title: Redundant and specific roles of EGFR ligands in the ERK activation waves during collective cell migration of MDCK cells

abstract: Epidermal growth factor receptor (EGFR) plays a pivotal role in collective cell migration by mediating cell-to-cell propagation of extracellular signal-regulated kinase (ERK) activation. Here, we aimed to determine which EGFR ligands mediate the ERK activation waves by gene knockout. Four of the seven known EGFR ligands are expressed in MDCK cells. We found that epidermal growth factor (EGF)-deficient cells exhibited lower basal ERK activity than the cells deficient in heparin-binding EGF (HBEGF), transforming growth factor alpha (TGF) or epiregulin (EREG), but all cell lines deficient in a single EGFR ligand retained the ERK activation waves. Therefore, we knocked out the EGFR ligand genes in decreasing order of expression. ERK activation waves were markedly suppressed, albeit incompletely, only when all four EGFR ligands were knocked-out. Re-expression of the EGFR ligands revealed that all but HBEGF could restore the ERK activation waves. Aiming at complete elimination of the ERK activation waves, we further attempted to knockout Nrg1, a ligand for ErbB3 and ErbB4, and found that Nrg1 deficiency induced growth arrest in the absence of all four EGFR ligand genes expressed in MDCK cells. Collectively, these results showed that EGFR ligands exhibit remarkable redundancy in the propagation of ERK activation waves during collective cell migration.

category: cell biology


title: Subcellular micropatterning for visual immunoprecipitation reveals differences in cytosolic protein complexes downstream the EGFR

abstract: Analysis of protein-protein interactions in living cells by protein micropatterning is currently limited to the spatial arrangement of transmembrane proteins and their corresponding downstream molecules. Here we present a robust method for visual immunoprecipitation of cytosolic protein complexes by use of an artificial transmembrane bait construct in combination with micropatterned antibody arrays on cyclic olefin polymer (COP) substrates. The method was used to characterize Grb2-mediated signalling pathways downstream the epidermal growth factor receptor (EGFR). Ternary protein complexes (Shc1:Grb2:SOS1 and Grb2:Gab1:PI3K) were identified and we found that EGFR downstream signalling is based on constitutively bound (Grb2:SOS1 and Grb2:Gab1) as well as on agonist-dependent protein associations with transient interaction properties (Grb2:Shc1 and Grb2:PI3K). Spatiotemporal analysis further revealed significant differences in stability and exchange kinetics of protein interactions. Furthermore, we could show that this approach is well suited to study the efficacy and specificity of SH2 and SH3 protein domain inhibitors in a live cell context. Altogether, this method represents a significant enhancement of quantitative subcellular micropatterning approaches as an alternative to standard biochemical analyses.


title: Evaluation of podocyte Rac-1 induced kidney disease by modulation of TRPC5

abstract:
BackgroundTransient receptor potential channel 5 (TRPC5) is a non-selective cationic ion channel expressed in brain, kidney and other organs where its activation underlies podocyte injury in chronic kidney diseases. Specifically, it has been suggested that a podocyte TRPC5 plasma membrane relocation and channel activation following injury results from activation of Rac-1, propagating podocyte dysfunction and proteinuria. However, previous TRPC5 transgenic mouse studies had questioned a pathogenic role for TRPC5 in podocytes. This investigation was designed to specifically evaluate podocyte Rac-1 activation in the context of functional TRPC5 or a TRPC5 pore mutant to assess effects on proteinuria.

Materials and MethodsWe employed single cell patch-clamp studies of cultured podocytes and studied proteinuria in transgenic mouse models to characterize the effects of TRPC5 following podocyte Rac-1 activation.

ResultsInhibition of TRPC5 by small molecules reportedly ameliorated proteinuria in murine models of proteinuric kidney diseases. In order to directly examine TRPC5 function following Rac-1-induced podocyte injury, we analyzed TRPC5 inhibition in podocyte specific Rac-1 (active) transgenic mice. In addition, we generated a double-transgenic mouse constitutively overexpressing either TRPC5 (TRPC5WT) or a TRPC5 dominant-negative pore mutant (TRPC5DN) in concert with podocyte specific and inducible activation of active Rac-1 (Rac-1Dtg). In electrophysiological experiments, active TRPC5 was detected in primary podocytes overexpressing TRPC5 but not in podocytes with endogenous TRPC5 expression, nor with Rac-1 overexpressing podocytes. TRPC5 inhibition did not change proteinuria in mice with active podocyte Rac-1, nor did an increase or loss of TRPC5 activity affected podocyte injury in Rac-1Dtg animals. Administration of TRPC5 inhibitors, ML204 and AC1903, did not alleviate podocyte Rac-1 induced proteinuria.

ConclusionTRPC5 inhibition did not modify podocyte Rac-1 induced proteinuria in mice.

Significance StatementTRPC5 is a calcium conducting ion channel involved in a plethora of biological functions in the brain, kidney and other organs. In proteinuric kidney diseases, others proposed a model that links activation of small GTPase Rac-1 in podocytes to activation of TRPC5 channels propagating cellular injury and eventually leading to progressive kidney disease. To test this hypothesis, we have developed a novel transgenic mouse model that employs podocyte Rac-1 activation in the presence or absence of a functional TRPC5 channel. Our data shows that transgenic mice with activated Rac-1 in podocytes did not enhance endogenous TRPC5 expression or its activity. Furthermore, TRPC5 blockade or activation did not modify Rac-1 induced proteinuria in mice.


title: Species-specific deployment of Runx2 isoforms and differential regulation of target genes during avian jaw development and evolution

abstract: Developmental regulation of bone formation in the jaw skeleton is essential to species-specific adaptation. The jaws are derived from neural crest mesenchyme (NCM), a progenitor population that directs skeletal patterning by exerting temporal and spatial control over molecular and cellular programs for osteogenesis. One important NCM-mediated gene is Runx2, which is a transcription factor required for osteoblast differentiation. RUNX2 protein binds many target genes involved in the deposition and resorption of bone. To determine the extent to which changes in Runx2 structure, function, and expression underlie the evolution of the jaw skeleton, we compare Runx2 across vertebrates and within birds. Runx2 contains two alternative promoters, tandem repeats of glutamine and alanine with variable lengths in different species, a conserved DNA-binding domain, an exon that is alternatively spliced, as well as two possible C-termini. Such alternative splicing produces eight potential isoforms that show distinct stage- and species-specific patterns in the jaw primordia of chick, quail and duck embryos. We also find that certain isoforms are strongly induced by TGF{beta} signaling whereas others are not. Overexpressing Runx2 isoforms in NCM reveals that some are transcriptionally activating, while others are repressive. But context appears to be relevant since species-specific polymorphisms in the promoter of target genes like Mmp13, can modulate the effects of different isoforms. Overall, our study indicates that the structure and species-specific deployment of Runx2 isoforms affect the transcriptional activity of target genes in ways that may have played a generative and regulatory role in the evolution of the avian jaw skeleton.

category: developmental biology


title: The zebrafish meiotic cohesion complex protein Smc1b is required for key events in meiotic prophase I

abstract: The eukaryotic structural maintenance of chromosomes (SMC) proteins are involved in key processes of chromosome structure and dynamics. SMC1{beta} was identified as a component of the meiotic cohesion complex in vertebrates, which aids in keeping sister chromatids together prior to segregation in meiosis II and is involved in association of homologous chromosomes in meiosis I. The role of SMC1{beta} in meiosis has primarily been studied in mice, where mutant male and female mice are infertile due to germ cell arrest at pachytene and metaphase II stages, respectively. Here, we investigate the function of zebrafish Smc1b to understand the role of this protein more broadly in vertebrates. We found that zebrafish smc1b is necessary for fertility and has important roles in meiosis, yet has no other apparent roles in development. Therefore, smc1b functions primarily in meiosis in both fish and mammals. In zebrafish, we showed that smc1b mutant spermatocytes initiated telomere clustering in leptotene, but failed to complete this process and progress into zygotene. Furthermore, mutant spermatocytes displayed a complete failure of homolog pairing and synapsis. Interestingly, meiotic DNA double strand breaks occurred in the absence of Smc1b despite failed pairing and synapsis. Overall, our findings point to an essential role of Smc1b in the leptotene to zygotene transition during zebrafish spermatogenesis. In addition, ovarian follicles failed to form in smc1b mutants, suggesting an essential role in female meiosis as well. Our results indicate that there are some key differences in Smc1b requirement in meiosis among vertebrates: while Smc1b is not required for homologue pairing and synapsis in mice, it is essential for these processes in zebrafish.


title: SARS-CoV-2 convergent evolution as a guide to explore adaptive advantage

abstract: Much can be learned from 1.2 million sequences of SARS-CoV-2 generated during the last 15 months. Out of the overwhelming number of mutations sampled so far, only few rose to prominence in the viral population. Many of these emerged recently and independently in multiple lineages. Such a textbook example of convergent evolution at the molecular level is not only curiosity but a guide to uncover the basis for adaptive advantage behind these events. Focusing on the extent of the convergent evolution in the spike (S) protein, our report confirms that the most concerning SARS-CoV-2 lineages carry the heaviest burden of convergent S-protein mutations, suggesting their fundamental adaptive advantage. The great majority (21/25) of S-protein sites under convergent evolution tightly cluster in three functional domains; N-terminal domain, receptor-binding domain, and Furin cleavage site. We further show that among the S-protein receptor-binding motif mutations, ACE2 affinity-improving substitutions are favored. While the probed mutation space in the S protein covered all amino-acids reachable by single nucleotide changes, substitutions requiring two nucleotide changes or epistatic mutations of multiple-residues have only recently started to emerge. Unfortunately, despite their convergent emergence and physical association, most of these adaptive mutations and their combinations remain understudied. We aim to promote research of current variants which are currently understudied but may become important in the future.

category: evolutionary biology


title: Variation in upstream open reading frames contributes to allelic diversity in protein abundance

abstract: The 5 untranslated region (UTR) sequence of eukaryotic mRNAs may contain upstream open reading frames (uORFs), which can regulate translation of the main open reading frame (mORF). The current model of translational regulation by uORFs posits that when a ribosome scans an mRNA and encounters a uORF, translation of that uORF can prevent ribosomes from reaching the mORF and cause decreased mORF translation. In this study, we first observed that rare variants in the 5 UTR dysregulate protein abundance. Upon further investigation, we found that rare variants near the start codon of uORFs can repress or derepress mORF translation, causing allelic changes in protein abundance. This finding holds for common variants as well, and common variants that modify uORF start codons also contribute disproportionately to metabolic and whole-plant phenotypes, suggesting that translational regulation by uORFs serves an adaptive function. These results provide evidence for the mechanisms by which natural sequence variation modulates gene expression, and ultimately, phenotype.

category: genomics


title: Bacterial CRISPR abundance jumps up at around 45°C

abstract: Although performing adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. Here, we observed an abrupt transition of bacterial CRISPR-Cas abundance at around 45{degrees}C. Phylogenetic comparative analyses confirmed that the abundance correlates with growth temperature only at the temperature range around 45{degrees}C. Meanwhile, we noticed that the diversities of cellular predators have a precipitous decline at this temperature range. The grazing risk faced by bacteria reduces substantially at around 45{degrees}C and almost disappears above 60{degrees}C. So viral lysis would become the dominating factor of bacterial mortality, and antivirus immunity has a higher priority. In temperature ranges where the abundance of cellular predators does not change with temperature, temperatures would have negligible effects on CRISPR-Cas abundance. The hypothesis predicts that bacteria should also be rich in CRISPR-Cas systems if they live in other extreme conditions inaccessible to grazing predators.


title: Bacterial CRISPR-Cas Abundance Increases Precipitously at Around 45°C: Linking Antivirus Immunity to Grazing Risk


title: Distinct allosteric mechanisms of first-generation MsbA inhibitors

abstract: Present in all kingdoms of life, ATP-binding cassette (ABC) transporters couple ATP hydrolysis to mechanical force and facilitate trafficking of diverse substrates across biological membranes. Although many ABC transporters are promising drug targets, their mechanisms of regulation by small molecule inhibitors remain largely unknown. Herein, we used the lipopolysaccharide (LPS) flippase MsbA, a prototypical ABC exporter, as a model system to probe mechanisms of allosteric modulation by compounds binding to the transmembrane domains (TMDs). Recent chemical screens have identified intriguing LPS transport inhibitors targeting MsbA: the ATPase stimulator TBT1 and the ATPase inhibitor G247. Despite preliminary biochemical and structural data, it is unclear how TBT1 and G247 bind to the MsbA TMDs yet induce opposite allosteric effect in the nucleotide-binding domains (NBDs). Through single-particle EM, mutagenesis and activity assay, we show that TBT1 and G247 bind adjacent yet separate locations in the TMDs, inducing drastic changes in TMD conformation and NBD positioning. Two TBT1 molecules asymmetrically occupy the LPS binding site to break the symmetry of MsbA, resulting in disordered transmembrane helices and decreased NBD distance. In this novel inhibited ABC transporter state, decreased distance between the NBDs causes stimulation of ATP hydrolysis yet LPS transport blockage. In contrast, G247 acts as a TMDs wedge, symmetrically increasing NBD separation and preventing conformational transition of MsbA. Our study uncovers the distinct mechanisms of the first-generation MsbA-specific inhibitors and demonstrates that rational design of substrate-mimicking compounds can be exploited to develop useful ABC transporter modulators.

category: biochemistry


title: Diversity of satellite glia in sympathetic and sensory ganglia

abstract: Satellite glia are the major glial type found in ganglia of the peripheral nervous system and wrap around cell bodies of sympathetic and sensory neurons that are very diverse. Other than their close physical association with peripheral neurons, little is known about this glial population. Here, we performed single cell RNA sequencing analysis and identified five different populations of satellite glia from sympathetic and sensory ganglia. We identified three shared populations of satellite glia enriched in immune-response genes, immediate-early genes and ion channels/ECM-interactors, respectively. Sensory- and sympathetic-specific satellite glia are differentially enriched for modulators of lipid synthesis and metabolism. Sensory glia are also specifically enriched for genes involved in glutamate turnover. Further, satellite glia and Schwann cells can be distinguished by unique transcriptional signatures. This study reveals remarkable heterogeneity of satellite glia in the peripheral nervous system.

category: neuroscience


title: A metabolomics pipeline enables mechanistic interrogation of the gut microbiome

abstract: Gut microbes modulate host phenotypes and are associated with numerous health effects in humans, ranging from cancer immunotherapy response to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microbes has hindered defining mechanistic connections between individual microbial strains and host phenotypes. One key way the gut microbiome influences host physiology is through the production of small molecules1-3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites (MDMs) in diverse sample types. We report the metabolic profiles of 178 gut microbe strains using our library of 833 metabolites. Leveraging this metabolomics resource we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover novel metabolism in Bacteroides, and employ comparative genomics-based discovery of candidate biochemical pathways. MDMs can be detected in diverse biofluids in gnotobiotic and conventional mice and traced back to corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microbe and microbe-host interactions.

category: microbiology


title: Force and step size of gliding motility in human pathogenic bacterium Mycoplasma pneumoniae

abstract:
Mycoplasma pneumoniae, a human pathogenic bacterium, binds to sialylated oligosaccharides and glides on host cell surfaces via a unique mechanism. Gliding motility is essential for initiating the infectious process. In the present study, we measured the stall force of an M. pneumoniae cell carrying a bead that was manipulated using optical tweezers on two strains. The stall forces of M129 and FH strains were averaged to be 23.7 and 19.7 pN, respectively, much weaker than those of other bacterial surface motilities. The binding activity and gliding speed of the M129 strain on sialylated oligosaccharides were eight and two times higher than those of the FH strain, respectively, showing that binding activity is not linked to gliding force. Gliding speed decreased when cell binding was reduced by addition of free sialylated oligosaccharides, indicating the existence of a drag force during gliding. We detected stepwise movements, likely caused by a single leg under 0.2-0.3 mM free sialylated oligosaccharides. A step size of 14-19 nm showed that 25-35 propulsion steps per second are required to achieve the usual gliding speed. The step size was reduced to less than half with the load applied using optical tweezers, showing that a 2.5 pN force from a cell is exerted on a leg. The work performed in this step was 16%-30% of the free energy of the hydrolysis of ATP molecules, suggesting that this step is linked to the elementary process of M. pneumoniae gliding.

IMPORTANCEHuman mycoplasma pneumonia is caused by the bacterium Mycoplasma pneumoniae. This tiny bacterium, shaped like a missile, binds to human epithelial surfaces and spreads using a unique gliding mechanism to establish infection. Here, we analyzed the movements and force of this motility using a special setup: optical tweezers. We then obtained detailed mechanical data to understand this mechanism. Furthermore, we succeeded in detecting small steps of nanometers in its gliding, which is likely linked to the elementary process of the core reaction: chemical to mechanical energy conversion. These data provide critical information to both control this human pathogen and explore new ideas for artificial molecular machines.


title: Locus-associated R-loop repression in cis

abstract: R-loops exert varied beneficial or detrimental effects. To assess the function of an R-loop at a specific genetic locus, we had developed an inducible RNaseH1-EGFP-dCas9 (RED) protein chimaera as part of a locus-associated R-loop-modulating system (LasR). LasR is compatible with R-loop modulation in trans, which targets RED to one locus to repress R-loops at another spatially proximal site. Here we use the LasR system for R-loop modulation in cis, which consists of targeting RED directly to an R-loop. The combination of LasR in cis and trans will be essential to ascribe functions to specific R-loops within varied molecular contexts and study designs.

category: molecular biology


title: Building the cytokinetic contractile ring in an early embryo: initiation as clusters of myosin II, anillin and septin, and visualization of a septin filament network

abstract: The cytokinetic contractile ring (CR) was first described some 50 years ago, however our understanding of the assembly and structure of the animal cell CR remains incomplete. We recently reported that mature CRs in sea urchin embryos contain myosin II mini-filaments organized into aligned concatenated arrays, and that in early CRs myosin II formed discrete clusters that transformed into the linearized structure over time. The present study extends our previous work by addressing the hypothesis that these myosin II clusters also contain the crucial scaffolding proteins anillin and septin, known to help link actin, myosin II, RhoA, and the membrane during cytokinesis. Super-resolution imaging of cortices from dividing embryos indicates that within each cluster, anillin and septin2 occupy a centralized position relative to the myosin II mini-filaments. As CR formation progresses, the myosin II, septin and anillin containing clusters enlarge and coalesce into patchy and faintly linear patterns. Our super-resolution images provide the initial visualization of anillin and septin nanostructure within an animal cell CR, including evidence of a septin filament network. Furthermore, Latrunculin-treated embryos indicated that the localization of septin or anillin to the myosin II clusters in the early CR was not dependent on actin filaments. These results highlight the structural progression of the CR in sea urchin embryos from an array of clusters to a linearized purse string, the association of anillin and septin with this process, and provide, for the first time, the visualization of septin filament higher order structure in an animal cell CR.


title: Phosphatidylinositol 3-kinase-independent synthesis of PtdIns(3,4)P2 by a phosphotransferase

abstract: Despite their comparatively low abundance, phosphoinositides play a central role in membrane traffic and signalling. PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are uniquely important, as they promote cell growth, survival, and migration. Pathogenic organisms have developed means to subvert phosphoinositide metabolism to promote successful infection and their survival within host organisms. We demonstrate that PtdIns(3,4)P2 is generated in host cells by effectors of the enteropathogenic bacteria Salmonella and Shigella. Pharmacological, gene silencing and heterologous expression experiments revealed that, remarkably, the biosynthesis of PtdIns(3,4)P2 occurs independently of phosphoinositide 3-kinases. Instead, we found that the Salmonella effector SopB, heretofore believed to be a phosphatase, generates PtdIns(3,4)P2 de novo via a phosphotransferase/phosphoisomerase mechanism. Recombinant SopB is capable of generating PtdIns(3,4)P2 from PtdIns(4,5)P2 in a cell-free system. Through a remarkable instance of convergent evolution, bacterial effectors acquired the ability to synthesize 3-phosphorylated phosphoinositides by an ATP- and kinase-independent mechanism, thereby subverting host signaling to gain entry and even provoke oncogenic transformation.


title: Transcriptional Reprogramming of Skeletal Muscle Stem Cells by the Niche Environment

abstract: Adult stem cells are indispensable for tissue regeneration. Tissue-specific stem cells reside in a specialized location called their niche, where they are in constant cross talk with neighboring niche cells and circulatory signals from their environment. Aging has a detrimental effect on the number and the regenerative function of various stem cells. However, whether the loss of stem cell function is a cause or consequence of their aging niche is unclear. Using skeletal muscle stem cells (MuSCs) as a model, we decouple cell-intrinsic from niche-mediated extrinsic effects of aging on their transcriptome. By combining in vivo MuSC heterochronic transplantation models and computational methods, we show that on a genome-wide scale, age-related altered genes fall into two distinct categories regarding their response to the niche environment. Genes that are inelastic in their response to the niche exhibit altered chromatin accessibility and are associated with differentially methylated regions (DMRs) between young and aged cells. On the other hand, genes that are restorable by niche exposure exhibit altered transcriptome but show no change in chromatin accessibility or DMRs. Taken together, our data suggest that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs, and exposure to a young niche can reverse approximately half of all age-associated changes that are not epigenetically encoded. The muscle niche therefore serves as an important therapeutic venue to mitigate the negative consequence of aging on tissue regeneration.

category: genetics


title: Survey and Molecular Detection of Sri Lankan Cassava Mosaic Virus in Thailand

abstract: Cassava plantations in an area of 458 ha spanning five provinces along the Thailand- Cambodia border were surveyed from October 2018 to July 2019 to determine the prevalence of cassava mosaic disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV) in the region. CMD prevalence was 40% in the whole area and 80% in Prachinburi, 43% in Sakaeo, 37% in Burium, 25% in Surin, and 19% in Sisaket provinces. Disease severity was generally scored as 2-3. The highest average disease severity was in Sakaeo province (3.7), followed by Buriram (3.6), Prachinburi (2.88), Surin (2.5), and Sisaket (2.4) provinces. Asymptomatic plants were identified in Surin (12%), Prachinburi (5%), Sakaeo (0.2%), and Buriram (0.1%) by PCR analysis. Interestingly, cassava cultivars CMR-89 and Rayong 11 were susceptible to CMD. In approximately 95% of cases, the infection was transmitted by whitefly (Bemisia tabaci), which had a high population density in Prachinburi but was sparse in Surin, with the largest populations observed in May and June. Nucleotide sequencing of the mitochondrial cytochrome oxidase 1 (mtCO1) gene of whitefly (Bemisia tabaci) in Thailand revealed a similarity to the Asia II 1 whitefly gene. Furthermore, the AV1 gene--which encodes the capsid protein--showed 90% nucleotide identity with SLCMV. Phylogenetic analysis of completed nucleotide sequences of DNA-A and DNA-B components of the SLCMV genome determined by rolling circle amplification (RCA) indicated that they were similar to the nucleotide sequence of SLCMV isolates from Thailand, Vietnam, and Cambodia. These results provide important insights into the distribution, impact, and spread of CMD and SLCMV in Thailand.

category: pathology


title: Orthogonal translation initiation using the non-canonical initiator tRNA(AAC) alters protein sequence and stability in vivo

abstract: Biological engineers seek to have better control and a more complete understanding of the process of translation initiation within cells so that they may produce proteins more efficiently, as well as to create orthogonal translation systems. Previously, initiator tRNA variants have been created that initiate translation from non-AUG start codons, but their orthogonality has never been measured and the detailed characteristics of proteins produced from them have not been well defined. In this study we created an initiator tRNA mutant with anticodon altered to AAC to be complementary to GUU start codons. We deploy this i-tRNA(AAC) into E. coli cells and measure translation initiation efficiency against all possible start codons. Using parallel reaction monitoring targeted mass spectrometry we identify the N-terminal amino acids of i-tRNA(AAC)-initiated reporter proteins and show these proteins have altered stability within cells. We also use structural modeling of the peptide deformylase enzyme interaction with position 1 valine peptides to interrogate a potential mechanism for accumulation of formylated-valine proteins observed by mass spectrometry. Our results demonstrate that mutant initiator tRNAs have potential to initiate translation more orthogonally than the native initiator tRNA but their interactions with cellular formyltransferases and peptide deformylases can be inefficient because of the amino acid they are charged with. Additionally, engineered initiator tRNAs may enable tuning of in vivo protein stability through initiation with non-methionine amino acids that alter their interaction with cellular proteases.

category: synthetic biology


title: Functional characterization of RELN missense mutations involved in recessive and dominant forms of Neuronal Migration Disorders

abstract: RELN is a large secreted glycoprotein that acts at multiple steps of cerebral cortex development, including neuronal migration. Only recessive mutations of the Reelin gene (RELN) have been associated with human cortical malformations and none has been functionally characterized. We identified novel missense RELN mutations in both compound and de novo heterozygous patients exhibiting an array of neuronal migration disorders (NMDs) as diverse as pachygyria, polymicrogyria and heterotopia. Most mutations caused defective RELN secretion in vitro and, when ectopically expressed in the embryonic mouse cortex, affected neuronal aggregation and/or migration in vivo. We determined the de novo heterozygous mutations acted as dominant negative and demonstrated that RELN mutations mediate not only recessive, but also dominant NMDs. This work assesses for the first time the pathogenicity of RELN mutations showing a strong genotype-phenotype correlation. In particular, the behavior of the mutant proteins in vitro and in vivo predicts the severity of cortical malformations and provides valuable insight into the pathogenesis of these disorders.


title: Mu opioid receptors acutely regulate adenosine signaling in a thalamo-striatal circuit.

abstract:
Endogenous adenosine plays a crucial role in maintaining energy homeostasis and adenosine levels are tightly regulated across neural circuits. In the dorsal medial striatum (DMS) adenosine inhibits neurotransmitter release, but the source and mechanism underlying its accumulation are largely unknown. Opioids also inhibit neurotransmitter release in the DMS and influences adenosine accumulation after prolonged exposure. However, how these two neurotransmitter systems interact acutely is also largely unknown. This study demonstrates that activation of opioid receptors (MORs), but not {delta} opioid receptors (DORs) or {kappa} opioid receptors (KORs), inhibits tonic activation of adenosine A1Rs via a cyclic adenosine monophosphate (cAMP) dependent mechanism in both male and female mice. Further, selectively knocking-out MORs from presynaptic terminals and postsynaptic medium spiny neurons (MSNs) revealed that activation of MORs on D1R positive MSNs, but not D2R positive MSNs, is necessary to inhibit tonic adenosine signaling on presynaptic terminals. Given the role of D1R positive MSNs in movement and motivated behaviors, these findings reveal a novel mechanism by which these neurons regulate their own synaptic inputs.

Significance StatementUnderstanding interactions between neuromodulatory systems within brain circuits is a fundamental question in neuroscience. The present work uncovers a novel role of opioids in acutely inhibiting adenosine accumulation and subsequent adenosine receptor signaling in the striatum by inhibiting the production of cAMP. Adenosine receptor signaling regulates striatal neurotransmitters including glutamate, GABA, dopamine and acetylcholine. Furthermore, interactions between adenosine2A receptors and numerous other GPCRs, including D2 dopamine and CB1 cannabinoid receptors, suggest that endogenous adenosine broadly modulates striatal GPCR signaling. Additionally, this work discovered that resting endogenous adenosine is released by D1, but not D2 receptor positive MSNs, suggesting that opioid signaling and manipulation of D1R-expressing MSN cAMP activity can broadly affect striatal function and behavior.


title: Plasticity of olfactory bulb inputs mediated by dendritic NMDA-spikes in piriform cortex

abstract: The piriform cortex (PCx) is essential for learning of odor information. The current view postulates odor learning in the PCx is mainly due to plasticity in intracortical (IC) synapses, while odor information from the olfactory bulb carried via the lateral olfactory tract (LOT) is "hardwired". Here we revisit this notion by studying location and pathway dependent plasticity rules. We find that in contrast to the prevailing view, synaptic and optogenetically activated LOT synapses undergo strong and robust long-term potentiation (LTP) mediated by only few local NMDA-spikes delivered at theta frequency, while global spike timing dependent plasticity protocols (STDP) failed to induce LTP in these distal synapses. An inverse result was observed for more proximal apical IC synapses; they undergo plasticity with STDP but are refractive to local NMDA-spike protocols. These results are consistent with a self-potentiating mechanism of odor information via NMDA-spikes which can form branch-specific memory traces of odors.


title: Long lasting anxiety following early life stress is dependent on glucocorticoid signaling in zebrafish

abstract: Chronic adversity in early childhood is associated with increased anxiety and a propensity for substance abuse later in adulthood, yet the effects of early life stress (ELS) on brain development remains poorly understood. The zebrafish, Danio rerio, is a powerful model for studying neurodevelopment and stress. Here, we describe a zebrafish model of ELS and identify a role for glucocorticoid signaling during a critical window in development that leads to long-term changes in brain function. Larval fish subjected to chronic stress in early development exhibited increased anxiety-like behavior and elevated glucocorticoid levels later in life. Increased stress-like behavior was only observed when fish were subjected to ELS within a precise time window in early development, revealing a temporal critical window of sensitivity. Moreover, enhanced anxiety-like behavior only emerges after two months post-ELS, revealing a developmentally specified delay in the effects of ELS. ELS leads to increased levels of baseline cortisol, and resulted in a dysregulation of cortisol receptors, suggesting long-term effects on cortisol signaling. Together, these findings reveal a  critical window for ELS to affect developmental reprogramming of the glucocorticoid receptor pathway, resulting in chronic elevated stress.


title: Conditional immobilization for live imaging C. elegans using auxin-dependent protein depletion

abstract:
The visualization of biological processes using fluorescent proteins and dyes in living organisms has enabled numerous scientific discoveries. The nematode Caenorhabditis elegans is a widely used model organism for live imaging studies since the transparent nature of the worm enables imaging of nearly all tissues within a whole, intact animal. While current techniques are optimized to enable the immobilization of hermaphrodite worms for live imaging, many of these approaches fail to successfully restrain the smaller male worms. To enable live imaging of worms of both sexes, we developed a new genetic, conditional immobilization tool that uses the auxin inducible degron (AID) system to immobilize both hermaphrodites and male worms for live imaging. Based on chromosome location, mutant phenotype, and predicted germline consequence, we identified and AID-tagged three candidate genes (unc-18, unc-104, and unc-52). Strains with these AID-tagged genes were placed on auxin and tested for mobility and germline defects. Among the candidate genes, auxin-mediated depletion of UNC-18 caused significant immobilization of both hermaphrodite and male worms that was also partially reversible upon removal from auxin. Notably, we found that male worms require a higher concentration of auxin for a similar amount of immobilization as hermaphrodites, thereby suggesting a potential sex-specific difference in auxin absorption and/or processing. In both males and hermaphrodites, depletion of UNC-18 did not largely alter fertility, germline progression, nor meiotic recombination. Finally, we demonstrate that this new genetic tool can successfully immobilize both sexes enabling live imaging studies of sexually dimorphic features in C. elegans.

ARTICLE SUMMARYC. elegans is a powerful model system for visualizing biological processes in live cells. In addition to the challenge of suppressing the worm movement for live imaging, most immobilization techniques only work with hermaphrodites. Here, we describe a new genetic immobilization tool that conditionally immobilizes both worm sexes for live imaging studies. Additionally, we demonstrate that this tool can be used for live imaging the C. elegans germline without causing large defects to germline progression or fertility in either sex.


title: Retinal organoids derived from rhesus macaque iPSCs undergo accelerated differentiation compared to human stem cells

abstract:
PurposeTo compare the timing and efficiency of the development of non-human primate (NHP) derived retinal organoids in comparison to those derived from human embryonic stem cells.

MethodsHuman embryonic stem cells (hESCs) and induced-pluripotent stem cells (rhiPSCs) derived from non-human primates (Macaca mulatta) were differentiated into retinal organoids by using an established differentiation protocol. Briefly, embryoid bodies were formed from pluripotent stem cells and induced into a neural lineage with neural induction media with the addition of BMP4. Thereafter, self-formation of optic vesicles was allowed to form in a 2D culture in retinal differentiation media (RDM). Optic vesicles were then manually harvested and cultured in suspension in 3D-RDM media until analysis. Differences in the timing of differentiation and efficiency of retinal organoid development were assessed by light microscopy, electron microscopy, immunocytochemistry, and single-cell transcriptomics.

ResultsGeneration of retinal organoids was achieved from both human and several NHP pluripotent stem cells lines. All rhiPSC lines resulted in retinal differentiation with the formation of optic vesicle-like structures similar to what has been observed in hESC retinal organoids. NHP retinal organoids had laminated structure and were composed of mature retinal cell types including cone and rod photoreceptors. Single cell RNA sequencing was conducted at two time points, which allowed identification of cell types and characterization of developmental trajectory in the developing organoid. Important differences between rhesus and human cells were measured regarding the timing and efficiency of retinal organoid differentiation. While the culture of NHP-derived iPSCs is relatively difficult compared to human stem cells, the generation of retinal organoids is feasible and may be less time consuming due to an intrinsically faster timing of retinal differentiation.

ConclusionsRetinal organoids produced from iPSCs derived from Rhesus monkey using established protocols differentiate through the stages of organoid development faster than those derived from human stem cells. The production of NHP retinal organoids may be advantageous to reduce experimental time and cost for basic biology studies in retinogenesis as well as for preclinical trials in NHPs studying retinal allograft transplantation.


title: Lipid kinases VPS34 and PIKfyve coordinate a phosphoinositide cascade to regulate Retriever-mediated recycling on endosomes

abstract: Cell-surface receptors control how cells respond to their environment. Many cell-surface receptors recycle from endosomes to the plasma membrane via a recently discovered pathway, which includes sorting-nexin SNX17, Retriever, WASH and CCC complexes. Here we discover that PIKfyve and its upstream PI3-kinase VPS34 positively regulate this pathway. VPS34 produces PI3P, which is the substrate for PIKfyve to generate PI3,5P2. We show that PIKfyve controls recycling of cargoes including integrins, receptors that control cell migration. Furthermore, endogenous PIKfyve colocalizes with SNX17, Retriever, WASH and CCC complexes on endosomes. Importantly, PIKfyve inhibition causes a loss of Retriever and CCC from endosomes, and mutation of the lipid binding site on a CCC subunit impairs its endosomal localization and delays integrin recycling. In addition, we show that recruitment of SNX17 is an early step and requires VPS34. These discoveries suggest that VPS34 and PIKfyve coordinate an ordered pathway to regulate recycling from endosomes and suggest how PIKfyve functions in cell migration.


title: Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts

abstract: Reconstructing the histories of complex adaptations and identifying the evolutionary mechanisms underlying their origins are two of the primary goals of evolutionary biology. Taricha newts, which contain high concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator defense, have evolved resistance to self-intoxication, which is a complex adaptation requiring changes in six paralogs of the voltage-gated sodium channel (Nav) gene family, the physiological target of TTX. Here, we reconstruct the origins of TTX self-resistance by sequencing the entire Nav gene family in newts and related salamanders. We show that moderate TTX resistance evolved early in the salamander lineage in three of the six Nav paralogs, preceding the proposed appearance of tetrodotoxic newts by [~]100 million years. TTX-bearing newts possess additional unique substitutions across the entire Nav gene family that provide physiological TTX resistance. These substitutions coincide with signatures of positive selection and relaxed purifying selection, as well as gene conversion events, that together likely facilitated their evolution. We also identify a novel exon duplication within Nav1.4 encoding an expressed TTX-binding site. Two resistance-conferring changes within newts appear to have spread via nonallelic gene conversion: in one case, one codon was copied between paralogs, and in the second, multiple substitutions were homogenized between the duplicate exons of Nav1.4. Our results demonstrate that gene conversion can accelerate the coordinated evolution of gene families in response to a common selection pressure.


title: Expansion of the prime editing modality with Cas9 from Francisella novicida

abstract: Prime editing can induce a desired base substitution, insertion, or deletion in a target gene using reverse transcriptase (RT) after nick formation by CRISPR nickase. In this study, we developed a technology that can be used to insert or replace external bases in the target DNA sequence by linking reverse transcriptase to the Francisella novicida Cas 9 [FnCas9(H969A)] nickase module, which is a CRISPR-Cas9 ortholog. Using FnCas9(H969A) nickase, the targeting limitation of existing Streptococcus pyogenes Cas9 nickase [SpCas9(H840A)]-based prime editing was dramatically extended, and accurate prime editing was induced specifically for the target genes.

category: bioengineering


title: Internal and external features of wild birds after collisions without apparent trauma in Japan

abstract: Wild birds often require rehabilitation after collisions, even with no apparent injury. Information about aftermath of collisions is still scares. Here, we investigated external characteristics and clinical features of the internal organs of wild birds that experienced collision and compared them with birds admitted to rehabilitation center for other reasons. Necropsy was performed on 55 bird carcasses from Passeriformes and Coraciiform. Five external characteristics were recorded before necropsy including; cause of admission, keel score, life stage, fat score, and number of days before death. The median survival time was calculated by Kaplan-Meier estimates. Data on external and internal features were compared using univariate and multivariate multinomial regressions. There was no significant difference in the median survival time among the causes of admission: 1 day for collision, 2 days for trauma, and 2 days for malnutrition. Kidney discoloration was more significantly associated with collision than with other trauma (p = 0.01). Although no apparent kidney abnormality (including enlargement) were observed, anterior lobe was significantly larger than posterior lobe with collision compared with malnutrition (p = 0.045). Birds that experienced collision exhibited a higher fat score than malnourished birds (p = 0.03). Our results suggested that wild birds with abundant fat were more likely to be admitted due to collision. The gross characteristics of collision included kidney discoloration and anterior lobe extension, which was possibly due to rupture of renal blood vessels by blunt external force. From these findings, it was considered that collision caused major axis of anterior lobe significantly larger than posterior lobe, even though no abnormal finding in renal size such as hypertrophy was recognized. This was the first study to evaluate the cause of admission, necropsy results, and external characteristics in wild birds admitted to rehabilitation centers. Absolute cage rest should be adhered to restore renal function for those birds admitted due to collision, and handling and treatment should be minimized to avoid excess movement of the birds.

category: zoology


title: Dynamics of Functional Network Organization Through Graph Mixture Learning

abstract:
Understanding the organizational principles of human brain activity at the systems level remains a major challenge in network neuroscience. Here, we introduce a fully data-driven approach based on graph learning to extract meaningful repeating network patterns from regionally-averaged time-courses. We use the Graph Laplacian Mixture Model (GLMM), a generative model that treats functional data as a collection of signals expressed on multiple underlying graphs. By exploiting covariance between activity of brain regions, these graphs can be learned without resorting to structural information. To validate the proposed technique, we first apply it to task fMRI with a known experimental paradigm. The probability of each graph to occur at each time-point is found to be consistent with the task timing, while the spatial patterns associated to each epoch of the task are in line with previously established activation patterns using classical regression analysis. We further on apply the technique to resting state data, which leads to extracted graphs that correspond to well-known brain functional activation patterns. The GLMM allows to learn graphs entirely from the functional activity that, in practice, turn out to reveal high degrees of similarity to the structural connectome. We compared similarity of the default mode network estimated from different task data and comparing them to each other and to structure. Using different metrics, a similar distinction between high- and low-level cognitive tasks arises.

Overall, this method allows us to infer relevant functional brain networks without the need of structural connectome information. Moreover, we find that these networks correspond better to structure compared to traditional methods.


title: CBX4 regulates long-form thymic stromal lymphopoietin-mediated airway inflammation through SUMOylation in HDM-induced asthma

abstract:
RationaleThymic stromal lymphopoietin (TSLP) is present in two distinct isoforms, short-form (sfTSLP) and long-form (lfTSLP). lfTSLP promotes inflammation while sfTSLP inhibits inflammation in allergic asthma. However, little is known about the regulation of lfTSLP and sfTSLP during allergic attack in asthma airway epithelium.

Methods and ResultsHere, we report that SUMOylation was enhanced in HDM-induced allergic asthma airway epithelium. Inhibition of SUMOylation significantly alleviated airway Th2 inflammation and lfTSLP expression. Mechanistically, CBX4, a SUMOylation E3 ligase, enhanced lfTSLP, but not sfTSLP, mRNA translation through the RNA binding protein, MEX-3B. MEX-3B promoted lfTSLP translation through binding of its KH domains to the lfTSLP mRNA. Furthermore, CBX4 regulated MEX-3B transcription in HBE through enhancing SUMOylation levels of the transcription factor, TFII-I.

ConclusionWe demonstrate an important mechanism whereby CBX4 promotes MEX-3B transcription through enhancing TFII-I SUMOylation, and MEX-3B enhances the expression of lfTSLP through binding to the lfTSLP mRNA and promoting its translation. Our findings uncover a novel target of CBX4 for therapeutic agents to lfTSLP-mediated asthma.


title: A potential prokaryotic and microsporidian pathobiome that may cause shrimp white feces syndrome (WFS)

abstract:
White feces syndrome (WFS) in shrimp cultivation ponds is characterized by the occurrence of shrimp with abnormal, white intestines (midguts) combined with large floating mats of white, shrimp fecal strings. The etiology for WFS is complex, similar to diarrhea in humans. EHP-WFS is a type of WFS characterized by massive quantities of spores from the microsporidian parasite Enterocytozoon hepatopenaei (EHP) together with mixed, unidentified bacteria in the shrimp hepatopancreas, midgut and fecal strings. However, WFS does not always develop in shrimp with severe EHP infections in controlled laboratory challenges. Further, in EHP-WFS outbreak ponds, some shrimp show white midguts (WG) while others in the same pond show grossly normal midguts (NG). We hypothesized that comparison of the microbial flora between WG and NG from the same EHP-WFS pond would reveal probable combinations of microbes significantly associated with EHP-WFS. To test this hypothesis, we selected a pond exhibiting a severe EHP-WFS outbreak in cultivated Penaeus vannamei and used a combination of microscopic and microbial profiling analyses to compare WG and NG samples. By histology, EHP plasmodia and spores were confirmed in the hepatopancreas (HP) and midgut of WG and NG shrimp, but pathological severity and spore quantity was higher in the WG shrimp. In addition, intestinal microbiomes in WG shrimp were less diverse and had higher abundance of bacteria from the genera Vibrio and Propionigenium. Propionigenium quantity in the HP of WG shrimp was significantly higher (P = 1.08e-5) than in NG shrimp (4,506 vs. 3 copies /100 ng DNA, respectively). These findings supported our hypothesis by revealing two candidate bacterial genera that should be tested in combination with EHP as a potential eukaryote-prokaryote pathobiome that causes EHP-WFS in P. vannamei.

HighlightsO_LIWhite feces syndrome (WFS) shrimp often harbor the microsporidian Enterocytozoon hepatopenaei (EHP)
C_LIO_LIThe hepatopancreas (HP) and midgut of EHP-WFS shrimp had more EHP copies and spores than EHP-non.-WFS shrimp
C_LIO_LIVibrio spp., Propionigenium sp. and EHP dominated in HP microbiomes of EHP-WFS shrimp
C_LIO_LIPropionigenium copy numbers were uniquely high in the HP of EHP-WFS shrimp
C_LIO_LIEHP-WFS shrimp also showed intestinal microbiomes of reduced diversity but more heterogeneity
C_LI


title: Phenotypic plasticity triggers rapid morphological convergence

abstract: Phenotypic convergence, the independent evolution of similar traits, is ubiquitous in nature, happening at all levels of biological organizations and in most kinds of living beings. Uncovering its mechanisms remains a fundamental goal in biology. Evolutionary theory considers that convergence emerges through independent genetic changes selected over long periods of time. We show in this study that convergence can also arise through phenotypic plasticity. We illustrate this idea by investigating how plasticity drives Moricandia arvensis, a mustard species displaying within-individual polyphenism in flowers, across the morphological space of the entire Brassicaceae family. By compiling the multidimensional floral phenotype, the phylogenetic relationships, and the pollination niche of over 3000 Brassicaceae species, we demonstrated that Moricandia arvensis exhibits a plastic-mediated within-individual floral disparity greater than that found not only between species but also between higher taxonomical levels such as genera and tribes. As a consequence of this divergence, M. arvensis moves outside the morphospace region occupied by its ancestors and close relatives, crosses into a new region where it encounters a different pollination niche and converges phenotypically with distant Brassicaceae lineages. Our study suggests that, by inducing phenotypes that explore simultaneously different regions of the morphological space, plasticity triggers rapid phenotypic convergence.


title: Neurotrophin signaling is modulated by specific transmembrane domain interactions

abstract: The neurotrophin receptors p75 and TrkA play an important role in the development and survival of the nervous system. Biochemical data suggest that p75 and TrkA regulate the activities of each other. For instance, p75 is able to regulate the response of TrkA to lower concentrations of NGF and TrkA promotes p75 shedding by -secretases in a ligand-dependent manner. The current model is that p75 and TrkA are regulated by means of a physical direct interaction, however the nature of such interaction has been elusive so far. Here using NMR in micelles, multiscale molecular dynamics (MD), FRET and functional studies we identified and characterized the direct interaction between TrkA and p75 through the transmembrane domains (TMDs). MD of p75-TMD mutants suggests that although the interaction between TrkA and p75 TMDs is maintained, a specific protein interface is required to facilitate TrkA active homodimerization in the presence of NGF. The same mutations in the TMD protein interface of p75 reduced the activation of TrkA by NGF and cell differentiation. In summary we provide a structural model of the p75/TrkA receptor complex stabilized by transmembrane domain interactions.


title: GmSALT3 expression improves reactive oxygen species detoxification in salt-stressed soybean roots

abstract:
Soybean plants are salinity (NaCl) sensitive, with their yield significantly decreased under moderately saline conditions. GmSALT3 is the dominant gene underlying a major QTL for salt tolerance in soybean. GmSALT3 encodes a transmembrane protein belonging to the plant cation/proton exchanger (CHX) family. It is currently unknown through which molecular mechanism(s) the ER-localised GmSALT3 contributes to salinity tolerance, as its localisation excludes direct involvement in ion exclusion. In order to gain insights into potential molecular mechanism(s), we used RNA-seq analysis of roots from two soybean NILs (Near Isogenic Lines); NIL-S (salt-sensitive, Gmsalt3) and NIL-T (salt-tolerant, GmSALT3), grown under control and saline conditions (200 mM NaCl) at three time points (0h, 6h, and 3 days). Gene ontology (GO) analysis showed that NIL-T has greater responses aligned to oxidation reduction. ROS were shown less abundant and scavenging enzyme activity was higher in NIL-T, consistent with the RNA-seq data. Further analysis indicated that genes related to calcium signalling, vesicle trafficking and Casparian strip (CS) development were upregulated in NIL-T following salt treatment. We propose that GmSALT3 improves the ability of NIL-T to cope with saline stress through preventing ROS overaccumulation in roots, and potentially modulating Ca2+ signalling, vesicle trafficking and formation of diffusion barriers.

HighlightRNA-seq analysis revealed that GmSALT3, which confers improved salt tolerance on soybean, improves reactive oxygen species detoxification in roots.

category: plant biology


title: Gaining or cutting SLAC: the evolution of plant guard cell signalling pathways

abstract: The evolution of adjustable plant pores (stomata), enabling CO2 acquisition in cuticle wax-sealed tissues was one of the most significant events in the development of life on land. But how did the guard cell signalling pathways that regulate stomatal movements evolve? We investigate this through comparison of fern and angiosperm guard cell transcriptomes. We find that these divergent plant groups share expression of similar genes in guard cells including biosynthesis and signalling genes for the drought stress hormone abscisic acid (ABA). However, despite conserved expression in guard cells, S-type anion channels from the SLAC/SLAH family - known for ABA-mediated stomatal closure in angiosperms - are not activated by the same pathways in ferns, highlighting likely differences in functionality. Examination of other land plant channels revealed a complex evolutionary history, featuring multiple gains or losses of SLAC activation mechanisms, as these channels were recruited to a role in stomatal closure. Taken together, the guard cells of flowering and non-flowering plants share similar core features, but also show lineage-specific and ecological niche-related adaptations, likely underlying differences in behaviour.


title: Learning to Predict in Networks with Heterogeneous and Dynamic Synapses

abstract: AO_SCPLOWBSTRACTC_SCPLOWA salient difference between artificial and biological neural networks is the complexity and diversity of individual units in the latter (Tasic et al., 2018). This remarkable diversity is present in the cellular and synaptic dynamics. In this study we focus on the role in learning of one such dynamical mechanism missing from most artificial neural network models, short-term synaptic plasticity (STSP). Biological synapses have dynamics over at least two time scales: a long time scale, which maps well to synaptic changes in artificial neural networks during learning, and the short time scale of STSP, which is typically ignored. Recent studies have shown the utility of such short-term dynamics in a variety of tasks (Masse et al., 2019; Perez-Nieves et al., 2021), and networks trained with such synapses have been shown to better match recorded neuronal activity and animal behavior (Hu et al., 2020). Here, we allow the timescale of STSP in individual neurons to be learned, simultaneously with standard learning of overall synaptic weights. We study learning performance on two predictive tasks, a simple dynamical system and a more complex MNIST pixel sequence. When the number of computational units is similar to the task dimensionality, RNNs with STSP outperform standard RNN and LSTM models. A potential explanation for this improvement is the encoding of activity history in the short-term synaptic dynamics, a biological form of long short-term memory. Beyond a role for synaptic dynamics themselves, we find a reason and a role for their diversity: learned synaptic time constants become heterogeneous across training and contribute to improved prediction performance in feedforward architectures. These results demonstrate how biologically motivated neural dynamics improve performance on the fundamental task of predicting future inputs with limited computational resources, and how learning such predictions drives neural dynamics towards the diversity found in biological brains.


title: TRPA1 block protects against loss of white matter function during ischaemia in the mouse optic nerve

abstract: Oligodendrocytes produce myelin which provides insulation to axons and speeds up neuronal transmission. In ischaemic conditions myelin is damaged, resulting in mental and physical disabilities. Therefore, it is important to understand how the function of oligodendrocytes and myelin is affected by ischaemia. Recent evidence suggests that oligodendrocyte damage during ischaemia is mediated by TRPA1, whose activation raises intracellular Ca2+ concentrations and damages compact myelin. Here, we show that TRPA1 is constitutively active in oligodendrocytes and the optic nerve, as the specific TRPA1 antagonist, A-967079, decreases basal oligodendrocyte Ca2+ concentrations and increases the size of the compound action potential. Conversely, TRPA1 agonists reduce the size of the optic nerve compound action potential, and this effect is significantly reduced by the TRPA1 antagonist. These results indicate that glial TRPA1 regulates neuronal excitability in the white matter under physiological as well as pathological conditions. Importantly, we find that inhibition of TRPA1 prevents loss of compound action potentials during oxygen and glucose deprivation (OGD) and improves the recovery. TRPA1 block was effective when applied before, during or after OGD, indicating that the damage is occurring during ischaemia and during the recovery, but importantly, that therapeutic intervention is possible after the ischaemic insult. These results indicate that TRPA1 has an important role in the brain, and that its block may be effective in treating oligodendrocyte loss and damage in many white matter diseases.


title: Pollinator habitat plantings benefit wild, native bees, but do not necessarily favor rare species

abstract:
O_LIInstalling pollinator habitat is a ubiquitous conservation tool, but little is known about which pollinator taxa require support, or which benefit from habitat installations.
C_LIO_LIWe studied the response of rare and common bees to pollinator habitat enhancement. We used independent regional datasets to designate bee species as common or rare based on their rank according to one of three metrics: a) site occurrence frequency, b) local relative abundance, and c) geographic range size. We asked whether the abundance or richness of rare and common bees were greater in pollinator habitat, relative to old-field controls. Because we used an arbitrary, quantile-based cutoff to categorize species rarity, we conducted sensitivity analysis and controlled for rarity classification errors with a null model. With this null model, we determined whether rare and/or common species responded to pollinator habitat disproportionately, compared to the expectation for  typical bee species.
C_LIO_LIWe found that the number of individuals and of species designated as rare based on local relative abundance was greater in pollinator habitat enhancements. The number of individuals from bee species designated as rare based on site occurrence was lower in pollinator habitat enhancements, but the number of species was not clearly different between habitat types. We did not find a clear positive nor negative effect of habitat enhancement for species designated rare based on geographic range size. For all three rarity metrics, common species increased in abundance and richness in pollinator habitat relative to controls. Null models indicated that in most cases, neither rare nor common species disproportionately benefited from pollinator habitat.
C_LIO_LISynthesis and Applications: Our results suggest that pollinator habitat can lead to an increase in the abundance and richness of bees, including species that are rare and that are common. However, rare species appeared to respond differently than typical species, and depending on how species were classified as rare, could display muted or even negative responses to habitat enhancement. Targeting rare species with specific floral resources or unique habitat types may lead to better outcomes for rare and threatened species.
C_LI

category: ecology


title: Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives

abstract:
BackgroundConservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use.

We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were Musa acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples and 16 seed samples from one infructescence ( bunch) for each population.

ResultsAllelic richness of seeds compared to populations was 51%, 81% and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (>15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch.

ConclusionsWe demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.


title: Comprehensive assessment of Indian variations in the druggable kinome landscape highlights distinct insights at the sequence, structure and pharmacogenomic stratum

abstract: India confines more than 17% of the worlds population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where the diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes,the second most targeted group of drug targets. The sequence level analysis identified similarities and differences among different populations based on the nsSNVs and amino acid exchange frequencies whereas comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network were investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveal critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world, and investigating its implications in the sequence, structural and pharmacogenomic landscape. The preliminary investigation reported in this paper, supporting the screening and detection of ADRs specific to the Indian population could aid in the development of techniques for pre-clinical and post-market screening of drug-related adverse events in the Indian population.


title: Cooperative regulation of adherens junction elongation through Epidermal Growth Factor Receptor (EGFR) activation.

abstract: The mechanisms controlling the elongation rates of adherens junctions are poorly characterized and lag behind our understanding of those controlling their static properties. In suspended cell aggregates, we found that the speed of de novo junction formation between two cells increases with the number of junctions that the cells are already engaged in. This cooperative effect is driven by the transient activation of the Epidermal Growth Factor Receptor (EGFR) upon junction formation. EGFR activation then regulates the actin cytoskeleton turnover while cortical tension remains unaltered. Overall, we show that EGFR activation regulates the elongation speed of junctions (kinetype) without affecting their final size (phenotype) in such aggregates.

category: biophysics


title: High fidelity epigenetic inheritance: Information theoretic model predicts k-threshold filling of histone modifications post replication

abstract: Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the information encoded in the histone marks gets inherited, given that only half the parental nucleosomes are transferred to each daughter chromatin, is a puzzle. Mapping DNA replication and reconstruction of modifications to equivalent problems in communication of information, we ask how well enzymes can recover the parental modifications, if they were ideal computing machines. Studying a parameter regime where realistic enzymes can function, our analysis predicts that, pragmatically, enzymes may implement a threshold - k filling algorithm which fills unmodified regions of length at most k. This algorithm, motivated from communication theory, is derived from the maximum a posteriori probability (MAP) decoding which identifies the most probable modification sequence based on available observations. Simulations using our method produce modification patterns similar to what has been observed in recent experiments. We also show that our results can be naturally extended to explain inheritance of spatially distinct antagonistic modifications.


title: Peripheral Coupling Sites Formed by STIM1 Govern the Contractility of Vascular Smooth Muscle Cells

abstract: Peripheral coupling between the sarcoplasmic reticulum (SR) and plasma membrane (PM) forms signaling complexes that regulate the membrane potential and contractility of vascular smooth muscle cells (VSMCs), although the mechanisms responsible for these membrane interactions are poorly understood. In many cells, STIM1 (stromal-interaction molecule 1), a single transmembrane-domain protein that resides in the endoplasmic reticulum (ER), transiently moves to ER-PM junctions in response to depletion of ER Ca2+ stores and initiates store-operated Ca2+ entry (SOCE). Fully differentiated VSMCs express STIM1 but exhibit only marginal SOCE activity. We hypothesized that STIM1 is constitutively active in contractile VSMCs and maintains peripheral coupling. In support of this concept, we found that the number and size of SR-PM interacting sites were decreased and SR-dependent Ca2+ signaling processes were disrupted in freshly isolated cerebral artery SMCs from tamoxifen-inducible, SMC-specific STIM1-knockout (Stim1-smKO) mice. VSMCs from Stim1-smKO mice also exhibited a reduction in nanoscale colocalization between Ca2+-release sites on the SR and Ca2+-activated ion channels on the PM, accompanied by diminished channel activity. Stim1-smKO mice were hypotensive and resistance arteries isolated from them displayed blunted contractility. These data suggest that STIM1 - independent of SR Ca2+ store depletion - is critically important for stable peripheral coupling in contractile VSMCs.

category: physiology


title: Tapping into non-English-language science for the conservation of global biodiversity

abstract: The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,680 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate, and can expand the geographical (by 12-25%) and taxonomic (by 5-32%) coverage of English-language evidence, especially in biodiverse regions, albeit often based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges.

category: scientific communication and education


title: Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro

abstract: Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic digestion, extensive sample clean-up to remove MS-incompatible surfactants, and offline sample fractionation to reduce proteome complexity prior to online liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Thus, there is a need for a fast, robust, and reproducible method for protein identification and quantification from complex proteomes. Herein, we developed an ultrafast bottom-up proteomics method enabled by Azo, a photocleavable, MS-compatible surfactant that effectively solubilizes proteins and promotes rapid tryptic digestion, combined with the Bruker timsTOF Pro, which enables deeper proteome coverage through trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF) of peptides. We applied this method to analyze the complex human cardiac proteome and identified nearly 4,000 protein groups from as little as 1 mg of human heart tissue in a single one-dimensional LC-TIMS-MS/MS run with high reproducibility. Overall, we anticipate this ultrafast, robust, and reproducible bottom-up method empowered by both Azo and the timsTOF Pro will be generally applicable and greatly accelerate the throughput of large-scale quantitative proteomic studies. Raw data are available via the MassIVE repository with identifier MSV000087476.

category: systems biology


title: PERK Activation by SB202190 Attenuates Amyloidogenesis via TFEB-induced Autophagy-Lysosomal Pathway

abstract: The protein kinase R (PKR)-like endoplasmic reticulum (ER) kinase (PERK), a key ER stress sensor of the unfolded protein response (UPR), can confer beneficial effects by facilitating the removal of cytosolic aggregates through the autophagy-lysosome pathway (ALP). In neurodegenerative diseases, the ALP ameliorates the accumulation of intracellular protein aggregates in the brain. Transcription factor-EB (TFEB), a master regulator of the ALP, positively regulates key genes involved in the cellular degradative pathway. However, in neurons, the role of PERK activation in mitigating amyloidogenesis by ALP remains unclear. In this study, we found that SB202190 selectively activates PERK independently of its inhibition of p38 mitogen-activated protein kinase, but not inositol-requiring transmembrane kinase/endoribonuclease-1 (IRE1) or activating transcription factor 6 (ATF6), in human neuroblastoma cells. PERK activation by SB202190 was dependent on mitochondrial ROS production and promoted Ca2+-calcineurin activation. The activation of the PERK-Ca2+-calcineurin axis by SB202190 positively affects TFEB activity to increase ALP in neuroblastoma cells. Collectively, our study reveals a novel physiological mechanism underlying ALP activation, dependent on PERK activation, for ameliorating amyloidogenesis in neurodegenerative diseases.


title: Alpha phase-amplitude tradeoffs predict visual perception

abstract:
Spontaneous alpha oscillations (~10 Hz) have been associated with various cognitive functions, including perception. Their phase and amplitude independently predict cortical excitability and subsequent perceptual performance. Yet, the causal role of alpha phase-amplitude tradeoffs on visual perception remains ill-defined. We aimed to fill this gap and tested two clear predictions from the Pulsed Inhibition theory according to which alpha oscillations are associated with periodic functional inhibition. (1) High alpha amplitude induces cortical inhibition at specific phases, associated with low perceptual performance, while at opposite phases, inhibition decreases (potentially increasing excitation) and perceptual performance increases. (2) Low alpha amplitude is less susceptible to these phasic (periodic) pulses of inhibition, leading to overall higher perceptual performance. Here, cortical excitability was assessed in humans using phosphene (illusory) perception induced by single pulses of transcranial magnetic stimulation (TMS) applied over visual cortex at perceptual threshold, and its post-pulse evoked activity recorded with simultaneous electroencephalography (EEG). We observed that pre-pulse alpha phase modulates the probability to perceive a phosphene, predominantly for high alpha amplitude, with a non-optimal phase for phosphene perception between -{pi}/2 and -{pi}/4. The pre-pulse non-optimal phase further leads to an increase in post-pulse evoked activity (ERP), in phosphene-perceived trials specifically. Together, these results show that alpha oscillations create periodic inhibitory moments when alpha amplitude is high, leading to periodic decrease of perceptual performance. This study provides strong causal evidence in favor of the Pulsed Inhibition theory.

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O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/445552v3_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1c6e4f8org.highwire.dtl.DTLVardef@e26614org.highwire.dtl.DTLVardef@19bc93forg.highwire.dtl.DTLVardef@b97b36_HPS_FORMAT_FIGEXP  M_FIG C_FIG Significance StatementThe Pulsed Inhibition theory predicts that the functional inhibition induced by high alpha oscillations amplitude is periodic, with specific phases decreasing neural firing and perceptual performance. In turn, low alpha oscillations amplitude is less susceptible to phasic moments of pulsed inhibition leading to overall higher perceptual performance. Using TMS with simultaneous EEG recordings in humans, we found that specific phases of spontaneous alpha oscillations (~10 Hz) decrease cortical excitability and the subsequent perceptual outcomes predominantly when alpha amplitude is high. Our results provide strong causal evidence in favor of the Pulsed Inhibition theory.


title: Secreted Proteases Control the Timing of Aggregative Community Formation in Vibrio cholerae

abstract:
Bacteria orchestrate collective behaviors using the cell-cell communication process called quorum sensing (QS). QS relies on the synthesis, release, and group-wide detection of small molecules called autoinducers. In Vibrio cholerae, a multicellular community aggregation program occurs in liquid, during stationary phase, and in the high-cell-density QS state. Here, we demonstrate that this aggregation program consists of two subprograms. In one subprogram, which we call void formation, structures form that contain few cells but provide a scaffold within which cells can embed. The other subprogram relies on flagellar machinery and enables cells to enter voids. A genetic screen for factors contributing to void formation, coupled with companion molecular analyses, showed that four extracellular proteases, Vca0812, Vca0813, HapA, and PrtV control the onset timing of both void formation and aggregation, and moreover, proteolytic activity is required. These proteases, or their downstream products, can be shared between void-producing and non-void-forming cells and can elicit aggregation in a normally non-aggregating V. cholerae strain. Employing multiple proteases to control void formation and aggregation timing could provide a redundant and irreversible path to commitment to this community lifestyle.

ImportanceBacteria can work as collectives to form multicellular communities. Vibrio cholerae, the bacterium that causes the disease cholera in humans, forms aggregated communities in liquid. Aggregate formation relies on a chemical communication process called quorum sensing. Here we show that, beyond overarching control by quorum sensing, there are two aggregation subprograms. One subprogram, which we call void formation, creates a scaffold within which cells can embed. The second subprogram, which allows bacteria to enter the scaffold, requires motility. We discovered that four extracellular proteases control the timing of both void formation and aggregation. We argue that, by using redundant proteases, V. cholerae ensures the reliable execution of this community formation process. These findings may provide insight into how V. cholerae successfully alternates between the marine environment and the human host: transitions that are central to the spread of the disease cholera.


title: Additive and epistatic effects influence spectral tuning in molluscan retinochrome opsin

abstract:
The relationship between genotype and phenotype is nontrivial due to often complex molecular pathways that make it difficult to unambiguously relate phenotypes to specific genotypes. Photopigments, an opsin apoprotein bound to a light-absorbing chromophore, present an opportunity to directly relate the amino acid sequence to an absorbance peak phenotype ({lambda}max). We examined this relationship by conducting a series of site-directed mutagenesis experiments of retinochrome, a non-visual opsin, from two closely related species: the common bay scallop, Argopecten irradians, and the king scallop, Pecten maximus. Using protein folding models, we identified three amino acid sites of likely functional importance and expressed mutated retinochrome proteins in vitro. Our results show that the mutation of amino acids lining the opsin binding pocket are responsible for fine spectral tuning, or small changes in the {lambda}max of these light sensitive proteins Most mutations caused a blue shift regardless of the retinochrome background, with shifts ranging from a 12 nm blue shift to a 5 nm red shift from the wild-type {lambda}max. These mutations do not show an additive effect, but rather suggests the presence of epistatic interactions. This work highlights the importance of binding pocket shape in the evolution of spectral tuning and builds on our ability to relate genotypic changes to phenotypes in an emerging model for opsin functional analysis.

Author summarySite-directed mutagenesis determined that spectral tuning in retinochrome is not solely additive, but is influenced by intra-molecular epistasis.


title: Membrane architecture and adherens junctions contribute to strong Notch pathway activation

abstract: The Notch pathway mediates cell-to-cell communication in a variety of tissues, developmental stages and organisms. Pathway activation relies on the interaction between transmembrane ligands and receptors on adjacent cells. As such, pathway activity could be influenced by the size, composition or dynamics of contacts between membranes. The initiation of Notch signalling in the Drosophila embryo occurs during cellularization, when lateral cell membranes and adherens junctions are first being deposited, allowing us to investigate the importance of membrane architecture and specific junctional domains for signaling. By measuring Notch dependent transcription in live embryos we established that it initiates while lateral membranes are growing and that signalling onset correlates with a specific phase in their formation. However, the length of the lateral membranes per se was not limiting. Rather, the adherens junctions, which assemble concurrently with membrane deposition, contributed to the high levels of signalling required for transcription, as indicated by the consequences from depleting -Catenin. Together, these results demonstrate that the establishment of lateral membrane contacts can be limiting for Notch trans-activation and suggest that adherens junctions play an important role in modulating Notch activity.

category: developmental biology


title: Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement.

abstract:
The retinoic acid receptor-related orphan receptor {gamma} (ROR{gamma}) is a ligand-dependent transcription factor of the nuclear receptor super family that underpins metabolic activity, immune function, and cancer progression. Despite being a valuable drug target in health and disease, our understanding of the ligand-dependent activities of ROR{gamma} is far from complete. Like most nuclear receptors, ROR{gamma} must recruit coregulatory protein to enact the ROR{gamma} target gene program. To date, a majority of structural studies have been focused exclusively on the ROR{gamma} ligand-binding domain and the ligand-dependent recruitment of small peptide segments of coregulators. Herein, we examine the ligand-dependent assembly of full length ROR{gamma}:coregulator complexes on cognate DNA response elements using structural proteomics and small angle x-ray scattering. The results from our studies suggest that ROR{gamma} becomes elongated upon DNA recognition, preventing long range interdomain crosstalk. We also determined that the DNA binding domain adopts a sequence-specific conformation, and that coregulatory proteins may be able to  sense the ligand- and DNA-bound status of ROR{gamma}. We propose a model where ligand-dependent coregulator recruitment may be influenced by the sequence of the DNA to which ROR{gamma} is bound. Overall, the efforts described herein will illuminate important aspects of full length ROR{gamma} and monomeric orphan nuclear receptor target gene regulation through DNA-dependent conformational changes.

GRAPHICAL ABSTRACT

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title: Double face of cytochrome c in cancers.New look into human breast ducts with Raman imaging

abstract:
Cytochrome c (Cyt c) is a key protein that is needed to maintain life (respiration) and cell death (apoptosis). The dual-function of Cyt c comes from its capability to act as mitochondrial redox carrier that transfers electrons between the membrane-embedded complexes III and IV and to serve as a cytoplasmic apoptosis-triggering agent, activating the caspase cascade.1-6 However, the precise roles of Cyt c in mitochondria, cytoplasm and extracellular matrix under normal and pathological conditions are not completely understood.7-9

To date, no pathway of Cyt c release that results in caspase activation has been compellingly demon-strated in any invertebrate.10 The significance of mitochondrial dysfunctionality has not been studied in ductal carcinoma to the best of our knowledge.1

Here we show that proper concentration of monounsaturated fatty acids, saturated fatty acids, cardi-olipin and Cyt c is critical in the correct breast ductal functioning and constitutes an important parameter to assess breast epithelial cells integrity and homeostasis. We look inside human breast ducts answering fundamental questions about location and distribution of various biochemical components inside the lumen, epithelial cells of the duct and the extracellular matrix around the cancer duct during cancer development in situ. We found in histopathologically controlled breast cancer duct that Cyt c, cardi-olipin, and palmitic acid are the main components inside the lumen of cancerous duct in situ. The pre-sented results show direct evidence that Cyt c is released to the lumen from the epithelial cells in can-cerous duct. In contrast the lumen in normal duct is empty and free of Cyt c. Our results demonstrate how Cyt c is likely to function in cancer development. We anticipate our results to be a starting point for more sophisticated in vitro and in vivo animal models. For example, the correlation between concentration of Cyt c and cancer grade could be tested in various types of cancer. Furthermore, Cyt c is a target of anti-cancer drug development 11,12 and a well-defined and quantitative Raman based assay for oxidative phosphorylation and apoptosis will be relevant for such developments.

category: cancer biology


title: Hippocampal reconfiguration of events in mnemonic networks

abstract: It is widely assumed that episodic memories are not stored in isolation but rather in dynamic event networks. However, the mechanisms of the underlying dynamic of these representations, in particular how such networks are updated, remain elusive. In this study, we investigated the reconfiguration of events into event networks in the hippocampus by presenting new events that could update either one of two competing narratives. During the first session, participants viewed four animated movies, each representing a distinct narrative; two distinct narratives from the Jones family and two distinct narratives from the Smith family. During the second session, we re-exposed participants to snapshots of these narratives along with snapshots of new events from one of the two families, allowing updating of the acquired event networks of that family. Our findings show that the hippocampus integrated new events that relate to the old family, and then integrated these new events with the corresponding old events. Furthermore, hippocampal representations of the events within a narrative became better integrated after updating. Our results shed new light on the neural mechanisms underlying flexible mnemonic updating with realistic events and further advance our understanding of the structured reconfiguration of event networks in memory.


title: Feasibility of FreeSurfer processing for T1-weighted brain images of 5-year-olds: semiautomated protocol of FinnBrain Neuroimaging Lab

abstract: Pediatric neuroimaging is a quickly developing field that still faces important methodological challenges. One key challenge is the use of many different atlases, automated segmentation tools, manual edits in semiautomated protocols, and quality control protocols, which complicates comparisons between studies. In this article, we present our semiautomated segmentation protocol using FreeSurfer v6.0, ENIGMA consortium software, and the quality control protocol that was used in FinnBrain Birth Cohort Study. We used a dichotomous quality rating scale for inclusion and exclusion of images, and then explored the quality on a region of interest level to exclude all regions with major segmentation errors. The effects of manual edits on cortical thickness values were minor: less than 2% in all regions. Supplementary materials cover registration and additional edit options in FreeSurfer and comparison to the computational anatomy toolbox (CAT12). Overall, we conclude that despite minor imperfections FreeSurfer can be reliably used to segment cortical metrics from T1-weighted images of 5-year-old children with appropriate quality assessment in place. However, custom templates may be needed to optimize the results for the subcortical areas. Our semiautomated segmentation protocol provides high quality pediatric neuroimaging data and could help investigators working with similar data sets.


title: A neural network account of memory replay and knowledge consolidation

abstract: Replay can consolidate memories through offline neural reactivation related to past experiences. Category knowledge is learned across multiple experiences, and its subsequent generalisation is promoted by consolidation and replay during rest and sleep. However, aspects of replay are difficult to determine from neuroimaging studies. We provided insights into category knowledge replay by simulating these processes in a neural network which approximated the roles of the human ventral visual stream and hippocampus. Generative replay, akin to imagining new category instances, facilitated generalisation to new experiences. Consolidation-related replay may therefore help to prepare us for the future as much as remember the past. Generative replay was more effective in later network layers functionally similar to the lateral occipital cortex than layers corresponding to early visual cortex, drawing a distinction between neural replay and its relevance to consolidation. Category replay was most beneficial for newly acquired knowledge, suggesting replay helps us adapt to changes in our environment. Finally, we present a novel mechanism for the observation that the brain selectively consolidates weaker information; a reinforcement learning process in which categories were replayed according to their contribution to network performance. This reinforces the idea of consolidation-related replay as an active rather than passive process.


title: An efficient protocol for chromosome isolation from sterlet (A. ruthenus) embryos and larvae

abstract: In the present study, the development of an efficient and feasible protocol for chromosome preparation from sterlet (A. ruthenus) embryos and larvae was carried out. In the established protocol, the mean efficiency of chromosome extraction ranged from 70 to 100%. The average number of recorded metaphases per slide was between 9 to 15. In general, the most satisfactory results were obtained for embryos at 6 dpf and larvae at the age of up to 7 dph. In the 24 dpf group, chromosome isolation was possible without immersion in spindle poison, however; in successive developmental stages, the minimal immersion time exceeded 1.5 hours, regardless of chorionation. Immersion for 14 hours did not compromise the efficacy of chromosome isolation. In the current study, successful chromosome isolation was determined mainly by hypotonization conditions. Younger developmental stages generally require the shortest hypotonization times, whereas older larvae require longer hypotonization times. The optimal hypotonization period is 5-15 minutes for embryos at 24 dpf, 40 minutes for embryos at 4dpf, and 50-60 minutes for fish at 6 dpf-7 dph. The only exception was the 24 hpf group where only blastula cells were used. An additional overnight fixation step significantly enhanced chromosome quality and supported chromosome counting especially in the 24 dpf group. The quality and quantity of chromosome slides were also significantly determined by tissue type, and the slides prepared from heads (gill cells) produced the best results.

category: cell biology


title: A quantitative review of abundance-based species distribution models

abstract: The contributions of species to ecosystem functions or services depend not only on their presence in a given community, but also on their local abundance. Progress in predictive spatial modelling has largely focused on species occurrence, rather than abundance. As such, limited guidance exists on the most reliable methods to explain and predict spatial variation in abundance. We analysed the performance of 68 abundance-based species distribution models fitted to 800,000 standardised abundance records for more than 800 terrestrial bird and reef fish species. We found high heterogeneity in performance of abundance-based models. While many models performed poorly, a subset of models consistently reconstructed range-wide abundance patterns. The best predictions were obtained using random forests for frequently encountered and abundant species, and for predictions within the same environmental domain as model calibration. Extending predictions of species abundance outside of the environmental conditions used in model training generated poor predictions. Thus, interpolation of abundances between observations can help improve understanding of spatial abundance patterns, but extrapolated predictions of abundance, e.g. under climate change, have a much greater uncertainty. Our synthesis provides a roadmap for modelling abundance patterns, a key property of species distributions that underpins theoretical and applied questions in ecology and conservation.