Miracle-dz/UniFAR-FTUs huggingface dataset:
Overproduction of the AlgT Sigma Factor Is Lethal to Mucoid Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic bacterial pathogen capable of causing chronic lung infections. Phenotypes important for the long-term persistence and adaption to this unique lung ecosystem are largely regulated by the AlgT sigma factor. Chronic infection isolates often contain mutations in the anti-sigma factor mucA, resulting in uncontrolled AlgT and continuous production of alginate in addition to the expression of ∼300 additional genes. Here, we report that in the absence of wild-type MucA, AlgT overproduction is lethal and that suppressors of toxic AlgT production have mutations in the MucA protease, MucP. Since AlgT contributes to the establishment of chronic infections, understanding how AlgT is regulated will provide vital information on how P. aeruginosa is capable of causing long-term infections. ABSTRACT Pseudomonas aeruginosa isolates from chronic lung infections often overproduce alginate, giving rise to the mucoid phenotype. Isolation of mucoid strains from chronic lung infections correlates with a poor patient outcome. The most common mutation that causes the mucoid phenotype is called mucA22 and results in a truncated form of the anti-sigma factor MucA that is continuously subjected to proteolysis. When a functional MucA is absent, the cognate sigma factor, AlgT, is no longer sequestered and continuously transcribes the alginate biosynthesis operon, leading to alginate overproduction. In this work, we report that in the absence of wild-type MucA, providing exogenous AlgT is toxic. This is intriguing, since mucoid strains endogenously possess high levels of AlgT. Furthermore, we show that suppressors of toxic AlgT production have mutations in mucP, a protease involved in MucA degradation, and provide the first atomistic model of MucP. Based on our findings, we speculate that mutations in mucP stabilize the truncated form of MucA22, rendering it functional and therefore able to reduce toxicity by properly sequestering AlgT. IMPORTANCE Pseudomonas aeruginosa is an opportunistic bacterial pathogen capable of causing chronic lung infections. Phenotypes important for the long-term persistence and adaption to this unique lung ecosystem are largely regulated by the AlgT sigma factor. Chronic infection isolates often contain mutations in the anti-sigma factor mucA, resulting in uncontrolled AlgT and continuous production of alginate in addition to the expression of ∼300 additional genes. Here, we report that in the absence of wild-type MucA, AlgT overproduction is lethal and that suppressors of toxic AlgT production have mutations in the MucA protease, MucP. Since AlgT contributes to the establishment of chronic infections, understanding how AlgT is regulated will provide vital information on how P. aeruginosa is capable of causing long-term infections.
Task-dependent mixed selectivity in the subiculum

CA1 and subiculum (SUB) connect the hippocampus to numerous output regions. Cells in both areas have place-specific firing fields, although they are more dispersed in SUB. Weak responses to head direction and running speed have been reported in both regions. However, how such information is encoded in CA1 and SUB, and the resulting impact on downstream targets, is poorly understood. Here we estimate the tuning of simultaneously recorded CA1 and SUB cells to position, head direction, and speed. Individual neurons respond conjunctively to these covariates in both regions but the degree of mixed representation is stronger in SUB, and more so during goal-directed spatial navigation than free foraging. Each navigational variable could be decoded with higher precision, from a similar number of neurons, in SUB than CA1. The findings point to a possible contribution of mixed-selective coding in SUB to efficient transmission of hippocampal representations to widespread brain regions.
Area Under the Dry Down Curve (AUDDC): A Method to Evaluate Rate of Dry Down in Maize

Maize (Zea mays L.) hybrids with fast field dry down are economically desirable across production regions. However, accurately measuring this genetically complex trait in a simple way has been a challenge to maize breeders. The objective of this research was to propose and test an efficient, simple, and reliable procedure to select genotypes with fast dry down in maize. Area under the dry down curve (AUDDC), an index representing the dynamic progress of field dry down, was proposed. The main experiment included 144 hybrids arranged in a partially balanced lattice design across four short-season environments in North Dakota. Data collected were silking date, ear moisture at four 7-d intervals starting 45 d after pollination, harvest moisture, test weight, and grain yield. Results showed significant genotype × environment interaction for most traits including AUDDC. However, AUDDC had the largest broad-sense heritability (H) among traits (0.84), suggesting it can be effectively utilized to identify faster drier inbred lines and hybrids. Strong correlations were found between AUDDC and silking date, AUD and moisture content at physiological maturity, and AUDDC and harvest moisture. Area under the dry down curve is proposed as an indirect measurement for dry down rate and we encourage its use to develop lines and hybrids with faster dry down.
Selection of food and ranging behaviour in a sexually monomorphic folivorous lemur: Lepilemur ruficaudatus

Monomorphic lemurs of Madagascar allow us to investigate whether there are behavioural mechanisms that compensate for sex-specific differences in the costs of maintenance and reproduction in arboreal primates. Food selection of the pair-living Lepilemur ruficaudatus was studied in relation to food chemistry, and travel distances were measured as possible indications of differential investment in ranging activities (possibly related to the defence of territories and/or mating opportunities). Fourteen females and 14 males were radio-tracked for a total of 365 half-nights (from dusk to midnight or from midnight to dawn) at different times of the year (birth, lactation and weaning, pre-mating, post-mating). When based on monthly means, the two sexes did not differ in nightly travel distances. Food selection of females and males did not differ in relation to the chemical composition of leaves, but fruits consumed by females had lower fibre contents than fruits consumed by males. Even though other behavioural data are fragmentary, little evidence exists for behavioural mechanisms in L. ruficaudatus to compensate for the different energetic costs of females and males.
Effect of dietary copper sulphate on the performance of growing Japanese quail

SUMMARY The effect of 200, 400 and 600 mg dietary copper sulphate/kg was studied in 64 Japanese quail (Coturnix coturnix japonica) in 1987. The results indicated that addition of 200 or 400 mg/kg to conventional diets of quail 7–42 days old significantly increased (P < 0·05) body weight gain and significantly decreased (P < 0·05) feed intake. There were significant (P < 0·05) increases in carcass, breast and leg weights in some cases; the first two characters had the highest values in the quail fed the diet containing 200 mg Cu/kg. The addition of 600 mg Cu/kg to the diet had an adverse effect on liver weight compared with the addition of 200 and 400 mg/kg. Copper concentration in the liver was not influenced by any rate of copper supplementation.
Observation of an α-synuclein liquid droplet state and its maturation into Lewy body-like assemblies

Misfolded α-synuclein is a major component of Lewy bodies, which are a hallmark of Parkinson’s disease. A large body of evidence shows that α-synuclein can self-assemble into amyloid fibrils, but the relationship between amyloid formation and Lewy body formation still remains unclear. Here we show, both in vitro and in a C. elegans model of Parkinson’s disease, that α-synuclein undergoes liquid-liquid phase separation by forming a liquid droplet state, which converts into an amyloid-rich hydrogel. This maturation process towards the amyloid state is delayed in the presence of model synaptic vesicles in vitro. Taken together, these results suggest that the formation of Lewy bodies is linked to the arrested maturation of α-synuclein condensates in the presence of lipids and other cellular components.
Antioxidant and Free Radical-Scavenging Activities of Goby (Zosterisessor ophiocephalus) Muscle Protein Hydrolysates Obtained by Enzymatic Treatment

Antioxidant activities of protein hydrolysates prepared from goby muscle by treatment with various bacterial alkaline proteases from Bacillus mojavensis A21, Bacillus subtilis A1, Bacillus pumilus A26, and Bacillus licheniformis NH1 and Alcalase were investigated. All hydrolysates showed different degrees of hydrolysis. The antioxidant activities of protein hydrolysates at different concentrations were evaluated using various in vitro antioxidant assays, including 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical method, reducing power assays, β-carotene bleaching, and DNA nicking assay. All protein hydrolysates showed varying degrees of antioxidant activity. The hydrolysate prepared using A26 proteases showed the strongest DPPH radical-scavenging activity, followed by NH1 and A21 hydrolysates. Moreover, NH1 hydrolysate exhibited notable effects against the discoloration of β-carotene. A1, A21, and alcalase protein hydrolysates exhibited high protection against hydroxyl radical induced DNA breakage.
Wide-field Fluorescence Lifetime Imaging Microscopy with a High-Speed Mega-pixel SPAD Camera

Fluorescence lifetime imaging microscopy (FLIM) is a key technology that provides direct insight into cell metabolism, cell dynamics and protein activity. However, determining the lifetimes of different fluorescent proteins requires the detection of a relatively large number of photons, hence slowing down total acquisition times. Moreover, there are many cases, for example in studies of cell collectives, where wide-field imaging is desired. We report scan-less wide-field FLIM based on a 0.5 Megapixel resolution, time-gated Single Photon Avalanche Diode (SPAD) camera, with acquisition rates up to 1 Hz. Fluorescence lifetime estimation is performed via a pre-trained artificial neural network with 1000-fold improvement in processing times compared to standard least squares fitting techniques. We utilised our system to image HT1080 – human fibrosarcoma cell line as well as Convallaria. The results show promise for real-time FLIM and a viable route towards multi-megapixel fluorescence lifetime images, with a proof-of-principle mosaic image shown with 3.6 megapixels.
Neuromodulation Exerts Feedback and Feedforward Control of Action Selection

To be effective, behavioral choices must result in actions that are appropriate to an animal’s needs and environmental circumstances. In addition, the actions must be ones the animal can sustain until its needs are met. This aligning of goals, action, and motivation requires the coordinated activity of multiple brain circuits, but how such coordination is achieved is poorly understood. Here, we show how the insect hormone Bursicon coordinates the selection and sustains execution of a behavior in newly emerged adult Drosophila. Such flies must expand and harden their wings after metamorphosis, but they choose to delay expansion in confined conditions. We show that the decision to expand is mediated by an environmentally-sensitive, positive feedback loop in which Bursicon promotes its own sustained release. Released Bursicon then modulates motor neurons to promote wing expansion behavior. Bursicon thus exerts feedforward and feedback control to coordinately select and motivate a goal-directed action.
Local sleep during mind-wandering enhances processes of spatial attention allocation

Mind wandering (MW) is a subjective, cognitive phenomenon, in which thoughts move away from the task towards an internal train of thoughts, possibly during phases of neuronal sleep-like activity (local sleep, LS). MW decreases cortical processing of external stimuli and is assumed to decouple attention from the external world. Here, we directly tested how indicators of LS, cortical processing and attentional selection change in a pop-out visual search task during phases of MW. Participants brain activity was recorded using magnetoencephalography, MW was assessed via self-report using randomly interspersed probes. As expected, MW worsened performance being accompanied by a decrease in high frequency activity (HFA, 80-150Hz) and an increase in slow wave activity (SWA, 1-6Hz), consistent with the occurrence of LS. In contrast, visual attentional selection as indexed by the N2pc component was enhanced during MW with the N2pc amplitude being directly linked to participants’ performance. This observation clearly contradicts accounts of attentional decoupling predicting a decrease in attention-related responses to external stimuli during MW. Together our results suggest that MW occurs during phases of LS with processes of attentional target selection being upregulated, potentially to compensate for the mental distraction during MW.
DYNC1LI2 regulates localization of the chaperone-mediated autophagy receptor LAMP2A and improves cellular homeostasis in cystinosis

The dynein motor protein complex is required for retrograde transport but the functions of the intermediate-light chains that form the cargo-binding complex are not elucidated and the importance of individual subunits in the maintenance of cellular homeostasis is unknown. Here, using mRNA arrays and protein analysis, we show that the dynein subunit, intermediate chain 2 (DYNC1LI2) is downregulated in cystinosis, a lysosomal storage disorder caused by genetic defects in the lysosomal cystine transporter, cystinosin. Reconstitution of the expression of DYNC1LI2 in Ctns-/- cells re-established endolysosomal dynamics. Defective vesicular trafficking in cystinotic cells was rescued by DYNC1LI2 expression which correlated with decreased endoplasmic reticulum stress manifested as decreased expression levels of the chaperone Grp78. Mitochondrial fragmentation in cystinotic fibroblasts was also rescued by DYNC1LI2. Survival of cystinotic cells to oxidative stress insult was increased by DYNC1LI2 reconstitution but not by its paralog DYNC1LI1, which also failed to decrease ER stress levels and mitochondrial fragmentation. Restoring DYNC1LI2 expression rescued the localization of the chaperone-mediated autophagy receptor, LAMP2A, and restored cellular homeostasis of cystinotic proximal tubule cells, the primary cell type affected in cystinosis. DYNC1LI2 failed to rescue phenotypes in cystinotic cells when LAMP2A was downregulated or when co-expressed with dominant negative (DN) RAB7 or DN-RAB11, which impair LAMP2A trafficking. DYNC1LI2 emerges as a new target to repair underlying trafficking and CMA defects in cystinosis, a mechanism that is not restored by currently used lysosomal depletion therapies.
Biophysical characterization of the inactivation of E. coli transketolase by aqueous co-solvents

Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.
Computational support, not primacy, distinguishes compensatory memory reorganization in epilepsy

Temporal lobe epilepsy (TLE) is associated with impairment in episodic memory. A substantial sub-group, however, is able to maintain adequate memory despite temporal lobe pathology. What has been missing from prior work in the cognitive reorganization is a direct comparison of TLE patients with intact/compensated status from those who are memory impaired and uncompensated. Little is known about the particular regional activations, functional connectivities (FC’s), and/or network reconfigurations that implement changes in the primary computations or the support functions that drive adaptive plasticity and compensated memory. We utilized task fMRI on 54 unilateral TLE patients and 24 matched healthy controls (HC) during performance of a paired-associate memory (PAM) task to address three questions: 1) what regions implement PAM in TLE, and do such regions vary as a function of good versus poor performance, 2) are there unique FC’s present during memory encoding that accounts for intact status through the preservation of primary memory computations or the supportive computations that allow for compensated memory responses, and 3) what features during memory encoding are most distinctive: is it the magnitude and location of regional activations, or the presence of enhanced functional connections to key structures such as the hippocampus? Results revealed a unique profile of non-ictal, non-dominant hemisphere regions (e.g., right posterior temporal regions) were most important to intact/compensated status in LTLE, involving both increased regional activity and increased modulatory communication with the hippocampi, all feature that was missing in impaired/uncompensated LTLE. The profile involved areas that are neither contralateral homologues to left hemisphere memory areas, nor regions traditionally considered computationally primary for episodic memory. None of these areas of increased activation or functional connectivity were associated with advantaged memory in HC’s. Our emphasis on different performance levels yielded insight into two forms of cognitive reorganization. Computational primacy, where LTLE showed little change relative to HC’s, and computational support where Intact/Compensated LTLE patients showed adaptive abnormalities. The analyses isolated the unique regional activations and mediating FC’s that implement truly compensatory reorganization in LTLE. The results provided a new perspective on memory deficits by making clear that memory deficits arise not just from knockout of a functional hub, but from the failure to instantiate a complex set of reorganization responses. Such responses provided computational support to ensure successful memory. The findings demonstrated that by keeping track of performance levels, we can increase our understanding of adaptive brain responses and neuroplasticity in epilepsy.
Attention Differentially Affects Acoustic and Phonetic Feature Encoding in a Multispeaker Environment

Humans have the remarkable ability to selectively focus on a single talker in the midst of other competing talkers. The neural mechanisms that underlie this phenomenon remain incompletely understood. In particular, there has been longstanding debate over whether attention operates at an early or late stage in the speech processing hierarchy. One way to better understand this is to examine how attention might differentially affect neurophysiological indices of hierarchical acoustic and linguistic speech representations. In this study, we do this by using encoding models to identify neural correlates of speech processing at various levels of representation. Specifically, we recorded EEG from fourteen human subjects (nine female and five male) during a “cocktail party” attention experiment. Model comparisons based on these data revealed phonetic feature processing for attended, but not unattended speech. Furthermore, we show that attention specifically enhances isolated indices of phonetic feature processing, but that such attention effects are not apparent for isolated measures of acoustic processing. These results provide new insights into the effects of attention on different prelexical representations of speech, insights that complement recent anatomic accounts of the hierarchical encoding of attended speech. Furthermore, our findings support the notion that, for attended speech, phonetic features are processed as a distinct stage, separate from the processing of the speech acoustics. SIGNIFICANCE STATEMENT Humans are very good at paying attention to one speaker in an environment with multiple speakers. However, the details of how attended and unattended speech are processed differently by the brain is not completely clear. Here, we explore how attention affects the processing of the acoustic sounds of speech as well as the mapping of those sounds onto categorical phonetic features. We find evidence of categorical phonetic feature processing for attended, but not unattended speech. Furthermore, we find evidence that categorical phonetic feature processing is enhanced by attention, but acoustic processing is not. These findings add an important new layer in our understanding of how the human brain solves the cocktail party problem.
Multiple random phosphorylations provide long delays and switches in circadian clocks

Theory predicts that self-sustained oscillations require robust delays and nonlinearities (ultrasensitivity). We study the circadian rhythms in the filamentous fungus Neurospora crassa (wild type period 22.5 hours) to investigate the underlying clock mechanisms. Its transcription translation feedback loop (TTFL) includes the activator White Collar Complex (WCC), the inhibitory FFC complex, and Casein kinase 1a. Moreover, there are multiple phosphorylation sites on FRQ (around 100) and WCC (approximately 95). A phosphoswitch controls the activity status of the FFC complex. We investigate how multiple, slow and random phosphorylations govern delay and nonlinearity in a negative feedback. We model FRQ phosphorylations with turnover of FRQ and CK1a using ordinary differential equations. Our model helps to understand the underlying mechanisms leading to delays and ultrasensitivity. The model shows temporal and steady state switches for the free kinase and phosphorylated FRQ. We show that random phosphorylations and sequestration mechanisms allow high Hill coefficients required for self-sustained oscillations. Our conceptual models help to understand multiple phosphorylations dynamics and to elucidate mechanisms of delayed switch generation.