title: Parasite defensive limb movements enhance signal attraction in male little torrent frogs: insight into the evolution of multimodal signals

abstract: Many animals rely on complex sexual signals that target multiple senses to attract mates and repel rivals. These multimodal mating displays can however also attract unintended receivers, which can be an important driver of signal complexity. Despite being taxonomically widespread, we often lack insight into how multimodal signals evolve from unimodal signals and in particular what roles unintended eavesdroppers play. Here we assess whether the physical movements of parasite defense behavior increase the complexity and attractiveness of an acoustic sexual signal in the little torrent frog (Amolops torrentis). Calling males of this species often display limb movements in order to defend against blood-sucking parasites such as frog-biting midges that eavesdrop on their acoustic signal. Through mate choice tests we show that some of these midge-evoked movements influence female preference for acoustic signals. Our data suggest that midge-induced movements may be incorporated into a sexual display, targeting both hearing and vision in the intended receiver. Females may play an important role in incorporating these multiple components because they prefer signals which combine multiple programs. Our results thus help to understand the relationship between ecological and sexual selection pressure operating on signalers and how in turn this may influence multimodal signal evolution.


title: Cell type-specific interpretation of noncoding variants using deep learning-based methods

abstract: Interpretation of non-coding genomic variants is one of the most important challenges in human genetics. Machine learning methods have emerged recently as a powerful tool to solve this problem. State-of-the-art approaches allow prediction of transcriptional and epigenetic effects caused by non-coding mutations. However, these approaches require specific experimental data for training and can not generalize across cell types where required features were not experimentally measured. We show here that available epigenetic characteristics of human cell types are extremely sparse, limiting those approaches that rely on specific epigenetic input. We propose a new neural network architecture, DeepCT, which can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Furthermore, we show that DeepCT can learn cell type-specific properties, build biologically meaningful vector representations of cell types and utilize these representations to generate cell type-specific predictions of the effects of non-coding variations in the human genome.

category: genetics


title: Discovery of a MUC3B gene reconstructs the membrane mucin gene cluster on human chromosome 7

abstract: Human tissue surfaces are coated with mucins, a family of macromolecular sugar-laden proteins serving diverse functions from lubrication to formation of selective biochemical barriers against harmful microorganisms and molecules. Membrane mucins are a distinct group of mucins that are attached to epithelial cell surfaces where they create a dense glycocalyx facing the extracellular environment. All mucin proteins carry long stretches of tandemly repeated sequences that undergo extensive O-linked glycosylation to form linear mucin domains. However, the repetitive nature of mucin domains makes them prone to recombination and render their genetic sequences particularly difficult to read with standard sequencing technologies. As a result, human mucin genes suffer from significant sequence gaps that have hampered investigation of gene function in health and disease. Here we leveraged a recent human genome assembly to identify a previously unmapped MUC3B gene located within a cluster of four structurally related membrane mucin genes that we entitle the MUC3 cluster at q22 locus in chromosome 7. We found that MUC3B shares high sequence identity with the known MUC3A gene, and that the two genes are governed by evolutionarily conserved regulatory elements. Furthermore, we show that MUC3A, MUC3B, MUC12 and MUC17 in the human MUC3 cluster are exclusively expressed in intestinal epithelial cells. Our results complete existing genetic gaps in the MUC3 cluster that is a conserved genetic unit during primate evolution. We anticipate our results to be the starting point for detection of new polymorphisms in the MUC3 cluster associated with human diseases. Moreover, our study provides the basis for exploration of intestinal mucin gene function in widely used experimental models such as human intestinal organoids and genetic mouse models.


title: Vocal traits of shorebird chicks are related to body mass and sex

abstract: Acoustic communication is critical during early life phases in precocial birds. For example, adult alarm calls can elicit antipredator behaviour in young, and chick vocalisations can communicate information to parents about chick identity, condition, location, sex, or age. We investigated whether chick calls of two species of Australian Charadriidae vary with sex or body mass. We handled Red-capped Plover Charadrius ruficapillus and Southern Masked Lapwing Vanellus miles novaehollandiae chicks for purposes of measurement, blood sampling, and banding. We opportunistically recorded their distress calls while in the hand, and analysed the calls to determine whether call structure is related to sex or body mass (a proxy for age). We measured five traits per call, plus time intervals between successive calls, for 26 plover chicks (2600 calls) and 95 lapwing chicks (6835 calls). In plovers, inter-call intervals were shorter in males and both inter-call interval and the dominant frequency range of calls decreased with increasing body mass. In lapwings, frequency modulation (computed as the range in the rate of change of the dominant frequency) was lower in male calls. The dominant frequency range of lapwing calls decreased with mass in both sexes, but the decline was greater in males, resulting in a lower dominant frequency range in males. Frequency modulation and entropy of lapwing calls also decreased with increasing body mass. Minimum dominant frequency did not change with body mass or sex in either species. Our study provides the first evidence for charadriid chicks of (a) a sexual difference in call structure and rate and (b) gradual growth-related changes in call structure and rate, across chicks. Studies on calls from a greater range of chick ages and from more species within this large and diverse family would be valuable. We provide a foundation for further studies of shorebird vocalisations during growth, which may elucidate the development and functional significance of such vocalisations.

category: animal behavior and cognition


title: P-TEFb is degraded by Siah1/2 in quiescent cells

abstract: P-TEFb, composed of CycT1 and CDK9, regulates the elongation of transcription by RNA polymerase II. In proliferating cells, it is regulated by 7SK snRNA in the 7SK snRNP complex. In resting cells, P-TEFb is absent, because CycT1 is dephosphorylated, released from CDK9 and rapidly degraded. In this study, we identified the mechanism of this degradation. We mapped the ubiquitination and degradation of free CycT1 to its N-terminal region from positions 1 to 280. This region is ubiquitinated at six lysines, where E3 ligases Siah1 and Siah2 bind and degrade these sequences. Importantly, the inhibition of Siah1/2 rescued the expression of free CycT1 in proliferating as well as resting primary cells. We conclude that Siah1/2 are the E3 ligases that bind and degrade the dissociated CycT1 in resting, terminally differentiated, anergic and/or exhausted cells.

category: biochemistry


title: Cell adhesion strength and tractions are mechano-diagnostic features of cellular invasiveness

abstract: The adhesion of cells to substrates occurs via integrin clustering and binding to the actin cytoskeleton. Oncogenes modify anchorage-dependent mechanisms in cells during cancer progression. Fluid shear devices provide a label-free, non-invasive way to characterize cell-substrate interactions and heterogeneities in the cell populations. We quantified the critical adhesion strengths of MCF7, MDAMB-231, A549, HPL1D, HeLa, and NIH3T3 cells using a custom fluid shear device. The detachment response was sigmoidal for each cell type. A549 and MDAMB-231 cells had significantly lower adhesion strengths at {tau}50 than their non-invasive counterparts, HPL1D and MCF7. Detachment dynamics was inversely correlated with cell invasion potentials. A theoretical model, based on {tau}50 values and the distribution of cell areas on substrates, provided good fits to data from de-adhesion experiments. Quantification of cell tractions, using the Reg-FTTC method on 10 kPa polyacrylamide gels, showed highest values for invasive, MDAMB-231 and A549, cells compared to non-invasive cells. Immunofluorescence studies show differences in vinculin distributions: non-invasive cells have distinct vinculin puncta, whereas invasive cells have more dispersed distributions. The cytoskeleton in non-invasive cells was devoid of well-developed stress fibers, and had thicker cortical actin bundles in the boundary. These correlations in adhesion strengths with cell invasiveness, demonstrated here, may be useful in cancer diagnostics and other pathologies featuring misregulation in adhesion.

category: bioengineering


title: VRK1 is a Paralog Synthetic Lethal Target in VRK2-methylated Glioblastoma

abstract: Synthetic lethality -- a genetic interaction that results in cell death when two genetic deficiencies co-occur but not when either deficiency occurs alone -- can be co-opted for cancer therapeutics. A pair of paralog genes is among the most straightforward synthetic lethal interaction by virtue of their redundant functions. Here we demonstrate a paralog-based synthetic lethality by targeting Vaccinia-Related Kinase 1 (VRK1) in Vaccinia-Related Kinase 2 (VRK2)-methylated glioblastoma (GBM). VRK2 is silenced by promoter methylation in approximately two-thirds of GBM, an aggressive cancer with few available targeted therapies. Genetic knockdown of VRK1 in VRK2-null or VRK2-methylated cells results in decreased activity of the downstream substrate Barrier to Autointegration Factor (BAF), a regulator of post-mitotic nuclear envelope formation. VRK1 knockdown, and thus reduced BAF activity, causes nuclear lobulation, blebbing and micronucleation, which subsequently results in G2/M arrest and DNA damage. The VRK1-VRK2 synthetic lethal interaction is dependent on VRK1 kinase activity and is rescued by ectopic VRK2 expression. Knockdown of VRK1 leads to robust tumor growth inhibition in VRK2-methylated GBM xenografts. These results indicate that inhibiting VRK1 kinase activity could be a viable therapeutic strategy in VRK2-methylated GBM.

category: cancer biology


title: Novel enhancers of guanylyl cyclase-A activity via allosteric modulation

abstract: Natriuretic peptide receptor (NPR)-A (also known as NPR-A, NPR1 or guanylyl cyclase-A, GC-A) is an attractive but challenging target to activate with small molecules. GC-A is activated by endogenous atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP), and this activation leads to the production of 3,5-cyclic guanosine monophosphate (cGMP). This system plays an important role in the regulation of cardiovascular and renal homeostasis. However, utilization of this receptor as a drug target has so far been limited to peptides, even though small molecule modulators allow oral administration and longer half-life. We have identified small molecular allosteric enhancers of GC-A, which strengthened ANP or BNP activation in various in vitro and ex vivo systems. These compounds do not mediate their actions through previously described allosteric binding sites or via known mechanisms of action. In addition, their selectivity and activity are dependent on only one amino acid in GC-A. Our findings show that there is a novel allosteric binding site on GC-A, which can be targeted by small molecules that increase the signaling effects of ANP and BNP.

category: pharmacology and toxicology


title: Normal Reproductive function in male mice lacking pituitary kisspeptin receptor.

abstract: The anterior pituitary secretion of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) regulate gonadal development, gametogenesis and the secretion of the gonadal steroid hormones. The gonadotroph is primarily regulated by hypothalamic secretion of gonadotropin-releasing hormone (GnRH) from neurons of the rostral hypothalamus and is mediated by GnRH receptor signaling. Kisspeptin (KISS1)/kisspeptin receptor (KISS1R) signaling in GnRH neurons plays an essential role in reproductive function. As the kisspeptin receptor is present in the pituitary, kisspeptin signaling via the Kiss1r may regulate reproductive function at the level of pituitary. Using Cre/Lox technology, we deleted the Kiss1r gene in pituitary gonadotropes (PKiRKO). PKiRKO male and females have normal genital development, puberty onset, and fertility. Females have normal LH, FSH and estradiol while males had significantly increased basal serum FSH levels with no differences in basal serum LH, or testosterone levels. Overall, these findings indicate that the pituitary KISS1R does not play a role in male reproduction.

category: physiology


title: Thylakoid grana stacking revealed by multiplex genome editing of LHCII encoding genes

abstract: Land plant chloroplasts differ from algal ones for their thylakoid membranes being organized in grana: piles of vesicles paired by their stromal surface, forming domains including Photosystem (PS) II and its antenna while excluding PS I and ATPase to stroma membranes, connecting grana stacks. The molecular basis of grana stacking remain unclear. We obtained genotypes lacking the trimeric antenna complex (Lhcb1-2-3), the monomeric Lhcb4-5-6, or both. Full deletion caused loss of grana, while either monomers or trimers support 50% stacking. The expression of Lhcb5 alone restored stacking at 50%, while Lhcb2 alone produced huge grana which broke down upon light exposure. Cyclic electron transport was maintained in the lack of stacking, while excitation energy balance between photosystems and the repair efficiency of damaged Photosystem II were affected. We conclude that grana evolved for need of regulating energy balance between photosystems under terrestrial canopy involving rapid changes in photon spectral distribution.

category: plant biology


title: NETISCE: A Network-Based Tool for Cell Fate Reprogramming

abstract: The search for effective therapeutic targets in fields like regenerative medicine and cancer research has generated interest in cell fate reprogramming. This cellular reprogramming paradigm can drive cells to a desired target state from any initial state. However, methods for identifying reprogramming targets remain limited for biological systems that lack large sets of experimental data or a dynamical characterization. We present NETISCE, a novel computational tool for identifying cell fate reprogramming targets in static networks. In combination with machine learning algorithms, NETISCE estimates the attractor landscape and predicts reprogramming targets using Signal Flow Analysis and Feedback Vertex Set Control, respectively. Through validations in studies of cell fate reprogramming from developmental, stem cell, and cancer biology, we show that NETISCE can predict previously identified cell fate reprogramming targets and identify potentially novel combinations of targets. NETISCE extends cell fate reprogramming studies to larger-scale biological networks without the need for full model parameterization and can be implemented by experimental and computational biologists to identify parts of a biological system relevant to the desired reprogramming task.

category: systems biology


title: Patterns of Arc mRNA expression in the rat brain following dual recall of fear- and reward-based socially acquired information

abstract: The ability to learn new information and behaviors is a vital component of survival in most animal species. This learning can occur via direct experience or through observation of another individual (i.e., social learning). While research focused on understanding the neural mechanisms of direct learning is prevalent, less work has aimed at understanding the brain circuitry mediating the acquisition and recall of socially acquired information. We aimed to further elucidate the mechanisms underlying recall of socially acquired information by having rats sequentially recall a socially transmitted food preference (STFP) and a fear association via fear conditioning by-proxy (FCbP). Brain tissue was processed for mRNA expression of the immediate early gene (IEG) Arc, which reliably expresses in the cell nucleus following transcription before migrating to the cytoplasm over the next 25 minutes. Given this timeframe, we were able to identify whether Arc transcription was triggered by STFP recall, FCbP recall, or following recall of both memories. Surprisingly - and contrary to past research examining expression of other IEGs following STFP or FCbP recall separately - we found no differences in any of the Arc expression measures across a number of prefrontal regions and the vCA3 of the hippocampus between controls, demonstrators, and observers, though we did detect an overall effect of sex in a number of regions. We theorize that these results may indicate that relatively little Arc-dependent neural restructuring is taking place in the prefrontal cortices following recall of a recently socially acquired information or directly acquired fear associations in these areas.

category: neuroscience


title: White-matter degradation and dynamical compensation support age-related functional alterations in human brain

abstract: Structural connectivity of the brain at different ages is analyzed using diffusion-weighted Magnetic Resonance Imaging (MRI) data. The largest decrease of the number and average length of streamlines is found for the long inter-hemispheric links, with the strongest impact for frontal regions. From the BOLD functional MRI (fMRI) time series we identify age-related changes of dynamic functional connectivity (dFC) and spatial covariation features of the FC links captured by metaconnectivity (MC). They indicate more constant dFC, but wider range and variance of MC. Finally we applied computational whole-brain network model based on oscillators, which mechanistically expresses the impact of the spatio-temporal structure of the brain (weights and the delays) to the dynamics. With this we tested several hypothesis, which revealed that the spatio-temporal reorganization of the brain with ageing, supports the observed functional fingerprints only if the model accounts for: (i) compensation of the individual brains for the overall loss of structural connectivity, and (ii) decrease of propagation velocity due to the loss of myelination. We also show that having these two conditions, it is sufficient to decompose the time-delays as bimodal distribution that only distinguishes between intra- and inter-hemispheric delays, and that the same working point also captures the static FC the best.


title: The Rhizosphere Bacterial Communities Differ Among Domesticated Maize Landraces - An Experimental Confirmation

abstract:
O_LIThe plant-associated microbiome has been shown to vary considerably between species and across environmental gradients. The effects of genomic variation on the microbiome within single species are less clearly understood, with results often confounded by the larger effects of climatic and edaphic variation.
C_LIO_LIIn this study, the effect of genomic variation on the rhizosphere bacterial communities of maize was investigated by comparing different genotypes grown within controlled environments. Rhizosphere bacterial communities were profiled by metabarcoding the universal bacterial 16S rRNA v3-v4 region. Initially, plants from the inbred B73 line and the Ancho - More 10 landrace were grown for 12- weeks and compared. The experiment was then repeated with an additional four Mexican landraces (Apachito - Chih 172, Tehua - Chis 204, Serrano - Pueb 180 and Hairnoso de Ocho) that were grown alongside additional B73 and Ancho - More 10 genotypes.
C_LIO_LIIn both experiments there were significant genotypic differences in the rhizosphere bacteria. Additionally, the bacterial communities were significantly correlated with genomic distance between genotypes, with the more closely related landraces being more similar in rhizosphere bacterial communities.
C_LIO_LIDespite limited sampling numbers, here we confirm that genomic variation in maize landraces is associated with differences in the rhizosphere bacterial communities. Further studies that go beyond correlations to identify the mechanisms that determine the genotypic variation of the rhizosphere microbiome are required.
C_LI

category: microbiology


title: NeoRdRp: A comprehensive dataset for identifying RNA-dependent RNA polymerase of various RNA viruses from metatranscriptomic data

abstract: RNA viruses are distributed throughout various environments, and most RNA viruses have recently been identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify novel RNA viruses from metatranscriptome data. To overcome this issue, we created a dataset of RNA-dependent RNA polymerase (RdRp) domains that are essential for all RNA viruses belonging to Orthornavirae. Genes with RdRp domains from various RNA viruses were clustered based on their amino acid sequence similarity. For each cluster, a multiple sequence alignment was generated, and a hidden Markov model (HMM) profile was created if the number of sequences was greater than three. We further refined the 426 HMM profiles by detecting the RefSeq RNA virus sequences and subsequently combined the hit sequences with the RdRp domains. As a result, a total of 1,182 HMM profiles were generated from 12,502 RdRp domain sequences, and the dataset was named NeoRdRp. Almost all NeoRdRp HMM profiles successfully detected RdRp domains, specifically in the UniProt dataset. Furthermore, we compared the NeoRdRp dataset with two previously reported methods for RNA virus detection using metatranscriptome sequencing data. Our methods successfully identified most of the RNA viruses in the datasets; however, some RNA viruses were not detected, as in the cases of the other two methods. The NeoRdRp can be repeatedly improved by adding new RdRp sequences and is applicable as a system for detecting various RNA viruses from diverse metatranscriptome data.


title: Triple-helix potential of the mouse genome

abstract: Certain DNA sequences, including mirror-symmetric polypyrimidine/polypurine runs, are capable of folding into a triple-helix-containing non-B-form DNA structure called H-DNA. Such H-DNA-forming sequences are frequent in many eukaryotic genomes, including in mammals, and multiple lines of evidence indicate that these motifs are mutagenic and can impinge on DNA replication, transcription, and other aspects of genome function. In this study, we show that the triplex-forming potential of H-DNA motifs in the mouse genome can be evaluated using S1-sequencing (S1-seq), which uses the single-stranded DNA (ssDNA)-specific nuclease S1 to generate deep-sequencing libraries that report on the position of ssDNA throughout the genome. When S1-seq was applied to genomic DNA isolated from mouse testis cells and splenic B cells, we observed prominent clusters of S1-seq reads that appeared to be independent of endogenous double-strand breaks, that coincided with H-DNA motifs, and that correlated strongly with the triplex-forming potential of the motifs. Fine-scale patterns of S1-seq reads, including a pronounced strand asymmetry in favor of centrally-positioned reads on the pyrimidine-containing strand, suggested that this S1-seq signal is specific for one of the four possible isomers of H-DNA (H-y5). By leveraging the abundance and complexity of naturally occurring H-DNA motifs across the mouse genome, we further defined how polypyrimidine repeat length and the presence of repeat-interrupting substitutions modify the structure of H-DNA. This study provides a new approach for studying DNA secondary structure genome wide at high spatial resolution.

category: molecular biology


title: ZC3HC1 is a structural element of the nuclear basket effecting interlinkage of TPR polypeptides

abstract: The nuclear basket (NB), anchored to the nuclear pore complex (NPC), is commonly thought of as built solely of protein TPR polypeptides, the latter thus regarded as the NBs only scaffold-forming components. In the current study, we report ZC3HC1 as a second building element of the NB. Recently described as an NB-appended protein omnipresent in vertebrates, we now show that ZC3HC1, both in vivo and in vitro, enables in a step-wise fashion the recruitment of TPR subpopulations to the NB and their linkage to already NPC-anchored TPR polypeptides. We further demonstrate that the degron-mediated rapid elimination of ZC3HC1 results in the prompt detachment of the ZC3HC1-appended TPR polypeptides from the NB and their release back into the nucleoplasm again, underscoring the role of ZC3HC1 as a natural structural element of the NB. Finally, we show that ZC3HC1 can keep TPR polypeptides positioned even at sites remote from the NB, in line with ZC3HC1 functioning as a protein connecting TPR polypeptides.

category: cell biology


title: Functional Requirements for a Samd14-Capping Protein Complex in Stress Erythropoiesis

abstract: Acute anemia induces rapid expansion of erythroid precursors and accelerated differentiation to replenish erythrocytes. Paracrine signals - involving cooperation between SCF/c-Kit signaling and other signaling inputs - are required for the increased erythroid precursor activity in anemia. Our prior work revealed that the Sterile Alpha Motif (SAM) Domain 14 (Samd14) gene increases the regenerative capacity of the erythroid system and promotes stress-dependent c-Kit signaling. However, the mechanism underlying Samd14s role in stress erythropoiesis is unknown. We identified a protein- protein interaction between Samd14 and the - and {beta} heterodimers of the F-actin capping protein (CP) complex. Knockdown of the CP {beta} subunit increased erythroid maturation in ex vivo cultures and decreased colony forming potential of stress erythroid precursors. In a genetic complementation assay for Samd14 activity, our results revealed that the Samd14-CP interaction is a determinant of erythroid precursor cell levels and function. Samd14-CP promotes SCF/c-kit signaling in CD71med spleen erythroid precursors. Given the roles of c-Kit signaling in hematopoiesis and Samd14 in c-Kit pathway activation, this mechanism may have pathological implications in acute/chronic anemia.


title: Acoustic and vibrational signaling in true katydid Nesoecia nigrispina: three means of sound production in the one species

abstract: The males of Mexican katydids Nesoecia nigrispina (Stal, 1873) produce calling songs and protest sounds using the same stridulatory apparatus as in most of the other Ensifera at the base of the elytra. It includes pars stridens on the upper elytron and plectrum on the lower. Calling sounds of two types (fast and slow) are 2-pulse series, repeated with a frequency of 1.2-4.5 s-1. Protest signals in the form of short trills from the same pulse duration males produce with tactile stimulation. The pulse repetition rate is more higher than that of the calling sounds - up to 10 (mean c. 8) s-1. The frequency spectra of these signals have maxima in the band of 14-15 kHz. However, in addition to the sounds described, both males and females are capable to produce protest signals of the second type with the help of another sound apparatus, namely with the help of the wings. Insects with removed elytra are unable to produce an audible sound. Thus, the sound is produced by the friction of the wings on the elytra, but there are no specialized stridulatory structures on them. In individuals of both sexes, in response mainly to tactile stimulation, short clicks are recorded, which they make, apparently, by the mandibles. Vibrational signals at tremulation are emitted by individuals of both sexes during courtship and males, completing the calling signal cycle and after copulation. It is possible that vibrational signals are an additional factor in reproductive isolation in sympatric species, since the calling sound signals in representatives of the genus Nesoecia are similar and exhibit significant variability.


title: Escherichia coli chemotaxis to competing stimuli in a microfluidic device with a constant gradient

abstract: In natural systems bacteria are exposed to many chemical stimulants; some attract chemotactic bacteria as they promote survival, while others repel bacteria because they inhibit survival. When faced with a mixture of chemoeffectors, it is not obvious which direction the population will migrate. Predicting this direction requires an understanding of how bacteria process information about their surroundings. We used a multiscale mathematical model to relate molecular level details of their two-component signaling system to the probability that an individual cell changes its swimming direction to the chemotactic velocity of a bacterial population. We used a microfluidic device designed to maintain a constant chemical gradient to compare model predictions to experimental observations. We obtained parameter values for the multiscale model of Escherichia coli chemotaxis to individual stimuli, -methylaspartate and nickel ion, separately. Then without any additional fitting parameters, we predicted the response to chemoeffector mixtures. Migration of E. coli toward -methylaspartate was modulated by adding increasing concentrations of nickel ion. Thus, the migration direction was controlled by the relative concentrations of competing chemoeffectors in a predictable way. This study demonstrated the utility of a multiscale model to predict the migration direction of bacteria in the presence of competing chemoeffectors.


title: Genomic analyses identify biological processes in ZKSCAN3-deficient colorectal cancer cells

abstract: Zinc finger with KRAB and SCAN domain 3 (ZKSCAN3) is associated with cell differentiation, cell proliferation and apoptosis, which has been reported as a critical driver of colorectal cancer. However, the mechanism and function of ZKSCAN3 in colorectal cancer is still unclear. Here, our objective is to identify the functional molecules and signaling by analyzing the RNA-seq data. The GSE172201 was created by the Illumina NovaSeq 6000 (Homo sapiens). The KEGG and GO analyses indicated the immune defense response to virus and transcription activity are major processes in the ZKSCAN3 KO colorectal cancer cells. Moreover, we determined ten key molecules including STAT1, MX1, DDX58, PPARG, EGFR, APP, BST2, DLG4, OASL, and IFIT2. Therefore, our study may provide the novel knowledge of ZKSCAN3 mediated colorectal cancer.

category: bioinformatics


title: Structure-function relationships in mitochondrial transcriptional condensates

abstract:
Phase separation organizes many membraneless structures in cells. The functional consequences of concentrating cellular machinery into biomolecular condensates, however, are largely unclear. One fundamental cellular function that has been linked to condensate formation is transcription. Here, we have reconstituted mitochondrial transcription in condensates from purified components. We find that the core components of the mttranscriptional machinery form multi-phasic, viscoelastic condensates in vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than equivalent reactions in bulk solution. These condensate-mediated decreases in transcriptional rates are associated with the formation of dynamically arrested vesicular structures that are driven by the production and accumulation of RNA during transcription. Using coarse-grained, equilibrium simulations, we show that the generation of RNA alters the phase behavior and the organization of transcriptional components within condensates and that the in vitro mtcondensates are non-equilibrium structures. Together, our in vitro and in silico approaches shed light on how proteins and (ribo)nucleic acids biophysically self-assemble within mitochondria in vivo. Our results highlight the complex morphologies of transcribing, multicomponent condensates and they illustrate the interdependent structure-function relationships in condensates.

Significance StatementMitochondria condense their genome into transcriptionally active mt-nucleoids. These structures fit the definition of biomolecular condensates that form via macromolecular phase separation. We take advantage of the ability to reconstitute mitochondrial transcriptional condensates in vitro from minimal components. We find that the production and accumulation of RNA alters the phase behavior of transcriptional condensates. The altered phase behavior is linked to the formation of arrested, non-equilibrium vesicular structures. Similar changes to phase behavior of proteins and (ribo)nucleic acids can be recapitulated in live mitochondria through knockdown of mt-nucleoid core components. Computer simulations help identify biophysical mechanisms that are needed to maintain the steady-state structures of transcriptional condensates.

category: biophysics


title: The 24-chain core-shell nanostructure of wood cellulose microfibrils in seed plants

abstract: Wood cellulose microfibrils (CMFs) are the most abundant organic substance on earth, but their nanostructures are poorly understood. There are controversies regarding the glucan chain number (N) of CMFs during initial synthesis and whether they become fused afterwards. Here, we combined small-angle X-ray scattering (SAXS), solid-state nuclear magnetic resonance (ssNMR) and X-ray diffraction (XRD) analyses to resolve these controversies. We successfully developed SAXS measurement methods for the cross-section aspect ratio and area of the crystalline-ordered CMF core, which showed higher density than the semi-disordered shell. The 1:1 aspect ratio suggested that CMFs remain mostly segregated, not fused. The area measurement revealed the chain number in the core zone (Ncore). The ratio of ordered cellulose over total cellulose, termed Roc, was determined by ssNMR. Using the formula N = Ncore / Roc, we found that the majority of wood CMFs contain 24 chains, conserved between gymnosperm and angiosperm trees. The average wood CMF has a crystalline-ordered core of [~]2.2 nm diameter and a semi-disordered shell of [~]0.5 nm thickness. In naturally and artificially aged wood, we only observed CMF aggregation (contact without crystalline continuity) but not fusion (forming conjoined crystalline unit). This further argued against the existence of partially fused CMFs in new wood, overturning the recently proposed 18-chain fusion hypothesis. Our findings are important for advancing wood structural knowledge and more efficient utilization of wood resources in sustainable bio-economies.


title: Theta- and gamma-band oscillatory uncoupling in the macaque hippocampus

abstract: Nested hippocampal oscillations in the rodent gives rise to temporal coding that may underlie learning, memory, and decision making. Theta/gamma coupling in rodent CA1 occurs during exploration and sharp-wave ripples during quiescence. Whether these oscillatory regimes extend to primates is less clear. We therefore sought to identify correspondences in frequency bands, nesting, and behavioral coupling taken from macaque hippocampus. We found that, in contrast to the rodent, theta and gamma frequency bands in macaque CA1 were segregated by behavioral states. Beta/gamma (15-70Hz) had greater power during visual search while theta (7-10 Hz) dominated during quiescence. Moreover, delta/theta (3-8 Hz) amplitude was strongest when beta2/slow gamma (20-35 Hz) amplitude was weakest, though the low frequencies coupled with higher, ripple frequencies (60-150 Hz). The distribution of spike-field coherence revealed three peaks matching the 3-10 Hz, 20-30 Hz and 60-150 Hz bands; however, the low frequency effects were primarily due to sharp-wave ripples. Accordingly, no intrinsic theta spiking rhythmicity was apparent. These results support a role for beta2/slow gamma modulation in CA1 during active exploration in the primate that is decoupled from theta oscillations. These findings diverge from the rodent oscillatory canon and call for a shift in focus and frequency when considering the primate hippocampus.


title: Fast parametric curve matching (FPCM) for automatic spike detection

abstract: Epilepsy is a widely spread neurological disease, whose treatment often requires resection of the pathological cortical tissue. Interictal spike analysis observed in the non-invasively collected EEG or MEG data offers an attractive way to localize epileptogenic cortical structures for surgery planning purposes. Interictal spike detection in lengthy multichannel data is a daunting task that is still often performed manually. This frequently limits such an analysis to a small portion of the data which renders the appropriate risks of missing the potentially epileptogenic region. While a plethora of automatic spike detection techniques have been developed each with its own assumptions and limitations, non of them is ideal and the best results are achieved when the output of several automatic spike detectors are combined. This is especially true in the low signal-to-noise ratio conditions. To this end we propose a novel biomimetic approach for automatic spike detection based on a constrained mixed spline machinery that we dub as fast parametric curve matching (FPCM). Using the peak-wave shape parametrization, the constrained parametric morphological model is constructed and convolved with the observed multichannel data to efficiently determine mixed spline parameters corresponding to each time-point in the dataset. Then the logical predicates that directly map to verbalized text-book like descriptions of the expected interictal event morphology allow us to accomplish the spike detection task. The results of simulations mimicking typical low SNR scenario show the robustness and high ROC AUC values of the FPCM method as compared to the spike detection performed using more conventional approaches such as wavelet decomposition, template matching or simple amplitude thresholding. Applied to the real MEG and EEG data from the human patients and to rat ECoG data, the FPCM technique demonstrates reliable detection of the interictal events and localization of epileptogenic zones concordant with independent conclusions made by the epileptologist. Since the FPCM is computationally light, tolerant to high amplitude artifacts and flexible to accommodate verbalized descriptions of the arbitrary target morphology, it may complement the existing arsenal of means for analysis of noisy interictal datasets.


title: Prelimbic proBDNF facilitates memory destabilization by regulation of neuronal function in juveniles

abstract: Fear regulation changes as a function of age and adolescence is a key developmental period for the continued maturation of fear neural circuitry. The involvement of prelimbic proBDNF in fear memory extinction and its mediated signaling were reported previously. Given the inherent high level of proBDNF during juvenile period, we tested whether prelimbic proBDNF regulated synaptic and neuronal functions allowing to influencing retrieval-dependent memory processing. By examining freezing behavior of auditory fear conditioned rats, we found high levels of prelimbic proBDNF in juvenile rats enhanced destabilization of the retrieval-dependent weak but not strong fear memory through activating p75NTR-GluN2B signaling. This modification was attributed to the increment in proportion of thin type spine and promotion in synaptic function, as evidence by facilitation of NMDA-mediated EPSCs and GluN2B-dependent synaptic depression. The strong prelimbic theta- and gamma-oscillation coupling predicted the suppressive effect of proBDNF on the recall of post-retrieval memory. Our results critically emphasize the importance of developmental proBDNF for modification of retrieval-dependent memory and provide a potential critical targeting to inhibit threaten memories associated with neurodevelopment disorders.


title: Dynamic characteristics and Functional Analysis Provide new insights into the role of GauERF105 in resistance against Verticillium wilt in Cotton

abstract: Verticillium wilt is the most devastating disease of cotton and it results in huge yield losses every year in the fields. The underlying mechanisms of VW in cotton are not well explored yet. In the current approach we used the transcriptome data from G. australe in response to Verticillium wilt attack to mine the ERF TFs and prove their potential role in resistance against VW attack in cotton. We identified 23 ERFs in total, and on the basis of expression at different time points i.e., 24h, 48h and 72h post inoculation and selected GauERF105 for further validation. We performed VIGS in cotton and over expression in Arabidopsis respectively. Moreover, DAB and trypan staining also suggests that the impact of disease was more in the wildtype as compared to transgene lines. On the basis of our results, we confirmed that GauERF105 is the key candidate and playing a key role for defending cotton against VW attack. Current finding might be helpful for generating resistance germplasm in cotton and it will be beneficial to recover the yield losses in field.

category: pathology


title: Liquid condensate is a common state of proteins and polypeptides at the regime of high intermolecular interactions

abstract: Liquid-liquid phase separation (LLPS) has emerged as a crucial biological mechanism for sequestering macromolecules (such as proteins and nucleic acids) into membraneless organelles in cells. Unstructured and intrinsically disordered domains are known to facilitate multivalent interactions driving protein LLPS. We hypothesized that LLPS could be an intrinsic property of proteins/polypeptides at their high intermolecular interaction regime. To examine this, we studied many (a total of 23) proteins/polypeptides with different structures and sequences for LLPS study using molecular crowder polyethylene glycol (PEG-8000). We showed that all proteins and even highly charged polypeptides (under study) can undergo liquid condensate formation, however with different phase space and conditions. Using a single component and combinations of protein multicomponent (co-LLPS) systems, we establish that a variety of intermolecular interactions can drive proteins/polypeptides LLPS.


title: Interplay between LHCSR proteins and state transitions governs the NPQ response in intact cells of Chlamydomonas during light fluctuations.

abstract:
Photosynthetic organisms use sunlight as the primary energy source to fix CO2. However, in the environment, light energy fluctuates rapidly and often exceeds saturating levels for periods ranging from seconds to hours, which can lead to detrimental effects for cells. Safe dissipation of excess light energy occurs primarily by non-photochemical quenching (NPQ) processes. In the model green microalga Chlamydomonas reinhardtii, photoprotective NPQ is mostly mediated by pH-sensing light-harvesting complex stress-related (LHCSR) proteins and the redistribution of light-harvesting antenna proteins between the photosystems (state transition). Although each component underlying NPQ has been documented, their relative contributions to the dynamic functioning of NPQ under fluctuating light conditions remains unknown. Here, by monitoring NPQ throughout multiple high light-dark cycles with fluctuation periods ranging from 1 to 10 minutes, we show that the dynamics of NPQ depend on the frequency of light fluctuations. Mutants impaired in the accumulation of LHCSRs (npq4, lhcsr1, and npq4lhcsr1) showed significantly less quenching during illumination, demonstrating that LHCSR proteins are responsible for the majority of NPQ during repetitive exposure to high light fluctuations. Activation of NPQ was also observed during the dark phases of light fluctuations, and this was exacerbated in mutants lacking LHCSRs. By analyzing 77K chlorophyll fluorescence spectra and chlorophyll fluorescence lifetimes and yields in a mutant impaired in state transition, we show that this phenomenon arises from state transition. Finally, we quantified the contributions of LHCSRs and state transition to the overall NPQ amplitude and dynamics for all light periods tested and show that both processes interact to facilitate NPQ during light fluctuations. We further assess the role of LHCSRs in cell growth under various periods of fluctuating light. These results highlight the dynamic functioning of photoprotection under light fluctuations and open a new way to systematically characterize the photosynthetic response to an ever-changing light environment.

One sentence summaryThe roles of LHCSR and STT7 in NPQ vary with the light fluctuation period and duration of light fluctuation.


title: AVATAR: AI Vision Analysis for Three-dimensional Action in Real-time

abstract: Artificial intelligence (AI) is an emerging tool for high-resolution behavioural analysis and conduction of human-free behavioural experiments. Here, we applied an AI-based system, AVATAR, which automatically virtualises 3D motions from the detection of 9 body parts. This allows quantification, classification and detection of specific action sequences in real-time and facilitates closed-loop manipulation, triggered by the onset of specific behaviours, in freely moving mice.


title: Expectation violations produce error signals in mouse V1

abstract: Repeated exposure to visual sequences changes the form of evoked activity in the primary visual cortex (V1). Predictive coding theory provides a potential explanation for this, namely that plasticity shapes cortical circuits to encode spatiotemporal predictions and that subsequent responses are modulated by the degree to which actual inputs match these expectations. Here we use a recently developed statistical modeling technique called Model-Based Targeted Dimensionality Reduction (MbTDR) to study visually-evoked dynamics in mouse V1 in context of a previously described experimental paradigm called "sequence learning". We report that evoked spiking activity changed significantly with training, in a manner generally consistent with the predictive coding framework. Neural responses to expected stimuli were suppressed in a late window (100-150ms) after stimulus onset following training, while responses to novel stimuli were not. Omitting predictable stimuli led to increased firing at the expected time of stimulus onset, but only in trained mice. Substituting a novel stimulus for a familiar one led to changes in firing that persisted for at least 300ms. In addition, we show that spiking data can be used to accurately decode time within the sequence. Our findings are consistent with the idea that plasticity in early visual circuits is involved in coding spatiotemporal information.


title: Testing the state-dependent model of time perception against experimental evidence

abstract: Coordinated movements, speech and other actions are impossible without precise timing. Realistic computational models of interval timing in the mammalian brain are expected to provide key insights into the underlying mechanisms of timing. Existing computational models of time perception have only been partially replicating experimental observations, such as the linear increase of time, the dopaminergic modulation of this increase, and the scalar property, i.e., the linear increase of the standard deviation of temporal estimates. In this work, we incorporate the state-dependent computational model, which encodes time in the dynamic evolution of network states without the need for a specific network structure into a biologically plausible prefrontal cortex (PFC) model based on in vivo and in vitro recordings of rodents. Specifically, we stimulated 1000 neurons in the beginning and in the end of a range of different time intervals, extracted states of neurons and trained the readout layer based on these states using least squares to predict the respective inter stimulus interval. We show that the naturally occurring heterogeneity in cellular and synaptic parameters in the PFC is sufficient to encode time over several hundreds of milliseconds. The readout faithfully represents the duration between two stimuli applied to the superficial layers of the network, thus fulfilling the requirement of a linear encoding of time. A simulated activation of the D2 dopamine receptor leads to an overestimation and an inactivation to an underestimation of time, in line with experimental results. Furthermore, we show that the scalar property holds true for intervals of several hundred milliseconds, and provide a mechanistic explanation for the origin of the scalar property as well as its deviations. We conclude that this model can represent durations up to 750 ms in a biophysically plausible setting, compatible with experimental findings in this regime.


title: Adjunctive inhibition of the integrated stress response pathway accelerates bacterial clearance in a mouse model of tuberculosis

abstract: Tuberculosis (TB) is a devastating infectious disease that continues to cause millions of human deaths every year. Even though most cases of TB can be cured with a 6-month antibiotic combination therapy, these long treatment durations have led to the emergence of multi-drug resistance and pose a major hurdle to global TB control. Despite numerous advances in TB drug development, a substantially shortened treatment time has yet to be achieved. Given the rise in antibiotic resistance, an alternative strategy to the direct targeting of M. tuberculosis (M.tb) is the development of host-directed therapies (HDTs) that promote bacterial clearance and/or lung health when given adjunctive to standard TB antibiotics. We recently discovered that a small molecule inhibitor of the Integrated Stress Response (ISR), which is abnormally activated in TB and associated with the formation of necrotic granulomas, reduced M.tb numbers and lung inflammation in mice. Here, we evaluated the therapeutic potential of adjunctive ISR inhibition in the context of standard TB therapy. Throughout the course of treatment, ISR inhibition robustly lowered bacterial burdens compared to standard TB therapy alone and accelerated the time-to-sterility in mice, as demonstrated by significantly reduced relapse rates after 4 months of treatment. In addition, mice receiving adjunctive ISR inhibition tended to have reduced lung necrosis and inflammation. Together, our findings identify the ISR pathway as a promising therapeutic target with the potential of shortening TB treatment durations and improving lung health.


title: Production and cross-feeding of nitrite within Prochlorococcus populations

abstract:
Prochlorococcus is an abundant photosynthetic bacterium in the oligotrophic open ocean where nitrogen (N) often limits the growth of phytoplankton. Prochlorococcus has evolved into multiple phylogenetic clades of high-light (HL) adapted and low-light (LL) adapted cells. Within these clades, cells encode a variety of N assimilation traits that are differentially distributed among members of the population. Among these traits, nitrate (NO3-) assimilation is generally restricted to a few clades of high-light adapted cells (the HLI, HLII, and HLVI clades) and a single clade of low-light adapted cells (the LLI clade). Most, if not all, cells belonging to the LLI clade have the ability to assimilate nitrite (NO2-), with a subset of this clade capable of assimilating both NO3- and NO2-. Cells belonging to the LLI clade are maximally abundant at the top of the nitracline and near the primary NO2- maximum layer. In some ecosystems, this peak in NO2- concentration may be a consequence of incomplete assimilatory NO3- reduction by phytoplankton. This phenomenon is characterized by a bottleneck in the downstream half of the NO3- assimilation pathway and the concomitant accumulation and release of NO2- by phytoplankton cells. Given the association between LLI Prochlorococcus and the primary NO2- maximum layer, we hypothesized that some Prochlorococcus exhibit incomplete assimilatory NO3- reduction. To assess this, we monitored NO2- accumulation in batch culture for 3 Prochlorococcus strains (MIT0915, MIT0917, and SB) and 2 Synechococcus strains (WH8102 and WH7803) when grown on NO3- as the sole N source. Only MIT0917 and SB accumulated external NO2- during growth on NO3-. Approximately 20-30% of the NO3-transported into the cell by MIT0917 was released as NO2-, with the balance assimilated into biomass. We further observed that co-cultures using NO3- as the sole N source could be established for MIT0917 and a Prochlorococcus strain that can assimilate NO2- but not NO3-. In these co-cultures, the NO2- released by MIT0917 was efficiently consumed by its partner strain during balanced exponential growth. Our findings highlight the potential for emergent metabolic partnerships within Prochlorococcus populations that are mediated by the production and consumption of the N cycle intermediate, NO2-.

SIGNIFICANCEEarths biogeochemical cycles are substantially driven by microorganisms and their interactions. Given that N often limits marine photosynthesis, we investigated the potential for N cross-feeding within populations of Prochlorococcus, the numerically dominant photosynthetic cell in the subtropical open ocean. During growth on NO3-, some Prochlorococcus cells release up to 30% of their N uptake as extracellular NO2-. In the wild, Prochlorococcus populations are composed of multiple functional types, including those that cannot use NO3- but can still assimilate NO2-. We show that metabolic dependencies arise when Prochlorococcus strains with complementary NO2- production and consumption phenotypes are grown together on NO3-. These findings demonstrate the potential for emergent metabolic partnerships, possibly modulating ocean nutrient gradients, that are mediated by cross-feeding of N cycle intermediates.


title: Isoforms of the transcriptional cofactor SIN3 differentially regulate genes necessary for energy metabolism and cell survival

abstract: The SIN3 scaffolding protein is a conserved transcriptional regulator known to fine-tune gene expression. In Drosophila, there are two major isoforms of SIN3, SIN3 220 and SIN3 187, which each assemble into multi-subunit histone modifying complexes. The isoforms have distinct developmental expression patterns and non-redundant functions. Gene regulatory network analyses indicate that both isoforms affect genes encoding proteins in pathways such as the cell cycle and cell morphogenesis. Interestingly, the SIN3 187 isoform uniquely regulates a subset of pathways including post-embryonic development, phosphate metabolism and apoptosis. Target genes in the phosphate metabolism pathway include nuclear-encoded mitochondrial genes coding for proteins responsible for oxidative phosphorylation. Here, we investigate the physiological effects of SIN3 isoforms on energy metabolism and cell survival. We find that ectopic expression of SIN3 187 represses expression of several nuclear-encoded mitochondrial genes affecting production of ATP and generation of reactive oxygen species (ROS). Forced expression of SIN3 187 also activates several pro-apoptotic and represses a few anti-apoptotic genes. In the SIN3 187 expressing cells, these gene expression patterns are accompanied with an increased sensitivity to paraquat-mediated oxidative stress. These findings indicate that SIN3 187 influences the regulation of mitochondrial function, apoptosis and oxidative stress response in ways that are dissimilar from SIN3 220. The data suggest that the distinct SIN3 histone modifying complexes are deployed in different cellular contexts to maintain homeostasis.


title: oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera

abstract: Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterising the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, likely a result of non-homologous end joining, and a large deletion in the 3' UTR due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

category: developmental biology


title: Cyanopeptides Restriction and Degradation Co-mediate Microbiota Assembly During a Freshwater Cyanobacterial Harmful Algal Bloom (CyanoHAB)

abstract: Cyanobacterial harmful algal blooms (CyanoHABs) are globally intensifying and exacerbated by climate change and eutrophication. However, microbiota assembly mechanisms underlying CyanoHABs remain scenario specific and elusive. Especially, cyanopeptides, as a group of bioactive secondary metabolites of cyanobacteria, could affect microbiota assembly and ecosystem function. Here, the trajectory of cyanopeptides were followed and linked to microbiota during Microcystis-dominated CyanoHABs in lake Taihu, China. The most abundant cyanopeptide classes detected included microginin, spumigin, microcystin, nodularin and cyanopeptolin with total MC-LR-equivalent concentrations between 0.23 and 2051.54 ppb, of which cyanotoxins beyond microcystins (e.g., cyanostatin B and nodularin_R etc.) far exceeded reported organismal IC50 and negatively correlated with microbiota diversity, exerting potential collective eco-toxicities stronger than microcystins alone. The microbial communities were differentiated by size fraction and sampling date throughout CyanoHABs, and surprisingly, their variances were better explained by cyanopeptides (19-38%) than nutrients (0-16%). Cyanopeptides restriction (e.g., inhibition) and degradation are first quantitatively verified as the deterministic drivers governing community assembly, with stochastic processes being mediated by interplay between cyanopeptide dynamics and lake microbiota. This study presents an emerging paradigm in which cyanopeptides restriction and degradation co-mediate lake water microbiota assembly, unveiling new insights about the ecotoxicological significance of CyanoHABs to freshwater ecosystems.

category: ecology


title: Importance Of Small Diameter Woody Plants And Treelet Species In Tropical Wet Evergreen Forest Of Southern Western Ghats, India

abstract: Tropical forests have long been accepted for their productivity and ecosystem services on account of their high diversity and stand structural attributes. In spite of their significance, tropical forests, and especially those of Asia, remain understudied. Until recently, most forest inventories in Asia have concentrated on trees 10 cm in diameter. Floristic composition, plant species diversity, above ground biomass, basal area and diversity were investigated across different life form and two-diameter classes in a large scale 10-ha plot, in the undisturbed tropical seasonal rain forest of Southern Western Ghats, Kerala, India. Regeneration pattern of the study area was examined by evaluating fishers alpha and IVI (Important Value Index) across three layer of vegetation (seedling, sapling, and tree). Within the plot, we recorded 25,390 woody plant species[≥] 1 cm dbh from 45 families, 91 genera, and 106 species. Plant density was 2539 woody individuals per hectare, with a basal area of 47.72 m2/ha and an above-ground biomass of 421.77 Mg/ha. By basal area, density, and frequency, the Rubiaceae, Sapotaceae, and Malvaceae families were the most important. Small-diameter trees (1 cm [≤] dbh [≤]10 cm) found to be 78 percent of the total tree population, 20.2 percent of the basal area, and 1.4 percent of the aboveground biomass. They also possessed 6 percent more diversity at the family level, 10% more diversity at the genus level, and 12% more diversity at the species level than woody individuals under 10 cm dbh.. Woody individuals of treelets life form and small-diameter classes were much more diverse and dense than the other groups, indicating that results based only on larger canopy trees and larger diameter class may be not an appropriate representation of the diversity status of a particular tropical forest type. Lower density of individuals in initial girth class indicates the vulnerability of the forest system to anthropogenic, natural disturbance and a changing climate. Reduce the minimum diameter limit down to 1 cm, in contrast to 10 cm limit used in most of the evergreen forest inventories, revealed a high density and diversity in thelower stories.


title: Northward Expansion of Amblyomma americanum (Acari: Ixodidae) into Southern Michigan

abstract: Amblyomma americanum (Linnaeus) (Acari: Ixodidae) (lone star tick) is an aggressive, generalist parasite that vectors numerous important human and animal pathogens. In recent decades its geographic range has expanded northwards from endemic regions in the southeastern and southcentral US. In 2019 five questing A. americanum comprising two life stages were detected at one site in Berrien County, in southwestern Michigan, satisfying one CDC criterium for an established population for the first time in the state. To better characterize the northern extent of emerging A. americanum, we conducted active surveillance (i.e., drag sampling) in summer 2020 throughout Michigans southern counties and detected one adult A. americanum from each of six widespread sites, including where they had been detected in 2019. A larger established population was identified at another site in Berrien County, which yielded 691 A. americanum comprising three life stages. Questing tick phenologies at this site were similar to that reported for other regions. Statewide surveillance in 2021 revealed no A. americanum outside of Berrien County, but establishment criteria were met again at the two sites where established populations were first detected respectively in 2019 and 2020. These observations may represent the initial successful invasion of A. americanum into Michigan. Data from passive (1999-2020) and active surveillance (2004-2021) efforts, including a domestic animal sentinel program (2015-2018), are reported to provide context for this nascent invasion. Continued active surveillance is needed to help inform the public, medical professionals, and public health officials of the health risks associated with this vector.


title: Meta-analysis of the genetic loci of pigment pattern evolution in vertebrates

abstract: Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for meta-analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harboring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found that genes implicated in upstream developmental processes had greater cis-regulatory proportions than downstream cellular function genes, and that ligands were associated with higher cis-regulatory proportions than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.

category: evolutionary biology


title: The hidden structural variability in avian genomes

abstract: Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study, we used a combination of long-read and linked-read genome assemblies to investigate the occurrence of insertions and deletions across the chromosomes of 14 species of birds-of-paradise and two species of estrildid finches including highly repetitive W chromosomes. The species sampling encompasses most genera and representatives from all major clades of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. We found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turnover of transposable element insertions, especially endogenous retroviruses.


title: Pachytene karyotypes of 17 species of birds

abstract: Karyotypes of less than 10% of bird species are known. Using immunolocalization of the synaptonemal complex, the core structure of meiotic chromosomes at the pachytene stage, and centromere proteins we described male pachytene karyotypes of seventeen species of birds. This method enables higher resolution than the conventional analyses of metaphase chromosomes. We provided the first descriptions of the karyotypes of three species (Rook, Blyths reed warbler and European pied flycatcher), corrected the published data on the karyotypes of ten species and confirmed them for four species. All passerine species examined have highly conservative karyotypes, 2n=80-82 with seven pairs of macrochromosomes and 33-34 pairs of microchromosomes. In all of them but not in the Common cuckoo we revealed single copies of the germline restricted chromosomes varying in size and morphology even between closely related species. This indicates a fast evolution of this additional chromosome. The interspecies differences concern the sizes of the macrochromosomes, morphology of the microchromosomes and sizes of the centromeres. The pachytene cells of the Gouldian finch, Brambling and Common linnet contained heteromorphic synaptonemal complexes indicating heterozygosity for inversions or centromere shifts. The European pied flycatcher, Gouldian finch and Domestic canary have extended centromeres in several macro- and microchromosomes.

category: genetics


title: The TOG protein Stu2 is regulated by acetylation

abstract: Stu2 in S. cerevisiae is a member of the XMAP215/Dis1/Alp14/Msps/CKAP5/ch-TOG family of MAPs and has multiple functions in controlling microtubules, including microtubule polymerization, microtubule depolymerization, linking chromosomes to the kinetochore, and assembly of {gamma}-TuSCs at the SPB. Whereas phosphorylation has been shown to be critical for Stu2 localization at the kinetochore, other regulatory mechanisms that control Stu2 function are still poorly understood. Here, we show that a novel form of Stu2 regulation occurs through the acetylation of three lysine residues at K252, K469, and K870, which are located in three distinct domains of Stu2. Alteration of acetylation through acetyl-mimetic and acetyl-blocking mutations did not impact the essential function of Stu2. Instead, these mutations lead to both positive and negative changes in chromosome stability, as well as changes in resistance to the microtubule depolymerization drug, benomyl. In agreement with our in silico modeling, several acetylation-mimetic mutants displayed increased interactions with {gamma}-tubulin. Taken together, these data suggest that Stu2 acetylation can govern multiple Stu2 functions in both a positive and negative manner, including chromosome stability and interactions at the SPB.


title: Analyzing the relationship between distracted driving and eye movement using multimodal data collected during car driving

abstract: Human error is the leading cause of traffic accidents and originates from the distraction caused by various factors, such as the drivers physical condition and mental state. One of the significant factors causing driver distraction is the presence of stress. In a previous study, multiple stressors were used to examine distraction while driving. Multiple stressors were given to the driver and the corresponding driver biometric data were obtained, and a multimodal dataset was published thereafter. In this study, we reiterate the results of existing studies and investigated the relationship between gaze variability while driving and stressor intervention, which has not yet been examined. We also examined whether biometric and vehicle information can estimate the presence or absence of secondary tasks during driving.

category: bioengineering


title: STReTCh: a strategy for facile detection of mechanical forces across proteins in cells

abstract: Numerous proteins experience and respond to mechanical forces as an integral part of their cellular functions, but measuring these forces remains a practical challenge. Here, we present a compact, 11 kDa molecular tension sensor termed STReTCh (Sensing Tension by Reactive Tag Characterization). Unlike existing genetically encoded tension sensors, STReTCh does not rely on experimentally demanding Forster resonance energy transfer (FRET)-based measurements and is compatible with typical fix-and-stain protocols. Using a magnetic tweezers assay, we calibrate the STReTCh module and show that it responds to physiologically relevant, piconewton forces. As proof-of-concept, we use an extracellular STReTCh-based sensor to visualize cell-generated forces at integrin-based adhesion complexes. In addition, we incorporate STReTCh into vinculin, a cytoskeletal adaptor protein, and show that STReTCh reports on forces transmitted between the cytoskeleton and cellular adhesion complexes. These data illustrate the utility of STReTCh as a broadly applicable tool for the measurement molecular-scale forces in biological systems.


title: Robust hydrogel-integrated microsystems enabled by enhanced interfacial bonding strength

abstract: Noncovalent hydrogels, compared to covalent hydrogels, have distinctive advantages including biocompatibility and self-healing property but tend to have poor mechanical robustness, thus restricting their application spectrum. A clue to increase utility of such soft hydrogels without chemical bulk modification can be witnessed in biological organ walls where soft mucous epithelial layers are juxtaposed with tough connective tissues. Perhaps, similarly, bonding noncovalent hydrogels to stronger materials, such as tough hydrogels, might be a viable approach for increasing stability and scalability as well as creating novel functions for hydrogel-based systems. However when attempting to bond these two materials, each of the four existing hydrogel-hydrogel bonding method has practical shortcomings. In this work, we introduce a mucosa-inspired bonding method that realizes interfacial bonding of noncovalent hydrogels to tough, hybrid hydrogels without external glue or bulk modification of the noncovalent gel while preserving interfacial micropatterns. The procedure is simple and we confirmed broad applicability with various noncovalent hydrogels and tough hydrogels. We demonstrated the utility of our bonding method with novel applications regarding in vitro assay, soft robotics and biologically inspired systems.


title: Novel Methods for Elucidating Modality Importance in Multimodal Electrophysiology Classifiers

abstract: Multimodal classification is increasingly common in biomedical informatics studies. Many such studies use deep learning classifiers with raw data, which makes explainability difficult. As such, only a few studies have applied explainability methods, and new methods are needed. In this study, we propose sleep stage classification as a testbed for method development and train a convolutional neural network with electroencephalogram (EEG), electrooculogram, and electromyogram data. We then present a global approach that is uniquely adapted for electrophysiology analysis. We further present two local approaches that can identify subject-level differences in explanations that would be obscured by global methods and that can provide insight into the effects of clinical and demographic variables upon the patterns learned by the classifier. We find that EEG is globally the most important modality for all sleep stages, except non-rapid eye movement stage 1 and that local subject-level differences in importance arise. We further show that sex, followed by medication and age had significant effects upon the patterns learned by the classifier. Our novel methods enhance explainability for the growing field of multimodal classification, provide avenues for the advancement of personalized medicine, and yield novel insights into the effects of demographic and clinical variables upon classifiers.


title: Correlative cryogenic montage electron tomography for comprehensive in-situ whole-cell structural studies

abstract: Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here, we present robust tools for montage electron tomography tailored for vitrified specimens. The integration of correlative cryo-fluorescence microscopy, focused-ion beam milling, and micropatterning produces contextual three-dimensional architecture of cells. Montage tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.


title: Development, Structure, and Mechanism of Synthetic Antibodies that Target Claudin and Clostridium perfringens Enterotoxin Complexes

abstract: Strains of the Gram-positive bacterium Clostridium perfringens produce a two-domain enterotoxin (CpE) that afflict millions of humans and domesticated animals annually by causing prevalent gastrointestinal illnesses. CpEs C-terminal domain (cCpE) binds cell surface receptors then its N-terminal domain restructures to form a membrane-penetrating {beta}-barrel pore, which is toxic to epithelial cells of the gut. The claudin family of membrane proteins are the receptors for CpE, and also control the architecture and function of cell/cell contacts called tight junctions that create barriers to intercellular transport of solutes. CpE binding disables claudin and tight junction assembly and induces cytotoxicity via {beta}-pore formation, disrupting gut homeostasis. Here, we aimed to develop probes of claudin/CpE assembly using a phage display library encoding synthetic antigen-binding fragments (sFabs) and discovered two that bound complexes between human claudin-4 and cCpE. We established each sFabs unique modes of molecular recognition, their binding affinities and kinetics, and determined structures for each sFab bound to ~35 kDa claudin-4/cCpE in three-protein comprised complexes using cryogenic electron microscopy (cryoEM). The structures reveal a recognition epitope common to both sFabs but also that each sFab distinctly conforms to bind their antigen, which explain their unique binding equilibria. Mutagenesis of antigen/sFab interfaces observed therein result in further binding changes. Together, these findings validate the structures and uncover the mechanism of targeting claudin-4/cCpE complexes by these sFabs. Based on these structural insights we generate a model for CpEs cytotoxic claudin-bound {beta}-pore that predicted that these two sFabs would not prevent CpE cytotoxicity, which we verify in vivo with a cell-based assay. This work demonstrates the development and targeting mechanisms of sFabs against claudin/cCpE that enable rapid structural elucidation of these small membrane protein complexes using a cryoEM workflow. It further provides a structure-based framework and therapeutic strategies for utilizing these sFabs as molecular templates to target claudin/CpE assemblies, obstruct CpE cytotoxicity, and treat CpE-linked gastrointestinal diseases that cause substantial economic and quality of life losses throughout the world.


title: GNNQQNY: Methodology for biophysical and structural understanding of aggregation

abstract: GNNQQNY sequence offers crucial information about the formation and structure of an amyloid fibril. In this study, we demonstrate a reproducible solubilisation protocol where the reduction of pH to 2.0 resulted in the generation of GNNQQNY monomers. The subsequent ultracentrifugation step removes the residual insoluble peptide from the homogeneous solution. This procedure ensures and allows the peptides to remain monomers till their aggregation is triggered by adjusting the pH to 7.2. The aggregation kinetics analysis showed a distinct lag-phase that is concentration-dependent, indicating nucleation-dependent aggregation kinetics. Nucleation kinetics analysis suggested a critical nucleus of size [~]7 monomers at physiological conditions. The formed nucleus acts as a template for further self-assembly leading to the formation of highly ordered amyloid fibrils. These findings suggest that the proposed solubilisation protocol provides the basis for understanding the kinetics and thermodynamics of amyloid nucleation and elongation in GNNQQNY sequences. This procedure can also be used for solubilising such small amyloidogenic sequences for their biophysical studies.


title: Structure determination of protein-peptide complexes from NMR chemical shift data using MELD.

abstract: Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding upon binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine structures of peptide-protein complexes. Here, we demonstrate this approach for polypeptide complexes formed with the extraterminal (ET) domain of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can form different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only backbone chemical shift data, in excellent agreement with experimentally-determined structures. The approach also predicts relative binding affinities of different peptides. This hybrid MELD-NMR approach provides a powerful new tool for structural analysis of protein-polypeptide complexes in the low NMR information content regime, which can be used successfully for flexible systems where one polypeptide binding partner folds upon complex formation.


title: Viscoelastic RNA entanglement and advective flow underlie nucleolar form and function

abstract: The nucleolus facilitates transcription, processing, and assembly of ribosomal RNA (rRNA), the most abundant RNA in cells. Nucleolar function is facilitated by its multiphase liquid properties, but nucleolar fluidity and its connection to ribosome biogenesis remain unclear. Here, we used quantitative imaging, mathematical modeling, and pulse-chase nucleotide labelling to map nucleolar rRNA dynamics. Inconsistent with a purely diffusive process, rRNA steadily expands away from the transcriptional sites, moving in a slow (~1[A]/s), radially-directed fashion. This motion reflects the viscoelastic properties of a highly concentrated gel of entangled rRNA, whose constant polymerization drives steady outward flow. We propose a new viscoelastic rRNA release model, where nucleolar rRNA cleavage and processing reduce entanglement, fluidizing the nucleolar periphery to facilitate release of mature pre-ribosomal particles.


title: Transcriptomic changes in the pituitary of female mice with androgen excess through dihydrotestosterone (DHT) treatment

abstract: Androgen excess in women is associated with the development of PCOS and its abnormalities. The Hypothalamus Pituitary Ovarian axis signaling is altered with excessed androgens, leading to anovulation and infertility. Previous studies in the lab have shown that AR signaling in the pituitary alters gonadotrophin release. Hence, the present pioneering study was an approach to determine the transcriptomic changes responsible to the phenotype seen with DHT excess. RNA seq data showed that 583 genes were differentially regulated by DHT in pituitary, of which 344 were upregulated and 239 downregulated. Pathways involved for these genes included endoplasmic reticulum, Golgi apparatus, calcium signaling and vesicles. Meanwhile, Transcriptional factor analysis showed that majority of the genes changed had Androgen responsive elements.


title: Single-cell transcriptome reveals the redifferentiation trajectories of the early stage of de novo shoot regeneration in Arabidopsis thaliana

abstract: De novo shoot regeneration from a callus plays a crucial role in both plant biotechnology and the fundamental research of plant cell totipotency. Recent studies have revealed many regulatory factors involved in this developmental process. However. our knowledge of the cell heterogeneity and cell fate transition during de novo shoot regeneration is still limited. Here, we performed time-series single-cell transcriptome experiments to reveal the cell heterogeneity and redifferentiation trajectories during the early stage of de novo shoot regeneration. Based on the single-cell transcriptome data of 35,669 cells at five-time points, we successfully determined seven major cell populations in this developmental process and reconstructed the redifferentiation trajectories. We found that all cell populations resembled root identities and undergone gradual cell-fate transitions. In detail, the totipotent callus cells differentiated into pluripotent QC-like cells and then gradually developed into less differentiated cells that have multiple root-like cell identities, such as pericycle-like cells. According to the reconstructed redifferentiation trajectories, we discovered that the canonical regeneration-related genes were dynamically expressed at certain stages of the redifferentiation process. Moreover, we also explored potential transcription factors and regulatory networks that might be involved in this process. The transcription factors detected at the initial stage, QC-like cells, and the end stage provided a valuable resource for future functional verifications. Overall, this dataset offers a unique glimpse into the early stages of de novo shoot regeneration, providing a foundation for a comprehensive analysis of the mechanism of de novo shoot regeneration.


title: Multiplex labeling and manipulation of endogenous neuronal proteins using sequential CRISPR/Cas9 gene editing

abstract: Recent advances in CRISPR/Cas9-mediated knock-in methods enable labeling of individual endogenous proteins with fluorophores, to determine their spatiotemporal expression in intact biological preparations. However, multiplex knock-in methods remain limited, particularly in postmitotic cells, due to a high degree of crosstalk between genome editing events. We present Conditional Activation of Knock-in Expression (CAKE), which delivers efficient, flexible and accurate multiplex genome editing in neurons. CAKE is based on sequential gRNA expression operated by a Cre- or Flp-recombinase to control the time window for genomic integration of each donor sequence, which diminishes crosstalk between genome editing events. Importantly, CAKE is compatible with multiple CRISPR/Cas9 strategies, and we show the utilization of CAKE for co-localization of various endogenous proteins, including synaptic scaffolds, ion channels and neurotransmitter receptor subunits. Knock-in efficacy was highly sensitive to DNA vector amount, while knock-in crosstalk was dependent on the rate of donor DNA integration and timing of Cre activation. We applied CAKE to study the co-distribution of endogenous synaptic proteins using dual-color single-molecule localization microscopy, and we introduced dimerization modules to acutely control synaptic receptor dynamics in living neurons. Taken together, CAKE is a versatile method for multiplex protein labeling, enabling accurate detection, precise localization and acute manipulation of endogenous proteins in single cells.


title: Contribution of behavioural variability to representational drift

abstract: Neuronal responses to similar stimuli change dynamically over time, raising the question of how internal representations can provide a stable substrate for neural coding. While the drift of these representations is mostly characterized in relation to external stimuli or tasks, behavioural or internal state of the animal is also known to modulate the neural activity. We therefore asked how the variability of such modulatory mechanisms can contribute to representational drift. By analysing publicly available datasets from the Allen Brain Observatory, we found that behavioural variability significantly contributes to changes in stimulus-induced neuronal responses across various cortical areas in the mouse. This effect could not be explained by a gain model in which change in the behavioural state scaled the signal or the noise. A better explanation was provided by a model in which behaviour contributed independently to neuronal tuning. Our results are consistent with a view in which behaviour modulates the low-dimensional, slowly-changing setpoints of neurons, upon which faster operations like sensory processing are performed. Importantly, our analysis suggests that reliable but variable behavioural signals might be misinterpreted as representational drift, if neuronal representations are only characterized in the stimulus space and marginalised over behavioural parameters.


title: Maturation of prefrontal input to dorsal raphe increases behavioral persistence in mice

abstract: The ability to persist towards a desired objective is a fundamental aspect of behavioral control whose impairment is implicated in several behavioral disorders. One of the prominent features of behavioral persistence is that its maturation occurs relatively late in development. This is presumed to echo the developmental time course of a corresponding circuit within late-maturing parts of the brain, such as the prefrontal cortex, but the specific identity of the responsible circuits is unknown. Here, we describe the maturation of the projection from layer 5 neurons of the prefrontal cortex to the dorsal raphe nucleus in mice. We show using pathway-specific optogenetic stimulation that this connection undergoes a dramatic increase in synaptic potency between postnatal weeks 3 and 8, corresponding to the transition from juvenile to adult. We then show that this period corresponds to an increase in the behavioral persistence that mice exhibit in a foraging task. Finally, we use genetic targeting to selectively ablate this pathway in adulthood and show that mice revert to a behavioral phenotype similar to juveniles. These results suggest that the prefrontal to dorsal raphe pathway is a critical anatomical and functional substrate of the development and manifestation of behavioral control.


title: Maturation of prefrontal input to dorsal raphe nucleus increases behavioral persistence in mice


title: Post-Translational Tubulin Modifications in Differentiated Human Neural Stem Cells

abstract: The tubulin protein fulfills a variety of cellular functions that range from chromosomal separation to locomotion. The functional diversity of tubulin is achieved through the expression of tubulin isotypes in different cell types or developmental time periods. Post-translational modifications (PTMs) of tubulin also are vital for specific intracellular tasks, such as binding and recruiting motor proteins. In neurons, the isotypic expression profile for tubulin is well characterized, and the importance of PTMs for proper neuronal function has gained recent attention due to their implication in neurodegenerative disorders. In contrast, the role of tubulin specializations in the determination of neural cell fate has received minimal attention and studies of tubulin PTMs and isotypes in neuroglia such as astrocytes are relatively few. To bridge this knowledge gap, we undertook an analysis of PTMs in neurons and astrocytes derived from the federally approved H9 hESC-derived human neural stem cell (hNSC) line. In hNSCs, basal cells can be directed to assume neural fate as neurons or astrocytes by specifying different media growth conditions. Immunocytochemical methods, fluorescent antibody probes, and confocal microscopy facilitated image acquisition of fluorescent signals from class III {beta}-tubulin ({beta}III-tubulin), polyglutamylated tubulin, and acetylated tubulin. The EBImage package for the statistical programming language R was used to assess and compare fluorescent probe intensities using Students t-tests. Qualitative analysis indicated that {beta}III-tubulin, polyglutamylated tubulin, and acetylated tubulin were expressed to some degree in basal hNSCs and their media-differentiated hNSC neuronal and astroglial progeny. In media-differentiated hNSC astrocyte progeny, quantification and statistical analysis of fluorescence probe intensities showed that acetylated tubulin/ {beta}III-tubulin ratios were greater than polyglutamylated tubulin/ {beta}III-tubulin ratios. These findings represent a snapshot of the dynamic and varied changes tubulin expression profile during the specification of neural cell identity. Results imply that investigations of tubulin PTMs have the potential to further understanding of the generation and regeneration of nervous tissue.


title: Efficient learning in children with rapid GABA boosting after training

abstract:
It is unclear why and how children learn more efficiently than adults, although inhibitory systems, which play an important role in stabilizing learning, are immature in children. Here, we found that despite a lower baseline concentration of {gamma}-aminobutyric acid (GABA) in early visual cortical areas in children (8 to 11 years old) than adults (18 to 35 years old), children exhibited a rapid boost of GABA immediately after visual training, whereas the concentration of GABA in adults remained unchanged after training. Moreover, behavioral experiments showed that children stabilized visual learning much faster than adults, showing rapid development of resilience to retrograde interference. These results together suggest that inhibitory systems in childrens brains are more dynamic and adapt more quickly to stabilize learning than in adults.

One Sentence SummaryChildren learn more efficiently than adults due to faster stabilization of learning with rapid GABA boosting after training.


title: Reduced synaptic activity and dysregulated extracellular matrix pathways are common phenotypes in midbrain neurons derived from sporadic and mutation-associated Parkinson's disease patients

abstract: Several mutations that cause Parkinsons disease (PD) have been identified over the past decade. These account for 15-25% of PD cases; the rest of the cases are considered sporadic. Currently, it is accepted that PD is not a single monolithic disease but rather a constellation of diseases with some common phenotypes. While rodent models exist for some of the PD-causing mutations, research on the sporadic forms of PD is lagging due to a lack of cellular models. In our study, we differentiated PD patient-derived dopaminergic (DA) neurons from induced pluripotent stem cells (iPSCs) of several PD-causing mutations as well as from sporadic PD patients. Strikingly, we observed a common neurophysiological phenotype: Neurons derived from PD patients had a severe reduction in the rate of synaptic currents compared to those derived from healthy controls. While the relationship between mutations in genes such as the SNCA and LRRK2 and a reduction in synaptic transmission has been investigated before, here we show evidence that the pathogenesis of the synapses in neurons is a general phenotype in PD. Analysis of RNA sequencing results displayed changes in gene expression in different synaptic mechanisms as well as other affected pathways such as extracellular matrix-related pathways. Some of these dysregulated pathways are common to all PD patients (monogenic or idiopathic). Our data, therefore, shows changes that are central and convergent to PD and suggests a strong involvement of the tetra-partite synapse in PD pathophysiology.


title: Synthetic Data Resource and Benchmarks for Time Cell Analysis and Detection Algorithms

abstract: Hippocampal CA1 cells take part in reliable, time-locked activity sequences in tasks that involve an association between stimuli, in a manner that tiles the interval between the stimuli. Such cells have been termed time cells. Here we adopt a first-principles approach to comparing diverse analysis and detection algorithms for identifying time cells. We developed a resource for generating synthetic activity datasets using calcium signals recorded in vivo from mouse hippocampus using 2-photon imaging, for template response waveforms. We assigned known, ground truth values for properties of time cells in this synthetic dataset, including noise, timing imprecision, hit-trial ratio and calcium event width. These datasets were the input to a pipeline for testing multiple algorithms for time cell detection to determine the conditions for which they were best suited, and evaluate their effective operating ranges. We find that most algorithms are sensitive to noise. Only a few methods benefit from larger event widths. Reassuringly, most methods are insensitive to timing imprecision, and exhibit successful time cell detection even at low hit trial ratios. Importantly, all methods show good concordance in identifying cells as time cells.


title: Abnormal larval neuromuscular junction morphology and physiology in Drosophila Prickle isoform mutants with defective axonal transport and adult seizure behavior

abstract: Previous studies have demonstrated that mutations of the Drosophila planar cell polarity gene prickle (pk) result in altered microtubule-mediated vesicular transport in larval motor axons, as well as adult neuronal circuit hyperexcitability and epileptic behavior. It is also known that mutant alleles of the prickle-prickle (pkpk) and prickle-spiny-legs (pksple) isoforms differ in phenotype but display isoform counterbalancing effects in heteroallelic pkpk/pksple flies to ameliorate adult motor circuit and behavioral hyperexcitability. We have further investigated the larval neuromuscular junction (NMJ) and uncovered robust phenotypes in both pkpk and pksple alleles (heretofore referred to as pk and sple alleles, respectively), including synaptic terminal overgrowth, as well as irregular motor axon terminal excitability, poor vesicle release synchronicity, and altered efficacy of synaptic transmission. We observed significant increase in whole-cell excitatory junctional potential (EJP) in pk homozygotes, which was restored to near WT level in pk/sple heterozygotes. We further examined motor terminal excitability sustained by presynaptic Ca2+ channels, under the condition of pharmacological blockade of Na+ and K+ channel function. Such manipulation revealed extreme Ca2+ channel-dependent nerve terminal excitability in both pk and sple mutants. However, when combined in pk/sple heterozygotes, such terminal hyper-excitability was restored to nearly normal. Focal recording from individual synaptic boutons revealed asynchronous vesicle release in both pk and sple homozygotes, which nevertheless persisted in pk/sple heterozygotes without indications of isoform counter-balancing effects. Similarly, the overgrowth at NMJs was not compensated in pk/sple heterozygotes, exhibiting an extremity comparable to that in pk and sple homozygotes. Our observations uncovered differential roles of the pk and sple isoforms and their distinct interactions in the various structural and functional aspects of the larval NMJ and adult neural circuits.