Miracle-dz/UniFAR-FTUs huggingface dataset:
PERSISTENCE AND CARRY-OVER OF METRIBUZIN AND TRIALLATE IN SUBARCTIC SOILS

Persistence of metribuzin and triallate in soil was studied near Delta Junction, Alaska from 1982 to 1985. Metribuzin was applied at 0.3, 0.6 and 1.3 kg ha−1 and triallate was applied at 0.7, 1.4 or 2.8 kg ha−1 in 1982. Spring barley, oats, spring wheat and rapeseed were planted in the plots in 1983 and 1985 to determine whether herbicide residues would decrease populations or yield of rotational crops. Application rate had no effect on degradation rate of metribuzin or triallate. Twelve percent of the metribuzin and 61% of the triallate applied still remained after 115 d. Three years after application, 2% of the metribuzin and 14% of the triallate applied still remained. In 1983, oat stands and yields in plots where triallate was applied at 2.8 kg ha−1 were lower than control plots. In 1985, there were no carry-over effects. Key words: Herbicide persistence, metribuzin, triallate, subarctic soils
Delayed auditory encoding and variable representation of stimulus regularity in cerebellar lesion patients

The dynamic and fleeting nature of sound necessitates the rapid encoding and use of information distributed over time. Here we investigated cerebellar contributions to these abilities. We measured EEG from cerebellar patients and healthy controls while they listened to “oddball” sound sequences consisting of infrequent pitch-deviant and frequent standard tones. Inter-stimulus-intervals were temporally regular (600 ms) or irregular (200-1000 ms). This allowed probing early event-related potentials (ERP; P50, N100) that reflect repetitive and changing stimulus characteristics in temporally regular or less (irregular) predictable sequences. Further, time-frequency data provided an index of temporal processing variability at the stimulation frequencies. We expected that cerebellar lesions lead to aberrant encoding and use of auditory information, reflected in the ERP morphology of peak amplitudes, latencies and typical suppression effects linked to stimulus predictability. Results confirm longer P50 peak latencies in patients and variable processing at stimulation frequencies covarying with the location of cerebellar damage. These findings further support the idea that the cerebellum might play a generalizable role in the encoding of auditory stimulation over time.
Semi-continuous Propagation of Influenza A Virus and Its Defective Interfering Particles: Analyzing the Dynamic Competition To Select Candidates for Antiviral Therapy

Defective interfering particles (DIPs) emerge naturally during viral infection and typically show an internal deletion in the viral genome. Thus, DIPs are propagation-incompetent. ABSTRACT Defective interfering particles (DIPs) of influenza A virus (IAV) are naturally occurring mutants that have an internal deletion in one of their eight viral RNA (vRNA) segments, rendering them propagation-incompetent. Upon coinfection with infectious standard virus (STV), DIPs interfere with STV replication through competitive inhibition. Thus, DIPs are proposed as potent antivirals for treatment of the influenza disease. To select corresponding candidates, we studied de novo generation of DIPs and propagation competition between different defective interfering (DI) vRNAs in an STV coinfection scenario in cell culture. A small-scale two-stage cultivation system that allows long-term semi-continuous propagation of IAV and its DIPs was used. Strong periodic oscillations in virus titers were observed due to the dynamic interaction of DIPs and STVs. Using next-generation sequencing, we detected a predominant formation and accumulation of DI vRNAs on the polymerase-encoding segments. Short DI vRNAs accumulated to higher fractions than longer ones, indicating a replication advantage, yet an optimum fragment length was observed. Some DI vRNAs showed breaking points in a specific part of their bundling signal (belonging to the packaging signal), suggesting its dispensability for DI vRNA propagation. Over a total cultivation time of 21 days, several individual DI vRNAs accumulated to high fractions, while others decreased. Using reverse genetics for IAV, purely clonal DIPs derived from highly replicating DI vRNAs were generated. We confirm that these DIPs exhibit a superior in vitro interfering efficacy compared to DIPs derived from lowly accumulated DI vRNAs and suggest promising candidates for efficacious antiviral treatment. IMPORTANCE Defective interfering particles (DIPs) emerge naturally during viral infection and typically show an internal deletion in the viral genome. Thus, DIPs are propagation-incompetent. Previous research suggests DIPs as potent antiviral compounds for many different virus families due to their ability to interfere with virus replication by competitive inhibition. For instance, the administration of influenza A virus (IAV) DIPs resulted in a rescue of mice from an otherwise lethal IAV dose. Moreover, no apparent toxic effects were observed when only DIPs were administered to mice and ferrets. IAV DIPs show antiviral activity against many different IAV strains, including pandemic and highly pathogenic avian strains, and even against nonhomologous viruses, such as SARS-CoV-2, by stimulation of innate immunity. Here, we used a cultivation/infection system, which exerted selection pressure toward accumulation of highly competitive IAV DIPs. These DIPs showed a superior interfering efficacy in vitro, and we suggest them for effective antiviral therapy.
Development of the Entorhinal Cortex Occurs via Parallel Lamination During Neurogenesis

The entorhinal cortex (EC) is the spatial processing center of the brain and structurally is an interface between the three layered paleocortex and six layered neocortex, known as the periarchicortex. Limited studies indicate peculiarities in the formation of the EC such as early emergence of cells in layers (L) II and late deposition of LIII, as well as divergence in the timing of maturation of cell types in the superficial layers. In this study, we examine developmental events in the entorhinal cortex using an understudied model in neuroanatomy and development, the pig and supplement the research with BrdU labeling in the developing mouse EC. We determine the pig serves as an excellent anatomical model for studying human neurogenesis, given its long gestational length, presence of a moderate sized outer subventricular zone and early cessation of neurogenesis during gestation. Immunohistochemistry identified prominent clusters of OLIG2+ oligoprogenitor-like cells in the superficial layers of the lateral EC (LEC) that are sparser in the medial EC (MEC). These are first detected in the subplate during the early second semester. MRI analyses reveal an acceleration of EC growth at the end of the second trimester. BrdU labeling of the developing MEC, shows the deeper layers form first and prior to the superficial layers, but the LV/VI emerges in parallel and the LII/III emerges later, but also in parallel. We coin this lamination pattern parallel lamination. The early-born Reln+ stellate cells in the superficial layers express the classic LV marker, Bcl11b (Ctip2) and arise from a common progenitor that forms the late deep layer LV neurons. In summary, we characterize the developing EC in a novel animal model and outline in detail the formation of the EC. We further provide insight into how the periarchicortex forms in the brain, which differs remarkably to the inside-out lamination of the neocortex.
A modular platform for engineering function of natural and synthetic biomolecular condensates

Phase separation is emerging as a universal principle for how cells use dynamic subcompartmentalization to organize biochemical reactions in time and space1,2. Yet, whether the emergent physical properties of these biomolecular condensates are important for their biological function remains unclear. The intrinsically disordered protein PopZ forms membraneless condensates at the poles of the bacterium Caulobacter crescentus and selectively sequesters kinase-signaling cascades to regulate asymmetric cell division3–5. By dissecting the molecular grammar underlying PopZ phase separation, we find that unlike many eukaryotic examples, where unstructured regions drive condensation6,7, a structured domain of PopZ drives condensation, while conserved repulsive features of the disordered region modulate material properties. By generating rationally designed PopZ mutants, we find that the exact material properties of PopZ condensates directly determine cellular fitness, providing direct evidence for the physiological importance of the emergent properties of biomolecular condensates. Our work codifies a clear set of design principles illuminating how sequence variation in a disordered domain alters the function of a widely conserved bacterial condensate. We used these insights to repurpose PopZ as a modular platform for generating synthetic condensates of tunable function in human cells.
A structured reflective process supports student awareness of employability skills development in a science placement module

Placements are often an extra-curricular activity of a science degree. This study reports on the outcomes of a final year credit-bearing 6-week placement module that was specifically designed to develop and enhance students’ employability skills. A key element of this module was that the student placements were not just evaluated from a science perspective, but with an emphasis on meaningful reflection and evaluation of employability skills development. Students recorded their levels of confidence in skills before, during and after the placement via an Online Reflective Log, as part of a module’s summative assessment. First, results showed that taking part in the placement and conducting their own independent research helped students to make connections between their scientific knowledge, otherwise constrained within the walls of the undergraduate science lab, and the wider impact of their research on society. Another theme that emerged concerned career choices and aspirations, and the placement experience either confirmed prior choices or opened new horizons. The Online Reflective Log helped students to feel supported by their university supervisor who were at a distance, while feedback on their tasks challenged them to reflect on the scientific and personal skills as they were engaged in scientific activities during placement. Students agreed that they had further developed their employability skills during the placement. Students acknowledged it was challenging to have to acquire evidence of skills development but appreciated the usefulness of this reflection in relation to their future careers.
Expectation-Based Gist Facilitation: Rapid Scene Understanding and the Role of Top-Down Information

Scene meaning is processed rapidly, with ‘gist’ extracted even when presentation duration spans a few dozen milliseconds. This has led some to suggest a primacy of bottom-up information. However, gist research has typically relied on showing successions of unrelated scene images, contrary to our everyday experience in which the world unfolds around us in a predictable manner. Thus, we investigated whether top-down information – in the form of observers’ predictions of an upcoming scene – facilitates gist processing. Within each trial, participants (N=336) experienced a series of images, organised to represent an approach to a destination (e.g., walking down a sidewalk), followed by a final target scene either congruous or incongruous with the expected destination (e.g., a store interior or a bedroom). Over a series of behavioural experiments, we found that: appropriate expectations facilitated gist processing; inappropriate expectations interfered with gist processing; the effect of congruency was driven by provision of contextual information rather than the thematic coherence of approach images, and; expectation-based facilitation was most apparent when destination duration was most curtailed. We then investigated the neural correlates of predictability on scene processing using ERP (N=26). Congruency-related differences were found in a putative scene-selective ERP component, related to integrating visual properties (P2), and in later components related to contextual integration including semantic and syntactic coherence (N400 and P600, respectively). Taken together, these results suggest that in real-world situations, top-down predictions of an upcoming scene influence even the earliest stages of its processing, affecting both the integration of visual properties and meaning.
Five Hours Total Sleep Deprivation Does Not Affect CA1 Dendritic Length or Spine Density

Sleep is essential for long term memory function. However the neuroanatomical consequences of sleep loss are disputed. Sleep deprivation has been reported to cause both decreases and increases of dendritic spine density. Here we use Thy1-GFP expressing transgenic mice to investigate the effects of acute sleep deprivation on the dendritic architecture of hippocampal CA1 pyramidal neurons. We found that five hours of sleep deprivation had no effect on either dendritic length or dendritic spine density. Our work suggests that no major neuroanatomical changes result from one episode of sleep deprivation.
An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

The distribution of cellular resources across bacterial proteins has been quantified through phenomenological growth laws. Here, we describe a complementary bacterial growth law for RNA composition, emerging from optimal cellular resource allocation into ribosomes and ternary complexes. The predicted decline of the tRNA/rRNA ratio with growth rate agrees quantitatively with experimental data. Its regulation appears to be implemented in part through chromosomal localization, as rRNA genes are typically closer to the origin of replication than tRNA genes and thus have increasingly higher gene dosage at faster growth. At the highest growth rates in E. coli, the tRNA/rRNA ratio appears to be regulated entirely through this effect.
The SARS-CoV-2 Transcriptome and the Dynamics of the S Gene Furin Cleavage Site in Primary Human Airway Epithelia

Polarized human airway epithelia at an air-liquid interface (HAE-ALI) are an in vitro model that supports efficient infection of SARS-CoV-2. The spike (S) protein of SARS-CoV-2 contains a furin cleavage site (FCS) at the boundary of the S1 and S2 domains which distinguishes it from SARS-CoV. ABSTRACT The spike (S) polypeptide of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consists of the S1 and S2 subunits and is processed by cellular proteases at the S1/S2 boundary that contains a furin cleavage site (FCS), 682RRAR↓S686. Various deletions surrounding the FCS have been identified in patients. When SARS-CoV-2 propagated in Vero cells, it acquired deletions surrounding the FCS. We studied the viral transcriptome in Vero cell-derived SARS-CoV-2-infected primary human airway epithelia (HAE) cultured at an air-liquid interface (ALI) with an emphasis on the viral genome stability of the FCS. While we found overall the viral transcriptome is similar to that generated from infected Vero cells, we identified a high percentage of mutated viral genome and transcripts in HAE-ALI. Two highly frequent deletions were found at the FCS region: a 12 amino acid deletion (678TNSPRRAR↓SVAS689) that contains the underlined FCS and a 5 amino acid deletion (675QTQTN679) that is two amino acids upstream of the FCS. Further studies on the dynamics of the FCS deletions in apically released virions from 11 infected HAE-ALI cultures of both healthy and lung disease donors revealed that the selective pressure for the FCS maintains the FCS stably in 9 HAE-ALI cultures but with 2 exceptions, in which the FCS deletions are retained at a high rate of >40% after infection of ≥13 days. Our study presents evidence for the role of unique properties of human airway epithelia in the dynamics of the FCS region during infection of human airways, which is likely donor dependent. IMPORTANCE Polarized human airway epithelia at an air-liquid interface (HAE-ALI) are an in vitro model that supports efficient infection of SARS-CoV-2. The spike (S) protein of SARS-CoV-2 contains a furin cleavage site (FCS) at the boundary of the S1 and S2 domains which distinguishes it from SARS-CoV. However, FCS deletion mutants have been identified in patients and in vitro cell cultures, and how the airway epithelial cells maintain the unique FCS remains unknown. We found that HAE-ALI cultures were capable of suppressing two prevalent FCS deletion mutants (Δ678TNSPRRAR↓SVAS689 and Δ675QTQTN679) that were selected during propagation in Vero cells. While such suppression was observed in 9 out of 11 of the tested HAE-ALI cultures derived from independent donors, 2 exceptions that retained a high rate of FCS deletions were also found. Our results present evidence of the donor-dependent properties of human airway epithelia in the evolution of the FCS during infection.
A behavioral syndrome linking boldness and flexibility facilitates invasion success in sticklebacks

For a species to expand its range, it needs to be good at dispersing and also capable of exploiting resources and adapting to different environments. Therefore, behavioral and cognitive traits could play key roles in facilitating invasion success. Here, we show that dispersing sticklebacks are bold, while sticklebacks that have recently established in a new region are flexible. Moreover, boldness and flexibility are negatively correlated with one another at the individual, family and population levels. Multiple lines of evidence suggest that the divergence in boldness and flexibility is likely to be evolutionary in origin. If boldness is favored in invaders during the initial dispersal stage, while flexibility is favored in recent immigrants during the establishment stage, then the link between boldness and flexibility could generate positive correlations between successes during both dispersal and establishment, and therefore play a key role in facilitating colonization success in sticklebacks and other organisms.
Removal of Hydrogen Sulphide by Immobilized Thiobacillus sp. strain CH11 in a Biofilter

An autotropic Thiobacillus sp. CH11 was isolated from piggery wastewater containing hydrogen sulphide. The removal characteristics of hydrogen sulphide by Thiobacillus sp. CH11 were examined in the continuous system. The hydrogen sulphide removal capacity was elevated by the BDST (Bed Depth Service Time) method (physical adsorption) and an immobilized cell biofilter (biological conversion). The optimum pH to remove hydrogen sulphide ranged from 6 to 8. The average specific uptake rate of hydrogen sulphide was as 1.02 x 10 -13 mol-S cell -1 h -1 in continuous systems. The maximum removal rate and saturation constant for hydrogen sulphide were calculated to be V m = 30.1 mmol-S day -1 (kg-dry bead) -1 and K s = 1.28 μmol dm -3 , respectively. A criterion to design a scale-up biofilter was also studied. The maximum inlet loading in the linear region (95% removal) was 47 mmol-S day -l (kg-dry bead) -1 . Additionally, the biofilter exhibited high efficiency (>98.5%) in the removal of hydrogen sulphide at both low (<0.026 mg dm -3 ) and high (0-078 mg dm -3 ) concentrations. The results suggested that the Thiobacillus sp. CH11 immobilized with Ca-alginate is a potential method for the removal of hydrogen sulphide.
PML-Dependent Memory of Type I Interferon Treatment Results in a Restricted Form of HSV Latency

Herpes simplex virus (HSV) establishes latent infection in long-lived neurons. During initial infection, neurons are exposed to multiple inflammatory cytokines but the effects of immune signaling on the nature of HSV latency is unknown. We show that initial infection of primary murine neurons in the presence of type I interferon (IFN) results in a form of latency that is restricted for reactivation. We also found that the subnuclear condensates, promyelocytic leukemia-nuclear bodies (PML-NBs), are absent from primary sympathetic and sensory neurons but form with type I IFN treatment and persist even when IFN signaling resolves. HSV-1 genomes colocalized with PML-NBs throughout a latent infection of neurons only when type I IFN was present during initial infection. Depletion of PML prior to or following infection did not impact the establishment latency; however, it did rescue the ability of HSV to reactivate from IFN-treated neurons. This study demonstrates that viral genomes possess a memory of the IFN response during de novo infection, which results in differential subnuclear positioning and ultimately restricts the ability of genomes to reactivate.
The Cryo-EM Structure of Vesivirus 2117 Highlights Functional Variations in Entry Pathways for Viruses in Different Clades of the Vesivirus Genus

Vesivirus 2117 has caused significant losses in manufacturing of biopharmaceutical products following contamination of cell cultures used in their production. We report the structure of the vesivirus 2117 capsid, the shell that encloses the virus’s genome. ABSTRACT Vesivirus 2117 is an adventitious agent that has been responsible for lost productivity in biopharmaceutical production following contamination of Chinese hamster ovary cell cultures in commercial bioreactors. A member of the Caliciviridae, 2117 is classified within the Vesivirus genus in a clade that includes canine and mink caliciviruses but is distinct from the vesicular exanthema of swine virus (VESV) clade, which includes the extensively studied feline calicivirus (FCV). We have used cryogenic electron microscopy (cryo-EM) to determine the structure of the capsid of this small, icosahedral, positive-sense-RNA-containing virus. We show that the outer face of the dimeric capsomeres, which contains the receptor binding site and major immunodominant epitopes in all caliciviruses studied thus far, is quite different from that of FCV. This is a consequence of a 22-amino-acid insertion in the sequence of the FCV major capsid protein that forms a “cantilevered arm” that both plays an important role in receptor engagement and undergoes structural rearrangements thought to be important for genome delivery to the cytosol. Our data highlight a potentially important difference in the attachment and entry pathways employed by the different clades of the Vesivirus genus. IMPORTANCE Vesivirus 2117 has caused significant losses in manufacturing of biopharmaceutical products following contamination of cell cultures used in their production. We report the structure of the vesivirus 2117 capsid, the shell that encloses the virus’s genome. Comparison of this structure with that of a related vesivirus, feline calicivirus (FCV), highlighted potentially important differences related to virus attachment and entry. Our findings suggest that these two viruses may bind differently to receptors at the host cell surface. We also show that a region of the capsid protein of FCV that rearranges following receptor engagement is not present in vesivirus 2117. These structural changes in the FCV capsid have been shown to allow the assembly of a portal-like structure that is hypothesized to deliver the viral genome to the cell’s interior. Our data suggest that the 2117 portal assembly may employ a different means of anchoring to the outer face of the capsid.