Diffusion imaging genomics provides novel insight into early mechanisms of cerebral small vessel disease.

Cerebral small vessel disease (cSVD) is a leading cause of stroke and dementia. Genetic risk loci for white matter hyperintensities (WMH), the most common MRI-marker of cSVD in older age, were recently shown to be significantly associated with white matter (WM) microstructure on diffusion tensor imaging (signal-based) in young adults. To provide new insights into these early changes in WM microstructure and their relation with cSVD, we sought to explore the genetic underpinnings of cutting-edge tissue-based diffusion imaging markers across the adult lifespan. We conducted a genome-wide association study of neurite orientation dispersion and density imaging (NODDI) markers in young adults (i-Share study: N = 1 758, (mean[range]) 22.1[18-35] years), with follow-up in young middle-aged (Rhineland Study: N = 714, 35.2[30-40] years) and late middle-aged to older individuals (UK Biobank: N = 33 224, 64.3[45-82] years). We identified 21 loci associated with NODDI markers across brain regions in young adults. The most robust association, replicated in both follow-up cohorts, was with Neurite Density Index (NDI) at chr5q14.3, a known WMH locus in VCAN. Two additional loci were replicated in UK Biobank, at chr17q21.2 with NDI, and chr19q13.12 with Orientation Dispersion Index (ODI). Transcriptome-wide association studies showed associations of STAT3 expression in arterial and adipose tissue (chr17q21.2) with NDI, and of several genes at chr19q13.12 with ODI. Genetic susceptibility to larger WMH volume, but not to vascular risk factors, was significantly associated with decreased NDI in young adults, especially in regions known to harbor WMH in older age. Individually, seven of 25 known WMH risk loci were associated with NDI in young adults. In conclusion, we identified multiple novel genetic risk loci associated with NODDI markers, particularly NDI, in early adulthood. These point to possible early-life mechanisms underlying cSVD and to processes involving remyelination, neurodevelopment and neurodegeneration, with a potential for novel approaches to prevention.

Visual impairment and retinal and brain neurodegeneration: A population-based study.

Visual impairment and retinal neurodegeneration are intrinsically connected and both have been associated with cognitive impairment and brain atrophy, but the underlying mechanisms remain unclear. To investigate whether transneuronal degeneration is implicated, we systematically assessed the relation between visual function and retinal, visual pathway, hippocampal and brain degeneration. We analyzed baseline data from 3316 eligible Rhineland Study participants with visual acuity (VA), optical coherence tomography (OCT), and magnetic resonance imaging (MRI) data available. Regional volumes, cortical volume, and fractional anisotropy (FA) were derived from T1-weighted and diffusion-weighted 3 T MRI scans. Statistical analyses were performed using multivariable linear regression and structural equation modeling. VA and ganglion cell layer (GCL) thinning were both associated with global brain atrophy (SD effect size [95% CI] -0.090 [-0.118 to -0.062] and 0.066 [0.053-0.080], respectively), and hippocampal atrophy (-0.029 [-0.055 to -0.003] and 0.114 [0.087-0.141], respectively). The effect of VA on whole brain and hippocampal volume was partly mediated by retinal neurodegeneration. Similarly, the effect of retinal neurodegeneration on brain and hippocampal atrophy was mediated through intermediate visual tracts, accounting for 5.2%-23.9% of the effect. Visual impairment and retinal neurodegeneration were robustly associated with worse brain atrophy, FA, and hippocampal atrophy, partly mediated through disintegration of intermediate visual tracts. Our findings support the use of OCT-derived retinal measures as markers of neurodegeneration, and indicate that both general and transneuronal neurodegeneration along the visual pathway, partly reflecting visual impairment, account for the association between retinal neurodegeneration and brain atrophy.

MAPL1: q-space reconstruction using ℓ1 -regularized mean apparent propagator.

PURPOSE: To improve the quality of mean apparent propagator (MAP) reconstruction from a limited number of q-space samples. METHODS: We implement an ℓ1 -regularised MAP (MAPL1) to consider higher order basis functions and to improve the fit without increasing the number of q-space samples. We compare MAPL1 with the least-squares optimization subject to non-negativity (MAP), and the Laplacian-regularized MAP (MAPL). We use simulations of crossing fibers and compute the normalized mean squared error (NMSE) and the Pearson's correlation coefficient to evaluate the reconstruction quality in q-space. We also compare coefficient-based diffusion indices in the simulations and in in vivo data. RESULTS: Results indicate that MAPL1 improves NMSE in 1 to 3% when compared to MAP or MAPL in a high undersampling regime. Additionally, MAPL1 produces more reproducible and accurate results for all sampling rates when there are enough basis functions to meet the sparsity criterion for the regularizer. These improved reconstructions also produce better coefficient-based diffusion indices for in vivo data. CONCLUSIONS: Adding an ℓ1 regularizer to MAP allows the use of more basis functions and a better fit without increasing the number of q-space samples. The impact of our research is that a complete diffusion spectrum can be reconstructed from an acquisition time very similar to a diffusion tensor imaging protocol.

SHORE-based detection and imputation of dropout in diffusion MRI.

PURPOSE: In diffusion MRI, dropout refers to a strong attenuation of the measured signal that is caused by bulk motion during the diffusion encoding. When left uncorrected, dropout will be erroneously interpreted as high diffusivity in the affected direction. We present a method to automatically detect dropout, and to replace the affected measurements with imputed values. METHODS: Signal dropout is detected by deriving an outlier score from a simple harmonic oscillator-based reconstruction and estimation (SHORE) fit of all measurements. The outlier score is defined to detect measurements that are substantially lower than predicted by SHORE in a relative sense, while being less sensitive to measurement noise in cases of weak baseline signal. A second SHORE fit is based on detected inliers only, and its predictions are used to replace outliers. RESULTS: Our method is shown to reliably detect and accurately impute dropout in simulated data, and to achieve plausible results in corrupted in vivo dMRI measurements. Computational effort is much lower than with previously proposed alternatives. CONCLUSIONS: Deriving a suitable outlier score from SHORE results in a fast and accurate method for detection and imputation of dropout in diffusion MRI. It requires measurements with multiple b values (such as multi-shell or DSI), but is independent from the models used for analysis (such as DKI, NODDI, deconvolution, etc.).

THOC5 controls 3'end-processing of immediate early genes via interaction with polyadenylation specific factor 100 (CPSF100).

Transcription of immediate early genes (IEGs) in response to extrinsic and intrinsic signals is tightly regulated at multiple stages. It is known that untranslated regions of the RNA can play a role in these processes. Here we show that THOC5, a member of the TREX (transcription/export) complex, plays a role in expression of only a subset of constitutively active genes, however transcriptome analysis reveals that more than 90% of IEG were not induced by serum in THOC5 depleted cells. Furthermore, THOC5 depletion does not influence the expression of the most rapidly induced IEGs, e.g. Fos and Jun. One group of THOC5 target genes, including Id1, Id3 and Wnt11 transcripts, were not released from chromatin in THOC5 depleted cells. Genes in another group, including Myc and Smad7 transcripts, were released with shortening of 3'UTR by alternative cleavage, and were spliced but export was impaired in THOC5 depleted cells. By interactome analysis using THOC5 as bait, we show that upon stimulation with serum THOC5 forms a complex with polyadenylation-specific factor 100 (CPSF100). THOC5 is required for recruitment of CPSF100 to 3'UTR of THOC5 target genes. These data suggest the presence of a novel mechanism for the control of IEG response by THOC5 via 3'end-processing.

THOC5, a member of the mRNA export complex: a novel link between mRNA export machinery and signal transduction pathways in cell proliferation and differentiation.

Cell growth, differentiation, and commitment to a restricted lineage are guided by a timely expressed set of growth factor/cytokine receptors and their down-stream transcription factor genes. Transcriptional control mechanisms of gene expression during differentiation have been mainly studied by focusing on the cis- and trans-elements in promoters however, the role of mRNA export machinery during differentiation has not been adequately examined. THO (Suppressors of the transcriptional defects of hpr1 delta by overexpression) complex 5 (THOC5) is a member of THO complex which is a subcomplex of the transcription/export complex (TREX). THOC5 is evolutionarily conserved in higher eukaryotes, however the exact roles of THOC5 in transcription and mRNA export are still unclear. In this review, we focus on recently uncovered aspects of the role of THOC5 in signal transduction induced by extracellular stimuli. THOC5 is phosphorylated by several protein kinases at multiple residues upon extracellular stimuli. These include stimulation with growth factors/cytokines/chemokines, or DNA damage reagents. Furthermore, THOC5 is a substrate for several oncogenic tyrosine kinases, suggesting that THOC5 may be involved in cancer development. Recent THOC5 knockout mouse data reveal that THOC5 is an essential element in the maintenance of stem cells and growth factor/cytokine-mediated differentiation/proliferation. Furthermore, depletion of THOC5 influences less than 1% of total mRNA export in the steady state, however it influences more than 90% of growth factor/cytokine induced genes. THOC5, thereby contributes to the 3' processing and/or export of immediate-early genes induced by extracellular stimuli. These studies bring new insight into the link between the mRNA export complex and immediate-early gene response. The data from these studies also suggest that THOC5 may be a useful tool for studying stem cell biology, for modifying the differentiation processes and for cancer therapy.

Murine precision-cut liver slices (PCLS): a new tool for studying tumor microenvironments and cell signaling ex vivo.

BACKGROUND: One of the most insidious characteristics of cancer is its spread to and ability to compromise distant organs via the complex process of metastasis. Communication between cancer cells and organ-resident cells via cytokines/chemokines and direct cell-cell contacts are key steps for survival, proliferation and invasion of metastasized cancer cells in organs. Precision-cut liver slices (PCLS) are considered to closely reflect the in vivo situation and are potentially useful for studying the interaction of cancer cells with liver-resident cells as well as being a potentially useful tool for screening anti-cancer reagents. Application of the PCLS technique in the field of cancer research however, has not yet been well developed. RESULTS: We established the mouse PCLS system using perfluorodecalin (PFD) as an artificial oxygen carrier. Using this system we show that the adherence of green fluorescent protein (GFP) labeled MDA-MB-231 (highly invasive) cells to liver tissue in the PCLS was 5-fold greater than that of SK-BR-3 (less invasive) cells. In addition, we generated PCLS from THOC5, a member of transcription/export complex (TREX), knockout (KO) mice. The PCLS still expressed Gapdh or Albumin mRNAs at normal levels, while several chemokine/growth factor or metalloprotease genes, such as Cxcl12, Pdgfa, Tgfb, Wnt11, and Mmp1a genes were downregulated more than 2-fold. Interestingly, adhesion of cancer cells to THOC5 KO liver slices was far less (greater than 80% reduction) than to wild-type liver slices. CONCLUSION: Mouse PCLS cultures in the presence of PFD may serve as a useful tool for screening local adherence and invasiveness of individual cancer cells, since single cells can be observed. This method may also prove useful for identification of genes in liver-resident cells that support cancer invasion by using PCLS from transgenic liver.

THOC5, a member of the mRNA export complex, contributes to processing of a subset of wingless/integrated (Wnt) target mRNAs and integrity of the gut epithelial barrier.

BACKGROUND: THO (Suppressors of the transcriptional defects of hpr1 delta by overexpression) complex 5 (THOC5), an mRNA export protein, is involved in the expression of only 1% of all genes. Using an interferon inducible knockout mouse system, we have previously shown that THOC5 is an essential element in the maintenance of hematopoietic stem cells and cytokine-mediated hematopoiesis in adult mice. Here we interrogate THOC5 function in cell differentiation beyond the hematopoietic system and study pathological changes caused by THOC5 deficiency. RESULTS: To examine whether THOC5 plays a role in general differentiation processes, we generated tamoxifen inducible THOC5 knockout mice. We show here that the depletion of THOC5 impaired not only hematopoietic differentiation, but also differentiation and self renewal of the gut epithelium. Depletion of the THOC5 gene did not cause pathological alterations in liver or kidney. We further show that THOC5 is indispensable for processing of mRNAs induced by Wnt (wingless/integrated) signaling which play key roles in epithelial cell differentiation/proliferation. A subset of Wnt target mRNAs, SRY-box containing gene 9 (Sox9), and achaete-scute complex homolog 2 (Ascl2), but not Fibronectin 1 (Fn1), were down-regulated in THOC5 knockout intestinal cells. The down-regulated Wnt target mRNAs were able to bind to THOC5. Furthermore, pathological alterations in the gastrointestinal tract induced translocation of intestinal bacteria and caused sepsis in mice. The bacteria translocation may cause Toll-like receptor activation. We identified one of the Toll-like receptor inducible genes, prostaglandin-endoperoxidase synthase 2 (Ptgs2 or COX2) transcript as THOC5 target mRNA. CONCLUSION: THOC5 is indispensable for processing of only a subset of mRNAs, but plays a key role in processing of mRNAs inducible by Wnt signals. Furthermore, THOC5 is dispensable for general mRNA export in terminally differentiated organs, indicating that multiple mRNA export pathways exist. These data imply that THOC5 may be a useful tool for studying intestinal stem cells, for modifying the differentiation processes and for cancer therapy.

Identification of mRNAs that are spliced but not exported to the cytoplasm in the absence of THOC5 in mouse embryo fibroblasts.

The TREX (transcription/export) complex has been conserved throughout evolution from yeast to man and is required for coupled transcription elongation and nuclear export of mRNAs. The TREX complex in mammals and Drosophila is composed of the THO subcomplex (THOC1, THOC2, THOC5, THOC6, and THOC7), THOC3, UAP56, and Aly/THOC4. In human and Drosophila, various studies have shown that THO is required for the export of heat shock mRNAs, but nothing is known about other mRNAs. Our previous study using conditional THOC5 (or FMIP) knockout mice revealed that the presence of THOC5 is critical in hematopoietic cells but not for terminally differentiated cells. In this study, we describe the establishment of a mouse embryo fibroblast cell line (MEF), THOC5 flox/flox. Four days after infection of MEF THOC5 flox/flox with adenovirus carrying Cre-recombinase gene (Ad-GFP-Cre), THOC5 is down-regulated >95% at the protein level, and cell growth is strongly suppressed. Transcriptome analysis using cytoplasmic RNA isolated from cells lacking functional THOC5 reveals that only 2.9% of all genes were down-regulated more than twofold. Although we examined these genes in fibroblasts, one-fifth of all down-regulated genes (including HoxB3 and polycomb CBX2) are known to play a key role in hematopoietic development. We further identified 10 genes that are spliced but not exported to the cytoplasm in the absence of THOC5. These mRNAs were copurified with THOC5. Furthermore, Hsp70 mRNA was exported in the absence of THOC5 at 37°C, but not under heat shock condition (42°C), suggesting that THOC5 may be required for mRNA export under stress and/or upon signaling-induced conditions.

Conflict interference in an insect.

Response conflicts occur when the correct goal-congruent response is weaker than an alternative but incorrect response. To overcome response conflicts, the stronger response has to be inhibited, making the study of response conflicts an important research topic in higher order cognition. Response conflicts often result in conflict interference-an increase in error rates and response times. Here, we ask whether an invertebrate-the ant, Lasius niger-can solve such response conflicts and, if so, whether it suffers from conflict interference. We also ask whether ants show congruency sequence effects, where subjects show transiently reduced conflict inference when conflicts repeat. We developed task-mimicking aspects of the Stroop color-word test, in which ants must learn to follow a neutral cue (a scent) on a Y maze but ignore a dominant and innately meaningful signal (a pheromone trail). The pheromone can be congruent with the scent cue (lead to the same maze arm) or be incongruent. Both accuracy and task-solving latency suffered when the information sources were incongruent. There was no evidence of congruency sequence effects. Because of limitations of the experimental design, we cannot rule out that insects would also show a congruency sequence effect under a different experimental paradigm. Although the methodology is not directly comparable to human studies, the presence of clear conflict interference suggests parallels between insect and human information processing, in spite of completely different brains. This powerful and straightforward methodology opens the possibility of exploring conflict interference in the presence of prepotent response tendencies in an invertebrate model. We hope this work encourages the field of response competition to use the vast literature on response competition in animal behavior studies. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Retinal layer assessments as potential biomarkers for brain atrophy in the Rhineland Study.

Retinal assessments have been discussed as biomarkers for brain atrophy. However, available studies did not investigate all retinal layers due to older technology, reported inconsistent results, or were based on small sample sizes. We included 2872 eligible participants of the Rhineland Study with data on spectral domain-optical coherence tomography (SD-OCT) and brain magnetic resonance imaging (MRI). We used multiple linear regression to examine relationships between retinal measurements and volumetric brain measures as well as fractional anisotropy (FA) as measure of microstructural integrity of white matter (WM) for different brain regions. Mean (SD) age was 53.8 ± 13.2 years (range 30-94) and 57% were women. Volumes of the inner retina were associated with total brain and grey matter (GM) volume, and even stronger with WM volume and FA. In contrast, the outer retina was mainly associated with GM volume, while both, inner and outer retina, were associated with hippocampus volume. While we extend previously reported associations between the inner retina and brain measures, we found additional associations of the outer retina with parts of the brain. This indicates that easily accessible retinal SD-OCT assessments may serve as biomarkers for clinical monitoring of neurodegenerative diseases and merit further research.

Identification of novel target genes of nerve growth factor (NGF) in human mastocytoma cell line (HMC-1 (V560G c-Kit)) by transcriptome analysis.

BACKGROUND: Nerve growth factor (NGF) is a potent growth factor that plays a key role in neuronal cell differentiation and may also play a role in hematopoietic differentiation. It has been shown that NGF induced synergistic action for the colony formation of CD34 positive hematopoietic progenitor cells treated with macrophage-colony stimulating factor (M-CSF or CSF-1), or stem cell factor (SCF). However, the exact role of NGF in hematopoietic system is unclear. It is also not clear whether NGF mediated signals in hematopoietic cells are identical to those in neuronal cells. RESULTS: To study the signal transduction pathways induced by NGF treatment in hematopoietic cells, we utilized the mastocytoma cell line HMC-1(V560G c-Kit) which expresses the NGF receptor, tropomyosin-receptor-kinase (Trk)A, as well as the constitutively activated SCF receptor, V560G c-Kit, which can be inhibited completely by treatment with the potent tyrosine kinase inhibitor imatinib mesylate (imatinib). NGF rescues HMC-1(V560G c-Kit) cells from imatinib mediated cell death and promotes proliferation. To examine the NGF mediated proliferation and survival in these cells, we compared the NGF mediated upregulated genes (30 and 120 min after stimulation) to the downregulated genes by imatinib treatment (downregulation of c-Kit activity for 4 h) by transcriptome analysis. The following conclusions can be drawn from the microarray data: Firstly, gene expression profiling reveals 50% overlap of genes induced by NGF-TrkA with genes expressed downstream of V560G c-Kit. Secondly, NGF treatment does not enhance expression of genes involved in immune related functions that were down regulated by imatinib treatment. Thirdly, more than 55% of common upregulated genes are involved in cell proliferation and survival. Fourthly, we found Kruppel-like factor (KLF) 2 and Smad family member 7 (SMAD7) as the NGF mediated novel downstream genes in hematopoietic cells. Finally, the downregulation of KLF2 gene enhanced imatinib induced apoptosis. CONCLUSION: NGF does not induce genes which are involved in immune related functions, but induces proliferation and survival signals in HMC-1(V560G c-Kit) cells. Furthermore, the current data provide novel candidate genes, KLF2 and SMAD7 which are induced by NGF/TrkA activation in hematopoietic cells. Since the depletion of KLF2 causes enhanced apoptosis of HMC-1(V560G c-Kit), KLF2 may play a role in the NGF mediated survival signal.

THOC5/FMIP, an mRNA export TREX complex protein, is essential for hematopoietic primitive cell survival in vivo.

BACKGROUND: The transcription/export complex is evolutionarily conserved from yeast to man and is required for coupled transcription elongation and nuclear export of mRNAs. FMIP(Fms interacting protein) is a member of the THO (suppressors of the transcriptional defects of hpr1delta by overexpression) complex which is a subcomplex of the transcription/export complex. THO complex (THOC) components are not essential for bulk poly (A)+ RNA export in higher eukaryotes, but for the nuclear export of subset of mRNAs, however, their exact role is still unclear. RESULTS: To study the role of THOC5/Fms interacting protein in vivo, we generated THOC5/Fms interacting protein knockout mice. Since these mice are embryonic lethal, we then generated interferon inducible conditional THOC5/Fms interacting protein knockout mice. After three poly injections all of the mice died within 14 days. No pathological alterations, however, were observed in liver, kidney or heart. Thus we considered the hematopoietic system and found that seven days after poly injection, the number of blood cells in peripheral blood decreased drastically. Investigation of bone marrow cells showed that these became apoptotic within seven days after poly injection. Committed myeloid progenitor cells and cells with long term reconstituting potential were lost from bone marrow within four days after poly injection. Furthermore, infusion of normal bone marrow cells rescued mice from death induced by loss of THOC5/Fms interacting protein. CONCLUSION: THOC5/Fms interacting protein is an essential element in the maintenance of hematopoiesis. Furthermore, mechanistically depletion of THOC5/Fms interacting protein causes the down-regulation of its direct interacting partner, THOC1 which may contribute to altered THO complex function and cell death.

Multi-shell Diffusion MRI Models for White Matter Characterization in Cerebral Small Vessel Disease.

OBJECTIVE: To test the hypothesis that multi-shell diffusion models improve the characterization of microstructural alterations in cerebral small vessel disease (SVD), we assessed associations with processing speed performance, longitudinal change, and reproducibility of diffusion metrics. METHODS: We included 50 patients with sporadic and 59 patients with genetically defined SVD (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy [CADASIL]) with cognitive testing and standardized 3T MRI, including multi-shell diffusion imaging. We applied the simple diffusion tensor imaging (DTI) model and 2 advanced models: diffusion kurtosis imaging (DKI) and neurite orientation dispersion and density imaging (NODDI). Linear regression and multivariable random forest regression (including conventional SVD markers) were used to determine associations between diffusion metrics and processing speed performance. The detection of short-term disease progression was assessed by linear mixed models in 49 patients with sporadic SVD with longitudinal high-frequency imaging (in total 459 MRIs). Intersite reproducibility was determined in 10 patients with CADASIL scanned back-to-back on 2 different 3T MRI scanners. RESULTS: Metrics from DKI showed the strongest associations with processing speed performance (R 2 up to 21%) and the largest added benefit on top of conventional SVD imaging markers in patients with sporadic SVD and patients with CADASIL with lower SVD burden. Several metrics from DTI and DKI performed similarly in detecting disease progression. Reproducibility was excellent (intraclass correlation coefficient >0.93) for DTI and DKI metrics. NODDI metrics were less reproducible. CONCLUSION: Multi-shell diffusion imaging and DKI improve the detection and characterization of cognitively relevant microstructural white matter alterations in SVD. Excellent reproducibility of diffusion metrics endorses their use as SVD markers in research and clinical care. Our publicly available intersite dataset facilitates future studies. CLASSIFICATION OF EVIDENCE: This study provides Class I evidence that in patients with SVD, diffusion MRI metrics are associated with processing speed performance.

Acceptance and Feasibility of a Guideline for the Animal Welfare Assessment of Fattening Pigs from Farmers' Point of View.

The welfare of farm animals is being increasingly discussed in society and politics. To evaluate animal welfare, indicator systems are often used. Such a system has been developed by the German Association for Technology and Structures in Agriculture and suggested in the publication "Animal Welfare Indicators: Practical Guide-Pigs". The association's aim is to provide farmers with a useful method for recording the welfare of pigs. Crucial for the acceptance of the guide by farmers is a high degree of feasibility of the recommended indicators as well as the proposed methods for their recording. To evaluate this, 40 farmers keeping fattening pigs were interviewed. The guided semi-structured interview was conducted on the farms after the farmers evaluated the welfare of their fattening pigs according to the guide. The results are: Apart from the indicators faecal soiling and tail length, all the other eleven indicators are accepted for the assessment of fattening pig welfare by a majority of the interviewed farmers (between 57.5% and 90% acceptance per indicator). Furthermore, the feasibility of the individual indicators was assessed as being positive. The relationship between time expenditure and benefit was rated on a five-point scale at an average of 3.1 (medium), which clearly shows that there is a need for further development of this guide. Some possible changes with a potential for improvement could be identified; for example, the aggregation of the results after the collection of the individual indicators to an overall result that can be compared and interpreted.

Comparison of q-Space Reconstruction Methods for Undersampled Diffusion Spectrum Imaging Data.

PURPOSE: To compare different q-space reconstruction methods for undersampled diffusion spectrum imaging data. MATERIALS AND METHODS: We compared the quality of three methods: Mean Apparent Propagator (MAP); Compressed Sensing using Identity (CSI) and Compressed Sensing using Dictionary (CSD) with simulated data and in vivo acquisitions. We used retrospective undersampling so that the fully sampled reconstruction could be used as ground truth. We used the normalized mean squared error (NMSE) and the Pearson's correlation coefficient as reconstruction quality indices. Additionally, we evaluated two propagator-based diffusion indices: mean squared displacement and return to zero probability. We also did a visual analysis around the centrum semiovale. RESULTS: All methods had reconstruction errors below 5% with low undersampling factors and with a wide range of noise levels. However, the CSD method had at least 1-2% lower NMSE than the other reconstruction methods at higher noise levels. MAP was the second-best method when using a sufficiently high number of q-space samples. MAP reconstruction showed better propagator-based diffusion indices for in vivo acquisitions. With undersampling factors greater than 4, MAP and CSI have noticeably more reconstruction error than CSD. CONCLUSION: Undersampled data were best reconstructed by means of CSD in simulations and in vivo. MAP was more accurate in the extraction of propagator-based indices, particularly for in vivo data.

Voluntary switching in an invertebrate: The effect of cue and reward change.

When faced with multiple competing goals, individuals must decide which goal to attend to. Voluntary task switching is an important paradigm for testing cognitive flexibility and spontaneous decision-making when competing tasks are present. Of particular importance is the study of how reward affects task switching, as reward is perhaps the most commonly used tool for shaping both human and animal behavior. Recently, Fröber and Dreisbach (2016) demonstrated that it is not reward level per se, but reward change, which most strongly affects switching behavior in humans: Task switching was lowest when reward remained high and highest when reward is changed (increase or decrease), while the repetition of low reward showed intermediate switching levels. Here we replicate their experiment on individual foragers of the ant species Lasius niger. Using an adapted spontaneous alternation task, we find that ants' switching response in light of their immediate reward history is qualitatively identical to that of humans. In a second experiment, we show that some of this behavior can be explained by the cue change, rather than the rewards. However, patterns exist in the data which cue change cannot explain. The striking parallel in behavior between humans and insects raises questions about how reward shapes behavioral flexibility and stability in humans. (PsycINFO Database Record

Colony-stimulating factor-1 receptor provides a growth advantage in epithelial cancer cell line A431 in the presence of epidermal growth factor receptor inhibitor gefitinib.

Although epidermal growth factor receptor (EGFR) has been identified as a potent "oncogenic driver" in various tumors of epithelial origin, EGFR-targeted therapies are often of limited success. One of the challenges of improving targeted therapies is to overcome bypassing signaling pathways. Analysis of RNA-seq data of 1006 cell lines from the Cancer Cell Line Encyclopedia (CCLE) revealed that more than 12% of carcinoma cell lines expressed markedly elevated mRNA levels of colony-stimulating factor (CSF)-1 receptor (CSF-1R). Since epithelial cells also express CSF-1, elevated levels of CSF-1R may participate in providing alternative growth and survival signals under targeted therapies. To address this question, we ectopically expressed CSF-1R in A431 cells that express EGFR at high levels, but no biologically relevant level of CSF-1R. In the presence of EGFR inhibitor gefitinib, CSF-1R provided a significant growth advantage in A431 cells. As expected, activation of both receptors, EGFR or CSF-1R, induced phosphorylation of extracellular signal-regulated kinase (Erk)1/2, Akt, protein kinase C (PKC) and signal transducer and activator of transcription (STAT)3. However, EGFR, but not CSF-1R, also induced STAT5 phosphorylation. Inhibitor of phosphatidylinositol 3-kinase (PI3K) (AZD8186), MAPK/ERK kinase (MEK)1/2 (U0126), PKCs (Bisindolylmaleimide I or Gö6976) or STAT3 (Stattic) partially reduced proliferation of CSF-1R expressing A431 cells in the presence of gefitinib. Moreover, multi-kinase inhibitor, cabozantinib, suppressed CSF-1R activation and drastically reduced cell growth when combined with gefitinib. These data suggest that CSF-1R has the potential to reduce sensitivity to gefitinib and may be involved in resistance development.

The SH2-domian-containing inositol 5-phosphatase (SHIP)-2 binds to c-Met directly via tyrosine residue 1356 and involves hepatocyte growth factor (HGF)-induced lamellipodium formation, cell scattering and cell spreading.

Recently, evidence has been accumulating that inositol and phosphatidylinositol polyphosphate play important roles in a variety of signal transduction systems including membrane traffic, actin cytoskeleton rearrangement and cell motility. In this paper, we show for the first time that the SH2-domain-containing inositol 5-phosphatase (SHIP)-2 binds directly to the hepatocyte growth factor (HGF/SF) receptor, c-Met, via phosphotyrosine 1356. HGF induces the breakdown of cell junctions and the dispersion of colonies of epithelial cells including MDCK cells. Whereas only few lamellipodia are observed in MDCK cells 2 min after stimulation with HGF, both SHIP-2- and SHIP-1-overexpressing cells form large, broad lamellipodia. The number of lamellipodia is 2-4-fold greater than that of mock-transfected MDCK cells in the same time period and SHIP is found to colocalize with actin at the leading edge. Furthermore, overexpression of a catalytic inactive mutant of SHIP-2 suppresses HGF-potentiated cell scattering and cell spreading, although these mutant-expressing cells form enhanced number of lamellipodia 2 min after HGF stimulation. Interestingly, cells expressing a mutant lacking the proline-rich domain of SHIP-2 at the C-terminal form few lamellipodia, but still spread and scatter upon stimulation with HGF at a reduced rate. These data suggest that phosphatase activity is required for HGF-mediated cell spreading and scattering but not for alteration of lamellipodium formation, while the proline-rich region influences lamellipodium formation. Furthermore, treatment with 10 microM of phosphatidylinositol 3 (PI3) kinase inhibitor, LY294002, abrogates HGF-induced cell scattering of SHIP-2-overexpressing cells but not parental HEK293 cells, suggesting that a balance between PI3 kinase and SHIP is important for cell motility.

mRNA export protein THOC5 as a tool for identification of target genes for cancer therapy.

Recent evidence indicates that mRNA export is selective, giving priority to a subset of mRNAs that control diverse biological processes including cell proliferation, differentiation, stress response, and cell survival as well as tumor development. The depletion of a member of the mRNA export complex, the THO complex, impairs the expression of only a subset of genes, but causes dramatic changes in phenotype, such as cell cycle inhibition, abnormal differentiation, and importantly apoptosis of stem cells and cancer cells but not normal epithelial cells, hepatocytes, or fibroblasts. Recent exosome sequence data revealed that over 100 driver gene mutations with a number of signaling pathways are involved in human cancer formation, indicating that multiple signaling pathways will need to be inhibited for cancer therapy. In this review we firstly describe a basic feature and function of the mRNA export complex, THO, secondly, the biological alteration upon depletion of a member of the THO complex in normal and cancer cells, and thirdly, identification of its target genes. Finally we describe our recent data on selection of targeting candidates from THOC5 dependent genes for application in cancer therapy.