The C-Terminal TDP-43 Fragments Have a High Aggregation Propensity and Harm Neurons by a Dominant-Negative Mechanism

TAR DNA binding protein 43 KD (TDP-43) is an essential gene that regulates gene transcription, mRNA splicing and stability. In amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two fatal neurodegenerative diseases, TDP-43 is fragmented, generating multiple fragments that include the C-terminal fragment of ∼25 KD. The role of these fragments in the pathogenesis of ALS and FTD is not clear. Here we investigated the aggregation propensity in various polypeptide regions of TDP-43 in mammalian cells and the effect of these fragments on cultured neurons. By expressing the full length and various TDP-43 fragments in motor neuron-derived NSC-34 cells and primary neurons, we found that both N- and C-terminal fragments of TDP-43 are prone to aggregate and the C-terminal end of RRM2 region is required, though not sufficient, for aggregation. The aggregation of the TDP-43 fragments can drive co-aggregation with the full-length TDP-43, consequently reducing the nuclear TDP-43. In addition, the TDP-43 fragments can impair neurite growth during neuronal differentiation. Importantly, overexpression of the full-length TDP-43 rescues the neurite growth phenotype whereas knockdown of the endogenous TDP-43 reproduces this phenotype. These results suggest that TDP-43 fragments, particularly the pathologically relevant C-terminal fragments, can impair neuronal differentiation by dominant-negatively interfering with the function of the full length TDP-43, thus playing a role in pathogenesis in ALS and FTD

YTHDF1 Regulates Tumorigenicity and Cancer Stem Cell-Like Activity in Human Colorectal Carcinoma

YTH N6-methyladenosine (m6A) RNA binding protein 1 (YTHDF1) is a core factor in RNA methylation modification. Recent studies have shown that m6A is closely related to multiple tumors, thus YTHDF1 may also play a role in tumorigenesis. This study, aimed to explore the role of YTHDF1 in the colorectal cancer (CRC). In this study, we identified YTHDF1 as being highly expressed at the mRNA and protein levels in TCGA, GEO CRC and primary CRC. Furthermore, the YTHDF1 gene copy number was positively correlated with YTHDF1 mRNA expression in CRC. Knocking down the expression of YTHDF1 significantly inhibited the CRC cell's tumorigenicity in vitro and murine xenograft tumor growth in vivo. Furthermore, silencing of YTHDF1 inhibited the colonosphere formation ability in vitro. Mechanistically, we found that silencing YTHDF1 significantly inhibited Wnt/β-catenin pathway activity in CRC cells. Together, YTHDF1 is overexpressed in CRC and plays a vital oncogenic role in CRC, and this novel finding may provide a potential therapeutic target for CRC

Study of Promoter Methylation Patterns of HOXA2, HOXA5, and HOXA6 and Its Clinicopathological Characteristics in Colorectal Cancer

Research on DNA methylation offers great potential for the identification of biomarkers that can be applied for accurately assessing an individual's risk for cancer. In this article, we try to find the ideal epigenetic genes involved in colorectal cancer (CRC) based on a CRC database and our CRC cohort. The top 20 genes with an extremely high frequency of hypermethylation in CRC were identified in the latest database. Remarkably, 3 HOXA genes were included in this list and ranked at the top. The percentage of methylation in the HOXA5, HOXA2, and HOXA6 genes in CRC were up to 67.62, 58.36, and 31.32%, respectively, and ranked first in CRC among all human tumor tissues. Paired colorectal tumor samples and adjacent non-tumor colorectal tissue samples and four CRC cell lines were selected for MethylTarget™ assays. The results demonstrated that CRC tissues and cells had a stronger methylation status around the 3 HOXA gene promoter regions compared with adjacent non-tumor colonic tissue samples. The Receiver operator characteristic curve (ROC) curves for HOXA genes show excellent diagnostic ability in distinguishing tissue from healthy individuals and CRC patients, especially for Stage I patients (AUC = 0.9979 in HOXA2, 0.9309 in HOXA5, and 0.8025 in HOXA6). An association analysis between the methylation pattern of HOXA genes and clinical indicators was performed and found that HOXA2 methylation was significantly associated with age, N, stage, M, lymphovascular invasion, perineural invasion, lymph node number. HOXA5 methylation was associated with age, T, M, stage, and tumor status, and HOXA6 methylation was associated with age and KRAS mutation. Notably, we found that the highest methylation of HOXA5 and HOXA2 occurs in the early stages of colorectal cancer tissues such as stage I, N0, MO, and non-invasive tissues. The methylation levels declined as tumors progressed. However, methylation level at any stage of the tumor was still significantly higher than in normal tissues (p < 0.0001). The mRNA of the 3 HOXA genes was downregulated in early tumor stages due to hypermethylation of CpG islands adjacent to the promoters of the genes. In addition, hypermethylation of HOXA5 and HOXA6 mainly occurred in patients < 60 years old and with MSI-L, MSS, CIMP.L and non-CIMP tumors. Together, this suggests that epigenetic silencing of 3 adjacent HOXA genes may be an important event in the progression of colorectal cancer

Comparison of Linear Superconducting Magnetic Bearings using Isotropic and Anisotropic Materials

International audienceCritical current density anisotropy is a common property of high-temperature superconducting materials. We clarify here how it could impact the performances of superconducting magnetic bearings by comparing linear bearings using isotropic and anisotropic materials. To be fair, the comparison considers optimized designs. An H-formulation finite element model is used to obtain the levitation and guidance forces of the bearing for a given moving sequence. It is coupled with a stochastic optimization algorithm. For the considered bearing topology (single bulk above PM Halbach array), it was found that for applications requiring only levitation force, both isotropic and anisotropic materials are suitable. But for applications requiring both levitation and guidance forces, isotropic materials are more suitable than anisotropic ones since they can provide a stable guidance force for a given minimal levitation force at the smallest cost. This could serve as general design guidelines for future engineering applications

Functionality and substrate specificity of human box H/ACA guide RNAs

A large number of box H/ACA RNAs have been identified in human cells, and have been predicted to account for nearly all pseudouridylation sites in human rRNAs. However, the function of these mammalian H/ACA RNAs in directing pseudouridylation has been verified experimentally in only two cases. In this study, we used three in vitro reconstitution systems, including yeast and mammalian systems, to test the function of seven H/ACA RNAs guiding16 pseudouridylation sites. Our results verified 12 of these sites; four predictions were incorrect. Further analyses indicated that three components, including the stability of the hairpin structure harboring the pseudouridylation pocket, the stability of guide sequence–target RNA base-pairing interaction, and the distance between the target uridine and the box H or ACA, were critical for the guide function, as changes in these components were sufficient to alter the functionality and specificity of the pseudouridylation pocket. The dynamic functional changes in response to changes in these three important components were further tested in vivo, and the results were completely consistent with the in vitro results. Finally, we compared our results with predictions made by two computer programs, as well as predictions made by human experts using visual inspection. We found that the predictions of one program (snoGPS) agreed with our experimental results with 100% sensitivity (12/12) and 75% specificity (3/4)

Construction of a Multicomponent Molecular Model of Fugu Coal for ReaxFF-MD Pyrolysis Simulation

Proper description of chemical structure diversity is necessary for a coal model in exploring the coal pyrolysis mechanism by reactive molecular dynamics (ReaxFF-MD) simulation. This paper presents a strategy for constructing large and reasonable coal models manually with varied chemical structures. A multicomponent molecular model containing 23,898 atoms was constructed for Fugu subbituminous coal following the proposed strategy on the basis of characterization data obtained from the proximate and ultimate analysis, C-13 NMR, and solvent extraction experiments. The model consists of 7S macromolecules of 20 varied average structures for structural diversity and 29 varied small compounds to capture the mobile phase. The elemental composition and key structural parameters of the multicomponent model agree with the analytical data of Fugu coal sample on the whole. The weight loss profile obtained from slow heat-up (2 K/ps) ReaxFF-MD simulations agrees fairly with the observations from thermogravimetric experiments reported in the literature. The temporal evolution of a representative product (C2H4) from long-time (2000 ps) isothermal ReaxFF-MD simulations shows qualitative agreement with the results of the synchrotron radiation vacuum ultraviolet photoionization time-of-flight mass spectrometry (SVUV-PI-TOF-MS) pyrolysis experiments. These examinations indicate the applicability of the constructed model in ReaxFF-MD simulations to explore the coal pyrolysis mechanism. The proposed strategy suggests a feasible approach for manually constructing reasonable large coal models based on limited conventional characterization data

Adaptive Responses of the Sea Anemone Heteractis crispa to the Interaction of Acidification and Global Warming

Ocean acidification and warming are two of the most important threats to the existence of marine organisms and are predicted to co-occur in oceans. The present work evaluated the effects of acidification (AC: 24 ± 0.1 °C and 900 μatm CO2), warming (WC: 30 ± 0.1 °C and 450 μatm CO2), and their combination (CC: 30 ± 0.1 °C and 900 μatm CO2) on the sea anemone, Heteractis crispa, from the aspects of photosynthetic apparatus (maximum quantum yield of photosystem II (PS II), chlorophyll level, and Symbiodiniaceae density) and sterol metabolism (cholesterol content and total sterol content). In a 15-day experiment, acidification alone had no apparent effect on the photosynthetic apparatus, but did affect sterol levels. Upregulation of their chlorophyll level is an important strategy for symbionts to adapt to high partial pressure of CO2 (pCO2). However, after warming stress, the benefits of high pCO2 had little effect on stress tolerance in H. crispa. Indeed, thermal stress was the dominant driver of the deteriorating health of H. crispa. Cholesterol and total sterol contents were significantly affected by all three stress conditions, although there was no significant change in the AC group on day 3. Thus, cholesterol or sterol levels could be used as important indicators to evaluate the impact of climate change on cnidarians. Our findings suggest that H. crispa might be relatively insensitive to the impact of ocean acidification, whereas increased temperature in the future ocean might impair viability of H. crispa

A Single Injection of Recombinant Adeno-Associated Virus into the Lumbar Cistern Delivers Transgene Expression Throughout the Whole Spinal Cord

The lack of methods to deliver transgene expression in spinal cord has hampered investigation of gene function and therapeutic targets for spinal cord diseases. Here, we report that a single intrathecal injection of recombinant adeno-associated virus rhesus-10 (rAAVrh10) into the lumbar cistern led to transgene expression in 60 to 90 % of the cells in the spinal cord. The transgene was expressed in all cell types, including neurons, glia, ependymal cells, and endothelial cells. Additionally, the transgene was expressed in some brain areas up to the frontal cortex and the olfactory bulb. The rAAV was distributed predominantly in the spinal cord, where its genome copy was over ten times that of the peripheral organs. Compared with intravenous injection, another method for rAAV delivery to the broad central nervous system (CNS), the intrathecal injection reduced the dosage of rAAV required to achieve similar or higher levels of transgene expression in the CNS by ~100-fold. Finally, the transduced areas were co-localized with the perivascular spaces of Virchow-Robin, from which the rAAV spreads further into the CNS parenchyma, thus suggesting that rAAV penetrated the CNS parenchyma through this pathway. Taken together, we have defined a fast and efficient method to deliver widespread transgene expression in mature spinal cord in mice. This method can be applied to stably overexpress or silence gene expression in the spinal cord to investigate gene functions in mammalian CNS. Additionally, this method can be applied to validate therapeutic targets for spinal cord diseases