Miracle-dz/UniFAR-FTUs huggingface dataset:
Insulin secretion is highly sensitive to desorption of plasma membrane cholesterol

Cholesterol‐rich clusters of SNARE (soluble NSF attachment protein receptor) proteins have been implicated as being important for exocytosis. Here we demonstrate the significance of cholesterol for normal biphasic insulin secretion in mouse β cells by removal of cholesterol from the plasma membrane using methyl‐β‐cyclodextrin (MBCD). Maximal inhibition of insulin secretion in static incubations was achieved using 0.1 mM MBCD. In in situ pancreatic perfusion measurements, both first and second phase insulin secretions were reduced by ~50% (P<0.05). This was accompanied by a reduced number of docked large dense core vesicles (LDCVs) (~40%;P<0.01) and a reduced exocytotic response (>50%; P<0.01). Fur‐ther, subcellular fractionations demonstrated move‐ment of the synaptosomal protein of 25 kDa (SNAP‐25) from the plasma membrane to the cytosol after MBCD treatment. The inhibitory actions of MBCD were coun‐teracted by subsequent addition of cholesterol. We hypothesize that desorption of cholesterol leads to the disturbance of a basic exocytotic mechanism partly due to migration of SNAP‐25, and we conclude that insulin secretion is highly sensitive to changes in plasma mem‐brane cholesterol. —Vikman, J., Jimenez‐Feltstrom, J., Nyman, P., Thelin, J., Eliasson, L. Insulin secretion is highly sensitive to desorption of plasma membrane cholesterol. FASEBJ. 23, 58‐67 (2009)
Enhanced activation of a “nutrient‐sensing” pathway with age contributes to insulin resistance

Calorie restriction improves life span whereas nutrient excess leads to obesity and unfavorable metabolic consequences, supporting the role for a cellular “nutrient sensor” in aging. Hexosamine biosyn‐thetic pathway (HBP) is a candidate nutrient‐sensing pathway. We hypothesized that altered nutrient sensing (by HBP) with age may provide a link among aging, nutrient flux, and insulin resistance. Using a hyperinsulinemic clamp in young rats, we show that experimental activation of HBP, through the systemic infusion of glucosamine, induced severe insulin resistance (36% decline in peripheral insulin action; P<0.05), increased adipose tissue gene expression of fat‐derived peptides (PAI‐1 by 4‐fold, angiotensinogen 3‐fold, leptin 2‐fold, resistin 4‐fold, and adiponectin 4‐fold; P<0.01 compared with young saline‐infused), and enhanced glycosylation of transcription factors, thus mimicking a physiological and biological phenotype of aging. We further demonstrate a greater activation of nutrient‐sensing HBP with age in both old ad libitum‐fed and calorie‐restricted rats. Interestingly, old calorie‐restricted animals rapidly develop insulin resistance when exposed to glucosamine, despite their “young” phenotype. These results suggest that altered nutrient sensing by HBP with age may be the link among nutrients, insulin resistance, and age‐related diabetes. —Einstein, F. H. , Fishman, S. , Bauman, J., Thompson, R. F. , Huffman, D. M. , Atzmon, G. , Barzilai, N. , Muzumdar, R. H. Enhanced activation of a “nutrient‐sensing” pathway with age contributes to insulin resistance. FASEB J. 22, 3450–3457 (2008)
Effects of erythropoietin in skin wound healing are dose related

The hematopoietic growth factor erythropoietin (EPO) attracts attention due to its all‐tissue‐protective pleiotropic properties. We studied the effect of EPO on dermal regeneration using intravital microscopy in a model of full dermal thickness wounds in the skin‐fold chamber of hairless mice. Animals received repetitive low doses or high doses of EPO (RLD‐EPO or RHD‐EPO) or a single high dose of EPO (SHD‐EPO). SHD‐EPO accelerated wound epithelialization, reduced wound cellularity, and induced maturation of newly formed microvascular networks. In contrast, RHD‐EPO impaired the healing process, as indicated by delayed epithelialization, high wound cellularity, and lack of maturation of microvascular networks. Also, RHD‐EPO caused an excessive erythrocyte mass and rheological malfunction, further deteriorating vessel and tissue maturation. Moreover, RHD‐EPO altered fibroblast and keratinocyte migration in vitro, while both cell types exposed to RLD‐EPO, and, in particular, to SHD‐EPO showed accelerated wound scratch closure. In summary, our data show that a single application of a high dose of EPO accelerates and improves skin wound healing. —Sorg, H. , Krueger, C. , Schulz, T. , Menger, M. D. , Schmitz, F. , Vollmar, B. Effects of erythropoietin in skin wound healing are dose related. FASEBJ. 23, 3049–3058 (2009). www.fasebj. org
CD4+CD25+FoxP3+PD1— regulatory T cells in acute and stable relapsing‐remitting multiple sclerosis and their modulation by therapy

The intracellular expression of the programmed death receptor 1 (PD1) identifies a subset of naive Treg cells with enhanced suppressive ability;anti‐gen stimulation results in the surface expression of PD1. Because the role of Treg impairments in multiple sclerosis (MS) is still contradictory, we analyzed naive PD1— and PD1+ Treg cells in peripheral blood and cerebrospinal fluid (CSF) of relapsing‐remitting multiple sclerosis (RR‐MS) patients and of healthy control subjects. Results showed that 1) CSF PD1— Treg cells were significantly augmented in MS patients;2) PD1 — Treg cells were significantly increased in the peripheral blood of patients with stable disease (SMS) compared to those with acute (AMS) disease, and in patients responding to glatiramer acetate (COPA) compared to AMS‐ and COPA‐unresponsive patients;and 3) PD1 + Treg cells were similar in CSF and peripheral blood of all groups analyzed. PD1 — Treg cells were not increased in the peripheral blood of interferon‐β (IFNβ) ‐responsive patients, but the suppressive ability of Treg cells was significantly higher in SMS and in COPA‐ or IFNβ‐responsive compared to AMS‐ and COPA‐unresponsive individuals. The data herein suggest that PD1 — Treg cells play a pivotal role in MS and offer a biological explanation for disease relapse and for the mechanism associated with response to COPA and IFNβ. —Saresella, M. , Marventano, I. , Longhi, R. , Lissoni, F. , Trabattoni, D. , Mendozzi, L. , Caputo, D. , Clerici, M. CD4+CD25+FoxP3+PD1 – regulatory T cells in acute and stable relapsing‐remitting multiple sclerosis and their modulation by therapy. FASEB J. 22, 3500–3508 (2008)
Structure of the Z Ring-associated Protein, ZapD, Bound to the C-terminal Domain of the Tubulin-like Protein, FtsZ, Suggests Mechanism of Z Ring Stabilization through FtsZ Cross-linking*

Cell division in most bacteria is mediated by the tubulin-like FtsZ protein, which polymerizes in a GTP-dependent manner to form the cytokinetic Z ring. A diverse repertoire of FtsZ-binding proteins affects FtsZ localization and polymerization to ensure correct Z ring formation. Many of these proteins bind the C-terminal domain (CTD) of FtsZ, which serves as a hub for FtsZ regulation. FtsZ ring-associated proteins, ZapA–D (Zaps), are important FtsZ regulatory proteins that stabilize FtsZ assembly and enhance Z ring formation by increasing lateral assembly of FtsZ protofilaments, which then form the Z ring. There are no structures of a Zap protein bound to FtsZ; therefore, how these proteins affect FtsZ polymerization has been unclear. Recent data showed ZapD binds specifically to the FtsZ CTD. Thus, to obtain insight into the ZapD-CTD interaction and how it may mediate FtsZ protofilament assembly, we determined the Escherichia coli ZapD-FtsZ CTD structure to 2.67 Å resolution. The structure shows that the CTD docks within a hydrophobic cleft in the ZapD helical domain and adopts an unusual structure composed of two turns of helix separated by a proline kink. FtsZ CTD residue Phe-377 inserts into the ZapD pocket, anchoring the CTD in place and permitting hydrophobic contacts between FtsZ residues Ile-374, Pro-375, and Leu-378 with ZapD residues Leu-74, Trp-77, Leu-91, and Leu-174. The structural findings were supported by mutagenesis coupled with biochemical and in vivo studies. The combined data suggest that ZapD acts as a molecular cross-linking reagent between FtsZ protofilaments to enhance FtsZ assembly.
Identification and characterization of CTRP9, a novel secreted glycoprotein, from adipose tissue that reduces serum glucose in mice and forms heterotrimers with adiponectin

Adiponectin is a major insulin‐sensitizing, multimeric hormone derived from adipose tissue that acts on muscle and liver to regulate whole‐body glucose and lipid metabolism. Here, we describe a novel and highly conserved paralog of adiponectin designated as Clq/TNF‐related protein (CTRP) 9. Of all the CTRP paralogs, CTRP9 shows the highest degree of amino acid identity to adiponectin in its globular C1q domain. CTRP9 is expressed predominantly in adipose tissue and females expresses higher levels of the transcript than males. Moreover, its expression levels in ob/ob mice changed in an age‐dependent manner, with significant up‐regulation in younger mice. CTRP9 is a secreted glycoprotein with multiple post‐translational modifications in its collagen domain that include hydroxylated prolines and hydroxylated and glycosylated lysines. It is se‐creted as multimers (predominantly trimers) from transfected cells and circulates in the mouse serum with levels varying according to sex and metabolic state of mice. Furthermore, CTRP9 and adiponectin can be secreted as heterooligomers when cotrans‐fected into mammalian cells, and in vivo, adiponectin/ CTRP9 complexes can be reciprocally coimmuno‐precipitated from the serum of adiponectin and CTRP9 transgenic mice. Biochemical analysis demonstrates that adiponectin and CTRP9 associate via their globular C1q domain, and this interaction does not require their conserved N‐terminal cysteines or their collagen domains. Furthermore, we show that adiponectin and CTRP9 form heterotrimers. In cultured myotubes, CTRP9 specifically activates AMPK, Akt, and p44/42 MAPK signaling pathways. Adenovirus‐mediated over‐expression of CTRP9 in obese (ob/ob) mice signifi‐cantly lowered serum glucose levels. Collectively, these results suggest that CTRP9 is a novel adipokine, and further study of CTRP9 will yield novel mechanistic insights into its physiological and metabolic function. — Wong, G. W. , Krawczyk, S. A. , Kitidis‐Mitrokostas, C. , Ge, G. , Spooner, E. , Hug, C. , Gimeno, R. , Lodish, H. F. Identification and characterization of CTRP9, a novel secreted glycoprotein from adipose tissue that reduces serum glucose in mice and forms heterotrimers with adiponectin. FASEB J. 23, 241‐258 (2009)
Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly

The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions.
Ceramide activates JNK to inhibit a cAMP‐gated K+ conductance and Cl‐ secretion in intestinal epithelia

Sphingomyelinases (SMases) hydrolyze membrane sphingomyelin to ceramide and are ex‐pressed by diverse host and microbial cell types popu‐lating mucosal surfaces. Exogenous bacterial SMase acts on the basolateral membrane of polarized human intestinal epithelial cells to repress the cAMP‐induced Cl‐ secretory response, but how this occurs is un‐known. We show here that SMase acts by down‐regulating a cAMP‐gated basolateral membrane K+ conduc‐tance. Neither phosphocholine, ceramide‐1‐phosphate, nor sphingosine‐1‐phosphate recapitulates this effect, indicating that ceramide production is the decisive factor. Basolaterally applied SMase induced the phos‐phorylation of c‐Jun NH2‐terminal kinase (JNK), and inhibition of JNK rescued the effect of SMase on cAMP‐dependant secretion. SMase secreted by normal human fibroblasts specifically recapitulated the effect on cAMP‐induced Cl‐ secretion, indicating that cell types inhabiting the subepithelial space can provide such an activity to the basolateral membrane of intesti‐nal enterocytes in trans. Thus, conversion of sphingo‐myelin to ceramide in basolateral membranes of intes‐tinal cells rapidly activates JNK to inhibit a cAMP‐gated K+ conductance and thereby attenuates Cl‐ secretion. These results define a novel lipid‐mediated pathway for regulation of salt and water homeostasis at mucosal surfaces. —Saslowsky, D. E. , Tanaka, N. , Reddy, K. P., Lencer, W. I. Ceramide activates JNK to inhibit a cAMP‐gated K+ conductance and Cl‐ secretion in intestinal epithelia. FASEBJ. 23, 259‐270 (2009)
Monomeric C‐reactive protein activates endothelial cells via interaction with lipid raft microdomains

Emerging evidence indicates that in addition to native pentameric C‐reactive protein (CRP), monomeric CRP (mCRP) also plays an active role in inflammation associated with cardiovascular diseases. mCRP activates endothelial cells, one of the critical events in cardiovascular diseases;however, the underlying molecular mechanisms are incompletely understood. Here we report that association of mCRP with human aortic and coronary artery endothelial cells is predominantly due to membrane insertion rather than binding to the surface proteins FcyRs and proteoglycans. We identify lipid rafts as the preferential membrane microdomains for mCRP anchorage. mCRP binding depends on membrane cholesterol content and is synergistically mediated by the putative cholesterol binding consensus sequence of CRP (aa 35‐47) and the C‐terminal octapeptide (aa 199‐206). Conversely, disrupting lipid rafts with methyl‐β cyclodextrin or nystatin abrogated mCRP‐induced cytokine release, reactive oxygen species generation, and adhesion molecule expression in endothelial cells. Furthermore, ex vivo treatment of rabbit thoracic aorta and carotid artery segments with nystatin prevented mCRP‐inducedIL‐8 release. Our data identify mCRP‐lipid raft interaction as an important mechanism in mediating cellular responses to mCRP and lend further support to the notion of mCRP regulation of endothelial cell function during inflammation. —Ji, S. ‐R. , Ma, L. , Bai, C. ‐J., Shi, J.‐M. , Li, H. ‐Y. , Potempa, L.A. , Filep, J.G. , Zhao, J., Wu, Y. Monomeric C‐reactive protein activates endothelial cells via interaction with lipid raft microdomains. FASEB J. 23, 1806–1816 (2009)
Imitative Follower Deception in Stackelberg Games

Information uncertainty is one of the major challenges facing applications of game theory. In the context of Stackelberg games, various approaches have been proposed to deal with the leader's incomplete knowledge about the follower's payoffs, typically by gathering information from the leader's interaction with the follower. Unfortunately, these approaches rely crucially on the assumption that the follower will not strategically exploit this information asymmetry, i.e., the follower behaves truthfully during the interaction according to their actual payoffs. As we show in this paper, the follower may have strong incentives to deceitfully imitate the behavior of a different follower type and, in doing this, benefit significantly from inducing the leader into choosing a highly suboptimal strategy. This raises a fundamental question: how to design a leader strategy in the presence of a deceitful follower? To answer this question, we put forward a basic model of Stackelberg games with (imitative) follower deception and show that the leader is indeed able to reduce the loss due to follower deception with carefully designed policies. We then provide a systematic study of the problem of computing the optimal leader policy and draw a relatively complete picture of the complexity landscape; essentially matching positive and negative complexity results are provided for natural variants of the model. Our intractability results are in sharp contrast to the situation with no deception, where the leader's optimal strategy can be computed in polynomial time, and thus illustrate the intrinsic difficulty of handling follower deception. Through simulations we also examine the benefit of considering follower deception in randomly generated games.
Hair Segmentation on Time-of-Flight RGBD Images

Robust segmentation of hair from portrait images remains challenging: hair does not conform to a uniform shape, style or even color; dark hair in particular lacks features. We present a novel computational imaging solution that tackles the problem from both input and processing fronts. We explore using Time-of-Flight (ToF) RGBD sensors on recent mobile devices. We first conduct a comprehensive analysis to show that scattering and inter-reflection cause different noise patterns on hair vs. non-hair regions on ToF images, by changing the light path and/or combining multiple paths. We then develop a deep network based approach that employs both ToF depth map and the RGB gradient maps to produce an initial hair segmentation with labeled hair components. We then refine the result by imposing ToF noise prior under the conditional random field. We collect the first ToF RGBD hair dataset with 20k+ head images captured on 30 human subjects with a variety of hairstyles at different view angles. Comprehensive experiments show that our approach outperforms the RGB based techniques in accuracy and robustness and can handle traditionally challenging cases such as dark hair, similar hair/background, similar hair/foreground, etc.
Clinical Investigation : Gastrointestinal Cancer Optimal Timing for Assessment of Tumor Response to Neoadjuvant Chemoradiation in Patients With Rectal Cancer : Do All Patients Benefit From Waiting Longer Than 6 Weeks ?

Optimal Timing for Assessment of Tumor Response to Neoadjuvant Chemoradiation in Patients With Rectal Cancer: Do All Patients Benefit From Waiting Longer Than 6 Weeks? Rodrigo O. Perez, MD, PhD,*,y Angelita Habr-Gama, MD, PhD,y Guilherme P. São Julião, MD,* Joaquim Gama-Rodrigues, MD, PhD,y Afonso H.S. Sousa, Jr, MD,* Fabio Guilherme Campos, MD,* Antonio R. Imperiale, MD,* Patricio B. Lynn, MD,y Igor Proscurshim, MD,y Sergio Carlos Nahas, MD,* Carla Rachel Ono, MD,z,x and Carlos Alberto Buchpiguel, MDz,x
Heme Assimilation in Schizosaccharomyces pombe Requires Cell-surface-anchored Protein Shu1 and Vacuolar Transporter Abc3*

The Schizosaccharomyces pombe shu1+ gene encodes a cell-surface protein required for assimilation of exogenous heme. In this study, shaving experiments showed that Shu1 is released from membrane preparations when spheroplast lysates are incubated with phosphoinositide-specific phospholipase C (PI-PLC). Shu1 cleavability by PI-PLC and its predicted hydropathy profile strongly suggested that Shu1 is a glycosylphosphatidylinositol-anchored protein. When heme biosynthesis is selectively blocked in hem1Δ mutant cells, the heme analog zinc mesoporphyrin IX (ZnMP) first accumulates into vacuoles and then subsequently, within the cytoplasm in a rapid and Shu1-dependent manner. An HA4-tagged shu1+ allele that retained wild-type function localizes to the cell surface in response to low hemin concentrations, but under high hemin concentrations, Shu1-HA4 re-localizes to the vacuolar membrane. Inactivation of abc3+, encoding a vacuolar membrane transporter, results in hem1Δ abc3Δ mutant cells being unable to grow in the presence of hemin as the sole iron source. In hem1Δ abc3Δ cells, ZnMP accumulates primarily in vacuoles and does not sequentially accumulate in the cytosol. Consistent with a role for Abc3 as vacuolar hemin exporter, results with hemin-agarose pulldown assays showed that Abc3 binds to hemin. In contrast, an Abc3 mutant in which an inverted Cys-Pro motif had been replaced with Ala residues fails to bind hemin with high affinity. Taken together, these results show that Shu1 undergoes rapid hemin-induced internalization from the cell surface to the vacuolar membrane and that the transporter Abc3 participates in the mobilization of stored heme from the vacuole to the cytosol.
Two proteins for the price of one: Structural studies of the dual-destiny protein preproalbumin with sunflower trypsin inhibitor-1

Seed storage proteins are both an important source of nutrition for humans and essential for seedling establishment. Interestingly, unusual napin-type 2S seed storage albumin precursors in sunflowers contain a sequence that is released as a macrocyclic peptide during post-translational processing. The mechanism by which such peptides emerge from linear precursor proteins has received increased attention; however, the structural characterization of intact precursor proteins has been limited. Here, we report the 3D NMR structure of the Helianthus annuus PawS1 (preproalbumin with sunflower trypsin inhibitor-1) and provide new insights into the processing of this remarkable dual-destiny protein. In seeds, PawS1 is matured by asparaginyl endopeptidases (AEPs) into the cyclic peptide SFTI-1 (sunflower trypsin inhibitor-1) and a heterodimeric 2S albumin. The structure of PawS1 revealed that SFTI-1 and the albumin are independently folded into well-defined domains separated by a flexible linker. PawS1 was cleaved in vitro with recombinant sunflower HaAEP1 and in situ using a sunflower seed extract in a way that resembled the expected in vivo cleavages. Recombinant HaAEP1 cleaved PawS1 at multiple positions, and in situ, its flexible linker was removed, yielding fully mature heterodimeric albumin. Liberation and cyclization of SFTI-1, however, was inefficient, suggesting that specific seed conditions or components may be required for in vivo biosynthesis of SFTI-1. In summary, this study has revealed the 3D structure of a macrocyclic precursor protein and provided important mechanistic insights into the maturation of sunflower proalbumins into an albumin and a macrocyclic peptide.