Miracle-dz/UniFAR-FTUs huggingface dataset:
Cnr2 Is Important for Ribbon Synapse Maturation and Function in Hair Cells and Photoreceptors

The role of the cannabinoid receptor 2 (CNR2) is still poorly described in sensory epithelia. We found strong cnr2 expression in hair cells (HCs) of the inner ear and the lateral line (LL), a superficial sensory structure in fish. Next, we demonstrated that sensory synapses in HCs were severely perturbed in zebrafish larvae lacking cnr2. Appearance and distribution of presynaptic ribbons and calcium channels (Cav1.3) were profoundly altered in mutant animals. Clustering of membrane-associated guanylate kinase (MAGUK) in post-synaptic densities (PSDs) was also heavily affected, suggesting a role for cnr2 for maintaining the structure of the sensory synapse. Furthermore, vesicular trafficking in HCs was strongly perturbed suggesting a retrograde action of the endocannabinoid system (ECs) mediated via cnr2 that was modulating HC mechanotransduction. We found similar perturbations in retinal ribbon synapses. Finally, we showed that larval swimming behaviors after sound and light stimulations were significantly different in mutant animals. Thus, we propose that cnr2 is critical for the processing of sensory information in the developing larva.
A Precuneal Causal Loop Mediates External and Internal Information Integration in the Human Brain

Human brains interpret external stimuli based on internal representations. One untested hypothesis is that the default-mode network (DMN), widely considered responsible for internally oriented cognition, can decode external information. Here, we posit that the unique structural and functional fingerprint of the precuneus (PCu) supports a prominent role for the posterior part of the DMN in this process. By analyzing the imaging data of 100 participants performing two attention-demanding tasks, we found that the PCu is functionally divided into dorsal and ventral subdivisions. We then conducted a comprehensive examination of their connectivity profiles and found that at rest, both the ventral PCu (vPCu) and dorsal PCu (dPCu) are mainly connected with the DMN but also are differentially connected with internally oriented networks (IoN) and externally oriented networks (EoN). During tasks, the double associations between the v/dPCu and the IoN/EoN are correlated with task performance and can switch depending on cognitive demand. Furthermore, dynamic causal modeling (DCM) revealed that the strength and direction of the effective connectivity (EC) between v/dPCu is modulated by task difficulty in a manner potentially dictated by the balance of internal versus external cognitive demands. Our study provides evidence that the posterior medial part of the DMN may drive interactions between large-scale networks, potentially allowing access to stored representations for moment-to-moment interpretation of an ever-changing environment. SIGNIFICANCE STATEMENT The default-mode network (DMN) is widely known for its association with internalized thinking processes, e.g., spontaneous thoughts, which is the most interesting but least understood component in human consciousness. The precuneus (PCu), a posteromedial DMN hub, is thought to play a role in this, but a mechanistic explanation has not yet been established. In this study we found that the associations between ventral PCu (vPCu)/dorsal PCu (dPCu) subdivisions and internally oriented network (IoN)/externally oriented network (EoN) are flexibly modulated by cognitive demand and correlate with task performance. We further propose that the recurrent causal connectivity between the ventral and dorsal PCu supports conscious processing by constantly interpreting external information based on an internal model, meanwhile updating the internal model with the incoming information.
A mating-induced reproductive gene promotes Anopheles tolerance to Plasmodium falciparum infection

Anopheles mosquitoes have transmitted Plasmodium parasites for millions of years, yet it remains unclear whether they suffer fitness costs to infection. Here we report that the fecundity of virgin and mated females of two important vectors—Anopheles gambiae and Anopheles stephensi—is not affected by infection with Plasmodium falciparum, demonstrating that these human malaria parasites do not inflict reproductive costs to their natural mosquito hosts. Additionally, parasite development is not impacted by mating status. However, in field studies using different P. falciparum isolates in Anopheles coluzzii, we find that Mating-Induced Stimulator of Oogenesis (MISO), a female reproductive gene strongly induced after mating by the sexual transfer of the steroid hormone 20-hydroxyecdysone (20E), protects females from incurring fecundity costs to infection. MISO-silenced females produce fewer eggs as they become increasingly infected with P. falciparum, while parasite development is not impacted by this gene silencing. Interestingly, previous work had shown that sexual transfer of 20E has specifically evolved in Cellia species of the Anopheles genus, driving the co-adaptation of MISO. Our data therefore suggest that evolution of male-female sexual interactions may have promoted Anopheles tolerance to P. falciparum infection in the Cellia subgenus, which comprises the most important malaria vectors. Author summary Plasmodium falciparum, the deadliest form of human malaria, is transmitted when female Anopheles mosquitoes bite people and take a blood meal in order to develop eggs. To date, it is still poorly understood whether Anopheles mosquitoes that get infected with P. falciparum suffer fitness costs. Here, we find that the number of eggs produced by Anopheles gambiae and Anopheles stephensi females is not affected by P. falciparum infection, and that the mating status of the mosquitoes does not impact the parasite. However, in field experiments infecting a related species, Anopheles coluzzii, with P. falciparum using blood from donors in Burkina Faso, we find that interfering with the expression of a gene normally triggered by the sexual transfer of the steroid hormone 20-hydroxyecdysone induces increasing costs to egg development as females become more infected with P. falciparum, with no impacts on the parasite. The results of our study suggest that pathways triggered by mating may help Anopheles prevent reproductive costs associated with P. falciparum infection, providing new insights into evolutionary strategies adopted by anophelines in the face of a longstanding association with Plasmodium parasites.
CASP microdomain formation requires cross cell wall stabilization of domains between neighbors and non-cell autonomous action of LOTR1 cell wall protein

Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how these contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network requires neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction in lotr1 is associated with disrupted CSDs and establishment of fully functional CSD at ectopic positions, forming “half strips”. LOTR1 is expressed in stele and needs to be expressed there. Endodermal expression, by contrast, cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establish LOTR1 as a crucial player in CSD positioning acting in a non-cell-autonomous pathway to restrict and coordinate CS positioning.
Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys: a mitochondrial selective sweep?

The golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphism (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results support the true species status of Z. atricapilla and Z. leucophrys, and indicate deeper divergences between the two species than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.
Functions of Gle1 are governed by two distinct modes of self-association

Gle1 is a conserved, essential regulator of DEAD-box RNA helicases, with critical roles defined in mRNA export, translation initiation, translation termination, and stress granule formation. Mechanisms that specify which, where and when DDXs are targeted by Gle1 are critical to understand. In addition to roles for stress-induced phosphorylation and inositol hexakisphosphate (IP6) binding in specifying Gle1 function, Gle1 oligomerizes via its N-terminal domain in a phosphorylation-dependent manner. However, a thorough analysis of the role for Gle1 self-association is lacking. Here, we find that Gle1 self-association is driven by two distinct regions: a coiled-coil domain and a novel ten amino acid aggregation prone region, both of which are necessary for proper Gle1 oligomerization. By exogenous expression in HeLa cells, we tested the function of a series of mutations that impact the oligomerization domains of the Gle1A and Gle1B isoforms. Gle1 oligomerization is necessary for many, but not all aspects of Gle1A and Gle1B function, and the requirements for each interaction domain differ. Whereas the coiled-coil domain and aggregation prone region additively contribute to competent mRNA export and stress granule formation, both self-association domains are independently required for regulation of translation under cellular stress. In contrast, Gle1 self-association is dispensable for phosphorylation and non-stressed translation initiation. Collectively, we reveal self-association functions as an additional mode of Gle1 regulation to ensure proper mRNA export and translation. This work also provides further insight into the mechanisms underlying human gle1 disease mutants found in prenatally lethal forms of arthrogryposis.
SOX11 is a lineage-dependency factor and master epigenetic regulator in neuroblastoma

The pediatric extra-cranial tumor neuroblastoma (NB) is characterised by a low mutation burden while copy number alterations are present in most high-risk cases. We identified SOX11 as a strong lineage dependency transcription factor in adrenergic NB based on recurrent chromosome 2p focal gains and amplifications, its specific expression in the normal sympatho-adrenal lineage and adrenergic NBs and its regulation by multiple adrenergic specific cis-interacting (super-)enhancers. Adrenergic NBs are strongly dependent on high SOX11 expression levels for growth and proliferation. Through genome-wide DNA-binding and transcriptome analysis, we identified and validated functional SOX11 target genes, several of which implicated in chromatin remodeling and epigenetic modification. SOX11 controls chromatin accessibility predominantly affecting distal adrenergic lineage-specific enhancers marked by binding sites of the adrenergic core regulatory circuitry. During normal sympathoblast differentiation we find expression of SOX11 prior to members of the adrenergic core regulatory circuitry. Given the broad control of SOX11 of multiple epigenetic regulatory complexes and its presumed pioneer factor function, we propose that adrenergic NB cells have co-opted the normal role of SOX11 as a crucial regulator of chromatin accessibility and cell identity.
The deubiquitylase Ubp15 couples transcription to mRNA export

The nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed and exported. The role of ubiquitylation in this process is increasingly recognized as the ubiquitylation of many key players have been shown to affect mRNA nuclear export. While a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here, we identified the deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts both with RNA polymerase II and with the nuclear pore complex, and its deletion reverts the nuclear export defect of mutants of the E3 ligase Rsp5. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.
Distinct temporal difference error signals in dopamine axons in three regions of the striatum in a decision-making task

Different regions of the striatum regulate different types of behavior. However, how dopamine signals differ across striatal regions and how dopamine regulates different behaviors remain unclear. Here, we compared dopamine axon activity in the ventral, dorsomedial, and dorsolateral striatum, while mice performed in a perceptual and value-based decision task. Surprisingly, dopamine axon activity was similar across all three areas. At a glance, the activity multiplexed different variables such as stimulus-associated values, confidence and reward feedback at different phases of the task. Our modeling demonstrates, however, that these modulations can be inclusively explained by moment-by-moment changes in the expected reward, i.e. the temporal difference error. A major difference between these areas was the overall activity level of reward responses: reward responses in dorsolateral striatum (DLS) were positively shifted, lacking inhibitory responses to negative prediction error. Tenets of habit and skill can be explained by this positively biased dopamine signal in DLS.
Coronatine contributes Pseudomonas cannabina pv. alisalensis virulence by overcoming both stomatal and apoplastic defenses in dicot and monocot plants

P. cannabina pv. alisalensis (Pcal) is a causative agent of bacterial blight of crucifer including cabbage, radish, and broccoli. Importantly, Pcal can infect not only a wide range of Brassicaceae, but also green manure crops such as oat. However, Pcal virulence mechanisms have not been investigated and are not fully understood. We focused on coronatine (COR) function, which is one of the well-known P. syringae pv. tomato DC3000 virulence factors, in Pcal infection processes on both dicot and monocot plants. Cabbage and oat plants dip-inoculated with a Pcal KB211 COR mutant (ΔcmaA) exhibited reduced virulence compared to Pcal WT. Moreover, ΔcmaA failed to reopen stomata on both cabbage and oat, suggesting that COR facilitates Pcal entry through stomata into both plants. Furthermore, cabbage and oat plants syringe-infiltrated with ΔcmaA also showed reduced virulence, suggesting that COR is involved in overcoming not only stomatal-based defense, but also apoplastic defense. Indeed, defense related genes, including PR1 and PR2, were highly expressed in plants inoculated with ΔcmaA compared to Pcal WT, indicating that COR suppresses defense-related genes of both cabbage and oat. Additionally, SA accumulation increases after ΔcmaA inoculation compared to Pcal WT. Taken together, COR contributes to cause disease by suppressing stomatal-based defense and apoplastic defense in both dicot and monocot plants. This is the first study to investigate COR functions in the interaction of Pcal and different host plants (dicot and monocot plants) using genetically and biochemically defined COR deletion mutants. Author summary Disease outbreaks caused by new Pseudomonas syringae isolates are problems worldwide. P. cannabina pv. alisalensis (Pcal) causes bacterial blight on a wide range of cruciferous plants and bacterial brown spot on oat plants. Although P. syringae deploys a variety of virulence factors, Pcal virulence factors have not been investigated. We focused on coronatine (COR) function, which is one of the well-known P. syringae virulence factors. COR is a non-host-specific phytotoxin and contributes to P. syringae growth and lesion formation or expansion in several host plants. COR function has been mainly studied in the model pathogen P. syringae pv. tomato DC3000 and model the plant Arabidopsis thaliana. Thus, COR roles in Pcal infection especially on monocot plants have not been well studied. Therefore, we investigated COR role in Pcal interaction with both dicot and monocot plants. Here, we revealed that COR functions as a multifunctional suppressor to manage Pcal virulence on both plants.
Research progress on the medicinal and nutritional properties of sea buckthorn (Hippophae rhamnoides) – a review

Summary Common sea buckthorn, Hippophae rhamnoides L. (Elaeagnaceae), is a small fruit tree widely distributed throughout Europe and Asia. Because H. rhamnoides plants are actinorhizal and tolerant of abiotic stresses, they grow in nutritionally-poor environments where it is difficult to grow other crops. Furthermore, sea buckthorn is rich in vitamins, unsaturated fatty acids, and phenolic compounds, and is used for medicinal purposes and as food in some parts of the World. In this review, we discuss (i) the pharmaceutical efficacy of H. rhamnoides; (ii) research on the sugars and acids contents of H. rhamnoides fruit, because it is part of the diet in some cultures and also shows promise as a functional food; and (iii) the various fruit phenotypes of sea buckthorn found in India and Russia because a high level of genetic diversity is important for improving fruit quality and yield. Few reviews on the medicinal and nutritional properties of H. rhamnoides have been published in the field of horticultural science. Sharing knowledge on this topic will contribute to the goal of improving the characteristics of sea buckthorn and increasing fruit production.
Sensitivity-dependent Hierarchical Receptor Codes for Odors

In order to comprehend the strategy of odor encoding by odorant receptors, we isolated 2740 mouse receptor neurons from four olfactory epithelial zones and classified them in terms of their sensitivities and tuning specificities to a chiral pair of odorants, S(+)-carvone (caraway-like odor) and R(–)-carvone (spearmint-like odor). Our approach revealed that the majority of receptors at the lowest effective stimulus concentration represented the principal odor qualities characteristic of each enantiomer by means of the principal odor qualities of the odorants for which the receptors were most sensitive. The chiral-non-discriminating receptors became 3.7 times of R(–)-carvone-sensitive receptors in the subpopulations when the stimulus concentration was increased 10-fold. More than 80% of the responsive receptors (an estimated 70 ± α types) exhibited overlapping sensitivities between the enantiomers. The signals from the non-discriminating receptors may be reduced to decode the characteristic odor identity for R(–)-carvone in the brain over an adequate range of stimulus strengths. The information processing of odors appears to involve the selective weighting of the signals from the most sensitive receptors. An analysis of the overall receptor codes to carvones indicated that the system employs hierarchical receptor codes: principal odor qualities are encoded by the most sensitive receptors and lower-ranked odor qualities by less sensitive receptors.
Carbon‐13 Discrimination Can be Used to Evaluate Soybean Yield Variability

Diagnostic tools for assessing the cause of soybean [Glycine max (L.) Merr. ] yield variability in whole fields are needed. The objective of this study was to determine if 13 C discrimination (Δ) can be used to assess the factors responsible for soybean yield variability. Research was conducted in five eastern South Dakota fields between 1999 and 2001. Yields in the summit-shoulder areas of Brookings, Moody, South Dakota State University (SDSU), and Lovjoy were 20 to 60% less than the rest of the field. Adding water to plants growing in the summit-shoulder areas in Moody and SDSU increased yield and A. However, in the foot-slope position, adding water did not impact yield or Δ. Based on the spatial relationships among protein content, yields, chlorophyll meter readings, and A at Moody and SDSU, (i) the reduced yields in the summit-shoulder areas most likely resulted from reduced plant vigor resulting from water stress; (ii) lower protein concentrations in summit-shoulder areas in Moody had a limited impact on A; and (iii) interactions among water availability, protein content, and yield can occur. In a combined analysis in the four fields where grain samples were collected at harvest (Moody, SDSU, Lovjoy, and TE80), A explained 62% of the total yield variability. Results from this experiment suggest that A can be used to help assess water stress, provided that N stress is absent. By understanding the causes of yield variability, producers will be able to make better management decisions.
Functional MRI of human amygdala activity during Pavlovian fear conditioning: Stimulus processing versus response expression

Although laboratory animal studies have shown that the amygdala plays multiple roles in conditional fear, less is known about the human amygdala. Human subjects were trained in a Pavlovian fear conditioning paradigm during functional magnetic resonance imaging (fMRI). Brain activity maps correlated with reference waveforms representing the temporal pattern of visual conditional stimuli (CSs) and subject-derived autonomic responses were compared. Subjects receiving paired CS–shock presentations showed greater amygdala activity than subjects receiving unpaired CS–shock presentations when their brain activity was correlated with a waveform generated from their behavioral responses. Stimulusbased waveforms revealed learning differences in the visual cortex, but not in the amygdala. These data support the view that the amygdala is important for the expression of learned behavioral responses during Pavlovian fear conditioning.