bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aggregation controlled by condensate rheology
Authors: Pönisch Wolfram , Michaels Thomas C.T. , Weber Christoph A. 
Published: November 2021

ABSTRACTBiomolecular condensates in living cells can exhibit a complex rheology including viscoelastic and glassy behaviour. This rheological behavior of condensates was suggested to regulate polymerisation of cytoskeletal filaments and aggregation of amyloid fibrils. Here, we theoretically investigate how the rheological properties of condensates can control the formation of linear aggregates. To this end, we propose a kinetic theory for linear aggregation in coexisting phases, which accounts for the aggregate size distribution and the exchange of aggregates between inside and outside of condensates. The rheology of condensates is accounted in our model via aggregate mobilities that depend on aggregate size. We show that condensate rheology determines whether aggregates of all sizes or dominantly small aggregates are exchanged between condensate inside and outside on the time-scale of aggregation. As a result, the ratio of aggregate numbers inside to outside of condensates differs significantly. Strikingly, we also find that weak variations in the rheological properties of condensates can lead to a switch-like change of the number of aggregates. These results suggest a possible physical mechanism for how living cells could control linear aggregation in a switch-like fashion through variations in condensate rheology.SIGNIFICANCEThe intracellular space can be organized through phase-separated condensates that often exhibit rheological properties reminiscent of complex fluids. These condensates can affect biochemical processes such as the formation of linear aggregates, in particular biofilaments or amyloids. Here, we propose a theoretical model for how condensate rheology can control the irreversible formation of linear aggregates. A key finding is that size and number of aggregates change in a switch-like fashion upon weak changes in condensate rheology. Our model paves the way to unravel the physiochemical mechanisms of how the rheology of condensates can control aberrant protein aggregation. Such mechanisms may explain how rheological changes, such as ageing or the transition to dormancy, give rise to diseases related to protein aggregation.
Probabilistic Genotyping of Single Cell Replicates from Complex DNA Mixtures Recovers Higher Contributor LRs than Standard Analysis
Authors: Huffman Kaitlin , Hanson Erin , Ballantyne Jack 
Published: November 2021

AbstractDNA mixtures are a common source of crime scene evidence and are often one of the more difficult sources of biological evidence to interpret. With the implementation of probabilistic genotyping (PG), mixture analysis has been revolutionized allowing previously unresolvable mixed profiles to be analyzed and probative genotype information from contributors to be recovered. However, due to allele overlap, artifacts, or low-level minor contributors, genotype information loss inevitably occurs. In order to reduce the potential loss of significant DNA information from donors in complex mixtures, an alternative approach is to physically separate individual cells from mixtures prior to performing DNA typing thus obtaining single source profiles from contributors. In the present work, a simplified micromanipulation technique combined with enhanced single-cell DNA typing was used to collect one or few cells, referred to as direct single-cell subsampling (DSCS). Using this approach, single and 2-cell subsamples were collected from 2-6 person mixtures. Single-cell subsamples resulted in single source DNA profiles while the 2-cell subsamples returned either single source DNA profiles or new mini-mixtures that are less complex than the original mixture due to the presence of fewer contributors. PG (STRmix™) was implemented, after appropriate validation, to analyze the original bulk mixtures, single source cell subsamples, and the 2-cell mini mixture subsamples from the original 2-6-person mixtures. PG further allowed replicate analysis to be employed which, in many instances, resulted in a significant gain of genotype information such that the returned donor likelihood ratios (LRs) were comparable to that seen in their single source reference profiles (i.e., the reciprocal of their random match probabilities). In every mixture, the DSCS approach gave improved results for each donor compared to standard bulk mixture analysis. With the 5- and 6- person complex mixtures, DSCS recovered highly probative LRs (> 1020) from donors that had returned non-probative LRs (<103) by standard methods.
Molecular evolution of classic Hodgkin lymphoma revealed through whole genome sequencing of Hodgkin and Reed Sternberg cells
Authors: Maura Francesco , Ziccheddu Bachisio , Xiang Jenny Z. , Bhinder Bhavneet , Abascal Federico , Maclachlan Kylee H. , Eng Kenneth Wha , Uppal Manik , He Feng , Zhang Wei , Gao Qi , Yellapantula Venkata , Park Sunita , Oberley Matthew , Ruckdeschel Elizabeth , Lim Megan S. , Wertheim Gerald , Barth Matthew , Horton Terzah M. , Forlenza Christopher , Zhang Yanming , Landgren Ola , Moskowitz Craig H , Cesarman Ethel , Imielinski Marcin , Elemento Olivier , Roshal Mikhail , Giulino-Roth Lisa 
Published: November 2021

AbstractThe rarity of malignant Hodgkin and Reed Sternberg (HRS) cells within a classic Hodgkin lymphoma (cHL) biopsy limits the ability to study the genomics of cHL. To circumvent this, our group has previously optimized fluorescence-activated cell sorting to purify HRS cells. Here we leveraged this method to report the first whole genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events prior to the clinical diagnosis of cHL. We identified alterations in driver genes not previously described in cHL, a high activity of the APOBEC mutational signature, and the presence complex structural variants including chromothripsis. We found that the high ploidy observed in cHL is often acquired through multiple, independent large chromosomal gain events including whole genome duplication. The first of these likely occurs several years prior to the diagnosis of cHL, and the last gains typically occur very close to the time of diagnosis. Evolutionary timing analyses revealed that driver mutations in B2M, BCL7A, GNA13, and PTPN1, and the onset of AID driven mutagenesis usually preceded large chromosomal gains. The study provides the first temporal reconstruction of cHL pathogenesis and suggests a relatively long time course between the first pathogenic event and the clinical diagnosis.
Structure and Function of the Retina of Low-density Lipoprotein Receptor-related Protein 5 (Lrp5)-deficient Rats
Authors: Ubels John L. , Lin Cheng-Mao , Antonetti David A. , Diaz-Coranguez Monica , Diegel Cassandra R. , Williams Bart O. 
Published: November 2021

AbstractLoss-of-function mutations in the Wnt co-receptor, low-density lipoprotein receptor-related protein 5 (LRP5), result in familial exudative vitreoretinopathy (FEVR), osteoporosis-pseudoglioma syndrome (OPPG), and Norrie disease. CRISPR/Cas9 gene editing was used to produce rat strains deficient in Lrp5. The purpose of this study was to validate this rat model for studies of hypovascular, exudative retinopathies. The retinal vasculature of wildtype and Lrp5 knockout rats was stained with Giffonia simplifolia isolectin B4 and imaged by fluorescence microscopy. Effects on retinal structure were investigated by histology. The integrity of the blood-retina barrier was analyzed by staining for claudin-5 and measurement of permeability to Evans blue dye. Retinas were imaged by fundus photography and SD-OCT, and electroretinograms were recorded. Lrp5 gene deletion led to sparse superficial retinal capillaries and loss of the deep and intermediate plexuses. Autofluorescent exudates were observed, correlated with absence of claudin-5 expression in superficial vessels and increased Evans blue permeability. OCT images show pathology similar to OCT of humans with FEVR, and retinal thickness is reduced by 50% compared to wild-type rats. Histology and OCT reveal that photoreceptor and outer plexiform layers are absent. The retina failed to demonstrate an ERG response. CRISPR/Cas9 gene-editing produced a predictable rat Lrp5 knockout model with extensive defects in the retinal vascular and neural structure and function. This rat model should be useful for studies of exudative retinal vascular diseases involving the Wnt and norrin pathways.
Construction of lux-based promoter-reporter platforms in Mycobacterium bovis BCG for screening of drug repurposing small-molecule compounds as new anti-tuberculosis drugs
Authors: Zhu Li , Lee Annie Wing-Tung , Wu Kelvin Ka-Lok , Gao Peng , Tam Kingsley King-Gee , Rajwani Rahim , Chaburte Galata Chala , Ng Timothy Ting-Leung , Chan Chloe Toi-Mei , Lao Hiu Yin , Yam Wing Cheong , Kao Richard Yi-Tsun , Siu Gilman Kit Hang 
Published: November 2021

AbstractThe emergence of multidrug-resistant strains and hyper-virulent strains of Mycobacterium tuberculosis are big therapeutic challenges for tuberculosis (TB) control. Repurposing bioactive small-molecule compounds has recently become a new therapeutic approach against TB. This study aimed to construct a rapid screening system to identify novel anti-TB agents from a library of small-molecule compounds.In this study, a total of 320 small-molecule compounds were used to screen for their ability to suppress the expression of a key virulence gene, phoP, of M. tuberculosis complex using luminescence (lux)-based promoter-reporter platforms. The minimum inhibitory and bactericidal concentrations on drug-resistant M. tuberculosis and cytotoxicity to human macrophage were determined. RNA-sequencing (RNA-seq) was conducted to determine the drug mechanisms of the selected compounds as novel antibiotics or anti-virulent agents against the M. tuberculosis complex.Six compounds displayed bactericidal activity against M. bovis BCG, in which Ebselen demonstrated the lowest cytotoxicity to macrophage and was considered as a potential antibiotic for TB. Another ten compounds did not inhibit the in vitro growth of the M. tuberculosis complex but down-regulated the expression of phoP specifically. Of them, ST-193 and ST-193 (hydrochloride) showed low cytotoxicity and could dysregulate the entire phoP-associated gene network, and thus identified as potential anti-virulence agents for M. tuberculosis. This study provides a rapid screening platform coupled with a systematic validation and eventually suggested one potential antibiotic and two anti-virulence agents for M. tuberculosis infections.
Whole-genome sequencing of Chinese native goat offers biological insights into cashmere fiber formation
Authors: Han Hu , Yang Man-Man , Dan Jiang , Zhang Xing-Ju , Wei Qiang , Chen Tao , Wang Qi-Ju , Yang Cheng-Ye , Wulan Bater , Zhang Ting-Ting , Gen Gang , Mengkedala  , Li Bin , Deng Wei-Dong , Miao Ze-Pu , Wang Ran , Zhang Qing-Feng , Li Lin , Chao Sheng-Yu , Fang Ming , Li Yong 
Published: November 2021

AbstractCashmere evolved naturally in the goat, and almost all breeds of goat can produce more or less cashmere fibers. However, the genetic alterations underlying cashmere trait selection are still unclear.We sequenced 120 Chinese native goat including two cashmere goat breeds (Ujumain, Chaidamu) and six ordinary goat breeds (Jining Gray, Matou, Guizhou Black, Jintang Black, Yunnan Black Bone, Chengdu Brown). The genome-wide selective sweep of cashmere goat and ordinary goat revealed a novel set of candidate genes as well as pathways, such as Nuclear factor kappa-B and Wnt Signaling pathways. Of them, theLHX2gene regulating hair follicle development, was evident from the strongest selection signal when comparing the Uhumqin cashmere goat and ordinary goat. Interestingly, we identified a 582bp deletion at 367 kb upstream ofLHX2with higher frequency in cashmere goats and their ancient relatives. This mutation probably rises along the breeding procedures, and is putatively responsible for cashmere production and diameter, as revealed by association studies. Luciferase assay shows that the deletion, which acts as an insulator, restrains the expression ofLHX2by interfering its upstream enhancers.Our study discovers a novel insulator of theLHX2involved in regulating cashmere production and diameter, which would be beneficial to understanding hair follicle development and regeneration. Our findings also provide new insights into the genetic formation of cashmere, and facilitate subsequent molecular breeding for cashmere goat improvement.
The role of Imp and Syp RBPs in precise neuronal elimination by apoptosis through the regulation of TFs
Authors: Guan Wenyue , Nie Ziyan , Laurençon Anne , Bouchet Mathilde , Godin Christophe , Chérif Kabir , Darnas Aurélien , Enriquez Jonathan 
Published: November 2021

SUMMARYNeuronal stem cells generate a limited and consistent number of neuronal progenies, each possessing distinct morphologies and functions. The precise production of neurons with distinct identities must be meticulously regulated throughout development to ensure optimal brain function. In our study, we focused on a neuroblast lineage in Drosophila known as Lin A/15, which gives rise to motoneurons (MNs) and glia. Interestingly, the Lin A/15 neuroblast dedicates 40% of its time to producing immature MNs that are subsequently eliminated through apoptosis. Two RNA-binding proteins, Imp and Syp, play crucial roles in this process of neuronal elimination. We found that Imp+ MNs survive, while Imp-, Syp+ MNs undergo apoptosis. Our results indicate that Imp promotes survival, whereas Syp promotes cell death in immature MNs. Furthermore, our investigations revealed that late-born motoneurons face elimination due to their failure to express a functional code of transcription factors that control their morphological fate (mTFs).Late-born MNs possess a unique and distinct set of TFs compared to early-born MNs. By manipulating the expression of Imp and Syp in late-born motoneurons, we observed a shift in the TF code of late MNs towards that of early-born MNs, resulting in their survival. Additionally, introducing the TF code of early MNs into late-born MNs also promoted their survival. These findings demonstrate that the differential expression of Imp and Syp in immature MNs establishes a connection between generating a precise number of MNs and producing MNs with distinct identities through the regulation of mTFs.Importantly, both Imp and Syp are conserved in vertebrates, suggesting that they play a central role in determining the number of neurons produced during development. The Drosophila model, along with its genetic tools, provides a unique opportunity to further explore and decipher the functions of these RNA-binding proteins in neural stem cells versus immature neurons. The insights gained from these studies could shed light on the broader mechanisms of neurogenesis and neuronal identity determination in more complex organisms.
Malaria transmission relies on concavin-mediated maintenance ofPlasmodiumsporozoite cell shape
Authors: Kehrer Jessica , Formaglio Pauline , Muthinja Julianne Mendi , Weber Sebastian , Baltissen Danny , Lance Christopher , Ripp Johanna , Grech Janessa , Meissner Markus , Funaya Charlotta , Amino Rogerio , Frischknecht Friedrich 
Published: November 2021

ABSTRACTDuring transmission of malaria-causing parasites from mosquitoes to mammals,Plasmodiumsporozoites migrate rapidly in the skin to search for a blood vessel. The high migratory speed and narrow passages taken by the parasites suggest considerable strain on the sporozoites to maintain their shape. Here we report on a newly identified protein, concavin, that is important for maintenance of the sporozoite shape inside salivary glands of mosquitoes and during migration in the skin. Concavin-GFP localized at the cytoplasmic periphery of sporozoites andconcavin(−)sporozoites progressively rounded up upon entry of salivary glands. These roundedconcavin(−)sporozoites failed to pass through the narrow salivary ducts and were hence rarely ejected by mosquitoes. However, normally shapedconcavin(−)sporozoites could be transmitted and migrated in the skin or skin like environments. Strikingly, motileconcavin(−)sporozoites could disintegrate while migrating through narrow strictures in the skin leading to parasite arrest or death and decreased transmission efficiency. We suggest that concavin contributes to cell shape maintenance by riveting the plasma membrane to the subtending inner membrane complex.SIGNIFICANCEMalaria parasites are transmitted byAnophelesmosquitoes and rely on rapid migration for establishing an infection. We identified and characterized a protein, named concavin, essential for maintaining the shape of the sporozoite. Concavin is a membrane associated protein facing the cytoplasm suggesting that it contributes to riveting the plasma membrane to the subtending inner membrane complex. Sporozoites lacking concavin can round up in the salivary glands, are less well transmitted to mice and disintegrate while migrating in the skin. Hence, concavin is essential for parasite transmission and infectivity.Highlights- A membrane associated protein is essential forPlasmodiumshape maintenance-Migrating parasites disintegrate in the absence of concavin-First protein essential for cellular integrity ofPlasmodiumsporozoites-Thickened and deformedPlasmodiumsporozoites fail to be transmitted by mosquitoes
The IPF fibroblastic focus is an active collagen biosynthesis factory embedded in a distinct extracellular matrix
Authors: Herrera Jeremy A. , Dingle Lewis , Montero M. Angeles , Shah Rajesh , Venkateswaran Rajamiyer V , Blaikley John F. , Lawless Craig , Schwartz Martin A. 
Published: November 2021

AbstractBackgroundThe Fibroblastic Focus (FF) is the signature lesion of Idiopathic Pulmonary Fibrosis (IPF) where myofibroblasts accumulate and extracellular matrix (ECM) is produced. However, the molecular composition and function of the FF and surrounding tissue remain undefined.MethodsUtilizing laser capture microdissection coupled mass spectrometry (LCM-MS), we interrogated the FF, adjacent mature scar, and adjacent alveoli in 6 IPF specimens plus 6 non-fibrotic alveolar specimens as controls. The data were subject to qualitative and quantitative analysis, and validation by immunohistochemistry.ResultsWe found that the protein signature of IPF alveoli is defined by immune deregulation as the strongest category. The IPF mature scar was classified as end-stage fibrosis whereas the FF contained an overabundance of a distinctive ECM compared to non-fibrotic control.ConclusionSpatial proteomics demonstrated distinct protein compositions in the histologically defined regions of IPF tissue. These data revealed that the FF is the main site of collagen biosynthesis and that the alveoli adjacent to the FF are abnormal. This new and essential information will inform future mechanistic studies on mechanisms of IPF progression.
A Prospective Cohort Study Towards Improving Enhanced Recovery After Cesarean (ERAC) Pathways
Authors: Cojocaru Liviu , Pahlavan Autusa , Alton Suzanne , Coghlan Martha , Seung Hyunuk , Trilling Ariel , Kodali Bhavani S , Crimmins Sarah , Goetzinger Katherine 
Published: November 2021

ABSTRACTObjectiveTo evaluate whether Enhanced Recovery After Cesarean (ERAC) pathways reduces inpatient and outpatient opioid use, pain scores and improves the indicators of postoperative recovery.Study designThis is a prospective cohort study of all patients older than 18 undergoing an uncomplicated cesarean delivery (CD) at an academic medical center. We excluded complicated CD, patients with chronic pain disorders, chronic opioid use, acute postpartum depression, or mothers whose neonate demised before their discharge. Lastly, we excluded non-English and non-Spanish speaking patients. Our study compared the outcomes in patients before (pre-ERAC) and after (post-ERAC) implementation of an ERAC pathways. Primary outcomes were inpatient morphine milligram equivalent (MME) use and the patient’s delta pain scores. Secondary outcomes were outpatient MME prescriptions as well as indicators of postoperative recovery.ResultsOf 308 patients undergoing CD from October 2019 to September 2020, 196 were enrolled in the pre-ERAC cohort and 112 in the post-ERAC cohort. Patients in the post-ERAC cohort were less likely to require opioids in the postoperative period compared to the pre-ERAC cohort (35.7% vs. 18.4%, p<0.001). In addition, there was a significant reduction in the MME per stay in this cohort [16.8 MME (11.2-33.9) vs. 30 MME (20-49), p<0.001]. In the post-ERAC cohort, there was also a reduction in the number of patients who required prescribed opioids at the time of discharge (86.6 vs. 98%, p<0.001) as well as in the amount of MMEs prescribed [150 MME (112-150) vs. 150 MME (150-225), p<0.001; different shape of distribution]. Patients in the post-ERAC cohort had lower delta pain scores [2.2 (1.3-3.7) vs. 3.3 (2.3-4.7), p<0.001].ConclusionOur study has illustrated that our ERAC pathways reduced inpatient and outpatient opioid use as well as patient-reported pain scores while improving indicators of postoperative recovery.
Construction of a bioluminescence-based assay for bitter taste receptors (TAS2Rs)
Authors: Tan Shi Min , Seetoh Wei-Guang 
Published: November 2021

AbstractIn humans, a family of 25 bitter taste receptors (TAS2Rs) mediates bitter taste perception. A common approach to characterize bitter causative agents involves expressing TAS2Rs and the appropriate signal transducers in heterologous cell systems, and monitoring changes in the intracellular free calcium levels upon ligand exposure using a fluorescence-based modality, which typically suffers from a low signal window, and is susceptible to interference by autofluorescence, therefore prohibiting its application to screening of plant or food extracts, which are likely to contain autofluorescent compounds. Here, we report the development and validation of a bioluminescence-based intracellular calcium release assay for TAS2Rs that has a better assay performance than a fluorescence-based assay. Furthermore, the bioluminescence-based assay enables the evaluation of TAS2R agonists within an autofluorescent matrix, highlighting its potential utility in the assessment of the bitterness-inducing properties of plant or food fractions by the food industry. Additionally, improvement to the bioluminescence-based assay for some TAS2Rs was achieved by altering their N-terminal signal sequences, leading to signal window enhancement. Altogether, the bioluminescence-based TAS2R assay can be used to perform functional studies of TAS2Rs, evaluate TAS2R-modulating properties of autofluorescent samples, and facilitate the discovery of compounds that can function as promising bitter taste modulators.
Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography
Authors: Schulz Eike C. , Prester Andreas , von Stetten David , Gore Gargi , Hatton Caitlin E. , Bartels Kim , Leimkohl Jan-Philipp , Schikora Hendrik , Ginn Helen M. , Tellkamp Friedjof , Mehrabi Pedram 
Published: November 2021

AbstractWe present an environmental enclosure for fixed-target serial crystallography, enabling X-ray diffraction experiments in a temperature window from below 10 °C to above 70 °C - a universal parameter of protein function. Via 5D-SSX time-resolved experiments can now be carried out at physiological temperatures, providing fundamentally new insights into protein function. We show temperature-dependent modulation of turnover kinetics for the mesophilicβ-lactamase CTX-M-14 and for the hyperthermophilic enzyme xylose isomerase.