title: Interferon-Gamma Signaling Promotes Melanoma Progression and Metastasis

abstract: Interferon-gamma (IFNG) has long been regarded as the flag-bearer for the anti-cancer immunosurveillance mechanisms. However, relatively recent studies have suggested a dual role of IFNG, albeit there is no direct experimental evidence for its potential pro-tumor functions. Here we provide in vivo evidence that treatment of mouse melanoma cell lines with physiological levels of Ifng enhances their tumorigenicity and metastasis in lung colonization allograft assays performed in immunocompetent syngeneic host mice, but not in immunocompromised host mice. We also show that this enhancement is dependent on downstream signaling via Stat1 but not Stat3, providing evidence of an oncogenic function of Stat1 in melanoma. The experimental results suggest that melanoma cell-specific Ifng signaling modulates the tumor microenvironment and its pro-tumorigenic effects are dependent on the {gamma}{delta} T cells, as Ifng-enhanced tumorigenesis was inhibited in the TCR-{delta} knockout mice. Overall, these results show that Ifng signaling may have tumor-promoting effects in melanoma by modulating the immune cell composition of the tumor microenvironment.


title: Discovery of small molecule inhibitors of the PTK7/β-catenin interaction targeting the Wnt signaling pathway in colorectal cancer

abstract: Second cause of death due to cancer worldwide, colorectal cancer (CRC) is a major public health issue. The discovery of new therapeutic targets is thus essential. The pseudokinase PTK7 intervenes in the regulation of the Wnt/{beta}-catenin pathway signaling, in part, through a kinase-domain dependent interaction with the {beta}-catenin protein. PTK7 is overexpressed in CRC; an event associated with metastatic development and reduced survival of non-metastatic patient. In addition, numerous alterations have been identified in CRC inducing constitutive activation of Wnt/{beta}-catenin pathway signaling through {beta}-catenin accumulation. Thus, we thought that targeting PTK7/{beta}-catenin interaction could be of interest for future drug development. In this study, we have developed a NanoBRET screening assay recapitulating the interaction between PTK7 and {beta}-catenin to identify compounds able to disrupt this protein-protein interaction. A high-throughput screening allowed us to identify small molecule inhibitors targeting the Wnt pathway signaling and inducing anti-proliferative effect in vitro in CRC cells harboring {beta}-catenin or APC mutations downstream of PTK7. Thus, inhibition of the PTK7/{beta}-catenin interaction could represent, in the future, a new therapeutic strategy to inhibit cell growth dependent on Wnt signaling pathway. Moreover, despite a lack of enzymatic activity of its tyrosine kinase domain, targeting the PTK7 kinase domain-dependent functions appears to be of interest for further therapeutic development.

category: pharmacology and toxicology


title: DAF-2/insulin IGF-1 receptor regulates mobility during ageing by integrating opposite inputs from muscle and neuronal tissues

abstract:
During ageing, preservation of locomotion is generally considered an indicator of sustained good health, in elderlies and in animal models. In C. elegans, mutants of the insulin-IGF-1 receptor DAF-2/IIRc represent a paradigm of healthy ageing, as their increased lifespan is accompanied by a delay in age-related loss of motility. However, these animals are less mobile than wild-type animals in early adulthood. Here we investigated the DAF-2/IIRc- dependent relationship between longevity and motility using an auxin-inducible degron to trigger tissue-specific degradation of endogenous DAF-2/IIRc. As previously reported, inactivation of DAF-2/IIRc in neurons or intestine was sufficient to extend the lifespan of worms, whereas depletion in epidermis, germline or muscle was not. However, neither intestinal nor neuronal depletion of DAF-2/IIRc prevented the age-related loss of motility. In 1-day-old adults, DAF-2/IIRc depletion in neurons reduced motility in a DAF-16/FOXO dependent manner, while muscle depletion had no effect. By contrast, DAF-2 depletion in the muscle of middleage animals improved their motility independently of DAF-16/FOXO but required UNC-120/SRF.

Yet, neuronal or muscle DAF-2/IIRc depletion both preserved the mitochondria network in ageing muscle. Overall, these results show that the motility pattern of daf-2 mutants is determined by the sequential and opposing impact of neurons and muscle tissues and can be dissociated from the regulation of the lifespan. This work also provides the characterization of a versatile tool to analyze the tissue-specific contribution of insulin-like signaling in integrated phenotypes at the whole organism level.

category: physiology


title: Phosphatases are predicted to govern prolactin-mediated JAK-STAT signaling in pancreatic beta cells

abstract: Patients with diabetes are unable to produce a sufficient amount of insulin to properly regulate their blood-glucose levels. One potential method of treating diabetes is to increase the number of insulin-secreting beta cells in the pancreas to enhance insulin secretion. It is known that during pregnancy, pancreatic beta cells proliferate in response to the pregnancy hormone, prolactin. Leveraging this proliferative response to prolactin may be a strategy to restore endogenous insulin production for patients with diabetes. To investigate this potential treatment, we previously developed a computational model to represent the prolactin-mediated JAK-STAT signaling pathway in pancreatic beta cells. However, this model does not account for variability in protein expression that naturally occurs between cells. Here, we applied the model to understand how heterogeneity affects the dynamics of JAK-STAT signaling. We simulated a sample of 10,000 heterogeneous cells with varying initial protein concentrations responding to prolactin stimulation. We used partial least squares regression to analyze the significance and role of each of the varied protein concentrations in producing the response of the cell. Our regression models predict that the concentrations of the cytosolic and nuclear phosphatases strongly influence the response of the cell. The model also predicts that increasing prolactin receptor strengthens negative feedback mediated by the inhibitor SOCS. These findings reveal biological targets that can potentially be used to modulate the proliferation of pancreatic beta cells to enhance insulin secretion and beta cell regeneration in the context of diabetes.

category: systems biology


title: Sustained Ranavirus outbreak causes mass-mortality and morbidity in imperiled amphibians.

abstract: A persistent two-month long outbreak of Ranavirus in a natural community of amphibians contributed to a mass die-off of gopher frog tadpoles (Lithobates capito) and severe disease in striped newts (Notophthalmus perstriatus) in Florida. Ongoing mortality in L. capito and signs in N. perstriatus continued for five weeks after the first observation. Hemorrhagic disease and necrosis were diagnosed from pathological examination of L. capito tadpoles. We confirmed detection of a Frog Virus 3 (FV3)-like Ranavirus via quantitative PCR in all species. Our findings highlight the susceptibility of these species to Rv and the need for long-term disease surveillance during epizootics.

category: zoology


title: Human enteric viruses shape disease phenotype through divergent innate immunomodulation

abstract:
Altered enteric microorganisms in concert with host genetics shape inflammatory bowel disease (IBD) phenotypes. However, insight is limited to bacteria and fungi. We found virus like particles (VLPs) enriched from normal human colon resections, containing eukaryotic viruses and bacteriophages (collectively, the virome), actively elicited atypical anti-inflammatory innate immune programs. Conversely, IBD patient VLPs provoked inflammation, which was successfully dampened by healthy VLPs. The IBD colon tissue virome was perturbed, including enriched Picornovirus Enterovirus B, not previously observed in fecal virome studies. Mice with humanized healthy colon tissue viromes had attenuated intestinal inflammation while those with IBD-derived viromes exhibited exacerbated inflammation in a nucleic acid sensing-dependent fashion. Furthermore, there were detrimental consequences for IBD-associated MDA5 loss-of-function on patient intestinal epithelial cells exposed to healthy or IBD viromes. Our results demonstrate that innate recognition of either healthy or IBD human viromes autonomously influences disease phenotypes in IBD. Harnessing the virome may offer therapeutic and biomarker potential.

One Sentence SummaryHuman viromes divergently shape host immunity and disease

category: immunology


title: Human 5p-tailed Mirtrons are Processed by RNaseP

abstract:
Approximately a thousand microRNAs (miRNAs) are documented from human cells. A third appear to transit non-canonical pathways that typically bypass processing by Drosha, the dedicated nuclear miRNA producing enzyme. The largest class of non-canonical miRNAs are mirtrons which eschew Drosha to mature through spliceosome activity. While mirtrons are found in several configurations, the vast majority of human mirtron species are 5-tailed. For these mirtrons, a 3 splice site defines the 3 end of their hairpin precursor while a "tail" of variable length separates the 5 base of the hairpin from the nearest splice site. How this tail is removed is not understood. Here we examine sequence motifs in 5-tailed mirtrons and interactions with RNA turnover processes to characterize biogenesis processes. Through studying the high confidence 5-tailed mirtron, hsa-miR-5010, we identify RNaseP as necessary and sufficient for "severing" the 5 tail of this mirtron. Further, depletion of RNaseP activity globally decreased 5-tailed mirtron expression implicating this endoribonuclease in biogenesis of the entire class. Moreover, as 5-tailed mirtron biogenesis appears to be connected to tRNA processing we found a strong correlation between accumulation of tRNA fragments (tRFs) and 5-tailed mirtron abundance. This suggests that dysregulation of tRNA processing seen in cancers may also impact expression of the [~]400 5-tailed mirtrons encoded in the human genome.

SUMMARYAbundant non-canonical human miRNAs referred to as tailed mirtrons are processed by RNaseP, which "severs" tail nucleotides to yield a precursor hairpin suitable for Dicer processing. Biogenesis of these miRNAs is correlated with tRFs, which are also products of RNaseP processing.

category: molecular biology


title: Interferon-gamma Induces Melanogenesis Via Post-Translational Modification of Tyrosinase

abstract:
Melanogenesis (melanin pigment production) in melanocytes is canonically stimulated by the alpha-melanocyte stimulating hormone (MSH), which activates the cyclic-AMP-mediated expression of the melanocyte inducing transcription factor (MITF) and its downstream melanogenic genes, including the principal rate-limiting melanogenic enzyme tyrosinase (Tyr). Here we report that interferon-gamma (IFNG; type II interferon), but not IFN-alpha (a type I interferon), induces a noncanonical melanogenic pathway. Inhibition of IFNG pathway by the JAK inhibitor ruxolitinib or knocking out Stat1 abrogated the IFNG-induced melanogenesis. Interestingly, IFNG-induced melanogenesis was independent of MITF. IFNG markedly increased the Tyr protein expression but did not affect the mRNA expression, suggesting a post-translational regulatory mechanism. In contrast, IFNG had no effect on the expression of other melanogenesis-related proteins, e.g. tyrosinase-related protein 1 (Tyrp1) and dopachrome tautomerase (Dct). Glycosidase digestion assays revealed that IFNG treatment increased the mature glycosylated form of Tyr, but not its de novo synthesis. Moreover, cycloheximide chase assay showed that degradation of Tyr was decreased in IFNG-treated cells. These results suggest that the IFNG-STAT1 pathway regulates melanogenesis via modulation of the post-translational processing and protein stability of Tyr.

SIGNIFICANCEThe canonical pathway that controls melanogenesis in melanocytes is activated by the alpha melanocyte stimulating hormone (MSH) via its receptor MC1R, which activates the cyclic-AMP-mediated expression of the melanocyte master regulator MITF and its downstream target genes involved in the melanogenic process. Here we report a novel non-canonical melanogenic pathway that is mediated via the Interferon-gamma cytokine signaling. We show that this non-canonical pathway is independent of MITF-mediated gene expression, but rather functions via post-translational modification of the principal melanogenic enzyme Tyrosinase.


title: Cofilin regulates actin network homeostasis and microvilli length in mouse oocytes

abstract: How multiple actin networks coexist in a common cytoplasm, while competing for a shared pool of monomers, is still an ongoing question. This is exemplified by meiotic maturation in the mouse oocyte, which relies on the dynamic remodeling of distinct cortical and cytoplasmic F-actin networks. Here we show that the conserved actin-depolymerizing factor cofilin is activated in a switch-like manner at meiosis resumption from prophase arrest. Interfering with cofilin activation during maturation resulted in widespread microvilli elongation, while cytoplasmic F-actin was depleted, leading to defects in spindle migration and polar body extrusion. In contrast, cofilin inactivation in metaphase II-arrested oocytes resulted in a shutdown of F-actin dynamics, along with a dramatic overgrowth of the polarized actin cap. However, inhibition of the Arp2/3 complex to promote actin cap disassembly elicited ectopic microvilli outgrowth in the polarized cortex. These data establish cofilin as a key player in actin network homeostasis in oocytes, and reveal that microvilli can act as a sink for monomers upon disassembly of a competing network.

category: cell biology


title: Microtubule disassembly by caspases is the rate-limiting step of cell extrusion

abstract: Epithelial cell death is essential for tissue homeostasis, robustness and morphogenesis. The expulsion of epithelial cells following caspase activation requires well-orchestrated remodeling steps leading to cell elimination without impairing tissue sealing. While numerous studies have provided insight about the process of cell extrusion, we still know very little about the relationship between caspase activation and the remodeling steps of cell extrusion. Moreover, most studies of cell extrusion focused on the regulation of actomyosin and steps leading to the formation of a supracellular contractile ring. However, the contribution of other cellular factors to cell extrusion has been poorly explored. Using the Drosophila pupal notum, a single layer epithelium where most extrusion events are caspase-dependent, we first showed that the initiation of cell extrusion and apical constriction are surprisingly not associated with the modulation of actomyosin concentration/dynamics. Instead, cell apical constriction is initiated by the disassembly of a medio-apical mesh of microtubules which is driven by effector caspases. We confirmed that local and rapid increase/decrease of microtubules is sufficient to respectively expand/constrict cell apical area. Importantly, the depletion of microtubules is sufficient to bypass the requirement of caspases for cell extrusion. This study shows that microtubules disassembly by caspases is a key rate-limiting steps of extrusion, and outlines a more general function of microtubules in epithelial cell shape stabilisation.


title: Ubiquitin E3 ligases Atrogin-1 and MuRF1 protein contents are differentially regulated in the rapamycin-sensitive mTOR-S6K1 signaling pathway in C2C12 myotubes

abstract: Muscle-specific ubiquitin E3 ligases, Atrogin-1 and MuRF1, are highly expressed in multiple conditions of skeletal muscle atrophy. The PI3K/Akt/FoxO signaling pathway is well known to regulate Atrogin-1 and MuRF1 gene expressions. Evidence supporting this is largely based on stimuli by insulin and IGF-1, that activate anabolic signaling, including Akt and Akt-dependent transcription factors. However, Akt activation also activates the mammalian target of rapamycin complex 1 (mTORC1) which induces skeletal muscle hypertrophy. However, whether mTORC1-dependent signaling has a role in regulating Atrogin-1 and/or MuRF1 gene and protein expression is currently unclear. In this study, we confirmed that activation of insulin-mediated Akt signaling suppresses both Atrogin-1 and MuRF1 protein content and that inhibition of Akt increases both Atrogin-1 and MuRF1 protein content in C2C12 myotubes. Interestingly, inhibition of mTORC1 using a specific mTORC1 inhibitor, rapamycin, increased Atrogin-1, but not MuRF1, protein content. Furthermore, activation of AMP-activated protein kinase (AMPK), a negative regulator of the mTORC1 signaling pathway, also showed distinct time-dependent changes between Atrogin-1 and MuRF1 protein content, suggesting differential regulatory mechanisms between Atrogin-1 and MuRF1 protein content. To further explore the downstream of mTORC1 signaling, we employed a specific S6K1 inhibitor, PF-4708671, and found that Atrogin-1 protein content was dose-dependently increased with PF-4708671 treatment, whereas MuRF1 protein content was not significantly altered. Overall, our results indicate that Atrogin-1 and MuRF1 protein contents are regulated by different mechanisms, the downstream of Akt, and that Atrogin-1 protein content can be regulated by rapamycin-sensitive mTOR-S6K1 dependent signaling pathway.


title: A Novel 3D Co-culture Platform for Integrating Tissue Interfaces for Tumor Growth, Migration and Therapeutic Sensitivity: PP-3D-S

abstract: Metastatic cancers can be highly heterogeneous, show large patient variability and are typically hard to treat due to chemoresistance. Personalized therapies are therefore needed to suppress tumor growth and enhance patients quality of life. Identifying appropriate patient-specific therapies remains a challenge though, due mainly to non-physiological in vitro culture systems. Therefore, more complex and physiological in vitro human cancer microenvironment tools could drastically aid in development of new therapies. We developed a plasma-modified, electro-spun 3D scaffold (PP-3D-S) that can mimic the human cancer microenvironment for customized-cancer therapeutic screening. The PP-3D-S were characterized for optimal plasma-modifying treatment and scaffolds morphology including fiber diameter and pore size. PP-3D-S was then seeded with human fibroblasts to mimic a stromal tissue layer; cell adhesion on plasma-modified poly (lactic acid), PLA, electrospun mats vastly exceeded that on untreated controls. The cell-seeded scaffolds were then overlaid with alginate/gelatin-based hydrogel embedded with MDA-MB231 human breast cancer cells, representing a tumor-tissue interface. Among three different plasma treatments, we found that NH3 plasma promoted the most tumor cell migration to the scaffold surfaces after 7 days of culture. For all treated and non-treated mats, we observed a significant difference in tumor cell migration between small-sized and either medium- or large-sized scaffolds. In addition, we found that the PP-3D-S was highly comparable to the standard Matrigel(R) migration assays in two different sets of doxorubicin screening experiments, where 75% reduction in migration was achieved with 0.5M doxorubicin for both systems. Taken together, our data indicate that PP-3D-S is an effective, low-cost, and easy-to-use alternate 3D tumor migration model which may be suitable as a physiological drug screening tool for personalized medicine against metastatic cancers.

category: bioengineering


title: A Hydrogel Microneedle-assisted Assay Integrating Aptamer Probes and Fluorescence Detection for Reagentless Biomarker Quantification

abstract: Analyzing interstitial fluid (ISF) via microneedle (MN) devices enables patient health monitoring in a minimally invasive manner and at point-of-care settings. However, most MN-based diagnostic approaches require complicated fabrication processes or post-processing of the extracted ISF. Here we show in-situ and on-needle measurement of target analytes by integrating hydrogel microneedles (HMN) with aptamer probes as the target recognition elements. Fluorescently tagged aptamer probes are chemically attached to the hydrogel matrix while a crosslinked patch is formed. We use the assay for specific and sensitive quantification of glucose concentrations in an animal model of diabetes to track hypoglycemia, euglycemia, and hyperglycemia conditions. The assay can track the rising and falling concentrations of glucose and the extracted measurements closely match those from the gold standard techniques. The assay enables rapid and reagentless target detection and can be readily modified to measure other target analytes in vivo. Our system has the potential to improve the quality of life of patients who are in need of close monitoring of biomarkers of health and disease.


title: Evaluation of Deep Neural Network ProSPr for Accurate Protein Distance Predictions on CASP14 Targets

abstract: The field of protein structure prediction has recently been revolutionized through the introduction of deep learning. The current state-of-the-art tool AlphaFold2 can predict highly accurate structures, however, it has a prohibitively long inference time for applications that require the folding of hundreds of sequences. The prediction of protein structure annotations, such as amino acid distances, can be achieved at a higher speed with existing tools, such as the ProSPr network. Here, we report on important updates to the ProSPr network, its performance on the recent Critical Assessment of Structure Prediction (CASP14) competition, and an evaluation of its accuracy dependency on multiple sequence alignment depth. We also provide a detailed description of the architecture and the training process, accompanied by reusable code. This work is anticipated to provide a solid foundation for the further development of protein distance prediction tools.

category: biophysics


title: A New Mouse Model of Diffuse Midline Glioma to Test Targeted Immunotherapies

abstract:
BACKGROUNDDiffuse midline gliomas remain incurable, with consistently poor outcomes in children despite radiotherapy. Immunotherapeutic approaches hold promise, with the integration of the hosts immune system fundamental to their design. Here, we describe a new, genetically engineered immunocompetent model that incorporates interleukin 13 receptor alpha 2 (IL13R2), a tumor-associated antigen, which is suitable for further evaluation of the antitumor activity of IL13R2-targeted immunotherapeutics in preclinical studies.

METHODSThe RCAS-Tv-a delivery system was used to induce gliomagenesis through overexpression of PDGFB and p53 deletion with and without human IL13R2 in Nestin-Tva; p53fl/fl mice. Hindbrain or cerebral cortex nestin progenitors of neonatal pups were infected with Cre recombinase and PDGFB+IL13R2 or Cre recombinase and PDGFB to model diffuse midline glioma and supratentorial high-grade glioma, respectively. Immunoblotting and flow cytometry was used to confirm target expression. Kaplan-Meier survival curves were established to compare tumor latency in both models. Tumor tissue was analyzed through immunohistochemistry and H&E staining. Cell lines generated from tumor-bearing mice were used for in vitro studies and orthotopic injections.

RESULTSThe protein expression of PDGFB and IL13R2 was confirmed by flow cytometry and western blot. In both groups, de novo tumors developed without significant difference in median survival between PDGFB and p53 loss (n=25, 40 days) and PDGFB, IL13R2, and p53 loss (n=33, 38 days, p=0.62). Tumors demonstrated characteristics of high-grade glioma such as infiltration, palisading necrosis, microvascular proliferation, high Ki-67 index, heterogeneous IL13R2 expression, and CD11b+ macrophages, along with a low proportion of CD3+ T cells. Orthotopic tumors developed from cell lines retained histopathological characteristics of de novo tumors. Mice orthotopically implanted with cells in the hindbrain or right cortex showed a median survival of 42 days and 41 (p=0.56) days, respectively.

CONCLUSIONGeneration of de novo tumors using the RCAS-Tv-a delivery system was successful, with tumors possessing histopathologic features common to pediatric diffuse gliomas. The development of these models opens the opportunity for preclinical assessment of IL13R2-directed immunotherapies with the potential for clinical translation.

category: cancer biology


title: Food or physics: plankton communities structured across Gulf of Alaska eddies

abstract: Oceanic features, such as mesoscale eddies that entrap and transport water masses, create heterogeneous seascapes to which biological communities may respond. To date, however, our understanding of how internal eddy dynamics influence plankton community structuring is limited by sparse sampling of eddies and their associated biotic communities. In this paper, we used 10 years of archived Continuous Plankton Recorder (CPR) data (2002-2013) associated with 9 mesoscale eddies in the Northeast Pacific/Gulf of Alaska to test the hypothesis that eddy origin and rotational direction determines the structure and dynamics of entrained plankton communities. Using generalized additive models and accounting for confounding factors (e.g., timing of sampling), we found peak diatom abundance within both cyclonic and anticyclonic eddies near the eddy edge. Zooplankton abundances, however, varied with distance to the eddy center/edge by rotational type and eddy life stage, and differed by taxonomic group. For example, the greatest abundance of small copepods was found near the center of anticyclonic eddies during eddy maturation and decay, but near the edge of cyclonic eddies during eddy formation and intensification. Distributions of copepod abundances across eddy surfaces were not mediated by phytoplankton distribution. Our results therefore suggest that physical mechanisms such as internal eddy dynamics exert a direct impact on the structure of zooplankton communities rather than indirect mechanisms involving potential food resources.

category: ecology


title: Open-Source Low-Cost Cardiac Optical Mapping System

abstract: Fluorescent imaging with voltage- or calcium-sensitive dyes, i.e. optical mapping, is one of the indispensable modern techniques to study cardiac electrophysiology, unsurpassed by temporal and spatial resolution. High-speed CMOS cameras capable of optical registration of action potential propagation are in general very costly. We present a complete solution priced below US$ 1,000 (including camera and lens) at the moment of publication with an open-source image acquisition and processing software. We demonstrate that the iDS UI-3130CP rev.2 camera we used in this study is capable of 200x200 977 frames per second (FPS) action potential recordings from rodent hearts. The signal-to-noise-ratio of a conditioned signal was 16 {+/-} 10 for rodent hearts. A comparison with a specialized MiCAM Ultimate-L camera has shown that signal-to-noise ratio (SNR) is sufficient for accurate measurements of AP waveform, conduction velocity ({+/-} 0.04 m/s) and action potential duration ({+/-} 7ms) in mouse and rat hearts. We measured the action potential prolongation during 4-aminopyridine administration in mouse heart, showing that proposed system signal quality is adequate for drug studies.


title: Effect of different ambient temperatures on reproductive outcome and wellbeing of lactating females in two mouse strains

abstract: Ambient temperature is an important non-biotic environmental factor influencing immunological and oncological parameters in laboratory mice. It is under discussion which temperature is more appropriate and whether the commonly used room temperature in rodent facilities of about 21{degrees}C represents a chronic cold stress or the 30{degrees}C of the thermoneutral zone constitutes heat stress for the animals. In this study we selected the physiological challenging period of lactation to investigate the influence of a cage temperature of 20{degrees}C, 25{degrees}C, and 30{degrees}C, respectively, on reproductive performance and stress hormone levels in two frequently used mouse strains. We found that more pups were weaned from B6D2F1 hybrids compared to C57BL/6N mothers and that the number of weaned pups was strongly reduced if mothers of both strains were kept at 30{degrees}C. Furthermore, at 30{degrees}C mothers and pups showed reduced body weight at weaning and offspring had longer tails. Despite pronounced temperature effects on reproductive parameters, we did not find any impact on adrenocortical activity in breeding and control mice. Independent of the ambient temperature however, we found that females raising pups showed elevated levels of fecal corticosterone metabolites (FCMs) compared to controls. Increased levels of stress hormone metabolites were measured specially around birth and during the third week of lactation. Our results provide no evidence for reduced or improved wellbeing of lactating mice at different ambient temperatures, but we found that a 30{degrees}C cage temperature impairs reproductive performance.


title: A Golden Gate-based Plasmid Library for the Rapid Assembly of Biotin Ligase Constructs for Proximity Labelling

abstract: Proximity-labelling has emerged as a powerful tool for the detection of weak and transient interactions between proteins as well as the characterization of subcellular proteomes. One proximity labelling approach makes use of a promiscuous bacterial biotin ligase, termed BioID. Expression of BioID (or of its derivates TurboID and MiniTurbo) fused to a bait protein results in the biotinylation of proximal proteins. These biotinylated proteins can then be isolated by affinity purification using streptavidin-coated beads and identified by mass spectrometry. To facilitate the use of proximity-labelling in plants, we have generated a collection of constructs that can be used for the rapid cloning of TurboID and MiniTurbo fusion proteins using the Golden Gate cloning method. To allow for the use of the constructs in a range of experiments we have designed assembly modules that encode the biotin ligases fused to different linkers as well as different commonly used subcellular localization sequences. We demonstrate the functionality of these vectors through biotinylation assays in tobacco (Nicotiana benthamiana) plants.

category: plant biology


title: Reward timing matters in motor learning

abstract: Reward can improve motor learning and the consolidation of motor memories. Identifying the features of reward feedback that are critical for motor learning is a necessary step for successful integration into rehabilitation programs. One central feature of reward feedback that may affect motor learning is its timing - that is, the delay after which reward is delivered following movement execution. In fact, research on associative learning has shown that short and long reward delays (e.g., 1 and 6 s following action execution) activate preferentially the striatum and the hippocampus, respectively, which both contribute with varying degrees to motor learning. Given the distinct functional role of these two areas, we hypothesized that reward timing could modulate how people learn and consolidate a new motor skill. In sixty healthy participants, we found that delaying reward delivery by a few seconds influenced motor learning dynamics. Indeed, training with a short reward delay (i.e., 1 s) induced slow, yet continuous gains in performance, while a long reward delay (i.e., 6 s) led to initially high learning rates that were followed by an early plateau in the learning curve and a lower endpoint performance. Moreover, participants who successfully learned the skill with a short reward delay displayed overnight consolidation, while those who trained with a long reward delay exhibited an impairment in the consolidation of the motor memory. Overall, our data show that reward timing affects motor learning, potentially by modulating the engagement of different learning processes, a finding that could be exploited in future rehabilitation programs.

category: neuroscience


title: Targeted Tshz3 deletion in corticostriatal circuit components segregates core autistic behaviors

abstract: We previously linked TSHZ3 haploinsufficiency to autism spectrum disorder (ASD) and showed that embryonic or postnatal Tshz3 deletion in mice results in behavioral traits relevant to the two core domains of ASD, namely social interaction deficits and repetitive behaviors. Here, we provide evidence that cortical projection neurons (CPNs) and striatal cholinergic interneurons (SCINs) are two main and complementary players in the TSHZ3-linked ASD syndrome. We show that in the cerebral cortex, TSHZ3 is expressed in CPNs and in a proportion of GABA interneurons, while not in cholinergic interneurons or glial cells. TSHZ3-expressing cells, which are predominantly SCINs in the striatum, represent a low proportion of neurons in the ascending cholinergic projection system. We then characterized two new conditional knockout (cKO) models generated by crossing Tshz3flox/flox with Emx1-Cre (Emx1-cKO) or Chat-Cre (Chat-cKO) mice to decipher the respective role of CPNs and SCINs. Emx1-cKO mice show altered excitatory synaptic transmission onto CPNs and plasticity at corticostriatal synapses, with neither cortical neuron loss nor impaired layer distribution. These animals present social interaction deficits but no repetitive patterns of behavior. Chat-cKO mice exhibit no loss of SCINs but changes in the electrophysiological properties of these interneurons, associated with repetitive patterns of behavior without social interaction deficits. Therefore, dysfunction in either CPNs or SCINs segregates with a distinct ASD behavioral trait. These findings provide novel insights onto the implication of the corticostriatal circuitry in ASD by revealing an unexpected neuronal dichotomy in the biological background of the two core behavioral domains of this disorder.


title: Hepatocyte Cell Cycle Progression Depends on a Transcriptional Repressor Cascade Downstream of Wnt Signaling

abstract: Cell proliferation is tightly controlled by inhibitors that block cell cycle progression until growth signals relieve this inhibition. In several tissues including the liver, transcriptional repressors such as E2F7 and E2F8 function as inhibitors of mitosis and promote polyploidy, but how growth factors release these mitotic inhibitors to facilitate cell cycle progression is unknown. We describe here a newly identified mechanism of cell division control in which Wnt/{beta}catenin signaling in the postnatal liver maintains active hepatocyte proliferation through Tbx3, a Wnt target gene. TBX3 directly represses transcription of E2f7 and E2f8, promoting a low ploidy state and cell cycle progression. This sequential transcriptional repressor cascade, initiated by Wnts, provides a new paradigm for exploring how a commonly active developmental signal impacts cell cycle completion.


title: Single cell profiling of the Timp gene family

abstract: Tissue inhibitor of metalloproteinases (TIMPs/Timps) are an endogenous family of widely expressed matrisome-associated proteins that were initially identified as inhibitors of matrix metalloproteinase activity (Metzincin family proteases). Consequently, TIMPs are often considered simply as protease inhibitors by many investigators. However, an evolving list of new metalloproteinase-independent functions for TIMP family members suggests that this concept is outdated. These novel TIMP functions include direct agonism/antagonism of multiple transmembrane receptors, as well as interactions with matrisome targets. While the family was fully identified over 2 decades ago, there has yet to be an in-depth study describing the expression of TIMPs in normal tissues of adult mammals. An understanding of the tissues and cell-types that express TIMPs 1 through 4, in both normal and disease states are important to contextualize the growing functional capabilities of TIMP proteins, which are often dismissed as non-canonical. Using publicly available single cell RNA sequencing data from the Tabula Muris Consortium, we analyzed approximately 100,000 murine cells across nineteen tissues from non-diseased organs, representing seventy-three annotated cell types, to define the diversity in Timp gene expression across healthy tissues. We describe that Timp genes display unique expression profiles across tissues and organ-specific cell types. Within annotated cell-types, we identify clear and discrete cluster-specific patterns of Timp expression, particularly in cells of stromal and endothelial origins. Differential expression and gene set pathway analysis provide evidence of the biological significance of Timp expression in these identified cell sub-types, which are consistent with novel roles in normal tissue homeostasis and changing roles in disease progression. This understanding of the tissues, specific cell types and conditions of the microenvironment in which Timp genes are expressed adds important physiological context to the growing array of novel TIMP protein functions.


title: Maf is a regulator of differentiation for gut immune epithelial cell Microfold cell (M cell)

abstract: Microfold cells (M cells) are a specialized subset of epithelial intestinal cells responsible for immunosurveillance of the gastrointestinal tract. M cells are located in the Peyers patches and are crucial for monitoring and the transcytosis of antigens, microorganisms, and pathogens via their mature receptor GP2. A mature M cell with Gp2 receptor aids in the uptake of antigens, which are passed through the single layer of epithelium and presented to underlying antigen-presenting cells and processed further down-stream with B cells, T cells, and dendritic cells. Recent studies revealed several transcription factors and ligands responsible for the development and differentiation of mature M cells however, an exhaustive list of factors remains to be elucidated. Our recent work on the epigenetic regulation of M cell development found 12 critical transcription factors that were controlled by the polycomb recessive complex 2. Musculoaponeurotic fibrosarcoma transcription factor (Maf) was identified as a gene regulated by the polycomb repressive complex (PRC2) during the development of M cells. In this paper, we explore Mafs critical role in M cell differentiation and maturation. Maf falls under the purview of RANKL signaling, is localized in the Peyers patches of the intestine, and is expressed by M cells. Given that, complete knockout of the Maf gene leads to a lethal phenotype, organoids isolated from Maf knockout mice and treated with RANKL exhibited impaired M cell development and a significant decrease in Gp2 expression. These findings reveal that Maf is an important regulator for M cell development and differentiation.

category: developmental biology


title: Single-Shot Optical Projection tomography for high-speed volumetric imaging

abstract: We present a single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic samples. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio but the sequential acquisition of projection images required for volumetric reconstruction typically requires samples to be immobilised during the acquisition of an OPT data set. We present a proof-of-principle system capable of single-shot imaging of a 1 mm diameter volume, demonstrating camera-limited rates of up to 62.5 volumes/second, which we have applied to 3D imaging of a freely-swimming zebrafish embryo. This is achieved by recording 8 projection views simultaneously on 4 low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under {pound}5,000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including fluid dynamics.


title: Simulation atomic force microscopy to predict correlated conformational dynamics in proteins from topographic imaging

abstract: Atomic force microscopy (AFM) of proteins can detect only changes within the scanned molecular surface, missing all motions in other regions and thus information about functionally relevant conformational couplings. We show that simulation AFM can overcome this drawback by reconstruction of 3D molecular structures from topographic AFM images. A proof of principle demonstration is provided for an in-silico AFM experiment visualizing the conformational dynamics of a membrane transporter. The application shows that the alternating access mechanism underlying its operation can be retrieved from only AFM imaging of one membrane side. Simulation AFM is implemented in the freely available BioAFMviewer software platform, providing the convenient applicability to better understand experimental AFM observations.


title: Turning high-throughput structural biology into predictive inhibitor design

abstract: A common challenge in drug design pertains to finding chemical modifications to a ligand that increases its affinity to the target protein. An underutilised advance is the increase in structural biology throughput, which has progressed from an artisanal endeavour to a monthly throughput of up to 100 different ligands against a protein in modern synchrotrons. However, the missing piece is a framework that turns high throughput crystallography data into predictive models for ligand design. Here we designed a simple machine learning approach that predicts protein-ligand affinity from experimental structures of diverse ligands against a single protein paired with biochemical measurements. Our key insight is using physics-based energy descriptors to represent protein-ligand complexes, and a learning-to-rank approach that infers the relevant differences between binding modes. We ran a high throughput crystallography campaign against the SARS-CoV-2 Main Protease (MPro), obtaining parallel measurements of over 200 protein-ligand complexes and the binding activity. This allows us to design a one-step library syntheses which improved the potency of two distinct micromolar hits by over 10-fold, arriving at a non-covalent and non-peptidomimetic inhibitor with 120 nM antiviral efficacy. Crucially, our approach successfully extends ligands to unexplored regions of the binding pocket, executing large and fruitful moves in chemical space with simple chemistry.


title: Identifying tumor cells at the single cell level

abstract: Tumors are highly complex tissues composed of cancerous cells, surrounded by a heterogeneous cellular microenvironment. Tumor response to treatments is governed by an interaction of cancer cell intrinsic factors with external influences of the tumor microenvironment. Disentangling the heterogeneity within a tumor is a crucial step in developing and utilization of effective cancer therapies. The single cell sequencing technology enables an effective molecular characterization of single cells within the tumor. This technology can help deconvolute heterogeneous tumor samples and thus revolutionize personalized medicine. However, a governing challenge in cancer single cell analysis is cell annotation, the assignment of a particular cell type or a cell state to each sequenced cell. One of the critical cell type annotation challenges is identification of tumor cells within single cell or spatial sequencing experiments.This is a critical limiting step for a multitude of research, clinical, and commercial applications. A reliable method addressing that challenge is a prerequisite for automatic annotation of histopathological data, profiled using multichannel immunofluorescence or spatial sequencing. Here, we propose Ikarus, a machine learning pipeline aimed at distinguishing tumor cells from normal cells at the single cell level. We have tested ikarus on multiple single cell datasets to ascertain that it achieves high sensitivity and specificity in multiple experimental contexts.


title: Fetal programming by sodium saccharin and damage on male offspring reproductive

abstract: Male infertility is responsible for 20-70% of infertility in couples. We investigated the effects of fetal programming with sodium saccharin consumption in testis structure and function and in male offspring fertility. Feed intake and efficiency, organ and fat weight, quantification and expression of AR and PCNA proteins, sperm count and hormonal dosages were performed. Changes in consumption were found in the final weeks of the experiment. Decreases in the expression and quantification of AR and PCNA, tubular diameter and luminal volume, and increase in epithelial and interstitial relative volumes were observed. Lower sperm count and transit and lower estradiol concentration were also found. The consumption of sodium saccharin by the dams programmed the male offspring affecting the HPG axis with alterations in Sertoli cell proliferation, AR expression and quantification, and sperm count. We hypothesize that these changes may be due to the reduction of estradiol that caused the loosening of the tight junctions of the blood-testis-barrier (BTB), causing cell losses during spermatogenesis, also reflecting, under the decrease in tubular diameter with an increase in epithelial volume and consequent decrease in luminal volume. Sodium saccharin programming directly affected the reproductive parameters of male offspring and adult fertility.


title: Relapse to cotinine seeking in rats: Differential effects of sex

abstract:
Relapse is a defining feature of smoking and a significant challenge in cessation management. Elucidation of novel mechanisms underlying relapse may inform future treatments. Cotinine, the major metabolite of nicotine, has been shown to support intravenous self-administration in rats, suggesting it as one potential mechanism contributing to nicotine reinforcement. However, it remains unknown whether cotinine would induce relapse-like behaviors. The current study investigated relapse to cotinine seeking in two relapse models, the reinstatement of drug seeking and incubation of drug craving models. In the reinstatement model, rats were trained to self-administer cotinine, extinguished cotinine-associated responses, and underwent cue-, drug-, or stress-induced reinstatement. Conditioned cues associated with cotinine self-administration, cotinine (1-2 mg/kg), or the pharmacological stressor yohimbine (1.25-2.5 mg/kg) reinstated cotinine seeking. Female rats displayed more pronounced cue-induced, but not drug- or stress-induced reinstatement than male rats. In addition, an overall analysis revealed that female rats exhibited greater cotinine self-administration, but less extinction than male rats. In the incubation model, rats were trained to self-administer cotinine, and underwent forced withdrawal in home cages. Rats were tested for cue-induced cotinine seeking on both withdrawal day 1 and withdrawal day 18. Rats exhibited greater cotinine-seeking on withdrawal day 18 compared to withdrawal day 1, with no difference between male and female rats. These findings indicate that cotinine induces sex-dependent relapse to cotinine seeking in rats, suggesting that cotinine may be a novel mechanism contributing to relapse. These rat models are valuable preclinical tools for interrogation of neurobiological underpinnings of relapse to cotinine seeking.

Significance StatementRelapse is a defining feature of smoking and a significant challenge in cessation management. Elucidation of novel mechanisms underlying relapse may inform future treatment. Cotinine, the major metabolite of nicotine, has previously been shown as a potential mechanism underlying the development of nicotine reinforcement because it supports intravenous self-administration in rats. The current study found that conditioned cues, priming injection of cotinine, and acute exposure to the pharmacological stressor yohimbine induced robust cotinine-seeking behavior in rats with a history of cotinine self-administration. In addition, significant sex effects were revealed in that female rats exhibited greater cotinine self-administration, less extinction, and more robust cue-induced reinstatement of cotinine seeking than male rats. These findings suggest that cotinine may be a novel mechanism contributing to relapse to nicotine seeking. In addition, these rat models are valuable preclinical tools for interrogation of behavioral and neurobiological underpinnings to relapse to cotinine seeking, thus forming basis for developing effective therapeutic strategy to aid in smoking cessation.

category: animal behavior and cognition


title: Stimulus-dependent orientation strategies in monarch butterflies

abstract: Insects are well-known for their ability to keep track of their heading direction based on a combination of skylight cues and visual landmarks. This allows them to navigate back to their nest, disperse throughout unfamiliar environments, as well as migrate over large distances between their breeding and non-breeding habitats. The monarch butterfly (Danaus plexippus) for instance is known for its annual southward migration from North America to certain trees in Central Mexico. To maintain a constant flight route, these butterflies use a time-compensated sun compass for orientation which is processed in a region in the brain, termed the central complex. However, to successfully complete their journey, the butterflies brain must generate a multitude of orientation strategies, allowing them to dynamically switch from sun-compass orientation to a tactic behavior toward a certain target. To study if monarch butterflies exhibit different orientation modes and if they can switch between them, we observed the orientation behavior of tethered flying butterflies in a flight simulator while presenting different visual cues to them. We found that the butterflies behavior depended on the presented visual stimulus. Thus, while a dark stripe was used for flight stabilization, a bright stripe was fixated by the butterflies in their frontal visual field. If we replaced a bright stripe by a simulated sun stimulus, the butterflies switched their orientation behavior and exhibited compass orientation. Taken together, our data show that monarch butterflies rely on and switch between different orientation modes, allowing them to adjust orientation to the actual behavioral demands of the animal.


title: Post-injury born oligodendrocytes integrate into the glial scar and inhibit growth of regenerating axons by premature myelination

abstract:
Pathologies of the central nervous system (CNS) white matter often result in permanent functional deficits because mature mammalian projection neurons fail to regenerate long-distance axons after injury. A major barrier to axonal regenerative research is that the CNS axons that regenerate in response to experimental treatments stall growth before reaching their post-synaptic targets. Here, we test the hypothesis that premature, de novo, myelination of regenerating axons stalls their growth, even after bypassing the glial scar. To test this hypothesis, first, we used single cell RNA-seq (scRNA-seq) and immunohistological analysis to investigate whether post-injury born oligodendrocytes integrate into the glial scar after optic nerve injury. Then, we used a multiple sclerosis model of demyelination concurrently with the stimulation of axon regeneration by Pten knockdown (KD) in projection neurons after optic nerve injury. We found that post-injury born oligodendrocytes integrate into the glial scar, where they are susceptible to the demyelination treatment, which prevented premature myelination, and thereby enhanced Pten KD-stimulated axon regeneration. We also present a website for comparing the gene expression of scRNA-seq-profiled optic nerve oligodendrocytes under physiological and pathophysiological conditions.

SIGNIFICANCE STATEMENTMyelin debris from degenerating axons along with reactive astrocytes in the glial scar inhibit CNS axon regeneration. However, even with the recently developed experimental approaches which activate axons to regenerate passed the glial scar, almost all axons still stall growth before reaching their post-synaptic targets. Here, we show that post-injury born oligodendrocytes integrate into the glial scar, and that other than myelin debris, live oligodendrocytes prematurely myelinating the regenerating axons inhibit growth, even if the axons have already regenerated passed the glial scar.


title: Retroactive analysis of single cell transcriptome profiles using next-generation algorithms revised the identification of several resilient retinal ganglion cell types

abstract: The clustering of single cell RNA-sequencing (scRNA-seq) data enables the classification of cell types, and the development of integration algorithms has enabled the tracing of altered-from-baseline transcriptomes to their respective cell type origins. Here, we developed an algorithm that removes sources of noise from scRNA-seq datasets and improves the accuracy of their integration. We found that this improvement of integration is further increased by an algorithm we developed for auto-determination of optimal weight-assignment to anchors. As a proof-of-concept, we show that our algorithm determined the type-origin of the 17% of injured retinal ganglion cells (RGCs) that an existing integration algorithm could not identify. As we found that the majority of the originally unassigned cells belonged to only several out of 45 RGC types, a consequent change in the proportions of the surviving types resulted in a moderately different ranking of resiliency to injury. This updated standard for RGC type resilience ranking improved the understanding of RGC type biology and the ranking-dependent prediction of genes for therapeutic neuroprotective targeting. Additional bioinformatic analyses revealed single-gene cluster-markers for RGC types and contributed new insights into the global characteristics of RGC types and how axonal injury affects them, showing how the extent of variance between transcriptomes of RGC types increases differentially during maturation and after injury. We also show, for the first time, that specific global properties of the transcriptome can predict the resilience to injury of certain cell types. Furthermore, we developed a website for cluster-by-cluster comparison of gene expression between uninjured and injured RGC types. The publicly available R library package, CellTools, for denoising and improving the integration of scRNA-seq datasets, as well as for associating cell types with the global properties of the transcriptome, will assist scRNA-seq studies of developing, injured, or diseased cell types across biological fields.


title: Self-learning algorithm for denoising and advancing the integration of scRNA-seq datasets improves the identification of resilient and susceptible retinal ganglion cell types

category: bioinformatics


title: Assessing HD-EEG functional connectivity states using ahuman brain computational model

abstract: Electro/Magnetoencephalography (EEG/MEG) source-space network analysis is increasingly recognized as a powerful tool to track fast electrophysiological brain dynamics. However, an objective and quantitative evaluation of the various steps, from source localization and functional connectivity to clustering algorithms, is challenging, due to the lack of realistic  controlled data. Here, we used a human brain computational model containing both physiologically-based cellular GABAergic and Glutamatergic circuits coupled through Diffusion Tensor Imaging - based structural connectivity, to generate realistic High Density-EEG (256 channels) recordings. We designed a scenario of successive gamma-band oscillations in distinct cortical areas in order to emulate a virtual picture naming task. We identified the fast time-varying network states and quantified the performance of the key steps involved in the pipeline: (1) inverse models to reconstruct cortical-level sources, (2) functional connectivity measures to compute statistical interdependency between regional time series, and (3) dimensionality reduction methods to derive dominant brain network states (BNS). Using a systematic evaluation of the different independent/principal/non-negative decomposition techniques along with a clustering approach, results show significant variability among the tested algorithms in terms of spatial and temporal accuracy. We outlined the spatial precision, the temporal sensitivity, as well as the global accuracy of the extracted BNS relative to each method. Our findings suggest a good performance of wMNE/PLV combination to elucidate the appropriate functional networks and ICA techniques to derive relevant dynamic brain network states. Our aim here is twofold: 1) to provide quantitative assessment on the advantages and the limitations of each of the analyzed techniques and 2) to introduce (and share) a complete framework that can be used to optimize the entire pipeline of EEG/MEG source connectivity. With such framework, other tasks can be generated and used for validation and other methodological points can be also addressed.


title: An Optimal Policy Model for Concurrent Uncertainty Estimation During Decision Making

abstract: We often postpone or even avoid making decisions when we feel uncertain. Uncertainty estimation is not an afterthought of decision making but a dynamic process that accompanies decision making in parallel and affects decision making. To study concurrent uncertainty estimation during decision making, we adapted the classic random-dots motion direction discrimination task to allow a reaction-time measure of uncertainty responses. Subjects were asked to judge whether a patch of random dots was moving left or right. In addition, they could seek assistance by choosing to look at a second stimulus that had the same direction but high coherence any time during the task. The task allows us to measure the reaction time of both the perceptual decisions and the uncertainty responses. The subjects were more likely to choose the uncertainty response when the motion coherence was low, while their reaction times of the uncertainty responses showed individual variations. To account for the subjects behavior, we created an optimal policy decision model in which decisions are based on the value functions computed from the accumulated evidence using a drift-diffusion process. Model simulations captured key features of the subjects choices, reaction times, and proportions of uncertainty responses. Varying model parameters explained individual variations in the subjects and the correlations between decision accuracy, proportions of uncertainty responses, and reaction times at the individual level. Our model links perceptual decisions and value-based decisions and indicates that concurrent uncertainty estimation may be based on comparisons between values of uncertainty responses and perceptual decisions, both of which may be derived from the same evidence accumulation process during decision making. It provides a theoretical framework for future investigations, including the ones that aim at the underlying neural mechanism.


title: Spatial signatures of anesthesia-induced burst-suppression differ between primates and rodents

abstract: During deep anesthesia, the electroencephalographic (EEG) signal of the brain alternates between bursts of activity and periods of relative silence (suppressions). The origin of burst-suppression and its distribution across the brain remain matters of debate. In this work, we used functional magnetic resonance imaging (fMRI) to map the brain areas involved in anesthesia-induced burst-suppression across four mammalian species: humans, long-tailed macaques, common marmosets, and rats. At first, we determined the fMRI signatures of burst-suppression in human EEG-fMRI data. Applying this method to animal fMRI datasets, we found distinct burst-suppression signatures in all species. The burst-suppression maps revealed a marked inter-species difference: in rats the entire neocortex engaged in burst-suppression, while in primates most sensory areas were excluded--predominantly the primary visual cortex. We anticipate that the identified species-specific fMRI signatures and whole-brain maps will guide future targeted studies investigating the cellular and molecular mechanisms of burst-suppression in unconscious states.


title: Unifying turbulent dynamics framework distinguishes different brain states

abstract: Recently, significant advances have been made by identifying the levels of synchronicity of the underlying dynamics of a given brain state. This research has demonstrated that unconscious dynamics tend to be more synchronous than those found in conscious states, which are more asynchronous. Here we go beyond this dichotomy to demonstrate that the different brain states are always underpinned by spatiotemporal chaos but with dissociable turbulent dynamics. We investigated human neuroimaging data from different brain states (resting state, meditation, deep sleep, and disorders of consciousness after coma) and were able to distinguish between them using complementary model-free and model-based measures of turbulent information transmission. Our model-free approach used recent advances describing a measure of information cascade across spatial scales using tools from turbulence theory. Complementarily, our model-based approach used exhaustive in silico perturbations of whole-brain models fitted to the empirical neuroimaging data, which allowed us to study the information encoding capabilities of the brain states. Overall, the current framework demonstrates that different levels of turbulent dynamics are fundamental for describing and differentiating between brain states.


title: Dysfunctional temporal stages of eye-gaze perception in adults with ADHD: a high-density EEG study

abstract:
ADHD have been associated with social cognitive impairments across the lifespan, but no studies have specifically addressed the presence of abnormalities in eye-gaze processing in the adult brain.

This study investigated the neural basis of eye-gaze perception in adults with ADHD using event-related potentials (ERP). Twenty-three ADHD and 23 controls performed a delayed face-matching task with neutral faces that had either direct or averted gaze. ERPs were classified using microstate analyses.

ADHD and controls displayed similar P100 and N170 microstates. ADHD was associated with cluster abnormalities in the attention-sensitive P200 to direct gaze, and in the N250 related to facial recognition. For direct gaze, source localization revealed reduced activity in ADHD for the P200 in the left/midline cerebellum, as well as in a cingulate-occipital network at the N250. These results suggest brain impairments involving eye-gaze decoding in adults with ADHD, suggesting that neural deficits persist across the lifespan.


title: Decoding of cortex-wide brain activity from local recordings of neural potentials

abstract:
ObjectiveElectrical recordings of neural activity from brain surface have been widely employed in basic neuroscience research and clinical practice for investigations of neural circuit functions, brain-computer interfaces, and treatments for neurological disorders. Traditionally, these surface potentials have been believed to mainly reflect local neural activity. It is not known how informative the locally recorded surface potentials are for the neural activities across multiple cortical regions.

ApproachTo investigate that, we perform simultaneous local electrical recording and wide-field calcium imaging in awake head-fixed mice. Using a recurrent neural network model, we try to decode the calcium fluorescence activity of multiple cortical regions from local electrical recordings.

Main resultsThe mean activity of different cortical regions could be decoded from locally recorded surface potentials. Also, each frequency band of surface potentials differentially encodes activities from multiple cortical regions so that including all the frequency bands in the decoding model gives the highest decoding performance. Despite the close spacing between recording channels, surface potentials from different channels provide complementary information about the large-scale cortical activity and the decoding performance continues to improve as more channels are included. Finally, we demonstrate the successful decoding of whole dorsal cortex activity at pixel-level using locally recorded surface potentials.

SignificanceThese results show that the locally recorded surface potentials indeed contain rich information of the large-scale neural activities, which could be further demixed to recover the neural activity across individual cortical regions. In the future, our cross-modality inference approach could be adapted to virtually reconstruct cortex-wide brain activity, greatly expanding the spatial reach of surface electrical recordings without increasing invasiveness. Furthermore, it could be used to facilitate imaging neural activity across the whole cortex in freely moving animals, without requirement of head-fixed microscopy configurations.


title: Separating neural oscillations from aperiodic 1/f activity: challenges and recommendations

abstract:
Electrophysiological power spectra typically consist of two components: An aperiodic part usually following an 1/f power law P{propto}1/f{beta}and periodic components appearing as spectral peaks. While the investigation of the periodic parts, commonly referred to as neural oscillations, has received considerable attention, the study of the aperiodic part has only recently gained more interest. The periodic part is usually quantified by center frequencies, powers, and bandwidths, while the aperiodic part is parameterized by the y-intercept and the 1/f exponent {beta}. For investigation of either part, however, it is essential to separate the two components.

In this article, we scrutinize two frequently used methods, FOOOF (Fitting Oscillations & One-Over-F) and IRASA (Irregular Resampling Auto-Spectral Analysis), that are commonly used to separate the periodic from the aperiodic component. We evaluate these methods using diverse spectra obtained with electroencephalography (EEG), magnetoencephalography (MEG), and local field potential (LFP) recordings relating to three independent research datasets. Each method and each dataset poses distinct challenges for the extraction of both spectral parts. The specific spectral features hindering the periodic and aperiodic separation are highlighted by simulations of power spectra emphasizing these features. Through comparison with the simulation parameters defined a priori, the parameterization error of each method is quantified. Based on the real and simulated power spectra, we evaluate the advantages of both methods, discuss common challenges, note which spectral features impede the separation, assess the computational costs, and propose recommendations on how to use them.


title: The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in an agroecosystem

abstract: The relationship between soil microbial diversity and agroecosystem functioning is controversial due to the elevated diversity level and the functional redundancy of microorganisms. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of winter cover crops (WCC) in a conventional maize-soy rotation promotes microbial diversity and the biological sink of H2 in soil, while reducing N2O emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons. Soil acted as a net sink for H2 and as a net source for CO2 and N2O. CO2 flux was the most sensitive to WCC whereas a significant spatial variation was observed for H2 flux with soil uptake rates observed in the most productive area two-fold greater than the baseline level. Sequencing and quantification of taxonomic and functional genes were integrated to explain variation in trace gas fluxes with compositional changes in soil microbial communities. Fungal communities were the most sensitive to WCC, but neither community abundance nor beta diversity were found to be indicative of fluxes. The alpha diversity of taxonomic and functional genes, expressed as the number of effective species, was integrated into composite variables extracted from multivariate analyses. Only the composite variable computed with the inverse Simpsons concentration index displayed a reproducible pattern throughout both growing seasons, with functional genes and bacterial 16S rRNA gene defining the two most contrasting gradients. The composite variable was decoupled from WCC treatment and explained 19-20% spatial variation of H2 fluxes. Sensitivity of the trace gas exchange process to soil properties at the local scale was inconsistent among H2, N2O and CO2, with the former being the most related to microbial diversity distribution pattern.


title: Accounting for animal movement improves vaccination strategies against wildlife disease in heterogeneous landscapes

abstract: Oral baiting is used to deliver vaccines to wildlife to prevent, control, and eliminate infectious diseases. A central challenge is how to spatially distribute baits to maximize encounters by target animal populations, particularly in urban and suburban areas where wildlife like raccoons (Procyon lotor) are abundant and baits are delivered along roads. Methods from movement ecology that quantify movement and habitat selection could help to optimize baiting strategies by more effectively targeting wildlife populations across space. We developed a spatially explicit, individual-based model of raccoon movement and oral rabies vaccine seroconversion to examine whether and when baiting strategies that match raccoon movement patterns perform better than currently employed baiting strategies in an oral rabies vaccination zone in greater Burlington, Vermont, USA. Habitat selection patterns estimated from locally radio-collared raccoons were used to parameterize movement simulations. We then used our simulations to estimate raccoon population rabies seroprevalence under currently used baiting strategies (actual baiting) relative to habitat selection-based baiting strategies (habitat baiting). We conducted simulations on the Burlington landscape and artificial landscapes that varied in heterogeneity relative to Burlington in the proportion and patch size of preferred habitats. We found that the benefits of habitat baiting strongly depended on the magnitude and variability of raccoon habitat selection and the degree of landscape heterogeneity within the baiting area. Habitat baiting improved seroprevalence over actual baiting for raccoons characterized as habitat specialists but not for raccoons that displayed weak habitat selection similar to radio-collared individuals--except when baits were delivered off roads where preferred habitat coverage and complexity was more pronounced. In contrast, in artificial landscapes with either more strongly juxtaposed favored habitats and/or higher proportions of favored habitats, habitat baiting performed better than actual baiting, even when raccoons displayed weak habitat preferences and where baiting was constrained to roads. Our results suggest that habitat selection-based baiting could increase raccoon population seroprevalence in urban-suburban areas, where practical, given the heterogeneity and availability of preferred habitat types in those areas. Our novel simulation approach provides a flexible framework to test alternative baiting strategies in multiclass landscapes to optimize bait distribution strategies.


title: Competition for water and species coexistence in phenologically structured annual plant communities

abstract: Both competition for water and phenological variation are important determinants of plant community structure, but ecologists lack a synthetic theory for how they affect coexistence outcomes. We developed an analytically tractable model of water competition for Mediterranean annual communities and demonstrate that variation in phenology alone can maintain high diversity in spatially homogenous assemblages of water-limited plants. We modeled a system where all water arrives early in the season and species vary in their ability to grow under drying conditions. As a consequence, species differ in growing season length, and compete by shortening the growing season of their competitors. This model replicates and offers mechanistic explanations for qualitative patterns observed in prior empirical studies of how phenology influences coexistence among Mediterranean annuals. Additionally, we found that a decreasing, concave-up tradeoff between growth rate and access to water can theoretically maintain infinite diversity under simple but realistic assumptions. High diversity is possible because: 1) later plants escape competition after their earlier-season competitors have gone to seed and 2) early-season species are more than compensated for their shortened growing season by a growth-rate advantage. Together, these mechanisms provide an explanation for how annual plant species might coexist when competing only for water.


title: Synchronous seasonality in the gut microbiota of wild wood mouse populations

abstract:
O_LIThe gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, what factors drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood.
C_LIO_LIHere, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent set of  core gut microbes is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations.
C_LIO_LIBetween 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild UK mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species.
C_LIO_LIAlthough broadly similar at high taxonomic levels and despite being only 50km apart, the two wild populations did not share a single bacterial amplicon sequence variant (ASV). Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite strong taxonomic divergence in the microbiota, the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, seasonal convergence in the gut microbiota among individuals occurred in late winter/early spring.
C_LIO_LIThese findings reveal highly repeatable seasonal gut microbiota dynamics across distinct populations of this species, despite divergent taxa being involved. Providing a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.
C_LI


title: City climate and landscape structure shape pollinators, nectar and transported pollen along a gradient of urbanization

abstract:
O_LIUrbanization gradients influence both landscape and climate and provide opportunity for understanding how species, especially plants and pollinators, respond to artificially driven environmental transitions.
C_LIO_LIHere, we investigated several aspects of pollination along an urbanization gradient in landscape and climate. We quantified wild hoverfly and bee abundances with trapping, standing crop of nectar with spectrophotometer, and the pollen transported by flower-visitors with DNA-metabarcoding, in 40 independent sites from seminatural to built-up areas in Northern Italy.
C_LIO_LILinear and nonlinear relationships were detected along the urbanization gradient. Pollinator abundances increased until 22% of impervious surface, dropping by 34% after that, and it also decreased with green patch distance and urban park size. Thus, suburban landscapes host more pollinators than highly cemented or seminatural areas. Moreover, pollinators diminished by up to 45% in areas with low temperature seasonality: urbanized areas likely posing thermic stress. Furthermore, the sugar mass available in nectar increased by 91% with impervious cover, indicating that city nectars were less consumed or flowers more productive. Furthermore, the species richness of pollen decreased by 32% in highly urbanized areas, and with a high incidence of exotic plants, hinting for anthropized plant communities.
C_LIO_LISynthesis and applications. Urbanization influences pollinator abundances, nectar resources and transported pollen. Pollinators are negatively affected by a thermally harsh climate in highly urbanized areas with isolated green areas and large parks. Suburban landscapes demonstrated the highest pollinator presence. In the city core, flowers contained more nectary sugar, while pollinators collected pollen from a small number of plants, mainly exotic. These findings highlight the influence of urban landscape structure and climate on pollinators and plants, showing that cities are heterogenous realities. Patterns from this study will serve as basis for pollinator-friendly planning and management of urban landscapes.
C_LI


title: Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

abstract: The spatial structure of genomic and phenotypic variation across populations reflects historical and demographic processes as well as evolution via natural selection. Characterizing such variation can provide an important perspective for understanding the evolutionary consequences of changing climate and for guiding ecological restoration. While evidence for local adaptation has been traditionally evaluated using phenotypic data, modern methods for generating and analyzing landscape genomic data can directly quantify local adaptation by associating allelic variation with environmental variation. Here, we analyze both genomic and phenotypic variation of rubber rabbitbrush (Ericameria nauseosa), a foundational shrub species of western North America. To quantify landscape genomic structure and provide perspective on patterns of local adaptation, we generated reduced representation sequencing data for 17 wild populations (222 individuals; 38,615 loci) spanning a range of environmental conditions. Population genetic analyses illustrated pronounced landscape genomic structure jointly shaped by geography and environment. Genetic-environment association (GEA) analyses using both redundancy analysis (RDA) and a machine-learning approach (Gradient Forest) indicated environmental variables (precipitation seasonality, slope, aspect, elevation, and annual precipitation) influenced spatial genomic structure, and were correlated with allele frequency shifts indicative of local adaptation at a consistent set of genomic regions. We compared our GEA based inference of local adaptation with phenotypic data collected by growing seeds from each population in a greenhouse common garden. Population differentiation in seed weight, emergence, and seedling traits was associated with environmental variables (e.g., precipitation seasonality) that were also implicated in GEA analyses, suggesting complementary conclusions about the drivers of local adaptation across different methods and data sources. Our results provide a baseline understanding of spatial genomic structure for E. nauseosa across the western Great Basin and illustrate the utility of GEA analyses for detecting the environmental causes and genetic signatures of local adaptation in a widely distributed plant species of restoration significance.

category: evolutionary biology


title: Effects of early and late life environments on ageing

abstract: Early and late life environments can interact in complex ways to influence the fitness of individuals. Most studies investigating effects of the environment on fitness focus on environments experienced and traits expressed at a single point in an organisms life. However, environments vary with time, thus the environments organisms experience at different ages may interact to affect how traits change throughout life. Here, we test whether thermal stress experienced during development leads individuals to cope better with thermal stress as adults. We manipulated temperature during both development and adulthood and measured a range of life-history traits, including senescence, in male and female seed beetles, Callosobruchus maculatus. We found that favourable developmental conditions increased reproductive performance of females (i.e. silver-spoon effects). In contrast, non-reproductive traits such as lifespan and survival senescence were only affected by adult environments- high adult temperatures decreased longevity and survival. Additionally, developmental and adult environments interacted to affect age-dependent changes in male weight. Overall, our results show that effects of early and late environments can be both sex- and trait- specific, and that a full understanding of how environments interact to affect fitness and ageing requires the integrated study of conditions experienced during different stages of ontogeny.


title: A Genomic Perspective on the Evolutionary Diversification of Turtles

abstract: To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.


title: Distinct and common features of numerical and structural chromosomal instability across different cancer types

abstract:
A large proportion of tumours is characterised by numerical or structural chromosomal instability (CIN), defined as an increased rate of gaining or losing whole chromosomes (W-CIN) or of accumulating structural aberrations (S-CIN). Both W-CIN and S-CIN are associated with tumourigenesis, cancer progression, treatment resistance and clinical outcome. Although W-CIN and S-CIN can co-occur, they are initiated by different molecular events. By analysing tumour genomic data from 33 cancer types, we show that the majority of tumours with high levels of W-CIN underwent whole genome doubling, whereas S-CIN levels are strongly associated with homologous recombination deficiency. Both CIN phenotypes are prognostic in several cancer types. Most drugs are less efficient in high-CIN cell lines, but we also report compounds and drugs which should be investigated as targets for W-CIN or S-CIN. By analysing associations between CIN and bio-molecular entities with pathway and gene expression levels, we complement gene signatures of CIN and report that the drug resistance gene CKS1B is strongly associated with S-CIN. Finally, we propose a potential copy number-dependent mechanism to activate the PI3K pathway in high-S-CIN tumours.

1. Simple summaryMany cancer cells are chromosomally unstable, a phenotype describing a tendency for accumulating chromosomal aberrations. Entire chromosomes tend to be gained or lost, which is called whole chromosome instability (W-CIN). Structural chromosomal instability (S-CIN) describes an increased rate of gaining, losing or translocating smaller parts of chromosomes. Here, we analyse data from 33 cancer types to find differences and commonalities between W-CIN and S-CIN. We find that W-CIN is strongly linked to whole genome doubling (WGD), whereas S-CIN is associated with a specific DNA damage repair pathway. Both W-CIN and S-CIN are difficult to target using currently available compounds and have distinct prognostic values. The activity of the drug resistance gene CKS1B is associated with S-CIN, which merits further investigation. In addition, we identify a potential copy number-based mechanism promoting signalling of the important PI3K cancer pathway in high-S-CIN tumours.

category: genetics


title: Sex differences in parental response to offspring begging are associated with pair bond strength across birds

abstract: Mothers, fathers, and offspring regularly clash over how much care offspring receive. Offspring beg to solicit for more resources--but how much begging is rewarded can depend on who is listening. While both parents benefit from provisioning offspring, each would benefit from their partner shouldering more of the burden of care, leading to sexual conflict. Additionally, if the costs and benefits of provisioning differ by sex, parent-offspring conflict should vary by sex. How these evolutionary conflicts influence sex differences in parent-offspring communication is unknown. To determine whether the sexes differ in their response to offspring signals, we conducted a meta-analysis on 30 bird species, comparing responsiveness to social and physiological traits affecting conflict. We found that a species typical pair bond strength predicts whether males or females respond more to offspring begging. In species with stable and/or monogamous bonds, and thus lower sexual and paternal-offspring conflict, males provisioning effort is more strongly correlated with offspring begging than females. The opposite holds for species with weak pair bonds: females respond more to begging, perhaps compensating for males lower responsiveness. These results demonstrate that sex differences in parental care can arise via sex differences in parent-offspring communication, driven by evolutionary conflicts.


title: Remarkable Adsorption Performance of Rutile TiO2 (110) Nanosheet for DNA Nucleobases: A First-Principles Study

abstract: The remarkable biocompatibility and supreme physical properties of nanostructured TiO2 have promised itself a strong future for biomedical applications. The present study reported a theoretical study on the adsorption of rutile TiO2 (110) nanosheet for DNA nucleobases using first-principles calculations. The calculations of the binding energy and work function demonstrate that the TiO2 nanosheet has remarkable adsorption strength to the DNA nucleobases, being more than 20 times larger than that of graphene and its derivatives. Further electronic band structure and density of state calculations elucidate the interaction mechanisms, which originate from dramatically reduced energy levels and strong hybridization of the 2p orbital of C, N and/or O with 3d orbital of Ti atoms near the Fermi level. The study directs a promising material at applications in DNA sensors and sequencers.


title: SURFMAP: a software for mapping in two dimensions protein surface features

abstract: Molecular cartography using two-dimensional (2D) representation of protein surfaces has been shown to be very promising for protein surface analysis. Here, we present SURFMAP, a free standalone and easy-to-use software that enables the fast and automated 2D projection of either predefined features of protein surface (i.e., electrostatic potential, Kyte-Doolittle hydrophobicity, stickiness, and surface relief) or any descriptor encoded in the temperature factor column of a PDB file. SURFMAP uses a pseudo-cylindrical sinusoidal "equal-area" projection that has the advantage of preserving the area measures. It provides the user with (i) 2D maps that enable the easy and visual analysis of protein surface features of interest and (ii) maps in a text file format allowing the fast and straightforward quantitative comparison of 2D maps of homologous proteins.


title: Diet and Domestication Drive Evolution of the Gut Holobiome

abstract: The host microbiome encompasses all microorganisms of a host. Host and microbiome coevolution in the gut result in differing microbial compositions, functionality, and host diet [1]. Host diet modulates what macromolecules are used for gut microbial metabolism, which can determine digestion, health, and behavior [2, 3]. Microbial composition across animals provides data on how microbiomes segregate between species and diets [4]. Here we show that microbiome data from GenBank can model host evolution, providing a "holobiome" insight to the important roles of diet and domestication. The main findings of this study in respect to microbial composition among species were: (1) herbivores are more similar than hosts with other diets; (2) domesticated species are more similar than wild relatives; and (3) humans are distinct from primates. Microbial composition between diets indicates a difference in functionality, where protein and fiber degradation are seen more in carnivores and herbivores respectively. Additionally, herbivores show the most microbial diversity among the diets. Finally, this analysis informs us of gaps in current microbiome data collection, which is biased toward pathogens. Thus, the host-microbiome relationship depicts a complex web of microbial functionality, composition, and diet that impact coevolution.


title: Attention please: modeling global and local context in glycan structure-function relationships

abstract: Glycans are found across the tree of life with remarkable structural diversity enabling critical contributions to diverse biological processes, ranging from facilitating host-pathogen interactions to regulating mitosis & DNA damage repair. While functional motifs within glycan structures are largely responsible for mediating interactions, the contexts in which the motifs are presented can drastically impact these interactions and their downstream effects. Here, we demonstrate the first deep learning method to represent both local and global context in the study of glycan structure-function relationships. Our method, glyBERT, encodes glycans with a branched biochemical language and employs an attention-based deep language model to learn biologically relevant glycan representations focused on the most important components within their global structures. Applying glyBERT to a variety of prediction tasks confirms the value of capturing rich context-dependent patterns in this attention-based model: the same monosaccharides and glycan motifs are represented differently in different contexts and thereby enable improved predictive performance relative to the previous state-of-the-art approaches. Furthermore, glyBERT supports generative exploration of context-dependent glycan structure-function space, moving from one glycan to "nearby" glycans so as to maintain or alter predicted functional properties. In a case study application to altering glycan immunogenicity, this generative process reveals the learned contextual determinants of immunogenicity while yielding both known and novel, realistic glycan structures with altered predicted immunogenicity. In summary, modeling the context dependence of glycan motifs is critical for investigating overall glycan functionality and can enable further exploration of glycan structure-function space to inform new hypotheses and synthetic efforts.


title: Determining salmon provenance with automated otolith reading

abstract:
Synthetic otolith marks are used at hundreds of hatcheries throughout the Pacific Rim to record the release location of salmon. Each year, human readers examine tens of thousands of otolith samples to identify the marks in salmon that are caught. The data inform dynamic management practices that maximize allowable catch while preserving populations, and guide hatchery investments. However, the method is limited by the time required to process otoliths, the inability to distinguish between wild and un-marked hatchery fish, and in some cases classification processes are limited by the subjective decisions of human readers. Automated otolith reading using computer vision has the potential to improve on all three of these limitations. Our work advances the field of automated otolith reading through a novel otolith classification algorithm that uses two neural networks trained with an adversarial algorithm to achieve 93% classification accuracy between four hatchery marks and unmarked otoliths. The algorithm relies on hemisection images of the otolith exclusively: no additional biological data are needed. Our work demonstrates a novel technique with modest training requirements that achieves unprecedented accuracy. The method can be easily adopted in existing otolith labs, scaled to accommodate additional marks, and does not require tracking additional information about the fish that the otolith was retrieved from.

Author summaryMany fish harvested in commercial fisheries have a bone-like structure in their inner ear called an otolith. Otoliths are useful because as they grow changes in the fishs environment create unique patterns that can be interpreted years later--similar to the way tree rings can be used to determine a trees age and rate of growth in different seasons. Hatcheries use this phenomenon to create unique patterns in the otoliths of fish they release that identify their origin. Trained otolith "readers" examine tens of thousands of otolith samples as part of commercial fishery management every year. The data help resource managers protect returns to wild streams and help hatcheries track the survival rates of their releases. However, human reading is time consuming, limited in the types of patterns that can be identified and can be subjective. Applying modern machine learning techniques to otolith reading has the potential to improve on all of these challenges. We developed a computational method that identifies hatchery marks in digital images of salmon otoliths without human input. In a test with otoliths containing one of four hatchery marks and unmarked otoliths, the method accurately classified 93% of otoliths. The method can be adopted in otolith labs and can be further improved by expanding the sample size used to train and test the method.


title: findPC: An R package to automatically select number of principal components in single-cell analysis

abstract:
SummaryPrincipal component analysis (PCA) is widely used in analyzing single-cell genomic data. Selecting the optimal number of PCs is a crucial step for downstream analyses. The elbow method is most commonly used for this task, but it requires one to visually inspect the elbow plot and manually choose the elbow point. To address this limitation, we developed six methods to automatically select the optimal number of PCs based on the elbow method. We evaluated the performance of these methods on real single-cell RNA-seq data from multiple human and mouse tissues. The perpendicular line method with 20 PCs has the best overall performance, and its results are highly consistent with the numbers of PCs identified manually. We implemented the six methods in an R package, findPC, that objectively selects the number of PCs and can be easily incorporated into any automatic analysis pipeline.

Availability and ImplementationfindPC R package is freely available at https://github.com/haotian-zhuang/findPC

Contactzhicheng.ji@duke.edu

Supplementary informationSupplementary data are available at Bioinformatics online.