Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies

Significance The identification and subsequent grafting of a unique peptide binding site within the Fab domain offers a unique means of adding functionality to monoclonal antibodies through a noncovalent interaction including improved pretargeted imaging, alternative payload delivery, and cross-linking of mAbs on cell surfaces to enhance their therapeutic potential. Capitalizing on their extraordinary specificity, monoclonal antibodies (mAbs) have become one of the most reengineered classes of biological molecules. A major goal in many of these engineering efforts is to add new functionality to the parental mAb, including the addition of cytotoxins and imaging agents for medical applications. Herein, we present a unique peptide-binding site within the central cavity of the fragment antigen binding framework region of the chimeric, anti-epidermal growth factor receptor mAb cetuximab. We demonstrate through diffraction methods, biophysical studies, and sequence analysis that this peptide, a meditope, has moderate affinity for the Fab, is specific to cetuximab (i.e., does not bind to human IgGs), and has no significant effect on antigen binding. We further demonstrate by diffraction studies and biophysical methods that the meditope binding site can be grafted onto the anti-human epidermal growth factor receptor 2 mAb trastuzumab, and that the antigen binding affinity of the grafted trastuzumab is indistinguishable from the parental mAb. Finally, we demonstrate a bivalent meditope variant binds specifically and stably to antigen-bearing cells only in the presence of the meditope-enabled mAbs. Collectively, this finding and the subsequent characterization and engineering efforts indicate that this unique interface could serve as a noncovalent “linker” for any meditope-enabled mAb with applications in multiple mAb-based technologies including diagnostics, imaging, and therapeutic delivery.
Blockade of A2A receptors potently suppresses the metastasis of CD73+ tumors

CD73 inhibits antitumor immunity through the activation of adenosine receptors expressed on multiple immune subsets. CD73 also enhances tumor metastasis, although the nature of the immune subsets and adenosine receptor subtypes involved in this process are largely unknown. In this study, we revealed that A2A/A2B receptor antagonists were effective in reducing the metastasis of tumors expressing CD73 endogenously (4T1.2 breast tumors) and when CD73 was ectopically expressed (B16F10 melanoma). A2A−/− mice were strongly protected against tumor metastasis, indicating that host A2A receptors enhanced tumor metastasis. A2A blockade enhanced natural killer (NK) cell maturation and cytotoxic function in vitro, reduced metastasis in a perforin-dependent manner, and enhanced NK cell expression of granzyme B in vivo, strongly suggesting that the antimetastatic effect of A2A blockade was due to enhanced NK cell function. Interestingly, A2B blockade had no effect on NK cell cytotoxicity, indicating that an NK cell-independent mechanism also contributed to the increased metastasis of CD73+ tumors. Our results thus revealed that CD73 promotes tumor metastasis through multiple mechanisms, including suppression of NK cell function. Furthermore, our data strongly suggest that A2A or A2B antagonists may be useful for the treatment of metastatic disease. Overall, our study has potential therapeutic implications given that A2A/A2B receptor antagonists have already entered clinical trials in other therapeutic settings.
Auxetic Perforated Mechanical Metamaterials with Randomly Oriented Cuts

Perforated systems with quasi-disordered arrays of slits are found to exhibit auxetic characteristics almost as much as their traditional ordered "rotating-squares" counterparts. This provides a highly robust methodology for constructing auxetics that may be used for various practical applications such as skin grafting, where a high degree of precision may not always be achievable.
Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

Laccases, as early as 1959, were proposed to catalyze the oxidative polymerization of monolignols. Genetic evidence in support of this hypothesis has been elusive due to functional redundancy of laccase genes. An Arabidopsis double mutant demonstrated the involvement of laccases in lignin biosynthesis. We previously identified a subset of laccase genes to be targets of a microRNA (miRNA) ptr-miR397a in Populus trichocarpa. To elucidate the roles of ptr-miR397a and its targets, we characterized the laccase gene family and identified 49 laccase gene models, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed Ptr-MIR397a in transgenic P. trichocarpa. In each of all nine transgenic lines tested, 17 PtrLACs were down-regulated as analyzed by RNA-seq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an ∼40% decrease in the total laccase activity. Overexpression of Ptr-MIR397a in these transgenic lines also reduced lignin content, whereas levels of all monolignol biosynthetic gene transcripts remained unchanged. A hierarchical genetic regulatory network (GRN) built by a bottom-up graphic Gaussian model algorithm provides additional support for a role of ptr-miR397a as a negative regulator of laccases for lignin biosynthesis. Full transcriptome–based differential gene expression in the overexpressed transgenics and protein domain analyses implicate previously unidentified transcription factors and their targets in an extended hierarchical GRN including ptr-miR397a and laccases that coregulate lignin biosynthesis in wood formation. Ptr-miR397a, laccases, and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content.
Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain

P-glycoprotein (P-gp) is one of the best-known mediators of drug efflux-based multidrug resistance in many cancers. This validated therapeutic target is a prototypic, plasma membrane resident ATP-Binding Cassette transporter that pumps xenobiotic compounds out of cells. The large, polyspecific drug-binding pocket of P-gp recognizes a variety of structurally unrelated compounds. The transport of these drugs across the membrane is coincident with changes in the size and shape of this pocket during the course of the transport cycle. Here, we present the crystal structures of three inward-facing conformations of mouse P-gp derived from two different crystal forms. One structure has a nanobody bound to the C-terminal side of the first nucleotide-binding domain. This nanobody strongly inhibits the ATP hydrolysis activity of mouse P-gp by hindering the formation of a dimeric complex between the ATP-binding domains, which is essential for nucleotide hydrolysis. Together, these inward-facing conformational snapshots of P-gp demonstrate a range of flexibility exhibited by this transporter, which is likely an essential feature for the binding and transport of large, diverse substrates. The nanobody-bound structure also reveals a unique epitope on P-gp.
Iodine Migration and its Effect on Hysteresis in Perovskite Solar Cells

The migration and accumulation of iodide ions create a modulation of the respective interfacial barriers causing the hysteresis in solar cells based on methylammonium lead iodide perovskites. Iodide ions are identified as the migrating species by measuring temperature dependent current-transients and photoelectron spectroscopy. The involved changes in the built-in potential due to ion migration are directly measured by electroabsorption spectroscopy.
Translational profiling of cardiomyocytes identifies an early Jak1/Stat3 injury response required for zebrafish heart regeneration

Certain lower vertebrates like zebrafish activate proliferation of spared cardiomyocytes after cardiac injury to regenerate lost heart muscle. Here, we used translating ribosome affinity purification to profile translating RNAs in zebrafish cardiomyocytes during heart regeneration. We identified dynamic induction of several Jak1/Stat3 pathway members following trauma, events accompanied by cytokine production. Transgenic Stat3 inhibition in cardiomyocytes restricted injury-induced proliferation and regeneration, but did not reduce cardiogenesis during animal growth. The secreted protein Rln3a was induced in a Stat3-dependent manner by injury, and exogenous Rln3 delivery during Stat3 inhibition stimulated cardiomyocyte proliferation. Our results identify an injury-specific cardiomyocyte program essential for heart regeneration.
Predictors of successful ageing: findings from the longitudinal follow-up of the Lothian Birth Cohort 1921

The progressive ageing of the world's population implies that any age-associated deterioration will become ever more prevalent. Some individuals can be identified as ageing more 'successfully' than their peers; the maintenance ofmental abilities in old age is one marker of this. Isolating modifiable determinants of cognitive ageing is therefore a research priority. Factors from the domains ofwork, social support networks and activity participation were examined in an ageing group retrospectively and contemporaneously. Aged 11, these individuals had taken a test ofmental ability (the Moray House Test: MHT) as part of the 1932 Scottish Mental Survey. Some 550 survivors were recruited -79 years old into a longitudinal study of cognitive ageingthe Lothian Birth Cohort 1921-when they again took the MHT, plus a battery of tests (Raven's Progressive Matrices, Verbal Fluency and Logical Memory). A 2nd wave of testing was completed at -83 years old. Over the 4 years of follow-up, significant decline was observed in cognitive ability (composite of the 3 tests) and separately for Raven's and Verbal Fluency, but not for Logical Memory. In regression analyses, higher cognitive ability at age 79 assessed by the MHT (expressed as age-79 IQ) was predicted by less hazardous working conditions, a quieter working environment and receiving more supervisor support; living with a spouse/partner for a fewer number of years in young adulthood and having fewer close friends/relatives in old age; and increased activity in midlife and old age. Each factor explained about 1% to 3% of the variance, independent of age-11 IQ and sex. Less cognitive decline from 79 to 83 years old (on the general ability composite) was associated with increased support from coworkers and walking (versus not) at age 80, each accounting for about 2% of the variance (independent of age-11 IQ and sex). When the analyses were pooled across lifestyle domains and further potential confounders (including education, social class, depression and disease history) were controlled, measures of the hazards encountered at work and lifetime activity participation each accounted for 1% to 3% of the variance in age-79 IQ, whilst walking accounted for about 2% of the variance in later life cognitive change. Inactivity in midlife and a lack of exercise in old age are plausible risk factors for cognitive decline. They are, fortunately, potentially malleable; promoting activity may offer pathways to improved cognitive ageing.
Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules

Significance Some bacteria have evolved resistance to nearly every known class of antibiotic, creating an urgent need for new ones that work by different mechanisms. However, there has been no simple way to determine how new antibiotics work. We have developed a unique method that provides a shortcut for understanding how antibiotics kill bacteria. This method can be used to sift through compounds to rapidly identify and characterize antibiotics that work against multidrug-resistant pathogens. Identifying the mechanism of action for antibacterial compounds is essential for understanding how bacteria interact with one another and with other cell types and for antibiotic discovery efforts, but determining a compound's mechanism of action remains a serious challenge that limits both basic research and antibacterial discovery programs. Here, we show that bacterial cytological profiling (BCP) is a rapid and powerful approach for identifying the cellular pathway affected by antibacterial molecules. BCP can distinguish between inhibitors that affect different cellular pathways as well as different targets within the same pathway. We use BCP to demonstrate that spirohexenolide A, a spirotetronate that is active against methicillin-resistant Staphylococcus aureus, rapidly collapses the proton motive force. BCP offers a simple, one-step assay that can be broadly applied, solving the longstanding problem of how to rapidly determine the cellular target of thousands of compounds.
The HMG‐CoA inhibitor, simvastatin, triggers in vitro anti‐tumour effect and decreases IgM secretion in Waldenstrom macroglobulinaemia

Waldenstrom macroglobulinaemia (WM) is an incurable lymphoplasmacytic lymphoma with secretion of serum monoclonal immunoglobulin M (IgM). We previously showed that patients receiving cholesterol‐lowering statins, had the lowest IgM value in a large cohort of patients with WM. Simvastatin, a 3‐hydroxy‐3‐methyl‐glutaryl‐CoA reductase inhibitor, induced inhibition of proliferation, cytotoxic effect and apoptosis in IgM secreting cell lines as well as in primary CD19+ WM cells. Interestingly, those effects were reversed by addition of mevalonate and geranylgeranylpyrophosphate, demonstrating that simvastatin inhibited cell growth, survival and IgM secretion on BCWM.1 WM cells by inhibition of geranylgeranylated proteins. Furthermore, simvastatin overcame tumour cell growth induced by co‐culture of WM cells with bone‐marrow stromal cells. Simvastatin also decreased IgM secretion by BCWM.1 cells at an early time‐point that had not affected cell survival. Simvastatin‐induced cytotoxicity was preceded by a decrease in Akt (protein kinase B, PKB) and extracellular signal‐regulated kinase (ERK) mitogen‐activated protein kinase (MAPK) pathways at 18 h. In addition, simvastatin induced an increase in stress‐activated protein kinase/c‐Jun N‐terminal kinase (SAPK/JNK) MAPK followed by caspase‐8, ‐9, ‐3 and poly(ADP‐ribose) polymerase (PARP) cleavages at 18 h, leading to apoptosis. Furthermore, simvastatin enhanced the cytotoxicity induced by bortezomib, fludarabine and dexamethasone. Our studies therefore support our earlier observation of statin‐mediated anti‐WM activity and provide the framework for future clinical trials testing simvastatin in WM.
Spontaneous slow replication fork progression elicits mitosis alterations in homologous recombination-deficient mammalian cells

Significance Faithful genome duplication requires the precise coordination of DNA replication, repair/recombination and chromosome segregation. Homologous recombination (HR) plays a pivotal role in the resumption of blocked replication forks, and HR− cells exhibit both spontaneous slower genome-wide replication fork speed and mitotic extra centrosomes (MECs). We show that MECs result from slow replication kinetics and that MECs are associated with multipolar mitosis leading to general unbalanced chromosome segregation. Thus, low levels of replication stress, which are not detected by cell surveillance, allow cells to progress through the cell cycle, resulting in aberrant mitosis and chromosome instability. These data underline the essential role of HR facing endogenous stress at the interface between replication and mitosis for protection against spontaneous general chromosome instability. Homologous recombination deficient (HR−) mammalian cells spontaneously display reduced replication fork (RF) movement and mitotic extra centrosomes. We show here that these cells present a complex mitotic phenotype, including prolonged metaphase arrest, anaphase bridges, and multipolar segregations. We then asked whether the replication and the mitotic phenotypes are interdependent. First, we determined low doses of hydroxyurea that did not affect the cell cycle distribution or activate CHK1 phosphorylation but did slow the replication fork movement of wild-type cells to the same level than in HR− cells. Remarkably, these low hydroxyurea doses generated the same mitotic defects (and to the same extent) in wild-type cells as observed in unchallenged HR− cells. Reciprocally, supplying nucleotide precursors to HR− cells suppressed both their replication deceleration and mitotic extra centrosome phenotypes. Therefore, subtle replication stress that escapes to surveillance pathways and, thus, fails to prevent cells from entering mitosis alters metaphase progression and centrosome number, resulting in multipolar mitosis. Importantly, multipolar mitosis results in global unbalanced chromosome segregation involving the whole genome, even fully replicated chromosomes. These data highlight the cross-talk between chromosome replication and segregation, and the importance of HR at the interface of these two processes for protection against general genome instability.
Self‐Healing, Fully Functional, and Multiparametric Flexible Sensing Platform

A non-biological and flexible self-healing platform has tailored sensitivity toward one or a combination of pressure, strain, gas analytes, and temperature. For demonstration, a complete self-healing device is described in the form of a bendable and stretchable chemiresistor, where every part is self-healing.
Bioluminescent imaging of drug efflux at the blood–brain barrier mediated by the transporter ABCG2

Significance The blood–brain barrier (BBB) prevents ingress of small molecules into the brain partly by expression of drug efflux transporters. Although several transporters are known to be involved, the role ABCG2 plays in this process is not clear. We demonstrate the ability to image ABCG2 function at the BBB by using luciferin in a luciferase-expressing mouse. This represents a direct measurement of ABCG2 function at the BBB, and demonstrates that ABCG2 does play a functional role at the BBB. ATP-binding cassette (ABC) transporters are a group of transmembrane proteins that maintain chemical homeostasis through efflux of compounds out of organelles and cells. Among other functions, ABC transporters play a key role in protecting the brain parenchyma by efflux of xenobiotics from capillary endothelial cells at the blood–brain barrier (BBB). They also prevent the entry of therapeutic drugs at the BBB, thereby limiting their efficacy. One of the key transporters playing this role is ABCG2. Although other ABC transporters can be studied through various imaging modalities, no specific probe exists for imaging ABCG2 function in vivo. Here we show that d-luciferin, the endogenous substrate of firefly luciferase, is a specific substrate for ABCG2. We hypothesized that ABCG2 function at the BBB could be evaluated by using bioluminescence imaging in transgenic mice expressing firefly luciferase in the brain. Bioluminescence signal in the brain of mice increased with coadministration of the ABCG2 inhibitors Ko143, gefitinib, and nilotinib, but not an ABCB1 inhibitor. This method for imaging ABCG2 function at the BBB will facilitate understanding of the function and pharmacokinetic inhibition of this transporter.
The Inter-Sectoral Impact Model Intercomparison Project (ISI–MIP): Project framework

The Inter-Sectoral Impact Model Intercomparison Project offers a framework to compare climate impact projections in different sectors and at different scales. Consistent climate and socio-economic input data provide the basis for a cross-sectoral integration of impact projections. The project is designed to enable quantitative synthesis of climate change impacts at different levels of global warming. This report briefly outlines the objectives and framework of the first, fast-tracked phase of Inter-Sectoral Impact Model Intercomparison Project, based on global impact models, and provides an overview of the participating models, input data, and scenario set-up.
Improvements in Diagnostic Accuracy with Quantitative Dynamic Contrast-Enhanced MRI

Abstract : Scanning of patients with a research acquisition protocol and calibration phantoms has continued. We identified the major sources of variability and error in our quantitative analysis. B1, or transmit field, inhomogeneity is a large source of error in the estimation of concentration of contrast media. To account for this we have developed a method using fat as a reference signal to correct for spatial variations in the B1 field. Further analysis of patients scanned repeatedly at 1.5T and 3T had identified that parameters related to the shape of the signal enhancement versus time curves during DCEMRI of lesions show relatively low variability. Analysis of all the cases acquired to date with the refined methods is underway.
A dynamically assembled cell wall synthesis machinery buffers cell growth

Significance For complex biological processes, the formation of protein complexes is a strategy for coordinating the activities of many enzymes in space and time. It has been hypothesized that growth of the bacterial cell wall involves stable synthetic complexes, but neither the existence of such complexes nor the consequences of such a mechanism for growth efficiency have been demonstrated. Here, we use single-molecule tracking to demonstrate that the association between an essential cell wall synthesis enzyme and the cytoskeleton is highly dynamic, which allows the cell to buffer growth rate against large fluctuations in enzyme abundance. This indicates that dynamic association can be an efficient strategy for coordination of multiple enzymes, especially those for which excess abundance can be harmful to cells. Assembly of protein complexes is a key mechanism for achieving spatial and temporal coordination in processes involving many enzymes. Growth of rod-shaped bacteria is a well-studied example requiring such coordination; expansion of the cell wall is thought to involve coordination of the activity of synthetic enzymes with the cytoskeleton via a stable complex. Here, we use single-molecule tracking to demonstrate that the bacterial actin homolog MreB and the essential cell wall enzyme PBP2 move on timescales orders of magnitude apart, with drastically different characteristic motions. Our observations suggest that PBP2 interacts with the rest of the synthesis machinery through a dynamic cycle of transient association. Consistent with this model, growth is robust to large fluctuations in PBP2 abundance. In contrast to stable complex formation, dynamic association of PBP2 is less dependent on the function of other components of the synthesis machinery, and buffers spatially distributed growth against fluctuations in pathway component concentrations and the presence of defective components. Dynamic association could generally represent an efficient strategy for spatiotemporal coordination of protein activities, especially when excess concentrations of system components are inhibitory to the overall process or deleterious to the cell.