Neuropilin-1 is a co-receptor for NGF and TrkA-evoked pain

Nerve growth factor (NGF) monoclonal antibodies (mAb) are one of the few patient-validated non-opioid treatments for chronic pain, despite failing to gain FDA approval due to worsened joint damage in some osteoarthritis patients. Herein, we demonstrate that neuropilin-1 (NRP1) is a nociceptor-enriched co-receptor for NGF that is necessary for tropomyosin-related kinase A (TrkA) signaling of pain. NGF binds NRP1 with nanomolar affinity. NRP1 and G Alpha Interacting Protein C-terminus 1 (GIPC1), a NRP1/TrkA adaptor, are coexpressed with TrkA in human and mouse nociceptors. NRP1 small molecule inhibitors and blocking mAb prevent NGF-stimulated action potential firing and activation of Na+ and Ca2+ channels in human and mouse nociceptors and abrogate NGF-evoked and inflammatory nociception in mice. NRP1 knockdown blunts NGF-stimulated TrkA phosphorylation, kinase signaling and transcription, whereas NRP1 overexpression enhances NGF and TrkA signaling. As well as interacting with NGF, NRP1 forms a heteromeric complex with TrkA. NRP1 thereby chaperones TrkA from the biosynthetic pathway to the plasma membrane and then to signaling endosomes, which enhances NGF-induced TrkA dimerization, endocytosis and signaling. Knockdown of GIPC1, a PDZ-binding protein that scaffolds NRP1 and TrkA to myosin VI, abrogates NGF-evoked excitation of nociceptors and pain-like behavior in mice. We identify NRP1 as a previously unrecognized co-receptor necessary for NGF/TrkA pain signaling by direct NGF binding and by chaperoning TrkA to the plasma membrane and signaling endosomes via the adaptor protein GIPC1. Antagonism of NRP1 and GIPC1 in nociceptors offers a long-awaited alternative to systemic sequestration of NGF with mAbs for the treatment of pain.

Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D

Isozymes are enzymes that catalyze identical biological reactions, yet exhibit slight variations in structures and catalytic efficiency, which enables the precise adjustment of metabolism to fulfill the specific requirements of a particular tissue or stage of development. Methionine aminopeptidase (MetAP) isozymes function a critical role in cleaving N-terminal methionine from nascent proteins to generate functional proteins. In humans, two distinct MetAP types I and II have been identified, with type I further categorized into cytosolic (MetAP1) and mitochondrial (MetAP1D) variants. However, despite extensive structural studies on both bacterial and human cytosolic MetAPs, the structural information remains unavailable for human mitochondrial MetAP. This study was aimed to elucidate the high-resolution structures of human mitochondrial MetAP1D in its apo-, cobalt-, and methionine-bound states. Through a comprehensive analysis of the determined structures and a docking simulation model with mitochondrial substrate peptides, we present mechanistic insights into the cleavage process of the initiator methionine from mitochondrial proteins. Notably, despite the shared features at the active site between the cytosolic and mitochondrial MetAP type I isozymes, we identified distinct structural disparities within the active-site pocket primarily contributed by two specific loops that could play a role in accommodating specific substrates. These structural insights offer a basis for the further exploration of MetAP isozymes as critical players in cellular processes and potential therapeutic applications.

β-Arrestin-dependent and -independent endosomal G protein activation by the vasopressin type 2 receptor

The vasopressin type 2 receptor (V2R) is an essential G protein-coupled receptor (GPCR) in renal regulation of water homeostasis. Upon stimulation, the V2R activates Gαs and Gαq/11, which is followed by robust recruitment of β-arrestins and receptor internalization into endosomes. Unlike canonical GPCR signaling, the β-arrestin association with the V2R does not terminate Gαs activation, and thus, Gαs-mediated signaling is sustained while the receptor is internalized. Here, we demonstrate that this V2R ability to co-interact with G protein/β-arrestin and promote endosomal G protein signaling is not restricted to Gαs, but also involves Gαq/11. Furthermore, our data imply that β-arrestins potentiate Gαs/Gαq/11 activation at endosomes rather than terminating their signaling. Surprisingly, we found that the V2R internalizes and promote endosomal G protein activation independent of β-arrestins to a minor degree. These new observations challenge the current model of endosomal GPCR signaling and suggest that this event can occur in both β-arrestin-dependent and -independent manners.

β-arrestin-dependent and -independent endosomal G protein activation by the vasopressin type 2 receptor

The vasopressin type 2 receptor (V2R) is an essential GPCR in renal regulation of water homeostasis. Upon stimulation, the V2R activates Gαs and Gαq/11, which is followed by robust recruitment of β-arrestins and receptor internalization into endosomes. Unlike canonical GPCR signaling, the β-arrestin association with the V2R does not terminate Gαs activation, and thus, Gαs-mediated signaling is sustained while the receptor is internalized. Here, we demonstrate that this V2R ability to co-interact with G protein/β-arrestin and promote endosomal G protein signaling is not restricted to Gαs, but also involves Gαq/11. Furthermore, our data implies that β-arrestins potentiate Gαs/Gαq/11 activation at endosomes rather than terminating their signaling. Surprisingly, we found that the V2R internalizes and promote endosomal G protein activation independent of β-arrestins to a minor degree. These new observations challenge the current model of endosomal GPCR signaling and suggest that this event can occur in both β-arrestin-dependent and -independent manners.

Structural Basis of Inhibition of DCLK1 by Ruxolitinib

Given the functional attributes of Doublecortin-like kinase 1 (DCLK1) in tumor growth, invasion, metastasis, cell motility, and tumor stemness, it is emerging as a therapeutic target in gastrointestinal cancers. Although a series of specific or nonspecific ATP-competitive inhibitors were identified against DCLK1, different types of scaffolds that can be utilized for the development of highly selective inhibitors or structural understanding of binding specificities of the compounds remain limited. Here, we present our work to repurpose a Janus kinase 1 inhibitor, ruxolitinib as a DCLK1 inhibitor, showing micromolar binding affinity and inhibitory activity. Furthermore, to gain an insight into its interaction mode with DCLK1, a crystal structure of the ruxolitinib-complexed DCLK1 has been determined and analyzed. Ruxolitinib as a nonspecific DCLK1 inhibitor characterized in this work is anticipated to provide a starting point for the structure-guided discovery of selective DCLK1 inhibitors.

Ultra-low-vibration closed-cycle cryogenic surface-electrode ion trap apparatus

We describe the design, commissioning, and operation of an ultra-low-vibration closed-cycle cryogenic ion trap apparatus. One hundred lines for low-frequency signals and eight microwave/radio frequency coaxial feed-lines offer the possibility of implementing a small-scale ion-trap quantum processor or simulator. With all supply cables attached, more than 1.3 W of cooling power at 5 K is still available for absorbing energy from electrical pulses introduced to control ions. The trap itself is isolated from vibrations induced by the cold head using a helium exchange gas interface. The performance of the vibration isolation system has been characterized using a Michelson interferometer, finding residual vibration amplitudes on the order of 10 nm rms. Trapping of ⁹Be⁺ ions has been demonstrated using a combination of laser ablation and photoionization.

Tumor regression grading after neoadjuvant treatment of esophageal and gastroesophageal junction adenocarcinoma: results of an international Delphi consensus survey

Complete histopathologic tumor regression after neoadjuvant treatment is a well-known prognostic factor for survival among patients with adenocarcinomas of the esophagus and gastroesophageal junction. The aim of this international Delphi survey was to reach a consensus regarding the most useful tumor regression grading (TRG) system that could represent an international standard for histopathologic TRG grading of gastroesophageal carcinomas. Fifteen pathologists with special interest in esophageal and gastric pathology participated in the online survey. The initial questionnaire contained of 43 statements that addressed the following topics: (1) specimen processing, (2) gross examination, (3) cross sectioning, (4) staining, (5) Barrett's esophagus, (6) TRG systems, and (7) TRG in lymph node (LN). Participants rated the items using a 5-point Likert style scale and were encouraged to write comments for each statement. The expert panel recommended a 4-tiered TRG system for assessing the primary tumor: grade 1: No residual tumor (complete histopathologic tumor regression), grade 2: less than 10% residual tumor (near-complete regression), grade 3: 10%-50% residual tumor (partial regression), grade 4: greater than 50% residual tumor (minimal/no regression), combined with a 3-tiered system for grading therapeutic response in metastatic LNs: grade a: no residual tumor (complete histopathologic TRG), grade b: partial regression (tumor cells and regression), grade c: no regression (no sign of tumor response). This TRG grading system can be recommended as an international standard for histopathologic TRG grading in esophageal and gastroesophageal junction adenocarcinoma.

Deformation-Induced Chemical Inhomogeneity and Short-Circuit Diffusion in Shear Bands of a Bulk Metallic Glass

The compositional changes in shear bands of a Cu_{50}Zr_{50} metallic glass after plastic deformation at room temperature have been monitored by atom probe tomography. Across the width of the shear bands an asymmetry of the enriched and depleted zones of the constituent elements is observed, while no change of the composition within the surrounding matrix occurs. The diffusion coefficients determined from the concentration profiles are orders of magnitude larger than the values of bulk diffusion at room temperature. The asymmetric concentration profiles of the constituent elements (Cu and Zr) remain stable during annealing at a temperature of 543 K, even though fast and preferential diffusion of a Ni tracer has been found along the shear band at the same temperature. The results indicate that the atomic structure and stress distribution within the shear bands is altered from that of the surrounding amorphous matrix. The fact that the shear band structure is unaltered at elevated temperatures and that fast diffusion occurs preferentially within the shear bands leads to the conclusion that they are structurally stable.

The HDAC6 inhibitor 7b induces BCR-ABL ubiquitination and downregulation and synergizes with imatinib to trigger apoptosis in chronic myeloid leukemia

Despite the discovery of tyrosine kinase inhibitors (TKIs) for the treatment of breakpoint cluster region-Abelson (BCR-ABL)⁺ cancer types, patients with chronic myeloid leukemia (CML) treated with TKIs develop resistance and severe adverse effects. Combination treatment, especially with a histone deacetylase (HDAC) 6 inhibitor (HDAC6i), appears to be an attractive option to prevent TKI resistance, considering the potential capacity of an HDAC6i to diminish BCR-ABL expression. We first validated the in vivo anti-cancer potential of the compound 7b by significantly reducing the tumor burden of BALB/c mice xenografted with K-562 cells, without notable organ toxicity. Here, we hypothesize that the HDAC6i compound 7b can lead to BCR-ABL downregulation in CML cells and sensitize them to TKI treatment. The results showed that combination treatment with imatinib and 7b resulted in strong synergistic caspase-dependent apoptotic cell death and drastically reduced the proportion of leukemia stem cells, whereas this treatment only moderately affected healthy cells. Ultimately, the combination significantly decreased colony formation in a semisolid methylcellulose medium and tumor mass in xenografted zebrafish compared to each compound alone. Mechanistically, the combination induced BCR-ABL ubiquitination and downregulation followed by disturbance of key proteins in downstream pathways involved in CML proliferation and survival. Taken together, our results suggest that an HDAC6i potentiates the effect of imatinib and could overcome TKI resistance in CML cells.

Resveratrol suppresses gastric cancer cell proliferation and survival through inhibition of PIM-1 kinase activity

The proviral integration site for Moloney murine leukemia virus (PIM) family of serine/threonine-specific kinases consist of three isoforms, that regulate proliferation, apoptosis, metabolism, invasion, and metastasis of cancer cells. Among these, abnormally elevated kinase activity of PIM-1 contributes to the progression of gastric cancer and predicts poor prognosis and a low survival rate in gastric cancer patients. In the present study, we found that resveratrol, one of the representative chemopreventive and anticarcinogenic phytochemicals, directly binds to PIM-1 and thereby inhibits its catalytic activity in human gastric cancer SNU-601 cells. This resulted in suppression of phosphorylation of the proapoptotic Bad, a known substrate of PIM-1. Resveratrol, by inactivating PIM-1, also inhibited anchorage-independent growth and proliferation of SNU-601 cells. To understand the molecular interaction between resveratrol and PIM-1, we conducted docking simulation and found that resveratrol directly binds to the PIM-1 at the ATP-binding pocket. In conclusion, the proapototic and anti-proliferative effects of resveratrol in gastric cancer cells are likely to be mediated through suppression of PIM-1 kinase activity, which may represent a novel mechanism underlying its chemopreventive and anticarcinogenic actions.

Novel HDAC inhibitor MAKV-8 and imatinib synergistically kill chronic myeloid leukemia cells via inhibition of BCR-ABL/MYC-signaling: effect on imatinib resistance and stem cells

Background

Chronic myeloid leukemia (CML) pathogenesis is mainly driven by the oncogenic breakpoint cluster region-Abelson murine leukemia viral oncogene homolog 1 (BCR-ABL) fusion protein. Since BCR-ABL displays abnormal constitutive tyrosine kinase activity, therapies using tyrosine kinase inhibitors (TKis) such as imatinib represent a major breakthrough for the outcome of CML patients. Nevertheless, the development of TKi resistance and the persistence of leukemia stem cells (LSCs) remain barriers to cure the disease, justifying the development of novel therapeutic approaches. Since the activity of histone deacetylase (HDAC) is deregulated in numerous cancers including CML, pan-HDAC inhibitors may represent promising therapeutic regimens for the treatment of CML cells in combination with TKi.

Results

We assessed the anti-leukemic activity of a novel hydroxamate-based pan-HDAC inhibitor MAKV-8, which complied with the Lipinski’s “rule of five,” in various CML cells alone or in combination with imatinib. We validated the in vitro HDAC-inhibitory potential of MAKV-8 and demonstrated efficient binding to the ligand-binding pocket of HDAC isoenzymes. In cellulo, MAKV-8 significantly induced target protein acetylation, displayed cytostatic and cytotoxic properties, and triggered concomitant ER stress/protective autophagy leading to canonical caspase-dependent apoptosis. Considering the specific upregulation of selected HDACs in LSCs from CML patients, we investigated the differential toxicity of a co-treatment with MAKV-8 and imatinib in CML versus healthy cells. We also showed that beclin-1 knockdown prevented MAKV-8-imatinib combination-induced apoptosis. Moreover, MAKV-8 and imatinib co-treatment synergistically reduced BCR-ABL-related signaling pathways involved in CML cell growth and survival. Since our results showed that LSCs from CML patients overexpressed c-MYC, importantly MAKV-8-imatinib co-treatment reduced c-MYC levels and the LSC population. In vivo, tumor growth of xenografted K-562 cells in zebrafish was completely abrogated upon combined treatment with MAKV-8 and imatinib.

Conclusions

Collectively, the present findings show that combinations HDAC inhibitor-imatinib are likely to overcome drug resistance in CML pathology.

Robust and Resource-Efficient Microwave Near-Field Entangling ^{9}Be^{+} Gate

Microwave trapped-ion quantum logic gates avoid spontaneous emission as a fundamental source of decoherence. However, microwave two-qubit gates are still slower than laser-induced gates and hence more sensitive to fluctuations and noise of the motional mode frequency. We propose and implement amplitude-shaped gate drives to obtain resilience to such frequency changes without increasing the pulse energy per gate operation. We demonstrate the resilience by noise injection during a two-qubit entangling gate with ^{9}Be^{+} ion qubits. In the absence of injected noise, amplitude modulation gives an operation infidelity in the 10^{-3} range.

The DRS-AIMP2-EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex

Aminoacyl-tRNA synthetases (ARSs) play essential roles in protein biosynthesis as well as in other cellular processes, often using evolutionarily acquired domains. For possible cooperativity and synergistic effects, nine ARSs assemble into the multi-tRNA synthetase complex (MSC) with three scaffold proteins: aminoacyl-tRNA synthetase complex-interacting multifunctional proteins 1, 2 and 3 (AIMP1, AIMP2 and AIMP3). X-ray crystallographic methods were implemented in order to determine the structure of a ternary subcomplex of the MSC comprising aspartyl-tRNA synthetase (DRS) and two glutathione S-transferase (GST) domains from AIMP2 and glutamyl-prolyl-tRNA synthetase (AIMP2GST and EPRSGST, respectively). While AIMP2GST and EPRSGST interact via conventional GST heterodimerization, DRS strongly interacts with AIMP2GST via hydrogen bonds between the α7-β9 loop of DRS and the β2-α2 loop of AIMP2GST, where Ser156 of AIMP2GST is essential for the assembly. Structural analyses of DRS-AIMP2GST-EPRSGST reveal its pivotal architecture in the MSC and provide valuable insights into the overall assembly and conditionally required disassembly of the MSC.

Versatile Control of ^{9}Be^{+} Ions Using a Spectrally Tailored UV Frequency Comb

We demonstrate quantum control of ^{9}Be^{+} ions directly implemented by an optical frequency comb. Based on numerical simulations of the relevant processes in ^{9}Be^{+} for different magnetic field regimes, we demonstrate a wide applicability when controlling the comb's spectral properties. We introduce a novel technique for the selective and efficient generation of a spectrally tailored narrow-bandwidth optical frequency comb near 313 nm. We experimentally demonstrate internal state control and internal-motional state coupling of ^{9}Be^{+} ions implemented by stimulated-Raman manipulation using a spectrally optimized optical frequency comb. Our pulsed laser approach is a key enabling step for the implementation of quantum logic and quantum information experiments in Penning traps.

Modifying the transition temperature, 120 K ≤ Tc ≤ 1150 K, of amorphous Fe90-xCoxSc10 with simultaneous alteration of fluctuation of exchange integral up to zero

Amorphous (a-) Fe_90−xCo_xSc₁₀ alloys have been produced by rapid quenching from the melt. The Curie temperature, T_C, was determined using both mean field theory and Landau’s theory of second-order phase transitions in zero and non-zero external fields. The dependence of T_C on the atomic spacing can be explained by the empirical Bethe-Slater curve. The value of T_C of a- Fe₅Co₈₅Sc₁₀, determined by the above theoretical approaches is 1150 K, which is the highest T_C ever measured for amorphous alloys. The flattening of the measured normalized magnetization, M(T)/M(0), as a function of the reduced temperature, T/T_C, is explained within the framework of the Handrich- Kobe model. According to this model the fluctuation of the exchange integral is the main reason for the flattening of M(T)/M(0). In the case of a-Fe₉₀Sc₁₀ without Co, however, the fluctuation of the exchange integral is dominant only at zero external field, B_ex = 0. At B_ex = 9 T, however, the fluctuation of the exchange integral has no conspicuous effect on the reduction of the magnetization. It is shown that at B_ex = 9 T the frozen magnetic clusters control the behaviour of the reduced magnetization as function of T/T_C. In contrast to other ferromagnetic alloys, where the flattening of M(T)/M(0) is characteristic for an amorphous structure, the a- Fe₅Co₈₅Sc₁₀ does not exhibit any trace of the fluctuation of the exchange integral.

Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB

Vancomycin resistance in Enterococci and its transfer to methicillin-resistant Staphylococcus aureus are challenging problems in health care institutions worldwide. High-level vancomycin resistance is conferred by acquiring either transposable elements of the VanA or VanB type. Enterococcus faecalis VanY_B in the VanB-type operon is a d,d-carboxypeptidase that recognizes the peptidyl-d-Ala⁴-d-Ala⁵ extremity of peptidoglycan and hydrolyses the terminal d-Ala on the extracellular side of the cell wall, thereby increasing the level of glycopeptide antibiotics resistance. However, at the molecular level, it remains unclear how VanY_B manipulates peptidoglycan peptides for vancomycin resistance. In this study, we have determined the crystal structures of E. faecalis VanY_B in the d-Ala-d-Ala-bound, d-Ala-bound, and -unbound states. The interactions between VanY_B and d-Ala-d-Ala observed in the crystal provide the molecular basis for the recognition of peptidoglycan substrates by VanY_B. Moreover, comparisons with the related VanX and VanXY enzymes reveal distinct structural features of E. faecalis VanY_B around the active-site cleft, thus shedding light on its unique substrate specificity. Our results could serve as the foundation for unravelling the molecular mechanism of vancomycin resistance and for developing novel antibiotics against the vancomycin-resistant Enterococcus species.

Electrical resistivity and wave character of free electrons in amorphous and nanoglass Sc75Fe25

The residual electrical resistivity of metallic amorphous alloys, ρ ₀, is typically in the range 50 µΩ cm  <  ρ ₀  <  310 µΩ cm corresponding to a mean free path of conduction electrons of order a few interatomic distances. In crystalline metals with low defect levels such as Cu however, the residual electrical resistivity is about ρ ₀  ≈  1.54  ×  10^-2 µΩ cm, leading to extensive progression of free electrons through the crystalline material, of typically up to 4  ×  10⁶ nm. The relatively 'high' values for the electrical resistivity of distorted Sc₇₅Fe₂₅ alloys are discussed here within the framework of the wave character of electrons. The present investigation of amorphous and nanoglass Sc₇₅Fe₂₅ over the temperature range 1.9-320 K, focuses on clarification of the temperature dependence of the resistivity, ρ(T). These alloys systems, which show a range of behaviours for temperature dependent resistivity-including temperature independent residual resistivity, as well as positive and negative polarities for the slope dρ(T)/dT-are examined in detail.

Cervical cord and ventricle affection in neuromyelitis optica

OBJECTIVES

Cervical cord involvement is common in neuromyelitis optica (NMO) and multiple sclerosis (MS), but its impact on disability in NMO has rarely been studied. Recent publications on NMO examined the periventricular system, areas of high aquaporin-4 expression, but not yet by using ventricle volumetry.

PURPOSE

To compare cervical cord atrophy, ventricular widening, and supra- and infratentorial brain measures between NMO and MS, and study their impact on clinical disability.

METHODS

Magnet resonance imaging-based volumetry of upper cervical cord, third and fourth lateral ventricles, grey matter, white matter, brainstem, cerebellum and clinical status of 18 NMO and 20 MS patients, was compared between the groups and with 26 healthy controls. Patterns of ventricular widening relative to healthy controls were inspected by voxel-based morphometry of the cerebrospinal fluid.

RESULTS

Cervical cord atrophy was similar in NMO and MS (75.2 ± 10.0 mm² , respectively, 76.5 ± 9.5 mm² vs 84.1 ± 8.6 mm² in controls).Third ventricle increase in both groups, and specific fourth ventricle widening in MS were detected. Patient groups differed in third to fourth ventricle ratio (P = 0.002). In NMO, white matter correlated inversely with the affected cord segments (P = 0.001) and with cervical cord area (P = 0.043). The disability status was explained by cervical cord area and third ventricle volume (R² =0.524) in NMO, and by grey matter and fourth ventricle volume (R² =0.565) in MS.

CONCLUSION

Cervical cord atrophy and third ventricular enlargement are both clinically relevant in NMO. Third and fourth ventricle volumetry shows differences between NMO and MS regarding the involvement of periventricular structures.

The N-terminal region of organic anion transporting polypeptide 1B3 (OATP1B3) plays an essential role in regulating its plasma membrane trafficking

Organic anion transporting polypeptide 1B3 (OATP1B3) is a major influx transporter mediating the hepatic uptake of various endogenous substrates as well as clinically important drugs such as statins and anticancer drugs. However, molecular mechanisms controlling the membrane trafficking of OATP1B3 have been largely unknown. Several reports recently indicated the presence of a distinct, cancer-type OATP1B3 variant lacking the N-terminal 28 amino acids compared to OATP1B3 expressed in non-malignant hepatocytes. Interestingly, the cancer-type OATP1B3 variant is located predominantly in the cytoplasm, implicating the involvement of the N-terminal region of OATP1B3 in its membrane trafficking. In the current study, we set out to experimentally validate the importance of the N-terminal region of OATP1B3 and to identify responsible sequence motif(s) in that region. A number of truncation or point mutants of OATP1B3 were transiently expressed in HEK293T, HCT-8 or MDCK II cells and their expression in cytoplasmic and surface membrane fractions were analyzed by immunoblotting. Our results indicated that the N-terminal sequence of OATP1B3, in particular, at the amino acid positions between 12 and 28, may be indispensable in its membrane trafficking. Moreover, our results using a fusion construct indicated that the first 50 amino acids of OATP1B3 are sufficient for its membrane localization. The importance of the N-terminal region in membranous localization was shared among the other OATP1B subfamily members, OATP1B1 and rat Oatp1b2. Our efforts to identify the responsible amino acid(s) or structure motif(s) in the N-terminal region did not pinpoint individual amino acids or motifs with putative secondary structures. Our current findings however demonstrate that the N-terminal region is important for the membrane localization of the OATP1B subfamily members and should facilitate future investigations of the mechanisms involved in the regulation and membrane trafficking of these important transporter proteins.

Identification of a genetic contamination in a commercial mouse strain using two panels of polymorphic markers

Rapid detection of genetic contamination is critical in mouse studies involving inbred strains. During a Quantitative Trait Locus (QTL) study using simple sequence length polymorphism (SSLP) markers, we noticed heterozygosity at some loci of a commercially available inbred C57BL/6N mouse strain, suggesting a contamination by another mouse strain. A panel of 100 single-nucleotide polymorphism (SNP) markers was used to confirm and specify the genetic contamination suspected. Retrospective analyses demonstrated that the contamination took place as early as autumn 2003 and has persisted ever since at a fairly constant level. Contaminating alleles most probably originated from a DBA strain. Our data demonstrate the suitability of SNP markers for rapid detection and identification of the source of genetic contamination. Further, our results show the importance of a state-of-theart genetic monitoring of the authenticity of murine inbred strains.

The truth about the 1st cycle Coulombic efficiency of LiNi1/3Co1/3Mn1/3O2 (NCM) cathodes

High voltage issues of the NCM cathode could be attributed predominantly to structural instabilities and unexpected negligible electrolyte oxidation.

Structure and Stability of the Dimeric Triosephosphate Isomerase from the Thermophilic Archaeon Thermoplasma acidophilum

Thermoplasma acidophilum is a thermophilic archaeon that uses both non-phosphorylative Entner-Doudoroff (ED) pathway and Embden-Meyerhof-Parnas (EMP) pathway for glucose degradation. While triosephosphate isomerase (TPI), a well-known glycolytic enzyme, is not involved in the ED pathway in T. acidophilum, it has been considered to play an important role in the EMP pathway. Here, we report crystal structures of apo- and glycerol-3-phosphate-bound TPI from T. acidophilum (TaTPI). TaTPI adopts the canonical TIM-barrel fold with eight α-helices and parallel eight β-strands. Although TaTPI shares ~30% sequence identity to other TPIs from thermophilic species that adopt tetrameric conformation for enzymatic activity in their harsh physiological environments, TaTPI exists as a dimer in solution. We confirmed the dimeric conformation of TaTPI by analytical ultracentrifugation and size-exclusion chromatography. Helix 5 as well as helix 4 of thermostable tetrameric TPIs have been known to play crucial roles in oligomerization, forming a hydrophobic interface. However, TaTPI contains unique charged-amino acid residues in the helix 5 and adopts dimer conformation. TaTPI exhibits the apparent T_d value of 74.6°C and maintains its overall structure with some changes in the secondary structure contents at extremely acidic conditions (pH 1–2). Based on our structural and biophysical analyses of TaTPI, more compact structure of the protomer with reduced length of loops and certain patches on the surface could account for the robust nature of Thermoplasma acidophilum TPI.

Hedgehog/Patched-associated rhabdomyosarcoma formation from delta1-expressing mesodermal cells

Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma. In children, the 2 major RMS subtypes are alveolar and embryonal RMS. Aberrant Hedgehog/Patched1 (Hh/Ptch) signaling is a hallmark of embryonal RMS. We demonstrate that mice carrying a Ptch mutation in mesodermal Delta1-expressing cells develop embryonal-like RMS at a similar rate as mice harboring a Ptch mutation in the germline or the brachury-expressing mesoderm. The tumor incidence decreases dramatically when Ptch is mutated in Myf5- or Pax3-expressing cells. No RMS develop from Myogenin/Mef2c-expressing cells. This suggests that Hh/Ptch-associated RMS are derived from Delta1-positive, Myf5-negative, Myogenin-negative and Pax3-negative mesodermal progenitors that can undergo myogenic differentiation but lack stable lineage commitment. Additional preliminary genetic data and data on mesodermal progenitors further imply an interplay of Hh/Ptch and Delta/Notch signaling activity during RMS initiation. In contrast, Wnt signals supposedly suppress RMS formation because RMS multiplicity decreases after inactivation of the Wnt-inhibitor Wif1. Finally, our results strongly suggest that the tumor-initiating event determines the lineage of RMS origin.

Novel 3-substituted-2-oxoindoline-based N-hydroxypropenamides as histone deacetylase inhibitors and antitumor agents

Histone deacetylases (HDAC) are currently a group of validated targets for anticancer drug discovery and development. In our research program to find novel small molecules targeting these enzymes, we designed and synthesized two series of 3-hydroxyimino-2-oxoindoline- and 3- methoxyimino-2-oxoindoline-based N-hydroxypropenamides (3a-g, 6a-g). The results show that these propenamides potently inhibited HDAC2 with IC50 values in sub-micromolar range, approximately 10-fold lower than that of SAHA (also known as suberoylanilohydroxamic acid). Evaluation of cytotoxicity of these compounds in three human cancer cell lines revealed that most of the synthesized compounds were up to 5-fold more cytotoxic than SAHA. Docking studies showed that the compounds bound to HDAC2 at the binding site with higher binding affinities compared to SAHA. Our present results demonstrate that these novel 3-substituted-2-oxoindoline-based N-hydroxypropenamides are potential for further development as anticancer agents.

Controlling spin polarized band-structure by variation of vacancy intensity in nanostructures

In this study, the magnetic properties of FeAl alloys with different grain sizes produced by high-pressure torsion were probed by means of magnetic Compton scattering. The measurements were performed at 300 and 10 K. Magnetic Compton profiles of nanocrystalline (35 nm) and ultrafine-grained (160 nm) FeAl alloys were analyzed in terms of the integral area, the width, and the distinctive dip intensity at low momenta. The changes in total magnetic moment and the strength of spin-polarization of itinerant electrons are assumed to be caused by vacancies induced during the preparation of the samples. Despite local disordering due to interfacial regions and deviations in perfect stoichiometry for B2 structure, the effect of vacancies is considered as the major magnetic state contributor.

Normal values for transbulbar sonography and magnetic resonance imaging of the optic nerve sheath diameter (ONSD) in children and adolescents

PURPOSE

To establish normal values of the optic nerve sheath diameter (ONSD) in children and adolescents for transbulbar sonography and magnetic resonance imaging.

MATERIALS AND METHODS

In 99 children and adolescents (age: 5.6 - 18.6 years, mean: 12 years) without neurologic or ophthalmologic disease, measurements of the ONSD with transbulbar sonography were performed. For comparison 59 children and adolescents (age: 5.1 - 17.4 years, mean 12.3 years) with a normal MR examination of the brain had measurements of the ONSD on a T2-weighted thin section sequence of the orbit. Besides establishing modality-related normal values, age dependency, accuracy and reproducibility of measurements were assessed.

RESULTS

Overall the mean ONSD was 5.75 ± 0.52 mm for transbulbar sonography and 5.69 ± 0.31 mm for MRI. There was no statistical significance between the 95 % percentiles and age for both transbulbar sonography (p = 0.332) and MRI (p = 0.336). As a parameter for the reproducibility of measurements, the repeatability coefficient (RC) was between 0.34 mm and 0.46 mm. The concordance correlation coefficient (CCC) values revealed a high agreement between readers both for transbulbar sonography (0.868) and MRI (0.796).

CONCLUSION

Normal values for ONSD in children and adolescents found in this study are significantly higher than assumed. The values found for transbulbar sonography are confirmed by comparable results for MR measurements. A precise sonographic measurement technique and the consideration of normal values found hereby are essential for correct interpretation of ONSD measurements in children and adolescents.

A versatile apparatus for the fine-tuned synthesis of cluster-based materials

In this paper, a custom-designed experimental setup for the fine-tuned synthesis of various cluster-based materials is presented. Providing custom-designed deposition stages and special sample holders it offers a high degree of control over the sample characteristics such as the cluster size, cluster amounts, and sample homogeneity in combination with high sample purity. The system is capable of producing thin films of pure clusters and various cluster-matrix combinations with cluster sizes ranging from single atoms up to aggregates of several thousand atoms. Two custom-designed deposition stages are available, one utilizes the full cluster beam, yielding micrograms of pure clusters within a few hours and the second one uses mass-separated clusters (mass-resolution between 2% and 10%), yielding nanograms of pure clusters in the same timescale. Furthermore, at the second deposition stage, a variety of matrix materials can be co-deposited at a controlled sample temperature between 153 K and 673 K. In order to prove the capabilities of the apparatus, a series of experiments with Fe clusters embedded in Ag matrices with different volume fractions of clusters were carried out. Energy dispersive X-ray spectroscopy measurements revealed that the amount of deposited clusters as well as the sample homogeneity can be controlled with an outstanding accuracy of 10%. Additional measurements of the magnetic properties indicated the presence of separated clusters for volume fractions of clusters around 2 volume percent (vol. %), while above this concentration (10 vol. %) a partial aggregation of the clusters was observed. It was also shown that the resulting thin films are nearly oxygen free, which ascertains that oxygen sensitive materials can be safely handled in this newly developed apparatus.

The mechanically induced structural disorder in barium hexaferrite, BaFe12O19, and its impact on magnetism

The response of the structure of the M-type barium hexaferrite (BaFe₁₂O₁₉) to mechanical action through high-energy milling and its impact on the magnetic behaviour of the ferrite are investigated. Due to the ability of the ⁵⁷Fe Mössbauer spectroscopic technique to probe the environment of the Fe nuclei, a valuable insight on a local atomic scale into the mechanically induced changes in the hexagonal structure of the material is obtained. It is revealed that the milling of BaFe₁₂O₁₉ results in the deformation of its constituent polyhedra (FeO₆ octahedra, FeO₄ tetrahedra and FeO₅ triangular bi-pyramids) as well as in the mechanically triggered transition of the Fe³⁺ cations from the regular 12k octahedral sites into the interstitial positions provided by the magnetoplumbite structure. The response of the hexaferrite to the mechanical treatment is found to be accompanied by the formation of a non-uniform nanostructure consisting of an ordered crystallite surrounded/separated by a structurally disordered surface shell/interface region. The distorted polyhedra and the non-equilibrium cation distribution are found to be confined to the amorphous near-surface layers of the ferrite nanoparticles with the thickness extending up to about 2 nm. The information on the mechanically induced short-range structural disorder in BaFe₁₂O₁₉ is complemented by an investigation of its magnetic behaviour on a macroscopic scale. It is demonstrated that the milled ferrite nanoparticles exhibit a pure superparamagnetism at room temperature. As a consequence of the far-from-equilibrium structural disorder in the surface shell of the nanoparticles, the mechanically treated BaFe₁₂O₁₉ exhibits a reduced magnetization and an enhanced coercivity.

Measurement of the Optic Nerve Sheath Diameter in Children: Comparison Between Transbulbar Sonography and Magnetic Resonance Imaging

PURPOSE

 To evaluate the accuracy of measurements of the optic nerve sheath diameter (ONSD) in children by comparing transbulbar sonography with magnetic resonance imaging (MRI).

MATERIALS AND METHODS

 65 children (age: 3 mo- 17y; mean age: 11.3y) underwent MR imaging of the brain including a heavily T 2-w sequence of the orbit and transbulbar sonography using a 17 MHz linear array transducer. Measurements of the ONSD were performed retrospectively by two experienced readers and all images were evaluated regarding the image quality. Bland-Altman Plots were produced to assess the accuracy of measurements. The correlation between readers and between MR imaging and transbulbar sonography was calculated by the concordance correlation coefficient (CCC).

RESULTS

 Overall the mean values of the ONSD for MRI (5.86 ± 0.66 mm) and transbulbar sonography (5.86 ± 0.71 mm) were identical. There was a high correlation between readers for measurements of the ONSD both for transbulbar sonography (CCC = 0.93) as well as for MRI (CCC = 0.9). Comparing the measurement values between transbulbar sonography and MRI, the correlation of ONSD values was good to moderate with a high dependency on image quality (CCC [0.31, 0.68]).

CONCLUSION

 We were able to demonstrate that the ONSD values of transbulbar sonography in children correlate well with MRI if the relevant anatomic structures are depicted and the measuring points are set correctly. Based on the findings of our study, it seems necessary to define normal and cut-off values for the ONSD in children again to finally assess the clinical relevance of the ONSD as a noninvasive parameter for the evaluation of intracranial pressure.

Fourier transform infrared imaging analysis in discrimination studies of squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) of the oral cavity and oropharynx represents more than 95% of all malignant neoplasms in the oral cavity. Histomorphological evaluation of this cancer type is invasive and remains a time consuming and subjective technique. Therefore, novel approaches for histological recognition are necessary to identify malignancy at an early stage. Fourier transform infrared (FTIR) imaging has become an essential tool for the detection and characterization of the molecular components of biological processes, such as those responsible for the dynamic properties of tumor progression. FTIR imaging is a modern analytical technique enabling molecular imaging of a complex biological sample and is based on the absorption of IR radiation by vibrational transitions in covalent bonds. One major advantage of this technique is the acquisition of local molecular expression profiles, while maintaining the topographic integrity of the tissue and avoiding time-consuming extraction, purification, and separation steps. With this imaging technique, it is possible to obtain unique images of the spatial distribution of proteins, lipids, carbohydrates, cholesterols, nucleic acids, phospholipids, and small molecules with high spatial resolution. Analysis and visualization of FTIR imaging datasets are challenging and the use of chemometric tools is crucial in order to take advantage of the full measurement. Therefore, methodologies for this task based on the novel developed algorithm for multivariate image analysis (MIA) are often necessary. In the present study, FTIR imaging and data analysis methods were combined to optimize the tissue measurement mode after deparaffinization and subsequent data evaluation (univariate analysis and MIAs). We demonstrate that it is possible to collect excellent IR spectra from formalin-fixed paraffin-embedded (FFPE) tissue microarrays (TMAs) of OSCC tissue sections employing an optimised analytical protocol. The correlation of FTIR imaging to the morphological tissue features obtained by histological staining of the sections demonstrated that many histomorphological tissue patterns can be visualized in the colour images. The different algorithms used for MIAs of FTIR imaging data dramatically increased the information content of the IR images from squamous cell tissue sections. These findings indicate that intra-operative and surgical specimens of squamous cell carcinoma tissue can be characterized by FTIR imaging.