Miracle-dz/UniFAR-FTUs huggingface dataset:
Opportunities and Challenges in Global Quantification of RNA-Protein Interaction via UV Cross-Linking

RNA-binding proteins (RBPs) are key mediators of posttranscriptional gene expression control. However, the links between cell signaling on the one hand and RBP function on the other are understudied. While thousands of posttranslational modification (PTM) sites on RBPs have been identified, their functional roles are only poorly characterized. RNA-interactome capture (RIC) and cross-linking and immunoprecipitation (CLIP) are attractive methods that provide information about RBP-RNA interactions on a genome-wide scale. Both approaches rely on the in situ UV cross-linking of RBPs and RNAs, biochemical enrichment and analysis by RNA-sequencing (CLIP) or mass spectrometry (RIC). In principle, RIC- and CLIP-like methods could be used to globally quantify RBP-RNA interactions in response to perturbations. However, several biases have to be taken into account to avoid misinterpretation of the results obtained. Here, we focus on RIC-like methods and discuss four key aspects relevant for quantitative interpretation: (1) the RNA isolation efficiency, (2) the inefficient and highly variable UV cross-linking, (3) the baseline RNA occupancy of RBPs, and (4) indirect factors affecting RBP-RNA interaction. We highlight these points by presenting selected examples of PTMs that might induce differential quantification in RIC-like experiments without necessarily affecting RNA-binding. We conclude that quantifying RBP-RNA interactions via RIC or CLIP-like methods should not be regarded as an end in itself but rather as starting points for deeper analysis.
Why Dieters Succeed or Fail: The Relationship Between Reward and Punishment Sensitivity and Restrained Eating and Dieting Success

Background The current study set out to improve our understanding of the characteristics of individuals who are motivated to restrict their food intake yet who nevertheless fail to do so. We examined whether punishment sensitivity (PS) was related to restrained eating, and reward sensitivity (RS) to perceived dieting success. Additionally, it was examined whether executive control (EC) moderates the association between RS and perceived dieting success. Methods Female student participants (N = 290, aged 17–29, BMI between 18.5 and 38.0) completed questionnaires on restrained eating, perceived dieting success, RS and PS, and carried out a behavioral task to index EC. Results PS was indeed positively related to restrained eating. RS was positively related to perceived dieting success, yet, EC did not moderate this association. Conclusion The current study adds to the evidence that PS is related to individuals’ motivation to restrict their food intake. Furthermore, it shows support for the suggestion that RS may facilitate food restriction.
Detection of Jaguar (Panthera onca) From Genetic Material in Drinking Water

Jaguar (Panthera onca) are of conservation concern and occur at very low densities in the northern portion of their range in northern Mexico and the southwestern United States. Environmental DNA sampling to detect genetic material from drinking water may be an effective approach for jaguar detection in these arid landscapes. Here we develop a qPCR assay for the detection of jaguar mitochondrial DNA, show that large quantities of DNA (mean 66,820 copies/L) can be found in the drinking water of captive animals, and observe detectable levels of DNA (80 copies/L) in a wild habitat with known jaguar populations. We suggest that environmental DNA sampling may represent a useful, complementary sampling tool for detection of rare jaguars, although effective application would require careful consideration of DNA persistence time in the environment.
TRIM71 Deficiency Causes Germ Cell Loss During Mouse Embryogenesis and Is Associated With Human Male Infertility

Mutations affecting the germline can result in infertility or the generation of germ cell tumors (GCT), highlighting the need to identify and characterize the genes controlling germ cell development. The RNA-binding protein and E3 ubiquitin ligase TRIM71 is essential for embryogenesis, and its expression has been reported in GCT and adult mouse testes. To investigate the role of TRIM71 in mammalian germ cell embryonic development, we generated a germline-specific conditional Trim71 knockout mouse (cKO) using the early primordial germ cell (PGC) marker Nanos3 as a Cre-recombinase driver. cKO mice are infertile, with male mice displaying a Sertoli cell-only (SCO) phenotype which in humans is defined as a specific subtype of non-obstructive azoospermia characterized by the absence of germ cells in the seminiferous tubules. Infertility in male Trim71 cKO mice originates during embryogenesis, as the SCO phenotype was already apparent in neonatal mice. The in vitro differentiation of mouse embryonic stem cells (ESCs) into PGC-like cells (PGCLCs) revealed reduced numbers of PGCLCs in Trim71-deficient cells. Furthermore, TCam-2 cells, a human GCT-derived seminoma cell line which was used as an in vitro model for PGCs, showed proliferation defects upon TRIM71 knockdown. Additionally, in vitro growth competition assays, as well as proliferation assays with wild type and CRISPR/Cas9-generated TRIM71 mutant NCCIT cells showed that TRIM71 also promotes proliferation in this malignant GCT-derived non-seminoma cell line. Importantly, the PGC-specific markers BLIMP1 and NANOS3 were consistently downregulated in Trim71 KO PGCLCs, TRIM71 knockdown TCam-2 cells and TRIM71 mutant NCCIT cells. These data collectively support a role for TRIM71 in PGC development. Last, via exome sequencing analysis, we identified several TRIM71 variants in a cohort of infertile men, including a loss-of-function variant in a patient with an SCO phenotype. Altogether, our work reveals for the first time an association of TRIM71 deficiency with human male infertility, and uncovers further developmental roles for TRIM71 in the germline during mouse embryogenesis.
Adverse Childhood Experiences Predict Early Initiation of Opioid Use Behaviors

Introduction: Although a substantial body of research documents a relationship between traumatic stress in childhood and the initiation of substance use later in the life course, only limited research has examined potential linkages between adverse childhood experiences (ACEs) and the initiation of non-medical prescription opioid use and other opioid use behaviors. The present study contributes to this growing body of work by investigating the association of childhood trauma with early initiation of a series of opioid use behaviors. Methods: New York City young adults (n = 539) ages 18–29 who reported non-medical use of prescription opioids or heroin use in the past 30 days were recruited using Respondent-Driven Sampling in 2014–16. Ten ACEs were assessed via self-report with the ACE Questionnaire. Associations between number of ACEs and self-reported ages of initiating seven opioid use behaviors (e.g., non-medical prescription opioid use, heroin use, heroin injection) were estimated with multivariable logistic regression. Results: Eighty nine percent of participants reported at least one ACE, and 46% reported four or more ACEs, a well-supported threshold indicating elevated risk for negative health consequences. Every increase of one trauma was associated with a 12–23% increase in odds of early initiation across the seven opioid use behaviors. Findings also document that the mean age at initiation increased with increasing risk severity across the behaviors, contributing to evidence of a trajectory from opioid pill misuse to opioid injection. Discussion: Increasing number of childhood traumas was associated with increased odds of earlier initiation of multiple opioid misuse behaviors. In light of prior research linking earlier initiation of substance use with increased substance use severity, present findings suggest the importance of ACEs as individual-level determinants of increased opioid use severity. Efforts to prevent onset and escalation of opioid use among at-risk youth may benefit from trauma prevention programs and trauma-focused screening and treatment, as well as increased attention to ameliorating upstream socio-structural drivers of childhood trauma.
The Effect of CO2 on Resting-State Functional Connectivity: Isocapnia vs. Poikilocapnia

The normal variability in breath size and frequency results in breath-to-breath variability of end-tidal PCO2 (PETCO2), the measured variable, and arterial partial pressure of carbon dioxide (PaCO2), the independent variable affecting cerebral blood flow (CBF). This study examines the effect of variability in PaCO2 on the pattern of resting-state functional MRI (rs-fMRI) connectivity. A region of interest (ROI)-to-ROI and Seed-to-Voxel first-level bivariate correlation, hemodynamic response function (hrf)-weighted analysis for measuring rs-fMRI connectivity was performed during two resting-state conditions: (a) normal breathing associated with breath-to-breath variation in PaCO2 (poikilocapnia), and (b) normal breathing with breath-to-breath variability of PETCO2 dampened using sequential rebreathing (isocapnia). End-tidal PCO2 (PETCO2) was used as a measurable surrogate for fluctuations of PaCO2. During poikilocapnia, enhanced functional connections were found between the cerebellum and inferior frontal and supramarginal gyrus (SG), visual cortex and occipital fusiform gyrus; and between the primary visual network (PVN) and the hippocampal formation. During isocapnia, these associations were not seen, rather enhanced functional connections were identified in the corticostriatal pathway between the putamen and intracalacarine cortex, supracalcarine cortex (SCC), and precuneus cortex. We conclude that vascular responses to variations in PETCO2, account for at least some of the observed resting state synchronization of blood oxygenation level-dependent (BOLD) signals.
3D Bioprinting of Vascularized Tissues for in vitro and in vivo Applications

With a limited supply of organ donors and available organs for transplantation, the aim of tissue engineering with three-dimensional (3D) bioprinting technology is to construct fully functional and viable tissue and organ replacements for various clinical applications. 3D bioprinting allows for the customization of complex tissue architecture with numerous combinations of materials and printing methods to build different tissue types, and eventually fully functional replacement organs. The main challenge of maintaining 3D printed tissue viability is the inclusion of complex vascular networks for nutrient transport and waste disposal. Rapid development and discoveries in recent years have taken huge strides toward perfecting the incorporation of vascular networks in 3D printed tissue and organs. In this review, we will discuss the latest advancements in fabricating vascularized tissue and organs including novel strategies and materials, and their applications. Our discussion will begin with the exploration of printing vasculature, progress through the current statuses of bioprinting tissue/organoids from bone to muscles to organs, and conclude with relevant applications for in vitro models and drug testing. We will also explore and discuss the current limitations of vascularized tissue engineering and some of the promising future directions this technology may bring.
Antiepileptic Efficacy and Network Connectivity Modulation of Repetitive Transcranial Magnetic Stimulation by Vertex Suppression

A core feature of drug-resistant epilepsy is hyperexcitability in the motor cortex, and low-frequency repetitive transcranial magnetic stimulation (rTMS) is a suitable treatment for seizures. However, the antiepileptic effect causing network reorganization has rarely been studied. Here, we assessed the impact of rTMS on functional network connectivity (FNC) in resting functional networks (RSNs) and their relation to treatment response. Fourteen patients with medically intractable epilepsy received inhibitive rTMS with a figure-of-eight coil over the vertex for 10 days spread across two weeks. We designed a 6-week follow-up phase divided into four time points to investigate FNC and rTMS-induced timing-dependent plasticity, such as seizure frequency and abnormal interictal discharges on electroencephalography (EEG). For psychiatric comorbidities, the Hamilton Depression Scale (HAM-D) and the Hamilton Anxiety Scale (HAM-A) were applied to measure depression and anxiety before and after rTMS. FNC was also compared to that of a cohort of 17 healthy control subjects. The after-effects of rTMS included all subjects that achieved the significant decrease rate of more than 50% in interictal epileptiform discharges and seizure frequency, 12 (14) patients with the reduction rate above 50% compared to the baseline, as well as emotional improvements in depression and anxiety (p < 0.05). In the analysis of RSNs, we found a higher synchronization between the sensorimotor network (SMN) and posterior default-mode network (pDMN) in epileptic patients than in healthy controls. In contrast to pre-rTMS, the results demonstrated a weaker FNC between the anterior DMN (aDMN) and SMN after rTMS, while the FNC between the aDMN and dorsal attention network (DAN) was greater (p < 0.05, FDR corrected). Importantly, the depressive score was anticorrelated with the FNC of the aDMN-SMN (r = −0.67, p = 0.0022), which was markedly different in the good and bad response groups treated with rTMS (p = 0.0115). Based on the vertex suppression by rTMS, it is possible to achieve temporary clinical efficacy by modulating network reorganization in the DMN and SMN for patients with refractory epilepsy.
Viral Gene Therapy for Glioblastoma Multiforme: A Promising Hope for the Current Dilemma

Glioblastoma multiforme (GBM), as one of the most common malignant brain tumors, was limited in its treatment effectiveness with current options. Its invasive and infiltrative features led to tumor recurrence and poor prognosis. Effective treatment and survival improvement have always been a challenge. With the exploration of genetic mutations and molecular pathways in neuro-oncology, gene therapy is becoming a promising therapeutic approach. Therapeutic genes are delivered into target cells with viral vectors to act specific antitumor effects, which can be used in gene delivery, play an oncolysis effect, and induce host immune response. The application of engineering technology makes the virus vector used in genetics a more prospective future. Recent advances in viral gene therapy offer hope for treating brain tumors. In this review, we discuss the types and designs of viruses as well as their study progress and potential applications in the treatment of GBM. Although still under research, viral gene therapy is promising to be a new therapeutic approach for GBM treatment in the future.
Forecasting the Cumulative Effects of Multiple Stressors on Breeding Habitat for a Steeply Declining Aerial Insectivorous Songbird, the Olive-sided Flycatcher (Contopus cooperi)

To halt ongoing loss in biodiversity, there is a need for landscape-level management recommendations that address cumulative impacts of anthropogenic and natural disturbances on wildlife habitat. We examined the cumulative effects of logging, roads, land-use change, fire, and bark beetle outbreaks on future habitat for olive-sided flycatcher (Contopus cooperi), a steeply declining aerial insectivorous songbird, in Canada’s western boreal forest. To predict the occurrence of olive-sided flycatcher we developed a suite of habitat suitability models using point count surveys (1997–2011) spatially- and temporally-matched with forest inventory data. Flycatcher occurrence was positively associated with small (∼10 ha) 10- to 20-year-old clearcuts, and with 10–100% tree mortality due to mountain pine beetle (Dendroctonus ponderosae) outbreaks, but we found no association with roads or distance to water. We used the parameter estimates from the best-fit habitat suitability models to inform spatially explicit state-and-transition simulation models to project change in habitat availability from 2020 to 2050 under six alternative scenarios (three management × two fire alternatives). The simulation models projected that the cumulative effects of land use conversion, forest harvesting, and fire will reduce the area of olive-sided flycatcher habitat by 16–18% under Business As Usual management scenarios and by 11–13% under scenarios that include protection of 30% of the land base. Scenarios limiting the size of all clearcuts to ≤10 ha resulted in a median habitat loss of 4–6%, but projections were highly variable. Under all three management alternatives, a 50% increase in fire frequency (expected due to climate change) exacerbated habitat loss. The projected losses of habitat in western boreal forest, even with an increase in protected areas, imply that reversing the ongoing population declines of olive-sided flycatcher and other migratory birds will require attention to forest management beyond protected areas. Further work should examine the effects of multiple stressors on the demographic mechanisms driving change in aerial insectivore populations, including stressors on the wintering grounds in South America, and should aim to adapt the design of protected areas and forest management policies to projected climate-driven increases in the size and frequency of wildfires.
Parkin Levels Decrease in Fibroblasts With Progranulin (PGRN) Pathogenic Variants and in a Cellular Model of PGRN Deficiency

Frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative diseases with TDP-43 mislocalization and aggregation. Genetic forms of FTLD and ALS are caused by pathogenic variants in various genes, such as PGRN (progranulin). To date, depletion of parkin E3 ubiquitin protein ligase, a key mitophagy regulator, has been reported in sporadic ALS patients and ALS mice models with TDP-43 proteinopathy. In this work, we show parkin downregulation also in fibroblasts derived from FTLD patients with four different PGRN pathogenic variants. We corroborate this finding in control fibroblasts upon PGRN silencing, demonstrating additionally the decrease of parkin downstream targets, mitofusin 2 (MFN2) and voltage dependent anion channel 1 (VDAC1). Importantly, we show that TDP-43 overexpression rescues PRKN levels upon transient PGRN silencing, but not in FTLD fibroblasts with PGRN pathogenic variants, despite upregulating PGRN levels in both cases. Further observation of PRKN downregulation upon TDP-43 silencing, suggests that TDP-43 loss-of-function contributes to PRKN decrease. Our results provide further evidence that parkin downregulation might be a common and systemic phenomenon in neurodegenerative diseases with TDP- 43 loss-of-function.
The Potential Application of Giant Reed (Arundo donax) in Ecological Remediation

Giant reed is known as one of the most important energy plants as a consequence of its huge dry biomass production. It can be used for bioenergy or biopolymer production. Thus, it can replace maize and reduce the production cost of biomass and electricity. Giant reed and its products have different uses in industry. The use of giant reed as a raw material to obtain cellulose past for the production of rayon viscose and paper. Thanks to the flexible and strong of the material, giant reed can be used in the manufacture of fishing rods, brass musical instruments, canes and construction supplies. One of the most important characteristics of giant reed is that it shows strong growth capability in different soils with wide ranges of pH, salinity and high heavy metal contents and can be used for ecological remediation. Giant reed was able not only to decontaminate polluted soils with heavy metals, but also to purify the wastewater and decrease the pH and make red mud safer. Here, we review the available evidence regarding the utilization of giant reed in the field of phytoremediation and discuss the potential application of giant reed combined with advanced remediation technologies in ecological remediation.
Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development

The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog2 in human ES cell-derived retinal organoids. Single cell transcriptome analyses identify three states of proliferating retinal progenitors: pre-neurogenic, neurogenic, and cell cycle-exiting progenitors. Each shows different expression profile of bHLH factors. The cell cycle-exiting progenitors feed into a postmitotic heterozygous neuroblast pool that gives rise to early born neuronal lineages. Elevating ATOH7 or Neurog2 expression accelerates the transition from the pre-neurogenic to the neurogenic state, and expands the exiting progenitor and neuroblast populations. In addition, ATOH7 and Neurog2 significantly, yet differentially, enhance retinal ganglion cell and cone photoreceptor production. Moreover, single cell transcriptome analyses reveal that ATOH7 and Neurog2 each assert positive autoregulation, and both suppress key bHLH factors associated with the pre-neurogenic and states and elevate bHLH factors expressed by exiting progenitors and differentiating neuroblasts. This study thus provides novel insight regarding how ATOH7 and Neurog2 impact human retinal progenitor behaviors and neuroblast fate choices.
Optical Imaging-Based Guidance of Viral Microinjections and Insertion of a Laminar Electrophysiology Probe Into a Predetermined Barrel in Mouse Area S1BF

Wide-field Optical Imaging of Intrinsic Signals (OI-IS; Grinvald et al., 1986) is a method for imaging functional brain hemodynamic responses, mainly used to image activity from the surface of the cerebral cortex. It localizes small functional modules – such as cortical columns – with great spatial resolution and spatial specificity relative to the site of increases in neuronal activity. OI-IS is capable of imaging responses either through an intact or thinned skull or following a craniotomy. Therefore, it is minimally invasive, which makes it ideal for survival experiments. Here we describe OI-IS-based methods for guiding microinjections of optogenetics viral vectors in proximity to small functional modules (S1 barrels) of the cerebral cortex and for guiding the insertion of electrodes for electrophysiological recording into such modules. We validate our proposed methods by tissue processing of the cerebral barrel field area, revealing the track of the electrode in a predetermined barrel. In addition, we demonstrate the use of optical imaging to visualize the spatial extent of the optogenetics photostimulation, making it possible to estimate one of the two variables that conjointly determine which region of the brain is stimulated. Lastly, we demonstrate the use of OI-IS at high-magnification for imaging the upper recording contacts of a laminar probe, making it possible to estimate the insertion depth of all contacts relative to the surface of the cortex. These methods support the precise positioning of microinjections and recording electrodes, thus overcoming the variability in the spatial position of fine-scale functional modules.