Biology subjects

Koch, A.

Publications and source records attributed to Koch, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2021

Flow cytometry method for absolute counting and single-cell phenotyping of mycobacteria

Detection and accurate quantitation of viable Mycobacterium tuberculosis is fundamental to understanding mycobacterial pathogenicity, tuberculosis (TB) disease progression and outcomes; TB transmission; drug action, efficacy and drug resistance. Despite this importance, methods for determining numbers of viable bacilli are limited in accuracy and precision owing to inherent characteristics of mycobacterial cell biology - including the tendency to clump, and "differential" culturability - and technical challenges consequent on handling an infectious pathogen under biosafe conditions. We developed an absolute counting method for mycobacteria in liquid cultures using a bench-top flow cytometer, and the low-cost fluorescent dyes Calcein-AM (CA) and SYBR-gold (SG). During exponential growth CA+ cell counts are highly correlated with CFU counts and can be used as a real-time alternative to simplify the accurate standardisation of inocula for experiments. In contrast to CFU counting, this method can detect and enumerate cell aggregates in samples, which we show are a potential source of variance and bias when using established methods. We show that CFUs comprise a sub-population of intact, metabolically active mycobacterial cells in liquid cultures, with CFU-proportion varying by growth conditions. A pharmacodynamic application of the flow cytometry method, exploring kinetics of fluorescent probe defined subpopulations compared to CFU is demonstrated. Flow cytometry derived Mycobacterium bovis BCG time-kill curves differ for rifampicin and kanamycin versus isoniazid and ethambutol, as do the relative dynamics of discrete morphologically-distinct subpopulations of bacilli revealed by this high-throughput single-cell technique.

microbiology↗

bioRxiv2021

Isolation and characterization of barley (Hordeum vulgare) extracellular vesicles and their role in RNAi-based crop protection

The demonstration that spray-induced gene silencing (SIGS) can confer strong disease resistance bypassing the laborious and time-consuming transgenic expression of double-stranded (ds)RNA to induce gene silencing of pathogenic targets was groundbreaking. However, future field applications will require fundamental mechanistic knowledge on dsRNA uptake, processing, and its transfer. There is increasing evidence that extracellular vesicles (EVs) mediate the transfer of transgene-derived small interfering (si)RNAs in host-induced gene silencing (HIGS) applications. Here, we examined the role of EVs regarding the translocation of sprayed dsRNA from barley (Hordeum vulgare) to the target fungus Fusarium graminearum. We found barley EVs with 156 nm in size containing predominantly 21 and 19 nucleotide (nt) siRNAs starting with a 5-terminal Adenine. Notably, barley EVs contain less siRNA compared to EVs isolated from transgenic HIGS Arabidopsis plants. Together our results further underpin mechanistic differences between HIGS and SIGS applications and a minor role of EVs in SIGS.

plant biology↗

bioRxiv2021

Structures of active melanocortin-4 receptor--Gs-protein complexes with NDP-α-MSH and setmelanotide

The melanocortin-4 receptor (MC4R), a hypothalamic master regulator of energy homeostasis and appetite, is a G-protein coupled receptor and a prime target for the treatment of obesity. Here, we present cryo-electron microscopy structures of MC4R- Gs-protein complexes with two recently FDA-approved drugs, the peptide agonists NDP--MSH and setmelanotide, with 2.9 [A] and 2.6 [A] resolution. Together with signaling data, the complex structures reveal the agonist-induced origin of transmembrane helix (TM) 6 regulated receptor activation. In both structures, different ligand binding modes of NDP--MSH, a high-affinity variant of the endogenous agonist, and setmelanotide, an anti-obesity drug with biased signaling, underline the key role of TM3 for ligand-specific interactions and of calcium ion as a ligand-adaptable cofactor. The agonist-TM3 interplay subsequently impacts the receptor- Gs-protein interfaces, mainly at intracellular loop 2. These structures reveal mechanistic details of MC4R activation or inhibition and provide important insights into receptor selectivity that will facilitate the development of tailored anti-obesity drugs.

biochemistry↗

bioRxiv2021

Predicting tomato field-yield using continuous monitoring of young tomato water status

To address the challenge of predicting tomato yields in the field, we used whole-plant functional phenotyping to evaluate water relations under well-irrigated and drought conditions. The genotypes tested are known to exhibit variability in their yields in wet and dry fields. The examined lines included two lines with recessive mutations that affect carotenoid biosynthesis, zeta z2083 and tangerine t3406, both isogenic to the processing tomato variety M82. The two mutant lines were reciprocally grafted onto M82, and multiple physiological characteristics were measured continuously, before, during and after drought treatment in the greenhouse. A comparative analysis of greenhouse and field yields showed that the whole-canopy stomatal conductance (gsc) in the morning and cumulative transpiration (CT) were strongly correlated with field measurements of total yield (TY: r2 = 0.9 and 0.77, respectively) and plant vegetative weight (PW: r2 = 0.6 and 0.94, respectively). Furthermore, the minimum CT during drought and the rate of recovery when irrigation was resumed were both found to predict resilience.

physiology↗

bioRxiv2021

Somatosensory innervation of healthy human oral tissues

The oral somatosensory system relays essential information about mechanical stimuli to enable oral functions such as feeding and speech. The neurochemical and anatomical diversity of sensory neurons across oral cavity sites have not been systematically compared. To address this gap, we analyzed healthy human tongue and hard palate innervation. Biopsies were collected from 12 volunteers and underwent multiplex fluorescent immunohistochemistry ([≥]2 specimens per marker/structure). Afferents were analyzed for markers of neurons ({beta}III tubulin), myelinated afferents (neurofilament heavy, NFH), and Merkel cells and taste cells (keratin 20, K20). Hard-palate innervation included Meissners corpuscles, glomerular endings, Merkel cell-neurite complexes, and free nerve endings. The organization of these somatosensory endings is reminiscent of fingertips, suggesting that the hard palate is equipped with a rich repertoire of sensory neurons for pressure sensing and spatial localization of mechanical inputs, which are essential for speech production and feeding. Likewise, the tongue is innervated by afferents that impart it with exquisite acuity and detection of moving stimuli that support flavor construction and speech. Filiform papillae contain end bulbs of Krause, as well as endings that have not been previously reported, including subepithelial neuronal densities, and NFH+ neurons innervating basal epithelium. Fungiform papillae had Meissners corpuscles and densities of NFH+ intraepithelial neurons surrounding taste buds. The differing compositions of sensory endings within filiform and fungiform papillae suggest that these structures have distinct roles in mechanosensation. Collectively, this study has identified previously undescribed afferent endings in human oral tissues and provides an anatomical framework for understanding oral mechanosensory functions.

neuroscience↗

bioRxiv2020

A SARS-CoV-2 neutralizing antibody selected from COVID-19 patients by phage display is binding to the ACE2-RBD interface and is tolerant to known RBD mutations

The novel betacoranavirus SARS-CoV-2 causes a form of severe pneumonia disease, termed COVID-19 (coronavirus disease 2019). Recombinant human antibodies are proven potent neutralizers of viruses and can block the interaction of viral surface proteins with their host receptors. To develop neutralizing anti-SARS-CoV-2 antibodies, antibody gene libraries from convalescent COVID-19 patients were constructed and recombinant antibody fragments (scFv) against the receptor binding domain (RBD) of the S1 subunit of the viral spike (S) protein were selected by phage display. The selected antibodies were produced in the scFv-Fc format and 30 showed more than 80% inhibition of spike (S1-S2) binding to cells expressing ACE2, assessed by flow cytometry screening assay. The majority of these inhibiting antibodies are derived from the VH3-66 V-gene. The antibody STE90-C11 showed a sub nM IC50 in a plaque-based live SARS-CoV-2 neutralization assay. The in vivo efficacy of the antibody was demonstrated in the Syrian hamster and in the hACE2 mice model using a silenced human IgG1 Fc part. The crystal structure of STE90-C11 Fab in complex with SARS-CoV-2-RBD was solved at 2.0 [A] resolution showing that the antibody binds at the same region as ACE2 to RBD. The binding and inhibtion of STE90-C11 is not blocked by many known RBD mutations including N439K, L452R, E484K or L452R+E484Q (emerging B.1.617). STE90-C11 derived human IgG1 with Fc{gamma}R silenced Fc (COR-101) is currently undergoing Phase Ib/II clinical trials for the treatment of moderate to severe COVID-19. In BriefHuman antibodies were selected from convalescent COVID-19 patients using antibody phage display. The antibody STE90-C11 is neutralizing authentic SARS-CoV-2 virus in vitro and in vivo and the crystal structure of STE90-C11 in complex with SARS-CoV-2-RBD revealed that this antibody is binding in the RBD-ACE2 interface. S1 binding of STE90-C11 and inhibition of ACE2 binding is not blocked by many known RBD mutations.

bioengineering↗

bioRxiv2020

Reprogramming of stromal fibroblasts by chemotherapy-induced secretion of IFNβ1 drives re-growth of breast cancer cells after treatment.

Chemotherapy is still the standard of care for a large number of aggressive tumours including breast cancer. In breast cancer, chemotherapeutic regimens are administered in intervaled cycles of the maximum tolerated dose, allowing cancer cells to re-grow or adapt during the resting periods between cycles. However, how stromal fibroblasts impact the fate of cancer cells after chemotherapy treatment remains poorly understood. We show that cancer cells utilize paracrine signalling with stromal fibroblasts to drive their recovery after treatment withdrawal. Secretion of IFN{beta}1 by cancer cells after treatment with high doses of chemotherapy instigates the acquisition of an anti-viral state in stromal fibroblasts associated with the expression of several interferon stimulated genes (ISGs), including numerous pro-inflammatory cytokines. This crosstalk is an important driver of the expansion of breast cancer cells after chemotherapy and blocking of IFN{beta}1 in tumour cells abrogated their increased recovery potential. Analysis of human breast carcinomas supports the proposed role of IFN{beta}1 since its expression is inversely correlated with recurrence free survival (RFS). Moreover, expression of the interferon signature identified in stromal fibroblasts is equally associated with higher recurrence rates and a worse outcome in breast cancer patients. Our study unravels a novel paracrine communication between cancer cells and fibroblasts that ultimately results in the escape of malignant cells to treatment. Targeting of this axis could potentially improve the outcome of breast cancer patients to chemotherapy treatment.

cancer biology↗

bioRxiv2020

The endometrial transcription landscape of MRKH syndrome

The Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome (OMIM 277000) is characterized by agenesis of the uterus and upper part of the vagina in females with normal ovarian function. While genetic causes have been identified for a small subset of patients and epigenetic mechanisms presumably contribute to the pathogenic unfolding, too, the etiology of the syndrome has remained largely enigmatic. A comprehensive understanding of gene activity in the context of the disease is crucial to identify etiological components and their potential interplay. So far, this understanding is lacking, primarily due to the scarcity of samples and suitable tissue. In order to close this gap, we profiled endometrial tissue of uterus rudiments in a large cohort of MRKH patients using RNA-seq and thereby provide a genome-wide view on the altered transcription landscape of the MRKH syndrome. Differential and co-expression analyses of the data identified cellular processes and candidate genes that converge on a core network of interconnected regulators that emerge as pivotal for the perturbed expression space. With these results and browsable access to the rich data through an online tool we seek to accelerate research to unravel the underlying biology of this syndrome.

genomics↗

bioRxiv2020

Host-induced gene silencing involves transfer of dsRNA-derived siRNA via extracellular vesicles

Small (s)RNAs and their double-stranded (ds)RNA precursors have been adopted to control diseases in crop plants through expression in transgenic plants and targeted gene silencing (host-induced gene silencing, HIGS). While HIGS strategies proved to be effective, the mechanism of RNA transfer at the plant - pathogen interface is widely unknown. Here we show that extracellular vesicles (EVs) purified from Arabidopsis thaliana plants expressing CYP3RNA, a dsRNA originally designed to target the three CYP51 genes of the fungal pathogen Fusarium graminearum, contain CYP3RNA-derived small interfering (si)RNAs as shown by RNA sequencing (RNA-seq) analysis. These transgene specific siRNAs had a length of 21 and 22 nucleotides with a bias towards 5-uracil (U) and 5-adenine (A). Notably, stringent protease and RNase treated EV fractions contained >70% less CYP3RNA-derived siRNAs, suggesting the presence of co-purified extravesicular nucleoprotein complexes stabilizing siRNAs outside of EVs. In addition, mutants of the ESCRT-III complex showed a loss of HIGS-mediated disease resistance and EVs isolated from these mutants were free of CYP3RNA-derived siRNAs. Together, these findings support the view that endosomal vesicle trafficking is required for HIGS mediating the transfer of transgene-derived siRNAs between donor host cells and recipient fungal cells probably in an EV-independent manner.

plant biology↗

bioRxiv2019

Phloem-mediated spreading of SIGS-derived non-coding RNAs in Hordeum vulgare

Small (s)RNA molecules are crucial factors in the communication between hosts and their interacting pathogens/pests that can modulate both host defense and microbial virulence/pathogenicity known as cross-kingdom RNA interference (ckRNAi). Consistent with this, sRNAs and their double-stranded (ds)RNA precursors have been adopted to control plant diseases through exogenously applied RNA biopesticides, known as spray-induced gene silencing (SIGS). While RNA spray proved to be effective, the mechanisms underlying the transfer and uptake of SIGS-associated RNAs are inadequately understood. Moreover, the use of the SIGS-technology as a biopesticide will require the systemic spreading of dsRNA/siRNA signals. Our results strongly support the notion of phloem-mediated long-distance movement of SIGS-associated dsRNA and/or siRNA. These findings are significant contributions to our mechanistic understanding of RNA spray technology, as our previous data indicate that SIGS requires the processing of dsRNAs by the fungal RNAi machinery. In summary, our findings support the model that SIGS involves: (i) uptake of sprayed dsRNA by the plant (via stomata); (ii) transfer of apoplastic dsRNAs into the symplast (DCL processing into siRNAs); (iii) systemic translocation of siRNA or unprocessed dsRNA via the vascular system (phloem/xylem); (iv) uptake of apoplastic dsRNA or symplastic dsRNA/siRNA depending on the lifestyle/feeding behavior of the pathogen/pest.

plant biology↗

bioRxiv2019

Study on the efficacy of dsRNAs with increasing length in RNAi-based silencing of the Fusarium CYP51 genes

Previously, we have demonstrated that transgenic Arabidopsis and barley plants, expressing a 791 nucleotide (nt) dsRNA (CYP3RNA) that targets all three CYP51 genes (FgCYP51A, FgCYP51B, FgCYP51C) in Fusarium graminearum (Fg), inhibited fungal infection via a process designated as host-induced gene silencing (HIGS). More recently, we have shown that spray applications of CYP3RNA also protect barley from fungal infection via a process termed spray-induced gene silencing (SIGS). Thus, RNAi technology may have the potential to revolutionize plant protection in agriculture. Therefore, successful field application will require optimization of RNAi design necessary to maximize the efficacy of the RNA silencing construct for making RNAi-based strategies a realistic and sustainable approach.\n\nPrevious studies indicate that silencing is correlated with the number of siRNAs generated from a dsRNA precursor. To prove the hypothesis that silencing efficiency is correlated with the number of siRNAs processed out of the dsRNA precursor, we tested in a HIGS and SIGS approach dsRNA precursors of increasing length ranging from 400 nt to 1500 nt to assess gene silencing efficiency of individual FgCYP51 genes. Concerning HIGS-mediated disease control, we found that there is no significant correlation between the length of the dsRNA precursor and the reduction of Fg infection on CYP51-dsRNA expressing Arabidopsis plants. Importantly and in clear contrast to HIGS, we measured a decrease in SIGS-mediated Fg disease resistance that significantly correlates with the length of the dsRNA construct that was sprayed, indicating that the size of the dsRNA interferes with a sufficient uptake of dsRNAs by the fungus.

plant biology↗

bioRxiv2019

RNA-spray-mediated silencing of Fusarium graminearum AGO and DCL genes improve barley disease resistance

Over the last decade, several studies have revealed the enormous potential of RNA-silencing strategies as a potential alternative to conventional pesticides for plant protection. We have previously shown that targeted gene silencing mediated by an in planta expression of non-coding inhibitory double-stranded RNAs (dsRNAs) can protect host plants against various diseases with unprecedented efficiency. In addition to the generation of RNA-silencing (RNAi) signals in planta, plants can be protected from pathogens and pests by spray-applied RNA-based biopesticides. Despite the striking efficiency of RNA-silencing-based technologies holds for agriculture, the molecular mechanisms underlying spray-induced gene silencing (SIGS) strategies are virtually unresolved, a requirement for successful future application in the field. Based on our previous work, we predict that the molecular mechanism of SIGS is controlled by the fungal-silencing machinery. In this study, we used SIGS to compare the silencing efficiencies of computationally-designed versus manually-designed dsRNA constructs targeting ARGONAUTE and DICER genes of Fusarium graminearum (Fg). We found that targeting key components of the fungal RNAi machinery via SIGS could protect barley leaves from Fg infection and that the manual design of dsRNAs resulted in higher gene-silencing efficiencies than the tool-based design. Moreover, our results indicate the possibility of cross-kingdom RNA silencing in the Fg-barley interaction, a phenomenon in which sRNAs operate as effector molecules to induce gene silencing between species from different kingdoms, such as a plant host and their interacting pathogens.

plant biology↗

bioRxiv2019

Call for participation: Collaborative benchmarking of functional-structural root architecture models. The case of root water uptake.

Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore defining common inputs that allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute towards improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development.

plant biology↗

bioRxiv2019

Phenotypic plasticity as an important mechanism of cave colonization and adaptation in Astyanax cavefish

A widely accepted model for the evolution of cave animals posits colonization by surface ancestors followed by the acquisition of adaptations over many generations. However, the speed of cave adaptation in some species suggests mechanisms operating over shorter timescales. To address these mechanisms, we used Astyanax mexicanus, a teleost with ancestral surface morphs (surface fish, SF) and derived cave morphs (cavefish, CF). We exposed SF to completely dark conditions and identified numerous altered traits at both the gene expression and phenotypic levels. Remarkably, most of these alterations mimicked CF phenotypes. Our results indicate that cave-related traits can appear within a single generation by phenotypic plasticity. In the next generation, plasticity can be further refined. The initial plastic responses are random in adaptive outcome but may determine the subsequent course of evolution. Our study suggests that phenotypic plasticity contributes to the rapid evolution of cave-related traits in A. mexicanus.

evolutionary biology↗

bioRxiv2019

Various components of the RNAi pathway are required for conidiation, ascosporogenesis, virulence, DON production and SIGS-mediated fungal inhibition by exogenous dsRNA in the Head Blight pathogen Fusarium graminearum

Gene silencing through RNA interference (RNAi) shapes many biological processes in filamentous fungi, including pathogenicity. In this study we explored the requirement of key components of fungal RNAi machinery, including DICER-like 1 and 2 (FgDCL1, FgDCL2), ARGONAUTE 1 and 2 (FgAGO1, FgAGO2), AGO-interacting protein FgQIP (QDE2-interacting protein), RecQ helicase (FgQDE3), and four RNA-dependent RNA polymerases (FgRdRP1, FgRdRP2, FgRdRP3, FgRdRP4), in the ascomycete mycotoxin-producing fungal pathogen Fusarium graminearum (Fg) for sexual and asexual multiplication, pathogenicity, and its sensitivity to double-stranded (ds)RNA. We corroborate and extend earlier findings that conidiation, ascosporogenesis and Fusarium Head Blight (FHB) symptom development require an operable RNAi machinery. The involvement of RNAi in conidiation is dependent on environmental conditions as it is detectable only under low light (< 2 {micro}mol m-2s-1). Although both DCLs and AGOs partially share their functions, the sexual ascosporogenesis is mediated primarily by FgDCL1 and FgAGO2, while FgDCL2 and FgAGO1 contribute to asexual conidia formation and germination. FgDCL1 and FgAGO2 also account for pathogenesis as their knock-out (KO) results in reduced FHB development. Apart from KO mutants{Delta} dcl2 and{Delta} ago1, mutants{Delta} rdrp2, {Delta}rdrp3, {Delta}rdrp4, {Delta}qde3 and{Delta} qip are strongly compromised for conidiation, while KO mutations in all RdPRs, QDE3 and QIP strongly affect ascosporogenesis. Analysis of trichothecenes mycotoxins in wheat kernels showed that the relative amount of deoxynivalenol (DON), calculated as [DON] per amount of fungal genomic DNA, was reduced in all spikes infected with RNAi mutants, suggesting the possibility that the fungal RNAi pathways affect Fgs DON production in wheat spikes. Moreover, gene silencing by exogenous target gene specific dsRNA (spray-induced gene silencing, SIGS) is dependent on fungal DCLs, AGOs, and QIP, but not on QDE3. Together these data show that in F. graminearum different key components of the RNAi machinery are crucial in different steps of fungal development and pathogenicity.

pathology↗

bioRxiv2018

Spontaneous intake and long-term effects of essential oils after a negative postnatal experience in chicks

The postnatal period is critical for broiler chicks as they are exposed to, possibly stressful, environmental changes in the hatchery and during transportation to the rearing houses. The ability of broiler chicks to spontaneously drink essential oils (EO) to mitigate the effects of a negative postnatal experience was tested. Chicks were either immediately placed in the rearing facility (C group), or subjected to a 24h-delay period before their placement (D group), mimicking the possible transportation delay in commercial conditions.\n\nIn experiment 1, each group had access to either water only or to water and one EO (cardamom, marjoram or verbena) from D1 to D13. The verbena EO intake was higher in the D group than in the C group from D1 to D6 and the cardamom EO intake was lower in the D group than in the C group from D6 to D13.\n\nIn experiment 2, half of the groups had access to water only and the other half was offered water and the 3 EO simultaneously. The EO were not differently chosen by chicks between D and C groups except a lower cardamom EO intake was observed in the D group than in the C group from D6 to D12. The delayed placement of the D group reduced chicken growth until 34 days of age and temporarily increased the feed conversion ratio, but did not affect their welfare or the prevalence of health disorders. The EO intake did not allow the chicks in the D group to overcome the growth reduction, but did overcome the reduction in Pectoralis major muscle yield. In conclusion, chicks are able to make spontaneous choices regarding EO intake according to their postnatal experience when EO are presented individually, but in our experimental design, they were not when EO were simultaneously presented. The EO intake only partially mitigated the decrease in chicken performance after the negative postnatal experience.

animal behavior and cognition↗

bioRxiv2018

Oxygen restriction induces a viable but non-culturable population in bacteria

Induction of a non-culturable state has been demonstrated for many bacteria. In a clinical perspective, the lack of growth due to these non-culturable bacteria can have major consequences for the diagnosis and treatment of patients. Here we show how anoxic conditioning (restriction of molecular oxygen, O2) generates difficult-to-culture (DTC) bacteria during biofilm growth. A significant subpopulation of Pseudomonas aeruginosa entered a DTC state after anoxic conditioning, ranging from five to 90 % of the total culturable population, in both planktonic and biofilm models. Anoxic conditioning also generated DTC subpopulations of Staphylococcus aureus and Staphylococcus epidermidis. Growth of the DTC populations were achieved by substituting O2 with 10 mM NO3- as an alternative electron acceptor for anaerobic respiration or, in the case of P. aeruginosa, by adding sodium pyruvate or catalase as scavengers against reactive oxygen species (ROS) during aerobic respiration. An increase in normoxic plating due to addition of catalase suggests the molecule hydrogen peroxide as a possible mechanism for induction of DTC P. aeruginosa. Anoxic conditioning also generated a true viable but non-culturable (VBNC) population of P. aeruginosa that was not resurrected by substituting O2 with NO3- during anaerobic respiration. Moreover, bacterial detection in clinical samples was improved significantly by supplementing 10 mM NO3- to LB plates and incubating under anoxic conditions. These results demonstrate that habituation to an infectious anoxic micro-environment complicates diagnostic culturing of bacteria, especially in the case of chronic infections where oxygen is restricted due to the host immune response. ImportanceDiagnostics of bacteria from chronic infections by standard culture-based methods is challenging. Bacteria in a non-culturable state may contribute to the lack of culturing from these infections. Many stressors are known to induce a non-culturable state, among others the absence of molecular oxygen, which is evident in chronic infections due to high rates of oxygen consumption by the host response. In this study, we have shown that Pseudomonas aeruginosa, Staphylococcus aureus and Staphylococcus epidermidis can enter a difficult-to-culture state after oxygen restriction. Regrowth was not possible using conventional normoxic plating where oxygen served as electron acceptor. Instead, regrowth was enabled during anoxic conditions with added nitrate as alternative electron acceptor. Our findings show that bacteria can habituate to their environment and that it has to be taken into consideration especially when culturing clinical samples e.g. from chronic infections.

microbiology↗

bioRxiv2018

Small differences in learning speed for different food qualities can drive efficient collective foraging in ant colonies

Social insects frequently make important collective decisions, such as selecting the best food sources. Many collective decisions are achieved via communication, for example by differential recruitment depending on resource quality. However, even species without recruitment can respond to a changing environment on collective level by tracking food source quality.\n\nWe hypothesised that an apparent collective decision to focus on the highest quality food source can be explained by differential learning of food qualities. Ants may learn the location of higher quality food faster, with most ants finally congregating at the best food source.\n\nTo test the effect of reward quality and motivation on learning in Lasius niger, we trained individual ants to find a reward of various sucrose molarities on one arm of a T-maze in spring and in autumn after one or four days of starvation.\n\nAs hypothesised, ants learned fastest in spring and lowest in autumn, with reduced starvation leading to slower learning. Surprisingly, the effect of food quality and motivation on the learning speed of individuals which persisted in visiting the feeders was small. However, persistence rates varied dramatically: All ants in spring made all (6) return visits to all food qualities, in contrast to 33% of ants in autumn under low starvation.\n\nFitting the empirical findings into an agent-based model revealed that even a tendency of ants to memorise routes to high quality food sources faster can result in ecologically sensible colony-level behaviour. Low motivation colonies are also choosier, due to increasing sensitivity to food quality.\n\nSignificance statementCollective decisions of insects are often achieved via communication and/or other interactions between individuals. However, animals can also make collective decisions in the absence of communication.\n\nWe show that foraging motivation and food quality can affect both route memory and the likelihood to return to the food source and thus mediate selective food exploitation. An agent-based model, implemented with our empirical findings, demonstrates that, at the collective level, even small differences in learning lead to ecologically sensible behaviour: mildly starved colonies are selective for high quality food while highly starved colonies exploit all food sources equally.\n\nWe therefore suggest that non-interactive factors such as individual learning and the foraging motivation of a colony can mediate or even drive group level behaviour. Instead of accounting collective behaviour exclusively to social interactions, possible contributing individual processes should also be considered.

animal behavior and cognition↗