Biosymbiotic platform for chronic long-range monitoring of biosignals in limited resource settings

Remote patient monitoring is a critical component of digital medicine, and the COVID-19 pandemic has further highlighted its importance. Wearable sensors aimed at noninvasive extraction and transmission of high-fidelity physiological data provide an avenue toward at-home diagnostics and therapeutics; however, the infrastructure requirements for such devices limit their use to areas with well-established connectivity. This accentuates the socioeconomic and geopolitical gap in digital health technology and points toward a need to provide access in areas that have limited resources. Low-power wide area network (LPWAN) protocols, such as LoRa, may provide an avenue toward connectivity in these settings; however, there has been limited work on realizing wearable devices with this functionality because of power and electromagnetic constraints. In this work, we introduce wearables with electromagnetic, electronic, and mechanical features provided by a biosymbiotic platform to realize high-fidelity biosignals transmission of 15 miles without the need for satellite infrastructure. The platform implements wireless power transfer for interaction-free recharging, enabling long-term and uninterrupted use over weeks without the need for the user to interact with the devices. This work presents demonstration of a continuously wearable device with this long-range capability that has the potential to serve resource-constrained and remote areas, providing equitable access to digital health.

Catalysis by KDM6 Histone Demethylases - A Synergy between the Non-Heme Iron(II) Center, Second Coordination Sphere, and Long-Range Interactions

KDM6A (UTX) and KDM6B (JMJD3) are human non-heme Fe(II) and 2-oxoglutarate (2OG) dependent JmjC oxygenases that catalyze the demethylation of trimethylated lysine 27 in the N-terminal tail of histone H3, a post-translational modification that regulates transcription. A Combined Quantum Mechanics/ Molecular Mechanics (QM/MM) and Molecular Dynamics (MD) study on the catalytic mechanism of KDM6A/B reveals that the transition state for the rate-limiting hydrogen atom transfer (HAT) reaction in KDM6A catalysis is stabilized by polar (Asn217) and aromatic (Trp369)/non-polar (Pro274) residues in contrast to KDM4, KDM6B and KDM7 demethylases where charged residues (Glu, Arg, Asp) are involved. KDM6A employs both σ- and π-electron transfer pathways for HAT, whereas KDM6B employs the σ-electron pathway. Differences in hydrogen bonding of the Fe-chelating Glu252(KDM6B) contribute to the lower energy barriers in KDM6B vs. KDM6A. The study reveals a dependence of the activation barrier of the rebound hydroxylation on the Fe-O-C angle in the transition state of KDM6A. Anti-correlation of the Zn-binding domain with the active site residues is a key factor distinguishing KDM6A/B from KDM7/4s. The results reveal the importance of communication between the Fe center, second coordination sphere, and long-range interactions in catalysis by KDMs and, by implication, other 2OG oxygenases.

RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing

Over recent years, long-range RNA structure has emerged as a factor that is fundamental to alternative splicing regulation. An increasing number of human disorders are now being associated with splicing defects; hence it is essential to develop methods that assess long-range RNA structure experimentally. RNA in situ conformation sequencing (RIC-seq) is a method that recapitulates RNA structure within physiological RNA-protein complexes. In this work, we juxtapose pairs of conserved complementary regions (PCCRs) that were predicted in silico with the results of RIC-seq experiments conducted in seven human cell lines. We show statistically that RIC-seq support of PCCRs correlates with their properties, such as equilibrium free energy, presence of compensatory substitutions, and occurrence of A-to-I RNA editing sites and forked eCLIP peaks. Exons enclosed in PCCRs that are supported by RIC-seq tend to have weaker splice sites and lower inclusion rates, which is indicative of post-transcriptional splicing regulation mediated by RNA structure. Based on these findings, we prioritize PCCRs according to their RIC-seq support and show, using antisense nucleotides and minigene mutagenesis, that PCCRs in two disease-associated human genes, PHF20L1 and CASK, and also PCCRs in their murine orthologs, impact alternative splicing. In sum, we demonstrate how RIC-seq experiments can be used to discover functional long-range RNA structures, and particularly those that regulate alternative splicing.

Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets

Leveraging linkage disequilibrium (LD) patterns as representative of population substructure enables the discovery of additive association signals in genome-wide association studies (GWASs). Standard GWASs are well-powered to interrogate additive models; however, new approaches are required for invesigating other modes of inheritance such as dominance and epistasis. Epistasis, or non-additive interaction between genes, exists across the genome but often goes undetected because of a lack of statistical power. Furthermore, the adoption of LD pruning as customary in standard GWASs excludes detection of sites that are in LD but might underlie the genetic architecture of complex traits. We hypothesize that uncovering long-range interactions between loci with strong LD due to epistatic selection can elucidate genetic mechanisms underlying common diseases. To investigate this hypothesis, we tested for associations between 23 common diseases and 5,625,845 epistatic SNP-SNP pairs (determined by Ohta's D statistics) in long-range LD (>0.25 cM). Across five disease phenotypes, we identified one significant and four near-significant associations that replicated in two large genotype-phenotype datasets (UK Biobank and eMERGE). The genes that were most likely involved in the replicated associations were (1) members of highly conserved gene families with complex roles in multiple pathways, (2) essential genes, and/or (3) genes that were associated in the literature with complex traits that display variable expressivity. These results support the highly pleiotropic and conserved nature of variants in long-range LD under epistatic selection. Our work supports the hypothesis that epistatic interactions regulate diverse clinical mechanisms and might especially be driving factors in conditions with a wide range of phenotypic outcomes.

A potential long-range RNA-RNA interaction in the HIV-1 RNA

It is well-established that viral and cellular mRNAs alike harbour functional long-range intra-molecular RNA-RNA interactions. Despite the biological importance of such interactions, their identification and characterization remain challenging. Here we present a computational method for the identification of certain kinds of long-range intra-molecular RNA-RNA interactions involving the loop nucleotides of a hairpin loop. Using the computational method, we analysed 4272 HIV-1 genomic mRNAs. A potential long-range intra-molecular RNA-RNA interaction within the HIV-1 genomic RNA was identified. The long-range interaction is mediated by a kissing loop structure between two stem-loops of the previously reported SHAPE-based secondary structure of the entire HIV-1 genome. Structural modelling studies were carried out to show that the kissing loop structure not only is sterically feasible, but also contains a conserved RNA structural motif often found in compact RNA pseudoknots. The computational method should be generally applicable to the identification of potential long-range intra-molecular RNA-RNA interactions in any viral or cellular mRNA sequence.Communicated by Ramaswamy H. Sarma.

Three-Dimensional Confinement of Water: H2O Exhibits Long-Range (>50 nm) Structure while D2O Does Not

Water is the liquid of life thanks to its three-dimensional adaptive hydrogen (H)-bond network. Confinement of this network may lead to dramatic structural changes influencing chemical and physical transformations. Although confinement effects occur on a <1 nm length scale, the upper length scale limit is unknown. Here, we investigate 3D-confinement over lengths scales ranging from 58-140 nm. By confining water in zwitterionic liposomes of different sizes and measuring the change in H-bond network conformation using second harmonic scattering (SHS), we determined long-range confinement effects in light and heavy water. D₂O displays no detectable 3D-confinement effects <58 nm (<3 × 10⁶ D₂O molecules). H₂O is distinctly different. The vesicle enclosed inner H-bond network has a different conformation compared to the outside network and the SHS response scales with the volume of the confining space. H₂O displays confinement effects over distances >100 nm (>2 × 10⁷ H₂O molecules).

Improving Chromatin-Interaction Prediction Using Single-Cell Open-Chromatin Profiles and Making Insight Into the Cis-Regulatory Landscape of the Human Brain

Single-cell open-chromatin profiles have the potential to reveal the pattern of chromatin-interaction in a cell type. However, currently available cis-regulatory network prediction methods using single-cell open-chromatin profiles focus more on local chromatin interactions despite the fact that long-range interactions among genomic sites play a significant role in gene regulation. Here, we propose a method that predicts both short and long-range interactions among genomic sites using single-cell open chromatin profiles. Our method, termed as single-cell epigenome based chromatin-interaction analysis (scEChIA) exploits signal imputation and refined L1 regularization. For a few single-cell open-chromatin profiles, scEChIA outperformed other tools even in terms of accuracy of prediction. Using scEChIA, we predicted almost 0.7 million interactions among genomic sites across seven cell types in the human brain. Further analysis revealed cell type for connection between genes and expression quantitative trait locus (eQTL) in the human brain and making insight about target genes of human-accelerated-elements and disease-associated mutations. Our analysis enabled by scEChIA also hints about the possible action of a few transcription factors (TFs), especially through long-range interaction in brain endothelial cells.

Edge Structural Health Monitoring (E-SHM) Using Low-Power Wireless Sensing

Effective Structural Health Monitoring (SHM) often requires continuous monitoring to capture changes of features of interest in structures, which are often located far from power sources. A key challenge lies in continuous low-power data transmission from sensors. Despite significant developments in long-range, low-power telecommunication (e.g., LoRa NB-IoT), there are inadequate demonstrative benchmarks for low-power SHM. Damage detection is often based on monitoring features computed from acceleration signals where data are extensive due to the frequency of sampling (~100-500 Hz). Low-power, long-range telecommunications are restricted in both the size and frequency of data packets. However, microcontrollers are becoming more efficient, enabling local computing of damage-sensitive features. This paper demonstrates the implementation of an Edge-SHM framework through low-power, long-range, wireless, low-cost and off-the-shelf components. A bespoke setup is developed with a low-power MEM accelerometer and a microcontroller where frequency and time domain features are computed over set time intervals before sending them to a cloud platform. A cantilever beam excited by an electrodynamic shaker is monitored, where damage is introduced through the controlled loosening of bolts at the fixed boundary, thereby introducing rotation at its fixed end. The results demonstrate how an IoT-driven edge platform can benefit continuous monitoring.

Corticofugal VIP Gabaergic Projection Neurons in the Mouse Auditory and Motor Cortex

Anatomical and physiological studies have described the cortex as a six-layer structure that receives, elaborates, and sends out information exclusively as excitatory output to cortical and subcortical regions. This concept has increasingly been challenged by several anatomical and functional studies that showed that direct inhibitory cortical outputs are also a common feature of the sensory and motor cortices. Similar to their excitatory counterparts, subsets of Somatostatin- and Parvalbumin-expressing neurons have been shown to innervate distal targets like the sensory and motor striatum and the contralateral cortex. However, no evidence of long-range VIP-expressing neurons, the third major class of GABAergic cortical inhibitory neurons, has been shown in such cortical regions. Here, using anatomical anterograde and retrograde viral tracing, we tested the hypothesis that VIP-expressing neurons of the mouse auditory and motor cortices can also send long-range projections to cortical and subcortical areas. We were able to demonstrate, for the first time, that VIP-expressing neurons of the auditory cortex can reach not only the contralateral auditory cortex and the ipsilateral striatum and amygdala, as shown for Somatostatin- and Parvalbumin-expressing long-range neurons, but also the medial geniculate body and both superior and inferior colliculus. We also demonstrate that VIP-expressing neurons of the motor cortex send long-range GABAergic projections to the dorsal striatum and contralateral cortex. Because of its presence in two such disparate cortical areas, this would suggest that the long-range VIP projection is likely a general feature of the cortex’s network.

Wireless, battery-free, subdermally implantable platforms for transcranial and long-range optogenetics in freely moving animals

Wireless, battery-free, and fully subdermally implantable optogenetic tools are poised to transform neurobiological research in freely moving animals. Current-generation wireless devices are sufficiently small, thin, and light for subdermal implantation, offering some advantages over tethered methods for naturalistic behavior. Yet current devices using wireless power delivery require invasive stimulus delivery, penetrating the skull and disrupting the blood-brain barrier. This can cause tissue displacement, neuronal damage, and scarring. Power delivery constraints also sharply curtail operational arena size. Here, we implement highly miniaturized, capacitive power storage on the platform of wireless subdermal implants. With approaches to digitally manage power delivery to optoelectronic components, we enable two classes of applications: transcranial optogenetic activation millimeters into the brain (validated using motor cortex stimulation to induce turning behaviors) and wireless optogenetics in arenas of more than 1 m² in size. This methodology allows for previously impossible behavioral experiments leveraging the modern optogenetic toolkit.

Extended measuring depth dual-wavelength Fourier domain optical coherence tomography

In this work an enhanced wide range dual band spectral domain optical coherence tomography technique (SD-OCT) is presented to increase the depth and accuracy of the measurement of optical A-scan biometry. The setup uses a Michelson interferometer with two wide-spectrum Superluminescent Diodes (SLD). The emissions of the SLDs are filtered by a long-pass filter (900 nm) in front of the reference mirror. The light is spectrally decomposed using a single reflective diffraction grating (1,800 lines/mm) and the whole spectrum captured with two CCD line sensors. The capabilities of the system have been validated using a self-made human model eye.

Evaluation of Misalignment Effect in Vehicle-to-Vehicle Visible Light Communications: Experimental Demonstration of a 75 Meters Link

The use of visible light communications technology in communication-based vehicle applications is gaining more and more interest as the research community is constantly overcoming challenge after challenge. In this context, this article addresses the issues associated with the use of Visible Light Communications (VLC) technology in Vehicle-to-Vehicle (V2V) communications, while focusing on two crucial issues. On the one hand, it aims to investigate the achievable communication distance in V2V applications while addressing the least favorable case, namely the one when a standard vehicle rear lighting system is used as a VLC emitter. On the other hand, this article investigates another highly unfavorable use case scenario, i.e., the case when two vehicles are located on adjacent lanes, rather than on the same lane. In order to evaluate the compatibility of the VLC technology with the usage in inter-vehicle communication, a VLC prototype is intensively evaluated in outdoor conditions. The experimental results show a record V2V VLC distance of 75 m, while providing a Bit Error Ratio (BER) of 10⁻⁷–10⁻⁶. The results also show that the VLC technology is able to provide V2V connectivity even in a situation where the vehicles are located on adjacent lanes, without a major impact on the link performances. Nevertheless, this situation generates an initial no-coverage zone, which is determined by the VLC receiver reception angle, whereas in some cases, vehicle misalignment can generate a BER increase that can go up to two orders of magnitude.

Dorsal and ventral mossy cells differ in their axonal projections throughout the dentate gyrus of the mouse hippocampus

Glutamatergic hilar mossy cells (MCs) have axons that terminate both near and far from their cell body but stay within the DG, making synapses primarily in the molecular layer. The long-range axons are considered the primary projection, and extend throughout the DG ipsilateral to the soma, and project to the contralateral DG. The specificity of MC axons for the inner molecular layer (IML) has been considered to be a key characteristic of the DG. In the present study, we made the surprising finding that dorsal MC axons are an exception to this rule. We used two mouse lines that allow for Cre-dependent viral labeling of MCs and their axons: dopamine receptor D2 (Drd2-Cre) and calcitonin receptor-like receptor (Crlr-Cre). A single viral injection into the dorsal DG to label dorsal MCs resulted in labeling of MC axons in both the IML and middle molecular layer (MML). Interestingly, this broad termination of dorsal MC axons occurred throughout the septotemporal DG. In contrast, long-range axons of ventral MCs terminated in the IML, consistent with the literature. Taken together, these results suggest that dorsal and ventral MCs differ significantly in their axonal projections. Since MC projections in the ML are thought to terminate primarily on GCs, the results suggest a dorsal-ventral difference in MC activation of GCs. The surprising difference in dorsal and ventral MC projections should therefore be considered when evaluating dorsal-ventral differences in DG function.

Improving Resource Management for Unattended Observation of the Marginal Ice Zone Using Autonomous Underwater Gliders

We present control policies for use with a modified autonomous underwater glider that are intended to enable remote launch/recovery and long-range unattended survey of the Arctic's marginal ice zone (MIZ). This region of the Arctic is poorly characterized but critical to the dynamics of ice advance and retreat. Due to the high cost of operating support vessels in the Arctic, the proposed glider architecture minimizes external infrastructure requirements for navigation and mission updates to brief and infrequent satellite updates on the order of once per day. This is possible through intelligent power management in combination with hybrid propulsion, adaptive velocity control, and dynamic depth band selection based on real-time environmental state estimation. We examine the energy savings, range improvements, decreased communication requirements, and temporal consistency that can be attained with the proposed glider architecture and control policies based on preliminary field data, and we discuss a future MIZ survey mission concept in the Arctic. Although the sensing and control policies presented here focus on under ice missions with an unattended underwater glider, they are hardware independent and are transferable to other robotic vehicle classes, including in aerial and space domains.

Success Probability Characterization of Long-Range in Low-Power Wide Area Networks

In low-power wide area networks (LPWAN), a considerable number of end devices (EDs) communicate with the gateway in a certain area, whereas for transmitted data, a low data rate and high latency are allowed. Long-range (LoRa), as one of the LPWAN technologies, considers pure ALOHA and chirp spread spectrum (CSS) in the media access control (MAC) and physical (PHY) layers such that it can improve the energy efficiency while mitigating inter-cell interference (ICI). This paper investigates the system throughput of LoRa networks under the assumption that the interferences between EDs for exclusive regions are ignored using CSS. In order to establish an analytical model for the performance of LoRa, we introduce the pure ALOHA capture model, which is the power threshold model. For this model, we assume that the interfering power is proportional to the length of the time overlapped. In addition, we discuss LoRa gain by comparing the total throughput of LoRa with that of non-CSS.

Auditory Long-Range Parvalbumin Cortico-Striatal Neurons

Previous studies have shown that cortico-striatal pathways link auditory signals to action-selection and reward-learning behavior through excitatory projections. Only recently it has been demonstrated that long-range GABAergic cortico-striatal somatostatin-expressing neurons in the auditory cortex project to the dorsal striatum, and functionally inhibit the main projecting neuronal population, the spiny projecting neuron. Here we tested the hypothesis that parvalbumin-expressing neurons of the auditory cortex can also send long-range projections to the auditory striatum. To address this fundamental question, we took advantage of viral and non-viral anatomical tracing approaches to identify cortico-striatal parvalbumin neurons (CS-Parv inhibitory projections → auditory striatum). Here, we describe their anatomical distribution in the auditory cortex and determine the anatomical and electrophysiological properties of layer 5 CS-Parv neurons. We also analyzed their characteristic voltage-dependent membrane potential gamma oscillation, showing that intrinsic membrane mechanisms generate them. The inherent membrane mechanisms can also trigger intermittent and irregular bursts (stuttering) of the action potential in response to steps of depolarizing current pulses.

HCN2 Channel-Induced Rescue of Brain Teratogenesis via Local and Long-Range Bioelectric Repair

Embryonic exposure to the teratogen nicotine results in brain defects, by disrupting endogenous spatial pre patterns necessary for normal brain size and patterning. Extending prior work in Xenopus laevis that showed that misexpression of ion channels can rescue morphogenesis, we demonstrate and characterize a novel aspect of developmental bioelectricity: channel-dependent repair signals propagate long-range across the embryo. We show that distal HCN2 channel misexpression and distal transplants of HCN2-expressing tissue, non-cell-autonomously reverse profound defects, rescuing brain anatomy, gene expression, and learning. Moreover, such rescue can be induced by small-molecule HCN2 channel activators, even with delayed treatment initiation. We present a simple, versatile computational model of bioelectrical signaling upstream of key patterning genes such as OTX2 and XBF1, which predicts long-range repair induced by ion channel activity, and experimentally validate the predictions of this model. Our results and quantitative model identify a powerful morphogenetic control mechanism that could be targeted by future regenerative medicine exploiting ion channel modulating drugs approved for human use.

Somatostatin-Expressing Interneurons Form Axonal Projections to the Contralateral Hippocampus

Conscious memories are critically dependent upon bilateral hippocampal formation, and interhemispheric commissural projections made by mossy cells and CA3 pyramidal cells. GABAergic interneurons also make long-range axonal projections, but little is known regarding their commissural, inter-hippocampal connections. We used retrograde and adeno-associated viral tracing, immunofluorescence and electron microscopy, and in vitro optogenetics to assess contralateral projections of neurochemically defined interneuron classes. We found that contralateral-projecting interneurons were 24-fold less common compared to hilar mossy cells, and mostly consisted of somatostatin- and parvalbumin-expressing types. Somatostatin-expressing cells made denser contralateral axonal projections than parvalbumin-expressing cells, although this was typically 10-fold less than the ipsilateral projection density. Somatostatin-expressing cells displayed a topographic-like innervation according to the location of their somata, whereas parvalbumin-expressing cells mostly innervated CA1. In the dentate gyrus molecular layer, commissural interneuron post-synaptic targets were predominantly putative granule cell apical dendrites. In the hilus, varicosities in close vicinity to various interneuron subtypes, as well as mossy cells, were observed, but most contralateral axon varicosities had no adjacent immunolabeled structure. Due to the relative sparsity of the connection and the likely distal dendritic location of their synapses, commissural projections made by interneurons were found to be weak. We postulate that these projections may become functionally active upon intense network activity during tasks requiring increased memory processing.

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas

CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas

CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.

Probing long-range spin-spin coupling constants in 2-halo-substituted cyclohexanones and cyclohexanethiones: The role of solvent and stereoelectronic effects

Earlier studies with 2-bromocyclohexanone demonstrated a measurable long-range coupling constant (⁴ J_H2,H6 ) for the equatorial conformer, although ⁴ J_H2,H4 and ⁴ J_H4,H6 were not observed; as a consequence, it is inferred that the carbonyl group plays an important role particularly due to hyperconjugative interactions σ_C2H2 →π*_C═O and σ_C6H6 →π*_C═O. In the present study, NBO analysis and coupling constant calculations were performed to cyclohexanone and cyclohexanethione alpha substituted with F, Cl, and Br, aiming to evaluate the halogen effect and acceptor character of the π* orbital on the long-range coupling pathway. The σ_C2H2 →π*_C1═Y and σ_C6H6 →π*_C1═Y (Y═O and S) hyperconjugative interactions for the equatorial conformer indeed contribute for the ⁴ J_H2,H6 transmission mechanism_. Surprisingly, the ⁴ J_H2,H6 value is higher for the carbonyl compounds, although the interactions σ_C2H2 →π*_C═Y and σ_C6H6 →π*_C═Y are more efficient for the thiocarbonyl compounds. Accordingly, the Fermi contact (FC) contribution for the thiocarbonyl compounds decays deeper than in ketones, thus reducing more the ⁴ J_H2,H6 values. Moreover, both π_C═S →σ*_C─X and π_C═S →σ*_C─H interactions seem to be stronger in thiocarbonyl than in carbonylic compounds. The implicit solvent effect (DMSO and water) on the coupling constant values was negligible when compared with the gas phase. On the other hand, an explicit solvent effect was found and ⁴ J_H2,H6 for the thiocarbonyl compounds appeared to be more sensitive than for the cyclohexanones.

An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons

Alternative splicing is a commonly-used mechanism of diversifying gene products. Mutually exclusive exons (MXE) represent a particular type of alternative splicing, in which one and only one exon from an array is included in the mature RNA. A number of genes with MXE do so by using a mechanism that depends on RNA structure. Transcripts of these genes contain multiple sites called selector sequences that are all complementary to a regulatory element called the docking site; only one of the competing base pairings can form at a time, which exposes one exon from the cluster to the spliceosome. MXE tend to have similar lengths and sequence content and are believed to originate through tandem genomic duplications. Here, we report that pre-mRNAs of this class of exons have an increased capacity to fold into competing secondary structures. We propose an evolutionary mechanism for the generation of such structures via duplications that affect not only exons, but also their adjacent introns with stem-loop structures. If one of the two arms of a stem-loop is duplicated, it will generate two selector sequences that compete for the same docking site, a pattern that is associated with MXE splicing. A similar partial duplication of two independent stem-loops produces a pattern that is consistent with the so-called bidirectional pairing model. These models explain why tandem exon duplications frequently result in mutually exclusive splicing.

Altered Long- and Short-Range Functional Connectivity Density in Healthy Subjects After Sleep Deprivations

Objective: To investigate the brain functional organization induced by sleep deprivation (SD) using functional connectivity density (FCD) analysis.

Methods: Twenty healthy subjects (12 female, 8 male; mean age, 20.6 ± 1.9 years) participated a 24 h sleep deprivation (SD) design. All subjects underwent the MRI scan and attention network test twice, once during rested wakefulness (RW) status, and the other was after 24 h acute SD. FCD was divided into the shortFCD and longFCD. Receiver operating characteristic (ROC) curve was used to evaluate the discriminating ability of those FCD differences in brain areas during the SD status from the RW status, while Pearson correlations was used to evaluate the relationships between those differences and behavioral performances.

Results: Subjects at SD status exhibited lower accuracy rate and longer reaction time relative to RW status. Compared with RW, SD had a significant decreased shortFCD in the left cerebellum posterior lobe, right cerebellum anterior lobe, and right orbitofrontal cortex, and increased shortFCD in the left occipital gyrus, bilateral thalamus, right paracentral lobule, bilateral precentral gyrus, and bilateral postcentral gyrus. Compared with RW, SD had a significant increased longFCD in the right precentral gyrus, bilateral postcentral gyrus, and right visuospatial network, and decreased longFCD in the default mode network. The area under the curve values of those specific FCD differences in brain areas were (mean ± std, 0.933 ± 0.035; 0.863~0.977). Further ROC curve analysis demonstrated that the FCD differences in those brain areas alone discriminated the SD status from the RW status with high degree of sensitivities (89.19 ± 6%; 81.3~100%) and specificities (89.15 ± 6.87%; 75~100%). Reaction time showed a negative correlation with the right orbitofrontal cortex (r = −0.48, p = 0.032), and accuracy rate demonstrated a positive correlation with the right default mode network (r = 0.573, p = 0.008).

Conclusions: The longFCD and shortFCD analysis might be potential indicator biomarkers to locate the underlying altered intrinsic brain functional organization disturbed by SD. SD sustains the cognitive performance by the decreased high-order cognition related areas and the arousal and sensorimotor related areas.

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the &ldquo;first-align-then-fold&rdquo; principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite &ldquo;first-fold-then-align&rdquo; approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation

Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (∼360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.

Layer 5 Callosal Parvalbumin-Expressing Neurons: A Distinct Functional Group of GABAergic Neurons

Previous studies have shown that parvalbumin-expressing neurons (CC-Parv neurons) connect the two hemispheres of motor and sensory areas via the corpus callosum, and are a functional part of the cortical circuit. Here we test the hypothesis that layer 5 CC-Parv neurons possess anatomical and molecular mechanisms which dampen excitability and modulate the gating of interhemispheric inhibition. In order to investigate this hypothesis we use viral tracing to determine the anatomical and electrophysiological properties of layer 5 CC-Parv and parvalbumin-expressing (Parv) neurons of the mouse auditory cortex (AC). Here we show that layer 5 CC-Parv neurons had larger dendritic fields characterized by longer dendrites that branched farther from the soma, whereas layer 5 Parv neurons had smaller dendritic fields characterized by shorter dendrites that branched nearer to the soma. The layer 5 CC-Parv neurons are characterized by delayed action potential (AP) responses to threshold currents, lower firing rates, and lower instantaneous frequencies compared to the layer 5 Parv neurons. Kv1.1 containing K⁺ channels are the main source of the AP repolarization of the layer 5 CC-Parv and have a major role in determining both the spike delayed response, firing rate and instantaneous frequency of these neurons.

Distinct Corticostriatal GABAergic Neurons Modulate Striatal Output Neurons and Motor Activity

The motor cortico-basal ganglion loop is critical for motor planning, execution, and learning. Balanced excitation and inhibition in this loop is crucial for proper motor output. Excitatory neurons have been thought to be the only source of motor cortical input to the striatum. Here, we identify long-range projecting GABAergic neurons in the primary (M1) and secondary (M2) motor cortex that target the dorsal striatum. This population of projecting GABAergic neurons comprises both somatostatin-positive (SOM⁺) and parvalbumin-positive (PV⁺) neurons that target direct and indirect pathway striatal output neurons as well as cholinergic interneurons differentially. Notably, optogenetic stimulation of M1 PV⁺ and M2 SOM⁺ projecting neurons reduced locomotion, whereas stimulation of M1 SOM⁺ projecting neurons enhanced locomotion. Thus, corticostriatal GABAergic projections modulate striatal output and motor activity.

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Long-range GABAergic projections from the motor cortex directly innervate the striatum

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M1 and M2 long-range SOM⁺ and PV⁺ neurons differentially innervate striatal neurons

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Striatal cholinergic neurons are innervated mainly by M1 SOM⁺ projecting neurons

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Motor cortex PV⁺ and SOM⁺ projecting neurons differentially modulate locomotion

Experience-Dependent and Differential Regulation of Local and Long-Range Excitatory Neocortical Circuits by Postsynaptic Mef2c

Development of proper cortical circuits requires an interaction of sensory experience and genetic programs. Little is known of how experience and specific transcription factors interact to determine the development of specific neocortical circuits. Here, we demonstrate that the activity-dependent transcription factor, Myocyte enhancer factor-2C (Mef2c), differentially regulates development of local versus long-range excitatory synaptic inputs onto layer 2/3 neurons in the somatosensory neocortex in vivo. Postnatal, postsynaptic deletion of Mef2c in a sparse population of L2/3 neurons suppressed development of excitatory synaptic connections from all local input pathways tested. In the same cell population, Mef2c deletion promoted the strength of excitatory inputs originating from contralateral neocortex. Both the synapse promoting and synapse suppressing effects of Mef2c deletion required normal whisking experience. These results reveal a role of Mef2c in experience-dependent development of specific sensory neocortical circuits.

Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations

The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I) and imidazole-5-acetic (II) acids was monitored using the traditional hybrid functional (B3LYP) and the long-range corrected functionals (CAM-B3LYP and ωB97XD) with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital (HOMO-LUMO) energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750-0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14-H15). This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS), TS1 and TS2, having energy barriers of 47.67-49.92 and 49.55-52.69 kcal/mol, respectively, and an sp³-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed.

Somatostatinergic systems: an update on brain functions in normal and pathological aging

Somatostatin is highly expressed in mammalian brain and is involved in many brain functions such as motor activity, sleep, sensory, and cognitive processes. Five somatostatin receptors have been described: sst(1), sst(2) (A and B), sst(3), sst(4), and sst(5), all belonging to the G-protein-coupled receptor family. During the recent years, numerous studies contributed to clarify the role of somatostatin systems, especially long-range somatostatinergic interneurons, in several functions they have been previously involved in. New advances have also been made on the alterations of somatostatinergic systems in several brain diseases and on the potential therapeutic target they represent in these pathologies.

Evidence for widespread association of mammalian splicing and conserved long-range RNA structures

Pre-mRNA structure impacts many cellular processes, including splicing in genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each gene, we now report RNA structures that could be involved in the regulation of splicing in mammals. Statistically, we demonstrate strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. As an example, we validated the RNA structure in the human SF1 gene using minigenes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.