bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Alternative Conformational States of Pseudo-Symmetric Solute Carrier Transporters using Methods from Deep Learning
Authors: Swapna G.V.T. , Dube Namita , Roth Monica J. , Montelione Gaetano T. 
Published: July 2024

ABSTRACTThe Solute Carrier (SLC) superfamily of integral membrane proteins function to transport a wide array of small molecules across plasma and organelle membranes. SLC proteins also function as important drug transporters and as viral receptors. Despite being classified as a single superfamily, SLC proteins do not share a single common fold classification; however, most belong to multi-pass transmembrane helical protein fold families. SLC proteins populate different conformational states during the solute transport process, including outward-open, intermediate (occluded), and inward-open conformational states. For some SLC fold families this structural “flipping” corresponds to swapping between conformations of their N-terminal and C-terminal symmetry-related sub-structures. Conventional AlphaFold2, AlphaFold3, or Evolutionary Scale Modeling methods typically generate models for only one of these multiple conformational states of SLC proteins. Several modifications of these AI-based protocols for modeling multiple conformational states of proteins have been described recently. These methods are often impacted by “memorization” of one of the alternative conformational states, and do not always provide both the inward and outward facing conformations of SLC proteins. Here we describe a combined ESM – template-based-modeling process, based on a previously described template-based modeling method that relies on the internal pseudo-symmetry of many SLC proteins, to consistently model alternate conformational states of SLC proteins. We further demonstrate how the resulting multi-state models can be validated experimentally by comparison with sequence-based evolutionary co-variance data (ECs) that encode information about contacts present in the various conformational states adopted by the protein. This simple, rapid, and robust approach for modeling conformational landscapes of pseudo-symmetric SLC proteins is demonstrated for several integral membrane protein transporters, including SLC35F2 the receptor of a feline leukemia virus envelope protein required for viral entry into eukaryotic cells.
Simulations of the infant gut microbiota suggest that complex ecological interactions regulate effects of human milk oligosaccharides on microbial mucin consumption
Authors: Versluis David M. , Wijtkamp Clair , Looijesteijn Ellen , Geurts Jan M. W. , Merks Roeland M. H. 
Published: July 2024

ABSTRACTIntestinal mucin acts as a barrier protecting the infant gut wall against diseases such as colitis and rotavirus.In vitroexperiments have shown that the gut microbiota of breastfed infants consumes less mucin than the microbiota of non-breastfed infants, but the mechanisms are incompletely understood. The main difference between human milk and most infant formulas is the presence of human milk oligosaccharides (HMOs) in human milk. We hypothesize that HMOs protect mucin by stimulating non-mucin consuming bacteria. To understand the un-derlying mechanisms we developed a computational model that describes the metabolism and ecology of the infant gut microbiota. Model simulations suggest that extracellular digestion of the HMO 2’-fucosyllactose by the mucin-consumerBifidobacterium bifidummay make this species vulnerable to competitors. The digestion products of HMOs become ‘public goods’ that can be consumed by competing species such asBacteroides vulgatusinstead.Bifidobacterium longum, which does not consume mucin or produce public goods, can then become dominant, despite growing less efficiently on HMOs in monocultures thanB. bifidum. In conclusion, our model simulations suggest that, through complex ecological interactions, HMOs may help lower mucin consumption by stimulating the non-mucin consumerB. longumat the expense of the mucin consumerB. bifidum.
Automated Skin Lesion Detection and Prevalence Estimation in Tamanend’s Bottlenose Dolphins
Authors: Murphy Colin J. , Collier Melissa A. , Jacoby Ann-Marie , Patterson Eric M. , Wallen Megan M. , Mann Janet , Bansal Shweta 
Published: July 2024

AbstractAnthropogenic global change is occurring at alarming rates, leading to increased urgency in the ability to monitor wildlife health in real time. Monitoring sentinel marine species, such as bottlenose dolphins, is particularly important due to extensive anthropogenic modifications to their habitats. The most common non-invasive method of monitoring cetacean health is documentation of skin lesions, often associated with poor health or disease, but the current methodology is inefficient and imprecise. Recent advancements in technology, such as machine learning, can provide researchers with more efficient ecological monitoring methods to address health questions at both the population and the individual levels. Our work develops a machine learning model to classify skin lesions on the understudied Tamanend’s bottlenose dolphins (Tursiops erebennus) of the Chesapeake Bay, using manual estimates of lesion presence in photographs. We assess the model’s performance and find that our best model performs with a high mean average precision (65.6%-86.8%), and generally increased accuracy with improved photo quality. We also demonstrate the model’s ability to address ecological questions across scales by generating model-based estimates of lesion prevalence and testing the effect of gregariousness on health status. At the population level, our model accurately estimates a prevalence of 72.1% spot and 27.3% fringe ring lesions, with a slight underprediction compared to manual estimates (82.2% and 32.1%). On the other hand, we find that individual-level analyses from the model predictions may be more sensitive to data quality, and thus, some individual scale questions may not be feasible to address if data quality is inconsistent. Manually, we do find that lesion presence in individuals suggests a positive relationship between lesion presence and gregariousness. This work demonstrates that object detection models on photographic data are reasonably successful, highly efficient, and provide initial estimates on the health status of understudied populations of bottlenose dolphins.
Effect of Voltage-Gated K+Channel Inhibition by 4-aminopyridine in Spinal Cord Injury Recovery in Zebrafish
Authors: Hoffman Payge M. , Mruk Karen 
Published: July 2024

AbstractSpinal cord injury (SCI) affects between 250,000 to 500,000 individuals annually. After the initial injury, a delayed secondary cascade of cellular responses occurs causing progressive degeneration and permanent disability. One part of this secondary process is disturbance of ionic homeostasis. The K+channel blocker, 4-aminopyridine (4-AP), is used clinically to alleviate symptoms of multiple sclerosis (MS). Several ongoing studies are being conducted to explore additional areas where 4-AP may have an effect, including stroke, traumatic brain injury, and nervous system recovery after SCI. The goal of our study was to determine whether 4-AP affects recovery from SCI in zebrafish (Danio rerio). Using the transgenic lineTg(gfap:EGFP), we created a spinal transection and tracked swim recovery. We found that constant treatment with 10 µM 4-AP increases swimming distance 40%. Live imaging demonstrated that treatment with 4-AP increases radial glial cells bridging at the site of injury in the presence of 4-AP. We conclude that 10 µM 4-AP is pro-regenerative after SCI.Significance StatementIn this study, we found that 4-AP can enhance locomotor recovery in zebrafish after spinal cord injury. Our findings indicate that inhibition of K+channels with 4-AP may promote glial remodeling that is pro-regenerative.
Resistance to age-related hearing loss in the echolocating big brown bat (Eptesicus fuscus)
Authors: Capshaw Grace , Diebold Clarice A. , Adams Danielle M. , Rayner Jack , Wilkinson Gerald S. , Moss Cynthia F. , Lauer Amanda M. 
Published: July 2024

AbstractHearing mediates many behaviors critical for survival in echolocating bats, including foraging and navigation. Most mammals are susceptible to progressive age-related hearing loss; however, the evolution of biosonar, which requires the ability to hear low-intensity echoes from outgoing sonar signals, may have selected against the development of hearing deficits in echolocating bats. Although many echolocating bats exhibit exceptional longevity and rely on acoustic behaviors for survival to old age, relatively little is known about the aging bat auditory system. In this study, we used DNA methylation to estimate the ages of wild-caught big brown bats (Eptesicus fuscus) and measured hearing sensitivity in young and aging bats using auditory brainstem responses (ABRs) and distortion product otoacoustic emissions (DPOAEs). We found no evidence for hearing deficits in aging bats, demonstrated by comparable thresholds and similar ABR wave and DPOAE amplitudes across age groups. We additionally found no significant histological evidence for cochlear aging, with similar hair cell counts, afferent, and efferent innervation patterns in young and aging bats. Here we demonstrate that big brown bats show minimal evidence for age-related loss of peripheral hearing sensitivity and therefore represent informative models for investigating mechanisms that may preserve hearing function over a long lifetime.
The Neurobiology of Cognitive Fatigue and Its Influence on Effort-Based Choice
Authors: Steward Grace , Chib Vikram S. 
Published: July 2024

ABSTRACTFeelings of cognitive fatigue emerge through repeated mental exertion and are ubiquitous in our daily lives. However, there is a limited understanding of the neurobiological mechanisms underlying the influence of cognitive fatigue on decisions to exert. We use functional magnetic resonance imaging to examine brain activity while participants make choices to exert effort for reward, before and after bouts of fatiguing cognitive exertion. We found that when participants became cognitively fatigued, they were more likely to choose to forgo higher levels of reward that required more effort. We describe a mechanism by which signals related to cognitive exertion in dlPFC influence effort value computations, instantiated by the insula, thereby influencing an individual’s decisions to exert while fatigued. Our results suggest that cognitive fatigue plays a critical role in decisions to exert effort and provides a mechanistic link through which information about cognitive state shapes effort-based choice.
Mathematical model of transcription loss due to accumulated DNA damage
Authors: Raseta Marko , Dealy Shannon , Grint Jacinta van de , Chang Jiang , Hoeijmakers Jan , Pothof Joris 
Published: July 2024

AbstractWe offer a simple mathematical model of gene transcription loss due to accumulated DNA damage in time based on widely agreed biological axioms. Closed form formulae characterizing the distribution of the underlying stochastic processes representing the transcription loss upon specified number of DNA damages are obtained. Moreover, the asymptotic behavior of the stochastic process was analyzed. Finally, the distribution of the first hitting time of transcription loss to specified biologically relevant levels was studied both analytically and computationally on mice data.
State dependent motor cortex stimulation reveals distinct mechanisms for corticospinal excitability and cortical responses
Authors: Perera Nipun D , Wischnewski Miles , Alekseichuk Ivan , Shirinpour Sina , Opitz Alexander 
Published: July 2024

AbstractTranscranial magnetic stimulation (TMS) is a non-invasive brain stimulation method which can modulate brain activity by inducing electric fields in the brain. It is a popular tool to study causal brain-behavior relationships. However, brain states vary over time and affect the response of TMS. Neural oscillations can track the current brain state and are a promising marker to guide stimulation timing. Real-time, state-dependent brain stimulation has shown that neural oscillation phase modulates corticospinal excitability reflecting the connection from the primary motor cortex to a target muscle. However, such motor-evoked potentials (MEPs) only indirectly reflect motor cortex activation and are unavailable at other brain regions of interest. The direct and secondary cortical effects of phase-dependent brain stimulation remain an open question. In this study, we recorded the cortical responses during single-pulse transcranial magnetic stimulation (TMS) using electroencephalography (EEG) concurrently with the MEP measurements. TMS was delivered at peak, rising, trough, and falling phases of mu (8-13 Hz) and beta (14-30 Hz) oscillations in the motor cortex. The cortical responses were quantified through TMS-evoked potential components N15, P50, and N100 as peak-to-peak amplitudes (P50-N15 and P50-N100). We further analyzed whether the pre-stimulus frequency band power was predictive of the motor cortical responses. We found a significant main effect of neural oscillation phase on early evoked component (P50-N15). Furthermore, we found an interaction effect of oscillation phase and frequency on both early and late (P50-N100) components. Next, we compared the direct EEG response to the corticospinal excitability reflected by MEP amplitude. Interestingly, the preferred phase of the mu rhythm showed a 900phase shift between the early TEP components and MEPs. The late component showed the same phase preference between EEG and MEPs. However, such a well-defined relationship did not exist for either of the components during beta phase specific stimulation. In addition, pre-TMS mu oscillatory power and phase significantly predicted both early and late cortical EEG responses when mu rhythm was targeted, indicating the independent causal effects of phase and power. However, only pre-TMS beta power significantly predicted the early and late TEP components when beta rhythm was targeted. Further analysis indicated that both pre-TMS mu and beta power jointly affect early cortical responses. In contrast, the late cortical responses were only influenced by pre-TMS mu power. These findings provide insight to mechanistic understanding of neural oscillation states in cortical and corticospinal activation in humans.
Employing Steered MD simulations for Effective Virtual Screening: Active Pharmacophore Search by Dynamic Corrections to target MKK3-MYC Interactions
Authors: Ulug Muhammet Eren , Ikram Saima , Sayyah Ehsan , Durdağı Serdar 
Published: July 2024

AbstractThe intricate relationship between mitogen-activated protein kinase 3 (MKK3) and MYC proto-oncogene protein (MYC) activation holds deep implications for the progression of cancer, particularly in the context of triple negative breast cancer (TNBC). Despite significant progress, the challenge of discovering effective MYC-targeted drugs persists, demanding innovative approaches to control MYC-dependent malignancies. A promising avenue in this pursuit involves disrupting the protein-protein interactions (PPIs) between MKK3 and MYC. The significance of this interaction is emphasized by the activation of MYC by MKK3 in diverse cell types, presenting a novel perspective for therapeutic interventions in MYC-driven pathways. In the current study, a novelin silicostrategy to screen small molecule libraries that target the MKK3-MYC interaction was conducted. Dynamic structure-based pharmacophore models were developed and utilized for screening the small molecule libraries, enabling the identification of compounds exhibiting favorable alignment with the defined pharmacophore features. Subsequently, physics-based simulations approaches were conducted on these selected hit molecules. Steered molecular dynamics (sMD) simulations were utilized to assess the correlation between the necessary forces to dissociate candidate hit ligands from the binding pocket and their corresponding average binding free energies (MM/GBSA). Comparative analysis of the average binding free energies of the identified hits obtained from the small molecule libraries represent that the identified compounds have promising predicted binding affinities compared to the reference molecule SGI-1027. Therefore, these findings may signify a crucial advancement in our ability to control MYC activation in cancer.
Primary auditory thalamus relays directly to cortical layer 1 interneurons
Authors: Vattino Lucas G. , MacGregor Cathryn P. , Liu Christine Junhui , Sweeney Carolyn G. , Takesian Anne E. 
Published: July 2024

AbstractInhibitory interneurons within cortical layer 1 (L1-INs) integrate inputs from diverse brain regions to modulate sensory processing and plasticity, but the sensory inputs that recruit these interneurons have not been identified. Here we used monosynaptic retrograde tracing and whole-cell electrophysiology to characterize the thalamic inputs onto two major subpopulations of L1-INs in the mouse auditory cortex. We find that the vast majority of auditory thalamic inputs to these L1-INs unexpectedly arise from the ventral subdivision of the medial geniculate body (MGBv), the tonotopically-organized primary auditory thalamus. Moreover, these interneurons receive robust functional monosynaptic MGBv inputs that are comparable to those recorded in the L4 excitatory pyramidal neurons. Our findings identify a direct pathway from the primary auditory thalamus to the L1-INs, suggesting that these interneurons are uniquely positioned to integrate thalamic inputs conveying precise sensory information with top-down inputs carrying information about brain states and learned associations.
The Raf/LIN-45 C-terminal distal tail segment negatively regulates signaling inCaenorhabditis elegans
Authors: Townley Robert A. , Stacy Kennedy S. , Cheraghi Fatemeh , de la Cova Claire C. 
Published: July 2024

AbstractRaf protein kinases act as Ras-GTP sensing components of the ERK signal transduction pathway in animal cells, influencing cell proliferation, differentiation, and survival. In humans, somatic and germline mutations in the genesBRAFandRAF1are associated with malignancies and developmental disorders. Recent studies shed light on the structure of activated Raf, a heterotetramer consisting of Raf and 14-3-3 dimers, and raised the possibility that a Raf C-terminal distal tail segment (DTS) regulates activation. We investigated the role of the DTS using theCaenorhabditis elegans,which has a single Raf ortholog termedlin-45. We discovered that truncations removing the DTS strongly enhancedlin-45(S312A), a weak gain-of-function allele equivalent toRAF1mutations found in patients with Noonan Syndrome. We generated mutations to test three elements of the LIN-45 DTS, which we termed the active site binding sequence (ASBS), the KTP motif, and the aromatic cluster. In the context oflin-45(S312A),mutation of either the ASBS, KTP motif, or aromatic cluster enhanced activity. We used AlphaFold to predict DTS protein interactions for LIN-45, fly Raf, and human BRAF, within the activated heterotetramer complex. We propose distinct functions for the LIN-45 DTS elements: i) the ASBS binds the kinase active site as an inhibitor, ii) phosphorylation of the KTP motif modulates DTS-kinase domain interaction, and iii) the aromatic cluster anchors the DTS in an inhibitory conformation. This work establishes that the Raf/LIN-45 DTS negatively regulates signaling inC. elegansand provides a model for its function in other Raf proteins.
Circulating Micro-RNAs in Patients with Hypophosphatasia Results of the first micro-RNA analysis in HPP
Authors: Haschka Judith , Messner Zora , Feurstein Julia , Hadzimuratovic Benjamin , Zwerina Jochen , Diendorfer Andreas B. , Pultar Marianne , Hackl Matthias , Kuzma Martin , Payer Juraj , Resch Heinrich , Kocijan Roland 
Published: July 2024

AbstractIntroductionAdult hypophosphatasia (HPP) patients present with diffuse heterogenous symptoms often mimicking rheumatological diseases or osteoporosis and therefore accompanied by delayed diagnosis. The aim of this study was to identify circulating miRNAs in adult HPP patients and to identify potential associations with clinical patients’ characteristics.MethodsWe utilized untargeted miRNA biomarker discovery by small RNA-sequencing to investigate cell-free miRNA profiles in 24 adult HPP patients (pathogenic variant of theALPLgene, HPP-related clinical symptoms and repeatedly low ALP) and 24 healthy controls.ResultsPatients and CTRL were comparable in age (47.9±14.2 vs. 45.9±8.8y, p=0.980) and sex (55.5% vs. 47.8% females, p=1.000). In total, 91% of patients reported musculoskeletal pain, 41% diffuse neurological symptoms and 64% history of fractures. In total, 84 miRNAs were significantly differently expressed between HPP and CTRLs in next generation sequencing (NGS) analysis(p<0.05). Of these, 14 miRNAs were selected (selection criteria: p<0.05, tissue specificity index >0.7, log2FC >+0.8 or < −0.8) for validation using RT-qPCR, which verified 6 of 14 selected miRNAs (p<0.05; miR-122-3p, miR-140-5p, miR-143-3p, miR-155-5p, miR-451a, miR-92a-3p). Target prediction and enrichment analysis identified associations with the musculoskeletal system and the central nervous system. In total, 37 miRNAs correlated with ALP levels, but only three miRNAs with PLP (pyridoxal-5’- phosphate).ConclusionsThese findings highlight a profound involvement of multiple organ systems and the potential of miRNAs as biomarkers for the effect of HPP on various systems.
A Randomized, Double-Blind, Controlled Trial to Assess the Effects of Lactoferrin at Two Doses vs. Active Control on Immunological and Safety Parameters in Healthy Adults
Authors: Peterson Ross D. , Guarneiri Liana L. , Adams Caryn G. , Wilcox Meredith L. , Clark Anthony J. , Rudemiller Nathan P. , Maki Kevin C. , Malinczak Carrie-Anne 
Published: July 2024

ABSTRACTBackgroundRecombinant human lactoferrin (rhLF) is of commercial interest for support of the immune system and iron homeostasis but is not currently available as a food ingredient.ObjectiveThe objective was to evaluate the immunogenicity/alloimmunization potential of Helaina rhLF (effera™) fromK. phaffiiover a 28-day period compared to bovine LF (bLF). It was hypothesized that rhLF would have an equal or lower immunogenic potential compared to bLF, which is permitted for use in conventional foods and infant formula in the EU and US.MethodsStudy 1 was a randomized, double-blind, parallel arm, controlled trial where 66 healthy adults were randomly allocated to 1 of 3 groups: high-dose rhLF (3.4 g/d), low-dose rhLF (0.34 g/d), or bLF (3.4 g/d) (clinicaltrials.gov:NCT06012669). Participants completed a 28-day (Day 28) supplementation period followed by a 28-day washout period (Day 56) and an additional 28-day follow-up period (Day 84). Study 2 was a 12-week observational study with no intervention that enrolled 24 healthy adults. In both studies, fasting blood was obtained on Days 0, 28, 56, and 84 for analysis of anti-bLF and anti-hLF antibody levels as the primary endpoint as well as other secondary safety endpoints including complete blood count, iron biomarkers, and metabolic panel.ResultsIn Study 1, the change from baseline to Day 56 in serum anti-bLF antibodies in the bLF group (least squares geometric mean and 95% confidence interval for the post/pre ratio: 3.01; 2.08, 4.35) was greater than the changes in serum anti-hLF antibodies in the low-dose rhLF (1.07; 0.77, 1.49; P<0.001) and high-dose rhLF (1.02; 0.62, 1.70; P<0.001) groups. In Study 2, the post/pre ratio at Day 56 in serum anti-hLF and anti-bLF antibodies were 1.00 (0.93, 1.08) and 1.01 (0.94, 1.09), respectively, confirming no change in anti-hLF antibodies in Study 1 or Study 2. Changes in all safety outcomes in Study 1 were similar between groups and within normal ranges.ConclusionThese results support the safety and tolerability of efferaTMas a food ingredient at an intake level up to 3.4 g/d in healthy adults.