title: METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance

abstract: Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the {tau}-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation tuning. Indeed, genome-wide ribosome profiling revealed suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a "ribosome code" that ensures proteome integrity in cells.


title: Calcium-binding protein S100A6 interaction with VEGF receptors integrates signaling and trafficking pathways

abstract: The mammalian endothelium which lines all blood vessels responds to soluble factors which control vascular development and sprouting. Endothelial cells bind to vascular endothelial growth factor A via two different receptor tyrosine kinases (VEGFR1, VEGFR2) which regulate such cellular responses. The integration of VEGFR signal transduction and membrane trafficking is not well understood. Here, we used a yeast-based membrane protein screen to identify VEGFR-interacting factor(s) which modulate endothelial cell function. By screening a human endothelial cDNA library, we identified a calcium-binding protein, S100A6, which can interact with either VEGFR. We found that S100A6 binds in a calcium-dependent manner to either VEGFR1 or VEGFR2. S100A6 binding was mapped to the VEGFR2 tyrosine kinase domain. Depletion of S100A6 impacts on VEGF-A-regulated signaling through the canonical mitogen-activated protein kinase (MAPK) pathway. Furthermore, S100A6 depletion caused contrasting effects on biosynthetic VEGFR delivery to the plasma membrane. Co-distribution of S100A6 and VEGFRs on tubular profiles suggest the presence of transport carriers that facilitate VEGFR trafficking. We propose a mechanism whereby S100A6 acts as a calcium-regulated switch which facilitates biosynthetic VEGFR trafficking from the TGN-to-plasma membrane. VEGFR-S100A6 interactions thus enable integration of signaling and trafficking pathways in controlling the endothelial response to VEGF-A.

category: cell biology


title: Differential impact of a dyskeratosis congenita mutation in TPP1 on mouse hematopoiesis and germline

abstract: Telomerase extends chromosome ends in somatic and germline stem cells to ensure continued proliferation. Mutations in genes critical for telomerase function result in telomeropathies such as dyskeratosis congenita (DC), frequently resulting in spontaneous bone marrow failure. While knockout of telomerase in mice has been instrumental in highlighting the importance of telomere length maintenance at an organismal level, it may not be representative of human telomeropathy mutations in vivo. A DC mutation in the shelterin protein TPP1 (K170{Delta}) that compromises telomerase recruitment to telomeres but leaves other functions of TPP1 and the integrity of the telomerase holoenzyme intact is a physiologically relevant tool to evaluate telomerase-dependent telomere length maintenance in mice. We used CRISPR-Cas9 to generate a mutant mouse knocked in for the equivalent of the TPP1 K170{Delta} mutation (TPP1 K82{Delta}) and investigated both its bone marrow and germline compartments in unprecedented detail. TPP1 K82{Delta} caused progressive telomere erosion with increasing generation number but did not induce steady-state hematopoietic defects. Strikingly, K82{Delta} caused mouse infertility, consistent with gross morphological defects in the testis and sperm, the appearance of either empty or severely disorganized seminiferous tubules, and a decrease in both spermatogonia and spermatocytes. It is intriguing that both TPP1 K82{Delta} mice and previously characterized telomerase knockout mice show no spontaneous bone marrow failure but rather succumb to a robust infertility phenotype at steady state. We speculate that telomere length maintenance contributes differently to the evolutionary fitness of humans and mice. Telomere length maintenance in the human bone marrow can ensure progression to reproductive age, while that in the mouse germline can help meet the elevated demand for sperm to produce multiple offspring.


title: Endogenous protein tagging in medaka using a simplified CRISPR/Cas9 knock-in approach

abstract: The CRISPR/Cas9 system has been used to generate fluorescently labelled fusion proteins by homology directed repair in a variety of species. Despite its revolutionary success, there remains an urgent need for increased simplicity and efficiency of genome editing in research organisms. Here, we establish a simplified, highly efficient and precise strategy for CRISPR/Cas9 mediated endogenous protein tagging in medaka (Oryzias latipes). We use a cloning-free approach that relies on PCR amplified donor fragments containing the fluorescent reporter sequences flanked by short homology arms (30-40bp), a synthetic sgRNA and streptavidin tagged Cas9. We generate six novel knock-in lines with high efficiency of F0 targeting and germline transmission. Whole Genome Sequencing (WGS) results reveal single-copy integration events only at the targeted loci. We provide an initial characterization of these fusion-protein lines, significantly expanding the repertoire of genetic tools available in medaka. In particular, we show that the mScarlet-pcna knock-in line has the potential to serve as an organismal-wide label for proliferative zones and an endogenous cell cycle reporter.

category: developmental biology


title: A Non-Canonical Raf Function Is Required for Dorsal-Ventral Patterning During Drosophila Embryogenesis

abstract: Proper embryonic development requires directional axes to pattern cells into embryonic structures. In Drosophila, spatially discrete expression of transcription factors determines the anterior to posterior organization of the early embryo, while the Toll and TGF{beta} signalling pathways determine the early dorsal to ventral pattern. Embryonic MAPK/ERK signaling contributes to both anterior to posterior patterning in the terminal regions and to dorsal to ventral patterning during oogenesis and embryonic stages. Here we describe a novel loss of function mutation in the Raf kinase gene, which leads to loss of ventral cell fates as seen through the loss of the ventral furrow, the absence of Dorsal/NF{kappa}B nuclear localization, the absence of mesoderm determinants Twist and Snail, and the expansion of TGF{beta}. Gene expression analysis showed cells adopting ectodermal fates much like loss of Toll signaling. Our results combine novel mutants, live imaging, optogenetics and transcriptomics to establish a novel role for Raf, that appears to be independent of the MAPK cascade, in embryonic patterning.


title: Small extracellular vesicles from young mice prevent frailty and improve healthspan in old mice.

abstract: Aging is associated with an increased risk of frailty, disability, comorbidities, institutionalization, falls, fractures, hospitalization, and mortality. Searching for strategies to delay the degenerative changes associated with aging and frailty is interesting. We treated old animals intravenously with small extracellular vesicles (sEVs) derived from adipose mesenchymal stem cells (ADSCs) of young animals, and we found an improvement of several functional parameters usually altered with aging, such as motor coordination, grip strength, fatigue resistance, fur regeneration, and renal function. Frailty index analysis showed that 40% of old control mice were frail, whereas none of the old ADSCs-sEVs treated mice were. Molecular and structural benefits in muscle and kidney accompanied this functional improvement. ADSCs-sEVs induced pro-regenerative effects and a decrease in oxidative stress, inflammation, and senescence markers. Moreover, predicted epigenetic age was lower in tissues of old mice treated with ADSCs-sEVs and their metabolome changed to a youth-like pattern. Finally, we gained some insight into the miRNAs contained in sEVs that might be, at least in part, responsible for the effects observed. We propose that young sEVs treatment can be beneficial against frailty and therefore can promote healthy aging.

category: physiology


title: Small extracellular vesicles from young mice prevent frailty, improve healthspan and decrease epigenetic age in old mice.


title: WAPO-A1  is the causal gene of the 7AL QTL for spikelet number per spike in wheat

abstract:
Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Integrating results from this study and previous findings, we show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheats, so it might be particularly useful in durum wheat where H2 is rare.

AUTHOR SUMMARYA region on wheat chromosome 7A has been previously shown to affect the number of spikelets and grains per spike as well as total grain yield in multiple breeding programs. In this study, we show that loss-of-function mutations in the WAPO1 gene located within this region reduce the number of spikelets per spike and that additional transgenic copies of this gene increase this number. These results demonstrate that WAPO1 is the gene responsible for the differences in grain number and yield associated with the 7A chromosome region. Among the three main variants identified for this gene, we demonstrate in field experiments that the H2 variant is associated with the largest increases in number of spikelets and grains per spike. The H2 WAPO1 variant is frequent in bread wheat breeding programs but is almost absent in modern pasta wheat varieties. Therefore, the introgression of the H2 represents a promising opportunity to improve grain yield in pasta wheat breeding programs.

category: plant biology


title: Phenotypic architecture of sociality and its associated genetic polymorphisms in zebrafish

abstract:
Sociality is often seen as a single phenotypic trait, but it relies on motivational and cognitive components implemented by specific causal mechanisms. Hence, these components may have evolved independently, or may have been linked by phenotypic correlations driven by a shared selective pressure for increased social competence. Furthermore, these components may be domain-specific or of general domain across social and non-social contexts. Here we have characterized the phenotypic architecture of sociality in zebrafish, which has been increasingly used as a model organism in social neuroscience. For this purpose, we have behaviorally phenotyped zebrafish from different wild type lines in four tests: social tendency, social and non-social recognition, and open-field test. Our results indicate that: (1) sociality has two main components that are independent from each other (social tendency and social recognition), hence not supporting the occurrence of a sociality syndrome; (2) both social traits are phenotypically linked to non-social traits (non-social exploration and non-social memory, respectively), forming two general behavioral modules, general inspection and general recognition, and suggesting that sociality traits have been co-opted from general-domain motivational and cognitive traits. Moreover, the study of the association between genetic polymorphisms (i.e. single nucleotide polymorphisms, SNPs) and each behavioral module further supports this view, since several SNPs from a list of candidate "social" genes, are statistically associated with the general inspection (motivational), but not with a general recognition (cognitive), behavioral module. The SNPs associated with general inspection are widespread across different chromosomes and include neurotransmitters, neuromodulators, and synaptic plasticity genes, suggesting that this behavioral module is regulated by multiple genes, each of them with small effects. Together, these results support the occurrence of general domain motivational and cognitive behavioral modules in zebrafish, which have been co-opted for the social domain.

Author summarySocial living has been considered one of the major transitions in evolution and it has been considered to act as a major selective force shaping the evolution of brain and behavior in animals. Sociality relies on two basic behavioral mechanisms: (1) the willingness to approach and be near others (aka social tendency); and (2) the ability to distinguish between others (aka social recognition) in order to adjust the behavior expressed during social interactions according to the identity of the interactant. There is an ongoing debate on to what extent these social abilities have specifically evolved in response to social living and are domain specific, or if they were selected as a broad response to cognitive demands and are of general domain. Here, we used zebrafish to test the domain-specific vs. general domain hypotheses and to assess the association of social tendency and social recognition with a set of candidate "social" genes (i.e. genes that have been linked to social behavior in other studies with different vertebrate species). We found that both social traits are not correlated to each other and are of general domain, and that only social tendency is associated with candidate "social" genes, suggesting that social tendency and social recognition are independent behavioral modules that rely on separate genetic architectures and that can evolve separately.

category: animal behavior and cognition


title: Detection and quantification of the vacuolar H ATPase using the Legionella effector protein SidK

abstract: Acidification of secretory and endocytic organelles is required for proper receptor recycling, membrane traffic, protein degradation, and solute transport. Proton-pumping vacuolar ATPases (V-ATPases) are responsible for this luminal acidification, which increases progressively as secretory and endocytic vesicles mature. An increasing density of V-ATPase complexes is thought to account for the gradual decrease in pH, but available reagents have not been sufficiently sensitive nor specific to test this hypothesis. We introduce a new probe to localize and quantify V-ATPases in eukaryotic cells. The probe is derived from SidK, a Legionella pneumophila effector protein that binds to the V-ATPase A subunit. We generated plasmids encoding fluorescent chimeras of SidK1-278, and labeled recombinant SidK1-278 with AlexaFluor-568 to visualize and quantify V-ATPases with high specificity in live and fixed cells, respectively. We show that V-ATPases are acquired progressively during phagosome maturation, that they distribute in discrete membrane subdomains, and that their density in lysosomes depends on the subcellular localization of the lysosome.


title: Investigating molecular crowding during cell division in budding yeast with FRET

abstract: Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear how these events are coordinated and how they integrate with regulation of molecular crowding. We use the budding yeast Saccharomyces cerevisiae as a model system to study these questions using recent progress in optical fluorescence microscopy and crowding sensing probe technology. We used a Forster Resonance Energy Transfer (FRET) based sensor, illuminated by confocal microscopy for high throughput analyses and Slimfield microscopy for single-molecule resolution, to quantify molecular crowding. We determine crowding in response to cellular growth of both mother and daughter cells, in addition to osmotic stress, and reveal hot spots of crowding across the bud neck in the burgeoning daughter cell. This crowding might be rationalized by the packing of inherited material, like the vacuole, from mother cells. We discuss recent advances in understanding the role of crowding in cellular regulation and key current challenges and conclude by presenting our recent advances in optimizing FRET-based measurements of crowding whilst simultaneously imaging a third color, which can be used as a marker that labels organelle membranes. Our approaches can be combined with synchronised cell populations to increase experimental throughput and correlate molecular crowding information with different stages in the cell cycle.

category: biophysics


title: The role of the atypical chemokine receptor CCRL2 in myelodysplastic syndrome and secondary acute myeloid leukemia

abstract: The identification of new molecular pathways supporting the growth of myelodysplastic syndrome (MDS) stem and progenitor cells is needed to understand clinical variation and develop targeted therapies. Within myeloid malignancies, men have worse outcomes compared to women, suggesting male sex hormone driven effects in malignant hematopoiesis. The androgen receptor promotes the expression of five granulocyte-colony factor receptor regulated genes. Among them, CCRL2 encodes an atypical chemokine receptor that regulates cytokine signaling in differentiated granulocytes but its role in myeloid malignancies is unknown. Our study revealed that CCRL2 is upregulated in stem and progenitor cells from patients with MDS and secondary acute leukemia. CCRL2 knockdown suppressed the growth and clonogenicity of MDS92 and MDS-L cells in vitro and in vivo. Moreover, CCRL2 knockdown significantly suppressed the phosphorylation of JAK2, STAT3, and STAT5 in MDS cells. CCRL2 co-precipitated with JAK2 and its suppression decreased the interaction of JAK2 with STAT proteins. Cell lines expressing JAK2V617F showed less effect of CCRL2 knockdown on growth and clonogenicity compared to those expressing wild type. However, the selective JAK2 inhibitor fedratinib potentiated the effects of CCRL2 knockdown in MDS and leukemia cells expressing both wild type JAK2 and JAK2V617F. In conclusion, our results implicate CCRL2 as a mediator of MDS and secondary acute leukemia cell growth, in part through JAK2/STAT signaling.

category: cancer biology


title: An Oscillatory Mechanism for Multi-level Storage in Short-term Memory

abstract:
Oscillatory activity is commonly observed during the maintenance of information in short-term memory, but its role remains unclear. Non-oscillatory models of short-term memory storage are able to encode stimulus identity through their spatial patterns of activity, but are typically limited to either an all-or-none representation of stimulus amplitude or exhibit a biologically implausible exact-tuning condition. Here, we demonstrate a simple phase-locking mechanism by which oscillatory input enables a circuit to generate persistent or sequential activity patterns that encode information not only in their location but also in their discretely graded amplitudes.

SignificanceA core observation in many memory systems and tasks is the presence of oscillations during memory maintenance. Here, we demonstrate a mechanism for the accumulation and storage of information in short-term memory in which oscillatory activity enables a solution to long-standing challenges in modeling the persistent neural activity underlying working memory. These challenges include the ability to encode information with low firing rates, multi-level storage of stimulus amplitude without extreme fine tuning, and multi-level storage of information in sequential activity. Altogether, this work proposes a new class of models for the storage of information in working memory, a new potential role for brain oscillations, and a novel dynamical mechanism for multi-stability.

category: neuroscience


title: Distributed representations for human inference

abstract: Neural representations can be characterized as falling along a continuum, from distributed representations, in which neurons are responsive to many related features of the environment, to localist representations, where neurons orthogonalize activity patterns despite any input similarity. Distributed representations support powerful learning in neural network models and have been posited to exist throughout the brain, but it is unclear under what conditions humans acquire these representations and what computational advantages they may confer. In a series of behavioral experiments, we present evidence that interleaved exposure to new information facilitates the rapid formation of distributed representations in humans. As in neural network models with distributed representations, interleaved learning supports fast and automatic recognition of item relatedness, affords efficient generalization, and is especially critical for inference when learning requires statistical integration of noisy information over time. We use the data to adjudicate between several existing computational models of human memory and inference. The results demonstrate the power of interleaved learning and implicate the use of distributed representations in human inference.


title: Coherent mapping of position and head direction across auditory and visual cortex

abstract: Neurons in primary visual cortex (V1) may not only signal current visual input but also relevant contextual information such as reward expectancy and the subjects spatial position. Such location-specific representations need not be restricted to V1 but could participate in a coherent mapping throughout sensory cortices. Here we show that spiking activity in primary auditory cortex (A1) and lateral, secondary visual cortex (V2L) of freely moving rats coherently represents a location-specific mapping in a sensory detection task performed on a figure-8 maze. Single-unit activity of both areas showed extensive similarities in terms of spatial distribution, reliability and position coding. Importantly, reconstructions of subject position on the basis of spiking activity displayed decoding errors that were correlated between areas in magnitude and direction. In addition to position, we found that head direction, but not locomotor speed or head angular velocity, was an important determinant of activity in A1 and V2L. Finally, pairs of units within and across areas showed significant correlations in instantaneous variability of firing rates (noise correlations). These were dependent on the spatial tuning of cells as well as the spatial position of the animal. We conclude that sensory cortices participate in coherent, multimodal representations of the subjects sensory-specific location. These may provide a common reference frame for distributed cortical sensory and motor processes and may support crossmodal predictive processing.


title: A comparative study between state-of-the-art MRI deidentification and AnonyMI, a new method combining re-identification risk reduction and geometrical preservation

abstract: Deidentifying MRIs constitutes an imperative challenge, as it aims at precluding the possibility of re-identification of a research subject or patient, but at the same time it should preserve as much geometrical information as possible, in order to maximize data reusability and to facilitate interoperability. Although several deidentification methods exist, no comprehensive and comparative evaluation of deidentification performance has been carried out across them. Moreover, the possible ways these methods can compromise subsequent analysis has not been exhaustively tested. To tackle these issues, we developed AnonyMI, a novel MRI deidentification method, implemented as a user-friendly 3D Slicer plugin-in, which aims at providing a balance between identity protection and geometrical preservation. To test these features, we performed two series of analyses on which we compared AnonyMI to other two state-of-the-art methods, to evaluate, at the same time, how efficient they are at deidentifying MRIs and how much they affect subsequent analyses, with particular emphasis on source localization procedures. Our results show that all three methods significantly reduce the re-identification risk but AnonyMI provides the best geometrical conservation. Notably, it also offers several technical advantages such as a user-friendly interface, multiple input-output capabilities, the possibility of being tailored to specific needs, batch processing and efficient visualization for quality assurance.


title: Functional coupling of TRPM2 and NMDARs exacerbates excitotoxicity in ischemic brain injury

abstract:
Excitotoxicity caused by NMDA receptors (NMDARs) is a major cause of neuronal death in ischemic stroke. However, past efforts of directly targeting NMDARs have unfortunately failed in clinical ischemic stroke trials. Here we reveal an unexpected mechanism underlying NMDARs-mediated neurotoxicity, which leads to identification of a novel target and development of an effective therapeutic peptide for ischemic stroke. We show that NMDARs excitotoxicity upon ischemic insults is mediated by physical and functional coupling to TRPM2. The physical interaction of TRPM2 with NMDARs results in markedly increase in the surface expression of NMDARs, leading to enhanced NMDAR function and increased neuronal death. We identified a specific NMDAR-interacting domain on TRPM2, and developed a cell-permeable peptide to uncouple TRPM2-NMDARs. The disrupting-peptide protects neurons against ischemic injury in vitro and protects mice against ischemic stroke in vivo. These findings provide an unconventional strategy to eliminate excitotoxic neuronal death without directly targeting NMDARs.

HIGHLIGHTSO_LITRPM2 physically and functionally interacts with NMDARs
C_LIO_LIInteraction of TRPM2 with NMDARs exacerbates NMDARs extrasynaptic excitotoxicity by increasing NMDARs surface expression during ischemic injury
C_LIO_LITRPM2 recruits PKC{gamma} to the interacting complexes to increase NMDARs surface expression
C_LIO_LIUncoupling the interaction between TRPM2 and NMDARs with a disrupting peptide (TAT-EE3) protects neurons against ischemic stroke in vitro and in vivo
C_LI

GRAPHIC ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=175 HEIGHT=200 SRC="FIGDIR/small/454247v1_ufig1.gif" ALT="Figure 1">
View larger version (53K):
org.highwire.dtl.DTLVardef@e618c5org.highwire.dtl.DTLVardef@646350org.highwire.dtl.DTLVardef@b4478corg.highwire.dtl.DTLVardef@1c5742f_HPS_FORMAT_FIGEXP  M_FIG C_FIG TRPM2 excerbates NMDARs excitotoxicity by physically and functionally interacting with NMDARs. The disrupting pipette TAT-EE3 protects neurons against ischemic injury in vitro and in vivo.


title: Age-Related Differences in Ventral Striatal and Default Mode Network Function During Reciprocated Trust

abstract: Social relationships change across the lifespan as social networks narrow and motivational priorities shift to the present. Interestingly, aging is also associated with changes in executive function, including decision-making abilities, but it remains unclear how age-related changes in both domains interact to impact financial decisions involving other people. To study this problem, we recruited 50 human participants (Nyounger = 26, ages 18-34; Nolder = 24, ages 63-80) to play an economic trust game as the investor with three partners (friend, stranger, and computer) who played the role of investee. Investors underwent functional magnetic resonance imaging (fMRI) during the trust game while investees were seated outside of the scanner. Building on our previous work with younger adults showing both enhanced striatal responses and altered default-mode network (DMN) connectivity as a function of social closeness during reciprocated trust, we predicted that these relations would exhibit age-related differences. We found that striatal responses to reciprocated trust from friends relative to strangers and computers were blunted in older adults relative to younger adults, thus supporting our primary pre-registered hypothesis regarding social closeness. We also found that older adults exhibited enhanced DMN connectivity with the temporoparietal junction (TPJ) during reciprocated trust from friends compared to computers while younger adults exhibited the opposite pattern. Taken together, these results advance our understanding of age-related differences in sensitivity to social closeness in the context of trusting others.


title: Antibiotic treatment induces activation of microglia and impairment of cholinergic gamma oscillations in the hippocampus

abstract: Antibiotics are widely applied for the treatment of bacterial infections, but their long-term use may lead to gut flora dysbiosis and detrimental effects on brain physiology, behavior as well as cognitive performance. Still, a striking lack of knowledge exists concerning electrophysiological correlates of antibiotic-induced changes in gut microbiota and behavior. Here, we investigated changes in the synaptic transmission and plasticity together with behaviorally-relevant network activities from the hippocampus of antibiotic-treated mice. The prolonged antibiotic treatment led to a strong reduction of myeloid cell pools in bone marrow, circulation and those surveilling the brain. Upon antibiotic treatment, circulating Ly6Chi inflammatory monocytes adopted a proinflammatory phenotype with increased expression of CD40 and MHC II. In the central nervous system, microglia displayed typical signs of activation with elevated CD40 and MHC II expression, as well as increased IL-6 and TNF production. Concomitantly, we detected a substantial reduction in the synaptic transmission in the hippocampal CA1 after antibiotic treatment. In line, carbachol-induced cholinergic gamma oscillation were reduced upon antibiotic treatment while the incidence of hippocampal sharp waves was elevated. These changes were associated with the global changes in the expression of neurotrophin nerve growth factor and inducible nitric oxide synthase, both of which have been shown to influence cholinergic functions. Overall, our study demonstrates that antibiotic-induced changes in the gut microbiome and immune cell function are associated with a drastic reduction in the synaptic transmission and gamma oscillations in the hippocampus, a brain region that is critically involved in mediation of innate and cognitive behavior.


title: EEG Alpha Power and Pupil Diameter Reflect Endogenous Auditory Attention Switching and Listening Effort

abstract: Auditory attention describes a listeners focus on an acoustic source while they ignore other competing sources that might be present. In an environment with multiple talkers and background noise (i.e. the cocktail party effect), auditory attention can be difficult, requiring the listener to expend measurable cognitive effort. A listener will naturally interrupt sustained attention on a source when switching towards another source during conversation. This change in attention is potentially even more taxing than maintaining sustained attention due to the limits of human working memory, and this additional effort required has not been well studied. In this work, we evaluated an attention decoder algorithm for detecting the change in attention and investigated cognitive effort expended during attentional switching and sustained attention. Two variants of endogenous attention switching were explored: the switches either had in-the-moment decision making or a pre-defined attentional switch time. A least-squares, EEG-based, attention decoding algorithm achieved 64.1% accuracy with a 5-second correlation window and illustrated smooth transitions in the attended talker prediction through switches in sustained attention at approximately half of the analysis window size (2.2 seconds). The expended listening effort, as measured by simultaneous electroencephalography (EEG) and pupillometry, was also a strong indicator of switching. Specifically, centrotemporal alpha power [F(2, 18) = 7.473, P = 0.00434] and mean pupil diameter [F(2, 18) = 9.159, P = 0.0018] were significantly different for trials that contained a switch in comparison to sustained trials. We also found that relative attended and ignored talker locations modulate the EEG alpha topographic response. This alpha lateralization was found to be impacted by the interaction between experimental condition and whether the measure was computed before or after the switch [F(2,18) = 3.227, P = 0.0634]. These results suggest that expended listening effort is a promising feature that should be pursued in a decoding context, in addition to speech and location-based features.


title: A multimodal neuroprosthetic interface to record, modulate and classify electrophysiological correlates of cognitive function

abstract: Most mental disorders are characterised by impaired cognitive function and behaviour control. Their often chronic reoccurring nature and the lack of efficient therapies necessitate the development of new treatment strategies. Brain-computer interfaces, equipped with multiple sensing and stimulation abilities, offer a new toolbox, whose suitability for diagnosis and therapy of mental disorders has not yet been explored. Here, we developed a soft and multimodal neuroprosthesis to measure and modulate prefrontal neurophysiological features of neuropsychiatric symptoms. We implanted the device epidurally above the medial prefrontal cortex of rats and obtained auditory event-related brain potentials reflecting intact neural stimulus processing and alcohol-induced neural impairments. Moreover, implant-driven electrical and pharmacological stimulation enabled successful modulation of neural activity. Finally, we developed machine learning algorithms which can deal with sparsity in the data and distinguish effects with high accuracy. Our work underlines the potential of multimodal bioelectronic systems to enable a personalised and optimised therapy.


title: Determining the stability of genome-wide factors in BMI between ages 40 to 69 years.

abstract: Genome-wide association studies (GWAS) have successfully identified common variants associated with BMI. However, the stability of genetic variation influencing BMI from midlife and beyond is unknown. By analyzing BMI data collected from 165,717 men and 193,073 women from the UKBiobank, we performed BMI GWAS on six independent five-year age intervals between 40 and 73 years. We then applied genomic structural equation modeling (gSEM) to test competing hypotheses regarding the stability of genetic effects for BMI. LDSR genetic correlations between BMI assessed between ages 40 to 73 were all very high and ranged 0.89 to 1.00. Genomic structural equation modeling revealed that genetic variance in BMI at each age interval could not be explained by the accumulation of any age-specific genetic influences or autoregressive processes. Instead, a common set of stable genetic influences appears to underpin variation in BMI from middle to early old age in men and women alike.

category: genetics


title: A multi-omics study to investigate tacrolimus nephrotoxicity mechanisms

abstract:
BackgroundTacrolimus, an immunosuppressive drug prescribed to a majority of transplanted patients is nephrotoxic, through still unclear mechanisms. This study aims to evaluate the impact of tacrolimus on a lineage of proximal tubular cells using a multi-omics approach.

MethodsLLC-PK1 cells were exposed to 5 M of tacrolimus for 24h. Intracellular proteins and metabolites, and extracellular metabolites were extracted and analysed by LC-MS/MS. The transcriptional expression of the dysregulated proteins PCK-1, FBP1 and FBP2 was measured using RT-qPCR.

ResultsIn our cell model, tacrolimus impacted different metabolic pathways including those of arginine (e.g., citrulline, ornithine) (p < 0.0001), amino acids (e.g., valine, isoleucine, aspartic acid) (p < 0.0001) and pyrimidine (p<0.01). In addition, it induced oxidative stress (p < 0.01) as shown by a decrease in total cell glutathione quantity. It impacted cell energy through an increase in Krebs cycle intermediates (e.g., citrate, aconitate, fumarate) (p < 0.01) and down-regulation of PCK-1 (p < 0.05) and FPB1 (p < 0.01), which are key enzymes in gluconeogenesis. Apart from glucose synthesis, gluconeogenesis is an important process in kidney mediated acid-base balance control.

ConclusionThe variations found using this multi-omics approach clearly point towards a dysregulation of energy production in epithelial cells of the renal tubule, and potentially of their functions, that may be implicated in tacrolimus nephrotoxicity in the clinics.

category: pharmacology and toxicology


title: Multi-omics investigation of tacrolimus nephrotoxicity


title: A new protocol for multiple muscle mapping using nTMS

abstract: The representation of muscles in the cortex can be mapped using navigated transcranial magnetic stimulation. The mapping can be quantified via measures like the centre of gravity or the size of the region of excitability. Determining these measures typically relies only on stimulation points that yield motor-evoked potentials (MEPs); stimulations that do not elicit an MEP, i.e., non-MEP points, are ignored entirely. In this study, we show how incorporating non-MEP points may affect the estimates of the size and centroid of the excitable area in eight hand and forearm muscles after mono-phasic single-pulse TMS. We performed test-retest assessments in twenty participants and estimated the reliability of centroids and sizes of the corresponding areas using inter-class correlation coefficients. For most muscles, the reliability turned out good, if not excellent. As expected, removing the non-MEP points significantly decreased area sizes and area weights, suggesting that conventional approaches that do not account for non-MEP points are likely to overestimate the regions of excitability.


title: Accounting for stimulations that do not elicit motor-evoked potentials when mapping cortical representations of multiple muscles


title: Widespread nociceptive maps in the human neonatal somatosensory cortex

abstract: Topographic cortical maps are essential for spatial localisation of sensory stimulation and generation of appropriate task-related motor responses. Somatosensation and nociception are finely mapped and aligned in the adult somatosensory (S1) cortex, but in infancy, when pain behaviour is disorganised and poorly directed, nociceptive maps may be less refined. We compared the topographic pattern of S1 activation following noxious (clinically required heel lance) and innocuous (touch) mechanical stimulation of the same skin region in newborn infants (n=32) using multi-optode functional near-infrared spectroscopy (fNIRS). Signal to noise ratio and overall activation area did not differ with stimulus modality. Within S1 cortex, touch and lance of the heel elicit localised, partially overlapping increases in oxygenated haemoglobin (HbO), but while touch activation was restricted to the heel area, lance activation extended into cortical hand regions. The data reveals a widespread cortical nociceptive map in infant S1, consistent with their poorly directed pain behaviour.


title: The sensory code within sense of time

abstract: Sensory experiences are accompanied by the perception of the passage of time; a cell phone vibration, for instance, is sensed as brief or long. The neuronal mechanisms underlying the perception of elapsed time remain unknown1. Recent work agrees on a role for cortical processing networks2,3, however the causal function of sensory cortex in time perception has not yet been specified. We hypothesize that the mechanisms for time perception are embedded within primary sensory cortex and are thus governed by the basic rules of sensory coding. By recording and optogenetically modulating neuronal activity in rat vibrissal somatosensory cortex, we find that the percept of stimulus duration is dilated and compressed by optogenetic excitation and inhibition, respectively, during stimulus delivery. A second set of rats judged the intensity of tactile stimuli; here, optogenetic excitation amplified the intensity percept, demonstrating sensory cortex to be the common gateway to both time and stimulus feature processing. The coding algorithms for sensory features are well established4-10. Guided by these algorithms, we formulated a 3-stage model beginning with the membrane currents evoked by vibrissal and optogenetic drive and culminating in the representation of perceived time; this model successfully replicated rats choices. Our finding that stimulus coding is intrinsic to sense of time disagrees with dedicated pacemaker-accumulator operation models11-13, where sensory input acts only to trigger the onset and offset of the timekeeping process. Time perception is thus as deeply intermeshed within the sensory processing pathway as is the sense of touch itself14,15 and can now be treated through the computational language of sensory coding. The model presented here readily generalizes to humans14,16 and opens up new approaches to understanding the time misperception at the core of numerous neurological conditions17,18.


title: Microbiome structure of a wild Drosophila community along tropical elevational gradients and comparison to laboratory lines

abstract:
While the biogeography of free-living microbial communities is well-studied, community turnover along environmental gradients in host-associated communities is not well understood. In particular, patterns of host-microbiome diversity along elevational gradients remain largely uncharacterized. Because elevational gradients may serve as natural proxies for climate change, understanding these temperature-influenced patterns can inform our understanding of the threats facing hosts and their microbes in a warming world. In this study, we analysed microbiomes from pupae & adults of four Drosophila species native to Australian tropical rainforests. We sampled wild individuals at high and low elevation along two mountain gradients, to determine natural diversity patterns, and sampled laboratory-reared individuals from isofemale lines established from the same localities, to see if any natural patterns would be retained in the lab. In both environments, we controlled for diet to help elucidate other deterministic patterns of microbiome composition. Microbiome community composition differed radically between laboratory-reared and field-caught flies but did not significantly differ across elevation. We found some notable taxonomic differences in Drosophila microbiomes between different species and elevations. We also found similar microbiome composition from both types of provided food, and we therefore suggest the significant differences in richness are the products of environments with different bacterial species pools. We conclude that elevational differences in temperature are not a major factor in determining Drosophila microbiome composition and we caution against determining microbiome composition from lab-only specimens, particularly long-term cultures.

ImportanceBacteria form microbiome communities inside many different hosts. These communities vary widely in diversity, and form differently, depending on a wide variety of factors. Diet is often an important factor for microbiome composition. We controlled diet in our study by providing the same food sources. We looked at how host-microbiome communities differed in four Drosophila species over two mountain gradients in tropical Australia, to see if temperature-driven differences in elevation affected host-microbiomes. We also compared these results to individuals kept in the laboratory to understand how different settings changed microbiome communities. We found that field samples had substantially greater microbiome diversity than those from the lab and found minimal differences in microbiome communities over elevation. Our study shows that environmental sources of bacteria matter for Drosophila microbiome composition, and caution should be exercised when interpreting microbiome results from lab-only studies.

category: ecology


title: Control of neurotransmitter release and presynaptic plasticity by re-orientation of membrane-bound Munc13-1

abstract: Munc13-1 plays a central role in neurotransmitter release through its conserved C-terminal region, which includes a diacyglycerol (DAG)-binding C1 domain, a Ca2+/PIP2-binding C2B domain, a MUN domain and a C2C domain. Munc13-1 was proposed to bridge synaptic vesicles to the plasma membrane in two different orientations mediated by distinct interactions of the C1C2B region with the plasma membrane: i) one involving a polybasic face that yields a perpendicular orientation of Munc13-1 and hinders release; and ii) another involving the DAG-Ca2+-PIP2-binding face that induces a slanted orientation and facilitates release. Here we have tested this model and investigated the role of the C1C2B region in neurotransmitter release. We find that K603E or R769E point mutations in the polybasic face severely impair synaptic vesicle priming in primary murine hippocampal cultures, and Ca2+-independent liposome bridging and fusion in in vitro reconstitution assays. A K720E mutation in the polybasic face and a K706E mutation in the C2B domain Ca2+-binding loops have milder effects in reconstitution assays and do not affect vesicle priming, but enhance or impair Ca2+-evoked release, respectively. The phenotypes caused by combining these mutations are dominated by the K603E and R769E mutations. Our results show that the C1-C2B region of Munc13-1 plays a central role in vesicle priming and support the notion that re-orientation of Munc13-1 controls neurotransmitter release and short-term presynaptic plasticity.


title: The transcriptional cofactor IRF2BP2 plays a key role in T cell homeostasis and Treg cell expansion

abstract: The levels of the co-transcriptional regulator IRF2BP2 (Interferon Regulatory Factor-2 Binding Protein-2) decrease with T cell activation and, when ectopically expressed, it reduces T cell proliferation. To further characterize the function of IRF2BP2 in T cell responses in vivo, we generated a conditional transgenic knock-in mouse that overexpresses IRF2BP2 in T lymphocytes. Overexpression of IRF2BP2 leads to a reduction in the T cell compartment of naive animals, upregulation of Foxp3 and Ifng; an increase in the frequency of regulatory T cells (Tregs), a preferential Th1 differentiation with increase of IFN-{gamma} production and a reduction of T cell proliferation, suggesting a disruption in T cell homeostasis. Interestingly, knock-in mice displayed reduced clinical and inflammatory signs of Experimental Autoimmune Encephalomyelitis (EAE) when compared to the control mice, with an augmented frequency of Treg cells. Altogether, our findings indicate that IRF2BP2 might help to control exacerbated T cell responses and point to a role for IRF2BP2 in preventing T cell autoimmunity.

category: immunology


title: Viruses of Asgard archaea

abstract: Asgardarchaeota encode many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, Verdandiviruses, includes tailed viruses of the realm Duplodnaviria, the second one, Skuldviruses, consists of viruses with predicted icosahedral capsids that belong to the realm Varidnaviria, and the third group, Wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these putative viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of a specific evolutionary relationship between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses, similar to all other known spindle-shaped viruses, probably establish chronic infection and are released without host cell lysis. All three groups of viruses were identified in sediment samples from distinct geographical locations and are expected to play important roles in controlling the Asgard archaea populations in deep-sea ecosystems.

category: microbiology


title: Crocosphaera as a major consumer of fixed nitrogen despite its capability of nitrogen fixation

abstract: Crocosphaera watsonii (hereafter Crocosphaera) is a key nitrogen (N) fixer in the ocean, but its ability to consume combined N sources is still unclear. Using in situ microcosm incubations with an ecological model, we show that Crocosphaera has high competitive capability both under low and moderately high combined N concentrations. In field incubations, Crocosphaera accounted for the highest consumption of ammonium and nitrate, followed by pico-eukaryotes. The model analysis shows that cells have a high ammonium uptake rate ([~]7 mol N (mol N)-1 d-1 at the maximum), which allows them to compete against pico-eukaryotes and non-diazotrophic cyanobacteria when combined N is sufficiently available. Even when combined N is depleted, their capability of nitrogen fixation allows higher growth rates compared to potential competitors. These results suggest the high fitness of Crocosphaera in combined N limiting, oligotrophic oceans, and thus heightens its potential significance in its ecosystem and in biogeochemical cycling.


title: A cohesin traffic pattern genetically linked to gene regulation

abstract:
Cohesin-mediated loop extrusion folds interphase chromosomes at the ten to hundreds kilobases scale. This process produces structural features such as loops and topologically associating domains. We identify three types of cis-elements that define the chromatin folding landscape generated by loop extrusion. First, CTCF sites form boundaries by stalling extruding cohesin, as shown before. Second, transcription termination sites form boundaries by acting as cohesin unloading sites. RNA polymerase II contributes to boundary formation at transcription termination sites. Third, transcription start sites form boundaries that are mostly independent of cohesin, but are sites where cohesin can pause. Together with cohesin loading at enhancers, and possibly other cis-elements, these loci create a dynamic pattern of cohesin traffic along the genome that guides enhancer-promoter interactions. Disturbing this traffic pattern, by removing CTCF barriers, renders cells sensitive to knock-out of genes involved in transcription initiation, such as the SAGA and TFIID complexes, and RNA processing such DEAD-Box RNA helicases. In the absence of CTCF, several of these factors fail to be efficiently recruited to active promoters. We propose that the complex pattern of cohesin movement along chromatin contributes to appropriate promoter-enhancer interactions and localization of transcription and RNA processing factors to active genes.

HIGHLIGHTSO_LIAt least three types of chromatin boundaries regulate a cohesin traffic pattern.
C_LIO_LIThe cohesin traffic pattern guides enhancer-promoter interactions.
C_LIO_LIRemoving CTCF renders cells sensitive to deletion of RNA processing and gene regulation genes.
C_LIO_LIDepleting CTCF affects localization of RNA processing and gene regulatory proteins.
C_LI

category: genomics


title: NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene expression in single cells

abstract: Oligonucleotide-conjugated antibodies1 have allowed for joint measurement of surface protein abundance and the transcriptome in single cells using high-throughput sequencing. Extending these measurements to gene regulatory proteins in the nucleus would provide a powerful means to link changes in abundance of trans-acting TFs to changes in activity of cis-acting elements and expression of target genes. Here, we introduce Nuclear protein Epitope, chromatin Accessibility, and Transcriptome sequencing (NEAT-seq), a technique to simultaneously measure nuclear protein abundance, chromatin accessibility, and the transcriptome in single cells. We apply this technique to profile CD4 memory T cells using a panel of master transcription factors (TFs) that drive distinct helper T cell subsets and regulatory T cells (Tregs) and identify examples of TFs with regulatory activity gated by three distinct mechanisms: transcription, translation, and regulation of chromatin binding. Furthermore, we identify regulatory elements and target genes associated with each TF, which we use to link a non-coding GWAS SNP within a GATA motif to both strong allele-specific chromatin accessibility in cells expressing high levels of GATA3 protein, and a putative target gene.


title: A cationic motif in Engrailed-2 homeoprotein controls its internalization via selective cell-surface glycosaminoglycans interactions

abstract: Engrailed-2 (En2) is a transcription factor that possesses as most homeoproteins the unique and intriguing property to transfer from cell to cell through unconventional pathways. The internalization mechanism of this cationic protein is far from being fully understood and is proposed to require an initial interaction with cell-surface glycosaminoglycans (GAGs). To decipher the role of GAGs in the recognition of En2 at the cell surface, we have quantified the internalization of the homeodomain region in cell lines that differ in their content in cell-surface GAGs. The binding specificity to GAGs and the influence of this interaction on the structure and dynamics of En2 was also investigated at the amino acid level. Our results show that a high-affinity GAG-binding hexadecapeptide (RKPKKKNPNKEDKRPR) located upstream of the homeodomain controls internalization efficiency of En2 through selective interactions with highly-sulfated GAGs of heparan sulfate type. Our data underline the functional importance of the intrinsically disordered basic region that precedes the prominent internalization domain in En2, and demonstrate the critical role of GAGs as an entry gate for En2, finely tuning its capacity to internalize into cells.

category: biochemistry


title: Phosphorylation of PNKP mediated by CDKs promotes end-processing of Okazaki fragments during DNA replication

abstract: Polynucleotide kinase phosphatase (PNKP) has enzymatic activities as 3' phosphatase and 5' kinase of DNA ends to promote DNA ligation. Here, we show that PNKP is involved in progression of DNA replication through end-processing of Okazaki fragments (OFs). Cyclin-dependent kinases (CDKs) regulate phosphorylation on threonine 118 (T118) of PNKP, and which phosphorylation allows it to be recruited to OFs. Loss of PNKP and T118 phosphorylation significantly increased unligated OFs and high-speed DNA synthesis in replication forks, suggesting that PNKP T118 phosphorylation is required for OFs ligation for its maturation. Furthermore, phosphatase-dead PNKP also exhibited an accumulation of unligated OFs and high-speed DNA synthesis. Overall, our data suggested that CDK-mediated PNKP phosphorylation at T118 is important for its recruitment to OFs and PNKP subsequently promotes end-processing for OFs maturation for stable cell proliferation.

category: molecular biology


title: A sequence-based global map of regulatory activity for deciphering human genetics

abstract: Sequence is at the basis of how the genome shapes chromatin organization, regulates gene expression, and impacts traits and diseases. Epigenomic profiling efforts have enabled large-scale identification of regulatory elements, yet we still lack a sequence-based map to systematically identify regulatory activities from any sequence, which is necessary for predicting the effects of any variant on these activities. We address this challenge with Sei, a new framework for integrating human genetics data with sequence information to discover the regulatory basis of traits and diseases. Our framework systematically learns a vocabulary for the regulatory activities of sequences, which we call sequence classes, using a new deep learning model that predicts a compendium of 21,907 chromatin profiles across >1,300 cell lines and tissues, the most comprehensive to-date. Sequence classes allow for a global view of sequence and variant effects by quantifying diverse regulatory activities, such as loss or gain of cell-type-specific enhancer function. We show that sequence class predictions are supported by experimental data, including tissue-specific gene expression, expression QTLs, and evolutionary constraints based on population allele frequencies. Finally, we applied our framework to human genetics data. Sequence classes uniquely provide a non-overlapping partitioning of GWAS heritability by tissue-specific regulatory activity categories, which we use to characterize the regulatory architecture of 47 traits and diseases from UK Biobank. Furthermore, the predicted loss or gain of sequence class activities suggest specific mechanistic hypotheses for individual regulatory pathogenic mutations. We provide this framework as a resource to further elucidate the sequence basis of human health and disease.


title: Detection and Spatiotemporal analysis of in-vitro 3D migratory Triple-Negative Breast cancer cells

abstract: The invasion of cancer cells into the surrounding tissues is one of the hallmarks of cancer. However, a precise quantitative understanding of the spatiotemporal patterns of cancer cell migration and invasion still remains elusive. A promising approach to investigate these patterns are 3D cell cultures, which provide more realistic models of cancer growth compared to conventional 2D monolayers. Quantifying the spatial distribution of cells in these 3D cultures yields great promise for understanding the spatiotemporal progression of cancer. In the present study, we present an image processing and segmentation pipeline for the detection of 3D GFP-fluorescent Triple-Negative Breast Cancer cell nuclei, and we perform quantitative analysis of the formed spatial patterns and their temporal evolution. The performance of the proposed pipeline was evaluated using experimental 3D cell culture data, and was found to be comparable to manual segmentation, outperforming four alternative automated methods. The spatiotemporal statistical analysis of the detected distributions of nuclei revealed transient, non-random spatial distributions that consisted of clustered patterns across a wide range of neighbourhood distances, as well as dispersion for larger distances. Overall, the implementation of the proposed framework revealed the spatial organization of cellular nuclei with improved accuracy, providing insights into the 3 dimensional inter-cellular organization and its progression through time.

category: bioengineering


title: Automatic calibration of a functional-structural wheat model using an adaptive design and a metamodelling approach

abstract:
O_LIBackground and Aims
Functional-structural plant models are increasingly being used by plant scientists to address a wide variety of questions. However, the calibration of these complex models is often challenging, mainly because of their high computational cost. In this paper, we applied an automatic method to the calibration of WALTer: a functional-structural wheat model that simulates the plasticity of tillering in response to competition for light.
C_LIO_LIMethods
We used a Bayesian calibration method to estimate the values of 5 parameters of the WALTer model by fitting the model outputs to tillering dynamics data. The method presented in this paper is based on the Efficient Global Optimisation algorithm. It involves the use of Gaussian process metamodels to generate fast approximations of the model outputs. To account for the uncertainty associated with the metamodels approximations, an adaptive design was used. The efficacy of the method was first assessed using simulated data. The calibration was then applied to experimental data.
C_LIO_LIKey Results
The method presented here performed well on both simulated and experimental data. In particular, the use of an adaptive design proved to be a very efficient method to improve the quality of the metamodels predictions, especially by reducing the uncertainty in areas of the parameter space that were of interest for the fitting. Moreover, we showed the necessity to have a diversity of field data in order to be able to calibrate the parameters.
C_LIO_LIConclusions
The method presented in this paper, based on an adaptive design and Gaussian process metamodels, is an efficient approach for the calibration of WALTer and could be of interest for the calibration of other functional-structural plant models.
C_LI

category: bioinformatics


title: Adipogenic activity of chemicals used in plastic consumer products

abstract:
Bisphenols and phthalates, chemicals frequently used in plastic products, promote obesity in cell and animal models. However, these well-known metabolism disrupting chemicals (MDCs) represent only a minute fraction of all compounds found in plastics. To gain a comprehensive understanding of plastics as a source of exposure to MDCs, we characterized all chemicals present in 34 everyday products using nontarget high-resolution mass spectrometry and analyzed their joint adipogenic activities by high-content imaging. We detected 55,300 chemical features and tentatively identified 629 unique compounds, including 11 known MDCs. Importantly, chemicals that induced proliferation, growth, and triglyceride accumulation in 3T3-L1 adipocytes were found in one third of the products. Since the majority did not target peroxisome proliferator-activated receptor {gamma}, the effects are likely to be caused by unknown MDCs. Our study demonstrates that daily-use plastics contain potent mixtures of MDCs and can, therefore, be a relevant yet underestimated environmental factor contributing to obesity.

TeaserPlastics contain a potent mixture of chemicals promoting adipogenesis, a key process in developing obesity.


title: Vergence accuracy in an autostereoscopic display

abstract: When fixating an object, observers typically under or over-converge by a small amount, a phenomenon known as "fixation disparity". Fixation disparity is typically measured with physical fixation targets and dichotically presented nonius lines. Here we made fixation disparity measurements with an autostereoscopic display, varying the retinal eccentricity and disparity of the fixation targets. Measurements were made in a group of four practiced observers and in a group of thirteen experimentally naive observers. Fixation disparities with a zero-disparity target were in the direction of fixation behind the plane of the screen and the magnitude of the fixation disparity grew with the eccentricity of the fixation targets (1-5 deg in the practiced observers and 1 - 10 deg in the naive observers). Fixation disparity also increased with increasing disparity of the targets, especially when they were presented at crossed disparities. Fixation disparities were larger overall for naive observers who additionally did not converge in front of the screen when vergence demand was created by crossed disparity fusion locks presented at 5 and 10 deg eccentricities.


title: The spatiotemporal link of temporal expectations: contextual temporal expectation is independent of spatial attention

abstract:
Temporal expectation is the ability to construct predictions regarding the timing of events, based on previously-experienced temporal regularities of different types. For example, cue-based expectations are constructed when a cue validly indicates when a target is expected to occur. However, in the absence of such cues, expectations can be constructed based on contextual temporal information, including the events hazard-rate function - its moment-by-moment conditional probability that changes over time; and prior experiences, which provide probabilistic information regarding the events predicted timing (sequential effects).

It was previously suggested that cue-based temporal expectation is exerted via synchronization of spatially-specific neural activity at a target's predictable time, within receptive fields corresponding to the targets expected location. Here, we tested if the same theoretical model holds for contextual temporal effects. Participants (n = 40) performed a speeded spatial-cueing detection task, with two-thirds valid spatial cues. The targets hazard-rate function was modulated by varying the foreperiod - the interval between the spatial cue and the target - among trials, and was manipulated between groups by changing the interval distribution. Reaction times were analyzed using both frequentist and Bayesian generalized linear mixed models, accounting for hazard and sequential effects. Results showed that the effects of contextual temporal structures on reaction times were independent of spatial attention. This suggests that the spatiotemporal mechanisms, thought to account for cue-based expectation, cannot explain other sources of temporal expectations. We conclude that expectations based on contextual structures have different characteristics than cue-based temporal expectation, suggesting reliance on distinct neural mechanisms.

Significance statementTemporal expectation is the ability to predict an event onset based on temporal regularities. A neurophysiological model suggested that temporal expectation relies on the synchronization of spatially-specific neurons whose receptive fields represent the attended location. This model predicts that temporal expectation would be evident solely within the locus of spatial attention. Existing evidence supported this model for expectation based on associations between a temporal cue and a target, but here we show that it cannot account for another source of temporal expectation - expectation that is based on contextual information, i.e. hazard-rate and recent priors. These findings reveal the existence of different predictive mechanisms for cued and contextual temporal predictions, with the former depending on spatial attention and the latter non-spatially-specific.


title: Drivers of phylogenetic structure in Amazonian freshwater fish assemblages

abstract:
AimCommunity phylogenetics provides important information about the evolutionary and ecological factors help structure regional species assemblages. Here, we analyze phylogenetic diversity (phylodiversity) patterns among fish species in 97 sub-drainages of the Amazon basin, to evaluate the roles of historical and contemporary processes in generating and maintaining the exceptional richness and endemism of Amazonian fish species assemblages.

LocationAmazon River basin

TaxonFreshwater fishes

MethodsUsing a large comprehensive database of freshwater fish species distributions, and a well-sampled molecular phylogeny of ray-finned (actinopterygian) fishes, we develop of multivariate statistical model to correlate estimated historical and contemporary environmental parameters with sub-drainage phylodiversity patterns. The model employs three phylogenetic metrics: i.e.: phylogenetic diversity (PD) sensu stricto, mean pairwise phylogenetic distance (MPD) between species capturing phylodiversity variation at older evolutionary timescales), and mean nearest taxon distance (MNTD) capturing variation in phylodiversity at younger evolutionary timescales.

ResultsThe model recovered significant effects of elevation gradients, contemporary climate, habitat fragmentation, water types, and past marine incursions on assemblage phylodiversity patterns. The model also found significantly negative relationships among the three phylogenetic metrics, and between these metrics and distance to mouth of the Amazon, representing a West-East longitudinal gradient.

Main conclusionsOur study revealed a highly non-random spatial and environmental distribution of our three phylogenetic diversity metrics across the 97 sub-drainages of the Amazon basin. Beyond significant regional effects of several environmental and historical drivers, we also found a significant West-East gradient of increasing phylogenetic diversity and phylogenetic relatedness, both patterns suggesting deeper evolutionary divergences among taxa located to the east, and more diverse, more recent radiations in the western sub-drainages. We conclude that western Amazonia can be seen as an evolutionary "cradle" of biodiversity for freshwater fishes in the Amazon basin as a whole.

Significance StatementThis manuscript reveals spatial patterns of freshwater fish phylogenetic diversity and relatedness and explains its major contemporary and historical drivers in the Amazon basin. Amazon basin contains the highest freshwater biodiversity on Earth, as so investigate phylogenetic dimension of diversity is extremally relevant from the perspective of understanding the information on the evolutionary processes that had shaped Amazonian contemporary fish assemblages.


title: Patterns of morphological diversification in the Ramphastoidea reveal the dramatic divergence of toucans from a conserved morphotype

abstract:
BackgroundMorphological traits offer insights into an organisms ecological niche, species interactions, and patterns of community organisation. Pantropical lineages - animals and plants distributed across the three tropical continental regions of Asia, Africa, and America - provide a way to test how different environments and communities influence morphological diversification. Here, we examined a monophyletic group of frugivorous birds, the barbets and toucans (Ramphastoidea), which diversified independently on three continents, to investigate whether clades in each region exhibit similar (phylogenetically constrained) or distinct (ecologically influenced) patterns of morphological diversification.

ResultsOur results show that despite differences in community dynamics in these regions, lineage accumulation patterns through time on all three continents are broadly similar, putatively due to phylogenetic niche conservatism. We quantified morphological variation in light of phylogenetic relatedness to further reveal that all barbet lineages across continents occupy a conserved region of morphospace after correcting for variation in size. However, in the Neotropics, one lineage, the toucans, have diverged dramatically from typical barbet space and converged toward (yet are distinct from) the trait space occupied by the distantly related hornbills in Asia and Africa. Additionally, we found no link between climatic variables and morphological traits. We conclude that barbets exhibit a conserved morphotype across continents and have diversified by scaling mainly in body size. However, the absence of other large frugivorous birds may have allowed toucans to diversify into a different region of morphospace of increased bill/wing to tail/wing ratios.

ConclusionsA combination of photographic and specimen measurements enabled us to demonstrate the presence of a globally conserved barbet morphotype across three tropical continents. By examining different continental lineages of a single monophyletic bird group, we shed light on the contrasting effects of regional ecological factors and phylogenetic constraints on morphological diversification.


title: Complexity-stability relationship in empirical microbial ecosystems

abstract: Mays stability theory [1, 2], which holds that large ecosystems can be stable up to a critical level of complexity, a product of the number of resident species and the intensity of their interactions, has been a central paradigm in theoretical ecology [3-7]. So far, however, empirically demonstrating this theory in real ecological systems has been a long-standing challenge, with inconsistent results [8]. Especially, it is unknown whether this theory is pertinent in the rich and complex communities of natural microbiomes, mainly due to the challenge of reliably reconstructing such large ecological interaction networks [9-11]. Here, we introduce a novel computational framework for estimating an ecosystems complexity without relying on a priori knowledge of its underlying interaction network. By applying this method to human-associated microbial communities from different body sites [12] and sponge-associated microbial communities from different geographical locations [13], we found that in both cases the communities display a pronounced trade-off between the number of species and their effective connectance. These results suggest that natural microbiomes are shaped by stability constraints, which limit their complexity.


title: Plant-associate interactions and diversification across trophic levels

abstract: Interactions between species are widely understood to have promoted the diversification of life on earth, but how interactions spur the the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled published genetic data for host plants and intimately associated herbivores, parasites, and mutualists. We first tested whether host and associate population structures were correlated -- an indication of associates locally adapting to hosts -- and tested for confounding correlations with geographic distance or climate variation. We used Bayesian multiple regression to estimate the effect of host plant genetic differentiation on associate genetic differentiation over and above the confounding effects of geography and climate. We found that plant and associate genetic structures are indeed often congruent, but isolation by distance and by climate are also common. Multiple regressions established that the effect of host plants on associates is robust to accounting for geographic distance and climate. Finally, associate genetic structure was significantly explained by plant genetic structure more often in antagonistic interactions than in mutualistic ones. This supports a key prediction of coevolutionary theory, that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions promote diversity via the effect of hosts geographic distribution on mutualists dispersal.

category: evolutionary biology


title: Across-population genomic prediction in grapevine opens up promising prospects for breeding

abstract: Crop breeding involves two selection steps: choosing progenitors and selecting offspring within progenies. Genomic prediction, based on genome-wide marker estimation of genetic values, could facilitate these steps. However, its potential usefulness in grapevine (Vitis vinifera L.) has only been evaluated in non-breeding contexts mainly through cross-validation within a single population. We tested across-population genomic prediction in a more realistic breeding configuration, from a diversity panel to ten bi-parental crosses connected within a half-diallel mating design. Prediction quality was evaluated over 15 traits of interest (related to yield, berry composition, phenology and vigour), for both the average genetic value of each cross (cross mean) and the genetic values of individuals within each cross (individual values). Genomic prediction in these conditions was found useful: for cross mean, average per-trait predictive ability was 0.6, while per-cross predictive ability was halved on average, but reached a maximum of 0.7. Mean predictive ability for individual values within crosses was 0.26, about half the within-half-diallel value taken as a reference. For some traits and/or crosses, these across-population predictive ability values are promising for implementing genomic selection in grapevine breeding. This study also provided key insights on variables affecting predictive ability. Per-cross predictive ability was well predicted by genetic distance between parents and when this predictive ability was below 0.6, it was improved by training set optimization. For individual values, predictive ability mostly depended on trait-related variables (magnitude of the cross effect and heritability). These results will greatly help designing grapevine breeding programs assisted by genomic prediction.


title: Modeling memory T cell states at single-cell resolution identifies in vivo state-dependence of eQTLs influencing disease

abstract: Many non-coding genetic variants cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated by gene-regulation differences between cell states. T cells, for example, have fluid, multifaceted functional states in vivo that cannot be modeled in eQTL studies that aggregate cells. Here, we modeled T cell states and eQTLs at single-cell resolution. Using >500,000 resting memory T cells from 259 Peruvians, we found over one-third of the 6,511 cis-eQTLs had state-dependent effects. By integrating single-cell RNA and surface protein measurements, we defined continuous cell states that explained more eQTL variation than discrete states like CD4+ or CD8+ T cells and could have opposing effects on independent eQTL variants in a locus. Autoimmune variants were enriched in cell-state-dependent eQTLs, such as a rheumatoid-arthritis variant near ORMDL3 strongest in cytotoxic CD8+ T cells. These results argue that fine-grained cell state context is crucial to understanding disease-associated eQTLs.


title: A Kernel Method for Dissecting Genetic Signals in Tests of High-Dimensional Phenotypes

abstract: Genomewide association studies increasingly employ multivariate tests of multiple correlated phenotypes to exploit likely pleiotropy to improve power. Typical multivariate methods produce a global p-value of association between a variant (or set of variants) and multiple phenotypes. When the global test is significant, subsequent interest then focuses on dissecting the signal and, in particular, delineating the set of phenotypes where the genetic variant(s) have a direct effect from the remaining phenotypes where the genetic variant(s) possess either indirect or no effect. While existing techniques like mediation models can be utilized for this purpose, they generally cannot handle high-dimensional phenotypic and genotypic data. To assist in filling this important gap, we propose a modification of a kernel distance-covariance framework for gene mapping of multiple variants with multiple phenotypes to test instead whether the association between the variants and a group of phenotypes is driven through a direct association with just a subset of the phenotypes. We use simulated data to show that our new method controls for type I error and is powerful to detect a variety of models demonstrating different patterns of direct and indirect effects. We further illustrate our method using GWAS data from the Grady Trauma Project and show that an existing signal between genetic variants in the ZHX2 gene and 21 items within the Beck Depression Inventory appears to be due to a direct effect of these variants on only 3 of these items. Our approach scales to genomewide analysis, and is applicable to high-dimensional correlated phenotypes.


title: AnchorWave: sensitive alignment of genomes with high diversity, structural polymorphism and whole-genome duplication variation

abstract:
Millions of species are currently being sequenced and their genomes are being compared. Many of them have more complex genomes than model systems and raised novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication or polyploidy levels. Here we introduce AnchorWave, which performs whole-genome duplication informed collinear anchor identification between genomes and performs base-pair resolution global alignments for collinear blocks using the wavefront algorithm and a 2-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multi-kilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs between two maize lines. By contrast, other genome alignment tools showed almost zero power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome than the closest competitive approach, when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor binding sites (TFBSs) at a rate of 1.05-74.85 fold higher than other tools, while with significantly lower false positive alignments. AnchorWave shows obvious improvement when applied to genomes with dispersed repeats, active transposable elements, high sequence diversity and whole-genome duplication variation.

Significance statementOne fundamental analysis needed to interpret genome assemblies is genome alignment. Yet, accurately aligning regulatory and transposon regions outside of genes remains challenging. We introduce AnchorWave, which implements a genome duplication informed longest path algorithm to identify collinear regions and performs base-pair resolved, end-to-end alignment for collinear blocks using an efficient 2-piece affine gap cost strategy. AnchorWave improves alignment of partially synthetic and real genomes under a number of scenarios: genomes with high similarity, large genomes with high TE activity, genomes with many inversions, and alignments between species with deeper evolutionary divergence and different whole-genome duplication histories. Potential use cases for the method include genome comparison for evolutionary analysis of non-genic sequences and population genetics of taxa with complex genomes.


title: Automated Feeding and Fermentation Phase Transitions for the Production of Unspecific Peroxygenase by Pichia pastoris

abstract: Fungal peroxygenases are promising biocatalysts for hydroxylation steps in various industry-relevant synthesis pathways. In this application note we describe a bioprocess for the production of unspecific peroxygenase (UPO) in Pichia pastoris. The process was divided in four phases, with different carbon requirements. Precise timing of culture feeding was crucial for optimal cell growth and protein expression. We demonstrate how the automation of culture feeding reduced manual work as well as the risk of process failure due to operator error.


title: Cholesterol plays a decisive role in tetraspanin assemblies during bilayer deformations

abstract: The tetraspanin family plays key roles in many physiological processes, such as, tumour invasion, cell motility, virus infection, cell attachment and entry. Tetraspanins function as molecular scaffolds organised in microdomains with interesting downstream cellular consequences. However, despite their relevance in human physiology, the precise mechanisms of their various functions remain elusive. In particular, the full-length CD81 tetraspanin has interesting cholesterol-related properties that modulate its activity in cells. In this work, we study the opening transition of CD81 under different conditions. We propose that such conformational change is a collaborative process enhanced by simultaneous interactions between multiple identical CD81 tetraspanins. With molecular dynamics simulations we describe the crucial role of a ternary lipid bilayer with cholesterol in CD81 conformational dynamics, observing two emergent properties: first, clusters of CD81 collectively segregate one tetraspanin while favouring one opening transition, second, cumulative cholesterol sequestering by CD81 tetraspanins inhibits large membrane deformations due to local density variations.


title: Artificial Neural Networks for classification of single cell gene expression

abstract:
BackgroundSingle-cell transcriptome (SCT) sequencing technology has reached the level of high-throughput technology where gene expression can be measured concurrently from large numbers of cells. The results of gene expression studies are highly reproducible when strict protocols and standard operating procedures (SOP) are followed. However, differences in sample processing conditions result in significant changes in gene expression profiles making direct comparison of different studies difficult. Unsupervised machine learning (ML) uses clustering algorithms combined with semi-automated cell labeling and manual annotation of individual cells. They do not scale up well and a workflow used on a specific dataset will not perform well with other studies. Supervised ML classification shows superior classification accuracy and generalization properties as compared to unsupervised ML methods. We describe a supervised ML method that deploys artificial neural networks (ANN), for 5-class classification of healthy peripheral blood mononuclear cells (PBMC) from multiple diverse studies.

ResultsWe used 58 data sets to train ANN incrementally - over ten cycles of training and testing. The sample processing involved four protocols: separation of PBMC, separation of PBMC + enrichment (by negative selection), separation of PBMC + FACS, and separation of PBMC + MACS. The training data set included between 85 and 110 thousand cells, and the test set had approximately 13 thousand cells. Training and testing were done with various combinations of data sets from four principal data sources. The overall accuracy of classification on independent data sets reached 5-class classification accuracy of 94%. Classification accuracy for B cells, monocytes, and T cells exceeded 95%. Classification accuracy of natural killer (NK) cells was 75% because of the similarity between NK cells and T cell subsets. The accuracy of dendritic cells (DC) was low due to very low numbers of DC in the training sets.

ConclusionsThe incremental learning ANN model can accurately classify the main types of PBMC. With the inclusion of more DC and resolving ambiguities between T cell and NK cell gene expression profiles, we will enable high accuracy supervised ML classification of PBMC. We assembled a reference data set for healthy PBMC and demonstrated a proof-of-concept for supervised ANN method in classification of previously unseen SCT data. The classification shows high accuracy, that is consistent across different studies and sample processing methods.


title: SimpleForest - a comprehensive tool for 3d reconstruction of trees from forest plot point clouds

abstract:
The here-on presented SimpleForest is written in C++ and published under GPL v3. As input data SimpleForest utilizes forestry scenes recorded as terrestrial laser scan clouds. SimpleForest provides a fully automated pipeline to model the ground as a digital terrain model, then segment the vegetation and finally build quantitative structure models of trees (QSMs) consisting of up to thousands of topologically ordered cylinders. These QSMs allow us to calculate traditional forestry metrics such as diameter at breast height, but also volume and other structural metrics that are hard to measure in the field. Our volume evaluation on three data sets with destructive volumes show high prediction qualities with concordance correlation coefficient CCC [Formula] of 0.91 (0.87), 0.94 (0.92) and 0.97 (0.93) for each data set respectively.

We combine two common assumptions in plant modeling "The sum of cross sectional areas after a branch junction equals the one before the branch junction" (Pipe Model Theory) and "Twigs are self-similar" (West, Brown and Enquist model). As even sized twigs correspond to even sized cross sectional areas for twigs we define the Reverse Pipe Radius Branchorder (RPRB) as the square root of the number of supported twigs. The prediction model radius = B0 * RPRB relies only on correct topological information and can be used to detect and correct overestimated cylinders. In QSM building the necessity to handle overestimated cylinders is well known. The RPRB correction performs better with a CCC [Formula] of 0.97 (0.93) than former published ones 0.80 (0.88) and 0.86 (0.85) in our validation.

We encourage forest ecologists to analyze output parameters such as the GrowthVolume published in earlier works, but also other parameters such as the GrowthLength, VesselVolume and RPRB which we define in this manuscript.

Upload statementSelf-uploaded pre-print for peer-review submitted manuscript. The manuscript was submitted on 26th of July 2021 to Plos Computational Biology:

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title: SMGen: A generator of synthetic models of biochemical reaction networks

abstract: Several software tools for the simulation and analysis of biochemical reaction networks have been developed in the last decades; however, assessing and comparing their computational performance in executing the typical tasks of Computational Systems Biology can be limited by the lack of a standardized benchmarking approach. To overcome these limitations, we propose here a novel tool, named SMGen, designed to automatically generate synthetic models of reaction networks that, by construction, are characterized by both features (e.g., system connectivity, reaction discreteness) and non trivial emergent dynamics of real biochemical networks. The generation of synthetic models in SMGen is based on the definition of an undirected graph consisting of a single connected component, which generally results in a computationally demanding task. To avoid any burden in the execution time, SMGen exploits a Main-Worker paradigm to speed up the overall process. SMGen is also provided with a user-friendly Graphical User Interface that allows the user to easily set up all the parameters required to generate a set of synthetic models with any user-defined number of reactions and species. We analysed the computational performance of SMGen by generating batches of symmetric and asymmetric Reaction-based Models (RBMs) of increasing size, showing how a different number of reactions and/or species affects the generation time. Our results show that when the number of reactions is higher than the number of species, SMGen has to identify and correct high numbers of errors during the creation process of the RBMs, a circumstance that increases the overall running time. Still, SMGen can create synthetic models with 512 species and reactions in less than 7 seconds. The open-source code of SMGen is available on GitLab: https://gitlab.com/sgr34/smgen.

category: systems biology


title: Amazonian run-of-river dam reservoir impacts underestimated: Evidence from a Before-After Control-Impact study of freshwater turtle nesting areas

abstract:
O_LIConstruction of hydropower dams is associated with negative impacts on biodiversity, yet there remains a lack of robust scientific evidence documenting the magnitude of these impacts particularly across highly biodiverse tropical waterways. Hydropower expansion is an increasing threat to the Endangered yellow-spotted river turtle (Podocnemis unifilis) across its tropical South American range.
C_LIO_LIYellow-spotted river turtle nesting areas were monitored as an indicator of dry season river level changes following run-of-river dam reservoir filling. A Before-After-Control-Impact (BACI) study design was used with multi-year field campaigns monitoring turtle nesting areas upstream of the dam.
C_LIO_LIThe cause and extent of changes in nesting areas were established using Generalized Additive Models. Nesting area density was evaluated in relation to: time (before versus after), treatment (control versus impact), time treatment interaction (BACI), distance to the dam and precipitation. The extent of changes was examined by comparing the proportion of nesting areas remaining during four years after reservoir filling.
C_LIO_LIDam construction generated an immediate and apparently permanent dry season river level rise that extended more than 20 km beyond impact assessment limits. On average the density of nesting areas declined 69% (from 0.48 to 0.15 per km) across 33 km of river directly impacted by the dam. This loss was reflected in a significant BACI interaction. Nesting area density was not explained by seasonal precipitation.
C_LIO_LIStandardized monitoring of freshwater turtle nesting areas provided an effective means to quantify impacts of hydropower developments across biodiverse yet rapidly changing waterways. The negative impacts documented in this study should be preventable by mitigation actions including habitat creation and dry season flow regulation. Such measures would also likely benefit multiple species elsewhere in tropical rivers increasingly impacted by run-of-river dams.
C_LI

category: zoology