bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular imaging HDACs class IIa expression-activity and pharmacologic inhibition in intracerebral glioma models in rats using PET/CT/(MRI) with [18F]TFAHA
Authors: Laws Maxwell T. , Bonomi Robin E. , Kamal Swatabdi , Gelovani David J. , Llaniguez Jeremy , Potukutchi Shreya , Lu Xin , Mangner Thomas , Gelovani Juri G.
Published: March 2019

HDAC class IIa enzymes (HDAC4, 5, 7, 9) are important for glioma progression, invasion, responses to TMZ and radiotherapy, and prognosis. In this study, we demonstrated the efficacy of PET/CT/(MRI) with [18F]TFAHA for non-invasive and quantitative imaging of HDAC class IIa expression-activity in intracerebral 9L and U87-MG gliomas in rats. Increased accumulation of [18F]TFAHA in 9L and U87-MG tumors was observed at 20 min post radiotracer administration with SUV of 1.45 ± 0.05 and 1.08 ± 0.05, respectively, and tumor-to-cortex SUV ratios of 1.74 ± 0.07 and 1.44 ± 0.03, respectively. [18F]TFAHA accumulation was also observed in normal brain structures known to overexpress HDACs class IIa: hippocampus, n.accumbens, PAG, and cerebellum. These results were confirmed by immunohistochemical staining of brain tissue sections revealing the upregulation of HDACs 4, 5, and 9, and HIF-1α, hypoacetylation of H2AK5ac, H2BK5ac, H3K9ac, H4K8ac, and downregulation of KLF4. Significant reduction in [18F]TFAHA accumulation in 9L tumors was observed after administration of HDACs class IIa specific inhibitor MC1568, but not the SIRT1 specific inhibitor EX-527. Thus, PET/CT/(MRI) with [18F]TFAHA can facilitate studies to elucidate the roles of HDAC class IIa enzymes in gliomagenesis and progression and to optimize therapeutic doses of novel HDACs class IIa inhibitors in gliomas.
Crystallization processes in a nonvibrating magnetic granular system with short range repulsive interaction
Authors: Sánchez-Miranda M. J. , Carrillo-Estrada J. L. , Donado F.
Published: March 2019

Applying an unsteady magnetic field to a 2D nonvibrating magnetic granular system induces a random motion in the steel beads with characteristics analogous to that of molecules in a fluid. We investigate the structural characteristics of the solid-like structures generated by different quenching conditions. The applied field is generated by the superposition of a constant field and a collinear sinusoidal field. The system reaches a quasi steady state in which the effective temperature is proportional to the amplitude of the applied field. By reducing the effective temperature at different rates, different cooling rates are produced. A slight inclination of the surface allows us to investigate the effects of small particle concentration gradients. The formation of a wide and rich variety of condensed solid structures, from gel-like and glass-like structures up to crystalline structures, is observed and depends on the cooling rate. We focus our attention on the crystallization process and found this process to be a collective phenomenon. We discuss our results in terms of the measured time evolution of the mean squared displacement, the effective diffusion coefficient, and the radial distribution function.
Comparison of self-reported and register-based hospital medical data on comorbidities in women
Authors: Ho Peh Joo , Tan Chuen Seng , Shawon Shajedur Rahman , Eriksson Mikael , Lim Li Yan , Miao Hui , Png Eileen , Chia Kee Seng , Hartman Mikael , Ludvigsson Jonas F. , Czene Kamila , Hall Per , Li Jingmei
Published: March 2019

Breast cancer patients commonly present with comorbidities which are known to influence treatment decisions and survival. We aim to examine agreement between self-reported and register-based medical records (National Patient Register [NPR]). Ascertainment of nine conditions, using individually-linked data from 64,961 women enrolled in the Swedish KARolinska MAmmography Project for Risk Prediction of Breast Cancer (KARMA) study. Agreement was assessed using observed proportion of agreement (overall agreement), expected proportion of agreement, and Cohen’s Kappa statistic. Two-stage logistic regression models taking into account chance agreement were used to identify potential predictors of overall agreement. High levels of overall agreement (i.e. ≥86.6%) were observed for all conditions. Substantial agreement (Cohen’s Kappa) was observed for myocardial infarction (0.74), diabetes (0.71) and stroke (0.64) between self-reported and NPR data. Moderate agreement was observed for preeclampsia (0.51) and hypertension (0.46). Fair agreement was observed for heart failure (0.40) and polycystic ovaries or ovarian cysts (0.27). For hyperlipidemia (0.14) and angina (0.10), slight agreement was observed. In most subgroups we observed negative specific agreement of >90%. There is no clear reference data source for ascertainment of conditions. Negative specific agreement between NPR and self-reported data is consistently high across all conditions.
An agonist antibody prefers relapsed AML for induction of cells that kill each other
Authors: Yea Kyungmoo , Jones Teresa M. , Jung Dokyung , Shin Sanghee , Arlian Britni M. , Han Kyung Ho , Zha Zhao , Kim Minseok S. , Oh Yong-Seok , Zhang Hongkai , Lerner Richard A.
Published: March 2019

Previously, we reported an agonist antibody to a cytokine receptor, Thrombopoietin receptor (TPOR) that effectively induces cytotoxic killer cells from precursor tumor cells isolated from newly diagnosed AML patients. Here, we show that the TPOR agonist antibody can induce even relapsed AML cells into killer cells more potently than newly diagnosed AML cells. After stimulation by the agonist antibody, these relapsed leukemic cells enter into a differentiation process of killer cells. The antibody-induced killer cells express, Granzyme B and Perforin that assault and kill other members of the AML cell population. Particularly, the agonist antibody showed potent efficacy on the AML xenograft model in mice using the NOD/LtSz-scid IL2Rγc null (NSG) mice. These results show that the TPOR agonist antibody that induces AML cells to kill each other is effective on both relapsed AML cells and in vivo. Therefore, this study suggests a new strategy for the treatment of cancer relapse after chemotherapy.
Molecular characterization of thalassemia and hemoglobinopathy in Southeastern China
Authors: Huang Hailong , Xu Liangpu , Chen Meihuan , Lin Na , Xue Huili , Chen Lingji , Wang Yan , He Deqin , Zhang Min , Lin Yuan
Published: March 2019

Thalassemia and hemoglobinopathy are two common inherited disorders, which are highly prevalent in southern China. However, there is little knowledge on the genotypes of thalassemia and hemoglobinopathy in Southeastern China. In this study, we present a large-scale genetic detection and molecular characterization of thalassemia and hemoglobinopathy in Fujian province, Southeastern China. A total of 189414 subjects screened for thalassemia were recruited, and the hemoglobin components and levels were investigated. Furthermore, suspected common thalassemia was identified, and the suspected rare forms of common thalassemias and hemoglobinopathy were detected. Among the total subjects screened, the overall prevalence of thalassemia and hemoglobinopathy was 6.8% and 0.26%, and rare α-thalassemia genotypes HKαα, –THAI/αα and −α27.6/αα, and novel β-thalassemia gene mutations CD90(G → T) and IVS-I-110(G > A) were identified. Additionally, Hb Q-Thailand hemoglobinopathy and five other types of hemoglobinopathies (Hb New York, Hb J-Bangkok, Hb G-Taipei, Hb G-Coushatta and Hb Maputo) were found. The results of this 10-year large-scale study demonstrate high prevalence of thalassemia with complicated gene mutations in Southeastern China, which provides valuable baseline data for genetic counseling and prenatal diagnosis. In addition to detection of common thalassemia genes, detection of rare thalassemia genotypes and hemoglobinopathies is recommended.
Substantial fat mass loss reduces low-grade inflammation and induces positive alteration in cardiometabolic factors in normal-weight individuals
Authors: Sarin H. V. , Lee J. H. , Jauhiainen M. , Joensuu A. , Borodulin K. , Männistö S. , Jin Z. , Terwilliger J. D. , Isola V. , Ahtiainen J. P. , Häkkinen K. , Kristiansson K. , Hulmi J. J. , Perola M.
Published: March 2019

The accumulation of fat, especially in visceral sites, is a significant risk factor for several chronic diseases with altered cardiometabolic homeostasis. We studied how intensive long-term weight loss and subsequent weight regain affect physiological changes, by longitudinally interrogating the lipid metabolism and white blood cell transcriptomic markers in healthy, normal-weight individuals. The current study examined 42 healthy, young (age: 27.5 ± 4.0 years), normal-weight (body mass index, BMI: 23.4 ± 1.7 kg/m2) female athletes, of which 25 belong to the weight loss and regain group (diet group), and 17 to the control group. Participants were evaluated, and fasting blood samples were drawn at three time points: at baseline (PRE); at the end of the weight loss period (MID: 21.1 ± 3.1 weeks after PRE); and at the end of the weight regain period (POST: 18.4 ± 2.9 weeks after MID). Following the weight loss period, the diet group experienced a ~73% reduction (~0.69 kg) in visceral fat mass (false discovery rate, FDR < 2.0 × 10−16), accompanied by anti-atherogenic effects on transcriptomic markers, decreased low-grade inflammation (e.g., as α1–acid glycoprotein (FDR = 3.08 × 10−13) and hs-CRP (FDR = 2.44 × 10−3)), and an increase in functionally important anti-atherogenic high-density lipoprotein -associated metabolites (FDR < 0.05). This occurred even though these values were already at favorable levels in these participants, who follow a fitness-lifestyle compared to age- and BMI-matched females from the general population (n = 58). Following the weight regain period, most of the observed beneficial changes in visceral fat mass, and metabolomic and transcriptomic profiles dissipated. Overall, the beneficial anti-atherogenic effects of weight loss can be observed even in previously healthy, normal-weight individuals.
Cooling of a vial in a snapfreezing device without using sacrificial cryogens
Authors: van Limbeek Michiel A. J. , Jagga Sahil , Holland Harry , Ledeboer Koen , ter Brake Marcel , Vanapalli Srinivas
Published: March 2019

A fresh and frozen high-quality patient bio-sample is required in molecular medicine for the identification of disease-associated mechanism at molecular levels. A common cooling procedure is immersing the tissue enclosed in a vial in a coolant such as liquid nitrogen. This procedure is not user friendly and is laborious as reducing the lag time from excision time to freezing depends on the logistic organizational structure within a hospital. Moreover snapfreezing must be done as soon as possible after tissue excision to preserve the tissue quality for molecular tests. Herein, we report an electrically powered snap freezing device as an alternative to quenching the vial in liquid nitrogen and therefore can be used directly at the location where the tissue is acquired. This device also facilitates the study of the effect of freezing conditions on the various molecular processes in the samples. Cooling experiments of a vial in the snap freezing device show that the cooling rates similar to or faster than quenching in liquid nitrogen are feasible. We performed experiments with several set point conditions and compared the results with a mathematical model.
Gene expression analysis reveals early dysregulation of disease pathways and links Chmp7 to pathogenesis of spinal and bulbar muscular atrophy
Authors: Malik Bilal , Devine Helen , Patani Rickie , La Spada Albert R. , Hanna Michael G. , Greensmith Linda
Published: March 2019

Spinal and bulbar muscular atrophy (SBMA) results from a CAG repeat expansion within the androgen receptor gene (AR). It is unclear why motor neurons selectively degenerate and there are currently no treatments for this debilitating disease. To uncover the causative genes and pathways involved in motor neuron dysfunction, we undertook transcriptomic profiling of primary embryonic motor neurons from SBMA mice. We show that transcriptional dysregulation occurs early during development in SBMA motor neurons. One gene found to be dysregulated, Chmp7, was also altered in vivo in spinal cord before symptom onset in SBMA mice, and crucially in motor neuron precursor cells derived from SBMA patient stem cells, suggesting that Chmp7 may play a causal role in disease pathogenesis by disrupting the endosome-lysosome system. Furthermore, genes were enriched in SBMA motor neurons in several key pathways including p53, DNA repair, WNT and mitochondrial function. SBMA embryonic motor neurons also displayed dysfunctional mitochondria along with DNA damage, possibly resulting from DNA repair gene dysregulation and/or mitochondrial dysfunction. This indicates that a coordinated dysregulation of multiple pathways leads to development of SBMA. Importantly, our findings suggest that the identified pathways and genes, in particular Chmp7, may serve as potential therapeutic targets in SBMA.
Vegfa/vegfr2 signaling is necessary for zebrafish islet vessel development, but is dispensable for beta-cell and alpha-cell formation
Authors: Toselli Chiara M. , Wilkinson Brayden M. , Paterson Joshua , Kieffer Timothy J.
Published: March 2019

The mechanisms underlying zebrafish pancreatic islet vascularization have not been well characterized. We sought to determine the angiogenic factors responsible for islet vascularization and assess whether an absence of endothelial cells affects beta-cell and alpha-cell formation. We used a double transgenic zebrafish Tg(fli1:EGFP; insa:tagRFP) to label endothelial cells and beta-cells, respectively. Beta-cells developed adjacent to endothelial cells and by 72 hours post fertilization (hpf) the zebrafish pancreatic islet was highly vascularized. Zebrafish beta-cells express vascular endothelial growth factors (vegf), vegfaa and vegfab. Double knockdown of vegfaa and vegfab or the primary Vegfa receptors (Vegfr2), kdr and kdrl, resulted in vessel deficient islets. While beta-cell and alpha-cell numbers remained unchanged in vessel deficient islets, insulina expression was downregulated relative to controls. Vegfaa/Vegfab-Vegfr2 signaling is necessary for proper islet vessel development, but not for the initial formation of beta-cells and alpha-cells.
Resilience of Central Pacific reefs subject to frequent heat stress and human disturbance
Authors: Donner Simon D. , Carilli Jessica
Published: March 2019

Frequent occurrences of coral bleaching and associated coral mortality over recent decades have raised concerns about the survival of coral reefs in a warming planet. The El Niño-influenced coral reefs in the central Gilbert Islands of the Republic of Kiribati, which experience years with prolonged heat stress more frequently than 99% of the world’s reefs, may serve as a natural model for coral community response to frequent heat stress. Here we use nine years of survey data (2004–2012) and a suite of remote sensing variables from sites along gradients of climate variability and human disturbance in the region to evaluate the drivers of coral community response to, and recovery from, multiple heat stress events. The results indicate that the extent of bleaching was limited during the 2009–2010 El Niño event, in contrast to a similar 2004–2005 event, and was correlated with incoming light and historical temperature variability, rather than heat stress. Spatial and temporal patterns in benthic cover suggest growing resistance to bleaching-level heat stress among coral communities subject to high inter-annual temperature variability and local disturbance, due to the spread of “weedy” and temperature-tolerant species (e.g., Porites rus) and the cloudy conditions in the region during El Niño events.
Pet dogs’ relationships vary rather individually than according to partner’s species
Authors: Cimarelli G. , Marshall-Pescini S. , Range F. , Virányi Z.
Published: March 2019

Most dogs worldwide are free-ranging animals that form relationships mainly with conspecifics, yet research has focused mainly on the dog-human bond, leading to the hypothesis that dogs evolved specific abilities to form a unique relationship with humans. Although widespread, this hypothesis has not, as yet, been tested. Here we compared the relationships pet dogs form with their owner and with other dogs living in the same household. Using a bottom-up approach, we analyzed dogs’ behavior in a test battery with both dog and human partners. Results revealed that pet dogs’ relationships are characterized by three components (i.e. reference, affiliation and stress). A comparison between dogs’ intra- and inter-specific relationships found that overall dogs refer more to their owner, but also that some dogs form stronger affiliative bonds with conspecifics than with their owner. Moreover, we tested how different partners could help dogs cope with a stressful situation. We found that the type of relationship, rather than the partner species, predicts how dogs react to a social threat. Our results suggest that dogs can form relationships of comparable qualities with both humans and other dogs, and that these relationships vary along multiple components across different partners.
Striatal Interneurons in Transgenic Nonhuman Primate Model of Huntington’s Disease
Authors: Lallani Shoeb B. , Villalba Rosa M. , Chen Yiju , Smith Yoland , Chan Anthony W. S.
Published: March 2019

Huntington’s disease is an autosomal dominant neurodegenerative disorder associated with progressive motor and cognitive impairments, and the expansion of a cysteine-adenine-guanine trinucleotide (polyglutamine) repeats in exon one of the human huntingtin gene. The pathology of the disease is characterized by a profound degeneration of striatal GABAergic projection neurons with relative sparing of interneurons accompanied with astrogliosis. Here, we describe the striatal pathology in two genotypically different transgenic HD monkeys that exhibit degrees of disease progression that resembled those seen in juvenile- (rHD1) and adult-onset (rHD7) HD. The caudate nucleus and putamen underwent severe neuronal loss in both animals, while the striatal volume was reduced only in rHD1, the most severely affected monkey. The number of GABAergic (calretinin- and parvalbumin-positive) and cholinergic interneurons was also reduced in most striatal regions of these two monkeys, but to variable degrees. Overall, the density of interneurons was increased in rHD1, but not in rHD7, suggesting a relative sparing of interneurons over projection neurons in the striatum of the most affected HD monkey. The neuropil of both the caudate nucleus and putamen was invaded with reactive astrocytes in rHD1, while astrogliosis was much less severe in rHD7 and absent from control. Combined with behavioral data collected from these monkeys, our findings further demonstrate that transgenic HD monkeys share similar disease patterns with HD patients, making them a highly reliable preclinical HD animal model.
Autoreactivity profiles of influenza hemagglutinin broadly neutralizing antibodies
Authors: Bajic Goran , van der Poel Cees E. , Kuraoka Masayuki , Schmidt Aaron G. , Carroll Michael C. , Kelsoe Garnett , Harrison Stephen C.
Published: March 2019

Epitope-focused approaches for selective clonal induction of broadly neutralizing antibodies (bnAbs) inform most current vaccine strategies for influenza virus and other rapidly evolving pathogens. The two conserved epitopes on the influenza hemagglutinin (HA) - the “stem” and the receptor-binding site (RBS) on the “head” - are the focus of the current “universal” influenza vaccine development efforts. Because stem-directed serum bnAbs are much less abundant than head-directed ones, we hypothesized that the HA stem bnAbs may be autoreactive and thus eliminated through the mechanisms of self-tolerance. We compared autoreactivity profiles of a set of stem and head-directed bnAbs. Most of the stem bnAbs we examined bound autoantigens; several showed staining of HEp-2 cells. A smaller proportion of the head-directed bnAbs were polyreactive. Gene usage did not correlate with autoreactivity. We suggest that complex foreign antigens may often have surface patches resembling some host epitope; our results indicate that HA stem epitopes resemble a host epitope more frequently than does the RBS.
Unexpected genomic rearrangements at targeted loci associated with CRISPR/Cas9-mediated knock-in
Authors: Rezza Amélie , Jacquet Christelle , Le Pillouer Amélie , Lafarguette Florian , Ruptier Charlotte , Billandon Marion , Isnard Petit Patricia , Trouttet Séverine , Thiam Kader , Fraichard Alexandre , Chérifi Yacine
Published: March 2019

The CRISPR/Cas9 gene editing tool enables accessible and efficient modifications which (re)ignited molecular research in certain species. However, targeted integration of large DNA fragments using CRISPR/Cas9 can still be challenging in numerous models. To systematically compare CRISPR/Cas9’s efficiency to classical homologous recombination (cHR) for insertion of large DNA fragments, we thoroughly performed and analyzed 221 experiments targeting 128 loci in mouse ES cells. Although both technologies proved efficient, CRISPR/Cas9 yielded significantly more positive clones as detected by overlapping PCRs. It also induced unexpected rearrangements around the targeted site, ultimately rendering CRISPR/Cas9 less efficient than cHR for the production of fully validated clones. These data show that CRISPR/Cas9-mediated recombination can induce complex long-range modifications at targeted loci, thus emphasizing the need for thorough characterization of any genetically modified material obtained through CRISPR-mediated gene editing before further functional studies or therapeutic use.
Magnetic field-induced rubber-like behavior in Ni-Mn-Ga particles/polymer composite
Authors: Sratong-on P. , Chernenko V. A. , Feuchtwanger J. , Hosoda H.
Published: March 2019

Single crystalline Ni-Mn-Ga is well known as a prototype ferromagnetic shape memory alloy (FSMA) exhibiting a giant magnetic field-induced strain (MFIS), up to 12%, due to the magnetically driven twin boundary rearrangement. The large stroke and fast magnetomechanical response make it important for actuators and sensors. Polycrystalline Ni-Mn-Ga is inexpensive and technologically easy accessible, but constrains from the grain boundaries inhibit the twin boundary motion, whereby a very low MFIS is observed. Here, we have shown for the first time that a polycrystalline Ni-Mn-Ga can be split into the magnetostrain-active single grains which, being specially assembled in a silicone polymer matrix, caused large and fully reversible MFIS of the resulting composite. We termed the unique reversibility of a large MFIS of the composite as the magnetic field-induced rubber-like behavior. The magnetostrain of individual particles was explored by the X-ray μCT 3D imaging. The results suggest novel solutions for development of the low cost magnetic actuators and sensors for haptic applications.
Effect of CHK1 Inhibition on CPX-351 Cytotoxicity in vitro and ex vivo
Authors: Vincelette Nicole D. , Ding Husheng , Huehls Amelia M. , Flatten Karen S. , Kelly Rebecca L. , Kohorst Mira A. , Webster Jonathan , Hess Allan D. , Pratz Keith W. , Karnitz Larry M. , Kaufmann Scott H.
Published: March 2019

CPX-351 is a liposomally encapsulated 5:1 molar ratio of cytarabine and daunorubicin that recently received regulatory approval for the treatment of therapy-related acute myeloid leukemia (AML) or AML with myelodysplasia-related changes based on improved overall survival compared to standard cytarabine/daunorubicin therapy. Checkpoint kinase 1 (CHK1), which is activated by DNA damage and replication stress, diminishes sensitivity to cytarabine and anthracyclines as single agents, suggesting that CHK1 inhibitors might increase the effectiveness of CPX-351. The present studies show that CPX-351 activates CHK1 as well as the S and G2/M cell cycle checkpoints. Conversely, CHK1 inhibition diminishes the cell cycle effects of CPX-351. Moreover, CHK1 knockdown or addition of a CHK1 inhibitor such as MK-8776, rabusertib or prexasertib enhances CPX-351-induced apoptosis in multiple TP53-null and TP53-wildtype AML cell lines. Likewise, CHK1 inhibition increases the antiproliferative effect of CPX-351 on primary AML specimens ex vivo, offering the possibility that CPX-351 may be well suited to combine with CHK1-targeted agents.
Development of thermo-responsive polycaprolactone macrocarriers conjugated with Poly(N-isopropyl acrylamide) for cell culture
Authors: Nguyen Linh T. B. , Odeleye Akinlolu O. O. , Chui Chih–Yao , Baudequin Timothée , Cui Zhanfeng , Ye Hua
Published: March 2019

Poly(N-isopropyl acrylamide) (PNIPAAm) is a well-known ‘smart’ material responding to external stimuli such as temperature. PNIPAAm was successfully conjugated to polycaprolactone (PCL) bead surfaces through amidation reaction. Functionalization steps were characterized and confirmed by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy and Energy Dispersion Spectroscopy. PNIPAAm-conjugated PCL allowed human dermal fibroblast cells (HDF) and mesenchymal stem cells (MSC) to adhere, spread, and grow successfully. By reducing the temperature to 30 °C, more than 70% of HDF were detached from PNIPAAm-conjugated PCL macrocarriers with 85% viability. The cell detachment ratio by trypsin treatment was slightly higher than that induced by reduced temperature, however, cell detachment from PNIPAAm-conjugated macrocarriers by lowering the temperature significantly reduced cell death and increased both cell viability and the recovery potential of the detached cells. HDF attachment and detachment were also observed by Live-Dead staining and phase contrast imaging. The expression of extracellular matrix proteins such as Laminin and Fibronectin was also affected by the trypsinization process but not by the reduced temperature process. Taken together, our results showed that thermo-responsive macrocarriers could be a promising alternative method for the non-invasive detachment of cells, in particular for tissue engineering, clinical applications and the use of bioreactors.
Countershading in zebrafish results from an Asip1 controlled dorsoventral gradient of pigment cell differentiation
Authors: Cal Laura , Suarez-Bregua Paula , Comesaña Pilar , Owen Jennifer , Braasch Ingo , Kelsh Robert , Cerdá-Reverter José Miguel , Rotllant Josep
Published: March 2019

Dorso-ventral (DV) countershading is a highly-conserved pigmentary adaptation in vertebrates. In mammals, spatially regulated expression of agouti-signaling protein (ASIP) generates the difference in shading by driving a switch between the production of chemically-distinct melanins in melanocytes in dorsal and ventral regions. In contrast, fish countershading seemed to result from a patterned DV distribution of differently-coloured cell-types (chromatophores). Despite the cellular differences in the basis for counter-shading, previous observations suggested that Agouti signaling likely played a role in this patterning process in fish. To test the hypotheses that Agouti regulated counter-shading in fish, and that this depended upon spatial regulation of the numbers of each chromatophore type, we engineered asip1 homozygous knockout mutant zebrafish. We show that loss-of-function asip1 mutants lose DV countershading, and that this results from changed numbers of multiple pigment cell-types in the skin and on scales. Our findings identify asip1 as key in the establishment of DV countershading in fish, but show that the cellular mechanism for translating a conserved signaling gradient into a conserved pigmentary phenotype has been radically altered in the course of evolution.
Bone-Specific Overexpression of PITX1 Induces Senile Osteoporosis in Mice Through Deficient Self-Renewal of Mesenchymal Progenitors and Wnt Pathway Inhibition
Authors: Karam Nancy , Lavoie Jean-François , St-Jacques Benoit , Bouhanik Saadallah , Franco Anita , Ladoul Nihad , Moreau Alain
Published: March 2019

The cellular and molecular mechanisms underlying senile osteoporosis remain poorly understood. In this study, transgenic mCol1α1-Pitx1 mice overexpressing paired-like homeodomain 1 (PITX1), a homeobox transcription factor, rapidly develop a severe type-II osteoporotic phenotype with significant reduction in bone mass and biomechanical strength similar to that seen in humans and reminiscent of the phenotype previously observed in Sca-1 (Ly6a)-null mice. PITX1 plays a critical role in hind limb formation during fetal development, while loss of expression is associated with primary knee/hip osteoarthritis in aging humans. Through in vivo and in vitro analyses, we demonstrate that Pitx1 directly regulates the self-renewal of mesenchymal progenitors and indirectly regulates osteoclast differentiation through the upregulation of Wnt signaling inhibitors DKK1, SOST, and GSK3-β. This is confirmed by elevated levels of plasma DKK1 and the accumulation of phospho-β-catenin in transgenic mice osteoblasts. Furthermore, overexpressed Pitx1 in mice osteoblasts results in severe repression of Sca-1 (Ly6a) that was previously associated with senile osteoporosis. Our study is the first to demonstrate the novel roles of PITX1 in senile osteoporosis where PITX1 regulates the self-renewal of mesenchymal stem cells or progenitor cells through Sca-1 (Ly6a) repression and, in addition, inhibits the Wnt signaling pathway.
Development and validation of a nomogram for urothelial cancer in patients with chronic kidney disease
Authors: Chou Che-Yi , Shu Kuo-Hsiung , Chen Hung-Chun , Wang Ming-Chang , Chang Chia-Chu , Hsu Bang-Gee , Chen Tzen-Wen , Chen Chien-Lung , Huang Chiu-Ching
Published: March 2019

Urothelial cancer (UC) is a common kidney cancer in Taiwan and patients with chronic kidney disease (CKD) are more at risk for UC than the general population. The diagnostic value of urine analysis and urine cytology is limited, especially in CKD patients. The aim of the study is to develop a nomogram to predict the risk of UC in CKD patients. We enrolled 169 UC patients and 1383 CKD patients from 9 hospitals in Taiwan between 2012 and 2015. CA125, HE4, clinical characteristics, and medical history were analyzed using multivariable logistic regression for its association with UC. A nomogram was developed to predict the risk of UC and was validated using Bootstrap. CA125 was associated with UC in CKD patients (OR: 5.91, 95% CI: 3.24–10.77) but HE4 was not (OR: 1.29, 95% CI: 0.67–2.35). A nomogram based on patients’ age, estimated glomerular filtration rate, CA125 (log transformed), smoking, exposure of environmental toxin, use of nonsteroid anti-inflammatory drugs, and use of traditional Chinese medicine was conducted. The AUC of the nomogram was 0.90 (95% CI: 0.86–0.92, p < 0.01). Serum CA125 may identify UC patients from CKD patients but has limited diagnostic value due to low sensitivity. The diagnostic value of serum CA125 level can be improved by the combination with clinical characteristics including age, renal function, and medical history.
Element banding and organic linings within chamber walls of two benthic foraminifera
Authors: Geerken E. , de Nooijer L. J. , Roepert A. , Polerecky L. , King H. E. , Reichart G. J.
Published: March 2019

Trace and minor elements incorporated in foraminiferal shells are among the most used proxies for reconstructing past environmental conditions. A prominent issue concerning these proxies is that the inter-specimen variability in element composition is often considerably larger than the variability associated with the environmental conditions for which the proxy is used. Within a shell of an individual specimen the trace and minor elements are distributed in the form of bands of higher and lower concentrations. It has been hypothesized that differences in specimen-specific element banding patterns cause the inter-specimen and inter-species variability observed in average element composition, thereby reducing the reliability of proxies. To test this hypothesis, we compared spatial distributions of Mg, Na, Sr, K, S, P and N within chamber walls of two benthic foraminiferal species (Amphistegina lessonii and Ammonia tepida) with largely different average Mg content. For both species the selected specimens were grown at different temperatures and salinities to additionally assess how these parameters influence the element concentrations within the shell wall. Our results show that Mg, Na, Sr and K are co-located within shells, and occur in bands that coincide with organic linings but extend further into the calcite lamella. Changes in temperature or salinity modulate the element-banding pattern as a whole, with peak and trough heights co-varying rather than independently affected by these two environmental parameters. This means that independent changes in peak or trough height do not explain differences in average El/Ca between specimens. These results are used to evaluate and synthesize models of underlying mechanisms responsible for trace and minor element partitioning during calcification in foraminifera.
DESTINI: A deep-learning approach to contact-driven protein structure prediction
Authors: Gao Mu , Zhou Hongyi , Skolnick Jeffrey
Published: March 2019

The amino acid sequence of a protein encodes the blueprint of its native structure. To predict the corresponding structural fold from the protein’s sequence is one of most challenging problems in computational biology. In this work, we introduce DESTINI (deep structural inference for proteins), a novel computational approach that combines a deep-learning algorithm for protein residue/residue contact prediction with template-based structural modelling. For the first time, the significantly improved predictive ability is demonstrated in the large-scale tertiary structure prediction of over 1,200 single-domain proteins. DESTINI successfully predicts the tertiary structure of four times the number of “hard” targets (those with poor quality templates) that were previously intractable, viz, a “glass-ceiling” for previous template-based approaches, and also improves model quality for “easy” targets (those with good quality templates). The significantly better performance by DESTINI is largely due to the incorporation of better contact prediction into template modelling. To understand why deep-learning accomplishes more accurate contact prediction, systematic clustering reveals that deep-learning predicts coherent, native-like contact patterns compared to co-evolutionary analysis. Taken together, this work presents a promising strategy towards solving the protein structure prediction problem.
The NADPH oxidase 4 is a major source of hydrogen peroxide in human granulosa-lutein and granulosa tumor cells
Authors: Buck Theresa , Hack Carsten Theo , Berg Dieter , Berg Ulrike , Kunz Lars , Mayerhofer Artur
Published: March 2019

H2O2 is a reactive oxygen species (ROS), which can diffuse away from its site of generation and may act as a cell-to-cell signaling factor. The mechanisms responsible for the generation of H2O2 in human ovarian follicles and possible signaling role(s) of H2O2 are not well known. We identified a source of H2O2, the enzyme NADPH oxidase (NOX) 4, in isolated differentiated, in-vitro fertilisation-derived human granulosa-lutein cells (GCs), in proliferating human granulosa tumour cells (KGN), as well as in situ in cells of growing ovarian follicles. H2O2 was readily detected in the supernatant of cultured GCs and KGN cells. H2O2 levels were significantly lowered by the NOX4 blocker GKT137831, indicating a pronounced contribution of NOX4 to overall H2O2 generation by these cells. We provide evidence that extracellular H2O2 is taken up by GCs, which is facilitated by aquaporins (peroxiporins). We thus conclude that GC-derived H2O2 might act as autocrine/paracrine factor. Addition of H2O2 increased MAPK-phosphorylation in GCs. Moreover, reducing H2O2 production with GKT137831 slowed proliferation of KGN cells. Our results pinpoint NOX4 and H2O2 as physiological players in the regulation of GC functions.
Minimum viable population size and population growth rate of freshwater fishes and their relationships with life history traits
Authors: Wang Teng , Fujiwara Masami , Gao Xin , Liu Huanzhang
Published: March 2019

The minimum viable population (MVP) size has been compared for a wide range of organisms in conservation biology, but a limited number of studies investigated it for freshwater fishes, which exhibit diverse life history strategies. In this study, the MVP size and population growth rate of 36 fish species in the Yangtze River were estimated and compared with their life-history traits. The results indicated that the MVP size ranged from 42 to 320 individuals, and instantaneous per-capita population growth rate ranged from 0.009 to 0.188 per year. MVP size and population growth rate were significantly associated with three life history traits: the age at maturity, generation time, and fecundity. Long-lived species with delayed maturation, long generation time, and high fecundity had a greater MVP size and a lower population growth rate than short-lived species. Therefore, our results emphasize a need for prioritizing our conservation effort more on long-lived species.
TMEM10 Promotes Oligodendrocyte Differentiation and is Expressed by Oligodendrocytes in Human Remyelinating Multiple Sclerosis Plaques
Authors: de Faria Omar , Dhaunchak Ajit S. , Kamen Yasmine , Roth Alejandro D. , Kuhlmann Tanja , Colman David R. , Kennedy Timothy E.
Published: March 2019

Oligodendrocyte precursor cells (OPCs) differentiate during postnatal development into myelin-forming oligodendrocytes, in a process distinguished by substantial changes in morphology and the onset of myelin gene expression. A mammalian-specific CNS myelin gene, tmem10, also called Opalin, encodes a type 1 transmembrane protein that is highly upregulated during early stages of OPC differentiation; however, a function for TMEM10 has not yet been identified. Here, consistent with previous studies, we detect TMEM10 protein in mouse brain beginning at ~P10 and show that protein levels continue to increase as oligodendrocytes differentiate and myelinate axons in vivo. We show that constitutive TMEM10 overexpression in the Oli-neu oligodendroglial cell line promotes the expression of the myelin-associated genes MAG, CNP and CGT, whereas TMEM10 knock down in primary OPCs reduces CNP mRNA expression and decreases the percentage of MBP-positive oligodendrocytes that differentiate in vitro. Ectopic TMEM10 expression evokes an increase in process extension and branching, and blocking endogenous TMEM10 expression results in oligodendrocytes with abnormal cell morphology. These findings may have implications for human demyelinating disorders, as oligodendrocytes expressing TMEM10 are detected in human remyelinating multiple sclerosis lesions. Together, our findings provide evidence that TMEM10 promotes oligodendrocyte terminal differentiation and may represent a novel target to promote remyelination in demyelinating disorders.
New insights into the relationship between taste perception and oral microbiota composition
Authors: Cattaneo Camilla , Gargari Giorgio , Koirala Ranjan , Laureati Monica , Riso Patrizia , Guglielmetti Simone , Pagliarini Ella
Published: March 2019

Fairly poor data are available on the relationship between taste perception, food preferences and oral microbiota. In the present study, we investigated the hypothesis that subjects with higher responsiveness to 6-n-propylthiuracil (PROP) might be characterized by a different taste sensitivity and tongue microbiota composition. Indeed, the bacterial metabolism may modulate/enhance the concentration of tastants near the taste receptors, modifying taste perception through a sensorial adaptation mechanism or by a broad range of microbial metabolic pathways. The detection thresholds of sweet, sour, salty and bitter, the Fungiform Papillae Density (FPD) and the composition of bacteria lining the tongue were determined in Supertasters (high PROP responsiveness, ST) and Non-tasters (low PROP responsiveness, NT). An important inter-individual variability was found for all taste stimuli and FPD between the two groups, with NT subjects showing significant higher threshold values and a lower FPD than with STs. We found five bacterial genera whose relative abundances were significantly higher in STs than NTs. This study opens new avenues of research by highlighting associations between parameters usually studied independently.
Temporal changes in cell division rate and genotoxic stress tolerance in quiescent center cells of Arabidopsis primary root apical meristem
Authors: Timilsina Rupak , Kim Jin Hee , Nam Hong Gil , Woo Hye Ryun
Published: March 2019

Plant roots provide structural support and absorb nutrients and water; therefore, their proper development and function are critical for plant survival. Extensive studies on the early stage of ontogenesis of the primary root have revealed that the root apical meristem (RAM) undergoes dynamic structural and organizational changes during early germination. Quiescent center (QC) cells, a group of slowly dividing cells at the center of the stem-cell niche, are vital for proper function and maintenance of the RAM. However, temporal aspects of molecular and cellular changes in QC cells and their regulatory mechanisms have not been well studied. In the present study, we investigated temporal changes in QC cell size, expression of QC cell-specific markers (WOX5 and QC25), and genotoxic tolerance and division rate of QC cells in the Arabidopsis primary root. Our data revealed the decreased size of QC cells and the decreased expression of the QC cell-specific markers with root age. We also found that QC cell division frequency increased with root age. Furthermore, our study provides evidence supporting the link between the transition of QC cells from a mitotically quiescent state to the frequently dividing state and the decrease in tolerance to genotoxic stress.
A novel echocardiographic method closely agrees with cardiac magnetic resonance in the assessment of left ventricular function in infarcted mice
Authors: Russo Ilaria , Micotti Edoardo , Fumagalli Francesca , Magnoli Michela , Ristagno Giuseppe , Latini Roberto , Staszewsky Lidia
Published: March 2019

Cardiac Magnetic Resonance (CMR) is the gold standard for left ventricular (LV) function assessment in small rodents and, though echocardiography (ECHO) has been proposed as an alternative method, LV volumes may be underestimated when marked eccentric remodeling is present. In the present study we described a novel echocardiographic method and we tested the agreement with CMR for LV volumes and ejection fraction calculation in mice with experimental myocardial infarction. Sham-operated and infarcted mice, subjected to Coronary Artery Ligation, underwent ECHO and CMR. Volumes and ejection fraction were calculated by ECHO using a standard Simpson’s modified method (ECHO pLAX) or a method from sequential parasternal short axis (ECHO pSAX) acquired mechanically by translating the probe every 1 mm along the left ventricle. The mean differences ±1.96 standard deviation near to zero suggested close agreement between ECHO pSAX and CMR; contrarily ECHO pLAX agreement with CMR was lower. In addition, ECHO was three times shorter and cheaper (Relative cost difference: pLAX: −66% and pSAX −57%) than CMR. In conclusion, ECHO pSAX is a new, fast, cheap and accurate method for LV function assessment in mice.
Thalamic Reticular Nucleus Parvalbumin Neurons Regulate Sleep Spindles and Electrophysiological Aspects of Schizophrenia in Mice
Authors: Thankachan Stephen , Katsuki Fumi , McKenna James T. , Yang Chun , Shukla Charu , Deisseroth Karl , Uygun David S. , Strecker Robert E. , Brown Ritchie E. , McNally James M. , Basheer Radhika
Published: March 2019

The thalamic reticular nucleus (TRN) is implicated in schizophrenia pathology. However, it remains unclear whether alterations of TRN activity can account for abnormal electroencephalographic activity observed in patients, namely reduced spindles (10–15 Hz) during sleep and increased delta (0.5–4 Hz) and gamma-band activity (30–80 Hz) during wakefulness. Here, we utilized optogenetic and reverse-microdialysis approaches to modulate activity of the major subpopulation of TRN GABAergic neurons, which express the calcium-binding protein parvalbumin (PV), and are implicated in schizophrenia dysfunction. An automated algorithm with enhanced efficiency and reproducibility compared to manual detection was used for sleep spindle assessment. A novel, low power, waxing-and-waning optogenetic stimulation paradigm preferentially induced spindles that were indistinguishable from spontaneously occurring sleep spindles without altering the behavioral state, when compared to a single pulse laser stimulation used by us and others. Direct optogenetic inhibition of TRN-PV neurons was ineffective in blocking spindles but increased both wakefulness and cortical delta/gamma activity, as well as impaired the 40 Hz auditory steady-state response. For the first time we demonstrate that spindle density is markedly reduced by (i) optogenetic stimulation of a major GABA/PV inhibitory input to TRN arising from basal forebrain parvalbumin neurons (BF-PV) and; (ii) localized pharmacological inhibition of low-threshold calcium channels, implicated as a genetic risk factor for schizophrenia. Together with clinical findings, our results support impaired TRN-PV neuron activity as a potential cause of schizophrenia-linked abnormalities in cortical delta, gamma, and spindle activity. Modulation of the BF-PV input to TRN may improve these neural abnormalities.
A multimodal approach to cardiovascular risk stratification in patients with type 2 diabetes incorporating retinal, genomic and clinical features
Authors: Fetit Ahmed E. , Doney Alexander S. , Hogg Stephen , Wang Ruixuan , MacGillivray Tom , Wardlaw Joanna M. , Doubal Fergus N. , McKay Gareth J. , McKenna Stephen , Trucco Emanuele
Published: March 2019

Cardiovascular diseases are a public health concern; they remain the leading cause of morbidity and mortality in patients with type 2 diabetes. Phenotypic information available from retinal fundus images and clinical measurements, in addition to genomic data, can identify relevant biomarkers of cardiovascular health. In this study, we assessed whether such biomarkers stratified risks of major adverse cardiac events (MACE). A retrospective analysis was carried out on an extract from the Tayside GoDARTS bioresource of participants with type 2 diabetes (n = 3,891). A total of 519 features were incorporated, summarising morphometric properties of the retinal vasculature, various single nucleotide polymorphisms (SNPs), as well as routine clinical measurements. After imputing missing features, a predictive model was developed on a randomly sampled set (n = 2,918) using L1-regularised logistic regression (lasso). The model was evaluated on an independent set (n = 973) and its performance associated with overall hazard rate after censoring (log-rankp < 0.0001), suggesting that multimodal features were able to capture important knowledge for MACE risk assessment. We further showed through a bootstrap analysis that all three sources of information (retinal, genetic, routine clinical) offer robust signal. Particularly robust features included: tortuousity, width gradient, and branching point retinal groupings; SNPs known to be associated with blood pressure and cardiovascular phenotypic traits; age at imaging; clinical measurements such as blood pressure and high density lipoprotein. This novel approach could be used for fast and sensitive determination of future risks associated with MACE.