title: Exploiting flow cytometry for the unbiased quantification of protein inclusions in Caenorhabditis elegans

abstract: The aggregation of proteins into inclusions or plaques is a prominent hallmark of a diverse range of pathologies including neurodegenerative diseases. The quantification of such inclusions in Caenorhabditis elegans models of aggregation is usually achieved by fluorescence microscopy or other techniques involving biochemical fractionation of worm lysates. Here, we describe a simple and rapid flow cytometry-based approach that allows fluorescently-tagged inclusions to be enumerated in whole worm lysate in a quantitative and unbiased fashion. We demonstrate that this technique is applicable to multiple C. elegans models of aggregation and importantly, can be used to monitor the dynamics of inclusion formation in response to heat shock and during aging. This includes the characterisation of physicochemical properties of inclusions, such as their size, which may reveal how aggregate formation is distinct in different tissues or at different stages of pathology or aging. This new method can be used as a powerful technique for the medium- to high-throughput quantification of inclusions in future studies of genetic or chemical modulators of aggregation in C. elegans.


title: Loss of Secretory Pathway Ca2+ ATPase (SPCA1) Impairs Insulin Secretion and Reduces Autophagy in the Pancreatic Islet

abstract: The {beta} cell Golgi apparatus serves as a significant store of intracellular Ca2+ and an important site of proinsulin maturation. However, the contribution of Golgi Ca2+ to diabetes pathophysiology is unknown. The Golgi primarily utilizes the Secretory Pathway Ca2+ ATPase (SPCA1) to maintain intraluminal Ca2+ stores, and loss of SPCA1 has been linked to impaired Golgi function in other cell types. Here, we demonstrated that SPCA1 expression is decreased in islets from diabetic mice and human organ donors with type 2 diabetes, suggesting SPCA1 may impact diabetes development. INS-1 {beta} cells lacking SPCA1 (SPCA1KO) showed reduced intraluminal Golgi Ca2+ levels, reduced glucose-stimulated insulin secretion (GSIS), and increased insulin content. Islets from SPCA1 haploinsufficient mice (SPCA1+/-) exhibited reduced GSIS, altered glucose-induced Ca2+ oscillations, and altered insulin granule maturation. Autophagy can regulate granule homeostasis, therefore we induced autophagy with Torin1 and found that SPCA1KO cells and SPCA1+/- islets had reduced levels of the autophagosome marker LC3-II. Furthermore, SPCA1KO LC3-II were unchanged after blocking autophagy initiation or autophagolysosome fusion and acidification. Thus, we concluded that {beta} cell SPCA1 plays an important role in the maintenance of Golgi Ca2+ homeostasis and reduced Golgi Ca2+ impairs autophagy initiation and may impact insulin granule homeostasis.

category: cell biology


title: Liquid-crystalline lipid phase transitions in lipid droplets selectively remodel the LD proteome

abstract: Lipid droplets (LDs) are reservoirs for triglycerides (TGs) and sterol-esters (SEs). How lipids are organized within LDs and influence the LD proteome remains unclear. Using in situ cryo-electron tomography, we show that glucose restriction triggers lipid phase transitions within LDs generating liquid-crystalline lattices inside them. Mechanistically, this requires TG lipolysis, which alters LD neutral lipid composition and promotes SE transition to a liquid-crystalline phase. Fluorescence imaging and proteomics further reveal that LD liquid-crystalline lattices selectively remodel the LD proteome. Some canonical LD proteins including Erg6 re-localize to the ER network, whereas others remain on LDs. Model peptide LiveDrop also redistributes from LDs to the ER, suggesting liquid-crystalline-phases influence ER-LD inter-organelle transport. Proteomics also indicates glucose restriction elevates peroxisome lipid oxidation, suggesting TG mobilization provides fatty acids for cellular energetics. This suggests glucose restriction drives TG mobilization, which alters the phase properties of LD lipids and selectively remodels the LD proteome.


title: Kazrin C entraps early endosomes at the pericentriolar region and facilitates endocytic recycling

abstract: We identified kazrin C as a human protein that inhibits clathrin-mediated endocytosis when overexpressed. We now generated kazrin knock out and GFP-kazrin C expressing MEF lines to investigate in detail its function in endocytic traffic. We find that kazrin depletion delays recycling of internalized material and causes accumulation and dispersal of early endosomes (EE), indicating a role in transport from the early to the perinuclear recycling endosomes (RE). Consistently, we found that the C-terminal domain of kazrin C, predicted to be an intrinsically disordered region (IDR), specifically interacts with several endosomal components, including Epsin Homology Domain (EHD) proteins, {gamma}-adaptin, and phosphatidyl-inositol-3 phosphate. Further, kazrin C shares homology with dynein/dynactin adaptors, it directly interacts with the dynactin complex and the dynein light intermediate chain LIC1, and overexpressed GFP-kazrin C forms condensates that entrap EE in the vicinity of the centrosome, in a microtubule-dependent manner. Altogether, the data indicates that kazrin C facilitates cargo recycling by trapping EE or EE-derived transport intermediates at the perinuclear region, where transfer of cargo to the RE might occur.


title: Monosomies, trisomies and segmental aneuploidies differentially affect chromosomal stability

abstract: Aneuploidy and chromosomal instability are both commonly found in cancer. Chromosomal instability leads to karyotype heterogeneity in tumors and is associated with therapy resistance, metastasis and poor prognosis. It has been hypothesized that aneuploidy per se is sufficient to drive CIN, however due to limited models and heterogenous results, it has remained controversial which aspects of aneuploidy can drive CIN. In this study we systematically tested the impact of different types of aneuploidies on the induction of CIN. We generated a plethora of isogenic aneuploid clones harboring whole chromosome or segmental aneuploidies in human p53-deficient RPE-1 cells. We observed increased segregation errors in cells harboring trisomies that strongly correlated to the number of gained genes. Strikingly, we found that clones harboring only monosomies do not induce a CIN phenotype. Finally, we found that an initial chromosome breakage event and subsequent fusion can instigate breakage-fusion-bridge cycles in segmental aneuploidies. This suggests that monosomies, trisomies and segmental aneuploidies have fundamentally different effects on chromosomal instability and these results help us to decipher the complex relationship between aneuploidy and CIN.


title: Cosmopolitanism at the Roman Danubian Frontier, Slavic Migrations, and the Genomic Formation of Modern Balkan Peoples

abstract: The Roman Empire expanded through the Mediterranean shores and brought human mobility and cosmopolitanism across this inland sea to an unprecedented scale. However, if this was also common at the Empire frontiers remains undetermined. The Balkans and Danube River were of strategic importance for the Romans acting as an East-West connection and as a defense line against "barbarian" tribes. We generated genome-wide data from 70 ancient individuals from present-day Serbia dated to the first millennium CE; including Viminacium, capital of Moesia Superior province. Our analyses reveal large scale-movements from Anatolia during Imperial rule, similar to the pattern observed in Rome, and cases of individual mobility from as far as East Africa. Between [~]250-500 CE, we detect gene-flow from Central/Northern Europe harboring admixtures of Iron Age steppe groups. Tenth-century CE individuals harbored North-Eastern European-related ancestry likely associated to Slavic-speakers, which contributed >20% of the ancestry of todays Balkan people.

category: evolutionary biology


title: Gene drive escape from resistance depends on mechanism and ecology

abstract: Gene drives can potentially be used to suppress pest populations, and the advent of CRISPR technology has made it feasible to engineer them in many species, especially insects. What remains largely unknown for implementations is whether anti-drive resistance will evolve to block the population suppression. An especially serious threat to some kinds of drive is mutations in the CRISPR cleavage sequence that block the action of CRISPR, but designs have been proposed to avoid this type of resistance. Various types of resistance at loci away from the cleavage site remain a possibility, which is the focus here. It is known that modest-effect suppression drives can essentially  outrun unlinked resistance even when that resistance is present from the start. We demonstrate here how the risk of evolving (unlinked) resistance can be further reduced without compromising overall suppression by introducing multiple suppression drives or by designing drives with specific ecological effects. However, we show that even modest-effect suppression drives remain vulnerable to the evolution of extreme levels of inbreeding, which halt the spread of the drive without actually interfering with its mechanism. The landscape of resistance evolution against suppression drives is therefore complex, but avenues exist for enhancing gene drive success.


title: Dicer-to-Argonaute switch controls biogenesis of oncogenic miRNA

abstract: miRNAs are post-transcriptional regulators of gene expression, controlling biological processes from development to pathogenesis. We asked whether the reshaped functional miRNA landscape in cancers is driven by altered transcription of its precursors, or altered biogenesis and maturation of miRNAs. Integrated analysis of genomic and transcriptomic data in 9,111 samples across 10 cancer types and healthy tissues revealed a recurrent genomic switch from DICER-dependent to non-canonical Argonaute-mediated, DICER-independent, miRNA biogenesis. Experimental validation in AGO2-amplified clinical samples and cancer cell lines confirmed that canonical miRNAs can undergo maturation in a DICER-independent manner, and that elevated Argonaute levels promote selective maturation of the oncogenic miR-106b/25 cluster as shown by the altered ratio of mature miRNA to immature pri-miRNA levels. The preferential maturation of these oncogenic miRNAs, whose processing bypasses DICER1, promotes cancer progression and predicts poor prognosis. This highlights the evolution of non-canonical AGO2-dependent oncomiR processing as a novel driver pathway in cancer.

category: genomics


title: 5WBF: A low-cost and straightforward whole blood filtration method suitable for whole-genome sequencing of Plasmodium falciparum clinical isolates

abstract:
BackgroundWhole-genome sequencing (WGS) is becoming increasingly helpful to assist malaria control programs. A major drawback of this approach is the large amount of human DNA compared to parasite DNA extracted from unprocessed whole blood. As red blood cells (RBCs) have a diameter of about 7-8 m and exhibit some deformability, we hypothesized that cheap and commercially available 5 m filters might retain leukocytes but much less of Plasmodium falciparum-infected RBCs. This study aimed to test the hypothesis that such a filtration method, named 5WBF (for 5 m Whole Blood Filtration), may provide highly enriched parasite material suitable for P. falciparum WGS.

MethodsWhole blood was collected from five patients experiencing a P. falciparum malaria episode (ring-stage parasitemia range: 0.04-5.5%) and from mock samples obtained by mixing synchronized, ring-stage cultured P. falciparum 3D7 parasites with uninfected human whole blood (final parasitemia range: 0.02-1.1%). These whole blood samples (50 to 400 L) were diluted in RPMI 1640 medium or PBS 1X buffer and filtered with syringes connected to a 5 m commercial filter. DNA was extracted from filtered and unfiltered counterpart blood samples using a commercial kit. The 5WBF method was evaluated on the ratios of parasite:human DNA assessed by qPCR and by sequencing depth and percentages of coverage from WGS data (Illumina NextSeq 500). As a comparison, we also applied to the same unprocessed whole blood samples the selective whole-genome amplification (sWGA) method which does not rely on blood filtration.

ResultsAfter applying 5WBF, qPCR indicated an average of 2-fold loss in the amount of parasite template DNA (Pf ARN18S gene) and from 4,096- to 65,536-fold loss of human template DNA (human {beta} actin gene). WGS analyses revealed that > 95% of the nuclear genome and the entire whole organellar genomes were covered at [≥] 10x depth for all samples tested. In sWGA counterparts, none of the organellar genomes were covered, and from 47.7 to 82.1% of the nuclear genome was covered at [≥] 10x depth depending on parasitemia. Sequence reads were homogeneously distributed across gene sequences for 5WBF-treated samples (n = 5,460 genes; mean coverage: 91x; median coverage: 93x; 5th percentile: 70x; 95th percentile: 103x), allowing the identification of gene copy number variations such as for gch1. This later analysis was not possible for sWGA-treated samples, as we observed a much more heterogeneous distribution of reads among gene sequences (mean coverage: 80x; median coverage: 51x; 5th percentile: 7x; 95th percentile: 245x).

ConclusionsThe novel 5WBF leucodepletion method is simple to implement and based on commercially available, standardized, 5 m filters which cost from 1.0 to 1.7{euro} per unit, depending on suppliers. 5WBF permits extensive genome-wide analysis of P. falciparum DNA from minute amounts of whole blood even with parasitemias as low as 0.02%.


title: Towards a molecular mechanism underlying mitochondrial protein import through the TOM-TIM23 complex

abstract: Nearly all mitochondrial proteins need to be targeted for import from the cytosol. For the majority, the first port of call is the translocase of the outer membrane (TOM complex), followed by a procession of alternative molecular machines, conducting transport to their final destination. The pre-sequence translocase of the inner-membrane (TIM23-complex) imports proteins with cleavable pre-sequences, and comes in two flavours: the TIM23SORT complex mediates inner mitochondrial membrane (IMM) protein insertion and the TIM23MOTOR complex delivers proteins to the matrix. Progress in understanding these transport mechanisms has been hampered by the poor sensitivity and time-resolution of import assays. However, with the development of an assay based on split NanoLuc luciferase, we can now explore this process in greater detail. Here, we apply this new methodology to understand how {Delta}{psi} and ATP hydrolysis, the two main driving forces for import through the TIM23MOTOR complex, contribute to the import of pre-sequence-containing precursors (PCPs) with varying properties. Notably, we found that two major rate-limiting steps define PCP import time: passage of PCP across the OMM and initiation of IMM transport by the pre-sequence. The rates of these steps are influenced by PCP properties such as size and net charge, but not total amount of PCP imported - emphasising the importance of collecting rapid kinetic data, achieved here, to elucidate mechanistic detail. The apparent distinction between transport through the two membranes (passage through TOM is substantially complete before PCP-TIM engagement) is in contrast with the current view that import occurs through TOM and TIM in a single continuous step. Our results also indicate that PCPs spend very little time in the TIM23 channel - presumably rapid success or failure of import is critical for maintaining mitochondrial fitness.

category: biochemistry


title: Towards a molecular mechanism underlying mitochondrial protein import through the TOM and TIM23 complexes


title: SHED-dependent oncogenic signalling of the PEAK3 pseudo-kinase

abstract: The PEAK1 and pragmin/PEAK2 pseudo-kinases have emerged as important components of the protein tyrosine kinase pathway implicated in cancer progression. They can signal by a scaffolding mechanism that involves a conserved split helical dimerization (SHED) module. We recently identified PEAK3 as a novel member of this family based on structural homology; however, its signalling mechanism remains unclear. Here, we found that although it can self-associate, PEAK3 shows higher evolutionary divergence than PEAK1/2. Moreover, PEAK3 protein is strongly expressed in human haematopoietic cells, and is upregulated in acute myeloid leukaemia. Functionally, PEAK3 overexpression in U2OS sarcoma cells enhanced their growth and migratory properties, while its silencing in THP1 leukemic cells reduced these effects. Importantly, an intact SHED module was required for these PEAK3 oncogenic activities. Mechanistically, through a phosphokinase survey, we identified PEAK3 as a novel inducer of AKT signalling, independent of growth factor stimulation. Then, proteomic analyses revealed that PEAK3 interacts with the signalling proteins GRB2 and ASAP1/2 and the protein kinase PYK2, and that these interactions require the SHED domain. Moreover, PEAK3 activated PYK2 to promote AKT signalling. Thus, the PEAK1-3 pseudo-kinases may use a conserved SHED-dependent mechanism to activate specific signalling proteins to promote oncogenesis.

category: cancer biology


title: R-loop homeostasis and cancer mutagenesis promoted by the DNA cytosine deaminase APOBEC3B

abstract:
The single-stranded DNA cytosine-to-uracil deaminase APOBEC3B is an antiviral protein implicated in cancer. However, its substrates in cells are not fully delineated. Here, APOBEC3B proteomics reveal interactions with a surprising number of R-loop factors. Biochemical experiments show APOBEC3B binding to R-loops in human cells and in vitro. Genetic experiments demonstrate R-loop increases in cells lacking APOBEC3B and decreases in cells overexpressing APOBEC3B. Genome-wide analyses show major changes in the overall landscape of physiological and stimulus-induced R-loops with thousands of differentially altered regions as well as binding of APOBEC3B to many of these sites. APOBEC3 mutagenesis impacts overexpressed genes and splice factor mutant tumors preferentially, and APOBEC3-attributed kataegis are enriched in RTCW consistent with APOBEC3B deamination. Taken together with the fact that APOBEC3B binds single-stranded DNA and RNA and preferentially deaminates DNA, these results support a mechanism in which APOBEC3B mediates R-loop homeostasis and contributes to R-loop mutagenesis in cancer.

HighlightsO_LIUnbiased proteomics link antiviral APOBEC3B to R-loop regulation
C_LIO_LISystematic alterations of APOBEC3B levels trigger corresponding changes in R-loops
C_LIO_LIAPOBEC3B binds R-loops in living cells and in vitro
C_LIO_LIBioinformatics analyses support an R-loop deamination and mutation model
C_LI


title: Chloroplast photosystem I dimer and high resolution model of the complex with plastocyanin

abstract: Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular organization affects the dynamics of photosynthetic membranes. Here, we reveal a chloroplast PSI from the green alga Chlamydomonas reinhardtii that is organized as a homodimer, comprising 40 protein subunits with 118 transmembrane helices that provide scaffold for 568 pigments. Our cryo-EM structure identifies that the absence of PsaH and Lhca2 gives rise to a head-to-head relative orientation of the PSI-LHCI monomers in a way that is essentially different from the oligomer formation in cyanobacteria. The light-harvesting protein Lhca9 is the key element for mediating this dimerization. The interface between the monomers is lacking PsaH, and thus partially overlaps with the surface area that would bind one of the LHCII complexes in state transitions. We also define the most accurate available PSI-LHCI model at 2.3 [A] resolution, including a flexibly bound electron donor plastocyanin, and assign correct identities and orientations of all the pigments, as well as 621 water molecules that affect energy transfer pathways.

category: plant biology


title: Algal photosystem I dimer and high resolution model of PSI:plastocyanin complex


title: Songbird subthalamic neurons signal song timing and error and project to dopaminergic midbrain

abstract:
Skill learning requires motor output to be evaluated against internal performance benchmarks. In songbirds, ventral tegmental area (VTA) dopamine neurons (DA) signal performance errors important for learning, but it remains unclear which brain regions project VTA and how these inputs may implement the sensorimotor comparisons necessary for error computation. Here we find that the songbird subthalamic nucleus (STN) projects to VTA and that STN microstimulation can excite VTA neurons. We also discover that STN receives inputs from auditory cortical and ventral pallidal brain regions previously implicated in song evaluation. In the first neural recordings from songbird STN, we discover that the activity of most STN neurons is associated with body movements and not singing, but a small fraction of neurons exhibits precise song timing and performance error signals consistent with performance evaluation. Together our results implicate the STN-VTA projection as an evolutionarily conserved pathway important for motor learning and expand the territories of songbird brain associated with song learning.

New & NoteworthySongbird subthalamic (STN) neurons exhibit song-timing and performance error signals and are interconnected with auditory pallium, ventral pallidum and ventral tegmental area, three areas important for song learning.

category: neuroscience


title: Influenza A virus (H1N1) infection induces microglia activation and temporal dysbalance in glutamatergic synaptic transmission.

abstract: 3.Influenza A virus (IAV) causes respiratory tract disease and is responsible for seasonal and reoccurring epidemics affecting all age groups. Next to typical disease symptoms such as fever and fatigue, IAV infection has been associated with behavioral alterations presumably contributing to the development of major depression. Previous experiments using IAV/H1N1 infection models have shown impaired hippocampal neuronal morphology and cognitive abilities, but the underlying pathways have not been fully described. In this study, we demonstrate that infection with a low dose non-neurotrophic H1N1 strain of IAV causes ample peripheral immune response followed by a temporary blood-brain-barrier disturbance. Although histological examination did not reveal obvious pathological processes in the brains of IAV-infected mice, detailed multidimensional flow cytometric characterization of immune cells uncovered subtle alterations in the activation status of microglia cells. More specifically, we detected an altered expression pattern of major histocompatibility complex class I and II, CD80, and F4/80 accompanied by elevated mRNA levels of CD36, CD68, C1QA, and C3, suggesting evolved synaptic pruning. To closer evaluate how these profound changes affect synaptic balance, we established a highly sensitive multiplex flow cytometry-based approach called Flow Synaptometry. The introduction of this novel technique enabled us to simultaneously quantify the abundance of pre- and postsynapses from distinct brain regions. Our data reveal a significant reduction of VGLUT1 in excitatory presynaptic terminals in the Cortex and Hippocampus, identifying a subtle dysbalance in glutamatergic synapse transmission upon H1N1 infection in mice. In conclusion, our results highlight the consequences of systemic IAV-triggered inflammation on the central nervous system and the induction and progression of neuronal alterations.

category: immunology


title: BiomeHorizon: visualizing microbiome time series data in R

abstract:
SummaryA key aspect of microbiome research is analysis of longitudinal dynamics using time series data. A method to visualize both the proportional and absolute change in the abundance of multiple taxa across multiple subjects over time is needed. We developed BiomeHorizon, an open-source R package that visualizes longitudinal compositional microbiome data using horizon plots.

Availability and ImplementationBiomeHorizon is available at https://github.com/blekhmanlab/biomehorizon/ and released under the MIT license. A guide with step-by-step instructions for using the package is provided at https://blekhmanlab.github.io/biomehorizon/. The guide also provides code to reproduce all plots in this manuscript.

Contactlgrienei@umn.edu, blekhman@umn.edu, iafink@uchicago.edu

Supplementary informationNone

category: microbiology


title: The B chromosome of Pseudococcus viburni: a selfish chromosome that exploits whole-genome meiotic drive

abstract: Meiosis, the key process underlying sexual reproduction, is generally a fair process: each chromosome has a 50% chance of being included into each gamete. However in some organisms meiosis has become highly aberrant with some chromosomes having a higher chance of making it into gametes than others. Yet why and how such systems evolve remains unclear. Here we study the unusual reproductive genetics of mealybugs, in which only maternal-origin chromosomes are included into the gametes during male meiosis, while paternally-derived chromosomes degrade. This "whole genome meiotic drive" occurs in all males and is evolutionarily conserved. However one species - the obscure mealybug Pseudococcus viburni - has a segregating B chromosome that increases in frequency by escaping paternal genome elimination. Here we present whole-genome and gene expression data from laboratory lines with and without B chromosomes. These data allow us to identify B-linked sequences including >70 protein-coding genes as well as a B-specific satellite repeat that makes up a significant proportion of the chromosome. We also used these data to investigate the evolutionary origin of the B chromosome. The few paralogs between the B and the core genome are distributed throughout the genome, showing that it is unlikely that the B originated through a simple duplication of one of the autosomes. We also find that while many of the B-linked genes do not have paralogs within the P.viburni genome, but they do show orthology with genes in other hemipteran insects suggesting that the B might have originated from fission of one of the autosomes, possibly followed by further translocations of individual genes. Finally in order to understand the mechanisms by which the B is able to escape elimination when paternally-derived we generated gene expression data for males and females with and without B chromosomes. We find that at the developmental stage when meiosis is taking place only a small number of B-linked genes show significant expression. Only one gene was significantly over-expressed during male meiosis, which is when the drive occurs: a acetyltransferase involved in H3K56Ac, which has a putative role in meiosis and is therefore a promising candidate for further studies. Together, these results form a promising foundation for studying the mechanisms of meiotic drive in a system that is uniquely suited for this approach.


title: The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: identification of sex-related and lipid biosynthesis genes

abstract:
Paracentrotus lividus is the most abundant, distributed and desirable echinoid species in Europe. Although, economically important, this species has scarce genomic resources available. Here, we produced and comprehensively characterized the male and female gonad transcriptome of P. lividus. The P. lividus transcriptome assembly has 53,865 transcripts, an N50 transcript length of 1,842 bp and an estimated gene completeness of 97.4% and 95.6% in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses yielded a total of 3371 and 3351 up regulated genes in P. lividus male and female gonad tissues, respectively. Additionally, we analysed and validated a catalogue of pivotal transcripts involved in sexual development and determination (206 transcripts) as well as in biosynthesis and storage of lipids (119 transcripts) in male and female specimens. This study provides a valuable transcriptomic resource and will contribute for the future conservation of the species as well as the exploitation in aquaculture settings.

HighlightsAssembly of a reference transcriptome of Paracentrotus lividus gonads.

Differential gene expression between males and female gonads of Paracentrotus lividus.

Identification and validation of pivotal genes involved in biosynthesis and storage of lipids.


title: Recurrent Integration of Human Papillomavirus Genomes at Transcriptional Regulatory Hubs

abstract: Oncogenic human papillomavirus (HPV) genomes are often integrated into host chromosomes in HPV-associated cancers. HPV genomes are integrated either as a single copy, or as tandem repeats of viral DNA interspersed with, or without, host DNA. Integration occurs frequently in common fragile sites susceptible to tandem repeat formation, and the flanking or interspersed host DNA often contains transcriptional enhancer elements. When co-amplified with the viral genome, these enhancers can form super-enhancer-like elements that drive high viral oncogene expression. Here, we compiled highly curated datasets of HPV integration sites in cervical (CESC) and head and neck squamous cell carcinoma (HNSCC) cancers and assessed the number of breakpoints, viral transcriptional activity, and host genome copy number at each insertion site. Tumors frequently contained multiple distinct HPV integration sites, but often only one "driver" site that expressed viral RNA. Since common fragile sites and active enhancer elements are cell-type specific, we mapped these regions in cervical cell lines using FANCD2 and Brd4/H3K27ac ChIP-seq, respectively. Large enhancer clusters, or super-enhancers, were also defined using the Brd4/H3K27ac ChIP-seq dataset. HPV integration breakpoints were enriched at both FANCD2-associated fragile sites, and enhancer-rich regions, and frequently showed adjacent focal DNA amplification in CESC samples. We identified recurrent integration "hotspots" that were enriched for super-enhancers, some of which function as regulatory hubs for cell-identity genes. We propose that during persistent infection, extrachromosomal HPV minichromosomes associate with these transcriptional epicenters, and accidental integration could promote viral oncogene expression and carcinogenesis.


title: Trick or Treat? Pollinator attraction in Vanilla pompona (Orchidaceae)

abstract: Natural pollination of species belonging to the pantropical orchid genus Vanilla remains poorly understood. Based on sporadic records, euglossine bees have been observed visiting flowers of Neotropical Vanilla species. Our research aimed at better understanding the pollinator attraction mechanism of the Neotropical species Vanilla pompona, a crop wild relative with valuable traits for vanilla crop improvement programs. Using video footage, we identified floral visitors and examined their behavior. The flowers of V. pompona attracted Eulaema cingulata males, which distinctively displayed two behaviors: floral scent collection and nectar search; with the latter leading to pollen removal. Morphological measurements of floral and visitor traits showed that other Eulaema species may also act as potential pollinators. Additionally, we recorded natural fruit set in three populations and over a period of two years, tested for nectar presence and analyzed floral fragrances through gas chromatography - mass spectrometry. We observed a low natural fruit set (2.42%) and did not detect nectar. Twenty floral volatile compounds were identified, with the dominant compound trans-carvone oxide previously found to attract Eulaema cingulata males. We hypothesize a dual attraction of Eulaema cingulata males to V. pompona flowers, based on floral fragrance reward as the primary long-distance attraction, and food deception for successful pollen removal. Further research confirming this hypothesis is recommended to develop appropriate conservation policies for Vanilla crop wild relatives, which are the primary reserves of this crops genetic variation.


title: A Jacalin-like lectin-domain-containing protein of Sclerospora graminicola act as an apoplastic virulence effector in plant-oomycete interactions

abstract: The plant extracellular space, including the apoplast and plasma membrane, is the initial site of plant- pathogen interactions. Pathogens deliver numerous secreted proteins, called effectors, into this region to suppress plant immunity and establish infection. Downy mildew caused by the oomycete pathogen Sclerospora graminicola (Sg) is an economically important disease of Poaceae crops including foxtail millet (Setaria italica). We previously reported the genome sequence of Sg and showed that the Jacalin-related lectin (JRL) gene family has significantly expanded in this lineage. However, the biological functions of JRL proteins remained unknown. Here, we show that JRL from S. graminicola (SgJRL) functions as an apoplastic virulence effector. We identified eight SgJRLs via protein mass spectrometry analysis of extracellular fluid from S. graminicola-inoculated foxtail millet leaves. SgJRLs consist of a Jacalin-like lectin domain and an N-terminal putative secretion signal, and SgJRL expression is induced by Sg infection. Heterologous expression of three SgJRLs with N-terminal secretion signal peptides in Nicotiana benthamiana enhanced the virulence of the pathogen Phytophthora palmivora inoculated onto the same leaves. Of the three SgJRLs, SG06536 fused with GFP localized to the apoplastic space in N. benthamiana leaves. INF1-mediated induction of defense-related genes was suppressed by co-expression of SG06536-GFP. These findings suggest that JRLs are novel apoplastic effectors that contribute to pathogenicity by suppressing plant defense responses.


title: Hexose translocation mediated by SlSWEET5b is required for pollen maturation in Solanum lycopersicum

abstract:
Pollen fertility is critical for successful fertilization and, accordingly, for crop yield. While sugar unloading affects growth and development of all types of sink organs, the molecular nature for sugar import to tomato pollen is poorly understood. However, SWEET transporters have been proposed to function in pollen development. Here, qRT-PCR revealed that SlSWEET5b was markedly expressed in flowers when compared to the remaining tomato SlSWEETs; particularly, in the stamens of maturing flower buds undergoing mitosis. Distinct accumulation of SlSWEET5b-GUS fusion proteins was present in mature flower buds, especially in anther vascular and inner cells, symplasmic isolated pollen cells and styles. The demonstration that GFP fusion proteins located to the plasma membrane support the idea that the SlSWEET5b carrier functions in apoplasmic sugar translocation during pollen maturation. Such function is in line with data from yeast complementation experiments and radiotracer uptakes, showing that SlSWEET5b operates as a low affinity hexose-specific passive facilitator, with a KM of ~36 mM. Most importantly, RNAi-mediated suppression of SlSWEET5b expression resulted in shrunken nucleus-less pollen cells, impaired germination and low seed yield. Interestingly, stamens from SlSWEET5b-silenced tomato mutants contained significantly lower amounts of sucrose and increased invertase activity, pointing to reduced carbon supply and perturbed sucrose homeostasis in this tissue. Taken together, our findings reveal an essential role of SlSWEET5b in mediating apoplasmic hexose import into phloem unloading cells and into developing pollen cells to support pollen mitosis and maturation in tomato flowers.

One-sentence SummaryPlasma-membrane-localized SlSWEET5b facilitates a sequential hexose flux, from phloem to anther cells and from anther locule to pollen, to support pollen maturation and fertility in tomato flowers.


title: S-acylation is a positive regulator of FLS2-mediated plant immunity

abstract: Plant receptor kinases are key transducers of physical extracellular stimuli, such as the presence of beneficial or pathogenic microbes or secreted signalling molecules. Receptor kinases are regulated by numerous post-translational modifications. Here, using the bacterial flagellin perceiving receptor kinase FLS2, we show that S-acylation at an evolutionarily conserved cysteine is crucial for function. S-acylation involves the addition of long-chain fatty acids to cysteine residues within proteins, altering their biophysical properties and behaviour within the membrane environment. We observe S-acylation of FLS2 at C-terminal kinase domain cysteine residues within minutes of treatment with flg22 ligand, and in a BAK1 co-receptor dependent manner. We demonstrate that S-acylation is essential for FLS2-mediated immune signalling, including anti-bacterial immunity. Similarly, mutating the corresponding conserved cysteine residue in the immune receptor kinase EFR supressed elf18 mediated signalling. Biochemical analysis of unstimulated and activated FLS2 containing complexes using detergents and native membrane DIBMA nanodiscs indicates that S-acylation assists the stabilization of activated receptor kinase complexes withing the membrane environment to increase signalling efficiency.


title: S-acylation stabilizes ligand-induced receptor kinase complex formation during plant pattern-triggered immune signalling.


title: Cross-frequency slow oscillation-spindle coupling in a biophysically realistic thalamocortical neural mass model

abstract: Sleep manifests itself by the spontaneous emergence of characteristic oscillatory rhythms, which often timelock and are implicated in the memory formation. Here, we analyze a neural mass model of the thalamocortical loop of which the cortical node can generate slow oscillations (approx. 1 Hz) while its thalamic component can generate fast sleep spindles of{sigma} -band activity (12-15 Hz). We study the dynamics for different coupling strengths between the thalamic and cortical nodes, for different conductance values of the thalamic nodes potassium leak and anomalous rectifying currents, and for different parameter regimes of the cortical node. The latter are: (1) a low activity (DOWN) state with noise-induced, transient excursions into a high activity (UP) state, (2) an adaptation induced slow oscillation limit cycle with alternating UP and DOWN states, and (3) a high activity (UP) state with noise-induced, transient excursions into the low activity (DOWN) state. During UP states, thalamic spindling is abolished or reduced. During DOWN states, the thalamic node generates sleep spindles, which in turn can cause DOWN to UP transitions in the cortical node. Consequently, this leads to spindle-induced UP state transitions in parameter regime (1), thalamic spindles induced in some but not all DOWN states in regime (2), and thalamic spindles following UP to DOWN transitions in regime (3). The spindle-induced{sigma} -band activity in the cortical node, however, is typically strongest during the UP state, which follows a DOWN state "window of opportunity" for spindling. When the cortical node is parametrized in regime (3), the model well explains the interactions between slow oscillations and sleep spindles observed experimentally during Non-Rapid Eye Movement sleep. The model is computationally efficient and can be integrated into large-scale modeling frameworks to study spatial aspects like sleep wave propagation.


title: Does learning to read change the perception of speech? Evidence from perceptual recalibration of speech sounds in adult illiterates, semi-literates, and literates of Tamil

abstract: How do different levels of representation interact in the mind? Key evidence for answering this question comes from experimental work that investigates the influence of knowledge of written language on spoken language processing. Here we tested whether learning orthographic representations (through reading) influences pre-lexical phonological representations in spoken-word recognition using a perceptual learning paradigm. Perceptual learning is well suited to reveal differences in pre-lexical representations that might be caused by learning to read because it requires the functional use of pre-lexical representations in order to generalize a learning experience. In a large-scale behavioural study in Chennai, India, 97 native speakers of Tamil with varying reading experience (from completely illiterate to highly literate) participated. In marked contrast to their performance in other cognitive tasks, even completely illiterate participants showed a perceptual learning effect that was not moderated by reading experience. This finding suggests that pre-lexical phonological representations are not substantially changed by learning to read and thus poses important constraints for the debate about the degree of interactivity between different levels of representations during human information processing.


title: Real-Time Brain-Machine Interface Achieves High-Velocity Prosthetic Finger Movements using a Biologically-Inspired Neural Network Decoder

abstract: Despite the rapid progress and interest in brain-machine interfaces that restore motor function, the performance of prosthetic fingers and limbs has yet to mimic native function. The algorithm that converts brain signals to a control signal for the prosthetic device is one of the limitations in achieving rapid and realistic finger movements. To achieve more realistic finger movements, we developed a shallow feed-forward neural network, loosely inspired by the biological neural pathway, to decode real-time two-degree-of-freedom finger movements. Using a two-step training method, a recalibrated feedback intention-trained (ReFIT) neural network achieved a higher throughput with higher finger velocities and more natural appearing finger movements than the ReFIT Kalman filter, which represents the current standard. The neural network decoders introduced herein are the first to demonstrate real-time decoding of continuous movements at a level superior to the current state-of-the-art and could provide a starting point to using neural networks for the development of more naturalistic brain-controlled prostheses.


title: Idea Paper: Effects of gonad type and body mass on the time required for sex change in fishes

abstract: Sex change is a well-known phenomenon in teleost fishes, and it takes several days to a few months depending on the species and direction of sex change. However, the underlying factors influencing the time required for sex change (TS) remain unclear. Given that the time for producing a new gonad largely determines TS, the gonad type (i.e., whether fish retain the gonad of opposite sex or not [delimited or non-delimited]) and metabolic rate are the ultimate determinants of TS. This study sought to test two hypotheses: (1) the delimited gonad shortens TS; and (2) TS scales with mass0.1-0.2, because the metabolic scaling exponent ({beta}) in fishes is 0.8-0.9 and biological times scale with mass1-{beta} in general. We compiled data on TS for 12 female-to-male and 14 male-to-female sex-changing species from the literature. Results of individual examinations of the effects of gonad type and mass were consistent with our hypotheses. However, upon simultaneous examination of the effects of gonad type and mass, these effects became unclear because of their strong multicollinearity. The compiled data for delimited and non-delimited gonads were biased toward the smaller and larger species, respectively, precluding us from being able to statistically distinguish between these effects. Small species with non-delimited gonads and large species with delimited gonads exist; however, their TS has not been measured with high temporal resolution thus far. Therefore, additional experiments on these species are required to statistically distinguish between, as well as to better understand, the effects of gonad type and mass on TS.

category: animal behavior and cognition


title: Adaptation of anammox bacteria to low temperature via gradual acclimation and cold shocks: distinctions in protein expression, membrane composition and activities

abstract:
Anammox bacteria enable an efficient removal of nitrogen from sewage in processes involving partial nitritation and anammox (PN/A) or nitrification, partial denitrification, and anammox (N-PdN/A). In mild climates, anammox bacteria must be adapted to [≤]15 {degrees}C, typically by gradual temperature decrease; however, this takes months or years. To reduce the time necessary for the adaptation, an unconventional method of  cold shocks is promising, involving hours-long exposure of anammox biomass to extremely low temperatures. We compared the efficacies of gradual temperature decrease and cold shocks to increase the metabolic activity of anammox (fed batch reactor, planktonic "Ca. Kuenenia"). We assessed the cold shock mechanism on the level of protein expression (quantitative shot-gun proteomics, LC-HRMS/MS) and structure of membrane lipids (UPLC-HRMS/MS). The shocked culture was more active (0.66{+/-}0.06 vs 0.48{+/-}0.06 kg-N/kg-VSS/d) and maintained the relative content of N-respiration proteins at levels consistent levels with the initial state, whereas the content of these proteins decreased in gradually acclimated culture. Cold shocks also induced a more efficient up-regulation of cold shock proteins (e.g. CspB, TypA, ppiD). Ladderane lipids characteristic for anammox evolved to a similar end-point in both cultures which confirms their role in anammox bacteria adaptation to cold and indicates a three-pronged adaptation mechanism involving ladderane lipids (ladderane alkyl length, introduction of shorter non-ladderane alkyls, polar headgroup). Overall, we show the outstanding potential of cold shocks for low-temperature adaptation of anammox bacteria and provide yet unreported detailed mechanisms of anammox adaptation to low temperatures.

HighlightsO_LIAnammox bacteria were adapted to low T by gradual acclimation and cold shocks
C_LIO_LIThe shocked culture was more active (0.66{+/-}0.06 vs 0.48{+/-}0.06 kg-N/kg-VSS/d)
C_LIO_LIN-respiration proteins content decreased in gradually acclimated bacteria
C_LIO_LISeveral cold shock proteins were upregulated more efficiently by cold shocks
C_LIO_LIAt {downarrow}T, anammox adjusted ladderane membrane lipid composition in three aspects
C_LI

Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

category: bioengineering


title: Simpler and Faster Development of Tumor Phylogeny Pipelines

abstract:
In the recent years there has been an increasing amount of single-cell sequencing (SCS) studies, producing a considerable number of new datasets. This has particularly affected the field of cancer analysis, where more and more papers are published using this sequencing technique that allows for capturing more detailed information regarding the specific genetic mutations on each individually sampled cell.

As the amount of information increases, it is necessary to have more sophisticated and rapid tools for analyzing the samples. To this goal we developed plastic, an easy-to-use and quick to adapt pipeline that integrates three different steps: (1) to simplify the input data; (2) to infer tumor phylogenies; and (3) to compare the phylogenies.

We have created a pipeline submodule for each of those steps, and developed new in-memory data structures that allow for easy and transparent sharing of the information across the tools implementing the above steps.

While we use existing open source tools for those steps, we have extended the tool used for simplifying the input data, incorporating two machine learning procedures -- which greatly reduce the running time without affecting the quality of the downstream analysis. Moreover, we have introduced the capability of producing some plots to quickly visualize results.

category: bioinformatics


title: LectinOracle - A Generalizable Deep Learning Model for Lectin-Glycan Binding Prediction

abstract: Ranging from bacterial cell adhesion over viral cell entry to human innate immunity, glycan-binding proteins or lectins abound in nature. Widely used as staining and characterization reagents in cell biology, and crucial for understanding the interactions in biological systems, lectins are a focal point of study in glycobiology. Yet the sheer breadth and depth of specificity for diverse oligosaccharide motifs has made studying lectins a largely piecemeal approach, with few options to generalize. Here, we present LectinOracle, a model combining transformer-based representations for proteins and graph convolutional neural networks for glycans to predict their interaction. Using a curated dataset of 564,647 unique protein-glycan interactions, we show that LectinOracle predictions agree with literature-annotated specificities for a wide range of lectins. We further identify clusters of lectins with related binding specificity that are not clustered based on sequence similarity. Using a range of specialized glycan arrays, we show that LectinOracle predictions generalize to new glycans and lectins, with qualitative and quantitative agreement with experimental data. We further demonstrate that LectinOracle can analyze whole lectomes and their role in host-microbe interactions. We envision that the herein presented platform will advance both the study of lectins and their role in (glyco)biology.


title: nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

abstract: The analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install - all dependencies are provided within containers -, portable and reproducible. It is written in Nextflow and developed as part of the nf-core initiative for best-practice pipeline development. All code is hosted on GitHub under the nf-core organization https://github.com/nf-core/mag and released under the MIT license.


title: The polyglutamine amyloid nucleus in living cells is monomeric and has competing dimensions of order

abstract: A long-standing goal of the study of amyloids has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of that event has made it inaccessible to classical biochemistry, structural biology, and computational approaches. Here, we addressed that limitation by measuring the dependence of amyloid formation on concentration and conformational templates in living cells, whose volumes are sufficiently small to resolve the outcomes of independent nucleation events. We characterized numerous rationally designed sequence variants of polyglutamine (polyQ), a polypeptide that precipitates Huntingtons and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. This effort uncovered a pattern of approximately twelve Qs, only for polypeptides exceeding the clinical length threshold, that allow for amyloid nucleation to occur spontaneously within single polypeptides. Nucleation was inhibited by intermolecular phase separation. Using atomistic molecular dynamics simulations, we found that the pattern encodes a minimal steric zipper of interdigitated side chains. Lateral growth of the steric zipper competed with axial growth to produce "pre-amyloid" oligomers. By illuminating the structural mechanism of polyQ amyloid formation in cells, our findings reveal a potential molecular etiology for polyQ diseases, and may provide a roadmap for the design of new therapies.

category: biophysics


title: The polyglutamine amyloid nucleus in living cells is a monomer with competing dimensions of order


title: Generation of tumors in wing imaginal discs of Drosophila melanogaster third instar larvae to study temporal and spatial patterns of expression of major heat shock proteins

abstract: Cancer cells overexpress heat shock proteins (Hsps), the major components of cellular stress response, to overcome the diversity of stresses and to survive. However, the specific roles of Hsps in initiation and establishment of cancers remain unclear. Using loss of Lgl function-mediated epithelial tumorigenesis in Drosophila, we induced tumorigenic MARCM clones of different genetic backgrounds in wing imaginal discs to examine the temporal and spatial expression and roles of major heat shock proteins in tumor growth. The constitutively expressed Hsp83, Hsc70 (heat shock cognate), Hsp60 and Hsp27 show elevated levels in all cells of the tumorigenic clone since early stages, which persists till their transformation. However, the stress-inducible Hsp70 is expressd only in a few cells at later stage of established tumorous clones that show high F-actin aggregation. Intriguingly, levels of heat shock factor (HSF), the master regulator of Hsps, remain unaltered in these tumorous cells and its down-regulation does not affect tumorigenic growth of lgl- clones overexpressing Yorkie, although down-regulation of Hsp83 prevents their survival and growth. Interestingly, overexpression of HSF or Hsp83 in lgl- cells makes them competitively successful in establishing tumorous clones. These results show that the major constitutively expressed Hsps, but not the stress-inducible Hsp70, are involved in early as well as late stages of epithelial tumors and their elevated expression in lgl- clones co-overexpressing Yorkie is independent of HSF.


title: Elevation of major constitutive heat shock proteins is heat shock factor independent and essential for establishment and growth of Lgl loss and Yorkie gain-mediated tumors in Drosophila


title: NBI-921352, a First-in-Class, Na V 1.6 Selective, Sodium Channel Inhibitor That Prevents Seizures in Scn8a Gain-of- Function Mice, and Wild-Type Mice and Rats

abstract: NBI-921352 (formerly XEN901) is a novel sodium channel inhibitor designed to specifically target NaV1.6 channels. Such a molecule provides a precision-medicine approach to target SCN8A-related epilepsy syndromes (SCN8A-RES), where gain-of-function (GoF) mutations lead to excess NaV1.6 sodium current, or other indications where NaV1.6 mediated hyper-excitability contributes to disease (Gardella and Moller, 2019; Johannesen et al., 2019; Veeramah et al., 2012). NBI-921352 is a potent inhibitor of NaV1.6 (IC50 0.051 {micro}M), with exquisite selectivity over other sodium channel isoforms (selectivity ratios of 756X for NaV1.1, 134X for NaV1.2, 276X for NaV1.7, and >583X for NaV1.3, NaV1.4, and NaV1.5). NBI-921352 is a state-dependent inhibitor, preferentially inhibiting activated (inactivated or open) channels. The state dependence leads to potent stabilization of inactivation, inhibiting NaV1.6 currents, including resurgent and persistent NaV1.6 currents, while sparing the closed/rested channels. The isoform-selective profile of NBI-921352 led to a robust inhibition of action-potential firing in glutamatergic excitatory pyramidal neurons, while sparing fast-spiking inhibitory interneurons, where NaV1.1 predominates. Oral administration of NBI-921352 prevented electrically induced seizures in a Scn8a GoF mouse, as well as in wild-type mouse and rat seizure models. NBI-921352 was effective in preventing seizures at lower brain and plasma concentrations than commonly prescribed sodium channel inhibitor antiseizure medicines (ASMs) carbamazepine, phenytoin, and lacosamide. NBI-921352 was well tolerated at higher multiples of the effective plasma and brain concentrations than those ASMs. NBI-921352 is entering phase II proof-of-concept trials for the treatment of SCN8A-developmental epileptic encephalopathy (SCN8A-DEE) and adult focal-onset seizures.

category: pharmacology and toxicology


title: Novel System to Monitor In Vivo Neural Graft Activity After Spinal Cord Injury

abstract: Expectations for neural stem/progenitor cell (NS/PC) transplantation as a treatment for spinal cord injury (SCI) are increasing. However, whether and how grafted cells are incorporated into the host neural circuit and contribute to motor function recovery remain unknown. The aim of this project was to establish a novel non-invasive in vivo imaging system to visualize the activity of neural grafts by which we can simultaneously demonstrate the circuit-level integration between the graft and host, and the contribution of graft neuronal activity to host behaviour. We introduced Akaluc, a newly engineered luciferase, under control of a potent neuronal activity-dependent synthetic promoter, E-SARE, into NS/PCs and engrafted the cells into SCI model mice. Through the use of this system, we reveal that the activity of grafted cells was integrated with host behaviour and driven by host neural circuit inputs. This non-invasive system is expected to help elucidate the therapeutic mechanism of cell transplantation treatment for SCI and determine better therapy techniques that maximize the function of cells in the host circuit.


title: Neural signatures of teamwork: Evidence from real-world military training

abstract: Successful teamwork is fundamental for optimally functioning societies. However, little is known regarding the neural basis of real-world teamwork. Here, we recruited forty individuals paired as twenty dyads and recorded dual-EEG at rest and during realistic training scenarios of increasing complexity using virtual simulation systems. We estimated markers of intrinsic brain activity (i.e., individual alpha frequency and aperiodic activity), as well as task-related theta and alpha oscillations. Using nonlinear modelling and machine learning techniques, we found that resting-state EEG predicts performance and can also reliably differentiate between members within a dyad. Task-related theta and alpha activity during easy training tasks predicted later performance on complex training to a greater extent than prior behaviour. These findings complement laboratory-based research on both oscillatory and aperiodic activity in higher-order cognition and provide evidence that theta and alpha activity play a critical role in complex task performance in team environments.


title: Dissecting errors of the exogenously-driven and endogenously-driven saccadic tasks in the common marmoset

abstract: Various saccadic tasks used traditionally in oculomotor research, including both exogenously-driven and endogenously-driven saccades, have been proposed as clinical diagnostic for human movement disorders. Recently, common marmosets have been proven to be a good primate model for these movement disorders. However, whether similar saccadic measurements can be used for marmosets was not tested. Here, we trained three marmosets on the gap task, an exogenously-driven saccadic task, and the oculomotor delayed response (ODR) task, an endogenously-driven saccadic task. We demonstrated that with long-term training, they were able to learn and switch between the two tasks. The marmosets showed undershooting tendency in the gap and both under- and overshooting tendency in the ODR task when they made saccades to the target. We also categorized the error trails into distractive, impulsive, and visuomotor errors, depending on when a false saccade happened concerning the task progression, and interpreted possible causes of errors based on the saccade response time and the task history. Each error category may indicate specific failures in a particular aspect of cognitive or sensorimotor processes. Finally, and critically, we found that saccades from successful trials exhibited the highest saccade peak velocity and the shortest saccade duration comparing to the same saccade amplitude from error trials. Taken together, we showed the potential of training the same marmoset on conflicting oculomotor tasks simultaneously. We documented the baseline performance and compared successful and error trials in both gap and ODR tasks from the same animals. We propose that analyzing the error trials in sync with successful trials could provide a further understanding of the marmosets cognitive and sensorimotor processes in both healthy and disease conditions.


title: Dissecting errors of the exogenously-driven and endogenously-driven saccadic tasks in the common marmosets


title: Neural evidence for the successor representation in choice evaluation

abstract: Evaluating choices in multi-step tasks is thought to involve mentally simulating trajectories. Recent theories propose that the brain simplifies these laborious computations using temporal abstraction: storing actions consequences, collapsed over multiple timesteps (the Successor Representation; SR). Although predictive neural representations and, separately, behavioral errors ("slips of action") consistent with this mechanism have been reported, it is unknown whether these neural representations support choices in a manner consistent with the SR. We addressed this question by using fMRI to measure predictive representations in a setting where the SR implies specific errors in multi-step expectancies and corresponding behavioral errors. By decoding measures of state predictions from sensory cortex during choice evaluation, we identified evidence that behavioral errors predicted by the SR are accompanied by predictive representations of upcoming task states reflecting SR predicted erroneous multi-step expectancies. These results provide neural evidence for the SR in choice evaluation and contribute toward a mechanistic understanding of flexible and inflexible decision making.


title: Disruption of the grid cell network in a mouse model of early Alzheimer's disease

abstract: Early-onset familial Alzheimers disease (AD) is marked by an aggressive buildup of amyloid beta (A{beta}) proteins, yet the neural circuit operations impacted during the initial stages of A{beta} pathogenesis remain elusive. Here, we report a coding impairment of the medial entorhinal cortex (MEC) grid cell network in a transgenic mouse model of familial AD that over-expresses A{beta} throughout the hippocampus and entorhinal cortex. Grid cells showed reduced spatial periodicity, spatial stability, and synchrony with interneurons and head-direction cells. In contrast, the spatial coding of non-grid cells within the MEC, and place cells within the hippocampus, remained intact. Grid cell deficits emerged at the earliest incidence of A{beta} fibril deposition and coincided with impaired spatial memory performance in a path integration task. These results demonstrate that widespread A{beta}-mediated damage to the entorhinal-hippocampal circuit results in an early impairment of the entorhinal grid cell network.


title: Poly(A) tail length is a major regulator of maternal gene expression during the mammalian oocyte-to-embryo transition

abstract: Transcription is silent during the mammalian oocyte-to-embryo transition (OET) until zygotic genome activation (ZGA). Therefore, the OET relies on post-transcriptional regulation of maternal mRNA, among which poly(A) tail lengths have been found to regulate translation for a small number of genes1-3. However, transcriptome-wide poly(A) tail length dynamics and their role in gene expression during the mammalian OET remain unknown. Here, we quantified transcriptome-wide mRNA poly(A) tail length dynamics during the mammalian OET using PAIso-seq1 and PAIso-seq24,5, two methods with different underlying principles that preserve the poly(A) tail information. We revealed that poly(A) tail length was highly dynamic during the mouse OET, and Btg4 is responsible for global maternal mRNA deadenylation. We found that the poly(A) tail length positively associated with translational efficiency transcriptome-wide in mouse oocytes. In addition, genes with different alternative polyadenylation isoforms show longer poly(A) tails for isoforms with distal polyadenylation sites compared to those with proximal polyadenylation sites in mouse, rat, pig and human oocytes after meiotic resumption, which is not seen in cultured cell lines. Surprisingly, mammalian embryos, namely mouse, rat, pig, and human embryos, all experience highly conserved global mRNA re-polyadenylation after fertilization, providing molecular evidence that the early embryo development before ZGA is driven by re-polyadenylated maternal mRNAs rather than newly transcribed mRNAs. Together, our study reveals the conserved mRNA poly(A) tail length landscape. This resource can be used for exploring spatiotemporal post-transcriptional regulation throughout the mammalian OET.

category: developmental biology


title: Dynamics of poly(A) tail length and non-A residues during the human oocyte-to-embryo transition

abstract: Poly(A) tail-mediated post-transcriptional regulation of maternal mRNA has been shown to be vital in the oocyte-to-embryo transition (OET) in flies, fish, frogs, and mice1-8. However, nothing is known about poly(A) tail dynamics for even a single gene during the human OET, because of the limited availability of human oocytes and embryos in combination with the low sensitivity of previous methods. Here, we systematically profiled the transcriptome-wide mRNA poly(A) tails in human oocytes at the germ-vesicle (GV), metaphase I (MI), and metaphase II (MII) stages, as well as pre-implantation embryos at the 1-cell (1C), 2-cell (2C), 4-cell (4C), 8-cell (8C), morula (MO), and blastocyst (BL) stages using single-oocyte/embryo PAIso-seq1 and PAIso-seq2 methods. We show that poly(A) tail length is highly dynamic during the OET, with BTG4 responsible for global deadenylation. Moreover, we reveal that non-A residues occur primarily in poly(A) tails of maternal RNA, which begin to increase at the MI stage, become highly abundant after fertilization (with U residues occurring in about two thirds, G residues in about one third, and C residues in about one fifth of mRNAs), and decline at the 8C stage. Importantly, we reveal that TUT4/7 can add U residues to deadenylated mRNA, which can then be re- polyadenylated to produce 5'-end and internal U residues. In addition, the re- polyadenylated mRNA can be stabilized through the addition of G residues by TENT4A/B. Finally, we demonstrate that U residues in poly(A) tails mark the maternal transcripts for quicker degradation in 8C human embryos compared to those without U residues. Together, our results not only reveal the dynamics of poly(A) tail length and non-A residues, but also provide mechanistic insights into the regulation of the length and the role of non-A residues during human OET. These findings further scientific understanding and open a new door for studying the human OET.


title: Abundant non-A residues in the poly(A) tail orchestrate the mouse oocyte-to-embryo transition

abstract: Non-A (U, G, and C) residues can be added to the 5-end, internal, and 3-end positions of poly(A) tails of RNA transcripts1-3, and some of these have been shown to regulate mRNA stability4, 5. The mammalian oocyte-to-embryo transition (OET) relies on post-transcriptional regulation of maternal RNA, because transcription is silent during this process until the point of zygotic genome activation (ZGA)6-9. Although the regulation of mRNA translation by poly(A) tail length plays an important role in the mammalian OET, the dynamics and functions of non-A residues in poly(A) tails are completely unknown. In this study, we profiled the genome-wide presence, abundance, and roles of non-A residues during the OET in mice using PAIso-seq1 and PAIso-seq22, 10, two complementary methods of poly(A) tail analysis. We found that non-A residues are highly dynamic in maternal mRNA, following a general pattern of beginning to increase at the MII stage, becoming highly abundant after fertilization with U residues in about half of poly(A) tails in 1-cell embryos, and declining in 2-cell embryos. We revealed that Btg4-mediated global maternal mRNA deadenylation created the substrates for U residue addition by Tut4/7 at their 3-ends and further re-polyadenylation. In addition, G residues can be added by Tent4a/b. Finally, we demonstrate that G residues stabilize the modified mRNA, while the U residues mark maternal RNA for faster degradation in 2-cell mouse embryos. Taken together, these findings demonstrate that non-A residues are abundant and re-sculpt the maternal transcriptome to initiate zygotic development, which reveals the functional importance of the post-transcriptional regulation mediated by non-A residues in mRNA poly(A) tails.


title: Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris.

abstract: As-yet-undescribed branches in the tree of eukaryotes are potentially represented by some of "orphan" protists (unicellular micro-eukaryotes), of which phylogenetic affiliations have not been clarified in previous studies. By clarifying the phylogenetic positions of orphan protists, we may fill the previous gaps in the diversity of eukaryotes and further uncover the novel affiliation between two (or more) major lineages in eukaryotes. Microheliella maris was originally described as a member of the phylum Heliozoa, but a pioneering large-scale phylogenetic analysis failed to place this organism within the previously described species/lineages with confidence. In this study, we analyzed a 319-gene alignment and demonstrated that M. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name "Pancryptista" for Cryptista plus M. maris. The 319-gene analyses also indicated that M. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called as "CAM clade" here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia) and the particular phylogenetic "signal" most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies. We hypothesize that many cryptophycean genes (including those in the 319-gene alignment) recombined partially with the homologous genes transferred from the red algal endosymbiont during secondary endosymbiosis and bear a faint phylogenetic affinity to the rhodophytan genes.


title: Establishment of reference standards for multifaceted mosaic variant analysis

abstract: Detection of somatic mosaicism in non-proliferative cells is a new challenge in genome research, however, the accuracy of current detection strategies remains uncertain due to the lack of a ground truth. Herein, we sought to present a set of reference standards based on a total of 386,613 mosaic single-nucleotide variants (SNVs) and insertion-deletion mutations (INDELs) with variant allele frequencies (VAFs) ranging from 0.5% to 56%, as well as 35,113,417 non-variant and 19,936 germline variant sites as a negative control. The whole reference standard set mimics the cumulative aspect of mosaic variant acquisition in the early developmental stage owing to the progressive mixing of cell lines with established genotypes, ultimately unveiling 741 possible inter-sample relationships with respect to variant sharing and asymmetry in VAFs. We expect that our reference standards will be essential for optimizing the current use of mosaic variant detection strategies and for developing algorithms to enable future improvements.


title: Comparative assessment of genes driving cancer and somatic evolution.

abstract: Genetic alterations of somatic cells can drive nonmalignant clone formation and promote cancer initiation. However, the link between these processes remains unclear hampering our understanding of tissue homeostasis and cancer development. Here we collect a literature-based repertoire of 3355 well-known or predicted drivers of cancer and noncancer somatic evolution in 122 cancer types and 12 noncancer tissues. Mapping the alterations of these genes in 7953 pancancer samples reveals that, despite the large size, the known compendium of drivers is still incomplete and biased towards frequently occurring coding mutations. High overlap exists between drivers of cancer and noncancer somatic evolution, although significant differences emerge in their recurrence. We confirm and expand the unique properties of drivers and identify a core of evolutionarily conserved and essential genes whose germline variation is strongly counter-selected. Somatic alteration in even one of these genes is sufficient to drive clonal expansion but not malignant transformation. Our study offers a comprehensive overview of our current understanding of the genetic events initiating clone expansion and cancer revealing significant gaps and biases that still need to be addressed. The compendium of cancer and noncancer somatic drivers, their literature support and properties are accessible at http://www.network-cancer-genes.org/.


title: Remarkably stable copy-number profiles in osteosarcoma revealed using single-cell DNA sequencing

abstract: Osteosarcoma is an aggressive malignancy characterized by high genomic complexity. Identification of few recurrent mutations in protein coding genes suggests that somatic copy-number aberrations (SCNAs) are the genetic drivers of disease. Models around genomic instability conflict-it is unclear if osteosarcomas result from pervasive ongoing clonal evolution with continuous optimization of the fitness landscape or an early catastrophic event followed by stable maintenance of an abnormal genome. We address this question by investigating SCNAs in 12,019 tumor cells obtained from expanded patient tissues using single-cell DNA sequencing, in ways that were previously impossible with bulk sequencing. Using the CHISEL algorithm, we inferred allele- and haplotype-specific SCNAs from whole-genome single-cell DNA sequencing data. Surprisingly, we found that, despite extensive genomic aberrations, cells within each tumor exhibit remarkably homogeneous SCNA profiles with little sub-clonal diversification. Longitudinal analysis between two pairs of patient samples obtained at distant time points (early detection, relapse) demonstrated remarkable conservation of SCNA profiles over tumor evolution. Phylogenetic analysis suggests that the bulk of SCNAs was acquired early in the oncogenic process, with few new events arising in response to therapy or during adaptation to growth in distant tissues. These data suggest that early catastrophic events, rather than sustained genomic instability, drive formation of these extensively aberrant genomes. Overall, we demonstrate the power of combining single-cell DNA sequencing with an allele- and haplotype-specific SCNA inference algorithm to resolve longstanding questions regarding genetics of tumor initiation and progression, questioning the underlying assumptions of genomic instability inferred from bulk tumor data.


title: Depth-resolved intersubject functional correlation of 7T BOLD signals reveals increased stimulus related information sharing across deep layers in premotor and parietal nodes for predictable actions

abstract: While the brain regions involved in action observation are relatively well documented in humans and primates, how these regions communicate to help understand and predict actions remains poorly understood. Traditional views emphasized a feed-forward architecture in which visual features are organized into increasingly complex representations that feed onto motor programs in parietal and then premotor cortices where the matching of observed actions upon the observers own motor programs contributes to action understanding. Predictive coding models place less emphasis on feed-forward connections and propose that feed-back connections from premotor regions back to parietal and visual neurons represent predictions about upcoming actions that can supersede visual inputs when actions become predictable, with visual input then merely representing prediction errors. Here we leverage the notion that feed-back connections target specific cortical layers to help adjudicate across these views. Specifically, we test whether observing sequences of hand actions in their natural order, which permits participants to predict upcoming actions, triggers more feed-back input to parietal regions than seeing the same actions in a scrambled sequence that hinders making predictions. Using submillimeter fMRI acquisition at 7T, we find that watching predictable sequences triggers more action-related activity (as measured using intersubject functional correlation) in the parietal cortical area PFt at depths receiving feed-back connections (layers III and V/VI) than watching the exact same actions in scrambled and hence unpredictable sequence. In addition, functional connectivity analysis performed using intersubject functional connectivity confirms that these increased action-related signals in PFt could originate from ventral premotor region BA44. This data showcases the utility of intersubject functional correlation in combination with 7T MRI to explore the architecture of social cognition under more naturalistic conditions, and provides evidence for models that emphasize the importance of feed-back connections in action prediction.


title: Predictive coding during action observation - a depth-resolved intersubject functional correlation study at 7T


title: Dynamics of mitochondrial mRNA abundance and poly(A) tail during the mammalian oocyte-to-embryo transition

abstract: Mitochondria are responsible for producing a cells energy and play a central role in many metabolic tasks, as well as signaling transduction and cell death1. Mitochondria dysfunctions cause several human diseases and aging processes2-8. Mammalian oocytes contain far more mitochondria than somatic cells. The nuclear localization of mitochondrial tricarboxylic acid cycle (TCA) cycle enzymes, which normally localize in the mitochondria, is critical for zygotic genome activation (ZGA) and the oocyte-to-embryo transition (OET) in mice9. However, during the mammalian OET, the abundance and post-transcriptional regulation of mitochondrial mRNA (MT-mRNA), particularly the poly(A) tail, has never been studied. Here, we used two independent sequencing methods (PAIso-seq1 and PAIso-seq2) to describe the features of MT-mRNA in mouse cell lines, thirteen mouse tissues and during the OET in mouse, rat, pig, and humans. These features included expression abundance, poly(A) tail length, and non-A residues in poly(A) tails. Unlike nuclear mRNA, we discovered that MT-mRNA has a stable distribution pattern of poly(A) tail length in different cell lines, across tissues, and during mammalian OET. MT-mRNA possesses non-A residues in the poly(A) tail (non-A residues hereafter), which change slightly across tissues and during the OET. We also found that the abundance of MT-mRNA varies substantially across tissues, increases during the OET, and increases along major ZGA in mice, rats, pigs, and humans. These findings provide insights into changes in MT-mRNA abundance and poly(A) tail during the mammalian OET and provide a resource for future studies on the posttranscriptional regulation of mitochondrial transcripts.


title: Conservation and divergence of poly(A) tail regulation during the mammalian oocyte-to-embryo transition

abstract: Poly(A) tail length and non-A residues are vital for oocyte-to-embryo transition (OET) in mice and humans1-5. However, the role of poly(A) tail length and non-A residues during OET in other commonly used mammalian animal models for human diseases remains unexplored. In addition, the degree of conservation in maternal mRNA poly(A) tail dynamics during OET across different mammal species is unknown. Here, we conduct a comparative analysis of the poly(A) tails during OET across four species: mice, rats, pigs, and humans. Dynamics during OET found to be conserved across all four species include: maternal mRNA deadenylation during oocyte maturation and re-polyadenylation after fertilization; a fall-rise trend in poly(A) tail length distribution; a rise-fall trend in the ratio of poly(A) tails with non-A residues; higher abundance of non-A residues in poly(A) tails of maternal mRNA than in zygotic genome activation (ZGA) mRNA; maternal mRNA with U residues degrades faster than those without U residues at the stage when ZGA takes place. While in mice and rats maternal mRNA deadenylation is impaired in parthenogenetic embryos and ZGA inhibition leads to blocked maternal mRNA deadenylation in mice and humans. In contrast, the length of consecutive U residues and the duration time of U residues in poly(A) tail diverges across the four species. Together, these findings reveal that the poly(A) tail mediated maternal mRNA post-transcriptional regulation is highly conserved in mammals with unique divergences in the length and life-span of U residues, providing new insights for the further understanding of OET across different mammals.


title: Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates

abstract: In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various non-human species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and how to appropriately account for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a "Mutationathon", a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a two-fold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.


title: Recognition of natural objects in the archerfish

abstract: Recognition of individual objects and their categorization is a complex computational task. Nevertheless, visual systems are able to perform this task in a rapid and accurate manner. Humans and other animals can efficiently recognize objects despite countless variations in their projection on the retina due to different viewing angles, distance, illumination conditions, and other parameters. Numerous studies conducted in mammals have associated the recognition process with cortical activity. Although the ability to recognize objects is not limited to mammals and has been well-documented in other vertebrates that lack a cortex, the mechanism remains elusive. To address this gap, we explored object recognition in the archerfish, which lack a fully developed cortex. Archerfish hunt by shooting a jet of water at aerial targets. We leveraged this unique skill to monitor visual behavior in archerfish by presenting fish with a set of images on a computer screen above the water tank and observing the behavioral response. This methodology served to characterize the ability of the archerfish to perform ecologically relevant recognition of natural objects. We found that archerfish can recognize an individual object presented under different conditions and that they can also categorize novel objects into known categories. Manipulating features of these objects revealed that the fish were more sensitive to object contours than texture and that a small number of features was sufficient for categorization. Our findings suggest the existence of a complex visual process in the archerfish visual system that enables object recognition and categorization.


title: Evidence for Free Radical Drug Ligands in class A G-protein Coupled Receptors

abstract: We analyse the conformation of 22 cationic ligands bound to G-protein coupled receptors of known structure and find three ligands that are present inside receptors not in their closed shell cation form, but as neutral radicals, i.e. after addition of an electron to the ligand. The implications of this finding for GPCR function are discussed and a possible experimental test is proposed.


title: Input zone-selective dysrhythmia in motor thalamus after dopamine depletion

abstract: The cerebral cortex, basal ganglia and motor thalamus form circuits important for purposeful movement. In Parkinsonism, basal ganglia neurons often exhibit dysrhythmic activity during, and with respect to, the slow ([~]1 Hz) and beta-band (15-30 Hz) oscillations that emerge in cortex in a brain state-dependent manner. There remains, however, a pressing need to elucidate the extent to which motor thalamus activity becomes similarly dysrhythmic after dopamine depletion relevant to Parkinsonism. To address this, we recorded single-neuron and ensemble outputs in the  basal ganglia-recipient zone (BZ) and  cerebellar-recipient zone (CZ) of motor thalamus in anesthetized male dopamine-intact rats and 6-OHDA-lesioned rats during two brain states, respectively defined by cortical slow-wave activity and activation. Two forms of thalamic input zone-selective dysrhythmia manifested after dopamine depletion: First, BZ neurons, but not CZ neurons, exhibited abnormal phase-shifted firing with respect to cortical slow oscillations prevalent during slow-wave activity; secondly, BZ neurons, but not CZ neurons, inappropriately synchronized their firing and engaged with the exaggerated cortical beta oscillations arising in activated states. These dysrhythmias were not accompanied by the thalamic hypoactivity predicted by canonical firing rate-based models of circuit organization in Parkinsonism. Complementary recordings of neurons in substantia nigra pars reticulata suggested their altered activity dynamics could underpin the BZ dysrhythmias. Finally, pharmacological perturbations demonstrated that ongoing activity in the motor thalamus bolsters exaggerated beta oscillations in motor cortex. We conclude that BZ neurons are selectively primed to mediate the detrimental influences of abnormal slow and beta-band rhythms on circuit information processing in Parkinsonism.


title: Microstructural Properties of Human Brain Revealed by Fractional Anisotropy can Predict the After-effect of Intermittent Theta Burst Stimulation

abstract: Intermittent theta burst stimulation (iTBS) delivered by transcranial magnetic stimulation (TMS) produces a long term potentiation (LTP)-like after-effect useful for investigations of cortical function and of potential therapeutic value. However, the iTBS-evoked after-effect over the primary motor cortex (M1) as measured by changes in motor evoked potential (MEP) amplitude exhibits a largely unexplained variability across individuals. Here, we present evidence that individual differences in white and grey matter microstructural properties revealed by fractional anisotropy (FA) predict the magnitude of the iTBS-induced after-effect over M1. The MEP amplitude change in the early phase (5-10 min) post-iTBS was associated with FA values in white matter tracts such as right superior longitudinal fasciculus and corpus callosum. In contrast, the MEP amplitude change in the late phase (15-30 min) post-iTBS was associated with FA in grey matter, primarily in right frontal cortex. These results suggest that the microstructural properties of regions connected directly or indirectly to the target region (M1) are crucial determinants of the iTBS after-effect. FA values indicative of these microstructural differences can predict the potential effectiveness of rTMS for both investigational use and clinical application.


title: On co-activation pattern analysis and non- stationarity of resting brain activity

abstract:
The non-stationarity of resting-state brain activity has received increasing attention in recent years. Functional connectivity (FC) analysis with short sliding windows and coactivation pattern (CAP) analysis are two widely used methods for assessing the dynamic characteristics of brain activity observed with functional magnetic resonance imaging (fMRI). However, the statistical nature of the dynamics captured by these techniques needs to be verified. In this study, we found that the results of CAP analysis were similar for real fMRI data and simulated stationary data with matching covariance structures and spectral contents. We also found that, for both the real and simulated data, CAPs were clustered into spatially heterogeneous modules. Moreover, for each of the modules in the real data, a spatially similar module was found in the simulated data. The present results suggest that care needs to be taken when interpreting observations drawn from CAP analysis as it does not necessarily reflect non-stationarity or a mixture of states in resting brain activity.

HighlightsO_LICAP was conducted for real fMRI data and a stationary null model.
C_LIO_LIThe results of CAP analysis were similar for the real and simulated data.
C_LIO_LISimilar results for real and simulated data in both ROI- and voxel-based analyses.
C_LIO_LIResults of CAP analysis may not reflect non-stationarity of resting brain activity.
C_LI


title: On co-activation pattern analysis and non-stationarity of resting brain activity


title: Effects of intra-hippocampal corticosterone and sleep on consolidation of complex memory of aversive experience in rats

abstract:
Formation and consolidation of memories for highly stressful (traumatic) events is a complex process that involves interplay between multiple memory systems and has implications for etiology and treatment of stress- and trauma-related disorders. Here we study effects of sleep/wake state and high intra-hippocampal corticosterone on consolidation of aversive contextual memories as well as consolidation of association between simple trauma-related cues and fear response in rats. Animals were implanted with EEG and EMG electrodes for sleep assessment and cannulas for intra-hippocampal corticosterone application. They were familiarized to a "safe box" and then trained in fear conditioning paradigm in a distinct "shock box" with a prominent simple auditory cue serving as a phasic background cue. Immediately after conditioning, animals received bilateral intra-hippocampal saline (1l) or corticosterone (10ng in 1l saline) injection and were either allowed to sleep or were kept awake for a following two-hour consolidation period. Memory test twenty-four hours later revealed that the saline-injected animals with sleep during consolidation had significantly stronger freezing response in the shock box compared to the safe box as well as increased freezing in response to the tone. Lack of post-learning sleep in saline injected animals led to generalization of fear response to the safe context, while association between simple cue and fear response was preserved. High intra-hippocampal corticosterone level during memory consolidation led to generalization of fear response to the safe context, regardless of sleep/wake state, while enhancement of response to single stimulus was not observed. Our results show how manipulation of conditions during consolidation can lead to greatly variable complex memories for a traumatic episode and distinct behavioral outcomes.

HighlightsO_LIWe studied effect of sleep and intrahippocampal corticosterone on consolidation of memories surrounding stressful event modeled by fear conditioning in rats.
C_LIO_LISleep following traumatic fear conditioning event is important for subsequent manifestation of fear response (freezing) specifically in the context of traumatic event but not in a neutral safe context.
C_LIO_LILack of sleep or high intra-hippocampal corticosterone level during memory consolidation leads to generalization of fear response to both the traumatic and safe context.
C_LIO_LIIncreased freezing in response to a trauma-related auditory cue was observed in saline injected rats regardless of wake/sleep state during consolidation.
C_LIO_LIPost-learning intra-hippocampal corticosterone injection blocked response to a trauma-related auditory cue regardless of wake/sleep state during consolidation.
C_LI


title: Apelin signaling dependent endocardial protrusions promote cardiac trabeculation in zebrafish

abstract: During cardiac development, endocardial cells (EdCs) produce growth factors to promote myocardial morphogenesis and growth. In particular, EdCs produce Neuregulin which is required for ventricular cardiomyocytes (CMs) to seed the multicellular ridges known as trabeculae. Defects in Neuregulin signaling, or in endocardial sprouting towards CMs, cause hypotrabeculation. However, the mechanisms underlying endocardial sprouting remain largely unknown. Here, we first show by live imaging in zebrafish embryos that EdCs interact with CMs via dynamic membrane protrusions. After touching CMs, these protrusions remain in close contact with their target despite the vigorous cardiac contractions. Loss of the CM-derived peptide Apelin, or of the Apelin receptor, which is expressed in EdCs, leads to reduced endocardial sprouting and hypotrabeculation. Mechanistically, Neuregulin signaling requires endocardial protrusions to activate extracellular signal-regulated kinase (Erk) signaling in CMs and trigger their delamination. Altogether, these data show that Apelin signaling dependent endocardial protrusions modulate CM behavior during trabeculation.


title: Trace elements in grey seals from the Gulf of St. Lawrence

abstract:
We measured baseline levels of 19 trace element and mercury speciation for grey seals (Halichoerus grypus) from the Gulf of St. Lawrence (GSL), Quebec, Canada. With interest growing in commercializing grey seal products for human consumption in this region, the goal of this study was to measure essential and non-essential trace elements in grey seals to evaluate health concerns and nutritional benefits. From 2015 to 2019, 120 grey seals were sampled by hunters and researchers at 4 sites in the GSL. Muscle, liver, heart and kidney samples were analyzed for 10 non-essential elements (Sb, As, Be, B, Cd, Pb, Hg, Ni, Tl, Sn) and 9 essential elements (Co, Cr, Cu, Fe, Mg, Mn, Mo, Se, Zn). Both total mercury (THg) and methylmercury (MeHg) were analysed for a subset of samples. Many elements were undetected in liver (Sb, As, Be, B, Cr, Co, Pb, Ni, Tl, Sn) and muscle tissues (same, plus Cd, Mn, Mo). Results showed lower element concentrations in the muscle (Fe, Mg, Se) and livers (Cd, Cr, Hg, Mn, Mo, Se) of young-of-the-year harvested in the winter (< 6 weeks old) compared to older animals feeding at sea. For older seals ([~] 5 months to 29 years), we did not observe progressive age-dependent bioaccumulation. Sex-specific differences were not very pronounced, but a few elements were 30 - 70% higher in the muscle (THg, MeHg) and liver (Mn, Zn) of male seals. Comparison to Canadian dietary reference intakes shows that a weekly portion of liver from young-of-the-year (< 6 weeks old) is a good source of essential elements (Cu, Fe) and that muscle and liver from this age category does not exceed reference values for toxic elements (As, Cd, Pb, MeHg). Ongoing discussions with regional public health professionals will help to develop dietary recommendations for the consumption of older grey seals.

HIGHLIGHTSO_LIWe measured baseline levels of 19 trace elements in grey seals harvested from the Gulf of St. Lawrence.
C_LIO_LIWe evaluated nutritional benefits and health concerns of human consumption of grey seal products.
C_LIO_LIOnce seals began feeding at sea ([~] 5 mo), many element concentrations increased, but did not bioaccumulate progressively with age afterwards.
C_LIO_LISome elements were more concentrated in the muscle (mercury) and livers (manganese, zinc) of male seals.
C_LIO_LIYoung seal (< 6 we) livers are a good dietary sources of copper and iron, while its muscle and liver were below reference values for toxic elements.
C_LI

GRAPHICAL ABSTRACT

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category: ecology


title: Do closely related species interact with similar partners?Testing for phylogenetic signal in bipartite interaction networks

abstract:
Whether interactions between species are conserved on evolutionary time-scales has spurred the development of both correlative and model-based approaches for testing phylogenetic signal in interspecific interactions: do closely related species interact with similar partners? Here we use simulations to test the statistical performances of the two approaches that are the most widely used in the field: Mantel tests and the Phylogenetic Bipartite Linear Model (PBLM). Mantel tests investigate the correlation between phylogenetic distances and dissimilarities in sets of interacting partners, while PBLM is a model-based approach that relies on strong assumptions on how interactions evolve. We find that PBLM often detects phylogenetic signal when it should not. Simple Mantel tests instead have low type-I error rates and moderate statistical power; however, they often artifactually detect that closely related species interact with dissimilar partners. Partial Mantel tests, which are used to partial out the phylogenetic signal in the number of partners, actually fail at correcting for this confounding effect, and we instead propose the sequential use of simple Mantel tests. We also explore the ability of simple Mantel tests to analyze clade-specific phylogenetic signal. We provide general guidelines and an application on an interaction network between orchids and mycorrhizal fungi.

Supplementary datahttps://github.com/BPerezLamarque/Phylosignal_network/blob/master/Supplementary_figures_phylo_signal_network.pdf