Miracle-dz/UniFAR-FTUs huggingface dataset:
Profiling the transcallosal response of rat motor cortex evoked by contralateral optogenetic stimulation of glutamatergic cortical neurons

Background Efficient interhemispheric integration of neural activity between left and right primary motor cortex (M1) is critical for inter-limb motor control. Objective We employed optogenetic stimulation to establish a framework for probing transcallosal M1-M1 interactions in rats. Methods In male rats, we optogenetically stimulated glutamatergic neurons in right M1 and recorded the transcallosally evoked potential with chronically implanted electrodes in contralateral left M1 during dexmedetomidine anesthesia. We systematically varied the stimulation intensity and duration to characterize the relationship between stimulation parameters in right M1 and the characteristics of the evoked intracortical potentials in left M1. Results Optogenetic stimulation of right M1 consistently evoked a transcallosal response in left M1 with a consistent negative peak (N1) that sometimes was preceded by a smaller positive peak (P1). Higher stimulation intensity or longer stimulation duration gradually increased N1 amplitude and reduced N1 variability across trials. Median N1 latencies remained stable, once stimulation elicited a reliable N1 peak and did not display a systematic shortening with increasing stimulation intensity or duration. Conclusions Optogenetically stimulated glutamatergic neurons in M1 can reliably evoke a transcallosal response in anesthetized rats and can be used to characterize the relationship between “stimulation dose” and “response magnitude” (i.e., the gain function) of transcallosal M1-to-M1 glutamatergic connections. Detailed knowledge of the stimulus-response relationship is needed to optimize the efficacy of optogenetic stimulation. Since transcallosal M1-M1 interactions can also be probed non-invasively with transcranial magnetic stimulation in humans, our optogenetic stimulation approach bears translational potential for studying how unilateral M1 stimulation can induce interhemispheric plasticity.
An Infectious Rous Sarcoma Virus Gag Mutant That Is Defective in Nuclear Cycling

While mechanisms for retroviral Gag assembly at the plasma membrane are beginning to be characterized, characterization of intermediate trafficking locales remain elusive. This is in part due to the difficulty of tracking individual proteins from translation to plasma membrane binding. ABSTRACT During retroviral replication, unspliced viral genomic RNA (gRNA) must escape the nucleus for translation into viral proteins and packaging into virions. “Complex” retroviruses, such as human immunodeficiency virus (HIV), use cis-acting elements on the unspliced gRNA in conjunction with trans-acting viral proteins to facilitate this escape. “Simple” retroviruses, such as Mason-Pfizer monkey virus (MPMV) and murine leukemia virus (MLV), exclusively use cis-acting elements on the gRNA in conjunction with host nuclear export proteins for nuclear escape. Uniquely, the simple retrovirus Rous sarcoma virus (RSV) has a Gag structural protein that cycles through the nucleus prior to plasma membrane binding. This trafficking has been implicated in facilitating gRNA nuclear export and is thought to be a required mechanism. Previously described mutants that abolish nuclear cycling displayed enhanced plasma membrane binding, enhanced virion release, and a significant loss in genome incorporation resulting in loss of infectivity. Here, we describe a nuclear cycling-deficient RSV Gag mutant that has similar plasma membrane binding and genome incorporation to wild-type (WT) virus and surprisingly is replication competent, albeit with a slower rate of spread than observed in WT virus. This mutant suggests that RSV Gag nuclear cycling is not strictly required for RSV replication. IMPORTANCE While mechanisms for retroviral Gag assembly at the plasma membrane are beginning to be characterized, characterization of intermediate trafficking locales remain elusive. This is in part due to the difficulty of tracking individual proteins from translation to plasma membrane binding. Rous sarcoma virus (RSV) Gag nuclear cycling is a unique phenotype that may provide comparative insight to viral trafficking evolution and may present a model intermediate to cis- and trans-acting mechanisms for gRNA export.
The ChvG-ChvI and NtrY-NtrX Two-Component Systems Coordinately Regulate Growth of Caulobacter crescentus

TCSs enable bacteria to regulate gene expression in response to physiochemical changes in their environment. The ChvGI and NtrYX TCSs regulate diverse pathways associated with pathogenesis, growth, and cell envelope function in many α-proteobacteria. ABSTRACT Two-component signaling systems (TCSs) are comprised of a sensory histidine kinase and a response regulator protein. In response to environmental changes, sensor kinases directly phosphorylate their cognate response regulator to affect gene expression. Bacteria typically express multiple TCSs that are insulated from one another and regulate distinct physiological processes. There are examples of cross-regulation between TCSs, but this phenomenon remains relatively unexplored. We have identified regulatory links between the ChvG-ChvI (ChvGI) and NtrY-NtrX (NtrYX) TCSs, which control important and often overlapping processes in alphaproteobacteria, including maintenance of the cell envelope. Deletion of chvG and chvI in Caulobacter crescentus limited growth in defined medium, and a selection for genetic suppressors of this growth phenotype uncovered interactions among chvGI, ntrYX, and ntrZ, which encodes a previously uncharacterized periplasmic protein. Significant overlap in the experimentally defined ChvI and NtrX transcriptional regulons provided support for the observed genetic connections between ntrYX and chvGI. Moreover, we present evidence that the growth defect of strains lacking chvGI is influenced by the phosphorylation state of NtrX and, to some extent, by levels of the TonB-dependent receptor ChvT. Measurements of NtrX phosphorylation in vivo indicated that NtrZ is an upstream regulator of NtrY and that NtrY primarily functions as an NtrX phosphatase. We propose a model in which NtrZ functions in the periplasm to inhibit NtrY phosphatase activity; regulation of phosphorylated NtrX levels by NtrZ and NtrY provides a mechanism to modulate and balance expression of the NtrX and ChvI regulons under different growth conditions. IMPORTANCE TCSs enable bacteria to regulate gene expression in response to physiochemical changes in their environment. The ChvGI and NtrYX TCSs regulate diverse pathways associated with pathogenesis, growth, and cell envelope function in many alphaproteobacteria. We used Caulobacter crescentus as a model to investigate regulatory connections between ChvGI and NtrYX. Our work defined the ChvI transcriptional regulon in C. crescentus and revealed a genetic interaction between ChvGI and NtrYX, whereby modulation of NtrYX signaling affects the survival of cells lacking ChvGI. In addition, we identified NtrZ as a periplasmic inhibitor of NtrY phosphatase activity in vivo. Our work establishes C. crescentus as an excellent model to investigate multilevel regulatory connections between ChvGI and NtrYX in alphaproteobacteria.
Selection in a growing bacterial/yeast colony biases results of mutation accumulation experiments

Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments performed with organisms such as Drosophila have an effective population size of one. However, in MA experiments with bacteria and yeast, a single founder is allowed to grow to a size of a colony (~108). The effective population size in these experiments is of the order of 10. In this scenario, while it is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth and therefore, the MA experiment; this effect has not been tested explicitly. In this work, we simulate colony growth and perform an MA experiment, and demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over represented by a factor greater than two. The DFE of beneficial and deleterious mutations are accurately captured in an MA experiment. We show that the effect of selection in a growing colony varies non-monotonically and that, in the face of natural selection dictating an MA experiment, estimates of mutation rate of an organism is not trivial. We perform experiments with 160 MA lines of E. coli, and demonstrate that rate of change of mean fitness is a non-monotonic function of the colony size, and that selection acts differently in different sectors of a growing colony. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.
Age-related decreases of cortical visuo-phonological transformation of unheard

35 In a previous work we showed that the visual cortex tracks acoustic amplitude modulations 36 accompanying lip movements during silently presented visual speech. It is unknown whether 37 similar visuo-phonological transformation processes also exist for spectral modulations, which 38 altogether could support the integration of auditory and visual cues for speech processing. 39 Also, given increasing hearing difficulties in elderly individuals, we were interested in how 40 these processes change as a function of age. Participants watched silent videos of a speaker 41 and paid attention to the lip movements while being seated in the MEG. We found that the 42 visual cortex not only tracks the unheard speech envelope, but also the unheard modulations 43 of resonant frequencies (or formants) and the pitch (or fundamental frequency) linked to the 44 lip movements, a process that is in general related to speech comprehension. Interestingly, 45 only the processing of intelligible unheard formants decreases significantly with age in the 46 visual and also in the cingulate cortex. This is not the case for the processing of the unheard 47 speech envelope, the fundamental frequency or the purely visual information carried by lip 48 movements. These results show that not only the global unheard speech envelope, but also 49 unheard spectral fine-details are transformed from a mere visual to a phonological 50 representation. Aging affects especially the ability to derive spectral dynamics at formant 51 frequencies. Since listening in noisy environments should capitalize on the ability to track 52 spectral fine-details, our results provide a novel focus on compensatory processes in such 53 challenging situations. 54
CRTC2 regulates plasma cell metabolism and survival

Antibody secreting cell (ASC) function and longevity determines the strength and durability of a humoral immune response. Previously, we identified the inactivation of the CREB-regulated transcriptional coactivator-2 (CRTC2) in an in vitro B cell differentiation assay that produced functional ASCs. However, the requirement for CRTC2 inactivation in ASC physiology in vivo remains unknown. Using transgenic (TG) mice that express a constitutively active form of CRTC2 (Crtc2-AA) as an experimental tool, we demonstrate that Crtc2 repression in plasma cells (PCs) is an intrinsic requirement for ASC metabolic fitness. Sustained CRTC2 activity shortens the survival of splenic and bone marrow PCs, resulting in reduced numbers of long-lived PCs and antibody deficits against T cell dependent and independent antigens, and an acute viral infection. TG PCs resemble short-lived PCs with reductions in glycolysis, oxidative metabolism, spare respiratory capacity, and antibody secretion. Mechanistically, Crtc2 repression is necessary for the fidelity of PC gene expression and mRNA alternative-splicing programs. Combined, Crtc2 repression in PCs must occur to support PC metabolism and extend ASC survival during a humoral immune response.
Cholesterol promotes both head group visibility and clustering of PI(4,5)P2 driving unconventional secretion of Fibroblast Growth Factor 2

Fibroblast Growth Factor 2 (FGF2) is a cell survival factor involved in tumor-induced angiogenesis. FGF2 is secreted through an unconventional secretory pathway based upon direct protein translocation across the plasma membrane. Here we demonstrate that both PI(4,5)P2-dependent FGF2 recruitment at the inner plasma membrane leaflet and FGF2 membrane translocation into the extracellular space are positively modulated by cholesterol in living cells. We further reveal cholesterol to enhance FGF2 binding to PI(4,5)P2-containing lipid bilayers in a fully reconstituted system. Based on extensive atomistic molecular dynamics simulations and membrane tension experiments, we propose cholesterol to modulate FGF2 binding to PI(4,5)P2 by (i) increasing head group visibility of PI(4,5)P2 on the membrane surface, (ii) increasing avidity by cholesterol-induced clustering of PI(4,5)P2 molecules triggering FGF2 oligomerization and (iii) increasing membrane tension facilitating the formation of lipidic membrane pores. Our findings have general implications for phosphoinositide-dependent protein recruitment to membranes and explain the highly selective targeting of FGF2 towards the plasma membrane, the subcellular site of FGF2 membrane translocation during unconventional secretion of FGF2.
Assessing the efficacy of antibiotic treatment for the creation of axenic earthworms

Earthworms are an integral part of soil ecosystems, especially for their role in soil functions such as organic matter (OM) decomposition and nutrient cycling. Earthworms and microorganisms are interdependent, and a considerable portion of the contribution earthworms make to influencing OM fate is through interactions with microorganisms. However, the importance of the earthworm-associated microbiome is not fully understood, because it is difficult to separate the direct influence of the earthworms from the indirect influence of their microbiome. Here, we evaluated an antibiotic-based procedure for producing axenic ecologically-contrasting earthworm species (E. fetida, L. terrestris, A. chlorotica) as the first step towards soil studies aimed at understanding the importance of the earthworm microbiome for host health and function. Individual earthworms were exposed to antibiotics: cycloheximide (150 μg ml−1), ampicillin (100 μg ml−1), ciprofloxacin (50 μg ml−1), nalidixic acid (50 μg ml−1), and gentamicin (50 μg ml−1) either singly or in a cocktail via culture (96 h) in a semi-solid agar carrier. Compared to the non-antibiotic treated control, the cocktail (for all three species) and ciprofloxacin (for E. fetida and A. chlorotica) treatments significantly reduced (P<0.05) culturable microbial abundance on nutrient agar and potato dextrose agar. The microbial counts were reduced to below detection (<50 CFU individual−1) for E. fetida and A. chlorotica receiving the cocktail. Illumina 16S rDNA amplicon sequence analysis of culturable L. terrestris -associated bacteria showed that antibiotic treatment influenced community composition revealing putative sensitive (Comomonas, Kosakonia and Sphingobacterium) and insensitive (Aeromonas, Pseudochrobactrum) taxa. Overall, we report a rapid, with minimal earthworm-handling, process of creating ‘axenic’ E. fetida and A. chlorotica individuals or L. terrestris with a suppressed microbiome as a tool to be used in future ecological studies of earthworm microbial interactions affecting host health and function.
Generative AAV capsid diversification by latent interpolation

Adeno-associated virus (AAV) capsids have shown clinical promise as delivery vectors for gene therapy. However, the high prevalence of pre-existing immunity against natural capsids poses a challenge for widespread treatment. The generation of diverse capsids that are potentially more capable of immune evasion is challenging because introducing multiple mutations often breaks capsid assembly. Here we target a representative, immunologically relevant 28-amino-acid segment of the AAV2 capsid and show that a low-complexity Variational Auto-encoder (VAE) can interpolate in sequence space to produce diverse and novel capsids capable of packaging their own genomes. We first train the VAE on a 564-sample Multiple-Sequence Alignment (MSA) of dependo-parvoviruses, and then further augment this dataset by adding 22,704 samples from a deep mutational exploration (DME) on the target region. In both cases the VAE generated viable variants with many mutations, which we validated experimentally. We propose that this simple approach can be used to optimize and diversify other proteins, as well as other capsid traits of interest for gene delivery.
Genetic deletion of interleukin-15 is not associated with major structural changes following experimental post-traumatic knee osteoarthritis in rats

Post-traumatic Osteoarthritis (PTOA) is a degenerative joint disease, leading to articular cartilage breakdown, osteophyte formation, and synovitis, caused by an initial joint trauma. Pro-inflammatory cytokines increase catabolic activity and may perpetuate inflammation following joint trauma. Interleukin-15 (IL-15), a pro-inflammatory cytokine, is increased in OA patients, although its roles in OA pathophysiology are not well characterized. IL-15 levels appear to correlate to self-reported pain levels, and polymorphisms in the IL-15 receptor alpha gene correlate to a 1.5-fold increase in OA symptoms. This could be due to IL-15 effects on the activity of proteinases, such as matrix metalloproteinases (MMP) −1, −3, and −7. Here we utilized Il15 deficient rats to examine the role of IL-15 in PTOA pathogenesis in an injury-induced model of OA. OA was surgically induced in Il15 deficient rats and control wild-type rats to compare PTOA progression. Semi-quantitative scoring of the articular cartilage, subchondral bone, osteophyte size, and synovium was performed by two blinded observers. Analyses of articular cartilage damage, subchondral bone damage, and osteophyte formation revealed no significant difference between Il15 deficient rats and wild-type rats following PTOA-induction. Similarly, synovitis scoring across 6 parameters found no significant difference between genetic variants. Overall, IL-15 does not appear to play a key role in the development of structural changes in this surgically-induced rat model of PTOA.
Contrasting patterns and co-occurrence network of soil bacterial and fungal community along depth profiles in cold temperate montane forests of China

Soil bacterial and fungal communities with different key ecological functions play an important role in the boreal forest ecosystem. Despite several studies have reported the microbial altitudinal distribution patterns, our understanding about the characteristics of the microbial community and the core composition of the microbiome in cold-temperate mountain forests is still limited. In this study, Illumina MiSeq sequencing was used to investigate the changes in soil bacterial and fungal communities in surface and subsurface soils along at an altitudinal gradient (from 830 m to 1300 m) on Oakley Mountain in the northern Greater Khingan Mountains. Altitude and soil depth had significant impacts on the relative abundance of Proteobacteria, Acidobacteria and Actinobacteria (dominant phylum for bacteria), and altitude had significant impacts on the Ascomycota, Basidiomycota and Mucoromycota (dominant phylum for fungi). The diversity of bacterial and fungal communities showed a monotonous decrease and increase with altitude. The influence of altitude on bacterial and fungal community composition was greater than that of soil depth. The variation of pH and dissolved organic nitrogen (DON) content in different altitudes were the main factors driving the bacterial and fungal community structure, respectively. There is no obvious difference between the network structure of surface and subsurface soil fungal communities, while the network of subsurface soil bacterial communities was more complex and compact than the surface layer. The network nodes mainly belonging to Proteobacteria and Actinobacteria are the key species in the two soil layers. Our results demonstrated that the altitude had a stronger influence on soil bacterial and fungal communities than soil depth, and bacterial and fungal communities showed divergent patterns along the altitudes and soil profiles.
Sugar Signaling Induces Dynamic Changes during Meristem Development in Arabidopsis

Aerial parts of plants originate from pluripotent cells in the shoot apical meristem (SAM). This population of stem cells is maintained via a negative feedback loop involving stable expression of WUSCHEL (WUS) and CLAVATA3. SAM size is dynamic and undergoes a more than 2-fold expansion upon the transition to reproductive growth. The underlying mechanism controlling this process is largely unknown, but coinciding increased levels of trehalose 6-phosphate (T6P) suggest a participation of sugar signaling. Here we show that TREHALOSE PHOSPHATE PHOSPHATASE J, a component of the T6P pathway, is directly regulated by WUS, and controls SAM expansion at floral transition through WUS. Our findings demonstrate a dynamic feedback-regulation between central meristem maintenance and flowering time regulators with sugar signaling. One Sentence Summary The increase in meristem size during the floral transition is regulated via a feedback regulation involving sugar signaling.
Transcriptional Inactivation of TP53 and the BMP Pathway Mediates Therapy-induced Dedifferentiation and Metastasis in Prostate Cancer

Unsupervised clustering and deconvolution analysis identifies a novel subtype of M-CRPC endowed with hybrid epithelial/mesenchymal (E/M) and luminal progenitor-like traits (Mesenchymal and Stem-like PC, MSPC). Analysis of patient datasets and mechanistic studies indicate that MSPC arises as a consequence of therapy-induced lineage plasticity. AR blockade instigates two separate and complementary processes: 1) transcriptional silencing of TP53 and hence acquisition of hybrid E/M and stem-like traits; and 2) inhibition of the BMP signaling, which promotes resistance to the pro-apoptotic and anti-proliferative effects of AR inhibition. The drug-tolerant prostate cancer cells generated through reprogramming are rescued by neuregulin and generate metastases in mice. Combined inhibition of HER2/3 and AR or mTORC1 exhibit efficacy in preclinical models of mixed ARPC/MSPC or MSPC, respectively. These results identify a novel subtype of M-CRPC, trace its origin to therapy-induced lineage plasticity, and reveal its dependency on HER2/3 signaling.
Autonomous Lidar-Based Monitoring of Coastal Lagoon Entrances

Intermittently closed and open lakes or Lagoons (ICOLLs) are characterised by entrance barriers that form or break down due to the action of wind, waves and currents until the ocean-lagoon exchange becomes discontinuous. Entrance closure raises a variety of management issues that are regulated by monitoring. In this paper, those issues are investigated, and an automated sensor solution is proposed. Based upon a static Lidar paired with an edge computing device. This solar-powered remote sensing device provides an efficient way to automatically survey the lagoon entrance and estimate the berm profile. Additionally, it estimates the dry notch location and its height, critical factors in the management of the lagoon entrances. Generated data provide valuable insights into landscape evolution and berm behaviour during natural and mechanical breach events.