Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Lauric Acid on the Stability of Aβ42-Oligomers

While Alzheimer’s disease is correlated with the presence of Aβ fibrils in patient brains, the more likely agents are their precursors, soluble oligomers that may form pores or otherwise distort cell membranes. Using all-atom molecular dynamics simulation we study how presence of fatty acids such as lauric acid changes the stability of pore-forming oligomers built from three-stranded Aβ42 chains. Such a change would alter the distribution of amyloids in the fatty-acid rich brain environment, and therefore could explain the lower polymorphism observed in Aβ-fibrils derived from brains of patients with Alzheimer’s disease. We find that lauric acid stabilizes both ring-like and barrel-shaped models, with the effect being stronger for barrel-like models than for ring-like oligomers.
Post-transcriptional gene regulation by the RNA binding protein IGF2BP3 is critical for MLL-AF4 mediated leukemogenesis

Despite recent advances in therapeutic approaches, patients with MLL-rearranged leukemia still have poor outcomes and a high risk of relapse. Here, we found that MLL-AF4, the most common MLL fusion protein in patients, transcriptionally induces IGF2BP3 and that IGF2BP3 strongly amplifies MLL-Af4 mediated leukemogenesis. Deletion of Igf2bp3 significantly increases the survival of mice with MLL-Af4 driven leukemia and greatly attenuates disease, with a minimal impact on baseline hematopoiesis. At the cellular level, MLL-Af4 leukemia-initiating cells require Igf2bp3 for their function in leukemogenesis. eCLIP and transcriptome analysis of MLL-Af4 transformed stem and progenitor cells and MLL-Af4 bulk leukemia cells reveals a complex IGF2BP3-regulated post-transcriptional operon governing leukemia cell survival and proliferation. Regulated mRNA targets include important leukemogenic genes such as those in the Hoxa locus and numerous genes within the Ras signaling pathway. Together, our findings show that IGF2BP3 is an essential positive regulator of MLL-AF4 mediated leukemogenesis and represents an attractive therapeutic target in this disease.
Evaluation of Coulomb potential in a triclinic cell with periodic boundary conditions

Lekner [Molec. Simul. 20, 356 (1998)] and Sperb's [Molec. Simul. 13, 189 (1994)] work on the evaluation of Coulomb energy and forces under periodic boundary conditions is generalized. So, now it should be possible to use a triclinic unit cell in simulations in 3D rather than just an orthorhombic cell. The expressions obtained are in a similar form as previously obtained by Lekner and Sperb for the especial case of an orthorhombic cell.
Regional and age-dependent Effects of Cortical Magnetic Stimulation on Unconstrained Reaching Behavior

Background The specific and dynamic contributions of premotor and supplementary motor areas to reaching movements in aging humans are not well understood. Objective To better understand the role of cortical motor regions and age on the control of unconstrained reaches against gravity by neurologically intact, younger and older adults. Methods Double pulse transcranial magnetic stimulation (TMS) was applied at locations targeting primary motor cortex (M1), dorsal premotor area (PMA), supplementary motor area (SMA), or dorsolateral prefrontal cortex (DLPFC). Paired stimuli were delivered before or after a visual cue was presented to initiate self-paced right-handed reaches to one of three, vertically oriented target locations. Results Regional stimulation effects on movement amplitude were observed both early and late in the reach. PMA stimulation increased reach distance to a greater extent than M1, SMA, and DLPFC stimulation. M1 and PMA stimulation increased deviation from the straight-line path around the time of peak velocity to an extent that was greater than SMA and DLPFC stimulation. Cortical stimulation increased the time that elapsed after, but not before, peak velocity. Despite stronger effects of stimulation on reaches in the younger group, this group had shorter times to reach the target after reaching peak velocity. Conclusion These results provide support for a role of PMA in visually guided movement after movement initiation. For older subjects, the increased time to arrive at the target after peak velocity despite weaker stimulation effects suggests an age-related reduction in sensorimotor processing flexibility for online control of unconstrained reaching. Highlights Dorsal premotor area stimulation at any time during the reaction-time period and early reaching affected early reach kinematics at least as much as stimulation of primary motor cortex. Older individuals had more stimulation-related interference in the late components of reaching despite having less early effect of stimulation, suggesting a reduction in flexibility of dynamic motor control due to aging. The antigravity component of unconstrained reaching did not have special aspects for regional cortical effects of stimulation.
EloR Interacts with the Lytic Transglycosylase MltG at Midcell in Streptococcus pneumoniae R6

Bacterial cell division has been a successful target for antimicrobial agents for decades. How different pathogens regulate cell division is, however, poorly understood. ABSTRACT The ellipsoid shape of Streptococcus pneumoniae is determined by the synchronized actions of the elongasome and the divisome, which have the task of creating a protective layer of peptidoglycan (PG) enveloping the cell membrane. The elongasome is necessary for expanding PG in the longitudinal direction, whereas the divisome synthesizes the PG that divides one cell into two. Although there is still little knowledge about how these two modes of PG synthesis are coordinated, it was recently discovered that two RNA-binding proteins called EloR and KhpA are part of a novel regulatory pathway controlling elongation in S. pneumoniae. EloR and KhpA form a complex that works closely with the Ser/Thr kinase StkP to regulate cell elongation. Here, we have further explored how this regulation occurs. EloR/KhpA is found at midcell, a localization fully dependent on EloR. Using a bacterial two-hybrid assay, we probed EloR against several elongasome proteins and found an interaction with the lytic transglycosylase homolog MltG. By using EloR as bait in immunoprecipitation assays, MltG was pulled down, confirming that they are part of the same protein complex. Fluorescence microscopy demonstrated that the Jag domain of EloR is essential for EloR’s midcell localization and its interaction with MltG. Since MltG is found at midcell independent of EloR, our results suggest that MltG is responsible for the recruitment of the EloR/KhpA complex to the division zone to regulate cell elongation. IMPORTANCE Bacterial cell division has been a successful target for antimicrobial agents for decades. How different pathogens regulate cell division is, however, poorly understood. To fully exploit the potential for future antibiotics targeting cell division, we need to understand the details of how the bacteria regulate and construct the cell wall during this process. Here, we have revealed that the newly identified EloR/KhpA complex, regulating cell elongation in S. pneumoniae, forms a complex with the essential peptidoglycan transglycosylase MltG at midcell. EloR, KhpA, and MltG are conserved among many bacterial species, and the EloR/KhpA/MltG regulatory pathway is most likely a common mechanism employed by many Gram-positive bacteria to coordinate cell elongation and septation.
Aerial course stabilization is impaired in motion-blind flies

Visual motion detection is among the best understood neuronal computations. One assumed behavioural role is to detect self-motion and to counteract involuntary course deviations, extensively investigated in tethered walking or flying flies. In free flight, however, any deviation from a straight course is signalled by both the visual system as well as by proprioceptive mechanoreceptors called ‘halteres’, which are the equivalent of the vestibular system in vertebrates. Therefore, it is yet unclear to what extent motion vision contributes to course control, or whether straight flight is completely controlled by proprioceptive feedback from the halteres. To answer these questions, we genetically rendered flies motion-blind by blocking their primary motion-sensitive neurons and quantified their free-flight performance. We found that such flies have difficulties maintaining a straight flight trajectory, much like control flies in the dark. By unilateral wing clipping, we generated an asymmetry in propulsory force and tested the ability of flies to compensate for this perturbation. While wild-type flies showed a remarkable level of compensation, motion-blind animals exhibited pronounced circling behaviour. Our results therefore unequivocally demonstrate that motion vision is necessary to fly straight under realistic conditions.
Ranked choice voting for representative transcripts with TRaCE

Summary Genome sequencing projects annotate protein-coding gene models with multiple transcripts, aiming to represent all of the available transcript evidence. However, downstream analyses often operate on only one representative transcript per gene locus, sometimes known as the canonical transcript. To choose canonical transcripts, TRaCE (Transcript Ranking and Canonical Election) holds an ‘election’ in which a set of RNA-seq samples rank transcripts by annotation edit distance. These sample-specific votes are tallied along with other criteria such as protein length and InterPro domain coverage. The winner is selected as the canonical transcript, but the election proceeds through multiple rounds of voting to order all the transcripts by relevance. Based on the set of expression data provided, TRaCE can identify the most common isoforms from a broad expression atlas or prioritize alternative transcripts expressed in specific contexts. Availability and Implementation Transcript ranking code can be found on GitHub at {{https://github.com/warelab/TRaCE}} Contact olson@cshl.edu, ware@cshl.edu Supplementary information Additional data are available in the github repository.
Disentangling environmental drivers of circadian metabolism in desert-adapted mice

Metabolism is a complex phenotype shaped by natural environmental rhythms, as well as behavioral, morphological, and physiological adaptations. Although historically studied under constant environmental conditions, continuous metabolic phenotyping through environmental transitions now offers a window into the physiological responses of organisms to changing environments. Here, we use flow-through respirometry to compare metabolic responses of the desert-adapted cactus mouse (Peromyscus eremicus) between diurnally variable and constant environmental conditions. We contrast metabolic responses to circadian cycles in photoperiod, temperature, and humidity, against those recorded under constant hot-and-dry and constant cold-and-wet conditions. We found significant sexual dimorphism in metabolic responses, despite no measurable difference in body weight. Males seem to be more heat tolerant and females more cold tolerant. Under circadian environmental cycling, the ratio of CO2 produced to O2 consumed (the respiratory quotient or respiratory exchange ratio) reached greater than one, a pattern that strongly suggests that lipogenesis is contributing to the production of energy and endogenous water in this species. This hypothesis is consistent with the results of previous dehydration experiments in this species, which documented significant weight loss in response to dehydration, without other physiological impairment. Our results are also consistent with historical descriptions of circadian torpor in this species (torpid by day, active by night), but reject the hypothesis that this pattern is driven by food restriction or negative water balance, as both resources were available to animals throughout the experiments. SUMMARY STATEMENT Continuous metabolic phenotyping of desert-adapted cactus mice (Peromyscus eremicus) identifies significant metabolic differences between the sexes and circadian patterning consistent with lipogenesis and environmental entrainment.
Amino Acid Variants in Malignant Melanoma

13 14 Correspondence to: 15 Prof. Dr. Boris Macek 16 Chair, Quantitative Proteomics 17 Director, Proteome Center Tuebingen 18 Interfaculty Institute for Cell Biology 19 University of Tuebingen 20 Auf der Morgenstelle 15 21 72076 Tuebingen 22 Germany 23 Phone: +49/(0)7071/29-70556 24 E-Mail: boris.macek@uni-tuebingen.de 25 26 27 Dr. Nicolas Claude Nalpas 28 Quantitative Proteomics 29 Proteome Center Tuebingen 30 Interfaculty Institute for Cell Biology 31 University of Tuebingen 32 Auf der Morgenstelle 15 33 72076 Tuebingen 34 Germany 35 Phone: +49/(0)7071/29-70552 36 E-Mail: nicolas.nalpas@ifiz.uni-tuebingen.de 37
A systems biology analysis of lipolysis and fatty acid release from adipocytes in vitro and from adipose tissue in vivo

Lipolysis and the release of fatty acids to supply energy fuel to other organs, such as between meals, during exercise, and starvation, are fundamental functions of the adipose tissue. The intracellular lipolytic pathway in adipocytes is activated by adrenaline and noradrenaline, and inhibited by insulin. Circulating fatty acids are elevated in type 2 diabetic individuals. The mechanisms behind this elevation are not fully known, and to increase the knowledge a link between the systemic circulation and intracellular lipolysis is key. However, data on lipolysis and knowledge from in vitro systems have not been linked to corresponding in vivo data and knowledge in vivo. Here, we use mathematical modelling to provide such a link. We examine mechanisms of insulin action by combining in vivo and in vitro data into an integrated mathematical model that can explain all data. Furthermore, the model can describe independent data not used for training the model. We show the usefulness of the model by simulating new and more challenging experimental setups in silico, e.g. the extracellular concentration of fatty acids during an insulin clamp, and the difference in such simulations between individuals with and without type 2 diabetes. Our work provides a new platform for model-based analysis of adipose tissue lipolysis, under both non-diabetic and type 2 diabetic conditions.
Glucan Unmasking Identifies Regulators of Temperature-Induced Translatome Reprogramming in C. neoformans

Cryptococcus neoformans is a fungal pathogen that causes devastating morbidity and mortality in immunocompromised individuals. It possesses several virulence factors that aid in its evasion from the host immune system, including a large polysaccharide capsule that cloaks the antigenic cell wall. ABSTRACT The cell walls of fungi are critical for cellular structure and rigidity but also serve as a major communicator to alert the cell to the changing environment. In response to stresses encountered in human hosts, pathogenic fungi remodel their cell walls. Masking the β-1,3-glucan component of the cell wall is critical to escape detection by innate immune cells. We previously demonstrated that β-1,3-glucan is unmasked in response to host temperature stress when translatome reprogramming is defective in Cryptococcus neoformans. Here, we used β-1,3-glucan unmasking as an output to identify signaling modules involved both in masking and in translatome reprogramming in response to host temperature stress. We reveal that the high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway is involved in translatome reprogramming and that mutants in this pathway display moderate unmasking when grown at 37°C. Additionally, we show that mutants of the cell wall integrity (CWI)/Mpk1 MAPK pathway extensively unmask β-1,3-glucan. While the CWI pathway does not impact translatome reprogramming, our data suggest that it may play a role in the posttranslational regulation of transcription factors that govern masking. IMPORTANCE Cryptococcus neoformans is a fungal pathogen that causes devastating morbidity and mortality in immunocompromised individuals. It possesses several virulence factors that aid in its evasion from the host immune system, including a large polysaccharide capsule that cloaks the antigenic cell wall. Studies investigating how the cell wall is remodeled to keep this pathogen disguised in response to stress have been limited. We previously found that host temperature stress results in translatome reprogramming that is necessary for keeping the highly antigenic β-(1, 3)-glucan component masked. Our data reveal signaling modules that trigger these responses and suggest the points of regulation at which these pathways act in achieving masking. Understanding these mechanisms may allow for therapeutic manipulation that may promote the immune recognition and clearance of this fungal pathogen.
Alternative splicing of GluN1 gates glycine-primed internalization of NMDA receptors

N-methyl-D-aspartate receptors (NMDARs), a principal subtype of excitatory neurotransmitter receptor, are composed as tetrameric assemblies of two glycine-binding GluN1 subunits and two glutamate-binding GluN2 subunits. Gating of the NMDARs requires binding of four co-agonist molecules, but the receptors can signal non-ionotropically through binding of glycine, alone, to its cognate site on GluN1. A consequence of this signalling by glycine is that NMDARs are primed such that subsequent gating, produced by glycine and glutamate, drives receptor internalization. The GluN1 subunit is not a singular molecular species in the CNS, rather there are 8 alternatively spliced isoforms of this subunit produced by including or excluding the N1 and the C1, C2 or C2’ polypeptide cassettes. Whether alternative splicing affects glycine priming signalling is unknown. Here, using recombinant NMDARs expressed heterologously we discovered that glycine priming of NMDARs critically depends on alternative splicing: the four splice isoforms lacking the N1 cassette, encoded in exon 5, are primed by glycine whereas glycine priming is blocked in the four splice variants containing the N1 cassette. On the other hand, the C-terminal cassettes – C1, C2 or C2’ – had no effect on glycine priming signalling. Nor was glycine priming affected by the GluN2 subunit in the receptor. In wild-type mice we found that glycine primed internalization of synaptic NMDARs in CA1 hippocampal pyramidal neurons. With mice we engineered such that GluN1 obligatorily contained the N1 cassette, glycine did not prime synaptic NMDARs in pyramidal neurons. In contrast to pyramidal neurons, we discovered that in wild-type mice, synaptic NMDARs in CA1 inhibitory interneurons were resistant to glycine priming. But we recapitulated glycine priming in inhibitory interneurons in mice engineered such that GluN1 obligatorily lacked the N1 cassette. Our findings reveal a previously unsuspected molecular function for alternative splicing of GluN1 in controlling non-ionotropic signalling of NMDAR by glycine and the consequential cell surface dynamics of the receptors.
Prevalence of multiple subtypes of binocularly-modulated visual neurons in the mouse superior colliculus

A central role of the visual system is to integrate inputs from both eyes to form one coherent visual perception. The superior colliculus (SC) plays a central role in visual processing, gaze orientation and vergence eye movements necessary for binocular vision. Indeed, the SC receives direct inputs from both the contralateral and ipsilateral eye and binocularly-modulated neurons have been identified in the SC of multiple species. However, evidence for binocular processing in rodents, particularly mice, has not been functionally confirmed. In this study we recorded visually-evoked activity in the mouse SC while presenting visual stimuli to each eye individually or both together and reveal a surprising diversity of binocularly-modulated responses. Strikingly, we found that ~2/3 of all identified neurons in the anteromedial SC were binocularly-modulated. Furthermore, we identified four binocular subtypes based on their differential responses under varying ocularities of stimulus presentation. Interestingly, we found both orientation- and direction-selective (OS and DS, respectively) neurons in all four binocular subtypes. And, tuning properties of binocular neurons were distinct from neighboring monocular neurons, exhibiting more linear spatial summation. Together, these data suggest that binocular neurons are prevalent in the anteromedial SC of the mouse. Additionally, the distinct tuning properties of binocular neurons suggest a previously unappreciated complexity of visual processing in the SC, which may contribute to binocular perception.
An enhanced yeast display platform demonstrates the binding plasticity under various selection pressures

Yeast surface display is popular in vitro evolution method. Here, we enhanced the method by multiple rounds of DNA and protein engineering, resulting in increased protein stabilities, surface expression, and enhanced fluorescence. The pCTcon2 yeast display vector was rebuild, introducing surface exposure tailored reporters – eUnaG2 and DnbALFA, creating a new platform of C and N terminal fusion vectors. In addition to gains in simplicity, speed, and cost, new applications were included to monitor protein surface exposure and protein retention in the secretion pathway. The enhanced methodologies were applied to investigate de-novo evolution of protein-protein interaction sites. Selecting binding from a mix of 6 protein-libraries towards two targets using high stringency selection led to the isolations of single high-affinity binders to each of the targets, without the need for high complexity libraries. Conversely, low-stringency selection resulted in the creation of many solutions for weak binding, demonstrating the plasticity of weak de-novo interactions.
Structural insights into glycine reuptake inhibition

The human glycine transporter 1 (GlyT1) regulates glycine mediated neuronal excitation and inhibition through sodium- and chloride-dependent reuptake of the neurotransmitter1-3. Inhibition of glycine reuptake via GlyT1 prolongs neurotransmitter signaling and has long served as a key therapeutic development strategy for treatment of a broad range of central nervous system disorders including schizophrenia and cognitive impairments4. Using an inhibition state-selective sybody and serial synchrotron crystallography, we determined the structure of GlyT1 in complex with a benzoylpiperazine chemotype inhibitor at 3.4 Å resolution. The inhibitor locks GlyT1 in an inward-open conformation and binds at the intracellular gate of the release pathway, overlapping with the glycine release site. The inhibitor likely reaches GlyT1 from the cytoplasmic leaflet of the plasma membrane. The study defines the mechanism of non-competitive inhibition and enables the rational design of new, clinically efficacious GlyT1 inhibitors.