title: Selective logging shows no impact on the dietary breadth of the fawn leaf-nosed bat (Hipposideros cervinus)

abstract: Logging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed bat Hipposideros cervinus across a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Blattodea, Diptera and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites regardless of the bioinformatic procedures used.


title: Evolution of gene expression across species and specialized zooids in Siphonophora

abstract:
BackgroundSiphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework.

ResultsWithin and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression.

ConclusionsOur findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

category: evolutionary biology


title: Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants

abstract: The spread of the SARS-CoV-2 variants could seriously dampen the global effort to tackle the COVID-19 pandemic. Recently, we investigated the humoral antibody responses of SARS-CoV-2 convalescent patients and vaccinees towards circulating variants, and identified a panel of monoclonal antibodies (mAbs) that could efficiently neutralize the B.1.351 (Beta) variant. Here we investigate how these mAbs target the B.1.351 spike protein using cryo-electron microscopy. In particular, we show that two superpotent mAbs, BD-812 and BD-836, have non-overlapping epitopes on the receptor-binding domain (RBD) of spike. Both block the interaction between RBD and the ACE2 receptor; and importantly, both remain fully efficacious towards the B.1.617.1 (Kappa) and B.1.617.2 (Delta) variants. The BD-812/BD-836 pair could thus serve as an ideal antibody cocktail against the SARS-CoV-2 VOCs.

category: biochemistry


title: Production of human milk fat substitute by engineered strains of Yarrowia lipolytica

abstract: Human milk fat has a distinctive stereoisomeric structure where palmitic acid is esterified to the middle (sn-2) position on the glycerol backbone of the triacylglycerol and unsaturated fatty acids to the outer (sn-1/3) positions. This configuration allows for more efficient nutrient absorption in the infant gut. However, the fat used in most infant formulas originates from plants, which tend only to esterify palmitic acid to the sn-1/3 positions. Oleaginous yeasts provide an alternative source of lipids for human nutrition. However, these yeasts also exclude palmitic acid from the sn-2 position of their triacylglycerol. Here we show that Yarrowia lipolytica can be engineered to produce triacylglycerol with more than 60% of the palmitic acid in the sn-2 position, by expression of a lysophosphatidic acid phosphatase with palmitoyl-Coenzyme A specificity, such as LPAAT2 from Chlamydomonas reinhardtii. The engineered Y. lipolytica strains can be cultured on glycerol, glucose, palm oil or a mixture of substrates, under nitrogen limited condition, to produce triacylglycerol with a fatty acid composition that resembles human milk fat, in terms of the major molecular species; palmitic, oleic and linoleic acids. Culture on palm oil or a mixture of glucose and palm oil produced the highest lipid titre in shake flask culture and a triacylglycerol composition that is most similar with human milk fat. Our data show that an oleaginous yeast can be engineered to produce a human milk fat substitute ({beta}-palmitate), that could potentially be used as an ingredient in infant formulas.

category: bioengineering


title: A new single-cell level R-index for EGFR-TKI resistance and survival prediction in LUAD

abstract: EGFR-TKIs achieved excellent efficacy in EGFR-mutated patients. Unfortunately, most patients would inevitably develop progressive disease within a median of 10 to 14 months. Predicting the resistance probability remains a challenge. Therefore, we created an R-index model trained by single-cell RNA data with the OCLR algorithm. This model can be applied to estimate the level of EGFR-TKI resistance in cell line and xenograft mice models and predict prognosis in multiple cohorts. Comparing the high and the low R-index group, we found that the glycolysis pathway and KRAS up-regulation pathway were related to resistance, and MDSC was the leading cause of immunosuppression in the tumor microenvironment. These results are consistent with previous studies indicating that the R-index provides an insight into resistance status and a new way to explore resistance mechanisms and clinical treatment by the combination of Glucose metabolism-targeted or MDSC-targeted therapies. This is the first quantification method of EGFR-TKI resistance based on single-cell sequencing data solving the problem of the mixed resistance state of tumor cells and helping explore transcriptome characteristics of drug-resistant cell populations.

category: bioinformatics


title: Hypertension drives microbial translocation and shifts in the fecal microbiome of non-human primates

abstract:
Accumulating evidence indicates a link between gut barrier dysfunction and hypertension. However, it is unclear whether hypertension dictates gut barrier dysfunction or vice versa and whether the gut microbiome plays a role. To better understand this relationship, first, we cross-sectionally examined hypertension and other cardio-metabolic risk factors and gut barrier function in a population of 150 nonhuman primates. Interestingly, the animals with hypertension showed evidence of gut barrier dysfunction (i.e., translocation of microbes through the gut wall), as indicated by higher plasma levels of lipopolysaccharide-binding protein (LBP)-1, compared to normotensive animals. Further, plasma LBP-1 levels were strongly correlated with diastolic blood pressure, independent of age and other health markers, suggesting specificity of the effect of hypertension on microbial translocation. In a subsequent longitudinal study (analysis at baseline, 12 and 27 months), hypertensive animals had higher plasma levels of LBP-1 at all the time points and greater bacterial gene expression in mesenteric lymph nodes compared to normotensive animals, confirming microbe translocation. Concomitantly, we identified distinct dysbiosis in the gut microbial signature of hypertensive versus normotensive animals at 12 and 27 months. These results suggest that hypertension drives microbial translocation in the gut and eventually unhealthy shifts in the gut microbiome, possibly contributing to poor health outcomes, providing further impetus for the management of hypertension.

Graphical Abstract

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category: pathology


title: Brain structure and function predict adherence to an exercise intervention in older adults

abstract: Individualized and precision medicine approaches to exercise for cognitive and brain health in aging have the potential to improve intervention efficacy. Predicting adherence to an exercise intervention in older adults prior to its commencement will allow for adaptive and optimized approaches that could save time (no need to demonstrate failure before changing course) and money (cost of de-implementing approaches that do not work for certain individuals) which ultimately could improve health outcomes (e.g., preventative medicine approaches prior to the onset of symptoms). Individual differences in brain structure and function in older adults are potential proxies of brain and brain reserve or maintenance and may provide strong predictions of adherence. We hypothesized that brain-based measures would predict adherence to a six-month randomized controlled trial of exercise in older adults, alone and in combination with psychosocial, cognitive and health measures. In 131 older adults (aged 65.79 {+/-} 4.65 years, 63% female) we found, using regularized elastic net regression within a nested cross-validation framework, that brain structure (cortical thickness and cortical surface area) in somatosensory, inferior temporal, and inferior frontal regions and functional connectivity (degree count) in primary information processing (somatosensory, visual), executive control, default, and attentional networks, predicted exercise adherence (R2 = 0.15, p < 0.001). Traditional survey and clinical measures such as gait and walking self-efficacy, biological sex and perceived stress also predicted adherence (R2 = 0.06, p = 0.001) but a combined multimodal model achieved the highest predictive strength (R2 = 0.22, p <0.001). Neuroimaging features alone can predict adherence to a structured group-based exercise intervention in older adults which suggests there is substantial utility of these measures for future research into precision medicine approaches. The best performing model contained multimodal features suggesting that each modality provided independent relevant information in the prediction of exercise adherence.

category: neuroscience


title: Evolution of molecular pathways of Tregs mediated Suppression

abstract: Treg-mediated suppression of conventional T cells is a fundamental step in regulating the adaptive immune response. It is known that Treg first appeared in vertebrates. However, little is known about the of major suppression pathways mediated by Tregs. We employed artificial intelligence text mining system to highlight the suppression pathways currently known to be utilized by Tregs. Our system identified various pathways mediated by CTLA4, calcium signaling, NfkB and NFAT. We simultaneously employed detailed phylogenetic analysis including multiple sequence alignment, phylogenetic tree building, ancestral sequence reconstruction, neutrality tests and positive selection test to investigate the evolution of Treg mediated pathways. We found that CTLA4 first appeared in vertebrates possibly arising from an IGV containing protein in cartilaginous fish. Conversely, we found that Tregs repurposed ancient pathways such as Calcineurin and CAMP Response Element Modulator. Interestingly, these two pathways were highly conserved between vertebrates and lower invertebrates indicating conservation of function. Taken together, our research indicate that Tregs developed its regulatory systems through evolution in vertebrates as well as reusing conserved ancient regulatory systems that are related to the innate immune system.


title: Phylogenetic analysis of molecular pathways in Tregs Suppressor Function


title: Changes in movement characteristics in response to private and social information acquisition of socially foraging fish

abstract: To overcome the cost of competition resulting from foraging in a group, individuals may balance their use of private (i.e., acquired from personal sampling) and social (i.e., acquired by watching other individuals) information to adjust their foraging strategy accordingly. Reliability of private information about environmental characteristics, such as the spatial distribution of prey, is thus likely to affect individual movement and social interactions during foraging. Our aim was to investigate how movement characteristics of foraging individuals changed as they acquired reliable private information about the spatial occurrence of prey in a foraging context. We allowed guppies (Poecilia reticulata) to develop the reliability of their private knowledge about prey spatial occurrence by repeatedly testing shoals in a foraging task under three experimental distributions of prey: 1) aggregated prey forming three patches located in fixed locations, 2) scattered distribution of prey with random locations, or 3) no prey (used as control). We then applied tracking methods to obtain individual time series of spatial coordinates from which we computed a suite of movement variables reflecting search effort, social proximity and locomotion characteristics during foraging, to examine changes occurring over repeated trials and to investigate which best explained foraging success. We show that foraging shoals became more efficient at finding and consuming food over the first three days by increasing their time spent active. Over time, individuals foraging on either scattered or aggregated prey travelled greater distances, showed an increasing distance to their closest neighbour and became slightly more stochastic in their acceleration profile, compared to control individuals. We found that behaviour changed as private information increased over time, with a clear behavioural shift occurring on the third testing day. Social proximity was the major predictor of foraging success in the absence of prior foraging information, while search effort became the most important predictors of foraging success as information increased. In conclusion, we show that individual movement patterns changed as they acquired private information. Contrary to our predictions, the spatial distribution of prey did not affect any of the movement variables of interest. Our results emphasise the importance of information in shaping movement behaviour in animals.

category: animal behavior and cognition


title: Nest relief in the cryptically-incubating semipalmated sandpiper is quick but vocal

abstract:
Biparental care requires coordination between parents. Such coordination might prove difficult if opportunities to communicate are scarce, which might have led to the evolution of elaborate and noisy nest relief rituals in species facing a low risk of predation. However, whether such conspicuous rituals also evolved in species that avoid predation by relying on crypsis remains unclear. Here, we used a continuous monitoring system to describe nest relief behavior during incubation in an Arctic-breeding shorebird with passive nest defense, the semipalmated sandpiper (Calidris pusilla). We then explored whether nest relief behavior provides information about parental cooperation and predicts incubation effort. We found that incubating parents vocalized twice as much before the arrival of their partner than during other times of incubation. In 75% of nest reliefs, the incubating parent left the nest only after its partner had returned and initiated the nest relief. In these cases, exchanges were quick (25s, median) and shortened over the incubation period by 0.1 - 1.4s per day (95%CI), suggesting that parents became more synchronized. However, nest reliefs were not cryptic. In 90% of exchanges, at least one parent vocalized, and in 20% of nest reliefs the incubating parent left the nest only after its returning partner called instantaneously. In 30% of cases, the returning parent initiated the nest relief with a call; in 39% of these cases, the incubating partner replied. If the partner replied, the next off-nest bout was 1 - 4hr (95%CI) longer than when the partner did not reply, which corresponds to an 8 - 45% increase. Our results indicate that incubating semipalmated sandpipers, which rely on crypsis to avoid nest predation, have quick but acoustically conspicuous nest reliefs. Our results also suggest that vocalizations during nest reliefs may be important for the division of parental duties.

LAY SUMMARYO_LIBiparental care requires coordination between parents. In species where both parents incubate and nests are visible, parents often perform complex nest relief rituals. Is this also the case in species where nests are cryptic?
C_LIO_LIWe video-recorded nest relief behavior at nests of cryptically incubating semipalmated sandpipers.
C_LIO_LIParents relieved each other quickly, but they vocalized frequently. In 20% of nest reliefs the incubating parent left only after its returning partner called instantaneously. In 30% of cases the returning parent initiated the nest relief with a call. If the partner replied, its next off-nest bout was 1 - 4hr longer than when the partner did not reply, which corresponds to an 8 - 45% increase.
C_LIO_LIOur results suggest that vocalizations during nest relief may be important for the division of parental duties. Further work in sandpipers and other taxa is needed to elucidate the role of parental vocalization in coordinating and synchronizing parental duties.
C_LI


title: The Effects of Posture on the Three-Dimensional Gait Mechanics of Human Walking in Comparison to Bipedal Chimpanzees

abstract:
Humans walk with an upright posture on extended limbs during stance and with a double-peaked vertical ground reaction force. Our closest living relatives, chimpanzees, are facultative bipeds that walk with a crouched posture on flexed, abducted hind limbs and with a single-peaked vertical ground reaction force. Differences in human and bipedal chimpanzee three-dimensional kinematics have been well quantified; however, it is unclear what the independent effects of using a crouched posture are on three-dimensional gait mechanics for humans, and how they compare with chimpanzees. Understanding the relationships between posture and gait mechanics, with known differences in morphology between species, can help researchers better interpret the effects of trait evolution on bipedal walking. We quantified pelvis and lower limb three-dimensional kinematics and ground reaction forces as humans adopted a series of upright and crouched postures and compared them with data from bipedal chimpanzee walking. Human crouched posture gait mechanics were more similar to bipedal chimpanzee gait than normal human walking, especially in sagittal plane hip and knee angles. However, there were persistent differences between species, as humans walked with less transverse plane pelvis rotation, less hip abduction, and greater peak horizontal ground reaction force in late stance than chimpanzees. Our results suggest that human crouched posture walking reproduces only a small subset of the characteristics of three-dimensional kinematics and ground reaction forces of chimpanzee walking, with the remaining differences likely due in large part to the distinct musculoskeletal morphologies of humans and chimpanzees.

Summary StatementDifferences between human crouched posture gait and bipedal chimpanzee gait illustrate the limitations of using modern day humans to infer the evolution of hominin bipedalism.


title: Injury risk functions for the four primary knee ligaments

abstract: The purpose of this study was to scan the available literature and use the obtained literature data to develop Injury Risk Functions (IRFs) for the Anterior- and Posterior Cruciate Ligament (ACL and PCL, respectively) and the Medial- and Lateral Collateral Ligament (MCL and LCL, respectively) in the knee joint. The IRFs were developed from Post-Mortem Human Subject (PMHS) tensile failure strains of Bone-Ligament-Bone (BLB) or dissected LIGament (LIG) preparations. Insufficient sample size of experimental datapoints required utilization of available literature data by statistically generating failure strains based on mean- and standard deviation from experiments that did not provide specimen-specific results. All virtual and specimen-specific values were then categorised into groups of static and dynamic rates and tested for the best fitting theoretical distribution to formulate the ligament IRF. Nine IRFs were derived (3 for ACL, 2 for PCL, 1 for MCL and 3 for LCL). These IRFs are, to the best of the authors knowledge, the first attempt at knee ligament injury predicting tools based on PMHS data. For future improvements of the knee ligament IRFs, upcoming experiments should have comparable testing and strain measuring methods, a clear definition of failure and a transparent reporting of each specimen specific result.


title: Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0

abstract: Glimma 1.0 introduced intuitive, point-and-click interactive graphics for differential gene expression analysis. Here, we present a major update to Glimma which brings improved inter-activity and reproducibility using high-level visualisation frame-works for R and JavaScript. Glimma 2.0 plots are now readily embeddable in R Markdown, thus allowing users to create reproducible reports containing interactive graphics. The revamped multidimensional scaling plot features dashboard-style controls allowing the user to dynamically change the colour, shape and size of sample points according to different experimental conditions. Interactivity was enhanced in the MA-style plot for comparing differences to average expression, which now supports selecting multiple genes, export options to PNG, SVG or CSV formats and includes a new volcano plot function. Feature-rich and user-friendly, Glimma makes exploring data for gene expression analysis more accessible and intuitive and is available on Bioconductor and GitHub.


title: Molecular docking and molecular dynamics simulation of the anticancer active ligand from Mimosa pudica to the Fibronectin Extra Domain A (EDA).

abstract: Mimosa pudica was observed to have many useful characters the main aim of the experiment is to strengthen the multiple potential value of M. Pudica L. To study its secondary metabolites antioxidant, anti-cancerous, GCMS and in-silico studies. In general, the methanol method is employed for obtaining leaf extracts. The preliminary phytochemical screening of the M. pudica leaf extract showed the presence of bioactive components such as terpenoids, flavonoids, glycosides, alkaloids, quinines, phenols, tannins, saponins, and coumarins. An attempt is made to check the anticancer activity towards the cancer cell line A549 (Lung cancer cells) by MTT assay. For the identification of the compounds and to obtain its structure the crude extract is analyzed by GC-MS technique. The result of the GC-MS is analyzed using bioinformatics tool for in-silico docking to find out its targets against lung cancer receptors and PDB ID is obtained from the RCBS PDB database. The affinity of the identified ligand molecules to bind to the active site of the protein was studied through docking. And the effectiveness of the ligand molecules was obtained through molecular dynamics for longer simulation. The RMSD, RMSF and RG interaction were studied to the screened compounds. Further, MMPBSA analysis was carried out for the selected and standard drug like irigenin compounds. These selected lead molecules shown the better binding energy compare to irigenin drug in MMPBSA. The lead derivatives have shown potential results against lung cancer cell lines.


title: From contigs to chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

abstract:
Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow many laboratories to sequence their species of interest. Although there is a promise to obtain "perfect genomes" with long read technologies, the number of contigs often exceeds the number of chromosomes significantly, containing many insertion and deletion errors around homopolymer tracks. To overcome these issues, we implemented ILRA to correct long reads-based assemblies, a pipeline that orders, names, merges, and circularizes contigs, filters erroneous small contigs and contamination, and corrects homopolymer errors with Illumina reads. We successfully tested our approach to assemble the genomes of four novel Plasmodium falciparum samples, and on existing assemblies of Trypanosoma brucei and Leptosphaeria spp. We found that correcting homopolymer tracks reduced the number of genes incorrectly annotated as pseudogenes, but an iterative correction seems to be needed to reduce high numbers of homopolymer errors. In summary, we described and compared the performance of a new tool, which improves the quality of long read assemblies. It can be used to correct genomes of a size of up to 300 Mb.

AvailabilityThe tool is available at GitHub: https://github.com/ThomasDOtto/ILRA.


title: Anaplerotic flux into the Calvin-Benson cycle. Integration in carbon and energy metabolism of Helianthus annuus

abstract:
Plants assimilate carbon primarily via the Calvin-Benson cycle. Two companion papers reports evidence for anaplerotic carbon flux into this cycle. To estimate flux rates in Helianthus annuus leaves based on gas exchange measurements, we here expanded Farquhar-von Caemmerer-Berry photosynthesis models by terms accounting for anaplerotic respiration and energy recycling. In line with reported isotope evidence (companion papers), we found relative increases in anaplerotic flux as intercellular CO2 concentrations, Ci, decrease below a change point. At Ci=136 and 202 ppm, we found absolute rates of 2.99 and 2.39 mol Ru5P m-2 s-1 corresponding to 58.3 and 28.2% of net CO2 assimilation, 13.1 and 10.7% of ribulose 1,5-bisphosphate regeneration, and 22.2 and 15.8% of Rubisco carboxylation (futile carbon cycling), respectively. Anaplerotic respiration governs total day respiration with contributions of 81.3 and 77.6%, and anaplerotic relative to photorespiratory CO2 release amounts to 63.9 and 67%, respectively. Furthermore, anaplerotic flux significantly increases absolute ATP demands and ATP-to-NADPH demand ratios of photosynthesis and may explain increasing sucrose-to-starch carbon partitioning ratios with decreasing Ci. We propose that anaplerotic flux can occur under both Rubisco and RuBP-limited growth conditions. Overall, our work introduces the anaplerotic pathway as central component in carbon and energy metabolism of C3 plants.

This manuscript has two companion papers: O_LIWieloch T, Grabner M, Augusti A, Serk H, Ehlers I, Yu J, Schleucher J. 2021. Metabolism is the major driver of hydrogen isotope fractionation recorded in tree-ring glucose of Pinus nigra. bioRxiv.
C_LIO_LIWieloch T, Augusti A, Schleucher J. 2021. Anaplerotic flux into the Calvin-Benson cycle. Isotope evidence for in vivo occurrence in Helianthus annuus. bioRxiv.
C_LI

category: biophysics


title: An age-depth model and revised stratigraphy of vertebrate-bearing units in Natural Trap Cave, Wyoming

abstract: Almost a half-century ago excavations at Natural Trap Cave (NTC) began to yield evidence of the steppe paleoecology along the western slope of the Bighorn Mountains in north central Wyoming. The first decade of fieldwork led to the discovery of a diverse fauna that existed at the end of the Last Glacial Maximum. Stratigraphic deposits below the entrance of the cave were studied soon after excavations began, but never formally published. Although stratigraphy, taphonomy, and depositional circumstances were briefly discussed over the following years, little has been done to correlate the numerous stratigraphic schemes used by various authors. In this study, four stratigraphic sections were measured and analysed to establish an easily modifiable lithostratigraphic system of nomenclature. We provide the first correlations of all stratigraphic nomenclature used throughout excavations at NTC to facilitate comparisons with current and previous collections and publications. By leveraging more than 100 radioisotopic dates we developed an age-depth model and chronostratigraphic framework to further interrogate spatiotemporal relationships between strata, paleoenvironmental proxies, and fossil assemblages. Deposition is shown to be discontinuous; sediment accumulation in the study area is restricted to the buildup through peak penultimate and Last Glacial maxima. More recent (<10 ka) Holocene deposits unconformably cover the eroded surface of underlying Pleistocene strata. There is active reworking of sediments with transport and deposition of reactivated sediments within the Lower Chamber. We note that the two hiatuses coincide with interglacial periods and may reflect changing depositional circumstances within the cave such as extended periods of non-deposition, erosion, or bypass (possibly leading to deposition in the Lower Chamber). Contrary to previous reports, we demonstrate that it is unlikely a prominent snow cone existed or contributed to the pattern of sediment and fossil distribution within the study area, furthermore, we do not observe a continuous Pleistocene-Holocene transition in the study area. Further stratigraphic work will be needed to better understand the interrelationship between Main and Lower chamber deposits and the evolution of sediment accumulation in NTC.

category: paleontology


title: Near-infrared spectroscopy calibration strategies to predict multiple nutritional parameters of pasture species from different functional groups

abstract: Near-infrared reflectance spectroscopy (NIRS) has been used by the agricultural industry as a high-precision technique to quantify nutritional chemistry in plants both rapidly and inexpensively. The aim of this study was to evaluate the performance of NIRS calibrations in predicting the nutritional composition of ten pasture species that underpin livestock industries in many countries. These species comprised a range of functional diversity (C3 legumes; C3/C4 grasses; annuals/perennials) and origins (tropical/temperate; introduced/native) that grew under varied environmental conditions (control and experimentally induced warming and drought) over a period of more than 2 years (n = 2,622). A maximal calibration set including 391 samples was used to develop and evaluate calibrations for all ten pasture species (global calibrations), as well as for subsets comprised of the plant functional groups. We found that the global calibrations were appropriate to predict the six key nutritional quality parameters studied for our pasture species, with the highest accuracy found for ash (ASH), crude protein (CP), neutral detergent fibre and acid detergent fibre (ADF), and the lowest for ether extract (EE) and acid detergent lignin parameters. The plant functional group calibrations for C3 grasses performed better than the global calibrations for ASH, CP, ADF and EE parameters, whereas for C3 legumes and C4 grasses the functional group calibrations performed less well than the global calibrations for all nutritional parameters of these groups. Additionally, our calibrations were able to capture the range of variation in forage quality caused by future climate scenarios of warming and severe drought.

category: plant biology


title: Spatiotemporal Dynamics of Stemphylium Leaf Blight and Potential Inoculum Sources in New York Onion Fields

abstract: Stemphylium leaf blight (SLB) caused by Stemphylium vesicarium is the dominant foliar disease affecting large-scale onion production in New York. The disease is managed by fungicides, but control failures are prevalent and recently attributed to fungicide resistance. Little is known of the relative role of inoculum sources in initiation and spread of SLB epidemics. The spatial and spatiotemporal dynamics of SLB epidemics in six onion fields were evaluated along linear transects in 2017 and 2018. Average SLB incidence increased from 0 to 100% throughout the cropping seasons with an average final lesion length of 28.3 cm. Disease progress was typical of a polycyclic epidemic and the logistic model provided the best fit to 83.3% of the datasets. Spatial patterns were better described by the beta-binomial than binomial distribution in half of the datasets and random patterns were more frequently observed by the index of dispersion. Geostatistical analyses of spatial pattern also found a low frequency of datasets with aggregation. Spatiotemporal analysis of epidemics detected that the aggregation was influenced by disease incidence. However, diseased units were not associated with the previous time period according to the spatiotemporal association function of SADIE. Variable spatial patterns suggested mixed inoculum sources dependent upon location, and likely an external inoculum source at the sampling scale used in this study. Plate testing of 28 commercially available organic onion seedlots from 2017 and 2018 did not detect S. vesicarium. This finding suggests that although S. vesicarium has been reported as seed transmitted, this is unlikely to be a significant inoculum source in commercially available organic seed lots and even less so in fungicide-treated seed used to establish conventional fields. A small-plot replicated trial was also conducted in each of two years to quantify the effect of S. vesicarium-infested onion residue on SLB epidemics in a field isolated from other onion fields. SLB incidence was significantly reduced in plots without residue compared to those in which residue remained on the soil surface. Burial of infested residue also significantly reduced epidemic progress in one year. The effect of infested onion residue on SLB epidemics in the subsequent onion crop suggests rotation or residue management may have a substantial effect on epidemics. However, the presence of an inoculum source external to fields in onion production regions as indicated by a lack of spatial aggregation may reduce the efficacy of in-field management techniques.


title: Scaffold modelling captures the structure-function-dynamics relationship in brain microcircuits

abstract: 1Modelling brain networks with complex configuration and cellular properties requires a set of neuroinformatic tools and an organized staged workflow. We have therefore developed the Brain Scaffold Builder (BSB), a new modeling framework embedding multiple strategies for cell placement and connectivity and a flexible management of cellular and network mechanisms. With BSB, for the first time, the mouse cerebellar cortex was reconstructed and simulated at cellular resolution, using morphologically realistic multi-compartmental single-neuron models. Embedded connection rules allowed BSB to generate the cerebellar connectome, unifying a collection of scattered experimental data into a coherent construct. Naturalistic background and sensory-burst stimulation were used for functional validation against recordings in vivo, monitoring the impact of subcellular mechanisms on signal propagation and spatio-temporal processing and providing a new ground-truth about circuit organization for the prediction of neural dynamics.


title: Sex-Dependent Effects of Chronic Microdrive Implantation on Acquisition of Trace Eyeblink Conditioning

abstract: Neuroscience techniques, including in vivo recording, have allowed for a great expansion in knowledge; however, this technology may also affect the very phenomena researchers set out to investigate. Including both female and male mice in our associative learning experiments shed light on sex differences on the impact of chronic implantation of tetrodes on learning. While previous research showed intact female mice acquired trace eyeblink conditioning faster than male and ovariectomized females, implantation of chronic microdrive arrays showed sexually dimorphic effects on learning. Microdrive implanted male mice acquired the associative learning paradigm faster than both intact and ovariectomized females. These effects were not due to the weight of the drive alone, as there were no significant sex-differences in learning of animals that received "dummy drive" implants without tetrodes lowered into the brain. Tandem mass tag mass spectrometry and western blot analysis suggest that significant alterations in the MAPK pathway, acute inflammation, and brain derived neurotrophic factor may underlie these observed sex- and surgery-dependent effects on learning.


title: A phenomenological model of neuroimmune interactions in epileptogenesis

abstract: Epilepsy can have many different causes and its development (epileptogenesis) involves a bewildering complexity of interacting processes. Here, we present a first-of-its-kind computational model to better understand the role of neuroimmune interactions in the development of acquired epilepsy. Our model describes the interactions between neuroinflammation, blood-brain barrier disruption, neuronal loss, circuit remodeling, and seizures. Formulated as a system of nonlinear differential equations, the model is validated using data from animal models that mimic human epileptogenesis caused by infection, status epilepticus, and blood-brain barrier disruption. The mathematical model successfully explains characteristic features of epileptogenesis such as its paradoxically long timescales (up to decades) despite short and transient injuries, or its dependence on the intensity of an injury. Furthermore, stochasticity in the model captures the variability of epileptogenesis outcomes in individuals exposed to identical injury. Notably, in line with the concept of degeneracy, our simulations reveal multiple routes towards epileptogenesis with neuronal loss as a sufficient but non-necessary component. We show that our framework allows for in silico predictions of therapeutic strategies, providing information on injury-specific therapeutic targets and optimal time windows for intervention.


title: Neuronal correlates of attentional selectivity and intensity in visual area V4 are invariant of motivational context

abstract: Flexibly switching attentional strategies is crucial for adaptive behavior in changing environments. Depending on the context, task demand employs different degrees of the two fundamental components of attention- attentional selectivity (preferentially attending to one location in visual space) and effort (the total non-selective intensity of attention). Neuronal responses in the visual cortex that show modulation with changes in either selective attention or effort are reported to partially represent motivational aspect of the task context. The relative contributions and interactions of these two components of attention to modulate neuronal signals and their sensitivity to distinct motivational drives are poorly understood. To address this question, we independently controlled monkeys spatially selective attention and non-selective attentional intensity in the same experimental session during a novel visual orientation change detection task. Attention was controlled either by adjusting the relative difficulty of the orientation changes at the two locations or by the reward associated with stimuli at two locations while simultaneously recording spikes from populations of neurons in area V4. We found that V4 neurons are robustly modulated by either selective attention or attentional intensity. Notably, as attentional selectivity for a neurons receptive field location decreased, its responses became weaker, despite an increase in the animals overall attentional intensity. This strong interaction between attentional selectivity and intensity could be identified in single trial spike trains. A simple divisive normalization of spatially distributed attention performances can explain the interaction between attention components well at the single neuron level. The effects of attentional selectivity and attentional intensity on neuronal responses were the same regardless of whether the changes were motivated by reward or task difficulty. These results provide a detailed cellular-level mechanism of how fundamental components of attention integrate and affect sensory processing in varying motivational and stimulus contexts.


title: Neural temporal context reinstatement of event structure during memory recall

abstract: Although life unfolds continuously, experiences are generally perceived and remembered as discrete events. Accumulating evidence suggests that event boundaries disrupt temporal representations and weaken memory associations. However, less is known about the consequences of event boundaries on temporal representations during retrieval, especially when temporal information is not tested explicitly. Using a neural measure of temporal context extracted from scalp electroencephalography, we found reduced temporal context similarity between studied items separated by an event boundary when compared to items from the same event. Further, while participants free recalled list items, neural activity reflected reinstatement of temporal context representations from study, including temporal disruption. A computational model of episodic memory, the Context Maintenance and Retrieval model (CMR; Polyn, Norman & Kahana, 2009), predicted these results, and made novel predictions regarding the influence of temporal disruption on recall order. These findings implicate the impact of event structure on memory organization via temporal representations.


title: Recombinant single-cycle influenza virus as a new tool to augment antitumour immunity with immune checkpoint inhibitors

abstract: Virus-based tumour vaccines offer many advantages compared to other antigen delivering systems. They generate concerted innate and adaptive immune response, and robust CD8+T cell responses. We engineered a non-replicating pseudotyped influenza virus (S-FLU) to deliver the well-known cancer testis antigen, NY-ESO-1 (S-NY-ESO-1 FLU). Intranasal or intramuscular immunization of NY-ESO-1 S-FLU virus in mice elicited a strong NY-ESO-1 specific CD8+T cell response in lungs and spleen that resulted in the regression of NY-ESO-1 expressing lung tumour and subcutaneous tumour respectively. Combined administration with anti PD-1 antibody, NY-ESO-1 S-FLU virus augmented the tumour protection by reducing the tumour metastasis. We propose that the antigen delivery through S-FLU is highly efficient in inducing antigen specific CD8+T cell response and protection against tumour development in combination with PD-1 blockade.

category: immunology


title: Transcriptomic analysis of ribosome biogenesis and pre-rRNA processing during growth stress in Entamoeba histolytica

abstract: Ribosome biogenesis, a multi-step process involving the transcription, modification, folding and processing of rRNA is the major consumer of cellular energy. It involves the sequential assembly of ribosomal proteins (RP)s via more than 200 ribogenesis factors. Unlike model organisms where transcription of rRNA and RP genes slows down during stress, in Entamoeba histolytica, pre-rRNA synthesis continues, and unprocessed pre-rRNA accumulates. To gain insight into the vast repertoire of ribosome biogenesis factors and understand the major components playing role during stress we computationally identified the ribosome biogenesis factors in E. histolytica. Of the total [~]279 S. cerevisiae proteins, we could only find 188 proteins in E. histolytica. Some of the proteins missing in E. histolytica were also missing in humans. A number of proteins represented by multiple genes in S. cerevisiae had only a single copy in E. histolytica. It was interesting to note that E. histolytica lacked mitochondrial ribosome biogenesis factors and had far less RNase components as compared to S. cerevisiae. Northern hybridization using probes from different spacer regions depicted the accumulation of unprocessed intermediates during stress. Transcriptomic studies revealed the differential regulation of a number of ribosomal factors both in serum-starved and RRP6KD conditions. The ARB1 protein involved at multiple steps of ribosome biogenesis and NEP1 and TSR3 involved in chemical modification of 18S rRNA previously shown to accumulate pre-rRNA precursors upon downregulation in S. cerevisiae and humans were included. The data reveals the importance of some of the major factors required for regulating pre-rRNA processing during stress. This is the first report on the complete repertoire of ribosome biogenesis factors in E. histolytica.

category: microbiology


title: Repurposing brewery contaminant yeast as production strains for low-alcohol beer fermentation

abstract:
A number of fungal isolates were recently obtained from a survey of the microbiota of multiple breweries and brewery products. Here, we sought to explore whether any of these brewery contaminants could be repurposed for beneficial use in beer fermentations, with particular focus on low-alcohol beer. 56 yeast strains were first screened for the utilization of different carbon sources, ability to ferment brewers wort, and formation of desirable aroma compounds. A number of strains appeared maltose-negative and produced desirable aromas without obvious off-flavours. These were selected for further scaled-up wort fermentations. The selected strains efficiently reduced wort aldehydes during fermentation, thus eliminating undesirable wort-like off-flavours, and produced a diverse volatile aroma profile. Sensory analysis of the beer samples using projective mapping identified two strains, Trigonopsis cantarellii and Candida sojae, that produced beers similar to a commercial reference lager beer. 30 L-scale wort fermentations were performed with these two strains together with a commercial Saccharomycodes ludwigii reference strain. Both strains performed comparably to the commercial reference, and the T. cantarellii strain in particular, produced low amounts of off-flavours and a significantly higher amount of the desirable monoterpene alcohol trans-geraniol. The strain was also sensitive to common food preservatives and antifungal compounds, and unable to grow at 37 {degrees}C, suggesting it is relatively easily controllable in the brewery, and appears to have low risk of pathogenicity. This study shows how the natural brewery microbiota can be exploited as a source of non-conventional yeasts for low-alcohol beer production.

Take Away- Fungal isolates from brewery microbiota were screened for beer production
- Numerous maltose-negative strains were tested for low-alcohol beer fermentation
- Trigonopsis cantarellii showed promise compared to a commercial reference strain
- T. cantarellii produced no off-flavours and higher levels of trans-geraniol


title: EP300 (p300) mediated histone butyrylation is critical for adipogenesis

abstract:
The master epigenetic enzyme EP300 (p300) besides having lysine acetyltransferase activity can also catalyse other acylation modifications (propionylation, butyrylation, crotonylation etc.), the physiological implications of which are yet to be established. Here we report that lysine butyrylation concomittantly increases during adipogenesis, along with increased butyryl CoA levels due to upregulated fatty acid metabolic pathways. To delineate the role of p300 catalysed butyrylation in adipogenesis, we have identified a semi-synthetic derivative (LTK-14A) of garcinol which specifically inhibited histone butyrylation without affecting acetylation. Treatment of 3T3L1 cells with LTK-14A significantly abolished adipogenesis by downregulation of genes related to adipogenesis presumably through the inhibition of H4K5 butyrylation. Administering the specific inhibitor to high fat diet fed C57BL6/J mice as well as genetically obese db/db mice led to an attenuation/decrease in their weight gain respectively. The reduced obesity could be at least partially attributed to the targeted inhibition of H4K5 butyrylation, as observed by immunofluorescence staining of the inhibitor treated mice liver sections and immunoblotting with histones extracted from epididymal fat pads. This report therefore not only for the first time causally links histone butyrylation with adipogenesis but also presents a novel small molecule modulator that could be developed for anti-obesity therapeutics.

Significance StatementIn the modern era, obesity has become a highly prevalent disorder, characterized by adipose tissue hypertrophy. Excessive caloric intake with minimal energy expenditure leads to accumulation of lipids in the adipose tissue. Like in many other processes, adipogenesis is epigenetically regulated. Besides acetyltransferase activity,the epigenetic enzyme p300 also possesses acyltransferase activity such as butyrylation.Our findings not only demonsrate the physiological role of p300 catalysed butyrylation in adipogenesis but also report a selective inhibitor of butyrylation which could have high therapeutic potential.

category: molecular biology


title: The pace of modern life, revisited

abstract: Wild populations must continuously adapt to environmental changes or they risk extinction. Such adaptations can be measured as phenotypic rates of change and can allow us to predict patterns of contemporary evolutionary change. About two decades ago, a dataset of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this dataset to look at microevolutionary processes in relation to specific types of human disturbances. Here, we have updated the dataset adding 5675 estimates of phenotypic changes and used it to revisit established patterns of contemporary evolutionary change. Using this newer version, containing 7338 estimates of phenotypic changes, we revisit the conclusions of four published articles. We then synthesize the expanded dataset to compare rates of change across different types of human disturbance. Analyses of this expanded dataset suggests that: I. a small absolute difference in rates of change exists between human disturbed and natural populations, II. harvesting by humans results in larger rates of change than other types of disturbances, III. introduced populations have increased rates of change, and IV. body size does not increase through time. Overall, findings from earlier analyses have largely held-up in analyses of our new dataset that encompass a much larger breadth of species, traits, and human disturbances. Lastly, we found that types of human disturbances affect rates of phenotypic change, and we call for this database to serve as a steppingstone for further analyses to understand patterns of contemporary evolution.


title: In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations

abstract: RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal L11 C-terminal domain was selected from a [~]1010 library of partially randomized sequences, all composed of 10 prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with MD simulations uncover qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant L11 domain uses bridging ion (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues was compensated by acidic residues plus metal ions.


title: ALLSorts: a RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia.

abstract:
B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Subtypes within B-ALL are distinguished by characteristic structural variants and mutations, which in some instances strongly correlate with responses to treatment. The World Health Organisation (WHO) recognises seven distinct classifications, or subtypes, as of 2016. However, recent studies have demonstrated that B-ALL can be segmented into 23 subtypes based on a combination of genomic features and gene expression profiles. A method to identify a patients subtype would have clear clinical utility. Despite this, no publically available classification methods using RNA-Seq exist for this purpose.

Here we present ALLSorts: a publicly available method that uses RNA-Seq data to classify B-ALL samples to 18 known subtypes and five meta-subtypes. ALLSorts is the result of a hierarchical supervised machine learning algorithm applied to a training set of 1223 B-ALL samples aggregated from multiple cohorts. Validation revealed that ALLSorts can accurately attribute samples to subtypes and can attribute multiple subtypes to a sample. Furthermore, when applied to both paediatric and adult cohorts, ALLSorts was able to classify previously undefined samples into subtypes.

ALLSorts is available and documented on GitHub (https://github.com/Oshlack/AllSorts/).

Key PointsO_LIALLSorts is a gene expression classifier for B-cell acute lymphoblastic leukemia, which predicts 18 distinct genomic subtypes - including those designated by the World Health Organisation (WHO) and provisional entities.
C_LIO_LITrained and validated on over 2300 B-ALL samples, representing each subtype and a variety of clinical features.
C_LIO_LICorrectly identified subtypes in 91% of cases in a held-out dataset and between 82-93% across a newly combined cohort of paediatric and adult samples.
C_LIO_LIALLSorts assigned subtypes to samples with previously unknown driver events.
C_LI

ALLsorts is an accurate, comprehensive and freely available classification tool that distinguishes subtypes of B-cell acute lymphoblastic leukemia from RNA-sequencing.


title: Studying magnetic susceptibility, microstructural compartmentalisation and chemical exchange in a formalin-fixed ex vivo human brain specimen

abstract:
PurposeEx vivo imaging is a preferable method to study the biophysical mechanism of white matter orientation-dependent signal phase evolution. Yet, how formalin fixation, commonly used for tissue preservation, affects the phase measurement is not fully known. We, therefore, study the impacts of formalin fixation on magnetic susceptibility, microstructural compartmentalisation and chemical exchange measurement on human brain tissue.

MethodsA formalin-fixed, post-mortem human brain specimen was scanned with multiple orientations with respect to the main magnetic field direction for robust bulk magnetic susceptibility measurement with conventional quantitative susceptibility imaging models. Homogeneous white matter tissues were subsequently excised from the whole-brain specimen and scanned in multiple rotations on an MRI scanner to measure the anisotropic magnetic susceptibility and microstructure-related contributions in the signal phase. Electron microscopy was used to validate the MRI findings.

ResultsThe bulk isotropic magnetic susceptibility of ex vivo whole-brain imaging is comparable to in vivo imaging, with noticeable enhanced non-susceptibility contributions. The excised specimen experiment reveals that anisotropic magnetic susceptibility and compartmentalisation phase effect were considerably reduced in formalin-fixed white matter tissue.

ConclusionsDespite formalin-fixed white matter tissue has comparable bulk isotropic magnetic susceptibility to those measured via in vivo imaging, its orientation-dependent components in the signal phase related to the tissue microstructure is substantially weaker, making it less favourable in white matter microstructure studies using phase imaging.


title: Directional sensitivity of the cerebral pressure-flow relationship in middle and posterior cerebral arteries using the repeated squat-stand model: within-day reproducibility and impact of diurnal variation in young healthy men and women

abstract: We recently employed repeated squat-stands (RSS) to quantify directional sensitivity of the cerebral-pressure flow relationship (i.e. hysteresis) using a novel metric. Within-day reproducibility and diurnal variation impacts of this metric are unknown. We evaluated this metric for: 1) within-day reproducibility and the extent diurnal variation has in middle (MCA; {Delta}MCAvT/{Delta}MAPT) and posterior cerebral arteries (PCA; {Delta}PCAvT/{Delta}MAPT); 2) sex differences. Absolute ({Delta}MCAvT/{Delta}MAPT ; {Delta}PCAvT/{Delta}MAPT) and relative (%MCAvT/%MAPT, %PCAvT/%MAPT) metrics were calculated at seven time-points (08:00-17:00) in 18 participants (8 women; 24 {+/-} 3 yrs) using the minimum-to-maximum MCAv/PCAv and MAP for each RSS at 0.05 Hz and 0.10 Hz. Reproducibility was evaluated with intraclass correlation coefficient (ICC). For all metrics, reproducibility was good (0.75-0.90) to excellent (>0.90). The metric in both arteries was impacted by MAP direction at 0.10 Hz (all p < 0.024). Time-of-day influenced {Delta}MCAvT/{Delta}MAPT (0.05 Hz: p = 0.0028; 0.10 Hz: p = 0.0009), %MCAvT/%MAPT (0.05 Hz: p = 0.035; 0.10 Hz: p = 0.0087), and {Delta}PCAvT/{Delta}MAPT (0.05 Hz: p = 0.0236). Sex differences in the MCA (p = 0.0028) vanished in relative terms and was absent in the PCA. These findings demonstrate within-day reproducibility of this metric in both arteries. Moreover, hysteresis is not impacted by sex.

category: physiology


title: Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

abstract: Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation, and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe small RNAs, pseudogenes, and transposable elements, and highlight tissue specific expression and methylation patterns. Resequencing of forty wild accessions provides insights into genome-wide genetic variation as well as QTL regions for flowering time and a seedling color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.


title: A robust method of extraction and GC-MS analysis of Monophenols exhibited UV-B mediated accumulation in Arabidopsis

abstract: Studies on specialised metabolites like phenolics are of immense interest owing to their significance to agriculture, nutrition and health. In plants, phenolics accumulate and exhibits spatial and temporal regulations in response to growth conditions. Robust methodologies aimed at efficient extraction of plant phenolics, their qualitative and quantitative analysis is desired. We optimised the analytical and experimental bottlenecks that captured free, ester, glycoside and wall-bound phenolics after acid or alkali treatments of the tissue extracts and subsequent GC-MS analysis. Higher recovery of phenolics from the methanolic extracts was achieved by through a) Ultrasonication assisted extraction along with Methyl tert-butyl ether (MTBE) enrichment b) nitrogen gas drying and c) their derivatisation using MSTFA for GC-MS analysis. The optimised protocol was tested on Arabidopsis rosette exposed to UV-B radiation (280-315 nm) which triggered enhanced levels of 11 monophenols and might be attributed to photoprotection and other physiological roles. Interestingly, coumaric acid (308 m/z) and caffeic acid (396 m/z) levels were enhanced by 12-14 folds under UV-B. Other phenolics such as cinnamic acid (220 m/z), hydroxybenzoic acid (282 m/z), vanillic acid (312 m/z, gallic acid (458 m/z), ferulic acid (338 m/z), benzoic acid (194 m/z), hydroxycinnamic acid (368 m/z) and protocatechuic acid (370 m/z) also showed elevated levels by about 1 to 4 folds. Notably, vanillin (253 m/z) was detected only in the UV-B exposed tissues. The protocol also comprehensively captured the variations in the levels of ester, glycoside and wall-bounded phenolics with high reproducibility and sensitivity. The robust method of extraction and GC-MS analysis can readily be adopted for studying phenolics in plant systems.


title: Data Storage Based on Combinatorial Synthesis of DNA Shortmers

abstract:
Storage needs represent a significant burden on the economy and the environment. Some of this can potentially be offset by improved density molecular storage. The potential of using DNA for storing data is immense. DNA can be harnessed as a high density, durable archiving medium for compressing and storing the exponentially growing quantities of digital data that mankind generates. Several studies have demonstrated the potential of DNA-based data storage systems. These include exploration of different encoding and error correction schemes and the use of different technologies for DNA synthesis and sequencing. Recently, the use of composite DNA letters has been demonstrated to leverage the inherent redundancy in DNA based storage systems to achieve higher logical density, offering a more cost-effective approach. However, the suggested composite DNA approach is still limited due to its sensitivity to the stochastic nature of the process. Combinatorial assembly methods were also suggested to encode information on DNA in high density, while avoding the challenges of the stochastic system. These are based on enzynatic assembly processes for producing the synthetic DNA.

In this paper, we propose a novel method to encode information into DNA molecules using combinatorial encoding and shortmer DNA synthesis, in compatibility with current chemical DNA synthesis technologies. Our approach is based on a set of easily distinguishable DNA shortmers serving as building blocks and allowing for near-zero error rates. We construct an extended combinatorial alphabet in which every letter is a subset of the set of building blocks. We suggest different combinatorial encoding schemes and explore their theoretical properties and practical implications in terms of error probabilities and required sequencing depth. To demonstrate the feasibility of our approach, we implemented an end-to-end computer simulation of a DNA-based storage system, using our suggested combinatorial encodings. We use simulations to assess the performance of the system and the effect of different parameters.

Our simulations suggest that our combinatorial approach can potentially achieve up to 6.5-fold increase in the logical density over standard DNA based storage systems, with near zero reconstruction error.

Implementing our approach at scale to perform actual synthesis, requires minimal alterations to current technologies. Our work thus suggests that the combination of combinatorial encoding with standard DNA chemical synthesis technologies can potentially improve current solutions, achieving scalable, efficient and cost-effective DNA-based storage.

category: synthetic biology


title: Selective ablation of adult GFAP-expressing tanycytes leads to hypogonadotropic hypogonadism in males

abstract:
In adult mammals, neural stem cells emerge in three neurogenic regions, the subventricular zone of the lateral ventricle (SVZ), the subgranular zone of the dentate gyrus of the hippocampus (SGZ) and the hypothalamus. In the SVZ and the SGZ, neural stem/progenitor cells (NSPCs) express the glial fibrillary acidic protein (GFAP) and selective ablation of these NSPCs drastically decreases cell proliferation in vitro and in vivo. In the hypothalamus, GFAP is expressed by -tanycytes, which are specialized radial glia-like cells in the wall of the third ventricle. To explore the role of these hypothalamic GFAP-positive tanycytes, we used transgenic mice expressing herpes simplex virus thymidine kinase (HSV-Tk) under the control of the mouse Gfap promoter and 4-week intracerebroventricular infusion of the antiviral agent ganciclovir (GCV) that kills dividing cells expressing Tk. While GCV drastically reduced the number and growth of hypothalamus-derived neurospheres from adult transgenic mice in vitro, it caused hypogonadism in vivo. The selective death of dividing tanycytes expressing GFAP indeed caused a marked decrease in testosterone levels and testicular weight, as well as vacuolization of the seminiferous tubules and loss of spermatogenesis. In addition, GCV-treated GFAP-Tk mice showed impaired sexual behavior, but no alteration in food intake or body weight. Our results also show that the selective ablation of GFAP-expressing tanycytes leads to a sharp decrease in the number of gonadotropin-releasing hormone (GnRH)-immunoreactive neurons and blunted LH secretion. Altogether, our data show that GFAP-expressing tanycytes play a central role in the regulation of male reproductive function.

Main pointsKilling adult hypothalamic GFAP-expressing cells blunts neurosphere formation in vitro and leads to GnRH deficiency and hypogonadism in vivo. This work pinpoints an unreported role of dividing GFAP-expressing tanycytes in reproductive function.


title: STAT3 expression in dendritic cells protects mice from colitis by a gut microbiome-dependent mechanism

abstract: An imbalance in gut homeostasis results in local and systemic pathogenesis. It is still not well-understood how the immune system interacts with the gut microbiome and maintains a delicate balance. Here, we utilized a mouse model in which STAT3 expression is deleted in CD11c+ (i.e., dendritic) cells (STAT3 cKO); these mice developed an ulcerative colitis-like disease, colon carcinoma and myelodysplastic syndrome-like disease. Circulating IgE levels in STAT3 cKO mice were significantly elevated. The gut microbiome was indispensable for the observed pathogenesis, as treatment with broad-spectrum antibiotics or cross-fostering STAT3 cKO pups with mothers harboring a different microbiome prevented disease development. Gut microbiome analyses suggested that decreased commensal bacteria and increased pathogenic bacteria most likely contributed to disease. Our data suggest that STAT3 controls the manifestation of inflammation in the gut caused by the microbiome. Therefore, we conclude that a deficiency of STAT3 in DCs is sufficient to trigger uncontrolled inflammation and the development of inflammatory bowel disease.


title: Deep learning-enhanced morphological profiling predicts cell fate dynamics in real-time in hPSCs

abstract: Predicting how stem cells become patterned and differentiated into target tissues is key for optimising human tissue design. Here, we established DEEP-MAP - for deep learning-enhanced morphological profiling - an approach that integrates single-cell, multi-day, multi-colour microscopy phenomics with deep learning and allows to robustly map and predict cell fate dynamics in real-time without a need for cell state-specific reporters. Using human pluripotent stem cells (hPSCs) engineered to co-express the histone H2B and two-colour FUCCI cell cycle reporters, we used DEEP-MAP to capture hundreds of morphological- and proliferation-associated features for hundreds of thousands of cells and used this information to map and predict spatiotemporally single-cell fate dynamics across germ layer cell fates. We show that DEEP-MAP predicts fate changes as early or earlier than transcription factor-based fate reporters, reveals the timing and existence of intermediate cell fates invisible to fixed-cell technologies, and identifies proliferative properties predictive of cell fate transitions. DEEP-MAP provides a versatile, universal strategy to map tissue evolution and organisation across many developmental and tissue engineering contexts.

category: cell biology


title: Interactive effects of microplastic pollution and heat stress on reef-building corals

abstract:
Plastic pollution is an emerging stressor that increases pressure on ecosystems such as coral reefs that are already challenged by climate change. However, the effect of plastic pollution in combination with global warming is largely unknown. Thus, the goal of this study was to determine the cumulative effect of microplastic pollution with that of global warming on reef-building coral species and to compare the severity of both stressors. For this, we conducted a series of three controlled laboratory experiments and exposed a broad range of coral species (Acropora muricata, Montipora digitata, Porites lutea, Pocillopora verrucosa, and Stylophora pistillata) to microplastic particles in a range of concentrations (2.5-2,500 particles L-1) and mixtures (from different industrial sectors) at ambient temperatures and in combination with heat stress. We show that microplastic can occasionally have a negative effect on the corals thermal tolerance. In comparison to heat stress, however, microplastic constitutes a minor stressor. While heat stress led to decreased photosynthetic efficiency of algal symbionts, and increased bleaching, tissue necrosis, and mortality, treatment with microplastic particles had only minor effects on the physiology and health of the tested coral species at ambient temperatures. These findings underline that while efforts to reduce plastic pollution should continue, they should not replace more urgent efforts to halt global warming, which are immediately needed to preserve remaining coral reef ecosystems.

Graphical Abstract

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category: ecology


title: How do King Cobras move across a major highway? Unintentional wildlife crossing structures may facilitate movement.

abstract:
O_LIGlobal road networks continue to expand, and the wildlife responses to these landscape-level changes need to be understood to advise long-term management decisions. Roads have high mortality risk to snakes because snakes typically move slowly and can be intentionally targeted by drivers.
C_LIO_LIWe investigated how radio-tracked King Cobras (Ophiophagus hannah) traverse a major highway in northeast Thailand, and if reproductive cycles were associated with road hazards.
C_LIO_LIWe surveyed a 15.3km stretch of Highway 304 to determine if there were any locations where snakes, and other wildlife, could safely move across the road (e.g., culverts, bridges). We used recurse analysis to detect possible road-crossing events, and used subsets of King Cobra movement data to create dynamic Brownian Bridge Movement Models (dBBMM) in an attempt to show movement pathways association with possible unintentional crossing structures. We further used Integrated Step Selection Functions (ISSF) to assess seasonal differences in avoidance of major roads for adult King Cobras in relation to reproductive state.
C_LIO_LIWe discovered 32 unintentional wildlife crossing locations capable of facilitating King Cobra movement across the highway. Our dBBMMs failed to show if underpasses were being used by telemetered individuals; however, the tracking locations pre- and post-crossing provided strong evidence of underpass use. Our ISSF suggested a lower avoidance of roads during the breeding season, though the results were inconclusive. With the high volume of traffic, large size of King Cobras and a 98.8% success rate of crossing the road in our study, we strongly suspect that individuals are using the unintentional crossing structures to safely traverse the road.
C_LIO_LIFurther research is needed to determine the extent of wildlife underpass use at our study site and globally, alongside using previously proven fencing to facilitate their use. We propose that more consistent integration of drainage culverts and bridges could help mitigate the impacts of roads on some terrestrial wildlife, particularly in areas where roads fragment forests and wildlife corridors.
C_LI


title: Plant-associated microbiomes promote nutrient turnover in impoverished substrates of a biodiversity hotspot

abstract: The substrates of the Brazilian campos rupestres have extremely low concentrations of key nutrients, mainly phosphorus, imposing severe restrictions to plant growth. Regardless, this ecosystem harbors enormous biodiversity which raises the question of how nutrients are cycled and acquired by the biosphere. To uncover the nutrient turnover potential of plant-associated microorganisms in the campos rupestres, we investigated the compositions and functions of microbiomes associated with two species of the Velloziaceae family that grow over distinct substrates (soil and rock). Amplicon, metagenomic, and metagenome-assembled genome sequence data showed that the campos rupestres harbor a novel assemblage of plant-associated prokaryotes and fungi. Compositional analysis revealed that the plant-associated soil and rock communities differed in taxonomic structure but shared a core of highly efficient colonizers that were strongly coupled with nutrient mobilization. Investigation of functional and abundance data revealed that the plant hosts actively recruit communities by exuding organic compounds and that the root-associated microbiomes possess a diverse repertoire of phosphorus turnover mechanisms. We also showed that the microbiomes of both plant species encompass novel populations capable of mobilizing nitrogen and that the substrate strongly influences the dynamics of this cycle. Our results show that the interplay between plants and their microbiomes shapes nutrient turnover in the campos rupestres. We highlight that investigation of microbial diversity is fundamental to understand plant fitness in stressful environments.

category: genomics


title: Source tracking and global distribution of the mobilized tigecycline resistant gene tet(X)

abstract: The emergence of tet(X) genes has compromised the clinical use of the last-line antibiotic tigecycline. We identified 322 (1.21%) tet(X) positive samples from 12,829 human microbiome samples distributed in four continents (Asia, Europe, North America and South America) using retrospective data from worldwide. These tet(X) genes were dominated by tet(X2)-like orthologs but we also identified 12 samples carrying novel tet(X) genes, designed tet(X15) and tet(X16), that were resistant to tigecycline. The metagenomic analysis revealed these tet(X) genes distributed in anaerobes dominated by Bacteroidaceae (78.89%) of human-gut origin. The transmission of these tet(X2)-like orthologs between Bacteroidaceae and Riemerella anatipestifer was primarily promoted by the mobile elements ISBf11 and IS4351. tet(X2)-like orthologs was also developed during transmission by mutation to high-level tigecycline resistant determinants tet(X15) and tet(X16). Further tracing these tet(X) in single bacterial isolate from public repository indicated that tet(X) genes were present as early as 1960s in R. anatipestifer that was the primary tet(X) carrier at early stage (before 2000). The tet(X2) and non-tet(X2) orthologs were primarily distributed in humans and food animals respectively, and non-tet(X2) were dominated by tet(X3) and tet(X4). Genomic comparison indicated these tet(X) genes were likely to be generated during tet(X) transmission between Flavobacteriaceae and E. coli/Acinetobacter spp.., and ISCR2 played a key role in the transmission. These results suggest R. anatipestifer was the potential ancestral source of tet(X) gene. Additionally, Bacteroidaceae of human-gut origin was an important hidden reservoir and mutational incubator for the mobile tet(X) genes that enabled spread to facultative anaerobes and aerobes.


title: Epigenetic reprogramming of DCCs into dormancy suppresses metastasis via restored TGFβ-SMAD4 signaling.

abstract: Disseminated cancer cells (DCCs) identified in secondary organs, sometimes before the primary tumor becomes detectable and treated, can remain dormant for years to decades before manifesting. Microenvironmental and epigenetic mechanisms may control the onset and escape from dormancy, and here we reveal how a combination of the DNA methylation inhibitor 5-azacytidine (AZA) and retinoic acid receptor ligands all-trans retinoic acid (atRA), orchestrate a novel program of stable dormancy. Treatment of HNSCC tumor cells with AZA+atRA induced a SMAD2/3/4 dependent regulation of downstream transcriptional program that restored the anti-proliferative function of TGF{beta} signaling. Significantly, AZA+atRA or AZA+AM80, an RAR specific agonist, strongly suppresses lung metastasis formation. The metastatic suppression occurs via the induction and maintenance of phenotypically homogenous dormant SMAD4+/NR2F1+ non-proliferative DCCs. These findings suggest that strategies that maintain or induce dormancy programs may be a viable alternative strategy to improve patient outcomes by preventing or significantly delaying metastasis development.

category: cancer biology


title: Downregulation of Neurodevelopmental Gene Expression in iPSC-Derived Cerebral Organoids Upon Infection by Human Cytomegalovirus

abstract: Human cytomegalovirus (HCMV) is a beta herpesvirus that, upon congenital infection, can cause severe birth defects including vision and hearing loss, microcephaly, and seizures. Currently, no approved treatment options exist for in utero infections. We previously demonstrated that HCMV infection decreases calcium signaling responses and alters neuronal differentiation in induced pluripotent stem cell (iPSC) derived neural progenitor cells (NPCs). Here we aimed to determine the impact of infection on the transcriptome in developing human neurons using iPSC-derived 3-dimensional cerebral organoids. We infected iPSC-derived cerebral organoids with HCMV encoding eGFP and sorted cell populations based on GFP signal strength. Significant transcriptional downregulation was observed including in key neurodevelopmental gene pathways in both the GFP (+) and intermediate groups. Interestingly, the GFP (-) group also showed downregulation of the same targets indicating a mismatch between GFP expression and viral infection. Using a modified HCMV virus destabilizing IE 1 and 2 proteins, we still observed significant downregulation of neurodevelopmental gene expression in infected neural progenitor cells. Together, these data indicate that IE viral proteins are not the main drivers of neurodevelopmental gene dysregulation in HCMV infected neural tissues suggesting therapeutically targeting IE gene expression is insufficient to restore neural differentiation and function.


title: Naked mole-rat hematopoietic stem and progenitors are highly quiescent with an inherent myeloid bias

abstract:
Naked mole-rats (NMRs) are the longest-lived rodents yet their stem cell characteristics remain enigmatic. Here we comprehensively mapped the NMR hematopoietic landscape and identified unique features likely contributing to longevity. Adult NMRs form red blood cells in spleen and marrow, which is a neotenic trait. A myeloid bias towards granulopoiesis in concert with decreased B-lymphopoiesis defines the marrow composition, resembling fetal leukopoiesis. Very similar to primates, the primitive stem cell compartment is marked by CD34 and THY1. Remarkably, stem and progenitor respiration rates are as low as in human cells, while NMR cells show a strong expression signature for fatty acid metabolism. The pool of quiescent stem cells is higher than in mice, and the cell cycle of hematopoietic cells is prolonged. Our work provides a platform to study immunology and stem cell biology in an animal model of exceptional longevity.

TeaserJuvenile features of hematopoiesis shape the blood system of the longest-lived rodent.


title: Interaction between Discs large and GPSM2: A Comparison Across Species

abstract: The orientation of the mitotic spindle determines the direction of cell division, and therefore contributes to tissue shape and cell fate. Interaction between the multifunctional scaffolding protein Discs large (Dlg) and the canonical spindle orienting factor GPSM2 (also called Pins in Drosophila and LGN in vertebrates) has been established in bilaterian models, but its function remains unclear. We used a phylogenetic approach to test whether the interaction is obligate in animals, and in particular whether GPSM2 evolved in multicellular organisms as a Dlg-binding protein. We show that Dlg diverged in C. elegans and the syncytial sponge O. minuta and propose that this divergence may correspond to differences in spindle orientation requirements between these organisms and the canonical pathways described in bilaterians. We also demonstrate that GPSM2 is present in basal animals, but the established Dlg-interaction site cannot be found in either Placozoa or Porifera. Our results suggest that the interaction between GPSM2 and Dlg appeared in Cnidaria, and we therefore speculate that it may have evolved to promote accurate division orientation in the nervous system. This work reveals the evolutionary history of the GPSM2/Dlg interaction and suggests new possibilities for its importance in spindle orientation during epithelial and neural tissue development.


title: Coilin oligomerization and remodeling by Nopp140 reveals a hybrid assembly mechanism for Cajal bodies

abstract: Cajal bodies (CBs) are ubiquitous nuclear membraneless organelles (MLOs) that promote efficient biogenesis of RNA-protein complexes. Depletion of the CB scaffolding protein coilin is lethal for vertebrate embryogenesis, making CBs a strong model for understanding the structure and function of MLOs. Although it is assumed that CBs form through biomolecular condensation, the biochemical and biophysical principles that govern CB dynamics have eluded study. Here, we identify features of the coilin protein that drive CB assembly and shape. Focusing on coilins N-terminal domain (NTD), we discovered its unexpected capacity for oligomerization in vivo. Single amino acid mutational analysis of coilin revealed distinct molecular interactions required for oligomerization and binding to the Nopp140 ligand, which facilitates CB assembly. We demonstrate that the intrinsically disordered regions of Nopp140 have substantial condensation properties and suggest that Nopp140 binding thereby remodels stable coilin oligomers to form a particle that recruits other functional components.


title: Using attentive gated neural networks to quantify the impact of non-coding variants on transcription factor binding affinity

abstract: A large proportion of non-coding variants are present within binding sites of transcription factors(TFs), which play a significant role in gene regulation. Thus, deriving the impact of non-coding variants on TF binding is the first step towards unravelling their regulatory roles within their associated disease traits. Most of the modern algorithms used for this purpose are based on convolutional neural network(CNN) architectures. However, these models are incapable of capturing the positional effect of different sub-sequences within the TF binding sites on the binding affinity. In this paper, we utilize the attentive gated neural network(AGNet) architecture to build a set of TF-AGNet models for predicting in vivo TF binding intensities in the GM12878 lymphoblastoid cells. These models have novel layers capable of deriving the impact of relative positions of different DNA sub-sequences, within a binding site, on TF binding affinity, and of extracting the most relevant prediction features. We show that the TF-AGNet models are able to outperform conventional CNNs for predicting continuous values of TF binding affinity. We also train additional TF-AGNet models for 20 TFs using data from 4 other cell-lines to assess the generalizability of their prediction accuracy. Lastly, we show that the TF-AGNet based models more accurately classify non-coding variants that significantly affect TF binding compared to models based on 7 variant annotation tools. This accuracy can be leveraged to derive gene regulatory roles of millions of non-coding variants across the genome to further examine their mechanistic associations with complex disease traits.


title: Molecular dynamics simulation of a model brain membrane with and without a 14-3-3 tau protein

abstract: An unbalanced composition of lipids and proteins in brain membranes is related to the appearance neurodegenrative diseases and recent investigations show that the 14-3-3 tau protein might relate to some of these diseases. This article reports results from a coarse-grained model brain membrane with and without a 14-3-3{tau} /{theta} protein inside the membrane. We investigated the symmetrized partial density, thickness, diffusion coefficients, and deuterium order parameters of the membrane with and without protein. We observe a slight increase in heads and linkers in the symmetrized partial density of the membrane with the protein inserted and higher values of the deuterium order parameters for the brain model membrane with protein. We observe a reduction in the diffusion coefficient of the fluid membrane in the presence of the transmembrane tau protein. Our findings show that the protein can modify the structural and dynamical properties of the membrane. This work will serve as a guide for future investigations on the interactions of tau proteins with brain membrane models and their relation to neurodegenerative diseases.


title: Hemangiosarcoma cells induce M2 polarization and PD-L1 expression in macrophages

abstract: Hemangiosarcoma (HSA) is a malignant tumor derived from endothelial cells. Tumor-associated macrophages are one of the major components of tumor microenvironment and crucial for cancer development. The presence and function of macrophages in HSA have not been studied because there is no syngeneic model for HSA. In this study, we evaluated two mouse HSA cell lines and one immortalized mouse endothelial cells for their usefulness as syngeneic models for canine HSA. Our results show that the ISOS-1 cell line develops tumors with similar morphology to canine HSA. ISOS-1 cells highly express KDM2B and have similar KDM2B target expression patterns with canine HSA. Moreover, we determine that in both ISOS-1 and canine HSA tumors, macrophages are present as a major constituent of the tumor microenvironment. These macrophages are positive for CD204, an M2 macrophage marker, and express PD-L1. ISOS-1-conditioned medium can induce M2 polarization and PD-L1 expression in RAW264.7 mouse macrophage cell line. These results show that ISOS-1 can be used as a syngenic model for canine HSA and suggest that macrophages play an important role in immune evasion in HSA. Using the syngeneic mouse model for canine HSA, we can further study the role of immune cells in the pathology of HSA.


title: Gene regulatory networks controlling temporal patterning, neurogenesis and cell fate specification in the mammalian retina.

abstract: Gene regulatory networks (GRNs), consisting of transcription factors and their target cis- regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized. In this study, we performed integrated single-cell RNA- and scATAC-seq analysis in both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis. We identified multiple interconnected, evolutionarily-conserved GRNs consisting of cell type-specific transcription factors that both activate expression of genes within their own network and often inhibit expression of genes in other networks. These GRNs control state transitions within primary retinal progenitors that underlie temporal patterning, regulate the transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirmed the prediction of this analysis that the NFI transcription factors Nfia, Nfib, and Nfix selectively activate expression of genes that promote late-stage temporal identity in primary retinal progenitors. We also used GRNs to identify additional transcription factors that promote (Insm1/2) and inhibit (Tbx3, Tcf7l1/2) rod photoreceptor specification in postnatal retina. This study provides an inventory of cis- and trans-acting factors that control retinal development, identifies transcription factors that control the temporal identity of retinal progenitors and cell fate specification, and will potentially guide cell-based therapies aimed at replacing retinal neurons lost due to disease.


title: Postnatal SETD1B is essential for learning and the regulation of neuronal plasticity genes

abstract: Histone 3 lysine 4 methylation (H3K4me) is mediated by six different lysine methyltransferases. Amongst these enzymes SET domain containing 1b (SETD1B) has been linked to syndromic intellectual disability but its role in the postnatal brain has not been studied yet. Here we employ mice that lack Setd1b from excitatory neurons of the postnatal forebrain and combine neuron-specific ChIP-seq and RNA-seq approaches to elucidate its role in neuronal gene expression. We observe that SETD1B controls the expression of genes with a broad H3K4me3 peak at their promoters that represent neuronal enriched genes linked to learning and memory function. Comparative analysis to corresponding data from conditional Kmt2a and Kmt2b knockout mice suggests that this function is specific to SETD1B. Moreover, postnatal loss of Setd1b leads to severe learning impairment, suggesting that SETD1B-mediated regulation of H3K4me levels in postnatal neurons is critical for cognitive function.


title: Degrading intestinal DAF-2 nearly doubles Caenorhabditis elegans lifespan without affecting development or reproduction

abstract:
Twenty-eight years following the breakthrough discovery that a single-gene mutation of daf-2 can double the lifespan of Caenorhabditis elegans, it remains unclear where this gene, which encodes an insulin/IGF-1 receptor, is expressed and where it acts to regulate aging. Here, by inserting DNA sequences of fluorescent tags into the genomic locus of daf-2 and that of its downstream transcription factor daf-16, we determined that both genes are expressed in most or all tissues from embryos through adulthood, in line with their diverse functions. Using tissue-specific auxin-induced protein degradation, we determined that both DAF-2 and DAF-16 act in the intestine to regulate organismal aging. Strikingly, loss of DAF-2 in the intestine nearly doubled C. elegans lifespan but did not produce the adverse developmental or reproductive phenotypes associated with genetic daf-2 mutants. These findings unify the mechanism of lifespan regulation by genes and that by dietary restriction, and begin to focus anti-aging research on nutrient supply.

HighlightsO_LIdaf-2 and daf-16 are expressed in most or all cells of C. elegans using genome editing.
C_LIO_LIDAF-2 and DAF-16 both regulate lifespan from the intestine as determined using auxin-induced protein degradation.
C_LIO_LIReduced insulin signaling in the intestine nearly doubles C. elegans lifespan without adverse effects on development or reproduction.
C_LIO_LILifespan regulation by genes and dietary restriction are unified by intestinal supply of nutrients and metabolism.
C_LI


title: Centromere formation remodels chromatin fibre structure

abstract: Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. To test whether centromeres have a special chromatin structure we have analysed the architecture of a neocentromere. Centromere formation is accompanied by RNA pol II recruitment and active transcription to form a decompacted, negatively supercoiled domain enriched in  open chromatin fibres. In contrast, centromerisation causes a spreading of repressive epigenetic marks to surrounding regions, delimited by H3K27me3 polycomb boundaries and divergent genes. This flanking domain is transcriptionally silent and partially remodelled to form  compact chromatin, similar to satellite-containing DNA sequences, and exhibits genomic instability. We suggest transcription disrupts chromatin to provide a foundation for kine-tochore formation whilst compact pericentromeric heterochromatin generates mechanical rigidity.


title: Human centromere formation activates transcription and opens chromatin fibre structure


title: A recombinant baculovirus TnGV in Trichoplusia ni larvae using the PIG bombardment method and the CRISPR/Cas9 system

abstract: Baculoviruses have been used for the expression of heterologous proteins of biotechnological interest. However, most of these proteins are obtained by homologous co-transfection recombination in cell lines, limiting their use. Recently, the CRISPR/Cas9 system has excelled in its high efficiency in editing specific sequences without the need for insect cell lines. In this work, the CRISPR/Cas9 system was used to edit the genome of Trichopusia ni granulovirus (TnGV) and transformation of insects by the PIG bombardment method. A homologous repair vector (pTnGV101) was designed with regions orf5 and orf7, as well as sgRNA flanking TnGV P10 of this virus. The bombardment transformation was carried out at 175 psi with 40% of infected T. ni larvae, of which 38% expressed the reporter protein EGFP. These results demonstrate that the CRISPR/Cas9 system and PIG bombardment can be used for genetic modification of baculovirus in vivo.


title: A Computational Model of the Effect ofShort-Term Monocular Deprivation onBinocular Rivalry in the Context of Amblyopia

abstract: Treatments for amblyopia focus on vision therapy and patching of one eye. Predicting the success of these methods remains difficult, however. Recent research has used binocular rivalry to monitor visual cortical plasticity during occlusion therapy, leading to a successful prediction of the recovery rate of the amblyopic eye. The underlying mechanisms and their relation to neural homeostatic plasticity are not known. Here we propose a spiking neural network to explain the effect of short-term monocular deprivation on binocular rivalry. The model reproduces perceptual switches as observed experimentally. When one eye is occluded, inhibitory plasticity changes the balance between the eyes and leads to longer dominance periods for the eye that has been deprived. The model suggests that homeostatic inhibitory plasticity is a critical component of the observed effects and might play an important role in the recovery from amblyopia.


title: Asymmetrical adaptations to increases and decreases in environmental volatility

abstract: Humans adapt their learning strategies to changing environments by estimating the volatility of the reinforcement conditions. Here, we examine how volatility affects learning and the underlying functional brain organizations using a probabilistic reward reversal learning task. We found that the order of conditions was critically important; participants adjusted learning rate going from volatile to stable, but not from stable to volatile, environments. Subjective volatility of the environment was encoded in the striatal reward system and its dynamic connections with the prefrontal control system. Flexibility, which captures the dynamic changes of network modularity in the brain, was higher in the environmental transition from volatile to stable than from stable to volatile. These findings suggest that behavioral adaptations and dynamic brain organizations in transitions between stable and volatile environments are asymmetric, providing critical insights into the way that people learn under uncertainty.