Miracle-dz/UniFAR-FTUs huggingface dataset:
Etanercept treatment in Fanconi anaemia; combined US and Italian experience

therapeutic strategy to target c-Myc. Cell, 146, 904–917. Ferlay, J., Shin, H.R. , Bray, F. , Forman, D. , Mathers, C. & Parkin, D.M. (2010) GLOBOCAN 2008, Cancer Incidence and Mortality Worldwide: IARC CancerBase No. 10 [Internet]. International Agency for Research on Cancer, Lyon, France. International Myeloma Working Group. (2003) Criteria for the classification of monoclonal gammopathies, multiple myeloma and related disorders: a report of the International Myeloma Working Group. British Journal of Haematology, 121, 749–757. Raab, M.S., Podar, K. , Breitkreutz, I. , Richardson, P.G. & Anderson, K.C. (2009) Multiple myeloma. Lancet, 374, 324–339. Richardson, P.G. , Laubach, J., Mitsiades, C.S. , Schlossman, R. , Hideshima, T. , Redman, K. , Chauhan, D. , Ghobrial, I.M. , Munshi, N. & Anderson, K.C. (2011) Managing multiple myeloma: the emerging role of novel therapies and adapting combination treatment for higher risk settings. British Journal of Haematology, 154, 755–762.
Range of cell-wall alterations enhance saccharification in Brachypodium distachyon mutants

Significance Bioethanol produced from waste biomass from crops has the potential to provide a sustainable alternative to petroleum-based transportation fuel that does not compete with human food supply. The main obstacle to this approach is the resistance of this biomass to digestion. Thus, expensive energetic pretreatment and high enzyme inputs are needed to increase digestion. In this study, we screened a population of randomly mutated plants for digestibility with the aim of identifying novel factors that impact on this trait. We found a number of mutants with high digestibility and no impairments in growth or fitness. These mutants show a range of alterations in cell-wall composition, and we have mapped and characterized the mutant with the highest increase in digestibility. Lignocellulosic plant biomass is an attractive feedstock for the production of sustainable biofuels, but the commercialization of such products is hampered by the high costs of processing this material into fermentable sugars (saccharification). One approach to lowering these costs is to produce crops with cell walls that are more susceptible to hydrolysis to reduce preprocessing and enzyme inputs. To deepen our understanding of the molecular genetic basis of lignocellulose recalcitrance, we have screened a mutagenized population of the model grass Brachypodium distachyon for improved saccharification with an industrial polysaccharide-degrading enzyme mixture. From an initial screen of 2,400 M2 plants, we selected 12 lines that showed heritable improvements in saccharification, mostly with no significant reduction in plant size or stem strength. Characterization of these putative mutants revealed a variety of alterations in cell-wall components. We have mapped the underlying genetic lesions responsible for increased saccharification using a deep sequencing approach, and here we report the mapping of one of the causal mutations to a narrow region in chromosome 2. The most likely candidate gene in this region encodes a GT61 glycosyltransferase, which has been implicated in arabinoxylan substitution. Our work shows that forward genetic screening provides a powerful route to identify factors that impact on lignocellulose digestibility, with implications for improving feedstock for cellulosic biofuel production.
Equity theory and fair inequality: A neuroeconomic study

Significance People’s preferences for income distribution fundamentally affect their behavior and contribute to shaping important social and political institutions. The study of such preferences has become a major topic in behavioral research in social psychology and economics. Despite the large literature studying preferences for income distribution, there is no direct neuronal evidence of how the brain responds to income distributions when people have made different contributions in terms of work effort. The present paper reports from, to our knowledge, the first neuroimaging study designed to examine how the brain responds to the distribution of income in such situations. As such, to our knowledge it is also the first study to examine the neuronal basis for equity theory. The present paper reports results from, to our knowledge, the first study designed to examine the neuronal responses to income inequality in situations in which individuals have made different contributions in terms of work effort. We conducted an experiment that included a prescanning phase in which the participants earned money by working, and a neuronal scanning phase in which we examined how the brain responded when the participants evaluated different distributions of their earnings. We provide causal evidence for the relative contribution of work effort being crucial for understanding the hemodynamic response in the brain to inequality. We found a significant hemodynamic response in the striatum to deviations from the distribution of income that was proportional to work effort, but found no effect of deviations from the equal distribution of income. We also observed a striking correlation between the hemodynamic response in the striatum and the self-reported evaluation of the income distributions. Our results provide, to our knowledge, the first set of neuronal evidence for equity theory and suggest that people distinguish between fair and unfair inequalities.
Heterogeneity for IGF-II production maintained by public goods dynamics in neuroendocrine pancreatic cancer

Significance Cancer cells compete for space and nutrients against healthy cells and other cancer cells but also cooperate by secreting growth factors. Clones that do not produce growth factors, however, have a proliferation advantage because they can use the factors produced by neighboring cells without the cost of producing them. Therefore, the cooperative production of growth factors by tumor cells should collapse. What maintains cooperation within the tumor? Here, we use evolutionary game theory to explain how heterogeneity can persist, and we use experiments with pancreatic cancer cells to test the predictions of the theory. Cancer is a process of clonal selection, and studying cancer cell populations using methods and concepts from evolutionary biology can reveal potential evolutionarily stable therapies. The extensive intratumor heterogeneity revealed by sequencing cancer genomes is an essential determinant of tumor progression, diagnosis, and treatment. What maintains heterogeneity remains an open question because competition within a tumor leads to a strong selection for the fittest subclone. Cancer cells also cooperate by sharing molecules with paracrine effects, such as growth factors, and heterogeneity can be maintained if subclones depend on each other for survival. Without strict interdependence between subclones, however, nonproducer cells can free-ride on the growth factors produced by neighboring producer cells, a collective action problem known in game theory as the “tragedy of the commons,” which has been observed in microbial cell populations. Here, we report that similar dynamics occur in cancer cell populations. Neuroendocrine pancreatic cancer (insulinoma) cells that do not produce insulin-like growth factor II (IGF-II) grow slowly in pure cultures but have a proliferation advantage in mixed cultures, where they can use the IGF-II provided by producer cells. We show that, as predicted by evolutionary game theory, producer cells do not go extinct because IGF-II acts as a nonlinear public good, creating negative frequency-dependent selection that leads to a stable coexistence of the two cell types. Intratumor cell heterogeneity can therefore be maintained even without strict interdependence between cell subclones. Reducing the amount of growth factors available within a tumor may lead to a reduction in growth followed by a new equilibrium, which may explain relapse in therapies that target growth factors.
Type IV pili interactions promote intercellular association and moderate swarming of Pseudomonas aeruginosa

Significance The opportunistic pathogen Pseudomonas aeruginosa utilizes both its flagellum and type IV pili (TFP) to facilitate motility, attachment, and colonization. Surface motility such as swarming is thought to precede biofilm formation during infection. We combined laboratory and computational methods to probe the physical interactions of TFP during flagellar-mediated swarming and found that TFP of one cell strongly interact with TFP of other cells, which limits swarming expansion rate. Hence, wild-type P. aeruginosa use cell−cell physical interactions via their TFP to control self-organization within motile swarms. This collective mechanism of cell−cell coordination using TFP allows for moderation of swarming direction of individual cells and avoidance of a toxic environment. Pseudomonas aeruginosa is a ubiquitous bacterium that survives in many environments, including as an acute and chronic pathogen in humans. Substantial evidence shows that P. aeruginosa behavior is affected by its motility, and appendages known as flagella and type IV pili (TFP) are known to confer such motility. The role these appendages play when not facilitating motility or attachment, however, is unclear. Here we discern a passive intercellular role of TFP during flagellar-mediated swarming of P. aeruginosa that does not require TFP extension or retraction. We studied swarming at the cellular level using a combination of laboratory experiments and computational simulations to explain the resultant patterns of cells imaged from in vitro swarms. Namely, we used a computational model to simulate swarming and to probe for individual cell behavior that cannot currently be otherwise measured. Our simulations showed that TFP of swarming P. aeruginosa should be distributed all over the cell and that TFP−TFP interactions between cells should be a dominant mechanism that promotes cell−cell interaction, limits lone cell movement, and slows swarm expansion. This predicted physical mechanism involving TFP was confirmed in vitro using pairwise mixtures of strains with and without TFP where cells without TFP separate from cells with TFP. While TFP slow swarm expansion, we show in vitro that TFP help alter collective motion to avoid toxic compounds such as the antibiotic carbenicillin. Thus, TFP physically affect P. aeruginosa swarming by actively promoting cell−cell association and directional collective motion within motile groups to aid their survival.
Establishment of a gastric epithelial progenitor cell line from a transgenic mouse expressing the simian virus 40 large T antigen gene in the parietal cell lineage

Abstract. Objective: In this study the gastric mucosa of transgenic mice expressing the simian virus 40 large T antigen gene in the parietal cell lineage is used to establish and characterize a new epithelial progenitor cell line. In these mice, proliferation and amplification of preparietal cells preclude their maturation into acid‐secreting parietal cells leading to achlorohydria, hyperplasia, dysplasia and eventually gastric adenocarcinoma. Materials and methods: Enzymatically dispersed gastric epithelial cells were cultured, cloned and screened using immunohistochemical methods, for expression of a variety of biomarkers of differentiated pit, parietal, enteroendocrine and neck/zymogenic cells. Results: A biomarker‐deficient cell line whose ultrastructural features resembled those of mouse gastric epithelial progenitor cells was established. Treatment with either hydrocortisone or oestrogen significantly enhanced proliferation of these cells, whereas retinoic acid inhibited their growth. No change in differentiation was detected with any of these treatments; however, when these cells were injected subcutaneously into nude mice, they proliferated to form tumours and undergo partial differentiation towards parietal cell lineage. Conclusion: This mouse gastric epithelial progenitor cell line could be useful as an in vitro model to study growth properties, proliferation and differentiation of a subpopulation of gastric epithelial progenitor cells and also to study gastric carcinogenesis.
Clonal aspects of plant cell proliferation and their applications to animal cells and bacteria

Abstract. Objectives: Extensive mathematical studies have been made on cell clone development but little has been advanced in the mathematics of small clone formation and virtually no actual data of small clone size has been collected. Materials and methods: Small clone sizes in leaf marginal cells of the aquatic plant Elodea and aleurone spot sizes in the grain of Zea were counted for later statistical analyses of mean, variance and probability distribution frequencies. Results: Simple mathematical models were developed and their calculated results are comparable to data collected on actual plant clones. The parameters in these models were original cell size (s0), growth rate (T), duration of growth (t) and cell division inequality (i). Conclusions: Given T and t, the critical parameter is s0. Plant tissue is ideal material to collect data on clone development because growth rate is uniform across a tissue and cells remain in place, so clone size can be measured, unlike microbes and animal cells that have neither feature. In the light of the results, traditional methods for calculating cell cycle duration and mutation rate are questioned. The applications of these plant features to studies on animal cell populations are discussed.
Interleukin‐6 receptor superantagonist Sant7 inhibits TGF‐β‐induced proliferation of human lung fibroblasts

Abstract. Objectives: Both interleukin‐6 (IL‐6) and transforming growth factor‐β (TGF‐β) are crucially involved in fibrotic events that characterize interstitial lung diseases (ILD). Therefore, the aim of this study was to investigate in primary cultures of normal and fibrotic human lung fibroblasts (HLF), exposed to either IL‐6 or TGF‐β1, the effects on phosphorylation of mitogen‐activated protein kinases (MAPK) and cell growth of IL‐6 signalling inhibition, performed by the IL‐6 receptor superantagonist Sant7.Materials and methods: MAPK phosphorylation was detected by Western blotting, HLF viability and proliferation were evaluated using the trypan blue staining and the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay, respectively. Results: Sant7, at a concentration of 1 µg/mL, was capable of significantly inhibiting HLF proliferation and MAPK phosphorylation induced by cell exposure to IL‐6 (100 ng/mL) or TGF‐β1 (10 ng/mL), whose actions were more evident in fibrotic cells. Conclusions: These findings suggest that, in HLFs derived from patients with ILDs, the proliferative mechanisms activated by TGF‐β1 are at least in part mediated by an increased release of IL‐6, leading to phosphorylation‐dependent MAPK activation. Such preliminary findings may thus open new therapeutic perspectives for fibrogenic ILDs, based on inhibition of signal transduction pathways stimulated by the IL‐6 receptor.
Selection of the lamprey VLRC antigen receptor repertoire

Significance The alternative adaptive immune system of jawless vertebrates is based on three types of variable lymphocyte receptors (VLRs) that are differentially expressed by distinct B- and T-like lymphocyte lineages. Like the antibodies and T-cell receptors of jawed vertebrates, the highly variable VLR antigen receptors are generated by combinatorial assembly. However, it is not known whether VLRs are subjected to selection to mitigate the detrimental effects of self-reactivity. Here, we identify signatures for selection of the VLRC receptors that are expressed by one of the T-cell lineages of lamprey; selection concerns the length of the receptor molecules and their N-terminal sequence diversity. These findings pave the way to identifying the mechanistic basis of selection. The alternative adaptive immune system of jawless vertebrates is based on different isotypes of variable lymphocyte receptors (VLRs) that are composed of leucine-rich repeats (LRRs) and expressed by distinct B- and T-like lymphocyte lineages. VLRB is expressed by B-like cells, whereas VLRA and VLRC are expressed by two T-like lineages that develop in the thymoid, a thymus-like structure in lamprey larvae. In each case, stepwise combinatorial insertions of different types of short donor LRR cassettes into incomplete germ-line genes are required to generate functional VLR gene assemblies. It is unknown, however, whether the diverse repertoires of VLRs that are expressed by peripheral blood lymphocytes are shaped by selection after their assembly. Here, we identify signatures of selection in the peripheral repertoire of VLRC antigen receptors that are clonally expressed by one of the T-like cell types in lampreys. Selection strongly favors VLRC molecules containing four internal variable leucine-rich repeat (LRRV) modules, although VLRC assemblies encoding five internal modules are initially equally frequent. In addition to the length selection, VLRC molecules in VLRC+ peripheral lymphocytes exhibit a distinct pattern of high entropy sites in the N-terminal LRR1 module, which is inserted next to the germ-line–encoded LRRNT module. This is evident in comparisons to VLRC gene assemblies found in the thymoid and to VLRC gene assemblies found in some VLRA+ cells. Our findings are the first indication to our knowledge that selection operates on a VLR repertoire and provide a framework to establish the mechanism by which this selection occurs during development of the VLRC+ lymphocyte lineage.
Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation

Significance Na+/Ca2+ exchangers (NCXs) have a key role in the homeostasis of cellular Ca2+ and consequently are implicated in diverse human-health disorders, including neurodegenerative and cardiovascular diseases. A detailed understanding of the molecular mechanisms of these membrane proteins is therefore of interest from fundamental and biomedical standpoints. Here, we establish the structural mechanism of Na+ recognition in a prokaryotic NCX homolog, using atomistic molecular-dynamics simulations based on recently reported crystallographic data, as well as experimental transport assays of wild-type and mutagenized exchangers. The results have general implications pertaining to the ion exchange stoichiometry and electrogenicity of the Na+/Ca2+ transport cycle across the NCX family, and provide the basis for future investigations of the conformational mechanism of these important transporters. Na+/Ca2+ exchangers (NCXs) are ubiquitous membrane transporters with a key role in Ca2+ homeostasis and signaling. NCXs mediate the bidirectional translocation of either Na+ or Ca2+, and thus can catalyze uphill Ca2+ transport driven by a Na+ gradient, or vice versa. In a major breakthrough, a prokaryotic NCX homolog (NCX_Mj) was recently isolated and its crystal structure determined at atomic resolution. The structure revealed an intriguing architecture consisting of two inverted-topology repeats, each comprising five transmembrane helices. These repeats adopt asymmetric conformations, yielding an outward-facing occluded state. The crystal structure also revealed four putative ion-binding sites, but the occupancy and specificity thereof could not be conclusively established. Here, we use molecular-dynamics simulations and free-energy calculations to identify the ion configuration that best corresponds to the crystallographic data and that is also thermodynamically optimal. In this most probable configuration, three Na+ ions occupy the so-called Sext, SCa, and Sint sites, whereas the Smid site is occupied by one water molecule and one H+, which protonates an adjacent aspartate side chain (D240). Experimental measurements of Na+/Ca2+ and Ca2+/Ca2+ exchange by wild-type and mutagenized NCX_Mj confirm that transport of both Na+ and Ca2+ requires protonation of D240, and that this side chain does not coordinate either ion at Smid. These results imply that the ion exchange stoichiometry of NCX_Mj is 3:1 and that translocation of Na+ across the membrane is electrogenic, whereas transport of Ca2+ is not. Altogether, these findings provide the basis for further experimental and computational studies of the conformational mechanism of this exchanger.
Melanoma brain metastasis is independent of lactate dehydrogenase A expression.

BACKGROUND The key metabolic enzyme lactate dehydrogenase A (LDHA) is overexpressed in many cancers, and several preclinical studies have shown encouraging results of targeted inhibition. However, the mechanistic importance of LDHA in melanoma is largely unknown and hitherto unexplored in brain metastasis. METHODS We investigated the spatial, temporal, and functional features of LDHA expression in melanoma brain metastasis across multiple in vitro assays, in a robust and predictive animal model employing MRI and PET imaging, and in a unique cohort of 80 operated patients. We further assessed the genomic and proteomic landscapes of LDHA in different cancers, particularly melanomas. RESULTS LDHA expression was especially strong in early and small brain metastases in vivo and related to intratumoral hypoxia in late and large brain metastases in vivo and in patients. However, LDHA expression in human brain metastases was not associated with the number of tumors, BRAF(V600E) status, or survival. Moreover, LDHA depletion by small hairpin RNA interference did not affect cell proliferation or 3D tumorsphere growth in vitro or brain metastasis formation or survival in vivo. Integrated analyses of the genomic and proteomic landscapes of LDHA indicated that LDHA is present but not imperative for tumor progression within the CNS, or predictive of survival in melanoma patients. CONCLUSIONS In a large patient cohort and in a robust animal model, we show that although LDHA expression varies biphasically during melanoma brain metastasis formation, tumor progression and survival seem to be functionally independent of LDHA.