei contains a single mitochondrion with a singular genome the kinetoplast DNA (kDNA). Electron microscopy studies revealed the tripartite attachment complex (TAC) to physically connect the kDNA to the basal body of the flagellum and to ensure proper segregation of the mitochondrial genome via the basal bodies movement, during cell cycle. Using super-resolution microscopy we precisely localize each of the currently known unique TAC components. We demonstrate that the TAC is assembled in a hierarchical order from the base of the flagellum towards the mitochondrial genome and that the assembly is not dependent on the kDNA itself. Based on biochemical analysis the TAC consists of several non-overlapping subcomplexes suggesting an overall size of the TAC exceeding 2.8 mDa. We furthermore demonstrate that the TAC has an impact on mitochondrial organelle positioning however is not required for proper organelle biogenesis or segregation.\n\nSignificance StatementMitochondrial genome replication and segregation are essential processes in most eukaryotic cells. While replication has been studied in some detail much less is known about the molecular machinery required distribute the replicated genomes. Using super-resolution microscopy in combination with molecular biology and biochemistry we show for the first time in which order the segregation machinery is assembled and that it is assembled de novo rather than in a semi conservative fashion in the single celled parasite Trypanosoma brucei. Furthermore, we demonstrate that the mitochondrial genome itself is not required for assembly to occur. It seems that the physical connection of the mitochondrial genome to cytoskeletal elements is a conserved feature in most eukaryotes, however the molecular components are highly diverse.\n\nAbbreviation

cell biology↗

bioRxiv2017

Genome-Wide SNPs Reveal the Drivers of Gene Flow In An Urban Population of the Asian Tiger Mosquito, Aedes albopictus

Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Ae. albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations.\n\nAuthor SummaryAedes albopictus, the Asian Tiger Mosquito, is a highly invasive disease vector with a growing global distribution. Designing strategies to prevent invasion and to control Ae. albopictus populations in invaded regions requires knowledge of how Ae. albopictus disperses. Studies comparing Ae. albopictus populations have found little evidence of genetic structure even between distant populations, suggesting that dispersal along human transportation networks is common. However, a more specific understanding of dispersal processes has been unavailable due to an absence of studies using high-resolution genetic markers. Here we present a study using high-resolution markers, which investigates genetic structure among 152 Ae. albopictus from Guangzhou, China. We found that human transportation networks, particularly shipping terminals, had an influence on genetic structure. We also found genetic distance was correlated with geographical distance, the first such observation in this species. This study demonstrates how high-resolution markers can be used to investigate ecological processes that may otherwise escape detection. We conclude that strategies for controlling Ae. albopictus will have to consider both passive reinvasion along human transportation networks and active reinvasion from neighbouring regions.

ecology↗

bioRxiv2017

Addressing the digital divide in contemporary biology: Lessons from teaching UNIX

Researchers in the biomedical sciences increasingly rely on applications that lack a graphical interface and require inputting code that, such as UNIX. Scientists who are not trained in computer science face an enormous challenge in analyzing the high-throughput data their research groups generate. We present a training model for use of command-line tools when the learner has little to no prior knowledge of UNIX.

scientific communication and education↗