bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the novel amylin receptor activators with nanomolar potency by peptide mutagenesis
Authors: Lee Sangmin 
Published: August 2024

AbstractAmylin peptide hormone activates amylin receptors in brains and controls blood glucose and appetite. An amylin receptor activator pramlintide was developed for diabetes treatment. Currently, the amylin receptor activator with once-weekly injection has been tested for body weight reduction to treat obesity. Human amylin peptide was reported to form aggregates, while rat amylin has been shown soluble in aqueous solution. Here, multiple peptide activators for human amylin receptors were developed by introducing comprehensive mutagenesis to rat amylin peptide. The rat amylin peptide C-terminal fragment is known for interacting with human amylin receptor extracellular domain. The rat amylin peptide C-terminal fragment with eleven amino acids was used to screen for affinity-enhancing mutations. Up to twelve mutational combinations were found to significantly increase peptide affinity for amylin receptor extracellular domains by over 100-fold. Using these affinity-enhancing mutations, three representative rat amylin analogs with thirty-seven amino acids were made to test the potency increase for amylin receptor activation. All three mutated rat amylin analogs showed significant potency increases by 5- to 10-fold compared to endogenous rat amylin. These mutated peptide activators also showed higher potency for human amylin receptor activation than a clinical drug pramlintide. These amylin receptor activators developed in this study can be useful for the drug development targeting diabetes/obesity treatment.
Tissue and Peripheral T-cell Repertoire Predicts Immunotherapy Response and Progression-Free Survival in NSCLC Patients
Authors: Pino-González Manuel , Lázaro-Quintela Martín , Alonso-Álvarez Irene , Gallardo-Gómez María , Juaneda-Magdalena Laura , Francisco-Fernández Alejandro , Calabuig-Fariñas Silvia , Jantus-Lewintre Eloisa , Martínez-Fernández Mónica 
Published: August 2024

AbstractImmunotherapy has opened new avenues of treatment for patients with advanced non-small cell lung cancer (NSCLC) without previous hope of survival. Unfortunately, only a small percentage of patients benefit from it, and it is still not well understood which tumor characteristics can be used to predict immunotherapy response. As the key cellular effectors of antitumor immunity, T cells are endowed with specialized T cell receptors (TCRs) to recognize and eliminate cancer cells. Here, we evaluated the potential of TCR repertoire as a predictive biomarker in patients treated with immunotherapy. With this aim, advanced NSCLC patients treated with immunotherapy at first-line were included. After obtaining peripheral blood and tissue samples at baseline, next-generation sequencing targeting TCRβ/γ was performed. Beyond TCR metrics, clonal space of the most frequent clones was determined. We found a positive association between uneven tumor-infiltrating TCRβ repertoire and the immunotherapy response. Moreover, the use of various tumor-infiltrating and circulating TRBV/J genes predicted the immunotherapy response. Our results indicate the importance of evaluating tissue and circulating TCRβ repertoire prior immunotherapy, showing it as a promising immunotherapy response biomarker in NSCLC patients.
Characterization and forecast of global influenza (sub)type dynamics
Authors: Bonacina Francesco , Boëlle Pierre-Yves , Colizza Vittoria , Lopez Olivier , Thomas Maud , Poletto Chiara 
Published: August 2024

AbstractThe (sub)type composition of seasonal influenza waves varies in space and time. (Sub)types tend to have different impacts on population groups, therefore understanding the drivers of their co-circulation and anticipating their composition is important for epidemic preparedness and response. FluNet provides data on influenza specimens by (sub)type for more than one hundred fifty countries. However, due to surveillance variations across countries, global analyses usually focus on (sub)type compositions, a kind of data which is difficult to treat with advanced statistical methods. We used Compositional Data Analysis to circumvent the problem and study trajectories of annual (sub)type compositions of countries. First, we examined global trends from 2000 to 2022. We identified a few seasons which stood out for the strong within-country (sub)type dominance due to either a new virus/clade taking over (2003/2004 season, A/H1N1pdm pandemic) or (sub)types’ spatial segregation (COVID-19 pandemic). Second, we showed that the composition trajectories of countries between 2010 and 2019 clustered in two macroregions characterized by (sub)type alternation vs. persistent mixing. Finally, we defined five algorithms for forecasting the next-year composition and we found that taking into account the global history of (sub)type composition in a Bayesian Hierarchical Vector AutoRegressive model improved predictions compared with naive methods. The joint analysis of spatiotemporal dynamics of influenza (sub)types worldwide revealed a hidden structure in (sub)type circulation that can be used to improve predictions of the (sub)type composition of next year’s epidemic according to place.
PREVALENCE OF ABNORMAL SEMINAL FLUID AND ASSOCIATED FACTORS AMONG PATIENTS ATTENDING FERTILITY CLINICS IN OSOGBO: A CROSS SECTIONAL STUDY
Authors: Awodele Kehinde , Adeyemo Sunday Charles , Olabode Eniola Dorcas , Fasanu Adeniyi Olaonipekun , Olaitan Lanre , Akindele Akintunde Rasaq , Olagunju Olufunso Abidemi , Aderinwale Adeola Dorcas 
Published: August 2024

ABSTRACTBackgroundInfertility is a global health issue that affects millions of couples worldwide, In Nigeria, the prevalence of infertility is particularly high underscoring the need for a better understanding of the factors contributing to male infertility at which Seminal Fluid Analysis (SFA) is the most important characteristics. This study aimed to assess the prevalence of abnormal seminal fluid and its associated factors among patients attending fertility clinics in Osogbo, Nigeria.Methods and FindingsA descriptive cross-sectional study design was used among male patients attending fertility centers in Osogbo, Osun State. Fisher’s formula (n=z2pq/d2) was used to determine the sample size. 305 respondents were selected using multistage sampling technique. Pre-tested questionnaire was used to collect data from respondents. Patients who consented to the study were also made to undergo seminal fluid analysis. The results were analysed using IBM Statistical Product for Service Solution (SPSS) version 27. Descriptive statistics was used for all variables. Bivariate and multivariate analysis were done at p<0.05 as level of significance. Majority of the respondents, 257 (84.3%) had at least one abnormality of Seminal fluid. Multiple regression analysis revealed that respondents who were habitual drunkard were about five times more likely to have at least one abnormality in their seminal fluid (OR: 4.990, p: 0.004, C.I.: 1.688-14.749) and smokers were three times more likely to have at least one abnormality in their seminal fluid (p=0.005, OR=3.300 and C.I=1.396-4.273). Also, respondents with history of sexually transmitted infection were 3.5 times more likely to have at least one abnormality in their seminal fluid (p=0.039, OR=3.595 and C.I=1.072-14.146).ConclusionsThe study observed high prevalence of abnormal seminal fluid which was significantly associated with lifestyle habits such as smoking, alcohol as well as previous history of sexually transmitted infection. The study recommended that advocacy program for healthy lifestyle, early screening and public health education will further reduce the burden of abnormal seminal fluid and by implication, infertility among couples.
Protein degradation shapes developmental tempo in mouse and human neural progenitors
Authors: Nakanoh Shota , Stamataki Despina , Garcia-Perez Lorena , Azzi Chiara , Carr Hayley L , Pokhilko Alexandra , Yu Lu , Howell Steven , Skehel Mark , Oxley David , Andrews Simon , Briscoe James , Rayon Teresa 
Published: August 2024

ABSTRACTThe speed of embryonic development varies considerably between mammalian species, yet the underlying molecular mechanisms remain poorly understood. To investigate the basis for species-specific developmental tempo, we performed a comprehensive comparative analysis of protein dynamics in mouse and human neural progenitors (NPs). Through a combination of targeted protein labelling, quantitative mass spectrometry, and protein depletion with self-labeling tags, we demonstrate that protein degradation is a key driver of tempo differences between mouse and human NPs. We observe a systematic 1.5-fold increase in protein half-lives in human NPs compared to mouse, independent of cellular compartment or protein function. This difference persists in post-mitotic neurons, indicating active degradation as the primary mechanism. Proteasomal activity is also ∼1.5-fold higher in mouse NPs, consistent with upregulation of proteasome-associated proteins. Importantly, increasing the rate of proteolytic degradation of a key transcriptional repressor in neural progenitors accelerates the expression of its target gene. Despite differences in degradation rates, protein synthesis rates are similar between species, resulting in higher protein content in human NPs. Our findings highlight the central role of protein degradation in controlling developmental tempo and provide insight into the molecular basis of evolutionary changes in developmental timing across species.
Cyclin A/B RxL Macrocyclic Inhibitors to Treat Cancers with High E2F Activity
Authors: Singh Shilpa , Gleason Catherine E. , Fang Min , Laimon Yasmin N. , Khivansara Vishal , Xie Shanhai , Durmaz Yavuz T. , Sarkar Aniruddha , Ngo Kenneth , Savla Varunika , Li Yixiang , Abu-Remaileh Muhannad , Li Xinyue , Tuladhar Bishma , Odeh Ranya , Hamkins-Indik Frances , He Daphne , Membreno Miles W. , Nosrati Meisam , Gushwa Nathan N. , Leung Siegfried S.F. , Fraga-Walton Breena , Hernandez Luis , Baldomero Miguel P , Lent Bryan M. , Spellmeyer David , Luna Joshua F. , Hoang Dalena , Gritsenko Yuliana , Chand Manesh , DeMart Megan K. , Metobo Sammy , Bhatt Chinmay , Shapiro Justin A. , Yang Kai , Dupper Nathan J. , Bockus Andrew T. , Doench John G. , Aggen James B. , Liu Li-Fen , Levin Bernard , Wang Evelyn W. , Vendrell Iolanda , Fischer Roman , Kessler Benedikt , Gokhale Prafulla C. , Signoretti Sabina , Spektor Alexander , Kreatsoulas Constantine , Singh Rajinder , Earp David J. , Garcia Pablo D. , Nijhawan Deepak , Oser Matthew G. 
Published: August 2024

AbstractCancer cell proliferation requires precise control of E2F1 activity; excess activity promotes apoptosis. Here, we developed cell-permeable and bioavailable macrocycles that selectively kill small cell lung cancer (SCLC) cells with inherent high E2F1 activity by blocking RxL-mediated interactions of cyclin A and cyclin B with select substrates. Genome-wide CRISPR/Cas9 knockout and random mutagenesis screens found that cyclin A/B RxL macrocyclic inhibitors (cyclin A/Bi) induced apoptosis paradoxically by cyclin B- and Cdk2-dependent spindle assembly checkpoint activation (SAC). Mechanistically, cyclin A/Bi hyperactivate E2F1 and cyclin B by blocking their RxL-interactions with cyclin A and Myt1, respectively, ultimately leading to SAC activation and mitotic cell death. Base editor screens identified cyclin B variants that confer cyclin A/Bi resistance including several variants that disrupted cyclin B:Cdk interactions. Unexpectedly but consistent with our base editor and knockout screens, cyclin A/Bi induced the formation of neo-morphic Cdk2-cyclin B complexes that promote SAC activation and apoptosis. Finally, orally-bioavailable cyclin A/Bi robustly inhibited tumor growth in chemotherapy-resistant patient-derived xenograft models of SCLC. This work uncovers gain-of-function mechanisms by which cyclin A/Bi induce apoptosis in cancers with high E2F activity, and suggests cyclin A/Bi as a therapeutic strategy for SCLC and other cancers driven by high E2F activity.
Chronic contractile activity induced skeletal muscle-derived extracellular vesicles increase mitochondrial biogenesis in recipient myocytes via transmembrane or peripheral membrane proteins
Authors: Obi Patience O. , Souza Tamiris F. G. , Seif Samira , Bydak Benjamin , Klassen Nicholas , West Adrian R. , Gordon Joseph W. , Saleem Ayesha 
Published: August 2024

AbstractThe effect of chronic contractile activity (CCA) on the biophysical properties and functional activity of skeletal muscle extracellular vesicles (Skm-EVs) is poorly understood due to challenges in distinguishing Skm-EVs originating from exercising musclein vivo. To address this, myoblasts were differentiated into myotubes, and electrically paced (3 h/day, 4 days @ 14 V). CCA evoked an increase in mitochondrial biogenesis in stimulatedvs. non-stimulated (CON) myotubes as expected. EVs were isolated from conditioned media from control and stimulated myotubes using differential ultracentrifugation and characterized biophysically using tunable resistive pulse sensing (TRPS, Exoid), TEM and western blotting. TEM images confirmed isolated round-shaped vesicles of about 30 - 150 nm with an intact lipid bilayer. The mean size of EVs ranged from 98 -138 nm, and was not altered by CCA. Zeta potential and total EV protein yield remained unchanged between groups, and total EV secretion increased after 4 days of CCA. Concomitant analysis of EVs after each day of CCA also demonstrated a progressive increase in CCA-EV concentration, while size and zeta potential remained unaltered, and EV protein yield increased in both CON-EVs and CCA groups. CCA-EVs were enriched with small-EVsvs. CON-EVs, concomitant with higher expression of small-EV markers CD81, Tsg101 and HSP70. In whole cell lysates, CD63 and ApoA1 were reduced with CCA in myotubes, whereas CD81, Tsg101, Flotillin-1 and HSP70 levels remained unchanged. To evaluate the functional effect of EVs secreted post-CCA, we treated C2C12 myoblasts with all EVs isolated from CON or CCA myotubes after each day of stimulation, and measured cell count, cell viability, protein yield and mitochondrial biogenesis in recipient cells. There was no effect on cell count, viability and protein yield. Myoblasts treated with CCA-EVs exhibited increased mitochondrial biogenesis as indicated by enhanced MitoTracker Red staining, cytochromecoxidase activity, and protein expression of electron transport chain subunit, CIV-MTCO1. Further, CCA-EV treatment enhanced maximal oxygen consumption rates (OCR), and ATP production in treated myoblasts. This increase in maximal OCR was abrogated when CCA-EVs pre-treated with proteinase K were co-cultured with myoblasts, indicating the pro-metabolic effect was likely mediated by transmembrane or peripheral membrane proteins in CCA-EVs. Our data highlight the novel effect of Skm-EVs isolated post-CCA in mediating pro-metabolic effects in recipient cells and thereby transmitting the effects associated with traditional exercise. Further investigation to interrogate the underlying mechanisms involved in downstream cellular metabolic adaptations is warranted.
Visualizing Liquid Distribution Across Hyphal Networks with Cellular Resolution
Authors: Clark Amelia J. , Masters-Clark Emily , Moratto Eleonora , Junier Pilar , Stanley Claire E. 
Published: August 2024

ABSTRACTFilamentous fungi and fungal-like organisms contribute to a wide range of important ecosystem functions. Evidence has shown the movement of liquid across mycelial networks in unsaturated environments, such as soil. However, tools to investigate liquid movement along hyphae at the level of the single cell are still lacking. Microfluidic devices permit the study of fungal and fungal-like organisms with cellular resolution as they can confine hyphae to a single optical plane, which is compatible with microscopy imaging over longer timescales and allows for precise control of the microchannel environment. The aim of this study was to develop a method that enables the visualization and quantification of liquid movement on hyphae of fungal and fungal-like microorganisms. For this, the Fungal-Fungal Interaction (FFI) microfluidic device was modified to allow for the maintenance of unsaturated microchannel conditions. Fluorescein-containing growth medium solidified with agar was used to track liquid transported by hyphae via fluorescence microscopy. Our key findings highlight the suitability of this novel methodology for the visualization of liquid movement by hyphae over varying time scales and the ability to quantify the movement of liquid along hyphae. Furthermore, we showed that at the cellular level, extracellular hyphal liquid movement can be bidirectional and highly dynamic, uncovering a possible link between liquid movement and hyphal growth characteristics. We envisage that this method can be applied to facilitate future research probing the parameters contributing to hyphal liquid movement and is an essential step for studying the phenomenon of fungal highways.
Assessing the Impact of Selective Attention on the Cortical Tracking of the Speech Envelope in the Delta and Theta Frequency Bands and How Musical Training Does (Not) Affect It
Authors: Schüller Alina , Mücke Annika , Riegel Jasmin , Reichenbach Tobias 
Published: August 2024

AbstractOral communication regularly takes place amidst background noise, requiring the ability to selectively attend to a target speech stream. Musical training has been shown to be beneficial for this task. Regarding the underlying neural mechanisms, recent studies showed that the speech envelope is tracked by neural activity in the auditory cortex, which plays a role in the neural processing of speech, including speech in noise. The neural tracking occurs predominantly in two frequency bands, the delta and the theta band. However, much regarding the specifics of these neural responses, as well as their modulation through musical training, still remain unclear. Here, we investigated the delta- and theta-band cortical tracking of the speech envelope of attended and ignored speech using magnetoencephalography (MEG) recordings. We thereby assessed both musicians and non-musicians to explore potential differences between these groups. The cortical speech tracking was quantified through source-reconstructing the MEG data and subsequently relating the speech envelope in a certain frequency band to the MEG data using linear models. We thereby found the theta-band tracking to be dominated by early responses with comparable magnitudes for attended and ignored speech, whereas the delta band tracking exhibited both earlier and later responses that were modulated by selective attention. Almost no significant differences emerged in the neural responses between musicians and non-musicians. Our findings show that only the speech tracking in the delta but not in the theta band contributes to selective attention, but that this mechanism is essentially unaffected by musical training.
Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical Conditions
Authors: Weckel-Dahman Hannah , Carlsen Ryan , Swanson Jessica M.J. 
Published: August 2024

ABSTRACTAttaining a complete thermodynamic and kinetic characterization for processes involving multiple interconnected rare-event transitions remains a central challenge in molecular biophysics. This challenge is amplified when the process must be understood under a range of reaction conditions. Herein, we present a condition-responsive kinetic modeling framework that can combine the strengths of bottom-up rate quantification from multiscale simulations with top-down solution refinement using experimental data. Although this framework can be applied to any process, we demonstrate its use for electrochemically driven transport through channels and transporters. Using the Cl−/H+antiporter ClC-ec1 as a model system, we show how robust and predictive kinetic solutions can be obtained when the solution space is grounded by thermodynamic constraints, seeded through multiscale rate quantification, and further refined with experimental data, such as electrophysiology assays. Turning to the Shaker K+channel, we demonstrate that robust solutions and biophysical insights can also be obtained with sufficient experimental data. This multi-pathway method proves capable of identifying single-pathway dominant mechanisms but also highlights that competing and off-pathway flux is still essential to replicate experimental findings and to describe concentration-dependent channel rectification.
Flux balance analysis and peptide mapping elucidate the impact of bioreactor pH on Chinese Hamster Ovary (CHO) cell metabolism and N-linked glycosylation in the Fab and Fc regions of the produced IgG
Authors: Reddy Jayanth Venkatarama , Singh Sumit Kumar , Leibiger Thomas , Lee Kelvin H , Ierapetritou Marianthi , Papoutsakis Eleftherios Terry 
Published: August 2024

AbstractChinese Hamster Ovary (CHO) cells were grown at different bioreactor pH conditions to detail how bioreactor pH affects cell metabolism and site-specific N-linked glycosylation of the produced broadly neutralizing anti-HIV IgG monoclonal antibody VRC01. The data show that pH affects cell growth, glucose/lactate metabolism, IgG production rates, nonessential amino acid metabolism and ammonia accumulation. Parsimonious Flux Balance Analysis (pFBA) and Flux Variability Analysis (FVA) provide insight into the effect of pH on core intracellular reactions at the different pH conditions and culture durations. pFBA revealed the contribution of sources for the production of the toxic metabolite ammonia and provided insights into the switch from ammonia production to consumption. It also documented that culture duration and pH alter the complex bimodal patterns (production/uptake) of several essential and non-essential amino acids. The VRC01 IgG has N-linked glycosylation sites in both the Fc region and the Fab region. Site- specific N-linked glycan analysis using glycopeptide mapping demonstrated that pH significantly affects the glycosylation profiles of the two IgG sites. The Fc region glycans were completely fucosylated but did not contain any sialylation. The Fab region glycans were not completely fucosylated but contained sialylated glycans. Bioreactor pH affected both the fucosylation and sialylation indexes in the Fab region and the galactosylation index of the Fc region. However, fucosylation in the Fc region was unaffected thus demonstrating that the effect of pH on site- specific N-linked glycosylation is complex.